forked from lijiext/lammps
Merge branch 'sllod' into collected-post-stable-patches
This commit is contained in:
Axel Kohlmeyer
commit
0a610cb482
|
|
@ -126,3 +126,6 @@ python/* @rbberger
|
|||
doc/utils/*/* @rbberger
|
||||
doc/Makefile @rbberger
|
||||
doc/README @rbberger
|
||||
|
||||
# for releases
|
||||
src/version.h @sjplimp
|
||||
|
|
|
|||
|
|
@ -221,7 +221,7 @@ else()
|
|||
endif()
|
||||
|
||||
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
|
||||
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
|
||||
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
|
||||
|
|
@ -354,7 +354,7 @@ if(PKG_KSPACE)
|
|||
endif()
|
||||
endif()
|
||||
|
||||
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)
|
||||
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
|
||||
find_package(LAPACK)
|
||||
find_package(BLAS)
|
||||
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
|
||||
|
|
@ -569,7 +569,7 @@ if(PKG_USER-PLUMED)
|
|||
if(PLUMED_MODE STREQUAL "STATIC")
|
||||
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
|
||||
"${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})
|
||||
"${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
|
||||
elseif(PLUMED_MODE STREQUAL "SHARED")
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
|
||||
elseif(PLUMED_MODE STREQUAL "RUNTIME")
|
||||
|
|
@ -856,6 +856,9 @@ if(PKG_USER-AWPMD)
|
|||
endif()
|
||||
|
||||
if(PKG_USER-ATC)
|
||||
if(LAMMPS_SIZES STREQUAL BIGBIG)
|
||||
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
|
||||
endif()
|
||||
target_link_libraries(atc ${LAPACK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
# Makefile for LAMMPS documentation
|
||||
|
||||
SHELL = /bin/bash
|
||||
SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py)
|
||||
SHELL = /bin/bash
|
||||
SHA1 = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
|
||||
BUILDDIR = /tmp/lammps-docs-$(SHA1)
|
||||
RSTDIR = $(BUILDDIR)/rst
|
||||
VENV = $(BUILDDIR)/docenv
|
||||
|
|
|
|||
|
|
@ -621,8 +621,8 @@ The USER-ATC package requires the MANYBODY package also be installed.
|
|||
|
||||
[CMake build]:
|
||||
|
||||
No additional settings are needed besides "-D PKG_REAX=yes" and "-D
|
||||
PKG_MANYBODY=yes".
|
||||
No additional settings are needed besides "-D PKG_USER-ATC=yes"
|
||||
and "-D PKG_MANYBODY=yes".
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
|
|
@ -735,58 +735,69 @@ from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
|
|||
:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
|
||||
|
||||
PLUMED can be linked into MD codes in three different modes: static,
|
||||
shared, and runtime. With the "static" mode, all required PLUMED code
|
||||
is linked statically into the MD code. The MD code is then fully
|
||||
independent from the PLUMED installation, but also you have to
|
||||
rebuild/relink the MD code to update the PLUMED code inside it. With
|
||||
"shared" linkage mode, the MD code is linked to a shared library
|
||||
containing the PLUMED code, preferably after it was installed in a
|
||||
globally accessible location. This way the same installed PLUMED code
|
||||
can be shared across multiple MD packages and can be updated, for as
|
||||
long as the shared PLUMED library is ABI-compatible. The third linkage
|
||||
mode is "runtime" which allows to switch the PLUMED kernel at runtime
|
||||
between different variants through setting the PLUMED_KERNEL environment
|
||||
variable, which has to point to the location of the libplumedKernel.so
|
||||
dynamical shared object, which is then loaded at runtime. This is
|
||||
particularly convenient for doing PLUMED development and comparing
|
||||
multiple PLUMED versions without having to recompile the hosting MD
|
||||
code. All three linkage modes are supported by LAMMPS on selected
|
||||
operating systems (e.g. Linux) and using either CMake or traditional
|
||||
make build. The "static" mode should be most portable, the "runtime"
|
||||
mode support in LAMMPS makes the most assumptions about operating
|
||||
system and compiler environment. If one mode does not work, try a
|
||||
different one, or switch to a different build system, or consider
|
||||
a global PLUMED installation or downloading it during building LAMMPS.
|
||||
shared, and runtime. With the "static" mode, all the code that PLUMED
|
||||
requires is linked statically into LAMMPS. LAMMPS is then fully
|
||||
independent from the PLUMED installation, but you have to rebuild/relink
|
||||
it in order to update the PLUMED code inside it. With the "shared"
|
||||
linkage mode, LAMMPS is linked to a shared library that contains the
|
||||
PLUMED code. This library should preferably be installed in a globally
|
||||
accessible location. When PLUMED is linked in this way the same library
|
||||
can be used by multiple MD packages. Furthermore, the PLUMED library
|
||||
LAMMPS uses can be updated without the need for a recompile of LAMMPS
|
||||
for as long as the shared PLUMED library is ABI-compatible.
|
||||
|
||||
The third linkage mode is "runtime" which allows the user to specify
|
||||
which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
|
||||
environment variable. This variable should point to the location of the
|
||||
libplumedKernel.so dynamical shared object, which is then loaded at
|
||||
runtime. This mode of linking is particularly convenient for doing
|
||||
PLUMED development and comparing multiple PLUMED versions as these sorts
|
||||
of comparisons can be done without recompiling the hosting MD code. All
|
||||
three linkage modes are supported by LAMMPS on selected operating
|
||||
systems (e.g. Linux) and using either CMake or traditional make
|
||||
build. The "static" mode should be the most portable, while the
|
||||
"runtime" mode support in LAMMPS makes the most assumptions about
|
||||
operating system and compiler environment. If one mode does not work,
|
||||
try a different one, switch to a different build system, consider a
|
||||
global PLUMED installation or consider downloading PLUMED during the
|
||||
LAMMPS build.
|
||||
|
||||
[CMake build]:
|
||||
|
||||
When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
|
||||
must ensure that GSL is installed in locations that are specified in
|
||||
your environment. There are then two additional commands that control
|
||||
the manner in which PLUMED is obtained and linked into LAMMPS.
|
||||
|
||||
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
|
||||
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
|
||||
|
||||
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
|
||||
downloaded (the version of that is hard-coded to a vetted version of
|
||||
PLUMED, usually a recent stable release version) and built inside the
|
||||
CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default),
|
||||
CMake will try to detect an installed version of PLUMED and link to
|
||||
that. For this to work, the PLUMED library has to be installed into a
|
||||
location where the pkg-config tool can find it or the PKG_CONFIG_PATH
|
||||
environment variable has to be set up accordingly.
|
||||
downloaded (the version of PLUMED that will be downloaded is hard-coded
|
||||
to a vetted version of PLUMED, usually a recent stable release version)
|
||||
and built inside the CMake build directory. If DOWNLOAD_PLUMED is set
|
||||
to "no" (the default), CMake will try to detect and link to an installed
|
||||
version of PLUMED. For this to work, the PLUMED library has to be
|
||||
installed into a location where the pkg-config tool can find it or the
|
||||
PKG_CONFIG_PATH environment variable has to be set up accordingly.
|
||||
PLUMED should be installed in such a location if you compile it using
|
||||
the default make; make install commands.
|
||||
|
||||
The PLUMED_MODE setting determines the linkage mode of the PLUMED
|
||||
library. Allowed values are "static" (default), "shared", or "runtime".
|
||||
For a discussion of PLUMED linkage modes, please see above. When
|
||||
enabling DOWNLOAD_PLUMED, the static linkage mode is recommended.
|
||||
The PLUMED_MODE setting determines the linkage mode for the PLUMED
|
||||
library. The allowed values for this flag are "static" (default),
|
||||
"shared", or "runtime". For a discussion of PLUMED linkage modes,
|
||||
please see above. When DOWNLOAD_PLUMED is enabled the static linkage
|
||||
mode is recommended.
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
Before installing the USER-PLUMED package, first the PLUMED library
|
||||
needs to be configured so that LAMMPS can find the right settings when
|
||||
compiling and linking the LAMMPS executable itself. You can either
|
||||
download and build PLUMED inside the LAMMPS plumed library folder or use
|
||||
a previously installed PLUMED library and point LAMMPS to its
|
||||
location. You also have to choose the linkage mode: "static" (default),
|
||||
"shared" or "runtime". For a discussion of PLUMED linkage modes, please
|
||||
see above.
|
||||
PLUMED needs to be installed before the USER-PLUMED package is installed
|
||||
so that LAMMPS can find the right settings when compiling and linking
|
||||
the LAMMPS executable. You can either download and build PLUMED inside
|
||||
the LAMMPS plumed library folder or use a previously installed PLUMED
|
||||
library and point LAMMPS to its location. You also have to choose the
|
||||
linkage mode: "static" (default), "shared" or "runtime". For a
|
||||
discussion of PLUMED linkage modes, please see above.
|
||||
|
||||
Download/compilation/configuration of the plumed library can be done
|
||||
from the src folder through the following make args:
|
||||
|
|
@ -799,11 +810,11 @@ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installati
|
|||
:pre
|
||||
|
||||
Note that 2 symbolic (soft) links, "includelink" and "liblink" are
|
||||
created in lib/plumed to point into the location of the PLUMED build to
|
||||
use and also a new file lib/plumed/Makefile.lammps is created with
|
||||
settings suitable for LAMMPS to compile and link PLUMED in the desired
|
||||
linkage mode. After this step is completed, you can install the
|
||||
USER-PLUMED package and compile LAMMPS in the usual manner:
|
||||
created in lib/plumed that point to the location of the PLUMED build to
|
||||
use. A new file lib/plumed/Makefile.lammps is also created with settings
|
||||
suitable for LAMMPS to compile and link PLUMED using the desired linkage
|
||||
mode. After this step is completed, you can install the USER-PLUMED
|
||||
package and compile LAMMPS in the usual manner:
|
||||
|
||||
make yes-user-plumed
|
||||
make machine :pre
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="27 Nov 2018 version">
|
||||
<META NAME="docnumber" CONTENT="12 Dec 2018 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
27 Nov 2018 version :c,h2
|
||||
12 Dec 2018 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
|
|
|||
|
|
@ -485,7 +485,7 @@ README for more info on Pizza.py and how to use these scripts.
|
|||
|
||||
reax tool :h4,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alond codes that can
|
||||
The reax sub-directory contains stand-alone codes that can
|
||||
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
|
||||
the README.txt file for more info.
|
||||
|
|
|
|||
|
|
@ -461,10 +461,10 @@ last snapshot. This can be accomplished with something the following
|
|||
commands:
|
||||
|
||||
variable Dhop equal 0.6
|
||||
variable check atom "c_dsp[4] > v_Dhop"
|
||||
variable check atom "c_dsp\[4\] > v_Dhop"
|
||||
compute dsp all displace/atom refresh check
|
||||
dump 1 all custom 20 tmp.dump id type x y z
|
||||
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
|
||||
dump_modify 1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre
|
||||
|
||||
The "compute displace/atom"_compute_displace_atom.html command
|
||||
calculates the displacement of each atom from its reference position.
|
||||
|
|
|
|||
|
|
@ -32,11 +32,10 @@ enhance the sampling of phase space.
|
|||
|
||||
The documentation included here only describes the fix plumed command
|
||||
itself. This command is LAMMPS specific, whereas most of the
|
||||
functionality implemented in PLUMED, however, will work with a range of
|
||||
MD codes, and when PLUMED is used as a stand alone code for analysis.
|
||||
The full "documentation for PLUMED"_plumeddocs is available online and
|
||||
included in the PLUMED source code. The PLUMED library development is
|
||||
hosted at
|
||||
functionality implemented in PLUMED will work with a range of MD codes,
|
||||
and when PLUMED is used as a stand alone code for analysis. The full
|
||||
"documentation for PLUMED"_plumeddocs is available online and included
|
||||
in the PLUMED source code. The PLUMED library development is hosted at
|
||||
"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
|
||||
A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
|
||||
|
||||
|
|
@ -54,11 +53,12 @@ have been set.
|
|||
|
||||
The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
|
||||
to PLUMED and there can only be one instance of the plumed fix at a
|
||||
time. The plumed fix communicates the minimum amount of information
|
||||
required and the PLUMED supports multiple, completely independent
|
||||
collective variables, multiple independent biases and multiple
|
||||
independent forms of analysis. There is thus really no restriction in
|
||||
functionality by only allowing only one plumed fix in the LAMMPS input.
|
||||
time. The way the plumed fix is implemented ensures that the minimum
|
||||
amount of information required is communicated. Furthermore, PLUMED
|
||||
supports multiple, completely independent collective variables, multiple
|
||||
independent biases and multiple independent forms of analysis. There is
|
||||
thus really no restriction in functionality by only allowing only one
|
||||
plumed fix in the LAMMPS input.
|
||||
|
||||
The {plumedfile} keyword allows the user to specify the name of the
|
||||
PLUMED input file. Instructions as to what should be included in a
|
||||
|
|
|
|||
|
|
@ -160,7 +160,7 @@ unaffected by interactions with other particles. Note that if you
|
|||
expect a rigid body not to move or rotate by using these keywords, you
|
||||
must insure its initial center-of-mass translational or angular
|
||||
velocity is 0.0. Otherwise the initial translational or angular
|
||||
momentum the body has will persist.
|
||||
momentum, the body has, will persist.
|
||||
|
||||
An xflag, yflag, or zflag set to {off} means turn off the component of
|
||||
force or torque in that dimension. A setting of {on} means turn on
|
||||
|
|
@ -287,9 +287,10 @@ bodies. The number of columns is 28. Thus for each rigid body, 28
|
|||
values are stored: the xyz coords of the center of mass (COM), the xyz
|
||||
components of the COM velocity, the xyz components of the force acting
|
||||
on the COM, the components of the 4-vector quaternion representing the
|
||||
orientation of the rigid body, the xyz components of the angular momentum
|
||||
orientation of the rigid body, the xyz components of the angular velocity
|
||||
of the body around its COM, the xyz components of the torque acting on the
|
||||
COM, the 3 principal components of the moment of inertia and the xyz image
|
||||
COM, the 3 principal components of the moment of inertia, the xyz components
|
||||
of the angular momentum of the body around its COM, and the xyz image
|
||||
flags of the COM.
|
||||
|
||||
The center of mass (COM) for each body is similar to unwrapped
|
||||
|
|
|
|||
|
|
@ -86,6 +86,9 @@ package"_Build_package.html doc page for more info.
|
|||
Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
|
||||
This fix is not compatible with a hybrid pair style, long-range dispersion,
|
||||
TIP4P water support, or long-range point dipole support.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"kspace_style"_kspace_style.html, "boundary"_boundary.html
|
||||
|
|
|
|||
|
|
@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
|
|||
accuracy = desired relative error in forces
|
||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||
{scafacos} values = method accuracy
|
||||
method = fmm or p2nfft or ewald or direct
|
||||
method = fmm or p2nfft or p3m or ewald or direct
|
||||
accuracy = desired relative error in forces :pre
|
||||
:ule
|
||||
|
||||
|
|
@ -392,6 +392,8 @@ the same bond/angle/dihedral are weighted by the
|
|||
"special_bonds"_special_bonds.html command. Likewise it does not
|
||||
support the "TIP4P water style" where a fictitious charge site is
|
||||
introduced in each water molecule.
|
||||
Finally, the methods {p3m} and {ewald} do not support computing the
|
||||
virial, so this contribution is not included.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -63,7 +63,6 @@ aliceblue
|
|||
allocaters
|
||||
allosws
|
||||
AlO
|
||||
alond
|
||||
Alonso
|
||||
amap
|
||||
Amatrix
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
variable sname index h_atom
|
||||
log ${sname}.spe.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
|
|
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
|||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
|
||||
run 0
|
||||
run 10
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
variable sname index h_molecule
|
||||
log ${sname}.spe.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
|
|
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
|||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
|
||||
run 0
|
||||
run 10
|
||||
|
|
|
|||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h_atom
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
processors 1 * *
|
||||
|
||||
|
||||
atom_style wavepacket
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h_atom
|
||||
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
|
||||
#neighbor 2.0 nsq
|
||||
|
||||
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||
pair_coeff * *
|
||||
|
||||
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/awpmd
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute energies all pair awpmd/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.52918
|
||||
ghost atom cutoff = 2.52918
|
||||
binsize = 1.26459, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair awpmd/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
|
||||
1 -266.3192 -266.3192 0 266.32746 0 -532.64666 0 0 159.30733 -0
|
||||
2 -266.3192 -266.3192 1.7273458e-17 266.32797 0 -532.64718 0 5.7948873e-15 169.14686 6.6606909e-13
|
||||
3 -266.3192 -266.3192 4.6899813e-15 266.32927 0 -532.64847 0 1.5733915e-12 194.06892 1.8084691e-10
|
||||
4 -266.3192 -266.3192 1.4824973e-13 266.33199 0 -532.6512 0 4.9734712e-11 246.65762 5.7165485e-09
|
||||
5 -266.3192 -266.3192 1.9298888e-12 266.33712 0 -532.65632 0 6.4743771e-10 345.53056 7.441702e-08
|
||||
6 -266.3192 -266.3192 1.5343223e-11 266.34601 0 -532.66521 0 5.1473332e-09 516.91949 5.9163869e-07
|
||||
7 -266.3192 -266.3192 8.8661674e-11 266.36051 0 -532.6797 0 2.9744154e-08 796.4357 3.4188175e-06
|
||||
8 -266.31919 -266.31919 4.0865149e-10 266.38304 0 -532.70223 0 1.3709411e-07 1231.0302 1.5757709e-05
|
||||
9 -266.31918 -266.31918 1.5889509e-09 266.41674 0 -532.73592 0 5.3306012e-07 1881.1652 6.1270366e-05
|
||||
10 -266.31916 -266.31916 5.4070747e-09 266.46554 0 -532.7847 0 1.8139615e-06 2823.2238 0.00020849822
|
||||
Loop time of 0.000725031 on 1 procs for 10 steps with 2 atoms
|
||||
|
||||
Performance: 1.192 ns/day, 20.140 hours/ns, 13792.516 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00030851 | 0.00030851 | 0.00030851 | 0.0 | 42.55
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001204 | 0.0001204 | 0.0001204 | 0.0 | 16.61
|
||||
Output | 0.00028038 | 0.00028038 | 0.00028038 | 0.0 | 38.67
|
||||
Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.85
|
||||
Other | | 9.537e-06 | | | 1.32
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 248 ave 248 max 248 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 225 ave 225 max 225 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 225
|
||||
Ave neighs/atom = 112.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h_atom
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
processors 1 * *
|
||||
|
||||
|
||||
atom_style wavepacket
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h_atom
|
||||
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
|
||||
#neighbor 2.0 nsq
|
||||
|
||||
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||
pair_coeff * *
|
||||
|
||||
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/awpmd
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute energies all pair awpmd/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.52918
|
||||
ghost atom cutoff = 2.52918
|
||||
binsize = 1.26459, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair awpmd/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0
|
||||
1 -266.3192 -266.3192 0 266.32789 0 -532.64709 0 0 167.49891 -0
|
||||
2 -266.3192 -266.3192 1.219316e-15 266.3314 0 -532.6506 0 4.0905525e-13 235.2267 4.7017146e-11
|
||||
3 -266.3192 -266.3192 8.3179871e-14 266.34548 0 -532.66468 0 2.7905123e-11 506.68594 3.2074377e-09
|
||||
4 -266.3192 -266.3192 4.4091748e-12 266.39036 0 -532.70955 0 1.4791868e-09 1372.0565 1.7001894e-07
|
||||
5 -266.31916 -266.31916 9.8904198e-11 266.51357 0 -532.83273 0 3.3180309e-08 3748.6725 3.8137718e-06
|
||||
6 -266.31893 -266.31893 1.3132578e-09 266.81733 0 -533.13626 0 4.4057077e-07 9611.8807 5.0639565e-05
|
||||
7 -266.31762 -266.31762 1.2317167e-08 267.50719 0 -533.82481 0 4.1321544e-06 22950.26 0.00047495321
|
||||
8 -266.31123 -266.31123 9.0048883e-08 268.97689 0 -535.28812 0 3.0209534e-05 51470.197 0.0034723086
|
||||
9 -266.28324 -266.28324 5.4612621e-07 271.95757 0 -538.24082 0 0.00018321403 109735.25 0.02105877
|
||||
10 -266.17113 -266.17114 2.8729529e-06 277.79384 0 -543.96498 0 0.00096381615 225424.02 0.11078182
|
||||
Loop time of 0.00176561 on 4 procs for 10 steps with 2 atoms
|
||||
|
||||
Performance: 0.489 ns/day, 49.045 hours/ns, 5663.769 timesteps/s
|
||||
87.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.3419e-05 | 0.00012642 | 0.00030923 | 0.0 | 7.16
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00073171 | 0.00086534 | 0.001025 | 0.0 | 49.01
|
||||
Output | 0.00063562 | 0.00075388 | 0.00094962 | 0.0 | 42.70
|
||||
Modify | 3.8147e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.25
|
||||
Other | | 1.55e-05 | | | 0.88
|
||||
|
||||
Nlocal: 0.5 ave 2 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 249.5 ave 250 max 248 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 56.25 ave 225 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 225
|
||||
Ave neighs/atom = 112.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h_molecule
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
processors 1 * *
|
||||
|
||||
|
||||
atom_style wavepacket
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h_molecule
|
||||
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4 atoms
|
||||
|
||||
#neighbor 2.0 nsq
|
||||
|
||||
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||
pair_coeff * *
|
||||
|
||||
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/awpmd
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute energies all pair awpmd/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.52918
|
||||
ghost atom cutoff = 2.52918
|
||||
binsize = 1.26459, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair awpmd/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
|
||||
1 30360.49 30360.489 0.0009272222 39540.081 2.0463631e-12 -9179.5926 0 0.10368794 1.3476061e+09 35.753932
|
||||
2 67447.779 67447.776 0.00370884 80547.07 -1.1368684e-12 -13099.294 0 0.41474633 2.8529839e+09 143.01385
|
||||
3 3713046.5 3713046.5 0.0041850026 3803060.3 -1.29603e-10 -90013.788 0 0.46799388 1.4486958e+11 161.3748
|
||||
4 2445632.1 2445620 12.171486 2452194.4 -9.777068e-11 -6574.4062 0 1361.0937 -6.5572589e+08 469335.68
|
||||
5 2434860.1 2434845.9 14.215419 2433638.8 -1.0663825e-10 1207.1541 0 1589.6595 -359380.29 548150.31
|
||||
6 2444984.1 2444969.8 14.215428 2451100 5.1841198e-11 -6130.1373 0 1589.6605 -5.6327282e+08 548150.63
|
||||
7 2436128.7 2436110.9 17.793789 2434903.7 2.0190782e-10 1207.154 0 1989.8158 -221406.77 686133.18
|
||||
8 2444786.5 2444768.7 17.793798 2450583.8 -1.1027623e-10 -5815.0651 0 1989.8169 -5.0227031e+08 686133.54
|
||||
9 2437198.9 2437175.9 22.942086 2435968.8 2.2600943e-10 1207.1538 0 2565.5315 -22903.736 884652.88
|
||||
10 2444787.1 2444764.2 22.942097 2450333.1 -3.1832315e-11 -5568.9214 0 2565.5327 -4.5741803e+08 884653.3
|
||||
Loop time of 0.00158453 on 1 procs for 10 steps with 4 atoms
|
||||
|
||||
Performance: 0.545 ns/day, 44.015 hours/ns, 6311.020 timesteps/s
|
||||
85.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00088882 | 0.00088882 | 0.00088882 | 0.0 | 56.09
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00031352 | 0.00031352 | 0.00031352 | 0.0 | 19.79
|
||||
Output | 0.00036216 | 0.00036216 | 0.00036216 | 0.0 | 22.86
|
||||
Modify | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.38
|
||||
Other | | 1.407e-05 | | | 0.89
|
||||
|
||||
Nlocal: 4 ave 4 max 4 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 596 ave 596 max 596 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 966 ave 966 max 966 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 966
|
||||
Ave neighs/atom = 241.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index h_molecule
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
processors 1 * *
|
||||
|
||||
|
||||
atom_style wavepacket
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.h_molecule
|
||||
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4 atoms
|
||||
|
||||
#neighbor 2.0 nsq
|
||||
|
||||
pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press
|
||||
pair_coeff * *
|
||||
|
||||
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/awpmd
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute energies all pair awpmd/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.52918
|
||||
ghost atom cutoff = 2.52918
|
||||
binsize = 1.26459, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair awpmd/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.172 | 5.234 | 5.422 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0
|
||||
1 30360.982 30360.981 0.0009272222 39540.638 -1.1368684e-12 -9179.6571 0 0.10368794 1.3476263e+09 35.753932
|
||||
2 67459.392 67459.388 0.0037086548 80559.71 6.5938366e-12 -13100.322 0 0.41472561 2.8534514e+09 143.0067
|
||||
3 3732209.2 3732209.2 0.0041861902 3822452.2 -3.1604941e-11 -90242.984 0 0.46812669 1.4561246e+11 161.42059
|
||||
4 2482974.7 2482961.9 12.860712 2489531.2 -2.2896529e-10 -6569.2968 0 1438.1675 -6.5458119e+08 495912.44
|
||||
5 2472238.2 2472223.2 14.933049 2471015.7 -1.6120794e-10 1207.5188 0 1669.9095 -324992.65 575822.3
|
||||
6 2482233.1 2482218.1 14.933057 2488321.7 -2.0691004e-11 -6103.5677 0 1669.9104 -5.5786438e+08 575822.62
|
||||
7 2473498.5 2473479.8 18.61401 2472272.3 1.459739e-10 1207.5167 0 2081.5382 -183348.11 717761.12
|
||||
8 2481621.3 2481602.6 18.614019 2487299.1 7.0258466e-11 -5696.4589 0 2081.5393 -4.7962801e+08 717761.48
|
||||
9 2474506.2 2474482.2 24.021181 2473274.7 2.1395863e-10 1207.508 0 2686.2029 24318.554 926263.07
|
||||
10 2480376.3 2480352.2 24.021192 2485505 -8.5719876e-11 -5152.7478 0 2686.2041 -3.8355089e+08 926263.48
|
||||
Loop time of 0.00267726 on 4 procs for 10 steps with 4 atoms
|
||||
|
||||
Performance: 0.323 ns/day, 74.368 hours/ns, 3735.160 timesteps/s
|
||||
91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00011826 | 0.00027376 | 0.00073862 | 0.0 | 10.23
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00080514 | 0.0011864 | 0.001574 | 0.9 | 44.31
|
||||
Output | 0.00094914 | 0.0011944 | 0.0017326 | 0.9 | 44.61
|
||||
Modify | 3.3379e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.17
|
||||
Other | | 1.824e-05 | | | 0.68
|
||||
|
||||
Nlocal: 1 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 599 ave 600 max 596 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 241.5 ave 966 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 966
|
||||
Ave neighs/atom = 241.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Apr 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
dimension 3
|
||||
|
|
@ -21,7 +20,7 @@ pair_style table spline 15000
|
|||
|
||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
|
||||
neigh_modify delay 0 every 1 check yes one 10000
|
||||
neighbor 12.0 bin
|
||||
|
|
@ -90,54 +89,54 @@ Neighbor list info ...
|
|||
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 300 1061.5961 1926.3291 107.006 66250.679
|
||||
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
|
||||
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
|
||||
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
|
||||
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
|
||||
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
|
||||
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
|
||||
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
|
||||
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
|
||||
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
|
||||
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
|
||||
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
|
||||
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
|
||||
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
|
||||
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
|
||||
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
|
||||
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
|
||||
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
|
||||
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
|
||||
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
|
||||
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
|
||||
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
|
||||
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
|
||||
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
|
||||
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
|
||||
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
|
||||
2500 305.51905 1051.59 1932.2314 -34.076658 66487.327
|
||||
3000 291.76224 1053.524 1894.5121 45.522865 65879.535
|
||||
3500 297.65795 1017.1028 1875.085 -79.41965 67185.19
|
||||
4000 285.98779 1042.3622 1866.7058 88.549172 66357.051
|
||||
4500 295.35 1071.4505 1922.7801 -16.75965 65378.949
|
||||
5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38
|
||||
5500 292.40422 1085.3901 1928.2287 161.88502 65677.644
|
||||
6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05
|
||||
6500 308.03807 1046.1413 1934.0436 249.70237 66052.045
|
||||
7000 289.33716 1037.9657 1871.9636 47.662734 66782.578
|
||||
7500 297.3092 1032.356 1889.3329 -24.049617 66129.95
|
||||
8000 298.27827 1044.118 1903.8882 -26.61809 66720.381
|
||||
8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559
|
||||
9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4
|
||||
9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848
|
||||
10000 309.9256 1043.5321 1936.875 -103.81403 66222.21
|
||||
Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms
|
||||
|
||||
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
|
||||
Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
|
||||
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
|
||||
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
|
||||
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
|
||||
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
|
||||
Other | | 0.1252 | | | 0.36
|
||||
Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39
|
||||
Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44
|
||||
Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68
|
||||
Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00
|
||||
Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25
|
||||
Other | | 0.1042 | | | 0.25
|
||||
|
||||
Nlocal: 968 ave 968 max 968 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 9112 ave 9112 max 9112 min
|
||||
Nghost: 9215 ave 9215 max 9215 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 404392 ave 404392 max 404392 min
|
||||
Neighs: 411837 ave 411837 max 411837 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 404392
|
||||
Ave neighs/atom = 417.76
|
||||
Total # of neighbors = 411837
|
||||
Ave neighs/atom = 425.451
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:34
|
||||
Total wall time: 0:00:42
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Apr 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
dimension 3
|
||||
|
|
@ -21,7 +20,7 @@ pair_style table spline 15000
|
|||
|
||||
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
|
||||
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:481)
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
|
||||
neigh_modify delay 0 every 1 check yes one 10000
|
||||
neighbor 12.0 bin
|
||||
|
|
@ -90,54 +89,54 @@ Neighbor list info ...
|
|||
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 300 1061.5961 1926.3291 107.006 66250.679
|
||||
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
|
||||
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
|
||||
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
|
||||
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
|
||||
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
|
||||
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
|
||||
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
|
||||
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
|
||||
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
|
||||
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
|
||||
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
|
||||
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
|
||||
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
|
||||
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
|
||||
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
|
||||
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
|
||||
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
|
||||
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
|
||||
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
|
||||
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
|
||||
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
|
||||
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
|
||||
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
|
||||
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
|
||||
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
|
||||
2500 305.51905 1051.59 1932.2314 -34.076657 66487.327
|
||||
3000 291.76224 1053.524 1894.5121 45.522919 65879.535
|
||||
3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183
|
||||
4000 285.99141 1042.379 1866.733 88.735986 66356.756
|
||||
4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597
|
||||
5000 292.47 1012.3769 1855.405 -255.07433 67527.215
|
||||
5500 294.04431 1080.4547 1928.0208 192.6588 65811.742
|
||||
6000 300.45893 986.16669 1852.2225 -167.3405 67858.175
|
||||
6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704
|
||||
7000 312.11968 1032.7392 1932.4065 152.17956 66016.299
|
||||
7500 306.80585 1032.1157 1916.4662 51.07705 66875.727
|
||||
8000 292.30957 1048.9003 1891.4661 61.280503 65894.103
|
||||
8500 297.79592 1013.4061 1871.786 -133.01136 66842.574
|
||||
9000 290.36753 1043.7732 1880.7412 65.208248 66010.86
|
||||
9500 288.92211 1077.8835 1910.6851 46.291982 65674.639
|
||||
10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692
|
||||
Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms
|
||||
|
||||
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
|
||||
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
|
||||
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
|
||||
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
|
||||
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
|
||||
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
|
||||
Other | | 0.3112 | | | 1.08
|
||||
Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35
|
||||
Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33
|
||||
Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42
|
||||
Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02
|
||||
Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28
|
||||
Other | | 0.08323 | | | 0.60
|
||||
|
||||
Nlocal: 242 ave 244 max 239 min
|
||||
Nlocal: 242 ave 248 max 232 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 5718.5 ave 5736 max 5702 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 100703 ave 108064 max 93454 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 5845.75 ave 5877 max 5808 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Neighs: 104313 ave 113860 max 95507 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 402813
|
||||
Ave neighs/atom = 416.129
|
||||
Neighbor list builds = 14
|
||||
Total # of neighbors = 417252
|
||||
Ave neighs/atom = 431.045
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:28
|
||||
Total wall time: 0:00:14
|
||||
|
|
@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
run 10000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
|
||||
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 60875.649 tau/day, 70457.927 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
|
||||
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
|
||||
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
|
||||
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
|
||||
Other | | 0.002982 | | | 2.10
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 43 ave 43 max 43 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 43
|
||||
Ave neighs/atom = 4.3
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
|
||||
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 64220.659 tau/day, 74329.466 timesteps/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
|
||||
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
|
||||
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
|
||||
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
|
||||
Other | | 0.05989 | | | 44.52
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 17.5 ave 33 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 70
|
||||
Ave neighs/atom = 7
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
run 10000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
|
||||
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
|
||||
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
|
||||
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
|
||||
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
|
||||
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
|
||||
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
|
||||
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
|
||||
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
|
||||
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
|
||||
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
|
||||
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29234.801 tau/day, 33836.575 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
|
||||
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
|
||||
Other | | 0.003813 | | | 1.29
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 88 ave 88 max 88 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 88
|
||||
Ave neighs/atom = 5.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
|
||||
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
|
||||
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
|
||||
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
|
||||
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
|
||||
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
|
||||
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
|
||||
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
|
||||
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
|
||||
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
|
||||
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
|
||||
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 34303.820 tau/day, 39703.495 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
|
||||
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
|
||||
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
|
||||
Other | | 0.1208 | | | 47.96
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 9 ave 10 max 8 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 34.5 ave 67 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 138
|
||||
Ave neighs/atom = 8.625
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
run 10000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,178 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
|
||||
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
|
||||
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 57828.835 tau/day, 66931.522 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
|
||||
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
|
||||
Other | | 0.004268 | | | 2.86
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45 ave 45 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45
|
||||
Ave neighs/atom = 4.5
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,178 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
|
||||
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
|
||||
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 59247.054 tau/day, 68572.979 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
|
||||
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
|
||||
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
|
||||
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
|
||||
Other | | 0.06674 | | | 45.76
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 18.5 ave 35 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 74
|
||||
Ave neighs/atom = 7.4
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
run 10000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,178 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
|
||||
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
|
||||
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
|
||||
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
|
||||
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
|
||||
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
|
||||
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
|
||||
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
|
||||
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
|
||||
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
|
||||
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
|
||||
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 26356.746 tau/day, 30505.493 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
|
||||
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
|
||||
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
|
||||
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
|
||||
Other | | 0.003398 | | | 1.04
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 116 ave 116 max 116 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 116
|
||||
Ave neighs/atom = 7.25
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,178 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
|
||||
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
|
||||
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
|
||||
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
|
||||
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
|
||||
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
|
||||
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
|
||||
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
|
||||
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
|
||||
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
|
||||
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
|
||||
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29625.313 tau/day, 34288.557 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
|
||||
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
|
||||
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
|
||||
Other | | 0.139 | | | 47.65
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11 ave 14 max 8 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 46 ave 89 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 184
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
|
|
@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0
|
|||
|
||||
read_data data.pegc12e8.gz
|
||||
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
40140 atoms
|
||||
reading velocities ...
|
||||
|
|
@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0
|
|||
thermo_style multi
|
||||
thermo 200
|
||||
run 1000
|
||||
Memory usage per processor = 12.4188 Mbytes
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 15 15 45
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/sdk, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
|
||||
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
|
||||
---------------- Step 200 ----- CPU = 8.7547 (sec) ----------------
|
||||
---------------- Step 200 ----- CPU = 11.2079 (sec) ----------------
|
||||
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
|
||||
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
|
||||
---------------- Step 400 ----- CPU = 17.7479 (sec) ----------------
|
||||
---------------- Step 400 ----- CPU = 22.6137 (sec) ----------------
|
||||
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
|
||||
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
|
||||
---------------- Step 600 ----- CPU = 26.7299 (sec) ----------------
|
||||
---------------- Step 600 ----- CPU = 33.9441 (sec) ----------------
|
||||
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
|
||||
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
|
||||
---------------- Step 800 ----- CPU = 35.8941 (sec) ----------------
|
||||
---------------- Step 800 ----- CPU = 45.4291 (sec) ----------------
|
||||
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
|
||||
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
|
||||
---------------- Step 1000 ----- CPU = 45.1542 (sec) ----------------
|
||||
---------------- Step 1000 ----- CPU = 56.9328 (sec) ----------------
|
||||
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
|
||||
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
|
||||
Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms
|
||||
|
||||
Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms
|
||||
99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s
|
||||
Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27
|
||||
Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14
|
||||
Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34
|
||||
Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49
|
||||
Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00
|
||||
Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19
|
||||
Other | | 0.2571 | | | 0.57
|
||||
Pair | 50.734 | 50.734 | 50.734 | 0.0 | 89.11
|
||||
Bond | 0.94032 | 0.94032 | 0.94032 | 0.0 | 1.65
|
||||
Neigh | 4.5195 | 4.5195 | 4.5195 | 0.0 | 7.94
|
||||
Comm | 0.15045 | 0.15045 | 0.15045 | 0.0 | 0.26
|
||||
Output | 0.00056767 | 0.00056767 | 0.00056767 | 0.0 | 0.00
|
||||
Modify | 0.47228 | 0.47228 | 0.47228 | 0.0 | 0.83
|
||||
Other | | 0.1154 | | | 0.20
|
||||
|
||||
Nlocal: 20070 ave 20100 max 20040 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 20230.5 ave 20241 max 20220 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 40140 ave 40140 max 40140 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 25966 ave 25966 max 25966 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5686756
|
||||
Ave neighs/atom = 141.673
|
||||
|
|
@ -113,3 +124,4 @@ Neighbor list builds = 38
|
|||
Dangerous builds = 0
|
||||
#write_restart pegc12e8-1.restart
|
||||
|
||||
Total wall time: 0:00:57
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style angle
|
||||
|
||||
# enforce that in z-direction there is only one
|
||||
# processor (could be two) for optimal performance
|
||||
processors * * 1
|
||||
|
||||
# read topology and force field
|
||||
pair_style lj/sdk 15.0
|
||||
bond_style harmonic
|
||||
angle_style sdk
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
read_data data.pegc12e8.gz
|
||||
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
40140 atoms
|
||||
reading velocities ...
|
||||
40140 velocities
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
13284 bonds
|
||||
reading angles ...
|
||||
12177 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
neighbor 3.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 5.0
|
||||
#dump 1 all xtc 200 pegc12e8-1.xtc
|
||||
#dump_modify 1 unwrap yes
|
||||
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
|
||||
#dump_modify 2 unwrap yes
|
||||
|
||||
velocity all create 303.0 46659 mom yes rot yes dist gaussian
|
||||
|
||||
fix 1 all nvt temp 303.0 303.0 100.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 200
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 15 15 45
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/sdk, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
|
||||
PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
|
||||
---------------- Step 200 ----- CPU = 3.0597 (sec) ----------------
|
||||
TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
|
||||
PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
|
||||
---------------- Step 400 ----- CPU = 6.2514 (sec) ----------------
|
||||
TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
|
||||
PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
|
||||
---------------- Step 600 ----- CPU = 9.4073 (sec) ----------------
|
||||
TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
|
||||
PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
|
||||
---------------- Step 800 ----- CPU = 12.6096 (sec) ----------------
|
||||
TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
|
||||
PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
|
||||
---------------- Step 1000 ----- CPU = 15.9134 (sec) ----------------
|
||||
TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
|
||||
PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
|
||||
Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms
|
||||
|
||||
Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.325 | 13.6 | 13.755 | 4.7 | 85.46
|
||||
Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57
|
||||
Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79
|
||||
Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61
|
||||
Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00
|
||||
Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09
|
||||
Other | | 0.0768 | | | 0.48
|
||||
|
||||
Nlocal: 10035 ave 10084 max 9971 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 14548.8 ave 14610 max 14509 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 5686756
|
||||
Ave neighs/atom = 141.673
|
||||
Ave special neighs/atom = 1.26861
|
||||
Neighbor list builds = 38
|
||||
Dangerous builds = 0
|
||||
#write_restart pegc12e8-1.restart
|
||||
|
||||
Total wall time: 0:00:16
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
|
|
@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0
|
|||
|
||||
read_data data.pegc12e8.gz
|
||||
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
40140 atoms
|
||||
reading velocities ...
|
||||
|
|
@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0
|
|||
thermo_style multi
|
||||
thermo 200
|
||||
run 1000
|
||||
Memory usage per processor = 12.4188 Mbytes
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 15 15 45
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/sdk, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
|
||||
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
|
||||
---------------- Step 200 ----- CPU = 8.6552 (sec) ----------------
|
||||
---------------- Step 200 ----- CPU = 11.2074 (sec) ----------------
|
||||
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
|
||||
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
|
||||
---------------- Step 400 ----- CPU = 17.5807 (sec) ----------------
|
||||
---------------- Step 400 ----- CPU = 22.6113 (sec) ----------------
|
||||
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
|
||||
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
|
||||
---------------- Step 600 ----- CPU = 28.1043 (sec) ----------------
|
||||
---------------- Step 600 ----- CPU = 34.0551 (sec) ----------------
|
||||
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
|
||||
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
|
||||
---------------- Step 800 ----- CPU = 40.5132 (sec) ----------------
|
||||
---------------- Step 800 ----- CPU = 45.5316 (sec) ----------------
|
||||
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
|
||||
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
|
||||
---------------- Step 1000 ----- CPU = 52.8166 (sec) ----------------
|
||||
---------------- Step 1000 ----- CPU = 56.9111 (sec) ----------------
|
||||
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
|
||||
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
|
||||
Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms
|
||||
|
||||
Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms
|
||||
99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s
|
||||
Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79
|
||||
Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88
|
||||
Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42
|
||||
Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27
|
||||
Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00
|
||||
Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12
|
||||
Other | | 0.2731 | | | 0.52
|
||||
Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22
|
||||
Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55
|
||||
Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94
|
||||
Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26
|
||||
Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00
|
||||
Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83
|
||||
Other | | 0.1127 | | | 0.20
|
||||
|
||||
Nlocal: 20070 ave 20109 max 20031 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 20234 ave 20281 max 20187 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 40140 ave 40140 max 40140 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 25968 ave 25968 max 25968 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5691680
|
||||
Ave neighs/atom = 141.796
|
||||
|
|
@ -113,3 +124,4 @@ Neighbor list builds = 38
|
|||
Dangerous builds = 0
|
||||
#write_restart pegc12e8-1.restart
|
||||
|
||||
Total wall time: 0:00:57
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style angle
|
||||
|
||||
# enforce that in z-direction there is only one
|
||||
# processor (could be two) for optimal performance
|
||||
processors * * 1
|
||||
|
||||
# read topology and force field
|
||||
pair_style lj/sdk 15.0
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
read_data data.pegc12e8.gz
|
||||
orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
40140 atoms
|
||||
reading velocities ...
|
||||
40140 velocities
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
13284 bonds
|
||||
reading angles ...
|
||||
12177 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
neighbor 3.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 5.0
|
||||
#dump 1 all xtc 200 pegc12e8-1.xtc
|
||||
#dump_modify 1 unwrap yes
|
||||
#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
|
||||
#dump_modify 2 unwrap yes
|
||||
|
||||
velocity all create 303.0 46659 mom yes rot yes dist gaussian
|
||||
|
||||
fix 1 all nvt temp 303.0 303.0 100.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 200
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 15 15 45
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/sdk, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
|
||||
PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 105.8245
|
||||
---------------- Step 200 ----- CPU = 3.0107 (sec) ----------------
|
||||
TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
|
||||
PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
|
||||
---------------- Step 400 ----- CPU = 6.1324 (sec) ----------------
|
||||
TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
|
||||
PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
|
||||
---------------- Step 600 ----- CPU = 9.3443 (sec) ----------------
|
||||
TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
|
||||
PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
|
||||
---------------- Step 800 ----- CPU = 12.5388 (sec) ----------------
|
||||
TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
|
||||
PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
|
||||
---------------- Step 1000 ----- CPU = 15.7416 (sec) ----------------
|
||||
TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
|
||||
PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
|
||||
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
|
||||
E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
|
||||
Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms
|
||||
|
||||
Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.591 | 13.612 | 13.626 | 0.4 | 86.47
|
||||
Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47
|
||||
Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79
|
||||
Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65
|
||||
Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00
|
||||
Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13
|
||||
Other | | 0.07576 | | | 0.48
|
||||
|
||||
Nlocal: 10035 ave 10098 max 10004 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 14546.5 ave 14564 max 14503 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 5691680
|
||||
Ave neighs/atom = 141.796
|
||||
Ave special neighs/atom = 1.26861
|
||||
Neighbor list builds = 38
|
||||
Dangerous builds = 0
|
||||
#write_restart pegc12e8-1.restart
|
||||
|
||||
Total wall time: 0:00:15
|
||||
|
|
@ -0,0 +1,145 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# coarse grained SDS surfactant monolayer
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style full
|
||||
processors * * 1
|
||||
|
||||
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
|
||||
bond_style harmonic
|
||||
angle_style sdk
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
read_data data.sds.gz
|
||||
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
31280 atoms
|
||||
reading velocities ...
|
||||
31280 velocities
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
4096 bonds
|
||||
reading angles ...
|
||||
3072 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 4 coul/long # SO4 SOD
|
||||
pair_coeff 4 4 coul/long # SOD SOD
|
||||
pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4
|
||||
pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM
|
||||
pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT
|
||||
pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD
|
||||
pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W
|
||||
pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM
|
||||
pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM
|
||||
pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM
|
||||
pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM
|
||||
pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT
|
||||
pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT
|
||||
pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT
|
||||
pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD
|
||||
pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W
|
||||
pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W
|
||||
|
||||
|
||||
group charged type 1 4
|
||||
2048 atoms in group charged
|
||||
atom_modify first charged
|
||||
|
||||
kspace_style pppm/cg 0.00001
|
||||
kspace_modify order 3
|
||||
|
||||
comm_modify mode multi
|
||||
neighbor 2.0 multi
|
||||
neigh_modify delay 4 every 2 check yes
|
||||
|
||||
timestep 10.0
|
||||
|
||||
fix 1 all nvt temp 310.0 310.0 100.0
|
||||
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.0416781
|
||||
grid = 8 4 12
|
||||
stencil order = 3
|
||||
estimated absolute RMS force accuracy = 0.00248777
|
||||
estimated relative force accuracy = 7.49185e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1155 384
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 28.5
|
||||
ghost atom cutoff = 28.5
|
||||
binsize = 8.5, bins = 27 14 48
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/sdk, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton
|
||||
stencil: half/multi/3d/newton
|
||||
bin: standard
|
||||
(2) pair coul/long, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
PPPM/cg optimization cutoff: 1e-05
|
||||
Total charged atoms: 6.5%
|
||||
Min/max charged atoms/proc: 6.5% 6.5%
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.49 | 35.49 | 35.49 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
|
||||
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
|
||||
20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751
|
||||
30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129
|
||||
40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838
|
||||
50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457
|
||||
60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545
|
||||
70 310.13623 -249262.32 2595.874 -217750.35 -26.276067
|
||||
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
|
||||
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
|
||||
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
|
||||
Loop time of 9.61984 on 1 procs for 100 steps with 31280 atoms
|
||||
|
||||
Performance: 8.981 ns/day, 2.672 hours/ns, 10.395 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.2928 | 7.2928 | 7.2928 | 0.0 | 75.81
|
||||
Bond | 0.036198 | 0.036198 | 0.036198 | 0.0 | 0.38
|
||||
Kspace | 0.053125 | 0.053125 | 0.053125 | 0.0 | 0.55
|
||||
Neigh | 2.117 | 2.117 | 2.117 | 0.0 | 22.01
|
||||
Comm | 0.029731 | 0.029731 | 0.029731 | 0.0 | 0.31
|
||||
Output | 0.0014369 | 0.0014369 | 0.0014369 | 0.0 | 0.01
|
||||
Modify | 0.079014 | 0.079014 | 0.079014 | 0.0 | 0.82
|
||||
Other | | 0.01051 | | | 0.11
|
||||
|
||||
Nlocal: 31280 ave 31280 max 31280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 16629 ave 16629 max 16629 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.40168e+06 ave 3.40168e+06 max 3.40168e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3401676
|
||||
Ave neighs/atom = 108.749
|
||||
Ave special neighs/atom = 0.458312
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:10
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# coarse grained SDS surfactant monolayer
|
||||
|
||||
|
|
@ -58,7 +57,7 @@ atom_modify first charged
|
|||
kspace_style pppm/cg 0.00001
|
||||
kspace_modify order 3
|
||||
|
||||
communicate multi
|
||||
comm_modify mode multi
|
||||
neighbor 2.0 multi
|
||||
neigh_modify delay 4 every 2 check yes
|
||||
|
||||
|
|
@ -70,6 +69,7 @@ thermo 10
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.0416781
|
||||
grid = 8 4 12
|
||||
stencil order = 3
|
||||
|
|
@ -77,10 +77,27 @@ PPPM initialization ...
|
|||
estimated relative force accuracy = 7.49185e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 525 96
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 28.5
|
||||
ghost atom cutoff = 28.5
|
||||
binsize = 8.5, bins = 27 14 48
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/sdk, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton
|
||||
stencil: half/multi/3d/newton
|
||||
bin: standard
|
||||
(2) pair coul/long, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
PPPM/cg optimization cutoff: 1e-05
|
||||
Total charged atoms: 6.5%
|
||||
Min/max charged atoms/proc: 6.4% 6.7%
|
||||
Memory usage per processor = 7.66668 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.48 | 17.48 | 17.48 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
|
||||
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
|
||||
|
|
@ -93,22 +110,22 @@ Step Temp E_pair E_mol TotEng Press
|
|||
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
|
||||
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
|
||||
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
|
||||
Loop time of 2.54454 on 4 procs for 100 steps with 31280 atoms
|
||||
|
||||
Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 21.216 ns/day 1.131 hours/ns 24.556 timesteps/s
|
||||
Performance: 33.955 ns/day, 0.707 hours/ns, 39.300 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.082 | 3.0928 | 3.1091 | 0.6 | 75.95
|
||||
Bond | 0.021077 | 0.021421 | 0.021823 | 0.2 | 0.53
|
||||
Kspace | 0.042646 | 0.058859 | 0.069797 | 4.1 | 1.45
|
||||
Neigh | 0.79689 | 0.79696 | 0.79711 | 0.0 | 19.57
|
||||
Comm | 0.048668 | 0.049552 | 0.050446 | 0.3 | 1.22
|
||||
Output | 0.00072145 | 0.00095147 | 0.0016341 | 1.3 | 0.02
|
||||
Modify | 0.034767 | 0.035175 | 0.035714 | 0.2 | 0.86
|
||||
Other | | 0.01665 | | | 0.41
|
||||
Pair | 1.8639 | 1.8913 | 1.9283 | 1.8 | 74.33
|
||||
Bond | 0.0092797 | 0.0094567 | 0.0095828 | 0.1 | 0.37
|
||||
Kspace | 0.018389 | 0.056616 | 0.084424 | 10.7 | 2.23
|
||||
Neigh | 0.53553 | 0.53569 | 0.53605 | 0.0 | 21.05
|
||||
Comm | 0.023819 | 0.02433 | 0.02506 | 0.3 | 0.96
|
||||
Output | 0.00058866 | 0.00084978 | 0.0016243 | 0.0 | 0.03
|
||||
Modify | 0.021841 | 0.022059 | 0.022308 | 0.1 | 0.87
|
||||
Other | | 0.004233 | | | 0.17
|
||||
|
||||
Nlocal: 7820 ave 7866 max 7774 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
|
@ -125,3 +142,4 @@ Dangerous builds = 0
|
|||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,129 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# coarse grained SDS surfactant monolayer
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style full
|
||||
processors * * 1
|
||||
|
||||
pair_style lj/sdk/coul/long 15.0
|
||||
bond_style harmonic
|
||||
angle_style sdk
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
read_data data.sds.gz
|
||||
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
31280 atoms
|
||||
reading velocities ...
|
||||
31280 velocities
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
4096 bonds
|
||||
reading angles ...
|
||||
3072 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj9_6 0.7000 4.3210 # SO4 SO4
|
||||
pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM
|
||||
pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT
|
||||
pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD
|
||||
pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W
|
||||
pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM
|
||||
pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM
|
||||
pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM
|
||||
pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM
|
||||
pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT
|
||||
pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT
|
||||
pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT
|
||||
pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD
|
||||
pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W
|
||||
pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W
|
||||
|
||||
kspace_style pppm/cg 0.00001
|
||||
kspace_modify order 3
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 4 every 2 check yes
|
||||
|
||||
timestep 10.0
|
||||
|
||||
fix 1 all nvt temp 310.0 310.0 100.0
|
||||
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.0789325
|
||||
grid = 15 8 25
|
||||
stencil order = 3
|
||||
estimated absolute RMS force accuracy = 0.00275556
|
||||
estimated relative force accuracy = 8.29828e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 5544 3000
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 27 14 48
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/sdk/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
PPPM/cg optimization cutoff: 1e-05
|
||||
Total charged atoms: 6.5%
|
||||
Min/max charged atoms/proc: 6.5% 6.5%
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
|
||||
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
|
||||
20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631
|
||||
30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902
|
||||
40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066
|
||||
50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007
|
||||
60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965
|
||||
70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691
|
||||
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
|
||||
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
|
||||
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
|
||||
Loop time of 9.23618 on 1 procs for 100 steps with 31280 atoms
|
||||
|
||||
Performance: 9.355 ns/day, 2.566 hours/ns, 10.827 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7363 | 7.7363 | 7.7363 | 0.0 | 83.76
|
||||
Bond | 0.032901 | 0.032901 | 0.032901 | 0.0 | 0.36
|
||||
Kspace | 0.078907 | 0.078907 | 0.078907 | 0.0 | 0.85
|
||||
Neigh | 1.2706 | 1.2706 | 1.2706 | 0.0 | 13.76
|
||||
Comm | 0.026005 | 0.026005 | 0.026005 | 0.0 | 0.28
|
||||
Output | 0.0014131 | 0.0014131 | 0.0014131 | 0.0 | 0.02
|
||||
Modify | 0.079446 | 0.079446 | 0.079446 | 0.0 | 0.86
|
||||
Other | | 0.01055 | | | 0.11
|
||||
|
||||
Nlocal: 31280 ave 31280 max 31280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 15812 ave 15812 max 15812 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.3521e+06 ave 3.3521e+06 max 3.3521e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3352103
|
||||
Ave neighs/atom = 107.164
|
||||
Ave special neighs/atom = 0.458312
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:09
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# coarse grained SDS surfactant monolayer
|
||||
|
||||
|
|
@ -62,6 +61,7 @@ thermo 10
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.0789325
|
||||
grid = 15 8 25
|
||||
stencil order = 3
|
||||
|
|
@ -69,10 +69,22 @@ PPPM initialization ...
|
|||
estimated relative force accuracy = 8.29828e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 2156 840
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 4 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 27 14 48
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/sdk/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
PPPM/cg optimization cutoff: 1e-05
|
||||
Total charged atoms: 6.5%
|
||||
Min/max charged atoms/proc: 6.4% 6.7%
|
||||
Memory usage per processor = 8.05923 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.32 | 17.32 | 17.32 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
|
||||
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
|
||||
|
|
@ -85,22 +97,22 @@ Step Temp E_pair E_mol TotEng Press
|
|||
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
|
||||
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
|
||||
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
|
||||
Loop time of 2.45408 on 4 procs for 100 steps with 31280 atoms
|
||||
|
||||
Loop time of 3.44972 on 4 procs for 100 steps with 31280 atoms
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 25.046 ns/day 0.958 hours/ns 28.988 timesteps/s
|
||||
Performance: 35.207 ns/day, 0.682 hours/ns, 40.748 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.7883 | 2.817 | 2.8415 | 1.1 | 81.66
|
||||
Bond | 0.017868 | 0.018973 | 0.020636 | 0.7 | 0.55
|
||||
Kspace | 0.063881 | 0.088012 | 0.11571 | 6.2 | 2.55
|
||||
Neigh | 0.42765 | 0.42828 | 0.42882 | 0.1 | 12.41
|
||||
Comm | 0.043887 | 0.044575 | 0.045079 | 0.2 | 1.29
|
||||
Output | 0.00072694 | 0.00096422 | 0.0016718 | 1.3 | 0.03
|
||||
Modify | 0.035513 | 0.035955 | 0.036887 | 0.3 | 1.04
|
||||
Other | | 0.01597 | | | 0.46
|
||||
Pair | 2.0065 | 2.0143 | 2.0326 | 0.8 | 82.08
|
||||
Bond | 0.0084255 | 0.0086145 | 0.0088007 | 0.1 | 0.35
|
||||
Kspace | 0.033373 | 0.052041 | 0.060933 | 4.8 | 2.12
|
||||
Neigh | 0.32741 | 0.32748 | 0.32754 | 0.0 | 13.34
|
||||
Comm | 0.022403 | 0.023025 | 0.023735 | 0.4 | 0.94
|
||||
Output | 0.00060058 | 0.00086623 | 0.0016549 | 0.0 | 0.04
|
||||
Modify | 0.022533 | 0.022723 | 0.022876 | 0.1 | 0.93
|
||||
Other | | 0.005038 | | | 0.21
|
||||
|
||||
Nlocal: 7820 ave 7866 max 7775 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
|
@ -114,3 +126,4 @@ Ave neighs/atom = 107.164
|
|||
Ave special neighs/atom = 0.458312
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
|
|
@ -15,7 +14,7 @@ kspace_style pppm 0.0001
|
|||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
|
|
@ -78,134 +77,179 @@ thermo 10
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 6776 1800
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2013-10-22.
|
||||
colvars: # indexFile = "" [default]
|
||||
colvars: # analysis = off [default]
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # outputAccumulatedWork = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
|
|
@ -215,51 +259,52 @@ SHAKE stats (type/ave/delta) on step 0
|
|||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.4104 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
|
||||
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
|
||||
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
|
||||
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
|
||||
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.818 55.459511 0.20679816
|
||||
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
|
||||
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.62715 11.433633
|
||||
80 267.51476 -5206.4041 -6282.6428 1076.2386 -6456.6352 31.611841 6.3553235
|
||||
90 278.15512 -5245.383 -6364.4288 1119.0458 -6499.8036 28.849902 0.36938817
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97185e-05
|
||||
6 0.996996 1.00569e-05
|
||||
8 1.08 6.02346e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36078e-05
|
||||
31 104.52 0.00306008
|
||||
100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Loop time of 1.04673 on 2 procs for 100 steps with 2004 atoms
|
||||
99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.509 ns/day 1.454 hours/ns 95.536 timesteps/s
|
||||
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76537 | 0.76832 | 0.77127 | 0.3 | 73.40
|
||||
Bond | 0.0024452 | 0.0025067 | 0.0025682 | 0.1 | 0.24
|
||||
Kspace | 0.088877 | 0.092861 | 0.096845 | 1.3 | 8.87
|
||||
Neigh | 0.13657 | 0.13657 | 0.13658 | 0.0 | 13.05
|
||||
Comm | 0.0172 | 0.018169 | 0.019137 | 0.7 | 1.74
|
||||
Output | 0.0002296 | 0.00031686 | 0.00040412 | 0.5 | 0.03
|
||||
Modify | 0.025518 | 0.025554 | 0.025591 | 0.0 | 2.44
|
||||
Other | | 0.002431 | | | 0.23
|
||||
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
|
||||
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
|
||||
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
|
||||
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
|
||||
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
|
||||
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
|
||||
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
|
||||
Other | | 0.001615 | | | 0.07
|
||||
|
||||
Nlocal: 1002 ave 1013 max 991 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8629.5 ave 8641 max 8618 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354118 ave 356534 max 351703 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
|
|
@ -269,279 +314,316 @@ Dangerous builds = 2
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 6776 1800
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97185e-05
|
||||
6 0.996996 1.00569e-05
|
||||
8 1.08 6.02346e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36078e-05
|
||||
31 104.52 0.00306008
|
||||
Memory usage per processor = 10.4104 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866
|
||||
110 266.26279 -5341.2085 -6412.4103 1071.2018 -6552.7566 33.572973 1.9229795
|
||||
120 262.66439 -5386.2495 -6442.9746 1056.7251 -6587.5499 29.859549 2.712489
|
||||
130 252.83437 -5422.5446 -6439.7226 1017.1779 -6580.4751 25.979056 1.2031649
|
||||
140 253.85101 -5452.1904 -6473.4584 1021.268 -6609.4883 26.071526 0.30586448
|
||||
150 261.31821 -5490.4808 -6541.7901 1051.3093 -6646.615 16.258546 6.904992
|
||||
160 255.73714 -5521.6048 -6550.4609 1028.8561 -6658.1531 19.717543 12.339834
|
||||
170 253.42881 -5540.0985 -6559.668 1019.5695 -6656.6862 23.293616 10.289885
|
||||
180 248.51049 -5550.3254 -6550.1079 999.78252 -6661.4178 26.200082 3.4339077
|
||||
190 250.80375 -5555.2616 -6564.2702 1009.0086 -6666.1496 25.536628 3.3495235
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81287e-06
|
||||
6 0.997 7.79626e-07
|
||||
8 1.08 1.08933e-06
|
||||
10 1.111 2.96498e-07
|
||||
12 1.08 4.69169e-07
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76617e-06
|
||||
31 104.52 0.000411076
|
||||
200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Loop time of 1.00434 on 2 procs for 100 steps with 2004 atoms
|
||||
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 17.205 ns/day 1.395 hours/ns 99.568 timesteps/s
|
||||
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.78001 | 0.78091 | 0.78181 | 0.1 | 77.75
|
||||
Bond | 0.0025158 | 0.0025688 | 0.0026219 | 0.1 | 0.26
|
||||
Kspace | 0.093375 | 0.094821 | 0.096266 | 0.5 | 9.44
|
||||
Neigh | 0.080238 | 0.08025 | 0.080261 | 0.0 | 7.99
|
||||
Comm | 0.01671 | 0.017204 | 0.017699 | 0.4 | 1.71
|
||||
Output | 0.0002296 | 0.00031531 | 0.00040102 | 0.5 | 0.03
|
||||
Modify | 0.025788 | 0.025804 | 0.02582 | 0.0 | 2.57
|
||||
Other | | 0.002469 | | | 0.25
|
||||
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
|
||||
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
|
||||
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
|
||||
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
|
||||
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
|
||||
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
|
||||
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
|
||||
Other | | 0.001596 | | | 0.08
|
||||
|
||||
Nlocal: 1002 ave 1014 max 990 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8654 ave 8667 max 8641 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354044 ave 355332 max 352756 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708088
|
||||
Ave neighs/atom = 353.337
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 6776 1800
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2013-10-22.
|
||||
colvars: # indexFile = "" [default]
|
||||
colvars: # analysis = off [default]
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # outputAccumulatedWork = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81287e-06
|
||||
6 0.997 7.79626e-07
|
||||
8 1.08 1.08933e-06
|
||||
10 1.111 2.96498e-07
|
||||
12 1.08 4.69169e-07
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76617e-06
|
||||
31 104.52 0.000411076
|
||||
Memory usage per processor = 10.4104 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891
|
||||
210 253.15173 -5538.5647 -6557.0194 1018.4547 -6672.044 37.671405 0.61299805
|
||||
220 245.19832 -5522.5253 -6508.9826 986.45735 -6628.2043 36.656213 0.04862311
|
||||
230 258.65093 -5495.7204 -6536.2989 1040.5785 -6658.0891 34.855426 0.22044707
|
||||
240 260.80348 -5469.8527 -6519.0912 1049.2385 -6624.1806 31.576284 3.7570152
|
||||
250 269.06517 -5438.3941 -6520.8701 1082.4761 -6616.3835 25.443998 8.6642401
|
||||
260 266.10873 -5397.3229 -6467.905 1070.582 -6580.6583 26.873845 8.3331291
|
||||
270 272.81399 -5350.8435 -6448.4015 1097.5579 -6563.7941 23.11303 10.972811
|
||||
280 279.52614 -5307.9857 -6432.5473 1124.5616 -6557.7474 33.640052 8.5474491
|
||||
290 286.8015 -5260.87 -6414.7011 1153.8311 -6515.4961 28.571844 5.9093384
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
|
||||
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
|
||||
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
|
||||
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
|
||||
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
|
||||
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
|
||||
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
|
||||
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
|
||||
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79747e-05
|
||||
6 0.997005 1.02624e-05
|
||||
8 1.08 1.84986e-05
|
||||
10 1.111 9.9852e-06
|
||||
12 1.08 8.8315e-06
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98839e-06
|
||||
12 1.08 8.84111e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.84856e-05
|
||||
31 104.52 0.00169095
|
||||
300 291.51723 -5216.3366 -6389.1396 1172.803 -6503.1168 27.877108 2.2481775
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168383
|
||||
300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Loop time of 1.0092 on 2 procs for 100 steps with 2004 atoms
|
||||
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 17.123 ns/day 1.402 hours/ns 99.089 timesteps/s
|
||||
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.77015 | 0.77511 | 0.78007 | 0.6 | 76.80
|
||||
Bond | 0.0022984 | 0.0024998 | 0.0027013 | 0.4 | 0.25
|
||||
Kspace | 0.088884 | 0.093076 | 0.097267 | 1.4 | 9.22
|
||||
Neigh | 0.092871 | 0.092888 | 0.092905 | 0.0 | 9.20
|
||||
Comm | 0.016476 | 0.017 | 0.017524 | 0.4 | 1.68
|
||||
Output | 0.00022602 | 0.00031459 | 0.00040317 | 0.5 | 0.03
|
||||
Modify | 0.025814 | 0.025818 | 0.025823 | 0.0 | 2.56
|
||||
Other | | 0.002488 | | | 0.25
|
||||
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
|
||||
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
|
||||
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
|
||||
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
|
||||
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
|
||||
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
|
||||
Other | | 0.001731 | | | 0.08
|
||||
|
||||
Nlocal: 1002 ave 1024 max 980 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8717.5 ave 8755 max 8680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354073 ave 358151 max 349995 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708146
|
||||
Ave neighs/atom = 353.366
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
|
|
@ -0,0 +1,629 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
|
||||
Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
|
||||
Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
|
||||
Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
|
||||
Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
|
||||
Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
|
||||
Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
|
||||
Other | | 0.001141 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
|
||||
190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
|
||||
Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
|
||||
Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
|
||||
Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
|
||||
Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
|
||||
Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
|
||||
Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
|
||||
Other | | 0.001623 | | | 0.28
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
|
||||
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
|
||||
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
|
||||
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
|
||||
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
|
||||
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
|
||||
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
|
||||
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
|
||||
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98838e-06
|
||||
12 1.08 8.84113e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168382
|
||||
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
|
||||
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
|
||||
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
|
||||
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
|
||||
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
|
||||
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
|
||||
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
|
||||
Other | | 0.001705 | | | 0.29
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -1,5 +1,4 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
|
|
@ -15,7 +14,7 @@ kspace_style pppm 0.0001
|
|||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
|
|
@ -77,88 +76,122 @@ thermo 10
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 6776 1800
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2013-10-22.
|
||||
colvars: # indexFile = "" [default]
|
||||
colvars: # analysis = off [default]
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # disableForces = off [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 0.
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # outputAccumulatedWork = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
|
|
@ -168,58 +201,60 @@ SHAKE stats (type/ave/delta) on step 0
|
|||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.4103 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
|
||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
||||
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
|
||||
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
|
||||
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8833 26.28765 20.573958
|
||||
70 277.26045 -5224.8416 -6340.2881 1115.4465 -6447.8495 27.742889 0.69414895
|
||||
80 268.01458 -5281.8501 -6360.0996 1078.2495 -6496.6062 20.300729 5.260642
|
||||
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191466
|
||||
6 0.996989 3.5552e-05
|
||||
8 1.08 9.10001e-06
|
||||
10 1.111 1.58547e-05
|
||||
12 1.08 5.80613e-06
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92454e-05
|
||||
31 104.52 0.00239929
|
||||
100 260.35617 -5387.2298 -6434.6687 1047.4389 -6534.1957 20.246734 0.075048991
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Loop time of 1.07439 on 2 procs for 100 steps with 2004 atoms
|
||||
98.2% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.084 ns/day 1.492 hours/ns 93.076 timesteps/s
|
||||
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timings breakdown:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.77154 | 0.77308 | 0.77462 | 0.2 | 71.96
|
||||
Bond | 0.0023637 | 0.0025266 | 0.0026896 | 0.3 | 0.24
|
||||
Kspace | 0.095779 | 0.097411 | 0.099043 | 0.5 | 9.07
|
||||
Neigh | 0.15521 | 0.15521 | 0.15522 | 0.0 | 14.45
|
||||
Comm | 0.018134 | 0.018364 | 0.018594 | 0.2 | 1.71
|
||||
Output | 0.00024295 | 0.00032854 | 0.00041413 | 0.5 | 0.03
|
||||
Modify | 0.024936 | 0.024973 | 0.02501 | 0.0 | 2.32
|
||||
Other | | 0.002498 | | | 0.23
|
||||
Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
|
||||
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
|
||||
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
|
||||
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
|
||||
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
|
||||
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
|
||||
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
|
||||
Other | | 0.001465 | | | 0.06
|
||||
|
||||
Nlocal: 1002 ave 1010 max 994 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8645 ave 8652 max 8638 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354116 ave 356373 max 351860 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708233
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,260 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99
|
||||
Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18
|
||||
Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33
|
||||
Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56
|
||||
Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64
|
||||
Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05
|
||||
Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04
|
||||
Other | | 0.001264 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,163 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23
|
||||
Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15
|
||||
Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90
|
||||
Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88
|
||||
Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63
|
||||
Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02
|
||||
Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12
|
||||
Other | | 0.001613 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,163 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27
|
||||
Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19
|
||||
Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25
|
||||
Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57
|
||||
Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58
|
||||
Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09
|
||||
Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85
|
||||
Other | | 0.001274 | | | 0.21
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,158 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93
|
||||
Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15
|
||||
Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85
|
||||
Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27
|
||||
Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64
|
||||
Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01
|
||||
Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07
|
||||
Other | | 0.001546 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,158 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95
|
||||
Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18
|
||||
Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39
|
||||
Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80
|
||||
Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67
|
||||
Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05
|
||||
Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75
|
||||
Other | | 0.001239 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,516 +0,0 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 22.5866 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
|
||||
10 305.06198 -5058.8899 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
|
||||
20 311.00592 -4999.0544 -6250.2623 1251.2079 -6417.0984 47.695274 36.699706
|
||||
30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344163 10.563914
|
||||
40 297.87524 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.723201 3.8354392
|
||||
50 304.02086 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459508 0.20679801
|
||||
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.76729 0.69356508
|
||||
70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7015 39.627148 11.433632
|
||||
80 267.51473 -5206.4042 -6282.6427 1076.2385 -6456.6352 31.611843 6.3553235
|
||||
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938867
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.86583 (78.0347)
|
||||
Bond time (%) = 0.00628591 (0.262896)
|
||||
Kspace time (%) = 0.165128 (6.90614)
|
||||
Neigh time (%) = 0.314792 (13.1656)
|
||||
Comm time (%) = 0.0111108 (0.464687)
|
||||
Output time (%) = 0.000252724 (0.0105697)
|
||||
Modify time (%) = 0.0253747 (1.06125)
|
||||
Other time (%) = 0.0022521 (0.0941899)
|
||||
|
||||
FFT time (% of Kspce) = 0.0274372 (16.6158)
|
||||
FFT Gflps 3d (1d only) = 1.99867 2.86506
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0137
|
||||
colvars: Restarting collective variable "two" from value: 10.0649
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 3900175693153042431
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
Memory usage per processor = 22.5866 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
|
||||
110 266.26278 -5341.2103 -6412.412 1071.2018 -6552.7583 33.572968 1.9229782
|
||||
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859553 2.7124877
|
||||
130 252.8344 -5422.5446 -6439.7226 1017.1781 -6580.4752 25.979049 1.2031628
|
||||
140 253.85115 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071514 0.30586247
|
||||
150 261.31825 -5490.48 -6541.7895 1051.3095 -6646.6144 16.258548 6.9049974
|
||||
160 255.7368 -5521.6048 -6550.4596 1028.8547 -6658.1517 19.717533 12.339821
|
||||
170 253.42877 -5540.1003 -6559.6695 1019.5693 -6656.6878 23.293662 10.289878
|
||||
180 248.51086 -5550.3244 -6550.1084 999.78404 -6661.4182 26.200056 3.4339065
|
||||
190 250.8039 -5555.2614 -6564.2706 1009.0092 -6666.15 25.536594 3.3495152
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.7964e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69174e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411068
|
||||
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.84544 (82.572)
|
||||
Bond time (%) = 0.00609159 (0.27256)
|
||||
Kspace time (%) = 0.163201 (7.30223)
|
||||
Neigh time (%) = 0.183405 (8.20622)
|
||||
Comm time (%) = 0.00959301 (0.429227)
|
||||
Output time (%) = 0.000245094 (0.0109664)
|
||||
Modify time (%) = 0.0247326 (1.10663)
|
||||
Other time (%) = 0.00223875 (0.10017)
|
||||
|
||||
FFT time (% of Kspce) = 0.0272989 (16.7271)
|
||||
FFT Gflps 3d (1d only) = 2.0088 2.93901
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708088 ave 708088 max 708088 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708088
|
||||
Ave neighs/atom = 353.337
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: The trajectory file will be "out2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 3900175693153042431
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.7964e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69174e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411068
|
||||
Memory usage per processor = 22.5866 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
|
||||
210 253.15043 -5538.5668 -6557.0163 1018.4495 -6672.041 37.67158 0.61296982
|
||||
220 245.19746 -5522.5242 -6508.9781 986.4539 -6628.1999 36.656356 0.048624555
|
||||
230 258.65299 -5495.7177 -6536.3046 1040.5868 -6658.0952 34.855726 0.22046598
|
||||
240 260.80143 -5469.8517 -6519.0819 1049.2302 -6624.1723 31.576409 3.7570726
|
||||
250 269.06507 -5438.3971 -6520.8727 1082.4757 -6616.3871 25.444125 8.6640978
|
||||
260 266.10282 -5397.3162 -6467.8744 1070.5583 -6580.628 26.873936 8.3330854
|
||||
270 272.81993 -5350.8393 -6448.4211 1097.5819 -6563.8139 23.113421 10.972906
|
||||
280 279.52079 -5307.9855 -6432.5256 1124.5401 -6557.7274 33.641095 8.5474821
|
||||
290 286.81184 -5260.8728 -6414.7455 1153.8727 -6515.5418 28.572468 5.9092648
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79733e-05
|
||||
6 0.997005 1.02622e-05
|
||||
8 1.08 1.84996e-05
|
||||
10 1.111 9.98595e-06
|
||||
12 1.08 8.83195e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.84801e-05
|
||||
31 104.52 0.00169221
|
||||
300 291.51842 -5216.3285 -6389.1362 1172.8077 -6503.1141 27.877464 2.2482411
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 2.25031 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.83745 (81.6533)
|
||||
Bond time (%) = 0.00609803 (0.270987)
|
||||
Kspace time (%) = 0.162178 (7.20694)
|
||||
Neigh time (%) = 0.207886 (9.23812)
|
||||
Comm time (%) = 0.00977254 (0.434276)
|
||||
Output time (%) = 0.000240803 (0.0107009)
|
||||
Modify time (%) = 0.024461 (1.08701)
|
||||
Other time (%) = 0.00221944 (0.0986283)
|
||||
|
||||
FFT time (% of Kspce) = 0.0273609 (16.8709)
|
||||
FFT Gflps 3d (1d only) = 2.00425 2.94806
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11292 ave 11292 max 11292 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708145 ave 708145 max 708145 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708145
|
||||
Ave neighs/atom = 353.366
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -1,516 +0,0 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.1924 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
|
||||
10 305.06198 -5058.8898 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
|
||||
20 311.00592 -4999.0545 -6250.2624 1251.2079 -6417.0984 47.695274 36.699706
|
||||
30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344162 10.563914
|
||||
40 297.87524 -5020.8339 -6219.2157 1198.3819 -6389.85 27.723201 3.8354392
|
||||
50 304.02086 -5056.254 -6279.3603 1223.1063 -6456.8182 55.459508 0.206798
|
||||
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.767289 0.69356507
|
||||
70 277.835 -5163.9751 -6281.7331 1117.758 -6447.7014 39.627147 11.433632
|
||||
80 267.51474 -5206.4042 -6282.6428 1076.2385 -6456.6352 31.611843 6.3553237
|
||||
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8036 28.849898 0.36938879
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.686681 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.47104 (68.5966)
|
||||
Bond time (%) = 0.00184608 (0.26884)
|
||||
Kspace time (%) = 0.0808357 (11.7719)
|
||||
Neigh time (%) = 0.0772016 (11.2427)
|
||||
Comm time (%) = 0.0293136 (4.26888)
|
||||
Output time (%) = 0.000323951 (0.0471764)
|
||||
Modify time (%) = 0.0247293 (3.60128)
|
||||
Other time (%) = 0.00139064 (0.202516)
|
||||
|
||||
FFT time (% of Kspce) = 0.0117171 (14.4949)
|
||||
FFT Gflps 3d (1d only) = 4.68018 10.009
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181741 max 172943 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: The trajectory file will be "out.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0137
|
||||
colvars: Restarting collective variable "two" from value: 10.0649
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 8103505641670189088
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97184e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36077e-05
|
||||
31 104.52 0.00306008
|
||||
Memory usage per processor = 10.1967 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
|
||||
110 266.26278 -5341.2101 -6412.4119 1071.2018 -6552.7582 33.572969 1.9229778
|
||||
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859555 2.7124877
|
||||
130 252.83442 -5422.5444 -6439.7226 1017.1781 -6580.4752 25.979048 1.2031628
|
||||
140 253.85116 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071518 0.30586252
|
||||
150 261.31828 -5490.48 -6541.7895 1051.3096 -6646.6145 16.25855 6.9049978
|
||||
160 255.73681 -5521.6048 -6550.4596 1028.8548 -6658.1518 19.717536 12.339819
|
||||
170 253.42879 -5540.1004 -6559.6697 1019.5694 -6656.688 23.293657 10.289879
|
||||
180 248.51083 -5550.3244 -6550.1084 999.78393 -6661.4181 26.200057 3.433906
|
||||
190 250.80387 -5555.2613 -6564.2703 1009.009 -6666.1497 25.536596 3.3495164
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.79639e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69175e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411069
|
||||
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.653275 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.47279 (72.3723)
|
||||
Bond time (%) = 0.00182116 (0.278774)
|
||||
Kspace time (%) = 0.079544 (12.1762)
|
||||
Neigh time (%) = 0.0451868 (6.91696)
|
||||
Comm time (%) = 0.027427 (4.19838)
|
||||
Output time (%) = 0.000316501 (0.0484483)
|
||||
Modify time (%) = 0.0247022 (3.78129)
|
||||
Other time (%) = 0.00148731 (0.227671)
|
||||
|
||||
FFT time (% of Kspce) = 0.0109947 (13.8221)
|
||||
FFT Gflps 3d (1d only) = 4.98769 10.1728
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177022 ave 182261 max 172093 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708086
|
||||
Ave neighs/atom = 353.336
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: The trajectory file will be "out2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = two
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: Restarting harmonic bias "h_pot".
|
||||
colvars: Reading current stage from the restart.
|
||||
colvars: # stage = 8103505641670189088
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing step number as firstTimestep.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.8129e-06
|
||||
6 0.997 7.79639e-07
|
||||
8 1.08 1.08934e-06
|
||||
10 1.111 2.96501e-07
|
||||
12 1.08 4.69175e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76571e-06
|
||||
31 104.52 0.000411069
|
||||
Memory usage per processor = 10.201 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
|
||||
210 253.15047 -5538.5669 -6557.0165 1018.4497 -6672.0412 37.671574 0.61297094
|
||||
220 245.19752 -5522.5242 -6508.9784 986.45412 -6628.2001 36.656348 0.048624447
|
||||
230 258.65297 -5495.7177 -6536.3044 1040.5868 -6658.0951 34.855726 0.22046446
|
||||
240 260.8016 -5469.8518 -6519.0827 1049.2309 -6624.173 31.576408 3.757081
|
||||
250 269.06524 -5438.3971 -6520.8735 1082.4764 -6616.3878 25.444134 8.6641098
|
||||
260 266.10241 -5397.317 -6467.8736 1070.5566 -6580.6272 26.87393 8.333095
|
||||
270 272.82004 -5350.8402 -6448.4225 1097.5823 -6563.8152 23.113398 10.972914
|
||||
280 279.52006 -5307.9867 -6432.5238 1124.5371 -6557.7256 33.641067 8.5474809
|
||||
290 286.81221 -5260.8707 -6414.7449 1153.8742 -6515.5413 28.572449 5.9092582
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79733e-05
|
||||
6 0.997005 1.02621e-05
|
||||
8 1.08 1.84996e-05
|
||||
10 1.111 9.98591e-06
|
||||
12 1.08 8.83192e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.84805e-05
|
||||
31 104.52 0.00169223
|
||||
300 291.51901 -5216.3298 -6389.1399 1172.8101 -6503.1178 27.877408 2.2482392
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.662081 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.47307 (71.452)
|
||||
Bond time (%) = 0.00178617 (0.269781)
|
||||
Kspace time (%) = 0.0802494 (12.1208)
|
||||
Neigh time (%) = 0.0528576 (7.98355)
|
||||
Comm time (%) = 0.0277618 (4.19311)
|
||||
Output time (%) = 0.000293612 (0.0443469)
|
||||
Modify time (%) = 0.0245907 (3.71416)
|
||||
Other time (%) = 0.00147164 (0.222275)
|
||||
|
||||
FFT time (% of Kspce) = 0.011487 (14.3141)
|
||||
FFT Gflps 3d (1d only) = 4.77392 9.91625
|
||||
|
||||
Nlocal: 501 ave 514 max 471 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Nghost: 6609.75 ave 6681 max 6555 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177036 ave 180240 max 169752 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 708146
|
||||
Ave neighs/atom = 353.366
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -1,182 +0,0 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: The trajectory file will be "peptide2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 22.5865 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
|
||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.4169 21.367753 12.393269
|
||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
|
||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
||||
40 297.5581 -5088.2156 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
|
||||
50 296.80003 -5117.2926 -6311.3488 1194.0562 -6451.8274 30.631279 5.3320296
|
||||
60 281.72797 -5188.4941 -6321.9139 1133.4198 -6427.8834 26.287652 20.573958
|
||||
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742888 0.69414894
|
||||
80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606438
|
||||
90 270.43386 -5334.0846 -6422.067 1087.9824 -6563.2486 39.845993 1.1832496
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191466
|
||||
6 0.996989 3.5552e-05
|
||||
8 1.08 9.1e-06
|
||||
10 1.111 1.58547e-05
|
||||
12 1.08 5.80613e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92453e-05
|
||||
31 104.52 0.00239929
|
||||
100 260.3562 -5387.2263 -6434.6653 1047.439 -6534.1923 20.24674 0.075048834
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 2.37975 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.83713 (77.1984)
|
||||
Bond time (%) = 0.00636029 (0.267267)
|
||||
Kspace time (%) = 0.162295 (6.81981)
|
||||
Neigh time (%) = 0.336338 (14.1333)
|
||||
Comm time (%) = 0.0106671 (0.448243)
|
||||
Output time (%) = 0.000264168 (0.0111006)
|
||||
Modify time (%) = 0.024472 (1.02834)
|
||||
Other time (%) = 0.00222516 (0.0935038)
|
||||
|
||||
FFT time (% of Kspce) = 0.028162 (17.3524)
|
||||
FFT Gflps 3d (1d only) = 1.94723 2.85015
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708233 ave 708233 max 708233 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708233
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
|
@ -1,182 +0,0 @@
|
|||
LAMMPS (21 May 2012-ICMS)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268721
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.01614
|
||||
estimated relative force accuracy = 4.86052e-05
|
||||
using single precision FFTs
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2012-03-23.
|
||||
colvars: # analysis = off [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # colvarsTrajAppend = off [default]
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: The trajectory file will be "peptide2.colvars.traj".
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = one
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035.
|
||||
colvars: All components initialized.
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # lowerWallConstant = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # upperWallConstant = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputSystemForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = h_pot
|
||||
colvars: # colvars = { one }
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # targetForceConstant = 0 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.1924 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 2
|
||||
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
|
||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
|
||||
30 316.97689 -5025.5598 -6300.7896 1275.2297 -6422.5336 27.323113 6.7588863
|
||||
40 297.5581 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
|
||||
50 296.80003 -5117.2927 -6311.3488 1194.0562 -6451.8275 30.631279 5.3320297
|
||||
60 281.72797 -5188.494 -6321.9138 1133.4198 -6427.8833 26.287652 20.573959
|
||||
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742889 0.69414888
|
||||
80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606437
|
||||
90 270.43386 -5334.0846 -6422.067 1087.9825 -6563.2486 39.845992 1.1832495
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191466
|
||||
6 0.996989 3.5552e-05
|
||||
8 1.08 9.10001e-06
|
||||
10 1.111 1.58547e-05
|
||||
12 1.08 5.80613e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92453e-05
|
||||
31 104.52 0.00239929
|
||||
100 260.35619 -5387.2298 -6434.6688 1047.439 -6534.1958 20.24674 0.07504876
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.650999 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 0.466917 (71.7232)
|
||||
Bond time (%) = 0.00176847 (0.271655)
|
||||
Kspace time (%) = 0.0588512 (9.04015)
|
||||
Neigh time (%) = 0.0832494 (12.788)
|
||||
Comm time (%) = 0.0190871 (2.93197)
|
||||
Output time (%) = 0.000295341 (0.0453674)
|
||||
Modify time (%) = 0.0194815 (2.99255)
|
||||
Other time (%) = 0.00134867 (0.20717)
|
||||
|
||||
FFT time (% of Kspce) = 0.010457 (17.7686)
|
||||
FFT Gflps 3d (1d only) = 5.24412 9.93123
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181777 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708233
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
|
@ -1,150 +0,0 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 6776 1800
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 11.5952 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344
|
||||
20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706
|
||||
30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914
|
||||
40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396
|
||||
50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816
|
||||
60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527
|
||||
70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633
|
||||
80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235
|
||||
90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97185e-05
|
||||
6 0.996996 1.00569e-05
|
||||
8 1.08 6.02346e-06
|
||||
10 1.111 1.84257e-05
|
||||
12 1.08 7.27136e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36078e-05
|
||||
31 104.52 0.00306008
|
||||
100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866
|
||||
|
||||
Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms
|
||||
98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.126 ns/day 1.488 hours/ns 93.325 timesteps/s
|
||||
|
||||
MPI task timings breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45
|
||||
Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24
|
||||
Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70
|
||||
Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62
|
||||
Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77
|
||||
Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62
|
||||
Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36
|
||||
Other | | 0.002651 | | | 0.25
|
||||
|
||||
Nlocal: 1002 ave 1013 max 991 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8629.5 ave 8641 max 8618 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354118 ave 356534 max 351703 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
|
@ -1,145 +0,0 @@
|
|||
LAMMPS (20 Mar 2014-ICMS)
|
||||
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 6776 1800
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 11.5952 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond 3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
|
||||
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
|
||||
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
|
||||
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
|
||||
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
|
||||
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958
|
||||
70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895
|
||||
80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642
|
||||
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191466
|
||||
6 0.996989 3.5552e-05
|
||||
8 1.08 9.10001e-06
|
||||
10 1.111 1.58547e-05
|
||||
12 1.08 5.80613e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92454e-05
|
||||
31 104.52 0.00239929
|
||||
100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996
|
||||
|
||||
Loop time of 1.07264 on 2 procs for 100 steps with 2004 atoms
|
||||
98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.110 ns/day 1.490 hours/ns 93.228 timesteps/s
|
||||
|
||||
MPI task timings breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76647 | 0.77219 | 0.77792 | 0.7 | 71.99
|
||||
Bond | 0.0024974 | 0.0025403 | 0.0025833 | 0.1 | 0.24
|
||||
Kspace | 0.091998 | 0.096921 | 0.10184 | 1.6 | 9.04
|
||||
Neigh | 0.14764 | 0.14765 | 0.14767 | 0.0 | 13.77
|
||||
Comm | 0.018904 | 0.01937 | 0.019835 | 0.3 | 1.81
|
||||
Output | 0.005985 | 0.0067209 | 0.0074568 | 0.9 | 0.63
|
||||
Modify | 0.024529 | 0.024536 | 0.024542 | 0.0 | 2.29
|
||||
Other | | 0.002705 | | | 0.25
|
||||
|
||||
Nlocal: 1002 ave 1010 max 994 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 8645 ave 8652 max 8638 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 354116 ave 356373 max 351860 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708233
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
|
@ -1,22 +1,23 @@
|
|||
configuration {
|
||||
step 200
|
||||
dt 2.000000e+00
|
||||
version 2018-11-16
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00127641579482e+01
|
||||
x 1.00127732034965e+01
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.62235621950587e+00
|
||||
x 9.62235997490241e+00
|
||||
}
|
||||
|
||||
harmonic {
|
||||
restraint {
|
||||
configuration {
|
||||
step 200
|
||||
name h_pot
|
||||
stage 8103505641670189088
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,23 @@
|
|||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2018-11-16
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00136989326255e+01
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 1.00648830006091e+01
|
||||
}
|
||||
|
||||
restraint {
|
||||
configuration {
|
||||
step 100
|
||||
name h_pot
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1,102 +1,203 @@
|
|||
# step one two
|
||||
100 1.00136999784453e+01 1.00648820764882e+01
|
||||
101 1.00137686830422e+01 1.00611307186442e+01
|
||||
102 1.00135851804620e+01 1.00551774768670e+01
|
||||
103 1.00127019172615e+01 1.00448609599088e+01
|
||||
104 1.00107148677220e+01 1.00279880647254e+01
|
||||
105 1.00073753998706e+01 1.00031566249892e+01
|
||||
106 1.00026887490897e+01 9.97035299845099e+00
|
||||
107 9.99696380204809e+00 9.93114513453873e+00
|
||||
108 9.99079173947846e+00 9.88834426761621e+00
|
||||
109 9.98495634348822e+00 9.84525182069547e+00
|
||||
110 9.98029608653331e+00 9.80488128973958e+00
|
||||
111 9.97755063903513e+00 9.76956423088248e+00
|
||||
112 9.97722827031026e+00 9.74089978578719e+00
|
||||
113 9.97952719395978e+00 9.71964890219001e+00
|
||||
114 9.98433213818614e+00 9.70572160189541e+00
|
||||
115 9.99128820986690e+00 9.69882648932897e+00
|
||||
116 9.99993078708906e+00 9.69906675982844e+00
|
||||
117 1.00098268026590e+01 9.70676032193502e+00
|
||||
118 1.00206800068605e+01 9.72193925284532e+00
|
||||
119 1.00323638324515e+01 9.74392975114862e+00
|
||||
120 1.00448758513666e+01 9.77144823009299e+00
|
||||
121 1.00582368252610e+01 9.80293582393448e+00
|
||||
122 1.00723784561855e+01 9.83653845611926e+00
|
||||
123 1.00870571871815e+01 9.86996653086528e+00
|
||||
124 1.01018149909563e+01 9.90067054070927e+00
|
||||
125 1.01159957146856e+01 9.92637090832991e+00
|
||||
126 1.01288197202732e+01 9.94568593115900e+00
|
||||
127 1.01395051017779e+01 9.95858909349258e+00
|
||||
128 1.01474031546764e+01 9.96651060978132e+00
|
||||
129 1.01521102583250e+01 9.97197886676780e+00
|
||||
130 1.01535305336566e+01 9.97782726175993e+00
|
||||
131 1.01518703644018e+01 9.98617108245763e+00
|
||||
132 1.01475651582407e+01 9.99754271679455e+00
|
||||
133 1.01411660808109e+01 1.00106700599276e+01
|
||||
134 1.01332313643590e+01 1.00230219318765e+01
|
||||
135 1.01242577071328e+01 1.00317168123542e+01
|
||||
136 1.01146539200964e+01 1.00343611311947e+01
|
||||
137 1.01047327535065e+01 1.00296410219261e+01
|
||||
138 1.00947009258946e+01 1.00175740354601e+01
|
||||
139 1.00846525340704e+01 9.99930113951843e+00
|
||||
140 1.00745850435896e+01 9.97645596333061e+00
|
||||
141 1.00644392647413e+01 9.95041162930873e+00
|
||||
142 1.00541491709691e+01 9.92180111647481e+00
|
||||
143 1.00436823424749e+01 9.89050169056719e+00
|
||||
144 1.00330636529660e+01 9.85603208426972e+00
|
||||
145 1.00223839228086e+01 9.81818334237853e+00
|
||||
146 1.00118047065649e+01 9.77758921505729e+00
|
||||
147 1.00015612314349e+01 9.73590349870836e+00
|
||||
148 9.99195527218088e+00 9.69551788236989e+00
|
||||
149 9.98332631801527e+00 9.65911749675800e+00
|
||||
150 9.97599491711484e+00 9.62915810268995e+00
|
||||
151 9.97018870425343e+00 9.60717358806770e+00
|
||||
152 9.96597676149386e+00 9.59319263515552e+00
|
||||
153 9.96323912038658e+00 9.58560496094010e+00
|
||||
154 9.96168472712778e+00 9.58154384221214e+00
|
||||
155 9.96091708239459e+00 9.57764409185937e+00
|
||||
156 9.96053284836430e+00 9.57094226701891e+00
|
||||
157 9.96022340231744e+00 9.55966218699141e+00
|
||||
158 9.95984104841431e+00 9.54367921177888e+00
|
||||
159 9.95941115970323e+00 9.52452532866834e+00
|
||||
160 9.95909775592352e+00 9.50490062318069e+00
|
||||
161 9.95913472197875e+00 9.48781177595095e+00
|
||||
162 9.95973716567135e+00 9.47562216260840e+00
|
||||
163 9.96102283681378e+00 9.46939618474568e+00
|
||||
164 9.96297512061468e+00 9.46883909503368e+00
|
||||
165 9.96545450087319e+00 9.47284744786104e+00
|
||||
166 9.96824446676367e+00 9.48032505757766e+00
|
||||
167 9.97111490093449e+00 9.49080999053287e+00
|
||||
168 9.97388723087919e+00 9.50468382474366e+00
|
||||
169 9.97648454853684e+00 9.52297944488190e+00
|
||||
170 9.97895120221314e+00 9.54683939172159e+00
|
||||
171 9.98143439573287e+00 9.57673744631037e+00
|
||||
172 9.98412851702981e+00 9.61177677879831e+00
|
||||
173 9.98719912546727e+00 9.64941646139346e+00
|
||||
174 9.99071466036109e+00 9.68581516318204e+00
|
||||
175 9.99461255041478e+00 9.71674194992540e+00
|
||||
176 9.99871362276481e+00 9.73875618365856e+00
|
||||
177 1.00027752607551e+01 9.75023319932384e+00
|
||||
178 1.00065593228689e+01 9.75187374895997e+00
|
||||
179 1.00098932819698e+01 9.74651102922357e+00
|
||||
180 1.00127089751067e+01 9.73824323715410e+00
|
||||
181 1.00150539578018e+01 9.73118937807432e+00
|
||||
182 1.00170703552922e+01 9.72834303011533e+00
|
||||
183 1.00189424568686e+01 9.73087964994846e+00
|
||||
184 1.00208211796404e+01 9.73798531353725e+00
|
||||
185 1.00227525196798e+01 9.74722518450810e+00
|
||||
186 1.00246411639883e+01 9.75544038568881e+00
|
||||
187 1.00262714680409e+01 9.75985920611179e+00
|
||||
188 1.00273770464779e+01 9.75895332491778e+00
|
||||
189 1.00277296204562e+01 9.75275348211835e+00
|
||||
190 1.00272109105395e+01 9.74260945002776e+00
|
||||
191 1.00258469602549e+01 9.73056029017316e+00
|
||||
192 1.00238019119674e+01 9.71852969006276e+00
|
||||
193 1.00213411099718e+01 9.70760780505631e+00
|
||||
194 1.00187745961566e+01 9.69771723529251e+00
|
||||
195 1.00163957858114e+01 9.68783387106584e+00
|
||||
196 1.00144342355802e+01 9.67665900893200e+00
|
||||
197 1.00130379562453e+01 9.66342567131686e+00
|
||||
198 1.00122840592666e+01 9.64853643967174e+00
|
||||
199 1.00121986038636e+01 9.63383126934824e+00
|
||||
200 1.00127641579482e+01 9.62235621950587e+00
|
||||
# step one two
|
||||
0 9.93490813652661e+00 7.58366314453810e+00
|
||||
1 9.95511870046091e+00 7.60655947684375e+00
|
||||
2 9.97738607194270e+00 7.65732201855527e+00
|
||||
3 1.00007618482085e+01 7.73339023313853e+00
|
||||
4 1.00245083583281e+01 7.83083600267188e+00
|
||||
5 1.00481503915519e+01 7.94485550041547e+00
|
||||
6 1.00714236148569e+01 8.07022633606012e+00
|
||||
7 1.00941640085929e+01 8.20149351409018e+00
|
||||
8 1.01161917254501e+01 8.33270968029044e+00
|
||||
9 1.01372195147989e+01 8.45743087998851e+00
|
||||
10 1.01568094484822e+01 8.57063657043322e+00
|
||||
11 1.01744058364969e+01 8.66916428851601e+00
|
||||
12 1.01894584969823e+01 8.75011341291751e+00
|
||||
13 1.02015949657517e+01 8.81261373358815e+00
|
||||
14 1.02107634786499e+01 8.86010572643564e+00
|
||||
15 1.02172802335367e+01 8.89996164389908e+00
|
||||
16 1.02217586687617e+01 8.94046117354318e+00
|
||||
17 1.02249400729821e+01 8.98764357480963e+00
|
||||
18 1.02274821194763e+01 9.04385418276306e+00
|
||||
19 1.02297694921722e+01 9.10767828090644e+00
|
||||
20 1.02317948794015e+01 9.17521818721732e+00
|
||||
21 1.02331324174422e+01 9.24256921345538e+00
|
||||
22 1.02330115052436e+01 9.30670040650459e+00
|
||||
23 1.02304888847637e+01 9.36477739916766e+00
|
||||
24 1.02246905091409e+01 9.41471338314027e+00
|
||||
25 1.02150557312054e+01 9.45578119421866e+00
|
||||
26 1.02015018849614e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880334e+00
|
||||
28 1.01647618536435e+01 9.53348342780342e+00
|
||||
29 1.01435075836914e+01 9.54736918677922e+00
|
||||
30 1.01218448127414e+01 9.55679294480281e+00
|
||||
31 1.01008234685872e+01 9.56289707955055e+00
|
||||
32 1.00812605992407e+01 9.56689852729787e+00
|
||||
33 1.00636482078211e+01 9.57008522470066e+00
|
||||
34 1.00481219532447e+01 9.57404682801174e+00
|
||||
35 1.00345149123742e+01 9.58097344406653e+00
|
||||
36 1.00224896192326e+01 9.59352147402459e+00
|
||||
37 1.00117065902086e+01 9.61412496221624e+00
|
||||
38 1.00019625883763e+01 9.64369256665448e+00
|
||||
39 9.99324045988116e+00 9.68100279483232e+00
|
||||
40 9.98566198277188e+00 9.72340741886406e+00
|
||||
41 9.97939087537504e+00 9.76737558060000e+00
|
||||
42 9.97455220189940e+00 9.80830263552738e+00
|
||||
43 9.97120052013341e+00 9.84185625268822e+00
|
||||
44 9.96933202180119e+00 9.86623764187619e+00
|
||||
45 9.96891976615505e+00 9.88235950966856e+00
|
||||
46 9.96994868341340e+00 9.89287033859050e+00
|
||||
47 9.97242707411381e+00 9.90111363064262e+00
|
||||
48 9.97636549450466e+00 9.91016536955268e+00
|
||||
49 9.98173560597232e+00 9.92197275407224e+00
|
||||
50 9.98843048433684e+00 9.93674029911159e+00
|
||||
51 9.99624064138588e+00 9.95286099036568e+00
|
||||
52 1.00048525916104e+01 9.96759873289121e+00
|
||||
53 1.00138780764319e+01 9.97821328789638e+00
|
||||
54 1.00229204333232e+01 9.98289434996108e+00
|
||||
55 1.00316676518615e+01 9.98113328544968e+00
|
||||
56 1.00399758142293e+01 9.97358294450079e+00
|
||||
57 1.00479031641095e+01 9.96154574170506e+00
|
||||
58 1.00556838347250e+01 9.94624156425743e+00
|
||||
59 1.00636555959318e+01 9.92816580065099e+00
|
||||
60 1.00721640105110e+01 9.90692505955277e+00
|
||||
61 1.00814536313753e+01 9.88155118527262e+00
|
||||
62 1.00915547252798e+01 9.85098082230735e+00
|
||||
63 1.01021918256653e+01 9.81456141006142e+00
|
||||
64 1.01127650365675e+01 9.77251908261309e+00
|
||||
65 1.01224426616504e+01 9.72626626484817e+00
|
||||
66 1.01303500341168e+01 9.67844790721581e+00
|
||||
67 1.01357827497794e+01 9.63264342158540e+00
|
||||
68 1.01383594707679e+01 9.59267551611127e+00
|
||||
69 1.01380701059532e+01 9.56168371312923e+00
|
||||
70 1.01352290156399e+01 9.54132235576289e+00
|
||||
71 1.01303782422632e+01 9.53145207033862e+00
|
||||
72 1.01241807468998e+01 9.53052072472080e+00
|
||||
73 1.01173118912092e+01 9.53632715678295e+00
|
||||
74 1.01103471939659e+01 9.54668992740772e+00
|
||||
75 1.01036629090248e+01 9.55984803752009e+00
|
||||
76 1.00973931139318e+01 9.57467381743772e+00
|
||||
77 1.00914805900150e+01 9.59078681449290e+00
|
||||
78 1.00857806923796e+01 9.60849062320413e+00
|
||||
79 1.00801732463746e+01 9.62847591791803e+00
|
||||
80 1.00746211947647e+01 9.65137407697197e+00
|
||||
81 1.00691682828698e+01 9.67731006831009e+00
|
||||
82 1.00638992393184e+01 9.70564969348618e+00
|
||||
83 1.00589006124327e+01 9.73510953407921e+00
|
||||
84 1.00542402131510e+01 9.76420390471647e+00
|
||||
85 1.00499602946160e+01 9.79180385249033e+00
|
||||
86 1.00460706235439e+01 9.81755460563928e+00
|
||||
87 1.00425414168408e+01 9.84200765912343e+00
|
||||
88 1.00393046004480e+01 9.86642899323320e+00
|
||||
89 1.00362677210398e+01 9.89232615597538e+00
|
||||
90 1.00333326702222e+01 9.92077091295346e+00
|
||||
91 1.00304190984417e+01 9.95163431119817e+00
|
||||
92 1.00274924302484e+01 9.98320614724761e+00
|
||||
93 1.00245832030580e+01 1.00126809229005e+01
|
||||
94 1.00217818712298e+01 1.00372157022896e+01
|
||||
95 1.00192174478224e+01 1.00549229065348e+01
|
||||
96 1.00170334876474e+01 1.00654011519876e+01
|
||||
97 1.00153609154724e+01 1.00697015600771e+01
|
||||
98 1.00142801210350e+01 1.00698014812365e+01
|
||||
99 1.00137749686339e+01 1.00677656407202e+01
|
||||
100 1.00136989326255e+01 1.00648830006091e+01
|
||||
100 1.00136989326255e+01 1.00648830006091e+01
|
||||
101 1.00137674082083e+01 1.00611318434583e+01
|
||||
102 1.00135836692120e+01 1.00551787890126e+01
|
||||
103 1.00127001705469e+01 1.00448624179689e+01
|
||||
104 1.00107128955990e+01 1.00279896008852e+01
|
||||
105 1.00073732210918e+01 1.00031581615939e+01
|
||||
106 1.00026863896858e+01 9.97035446256176e+00
|
||||
107 9.99696129324890e+00 9.93114647843641e+00
|
||||
108 9.99078911556410e+00 9.88834547941894e+00
|
||||
109 9.98495363939735e+00 9.84525289783234e+00
|
||||
110 9.98029333636388e+00 9.80488218664815e+00
|
||||
111 9.97754787492958e+00 9.76956483721087e+00
|
||||
112 9.97722552172005e+00 9.74089998776836e+00
|
||||
113 9.97952448720610e+00 9.71964869280979e+00
|
||||
114 9.98432949668635e+00 9.70572109422863e+00
|
||||
115 9.99128565538624e+00 9.69882579496975e+00
|
||||
116 9.99992834152120e+00 9.69906594532193e+00
|
||||
117 1.00098244901113e+01 9.70675942684906e+00
|
||||
118 1.00206778548564e+01 9.72193838510829e+00
|
||||
119 1.00323618718055e+01 9.74392916146852e+00
|
||||
120 1.00448741144078e+01 9.77144817149792e+00
|
||||
121 1.00582353428180e+01 9.80293643028548e+00
|
||||
122 1.00723772537607e+01 9.83653980628752e+00
|
||||
123 1.00870562810006e+01 9.86996874359296e+00
|
||||
124 1.01018143847617e+01 9.90067377124461e+00
|
||||
125 1.01159953973120e+01 9.92637526075002e+00
|
||||
126 1.01288196652442e+01 9.94569135970445e+00
|
||||
127 1.01395052692626e+01 9.95859533688896e+00
|
||||
128 1.01474034953817e+01 9.96651718147533e+00
|
||||
129 1.01521107193303e+01 9.97198512417321e+00
|
||||
130 1.01535310646235e+01 9.97783256102044e+00
|
||||
131 1.01518709230597e+01 9.98617497185904e+00
|
||||
132 1.01475657142497e+01 9.99754506682891e+00
|
||||
133 1.01411666167305e+01 1.00106710657684e+01
|
||||
134 1.01332318751871e+01 1.00230220357698e+01
|
||||
135 1.01242581986854e+01 1.00317166064461e+01
|
||||
136 1.01146544066986e+01 1.00343612487317e+01
|
||||
137 1.01047332554016e+01 1.00296420246780e+01
|
||||
138 1.00947014667735e+01 1.00175763327172e+01
|
||||
139 1.00846531387645e+01 9.99930494674974e+00
|
||||
140 1.00745857366623e+01 9.97646128131491e+00
|
||||
141 1.00644400706802e+01 9.95041823440337e+00
|
||||
142 1.00541501159131e+01 9.92180857541951e+00
|
||||
143 1.00436834569978e+01 9.89050941872713e+00
|
||||
144 1.00330649757401e+01 9.85603943350860e+00
|
||||
145 1.00223855042347e+01 9.81818968302844e+00
|
||||
146 1.00118066120717e+01 9.77759398920638e+00
|
||||
147 1.00015635423691e+01 9.73590632972306e+00
|
||||
148 9.99195808427061e+00 9.69551862637489e+00
|
||||
149 9.98332973799261e+00 9.65911623085002e+00
|
||||
150 9.97599905761175e+00 9.62915505877515e+00
|
||||
151 9.97019367767784e+00 9.60716909686955e+00
|
||||
152 9.96598267281873e+00 9.59318709200410e+00
|
||||
153 9.96324605944343e+00 9.58559881047527e+00
|
||||
154 9.96169276126796e+00 9.58153758556819e+00
|
||||
155 9.96092625032814e+00 9.57763829311044e+00
|
||||
156 9.96054315607791e+00 9.57093750799266e+00
|
||||
157 9.96023482227745e+00 9.55965895377840e+00
|
||||
158 9.95985352165466e+00 9.54367776307569e+00
|
||||
159 9.95942460039566e+00 9.52452561463833e+00
|
||||
160 9.95911205589222e+00 9.50490226824346e+00
|
||||
161 9.95914975443396e+00 9.48781410600212e+00
|
||||
162 9.95975278911406e+00 9.47562429341561e+00
|
||||
163 9.96103890040379e+00 9.46939719079233e+00
|
||||
164 9.96299147170478e+00 9.46883821286236e+00
|
||||
165 9.96547099380307e+00 9.47284423942468e+00
|
||||
166 9.96826097146115e+00 9.48031949605208e+00
|
||||
167 9.97113131026389e+00 9.49080246783928e+00
|
||||
168 9.97390346515378e+00 9.50467508257787e+00
|
||||
169 9.97650055807565e+00 9.52297045210046e+00
|
||||
170 9.97896696852481e+00 9.54683120799382e+00
|
||||
171 9.98144993167344e+00 9.57673108800475e+00
|
||||
172 9.98414386605973e+00 9.61177309775590e+00
|
||||
173 9.98721435874383e+00 9.64941604907962e+00
|
||||
174 9.99072987081047e+00 9.68581828149366e+00
|
||||
175 9.99462784290560e+00 9.71674849920838e+00
|
||||
176 9.99872910050856e+00 9.73876571566039e+00
|
||||
177 1.00027910094647e+01 9.75024496509227e+00
|
||||
178 1.00065753933095e+01 9.75188677631197e+00
|
||||
179 1.00099096736715e+01 9.74652424002240e+00
|
||||
180 1.00127256239536e+01 9.73825559652692e+00
|
||||
181 1.00150707323506e+01 9.73120003142692e+00
|
||||
182 1.00170870650914e+01 9.72835138795971e+00
|
||||
183 1.00189588719574e+01 9.73088542644806e+00
|
||||
184 1.00208370553711e+01 9.73798855694274e+00
|
||||
185 1.00227676206971e+01 9.74722630488312e+00
|
||||
186 1.00246552838286e+01 9.75544013816019e+00
|
||||
187 1.00262844434324e+01 9.75985859738447e+00
|
||||
188 1.00273887691195e+01 9.75895345517658e+00
|
||||
189 1.00277400472209e+01 9.75275536148299e+00
|
||||
190 1.00272200725279e+01 9.74261382746486e+00
|
||||
191 1.00258549688160e+01 9.73056754269459e+00
|
||||
192 1.00238089567536e+01 9.71853980670345e+00
|
||||
193 1.00213474465750e+01 9.70762043885231e+00
|
||||
194 1.00187805230869e+01 9.69773175124558e+00
|
||||
195 1.00164016154513e+01 9.68784935173366e+00
|
||||
196 1.00144402674219e+01 9.67667427007303e+00
|
||||
197 1.00130444574495e+01 9.66343938720852e+00
|
||||
198 1.00122912607270e+01 9.64854739476250e+00
|
||||
199 1.00122066750836e+01 9.63383866331536e+00
|
||||
200 1.00127732034965e+01 9.62235997490241e+00
|
||||
|
|
|
|||
|
|
@ -1,22 +1,23 @@
|
|||
configuration {
|
||||
step 300
|
||||
dt 2.000000e+00
|
||||
version 2018-11-16
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 9.95354148699614e+00
|
||||
x 9.95315918568411e+00
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.79310294857288e+00
|
||||
x 9.79318883680258e+00
|
||||
}
|
||||
|
||||
harmonic {
|
||||
restraint {
|
||||
configuration {
|
||||
step 300
|
||||
name h_pot
|
||||
stage 8103505641670189088
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,102 +1,102 @@
|
|||
# step one two
|
||||
200 1.00127641579482e+01 9.62235621950587e+00
|
||||
201 1.00139098397954e+01 9.61766067322651e+00
|
||||
202 1.00154895322849e+01 9.62284260846102e+00
|
||||
203 1.00172625720562e+01 9.63964717046032e+00
|
||||
204 1.00188930177704e+01 9.66786064733448e+00
|
||||
205 1.00199761813056e+01 9.70519780219794e+00
|
||||
206 1.00200944106384e+01 9.74779969655747e+00
|
||||
207 1.00188963572281e+01 9.79111374012340e+00
|
||||
208 1.00161883604793e+01 9.83086787098858e+00
|
||||
209 1.00120201470551e+01 9.86403984083060e+00
|
||||
210 1.00067290723642e+01 9.88948240692241e+00
|
||||
211 1.00009114042457e+01 9.90790280320401e+00
|
||||
212 9.99530858712775e+00 9.92119319076851e+00
|
||||
213 9.99063126799011e+00 9.93149262690681e+00
|
||||
214 9.98737350983788e+00 9.94043951053174e+00
|
||||
215 9.98567811211086e+00 9.94878566374960e+00
|
||||
216 9.98529977833156e+00 9.95640488686023e+00
|
||||
217 9.98567740511041e+00 9.96270367197379e+00
|
||||
218 9.98609281741416e+00 9.96726160094494e+00
|
||||
219 9.98586784093273e+00 9.97033437532426e+00
|
||||
220 9.98454831898211e+00 9.97291246609646e+00
|
||||
221 9.98202887687821e+00 9.97627400695988e+00
|
||||
222 9.97858776161328e+00 9.98128372296812e+00
|
||||
223 9.97481791063232e+00 9.98787692577356e+00
|
||||
224 9.97146915301902e+00 9.99495319867179e+00
|
||||
225 9.96924741695340e+00 1.00005781312739e+01
|
||||
226 9.96863280571612e+00 1.00023562928510e+01
|
||||
227 9.96977462939505e+00 9.99793468396390e+00
|
||||
228 9.97249206995624e+00 9.98558877312050e+00
|
||||
229 9.97637419760570e+00 9.96476526430303e+00
|
||||
230 9.98093600414111e+00 9.93639297716863e+00
|
||||
231 9.98577334632368e+00 9.90279138444459e+00
|
||||
232 9.99066901099700e+00 9.86714667869485e+00
|
||||
233 9.99562704815141e+00 9.83274230148512e+00
|
||||
234 1.00008356809073e+01 9.80226834521352e+00
|
||||
235 1.00065772362800e+01 9.77744581513232e+00
|
||||
236 1.00131097048912e+01 9.75894408214992e+00
|
||||
237 1.00205553485494e+01 9.74639403983496e+00
|
||||
238 1.00288314258010e+01 9.73851464709533e+00
|
||||
239 1.00376482262668e+01 9.73355843502651e+00
|
||||
240 1.00465718867162e+01 9.72986544373201e+00
|
||||
241 1.00551241447104e+01 9.72616365347388e+00
|
||||
242 1.00628799016098e+01 9.72156081057173e+00
|
||||
243 1.00695359569141e+01 9.71533506969961e+00
|
||||
244 1.00749394351078e+01 9.70669135454371e+00
|
||||
245 1.00790729024702e+01 9.69470862769774e+00
|
||||
246 1.00820010382698e+01 9.67869454326621e+00
|
||||
247 1.00837917095021e+01 9.65894101136318e+00
|
||||
248 1.00844414119874e+01 9.63696223650643e+00
|
||||
249 1.00838441989246e+01 9.61423476365400e+00
|
||||
250 1.00818306797879e+01 9.59185059543549e+00
|
||||
251 1.00782686429397e+01 9.57154356576350e+00
|
||||
252 1.00731806695096e+01 9.55550278600070e+00
|
||||
253 1.00668200834919e+01 9.54554307033366e+00
|
||||
254 1.00596730176507e+01 9.54248962932697e+00
|
||||
255 1.00523895763009e+01 9.54590976255577e+00
|
||||
256 1.00456784264533e+01 9.55421544253452e+00
|
||||
257 1.00402005024002e+01 9.56513899116782e+00
|
||||
258 1.00364831006552e+01 9.57640458000444e+00
|
||||
259 1.00348576492106e+01 9.58619146455749e+00
|
||||
260 1.00354210621162e+01 9.59329709957898e+00
|
||||
261 1.00380245202744e+01 9.59728096353517e+00
|
||||
262 1.00422960600822e+01 9.59832037848005e+00
|
||||
263 1.00476990763950e+01 9.59672497993560e+00
|
||||
264 1.00536104533027e+01 9.59261911381189e+00
|
||||
265 1.00594002482137e+01 9.58602304006163e+00
|
||||
266 1.00644981793165e+01 9.57714719542419e+00
|
||||
267 1.00684482704210e+01 9.56662135439055e+00
|
||||
268 1.00709580655557e+01 9.55551489305294e+00
|
||||
269 1.00719418900228e+01 9.54518226195314e+00
|
||||
270 1.00715463773733e+01 9.53703197862875e+00
|
||||
271 1.00701345227997e+01 9.53228911010047e+00
|
||||
272 1.00682184887617e+01 9.53176321322706e+00
|
||||
273 1.00663378629920e+01 9.53558933249131e+00
|
||||
274 1.00649132448630e+01 9.54304329234477e+00
|
||||
275 1.00641243212406e+01 9.55266696753925e+00
|
||||
276 1.00638595454980e+01 9.56275901409309e+00
|
||||
277 1.00637587244679e+01 9.57196213233751e+00
|
||||
278 1.00633313189549e+01 9.57961568108488e+00
|
||||
279 1.00621123193119e+01 9.58575692732997e+00
|
||||
280 1.00598117112007e+01 9.59088855190189e+00
|
||||
281 1.00564177173993e+01 9.59570566223894e+00
|
||||
282 1.00522270044392e+01 9.60088836897012e+00
|
||||
283 1.00477888199161e+01 9.60693590561625e+00
|
||||
284 1.00437690523107e+01 9.61400570555926e+00
|
||||
285 1.00407622307256e+01 9.62182265962647e+00
|
||||
286 1.00391028258991e+01 9.62979902243492e+00
|
||||
287 1.00387366035163e+01 9.63738040674711e+00
|
||||
288 1.00391979793082e+01 9.64439605217689e+00
|
||||
289 1.00397008587343e+01 9.65118231683256e+00
|
||||
290 1.00393154139857e+01 9.65847479887268e+00
|
||||
291 1.00371856971467e+01 9.66716430247627e+00
|
||||
292 1.00327325013742e+01 9.67799413246555e+00
|
||||
293 1.00257889436952e+01 9.69130066948859e+00
|
||||
294 1.00166284740574e+01 9.70687426338097e+00
|
||||
295 1.00058767991341e+01 9.72395332252100e+00
|
||||
296 9.99433972822595e+00 9.74134088397850e+00
|
||||
297 9.98281255441855e+00 9.75768650006539e+00
|
||||
298 9.97193339524040e+00 9.77194269576588e+00
|
||||
299 9.96211387496966e+00 9.78370254738211e+00
|
||||
300 9.95354148699614e+00 9.79310294857288e+00
|
||||
# step one two
|
||||
200 1.00127732034965e+01 9.62235997490241e+00
|
||||
201 1.00139198864982e+01 9.61766167925624e+00
|
||||
202 1.00155004339120e+01 9.62284272858813e+00
|
||||
203 1.00172741972246e+01 9.63964899323068e+00
|
||||
204 1.00189052021826e+01 9.66786718571673e+00
|
||||
205 1.00199887119842e+01 9.70521202056400e+00
|
||||
206 1.00201070660155e+01 9.74782380666112e+00
|
||||
207 1.00189089093749e+01 9.79114913038349e+00
|
||||
208 1.00162005540278e+01 9.83091553260188e+00
|
||||
209 1.00120316562035e+01 9.86409994884863e+00
|
||||
210 1.00067394529596e+01 9.88955328455197e+00
|
||||
211 1.00009200584653e+01 9.90798080826055e+00
|
||||
212 9.99531475905311e+00 9.92127385542524e+00
|
||||
213 9.99063400342297e+00 9.93157198661852e+00
|
||||
214 9.98737188807678e+00 9.94051482696048e+00
|
||||
215 9.98567127567181e+00 9.94885527957784e+00
|
||||
216 9.98528704043382e+00 9.95646746111755e+00
|
||||
217 9.98565832937415e+00 9.96275739929720e+00
|
||||
218 9.98606724184677e+00 9.96730423246689e+00
|
||||
219 9.98583582550472e+00 9.97036378703713e+00
|
||||
220 9.98451001643477e+00 9.97292736129215e+00
|
||||
221 9.98198434901656e+00 9.97627439806637e+00
|
||||
222 9.97853678731273e+00 9.98127100659218e+00
|
||||
223 9.97475984191141e+00 9.98785371236258e+00
|
||||
224 9.97140286510626e+00 9.99492286335624e+00
|
||||
225 9.96917137580259e+00 1.00005443231922e+01
|
||||
226 9.96854523900174e+00 1.00023222923235e+01
|
||||
227 9.96967375964547e+00 9.99790273206806e+00
|
||||
228 9.97237636771905e+00 9.98555960216881e+00
|
||||
229 9.97624253505807e+00 9.96473792067690e+00
|
||||
230 9.98078777310055e+00 9.93636511602182e+00
|
||||
231 9.98560846780419e+00 9.90275990393703e+00
|
||||
232 9.99048787217569e+00 9.86710855077386e+00
|
||||
233 9.99543040822038e+00 9.83269539984149e+00
|
||||
234 1.00006246021103e+01 9.80221208335553e+00
|
||||
235 1.00063530848982e+01 9.77738136586701e+00
|
||||
236 1.00128741709083e+01 9.75887400813685e+00
|
||||
237 1.00203106975850e+01 9.74632163179798e+00
|
||||
238 1.00285805371730e+01 9.73844350416337e+00
|
||||
239 1.00373945897865e+01 9.73349215182819e+00
|
||||
240 1.00463194539327e+01 9.72980720779576e+00
|
||||
241 1.00548770491533e+01 9.72611599020063e+00
|
||||
242 1.00626421174965e+01 9.72152572108181e+00
|
||||
243 1.00693109823863e+01 9.71531423107737e+00
|
||||
244 1.00747300690509e+01 9.70668632474813e+00
|
||||
245 1.00788811512303e+01 9.69472082245661e+00
|
||||
246 1.00818281591535e+01 9.67872530149764e+00
|
||||
247 1.00836382918008e+01 9.65899116363609e+00
|
||||
248 1.00843077585461e+01 9.63702967428387e+00
|
||||
249 1.00837304601058e+01 9.61431312359133e+00
|
||||
250 1.00817369874724e+01 9.59193249256670e+00
|
||||
251 1.00781951382998e+01 9.57162234547176e+00
|
||||
252 1.00731274409141e+01 9.55557274350384e+00
|
||||
253 1.00667870632608e+01 9.54560001126946e+00
|
||||
254 1.00596598859158e+01 9.54253147668434e+00
|
||||
255 1.00523956909045e+01 9.54593692832520e+00
|
||||
256 1.00457028282132e+01 9.55423082330650e+00
|
||||
257 1.00402418669526e+01 9.56514761944992e+00
|
||||
258 1.00365397691695e+01 9.57641296971103e+00
|
||||
259 1.00349276270394e+01 9.58620624196598e+00
|
||||
260 1.00355019919770e+01 9.59332346959128e+00
|
||||
261 1.00381137097146e+01 9.59732188686984e+00
|
||||
262 1.00423905760179e+01 9.59837618250971e+00
|
||||
263 1.00477959188736e+01 9.59679324477687e+00
|
||||
264 1.00537068007149e+01 9.59269523141530e+00
|
||||
265 1.00594937260641e+01 9.58610120816249e+00
|
||||
266 1.00645870781682e+01 9.57722117048002e+00
|
||||
267 1.00685316571224e+01 9.56668493985151e+00
|
||||
268 1.00710357823615e+01 9.55556251047062e+00
|
||||
269 1.00720144042107e+01 9.54520978473172e+00
|
||||
270 1.00716144493745e+01 9.53703781183182e+00
|
||||
271 1.00701992199135e+01 9.53227489206590e+00
|
||||
272 1.00682808706064e+01 9.53173333554826e+00
|
||||
273 1.00663988075209e+01 9.53554943194497e+00
|
||||
274 1.00649733063520e+01 9.54299862049767e+00
|
||||
275 1.00641836485840e+01 9.55262143610080e+00
|
||||
276 1.00639178664285e+01 9.56271517955029e+00
|
||||
277 1.00638153921535e+01 9.57192148747872e+00
|
||||
278 1.00633853985923e+01 9.57957875475062e+00
|
||||
279 1.00621626720543e+01 9.58572327394556e+00
|
||||
280 1.00598570838615e+01 9.59085686511578e+00
|
||||
281 1.00564566071967e+01 9.59567423393283e+00
|
||||
282 1.00522576614697e+01 9.60085550637412e+00
|
||||
283 1.00478091897332e+01 9.60690040068280e+00
|
||||
284 1.00437767664032e+01 9.61396708331890e+00
|
||||
285 1.00407546813490e+01 9.62178118810825e+00
|
||||
286 1.00390773261870e+01 9.62975547860500e+00
|
||||
287 1.00386906040191e+01 9.63733595704590e+00
|
||||
288 1.00391292740982e+01 9.64435229335154e+00
|
||||
289 1.00396077171765e+01 9.65114124926381e+00
|
||||
290 1.00391967746350e+01 9.65843904962787e+00
|
||||
291 1.00370409303829e+01 9.66713735495098e+00
|
||||
292 1.00325613495850e+01 9.67798035621834e+00
|
||||
293 1.00255913568518e+01 9.69130440474672e+00
|
||||
294 1.00164044158125e+01 9.70689841022156e+00
|
||||
295 1.00056261321876e+01 9.72399810930261e+00
|
||||
296 9.99406221883501e+00 9.74140402524052e+00
|
||||
297 9.98250803362175e+00 9.75776438941627e+00
|
||||
298 9.97160202027972e+00 9.77203069297329e+00
|
||||
299 9.96175637151037e+00 9.78379375044905e+00
|
||||
300 9.95315918568411e+00 9.79318883680258e+00
|
||||
|
|
|
|||
|
|
@ -1,17 +1,18 @@
|
|||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2018-11-16
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00387424212228e+01
|
||||
x 1.00387423506482e+01
|
||||
}
|
||||
|
||||
harmonic {
|
||||
restraint {
|
||||
configuration {
|
||||
step 100
|
||||
name h_pot
|
||||
stage 4044288781530052640
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,102 +1,102 @@
|
|||
# step one
|
||||
0 1.23398428397332e+01
|
||||
1 1.23379000531837e+01
|
||||
2 1.22833752132682e+01
|
||||
3 1.21783464524822e+01
|
||||
4 1.20268109152646e+01
|
||||
5 1.18342676552027e+01
|
||||
6 1.16071240696111e+01
|
||||
7 1.13522568477758e+01
|
||||
8 1.10769760454451e+01
|
||||
9 1.07892333501017e+01
|
||||
10 1.04978607983300e+01
|
||||
11 1.02148368912480e+01
|
||||
12 9.95820967758655e+00
|
||||
13 9.74528082635713e+00
|
||||
14 9.59065550809125e+00
|
||||
15 9.49025917553263e+00
|
||||
16 9.43254360388750e+00
|
||||
17 9.41011962734900e+00
|
||||
18 9.41602364253240e+00
|
||||
19 9.44413444723206e+00
|
||||
20 9.49001191595699e+00
|
||||
21 9.55036186844267e+00
|
||||
22 9.62258413071055e+00
|
||||
23 9.70460340526413e+00
|
||||
24 9.79475248209609e+00
|
||||
25 9.89135077720185e+00
|
||||
26 9.99213105078110e+00
|
||||
27 1.00938499722663e+01
|
||||
28 1.01925349210626e+01
|
||||
29 1.02845107805173e+01
|
||||
30 1.03676652352347e+01
|
||||
31 1.04416367894860e+01
|
||||
32 1.05071334937552e+01
|
||||
33 1.05650452299048e+01
|
||||
34 1.06158824214188e+01
|
||||
35 1.06595186275218e+01
|
||||
36 1.06948928511102e+01
|
||||
37 1.07202580715959e+01
|
||||
38 1.07337399401028e+01
|
||||
39 1.07331885445159e+01
|
||||
40 1.07158932314825e+01
|
||||
41 1.06789136129953e+01
|
||||
42 1.06198862520319e+01
|
||||
43 1.05380120055201e+01
|
||||
44 1.04346603936480e+01
|
||||
45 1.03132931131809e+01
|
||||
46 1.01792839195940e+01
|
||||
47 1.00398967921774e+01
|
||||
48 9.90373826474332e+00
|
||||
49 9.77934819842326e+00
|
||||
50 9.67344128626180e+00
|
||||
51 9.58957431460176e+00
|
||||
52 9.52771755964755e+00
|
||||
53 9.48463676001684e+00
|
||||
54 9.45495927636316e+00
|
||||
55 9.43277262066999e+00
|
||||
56 9.41329687195946e+00
|
||||
57 9.39418023785890e+00
|
||||
58 9.37608079167942e+00
|
||||
59 9.36244026161597e+00
|
||||
60 9.35853356967195e+00
|
||||
61 9.36993825765332e+00
|
||||
62 9.40084295384763e+00
|
||||
63 9.45286334548428e+00
|
||||
64 9.52464492798022e+00
|
||||
65 9.61230778865749e+00
|
||||
66 9.71074173620872e+00
|
||||
67 9.81506921139973e+00
|
||||
68 9.92117599348263e+00
|
||||
69 1.00244217575122e+01
|
||||
70 1.01178260477346e+01
|
||||
71 1.01986938379172e+01
|
||||
72 1.02670956368544e+01
|
||||
73 1.03213051063305e+01
|
||||
74 1.03597191337854e+01
|
||||
75 1.03817745676591e+01
|
||||
76 1.03880610583944e+01
|
||||
77 1.03809103738027e+01
|
||||
78 1.03645558156884e+01
|
||||
79 1.03441497701913e+01
|
||||
80 1.03243653409000e+01
|
||||
81 1.03082112818858e+01
|
||||
82 1.02961296917318e+01
|
||||
83 1.02862106580352e+01
|
||||
84 1.02756069146933e+01
|
||||
85 1.02618115908758e+01
|
||||
86 1.02435132305408e+01
|
||||
87 1.02212121470422e+01
|
||||
88 1.01972799936680e+01
|
||||
89 1.01743931780361e+01
|
||||
90 1.01538342930689e+01
|
||||
91 1.01363020288600e+01
|
||||
92 1.01223080393853e+01
|
||||
93 1.01118050646187e+01
|
||||
94 1.01038513159042e+01
|
||||
95 1.00967020139234e+01
|
||||
96 1.00885782989097e+01
|
||||
97 1.00784257293241e+01
|
||||
98 1.00661428832570e+01
|
||||
99 1.00524912515310e+01
|
||||
100 1.00387424212228e+01
|
||||
# step one
|
||||
0 1.23398428397332e+01
|
||||
1 1.23379000532662e+01
|
||||
2 1.22833752135957e+01
|
||||
3 1.21783464514507e+01
|
||||
4 1.20268109095184e+01
|
||||
5 1.18342676394048e+01
|
||||
6 1.16071240372003e+01
|
||||
7 1.13522567926249e+01
|
||||
8 1.10769759646337e+01
|
||||
9 1.07892332454600e+01
|
||||
10 1.04978606745989e+01
|
||||
11 1.02148367517604e+01
|
||||
12 9.95820954052204e+00
|
||||
13 9.74528077043305e+00
|
||||
14 9.59065564952749e+00
|
||||
15 9.49025959957862e+00
|
||||
16 9.43254431868731e+00
|
||||
17 9.41012058917623e+00
|
||||
18 9.41602481112176e+00
|
||||
19 9.44413580740584e+00
|
||||
20 9.49001346044027e+00
|
||||
21 9.55036359015270e+00
|
||||
22 9.62258602486444e+00
|
||||
23 9.70460545744668e+00
|
||||
24 9.79475465622561e+00
|
||||
25 9.89135302429916e+00
|
||||
26 9.99213332770717e+00
|
||||
27 1.00938522423366e+01
|
||||
28 1.01925371414626e+01
|
||||
29 1.02845129002944e+01
|
||||
30 1.03676671987640e+01
|
||||
31 1.04416385355998e+01
|
||||
32 1.05071349561950e+01
|
||||
33 1.05650463398331e+01
|
||||
34 1.06158831174766e+01
|
||||
35 1.06595188661313e+01
|
||||
36 1.06948926085038e+01
|
||||
37 1.07202573517647e+01
|
||||
38 1.07337387802787e+01
|
||||
39 1.07331870068021e+01
|
||||
40 1.07158913924701e+01
|
||||
41 1.06789115566470e+01
|
||||
42 1.06198840652253e+01
|
||||
43 1.05380097743725e+01
|
||||
44 1.04346581978275e+01
|
||||
45 1.03132910149185e+01
|
||||
46 1.01792819503691e+01
|
||||
47 1.00398949454818e+01
|
||||
48 9.90373650268307e+00
|
||||
49 9.77934647164350e+00
|
||||
50 9.67343955381284e+00
|
||||
51 9.58957255517495e+00
|
||||
52 9.52771577288560e+00
|
||||
53 9.48463495848957e+00
|
||||
54 9.45495747488851e+00
|
||||
55 9.43277083061229e+00
|
||||
56 9.41329510571902e+00
|
||||
57 9.39417852043035e+00
|
||||
58 9.37607916767444e+00
|
||||
59 9.36243879601093e+00
|
||||
60 9.35853234890725e+00
|
||||
61 9.36993739187210e+00
|
||||
62 9.40084256925489e+00
|
||||
63 9.45286356660258e+00
|
||||
64 9.52464585631223e+00
|
||||
65 9.61230948096192e+00
|
||||
66 9.71074418990813e+00
|
||||
67 9.81507236552599e+00
|
||||
68 9.92117974657176e+00
|
||||
69 1.00244259961919e+01
|
||||
70 1.01178306268727e+01
|
||||
71 1.01986985644537e+01
|
||||
72 1.02671003889995e+01
|
||||
73 1.03213098011429e+01
|
||||
74 1.03597236984298e+01
|
||||
75 1.03817789163109e+01
|
||||
76 1.03880650963390e+01
|
||||
77 1.03809140245635e+01
|
||||
78 1.03645590344102e+01
|
||||
79 1.03441525373194e+01
|
||||
80 1.03243676495902e+01
|
||||
81 1.03082131278348e+01
|
||||
82 1.02961310659179e+01
|
||||
83 1.02862115513553e+01
|
||||
84 1.02756073299153e+01
|
||||
85 1.02618115461408e+01
|
||||
86 1.02435127550163e+01
|
||||
87 1.02212112849545e+01
|
||||
88 1.01972788307491e+01
|
||||
89 1.01743918261207e+01
|
||||
90 1.01538328424605e+01
|
||||
91 1.01363005552771e+01
|
||||
92 1.01223066231827e+01
|
||||
93 1.01118037967830e+01
|
||||
94 1.01038502876980e+01
|
||||
95 1.00967012947728e+01
|
||||
96 1.00885779123137e+01
|
||||
97 1.00784256309007e+01
|
||||
98 1.00661429612272e+01
|
||||
99 1.00524913461711e+01
|
||||
100 1.00387423506482e+01
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
variable A string bulkNi
|
||||
log $A.log
|
||||
|
||||
boundary p p p
|
||||
|
||||
|
|
@ -26,7 +25,7 @@ fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
|
|||
|
||||
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
||||
|
||||
dump 1 all custom 1 $A.dump id x y z
|
||||
#dump 1 all custom 1 $A.dump id x y z
|
||||
run 0
|
||||
|
||||
unfix 1
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable A string bulkNi
|
||||
|
||||
boundary p p p
|
||||
|
||||
units metal
|
||||
timestep 0.001
|
||||
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.0037179 secs
|
||||
|
||||
pair_style none
|
||||
mass * 58.71
|
||||
atom_modify sort 0 0
|
||||
|
||||
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
|
||||
|
||||
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 0 0 0 c 0.025 0.025 0.025 dR_Ewald 0.01 echo manual
|
||||
|
||||
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file $A.hist.xrd
|
||||
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file bulkNi.hist.xrd
|
||||
|
||||
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
||||
fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed
|
||||
|
||||
#dump 1 all custom 1 $A.dump id x y z
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.91 | 21.91 | 21.91 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 32000 atoms
|
||||
|
||||
314.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2461 ave 2461 max 2461 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
unfix 2
|
||||
uncompute XRD
|
||||
uncompute SAED
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:03:30
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable A string bulkNi
|
||||
|
||||
boundary p p p
|
||||
|
||||
units metal
|
||||
timestep 0.001
|
||||
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
Time spent = 0.0010488 secs
|
||||
|
||||
pair_style none
|
||||
mass * 58.71
|
||||
atom_modify sort 0 0
|
||||
|
||||
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
|
||||
|
||||
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 0 0 0 c 0.025 0.025 0.025 dR_Ewald 0.01 echo manual
|
||||
|
||||
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file $A.hist.xrd
|
||||
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file bulkNi.hist.xrd
|
||||
|
||||
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
|
||||
fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed
|
||||
|
||||
#dump 1 all custom 1 $A.dump id x y z
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.08 | 16.08 | 16.08 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
Loop time of 1.84774e-06 on 4 procs for 0 steps with 32000 atoms
|
||||
|
||||
162.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.848e-06 | | |100.00
|
||||
|
||||
Nlocal: 8000 ave 8000 max 8000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1041 ave 1041 max 1041 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
unfix 2
|
||||
uncompute XRD
|
||||
uncompute SAED
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:54
|
||||
|
|
@ -0,0 +1,193 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 butane system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 79507 46656
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655
|
||||
50 1.8285224 3442.9216 2047.8425 187.41713 1395.0792 844.61103 802.43438 114.10967 0 -765.532 595242.44 -594842.98 3027.409 55742.797 200.4343 152.51723
|
||||
100 3.7075663 2949.9137 1973.6229 180.62461 976.29073 358.0742 923.62856 174.43734 0 -919.88297 595306.76 -594866.72 2009.106 55742.797 229.49986 50.10998
|
||||
150 5.5383921 2885.0697 1951.4547 178.59578 933.61499 234.26452 991.10197 194.44106 0 -910.03339 595293.22 -594869.38 4963.8801 55742.797 240.13548 14.311317
|
||||
200 7.4217758 2890.343 1901.2801 174.00384 989.06297 227.57533 1077.5605 200.01467 0 -943.83325 595298.11 -594870.36 2977.5804 55742.797 237.27186 5.1150968
|
||||
250 9.2994335 2922.348 1945.2702 178.02978 977.07781 212.26144 1127.8726 194.65284 0 -984.2934 595297.59 -594871.01 1592.2372 55742.797 243.81864 2.4147813
|
||||
300 11.125204 2986.575 2013.159 184.24291 973.41608 212.85963 1130.6272 194.90599 0 -992.98724 595299.3 -594871.29 2816.8628 55742.797 252.63444 1.681279
|
||||
350 12.99769 3051.4916 1978.4541 181.06675 1073.0375 228.43411 1195.4688 205.43169 0 -982.55178 595297.25 -594871 1408.7973 55742.797 248.34887 1.4666749
|
||||
400 14.865399 3011.3983 1995.0047 182.58145 1016.3936 237.79955 1167.8185 197.49857 0 -1014.9362 595298.99 -594870.78 1456.5007 55742.797 250.45674 1.3981189
|
||||
450 16.681866 3010.262 1976.9744 180.93133 1033.2876 216.3478 1196.7189 197.65964 0 -1005.6015 595298.72 -594870.56 1296.528 55742.797 248.1869 1.4022273
|
||||
500 18.553431 3051.4554 2022.049 185.05652 1029.4064 220.84993 1196.1502 199.57249 0 -1014.3775 595298.27 -594871.05 2481.7571 55742.797 253.85835 1.3999256
|
||||
550 20.416665 3086.0021 2018.9226 184.7704 1067.0796 221.95877 1215.9767 213.3405 0 -1012.5564 595299.48 -594871.12 1694.9376 55742.797 253.47686 1.3683935
|
||||
600 22.27849 3110.9928 2030.8992 185.86649 1080.0935 220.35725 1253.9571 208.13083 0 -1030.4314 595298.96 -594870.88 -76.102661 55742.797 254.95682 1.4397403
|
||||
650 24.087152 3154.373 2024.8469 185.31258 1129.5261 221.85968 1283.352 210.69451 0 -1015.2311 595299.67 -594870.82 1280.5683 55742.797 254.20302 1.4194509
|
||||
700 25.941822 3133.85 2054.2045 187.99938 1079.6454 225.19338 1242.7819 192.54094 0 -1010.8971 595301.2 -594871.18 696.8538 55742.797 257.8878 1.4422435
|
||||
750 27.79477 3189.0815 2103.7507 192.53381 1085.3308 219.46949 1243.7676 203.10695 0 -1010.2442 595299.93 -594870.7 483.46393 55742.797 264.14441 1.3796789
|
||||
800 29.64589 3173.663 2053.4832 187.93336 1120.1799 219.59931 1256.2721 218.76191 0 -1003.0067 595299.37 -594870.81 543.09774 55742.797 257.81268 1.4005681
|
||||
850 31.44585 3221.2873 2083.5215 190.68244 1137.7658 224.0492 1276.9143 219.91997 0 -1011.193 595298.47 -594870.4 143.54962 55742.797 261.60038 1.3772624
|
||||
900 33.293605 3214.96 2053.8414 187.96614 1161.1187 222.21434 1296.0291 226.57612 0 -1013.6289 595300.61 -594870.68 473.39553 55742.797 257.85596 1.4053153
|
||||
950 35.166863 3213.1086 2123.777 194.3666 1089.3317 221.79126 1251.6851 200.63798 0 -1014.0889 595300.01 -594870.7 1206.8497 55742.797 266.62111 1.4935247
|
||||
1000 36.983663 3211.3103 2079.738 190.33618 1131.5723 225.4767 1260.2162 204.61245 0 -986.95685 595298.7 -594870.48 787.31501 55742.797 261.0928 1.4615275
|
||||
1050 38.806926 3199.3221 2095.9148 191.81667 1103.4073 212.62976 1255.417 208.36886 0 -1001.9237 595299.13 -594870.21 239.45594 55742.797 263.14173 1.4246893
|
||||
1100 40.634771 3199.8694 2067.6467 189.2296 1132.2227 235.50505 1264.2214 198.42446 0 -994.78564 595299.12 -594870.26 830.67515 55742.797 259.58627 1.4225726
|
||||
1150 42.427903 3172.4663 2083.0988 190.64376 1089.3675 209.20043 1236.7213 204.50261 0 -990.26027 595299.43 -594870.22 1355.1408 55742.797 261.54264 1.389433
|
||||
1200 44.302469 3178.2153 2055.1801 188.08866 1123.0351 230.76616 1258.2175 205.04893 0 -999.28826 595298.25 -594869.96 819.5423 55742.797 258.01926 1.4189827
|
||||
1250 46.164956 3224.5367 2108.1449 192.93596 1116.3918 235.56939 1247.0387 212.74774 0 -1007.3896 595298.16 -594869.74 -146.38102 55742.797 264.67477 1.4395372
|
||||
1300 48.015128 3286.0631 2125.3364 194.50931 1160.7267 236.69229 1272.7247 218.49151 0 -995.46842 595298.38 -594870.1 434.46496 55742.797 266.83295 1.451771
|
||||
1350 49.79655 3247.1808 2087.4518 191.04214 1159.7291 215.07571 1301.219 211.43766 0 -995.15128 595297.24 -594870.09 1501.3496 55742.797 262.07016 1.44305
|
||||
1400 51.624074 3194.7716 2041.9251 186.87557 1152.8466 236.94802 1261.0635 209.14663 0 -982.03995 595297.35 -594869.63 346.64925 55742.797 256.31352 1.5208162
|
||||
1450 53.450535 3229.6083 2087.4545 191.04239 1142.1538 246.85361 1264.077 205.22437 0 -1003.5382 595299.44 -594869.9 278.1536 55742.797 262.08335 1.4087832
|
||||
1500 55.288627 3249.6608 2089.8541 191.262 1159.8067 238.99337 1274.9502 206.61799 0 -988.99015 595297.98 -594869.75 636.34142 55742.797 262.36618 1.4595924
|
||||
1550 57.093174 3273.2213 2122.5463 194.25397 1150.675 230.16428 1274.9965 195.7686 0 -979.24728 595298.84 -594869.85 528.01943 55742.797 266.47594 1.4678006
|
||||
1600 58.978489 3288.6787 2120.7284 194.0876 1167.9503 229.10278 1274.2494 205.30619 0 -969.94195 595298.85 -594869.62 1126.6579 55742.797 266.23416 1.5026913
|
||||
1650 60.803467 3286.3327 2148.1031 196.59291 1138.2295 234.18582 1256.2009 214.69184 0 -995.41699 595298.38 -594869.81 -457.07393 55742.797 269.67989 1.4977223
|
||||
1700 62.624963 3296.9487 2092.8432 191.53556 1204.1055 238.05554 1313.8592 213.47968 0 -989.09874 595297.16 -594869.35 981.42569 55742.797 262.7423 1.4593707
|
||||
1750 64.39829 3310.3958 2097.6547 191.97591 1212.7411 243.56621 1309.681 210.07115 0 -978.63733 595297.78 -594869.72 -41.877565 55742.797 263.31945 1.5344885
|
||||
1800 66.216881 3229.7417 2079.7567 190.33789 1149.985 226.57585 1276.3941 202.60118 0 -984.26122 595298.62 -594869.94 515.97995 55742.797 261.07174 1.5239416
|
||||
1850 68.038292 3199.6375 2033.1459 186.0721 1166.4916 242.84458 1267.7768 212.87764 0 -984.52187 595296.72 -594869.21 440.77319 55742.797 255.22287 1.4839954
|
||||
1900 69.841965 3155.3872 2019.0731 184.78417 1136.3141 213.38104 1263.0105 213.0042 0 -980.43253 595296.92 -594869.57 469.76979 55742.797 253.48524 1.3965366
|
||||
1950 71.702563 3191.9366 2051.5475 187.75621 1140.3891 211.61608 1278.9441 206.1048 0 -984.04544 595297.56 -594869.79 758.07165 55742.797 257.54478 1.4655839
|
||||
2000 73.520102 3214.3938 2041.9357 186.87654 1172.4582 237.13198 1275.4194 218.0467 0 -985.25597 595296.76 -594869.64 375.81502 55742.797 256.33161 1.4761528
|
||||
Loop time of 73.5201 on 1 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Performance: 1.175 ns/day, 20.422 hours/ns, 27.203 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 50.346 | 50.346 | 50.346 | 0.0 | 68.48
|
||||
Bond | 3.3227 | 3.3227 | 3.3227 | 0.0 | 4.52
|
||||
Kspace | 16.003 | 16.003 | 16.003 | 0.0 | 21.77
|
||||
Neigh | 1.3495 | 1.3495 | 1.3495 | 0.0 | 1.84
|
||||
Comm | 0.33013 | 0.33013 | 0.33013 | 0.0 | 0.45
|
||||
Output | 0.0044131 | 0.0044131 | 0.0044131 | 0.0 | 0.01
|
||||
Modify | 2.1068 | 2.1068 | 2.1068 | 0.0 | 2.87
|
||||
Other | | 0.05755 | | | 0.08
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8703 ave 8703 max 8703 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 860806 ave 860806 max 860806 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 860806
|
||||
Ave neighs/atom = 191.29
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:13
|
||||
|
|
@ -0,0 +1,193 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 butane system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 26875 11664
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655
|
||||
50 0.60067916 3418.0026 2021.3092 184.98882 1396.6934 835.43668 808.1357 113.8069 0 -759.89265 595242.48 -594843.28 3040.8412 55742.797 197.07838 152.67751
|
||||
100 1.1808443 2892.8432 1932.7674 176.88554 960.07578 363.31823 924.84568 164.52097 0 -931.84989 595306.29 -594867.05 1694.4336 55742.797 224.44681 49.87859
|
||||
150 1.7504072 2833.9225 1947.7257 178.2545 886.19681 243.64601 972.03324 186.73658 0 -941.85405 595295.47 -594869.83 4603.775 55742.797 239.63159 14.40403
|
||||
200 2.3280952 2870.6299 1920.2424 175.73925 950.38759 226.3737 1061.7175 186.27763 0 -950.17253 595296.43 -594870.24 2606.5041 55742.797 239.64552 5.1468097
|
||||
250 2.9009523 2894.0913 1933.574 176.95936 960.51728 215.18824 1118.0957 195.43563 0 -993.95102 595296.54 -594870.8 1812.6379 55742.797 242.26101 2.6446653
|
||||
300 3.4866827 2959.1219 1970.1936 180.31075 988.92834 209.63552 1155.4811 193.64322 0 -996.9511 595297.92 -594870.8 3371.5528 55742.797 247.17325 1.8304564
|
||||
350 4.1206505 2988.7765 1988.8664 182.01968 999.91007 217.65998 1148.4029 204.96757 0 -996.5586 595296.05 -594870.61 3021.4005 55742.797 249.63956 1.5179762
|
||||
400 4.7467482 3014.5638 1983.6589 181.54309 1030.9049 225.81008 1174.5083 214.70193 0 -1012.492 595298.89 -594870.51 668.28879 55742.797 249.02834 1.40089
|
||||
450 5.3385043 3065.528 2028.5299 185.64965 1036.9981 206.85828 1232.536 204.7453 0 -1034.5447 595297.52 -594870.12 1276.895 55742.797 254.65283 1.4568976
|
||||
500 5.8841732 3087.3359 1998.9143 182.93925 1088.4216 209.84037 1244.2781 211.45124 0 -1004.5214 595297.9 -594870.53 1811.1357 55742.797 250.95893 1.3696214
|
||||
550 6.495003 3082.7524 2000.662 183.0992 1082.0904 218.46927 1229.7948 204.12764 0 -997.16039 595297.23 -594870.37 2005.0512 55742.797 251.16775 1.399994
|
||||
600 7.0529547 3089.1148 2008.9702 183.85957 1080.1445 215.63956 1239.6501 205.6559 0 -1008.3414 595297.61 -594870.07 1579.3906 55742.797 252.19307 1.453043
|
||||
650 7.6147993 3094.7607 1984.215 181.59398 1110.5457 217.2587 1270.5436 217.11567 0 -1021.7236 595297.37 -594870.02 922.17911 55742.797 249.09972 1.3970954
|
||||
700 8.1847589 3085.7974 1977.7443 181.00179 1108.0531 226.89107 1263.0937 209.93619 0 -1019.8382 595298.21 -594870.24 1358.6744 55742.797 248.27153 1.4348071
|
||||
750 8.7551639 3098.7075 1990.5214 182.17114 1108.186 210.53964 1263.8112 208.67005 0 -1002.6807 595298.31 -594870.47 1389.4827 55742.797 249.86686 1.4670711
|
||||
800 9.3312614 3106.7743 2001.1286 183.14191 1105.6457 223.39008 1267.3688 200.94765 0 -1014.1025 595298.4 -594870.36 498.96153 55742.797 251.20537 1.4561965
|
||||
850 9.9120548 3162.1905 2015.7594 184.4809 1146.4311 238.91403 1296.3319 216.49567 0 -1033.2993 595298.07 -594870.08 -146.24973 55742.797 253.06241 1.4124079
|
||||
900 10.506582 3151.6622 2017.7351 184.66172 1133.9272 225.66798 1259.6857 214.41352 0 -993.82625 595298.42 -594870.44 855.52595 55742.797 253.32946 1.3630807
|
||||
950 11.073148 3108.5571 1984.4638 181.61676 1124.0933 219.09683 1258.9728 215.5009 0 -998.11162 595299.1 -594870.46 742.29532 55742.797 249.13228 1.3937456
|
||||
1000 11.712476 3151.1431 2010.1073 183.96363 1141.0358 234.62673 1262.3296 218.152 0 -1001.9319 595297.94 -594870.08 -15.429859 55742.797 252.31702 1.5039719
|
||||
1050 12.416933 3154.9906 2025.2409 185.34864 1129.7498 240.28475 1245.2732 211.12104 0 -994.07995 595297.56 -594870.41 220.34341 55742.797 254.21036 1.5313366
|
||||
1100 13.000971 3146.7058 2015.0512 184.41609 1131.6546 217.69098 1255.773 216.52818 0 -985.5434 595297.52 -594870.32 245.54987 55742.797 252.9731 1.4117211
|
||||
1150 13.566174 3184.3315 2097.0388 191.91954 1087.2926 210.06417 1226.6616 216.15719 0 -994.73562 595299.65 -594870.51 960.8241 55742.797 263.29333 1.3975188
|
||||
1200 14.098352 3181.1191 2062.3454 188.74443 1118.7737 228.90526 1255.3357 202.92363 0 -997.73355 595299.52 -594870.18 341.31357 55742.797 258.91222 1.4415835
|
||||
1250 14.653097 3174.3638 2030.9146 185.8679 1143.4492 239.32477 1267.7689 201.40964 0 -992.67835 595297.78 -594870.16 399.69023 55742.797 254.97189 1.4037218
|
||||
1300 15.198202 3181.4157 2020.4604 184.91114 1160.9553 213.94195 1283.8134 212.79399 0 -977.52401 595298.12 -594870.19 141.81633 55742.797 253.64065 1.447907
|
||||
1350 15.763844 3221.4526 2077.8786 190.16601 1143.574 237.97099 1261.8854 206.43835 0 -991.01514 595298.43 -594870.14 293.86155 55742.797 260.85797 1.4643006
|
||||
1400 16.36341 3273.4082 2117.3713 193.78035 1156.0369 241.63847 1257.3077 215.03947 0 -986.42491 595298.6 -594870.13 881.28305 55742.797 265.82788 1.4598428
|
||||
1450 16.907335 3277.2159 2086.1619 190.92409 1191.054 245.42292 1289.0177 220.33432 0 -991.71405 595297.92 -594869.93 24.577369 55742.797 261.91752 1.4173689
|
||||
1500 17.461373 3277.8652 2139.2814 195.78556 1138.5838 230.79453 1253.5268 210.7018 0 -984.94169 595298.66 -594870.16 612.24618 55742.797 268.59444 1.432741
|
||||
1550 17.996041 3247.9903 2120.4397 194.06118 1127.5505 237.85251 1244.2413 207.38138 0 -989.02975 595297.17 -594870.07 908.40409 55742.797 266.20105 1.4941148
|
||||
1600 18.546506 3263.2065 2095.2604 191.75678 1167.9461 222.27478 1287.0828 217.80256 0 -988.01164 595299.17 -594870.37 372.09439 55742.797 263.06244 1.4165997
|
||||
1650 19.087156 3279.007 2102.6708 192.43497 1176.3363 228.35925 1287.432 218.78886 0 -987.87117 595299.94 -594870.32 -277.43091 55742.797 263.9961 1.4129192
|
||||
1700 19.665064 3297.4084 2103.7436 192.53316 1193.6648 248.40926 1304.8649 202.53258 0 -989.5236 595297.12 -594869.74 1158.9952 55742.797 264.11122 1.4655993
|
||||
1750 20.367483 3280.0391 2075.6964 189.9663 1204.3427 240.06411 1311.9499 213.18798 0 -987.79028 595296.5 -594869.56 437.83034 55742.797 260.60055 1.4183112
|
||||
1800 20.942509 3272.2429 2082.8406 190.62013 1189.4023 235.68331 1306.7318 216.11438 0 -997.06553 595297.79 -594869.86 1293.8956 55742.797 261.49937 1.4181999
|
||||
1850 21.546463 3288.8649 2088.0429 191.09624 1200.822 239.22801 1297.8732 214.15066 0 -979.04152 595298.01 -594869.39 217.43385 55742.797 262.15237 1.4245994
|
||||
1900 22.118972 3213.0018 2032.382 186.00219 1180.6198 222.35796 1278.9261 222.52754 0 -969.8068 595296.01 -594869.39 563.16684 55742.797 255.16077 1.393322
|
||||
1950 22.701752 3228.1804 2084.1556 190.74048 1144.0248 232.43889 1247.3333 216.54358 0 -981.18306 595298.59 -594869.7 -309.06733 55742.797 261.65433 1.4460719
|
||||
2000 23.402514 3297.5065 2091.6171 191.42335 1205.8894 238.75396 1287.293 220.47084 0 -968.78447 595297.97 -594869.81 128.84944 55742.797 262.59803 1.4363623
|
||||
Loop time of 23.4026 on 4 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Performance: 3.692 ns/day, 6.501 hours/ns, 85.461 timesteps/s
|
||||
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.545 | 13.094 | 13.896 | 14.0 | 55.95
|
||||
Bond | 0.83177 | 0.90776 | 0.96459 | 5.1 | 3.88
|
||||
Kspace | 6.3904 | 7.1918 | 7.7297 | 18.8 | 30.73
|
||||
Neigh | 0.38941 | 0.38974 | 0.38988 | 0.0 | 1.67
|
||||
Comm | 0.65148 | 0.70795 | 0.7821 | 5.6 | 3.03
|
||||
Output | 0.0028274 | 0.0036304 | 0.0057163 | 2.0 | 0.02
|
||||
Modify | 1.0483 | 1.0571 | 1.0693 | 0.9 | 4.52
|
||||
Other | | 0.05109 | | | 0.22
|
||||
|
||||
Nlocal: 1125 ave 1207 max 1003 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 5763 ave 5904 max 5656 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 214633 ave 220347 max 204542 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 858532
|
||||
Ave neighs/atom = 190.785
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:23
|
||||
|
|
@ -0,0 +1,199 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 butane system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_CORE gCORES temp/com
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDIRECT all drude/transform/direct
|
||||
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||
fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 79507 46656
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655
|
||||
50 1.9199426 2090.3465 1466.1274 134.17896 624.21909 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015
|
||||
100 3.8672287 2131.9775 1633.3979 149.48744 498.57958 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587
|
||||
150 5.7598403 2177.6381 1711.4959 156.63492 466.14214 134.74039 700.59918 168.27759 0 -965.58407 595300.38 -594872.27 4413.0226 55742.797 215.26856 0.12192183
|
||||
200 7.7044377 2233.5218 1730.4556 158.3701 503.06611 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5946 55742.797 217.61368 0.22886584
|
||||
250 9.6830325 2297.301 1773.2292 162.28471 524.07183 151.53589 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0574 55742.797 222.691 1.0389647
|
||||
300 11.612487 2368.3956 1891.828 173.13879 476.56753 142.49028 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9226 55742.797 236.85673 3.051144
|
||||
350 13.534112 2414.4805 1843.9331 168.75548 570.54737 181.42276 808.67959 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5958 55742.797 231.57282 1.0738202
|
||||
400 15.432559 2466.7093 1924.3089 176.11142 542.40037 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79722 55742.797 241.94266 0.38534823
|
||||
450 17.325742 2522.7871 1875.8855 171.67974 646.90166 133.40905 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.401476 55742.797 235.86638 0.34369113
|
||||
500 19.162983 2580.277 1955.7507 178.98895 624.52624 185.08446 827.39298 175.04156 0 -984.94513 595290.88 -594868.93 3484.9214 55742.797 245.79119 0.67067789
|
||||
550 21.070935 2640.6835 1866.0349 170.77823 774.64852 176.89611 988.92025 176.49761 0 -991.07213 595292.32 -594868.91 1773.3487 55742.797 234.10561 1.7344182
|
||||
600 22.994624 2690.8564 1876.0664 171.6963 814.79004 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72494 55742.797 235.38014 1.7010295
|
||||
650 24.877667 2732.1824 1963.5421 179.70202 768.64029 165.39218 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9019 55742.797 246.76774 0.68037803
|
||||
700 26.759878 2775.7295 1921.9362 175.89427 853.7933 175.21242 987.66711 186.48684 0 -918.75412 595291.36 -594868.18 670.06325 55742.797 241.62283 0.44222016
|
||||
750 28.615888 2820.0743 2038.1503 186.53011 781.92393 168.58533 929.80575 193.62705 0 -939.93789 595298.09 -594868.25 398.72744 55742.797 256.20117 0.55407341
|
||||
800 30.410775 2865.9592 1943.5754 177.87467 922.38383 197.16018 1009.2236 201.50387 0 -914.81706 595297.54 -594868.23 -717.10982 55742.797 244.0452 1.2420646
|
||||
850 32.248099 2909.1134 2101.5572 192.33306 807.55624 195.1889 876.12791 184.47417 0 -876.31499 595296.17 -594868.09 -1403.423 55742.797 263.69793 1.8344087
|
||||
900 34.102496 2938.1375 2038.9241 186.60092 899.21338 183.32678 989.0166 184.31256 0 -889.86015 595300.05 -594867.63 -1087.2756 55742.797 256.12731 1.0106116
|
||||
950 35.940632 2965.6943 2007.942 183.76546 957.75234 227.45507 972.71509 206.37948 0 -880.42319 595299.46 -594867.83 -1848.76 55742.797 252.40652 0.53885795
|
||||
1000 37.768527 2994.2318 2058.0187 188.34845 936.2131 170.68954 965.88084 205.36587 0 -833.14442 595294.86 -594867.44 327.63778 55742.797 258.71295 0.52143526
|
||||
1050 39.603905 3022.9502 2095.3849 191.76817 927.56532 203.90713 935.91395 205.082 0 -845.07245 595294.32 -594866.59 -355.70498 55742.797 263.25608 0.94199109
|
||||
1100 41.345196 3051.1765 2047.7198 187.4059 1003.4567 212.39896 989.65688 227.20813 0 -856.11279 595297.04 -594866.74 -1402.0226 55742.797 256.98382 1.677375
|
||||
1150 43.126233 3071.8156 2127.8628 194.74053 943.95283 188.38429 926.24314 223.28057 0 -821.63214 595294.06 -594866.38 550.31162 55742.797 267.19152 1.343134
|
||||
1200 44.919531 3087.7694 2015.2957 184.43847 1072.4737 199.90941 1034.9531 215.15479 0 -804.43316 595293.38 -594866.49 -333.57889 55742.797 253.2678 0.70913779
|
||||
1250 46.708812 3102.5825 2176.9514 199.23308 925.63109 155.81514 956.83605 230.07299 0 -847.4765 595296.65 -594866.26 -932.66378 55742.797 273.66546 0.54750847
|
||||
1300 48.515239 3116.8403 2087.6042 191.05609 1029.2361 209.96221 974.81036 241.13636 0 -823.38395 595292.74 -594866.03 -825.75374 55742.797 262.34482 0.76176534
|
||||
1350 50.311301 3131.0791 2089.6528 191.24358 1041.4264 186.48162 998.11153 233.70979 0 -801.36955 595290.06 -594865.57 684.79541 55742.797 262.36803 1.3871258
|
||||
1400 52.135502 3138.996 2186.2583 200.08485 952.73772 168.60362 957.20176 227.71916 0 -826.52254 595291.08 -594865.34 1796.7314 55742.797 274.47405 1.5135697
|
||||
1450 53.920154 3139.5791 2010.7381 184.02136 1128.841 192.80138 1074.5202 245.37245 0 -807.31625 595288.01 -594864.55 -16.506503 55742.797 252.6314 0.8772328
|
||||
1500 55.713369 3143.899 2099.4529 192.14047 1044.4461 186.04036 980.83507 242.01351 0 -784.81179 595285 -594864.63 2343.8872 55742.797 263.89144 0.6124176
|
||||
1550 57.492258 3149.7317 2086.0668 190.91539 1063.6649 165.80538 1056.0892 230.89557 0 -813.37736 595289.09 -594864.84 2260.7336 55742.797 262.17651 0.69483863
|
||||
1600 59.30172 3156.5347 2013.4253 184.26729 1143.1093 210.65899 1098.2888 243.95147 0 -835.61974 595290.47 -594864.64 -838.56538 55742.797 252.86557 1.1543025
|
||||
1650 61.139585 3160.0034 2081.0689 190.45799 1078.9345 212.2197 1005.7495 250.37949 0 -813.72039 595289.15 -594864.85 796.20008 55742.797 261.22489 1.5557795
|
||||
1700 62.942445 3155.5695 2113.3768 193.41478 1042.1927 146.0358 1019.0909 249.77844 0 -798.16322 595290.59 -594865.14 359.703 55742.797 265.47004 1.0739924
|
||||
1750 64.762126 3151.7963 2063.5473 188.85442 1088.249 224.89092 997.01992 247.37169 0 -807.87664 595291.82 -594864.98 -1081.2896 55742.797 259.34344 0.69485895
|
||||
1800 66.592646 3150.4284 2097.9263 192.00076 1052.5021 202.22769 974.42253 248.58755 0 -799.53819 595291.61 -594864.8 94.59915 55742.797 263.68436 0.65251966
|
||||
1850 68.418504 3153.4497 2106.6304 192.79735 1046.8193 177.57201 971.73173 249.90467 0 -777.13268 595289.76 -594865.02 881.42667 55742.797 264.65056 0.99601086
|
||||
1900 70.216536 3159.2067 2092.2719 191.48328 1066.9348 198.78887 969.41481 260.03017 0 -787.26086 595290.41 -594864.45 606.42691 55742.797 262.6612 1.4839999
|
||||
1950 72.044671 3164.5166 2059.5681 188.49025 1104.9485 214.12266 1000.4479 263.39571 0 -799.45144 595291.13 -594864.69 -1248.7635 55742.797 258.62997 1.2624764
|
||||
2000 73.841754 3171.2996 2080.1586 190.37468 1091.1409 179.21893 996.41501 248.41662 0 -760.00915 595292.04 -594864.94 940.6962 55742.797 261.39988 0.78376244
|
||||
Loop time of 73.8418 on 1 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Performance: 1.170 ns/day, 20.512 hours/ns, 27.085 timesteps/s
|
||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 48.171 | 48.171 | 48.171 | 0.0 | 65.23
|
||||
Bond | 3.3962 | 3.3962 | 3.3962 | 0.0 | 4.60
|
||||
Kspace | 16.344 | 16.344 | 16.344 | 0.0 | 22.13
|
||||
Neigh | 1.6599 | 1.6599 | 1.6599 | 0.0 | 2.25
|
||||
Comm | 0.35976 | 0.35976 | 0.35976 | 0.0 | 0.49
|
||||
Output | 0.0045705 | 0.0045705 | 0.0045705 | 0.0 | 0.01
|
||||
Modify | 3.8475 | 3.8475 | 3.8475 | 0.0 | 5.21
|
||||
Other | | 0.05927 | | | 0.08
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10103 ave 10103 max 10103 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 774433 ave 774433 max 774433 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 774433
|
||||
Ave neighs/atom = 172.096
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:14
|
||||
|
|
@ -0,0 +1,199 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 butane system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_CORE gCORES temp/com
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDIRECT all drude/transform/direct
|
||||
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||
fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 26875 11664
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 8 8 8
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655
|
||||
50 0.63524747 2090.3465 1466.1274 134.17896 624.2191 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015
|
||||
100 1.2804167 2131.9774 1633.3979 149.48744 498.57955 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587
|
||||
150 1.9264774 2177.6381 1711.4959 156.63492 466.14218 134.74039 700.59917 168.27759 0 -965.58407 595300.38 -594872.27 4413.0227 55742.797 215.26856 0.12192187
|
||||
200 2.5798194 2233.5217 1730.4557 158.3701 503.06601 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5944 55742.797 217.61368 0.22886584
|
||||
250 3.234822 2297.3011 1773.2292 162.28471 524.07191 151.5359 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0577 55742.797 222.691 1.0389643
|
||||
300 3.9885037 2368.3956 1891.828 173.13879 476.56759 142.49027 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9227 55742.797 236.85673 3.0511439
|
||||
350 4.7276039 2414.4804 1843.9331 168.75548 570.54727 181.42277 808.6796 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5954 55742.797 231.57282 1.0738212
|
||||
400 5.3416793 2466.7094 1924.3089 176.11142 542.40044 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79737 55742.797 241.94266 0.38534799
|
||||
450 6.0018888 2522.7872 1875.8855 171.67974 646.90169 133.40906 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.40141 55742.797 235.86638 0.34369111
|
||||
500 6.6298664 2580.2771 1955.7507 178.98895 624.52635 185.08445 827.39297 175.04156 0 -984.94513 595290.88 -594868.93 3484.9216 55742.797 245.79119 0.67067791
|
||||
550 7.2369561 2640.6835 1866.035 170.77823 774.64858 176.89609 988.92025 176.49761 0 -991.07212 595292.32 -594868.91 1773.3486 55742.797 234.10561 1.7344207
|
||||
600 7.8453741 2690.8569 1876.0664 171.6963 814.7905 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72487 55742.797 235.38014 1.7010285
|
||||
650 8.4387105 2732.1825 1963.5421 179.70202 768.64035 165.39219 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9017 55742.797 246.76774 0.68037827
|
||||
700 9.0765064 2775.7294 1921.9362 175.89427 853.79318 175.21242 987.66712 186.48684 0 -918.75413 595291.36 -594868.18 670.06264 55742.797 241.62283 0.44222019
|
||||
750 9.6925657 2820.0741 2038.1504 186.53011 781.92376 168.58531 929.80574 193.62706 0 -939.9379 595298.09 -594868.25 398.72752 55742.797 256.20117 0.55407442
|
||||
800 10.302839 2865.959 1943.5754 177.87467 922.38359 197.16019 1009.2236 201.50386 0 -914.81706 595297.54 -594868.23 -717.10975 55742.797 244.0452 1.2420644
|
||||
850 10.916842 2909.1138 2101.5572 192.33306 807.55656 195.18897 876.12792 184.47417 0 -876.31499 595296.17 -594868.09 -1403.4232 55742.797 263.69793 1.8344028
|
||||
900 11.513051 2938.1376 2038.9242 186.60093 899.21343 183.32681 989.01659 184.31258 0 -889.86018 595300.05 -594867.63 -1087.2761 55742.797 256.12732 1.0106144
|
||||
950 12.11419 2965.6942 2007.942 183.76546 957.75216 227.45503 972.71506 206.37949 0 -880.4232 595299.46 -594867.83 -1848.7603 55742.797 252.40653 0.53885876
|
||||
1000 12.740639 2994.2317 2058.0187 188.34845 936.21302 170.68957 965.88085 205.36589 0 -833.14441 595294.86 -594867.44 327.6391 55742.797 258.71295 0.52143283
|
||||
1050 13.346812 3022.9501 2095.3848 191.76817 927.56526 203.90712 935.91396 205.08197 0 -845.07232 595294.32 -594866.59 -355.70418 55742.797 263.25608 0.94198602
|
||||
1100 13.938097 3051.1769 2047.7199 187.4059 1003.457 212.39892 989.65684 227.20812 0 -856.11277 595297.04 -594866.74 -1402.022 55742.797 256.98383 1.6773742
|
||||
1150 14.508841 3071.8157 2127.8626 194.74051 943.95311 188.38445 926.24309 223.28071 0 -821.63207 595294.06 -594866.38 550.31236 55742.797 267.1915 1.3431353
|
||||
1200 15.110682 3087.7694 2015.2955 184.43845 1072.4739 199.90932 1034.9531 215.15511 0 -804.43314 595293.38 -594866.49 -333.57793 55742.797 253.26777 0.70913778
|
||||
1250 15.728746 3102.5825 2176.9518 199.23312 925.63076 155.81519 956.83624 230.0728 0 -847.47674 595296.65 -594866.26 -932.66685 55742.797 273.66551 0.54750805
|
||||
1300 16.365541 3116.8403 2087.6045 191.05612 1029.2357 209.96201 974.81053 241.13608 0 -823.38398 595292.74 -594866.03 -825.75383 55742.797 262.34486 0.76175709
|
||||
1350 16.943579 3131.0787 2089.6524 191.24354 1041.4264 186.48189 998.11168 233.71019 0 -801.37003 595290.06 -594865.57 684.79151 55742.797 262.36797 1.3871293
|
||||
1400 17.542898 3138.996 2186.2582 200.08483 952.73785 168.60338 957.20178 227.71944 0 -826.52269 595291.08 -594865.34 1796.7295 55742.797 274.47403 1.5135537
|
||||
1450 18.144658 3139.5791 2010.7377 184.02132 1128.8414 192.8015 1074.5205 245.37206 0 -807.3159 595288.01 -594864.55 -16.504608 55742.797 252.63135 0.87723467
|
||||
1500 18.759382 3143.8991 2099.4529 192.14048 1044.4462 186.04014 980.83524 242.01309 0 -784.81131 595285 -594864.63 2343.8986 55742.797 263.89145 0.61241549
|
||||
1550 19.331644 3149.7316 2086.068 190.9155 1063.6635 165.80546 1056.0893 230.89463 0 -813.37768 595289.09 -594864.84 2260.7364 55742.797 262.17666 0.69483626
|
||||
1600 19.91757 3156.535 2013.4276 184.2675 1143.1073 210.65881 1098.2892 243.94955 0 -835.62037 595290.47 -594864.64 -838.57356 55742.797 252.86585 1.1542996
|
||||
1650 20.503137 3160.0031 2081.0656 190.45768 1078.9375 212.2197 1005.7509 250.38023 0 -813.71955 595289.15 -594864.85 796.21731 55742.797 261.22447 1.5557945
|
||||
1700 21.130273 3155.5677 2113.3761 193.41472 1042.1916 146.036 1019.0909 249.77802 0 -798.16357 595290.59 -594865.14 359.69262 55742.797 265.46995 1.074008
|
||||
1750 21.735444 3151.796 2063.5487 188.85455 1088.2472 224.89093 997.02075 247.36817 0 -807.87592 595291.82 -594864.98 -1081.2667 55742.797 259.34362 0.69484916
|
||||
1800 22.302735 3150.4232 2097.9294 192.00105 1052.4938 202.22751 974.42358 248.58229 0 -799.53722 595291.6 -594864.8 94.58692 55742.797 263.68474 0.65252808
|
||||
1850 22.902581 3153.4477 2106.6272 192.79706 1046.8205 177.57166 971.73469 249.90348 0 -777.13298 595289.76 -594865.02 881.42516 55742.797 264.65016 0.99601444
|
||||
1900 23.480426 3159.2037 2092.2693 191.48304 1066.9343 198.78895 969.41309 260.03288 0 -787.26163 595290.41 -594864.45 606.40366 55742.797 262.66088 1.4839893
|
||||
1950 24.086136 3164.5139 2059.5653 188.48999 1104.9485 214.12027 1000.4493 263.39543 0 -799.45067 595291.13 -594864.69 -1248.7209 55742.797 258.62963 1.2624825
|
||||
2000 24.655188 3171.2963 2080.1555 190.37439 1091.1408 179.21892 996.41486 248.41626 0 -760.00877 595292.04 -594864.94 940.70366 55742.797 261.39948 0.7837686
|
||||
Loop time of 24.6553 on 4 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Performance: 3.504 ns/day, 6.849 hours/ns, 81.119 timesteps/s
|
||||
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 11.825 | 12.439 | 13.012 | 12.2 | 50.45
|
||||
Bond | 0.82239 | 0.89713 | 0.95859 | 5.7 | 3.64
|
||||
Kspace | 6.6353 | 7.2001 | 7.8139 | 15.7 | 29.20
|
||||
Neigh | 0.44976 | 0.44994 | 0.45003 | 0.0 | 1.82
|
||||
Comm | 0.55452 | 0.62432 | 0.70013 | 6.6 | 2.53
|
||||
Output | 0.003664 | 0.0043042 | 0.0061252 | 1.6 | 0.02
|
||||
Modify | 2.9457 | 2.959 | 2.9736 | 0.7 | 12.00
|
||||
Other | | 0.08099 | | | 0.33
|
||||
|
||||
Nlocal: 1125 ave 1166 max 1096 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 5867.25 ave 5956 max 5793 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 193608 ave 200510 max 186198 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 774433
|
||||
Ave neighs/atom = 172.096
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:24
|
||||
|
|
@ -1,171 +0,0 @@
|
|||
LAMMPS (18 Jul 2015)
|
||||
# 250 butane system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 79507 46656
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
Memory usage per processor = 20.1567 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655
|
||||
50 2.8944459 3475.1575 2067.5082 189.21692 1407.6493 846.00752 810.92425 115.58516 0 -764.28457 595242.38 -594842.96 3029.5187 55742.797 202.89871 152.54291
|
||||
100 5.6009829 2975.2938 1988.4777 181.98411 986.81605 358.65377 931.63831 175.54125 0 -919.10691 595306.8 -594866.71 2010.6143 55742.797 231.36532 50.118891
|
||||
150 8.2652578 2904.7202 1962.6821 179.62331 942.03808 234.91712 997.34884 195.22618 0 -909.31364 595293.23 -594869.37 4956.5664 55742.797 241.54715 14.313437
|
||||
200 10.97319 2905.616 1909.813 174.78477 995.80302 228.33514 1082.3513 200.51771 0 -943.19777 595298.16 -594870.37 2973.6338 55742.797 238.34584 5.1137785
|
||||
250 13.676164 2934.0626 1952.0155 178.6471 982.0471 212.76463 1131.5055 194.94566 0 -983.79846 595297.63 -594871 1591.8677 55742.797 244.66672 2.4161409
|
||||
300 16.381759 2995.4781 2017.7772 184.66557 977.70088 213.25867 1133.9492 195.13329 0 -992.6543 595299.31 -594871.29 2817.7518 55742.797 253.21545 1.6812532
|
||||
350 19.14905 3058.4882 1982.338 181.4222 1076.1502 228.54692 1197.9766 205.68279 0 -982.30502 595297.25 -594871 1408.2609 55742.797 248.83728 1.4672371
|
||||
400 21.914272 3016.5895 1998.3531 182.8879 1018.2363 238.06518 1169.309 197.52924 0 -1014.8678 595298.98 -594870.78 1454.1926 55742.797 250.8778 1.3985907
|
||||
450 24.629148 3014.232 1979.0496 181.12125 1035.1824 216.45567 1198.2831 197.81853 0 -1005.5029 595298.68 -594870.56 1296.2887 55742.797 248.44786 1.4025051
|
||||
500 27.390589 3054.4694 2023.8824 185.22432 1030.587 220.97548 1197.2137 199.51957 0 -1014.3543 595298.28 -594871.05 2481.3102 55742.797 254.08894 1.4000969
|
||||
550 30.147365 3088.0877 2020.1967 184.887 1067.8909 221.93439 1216.8427 213.27263 0 -1012.4867 595299.44 -594871.11 1697.8283 55742.797 253.63701 1.3687703
|
||||
600 32.854639 3112.7966 2031.7038 185.94013 1081.0928 220.37419 1254.8806 208.09272 0 -1030.3329 595298.95 -594870.87 -75.358619 55742.797 255.05809 1.439614
|
||||
650 35.725004 3155.4753 2025.6962 185.39031 1129.7792 221.82928 1284.1281 210.16702 0 -1015.1565 595299.63 -594870.82 1286.1601 55742.797 254.30974 1.4197689
|
||||
700 38.70379 3134.5524 2054.9292 188.0657 1079.6232 225.36387 1243.5643 191.53984 0 -1010.9148 595301.25 -594871.18 700.78109 55742.797 257.97902 1.4421042
|
||||
750 41.679769 3189.6098 2103.3042 192.49294 1086.3056 219.5641 1243.9772 203.81533 0 -1010.2161 595299.86 -594870.7 482.90086 55742.797 264.08828 1.3795515
|
||||
800 44.637671 3173.7718 2053.4131 187.92694 1120.3587 219.52183 1256.8457 218.62858 0 -1003.175 595299.34 -594870.81 538.9293 55742.797 257.80398 1.4002525
|
||||
850 47.531367 3221.5884 2084.0326 190.72922 1137.5559 224.32279 1277.7167 218.74781 0 -1011.3685 595298.54 -594870.4 145.40179 55742.797 261.66451 1.3777132
|
||||
900 50.379314 3214.7916 2054.2398 188.00261 1160.5518 222.07439 1296.738 225.4151 0 -1013.6054 595300.61 -594870.68 490.09072 55742.797 257.90629 1.4047863
|
||||
950 53.038527 3213.4974 2122.2134 194.2235 1091.284 221.85551 1252.3002 201.89089 0 -1014.1089 595300.04 -594870.69 1203.4321 55742.797 266.42418 1.4941572
|
||||
1000 55.653448 3212.7244 2079.8287 190.34449 1132.8956 225.42816 1261.5078 204.71764 0 -986.95829 595298.68 -594870.48 790.47665 55742.797 261.10437 1.4611106
|
||||
1050 58.290098 3216.1124 2106.2454 192.76212 1109.8669 213.54607 1261.1068 207.93437 0 -1001.5715 595299.05 -594870.2 69.145866 55742.797 264.43815 1.4332898
|
||||
1100 60.921228 3218.0797 2082.4185 190.5815 1135.6611 236.95827 1266.8625 198.25038 0 -995.08857 595298.88 -594870.2 694.35787 55742.797 261.43907 1.4374087
|
||||
1150 63.510285 3208.3968 2119.1968 193.94742 1089.2 210.20908 1236.1825 202.19163 0 -988.56762 595299.35 -594870.17 1528.4475 55742.797 266.08185 1.3950176
|
||||
1200 66.140576 3219.1289 2078.071 190.18362 1141.0579 234.57015 1268.2146 206.93186 0 -997.01686 595298.32 -594869.97 939.70203 55742.797 260.89628 1.4263352
|
||||
1250 68.774998 3268.5006 2115.3231 193.5929 1153.1775 241.50662 1262.3711 220.71001 0 -1000.1626 595298.37 -594869.62 -187.61926 55742.797 265.57695 1.4418423
|
||||
1300 71.409732 3324.099 2138.7146 195.73368 1185.3844 242.3031 1279.7915 223.94399 0 -989.04901 595298.47 -594870.08 258.69655 55742.797 268.51674 1.4497832
|
||||
1350 73.990336 3290.8471 2103.0993 192.47419 1187.7477 219.60844 1312.8653 221.57552 0 -993.69832 595297.61 -594870.21 1651.4259 55742.797 264.03877 1.4428477
|
||||
1400 76.620059 3227.0141 2052.6998 187.86167 1174.3143 236.01325 1272.4804 217.65692 0 -979.6779 595297.5 -594869.66 595.11702 55742.797 257.67276 1.5108922
|
||||
1450 79.249466 3253.5975 2107.984 192.92124 1145.6135 248.51645 1261.8304 208.79164 0 -1002.8333 595299.15 -594869.84 170.12671 55742.797 264.66781 1.4041436
|
||||
1500 81.830899 3276.1976 2101.6206 192.33886 1174.577 242.38394 1288.61 204.9722 0 -989.7383 595298.02 -594869.67 619.26135 55742.797 263.84288 1.4691362
|
||||
1550 84.449908 3271.9376 2117.6914 193.80965 1154.2463 234.62432 1268.5368 202.02117 0 -979.66071 595298.65 -594869.92 568.43047 55742.797 265.86458 1.4693675
|
||||
1600 87.073373 3281.1387 2105.1447 192.66139 1175.994 219.69265 1288.3244 205.52796 0 -966.68015 595298.79 -594869.67 1351.6273 55742.797 264.27256 1.5056051
|
||||
1650 89.695136 3287.675 2131.7955 195.10045 1155.8795 235.54527 1262.9178 220.26583 0 -991.68887 595298.56 -594869.72 -750.34342 55742.797 267.63101 1.4905169
|
||||
1700 92.342235 3295.9626 2079.4982 190.31424 1216.4644 232.74928 1329.4691 218.51323 0 -992.04439 595297.16 -594869.38 589.94184 55742.797 261.06357 1.4590401
|
||||
1750 94.911541 3315.2639 2097.2605 191.93983 1218.0035 241.24927 1312.3575 214.88139 0 -978.98823 595298.34 -594869.84 -92.971422 55742.797 263.26817 1.5389785
|
||||
1800 97.525025 3241.5219 2086.8653 190.98847 1154.6566 221.03432 1282.1774 209.03793 0 -986.54668 595299 -594870.05 456.17335 55742.797 261.96332 1.5311996
|
||||
1850 100.13804 3222.7069 2040.0335 186.70245 1182.6734 242.74754 1272.8794 221.80974 0 -982.51665 595296.99 -594869.24 279.00233 55742.797 256.09213 1.4766233
|
||||
1900 102.70693 3190.3766 2032.3946 186.00335 1157.9819 213.06329 1268.187 220.21025 0 -971.50314 595297.54 -594869.51 499.15225 55742.797 255.16226 1.3935863
|
||||
1950 105.30868 3208.3096 2053.9844 187.97923 1154.3252 212.46296 1277.2726 210.16078 0 -974.19087 595298.44 -594869.82 807.22906 55742.797 257.85261 1.4622515
|
||||
2000 107.9105 3231.8811 2053.6913 187.9524 1178.1899 229.11239 1280.6492 220.1084 0 -979.25259 595297.02 -594869.45 474.05197 55742.797 257.80782 1.4833297
|
||||
Loop time of 107.911 on 1 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Pair time (%) = 65.8442 (61.0173)
|
||||
Bond time (%) = 16.6061 (15.3887)
|
||||
Kspce time (%) = 20.7451 (19.2244)
|
||||
Neigh time (%) = 1.24307 (1.15195)
|
||||
Comm time (%) = 0.386346 (0.358024)
|
||||
Outpt time (%) = 0.00603366 (0.00559135)
|
||||
Other time (%) = 3.07976 (2.854)
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8739 ave 8739 max 8739 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 860638 ave 860638 max 860638 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 860638
|
||||
Ave neighs/atom = 191.253
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,171 +0,0 @@
|
|||
LAMMPS (18 Jul 2015)
|
||||
# 250 butane system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nve
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 26875 11664
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
Memory usage per processor = 14.7792 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655
|
||||
50 0.91017509 3449.6475 2040.7698 186.76984 1408.8777 836.85155 816.32124 115.24642 0 -758.7276 595242.44 -594843.26 3042.2937 55742.797 199.51659 152.7045
|
||||
100 1.829694 2917.9137 1947.102 178.19743 970.81176 363.96553 932.94225 165.60761 0 -931.00296 595306.34 -594867.04 1697.0127 55742.797 226.24749 49.885738
|
||||
150 2.6620312 2853.3142 1959.0731 179.29301 894.24108 244.19792 978.17893 187.28366 0 -941.03478 595295.44 -594869.82 4597.2005 55742.797 241.05848 14.405808
|
||||
200 3.4969041 2885.6715 1928.6381 176.50762 957.03347 227.09245 1066.5297 186.6858 0 -949.52603 595296.49 -594870.24 2602.8275 55742.797 240.70211 5.1458056
|
||||
250 4.621171 2905.8961 1939.7876 177.52802 966.10847 215.77945 1122.1238 195.98218 0 -993.52132 595296.54 -594870.79 1808.1681 55742.797 243.04306 2.643716
|
||||
300 5.5216351 2968.5517 1974.9277 180.74402 993.624 210.11413 1158.7871 194.142 0 -996.53154 595297.91 -594870.79 3371.8618 55742.797 247.7682 1.8321312
|
||||
350 6.3789251 2996.151 1992.9982 182.39782 1003.1527 217.80518 1150.726 205.32316 0 -996.14478 595296.05 -594870.61 3022.9945 55742.797 250.15947 1.5176819
|
||||
400 7.208317 2991.7201 1975.3852 180.78589 1016.3349 221.46133 1169.8254 213.90874 0 -1016.9906 595298.44 -594870.31 753.59124 55742.797 247.99744 1.3743032
|
||||
450 8.0359671 3061.6051 2009.1302 183.87421 1052.4749 212.54169 1234.7697 205.71762 0 -1028.2259 595297.95 -594870.28 996.71341 55742.797 252.23801 1.3870863
|
||||
500 8.8456361 3127.3783 2009.8033 183.93581 1117.5749 222.16507 1246.5854 215.82607 0 -994.66665 595298.3 -594870.63 2537.6157 55742.797 252.32947 1.367397
|
||||
550 9.6647151 3181.037 2069.9836 189.44346 1111.0534 218.00575 1246.961 212.55852 0 -992.83597 595296.16 -594869.79 1333.8768 55742.797 259.86467 1.4641506
|
||||
600 10.484356 3194.2009 2007.5349 183.7282 1186.666 228.93838 1309.4718 215.93595 0 -995.70641 595297.81 -594869.79 1336.7994 55742.797 252.00698 1.4677515
|
||||
650 11.30116 3145.4387 2028.2544 185.62444 1117.1843 209.73722 1277.9793 217.12799 0 -1015.2398 595297.88 -594870.3 1442.6875 55742.797 254.61499 1.4639962
|
||||
700 12.106719 3163.3345 2053.2645 187.91335 1110.07 209.45249 1257.3108 216.7541 0 -1000.1505 595296.63 -594869.92 1093.9724 55742.797 257.76091 1.4652884
|
||||
750 12.924665 3145.6215 2010.7195 184.01966 1134.902 224.53065 1248.3301 222.25374 0 -988.4479 595298.83 -594870.59 470.73988 55742.797 252.39115 1.5116555
|
||||
800 13.736913 3191.2614 2043.4195 187.01234 1147.842 225.71717 1239.3564 234.89539 0 -980.97352 595299.07 -594870.22 1472.0305 55742.797 256.53524 1.4309304
|
||||
850 14.550736 3157.6279 2004.8472 183.48223 1152.7806 217.72587 1269.3398 224.40554 0 -987.51794 595299.15 -594870.32 293.76575 55742.797 251.69397 1.4007963
|
||||
900 15.344895 3188.5027 2077.065 190.09155 1111.4377 216.92608 1251.4141 213.7672 0 -1000.1269 595299.5 -594870.05 702.56821 55742.797 260.7853 1.3847905
|
||||
950 16.157597 3205.6761 2090.9807 191.3651 1114.6954 223.7729 1252.7887 225.91029 0 -1016.3682 595299.15 -594870.56 -19.492925 55742.797 262.50762 1.4603579
|
||||
1000 16.969809 3231.5931 2078.7058 190.24172 1152.8873 228.77504 1273.1611 219.28923 0 -995.58473 595296.82 -594869.57 1292.4071 55742.797 260.98775 1.3954023
|
||||
1050 17.771785 3264.2837 2106.0113 192.7407 1158.2724 224.16481 1278.5557 212.91309 0 -985.93386 595298.71 -594870.14 1357.1588 55742.797 264.40381 1.4463397
|
||||
1100 18.572331 3243.3355 2125.1664 194.49376 1118.1691 227.38559 1247.5134 210.61488 0 -996.85878 595299.68 -594870.17 650.53225 55742.797 266.82195 1.4240918
|
||||
1150 19.40463 3255.4144 2096.5982 191.87922 1158.8162 234.11389 1267.4257 217.02225 0 -989.70892 595299.81 -594869.84 688.78475 55742.797 263.2133 1.4631154
|
||||
1200 20.321045 3266.2609 2088.3727 191.12642 1177.8882 225.40174 1284.1097 225.77008 0 -985.63518 595297.81 -594869.57 182.80287 55742.797 262.21901 1.3550749
|
||||
1250 21.233994 3277.4365 2093.1481 191.56346 1184.2884 250.33569 1267.9985 235.70102 0 -999.80819 595299.96 -594869.9 780.87528 55742.797 262.80001 1.4077597
|
||||
1300 22.113268 3280.4141 2121.4996 194.15818 1158.9145 228.23585 1259.7304 230.65174 0 -989.06345 595298.99 -594869.63 932.19341 55742.797 266.34543 1.4646736
|
||||
1350 23.007421 3272.2214 2088.047 191.09662 1184.1744 224.66504 1284.656 217.03214 0 -970.5252 595297.72 -594869.37 63.097535 55742.797 262.16781 1.3823451
|
||||
1400 23.903494 3239.3096 2099.1837 192.11584 1140.1259 221.3215 1252.8691 215.64014 0 -978.70393 595298.89 -594869.89 1125.3057 55742.797 263.59141 1.3221979
|
||||
1450 24.833224 3226.293 2042.7354 186.94973 1183.5576 241.40449 1273.025 233.66813 0 -994.70934 595299.55 -594869.38 -412.31857 55742.797 256.45155 1.4245996
|
||||
1500 25.736203 3245.4596 2097.0431 191.91994 1148.4164 250.3854 1248.1507 212.36871 0 -990.48467 595297.36 -594869.36 245.49743 55742.797 263.28349 1.4252034
|
||||
1550 26.633033 3308.5518 2113.8467 193.45778 1194.7051 234.5293 1286.7563 233.20552 0 -987.36764 595297.06 -594869.48 1324.7098 55742.797 265.37419 1.4864431
|
||||
1600 27.530123 3319.786 2130.8949 195.01803 1188.8911 234.06508 1292.3987 225.94876 0 -992.81161 595299.1 -594869.81 343.14209 55742.797 267.51024 1.5104547
|
||||
1650 28.41116 3239.0425 2066.8485 189.15654 1172.194 219.46922 1303.0071 210.00869 0 -989.28577 595298.63 -594869.64 -505.97551 55742.797 259.48305 1.4300292
|
||||
1700 29.313339 3281.3023 2054.581 188.03383 1226.7213 224.72686 1339.1948 208.65914 0 -974.24634 595297.79 -594869.4 331.11846 55742.797 257.92342 1.4735531
|
||||
1750 30.216241 3237.8348 2043.3835 187.00904 1194.4513 238.16066 1281.9383 221.74494 0 -976.72731 595299.4 -594870.06 612.69867 55742.797 256.53793 1.4116726
|
||||
1800 31.113153 3242.1274 2087.94 191.08683 1154.1873 240.53142 1256.6966 210.49591 0 -983.16111 595299.34 -594869.72 -8.1277769 55742.797 262.14149 1.4166426
|
||||
1850 31.993161 3249.8016 2079.8947 190.35052 1169.9069 233.21641 1269.4077 215.23716 0 -975.12835 595296.5 -594869.33 1156.1724 55742.797 261.13101 1.4122227
|
||||
1900 32.891621 3251.9579 2097.6037 191.97124 1154.3541 243.13703 1228.3357 235.37914 0 -983.06313 595300.37 -594869.8 293.60486 55742.797 263.33664 1.4715416
|
||||
1950 33.791255 3202.0703 2076.0894 190.00227 1125.9809 233.71337 1217.6976 227.58496 0 -981.8352 595298.07 -594869.25 -544.65606 55742.797 260.61868 1.5018224
|
||||
2000 34.690323 3215.7987 2015.5993 184.46625 1200.1994 242.43605 1281.6846 227.48326 0 -980.70325 595298.82 -594869.52 248.82508 55742.797 253.04055 1.4169879
|
||||
Loop time of 34.6904 on 4 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Pair time (%) = 16.514 (47.6038)
|
||||
Bond time (%) = 4.35555 (12.5555)
|
||||
Kspce time (%) = 10.6198 (30.613)
|
||||
Neigh time (%) = 0.393407 (1.13405)
|
||||
Comm time (%) = 1.18699 (3.42165)
|
||||
Outpt time (%) = 0.00467861 (0.0134867)
|
||||
Other time (%) = 1.6161 (4.65863)
|
||||
|
||||
Nlocal: 1125 ave 1219 max 1009 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 5768 ave 5890 max 5664 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 215002 ave 223956 max 206872 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 860008
|
||||
Ave neighs/atom = 191.113
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 29
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,177 +0,0 @@
|
|||
LAMMPS (18 Jul 2015)
|
||||
# 250 butane system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_CORE gCORES temp/com
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDIRECT all drude/transform/direct
|
||||
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||
fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 79507 46656
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
Memory usage per processor = 20.1567 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655
|
||||
50 2.8816051 2130.0808 1490.8248 136.43926 639.25601 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137
|
||||
100 5.569447 2172.0554 1656.5476 151.60609 515.50773 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117
|
||||
150 8.2248161 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6234 55742.797 218.02975 0.12336382
|
||||
200 10.911476 2271.1314 1750.9955 160.2499 520.13587 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.4949 55742.797 220.19714 0.23035017
|
||||
250 13.588019 2333.7822 1793.0252 164.09642 540.75705 153.18169 833.95287 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339004
|
||||
300 16.26521 2403.6147 1909.3441 174.74185 494.27059 144.27299 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3721 55742.797 239.06243 3.0455686
|
||||
350 18.937858 2448.2389 1862.67 170.47027 585.56885 181.70523 821.7917 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806435
|
||||
400 21.590191 2498.6994 1942.5496 177.7808 556.14976 168.5792 828.99117 182.0756 0 -1050.149 595296.43 -594869.77 485.86761 55742.797 244.23632 0.3882729
|
||||
450 24.247025 2552.9641 1890.0917 172.97989 662.87241 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452669 55742.797 237.65323 0.34464588
|
||||
500 26.850275 2608.55 1970.0729 180.29971 638.4771 187.01392 838.62129 176.10775 0 -985.23355 595290.89 -594868.93 3471.1633 55742.797 247.59402 0.66791252
|
||||
550 29.482354 2667.002 1875.8227 171.67399 791.17931 178.48765 1003.6885 176.78989 0 -991.21705 595292.35 -594868.92 1767.0543 55742.797 235.34039 1.7252619
|
||||
600 32.10773 2715.2399 1883.279 172.35639 831.96094 186.79504 1047.6877 183.04311 0 -1010.5423 595293.27 -594868.29 931.85523 55742.797 236.28437 1.7094253
|
||||
650 34.715398 2754.4497 1970.794 180.3657 783.65568 166.02823 963.09399 184.8464 0 -952.45217 595290.25 -594868.11 2640.017 55742.797 247.67755 0.68709275
|
||||
700 37.337317 2795.9461 1928.2674 176.4737 867.67874 176.09641 1002.4636 186.11483 0 -920.14356 595291.32 -594868.18 664.78904 55742.797 242.41897 0.44316381
|
||||
750 39.927419 2838.2052 2043.2258 186.99461 794.97945 170.34991 941.73148 193.53082 0 -940.49604 595298.1 -594868.23 410.24758 55742.797 256.84035 0.55229077
|
||||
800 42.469991 2881.9788 1945.9722 178.09402 936.00667 197.5203 1021.5571 202.83524 0 -915.18511 595297.49 -594868.21 -716.81442 55742.797 244.35112 1.2303511
|
||||
850 45.05362 2923.3858 2106.5752 192.79231 816.81052 195.94987 886.41681 184.36064 0 -878.10485 595296.29 -594868.1 -1407.5711 55742.797 264.3276 1.8387296
|
||||
900 47.651245 2950.6673 2039.6221 186.6648 911.04515 183.79618 1000.7954 184.49766 0 -890.38965 595299.97 -594867.63 -1085.794 55742.797 256.21167 1.0198208
|
||||
950 50.451391 2976.6436 2006.5932 183.64202 970.05039 228.60059 985.21322 206.18529 0 -881.65815 595299.54 -594867.83 -1851.9703 55742.797 252.23637 0.54012241
|
||||
1000 53.018937 3003.743 2056.8471 188.24122 946.89587 171.73287 976.85675 207.05097 0 -836.24563 595294.95 -594867.45 282.61914 55742.797 258.5658 0.52076804
|
||||
1050 55.532595 3031.3535 2095.4846 191.7773 935.86887 203.54188 945.75569 204.8504 0 -846.10969 595294.45 -594866.62 -376.91112 55742.797 263.27093 0.93584407
|
||||
1100 58.115412 3058.5347 2047.3098 187.36838 1011.2249 211.94076 1001.093 223.66214 0 -855.82424 595297.13 -594866.78 -1381.6531 55742.797 256.93409 1.6724456
|
||||
1150 60.799698 3078.3996 2123.1811 194.31206 955.21855 189.50189 937.18685 224.21465 0 -823.63222 595294.38 -594866.43 524.70113 55742.797 266.5974 1.3568376
|
||||
1200 63.295243 3093.556 2005.8939 183.57802 1087.6621 201.3428 1044.9909 219.39202 0 -805.37122 595293.83 -594866.52 -370.32492 55742.797 252.0829 0.71475597
|
||||
1250 65.797931 3108.5155 2175.8972 199.13661 932.61826 156.6571 969.72254 225.30586 0 -850.00503 595297.25 -594866.31 -1015.3093 55742.797 273.53154 0.55100418
|
||||
1300 68.300441 3122.9792 2090.3719 191.30939 1032.6073 209.92015 984.36624 236.75408 0 -825.27583 595292.92 -594866.08 -798.51816 55742.797 262.69421 0.75855207
|
||||
1350 70.793202 3136.8213 2084.47 190.76925 1052.3513 186.49827 1004.7564 234.55362 0 -798.08335 595290.25 -594865.63 702.53782 55742.797 261.71553 1.3884089
|
||||
1400 73.326733 3144.9028 2180.3659 199.54558 964.53687 170.02484 962.43948 235.07761 0 -829.27156 595291.77 -594865.51 1682.2488 55742.797 273.7286 1.5246324
|
||||
1450 75.821906 3146.3365 2013.3816 184.26329 1132.9549 193.77936 1084.1403 252.3227 0 -821.23045 595288.54 -594864.6 -160.21484 55742.797 252.96375 0.87780357
|
||||
1500 78.325264 3150.6861 2107.4863 192.87569 1043.1998 185.11752 988.72532 245.47682 0 -796.86739 595285.46 -594864.71 2242.3101 55742.797 264.90216 0.61222547
|
||||
1550 80.779931 3156.3483 2074.5953 189.86552 1081.7531 166.52863 1062.4971 238.93518 0 -810.65247 595289.34 -594864.9 2224.9015 55742.797 260.73559 0.68881715
|
||||
1600 83.275807 3163.8714 2000.6756 183.10045 1163.1958 210.70823 1110.4519 256.16493 0 -840.1463 595290.73 -594864.71 -830.17884 55742.797 251.26533 1.1443116
|
||||
1650 85.768304 3169.3489 2056.4309 188.20313 1112.918 214.6419 1021.762 268.00157 0 -815.69477 595289 -594864.8 813.12089 55742.797 258.12835 1.5476743
|
||||
1700 88.261463 3168.7666 2119.4079 193.96675 1049.3587 147.25006 1027.6415 246.49221 0 -797.55007 595290.74 -594865.22 412.59618 55742.797 266.23017 1.0703149
|
||||
1750 90.746918 3168.2304 2066.7675 189.14913 1101.463 224.44009 1005.0052 243.56874 0 -797.83359 595291.25 -594864.96 -858.91314 55742.797 259.74684 0.69942293
|
||||
1800 93.246077 3169.7579 2109.6017 193.06929 1060.1562 204.57678 981.05867 249.37843 0 -801.42006 595291.51 -594864.95 137.05559 55742.797 265.15197 0.65571606
|
||||
1850 95.734661 3174.8532 2133.5052 195.25692 1041.348 175.87566 982.18775 244.55231 0 -786.49546 595290.43 -594865.21 882.03323 55742.797 268.02768 1.006296
|
||||
1900 98.221874 3180.3842 2106.4808 192.78367 1073.9034 207.8879 977.47746 250.68948 0 -788.04039 595290.55 -594864.66 574.40162 55742.797 264.45175 1.4759897
|
||||
1950 100.72148 3182.921 2084.8893 190.80763 1098.0317 207.26976 1007.5583 256.52302 0 -800.37789 595291.76 -594864.71 -981.75066 55742.797 261.81202 1.271779
|
||||
2000 103.20588 3185.2881 2079.8136 190.3431 1105.4745 185.44441 1008.6997 251.0561 0 -766.97142 595292.22 -594864.97 661.65951 55742.797 261.35563 0.78600155
|
||||
Loop time of 103.206 on 1 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Pair time (%) = 60.3651 (58.49)
|
||||
Bond time (%) = 16.8315 (16.3087)
|
||||
Kspce time (%) = 20.1106 (19.4859)
|
||||
Neigh time (%) = 1.52801 (1.48054)
|
||||
Comm time (%) = 0.328804 (0.318591)
|
||||
Outpt time (%) = 0.00495553 (0.00480159)
|
||||
Other time (%) = 4.03695 (3.91155)
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10060 ave 10060 max 10060 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 774908 ave 774908 max 774908 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 774908
|
||||
Ave neighs/atom = 172.202
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,177 +0,0 @@
|
|||
LAMMPS (18 Jul 2015)
|
||||
# 250 butane system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
|
||||
pair_modify mix geometric tail yes
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.butane
|
||||
orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
4250 bonds
|
||||
reading angles ...
|
||||
6000 angles
|
||||
reading dihedrals ...
|
||||
6750 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
12 = max # of 1-4 neighbors
|
||||
17 = max # of special neighbors
|
||||
|
||||
group gBUTANE molecule 1:250
|
||||
4500 atoms in group gBUTANE
|
||||
group gCORES type 1 2 3
|
||||
3500 atoms in group gCORES
|
||||
group gDRUDES type 4 5
|
||||
1000 atoms in group gDRUDES
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 * thole 1.368000
|
||||
pair_coeff 2 * thole 1.368000
|
||||
pair_coeff 4 * thole 1.368000
|
||||
pair_coeff 5 * thole 1.368000
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 260.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gCORES create ${vTEMP} 12345
|
||||
velocity gCORES create 260 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N D D
|
||||
|
||||
fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
|
||||
0 = # of size 2 clusters
|
||||
500 = # of size 3 clusters
|
||||
500 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_CORE gCORES temp/com
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDIRECT all drude/transform/direct
|
||||
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
|
||||
fix fNVT1 gCORES nvt temp 260 260 100.0
|
||||
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
|
||||
fix fNVT2 gDRUDES nvt temp 1 1 20.0
|
||||
fix fINVERSE all drude/transform/inverse
|
||||
|
||||
fix fMOMENTUM all momentum 100 linear 1 1 1
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 50
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.367867
|
||||
grid = 36 36 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.031354
|
||||
estimated relative force accuracy = 9.44215e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 26875 11664
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 17
|
||||
New max number of 1-2 to 1-4 neighbors: 17 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
Memory usage per processor = 14.7792 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655
|
||||
50 1.019057 2130.0808 1490.8248 136.43926 639.25599 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137
|
||||
100 2.043848 2172.0553 1656.5476 151.60609 515.50769 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117
|
||||
150 3.0405529 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6233 55742.797 218.02975 0.12336381
|
||||
200 4.0440719 2271.1314 1750.9955 160.2499 520.13584 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.495 55742.797 220.19714 0.23035002
|
||||
250 5.0482569 2333.7821 1793.0252 164.09642 540.75694 153.18169 833.95288 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339003
|
||||
300 6.044857 2403.6147 1909.3441 174.74185 494.27053 144.273 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3723 55742.797 239.06243 3.0455683
|
||||
350 7.0382209 2448.239 1862.67 170.47027 585.56896 181.70522 821.79171 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806438
|
||||
400 8.025661 2498.6992 1942.5496 177.78079 556.14963 168.5792 828.99116 182.0756 0 -1050.149 595296.43 -594869.77 485.86784 55742.797 244.23632 0.38827289
|
||||
450 9.010309 2552.9639 1890.0917 172.97988 662.87225 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452466 55742.797 237.65323 0.34464586
|
||||
500 9.979717 2608.5501 1970.0729 180.29971 638.47718 187.01392 838.62128 176.10774 0 -985.23355 595290.89 -594868.93 3471.1636 55742.797 247.59402 0.66791289
|
||||
550 10.965174 2667.002 1875.8227 171.674 791.17932 178.48766 1003.6885 176.78987 0 -991.21707 595292.35 -594868.92 1767.0547 55742.797 235.34039 1.7252612
|
||||
600 11.944224 2715.2397 1883.279 172.35639 831.96067 186.79504 1047.6877 183.0431 0 -1010.5423 595293.27 -594868.29 931.85415 55742.797 236.28437 1.7094243
|
||||
650 12.916431 2754.4495 1970.794 180.36571 783.65547 166.02823 963.09393 184.84638 0 -952.45216 595290.25 -594868.11 2640.0169 55742.797 247.67755 0.68709272
|
||||
700 13.889729 2795.9463 1928.2674 176.47369 867.67893 176.09642 1002.4636 186.11482 0 -920.14357 595291.32 -594868.18 664.78857 55742.797 242.41896 0.44316458
|
||||
750 14.849284 2838.2051 2043.2257 186.9946 794.97938 170.34989 941.73149 193.53082 0 -940.49605 595298.1 -594868.23 410.24692 55742.797 256.84034 0.55228895
|
||||
800 15.765569 2881.9786 1945.9721 178.09402 936.00653 197.52035 1021.5571 202.83523 0 -915.18508 595297.49 -594868.21 -716.8133 55742.797 244.35111 1.2303486
|
||||
850 16.62147 2923.386 2106.5752 192.79231 816.81079 195.9499 886.4168 184.36063 0 -878.10486 595296.29 -594868.1 -1407.5716 55742.797 264.3276 1.8387295
|
||||
900 17.476931 2950.6672 2039.6221 186.6648 911.04508 183.7962 1000.7955 184.49765 0 -890.38971 595299.97 -594867.63 -1085.795 55742.797 256.21167 1.0198179
|
||||
950 18.332394 2976.6435 2006.5931 183.64202 970.05037 228.60059 985.21322 206.18531 0 -881.65816 595299.54 -594867.83 -1851.9704 55742.797 252.23636 0.54012295
|
||||
1000 19.192022 3003.7432 2056.8471 188.24122 946.89612 171.73291 976.85679 207.05089 0 -836.24565 595294.95 -594867.45 282.61893 55742.797 258.5658 0.52076763
|
||||
1050 20.070536 3031.3535 2095.4845 191.77729 935.86893 203.54188 945.75571 204.85039 0 -846.10968 595294.45 -594866.62 -376.91144 55742.797 263.27092 0.93584075
|
||||
1100 20.978902 3058.5346 2047.3099 187.36839 1011.2247 211.94079 1001.093 223.66207 0 -855.82432 595297.13 -594866.78 -1381.6546 55742.797 256.93411 1.6724371
|
||||
1150 21.886788 3078.3992 2123.1811 194.31206 955.21814 189.50191 937.18689 224.21463 0 -823.63239 595294.38 -594866.43 524.69914 55742.797 266.59741 1.3568273
|
||||
1200 22.731807 3093.5558 2005.8937 183.57801 1087.6621 201.34278 1044.991 219.39206 0 -805.37129 595293.83 -594866.52 -370.32731 55742.797 252.08289 0.71475598
|
||||
1250 23.577332 3108.5154 2175.8971 199.1366 932.61825 156.65715 969.72264 225.30585 0 -850.00508 595297.25 -594866.31 -1015.3099 55742.797 273.53152 0.55101046
|
||||
1300 24.41954 3122.979 2090.3725 191.30944 1032.6065 209.92008 984.36627 236.75348 0 -825.27575 595292.92 -594866.08 -798.51517 55742.797 262.69428 0.75855174
|
||||
1350 25.260247 3136.8213 2084.4701 190.76926 1052.3512 186.49846 1004.7564 234.55382 0 -798.08358 595290.25 -594865.63 702.53502 55742.797 261.71554 1.3884097
|
||||
1400 26.111855 3144.9027 2180.3656 199.54555 964.53705 170.02479 962.43949 235.07796 0 -829.2718 595291.77 -594865.51 1682.2458 55742.797 273.72857 1.5246347
|
||||
1450 26.950639 3146.3362 2013.3813 184.26326 1132.955 193.77936 1084.1402 252.32287 0 -821.23025 595288.54 -594864.6 -160.21134 55742.797 252.96371 0.87779957
|
||||
1500 27.790502 3150.6919 2107.4861 192.87567 1043.2058 185.11758 988.72513 245.47693 0 -796.86696 595285.47 -594864.71 2242.3607 55742.797 264.90213 0.61222945
|
||||
1550 28.619789 3156.3482 2074.5978 189.86575 1081.7504 166.52858 1062.4966 238.93331 0 -810.65249 595289.34 -594864.9 2224.9023 55742.797 260.7359 0.68881915
|
||||
1600 29.460929 3163.8714 2000.6737 183.10027 1163.1978 210.70797 1110.4522 256.16659 0 -840.14623 595290.73 -594864.71 -830.17835 55742.797 251.26509 1.1443132
|
||||
1650 30.299437 3169.3484 2056.4317 188.20321 1112.9167 214.64223 1021.7623 268.00145 0 -815.6963 595289 -594864.8 813.10459 55742.797 258.12846 1.5476742
|
||||
1700 31.139599 3168.7665 2119.4084 193.96679 1049.3581 147.25025 1027.6419 246.49323 0 -797.55219 595290.74 -594865.22 412.56019 55742.797 266.23023 1.0703144
|
||||
1750 31.982883 3168.2311 2066.7649 189.14889 1101.4662 224.43981 1005.0038 243.56888 0 -797.82899 595291.25 -594864.96 -858.8853 55742.797 259.74652 0.69941609
|
||||
1800 32.826623 3169.7582 2109.6043 193.06952 1060.154 204.57671 981.05578 249.38028 0 -801.42264 595291.51 -594864.95 137.07377 55742.797 265.1523 0.65571522
|
||||
1850 33.670608 3174.8602 2133.4946 195.25594 1041.3657 175.87741 982.18471 244.56078 0 -786.49062 595290.44 -594865.21 882.07943 55742.797 268.02634 1.0063027
|
||||
1900 34.515605 3180.392 2106.493 192.78478 1073.8991 207.88481 977.47602 250.68433 0 -788.04013 595290.55 -594864.66 574.47687 55742.797 264.45328 1.4759962
|
||||
1950 35.361549 3182.9198 2084.8984 190.80846 1098.0214 207.26715 1007.5534 256.52264 0 -800.37486 595291.76 -594864.71 -981.72234 55742.797 261.81317 1.2717649
|
||||
2000 36.208456 3185.292 2079.8093 190.34271 1105.4827 185.44479 1008.7001 251.06381 0 -766.97114 595292.22 -594864.97 661.65731 55742.797 261.3551 0.78598984
|
||||
Loop time of 36.2086 on 4 procs for 2000 steps with 4500 atoms
|
||||
|
||||
Pair time (%) = 15.6569 (43.2408)
|
||||
Bond time (%) = 4.33273 (11.966)
|
||||
Kspce time (%) = 10.271 (28.3662)
|
||||
Neigh time (%) = 0.435532 (1.20284)
|
||||
Comm time (%) = 0.83936 (2.31813)
|
||||
Outpt time (%) = 0.00456434 (0.0126057)
|
||||
Other time (%) = 4.66849 (12.8933)
|
||||
|
||||
Nlocal: 1125 ave 1165 max 1096 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 5854.5 ave 5931 max 5788 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 193727 ave 200966 max 187020 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 774908
|
||||
Ave neighs/atom = 172.202
|
||||
Ave special neighs/atom = 13.3333
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,277 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 1 500.0
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 50653 27000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.48 | 22.48 | 22.48 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301
|
||||
20 0.81254506 10970.11 5646.659 758.03805 5323.451 2059.6082 2216.9981 125.92585 0 1728.656 514096.92 -514904.66 75437.598 22442.383 899.52209 426.89792
|
||||
40 1.7067263 8946.2741 5328.0351 715.26425 3618.239 1462.1404 1696.2927 256.70344 0 1227.0694 513938.28 -514962.25 46636.214 23048.268 913.15414 252.56747
|
||||
60 2.5404506 7510.8082 4723.1172 634.0568 2787.6909 1200.8053 1745.3972 301.30817 0 557.80687 513950.19 -514967.82 37794.247 23517.363 840.69812 151.04831
|
||||
80 3.3801596 6348.9157 4602.0926 617.80981 1746.8231 881.76663 1380.8166 300.54007 0 204.03797 513929.56 -514949.9 33851.301 23924.559 841.20021 95.741792
|
||||
100 4.2437606 5485.1689 4144.6876 556.40528 1340.4814 784.82013 1301.8493 289.61476 0 -77.16227 514016.31 -514974.95 23853.877 24319.093 768.90717 59.825643
|
||||
120 5.0577445 4861.8148 3777.2483 507.07825 1084.5665 621.85238 1297.2272 283.15722 0 -165.13412 514030.3 -514982.83 17461.708 24661.819 708.89192 35.503576
|
||||
140 5.8777206 4340.7393 3447.4973 462.81068 893.24198 643.1178 1248.6088 275.35463 0 -264.6674 513962.95 -514972.12 14977.074 24942.76 650.90916 23.297159
|
||||
160 6.688663 3926.6789 3280.6852 440.41693 645.99367 590.74309 1125.6956 275.31466 0 -402.41978 514040.08 -514983.42 17550.63 25183.539 623.01495 13.767656
|
||||
180 7.4729645 3510.0638 3034.3628 407.34927 475.70103 580.84695 1065.6783 271.61808 0 -478.33275 514008.17 -514972.28 9895.4157 25410.444 577.92533 8.7953368
|
||||
200 8.2036176 3232.9542 2804.7026 376.51845 428.25158 560.53426 1096.7584 268.56297 0 -524.94297 514009.86 -514982.53 8536.536 25604.126 535.28025 5.5722323
|
||||
220 8.9682925 3019.8368 2679.2202 359.67301 340.61655 534.32413 1086.0764 252.71411 0 -554.59208 514001.04 -514978.94 7625.0406 25766.134 511.84268 4.1308947
|
||||
240 9.730809 2817.4084 2557.6953 343.35885 259.71311 533.47006 1096.7331 235.22275 0 -594.9152 513968.32 -514979.12 6062.2975 25913.841 489.03736 2.9845074
|
||||
260 10.499042 2630.9155 2460.3336 330.28849 170.58193 520.16741 1043.8106 228.53526 0 -637.28205 514004.22 -514988.87 5628.429 26050.517 470.64131 2.358198
|
||||
280 11.217016 2462.5369 2379.2296 319.40065 83.307285 525.29091 971.98774 226.2588 0 -624.49241 513966.97 -514982.71 4755.8332 26171.267 455.29613 1.8853352
|
||||
300 11.964113 2313.8618 2233.2275 299.80054 80.634294 520.99642 985.55834 216.66019 0 -623.05887 513969.74 -514989.27 3495.3603 26275.734 427.3819 1.7109763
|
||||
320 12.723562 2171.4928 2215.8464 297.4672 -44.353519 513.03114 926.86216 206.3972 0 -647.51178 513946.73 -514989.86 3549.145 26372.81 424.12312 1.5400892
|
||||
340 13.426266 2048.6698 2102.88 282.30198 -54.210215 517.14417 972.13286 198.86927 0 -648.61225 513890.91 -514984.65 3715.5702 26466.519 402.53006 1.3933858
|
||||
360 14.168186 1940.223 2045.0378 274.53693 -104.81473 499.08868 932.31216 187.54718 0 -652.27824 513915.74 -514987.22 2294.4616 26556.528 391.47399 1.3177584
|
||||
380 14.864166 1826.4204 1933.7705 259.59981 -107.3501 518.46244 919.38664 182.02964 0 -651.82587 513909.74 -514985.14 2611.0855 26637.685 370.14008 1.326376
|
||||
400 15.599668 1760.0086 1974.1623 265.02222 -214.15371 494.76522 905.22476 184.88378 0 -673.22096 513861.68 -514987.49 2090.4168 26713.916 377.90359 1.2789937
|
||||
420 16.2925 1674.2391 1874.8006 251.68337 -200.56147 494.23164 919.14316 191.46494 0 -660.1575 513844.17 -514989.42 350.12478 26785.636 358.83667 1.3234235
|
||||
440 17.041535 1636.4128 1886.5254 253.25737 -250.11252 501.29431 885.94965 180.12472 0 -646.62075 513813.8 -514984.66 458.70321 26849.461 361.09661 1.2948048
|
||||
460 17.740912 1593.2246 1860.4472 249.7565 -267.22259 491.27176 906.91419 174.59456 0 -666.47423 513815.28 -514988.81 115.45351 26902.557 356.10559 1.2755931
|
||||
480 18.472947 1505.1612 1836.7228 246.5716 -331.56157 509.71008 860.32948 173.58748 0 -651.36822 513766.31 -514990.13 1635.9711 26947.857 351.56234 1.2644252
|
||||
500 19.162812 1442.4712 1798.4284 241.43076 -355.95719 522.31402 861.73677 168.27586 0 -655.15129 513739.29 -514992.42 1516.6732 26993.542 344.22674 1.2515652
|
||||
520 19.89256 1429.3971 1796.9572 241.23326 -367.5601 524.35274 871.7445 162.49855 0 -664.89069 513732.49 -514993.75 -691.80782 27036.842 343.93996 1.2626321
|
||||
540 20.616937 1386.8087 1788.7933 240.13729 -401.98456 549.1041 874.95416 154.29758 0 -656.88358 513668.46 -514991.91 -119.32561 27073.387 342.35804 1.3020275
|
||||
560 21.306129 1344.6077 1829.0478 245.54127 -484.44012 543.60765 827.52373 145.03505 0 -643.55003 513639.44 -514996.5 693.36148 27104.757 350.07417 1.3037885
|
||||
580 22.040812 1286.9423 1718.4962 230.70022 -431.5539 560.81872 873.95523 152.40482 0 -615.47818 513591.3 -514994.56 817.2745 27136.551 328.90573 1.2464245
|
||||
600 22.724418 1275.6074 1701.8955 228.47166 -426.28816 557.82466 895.29544 163.06547 0 -608.8133 513562.03 -514995.69 275.46334 27163.636 325.68453 1.3370122
|
||||
620 23.44057 1274.2239 1712.0781 229.83862 -437.85423 558.25658 859.2033 175.17918 0 -603.74788 513569.12 -514995.87 -810.10874 27182.704 327.68601 1.2216086
|
||||
640 24.123536 1217.5949 1736.1449 233.06948 -518.54993 572.30838 823.15943 163.38189 0 -606.64686 513521.66 -514992.42 -536.21523 27199.467 332.28881 1.2469404
|
||||
660 24.805612 1140.2496 1676.0527 225.00239 -535.80312 572.19423 829.86027 152.55649 0 -620.66616 513527.68 -514997.43 120.66196 27215.98 320.75861 1.2712041
|
||||
680 25.520239 1133.2378 1685.4319 226.26149 -552.19407 578.85784 824.91421 153.63895 0 -613.65105 513498.02 -514993.97 -379.30914 27230.138 322.5583 1.2672644
|
||||
700 26.205342 1124.125 1689.5449 226.81364 -565.41988 579.11835 817.50558 160.54964 0 -604.5409 513474.09 -514992.14 528.42535 27241.45 323.33965 1.2838662
|
||||
720 26.921122 1109.6569 1678.6607 225.35249 -569.00385 580.40773 815.63482 166.4848 0 -599.13557 513461.32 -514993.72 1376.5605 27253.659 321.24203 1.3097627
|
||||
740 27.601695 1104.3735 1664.4944 223.45073 -560.12097 598.18143 826.47186 162.20687 0 -577.40038 513419.67 -514989.25 -685.80791 27266.235 318.55379 1.2456749
|
||||
760 28.28271 1069.6794 1657.3304 222.48899 -587.65098 602.19554 832.68475 153.62759 0 -575.90127 513395.19 -514995.45 28.38921 27277.988 317.17055 1.268719
|
||||
780 28.996149 1035.0873 1654.5397 222.11435 -619.45236 585.73597 809.21796 152.24623 0 -573.92716 513400.09 -514992.82 -549.23892 27289.878 316.65381 1.2261365
|
||||
800 29.675426 1040.0427 1664.7856 223.48982 -624.74286 604.87479 803.38738 148.64588 0 -581.4825 513396.97 -514997.14 530.67038 27299.723 318.5938 1.2825531
|
||||
820 30.402455 1058.8049 1736.3913 233.10256 -677.58644 598.66467 784.93293 144.90816 0 -597.9166 513390.25 -514998.43 653.33362 27310.17 332.34765 1.2198792
|
||||
840 31.118422 1045.2817 1676.2729 225.03194 -630.99122 612.88019 813.4753 148.32663 0 -579.43245 513373.31 -514999.55 -720.22991 27320.116 320.80475 1.2620189
|
||||
860 31.799375 1020.82 1671.7525 224.4251 -650.93249 601.80247 814.81617 150.65389 0 -579.97174 513366.24 -515004.47 -498.60966 27326.379 319.94744 1.2404059
|
||||
880 32.481784 989.86496 1624.1319 218.03225 -634.26695 614.48607 850.33389 145.79505 0 -574.15578 513329.88 -515000.6 644.59976 27330.958 310.79513 1.2948148
|
||||
900 33.198209 951.41059 1655.2127 222.20471 -703.80214 612.33731 803.86098 146.44258 0 -578.12695 513314.46 -515002.78 -25.904297 27339.169 316.76616 1.2650626
|
||||
920 33.878012 990.08562 1682.4801 225.86523 -692.39448 625.27768 804.9682 145.49836 0 -566.22584 513298.29 -515000.2 -208.28417 27347.438 322.01282 1.2196912
|
||||
940 34.556311 974.83201 1654.4008 222.09571 -679.56876 644.46748 830.40192 142.42832 0 -571.21787 513274.72 -515000.37 -71.952805 27352.639 316.60661 1.2741508
|
||||
960 35.269557 970.36001 1647.0909 221.11439 -676.73092 621.42437 860.53358 137.22199 0 -570.51798 513277.98 -515003.38 339.47273 27355.862 315.21012 1.2628848
|
||||
980 35.951764 922.33531 1622.6042 217.82716 -700.2689 618.59396 850.9916 132.49991 0 -567.44171 513265.42 -515000.33 -3.755395 27360.701 310.51565 1.2635959
|
||||
1000 36.662547 903.55733 1693.4113 227.3327 -789.854 615.39097 786.15607 135.3415 0 -548.74582 513226.2 -515004.2 -1219.6014 27365.318 324.08684 1.2699177
|
||||
1020 37.341981 880.90138 1612.1831 216.42818 -731.2817 641.82697 825.92774 137.67854 0 -547.87626 513212.88 -515001.72 -125.90779 27364.725 308.51463 1.2712085
|
||||
1040 38.019606 859.45089 1636.4941 219.69182 -777.04323 642.81093 781.73583 128.96061 0 -535.59867 513206.15 -515001.1 -135.59253 27365.446 313.17007 1.2829993
|
||||
1060 38.725149 841.77495 1587.4484 213.10766 -745.67345 645.21049 847.89954 128.65218 0 -530.86511 513167.42 -515003.99 -78.288456 27368.183 303.75381 1.3158354
|
||||
1080 39.38038 821.88019 1590.6204 213.53349 -768.74022 655.77353 810.91879 133.42328 0 -519.68745 513152.23 -515001.39 -104.67266 27368.299 304.3695 1.2980829
|
||||
1100 40.035902 809.65728 1576.7543 211.67203 -767.09702 656.19162 822.82454 142.23371 0 -516.69506 513132.98 -515004.64 1031.9055 27367.566 301.722 1.273181
|
||||
1120 40.726126 820.5289 1619.3681 217.39273 -798.83918 672.50004 801.37058 138.45512 0 -522.82421 513115.49 -515003.84 754.43464 27372.483 309.87476 1.3114682
|
||||
1140 41.387774 841.02858 1618.789 217.315 -777.76045 662.62238 819.67645 137.92965 0 -530.61485 513139.41 -515006.78 -1113.1328 27379.657 309.76952 1.298026
|
||||
1160 42.057621 817.85003 1643.6698 220.65512 -825.81977 662.19692 793.93829 135.32496 0 -560.64736 513151.2 -515007.83 -185.68314 27379.995 314.55458 1.262201
|
||||
1180 42.715174 828.80176 1642.913 220.55353 -814.11124 676.87917 807.99197 132.86256 0 -551.49814 513123.1 -515003.45 -1104.1521 27375.422 314.43929 1.1926696
|
||||
1200 43.406653 824.66892 1602.5917 215.14058 -777.92278 660.24947 818.58601 137.75245 0 -536.80435 513150.81 -515008.52 417.52586 27368.971 306.71463 1.1809397
|
||||
1220 44.070962 793.59171 1650.4888 221.57054 -856.89708 643.52358 800.09599 140.67504 0 -559.82512 513124.22 -515005.59 -2053.0708 27364.593 315.86306 1.2592409
|
||||
1240 44.763665 784.17746 1595.2933 214.1608 -811.11582 645.81703 823.62179 144.27417 0 -541.81494 513125.24 -515008.25 -522.45199 27354.125 305.31945 1.1717212
|
||||
1260 45.426509 771.80674 1579.9594 212.1023 -808.15267 647.37467 839.39464 139.48231 0 -533.91983 513105.35 -515005.84 -236.36749 27340.092 302.33234 1.2827322
|
||||
1280 46.090314 757.30829 1571.2053 210.9271 -813.89703 677.57798 806.17559 134.09538 0 -505.01959 513077.27 -515003.99 811.20493 27324.568 300.65658 1.2770862
|
||||
1300 46.786592 784.63599 1620.5544 217.55198 -835.91837 658.42232 810.22801 135.68533 0 -515.37984 513080.18 -515005.05 -382.12012 27312.082 310.1031 1.3093104
|
||||
1320 47.448243 775.54897 1628.6454 218.63816 -853.0964 663.39683 830.11901 133.1559 0 -535.66369 513055.76 -514999.87 -555.79114 27302.584 311.6778 1.2541558
|
||||
1340 48.112453 748.355 1610.6902 216.22777 -862.33523 657.81748 804.32588 131.93735 0 -513.6202 513058.67 -515001.47 313.47767 27291.01 308.20033 1.3368285
|
||||
1360 48.811392 751.32155 1595.4402 214.18052 -844.11861 657.51903 845.03718 137.87132 0 -513.62167 513031.45 -515002.37 -79.880845 27279.506 305.28326 1.321866
|
||||
1380 49.475022 731.26314 1608.1608 215.88821 -876.89769 669.57446 814.19938 135.69586 0 -498.14752 513005.56 -515003.78 494.44462 27274.725 307.73144 1.2994877
|
||||
1400 50.172106 710.15416 1589.3213 213.35909 -879.16715 684.55854 812.02642 130.05555 0 -491.32449 512986.97 -515001.46 -1873.3431 27271.561 304.096 1.3551531
|
||||
1420 50.837606 696.15497 1589.6894 213.40851 -893.53445 692.24474 827.32888 125.48151 0 -496.67739 512958.77 -515000.68 -534.37168 27263.105 304.19764 1.2826528
|
||||
1440 51.508246 698.08943 1637.5392 219.83212 -939.44977 695.24634 786.95383 130.67316 0 -494.65965 512945.4 -515003.07 -237.78467 27250.78 313.40258 1.2079267
|
||||
1460 52.205405 699.73512 1625.071 218.15832 -925.33587 701.89168 802.08732 135.45068 0 -501.703 512938.62 -515001.68 28.171339 27240.652 310.98643 1.268512
|
||||
1480 52.872982 689.70566 1597.6417 214.47607 -907.93608 674.72811 845.78451 136.8906 0 -497.50953 512935.14 -515002.97 -602.11556 27230.827 305.70908 1.3130701
|
||||
1500 53.569404 691.1995 1561.7613 209.65929 -870.56183 692.08042 858.4753 135.61947 0 -493.28793 512938.1 -515001.55 -597.63867 27214.771 298.8608 1.2428754
|
||||
1520 54.234223 674.25149 1622.6123 217.82825 -948.36077 668.17586 834.50429 135.26557 0 -517.17765 512934.73 -515003.86 -104.64931 27195.923 310.52105 1.2545913
|
||||
1540 54.899103 660.26416 1645.0423 220.83937 -984.77813 693.47571 799.50207 124.8185 0 -510.40009 512910.64 -515002.81 -1254.5226 27176.861 314.81806 1.2613124
|
||||
1560 55.595102 664.64562 1650.033 221.50935 -985.38737 697.98896 795.13498 120.20295 0 -510.91599 512918.67 -515006.46 -950.50992 27153.028 315.75626 1.3045633
|
||||
1580 56.262 663.46124 1633.8238 219.33335 -970.36258 704.49765 795.17437 132.71647 0 -502.08537 512906.5 -515007.16 -205.86006 27124.708 312.66475 1.2676295
|
||||
1600 56.928335 645.68029 1598.5467 214.59755 -952.86639 706.45777 828.29528 135.72398 0 -513.58629 512891.73 -515001.49 -1147.6441 27091.638 305.87496 1.3308059
|
||||
1620 57.629507 637.7525 1562.3603 209.7397 -924.60782 721.14412 846.17365 136.34063 0 -517.2706 512894.92 -515005.91 -1271.6076 27054.822 298.95752 1.2851255
|
||||
1640 58.297866 616.11852 1583.9447 212.63731 -967.82623 714.38783 803.96933 137.27846 0 -500.85436 512879.67 -515002.28 -1169.7751 27016.776 303.10683 1.2582529
|
||||
1660 58.96682 632.47606 1599.1228 214.6749 -966.64675 723.96119 799.81022 125.78728 0 -480.98243 512865.44 -515000.66 -688.27485 26977.191 305.98571 1.3301015
|
||||
1680 59.679934 614.14317 1630.4077 218.87475 -1016.2646 712.35781 795.2823 112.38484 0 -463.91464 512831.48 -515003.86 -303.49292 26939.363 311.98958 1.314989
|
||||
1700 60.35184 607.54886 1616.1532 216.96114 -1008.6043 724.48093 799.01068 115.53655 0 -450.47755 512806.86 -515004.02 1086.8644 26904.035 309.27252 1.2786556
|
||||
1720 61.066244 609.2294 1580.6054 212.18902 -971.37599 725.61177 813.06406 121.47504 0 -440.04715 512818.91 -515010.39 5.983342 26873.897 302.44224 1.3152539
|
||||
1740 61.74157 625.35389 1606.0174 215.60047 -980.66354 721.92477 812.41005 127.04476 0 -435.05634 512799.07 -515006.06 333.20671 26849.324 307.31957 1.3017468
|
||||
1760 62.417318 594.94962 1568.3514 210.54397 -973.40177 730.56559 805.35837 129.49326 0 -450.75311 512821.57 -515009.64 891.72675 26828.071 300.13536 1.2166782
|
||||
1780 63.140649 600.36677 1620.4389 217.53648 -1020.0721 722.22052 795.19804 123.74183 0 -460.16037 512805.38 -515006.45 6.5230083 26812.903 310.0854 1.2989361
|
||||
1800 63.824508 579.73219 1609.3524 216.04817 -1029.6202 711.53963 793.77661 123.12265 0 -451.25398 512797.31 -515004.11 -1303.7286 26799.27 307.96564 1.2860154
|
||||
1820 64.545172 598.84205 1608.9687 215.99665 -1010.1266 714.09002 799.02749 122.43878 0 -453.90843 512813.78 -515005.56 632.28614 26785.698 307.91501 1.2325029
|
||||
1840 65.22587 586.50951 1587.5928 213.12705 -1001.0833 727.94474 823.60521 129.12956 0 -460.11816 512780.21 -515001.85 1024.9885 26777.699 303.8049 1.2612311
|
||||
1860 65.909234 575.80278 1557.8819 209.13849 -982.07909 727.5608 800.91998 138.66389 0 -454.06531 512808.05 -515003.21 -696.69404 26772.219 298.09238 1.3005467
|
||||
1880 66.632258 611.28789 1604.6616 215.41846 -993.37373 737.40385 802.26484 139.2269 0 -450.63031 512780.24 -515001.88 -40.643962 26765.841 307.08153 1.2507275
|
||||
1900 67.314627 606.24473 1611.9641 216.39878 -1005.7194 718.10757 783.64683 141.16739 0 -478.54415 512835.51 -515005.61 564.61472 26761.053 308.45922 1.3025385
|
||||
1920 67.997687 622.32128 1652.1009 221.78697 -1029.7797 709.21175 808.86628 140.79666 0 -489.67469 512806.75 -515005.73 -2045.2966 26762.21 316.16296 1.280607
|
||||
1940 68.720055 585.91734 1580.5482 212.18134 -994.63085 701.86656 823.41307 141.76963 0 -476.56128 512820.97 -515006.09 -1477.9457 26758.847 302.44297 1.2879495
|
||||
1960 69.400974 599.23183 1573.8307 211.27954 -974.59884 703.80549 834.20676 141.74855 0 -473.96154 512825.62 -515006.02 -555.31861 26748.97 301.16698 1.2604779
|
||||
1980 70.082469 604.67649 1570.9488 210.89266 -966.27229 709.67328 842.22196 142.29376 0 -479.29842 512823.2 -515004.37 220.13578 26738.567 300.59944 1.2956585
|
||||
2000 70.804962 610.11958 1559.2324 209.31979 -949.11278 723.21777 823.79015 145.64191 0 -461.27302 512827.63 -515008.12 -226.50414 26731.515 298.36269 1.2739114
|
||||
Loop time of 70.805 on 1 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 1.220 ns/day, 19.668 hours/ns, 28.247 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 46.358 | 46.358 | 46.358 | 0.0 | 65.47
|
||||
Bond | 1.8097 | 1.8097 | 1.8097 | 0.0 | 2.56
|
||||
Kspace | 10.643 | 10.643 | 10.643 | 0.0 | 15.03
|
||||
Neigh | 1.8814 | 1.8814 | 1.8814 | 0.0 | 2.66
|
||||
Comm | 0.38412 | 0.38412 | 0.38412 | 0.0 | 0.54
|
||||
Output | 0.008601 | 0.008601 | 0.008601 | 0.0 | 0.01
|
||||
Modify | 9.6728 | 9.6728 | 9.6728 | 0.0 | 13.66
|
||||
Other | | 0.04689 | | | 0.07
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10022 ave 10022 max 10022 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 721937 ave 721937 max 721937 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 721937
|
||||
Ave neighs/atom = 240.646
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 49
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:10
|
||||
|
|
@ -0,0 +1,277 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 1 500.0
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 17908 7200
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.7 | 15.72 | 15.75 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301
|
||||
20 0.24885726 10977.523 5649.4234 758.40916 5328.0995 2062.3542 2228.2406 127.20787 0 1716.2655 514097.62 -514903.59 75540.788 22441.711 900.66455 425.71754
|
||||
40 0.52037597 8971.222 5307.0197 712.44303 3664.2023 1468.3101 1727.552 263.87374 0 1220.3688 513944.03 -514959.93 46704.125 23047.094 909.55742 251.59686
|
||||
60 0.7807281 7598.3479 4774.3053 640.92856 2824.0427 1194.6424 1771.6653 314.85756 0 553.7151 513952.94 -514963.78 37329.2 23513.994 850.78607 150.29302
|
||||
80 1.1572349 6500.0058 4632.0732 621.83456 1867.9325 914.32396 1444.2432 317.24546 0 213.11185 513930.12 -514951.11 33256.762 23919.646 847.27963 94.966975
|
||||
100 1.4178512 5591.472 4319.1968 579.83234 1272.2752 772.47756 1235.8385 306.35435 0 -56.189361 513990.32 -514976.52 21842.59 24315.598 802.33641 59.89227
|
||||
120 1.6625795 4952.7621 3881.7096 521.1017 1071.0525 630.88446 1260.1912 299.84296 0 -147.16305 514014.9 -514987.6 17191.638 24657.729 728.78527 35.811873
|
||||
140 1.8984792 4373.9331 3440.7548 461.90553 933.1783 670.28429 1238.1308 300.44834 0 -260.57044 513963.56 -514978.68 17252.83 24939.26 649.60264 23.329745
|
||||
160 2.1378865 3923.229 3251.2581 436.46647 671.97091 632.15143 1144.4146 307.32283 0 -436.68046 514014.07 -514989.31 17845.825 25185.451 617.37678 13.751529
|
||||
180 2.3720722 3558.1557 3060.4382 410.84977 497.71755 621.70998 1085.8204 297.1556 0 -495.34468 513968.54 -514980.16 9885.361 25415.428 582.93783 8.7536435
|
||||
200 2.6049569 3228.4936 2864.4301 384.53659 364.06344 591.33636 1077.5366 257.50944 0 -521.78289 513950.34 -514990.87 5925.7217 25605.563 546.61818 5.8335105
|
||||
220 2.8426785 2922.7424 2668.2075 358.19461 254.5349 552.38924 1045.2135 238.94168 0 -548.4004 513955.45 -514989.06 7136.0052 25761.984 509.82785 3.9098309
|
||||
240 3.1155882 2721.0612 2574.2915 345.58681 146.76969 547.99652 1035.0606 226.51837 0 -609.21222 513928.45 -514982.05 6971.5001 25907.597 492.18737 3.0535008
|
||||
260 3.3265111 2525.7518 2460.9077 330.36557 64.844061 536.78625 1022.3311 211.32544 0 -633.92783 513919.8 -514991.47 4534.5804 26040.845 470.74694 2.3688839
|
||||
280 3.5478129 2338.039 2324.3983 312.03981 13.640708 519.09042 970.16233 197.76897 0 -621.27548 513937.32 -514989.43 2909.3322 26151.714 444.74626 1.9753672
|
||||
300 3.7687361 2194.851 2189.0474 293.86956 5.8036062 530.74509 982.33557 190.99311 0 -652.24555 513946.83 -514992.86 4224.0345 26246.212 418.93917 1.6487718
|
||||
320 3.9801922 2045.4487 2132.0617 286.21949 -86.613049 531.53518 935.90803 188.46605 0 -683.41226 513935.36 -514994.47 1710.734 26338.321 408.05555 1.5540687
|
||||
340 4.1992741 1929.4058 2083.452 279.69387 -154.04619 509.02677 906.15126 186.62933 0 -668.19644 513908.44 -514996.09 2736.2098 26423.379 398.77795 1.4580758
|
||||
360 4.4171088 1853.7062 1992.5995 267.49733 -138.89334 525.34864 891.90355 178.21101 0 -654.64078 513920.99 -515000.71 3816.7092 26502.12 381.4127 1.3381612
|
||||
380 4.6217661 1760.9358 1947.0158 261.37793 -186.07997 516.89889 919.58404 172.53796 0 -676.7004 513879.46 -514997.86 2960.1316 26580.115 372.6985 1.2814406
|
||||
400 4.8376818 1687.8988 1905.9227 255.86137 -218.0239 535.53769 922.01769 176.20545 0 -684.03744 513833.88 -515001.63 1297.7806 26648.895 364.81828 1.2874209
|
||||
420 5.0580292 1605.7787 1889.0825 253.60065 -283.30381 517.08427 857.72563 180.14818 0 -663.15367 513826.27 -515001.38 2609.7387 26710.911 361.58795 1.2934789
|
||||
440 5.2613502 1518.1412 1794.5719 240.91304 -276.43077 531.12246 893.04683 188.1283 0 -667.41934 513778.75 -515000.06 1448.9344 26771.955 343.49864 1.2323194
|
||||
460 5.474973 1455.6369 1796.1847 241.12955 -340.54775 527.17043 846.65061 188.73693 0 -650.46422 513749.2 -515001.84 161.63078 26825.587 343.80003 1.2432983
|
||||
480 5.6766918 1423.3951 1780.4686 239.01974 -357.07349 555.37302 861.62016 179.25213 0 -642.3686 513685.22 -514996.17 1728.4109 26870.018 340.77367 1.2753301
|
||||
500 5.8963647 1414.5107 1792.5124 240.63656 -378.00171 562.06965 865.1732 172.51081 0 -638.43613 513657.38 -514996.7 2852.5688 26914.25 343.08652 1.2642269
|
||||
520 6.1024427 1359.8646 1801.0839 241.78725 -441.21931 573.29268 804.68005 169.59419 0 -635.98014 513644.06 -514996.86 917.97283 26965.499 344.72952 1.264948
|
||||
540 6.3182905 1320.129 1763.768 236.77776 -443.63898 564.54015 851.18104 169.65891 0 -632.69528 513601.13 -514997.45 393.78094 27008.775 337.59196 1.2311182
|
||||
560 6.5340965 1288.8769 1741.0597 233.72927 -452.18283 588.80641 843.7906 164.29947 0 -639.61003 513594.25 -515003.72 2022.6586 27046.802 333.24957 1.2004945
|
||||
580 6.738924 1250.8612 1701.7462 228.45162 -450.88502 575.95012 877.76059 153.10544 0 -632.21312 513575.06 -515000.54 319.43567 27087.59 325.68988 1.258461
|
||||
600 6.9839265 1237.7875 1721.861 231.15193 -484.0735 586.2774 851.82884 147.45104 0 -635.34134 513566.1 -515000.39 -1495.8007 27125.397 329.56435 1.2147693
|
||||
620 7.1886187 1255.6883 1741.6598 233.80983 -485.97147 593.81316 838.06474 152.61844 0 -618.48814 513546.09 -514998.07 -239.76675 27153.275 333.35756 1.2207133
|
||||
640 7.403686 1231.453 1734.6085 232.86323 -503.15553 592.94732 847.14537 157.31902 0 -622.72191 513517.06 -514994.9 1262.739 27174.105 331.96914 1.3100227
|
||||
660 7.6087363 1205.9453 1720.7921 231.00844 -514.84686 605.97637 844.61854 156.72343 0 -608.38182 513480.7 -514994.48 541.26917 27199.495 329.34901 1.2412012
|
||||
680 7.8241618 1168.82 1693.3809 227.32862 -524.5609 610.91696 859.82389 152.3176 0 -616.40743 513464.95 -514996.17 -529.37821 27221.433 324.05587 1.3283313
|
||||
700 8.0318077 1139.7968 1686.9214 226.46146 -547.12461 600.49589 835.94756 154.05863 0 -606.7429 513467.63 -514998.52 679.06473 27236.703 322.81056 1.3423643
|
||||
720 8.2363923 1092.9537 1676.7232 225.09239 -583.76953 599.79941 810.70949 154.32485 0 -586.40642 513433.08 -514995.27 -585.69662 27255.925 320.84689 1.3625931
|
||||
740 8.4505181 1128.5561 1686.198 226.36434 -557.64189 608.39888 814.40376 148.31341 0 -576.35219 513440.47 -514992.87 1244.5446 27274.826 322.70284 1.2739521
|
||||
760 8.6553326 1117.7278 1739.2464 233.48585 -621.51863 612.4462 767.55338 143.8046 0 -557.71655 513408.23 -514995.84 1093.5729 27295.505 332.85864 1.3081834
|
||||
780 8.8741109 1106.8963 1694.5955 227.49166 -587.69917 621.94129 814.60472 148.54444 0 -544.5269 513368.24 -514996.5 1020.894 27319.829 324.31438 1.2670368
|
||||
800 9.0792463 1119.8416 1718.8899 230.75307 -599.04828 615.79521 822.09893 150.20192 0 -544.21016 513354.51 -514997.44 -145.29684 27346.503 328.96744 1.27833
|
||||
820 9.2923503 1100.7099 1661.8207 223.0918 -561.11086 634.74953 843.11877 146.78045 0 -554.19608 513367.17 -514998.73 1869.737 27372.705 318.03624 1.2563109
|
||||
840 9.4957469 1050.0874 1692.7796 227.24789 -642.69222 601.30056 816.98683 139.43809 0 -553.50651 513352.19 -514999.1 1348.2664 27400.511 323.96534 1.2729707
|
||||
860 9.7094629 1042.7553 1659.2043 222.74056 -616.44901 621.75625 821.47309 138.21191 0 -555.05691 513354.19 -514997.03 -727.5674 27429.255 317.50236 1.3339135
|
||||
880 9.9195423 1033.8676 1659.2249 222.74333 -625.35739 603.51906 847.42057 149.36712 0 -565.95565 513337.79 -514997.5 -313.44149 27451.297 317.53888 1.2570577
|
||||
900 10.142613 1033.7624 1637.6339 219.84483 -603.87149 622.06547 811.88787 155.52952 0 -542.52312 513343.54 -514994.37 1047.3137 27471.84 313.40683 1.2403795
|
||||
920 10.345829 1008.6446 1641.2497 220.33024 -632.60508 603.07732 856.65655 154.41458 0 -548.68151 513295.17 -514993.24 103.24221 27494.927 314.0879 1.2685922
|
||||
940 10.547752 1014.9632 1643.6054 220.64648 -628.64224 651.79962 816.08408 149.02041 0 -527.85081 513276.54 -514994.23 -364.67163 27515.823 314.56245 1.2150283
|
||||
960 10.760628 1032.4206 1694.3296 227.45598 -661.90901 631.32636 826.29861 143.25116 0 -525.82257 513258.93 -514995.89 1416.1446 27534.39 324.25519 1.2878583
|
||||
980 10.96867 997.2143 1637.471 219.82297 -640.25673 649.17389 840.91105 145.10691 0 -527.22384 513248.84 -514997.07 1027.4324 27556.624 313.33467 1.3359011
|
||||
1000 11.181152 980.70328 1679.6252 225.48198 -698.92196 616.29851 808.49173 143.96963 0 -518.492 513246.09 -514995.28 328.95214 27580.508 321.45785 1.23763
|
||||
1020 11.385127 964.62633 1655.3416 222.22201 -690.71527 637.09502 844.75137 135.25445 0 -525.02956 513212.27 -514995.06 80.148272 27602.021 316.79063 1.2656102
|
||||
1040 11.594135 956.01316 1683.0451 225.94108 -727.03194 631.81212 818.33077 128.9891 0 -520.68359 513210.27 -514995.75 470.78306 27620.292 322.12502 1.2135338
|
||||
1060 11.787688 933.22039 1693.9231 227.4014 -760.70274 646.39135 803.29817 130.04881 0 -528.24124 513182.71 -514994.91 239.4629 27638.164 324.20286 1.2314242
|
||||
1080 12.019302 924.08701 1655.3855 222.2279 -731.29849 657.61421 824.59227 129.04796 0 -511.96678 513168.73 -514999.31 303.67371 27653.716 316.81728 1.223067
|
||||
1100 12.213108 898.91261 1623.3761 217.93078 -724.46344 664.01917 828.5969 133.99752 0 -516.0614 513164.69 -514999.71 -222.62542 27666.941 310.68427 1.2153994
|
||||
1120 12.41604 853.75082 1604.1305 215.34715 -750.37966 641.42123 819.9451 135.53827 0 -522.84677 513174.17 -514998.61 -712.60931 27680.156 306.99082 1.2247886
|
||||
1140 12.609285 856.11685 1597.8188 214.49984 -741.70197 667.36627 802.82977 138.4139 0 -519.32453 513168.41 -514999.4 -102.39627 27691.615 305.78084 1.224836
|
||||
1160 12.804644 841.06502 1588.8444 213.29507 -747.7794 639.48731 820.18846 145.23411 0 -514.61341 513163.68 -515001.76 -1183.509 27699.206 304.05355 1.2408942
|
||||
1180 13.054664 860.51613 1621.2063 217.6395 -760.69016 641.94901 812.05607 135.63519 0 -518.65348 513173.02 -515004.7 281.47746 27701.81 310.24087 1.2817118
|
||||
1200 13.250304 837.02718 1605.8013 215.57145 -768.77412 647.08878 819.62137 134.70383 0 -535.25329 513169.92 -515004.85 -741.61789 27704.108 307.27044 1.3202509
|
||||
1220 13.454972 847.88424 1630.4606 218.88185 -782.57635 632.73877 814.55949 134.45986 0 -543.58866 513187.28 -515008.03 301.16905 27705.337 312.02884 1.2480776
|
||||
1240 13.650697 847.8463 1613.1526 216.55833 -765.3063 657.26308 817.09263 131.44411 0 -533.77746 513168.85 -515006.17 -1738.246 27705.837 308.69599 1.2825009
|
||||
1260 13.848417 864.10938 1604.3359 215.37473 -740.22655 654.64386 830.80471 136.50167 0 -518.80899 513162.82 -515006.19 -457.58037 27701.516 306.99469 1.3056189
|
||||
1280 14.058141 892.58539 1622.354 217.79358 -729.76865 654.56025 853.72132 146.37045 0 -502.50853 513124.64 -515006.56 1617.9621 27698.218 310.47185 1.2538957
|
||||
1300 14.25655 910.15714 1649.6144 221.45317 -739.4573 669.55948 824.60696 152.88156 0 -495.91044 513118.29 -515008.89 -947.37179 27701.819 315.68715 1.2786016
|
||||
1320 14.462712 881.86464 1653.5515 221.98169 -771.68682 667.15825 811.67934 146.31009 0 -501.83979 513113.06 -515008.06 -836.07194 27703.296 316.44487 1.2716419
|
||||
1340 14.66221 870.89257 1685.0409 226.20901 -814.14836 639.83879 820.7611 137.05399 0 -502.59799 513100.73 -515009.93 1322.9199 27705.806 322.51431 1.1950205
|
||||
1360 14.876581 853.37228 1650.3504 221.55197 -796.97814 646.59807 828.89771 128.53685 0 -518.68585 513127.01 -515009.33 -685.77178 27711.07 315.84173 1.2552323
|
||||
1380 15.07645 846.05537 1652.3957 221.82654 -806.34037 655.80177 845.42057 123.99858 0 -508.17399 513084.95 -515008.34 -1611.4393 27715.739 316.20591 1.3081133
|
||||
1400 15.290876 845.61911 1643.3419 220.6111 -797.72277 681.7704 794.40988 122.51167 0 -491.96431 513103.8 -515008.25 1340.3832 27715.764 314.49703 1.249787
|
||||
1420 15.489104 803.39863 1630.1296 218.83742 -826.73099 671.35628 807.63619 122.01003 0 -484.93762 513065.22 -515008.01 1599.9415 27715.83 311.97673 1.2205741
|
||||
1440 15.695448 798.11794 1586.2583 212.94789 -788.14035 691.5246 832.65594 120.76201 0 -465.82995 513043.17 -515010.42 693.27083 27722.616 303.53977 1.2829192
|
||||
1460 15.91282 786.25408 1614.9027 216.79327 -828.64859 657.62541 813.69119 123.75957 0 -476.8708 513064.69 -515011.54 411.32225 27731.39 309.03286 1.2785029
|
||||
1480 16.12012 763.25782 1608.2178 215.89585 -844.95995 668.25992 798.0135 125.60791 0 -501.0795 513074.18 -515009.94 -210.6788 27739.429 307.75344 1.2722038
|
||||
1500 16.31711 742.2781 1642.6489 220.51807 -900.3708 642.57755 747.85628 128.7751 0 -506.59888 513093.85 -515006.83 657.03263 27745.692 314.34071 1.3056262
|
||||
1520 16.523088 729.1993 1560.7352 209.52153 -831.53586 684.2385 779.3475 135.75119 0 -498.45899 513072.79 -515005.21 64.426284 27753.859 298.64905 1.276366
|
||||
1540 16.719949 744.18971 1581.6321 212.32685 -837.44244 684.68705 806.72314 139.08406 0 -507.07664 513045.21 -515006.07 -1592.594 27760.726 302.65236 1.2826649
|
||||
1560 16.955894 732.25034 1589.2114 213.34434 -856.96111 671.90468 790.0602 135.77523 0 -516.63197 513069.7 -515007.77 -483.90212 27760.814 304.08818 1.324249
|
||||
1580 17.152081 767.01867 1612.3153 216.44593 -845.29663 682.6108 787.28261 132.5621 0 -507.32097 513069.61 -515010.04 -555.1036 27759.537 308.50615 1.3501402
|
||||
1600 17.357651 765.40129 1608.2406 215.89892 -842.8393 685.49537 792.49876 133.14916 0 -503.66586 513056.44 -515006.76 205.34219 27753.467 307.76245 1.2628065
|
||||
1620 17.55409 772.17408 1631.4594 219.01594 -859.28536 668.94991 789.22477 139.7312 0 -488.80931 513038.28 -515006.66 869.15057 27745.263 312.19213 1.312809
|
||||
1640 17.750204 790.00313 1585.8898 212.89842 -795.88666 698.581 834.90324 141.30234 0 -480.2032 513014.32 -515004.79 425.63098 27741.564 303.48802 1.2388328
|
||||
1660 17.9655 747.54165 1583.9657 212.64013 -836.4241 681.84949 818.22116 144.32659 0 -480.9488 513005 -515004.87 393.07342 27741.508 303.09446 1.2953283
|
||||
1680 18.160659 733.30069 1561.2237 209.58711 -827.92298 700.21145 825.04894 140.46392 0 -471.32136 512986.07 -515008.4 358.86819 27742.435 298.74386 1.2734665
|
||||
1700 18.356133 711.44468 1578.4996 211.90632 -867.05487 695.93174 805.45219 136.97231 0 -472.62368 512976.67 -515009.46 536.5943 27744.152 302.06506 1.2553362
|
||||
1720 18.560144 721.96636 1575.331 211.48095 -853.36463 702.17681 830.22534 135.88637 0 -477.83518 512966.99 -515010.81 -645.91282 27748.165 301.45254 1.2652763
|
||||
1740 18.756074 711.63956 1586.0957 212.92606 -874.45612 689.4748 798.79974 136.08847 0 -473.58719 512984.43 -515009.66 -1624.8445 27748.356 303.52048 1.2551975
|
||||
1760 18.958437 724.24881 1594.573 214.0641 -870.32418 693.92297 821.07919 134.86949 0 -499.044 512991.53 -515012.68 -67.704697 27743.489 305.14895 1.2473787
|
||||
1780 19.161341 715.10685 1646.5039 221.03559 -931.39709 696.96446 758.9442 137.66678 0 -506.22154 512995.87 -515014.62 -40.253747 27743.38 315.10841 1.2414332
|
||||
1800 19.355029 729.61134 1620.3158 217.51995 -890.70444 705.93766 795.61246 140.68696 0 -489.30347 512967.54 -515011.18 -766.11724 27742.605 310.0618 1.2972844
|
||||
1820 19.55902 729.31305 1608.8589 215.98192 -879.54588 679.10327 811.20714 148.4305 0 -487.995 512981.33 -515011.62 -171.78807 27733.221 307.90957 1.1975335
|
||||
1840 19.753109 755.00585 1604.0683 215.33881 -849.06248 704.5529 836.72831 145.47772 0 -486.71807 512964.36 -515013.46 214.63499 27724.953 306.97134 1.2429474
|
||||
1860 19.967638 750.425 1611.9697 216.39953 -861.54467 681.08979 817.41958 140.85922 0 -481.23461 512994.18 -515013.86 458.39691 27723.378 308.4884 1.2369562
|
||||
1880 20.162438 731.26375 1599.4322 214.71642 -868.16842 699.34308 809.01864 139.89206 0 -501.58244 512999.06 -515013.9 -1549.9632 27725.425 306.09592 1.211311
|
||||
1900 20.356956 708.62541 1610.6874 216.22739 -902.06199 683.06943 810.51769 134.55613 0 -508.02851 512990.33 -515012.5 675.39868 27720.583 308.23181 1.2620963
|
||||
1920 20.560648 703.81181 1586.8847 213.03199 -883.0729 690.93049 825.78591 131.84894 0 -498.42445 512977.68 -515010.9 367.15667 27713.888 303.69961 1.1917227
|
||||
1940 20.754765 701.93422 1590.5107 213.51875 -888.57645 687.55932 818.62417 128.12087 0 -485.00453 512971.02 -515008.9 1457.2723 27711.175 304.3668 1.2586653
|
||||
1960 20.966151 702.58467 1615.2174 216.83553 -912.63277 695.227 811.79161 131.25635 0 -468.08028 512925.61 -515008.44 812.93978 27708.617 309.10899 1.2402714
|
||||
1980 21.169778 704.12312 1614.6957 216.76549 -910.5726 710.51045 811.95687 140.34792 0 -452.87904 512887.51 -515008.02 -604.37886 27705.003 309.00871 1.242271
|
||||
2000 21.363046 700.52702 1604.4991 215.39664 -903.9721 726.08016 810.67383 139.90807 0 -443.00664 512870.59 -515008.22 148.09738 27699.21 307.02152 1.3180547
|
||||
Loop time of 21.3631 on 4 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 4.044 ns/day, 5.934 hours/ns, 93.619 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.835 | 11.289 | 12.258 | 17.2 | 52.85
|
||||
Bond | 0.4537 | 0.48285 | 0.50792 | 3.1 | 2.26
|
||||
Kspace | 4.2572 | 5.2354 | 5.6853 | 25.4 | 24.51
|
||||
Neigh | 0.54701 | 0.5472 | 0.54747 | 0.0 | 2.56
|
||||
Comm | 0.60596 | 0.64067 | 0.67884 | 3.8 | 3.00
|
||||
Output | 0.0058618 | 0.0073152 | 0.011671 | 2.9 | 0.03
|
||||
Modify | 2.769 | 2.9549 | 3.1306 | 8.9 | 13.83
|
||||
Other | | 0.2055 | | | 0.96
|
||||
|
||||
Nlocal: 750 ave 757 max 742 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 5838 ave 5894 max 5784 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 175398 ave 186533 max 165750 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 701594
|
||||
Ave neighs/atom = 233.865
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:21
|
||||
|
|
@ -0,0 +1,286 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_ATOM gATOMS temp
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDTDIR all drude/transform/direct
|
||||
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500
|
||||
fix_modify fNPT temp cTEMP_ATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
|
||||
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 1 100.0
|
||||
fix fDTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 50653 27000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.48 | 22.48 | 22.48 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301
|
||||
20 0.82186079 11385.283 5995.2608 804.83624 5390.0219 2039.7455 2312.5467 131.6964 0 1710.3725 514098.33 -514902.67 75869.034 22408.215 975.27381 406.07545
|
||||
40 1.7293625 9812.345 6009.1868 806.70574 3803.1582 1442.3552 1826.1503 275.19417 0 1288.22 513934.99 -514963.75 48672.13 22980.211 1057.0198 221.56388
|
||||
60 2.5726278 8857.8006 5779.5918 775.88366 3078.2088 1190.8886 1938.5953 328.68401 0 619.17987 513971 -514970.14 39706.347 23441.277 1050.8999 133.14459
|
||||
80 3.4535189 8115.6222 5997.8743 805.18709 2117.7479 901.83124 1587.5299 325.40736 0 288.22238 513957.46 -514942.7 37586.493 23835.221 1111.6406 89.055348
|
||||
100 4.2757752 7496.057 5770.3042 774.63685 1725.7528 829.61731 1420.6409 325.39973 0 62.226626 514051.66 -514963.79 27290.384 24226.433 1080.2534 60.498681
|
||||
120 5.1343639 6986.3331 5396.8054 724.49634 1589.5277 678.23213 1535.5139 325.88286 0 -9.8121501 514027.1 -514967.39 21714.378 24578.965 1016.2738 42.716174
|
||||
140 5.9375162 6548.6966 5126.4765 688.20593 1422.2201 724.92776 1477.7366 315.11557 0 -99.615083 513960.65 -514956.6 19741.549 24878.09 969.48208 30.977308
|
||||
160 6.7352271 6130.9708 5000.2242 671.25714 1130.7466 703.21482 1302.0806 314.9338 0 -258.62211 514042.38 -514973.24 23045.182 25144.056 948.68855 23.022183
|
||||
180 7.5256455 5749.5567 4700.6896 631.046 1048.867 674.90328 1301.3631 310.04329 0 -326.92492 514044.37 -514954.88 14218.695 25401.78 893.70987 17.322259
|
||||
200 8.3062081 5429.1755 4392.2849 589.64408 1036.8906 611.96666 1296.169 303.15486 0 -300.5535 514093.83 -514967.68 10827.179 25624.937 836.11247 13.764989
|
||||
220 9.0794528 5133.41 4290.3608 575.96124 843.04924 572.47213 1261.7692 289.97557 0 -383.86544 514078.49 -514975.79 12503.3 25816.637 817.71346 11.104784
|
||||
240 9.8436809 4849.9512 4119.9044 553.07825 730.04677 553.72774 1263.639 278.92306 0 -487.89901 514091.57 -514969.91 10886.302 25998.932 785.78404 9.3606461
|
||||
260 10.605034 4583.5435 3910.7331 524.99797 672.81042 541.41982 1175.0582 273.43969 0 -475.41044 514139.92 -514981.62 8078.6171 26172.119 746.49788 7.4648407
|
||||
280 11.362397 4348.81 3691.9428 495.62637 656.86725 598.7722 1148.0372 278.86509 0 -444.28194 514045.6 -514970.12 5115.8688 26326.635 704.97777 6.4789284
|
||||
300 12.115575 4128.489 3579.1998 480.49114 549.2892 583.98038 1089.487 267.65383 0 -457.0616 514043.78 -514978.55 8341.4597 26460.833 683.88483 5.2652332
|
||||
320 12.823282 3913.3823 3456.6176 464.03504 456.76476 556.22095 1103.3421 263.7791 0 -485.68641 514000.55 -514981.44 9109.6369 26597.284 660.68384 4.5691163
|
||||
340 13.570274 3712.2734 3258.0793 437.38219 454.19409 533.60879 1068.9434 271.82635 0 -454.64507 514002.17 -514967.71 7179.0605 26741.746 622.91874 3.8804069
|
||||
360 14.315206 3532.9579 3023.6802 405.91518 509.27768 522.48836 1104.2686 276.28278 0 -456.22486 514036.79 -514974.33 4545.215 26882.126 578.23151 3.3025371
|
||||
380 15.055002 3366.746 2970.7631 398.8113 395.98299 508.12217 1059.1562 257.91185 0 -499.79406 514032.85 -514962.26 5636.5329 27008.105 568.28965 2.830075
|
||||
400 15.75335 3204.5091 2873.415 385.74277 331.09416 543.77882 1018.7946 231.10838 0 -519.43553 514029.65 -514972.81 7243.9791 27130.53 549.73386 2.5825543
|
||||
420 16.480976 3050.3022 2775.7673 372.63402 274.53487 517.37336 953.14854 225.86836 0 -505.67105 514057.58 -514973.77 4018.2502 27257.578 531.12039 2.3356262
|
||||
440 17.20372 2915.9612 2639.1922 354.29944 276.76899 507.07374 983.90795 236.07195 0 -534.71742 514060.31 -514975.87 1699.7076 27372.134 505.04906 2.0779128
|
||||
460 17.925103 2787.2795 2609.7668 350.34921 177.51264 485.49348 933.6558 234.43516 0 -560.63202 514070.07 -514985.51 3390.2752 27466.686 499.52337 1.8090485
|
||||
480 18.647898 2662.2222 2514.1136 337.50821 148.10854 464.53566 928.19247 239.15967 0 -570.39028 514071.12 -514984.5 5075.4159 27556.806 481.25552 1.6478036
|
||||
500 19.332267 2540.2584 2432.8576 326.59997 107.40071 473.20947 888.84623 239.12328 0 -565.53809 514057.83 -514986.07 3129.6192 27653.186 465.74774 1.486379
|
||||
520 20.047809 2431.9884 2374.7243 318.79583 57.264134 460.05267 838.76564 228.73042 0 -579.0486 514094.39 -514985.63 462.28535 27743.092 454.64978 1.3782218
|
||||
540 20.762916 2328.6134 2274.6313 305.35881 53.982075 473.12149 875.45698 220.60795 0 -604.15461 514076.11 -514987.16 2622.3468 27815.745 435.47546 1.3461692
|
||||
560 21.477821 2228.4408 2278.1084 305.82559 -49.667558 455.45537 820.96545 214.46954 0 -604.66916 514053.07 -514988.96 3774.7454 27887.17 436.23203 1.136117
|
||||
580 22.156966 2134.2145 2127.7975 285.64705 6.4169804 480.53632 836.99951 218.25579 0 -563.43994 514020.11 -514986.04 1347.9073 27963.805 407.4267 1.1136558
|
||||
600 22.868461 2048.3341 2102.8549 282.29862 -54.520854 486.1799 795.85772 224.19443 0 -574.58492 514004 -514990.16 -100.5692 28031.415 402.6784 1.0360651
|
||||
620 23.582384 1967.2649 2050.2745 275.23994 -83.009549 477.31366 785.52916 222.26776 0 -570.5843 513998.54 -514996.08 1809.6235 28084.448 392.60381 1.0239108
|
||||
640 24.25969 1887.8882 1984.0464 266.34912 -96.158235 482.78351 800.40092 220.19212 0 -557.48535 513952.64 -514994.69 3804.7495 28138.319 379.94961 0.92618662
|
||||
660 24.968904 1812.5853 1960.7266 263.21855 -148.1413 497.47994 750.65798 215.15703 0 -556.35598 513938.64 -514993.72 1173.0953 28202.964 375.50038 0.8766551
|
||||
680 25.642951 1744.2287 1912.3074 256.71848 -168.07864 497.12304 725.28297 210.74936 0 -554.7656 513943.75 -514990.22 81.489372 28262.329 366.24876 0.80553628
|
||||
700 26.349596 1677.5524 1912.8593 256.79258 -235.30692 490.36723 720.72019 204.81758 0 -570.32399 513908.13 -514989.01 2139.1872 28311.757 366.38002 0.74614938
|
||||
720 27.054473 1611.7133 1859.3776 249.61291 -247.66437 499.44111 727.86981 195.52975 0 -552.65485 513871.24 -514989.09 3009.9637 28365.384 356.12743 0.74621105
|
||||
740 27.725048 1549.685 1790.3493 240.34617 -240.66425 496.25123 737.75419 180.00468 0 -548.11159 513879.93 -514986.49 718.56841 28427.109 342.91326 0.7024951
|
||||
760 28.446277 1492.9982 1801.2374 241.80786 -308.23923 502.49459 708.38808 172.24218 0 -560.93888 513860.87 -514991.3 -859.12137 28481.474 345.01555 0.6674887
|
||||
780 29.148375 1436.9239 1823.9643 244.85884 -387.0404 509.26814 663.93976 171.61087 0 -556.48284 513815.66 -514991.04 1168.7449 28521.446 349.36331 0.6885803
|
||||
800 29.818515 1382.5968 1737.4206 233.24074 -354.82378 513.00178 695.57772 172.42262 0 -552.28591 513804.68 -514988.22 1805.011 28561.249 332.78321 0.66397175
|
||||
820 30.524059 1332.0207 1689.2759 226.77754 -357.25521 509.51717 686.84564 172.57648 0 -548.44359 513812.21 -514989.96 -66.311617 28604.787 323.58511 0.59083949
|
||||
840 31.201142 1285.6252 1683.5729 226.01193 -397.94769 507.59079 662.90068 169.36995 0 -553.69874 513804.36 -514988.47 -621.19538 28640.472 322.48932 0.59667555
|
||||
860 31.914963 1240.0349 1703.7814 228.72483 -463.74645 497.11887 658.78716 169.54588 0 -569.52851 513767.79 -514987.46 792.58789 28666.426 326.36247 0.59868606
|
||||
880 32.585058 1195.4713 1670.1212 224.2061 -474.64983 499.64545 651.51445 170.02281 0 -554.71997 513740.96 -514982.07 1233.1339 28693.075 319.91881 0.57749338
|
||||
900 33.283366 1153.5526 1643.4626 220.62731 -489.90999 500.29806 640.14014 177.39649 0 -558.06916 513735.19 -514984.87 -525.66059 28722.393 314.81615 0.5591618
|
||||
920 33.951266 1114.6093 1618.9458 217.33604 -504.3365 511.75888 633.60684 175.10475 0 -554.17306 513720.73 -514991.36 -1519.3862 28743.137 310.10475 0.58591773
|
||||
940 34.650169 1076.5361 1629.6248 218.76965 -553.08868 510.90659 619.76241 167.78799 0 -557.43468 513695.73 -514989.85 296.76427 28751.218 312.16525 0.55489087
|
||||
960 35.315701 1040.3478 1609.1044 216.01487 -568.7566 511.15544 602.92746 166.01646 0 -548.67061 513692.97 -514993.15 742.32048 28759.401 308.22081 0.57967815
|
||||
980 36.013822 1006.0783 1560.5473 209.49631 -554.46902 516.03243 629.22012 171.82488 0 -544.97376 513663.64 -514990.21 -1243.6962 28769.845 298.9291 0.54046046
|
||||
1000 36.709116 974.24875 1558.0215 209.15723 -583.77273 506.6472 601.9316 165.11551 0 -553.06573 513688.1 -514992.5 -1282.1536 28770.759 298.43904 0.55412832
|
||||
1020 37.34906 943.47684 1567.4776 210.42667 -624.00074 507.7679 618.07297 152.13649 0 -569.64661 513661.22 -514993.55 -186.03132 28762.516 300.24615 0.56731507
|
||||
1040 38.021245 913.48747 1599.9646 214.7879 -686.47709 487.43669 574.25818 153.42118 0 -593.34764 513684.82 -514993.06 479.26449 28754.262 306.47982 0.55368609
|
||||
1060 38.667195 884.53789 1558.1773 209.17815 -673.63945 500.21603 593.70139 157.67768 0 -604.58442 513672.34 -514992.99 -2207.1953 28748.02 298.45285 0.59162362
|
||||
1080 39.342256 857.28828 1538.9142 206.59217 -681.62596 503.64978 574.76485 165.14388 0 -584.10927 513643.02 -514984.09 -1836.7583 28728.357 294.75731 0.59805527
|
||||
1100 39.987321 832.19678 1479.2179 198.57822 -647.02114 514.08633 608.91942 165.26491 0 -569.63464 513616.87 -514982.52 -27.127273 28698.734 283.30588 0.61555857
|
||||
1120 40.665662 809.16107 1516.8748 203.63348 -707.71373 513.27211 567.99212 169.86948 0 -560.7949 513584.25 -514982.3 -372.41735 28671.493 290.52752 0.60920143
|
||||
1140 41.313559 787.50744 1484.3806 199.27128 -696.87314 526.25364 582.78208 167.73401 0 -550.7679 513559.52 -514982.4 -1728.2274 28644.545 284.28679 0.6360583
|
||||
1160 41.993408 767.41852 1497.6302 201.04998 -730.21173 515.9345 580.51745 159.02047 0 -534.99467 513529.39 -514980.08 -1872.4418 28608.964 286.81617 0.66081293
|
||||
1180 42.642904 750.18943 1492.2376 200.32605 -742.04816 532.34349 570.6807 154.35233 0 -512.26701 513492.93 -514980.09 926.11765 28566.848 285.74878 0.73922998
|
||||
1200 43.293101 735.32682 1504.5521 201.97921 -769.22524 536.2319 594.47464 155.80234 0 -515.01641 513442.47 -514983.19 33.948973 28534.509 288.11106 0.73558261
|
||||
1220 43.977824 720.73905 1495.8029 200.80467 -775.06381 558.11107 561.07651 159.20703 0 -503.03817 513434.59 -514985.01 -986.07615 28506.699 286.43244 0.73880049
|
||||
1240 44.630923 707.60909 1486.697 199.58224 -779.08789 564.73341 574.9815 160.19665 0 -467.65622 513371.76 -514983.1 39.386144 28476.751 284.65743 0.8073656
|
||||
1260 45.316338 696.90935 1495.2634 200.73224 -798.35401 576.91144 565.71232 154.53813 0 -455.98096 513344.03 -514983.57 859.74504 28450.875 286.27774 0.85844048
|
||||
1280 45.972141 687.90416 1485.152 199.37484 -797.24786 581.1043 593.28449 150.90626 0 -447.852 513310.83 -514985.52 746.2051 28434.182 284.33627 0.86567683
|
||||
1300 46.659596 680.05111 1479.108 198.56346 -799.05687 585.50039 589.75255 148.14575 0 -422.7668 513283.23 -514982.92 -524.66474 28424.119 283.14576 0.93998516
|
||||
1320 47.315349 673.52979 1476.4577 198.20767 -802.9279 572.81659 595.26192 147.37054 0 -424.83034 513287.53 -514981.08 106.77633 28412.923 282.64612 0.92033657
|
||||
1340 48.004338 668.69073 1484.7214 199.31704 -816.03069 582.3039 588.40727 153.74406 0 -434.27973 513271.16 -514977.36 731.28971 28403.842 284.19266 1.0081579
|
||||
1360 48.666622 665.51033 1519.3878 203.97084 -853.87752 575.99453 554.12668 159.19953 0 -458.43153 513293.36 -514978.13 422.98973 28400.634 290.81807 1.0553453
|
||||
1380 49.357293 663.82821 1467.8065 197.04629 -803.97832 578.21925 592.65789 156.17923 0 -458.90398 513308.34 -514980.47 -203.04754 28400.637 280.90634 1.1101023
|
||||
1400 50.048356 663.49309 1516.9007 203.63695 -853.40759 571.04838 580.61589 146.23345 0 -462.76173 513293.95 -514982.5 -448.98731 28399.279 290.29749 1.1575012
|
||||
1420 50.708454 664.15896 1499.9167 201.35693 -835.75773 566.58488 603.52748 148.50712 0 -471.56553 513299.67 -514982.48 260.66933 28395.449 287.02615 1.1936028
|
||||
1440 51.401936 665.7749 1505.3913 202.09187 -839.61636 568.31696 588.02115 157.51085 0 -462.77296 513294.54 -514985.23 686.32226 28393.937 288.0844 1.1731726
|
||||
1460 52.062043 668.60203 1501.3101 201.54398 -832.70805 581.33476 579.96642 157.99886 0 -456.96282 513291.57 -514986.61 -271.294 28396.763 287.25414 1.2848928
|
||||
1480 52.756437 672.78069 1509.7227 202.67334 -836.94203 577.59283 567.71153 162.7344 0 -467.11093 513309.03 -514986.9 -936.72661 28397.351 288.85976 1.3014708
|
||||
1500 53.420877 678.15981 1516.2442 203.54882 -838.08436 568.973 592.07243 169.01021 0 -495.80017 513315.7 -514988.04 88.20689 28392.187 290.08472 1.3603151
|
||||
1520 54.114697 684.70508 1526.4386 204.91738 -841.73356 557.42832 581.42465 168.54996 0 -496.59211 513336.95 -514989.5 515.33669 28387.812 292.03285 1.3747328
|
||||
1540 54.776816 692.26725 1535.4798 206.13111 -843.21253 551.89278 584.81969 156.31938 0 -472.91843 513327.8 -514991.12 -260.08916 28386.831 293.74312 1.4282442
|
||||
1560 55.471466 700.38373 1542.1981 207.03301 -841.81433 551.6024 611.83194 152.66068 0 -499.25336 513334.3 -514992.96 -881.89875 28383.701 295.04052 1.4061086
|
||||
1580 56.134557 708.58784 1550.4384 208.13924 -841.85055 556.69767 582.39421 162.30767 0 -515.06887 513365.13 -514993.31 317.46976 28375.679 296.61441 1.4196493
|
||||
1600 56.831572 717.16972 1560.1894 209.44826 -843.01966 549.14904 592.56757 172.02873 0 -494.96769 513331.32 -514993.12 268.64262 28369.888 298.46813 1.4559812
|
||||
1620 57.496371 726.01824 1544.6646 207.36413 -818.64636 564.25447 620.2534 171.6366 0 -481.33955 513299.03 -514992.48 -928.98251 28365.608 295.50693 1.4211187
|
||||
1640 58.192956 734.97748 1599.5833 214.73672 -864.60585 559.51067 584.21101 166.15126 0 -484.99381 513300.49 -514989.98 -395.19323 28356.094 306.02332 1.448322
|
||||
1660 58.859821 743.85098 1568.6598 210.58537 -824.80879 567.20594 620.40617 159.81333 0 -485.47565 513302.38 -514989.14 275.6277 28344.463 300.08676 1.4680092
|
||||
1680 59.556888 752.397 1614.4574 216.7335 -862.06044 567.74587 617.24576 156.34105 0 -474.64789 513259.55 -514988.29 153.36452 28335.561 308.89368 1.4040884
|
||||
1700 60.222487 760.11363 1574.8766 211.41996 -814.76301 589.13636 635.26767 165.24375 0 -441.39255 513225.54 -514988.56 -449.5961 28328.169 301.30175 1.4138952
|
||||
1720 60.92238 767.32908 1633.2653 219.25837 -865.93623 593.92768 614.12149 168.83762 0 -435.93625 513180.07 -514986.96 625.88498 28319.407 312.50976 1.3794422
|
||||
1740 61.588997 773.58335 1604.1264 215.34661 -830.5431 611.54553 634.6288 170.13873 0 -425.1955 513161.11 -514982.77 1258.1591 28315.688 306.93109 1.3623528
|
||||
1760 62.288118 778.46232 1604.1065 215.34394 -825.64421 601.28947 635.92844 169.10255 0 -409.79824 513164.39 -514986.55 923.97553 28321.077 306.93241 1.3503708
|
||||
1780 62.95488 782.68573 1585.9867 212.91143 -803.30098 634.82805 637.66853 173.52039 0 -396.05083 513134.96 -514988.23 308.41322 28332.765 303.45213 1.3659282
|
||||
1800 63.656662 786.45168 1632.4834 219.1534 -846.0317 626.46808 612.859 170.73849 0 -389.28328 513124.73 -514991.55 434.99541 28346.181 312.38153 1.3288883
|
||||
1820 64.322505 789.07103 1622.34 217.7917 -833.26902 631.84388 628.97419 164.08777 0 -403.37081 513135.19 -514989.99 1423.3137 28362.768 310.45751 1.2810964
|
||||
1840 65.020631 790.43307 1598.2845 214.56235 -807.85142 593.52496 652.49021 167.51591 0 -408.69698 513177.63 -514990.32 862.95994 28387.747 305.87197 1.2204936
|
||||
1860 65.687176 791.36821 1585.9825 212.91087 -794.61429 619.37616 661.00216 170.47785 0 -410.28902 513156.18 -514991.36 -22.140042 28417.059 303.51149 1.2255437
|
||||
1880 66.353485 791.94788 1630.1749 218.8435 -838.22706 591.52981 652.79092 178.67552 0 -433.7293 513160.08 -514987.57 -35.653011 28444.349 312.01504 1.151451
|
||||
1900 67.051143 791.5025 1611.2186 216.2987 -819.71613 604.66631 614.52658 185.27138 0 -426.58089 513192.07 -514989.67 1492.9051 28470.603 308.39205 1.1258287
|
||||
1920 67.749766 789.33745 1638.8687 220.0106 -849.53124 604.75057 634.21383 186.54046 0 -427.33715 513139.73 -514987.43 863.10157 28504.605 313.697 1.1156351
|
||||
1940 68.417711 786.91982 1566.7995 210.33564 -779.87972 606.00187 648.68271 182.72186 0 -430.75201 513205.37 -514991.9 -1132.9713 28541.397 299.9167 1.0327394
|
||||
1960 69.114583 784.25672 1592.2094 213.7468 -807.95267 595.81907 669.03472 172.75782 0 -436.10776 513181.4 -514990.86 78.431195 28569.12 304.79729 1.0106551
|
||||
1980 69.778898 780.04995 1637.1409 219.77865 -857.09092 606.44426 629.01991 163.80784 0 -440.75819 513180.63 -514996.23 1330.6593 28595.247 313.42473 0.97808647
|
||||
2000 70.476083 774.653 1633.3807 219.27386 -858.72771 607.3352 611.62149 162.37854 0 -449.5387 513203.88 -514994.4 -192.50999 28627.445 312.71969 0.94122657
|
||||
Loop time of 70.4761 on 1 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 1.226 ns/day, 19.577 hours/ns, 28.378 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 43.881 | 43.881 | 43.881 | 0.0 | 62.26
|
||||
Bond | 1.8093 | 1.8093 | 1.8093 | 0.0 | 2.57
|
||||
Kspace | 10.585 | 10.585 | 10.585 | 0.0 | 15.02
|
||||
Neigh | 2.3196 | 2.3196 | 2.3196 | 0.0 | 3.29
|
||||
Comm | 0.38965 | 0.38965 | 0.38965 | 0.0 | 0.55
|
||||
Output | 0.0086887 | 0.0086887 | 0.0086887 | 0.0 | 0.01
|
||||
Modify | 11.438 | 11.438 | 11.438 | 0.0 | 16.23
|
||||
Other | | 0.04561 | | | 0.06
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10476 ave 10476 max 10476 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 658684 ave 658684 max 658684 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 658684
|
||||
Ave neighs/atom = 219.561
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 65
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:10
|
||||
|
|
@ -0,0 +1,286 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_ATOM gATOMS temp
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDTDIR all drude/transform/direct
|
||||
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500
|
||||
fix_modify fNPT temp cTEMP_ATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
|
||||
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 1 100.0
|
||||
fix fDTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 17908 7200
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.7 | 15.72 | 15.75 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301
|
||||
20 0.26940155 11385.283 5995.2608 804.83624 5390.0219 2039.7455 2312.5467 131.6964 0 1710.3725 514098.33 -514902.67 75869.034 22408.215 975.27381 406.07545
|
||||
40 0.56039548 9812.345 6009.1868 806.70574 3803.1582 1442.3552 1826.1503 275.19417 0 1288.22 513934.99 -514963.75 48672.13 22980.211 1057.0198 221.56388
|
||||
60 0.88414049 8857.8007 5779.5918 775.88366 3078.2089 1190.8886 1938.5954 328.68401 0 619.17987 513971 -514970.14 39706.347 23441.277 1050.8999 133.14459
|
||||
80 1.1696272 8115.6221 5997.8743 805.18709 2117.7478 901.83126 1587.5299 325.40736 0 288.22238 513957.46 -514942.7 37586.493 23835.221 1111.6406 89.055345
|
||||
100 1.4401748 7496.0571 5770.3042 774.63685 1725.7529 829.6173 1420.6409 325.39973 0 62.226624 514051.66 -514963.79 27290.384 24226.433 1080.2534 60.498679
|
||||
120 1.7223158 6986.3333 5396.8053 724.49634 1589.528 678.23214 1535.5139 325.88286 0 -9.8121501 514027.1 -514967.39 21714.378 24578.965 1016.2738 42.716172
|
||||
140 1.9845128 6548.697 5126.4765 688.20593 1422.2205 724.92774 1477.7367 315.11557 0 -99.615085 513960.65 -514956.6 19741.55 24878.09 969.48208 30.977306
|
||||
160 2.2419188 6130.9704 5000.2242 671.25714 1130.7463 703.21482 1302.0806 314.9338 0 -258.62211 514042.38 -514973.24 23045.181 25144.056 948.68855 23.022185
|
||||
180 2.4937162 5749.5572 4700.6896 631.046 1048.8675 674.90328 1301.3631 310.04329 0 -326.92492 514044.37 -514954.88 14218.696 25401.78 893.70987 17.322259
|
||||
200 2.7779307 5429.1755 4392.2849 589.64408 1036.8906 611.96667 1296.169 303.15487 0 -300.55349 514093.83 -514967.68 10827.18 25624.937 836.11247 13.764988
|
||||
220 3.0248075 5133.4101 4290.3608 575.96124 843.04929 572.47215 1261.7692 289.97559 0 -383.86544 514078.49 -514975.79 12503.299 25816.637 817.71346 11.104783
|
||||
240 3.2623236 4849.9512 4119.9045 553.07826 730.04673 553.72776 1263.639 278.92307 0 -487.89902 514091.57 -514969.91 10886.301 25998.932 785.78405 9.3606436
|
||||
260 3.4997547 4583.5434 3910.7331 524.99797 672.81028 541.41985 1175.0582 273.43967 0 -475.41047 514139.92 -514981.62 8078.6153 26172.119 746.49788 7.4648392
|
||||
280 3.7359712 4348.8096 3691.9428 495.62637 656.86681 598.77221 1148.0372 278.86509 0 -444.28193 514045.6 -514970.12 5115.867 26326.635 704.97778 6.478926
|
||||
300 3.9722769 4128.4892 3579.1998 480.49114 549.28936 583.98039 1089.487 267.65383 0 -457.0616 514043.78 -514978.55 8341.4601 26460.833 683.88483 5.2652305
|
||||
320 4.1924908 3913.3825 3456.6177 464.03505 456.76481 556.22097 1103.342 263.77912 0 -485.6864 514000.55 -514981.44 9109.6369 26597.284 660.68387 4.569117
|
||||
340 4.4220572 3712.2735 3258.0794 437.3822 454.19406 533.60886 1068.9435 271.82625 0 -454.64506 514002.17 -514967.71 7179.0608 26741.746 622.91875 3.8804079
|
||||
360 4.651022 3532.9576 3023.6802 405.91518 509.27748 522.48821 1104.2686 276.28277 0 -456.22485 514036.79 -514974.33 4545.2157 26882.126 578.2315 3.3025369
|
||||
380 4.8867376 3366.7464 2970.763 398.8113 395.98341 508.12225 1059.1562 257.91185 0 -499.7941 514032.85 -514962.26 5636.5327 27008.105 568.28964 2.8300765
|
||||
400 5.1070464 3204.509 2873.4151 385.74278 331.09386 543.77873 1018.7946 231.10847 0 -519.43554 514029.65 -514972.81 7243.9777 27130.53 549.73389 2.582555
|
||||
420 5.3353672 3050.3029 2775.7676 372.63405 274.53536 517.37318 953.14843 225.86866 0 -505.67104 514057.59 -514973.77 4018.2518 27257.578 531.12044 2.3356247
|
||||
440 5.5616498 2915.9614 2639.1925 354.29947 276.76893 507.07348 983.90798 236.07196 0 -534.7174 514060.31 -514975.87 1699.7058 27372.134 505.04911 2.0779123
|
||||
460 5.7944629 2787.2801 2609.7652 350.34899 177.51494 485.49336 933.65567 234.4359 0 -560.632 514070.07 -514985.51 3390.2812 27466.685 499.52306 1.8090438
|
||||
480 6.0186839 2662.2225 2514.1129 337.50812 148.10954 464.53577 928.19233 239.15956 0 -570.39024 514071.12 -514984.5 5075.4176 27556.806 481.25539 1.6478044
|
||||
500 6.2357466 2540.259 2432.8587 326.60011 107.40032 473.20958 888.84591 239.12382 0 -565.53821 514057.83 -514986.07 3129.6111 27653.186 465.74794 1.4863829
|
||||
520 6.462676 2431.9888 2374.7256 318.79601 57.263157 460.05319 838.76524 228.73041 0 -579.04849 514094.39 -514985.63 462.28097 27743.092 454.65004 1.3782188
|
||||
540 6.6893921 2328.6141 2274.6316 305.35885 53.982526 473.12143 875.45686 220.60764 0 -604.15443 514076.11 -514987.16 2622.3509 27815.745 435.4755 1.3461673
|
||||
560 6.915879 2228.4408 2278.108 305.82554 -49.667226 455.45527 820.9654 214.46985 0 -604.66926 514053.07 -514988.96 3774.7446 27887.17 436.23196 1.1361161
|
||||
580 7.129838 2134.2136 2127.7972 285.64701 6.4164029 480.53569 836.9992 218.2561 0 -563.43996 514020.11 -514986.04 1347.8991 27963.805 407.42665 1.1136548
|
||||
600 7.3513916 2048.334 2102.8555 282.2987 -54.521528 486.17968 795.85755 224.19382 0 -574.58522 514004 -514990.17 -100.56264 28031.415 402.67851 1.0360672
|
||||
620 7.571908 1967.2653 2050.2743 275.23991 -83.008964 477.31341 785.52964 222.26773 0 -570.58461 513998.54 -514996.08 1809.6139 28084.448 392.60377 1.023916
|
||||
640 7.822695 1887.8873 1984.0468 266.34918 -96.159502 482.78324 800.4011 220.19183 0 -557.48586 513952.64 -514994.69 3804.7387 28138.319 379.94969 0.92618308
|
||||
660 8.0473323 1812.5849 1960.7275 263.21866 -148.14251 497.48053 750.6579 215.15723 0 -556.35642 513938.64 -514993.72 1173.0782 28202.964 375.50053 0.87666213
|
||||
680 8.2574785 1744.229 1912.3049 256.71816 -168.07594 497.12359 725.28373 210.75068 0 -554.76517 513943.75 -514990.22 81.483029 28262.329 366.2483 0.80553356
|
||||
700 8.4756997 1677.5494 1912.8562 256.79217 -235.30682 490.36725 720.72028 204.81842 0 -570.32326 513908.12 -514989.01 2139.1574 28311.757 366.37944 0.74614771
|
||||
720 8.6941352 1611.7137 1859.3792 249.61312 -247.66551 499.4419 727.86911 195.529 0 -552.65432 513871.24 -514989.09 3009.9813 28365.384 356.12774 0.74621707
|
||||
740 8.9091365 1549.6852 1790.3521 240.34656 -240.66693 496.25202 737.75393 180.00372 0 -548.11093 513879.92 -514986.49 718.57423 28427.108 342.91382 0.70248974
|
||||
760 9.1269078 1492.9984 1801.2402 241.80823 -308.24181 502.49565 708.38773 172.24112 0 -560.93884 513860.87 -514991.3 -859.1512 28481.473 345.01608 0.66749339
|
||||
780 9.3445795 1436.924 1823.9645 244.85885 -387.04046 509.26901 663.94064 171.61073 0 -556.48262 513815.66 -514991.04 1168.7425 28521.446 349.36333 0.68859382
|
||||
800 9.5536196 1382.5971 1737.4248 233.2413 -354.82766 513.0037 695.57852 172.42075 0 -552.28635 513804.68 -514988.22 1805.0199 28561.249 332.78401 0.66398258
|
||||
820 9.778646 1332.0198 1689.275 226.77742 -357.25518 509.51804 686.84757 172.57573 0 -548.44337 513812.21 -514989.96 -66.330382 28604.787 323.58493 0.59085762
|
||||
840 9.9888568 1285.6245 1683.5728 226.01192 -397.9483 507.59294 662.89974 169.37203 0 -553.69839 513804.35 -514988.47 -621.21477 28640.472 322.48931 0.59668678
|
||||
860 10.20852 1240.0357 1703.7808 228.72476 -463.74517 497.12172 658.78743 169.54895 0 -569.53018 513767.79 -514987.46 792.62408 28666.425 326.36236 0.5987066
|
||||
880 10.41846 1195.4711 1670.1197 224.2059 -474.64858 499.64663 651.5165 170.02534 0 -554.71869 513740.96 -514982.08 1233.144 28693.074 319.91853 0.57749627
|
||||
900 10.636871 1153.5523 1643.4571 220.62657 -489.90477 500.29822 640.14056 177.40242 0 -558.06881 513735.19 -514984.87 -525.65607 28722.392 314.8151 0.5591483
|
||||
920 10.892932 1114.609 1618.9439 217.33579 -504.33488 511.75888 633.60856 175.1138 0 -554.17472 513720.72 -514991.36 -1519.4599 28743.136 310.10438 0.58594249
|
||||
940 11.111583 1076.5388 1629.6394 218.77161 -553.10061 510.90787 619.76339 167.7895 0 -557.43647 513695.72 -514989.85 296.67789 28751.217 312.16803 0.5549268
|
||||
960 11.321271 1040.3467 1609.1144 216.01622 -568.76774 511.14781 602.93181 166.00661 0 -548.6701 513692.97 -514993.16 742.31157 28759.398 308.22272 0.57970476
|
||||
980 11.542122 1006.0767 1560.5644 209.4986 -554.48764 516.02585 629.21936 171.81429 0 -544.97384 513663.64 -514990.21 -1243.6779 28769.841 298.93237 0.54048524
|
||||
1000 11.766886 974.24702 1558.0041 209.15489 -583.75705 506.64122 601.93463 165.12035 0 -553.064 513688.11 -514992.5 -1282.0718 28770.754 298.4357 0.55413455
|
||||
1020 11.970261 943.47512 1567.4558 210.42375 -623.98071 507.76272 618.07613 152.14193 0 -569.64333 513661.22 -514993.54 -185.99703 28762.511 300.24196 0.56735077
|
||||
1040 12.182541 913.49183 1599.9518 214.78618 -686.45996 487.4406 574.26298 153.41685 0 -593.34617 513684.82 -514993.05 479.3652 28754.257 306.47736 0.55370848
|
||||
1060 12.385323 884.5384 1558.1791 209.17839 -673.64068 500.22922 593.70741 157.65505 0 -604.58403 513672.33 -514992.98 -2207.1147 28748.016 298.45318 0.59162923
|
||||
1080 12.597323 857.28841 1538.9194 206.59286 -681.63097 503.67593 574.77226 165.12151 0 -584.10752 513643 -514984.09 -1836.8716 28728.353 294.7583 0.59804385
|
||||
1100 12.806903 832.2002 1479.2217 198.57873 -647.02154 514.11416 608.92484 165.24735 0 -569.63674 513616.86 -514982.53 -27.131764 28698.73 283.30662 0.61552981
|
||||
1120 13.021407 809.16206 1516.8721 203.63312 -707.71008 513.30089 567.99641 169.86685 0 -560.80062 513584.24 -514982.32 -372.41029 28671.488 290.52701 0.60920306
|
||||
1140 13.226424 787.50897 1484.3443 199.26641 -696.83535 526.29673 582.76992 167.79235 0 -550.76364 513559.47 -514982.41 -1728.2731 28644.54 284.27985 0.6360204
|
||||
1160 13.439471 767.42267 1497.5383 201.03765 -730.11567 515.96405 580.5165 159.12444 0 -534.97892 513529.33 -514980.08 -1872.3497 28608.958 286.79856 0.66079274
|
||||
1180 13.643181 750.19166 1492.1028 200.30795 -741.9111 532.36765 570.69633 154.43336 0 -512.25199 513492.9 -514980.06 926.80786 28566.842 285.72289 0.73932156
|
||||
1200 13.878355 735.34196 1504.4584 201.96663 -769.11641 536.29872 594.4765 155.773 0 -514.98695 513442.46 -514983.13 34.590808 28534.508 288.09313 0.73549598
|
||||
1220 14.095265 720.75191 1495.8784 200.81481 -775.12649 558.18322 561.11868 159.16072 0 -503.00794 513434.4 -514984.98 -986.83251 28506.707 286.44694 0.73874965
|
||||
1240 14.302587 707.62702 1486.8261 199.59958 -779.19911 564.76327 574.98748 160.18253 0 -467.67421 513371.66 -514983.12 38.339148 28476.761 284.68236 0.80695809
|
||||
1260 14.5169 696.93229 1495.1997 200.7237 -798.26742 576.84276 565.66929 154.59183 0 -456.04034 513344.28 -514983.61 859.97875 28450.881 286.26551 0.85851389
|
||||
1280 14.723275 687.92791 1485.1331 199.3723 -797.20519 581.04737 593.2454 150.87332 0 -447.80111 513310.98 -514985.55 747.71864 28434.188 284.33268 0.86557314
|
||||
1300 14.940926 680.08292 1479.193 198.57487 -799.11011 585.53803 589.87487 148.01029 0 -422.72639 513283.11 -514982.92 -525.51472 28424.13 283.16208 0.93995449
|
||||
1320 15.146466 673.56377 1476.0598 198.15425 -802.496 572.76673 595.29767 147.53133 0 -424.76316 513287.72 -514981.04 109.20091 28412.937 282.56994 0.92008603
|
||||
1340 15.360807 668.74056 1484.8781 199.33807 -816.13759 582.36447 588.33732 153.88508 0 -434.18175 513270.79 -514977.34 733.42094 28403.872 284.22277 1.0080038
|
||||
1360 15.565801 665.56738 1519.4405 203.97791 -853.8731 575.96075 554.2097 159.14168 0 -458.4083 513293.33 -514978.1 423.26533 28400.693 290.82823 1.0551985
|
||||
1380 15.785992 663.88904 1467.7833 197.04317 -803.89424 578.34934 592.76078 156.17583 0 -458.96296 513308.25 -514980.47 -202.88792 28400.724 280.90163 1.1107077
|
||||
1400 16.000381 663.53838 1516.5314 203.58738 -852.99304 571.11885 580.68736 146.25518 0 -462.81788 513294.24 -514982.47 -449.44011 28399.391 290.22677 1.1573629
|
||||
1420 16.208723 664.23926 1499.3076 201.27517 -835.06836 566.43752 603.59629 148.52977 0 -471.69399 513300.52 -514982.46 261.17724 28395.582 286.90991 1.1923832
|
||||
1440 16.424351 665.87924 1504.925 202.02927 -839.04575 568.21243 588.179 157.65461 0 -462.88044 513294.99 -514985.2 684.75502 28394.09 287.99547 1.1721041
|
||||
1460 16.630685 668.71536 1501.3751 201.55271 -832.6597 581.26842 579.88403 157.98256 0 -456.9524 513291.74 -514986.58 -272.14551 28396.923 287.26686 1.284286
|
||||
1480 16.851607 672.94191 1510.1794 202.73465 -837.23749 577.53887 567.63332 162.86706 0 -467.21952 513308.9 -514986.95 -937.06962 28397.511 288.94723 1.3016431
|
||||
1500 17.060401 678.34496 1516.5383 203.58831 -838.19335 568.9071 592.24094 169.15958 0 -495.91214 513315.52 -514988.11 85.894805 28392.343 290.14127 1.359925
|
||||
1520 17.280722 684.91448 1526.955 204.9867 -842.04054 557.53201 581.42008 168.46993 0 -496.76555 513336.83 -514989.52 513.1704 28387.948 292.13159 1.3753055
|
||||
1540 17.489951 692.4859 1536.0578 206.20871 -843.5719 552.11665 584.87851 156.09211 0 -473.22273 513327.75 -514991.18 -267.31574 28386.929 293.85398 1.4281354
|
||||
1560 17.713041 700.59595 1541.593 206.95178 -840.99701 551.44763 612.32187 152.35924 0 -499.17884 513335.07 -514993.01 -882.17955 28383.721 294.92477 1.4055318
|
||||
1580 17.929113 708.77379 1550.3407 208.12612 -841.56691 556.60852 582.39053 162.12325 0 -515.10224 513365.77 -514993.35 322.32831 28375.626 296.59534 1.4204419
|
||||
1600 18.144745 717.39964 1559.9665 209.41835 -842.56689 549.07216 592.74611 171.9088 0 -494.99998 513331.85 -514993.14 267.08424 28369.799 298.42556 1.4556193
|
||||
1620 18.363554 726.25369 1544.67 207.36486 -818.41631 564.24547 620.11593 171.47239 0 -481.42668 513299.67 -514992.5 -929.2129 28365.483 295.50817 1.4206365
|
||||
1640 18.578192 735.20307 1599.669 214.74822 -864.46597 559.44554 584.31101 166.36248 0 -485.25281 513300.68 -514990.01 -400.32794 28355.927 306.03975 1.4483397
|
||||
1660 18.788682 744.13508 1567.4804 210.42705 -823.34534 567.22939 620.98009 160.76689 0 -485.86239 513302.82 -514989.28 275.23727 28344.229 299.86144 1.466234
|
||||
1680 19.002967 752.73626 1613.0757 216.548 -860.33939 567.6576 617.82475 157.94412 0 -474.89518 513259.71 -514988.58 145.60417 28335.257 308.62904 1.4035192
|
||||
1700 19.208987 760.45858 1575.0294 211.44047 -814.57086 588.97206 634.68664 166.27782 0 -441.79702 513226.22 -514988.93 -455.69419 28327.746 301.33081 1.4144311
|
||||
1720 19.424031 767.76378 1634.9553 219.48525 -867.19156 594.28118 613.97792 169.57851 0 -435.89528 513178.39 -514987.52 624.6147 28318.833 312.83371 1.3795127
|
||||
1740 19.630425 774.0707 1607.3304 215.77673 -833.25975 612.27366 635.89702 170.90768 0 -425.06946 513156.42 -514983.69 1245.2476 28314.962 307.54418 1.3649994
|
||||
1760 19.88556 778.94063 1606.5499 215.67195 -827.60929 602.10334 636.54708 169.93908 0 -409.46967 513160.13 -514986.86 900.23197 28320.117 307.40099 1.3499664
|
||||
1780 20.156405 783.13015 1582.8925 212.49605 -799.76233 635.8022 637.81662 173.60641 0 -395.27083 513136.4 -514988.12 303.67422 28331.437 302.86049 1.3623691
|
||||
1800 20.394003 786.8472 1629.8795 218.80383 -843.03226 626.87797 613.50519 171.66383 0 -388.22631 513124.5 -514991.35 452.45767 28344.488 311.88054 1.3331104
|
||||
1820 20.604631 789.49317 1623.8201 217.99039 -834.32693 632.3375 629.50791 165.54164 0 -402.81199 513130.95 -514989.85 1435.9558 28360.845 310.74273 1.2776203
|
||||
1840 20.882926 790.84026 1595.8459 214.23498 -805.0056 593.44998 654.04584 168.32988 0 -408.05005 513177.2 -514989.98 869.17595 28385.701 305.40649 1.2158021
|
||||
1860 21.104003 791.82787 1587.2175 213.07667 -795.38968 618.69585 660.77302 168.60246 0 -408.77525 513157.18 -514991.87 14.63364 28414.975 303.75155 1.217843
|
||||
1880 21.318712 792.39264 1628.8097 218.66022 -836.41704 590.23683 653.83304 177.71688 0 -432.28625 513162.12 -514988.04 -17.001449 28442.457 311.75357 1.1508692
|
||||
1900 21.52406 792.00166 1611.7686 216.37254 -819.76695 604.55866 613.59005 183.84763 0 -425.02508 513192.41 -514989.15 1501.7473 28469.05 308.49923 1.1217532
|
||||
1920 21.740008 789.87504 1640.0559 220.16997 -850.18086 603.67271 634.84308 183.31253 0 -426.75252 513142.08 -514987.34 889.51113 28503.487 313.92438 1.1161317
|
||||
1940 21.949681 787.46267 1570.9429 210.89187 -783.48022 605.27114 651.32573 181.65051 0 -435.56723 513206.5 -514992.66 -1213.4071 28540.767 300.71188 1.0306517
|
||||
1960 22.16336 784.79852 1591.8755 213.70197 -807.07695 594.43439 669.69922 174.81078 0 -440.94269 513185.58 -514990.66 -9.1610879 28568.421 304.73308 1.0111234
|
||||
1980 22.368034 780.57674 1632.8138 219.19775 -852.23704 605.41038 630.06225 169.19473 0 -441.49651 513181.33 -514996.74 1265.2908 28593.818 312.59942 0.96826781
|
||||
2000 22.581326 775.20404 1636.2577 219.66008 -861.05366 609.0993 612.37884 163.97498 0 -448.27188 513197.01 -514995.24 -167.85231 28624.885 313.26825 0.94815628
|
||||
Loop time of 22.5814 on 4 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Performance: 3.826 ns/day, 6.273 hours/ns, 88.568 timesteps/s
|
||||
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.479 | 10.867 | 11.348 | 9.5 | 48.12
|
||||
Bond | 0.47013 | 0.48392 | 0.50035 | 1.7 | 2.14
|
||||
Kspace | 4.4559 | 4.9538 | 5.3493 | 14.5 | 21.94
|
||||
Neigh | 0.65502 | 0.65523 | 0.65539 | 0.0 | 2.90
|
||||
Comm | 0.47358 | 0.47448 | 0.47606 | 0.1 | 2.10
|
||||
Output | 0.0062618 | 0.0089129 | 0.014062 | 3.2 | 0.04
|
||||
Modify | 5.0877 | 5.0948 | 5.1016 | 0.3 | 22.56
|
||||
Other | | 0.04382 | | | 0.19
|
||||
|
||||
Nlocal: 750 ave 769 max 722 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 5829.25 ave 5873 max 5791 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 164687 ave 168810 max 157995 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 658749
|
||||
Ave neighs/atom = 219.583
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 65
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:22
|
||||
|
|
@ -1,254 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 1 500.0
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 50653 27000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
Memory usage per processor = 17.0416 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
|
||||
20 1.385576 10970.012 5646.6301 758.03417 5323.3819 2059.5936 2216.9884 125.92554 0 1728.6053 514096.92 -514904.65 75436.064 22442.45 899.51659 426.89782
|
||||
40 2.8551838 8946.3004 5328.0205 715.26229 3618.2799 1462.1369 1696.2859 256.70292 0 1227.1291 513938.28 -514962.25 46638.926 23048.183 913.15135 252.56746
|
||||
60 4.256644 7510.9138 4723.1153 634.05655 2787.7985 1200.8153 1745.4103 301.30777 0 557.91727 513950.17 -514967.82 37797.472 23517.111 840.69781 151.04819
|
||||
80 5.6700039 6349.0396 4602.1226 617.81383 1746.917 881.77472 1380.8268 300.54011 0 204.13917 513929.54 -514949.9 33853.354 23924.249 841.20585 95.742025
|
||||
100 7.1165569 5485.3222 4144.7402 556.41234 1340.582 784.84009 1301.8671 289.61557 0 -77.062714 514016.28 -514974.95 23857.465 24318.637 768.91722 59.825738
|
||||
120 8.510273 4862.0053 3777.3363 507.09006 1084.669 621.87069 1297.2363 283.15963 0 -165.00092 514030.24 -514982.84 17467.301 24661.1 708.90876 35.503627
|
||||
140 9.89271 4340.9652 3447.5936 462.82361 893.3716 643.1449 1248.6314 275.36087 0 -264.51028 513962.87 -514972.13 14982.178 24941.74 650.92753 23.297372
|
||||
160 11.266981 3926.9368 3280.8104 440.43373 646.12637 590.77624 1125.7232 275.3221 0 -402.26335 514039.99 -514983.43 17555.529 25182.215 623.03896 13.767615
|
||||
180 12.636709 3510.3411 3034.5182 407.37013 475.82289 580.88726 1065.7063 271.62555 0 -478.17514 514008.07 -514972.29 9901.7384 25408.806 577.95511 8.7953435
|
||||
200 13.951961 3233.2057 2804.8754 376.54165 428.33026 560.57334 1096.7788 268.56938 0 -524.79217 514009.74 -514982.54 8543.4492 25602.16 535.31334 5.5723047
|
||||
220 15.315 3020.0557 2679.3857 359.69523 340.66996 534.37676 1086.1078 252.72365 0 -554.44877 514000.87 -514978.96 7630.6161 25763.835 511.8744 4.1309201
|
||||
240 16.66608 2817.6362 2557.8968 343.3859 259.73947 533.53125 1096.7513 235.23483 0 -594.78212 513968.14 -514979.14 6067.9397 25911.192 489.07601 2.9844639
|
||||
260 18.020921 2631.1316 2460.4934 330.30994 170.63824 520.23801 1043.849 228.55335 0 -637.15729 514004.04 -514988.88 5635.1903 26047.493 470.67196 2.358136
|
||||
280 19.327414 2462.7215 2379.403 319.42393 83.318543 525.36331 972.01762 226.26993 0 -624.36335 513966.76 -514982.73 4763.2439 26167.845 455.32938 1.8853017
|
||||
300 20.664073 2314.007 2233.3945 299.82295 80.612529 521.07514 985.58156 216.6623 0 -622.92535 513969.51 -514989.29 3501.9257 26271.903 427.41388 1.7110326
|
||||
320 21.998284 2171.6005 2216.0458 297.49398 -44.445373 513.1225 926.87268 206.39293 0 -647.39127 513946.45 -514989.89 3556.0249 26368.557 424.16134 1.5401544
|
||||
340 23.295565 2048.7645 2103.0412 282.32362 -54.276671 517.24017 972.17593 198.86832 0 -648.49462 513890.61 -514984.68 3723.4258 26461.822 402.56097 1.3933654
|
||||
360 24.639426 1940.255 2045.2119 274.5603 -104.95688 499.1817 932.32957 187.5616 0 -652.16846 513915.39 -514987.25 2301.433 26551.361 391.50737 1.3177372
|
||||
380 25.919177 1826.4337 1933.9251 259.62057 -107.49138 518.5733 919.38362 182.08763 0 -651.72644 513909.35 -514985.16 2618.7931 26632.025 370.16974 1.3263382
|
||||
400 27.23436 1760.0079 1974.3468 265.04699 -214.33884 494.88766 905.27809 184.94874 0 -673.15814 513861.2 -514987.5 2096.731 26707.742 377.93896 1.2790015
|
||||
420 28.50932 1674.2459 1875.0429 251.7159 -200.79701 494.32791 919.1307 191.42967 0 -660.09631 513843.82 -514989.41 358.06627 26778.924 358.8831 1.3234648
|
||||
440 29.823068 1636.3668 1886.8736 253.30412 -250.50682 501.37304 885.96911 179.94725 0 -646.55634 513813.44 -514984.68 465.97294 26842.197 361.1633 1.2949713
|
||||
460 31.092765 1593.0934 1860.7484 249.79693 -267.65503 491.39115 906.9344 174.33035 0 -666.38274 513814.92 -514988.85 126.16052 26894.743 356.1632 1.2759204
|
||||
480 32.406062 1505.0407 1837.1657 246.63106 -332.12503 509.85902 860.16645 173.43061 0 -651.2259 513765.85 -514990.2 1646.3283 26939.521 351.6473 1.2643358
|
||||
500 33.677199 1442.2558 1798.394 241.42613 -356.13819 522.53768 861.77071 168.42903 0 -655.02572 513738.55 -514992.4 1526.9168 26984.71 344.22043 1.2508825
|
||||
520 34.98888 1429.2148 1796.9298 241.22958 -367.71495 524.55666 871.69773 162.68814 0 -664.81406 513731.94 -514993.79 -680.86121 27027.519 343.9346 1.2628675
|
||||
540 36.290854 1386.5466 1788.8853 240.14964 -402.33868 549.35219 874.93475 154.34652 0 -656.82759 513667.79 -514991.93 -112.10182 27063.585 342.37563 1.3021222
|
||||
560 37.52542 1344.4167 1829.4102 245.58992 -484.99349 543.86102 827.43025 144.96524 0 -643.51447 513638.79 -514996.53 701.10406 27094.487 350.14354 1.3040182
|
||||
580 38.796225 1286.7629 1718.567 230.70973 -431.80414 561.04865 874.04358 152.41827 0 -615.40981 513590.72 -514994.62 826.08615 27125.818 328.91939 1.2462575
|
||||
600 40.032106 1275.3861 1701.9169 228.47454 -426.53082 558.07219 895.26591 163.23964 0 -608.79386 513561.43 -514995.74 284.53547 27152.441 325.68878 1.3366627
|
||||
620 41.297358 1273.8918 1712.1906 229.85372 -438.29876 558.54787 859.08268 175.40704 0 -603.76978 513568.36 -514995.92 -799.98388 27171.09 327.70761 1.2215062
|
||||
640 42.526453 1217.1518 1736.1072 233.06442 -518.95534 572.52862 823.16123 163.5653 0 -606.82177 513521.07 -514992.46 -528.59646 27187.499 332.28172 1.2466277
|
||||
660 43.751388 1139.8934 1675.8281 224.97222 -535.93471 572.5104 829.99341 152.69698 0 -620.77477 513527.1 -514997.46 127.63393 27203.689 320.71564 1.270961
|
||||
680 44.951294 1132.7801 1684.9691 226.19937 -552.18903 579.17897 824.9868 153.95243 0 -613.89121 513497.59 -514994 -375.69988 27217.538 322.46995 1.266406
|
||||
700 46.114508 1123.7259 1689.7673 226.8435 -566.04141 579.34852 817.35591 160.76324 0 -604.95952 513473.67 -514992.22 539.9968 27228.562 323.38291 1.2824201
|
||||
720 47.311101 1109.2452 1679.3944 225.45099 -570.14919 580.49864 815.37954 166.39557 0 -599.53737 513460.9 -514993.78 1379.628 27240.51 321.38269 1.3097525
|
||||
740 48.482072 1103.9038 1664.1003 223.39782 -560.19651 598.28549 826.45607 162.40108 0 -577.67737 513419.55 -514989.21 -688.06905 27252.803 318.47888 1.2441535
|
||||
760 49.66032 1069.6322 1656.8299 222.42181 -587.19776 602.32252 832.89566 153.82032 0 -575.90234 513395.07 -514995.41 40.843646 27264.248 317.07409 1.2699292
|
||||
780 50.861186 1034.9853 1655.3151 222.21845 -620.3298 585.98097 809.14501 152.10567 0 -574.09092 513399.41 -514992.88 -542.13898 27275.872 316.80217 1.2268067
|
||||
800 52.028532 1040.3169 1665.5678 223.59483 -625.25085 605.03042 803.57295 148.68705 0 -581.69335 513396.32 -514997.16 535.8591 27285.478 318.74392 1.2821524
|
||||
820 53.219595 1058.9481 1736.3976 233.1034 -677.4495 598.69968 784.98413 145.24433 0 -598.32684 513390.35 -514998.4 661.30446 27295.669 332.34879 1.2200226
|
||||
840 54.41621 1045.3784 1676.8277 225.10642 -631.4493 612.87881 813.63091 148.70121 0 -579.94856 513372.94 -514999.65 -709.36037 27305.36 320.91078 1.2627849
|
||||
860 55.601647 1020.7309 1672.697 224.55189 -651.96607 601.90752 814.84165 150.80576 0 -580.50172 513365.58 -515004.6 -495.61008 27311.4 320.12878 1.239739
|
||||
880 56.769503 989.87899 1623.5853 217.95888 -633.70636 614.6379 850.57766 146.023 0 -574.97001 513330.69 -515000.67 642.87966 27315.764 310.68993 1.2958041
|
||||
900 57.983504 951.29928 1656.7713 222.41394 -705.47199 612.66694 803.70933 146.11306 0 -578.97014 513313.84 -515002.83 -24.66438 27323.702 317.06441 1.2662666
|
||||
920 59.146542 990.23712 1682.9256 225.92504 -692.68849 625.49291 805.11902 145.39781 0 -566.50947 513298.1 -515000.28 -197.4677 27331.656 322.09842 1.2192545
|
||||
940 60.311439 975.32007 1655.1496 222.19623 -679.82952 644.56888 830.44185 142.39994 0 -571.05582 513274.28 -515000.46 -57.36251 27336.591 316.75027 1.2738836
|
||||
960 61.537265 970.70957 1646.9748 221.0988 -676.26523 621.55653 860.81553 137.50196 0 -570.35847 513277.66 -515003.44 356.66027 27339.657 315.18748 1.2637636
|
||||
980 62.841358 922.60821 1622.7907 217.8522 -700.18247 618.71597 851.23286 133.07652 0 -567.79027 513264.96 -515000.37 5.1281321 27344.467 310.55109 1.2643077
|
||||
1000 64.061049 903.52078 1692.943 227.26982 -789.4222 615.63909 786.17473 136.0751 0 -548.92889 513225.82 -515004.21 -1215.8274 27349.08 323.99743 1.2690479
|
||||
1020 65.198298 880.82937 1611.9406 216.39562 -731.11119 641.95133 825.78985 138.47494 0 -548.19881 513212.76 -515001.89 -120.47994 27348.478 308.46852 1.2703282
|
||||
1040 66.338573 859.35882 1637.2347 219.79124 -777.87584 642.91383 781.96671 129.07882 0 -535.68978 513205.22 -515001.36 -128.41699 27349.25 313.3121 1.2828435
|
||||
1060 67.506762 843.6634 1588.9732 213.31236 -745.30982 645.93104 848.24527 128.71177 0 -531.00457 513167.02 -515004.21 111.3449 27352.063 304.04699 1.3138151
|
||||
1080 68.625545 819.34273 1604.5527 215.40383 -785.20997 653.64454 797.74835 132.82208 0 -520.03981 513152.36 -515001.74 -705.09278 27353.042 307.03668 1.306641
|
||||
1100 69.741567 799.10089 1574.7957 211.40909 -775.69478 654.13763 825.37479 142.68152 0 -514.52184 513120.3 -515003.67 1350.915 27353.287 301.3473 1.2713755
|
||||
1120 70.887971 807.77511 1606.5291 215.66916 -798.75403 677.02 802.76738 138.71115 0 -519.19695 513103.61 -515001.67 551.01047 27358.309 307.4238 1.2874498
|
||||
1140 72.009922 822.40019 1605.593 215.54349 -783.19283 664.08656 825.14971 139.5036 0 -525.0726 513119.2 -515006.06 -1500.6927 27365.732 307.25006 1.2741015
|
||||
1160 73.11993 799.60355 1627.1824 218.44176 -827.57881 660.53797 810.61642 135.99659 0 -549.15929 513120.99 -515006.56 -463.83247 27365.87 311.39885 1.2506312
|
||||
1180 74.237157 808.71869 1627.4862 218.48255 -818.76747 671.07453 814.08104 132.68184 0 -536.0374 513101.27 -515001.83 -1497.9686 27360.344 311.48219 1.1920705
|
||||
1200 75.389495 800.76402 1602.0973 215.0742 -801.33325 661.27319 818.56681 137.56688 0 -528.29009 513116.11 -515006.56 727.09082 27352.249 306.62538 1.1680129
|
||||
1220 76.512266 786.90424 1625.6159 218.23148 -838.7117 654.42667 808.06282 144.23638 0 -544.37793 513103.11 -515004.17 -1016.333 27347.251 311.10383 1.2383451
|
||||
1240 77.618425 784.43915 1618.0202 217.21178 -833.58101 652.75565 810.84854 144.21786 0 -538.55907 513104.01 -515006.86 -1688.0609 27338.945 309.66351 1.2014646
|
||||
1260 78.767789 792.64493 1616.6996 217.03449 -824.05464 659.33158 832.96211 136.95679 0 -535.25333 513087.8 -515005.85 -240.86746 27324.585 309.38787 1.2538953
|
||||
1280 79.890153 772.02964 1579.0067 211.9744 -806.97707 680.62465 825.10068 128.65485 0 -522.39638 513085.1 -515004.06 1026.3484 27308.077 302.15133 1.2789362
|
||||
1300 81.045542 794.71268 1640.9493 220.28991 -846.23661 653.48559 809.8286 126.57126 0 -529.35975 513101 -515007.77 -222.24259 27295.577 314.02093 1.2904787
|
||||
1320 82.165808 784.00371 1619.7825 217.44836 -835.77876 666.10367 843.1839 129.04786 0 -537.48412 513064.75 -515001.38 -904.29245 27284.448 309.98624 1.2367093
|
||||
1340 83.287128 768.52183 1621.7783 217.71629 -853.25649 658.65554 797.98287 135.92558 0 -517.31157 513072.35 -515000.86 556.43774 27269.699 310.3284 1.3310985
|
||||
1360 84.450531 750.55548 1561.8653 209.67325 -811.30983 659.33682 849.22159 146.12076 0 -514.99584 513050.84 -515001.83 156.64838 27254.169 298.83628 1.3466087
|
||||
1380 85.572197 744.55824 1600.9118 214.91506 -856.35357 669.28688 822.92318 135.57716 0 -509.75984 513027.33 -515001.71 395.88113 27246.862 306.32946 1.3282506
|
||||
1400 86.727889 740.37698 1618.0191 217.21163 -877.6421 680.34192 804.16104 122.37614 0 -510.05578 513028.7 -515003.17 -1778.0909 27242.463 309.60983 1.3262175
|
||||
1420 87.853329 707.95242 1606.2301 215.62901 -898.27766 681.75825 834.81666 117.56052 0 -511.14444 512980.84 -515002.11 132.87977 27231.78 307.36642 1.2875563
|
||||
1440 88.999557 701.0459 1631.5857 219.03289 -930.53982 689.29026 778.55166 121.13791 0 -503.03703 512986.74 -515003.22 502.08629 27220.348 312.26072 1.2092436
|
||||
1460 90.173845 691.9965 1611.7145 216.36527 -919.71797 691.89285 800.91685 123.97376 0 -504.76462 512970.72 -515002.46 530.64797 27214.26 308.41315 1.2983911
|
||||
1480 91.318457 691.7249 1594.0369 213.99213 -902.31197 688.47809 838.61898 125.21502 0 -504.16566 512953.09 -515003.55 -1094.2326 27210.327 305.01536 1.3192889
|
||||
1500 92.483926 665.64633 1571.5229 210.96973 -905.87653 681.91529 823.02708 127.30163 0 -506.25486 512973.62 -515005.48 -1022.5661 27200.233 300.72872 1.2507982
|
||||
1520 93.612424 675.29951 1631.0635 218.96279 -955.76401 670.77264 825.29942 133.56984 0 -531.08736 512951.49 -515005.81 -389.61365 27187.165 312.13799 1.2620465
|
||||
1540 94.741199 653.89323 1632.9694 219.21864 -979.07615 678.96106 792.69599 132.07987 0 -515.25022 512939.14 -515006.7 -1030.2457 27174.091 312.51532 1.234099
|
||||
1560 95.9062 636.91726 1590.0999 213.46361 -953.18262 687.04134 809.44011 127.54619 0 -523.45302 512956.52 -515010.28 -951.93121 27155.942 304.27362 1.288966
|
||||
1580 97.028125 627.56968 1601.8646 215.04297 -974.29496 686.96797 803.53231 128.08068 0 -517.28126 512935.11 -515010.71 -1043.2395 27131.362 306.54052 1.2619672
|
||||
1600 98.159189 639.59673 1591.5973 213.66464 -952.00062 695.73225 820.03411 126.92265 0 -523.57295 512936.97 -515008.08 -516.36154 27101.901 304.53745 1.3431812
|
||||
1620 99.322595 631.83759 1582.6681 212.46592 -950.83047 708.36138 817.50888 123.99588 0 -518.92537 512930.72 -515012.49 -2198.9765 27071.135 302.85679 1.2706043
|
||||
1640 100.45901 621.88183 1569.4451 210.6908 -947.56326 703.57599 823.87187 132.80048 0 -497.70649 512900.32 -515010.43 -1335.78 27038.969 300.32548 1.2622751
|
||||
1660 101.60839 642.07332 1595.5476 214.19493 -953.47423 705.46998 794.82235 141.09052 0 -484.29874 512898.11 -515008.66 -403.23344 27004.83 305.30235 1.3253687
|
||||
1680 102.77636 620.05889 1604.721 215.42642 -984.66208 704.63874 808.2235 139.26176 0 -475.937 512849.25 -515010.1 -336.0674 26974.635 307.06907 1.3063348
|
||||
1700 103.9216 625.14905 1627.936 218.54293 -1002.7869 700.41444 790.63143 141.47429 0 -472.95296 512847.83 -515010.18 432.43074 26948.842 311.5388 1.2611748
|
||||
1720 105.07527 635.67026 1585.5068 212.84701 -949.83654 711.22133 826.38676 138.90157 0 -470.74615 512857.96 -515013.56 -927.08791 26927.403 303.39054 1.2949652
|
||||
1740 106.19526 622.55036 1629.9419 218.81221 -1007.3915 701.72972 807.03841 133.88234 0 -462.62233 512821.73 -515009.15 60.724835 26906.734 311.91698 1.2759906
|
||||
1760 107.3157 601.07861 1563.031 209.82973 -961.95237 721.05163 813.03641 135.83107 0 -472.1521 512852.13 -515011.85 1071.0762 26889.11 299.11764 1.211508
|
||||
1780 108.47195 615.76689 1612.7311 216.50175 -996.96425 712.00335 812.2101 135.93651 0 -469.54632 512821.55 -515009.11 -1171.9908 26876.291 308.62781 1.2522701
|
||||
1800 109.60652 590.39061 1576.6095 211.65259 -986.21891 706.7567 822.39219 137.15671 0 -470.15251 512825.84 -515008.21 -1051.5297 26860.1 301.6752 1.3176335
|
||||
1820 110.78553 603.65994 1596.51 214.32414 -992.85007 711.49043 808.94991 132.38543 0 -461.89866 512827.37 -515011.15 180.50052 26844.34 305.50815 1.2756752
|
||||
1840 111.93685 591.93917 1596.2013 214.2827 -1004.2621 720.41618 814.51338 137.96161 0 -460.4745 512793.12 -515009.8 605.10058 26833.73 305.47844 1.2069138
|
||||
1860 113.12134 609.8248 1577.7772 211.80934 -967.95236 716.21723 808.30329 144.61624 0 -461.04538 512833.46 -515009.51 -1143.3982 26826.019 301.93343 1.2373879
|
||||
1880 114.2602 614.25513 1599.756 214.7599 -985.50088 748.39555 792.89735 140.36606 0 -460.16996 512800.85 -515007.84 -261.10141 26816.306 306.15319 1.2225442
|
||||
1900 115.40316 615.77501 1599.1853 214.68329 -983.41029 729.35936 798.81735 146.34452 0 -492.16069 512844.21 -515009.98 493.95161 26806.893 306.01603 1.2873103
|
||||
1920 116.55442 628.99417 1652.3184 221.81616 -1023.3242 715.08536 813.8821 147.49091 0 -508.7856 512818.33 -515009.33 -2250.9701 26803.895 316.19125 1.3118467
|
||||
1940 117.73809 613.28705 1595.717 214.21768 -982.42996 719.54904 821.80704 150.0739 0 -493.66309 512828.25 -515008.45 -2187.7221 26796.819 305.33907 1.3154875
|
||||
1960 118.91834 594.22322 1584.9306 212.76966 -990.7074 717.75467 820.27772 151.35897 0 -491.90915 512819.49 -515007.68 -736.31063 26780.283 303.29276 1.2654066
|
||||
1980 120.06148 614.4096 1572.4353 211.09222 -958.02568 732.31342 826.01815 154.79578 0 -487.35165 512824.93 -515008.73 39.731855 26764.092 300.89417 1.2728833
|
||||
2000 121.20194 604.51985 1580.7247 212.20504 -976.20489 716.50209 820.59198 155.66948 0 -482.48478 512823.08 -515009.56 -465.82593 26752.509 302.47674 1.2881296
|
||||
Loop time of 121.202 on 1 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 58.9106 (48.6053)
|
||||
Bond time (%) = 7.9266 (6.53999)
|
||||
Kspce time (%) = 14.2366 (11.7462)
|
||||
Neigh time (%) = 1.79608 (1.48189)
|
||||
Comm time (%) = 0.562635 (0.464213)
|
||||
Outpt time (%) = 0.0137095 (0.0113113)
|
||||
Other time (%) = 37.7558 (31.1511)
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10007 ave 10007 max 10007 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 720894 ave 720894 max 720894 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 720894
|
||||
Ave neighs/atom = 240.298
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 49
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,254 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
|
||||
fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes
|
||||
fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 ${vPRESS} 500.0
|
||||
fix fNPH all nph iso 1 1 500.0
|
||||
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 17908 7200
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
Memory usage per processor = 13.7041 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
|
||||
20 0.44569397 10977.424 5649.3945 758.40528 5328.0296 2062.3394 2228.2308 127.20754 0 1716.2152 514097.63 -514903.59 75539.256 22441.778 900.65907 425.71739
|
||||
40 0.90527296 8971.2482 5307.0059 712.44118 3664.2423 1468.3059 1727.5451 263.87315 0 1220.4282 513944.02 -514959.93 46706.836 23047.009 909.55477 251.59684
|
||||
60 1.361037 7598.4556 4774.303 640.92826 2824.1526 1194.6529 1771.6791 314.85714 0 553.82536 513952.92 -514963.78 37332.483 23513.741 850.78562 150.29304
|
||||
80 1.7987111 6500.1249 4632.1069 621.83909 1868.0179 914.33309 1444.251 317.2453 0 213.21366 513930.08 -514951.11 33258.709 23919.334 847.28599 94.967207
|
||||
100 2.243571 5591.6251 4319.2496 579.83942 1272.3755 772.49711 1235.8559 306.35507 0 -56.084846 513990.28 -514976.52 21846.137 24315.14 802.34652 59.892261
|
||||
120 2.672169 4952.948 3881.7989 521.11369 1071.1491 630.90018 1260.1994 299.84546 0 -147.02839 514014.84 -514987.6 17197.209 24657.008 728.80233 35.812029
|
||||
140 3.0969729 4374.1711 3440.8515 461.91852 933.31957 670.31509 1238.1527 300.45294 0 -260.41129 513963.49 -514978.68 17258.201 24938.237 649.62114 23.329848
|
||||
160 3.522228 3923.495 3251.4038 436.48603 672.0912 632.18705 1144.4394 307.33026 0 -436.52375 514013.97 -514989.32 17850.515 25184.125 617.40474 13.751472
|
||||
180 3.939676 3558.426 3060.6065 410.87237 497.81946 621.75343 1085.8467 297.16091 0 -495.18434 513968.41 -514980.17 9891.4148 25413.786 582.97006 8.7537197
|
||||
200 4.3550711 3228.7597 2864.5929 384.55845 364.16674 591.37767 1077.5669 257.51603 0 -521.62174 513950.21 -514990.89 5932.7994 25603.593 546.64932 5.8336845
|
||||
220 4.781127 2922.9928 2668.3732 358.21686 254.61956 552.45115 1045.2477 238.95571 0 -548.2597 513955.3 -514989.07 7141.8585 25759.687 509.85961 3.9098706
|
||||
240 5.195529 2721.2831 2574.4897 345.61343 146.79339 548.06208 1035.0795 226.53387 0 -609.08183 513928.26 -514982.06 6976.8028 25904.957 492.22535 3.0535597
|
||||
260 5.5978601 2525.9513 2461.0955 330.39077 64.855761 536.85769 1022.3488 211.33422 0 -633.79065 513919.59 -514991.49 4541.0707 26037.832 470.78293 2.3688827
|
||||
280 6.0106721 2338.1989 2324.5678 312.06255 13.63115 519.14801 970.18634 197.76634 0 -621.14257 513937.12 -514989.44 2916.5572 26148.311 444.7787 1.975451
|
||||
300 6.4294651 2194.9975 2189.2141 293.89194 5.7833943 530.82824 982.37216 190.98549 0 -652.12498 513946.6 -514992.88 4231.0047 26242.419 418.97109 1.6488796
|
||||
320 6.825505 2045.5803 2132.2428 286.24381 -86.66256 531.61575 935.95137 188.46723 0 -683.29899 513935.09 -514994.49 1717.7425 26334.126 408.09021 1.554221
|
||||
340 7.23614 1929.4862 2083.5954 279.71312 -154.10925 509.11673 906.18183 186.63991 0 -668.08147 513908.15 -514996.11 2743.5013 26418.758 398.8054 1.4581893
|
||||
360 7.6401701 1853.7734 1992.7639 267.5194 -138.99054 525.44894 891.90785 178.2228 0 -654.5178 513920.68 -515000.73 3824.9512 26497.054 381.4442 1.3381947
|
||||
380 8.035013 1760.9758 1947.1807 261.40007 -186.20493 517.02356 919.61194 172.55666 0 -676.58938 513879.08 -514997.89 2968.2379 26574.581 372.73009 1.2814975
|
||||
400 8.439594 1687.9145 1906.019 255.8743 -218.10451 535.676 922.06535 176.24936 0 -683.92633 513833.49 -515001.66 1305.3348 26642.871 364.83666 1.2876267
|
||||
420 8.849108 1605.8081 1889.1783 253.61351 -283.37015 517.23187 857.77943 180.22369 0 -663.03698 513825.85 -515001.41 2618.2332 26704.387 361.60626 1.2936035
|
||||
440 9.2419581 1518.1322 1794.7348 240.93491 -276.60265 531.28729 893.06522 188.20612 0 -667.29018 513778.24 -515000.11 1458.8151 26764.917 343.52984 1.2323667
|
||||
460 9.6461852 1455.546 1796.4 241.15845 -340.85398 527.34366 846.65226 188.77031 0 -650.31889 513748.59 -515001.89 169.77154 26818.027 343.8413 1.2433195
|
||||
480 10.037471 1423.2564 1780.6643 239.04601 -357.40797 555.56132 861.65053 179.25353 0 -642.23744 513684.59 -514996.23 1737.2169 26861.945 340.81112 1.2754844
|
||||
500 10.442603 1414.4159 1792.7736 240.67163 -378.35771 562.25347 865.25285 172.51254 0 -638.36916 513656.76 -514996.77 2862.5086 26905.68 343.13664 1.264128
|
||||
520 10.840656 1359.8057 1801.5592 241.85105 -441.75349 573.49082 804.76936 169.51784 0 -635.89324 513643.32 -514996.96 927.77773 26956.407 344.82065 1.2649106
|
||||
540 11.24422 1319.969 1763.9685 236.80467 -443.9995 564.76203 851.23442 169.85422 0 -632.66442 513600.38 -514997.57 402.68456 26999.135 337.63034 1.2312338
|
||||
560 11.656965 1288.5175 1741.1847 233.74605 -452.66718 589.0843 843.68941 164.33111 0 -639.59483 513593.61 -515003.78 2031.8562 27036.616 333.27376 1.1999696
|
||||
580 12.050085 1250.4981 1701.8135 228.46065 -451.3154 576.17535 877.82925 152.94556 0 -632.24298 513574.54 -515000.56 328.36451 27076.846 325.70282 1.2583556
|
||||
600 12.463133 1212.0751 1699.8202 228.19306 -487.74513 586.11242 850.6289 146.9891 0 -635.87543 513564.76 -515000.36 -593.07635 27114.131 325.34702 1.1966401
|
||||
620 12.857609 1202.6969 1724.5891 231.51816 -521.8922 586.546 815.3615 149.33058 0 -627.92161 513553.83 -514999.04 -16.881985 27141.295 330.08328 1.2224592
|
||||
640 13.267988 1180.7392 1717.1928 230.52525 -536.45363 595.45079 837.47314 150.14341 0 -635.92342 513512.84 -514996.44 1253.4658 27161.366 328.61164 1.3535393
|
||||
660 13.661833 1146.6245 1693.9969 227.4113 -547.37231 603.66965 823.99031 147.75109 0 -616.07296 513489.44 -514996.15 -632.85642 27186.187 324.23124 1.1905446
|
||||
680 14.057714 1112.6845 1649.8772 221.48844 -537.19275 594.76928 869.75332 148.3474 0 -610.67856 513459.02 -514998.41 -656.86895 27208.556 315.75904 1.2280206
|
||||
700 14.46045 1080.853 1662.6225 223.19944 -581.76952 607.13692 800.72097 155.37025 0 -590.53466 513444.43 -514998.9 1478.4986 27230.38 318.17518 1.2929123
|
||||
720 14.858115 1074.1453 1681.4035 225.7207 -607.2582 602.55649 804.73664 155.69335 0 -578.62035 513406.54 -514998.16 -312.12065 27255.88 321.76305 1.3178416
|
||||
740 15.262165 1057.2173 1626.1913 218.30872 -568.97405 614.54113 851.40449 158.65878 0 -585.61227 513391.12 -514999.09 -252.45558 27276.192 311.20516 1.2592718
|
||||
760 15.664885 1062.4809 1661.9166 223.10468 -599.4357 613.01783 805.30824 157.10102 0 -572.92999 513401.46 -515003.4 8.2424603 27294.015 318.05423 1.2582564
|
||||
780 16.067218 1054.4338 1611.1036 216.28327 -556.66986 619.88711 869.25572 154.03862 0 -563.00792 513365.76 -515002.61 -325.5131 27313.202 308.30577 1.2766112
|
||||
800 16.469454 1045.3661 1667.4808 223.85165 -622.11476 607.72536 819.84304 154.6324 0 -551.0017 513351.46 -515004.78 -711.73517 27333.225 319.1255 1.2459692
|
||||
820 16.874566 1025.6074 1655.4437 222.23572 -629.83638 617.12876 822.09062 147.69173 0 -566.57998 513354.87 -515005.04 399.28085 27347.385 316.79906 1.2953686
|
||||
840 17.272044 995.37917 1669.6204 224.13888 -674.24128 600.79611 821.7655 140.46192 0 -568.05887 513337.46 -515006.66 583.69527 27361.364 319.5132 1.2991152
|
||||
860 17.673279 971.05977 1639.0518 220.03518 -667.99202 608.93496 824.23202 133.94234 0 -564.33929 513334.29 -515005.05 -413.73876 27378.37 313.69629 1.2004828
|
||||
880 18.080302 944.37506 1628.7217 218.64842 -684.34669 617.46083 825.05882 135.40531 0 -569.6048 513312.82 -515005.49 512.87669 27389.533 311.69643 1.2448601
|
||||
900 18.477336 949.5982 1677.4393 225.18853 -727.84115 624.49844 772.75351 136.94704 0 -549.4139 513292.05 -515004.67 271.20937 27400.579 321.05001 1.211493
|
||||
920 18.873705 932.25995 1610.381 216.18626 -678.12109 623.29028 843.94403 144.55915 0 -557.17786 513270.07 -515002.81 1097.4299 27412.447 308.17027 1.2686712
|
||||
940 19.284093 916.57919 1640.5258 220.23305 -723.94658 619.65583 814.76133 144.02609 0 -552.83588 513253.39 -515002.95 -342.60513 27424.209 313.98093 1.1943711
|
||||
960 19.678839 941.9627 1630.8148 218.9294 -688.85213 647.73279 836.44195 147.48183 0 -533.27218 513217.4 -515004.64 -291.64501 27431.009 312.08648 1.2709839
|
||||
980 20.091488 888.07492 1615.6407 216.89235 -727.56578 644.39061 818.66717 151.18945 0 -530.05167 513198.49 -515010.26 835.04931 27433.771 309.19916 1.2205907
|
||||
1000 20.484026 903.45687 1626.7477 218.38341 -723.29085 660.33039 814.13089 154.52432 0 -517.32081 513174.16 -515009.12 -597.08083 27441.855 311.29984 1.2872278
|
||||
1020 20.884939 884.61313 1628.0576 218.55926 -743.44446 659.18164 792.2445 148.42138 0 -501.95147 513167.72 -515009.06 -227.27612 27447.478 311.54441 1.3024911
|
||||
1040 21.279846 852.14085 1593.0292 213.85686 -740.88834 648.79571 822.31823 141.59479 0 -492.90372 513148.22 -515008.91 1544.7468 27454.311 304.83469 1.2878493
|
||||
1060 21.655111 848.20594 1615.8134 216.91553 -767.60742 629.3671 795.01871 137.79728 0 -487.7332 513167.91 -515009.96 818.90975 27467.219 309.21127 1.2684583
|
||||
1080 22.037992 831.86637 1618.7361 217.30789 -786.86971 636.48473 828.1039 138.80398 0 -531.02117 513152.33 -515011.57 -796.09024 27482.281 309.76171 1.2933978
|
||||
1100 22.412974 796.80267 1592.7483 213.81915 -795.94567 625.90981 798.78644 146.80857 0 -536.96836 513184.36 -515014.85 -84.200922 27491.353 304.78282 1.2860228
|
||||
1120 22.801171 772.10069 1567.5834 210.44088 -795.48274 658.82509 788.14264 148.88807 0 -539.176 513162.6 -515014.76 867.66407 27496.215 299.95125 1.3027473
|
||||
1140 23.17888 770.63813 1565.9379 210.21998 -795.2998 640.7064 799.36864 147.80124 0 -535.9357 513166.65 -515013.89 -1183.537 27499.574 299.64709 1.2856405
|
||||
1160 23.563832 764.75496 1564.5598 210.03497 -799.80482 647.22053 811.27899 146.29888 0 -543.29534 513150.92 -515012.23 -1228.125 27500.914 299.39235 1.2526237
|
||||
1180 23.941609 764.17598 1617.4255 217.13195 -853.24954 659.94837 768.65464 144.94873 0 -529.07191 513110.91 -515008.64 107.09246 27498.487 309.51287 1.287252
|
||||
1200 24.317012 762.98696 1589.6792 213.40714 -826.69227 651.88091 816.19739 145.19502 0 -517.91574 513088.48 -515010.53 -1052.4085 27492.624 304.22381 1.2172354
|
||||
1220 24.706198 764.88104 1566.9504 210.3559 -802.06936 679.17803 822.8538 134.80594 0 -509.18914 513076.83 -515006.55 694.03102 27483.433 299.85098 1.253554
|
||||
1240 25.083107 767.93518 1615.6009 216.887 -847.66571 671.38696 801.01511 123.2586 0 -498.24308 513061.33 -515006.42 -367.46541 27476.952 309.13859 1.3441052
|
||||
1260 25.461219 769.84629 1597.441 214.44912 -827.59471 670.93506 820.00134 122.64096 0 -489.27375 513053.94 -515005.84 -58.54717 27470.667 305.70834 1.2250043
|
||||
1280 25.850924 761.02257 1637.0908 219.77192 -876.06819 685.99978 801.7347 121.99508 0 -498.90642 513022.12 -515009.01 667.72097 27460.84 313.30874 1.2269128
|
||||
1300 26.230407 725.15653 1614.5991 216.75252 -889.44257 676.06266 795.73111 129.44616 0 -500.04123 513019.86 -515010.51 346.28961 27453.003 309.01166 1.1958813
|
||||
1320 26.616651 690.04147 1555.4057 208.80608 -865.36428 674.77824 814.17441 138.30234 0 -503.84683 513024.03 -515012.8 -953.72011 27450.174 297.64076 1.2471902
|
||||
1340 26.997168 731.37012 1629.8044 218.79375 -898.43423 672.50861 814.71248 139.58285 0 -509.67436 512995.22 -515010.78 -1831.2948 27443.855 311.896 1.2621742
|
||||
1360 27.377617 745.65434 1610.5181 216.20467 -864.8638 691.11602 810.45797 140.60405 0 -508.77522 513011.95 -515010.21 -479.36536 27427.931 308.19958 1.2616878
|
||||
1380 27.768431 746.41678 1674.6182 224.8098 -928.2014 661.11056 795.29365 134.53957 0 -512.17435 513003.03 -515010 726.71849 27412.674 320.49072 1.2545772
|
||||
1400 28.151466 706.81871 1607.416 215.78822 -900.5973 709.47611 804.4224 129.7539 0 -509.52634 512973.57 -515008.29 -712.21584 27401.879 307.61219 1.2445794
|
||||
1420 28.544365 667.95202 1582.3831 212.42766 -914.43103 664.88892 801.83372 136.47795 0 -514.32654 513008.75 -515012.06 -674.60825 27385.407 302.81863 1.2330197
|
||||
1440 28.92417 662.21363 1572.2132 211.0624 -909.99957 695.6883 812.01519 141.73013 0 -511.80853 512960.55 -515008.18 -73.453766 27362.02 300.86905 1.233181
|
||||
1460 29.303746 673.3058 1590.356 213.49799 -917.05016 660.8122 809.16185 137.34151 0 -506.78651 512991.4 -515008.98 487.20204 27337.657 304.34864 1.2293292
|
||||
1480 29.683979 690.74904 1599.4915 214.72439 -908.74246 688.89665 819.23241 129.49598 0 -495.16925 512954.44 -515005.64 487.60757 27316.061 306.12959 1.159563
|
||||
1500 30.073856 696.13426 1627.5685 218.49359 -931.4342 677.25983 808.26514 125.60011 0 -489.59764 512955.4 -515008.36 519.17541 27293.341 311.4741 1.2480919
|
||||
1520 30.451939 716.4485 1613.3483 216.5846 -896.89978 696.36687 820.98027 134.70464 0 -469.43851 512929.25 -515008.76 544.98379 27271.903 308.73614 1.2765559
|
||||
1540 30.839949 711.84578 1602.4823 215.1259 -890.63656 708.76314 793.80104 146.48285 0 -451.73842 512918.02 -515005.96 454.52189 27257.543 306.63893 1.3081885
|
||||
1560 31.255883 702.95447 1604.1384 215.34821 -901.1839 701.09472 795.80519 150.09855 0 -450.00841 512908.1 -515006.27 -175.16964 27248.208 306.99599 1.217717
|
||||
1580 31.634972 666.16399 1593.9574 213.98146 -927.79341 709.48317 798.22341 141.85062 0 -483.91855 512915.54 -515008.98 -174.37068 27241.403 305.02798 1.2549165
|
||||
1600 32.013681 688.42678 1613.6536 216.62559 -925.22683 708.7011 810.24587 137.18807 0 -474.54073 512902.73 -515009.55 175.74764 27236.695 308.81599 1.2269417
|
||||
1620 32.377997 686.38631 1599.6555 214.7464 -913.26914 723.55612 796.07516 144.8931 0 -474.73319 512907.37 -515010.43 33.582792 27234.316 306.09396 1.3145429
|
||||
1640 32.739099 705.79223 1615.3667 216.85556 -909.57442 705.06325 806.35123 150.08668 0 -479.53397 512919.18 -515010.72 -276.47112 27230.877 309.12408 1.2740414
|
||||
1660 33.111364 701.27726 1607.2688 215.76845 -905.99149 721.97907 787.92231 144.01692 0 -463.68107 512916.64 -515012.87 929.51954 27224.725 307.57382 1.2682264
|
||||
1680 33.474256 700.51394 1604.7821 215.43463 -904.2682 712.18636 816.32021 135.23856 0 -471.34583 512915.88 -515012.55 169.46579 27223.825 307.07661 1.316103
|
||||
1700 33.847599 653.51775 1574.3177 211.34492 -920.79992 708.22805 829.01689 135.77013 0 -456.72703 512872.35 -515009.44 -1331.9277 27225.869 301.24451 1.2944188
|
||||
1720 34.210801 646.19978 1583.018 212.5129 -936.81823 721.83771 788.24431 140.19453 0 -469.87575 512893.23 -515010.45 722.29697 27224.305 302.91185 1.3016769
|
||||
1740 34.57351 650.08331 1600.9298 214.91747 -950.84647 709.99119 789.79721 138.23225 0 -460.97413 512880.98 -515008.87 1102.6045 27225.414 306.34618 1.3045986
|
||||
1760 34.947762 647.44786 1591.6127 213.6667 -944.16484 703.25888 831.27698 133.1631 0 -463.47718 512860.59 -515008.98 1152.8885 27230.97 304.56068 1.2966664
|
||||
1780 35.311829 634.92036 1581.508 212.31019 -946.58767 707.7771 807.97758 140.70709 0 -473.2579 512882.95 -515012.74 229.64632 27235.632 302.63254 1.2770484
|
||||
1800 35.686407 609.58199 1563.2412 209.85795 -953.65919 706.83652 811.29431 136.56443 0 -482.58705 512887.2 -515012.97 -1428.3239 27239.537 299.14762 1.235579
|
||||
1820 36.050632 615.78755 1553.6653 208.57243 -937.87771 721.32849 827.06658 126.75248 0 -476.19143 512873.72 -515010.55 -1558.7353 27240.307 297.30295 1.2564383
|
||||
1840 36.425851 595.24691 1623.2931 217.91965 -1028.0462 715.62813 759.44377 125.14223 0 -486.38933 512873.86 -515015.73 -393.40048 27233.914 310.63049 1.3037899
|
||||
1860 36.791862 584.14833 1580.8506 212.22194 -996.70229 725.49209 786.41557 129.34385 0 -497.01606 512871.73 -515012.67 -445.7964 27227.234 302.53512 1.2082224
|
||||
1880 37.159068 571.94192 1587.3128 213.08945 -1015.3709 727.21492 776.53831 128.97058 0 -472.95741 512835.25 -515010.39 -2430.0222 27217.82 303.74009 1.2871788
|
||||
1900 37.534434 588.18296 1575.532 211.50794 -987.34908 735.18962 822.01431 121.27343 0 -474.15326 512820.83 -515012.5 -1004.9937 27200.966 301.48221 1.2875721
|
||||
1920 37.899018 595.6429 1593.2862 213.89136 -997.64331 728.16052 813.67464 116.25522 0 -474.41478 512829.4 -515010.72 56.20061 27185.033 304.87735 1.3063391
|
||||
1940 38.263855 552.10655 1586.7384 213.01234 -1034.6318 727.69915 794.08444 116.66262 0 -474.42985 512811.77 -515010.42 229.42949 27173.976 303.61874 1.3140118
|
||||
1960 38.637106 571.50083 1614.8554 216.78693 -1043.3546 729.51741 761.23804 128.23909 0 -464.44507 512811.41 -515009.31 -496.32744 27162.867 309.02606 1.2732453
|
||||
1980 38.999486 554.31018 1603.5237 215.26569 -1049.2135 738.87358 785.7371 126.13553 0 -468.044 512779.36 -515011.27 467.45037 27149.813 306.82565 1.3387674
|
||||
2000 39.362048 570.16479 1585.0529 212.78608 -1014.8882 754.53304 813.00379 125.06015 0 -448.86583 512751.21 -515009.83 -257.98779 27141.691 303.29539 1.313977
|
||||
Loop time of 39.3621 on 4 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 15.1636 (38.5233)
|
||||
Bond time (%) = 2.04281 (5.18978)
|
||||
Kspce time (%) = 8.76608 (22.2704)
|
||||
Neigh time (%) = 0.513343 (1.30415)
|
||||
Comm time (%) = 1.60174 (4.06924)
|
||||
Outpt time (%) = 0.00888807 (0.0225803)
|
||||
Other time (%) = 11.2657 (28.6206)
|
||||
|
||||
Nlocal: 750 ave 771 max 713 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 5881.75 ave 5954 max 5826 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 178004 ave 198102 max 168052 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 712018
|
||||
Ave neighs/atom = 237.339
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,263 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_ATOM gATOMS temp
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDTDIR all drude/transform/direct
|
||||
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500
|
||||
fix_modify fNPT temp cTEMP_ATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349)
|
||||
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 1 100.0
|
||||
fix fDTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 50653 27000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
Memory usage per processor = 17.0416 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
|
||||
20 1.485518 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565
|
||||
40 2.9579411 9812.3728 6009.1747 806.70411 3803.1981 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0176 221.56359
|
||||
60 4.3728549 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.61 23440.966 1050.9011 133.14424
|
||||
80 5.817939 8115.7843 5997.9225 805.19356 2117.8618 901.84106 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.951 23834.833 1111.65 89.054921
|
||||
100 7.207612 7496.2553 5770.3833 774.64747 1725.872 829.63908 1420.6659 325.4016 0 62.343574 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498472
|
||||
120 8.656971 6986.593 5396.9479 724.51547 1589.6452 678.24993 1535.5197 325.88462 0 -9.6649617 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715636
|
||||
140 10.075453 6549.0006 5126.6341 688.22709 1422.3665 724.95472 1477.7714 315.11964 0 -99.456486 513960.58 -514956.6 19747.307 24877.008 969.51239 30.977085
|
||||
160 11.492728 6131.3317 5000.4421 671.2864 1130.8896 703.24858 1302.1192 314.93994 0 -258.4539 514042.29 -514973.25 23050.008 25142.654 948.73049 23.021806
|
||||
180 12.899685 5749.9765 4700.9451 631.0803 1049.0314 674.94525 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.485 25400.048 893.75893 17.322076
|
||||
200 14.301162 5429.601 4392.5738 589.68286 1037.0272 612.00108 1296.2432 303.16019 0 -300.38658 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486
|
||||
220 15.696118 5133.8318 4290.7369 576.01173 843.09487 572.51989 1261.8055 289.99072 0 -383.71584 514078.3 -514975.81 12509.826 25814.229 817.78562 11.104636
|
||||
240 17.080213 4850.3856 4120.3632 553.13985 730.0224 553.79224 1263.6533 278.92142 0 -487.76523 514091.35 -514969.93 10891.878 25996.167 785.87194 9.360776
|
||||
260 18.465174 4583.9875 3911.0361 525.03865 672.95138 541.52251 1175.1552 273.43365 0 -475.23638 514139.68 -514981.61 8086.1512 26168.96 746.55574 7.4653786
|
||||
280 19.852883 4349.224 3692.2792 495.67153 656.9448 598.81912 1148.0997 278.8781 0 -444.09603 514045.38 -514970.13 5124.6373 26323.056 705.04252 6.4783461
|
||||
300 21.231065 4128.9017 3579.5067 480.53234 549.39506 584.06591 1089.5131 267.69425 0 -456.87099 514043.55 -514978.56 8350.7757 26456.831 683.9437 5.2650983
|
||||
320 22.561911 3913.7712 3456.9151 464.07498 456.85609 556.31985 1103.3901 263.88855 0 -485.54294 514000.27 -514981.47 9117.6459 26592.844 660.74075 4.5694113
|
||||
340 23.929412 3712.7166 3258.4133 437.42702 454.30336 533.72419 1069.0448 271.85689 0 -454.53939 514001.97 -514967.75 7187.6779 26736.819 622.98237 3.8812919
|
||||
360 25.298241 3533.3834 3024.1004 405.9716 509.283 522.55431 1104.3208 276.30858 0 -456.06655 514036.53 -514974.36 4554.9866 26876.658 578.31181 3.3031408
|
||||
380 26.653809 3367.1792 2971.2716 398.87957 395.9076 508.27241 1059.2248 257.85685 0 -499.68496 514032.55 -514962.31 5645.8914 27002.069 568.38695 2.8305175
|
||||
400 27.984353 3204.91 2874.2403 385.85357 330.6697 543.88404 1018.8809 231.0702 0 -519.33317 514029.07 -514972.9 7250.7332 27123.905 549.89179 2.5832582
|
||||
420 29.327209 3050.6948 2776.6044 372.74639 274.09045 517.42853 953.07587 226.06727 0 -505.60565 514057.02 -514973.9 4026.2599 27250.314 531.28066 2.3360848
|
||||
440 30.659683 2916.2839 2640.2361 354.43958 276.04784 507.06292 983.97321 236.01275 0 -534.64355 514059.65 -514976.01 1708.709 27364.195 505.24974 2.0766005
|
||||
460 31.992583 2787.525 2609.5902 350.32551 177.93474 485.64363 933.57925 234.95003 0 -560.61762 514069.83 -514985.45 3400.5279 27458.081 499.48923 1.8097259
|
||||
480 33.31755 2662.4984 2514.178 337.51686 148.32032 464.67048 928.26208 239.37956 0 -570.38407 514070.86 -514984.47 5084.8141 27547.559 481.26944 1.6441427
|
||||
500 34.613889 2540.5549 2433.5506 326.693 107.00428 473.2945 888.73268 239.40601 0 -565.68704 514057.33 -514986.07 3134.3501 27643.279 465.87942 1.4891047
|
||||
520 35.938482 2432.2066 2375.3401 318.8785 56.866542 460.28751 838.60926 229.00792 0 -579.13212 514093.74 -514985.64 468.2133 27732.471 454.76753 1.3789356
|
||||
540 37.265891 2328.8169 2275.0595 305.41629 53.757389 473.08203 875.54175 220.60944 0 -604.11384 514075.79 -514987.16 2632.7788 27804.408 435.55773 1.3457265
|
||||
560 38.585909 2228.615 2278.3234 305.85446 -49.708475 455.58479 820.87878 215.10334 0 -604.72924 514052.45 -514989 3784.1482 27875.141 436.2741 1.1341618
|
||||
580 39.864162 2134.4158 2127.9962 285.67372 6.4195621 480.68268 836.80009 219.13915 0 -563.30768 514019.28 -514986.18 1359.5813 27951.068 407.46382 1.1159366
|
||||
600 41.132397 2048.4786 2102.9549 282.31205 -54.476369 486.301 796.4297 225.04029 0 -574.89865 514003.04 -514990.39 -91.415091 28017.963 402.69767 1.0358319
|
||||
620 42.405012 1967.4398 2048.4364 274.99318 -80.996617 477.38045 786.20744 223.98682 0 -570.14553 513997.93 -514996.35 1828.8595 28070.312 392.2521 1.022392
|
||||
640 43.643353 1888.1318 1981.566 266.01614 -93.434276 482.74658 801.17689 222.6863 0 -557.43781 513952.32 -514994.92 3812.5364 28123.574 379.47296 0.92888928
|
||||
660 44.915581 1813.0614 1959.0105 262.98817 -145.94913 498.25019 750.64037 217.17325 0 -556.66234 513938.55 -514993.9 1151.2432 28187.531 375.17108 0.87739869
|
||||
680 46.131009 1744.832 1911.6741 256.63347 -166.84215 497.042 725.1867 211.01897 0 -553.89849 513944.3 -514990.49 108.93436 28245.999 366.12859 0.80270448
|
||||
700 47.378681 1678.1626 1915.3894 257.13223 -237.22675 490.51486 719.69339 202.0347 0 -569.53306 513909.13 -514989.07 2213.2126 28294.676 366.86703 0.7415387
|
||||
720 48.690897 1612.159 1862.0857 249.97645 -249.92665 500.42275 728.44427 190.27551 0 -551.64449 513871.72 -514989.15 3052.5203 28347.921 356.64837 0.74199709
|
||||
740 49.934569 1549.9154 1792.3586 240.61591 -242.44316 497.29161 738.6029 175.53735 0 -547.70029 513880.64 -514986.81 738.07583 28409.346 343.29748 0.7047584
|
||||
760 51.094031 1493.142 1799.8956 241.62772 -306.75355 503.57846 709.28495 169.315 0 -559.17689 513862.16 -514991.92 -783.63021 28463.359 344.75885 0.66625263
|
||||
780 52.252971 1437.0347 1824.9884 244.99631 -387.95371 510.42774 661.31982 170.22096 0 -556.6031 513818.26 -514991.58 1267.2418 28503.342 349.56302 0.68065177
|
||||
800 53.379442 1382.5833 1736.7991 233.1573 -354.21576 514.27927 697.39594 172.11416 0 -554.93314 513805.74 -514988.82 1744.7887 28543.483 332.6636 0.66505935
|
||||
820 54.535354 1332.0444 1690.9869 227.00722 -358.94246 509.37721 686.56084 172.95747 0 -552.9503 513815.42 -514990.31 -146.04973 28586.706 323.91193 0.59356881
|
||||
840 55.662329 1285.5292 1685.7755 226.30763 -400.2463 507.19453 662.75433 170.55434 0 -559.51859 513807.26 -514988.49 -690.17907 28621.308 322.91069 0.59874377
|
||||
860 56.818479 1239.7941 1704.701 228.84829 -464.90694 495.88426 658.89439 170.35 0 -574.82793 513772.87 -514988.08 747.19844 28645.708 326.53594 0.60530564
|
||||
880 57.943864 1195.2063 1673.557 224.66734 -478.35068 498.99876 648.88199 170.51747 0 -557.50857 513743.81 -514983.05 1172.7738 28670.551 320.58027 0.57096305
|
||||
900 59.0976 1153.211 1639.9315 220.15327 -486.72046 502.47627 643.51354 178.69816 0 -556.38628 513730.32 -514985.34 -511.45034 28697.8 314.13849 0.56088797
|
||||
920 60.220959 1114.1597 1616.0109 216.94205 -501.85117 514.79499 630.19604 179.36393 0 -549.5453 513714.55 -514991.21 -1422.3991 28716.8 309.54311 0.58363424
|
||||
940 61.375362 1076.2186 1627.0408 218.42275 -550.82218 512.57892 621.31041 171.65194 0 -553.00757 513686.04 -514989.39 298.61672 28723.941 311.6754 0.54200743
|
||||
960 62.499341 1040.0389 1613.5611 216.61317 -573.52223 511.50602 601.98148 170.02159 0 -546.21393 513682.82 -514993.64 795.9161 28731.421 309.07527 0.57946382
|
||||
980 63.655075 1005.556 1568.0264 210.50035 -562.47043 514.81982 629.32987 175.28567 0 -544.55487 513654.62 -514991.97 -1246.9263 28741.462 300.35589 0.55675479
|
||||
1000 64.806202 973.43261 1565.2247 210.12423 -591.79208 505.29272 600.76239 165.17131 0 -554.93533 513685.36 -514993.44 -1299.5982 28742.028 299.81847 0.55749205
|
||||
1020 65.904504 942.29451 1571.0425 210.90525 -628.74802 506.25414 614.54444 152.41332 0 -569.19989 513660.6 -514993.36 -197.56562 28733.474 300.93111 0.56370125
|
||||
1040 67.002294 912.00673 1595.282 214.15928 -683.27525 489.63949 569.70488 159.39981 0 -590.61096 513680.38 -514991.79 467.80409 28724.916 305.58073 0.55701412
|
||||
1060 68.131496 883.21094 1542.2424 207.03896 -659.03142 503.00762 589.40955 165.92561 0 -599.75208 513674.64 -514992.26 -2147.8302 28718.434 295.39729 0.59345978
|
||||
1080 69.232333 856.19557 1533.4133 205.85369 -677.21769 507.87992 576.5184 168.18594 0 -578.48413 513634.34 -514985.66 -1762.0347 28699.147 293.70385 0.59551254
|
||||
1100 70.364775 831.37376 1484.1452 199.23968 -652.77147 514.07523 608.66719 163.10107 0 -567.48676 513613.52 -514984.65 33.310994 28670.682 284.25195 0.61206838
|
||||
1120 71.467535 808.52739 1521.0421 204.19292 -712.51473 513.69276 561.64386 163.23813 0 -559.45919 513591.61 -514983.24 -310.61111 28645.19 291.32265 0.61797603
|
||||
1140 72.601129 786.87835 1489.4671 199.95412 -702.58878 523.98829 584.70722 162.29577 0 -549.08561 513559.92 -514984.41 -1685.4255 28620.437 285.26086 0.63846185
|
||||
1160 73.705792 766.63847 1508.1762 202.46573 -741.53775 514.32182 584.88936 152.54558 0 -535.15913 513525.59 -514983.73 -1902.1776 28587.352 288.83351 0.67096701
|
||||
1180 74.841457 749.02843 1510.9898 202.84344 -761.96133 536.04857 571.2202 147.21017 0 -519.34217 513485.23 -514982.33 867.83936 28547.617 289.35403 0.71492747
|
||||
1200 75.948637 733.34578 1503.6833 201.86257 -770.33748 533.86604 589.40444 152.04389 0 -519.58392 513457.87 -514983.94 16.285861 28517.381 287.94489 0.73468233
|
||||
1220 77.086539 718.25616 1498.0744 201.1096 -779.81819 559.89022 564.22113 156.14265 0 -507.10566 513432.51 -514985.47 -1279.2454 28491.203 286.86449 0.74672427
|
||||
1240 78.196455 704.4456 1488.8421 199.87022 -784.3965 566.03391 579.8182 161.3278 0 -468.50406 513361.56 -514984.64 -54.414997 28461.145 285.0822 0.7757678
|
||||
1260 79.336046 693.03071 1494.0932 200.57516 -801.06253 573.59408 573.29809 158.50778 0 -453.3769 513333.73 -514986.81 977.78497 28434.874 286.06644 0.82806578
|
||||
1280 80.450187 683.34372 1478.8974 198.53519 -795.55372 580.51573 596.90975 153.51449 0 -437.44107 513297.84 -514986.89 809.72996 28418.785 283.14058 0.85789606
|
||||
1300 81.562086 675.21003 1490.4096 200.08064 -815.19955 586.94949 575.877 144.63393 0 -412.94901 513274.99 -514984.7 -448.50658 28409.979 285.3107 0.94374006
|
||||
1320 82.704837 668.21879 1489.4584 199.95295 -821.23962 576.22292 605.97557 140.59647 0 -423.93742 513262.85 -514982.94 -41.054413 28400.286 285.13719 0.9231239
|
||||
1340 83.820401 662.582 1506.0415 202.17916 -843.45952 580.69502 578.24319 144.89986 0 -430.94868 513260.2 -514976.55 977.60126 28392.044 288.28069 1.0060194
|
||||
1360 84.965785 658.24059 1527.9683 205.12273 -869.7277 577.91541 570.19843 152.39114 0 -451.12207 513259.47 -514978.58 371.63239 28390.774 292.47304 1.0318294
|
||||
1380 86.080907 654.92452 1486.6437 199.57509 -831.71915 580.08964 585.152 157.63831 0 -437.00747 513263.59 -514981.18 -247.9673 28392.439 284.5256 1.0911219
|
||||
1400 87.195704 652.93764 1510.6586 202.79899 -857.721 568.92903 573.37125 151.89337 0 -426.43036 513257.39 -514982.88 -51.617883 28392.618 289.11402 1.1268379
|
||||
1420 88.34689 651.93794 1494.4977 200.62946 -842.55979 571.38046 600.63765 145.50987 0 -443.12588 513270.14 -514987.1 743.13616 28392.861 285.98783 1.1924311
|
||||
1440 89.493044 651.84231 1520.3977 204.10641 -868.55537 569.30886 591.50444 144.87083 0 -452.53315 513268.23 -514989.93 461.56063 28397.854 290.94803 1.2038182
|
||||
1460 90.608597 652.79726 1538.7134 206.56522 -885.91619 576.98896 569.0177 144.49629 0 -461.96923 513277.97 -514992.42 -706.12558 28404.942 294.4277 1.2773313
|
||||
1480 91.757208 654.35279 1560.3813 209.47403 -906.02856 573.31257 551.02062 151.79154 0 -471.83285 513285.31 -514995.63 -636.13512 28406.735 298.57005 1.3040147
|
||||
1500 92.886091 656.18474 1535.2238 206.09675 -879.03909 565.77757 581.30733 155.02848 0 -493.04533 513302.18 -514990.29 143.11549 28404.04 293.73748 1.3269254
|
||||
1520 94.042872 658.68485 1540.4536 206.79882 -881.76871 562.4227 566.55678 153.51217 0 -481.25224 513306.12 -514989.13 320.11741 28402.365 294.71422 1.3871403
|
||||
1540 95.163877 662.00561 1525.2953 204.7639 -863.28974 547.96338 591.50659 150.34534 0 -461.18073 513297.4 -514989.32 -131.34055 28402.834 291.79671 1.4143192
|
||||
1560 96.312922 666.1124 1506.6675 202.2632 -840.55513 559.7266 593.99441 157.20165 0 -475.77029 513317.32 -514993.02 -361.762 28402.279 288.23662 1.3888658
|
||||
1580 97.430754 670.56531 1535.7659 206.16953 -865.20063 562.32491 577.33497 164.90914 0 -495.18787 513321.56 -514996.14 281.32907 28399.686 293.815 1.3885206
|
||||
1600 98.548553 676.03467 1559.0361 209.29344 -883.00142 570.63265 568.63747 171.76131 0 -497.53636 513299.62 -514996.12 -83.071675 28398.615 298.25471 1.4380743
|
||||
1620 99.69614 681.61565 1551.6098 208.29649 -869.99417 572.80627 589.25676 175.66645 0 -486.29635 513275.79 -514997.22 -1208.1908 28396.28 296.81124 1.4843702
|
||||
1640 100.81368 687.56466 1565.2232 210.12403 -877.65855 578.7743 586.81939 173.9181 0 -490.97778 513266.56 -514992.76 -587.86248 28386.365 299.44244 1.4342399
|
||||
1660 101.96336 693.76095 1558.3222 209.1976 -864.56124 583.58497 605.24119 171.44101 0 -488.52963 513255.46 -514991.76 335.92415 28373.356 298.0981 1.4841753
|
||||
1680 103.08285 699.76249 1608.1314 215.88426 -908.36892 585.35458 590.64567 171.79357 0 -478.93732 513211.41 -514988.64 91.212095 28363.527 307.67509 1.4177962
|
||||
1700 104.23343 705.16423 1586.5697 212.9897 -881.40546 609.44211 582.01973 172.76356 0 -457.12517 513197.39 -514985.89 -662.76266 28354.912 303.56619 1.3605633
|
||||
1720 105.38429 709.98606 1609.0843 216.01219 -899.09829 612.02708 597.82638 167.68834 0 -444.72348 513153.41 -514985.33 -92.038463 28343.124 307.84128 1.4562833
|
||||
1740 106.50511 714.51622 1579.8945 212.09359 -865.37833 624.49924 619.60972 166.03466 0 -425.9731 513136.37 -514985.92 1173.1099 28332.574 302.27863 1.3790325
|
||||
1760 107.65668 718.07347 1624.056 218.02206 -905.9825 608.96798 597.96224 154.72096 0 -409.37211 513132.37 -514990.63 786.32681 28330.712 310.74964 1.3669913
|
||||
1780 108.77729 720.46707 1606.3817 215.64937 -885.91465 639.71765 615.06161 152.57928 0 -394.48439 513088.38 -514987.17 -271.86201 28334.236 307.3761 1.3327989
|
||||
1800 109.92899 721.98649 1608.1038 215.88055 -886.11732 621.68949 602.68633 163.61329 0 -397.09967 513111.57 -514988.58 587.45646 28336.693 307.73281 1.2707867
|
||||
1820 111.05093 722.92155 1567.2948 210.40212 -844.3732 657.9717 609.80843 174.58395 0 -387.74403 513087.19 -514986.18 1657.5204 28343.522 299.9292 1.2250789
|
||||
1840 112.17289 723.61458 1561.6308 209.64177 -838.01626 621.38222 638.008 181.56394 0 -392.76804 513100.91 -514987.12 951.04423 28360.92 298.8574 1.192447
|
||||
1860 113.32517 724.57888 1559.5079 209.35678 -834.92903 648.61916 621.88348 182.62731 0 -413.59874 513115.13 -514989.59 -474.05956 28382.975 298.4495 1.1946089
|
||||
1880 114.44655 725.74322 1588.6378 213.26733 -862.89459 616.10137 598.6142 185.03327 0 -431.03949 513153.5 -514985.11 326.23753 28401.004 304.06324 1.1258592
|
||||
1900 115.60092 726.63642 1552.6045 208.43002 -825.96805 615.20719 632.90186 175.31959 0 -439.29325 513177.07 -514987.17 1080.7061 28419.738 297.15171 1.1348451
|
||||
1920 116.72882 727.57597 1579.3221 212.01674 -851.74611 606.50987 618.17792 169.75157 0 -442.63284 513179.83 -514983.38 -43.794187 28443.345 302.3028 1.0665772
|
||||
1940 117.88137 728.52961 1573.1141 211.18335 -844.58454 624.72383 626.3057 166.98593 0 -453.41808 513175.12 -514984.3 -900.58801 28464.403 301.13166 1.0223996
|
||||
1960 119.003 728.94698 1626.2629 218.31833 -897.31596 599.28223 602.89095 166.05528 0 -470.08979 513190.07 -514985.52 -260.33773 28477.732 311.33029 0.99933978
|
||||
1980 120.15553 728.20483 1628.3695 218.60113 -900.16467 612.33461 601.10447 163.81406 0 -448.48915 513155.61 -514984.54 821.49207 28488.285 311.74795 0.96708127
|
||||
2000 121.27853 726.32991 1617.7225 217.17182 -891.39259 608.69121 604.99032 169.22497 0 -445.16887 513154.27 -514983.4 -472.67394 28502.073 309.74198 0.88520672
|
||||
Loop time of 121.279 on 1 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 55.4018 (45.6815)
|
||||
Bond time (%) = 7.86978 (6.48901)
|
||||
Kspce time (%) = 13.9231 (11.4803)
|
||||
Neigh time (%) = 2.17099 (1.79008)
|
||||
Comm time (%) = 0.43024 (0.354754)
|
||||
Outpt time (%) = 0.0126977 (0.0104699)
|
||||
Other time (%) = 41.4699 (34.194)
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10468 ave 10468 max 10468 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 662422 ave 662422 max 662422 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 662422
|
||||
Ave neighs/atom = 220.807
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 63
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,263 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
read_data data.ethanol
|
||||
orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
scanning bonds ...
|
||||
5 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2750 bonds
|
||||
reading angles ...
|
||||
3250 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
11 = max # of special neighbors
|
||||
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
|
||||
pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
|
||||
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH
|
||||
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH
|
||||
pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO
|
||||
pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO
|
||||
pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
|
||||
pair_coeff 1 1 thole 2.051000
|
||||
pair_coeff 1 2 thole 1.580265
|
||||
pair_coeff 1 4 thole 1.416087
|
||||
pair_coeff 1 6 thole 2.051000
|
||||
pair_coeff 1 7 thole 1.580265
|
||||
pair_coeff 1 8 thole 1.416087
|
||||
pair_coeff 2 2 thole 1.217570
|
||||
pair_coeff 2 4 thole 1.091074
|
||||
pair_coeff 2 6 thole 1.580265
|
||||
pair_coeff 2 7 thole 1.217570
|
||||
pair_coeff 2 8 thole 1.091074
|
||||
pair_coeff 4 4 thole 0.977720
|
||||
pair_coeff 4 6 thole 1.416087
|
||||
pair_coeff 4 7 thole 1.091074
|
||||
pair_coeff 4 8 thole 0.977720
|
||||
pair_coeff 6 6 thole 2.051000
|
||||
pair_coeff 6 7 thole 1.580265
|
||||
pair_coeff 6 8 thole 1.416087
|
||||
pair_coeff 7 7 thole 1.217570
|
||||
pair_coeff 7 8 thole 1.091074
|
||||
pair_coeff 8 8 thole 0.977720
|
||||
|
||||
group gETHANOL molecule 1:250
|
||||
3000 atoms in group gETHANOL
|
||||
group gATOMS type 1 2 3 4 5
|
||||
2250 atoms in group gATOMS
|
||||
group gDRUDES type 6 7 8
|
||||
750 atoms in group gDRUDES
|
||||
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
variable vTEMP equal 300.0
|
||||
variable vTEMP_D equal 1.0
|
||||
variable vPRESS equal 1.0
|
||||
|
||||
velocity gATOMS create ${vTEMP} 12345
|
||||
velocity gATOMS create 300 12345
|
||||
velocity gDRUDES create ${vTEMP_D} 12345
|
||||
velocity gDRUDES create 1 12345
|
||||
|
||||
fix fDRUDE all drude C C N C N D D D
|
||||
|
||||
fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
|
||||
250 = # of size 2 clusters
|
||||
250 = # of size 3 clusters
|
||||
250 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
|
||||
comm_modify vel yes
|
||||
compute cTEMP_ATOM gATOMS temp
|
||||
compute cTEMP all temp/drude
|
||||
|
||||
fix fDTDIR all drude/transform/direct
|
||||
fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500
|
||||
fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500
|
||||
fix_modify fNPT temp cTEMP_ATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349)
|
||||
fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0
|
||||
fix fNVT gDRUDES nvt temp 1 1 100.0
|
||||
fix fDTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
|
||||
thermo 20
|
||||
|
||||
timestep 0.5
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.379738
|
||||
grid = 30 30 30
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0289979
|
||||
estimated relative force accuracy = 8.73262e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 17908 7200
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 11
|
||||
New max number of 1-2 to 1-4 neighbors: 11 (+0)
|
||||
Neighbor list info ...
|
||||
2 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 10
|
||||
Memory usage per processor = 13.7041 Mbytes
|
||||
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2]
|
||||
0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301
|
||||
20 0.48582006 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565
|
||||
40 0.99611902 9812.3727 6009.1747 806.70411 3803.198 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0177 221.56359
|
||||
60 1.4878449 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.611 23440.966 1050.9011 133.14424
|
||||
80 1.9926319 8115.7842 5997.9225 805.19356 2117.8617 901.84105 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.95 23834.833 1111.65 89.05492
|
||||
100 2.476769 7496.2555 5770.3833 774.64747 1725.8722 829.63908 1420.6659 325.4016 0 62.343573 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498473
|
||||
120 2.9719281 6986.5933 5396.9479 724.51547 1589.6454 678.24993 1535.5197 325.88462 0 -9.6649715 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715633
|
||||
140 3.4472849 6549.0004 5126.6341 688.22709 1422.3663 724.95473 1477.7714 315.11964 0 -99.456489 513960.58 -514956.6 19747.305 24877.008 969.51239 30.977084
|
||||
160 3.8980451 6131.3313 5000.4421 671.2864 1130.8892 703.24856 1302.1192 314.93994 0 -258.4539 514042.28 -514973.25 23050.008 25142.654 948.73049 23.021804
|
||||
180 4.3219371 5749.9765 4700.9451 631.0803 1049.0314 674.94524 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.484 25400.048 893.75892 17.322075
|
||||
200 4.740237 5429.6012 4392.5738 589.68286 1037.0274 612.00109 1296.2432 303.16019 0 -300.38659 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486
|
||||
220 5.15255 5133.8314 4290.7369 576.01173 843.09448 572.5199 1261.8055 289.99074 0 -383.71584 514078.3 -514975.81 12509.825 25814.229 817.78562 11.104636
|
||||
240 5.5619049 4850.3859 4120.3634 553.13987 730.0225 553.79223 1263.6533 278.92141 0 -487.76524 514091.35 -514969.93 10891.878 25996.167 785.87197 9.3607763
|
||||
260 5.9694359 4583.988 3911.0361 525.03865 672.95183 541.52258 1175.1553 273.43363 0 -475.23639 514139.68 -514981.61 8086.1508 26168.96 746.55574 7.4653781
|
||||
280 6.3831999 4349.2238 3692.2792 495.67153 656.94461 598.81909 1148.0997 278.87809 0 -444.09603 514045.38 -514970.13 5124.6371 26323.056 705.04252 6.4783461
|
||||
300 6.8002019 4128.9011 3579.5067 480.53234 549.39444 584.0659 1089.513 267.69426 0 -456.87099 514043.55 -514978.56 8350.7748 26456.831 683.94371 5.2650989
|
||||
320 7.2020841 3913.7715 3456.9151 464.07498 456.85644 556.31985 1103.3901 263.8886 0 -485.54294 514000.27 -514981.47 9117.645 26592.844 660.74075 4.5694128
|
||||
340 7.614501 3712.7165 3258.4132 437.42702 454.30329 533.72422 1069.0449 271.85681 0 -454.53938 514001.97 -514967.75 7187.6789 26736.819 622.98237 3.8812925
|
||||
360 8.0251679 3533.3831 3024.1004 405.97159 509.28269 522.55432 1104.3208 276.30864 0 -456.06652 514036.53 -514974.36 4554.9866 26876.658 578.3118 3.3031414
|
||||
380 8.4368989 3367.1791 2971.2717 398.87959 395.90735 508.27248 1059.2247 257.85692 0 -499.68504 514032.55 -514962.31 5645.8885 27002.069 568.38697 2.8305185
|
||||
400 8.841274 3204.9102 2874.2407 385.85361 330.66952 543.884 1018.8809 231.07032 0 -519.33317 514029.07 -514972.9 7250.7314 27123.905 549.89185 2.58326
|
||||
420 9.2528131 3050.6946 2776.6047 372.74643 274.08991 517.42853 953.07588 226.06762 0 -505.60561 514057.02 -514973.9 4026.258 27250.314 531.28072 2.3360857
|
||||
440 9.6643951 2916.2842 2640.2367 354.43965 276.04748 507.06285 983.97334 236.01271 0 -534.64347 514059.65 -514976.01 1708.7076 27364.195 505.24986 2.0765971
|
||||
460 10.070477 2787.525 2609.5902 350.3255 177.93484 485.64382 933.57906 234.95019 0 -560.61753 514069.83 -514985.45 3400.5283 27458.081 499.48921 1.8097272
|
||||
480 10.475857 2662.4983 2514.1778 337.51682 148.3205 464.67048 928.2622 239.37954 0 -570.38391 514070.86 -514984.47 5084.8137 27547.559 481.26939 1.6441432
|
||||
500 10.904204 2540.5544 2433.5504 326.69297 107.00399 473.29419 888.73276 239.40578 0 -565.68691 514057.33 -514986.07 3134.3575 27643.279 465.87938 1.4891037
|
||||
520 11.343421 2432.2068 2375.3395 318.87842 56.867315 460.28707 838.60936 229.00812 0 -579.13202 514093.74 -514985.64 468.2212 27732.471 454.76741 1.3789343
|
||||
540 11.792302 2328.8171 2275.0598 305.41633 53.757301 473.0817 875.54202 220.60952 0 -604.11383 514075.79 -514987.16 2632.7729 27804.408 435.55777 1.3457292
|
||||
560 12.22888 2228.6146 2278.324 305.85454 -49.709377 455.5848 820.87873 215.10398 0 -604.72916 514052.45 -514989 3784.1433 27875.141 436.27421 1.1341637
|
||||
580 12.654423 2134.4153 2127.9966 285.67378 6.418699 480.68271 836.79983 219.13997 0 -563.30761 514019.28 -514986.18 1359.5795 27951.068 407.46389 1.1159357
|
||||
600 13.083667 2048.478 2102.9555 282.31212 -54.477504 486.30135 796.43014 225.04094 0 -574.89912 514003.04 -514990.39 -91.420338 28017.963 402.69778 1.0358317
|
||||
620 13.5203 1967.44 2048.4369 274.99325 -80.99691 477.38009 786.20772 223.98767 0 -570.14552 513997.92 -514996.35 1828.852 28070.312 392.2522 1.022388
|
||||
640 13.946543 1888.1309 1981.5653 266.01604 -93.434406 482.74621 801.17707 222.68721 0 -557.43764 513952.32 -514994.92 3812.5405 28123.574 379.47281 0.92888841
|
||||
660 14.383896 1813.0614 1959.0076 262.98777 -145.94621 498.24936 750.64093 217.17501 0 -556.66175 513938.55 -514993.9 1151.2704 28187.531 375.17051 0.8773937
|
||||
680 14.80455 1744.8321 1911.6727 256.63328 -166.84059 497.04089 725.18698 211.02114 0 -553.89822 513944.3 -514990.49 108.9445 28245.999 366.1283 0.80270876
|
||||
700 15.246875 1678.1628 1915.389 257.13218 -237.22624 490.51443 719.69473 202.03683 0 -569.53274 513909.13 -514989.07 2213.2168 28294.676 366.86695 0.74153849
|
||||
720 15.683303 1612.159 1862.0857 249.97646 -249.9267 500.42186 728.44302 190.2785 0 -551.64436 513871.73 -514989.15 3052.5153 28347.921 356.64838 0.74199104
|
||||
740 16.103407 1549.912 1792.3564 240.61562 -242.44438 497.29156 738.60345 175.54129 0 -547.7015 513880.63 -514986.81 737.97658 28409.346 343.29706 0.70477013
|
||||
760 16.533572 1493.1418 1799.8951 241.62766 -306.75333 503.57865 709.28516 169.31508 0 -559.17797 513862.16 -514991.92 -783.64904 28463.359 344.75876 0.66625709
|
||||
780 16.963103 1437.0356 1824.9946 244.99715 -387.959 510.43018 661.31998 170.2197 0 -556.60498 513818.25 -514991.58 1267.2099 28503.341 349.56422 0.68065257
|
||||
800 17.384911 1382.5837 1736.8044 233.15801 -354.22065 514.28158 697.39733 172.11237 0 -554.93413 513805.74 -514988.82 1744.7575 28543.482 332.66462 0.66506284
|
||||
820 17.818295 1332.0449 1690.9863 227.00714 -358.94137 509.37962 686.56323 172.95557 0 -552.94994 513815.42 -514990.31 -146.04099 28586.704 323.91181 0.59356692
|
||||
840 18.239769 1285.5293 1685.7656 226.30629 -400.23625 507.19659 662.75791 170.55111 0 -559.5183 513807.26 -514988.49 -690.12588 28621.306 322.90879 0.59871543
|
||||
860 18.672279 1239.7943 1704.6913 228.84697 -464.89697 495.88249 658.89516 170.34465 0 -574.82534 513772.88 -514988.07 747.30519 28645.706 326.53407 0.60529545
|
||||
880 19.094243 1195.2074 1673.5516 224.66662 -478.34417 498.99767 648.88222 170.51909 0 -557.50585 513743.81 -514983.05 1172.8191 28670.55 320.57923 0.57095732
|
||||
900 19.530344 1153.213 1639.9317 220.1533 -486.71872 502.48114 643.51414 178.70544 0 -556.38218 513730.3 -514985.34 -511.40662 28697.799 314.13852 0.56091919
|
||||
920 19.954644 1114.1622 1615.9735 216.93702 -501.81127 514.7973 630.19712 179.3982 0 -549.54237 513714.55 -514991.21 -1422.316 28716.8 309.53594 0.58362776
|
||||
940 20.390261 1076.2212 1626.9734 218.41371 -550.75226 512.58732 621.31396 171.70796 0 -553.00677 513686.03 -514989.39 298.59388 28723.942 311.66248 0.54203006
|
||||
960 20.813949 1040.0451 1613.5266 216.60854 -573.48149 511.51922 601.98585 170.02867 0 -546.21382 513682.83 -514993.63 795.90454 28731.424 309.06864 0.57947773
|
||||
980 21.252467 1005.5683 1568.0671 210.50581 -562.49882 514.83412 629.32638 175.23649 0 -544.55558 513654.63 -514991.97 -1246.8402 28741.467 300.36369 0.55676445
|
||||
1000 21.687328 973.43654 1565.2947 210.13362 -591.85814 505.31069 600.76156 165.13032 0 -554.93709 513685.33 -514993.45 -1299.6769 28742.033 299.8319 0.55747244
|
||||
1020 22.104826 942.30585 1571.1252 210.91634 -628.81931 506.25625 614.52982 152.39206 0 -569.20109 513660.58 -514993.37 -197.40138 28733.481 300.94692 0.5637722
|
||||
1040 22.524452 912.01118 1595.3373 214.16671 -683.32616 489.65166 569.71087 159.37841 0 -590.61264 513680.34 -514991.8 467.8096 28724.925 305.59134 0.55703469
|
||||
1060 22.949422 883.20635 1542.2363 207.03814 -659.02996 503.02658 589.43979 165.92415 0 -599.75711 513674.6 -514992.27 -2148.0784 28718.444 295.39616 0.59339691
|
||||
1080 23.371693 856.19688 1533.476 205.86212 -677.27914 507.92146 576.49892 168.14482 0 -578.48635 513634.3 -514985.66 -1762.3643 28699.157 293.71591 0.59543987
|
||||
1100 23.796874 831.36718 1484.0494 199.22681 -652.68218 514.09435 608.64804 163.13622 0 -567.49464 513613.56 -514984.63 33.441222 28670.69 284.23352 0.61219688
|
||||
1120 24.215957 808.52756 1520.8457 204.16656 -712.31817 513.70662 561.61909 163.36198 0 -559.46566 513591.68 -514983.22 -310.69178 28645.197 291.28494 0.61812087
|
||||
1140 24.641242 786.87445 1489.3947 199.9444 -702.52028 523.97711 584.65081 162.32286 0 -549.07998 513560 -514984.39 -1685.574 28620.442 285.24697 0.63849523
|
||||
1160 25.055568 766.64827 1508.2693 202.47822 -741.62101 514.35266 584.91055 152.45332 0 -535.165 513525.54 -514983.72 -1901.0493 28587.357 288.85135 0.67096559
|
||||
1180 25.482658 749.02928 1511.1172 202.86054 -762.08788 536.05747 571.22043 147.19144 0 -519.37083 513485.14 -514982.32 866.88063 28547.627 289.37844 0.71496578
|
||||
1200 25.894749 733.35099 1503.6268 201.85499 -770.27581 533.87098 589.37041 152.16808 0 -519.57804 513457.84 -514983.94 14.805399 28517.39 287.93411 0.73458768
|
||||
1220 26.325628 718.27504 1498.0867 201.11126 -779.81165 559.91487 564.18647 156.27378 0 -507.13199 513432.42 -514985.48 -1279.1075 28491.202 286.86673 0.74700594
|
||||
1240 26.738918 704.4507 1488.7649 199.85985 -784.31417 566.05166 579.79847 161.35046 0 -468.44357 513361.55 -514984.62 -53.3159 28461.135 285.06732 0.77592838
|
||||
1260 27.171522 693.03769 1494.1149 200.57807 -801.07721 573.62194 573.3094 158.43371 0 -453.27917 513333.62 -514986.78 977.9179 28434.863 286.07064 0.82794452
|
||||
1280 27.586875 683.35215 1479.0049 198.54962 -795.65277 580.54264 596.95031 153.53994 0 -437.44286 513297.62 -514986.86 808.24663 28418.774 283.16101 0.85830865
|
||||
1300 28.005456 675.21985 1490.3973 200.079 -815.1775 586.97926 575.85031 144.74048 0 -412.9591 513274.88 -514984.67 -448.16581 28409.96 285.30833 0.9437975
|
||||
1320 28.436763 668.22782 1489.1302 199.90889 -820.90236 576.19343 605.89694 140.779 0 -423.95547 513263.1 -514982.91 -40.766531 28400.261 285.0744 0.92283057
|
||||
1340 28.854671 662.60827 1506.0283 202.17738 -843.42002 580.70797 578.1842 144.8341 0 -430.96333 513260.37 -514976.56 977.60336 28392.015 288.27815 1.0060347
|
||||
1360 29.284718 658.23752 1527.6526 205.08035 -869.41511 577.91716 570.16602 152.14574 0 -451.11548 513260.04 -514978.56 374.82603 28390.744 292.41271 1.031412
|
||||
1380 29.707547 654.96847 1486.4979 199.55551 -831.52939 580.08595 585.05597 157.33942 0 -437.07207 513264.24 -514981.18 -245.84993 28392.431 284.49746 1.0915693
|
||||
1400 30.132399 652.9829 1510.7519 202.81151 -857.76902 568.8718 573.40304 151.53282 0 -426.40132 513257.71 -514982.89 -48.059208 28392.645 289.13172 1.1272637
|
||||
1420 30.56509 652.00089 1494.6519 200.65015 -842.65097 571.38637 600.46686 145.25854 0 -443.09809 513270.44 -514987.1 744.84418 28392.941 286.01743 1.1922923
|
||||
1440 30.993519 651.93656 1520.3356 204.09807 -868.39904 569.20772 591.53184 144.73613 0 -452.45231 513268.58 -514990 462.47894 28397.996 290.93612 1.2038241
|
||||
1460 31.413554 652.8797 1538.7905 206.57555 -885.91076 576.968 569.3361 144.29397 0 -461.95958 513278 -514992.55 -703.88926 28405.143 294.44272 1.2767432
|
||||
1480 31.854234 654.43984 1560.998 209.55681 -906.55813 573.32119 550.83703 151.55603 0 -471.87704 513285.3 -514995.69 -634.5939 28407.003 298.6883 1.3039308
|
||||
1500 32.258767 656.25668 1535.2085 206.0947 -878.95186 565.7821 581.34544 155.11099 0 -493.26681 513302.34 -514990.27 141.09795 28404.376 293.73526 1.3252685
|
||||
1520 32.667376 658.76245 1540.1255 206.75478 -881.36305 562.28162 566.2439 153.62339 0 -481.21787 513306.74 -514989.04 320.45957 28402.754 294.65144 1.3869014
|
||||
1540 33.067487 662.13708 1524.8473 204.70375 -862.71024 547.98628 591.76817 150.15973 0 -460.97843 513297.6 -514989.25 -130.86158 28403.27 291.71099 1.413931
|
||||
1560 33.480413 666.19858 1506.8716 202.29059 -840.67298 559.57219 594.04584 156.75269 0 -475.69342 513317.61 -514992.96 -357.4244 28402.761 288.27566 1.3890257
|
||||
1580 33.881172 670.71346 1535.3958 206.11984 -864.68236 562.04024 577.64202 164.82634 0 -495.24757 513322.21 -514996.15 278.58466 28400.233 293.74325 1.3903967
|
||||
1600 34.282713 676.13061 1559.338 209.33397 -883.20743 570.25038 568.59163 172.20015 0 -497.5923 513299.59 -514996.24 -86.394917 28399.201 298.31271 1.4378209
|
||||
1620 34.693053 681.80099 1552.6868 208.44108 -870.88582 572.69475 589.3952 176.11924 0 -485.89655 513274.18 -514997.38 -1204.2981 28396.883 297.01677 1.4865321
|
||||
1640 35.094327 687.72244 1565.9114 210.21642 -878.189 578.48421 587.25138 174.28163 0 -490.691 513265.29 -514992.8 -581.44816 28387.006 299.57429 1.4344443
|
||||
1660 35.50466 693.90688 1558.2867 209.19283 -864.37979 583.51938 605.39763 171.58103 0 -488.26355 513255.15 -514991.76 341.26177 28374.079 298.09208 1.4823162
|
||||
1680 35.905614 699.81947 1608.5571 215.9414 -908.73759 585.45342 590.42357 171.65094 0 -478.75081 513211.28 -514988.8 77.131096 28364.346 307.75695 1.4172031
|
||||
1700 36.320681 705.27021 1587.164 213.06948 -881.89376 609.44479 581.8672 172.3033 0 -457.17018 513197.71 -514986.05 -666.39751 28355.734 303.6806 1.3594258
|
||||
1720 36.728727 710.00906 1608.1379 215.88513 -898.12885 612.49125 598.01777 167.03198 0 -445.09105 513154.85 -514985.42 -87.720392 28343.913 307.66062 1.454487
|
||||
1740 37.130271 714.53567 1580.0753 212.11786 -865.53967 624.57295 619.34825 165.15138 0 -426.77348 513138.14 -514985.98 1176.8164 28333.357 302.31339 1.3787996
|
||||
1760 37.542675 718.03805 1624.8218 218.12487 -906.78379 608.77029 596.31671 153.7484 0 -409.62158 513134.59 -514990.59 800.3654 28331.535 310.89569 1.3688034
|
||||
1780 37.943518 720.37511 1609.0275 216.00455 -888.65236 640.15257 613.63079 151.83793 0 -394.53333 513087.34 -514987.08 -257.84624 28335.192 307.88341 1.3325434
|
||||
1800 38.353172 721.7956 1606.901 215.71908 -885.1054 621.86791 602.54827 163.37359 0 -396.5738 513111.86 -514988.19 600.83028 28337.874 307.50221 1.2708112
|
||||
1820 38.755103 722.6791 1563.6639 209.9147 -840.98481 658.28036 609.55302 175.97253 0 -386.62661 513087.76 -514985.92 1673.6509 28345.014 299.23272 1.2261086
|
||||
1840 39.156883 723.36526 1560.0643 209.43147 -836.69905 621.56238 639.2919 183.25684 0 -391.12333 513097.3 -514986.98 948.98786 28362.795 298.55837 1.1894608
|
||||
1860 39.568864 724.34062 1560.3485 209.46963 -836.00792 648.95076 621.00344 183.45409 0 -412.61997 513112.89 -514989.69 -494.41519 28385.176 298.60946 1.1973936
|
||||
1880 39.96934 725.55016 1589.2514 213.34971 -863.70126 617.1181 598.13412 185.78351 0 -430.81566 513151.32 -514985.25 301.61577 28403.364 304.1812 1.1250834
|
||||
1900 40.379241 726.4494 1555.4145 208.80726 -828.96513 616.25066 631.90687 175.77829 0 -439.44651 513173.5 -514986.96 1079.4893 28422.072 297.69125 1.1328664
|
||||
1920 40.778163 727.328 1577.4105 211.76012 -850.08251 606.30559 616.55697 170.46944 0 -442.17245 513181.84 -514983.08 4.4471417 28445.679 301.93699 1.065083
|
||||
1940 41.186491 728.19228 1574.1105 211.3171 -845.91818 625.03022 624.89302 167.86917 0 -451.74938 513172.29 -514984.25 -891.08022 28467.03 301.3211 1.026012
|
||||
1960 41.58233 728.61768 1624.4163 218.07043 -895.79862 599.93561 599.92993 167.38843 0 -465.99755 513188.14 -514985.2 -216.32489 28480.762 310.97645 0.99894847
|
||||
1980 41.996931 727.92162 1627.8345 218.52931 -899.91293 612.92861 601.82319 165.16403 0 -447.59836 513151.59 -514983.82 865.41931 28491.981 311.64212 0.97473559
|
||||
2000 42.398021 726.10625 1615.3704 216.85607 -889.26418 609.59944 604.55036 169.50136 0 -443.24252 513152.61 -514982.28 -436.06261 28506.736 309.2898 0.88821892
|
||||
Loop time of 42.3981 on 4 procs for 2000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 14.495 (34.1878)
|
||||
Bond time (%) = 2.06082 (4.86065)
|
||||
Kspce time (%) = 7.76109 (18.3053)
|
||||
Neigh time (%) = 0.634993 (1.49769)
|
||||
Comm time (%) = 1.07386 (2.53281)
|
||||
Outpt time (%) = 0.0100121 (0.0236145)
|
||||
Other time (%) = 16.3623 (38.5921)
|
||||
|
||||
Nlocal: 750 ave 774 max 711 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 5796.5 ave 5864 max 5731 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 165579 ave 169096 max 157793 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 662315
|
||||
Ave neighs/atom = 220.772
|
||||
Ave special neighs/atom = 10.5
|
||||
Neighbor list builds = 63
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,246 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
|
||||
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix NVE DRUDES nve
|
||||
|
||||
compute TEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 36.15 | 36.15 | 36.15 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 1.2941742 2882.4586 4527.8074 -1645.3488 561.72856 0 600.34616 155114.77 -157922.19 27167.701 14058.741 1013.3326 1438.6699 160.63128
|
||||
40 2.6812835 1331.3822 3348.9313 -2017.5492 681.52311 0 553.09465 154668.62 -157920.79 17925.928 14484.215 749.4977 1105.2032 36.587791
|
||||
60 4.0337768 297.35951 2604.4137 -2307.0542 583.99973 0 409.03992 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335647
|
||||
80 5.3483341 -374.31059 2263.3247 -2637.6353 534.80336 0 212.27979 154543.18 -157927.9 6155.9233 15645.855 506.53672 755.45209 7.6929097
|
||||
100 6.6217718 -905.58895 1911.7191 -2817.308 532.30402 0 87.570164 154497.48 -157934.66 2149.3102 16288.797 427.84665 639.27768 4.1289095
|
||||
120 7.8588221 -1233.6892 1675.0884 -2908.7776 544.76423 0 59.500422 154422.72 -157935.76 233.49801 16915.818 374.88821 560.54178 2.8313109
|
||||
140 8.9570706 -1463.4914 1468.7447 -2932.2361 539.69696 0 41.083518 154424.91 -157937.93 -1492.9875 17509.345 328.70809 491.66367 2.1395091
|
||||
160 10.032995 -1695.7544 1385.9606 -3081.7149 552.9156 0 30.022825 154274.72 -157939.37 -3010.5044 18061.925 310.18082 463.9681 1.9858861
|
||||
180 11.181687 -1818.1852 1253.1677 -3071.3529 559.57415 0 20.017285 154289.69 -157940.63 -3354.2207 18564.877 280.4615 419.5755 1.6725842
|
||||
200 12.212811 -1949.6488 1210.0648 -3159.7136 570.0554 0 16.320167 154195.04 -157941.13 -4117.951 19014.456 270.81499 405.06855 1.7662371
|
||||
220 13.224296 -2031.6068 1148.1459 -3179.7527 598.02848 0 30.832907 154127.13 -157935.75 -4514.6121 19406.767 256.95741 384.33718 1.6839577
|
||||
240 14.315843 -2118.6272 1120.0031 -3238.6303 613.29235 0 59.889003 154030.6 -157942.41 -4415.1885 19738.97 250.659 374.93927 1.5971322
|
||||
260 15.300218 -2203.4151 1065.8468 -3269.2619 614.19212 0 77.618884 153980.71 -157941.79 -4563.8872 20011.077 238.53871 356.80712 1.5248251
|
||||
280 16.273073 -2317.9388 1033.2702 -3351.2091 650.51355 0 126.14935 153811.62 -157939.49 -4722.8063 20224.149 231.248 345.84878 1.5839508
|
||||
300 17.240341 -2377.6039 992.48386 -3370.0878 688.02302 0 179.7828 153701.2 -157939.1 -4125.8573 20378.438 222.11992 332.08746 1.7406198
|
||||
320 18.20275 -2419.6151 1023.0261 -3442.6412 720.31006 0 227.7006 153549.39 -157940.04 -4083.286 20479.24 228.95535 342.33558 1.7369708
|
||||
340 19.161978 -2456.7614 1048.823 -3505.5844 754.12989 0 264.46876 153415.73 -157939.91 -3894.4573 20529.72 234.72874 351.04481 1.6271431
|
||||
360 20.2149 -2504.7183 1041.9917 -3546.71 785.42914 0 335.38633 153271.5 -157939.03 -3464.0342 20531.324 233.19988 348.66948 1.7942822
|
||||
380 21.17402 -2596.3611 1000.1227 -3596.4839 825.3161 0 390.15783 153129.43 -157941.39 -3357.8641 20490.649 223.82952 334.61582 1.8092697
|
||||
400 22.139238 -2666.6886 1006.4834 -3673.172 866.01231 0 422.49717 152978.53 -157940.22 -3329.7321 20411.001 225.25305 336.79329 1.7220591
|
||||
420 23.107117 -2676.0182 1036.9614 -3712.9796 909.17035 0 490.73558 152826 -157938.88 -2909.4385 20294.307 232.07409 346.93054 1.8970578
|
||||
440 24.079176 -2731.6451 1054.3541 -3785.9992 935.99044 0 530.99271 152684.71 -157937.69 -2566.5271 20147.069 235.96661 352.81301 1.8018782
|
||||
460 25.058476 -2808.7306 996.20963 -3804.9403 986.66566 0 582.2501 152565.84 -157939.7 -2490.6211 19973.642 222.95376 333.32458 1.7662208
|
||||
480 26.045001 -2862.5602 1012.8284 -3875.3886 1005.2147 0 610.1273 152450.46 -157941.19 -2032.2463 19777.578 226.67307 338.84478 1.876307
|
||||
500 27.043275 -2935.1165 989.42859 -3924.5451 1019.8833 0 633.91479 152362.53 -157940.87 -2210.2423 19561.788 221.43615 331.0551 1.7553824
|
||||
520 28.052607 -2989.5984 969.48801 -3959.0864 1057.825 0 655.88112 152268.64 -157941.44 -2303.725 19328.454 216.97341 324.39473 1.6968168
|
||||
540 29.169729 -3036.3745 1016.2059 -4052.5804 1091.3747 0 658.52433 152140.18 -157942.65 -2235.4034 19080.73 227.42896 340.04854 1.7349328
|
||||
560 30.202366 -3093.8922 946.57093 -4040.4631 1140.9835 0 764.01213 151997.25 -157942.71 -1159.9486 18819.788 211.84452 316.62558 1.85871
|
||||
580 31.245469 -3165.5156 988.32907 -4153.8446 1198.6661 0 795.79314 151795.81 -157944.12 -1299.7687 18555.467 221.19007 330.67963 1.7685771
|
||||
600 32.305233 -3193.4945 981.48315 -4174.9776 1207.1636 0 842.25251 151717.63 -157942.02 -845.49527 18290.083 219.65794 328.37122 1.7920774
|
||||
620 33.378728 -3254.0556 966.92094 -4220.9766 1219.0239 0 848.81235 151653.93 -157942.75 -633.10425 18027.72 216.39889 323.4395 1.8848743
|
||||
640 34.465769 -3267.9659 1003.5996 -4271.5655 1273.644 0 929.19275 151468.58 -157942.99 146.55456 17770.457 224.60765 335.70351 1.9667214
|
||||
660 35.565967 -3292.3649 1001.1012 -4293.4661 1299.7838 0 957.48532 151393.06 -157943.79 252.79622 17523.772 224.0485 334.86273 1.9719336
|
||||
680 36.678817 -3311.7859 1008.4763 -4320.2622 1356.4829 0 987.54908 151279.12 -157943.41 715.95691 17290.15 225.69907 337.35795 1.9299071
|
||||
700 37.804361 -3384.7539 970.95734 -4355.7113 1376.9176 0 1003.218 151209.28 -157945.12 602.03837 17070.444 217.30224 324.76399 1.9441468
|
||||
720 38.944631 -3389.983 1003.4282 -4393.4112 1388.0708 0 1009.042 151153.78 -157944.31 799.15462 16864.409 224.5693 335.74485 1.7690575
|
||||
740 40.095444 -3390.8892 1011.8969 -4402.786 1395.7801 0 1060.0508 151084.65 -157943.27 1475.2637 16672.377 226.4646 338.45322 2.034426
|
||||
760 41.257411 -3430.7027 1037.7609 -4468.4636 1415.8714 0 1069.0374 150989.87 -157943.24 1304.5866 16496.661 232.25301 347.18143 1.9316673
|
||||
780 42.432308 -3457.167 1031.0329 -4488.1999 1428.7433 0 1114.4772 150912.91 -157944.33 1885.5157 16338.236 230.74728 344.90463 1.9710957
|
||||
800 43.614638 -3510.8663 985.5619 -4496.4282 1454.853 0 1136.1159 150858.74 -157946.14 1646.2494 16199.542 220.57078 329.56096 2.1492639
|
||||
820 44.806214 -3561.3122 954.7588 -4516.071 1480.1009 0 1122.7071 150826.81 -157945.69 1635.0446 16080.49 213.67698 319.29136 2.0208705
|
||||
840 46.008772 -3574.3488 957.87693 -4532.2258 1470.2766 0 1075.5497 150865.51 -157943.56 1501.6257 15978.031 214.37482 320.32468 2.0463654
|
||||
860 47.215247 -3579.685 964.25763 -4543.9426 1434.0326 0 1038.1021 150929.67 -157945.75 1011.7367 15888.91 215.80284 322.50392 1.9690629
|
||||
880 48.426587 -3621.2356 959.70408 -4580.9397 1439.8947 0 1036.0768 150886.22 -157943.13 506.78826 15810.176 214.78374 320.9264 2.0688639
|
||||
900 49.644699 -3666.1303 946.8746 -4613.0049 1466.4484 0 1064.2478 150801.81 -157945.51 1109.1589 15739.244 211.91248 316.66479 1.9840376
|
||||
920 50.870043 -3689.2489 931.40538 -4620.6543 1504.5475 0 1112.6525 150708.42 -157946.28 1403.0057 15677.776 208.45044 311.4521 2.0302083
|
||||
940 52.10243 -3721.3501 909.43101 -4630.7811 1542.2534 0 1138.863 150634.25 -157946.14 1347.0651 15627.828 203.53253 304.13886 1.9127999
|
||||
960 53.227722 -3765.0247 879.73583 -4644.7606 1542.4842 0 1151.7551 150607.39 -157946.39 1704.8479 15589.06 196.88668 294.16244 1.9413966
|
||||
980 54.463265 -3768.795 907.84469 -4676.6397 1541.4855 0 1133.986 150593.62 -157945.73 1307.1066 15561.731 203.1775 303.56604 1.9940794
|
||||
1000 55.701727 -3785.8075 880.81809 -4666.6256 1521.7209 0 1096.2695 150662.35 -157946.97 970.21043 15543.592 197.1289 294.56486 1.8627129
|
||||
1020 56.889708 -3802.4725 921.96298 -4724.4355 1530.0248 0 1066.8927 150623.76 -157945.11 4.0693062 15531.676 206.33721 308.27171 2.0555342
|
||||
1040 58.073551 -3805.5983 892.97259 -4698.5709 1517.1505 0 1090.904 150638.66 -157945.28 814.78747 15522.075 199.8491 298.65131 1.8449766
|
||||
1060 59.268992 -3814.9754 904.37152 -4719.3469 1516.0462 0 1073.1076 150635.42 -157943.93 352.09813 15517.26 202.4002 302.40986 1.9760806
|
||||
1080 60.368197 -3799.7772 900.93602 -4700.7132 1525.3102 0 1076.0639 150645.06 -157947.15 399.96911 15516.854 201.63133 301.25571 1.9793146
|
||||
1100 61.57456 -3802.9637 891.80847 -4694.7721 1493.3846 0 1048.571 150708.35 -157945.08 296.41566 15520.259 199.58857 298.21614 1.9342423
|
||||
1120 62.780309 -3783.7153 915.24553 -4698.9609 1504.5486 0 1057.5171 150684.14 -157945.17 489.89871 15526.377 204.83383 306.05465 1.9825112
|
||||
1140 63.986179 -3799.4039 915.28328 -4714.6872 1498.182 0 1037.3595 150696.49 -157946.72 -57.392244 15535.825 204.84228 306.06136 1.9944283
|
||||
1160 65.193113 -3821.1813 889.41687 -4710.5981 1485.5696 0 1035.222 150714.63 -157946.02 -132.88199 15546.599 199.05332 297.34747 2.0669157
|
||||
1180 66.295017 -3815.3668 883.81796 -4699.1847 1475.1971 0 1029.0735 150742.62 -157946.07 -12.015088 15557.826 197.80027 295.60821 1.7888039
|
||||
1200 67.501339 -3799.2243 924.83203 -4724.0563 1503.6728 0 1039.8081 150676.17 -157943.71 -279.42673 15568.706 206.97931 309.25452 2.0149166
|
||||
1220 68.70749 -3793.2571 918.16669 -4711.4238 1500.7028 0 1072.1543 150660.33 -157944.61 396.95956 15579.039 205.48759 307.10011 1.8515828
|
||||
1240 69.913097 -3807.1761 903.62796 -4710.804 1518.0566 0 1098.727 150617.61 -157945.19 571.77344 15592.05 202.23379 302.09539 2.1061249
|
||||
1260 71.120192 -3813.0785 928.88909 -4741.9676 1522.8082 0 1080.2068 150602.14 -157947.12 143.45803 15608.285 207.88729 310.67334 1.8994019
|
||||
1280 72.221799 -3825.0477 896.43989 -4721.4876 1498.3409 0 1057.1098 150667.73 -157944.67 -469.23041 15626.738 200.62509 299.78768 1.8986521
|
||||
1300 73.424948 -3846.2307 907.67631 -4753.907 1477.8354 0 1013.4733 150700.69 -157945.9 -661.19665 15644.394 203.13982 303.56549 1.8822105
|
||||
1320 74.627469 -3829.941 882.93628 -4712.8773 1476.7417 0 1016.2042 150741.02 -157946.85 -14.196904 15658.043 197.60295 295.24326 1.9271172
|
||||
1340 75.833837 -3851.5034 857.32804 -4708.8314 1465.5881 0 1021.2072 150749.47 -157945.1 -96.242387 15669.364 191.87178 286.7037 1.8241831
|
||||
1360 76.936204 -3860.3024 888.18647 -4748.4888 1464.1796 0 984.93111 150747.8 -157945.4 -974.33424 15678.357 198.77795 297.0089 1.9185093
|
||||
1380 78.140865 -3836.5819 880.98802 -4717.5699 1461.9764 0 985.01748 150781.29 -157945.85 -872.9259 15682.263 197.16693 294.58145 1.9435476
|
||||
1400 79.344863 -3828.5386 906.27947 -4734.8181 1482.8705 0 991.46422 150736.59 -157945.74 -1233.9461 15680.599 202.82721 303.0834 1.909166
|
||||
1420 80.548134 -3814.3258 902.48807 -4716.8139 1475.6502 0 1014.0056 150738.18 -157944.65 -555.01708 15672.591 201.97868 301.83062 1.8708541
|
||||
1440 81.755274 -3856.0851 862.48793 -4718.573 1498.2382 0 1065.2356 150663.3 -157945.35 32.56482 15661.106 193.02657 288.38598 1.9216938
|
||||
1460 82.860741 -3844.5162 901.31045 -4745.8266 1509.4529 0 1079.4605 150610.73 -157945.47 187.59843 15650.274 201.71513 301.41292 1.9161214
|
||||
1480 84.068614 -3830.9341 924.4504 -4755.3845 1492.3743 0 1043.7244 150654.84 -157946.33 -493.49005 15640.167 206.8939 309.17217 1.9235617
|
||||
1500 85.277247 -3837.3277 905.31407 -4742.6418 1493.7224 0 1030.5512 150679.62 -157946.53 -614.09435 15628.452 202.61115 302.74791 1.9324006
|
||||
1520 86.48688 -3826.0085 909.05297 -4735.0615 1484.1418 0 1034.4558 150691.85 -157945.51 -146.17552 15614.976 203.44792 304.03751 1.8618391
|
||||
1540 87.592599 -3841.6696 938.60068 -4780.2703 1507.974 0 1041.0705 150616.87 -157946.18 -507.85898 15599.499 210.06076 313.85613 2.0498944
|
||||
1560 88.805017 -3826.9957 909.65333 -4736.649 1544.8227 0 1126.866 150538.2 -157946.54 606.26354 15581.816 203.58228 304.19548 1.9487298
|
||||
1580 90.020651 -3832.1768 912.93266 -4745.1095 1574.5895 0 1176.6062 150449.01 -157945.31 1282.9622 15569.746 204.3162 305.24469 2.0505914
|
||||
1600 91.237675 -3854.9438 913.45738 -4768.4012 1573.5937 0 1137.9072 150465.94 -157945.85 833.4472 15566.901 204.43364 305.43089 2.0302658
|
||||
1620 92.456385 -3858.2579 926.48289 -4784.7408 1547.7966 0 1104.6836 150506.72 -157943.94 175.66142 15569.538 207.34877 309.84283 1.9459647
|
||||
1640 93.67173 -3891.1815 918.17278 -4809.3543 1552.442 0 1100.5019 150484.4 -157946.7 -21.914006 15574.644 205.48895 307.0691 1.9176872
|
||||
1660 94.887992 -3919.3626 865.63387 -4784.9964 1520.4861 0 1071.2498 150569.18 -157945.91 76.169452 15580.674 193.73064 289.45503 1.8943961
|
||||
1680 96.104407 -3895.1048 904.57852 -4799.6834 1528.5992 0 1025.321 150591.92 -157945.52 -806.96969 15586.13 202.44653 302.49383 1.9470391
|
||||
1700 97.217725 -3867.858 892.51088 -4760.3689 1529.7738 0 1070.8486 150584.86 -157945.86 140.65618 15587.548 199.74577 298.38679 2.0642365
|
||||
1720 98.434344 -3893.3744 901.29331 -4794.6677 1574.0498 0 1116.4639 150460.62 -157945.8 58.347282 15588.502 201.71129 301.37785 1.974756
|
||||
1740 99.650283 -3863.7002 920.58199 -4784.2822 1591.6512 0 1158.7562 150411.66 -157946.35 690.62331 15590.533 206.02814 307.90557 1.8612258
|
||||
1760 100.86726 -3861.1571 936.31333 -4797.4705 1577.1868 0 1147.145 150425.93 -157947.74 479.33327 15596.819 209.54885 313.12745 1.9725316
|
||||
1780 102.08407 -3902.9055 937.9542 -4840.8597 1574.1479 0 1089.8436 150439.21 -157944.06 -423.26154 15606.503 209.91608 313.72161 1.8851726
|
||||
1800 103.30044 -3924.3367 882.83761 -4807.1743 1548.9296 0 1083.4742 150506.67 -157946.25 -165.30212 15613.782 197.58087 295.18333 1.9807824
|
||||
1820 104.51493 -3933.257 906.13467 -4839.3917 1566.2208 0 1066.4802 150474.1 -157946.19 -704.84936 15618.451 202.7948 303.015 1.948802
|
||||
1840 105.73189 -3925.7774 886.11608 -4811.8935 1541.3194 0 1071.3574 150522.01 -157946.58 -603.17056 15617.998 198.3146 296.30423 1.9386975
|
||||
1860 106.94721 -3888.206 921.52432 -4809.7304 1579.4857 0 1109.6812 150447.64 -157946.54 104.6013 15613.197 206.23903 308.2177 1.8692298
|
||||
1880 108.06014 -3916.0862 918.21234 -4834.2985 1583.1417 0 1094.2365 150433.88 -157945.56 -253.01422 15607.47 205.49781 306.96538 2.1516579
|
||||
1900 109.27602 -3899.0882 918.64022 -4817.7285 1556.1431 0 1115.1484 150457.92 -157946.94 -143.94816 15600.312 205.59357 307.17307 2.0233622
|
||||
1920 110.49415 -3920.9798 896.1905 -4817.1703 1548.5569 0 1085.0712 150496.68 -157947.48 -337.28194 15592.107 200.56927 299.64783 2.0110119
|
||||
1940 111.71421 -3968.3536 874.10309 -4842.4567 1572.4606 0 1094.9587 150436.32 -157946.19 -303.02321 15581.696 195.62607 292.28508 1.9167899
|
||||
1960 112.93472 -3934.8475 883.5952 -4818.4427 1591.4146 0 1141.0692 150394.9 -157945.83 393.7304 15568.475 197.75042 295.48636 1.883029
|
||||
1980 114.15483 -3907.4423 937.55746 -4844.9997 1643.691 0 1216.6376 150240.27 -157945.59 815.94743 15556.713 209.82728 313.50122 2.0597469
|
||||
2000 115.37626 -3925.4165 915.08958 -4840.506 1623.4406 0 1190.2236 150292.14 -157946.31 519.99833 15550.966 204.79893 305.95187 2.083444
|
||||
Loop time of 115.376 on 1 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Performance: 1.498 ns/day, 16.024 hours/ns, 17.335 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 97.091 | 97.091 | 97.091 | 0.0 | 84.15
|
||||
Bond | 0.031897 | 0.031897 | 0.031897 | 0.0 | 0.03
|
||||
Kspace | 3.7648 | 3.7648 | 3.7648 | 0.0 | 3.26
|
||||
Neigh | 10.041 | 10.041 | 10.041 | 0.0 | 8.70
|
||||
Comm | 0.79701 | 0.79701 | 0.79701 | 0.0 | 0.69
|
||||
Output | 0.0071344 | 0.0071344 | 0.0071344 | 0.0 | 0.01
|
||||
Modify | 3.5966 | 3.5966 | 3.5966 | 0.0 | 3.12
|
||||
Other | | 0.0467 | | | 0.04
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21222 ave 21222 max 21222 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.30826e+06 ave 2.30826e+06 max 2.30826e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2308257
|
||||
Ave neighs/atom = 923.303
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 6
|
||||
|
||||
Total wall time: 0:01:55
|
||||
|
|
@ -0,0 +1,246 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
|
||||
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix NVE DRUDES nve
|
||||
|
||||
compute TEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 0.3966074 2915.1579 4579.5774 -1664.4194 561.91893 0 600.76451 155095.13 -157922.23 27379.771 14058.574 1024.9188 1455.9194 160.86778
|
||||
40 0.81358027 1320.1722 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914
|
||||
60 1.2173033 284.06793 2671.4324 -2387.3645 575.54155 0 387.8792 154580.74 -157931.53 12104.74 15031.425 597.87206 886.98502 18.450412
|
||||
80 1.6120358 -462.53073 2214.284 -2676.8148 560.36346 0 254.65244 154447.22 -157939.05 6285.2446 15651.216 495.56131 739.13811 7.4024414
|
||||
100 1.9901412 -965.1962 1839.8309 -2805.0271 544.5953 0 115.80813 154469.59 -157935.02 2361.9408 16295.72 411.75794 615.12768 4.1969771
|
||||
120 2.4076366 -1316.6354 1649.5851 -2966.2205 554.66642 0 50.928948 154365.49 -157937.3 -493.85718 16925.293 369.18054 552.03453 2.7331858
|
||||
140 2.7559175 -1590.9197 1440.667 -3031.5867 526.07695 0 -24.440541 154404.35 -157937.57 -2586.3198 17517.285 322.42423 482.1612 2.2975751
|
||||
160 3.1113834 -1742.3406 1326.8813 -3069.2219 539.49038 0 -43.846686 154369.1 -157933.96 -3549.2199 18059.707 296.95875 444.11027 2.0644718
|
||||
180 3.4379854 -1895.133 1224.1815 -3119.3145 555.27915 0 -18.261199 154275.94 -157932.27 -3762.2323 18545.519 273.97433 409.78407 1.8069068
|
||||
200 3.772357 -2004.4681 1176.8827 -3181.3508 565.04401 0 0.21397152 154190.38 -157936.99 -4346.6082 18973.343 263.38877 393.94854 1.740057
|
||||
220 4.0741081 -2094.1886 1098.386 -3192.5745 592.45711 0 36.50232 154113.36 -157934.89 -4135.0776 19341.735 245.82103 367.67719 1.6170754
|
||||
240 4.3758588 -2178.9977 1086.8337 -3265.8313 617.63759 0 96.837785 153957.25 -157937.56 -4121.8002 19651.8 243.23561 363.77451 1.6722528
|
||||
260 4.6875975 -2264.8204 1078.4367 -3343.2571 663.36053 0 167.77029 153763.13 -157937.51 -3799.2337 19907.053 241.35634 360.97449 1.6377088
|
||||
280 4.9870708 -2325.8017 1097.4329 -3423.2346 717.74153 0 235.01385 153562.93 -157938.92 -3696.4866 20111.415 245.60773 367.30986 1.7042226
|
||||
300 5.2866828 -2390.4714 1068.102 -3458.5734 751.64774 0 295.31519 153435.36 -157940.9 -3511.7651 20268.755 239.04342 357.49315 1.6658672
|
||||
320 5.587172 -2455.1882 1041.7365 -3496.9247 765.89806 0 331.14936 153345 -157938.97 -3020.2521 20383.476 233.14276 348.62201 1.7179837
|
||||
340 5.8844874 -2536.9586 1050.7417 -3587.7004 793.64691 0 352.69902 153205.76 -157939.81 -3447.4347 20457.614 235.15816 351.64191 1.7214644
|
||||
360 6.1785333 -2603.5522 966.91828 -3570.4705 819.14562 0 391.00832 153158.88 -157939.51 -3164.7275 20490.766 216.3983 323.52165 1.7255664
|
||||
380 6.475884 -2594.7716 1024.7965 -3619.5682 836.45788 0 434.31956 153047.12 -157937.46 -2902.8144 20485.924 229.35156 342.91613 1.7641391
|
||||
400 6.7656763 -2647.3629 982.4772 -3629.8401 864.60508 0 479.09794 152963.5 -157937.04 -2535.5559 20447.667 219.88041 328.70004 1.8030439
|
||||
420 7.0558476 -2687.5292 1023.0073 -3710.5365 928.03183 0 538.52272 152760.85 -157937.94 -2383.1875 20380.424 228.95113 342.29995 1.8044464
|
||||
440 7.3502834 -2765.1784 999.349 -3764.5274 966.2891 0 577.16135 152631.19 -157939.17 -2390.6308 20286.677 223.65636 334.36519 1.794568
|
||||
460 7.6480289 -2806.7277 1004.2012 -3810.9289 996.86402 0 599.42684 152532.82 -157940.04 -2476.2951 20168.787 224.74229 335.9677 1.8474231
|
||||
480 7.9473393 -2830.1149 1013.7084 -3843.8233 1009.5457 0 624.67244 152464.69 -157942.73 -2208.5836 20027.763 226.87003 339.15378 1.8588625
|
||||
500 8.2545588 -2849.2101 1033.8059 -3883.016 1018.8936 0 665.65423 152373.57 -157941.13 -1864.5049 19866.3 231.36788 345.90443 1.8323172
|
||||
520 8.591975 -2883.363 982.80834 -3866.1713 1046.7496 0 716.08257 152311.55 -157940.55 -1180.4653 19690.017 219.95452 328.79387 1.8393955
|
||||
540 8.9018662 -2922.4604 979.55307 -3902.0135 1068.293 0 739.88796 152230.57 -157940.76 -1048.6961 19504.92 219.22599 327.7909 1.6577051
|
||||
560 9.2518864 -2966.9519 973.53114 -3940.4831 1078.4149 0 742.20771 152177.5 -157938.6 -840.75895 19313.099 217.87827 325.70841 1.7798986
|
||||
580 9.5821679 -3053.0997 924.19412 -3977.2939 1102.7966 0 751.05657 152109.51 -157940.66 -919.12753 19115.431 206.83654 309.16882 1.7634757
|
||||
600 9.9095862 -3062.7056 960.18758 -4022.8932 1105.4131 0 725.33328 152088.02 -157941.66 -1565.9872 18911.303 214.89195 321.19255 1.860965
|
||||
620 10.237109 -3087.2168 1011.0151 -4098.2319 1138.4545 0 715.92859 151990.05 -157942.66 -1858.9668 18697.232 226.26725 338.29838 1.752463
|
||||
640 10.571446 -3104.3903 1013.9671 -4118.3574 1151.4213 0 771.17657 151902.66 -157943.62 -1042.667 18472.317 226.92791 339.23913 1.8477429
|
||||
660 10.904144 -3140.5527 1003.0482 -4143.6009 1209.2262 0 856.88154 151734.42 -157944.13 -209.63558 18243.884 224.48425 335.54573 1.90792
|
||||
680 11.269296 -3178.318 984.55406 -4162.872 1244.5687 0 912.27932 151624.96 -157944.68 342.27035 18019.714 220.34522 329.38006 1.8427138
|
||||
700 11.61204 -3220.4931 991.39835 -4211.8914 1287.1899 0 958.87881 151484.75 -157942.71 561.06968 17805.512 221.87699 331.61354 1.9544592
|
||||
720 11.956387 -3270.5677 968.72596 -4239.2937 1318.9328 0 1005.2488 151379.5 -157942.98 980.32825 17604.484 216.80286 324.06313 1.8724276
|
||||
740 12.307601 -3290.3786 992.65117 -4283.0298 1300.6067 0 994.6404 151364.88 -157943.15 981.03868 17418.67 222.15737 332.13302 1.7636245
|
||||
760 12.709807 -3328.535 955.47413 -4284.0092 1326.3889 0 996.60158 151337.63 -157944.63 1057.2942 17247.311 213.83707 319.58671 1.9099364
|
||||
780 13.073534 -3357.4814 992.18506 -4349.6664 1339.5541 0 988.34064 151267.55 -157945.11 569.82212 17090.619 222.05305 331.88822 1.9447924
|
||||
800 13.464632 -3375.243 920.44154 -4295.6846 1344.9357 0 1033.5805 151270.88 -157945.08 1522.7002 16947.373 205.99671 307.8875 1.8152213
|
||||
820 13.825511 -3384.8564 957.24296 -4342.0994 1353.9907 0 1040.4762 151209.02 -157945.59 1664.2884 16820.422 214.23294 320.13875 1.9919112
|
||||
840 14.161551 -3422.503 978.5056 -4401.0087 1362.0589 0 1015.2074 151166.38 -157944.65 799.30788 16709.133 218.99156 327.32752 1.887971
|
||||
860 14.533048 -3467.9469 967.207 -4435.1539 1359.5363 0 1012.6359 151135.59 -157942.92 781.21407 16610.402 216.46291 323.49791 1.9571626
|
||||
880 14.90632 -3453.3858 998.28194 -4451.6677 1357.904 0 965.66218 151167.88 -157943.11 327.66041 16521.416 223.41755 333.88219 2.0414314
|
||||
900 15.304111 -3462.8392 980.22919 -4443.0684 1356.3167 0 986.69144 151157.82 -157943.9 1027.2464 16438.193 219.37731 327.82432 2.0328217
|
||||
920 15.679265 -3447.1555 973.44396 -4420.5994 1360.7957 0 1016.6188 151146.99 -157945 1288.3873 16362.953 217.85876 325.51992 2.1081109
|
||||
940 16.057773 -3481.2586 989.56656 -4470.8252 1370.2709 0 978.71463 151124.98 -157944.79 462.51008 16297.794 221.46703 330.96437 2.0294765
|
||||
960 16.417333 -3513.0231 967.65653 -4480.6797 1332.0395 0 924.14851 151207.66 -157944.53 130.65949 16238.731 216.56352 323.68471 1.8694768
|
||||
980 16.809043 -3552.9742 930.52856 -4483.5028 1369.5671 0 943.1948 151148.51 -157944.78 162.05947 16182.544 208.2542 311.18346 1.9699974
|
||||
1000 17.204374 -3547.8316 928.6749 -4476.5065 1345.2729 0 939.82999 151183.66 -157945.27 165.47858 16127.801 207.83935 310.6291 1.8515304
|
||||
1020 17.596776 -3544.884 939.68436 -4484.5683 1339.8295 0 954.31534 151165.65 -157944.37 520.88879 16074.311 210.30329 314.30017 1.8816955
|
||||
1040 17.979123 -3574.7347 918.01852 -4492.7532 1348.2798 0 985.63357 151118.04 -157944.71 667.98123 16024.2 205.45443 307.00947 1.9378696
|
||||
1060 18.387169 -3558.0092 961.56557 -4519.5748 1357.9517 0 960.15956 151105.93 -157943.62 125.05193 15979.251 215.20035 321.61047 1.9569155
|
||||
1080 18.773684 -3578.9948 924.98329 -4503.9781 1328.198 0 963.29308 151149.83 -157945.3 446.98896 15936.835 207.01316 309.36635 1.8873208
|
||||
1100 19.16304 -3608.0441 897.53939 -4505.5835 1374.0861 0 1014.8258 151052.01 -157946.5 903.7649 15898.367 200.87116 300.13546 1.9333063
|
||||
1120 19.575293 -3614.8945 952.97919 -4567.8736 1384.5634 0 1021.0735 150973.5 -157947.01 900.30601 15866.787 213.2787 318.78179 1.850125
|
||||
1140 19.971095 -3618.8945 941.15802 -4560.0526 1413.1629 0 1052.0922 150920.8 -157946.1 946.48705 15842.856 210.6331 314.72329 2.0381081
|
||||
1160 20.367334 -3593.6555 965.54035 -4559.1959 1410.1926 0 1056.4577 150917.31 -157943.16 1255.7185 15827.388 216.08991 322.92339 1.9871263
|
||||
1180 20.80204 -3616.5746 928.17105 -4544.7457 1396.8419 0 1016.2295 150986.13 -157943.95 787.12503 15820.166 207.72659 310.40871 1.9519704
|
||||
1200 21.354242 -3640.0065 913.1866 -4553.1931 1389.564 0 1003.0365 150999.43 -157945.23 124.9066 15819.562 204.37304 305.34426 2.0128932
|
||||
1220 21.797356 -3633.6726 951.90864 -4585.5813 1378.6589 0 960.35277 151020.87 -157945.46 18.165228 15822.414 213.03911 318.39602 1.9062762
|
||||
1240 22.183053 -3647.5993 945.94087 -4593.5401 1389.2708 0 951.90886 151011.29 -157946.01 -36.466949 15826.558 211.70351 316.39869 1.8959
|
||||
1260 22.604321 -3652.8431 945.01497 -4597.8581 1429.1559 0 1004.3575 150913.05 -157944.42 362.05633 15830.563 211.49629 316.0745 1.946701
|
||||
1280 22.99465 -3653.7982 950.39456 -4604.1928 1435.3114 0 1049.5949 150856.36 -157945.46 625.62312 15836.724 212.70025 317.85889 1.9726129
|
||||
1300 23.381442 -3629.7936 957.73231 -4587.5259 1443.1612 0 1053.2561 150860.98 -157944.93 702.06174 15846.916 214.34246 320.25498 2.0929604
|
||||
1320 23.76752 -3646.7132 952.84473 -4599.5579 1452.1034 0 1053.24 150842.08 -157946.98 574.37181 15862.45 213.24861 318.70565 1.9106871
|
||||
1340 24.144538 -3671.1813 963.35534 -4634.5366 1444.4873 0 998.25657 150869.14 -157946.42 -322.65814 15883.001 215.6009 322.16079 2.04787
|
||||
1360 24.525885 -3706.8433 911.96869 -4618.812 1408.7597 0 994.56958 150923.67 -157945.81 -57.178556 15902.95 204.10046 304.98731 1.9206183
|
||||
1380 24.900833 -3729.8666 893.54172 -4623.4083 1421.5285 0 989.13168 150911.03 -157945.1 -299.2294 15921.536 199.97647 298.78606 1.9572022
|
||||
1400 25.273009 -3793.6665 896.59455 -4690.261 1407.5033 0 927.03218 150922.27 -157947.07 -1625.2355 15935.372 200.6597 299.82059 1.9326242
|
||||
1420 25.649713 -3798.9041 894.49834 -4693.4024 1387.2314 0 908.98338 150956.58 -157946.2 -1336.2681 15939.126 200.19057 299.08979 1.99336
|
||||
1440 26.019568 -3770.2203 926.96956 -4697.1899 1408.3234 0 930.94218 150909.09 -157945.54 -1479.4839 15931.76 207.45769 309.99863 1.9420101
|
||||
1460 26.391048 -3765.611 925.8388 -4691.4498 1453.7458 0 991.60997 150809.05 -157945.85 -840.19764 15915.083 207.20462 309.58977 2.0206113
|
||||
1480 26.764417 -3775.5533 897.45722 -4673.0106 1448.3682 0 1017.1514 150806.55 -157945.08 -350.56805 15893.71 200.85277 300.10571 1.945031
|
||||
1500 27.13281 -3774.5729 890.65309 -4665.226 1446.7764 0 1001.4176 150830.42 -157943.84 -410.46342 15870.464 199.32999 297.86004 1.8712264
|
||||
1520 27.500265 -3789.599 873.98319 -4663.5822 1442.1868 0 1012.8814 150826.03 -157944.68 24.399796 15844.317 195.59923 292.31265 1.7812003
|
||||
1540 27.868039 -3799.4214 879.9876 -4679.409 1470.7765 0 1043.5857 150751.8 -157945.57 -117.3494 15817.531 196.94303 294.27937 1.8764714
|
||||
1560 28.237804 -3808.5737 884.02221 -4692.5959 1476.2544 0 1031.065 150745.8 -157945.71 -134.38328 15790.497 197.84599 295.60533 1.9624808
|
||||
1580 28.614069 -3810.3826 881.02258 -4691.4052 1494.8044 0 1056.2914 150703.91 -157946.41 143.72796 15761.802 197.17466 294.61532 1.9194335
|
||||
1600 28.98594 -3811.3999 900.38301 -4711.7829 1484.7896 0 1008.1585 150740.82 -157945.55 -606.18902 15732.936 201.50757 301.08426 1.975131
|
||||
1620 29.390152 -3806.3652 923.83116 -4730.1964 1451.5712 0 974.75532 150788.99 -157945.52 -803.66402 15700.793 206.75531 308.94868 1.9548773
|
||||
1640 29.770757 -3780.4823 926.08598 -4706.5682 1473.3966 0 1001.2541 150764.99 -157946.2 -267.61953 15664.228 207.25994 309.69886 1.9804041
|
||||
1660 30.150359 -3781.8554 904.38999 -4686.2453 1480.8669 0 1044.4828 150733.32 -157944.92 334.93631 15626.039 202.40434 302.41882 1.9682532
|
||||
1680 30.535691 -3806.1604 913.1776 -4719.338 1495.1709 0 1047.1796 150684.96 -157946.64 187.42287 15589.003 204.37102 305.37701 1.9489831
|
||||
1700 30.914774 -3833.9683 889.78762 -4723.756 1506.0651 0 1085.1426 150631.7 -157946.67 484.91155 15553.147 199.1363 297.62268 1.7777001
|
||||
1720 31.295628 -3842.1369 894.05081 -4736.1877 1523.554 0 1111.0586 150574.13 -157944.93 644.7439 15520.678 200.09041 298.99568 1.8760829
|
||||
1740 31.688478 -3846.6021 868.65036 -4715.2525 1537.3591 0 1138.8056 150555.14 -157946.56 899.91638 15492.771 194.40573 290.47895 1.8712221
|
||||
1760 32.046871 -3857.9528 883.26637 -4741.2192 1542.993 0 1087.2616 150575.49 -157946.97 551.51344 15470.089 197.67683 295.29782 2.0345443
|
||||
1780 32.474213 -3871.4941 935.07928 -4806.5734 1526.7468 0 1036.0478 150576.57 -157945.93 -636.02229 15449.192 209.27266 312.71251 1.9801693
|
||||
1800 32.86394 -3840.4408 916.271 -4756.7118 1576.9326 0 1100.9058 150511.02 -157945.57 628.83596 15425.726 205.06333 306.41471 1.9480945
|
||||
1820 33.2544 -3863.8057 928.94676 -4792.7524 1566.8662 0 1091.867 150492.97 -157944.46 127.39479 15404.045 207.90019 310.61713 2.0438685
|
||||
1840 33.654639 -3866.4315 882.39729 -4748.8287 1571.1231 0 1116.2191 150510.49 -157946.66 775.21837 15384.034 197.48232 295.08631 1.8701078
|
||||
1860 34.049358 -3854.7362 943.50575 -4798.2419 1598.0765 0 1094.2606 150455.31 -157945.89 -185.76137 15367.771 211.15852 315.55119 1.9664963
|
||||
1880 34.452703 -3862.4907 910.1166 -4772.6073 1551.4788 0 1069.6982 150551.3 -157945.09 75.157314 15353.364 203.68596 304.30419 2.0643731
|
||||
1900 34.820253 -3879.6568 921.99593 -4801.6528 1541.8636 0 1071.1404 150530.01 -157944.67 -243.29034 15340.544 206.34458 308.28647 2.0409636
|
||||
1920 35.24159 -3914.6053 894.91511 -4809.5205 1545.6295 0 1087.8419 150502.25 -157945.24 585.4907 15327.629 200.28384 299.29163 1.8721306
|
||||
1940 35.641894 -3916.7204 893.69522 -4810.4157 1558.0228 0 1078.6893 150498.47 -157945.6 -213.58892 15315.774 200.01082 298.82901 1.9662798
|
||||
1960 36.036489 -3916.4155 889.43523 -4805.8507 1569.5342 0 1087.2216 150483.46 -157946.07 197.26075 15304.142 199.05743 297.4414 1.897782
|
||||
1980 36.439917 -3885.2222 890.76008 -4775.9823 1562.1737 0 1087.3549 150520.37 -157945.88 448.96019 15293.261 199.35393 297.81895 2.0239285
|
||||
2000 36.842032 -3890.9997 883.71903 -4774.7187 1561.3244 0 1092.1688 150517.76 -157945.97 292.74093 15284.861 197.77813 295.50959 1.9186189
|
||||
Loop time of 36.8421 on 4 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Performance: 4.690 ns/day, 5.117 hours/ns, 54.286 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 24.965 | 26.526 | 28.829 | 27.6 | 72.00
|
||||
Bond | 0.011653 | 0.012315 | 0.013344 | 0.6 | 0.03
|
||||
Kspace | 1.5367 | 3.8315 | 5.3771 | 72.2 | 10.40
|
||||
Neigh | 2.6221 | 2.6225 | 2.6227 | 0.0 | 7.12
|
||||
Comm | 1.2339 | 1.2536 | 1.2758 | 1.3 | 3.40
|
||||
Output | 0.0057538 | 0.0073775 | 0.012186 | 3.2 | 0.02
|
||||
Modify | 2.4848 | 2.5068 | 2.5296 | 1.2 | 6.80
|
||||
Other | | 0.08209 | | | 0.22
|
||||
|
||||
Nlocal: 625 ave 639 max 613 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 13529.2 ave 13635 max 13449 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 587190 ave 645917 max 526348 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2348759
|
||||
Ave neighs/atom = 939.504
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 102
|
||||
Dangerous builds = 7
|
||||
|
||||
Total wall time: 0:00:36
|
||||
|
|
@ -0,0 +1,252 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
comm_modify vel yes
|
||||
compute TATOM ATOMS temp/com
|
||||
compute TEMP all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix_modify RIGID temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1338)
|
||||
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 1 100.0
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 36.15 | 36.15 | 36.15 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 1.3635511 3742.6843 5338.7884 -1596.1041 567.30749 0 662.23765 155098.37 -157924.01 31679.425 13979.574 1194.8318 1690.2246 201.65659
|
||||
40 2.8319206 2752.8326 4407.7651 -1654.9326 793.00136 0 870.3308 154593.76 -157912.03 27394.569 14278.56 986.46689 1450.7477 55.932383
|
||||
60 4.2769592 1995.5898 3982.037 -1986.4472 660.67727 0 750.60931 154536.67 -157934.4 22230.525 14691.401 891.18805 1315.7323 40.317105
|
||||
80 5.6864653 1376.4611 3451.5427 -2075.0816 617.739 0 606.36728 154625.69 -157924.88 17342.361 15201.343 772.46234 1147.1933 21.455572
|
||||
100 7.0593393 885.62035 3037.6307 -2152.0103 536.23281 0 448.92338 154793.05 -157930.22 13263.277 15783.251 679.82798 1011.6853 14.753602
|
||||
120 8.3966329 487.59021 2926.9825 -2439.3923 534.45241 0 332.92674 154624.58 -157931.35 8680.1218 16409.225 655.06468 977.01117 9.8615821
|
||||
140 9.6922171 159.94255 2531.0921 -2371.1495 507.26507 0 248.61566 154802.72 -157929.75 6400.0155 17052.819 566.4636 845.55884 7.140197
|
||||
160 10.950651 -100.91956 2408.1664 -2509.0859 490.99483 0 134.36058 154800.6 -157935.04 3836.9925 17698.151 538.95257 805.1915 5.3968131
|
||||
180 12.172047 -313.40678 2221.7371 -2535.1439 469.97826 0 75.806422 154853.24 -157934.17 1959.0003 18334.826 497.22932 743.13919 4.4151403
|
||||
200 13.369177 -490.93825 2067.2564 -2558.1946 455.16083 0 77.543554 154841.16 -157932.06 1193.4025 18956.449 462.65622 691.72198 3.5993868
|
||||
220 14.438093 -642.88359 1962.7222 -2605.6058 481.40176 0 64.823738 154779.31 -157931.14 258.47931 19559.018 439.26127 657.06568 2.7739198
|
||||
240 15.577558 -770.43472 1795.7362 -2566.1709 467.25739 0 68.825446 154830.01 -157932.26 19.605411 20139.418 401.88945 601.23804 2.3884997
|
||||
260 16.688265 -878.62151 1752.9509 -2631.5724 476.39236 0 71.926651 154747.16 -157927.05 -779.07206 20696.166 392.31402 587.06568 2.0260792
|
||||
280 17.682964 -971.81622 1649.6272 -2621.4434 473.84812 0 58.450385 154779.58 -157933.32 -1008.5258 21226.441 369.18995 552.55677 1.7179235
|
||||
300 18.755012 -1057.4737 1581.0153 -2638.4889 480.33302 0 92.047223 154721.85 -157932.72 -1272.4892 21728.979 353.83447 529.64527 1.5051853
|
||||
320 19.774572 -1132.8157 1506.8725 -2639.6882 477.53234 0 107.39639 154707.65 -157932.27 -1097.9626 22203.697 337.24116 504.84512 1.3587573
|
||||
340 20.69206 -1199.489 1494.9584 -2694.4474 479.87519 0 106.49874 154656.38 -157937.2 -1428.8049 22652.416 334.57476 500.90442 1.2462835
|
||||
360 21.652272 -1264.9018 1440.9759 -2705.8778 491.74088 0 107.21802 154624.72 -157929.55 -1585.5815 23073.033 322.49337 482.81675 1.2016239
|
||||
380 22.541014 -1323.4812 1376.8139 -2700.295 497.62389 0 130.73162 154602.95 -157931.6 -1822.4176 23465.34 308.13377 461.36583 1.0533711
|
||||
400 23.429899 -1373.4313 1375.7746 -2749.2059 504.5216 0 124.40122 154554.57 -157932.7 -2024.2519 23828.151 307.90118 461.05182 0.98409512
|
||||
420 24.30185 -1426.2004 1375.0825 -2801.2829 515.4234 0 141.95789 154473.92 -157932.58 -2211.7434 24159.844 307.74628 460.87881 0.86572884
|
||||
440 25.220268 -1475.8906 1324.8476 -2800.7382 535.08125 0 196.94504 154398.6 -157931.36 -1603.3424 24460.372 296.50361 443.98822 0.94139759
|
||||
460 26.069995 -1526.8146 1312.6512 -2839.4658 567.30401 0 263.15706 154263.01 -157932.94 -1446.573 24734.601 293.77403 439.95008 0.83440493
|
||||
480 26.912804 -1575.0902 1310.7022 -2885.7924 595.89933 0 312.71625 154137.37 -157931.78 -1115.9617 24986.067 293.33784 439.29118 0.84448526
|
||||
500 27.750046 -1625.867 1316.9545 -2942.8215 622.71944 0 334.05272 154029.75 -157929.34 -1178.3349 25218.467 294.73713 441.38984 0.84223525
|
||||
520 28.580007 -1677.8147 1275.1901 -2953.0048 636.81498 0 364.43482 153975.25 -157929.51 -1185.7191 25432.383 285.39015 427.42176 0.75616765
|
||||
540 29.461706 -1724.6335 1253.4762 -2978.1096 632.62875 0 336.7701 153984.65 -157932.16 -1475.652 25627.637 280.53054 420.14989 0.73078744
|
||||
560 30.284055 -1768.8039 1262.2867 -3031.0907 642.26972 0 309.98943 153946.77 -157930.12 -1811.8157 25800.729 282.50237 423.09732 0.74744177
|
||||
580 31.099254 -1811.2401 1227.9083 -3039.1484 678.22201 0 368.41929 153846.44 -157932.23 -1409.4088 25948.882 274.80841 411.53414 0.80732891
|
||||
600 31.912324 -1853.2774 1206.9943 -3060.2717 700.63403 0 436.68693 153737.89 -157935.48 -992.41608 26077.285 270.12781 404.5385 0.76616257
|
||||
620 32.720867 -1895.189 1204.3588 -3099.5478 691.72649 0 400.33253 153741.91 -157933.52 -1388.6703 26189.589 269.53797 403.65884 0.75715127
|
||||
640 33.582986 -1935.0173 1187.9183 -3122.9356 705.21393 0 424.23263 153679.52 -157931.9 -1350.2348 26282.622 265.85856 398.13366 0.77665339
|
||||
660 34.390937 -1971.7086 1162.7479 -3134.4565 702.26031 0 428.42789 153668.92 -157934.06 -1188.7971 26357.244 260.22536 389.70613 0.74337722
|
||||
680 35.194277 -2009.3204 1181.9615 -3191.282 730.54911 0 440.01944 153571.31 -157933.16 -1362.8153 26413.989 264.52542 396.12452 0.79816042
|
||||
700 35.997317 -2050.9709 1191.8391 -3242.8101 753.00327 0 467.6939 153468.36 -157931.87 -1482.0887 26451.007 266.73604 399.41272 0.84921753
|
||||
720 36.797657 -2089.4271 1150.0076 -3239.4347 754.31976 0 503.35736 153436.75 -157933.87 -1244.458 26468.888 257.37407 385.38778 0.83191363
|
||||
740 37.600469 -2125.3798 1154.3541 -3279.7339 774.13557 0 529.42004 153350.85 -157934.14 -1118.7575 26470.499 258.34683 386.83315 0.85749243
|
||||
760 38.401939 -2161.7135 1130.3511 -3292.0647 796.77441 0 536.43801 153307.45 -157932.73 -1175.0129 26456.703 252.9749 378.79415 0.83045948
|
||||
780 39.260591 -2198.2814 1150.3816 -3348.6631 831.65486 0 563.13944 153188.89 -157932.35 -1176.261 26427.139 257.45777 385.51594 0.82651674
|
||||
800 40.064371 -2234.1521 1110.6647 -3344.8168 855.23508 0 601.01417 153131.92 -157932.98 -862.30786 26382.746 248.56904 372.17004 0.86990233
|
||||
820 40.870016 -2267.8439 1102.4715 -3370.3153 860.65298 0 594.70187 153108.56 -157934.23 -1010.8125 26326.235 246.73537 369.40044 0.91177598
|
||||
840 41.681368 -2299.1566 1078.3708 -3377.5273 859.59901 0 593.35932 153101.25 -157931.73 -865.53535 26257.386 241.34159 361.33643 0.86924241
|
||||
860 42.495518 -2331.8875 1107.384 -3439.2715 881.30207 0 614.64915 152998.03 -157933.26 -1071.9258 26177.36 247.83481 371.04249 0.92379597
|
||||
880 43.30765 -2362.8811 1111.5783 -3474.4594 878.94272 0 592.04533 152990.05 -157935.5 -1381.2745 26084.115 248.77351 372.40018 1.0226212
|
||||
900 44.121972 -2394.8169 1068.126 -3462.9429 875.67985 0 600.20259 152996.32 -157935.15 -1082.6484 25975.468 239.0488 357.84385 0.98060155
|
||||
920 44.942671 -2427.7497 1051.3836 -3479.1333 900.00235 0 630.10877 152926.67 -157935.91 -1219.7107 25853.048 235.30182 352.19248 1.049881
|
||||
940 45.823624 -2454.734 1033.0018 -3487.7359 898.98611 0 622.98212 152924.56 -157934.26 -1017.3685 25716.622 231.18793 346.03843 1.0245683
|
||||
960 46.651637 -2482.3376 1051.4989 -3533.8365 882.79039 0 607.4772 152907.91 -157932.02 -1287.7224 25567.669 235.32761 352.20104 1.1100984
|
||||
980 47.483709 -2510.9021 1063.1436 -3574.0457 917.45654 0 628.78148 152815.06 -157935.34 -1318.0782 25404.812 237.93373 356.07751 1.1703057
|
||||
1000 48.3218 -2539.3123 1076.5262 -3615.8385 929.24497 0 620.5376 152770.95 -157936.57 -1437.1421 25228.96 240.92878 360.5539 1.1966823
|
||||
1020 49.120018 -2568.5635 1047.1393 -3615.7027 927.28535 0 622.11842 152769.9 -157935 -1455.4685 25039.532 234.35192 350.71529 1.1564745
|
||||
1040 49.90245 -2600.2331 1062.6806 -3662.9136 955.48542 0 644.04662 152672.56 -157935.01 -1384.5306 24836.175 237.83009 355.87178 1.2710552
|
||||
1060 50.69897 -2630.1462 1061.5152 -3691.6614 986.58819 0 682.07977 152579.13 -157939.46 -1344.1472 24620.038 237.56929 355.4358 1.3611209
|
||||
1080 51.503865 -2659.3124 1028.5625 -3687.8749 1013.1448 0 748.60853 152486.11 -157935.74 -632.77731 24393.781 230.1944 344.4159 1.2910154
|
||||
1100 52.317019 -2686.7631 1046.6402 -3733.4033 1010.8277 0 734.27617 152460.31 -157938.82 -853.90087 24163.398 234.24022 350.47672 1.2987412
|
||||
1120 53.191877 -2717.3602 1100.2788 -3817.639 1053.1519 0 729.94563 152339.1 -157939.84 -1341.3046 23928.078 246.24466 368.47141 1.2986799
|
||||
1140 54.021756 -2749.0229 1075.5657 -3824.5886 1053.2247 0 772.2959 152288.35 -157938.46 -589.3316 23686.107 240.71381 360.21003 1.2399432
|
||||
1160 54.861993 -2781.7214 1067.9567 -3849.6781 1074.5488 0 806.08569 152208.08 -157938.39 -831.19568 23442.775 239.0109 357.6544 1.2458686
|
||||
1180 55.710942 -2810.148 1089.8079 -3899.9559 1109.6809 0 845.87985 152083.25 -157938.76 -222.17835 23198.413 243.90125 365.01942 1.1770946
|
||||
1200 56.57052 -2842.1991 1074.027 -3916.2261 1125.4801 0 878.8665 152014.69 -157935.26 -448.25353 22957.682 240.36945 359.7275 1.1726032
|
||||
1220 57.436566 -2870.9683 1065.5007 -3936.469 1121.3024 0 895.48147 151984.11 -157937.36 -49.04933 22721.016 238.46125 356.86483 1.1771853
|
||||
1240 58.31029 -2898.6134 1082.9239 -3981.5374 1156.8878 0 872.68215 151926.15 -157937.26 -519.72203 22490.6 242.3606 362.72866 1.139753
|
||||
1260 59.192157 -2928.7913 1040.5848 -3969.3761 1145.0651 0 909.81511 151912.71 -157936.97 -29.590267 22264.147 232.88502 348.55509 1.0791106
|
||||
1280 60.142411 -2955.6846 1022.8912 -3978.5758 1140.672 0 883.63602 151933.74 -157936.62 -175.91605 22043.467 228.92516 342.58962 1.1383994
|
||||
1300 61.07528 -2981.9373 1075.9497 -4057.887 1158.7075 0 849.86519 151871.92 -157938.38 -934.6555 21827.24 240.79975 360.40764 1.1023778
|
||||
1320 62.024172 -3008.7547 1034.6665 -4043.4212 1150.8314 0 884.82764 151858.67 -157937.75 -365.70526 21611.763 231.56049 346.60301 1.0123134
|
||||
1340 62.982555 -3034.4981 1059.0543 -4093.5524 1167.4937 0 873.78686 151802.9 -157937.73 -607.20768 21399.603 237.01853 354.83546 0.91062335
|
||||
1360 63.941291 -3061.6404 1086.842 -4148.4824 1203.2944 0 877.27308 151711.62 -157940.67 -877.19102 21189.111 243.23747 364.15541 0.91512372
|
||||
1380 64.90951 -3092.7485 1046.5902 -4139.3388 1239.0597 0 915.00432 151646.1 -157939.51 -519.03533 20978.348 234.22904 350.66459 0.8894947
|
||||
1400 65.889121 -3121.488 1051.0689 -4172.5569 1298.7247 0 989.25234 151480.54 -157941.07 -54.596483 20769.447 235.23138 352.15827 0.90714599
|
||||
1420 66.880954 -3149.3299 1046.1867 -4195.5166 1316.5513 0 1013.5453 151416.57 -157942.18 -12.199056 20566.196 234.13872 350.49775 0.95239313
|
||||
1440 67.876446 -3172.8201 1046.5913 -4219.4114 1319.1146 0 989.68846 151410.33 -157938.54 -145.84664 20369.571 234.22928 350.68677 0.84585946
|
||||
1460 68.88107 -3200.8425 1052.2514 -4253.0939 1296.3997 0 914.27128 151478.83 -157942.59 -1047.6067 20177.139 235.49603 352.58952 0.83805114
|
||||
1480 69.894247 -3229.1329 1032.538 -4261.6708 1273.6899 0 884.58641 151521.54 -157941.48 -877.62887 19983.452 231.08411 345.95296 0.88426485
|
||||
1500 71.009717 -3256.5597 1060.231 -4316.7907 1291.1374 0 874.13592 151461.84 -157943.91 -1479.1729 19788.536 237.28186 355.23846 0.89410552
|
||||
1520 72.041054 -3283.4789 1004.9547 -4288.4336 1248.3551 0 849.40507 151555.63 -157941.83 -1210.342 19590.335 224.91093 336.73148 0.81999833
|
||||
1540 73.084395 -3307.2541 1008.328 -4315.5821 1259.4211 0 846.2933 151520.12 -157941.42 -1328.6534 19389.457 225.66587 337.86416 0.81796565
|
||||
1560 74.135646 -3333.4164 1009.8078 -4343.2242 1290.3482 0 843.72954 151464.8 -157942.1 -1492.5376 19185.011 225.99706 338.35783 0.82352496
|
||||
1580 75.198241 -3359.5746 1031.9507 -4391.5253 1301.979 0 907.32598 151341.72 -157942.55 -931.21229 18977.005 230.95268 345.78871 0.81873619
|
||||
1600 76.272058 -3383.7255 977.90216 -4361.6277 1350.9107 0 1005.0889 151225.61 -157943.23 -265.11417 18769.775 218.85651 327.62822 0.87537743
|
||||
1620 77.356282 -3399.3062 994.75129 -4394.0575 1387.4383 0 1059.1407 151101.4 -157942.03 574.54697 18568.615 222.62738 333.25885 0.91918263
|
||||
1640 78.448545 -3415.8361 1023.468 -4439.304 1398.4672 0 1052.931 151054.15 -157944.85 470.27927 18377.301 229.05423 342.8805 0.94357863
|
||||
1660 79.550247 -3434.561 975.54176 -4410.1027 1429.1617 0 1081.052 151023.2 -157943.52 1049.9178 18195.592 218.32825 326.8381 0.87189374
|
||||
1680 80.667191 -3451.4085 987.31735 -4438.7259 1473.5691 0 1116.4474 150914.31 -157943.05 1058.2306 18025.735 220.96365 330.80265 0.84371639
|
||||
1700 81.797154 -3467.686 964.72099 -4432.407 1455.6679 0 1109.6516 150945 -157942.73 1282.6999 17867.835 215.90654 323.18716 0.91347876
|
||||
1720 82.926758 -3484.8522 984.05698 -4468.9092 1459.9348 0 1102.3739 150911.78 -157943 919.74849 17722.037 220.23397 329.6527 0.95604421
|
||||
1740 84.064705 -3497.8606 976.97179 -4474.8324 1401.3809 0 1034.3626 151032.67 -157943.25 535.35483 17586.464 218.64829 327.27748 0.95261024
|
||||
1760 85.25497 -3516.3474 990.65511 -4507.0025 1393.0104 0 1015.5429 151026.85 -157942.4 -45.078457 17457.877 221.71065 331.88315 0.92222263
|
||||
1780 86.432811 -3532.5203 981.67325 -4514.1936 1381.8497 0 1018.8916 151028.12 -157943.05 419.25311 17333.542 219.70049 328.86023 0.94159899
|
||||
1800 87.629265 -3551.0627 978.09831 -4529.161 1409.4225 0 1023.8144 150980.45 -157942.84 -136.21958 17214.117 218.90041 327.67684 0.90973891
|
||||
1820 88.810324 -3566.367 953.86873 -4520.2357 1386.004 0 1027.6913 151009.66 -157943.59 272.29498 17097.552 213.47778 319.53574 0.93491142
|
||||
1840 89.996806 -3581.9401 989.35892 -4571.299 1438.2511 0 1011.4985 150924.05 -157945.1 -277.89182 16984.647 221.42056 331.39393 1.0309706
|
||||
1860 91.192728 -3597.0855 939.72505 -4536.8105 1424.7503 0 1045.0751 150938.2 -157944.83 769.1418 16874.282 210.31239 314.73818 1.0402053
|
||||
1880 92.395072 -3609.1452 988.80243 -4597.9477 1452.2757 0 1054.8324 150839.43 -157944.48 448.42199 16769.952 221.29601 331.17499 1.095477
|
||||
1900 93.599308 -3623.9274 981.88757 -4605.815 1467.8981 0 1058.3428 150811.66 -157943.72 440.93441 16671.114 219.74845 328.86095 1.0839713
|
||||
1920 94.800441 -3637.4995 962.46738 -4599.9668 1472.6584 0 1100.9414 150770.55 -157944.12 927.11674 16577.506 215.40217 322.39885 0.97801499
|
||||
1940 96.006696 -3649.8745 932.46317 -4582.3377 1482.9302 0 1127.1576 150751.01 -157943.44 1275.661 16490.871 208.68717 312.30264 1.0388692
|
||||
1960 97.217233 -3660.5717 957.9057 -4618.4774 1471.5387 0 1090.5959 150763.08 -157943.69 926.00133 16412.162 214.38126 320.81698 1.081062
|
||||
1980 98.432616 -3673.974 955.97217 -4629.9462 1448.9016 0 1043.2494 150823.46 -157945.55 585.7993 16339.534 213.94853 320.15896 1.0997884
|
||||
2000 99.651307 -3687.9477 943.17863 -4631.1263 1431.8862 0 1028.9334 150853.1 -157945.05 406.94681 16271.378 211.08531 315.85857 1.1166274
|
||||
Loop time of 99.6513 on 1 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Performance: 1.734 ns/day, 13.840 hours/ns, 20.070 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 78.424 | 78.424 | 78.424 | 0.0 | 78.70
|
||||
Bond | 0.032606 | 0.032606 | 0.032606 | 0.0 | 0.03
|
||||
Kspace | 3.7865 | 3.7865 | 3.7865 | 0.0 | 3.80
|
||||
Neigh | 9.511 | 9.511 | 9.511 | 0.0 | 9.54
|
||||
Comm | 0.71185 | 0.71185 | 0.71185 | 0.0 | 0.71
|
||||
Output | 0.0071998 | 0.0071998 | 0.0071998 | 0.0 | 0.01
|
||||
Modify | 7.1361 | 7.1361 | 7.1361 | 0.0 | 7.16
|
||||
Other | | 0.04205 | | | 0.04
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 20897 ave 20897 max 20897 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.20428e+06 ave 2.20428e+06 max 2.20428e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2204275
|
||||
Ave neighs/atom = 881.71
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 122
|
||||
Dangerous builds = 16
|
||||
|
||||
Total wall time: 0:01:39
|
||||
|
|
@ -0,0 +1,252 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
comm_modify vel yes
|
||||
compute TATOM ATOMS temp/com
|
||||
compute TEMP all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix_modify RIGID temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1338)
|
||||
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 1 100.0
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 0.45823026 3742.7989 5338.7966 -1595.9977 567.29056 0 662.23349 155098.48 -157924 31679.045 13979.575 1194.8336 1690.2267 201.65776
|
||||
40 0.95719695 2752.9392 4407.9332 -1654.994 792.86724 0 870.27523 154593.92 -157912.06 27392.303 14278.564 986.5045 1450.7624 56.079839
|
||||
60 1.4402499 1995.9776 3980.851 -1984.8734 660.64219 0 750.43211 154538.47 -157934.42 22242.677 14691.413 890.92262 1315.3403 40.305318
|
||||
80 1.9050057 1377.133 3449.7879 -2072.6549 617.64238 0 605.75691 154628.64 -157924.69 17345.359 15201.397 772.06961 1146.6088 21.447181
|
||||
100 2.3745039 886.38999 3038.411 -2152.021 537.89929 0 450.99966 154789.13 -157930.05 13299.226 15783.335 680.00261 1011.6773 15.016235
|
||||
120 2.8589215 488.05512 2928.1336 -2440.0785 536.23142 0 334.886 154620.05 -157931.25 8694.3495 16409.509 655.32232 977.40122 9.853881
|
||||
140 3.2965367 160.14918 2538.5119 -2378.3627 509.19544 0 249.89187 154793.34 -157930.79 6363.0936 17053.486 568.12418 847.92535 7.2744487
|
||||
160 3.7223189 -103.57483 2403.1617 -2506.7365 494.69852 0 144.07166 154790.83 -157936.34 4017.2081 17699.095 537.83252 803.44789 5.3901447
|
||||
180 4.1554348 -315.60495 2216.8001 -2532.405 477.29347 0 80.852028 154842.41 -157932.96 1958.2418 18336.716 496.1244 741.47039 4.4401782
|
||||
200 4.5533779 -490.60343 2058.8989 -2549.5023 470.22934 0 80.797892 154831.65 -157932.18 1260.3909 18960.132 460.78579 688.924 3.5878094
|
||||
220 4.9085493 -644.11131 2001.1202 -2645.2315 494.11411 0 53.067462 154741.64 -157934.05 -16.783051 19564.819 447.8548 669.94702 2.7746354
|
||||
240 5.2955835 -773.77077 1911.0789 -2684.8496 491.56671 0 36.573942 154722.87 -157935.86 -773.28467 20144.754 427.70337 639.97783 2.2990474
|
||||
260 5.7046614 -886.74825 1719.7065 -2606.4547 462.97836 0 47.58745 154814.53 -157931.55 -695.31939 20696.484 384.87384 575.96438 1.9230094
|
||||
280 6.0633757 -983.59043 1659.2126 -2642.803 476.05207 0 65.528 154749.28 -157933.67 -1099.7766 21220.608 371.33519 555.77921 1.7044743
|
||||
300 6.4097662 -1069.381 1531.6365 -2601.0175 487.38768 0 130.0599 154709.01 -157927.47 -548.94313 21717.512 342.78339 513.13082 1.4029607
|
||||
320 6.7455602 -1144.854 1562.925 -2707.779 508.98546 0 127.16624 154591.4 -157935.34 -1515.6429 22190.677 349.78582 523.6096 1.414493
|
||||
340 7.0504746 -1216.4848 1511.8539 -2728.3386 518.41635 0 144.67031 154541.86 -157933.28 -1346.5299 22636.537 338.356 506.57907 1.2331509
|
||||
360 7.3652327 -1279.8842 1434.5465 -2714.4306 524.92137 0 153.81139 154537.16 -157930.32 -1445.625 23056.451 321.05444 480.69079 1.1396531
|
||||
380 7.6638732 -1340.1922 1391.8227 -2732.0149 537.12747 0 180.48607 154482.89 -157932.52 -1316.0441 23450.122 311.49278 466.4254 1.0045437
|
||||
400 7.9763258 -1398.97 1401.3049 -2800.275 547.10484 0 190.74701 154394.07 -157932.19 -1697.8502 23818.202 313.61492 469.64586 0.92579849
|
||||
420 8.2703266 -1450.483 1357.937 -2808.4199 555.88824 0 178.22829 154390.11 -157932.65 -1958.9883 24158.533 303.90908 455.10587 0.90768013
|
||||
440 8.5902264 -1501.4161 1341.5516 -2842.9677 573.14949 0 195.16753 154320.41 -157931.7 -1876.025 24469.636 300.24201 449.65628 0.81297929
|
||||
460 8.8937869 -1551.3256 1326.1262 -2877.4518 581.25352 0 206.82716 154267.73 -157933.26 -2033.2771 24752.01 296.78977 444.48443 0.8068672
|
||||
480 9.1780484 -1598.4261 1289.0614 -2887.4875 599.31424 0 250.55266 154195.32 -157932.67 -1734.9907 25004.733 288.4946 432.05986 0.78706924
|
||||
500 9.4627533 -1647.1265 1310.6504 -2957.7768 620.75343 0 278.84436 154075.73 -157933.11 -1819.9564 25230.755 293.32624 439.2975 0.79707067
|
||||
520 9.744127 -1694.4448 1256.1824 -2950.6272 640.46082 0 300.05753 154043.8 -157934.95 -1676.1925 25430.395 281.13621 421.05228 0.74177674
|
||||
540 10.022904 -1741.636 1235.1581 -2976.794 663.79651 0 343.79844 153947.6 -157931.99 -1450.0194 25605.442 276.43091 414.00136 0.73713962
|
||||
560 10.317977 -1784.6341 1213.4226 -2998.0567 667.043 0 361.93171 153904.04 -157931.07 -1633.3649 25757.73 271.56648 406.71944 0.71740617
|
||||
580 10.599227 -1824.7401 1203.2527 -3027.9928 695.49991 0 399.21355 153809.37 -157932.08 -1210.3391 25887.112 269.29042 403.29611 0.74045254
|
||||
600 10.872629 -1865.8971 1201.7743 -3067.6714 714.59075 0 432.45767 153718.17 -157932.89 -1199.4783 25998.228 268.95956 402.78195 0.77684613
|
||||
620 11.144566 -1905.4349 1175.2733 -3080.7082 746.97979 0 456.14057 153649.58 -157933.41 -952.82994 26092.511 263.02858 393.89597 0.76773558
|
||||
640 11.426686 -1943.5065 1165.9307 -3109.4372 755.41374 0 483.29607 153585.09 -157933.23 -984.52156 26172.87 260.93768 390.78613 0.7189019
|
||||
660 11.699499 -1980.6601 1149.4782 -3130.1383 744.34638 0 460.44858 153597.74 -157932.67 -1312.9908 26238.692 257.25559 385.23533 0.78159645
|
||||
680 12.011345 -2017.8555 1159.1341 -3176.9896 734.22636 0 422.37481 153599.86 -157933.45 -1747.0103 26285.639 259.41659 388.49552 0.73989774
|
||||
700 12.310963 -2054.4791 1156.1376 -3210.6166 733.10466 0 423.00212 153565.55 -157932.27 -1636.1386 26309.504 258.74596 387.47025 0.77987596
|
||||
720 12.582198 -2091.6681 1174.8015 -3266.4696 739.49203 0 428.4236 153500.55 -157934.93 -1696.6642 26311.163 262.923 393.72409 0.79497316
|
||||
740 12.970993 -2130.5966 1159.8063 -3290.403 749.2778 0 449.89501 153443.16 -157932.74 -1820.153 26290.013 259.56704 388.70043 0.78112554
|
||||
760 13.328577 -2169.5713 1138.8137 -3308.385 783.90384 0 538.06269 153303 -157933.35 -1011.1163 26246.385 254.86884 381.62657 0.84363887
|
||||
780 13.701648 -2205.5168 1142.2259 -3347.7427 832.2034 0 585.43846 153169.83 -157935.21 -877.81856 26188.431 255.63251 382.73539 0.91548041
|
||||
800 14.064343 -2244.3113 1142.1063 -3386.4176 846.00692 0 618.31624 153083.94 -157934.68 -661.72264 26119.157 255.60573 382.69013 0.92572469
|
||||
820 14.33644 -2280.7153 1109.9081 -3390.6234 858.49264 0 654.04808 153031.02 -157934.18 -465.91138 26042.068 248.39971 371.86079 0.98075233
|
||||
840 14.635953 -2313.2679 1104.4689 -3417.7368 870.71302 0 653.66264 152993.54 -157935.66 -613.02846 25959.467 247.1824 370.05309 0.94666727
|
||||
860 14.907509 -2345.7077 1108.2969 -3454.0045 887.72574 0 641.79104 152948.54 -157932.06 -761.70678 25870.075 248.03912 371.27357 1.0741475
|
||||
880 15.183513 -2377.4774 1063.4515 -3440.9289 869.82787 0 628.04321 152993.89 -157932.69 -855.49925 25771.822 238.00263 356.26939 0.99311617
|
||||
900 15.507916 -2408.6686 1102.0685 -3510.7371 895.2471 0 633.04968 152893.8 -157932.84 -816.76925 25662.984 246.64518 369.19309 1.0560774
|
||||
920 15.786689 -2440.9159 1064.6296 -3505.5455 907.99426 0 640.59576 152879.85 -157933.98 -771.43262 25544.45 238.26628 356.60949 1.103337
|
||||
940 16.081306 -2471.511 1069.129 -3540.64 935.37062 0 676.1306 152783.76 -157935.9 -835.05654 25417.183 239.27326 358.07731 1.186596
|
||||
960 16.361392 -2501.4199 1106.6503 -3608.0702 940.89653 0 655.04578 152730.01 -157934.03 -1188.2588 25280.379 247.6706 370.62835 1.259746
|
||||
980 16.6468 -2536.7151 1106.7401 -3643.4553 955.83568 0 689.00094 152647 -157935.3 -1034.563 25131.304 247.69072 370.65118 1.2744144
|
||||
1000 16.935502 -2570.2795 1086.764 -3657.0436 980.59572 0 714.89208 152582.49 -157935.02 -778.85654 24971.385 243.22002 363.90242 1.3687958
|
||||
1020 17.227137 -2602.1046 1057.6875 -3659.7921 986.13374 0 727.61595 152561.35 -157934.9 -733.05283 24804.434 236.71263 354.20236 1.2597408
|
||||
1040 17.498504 -2630.2834 1061.6996 -3691.9831 979.55337 0 702.15346 152561.09 -157934.78 -845.34279 24631.58 237.61056 355.56436 1.2277288
|
||||
1060 17.773529 -2662.6359 1059.732 -3722.3679 987.68613 0 704.67809 152519.16 -157933.89 -870.46195 24451.603 237.17019 354.91872 1.1988053
|
||||
1080 18.050301 -2692.4034 1097.314 -3789.7174 1025.2827 0 758.27603 152361.94 -157935.22 -859.61672 24264.679 245.58112 367.45939 1.3334136
|
||||
1100 18.32944 -2721.6082 1035.0808 -3756.689 1024.3757 0 793.48607 152361.85 -157936.4 -398.00889 24072.334 231.65321 346.6143 1.2677215
|
||||
1120 18.641844 -2749.785 1044.4525 -3794.2375 1055.3749 0 824.30266 152262.04 -157935.96 -237.96338 23879.17 233.75062 349.76962 1.2451155
|
||||
1140 18.960959 -2772.8286 1065.2495 -3838.078 1064.0529 0 819.37794 152214.82 -157936.33 -419.50711 23686.912 238.40502 356.77133 1.1955971
|
||||
1160 19.294018 -2799.8843 1046.0072 -3845.8914 1068.2773 0 805.55181 152215.61 -157935.33 -627.01178 23494.818 234.09856 350.34221 1.1430413
|
||||
1180 19.649965 -2828.7115 1062.1027 -3890.8142 1081.854 0 768.64664 152195.11 -157936.43 -1113.3883 23300.677 237.70076 355.77198 1.0829394
|
||||
1200 19.96859 -2856.704 1046.499 -3903.203 1081.2546 0 753.81059 152196.72 -157934.99 -1184.6559 23100.615 234.20861 350.52914 1.0991524
|
||||
1220 20.326653 -2886.057 1023.9211 -3909.9781 1088.5712 0 740.41133 152197.78 -157936.75 -1477.5653 22893.4 229.15565 343.00067 1.0072919
|
||||
1240 20.659779 -2913.7708 995.31097 -3909.0818 1069.874 0 758.11146 152202.13 -157939.2 -1090.4758 22677.17 222.75264 333.41163 0.98913753
|
||||
1260 20.982659 -2936.9388 1011.886 -3948.8248 1101.8407 0 796.10406 152091.56 -157938.33 -917.17194 22454.903 226.46216 338.97372 0.98612749
|
||||
1280 21.296781 -2960.7771 994.15899 -3954.9361 1129.3448 0 823.90727 152029.43 -157937.61 -820.42886 22229.299 222.49482 333.04692 0.94562797
|
||||
1300 21.610997 -2984.3569 1049.8825 -4034.2394 1141.808 0 815.97434 151946.6 -157938.63 -777.81536 22002.292 234.96586 351.7259 0.97584665
|
||||
1320 21.939147 -3010.5287 1015.4181 -4025.9468 1162.122 0 814.19766 151933.87 -157936.14 -896.97771 21774.771 227.25266 340.00602 1.1005558
|
||||
1340 22.290971 -3038.0553 985.5931 -4023.6484 1161.8588 0 834.2486 151919.16 -157938.92 -776.69761 21546.055 220.57776 330.09107 1.0139801
|
||||
1360 22.647999 -3060.107 995.10747 -4055.2145 1155.9364 0 823.15336 151904.81 -157939.11 -1060.7954 21316.783 222.70709 333.36443 0.91659915
|
||||
1380 23.10948 -3084.6301 1045.0151 -4129.6452 1182.7352 0 811.15693 151815.78 -157939.31 -1245.9569 21085.59 233.87652 350.01917 1.0453875
|
||||
1400 23.508905 -3109.9777 987.57375 -4097.5514 1174.5153 0 826.73317 151839.75 -157938.55 -936.38803 20851.737 221.02103 330.8031 0.91405623
|
||||
1420 23.906708 -3133.4897 996.08018 -4129.5698 1204.428 0 883.9796 151722.31 -157940.29 -279.27606 20617.831 222.92479 333.68351 0.93320818
|
||||
1440 24.340815 -3156.6284 1002.5391 -4159.1675 1256.8861 0 938.67074 151584.42 -157939.15 -252.37357 20388.73 224.3703 335.78661 1.0353205
|
||||
1460 24.814756 -3174.2482 1025.2447 -4199.493 1219.0264 0 890.12474 151633.42 -157942.07 -472.20532 20165.369 229.45188 343.47039 0.91379457
|
||||
1480 25.194546 -3199.1381 1019.3011 -4218.4392 1263.6197 0 907.8062 151551.73 -157941.59 -357.34642 19946.233 228.12168 341.47893 0.95052162
|
||||
1500 25.6163 -3221.8311 999.94752 -4221.7787 1277.1026 0 966.69277 151477.62 -157943.19 163.84163 19732.291 223.79031 334.84833 1.1106364
|
||||
1520 26.062775 -3240.6737 1026.9402 -4267.6139 1307.0169 0 971.17205 151397.27 -157943.07 300.59837 19526.783 229.83132 344.05076 0.92328807
|
||||
1540 26.51185 -3263.1162 1054.1755 -4317.2916 1310.0417 0 972.81145 151342.02 -157942.16 -71.812538 19330.083 235.92663 353.19321 0.92162655
|
||||
1560 26.975349 -3285.1217 1012.3967 -4297.5183 1317.4278 0 1037.4478 151290.29 -157942.68 862.26427 19140.892 226.57645 339.17946 0.91729521
|
||||
1580 27.358741 -3305.5601 989.56962 -4295.1297 1340.9939 0 1081.7847 151223.92 -157941.82 1218.8084 18963.059 221.46771 331.53455 0.89110049
|
||||
1600 27.75085 -3325.3691 1029.8506 -4355.2197 1351.2586 0 1061.6722 151170.95 -157939.1 749.81991 18797.795 230.48267 344.98106 1.0044287
|
||||
1620 28.144375 -3345.1891 1016.654 -4361.8431 1337.3071 0 1043.5237 151199.64 -157942.31 600.76159 18642.93 227.52925 340.61677 0.89914217
|
||||
1640 28.539596 -3364.6709 980.13009 -4344.801 1354.0177 0 1066.4673 151176.84 -157942.13 1010.3991 18496.839 219.35513 328.33786 0.95094445
|
||||
1660 28.935194 -3382.7945 996.82121 -4379.6158 1343.4606 0 1016.5523 151199.22 -157938.85 546.93155 18360.15 223.09063 333.92162 0.96051901
|
||||
1680 29.338179 -3403.1864 976.66081 -4379.8472 1355.1038 0 1029.6963 151176.44 -157941.09 748.54459 18230.922 218.57869 327.20355 0.89183674
|
||||
1700 29.743355 -3417.6904 994.06517 -4411.7556 1368.1157 0 1013.9323 151145.57 -157939.38 351.45668 18109.291 222.47382 332.98346 0.9529814
|
||||
1720 30.14859 -3434.6282 979.89215 -4414.5203 1377.0869 0 1043.321 151104.18 -157939.11 1004.1915 17993.82 219.30187 328.11073 1.0747474
|
||||
1740 30.591568 -3451.0422 966.54361 -4417.5858 1376.9794 0 1050.8109 151097.44 -157942.82 1079.9737 17886.467 216.31444 323.72083 1.0159044
|
||||
1760 31.006144 -3469.3784 980.75469 -4450.1331 1396.5756 0 1015.9581 151078.09 -157940.75 190.14272 17786.919 219.49491 328.49844 0.97971363
|
||||
1780 31.424875 -3485.9292 1008.375 -4494.3041 1373.9658 0 984.95385 151090.2 -157943.42 -155.51723 17691.03 225.67639 337.7992 0.97942677
|
||||
1800 31.849784 -3502.475 976.23102 -4478.706 1385.4591 0 994.63329 151084.94 -157943.74 288.55406 17597.361 218.48251 327.04845 0.91364963
|
||||
1820 32.275504 -3520.5204 971.19507 -4491.7155 1407.4082 0 1049.909 150992.97 -157942.01 526.1499 17507.18 217.35545 325.30923 0.99414761
|
||||
1840 32.701591 -3535.2936 982.97322 -4518.2668 1419.0124 0 1050.2222 150955.57 -157943.08 420.31843 17421.408 219.99142 329.22593 1.0824421
|
||||
1860 33.133267 -3551.8598 947.45359 -4499.3134 1430.136 0 1069.4805 150943.73 -157942.66 669.02599 17340.063 212.04206 317.36556 0.97096264
|
||||
1880 33.56593 -3564.7527 963.54319 -4528.2959 1418.0293 0 1050.1008 150947.78 -157944.21 529.33841 17263.982 215.64294 322.72997 0.96836521
|
||||
1900 34.00203 -3580.0607 963.5239 -4543.5846 1424.6268 0 1048.9836 150925.17 -157942.36 464.00157 17192.083 215.63863 322.69033 1.0695571
|
||||
1920 34.44279 -3593.8573 957.94124 -4551.7986 1437.3475 0 1061.2427 150893.58 -157943.97 400.78058 17123.621 214.38922 320.8512 1.015936
|
||||
1940 34.877758 -3608.3005 951.71962 -4560.0201 1421.2611 0 1059.2678 150903.97 -157944.52 332.6227 17058.096 212.9968 318.72703 1.0660417
|
||||
1960 35.315982 -3623.3562 948.66706 -4572.0233 1438.6049 0 1066.4475 150868.57 -157945.64 448.04656 16995.11 212.31364 317.61154 1.1874864
|
||||
1980 35.79727 -3635.1448 958.32383 -4593.4687 1448.1655 0 1056.2971 150846.27 -157944.2 110.28409 16935.142 214.47484 320.97102 1.0535213
|
||||
2000 36.231822 -3649.7345 959.87855 -4609.6131 1458.7554 0 1080.5488 150796.28 -157945.2 615.27816 16877.582 214.82279 321.49302 1.0526861
|
||||
Loop time of 36.2319 on 4 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Performance: 4.769 ns/day, 5.032 hours/ns, 55.200 timesteps/s
|
||||
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.246 | 21.089 | 23.446 | 32.8 | 58.21
|
||||
Bond | 0.012314 | 0.012709 | 0.013402 | 0.4 | 0.04
|
||||
Kspace | 2.0259 | 4.3875 | 6.228 | 72.1 | 12.11
|
||||
Neigh | 2.6629 | 2.6673 | 2.6718 | 0.3 | 7.36
|
||||
Comm | 0.95863 | 0.96795 | 0.97884 | 0.9 | 2.67
|
||||
Output | 0.0071304 | 0.0093493 | 0.0142 | 2.9 | 0.03
|
||||
Modify | 7.0096 | 7.0134 | 7.0186 | 0.1 | 19.36
|
||||
Other | | 0.08472 | | | 0.23
|
||||
|
||||
Nlocal: 625 ave 683 max 565 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 12687 ave 12923 max 12461 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 531145 ave 625145 max 458041 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2124581
|
||||
Ave neighs/atom = 849.832
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 122
|
||||
Dangerous builds = 16
|
||||
|
||||
Total wall time: 0:00:36
|
||||
|
|
@ -1,230 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 14
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
|
||||
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix NVE DRUDES nve
|
||||
|
||||
compute TEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Memory usage per processor = 24.8361 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 1.529202 2882.459 4527.8074 -1645.3484 561.72857 0 600.34616 155114.77 -157922.19 27167.702 14058.741 1013.3326 1438.6699 160.63128
|
||||
40 3.073256 1331.3826 3348.9313 -2017.5487 681.52309 0 553.09465 154668.62 -157920.79 17925.93 14484.215 749.4977 1105.2032 36.587791
|
||||
60 4.584862 297.35979 2604.4137 -2307.0539 583.99971 0 409.0399 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335649
|
||||
80 6.053256 -374.31023 2263.3247 -2637.635 534.80338 0 212.27981 154543.18 -157927.9 6155.9261 15645.855 506.53672 755.45209 7.6929084
|
||||
100 7.4787509 -905.58889 1911.7191 -2817.308 532.30405 0 87.570168 154497.48 -157934.66 2149.3099 16288.797 427.84666 639.27768 4.1289101
|
||||
120 8.8570309 -1233.6894 1675.0881 -2908.7775 544.7643 0 59.500519 154422.72 -157935.76 233.4994 16915.818 374.88816 560.54169 2.8313123
|
||||
140 10.102229 -1463.4927 1468.7443 -2932.237 539.69692 0 41.083584 154424.91 -157937.93 -1492.9865 17509.345 328.70799 491.66353 2.1394958
|
||||
160 11.319324 -1695.7535 1385.9603 -3081.7137 552.91518 0 30.022893 154274.72 -157939.37 -3010.4983 18061.925 310.18075 463.968 1.9858941
|
||||
180 12.62008 -1818.1958 1253.169 -3071.3648 559.57456 0 20.01719 154289.67 -157940.63 -3354.4536 18564.877 280.4618 419.57594 1.6725953
|
||||
200 13.836408 -1949.6497 1210.0669 -3159.7167 570.055 0 16.319449 154195.04 -157941.13 -4118.0013 19014.456 270.81546 405.06925 1.766255
|
||||
220 15.032024 -2031.6125 1148.1454 -3179.7579 598.02981 0 30.833041 154127.13 -157935.75 -4514.7299 19406.767 256.9573 384.33701 1.6839691
|
||||
240 16.302775 -2118.6259 1120.0048 -3238.6307 613.2903 0 59.888138 154030.6 -157942.41 -4415.1944 19738.97 250.65937 374.93983 1.5971234
|
||||
260 17.465169 -2203.4348 1065.8476 -3269.2823 614.19171 0 77.619746 153980.69 -157941.79 -4564.2677 20011.077 238.53887 356.80737 1.5247856
|
||||
280 18.614435 -2317.9282 1033.2676 -3351.1958 650.51218 0 126.14976 153811.64 -157939.49 -4722.7543 20224.149 231.24742 345.8479 1.5839508
|
||||
300 19.757547 -2377.6306 992.4842 -3370.1148 688.02217 0 179.77994 153701.18 -157939.1 -4126.4983 20378.439 222.12 332.08757 1.7406267
|
||||
320 20.888309 -2419.6547 1023.0345 -3442.6892 720.31567 0 227.70007 153549.33 -157940.04 -4083.8776 20479.241 228.95722 342.33844 1.7368676
|
||||
340 22.018005 -2456.7661 1048.83 -3505.5961 754.13021 0 264.44865 153415.74 -157939.91 -3894.7125 20529.721 234.73031 351.04714 1.6271854
|
||||
360 23.241519 -2504.7475 1041.9912 -3546.7386 785.42547 0 335.38743 153271.47 -157939.03 -3464.4465 20531.323 233.19976 348.66924 1.7943874
|
||||
380 24.370763 -2596.2223 1000.109 -3596.3313 825.31479 0 390.18238 153129.56 -157941.39 -3355.5804 20490.646 223.82645 334.61119 1.8093168
|
||||
400 25.499192 -2666.6702 1006.474 -3673.1442 865.9858 0 422.51674 152978.57 -157940.21 -3329.4637 20411.001 225.25095 336.79016 1.7220267
|
||||
420 26.635042 -2675.8885 1036.9567 -3712.8452 909.14044 0 490.71452 152826.18 -157938.88 -2907.7096 20294.317 232.07303 346.92895 1.8970394
|
||||
440 27.774963 -2731.5399 1054.4488 -3785.9886 935.99349 0 530.9675 152684.75 -157937.7 -2566.587 20147.094 235.9878 352.84462 1.8021906
|
||||
460 28.922784 -2808.5929 996.20283 -3804.7957 986.6991 0 582.25374 152565.95 -157939.7 -2489.2912 19973.682 222.95224 333.32237 1.7660757
|
||||
480 30.07189 -2862.64 1012.7035 -3875.3436 1005.1596 0 610.07691 152450.62 -157941.2 -2031.6453 19777.635 226.64513 338.80268 1.8767218
|
||||
500 31.210731 -2935.4679 989.23412 -3924.702 1019.9115 0 633.87354 152362.4 -157940.89 -2214.2821 19561.863 221.39263 330.98935 1.7563884
|
||||
520 32.363073 -2989.4684 968.83888 -3958.3072 1057.5825 0 655.88302 152269.68 -157941.45 -2298.887 19328.548 216.82813 324.17678 1.6971802
|
||||
540 33.631173 -3036.6833 1016.2589 -4052.9421 1091.2498 0 658.37327 152140.1 -157942.67 -2240.561 19080.875 227.44082 340.06628 1.7350202
|
||||
560 34.815099 -3093.7794 947.7515 -4041.5309 1141.2318 0 764.1603 151995.79 -157942.71 -1157.5191 18819.961 212.10873 317.02152 1.858938
|
||||
580 36.012327 -3166.4133 987.9563 -4154.3696 1199.2171 0 796.34125 151794.12 -157944.05 -1304.4967 18555.635 221.10665 330.55449 1.7687509
|
||||
600 37.228579 -3194.8572 979.66264 -4174.5199 1206.8265 0 842.68836 151717.96 -157941.99 -843.16439 18290.222 219.25051 327.76152 1.7899831
|
||||
620 38.457464 -3255.2052 965.87596 -4221.0812 1218.8406 0 849.13897 151653.64 -157942.7 -628.0114 18027.862 216.16502 323.08905 1.8846337
|
||||
640 39.700987 -3269.6729 1003.1309 -4272.8038 1273.0417 0 928.68865 151468.54 -157943.07 117.71698 17770.578 224.50275 335.54575 1.9677468
|
||||
660 40.961165 -3293.6967 1002.4504 -4296.1471 1299.7531 0 955.60765 151392.37 -157943.87 207.76414 17523.763 224.35045 335.3089 1.9848634
|
||||
680 42.237597 -3310.539 1011.7934 -4322.3324 1358.9202 0 986.69345 151275.62 -157943.56 677.05046 17289.864 226.44145 338.46824 1.9349743
|
||||
700 43.530486 -3380.6882 976.5597 -4357.2479 1378.7945 0 1003.8845 151205.15 -157945.07 605.30766 17069.732 218.55607 326.63938 1.9523301
|
||||
720 44.837568 -3385.7377 1005.1302 -4390.8679 1389.9512 0 1012.3035 151151.06 -157944.19 817.35931 16863.381 224.95021 336.31657 1.7675955
|
||||
740 46.162222 -3378.6942 1023.8252 -4402.5194 1400.0688 0 1063.4211 151077.64 -157943.65 1513.5741 16671.518 229.13418 342.45655 2.0311926
|
||||
760 47.500172 -3425.4378 1036.4011 -4461.8389 1408.8321 0 1068.7339 151003.75 -157943.15 1350.0894 16496.502 231.9487 346.7108 1.9605952
|
||||
780 48.851472 -3453.9533 1021.8895 -4475.8428 1425.2091 0 1104.5857 150938.44 -157944.08 1801.2205 16339.019 228.70097 341.83264 1.9802343
|
||||
800 50.2129 -3497.6136 979.31494 -4476.9285 1441.1399 0 1119.8292 150908.27 -157946.17 1649.8638 16200.982 219.17269 327.47284 2.1340593
|
||||
820 51.586885 -3545.7792 969.50276 -4515.282 1479.3831 0 1103.1191 150847.98 -157945.76 1410.2174 16081.771 216.97671 324.23659 2.0229826
|
||||
840 52.968935 -3562.4777 972.83071 -4535.3084 1470.5582 0 1079.9217 150857.46 -157943.25 1608.0813 15977.891 217.72151 325.33963 2.0498221
|
||||
860 54.3603 -3569.1307 987.8631 -4556.9938 1446.8392 0 1055.8137 150885.62 -157945.27 1110.2002 15887.947 221.08579 330.4231 1.9689916
|
||||
880 55.752677 -3612.6783 957.13055 -4569.8088 1435.3619 0 1056.264 150883.35 -157944.78 914.27883 15809.361 214.20778 320.06673 2.0614732
|
||||
900 57.105164 -3660.821 939.51428 -4600.3353 1463.6114 0 1070.121 150812.25 -157946.31 1261.3306 15740.285 210.26522 314.20385 1.967446
|
||||
920 58.464501 -3685.0371 941.21956 -4626.2567 1483.8487 0 1096.8187 150737.38 -157944.31 1236.4144 15680.989 210.64687 314.81024 1.89883
|
||||
940 59.82202 -3719.0907 915.61639 -4634.7071 1515.6474 0 1104.1119 150691.39 -157945.86 1066.5855 15632.292 204.91683 306.20627 1.9280979
|
||||
960 61.189826 -3752.7758 893.54303 -4646.3189 1517.1996 0 1125.6182 150656.81 -157945.94 1449.4275 15593.029 199.97676 298.74917 2.0320058
|
||||
980 62.459059 -3752.1139 925.61635 -4677.7302 1528.3468 0 1137.3575 150600.83 -157944.27 1493.1803 15564.263 207.15484 309.5242 2.0018169
|
||||
1000 63.8395 -3737.7642 905.82477 -4643.589 1505.254 0 1110.1192 150686.75 -157945.72 1296.1084 15546.258 202.72544 302.92529 1.9202879
|
||||
1020 65.169118 -3767.2178 892.14155 -4659.3593 1493.2162 0 1085.8721 150707.12 -157945.57 922.80521 15537.177 199.66311 298.24598 2.0980372
|
||||
1040 66.474103 -3783.5702 891.57404 -4675.1442 1484.1631 0 1076.2171 150710.25 -157945.77 707.15481 15535.102 199.5361 298.15469 1.8998396
|
||||
1060 67.68596 -3816.1219 868.55884 -4684.6807 1478.7568 0 1060.3026 150723.2 -157946.94 638.16846 15538.641 194.38525 290.46937 1.8282435
|
||||
1080 69.003517 -3807.3485 875.34276 -4682.6913 1482.2148 0 1055.6143 150725.66 -157946.19 416.14661 15546.427 195.90351 292.75831 1.802085
|
||||
1100 70.315532 -3814.5517 894.42504 -4708.9768 1492.6318 0 1053.4891 150692.22 -157947.31 341.55654 15557.253 200.17416 299.12904 1.8640462
|
||||
1120 71.62724 -3837.42 886.31149 -4723.7315 1497.9422 0 1047.1133 150677.33 -157946.12 4.9308474 15569.465 198.35833 296.42678 1.8247148
|
||||
1140 72.956868 -3802.3965 899.40687 -4701.8034 1479.6329 0 1020.1254 150744.44 -157946 -142.99064 15582.446 201.2891 300.81318 1.8383791
|
||||
1160 74.274932 -3810.7658 902.84695 -4713.6127 1472.5916 0 1018.8174 150740.5 -157945.52 12.783208 15594.928 202.059 301.90406 1.9647721
|
||||
1180 75.595463 -3786.4338 929.44447 -4715.8783 1477.4053 0 1016.2942 150735.81 -157945.39 -53.70556 15606.416 208.01158 310.85718 1.9043666
|
||||
1200 76.915409 -3800.0338 897.43664 -4697.4705 1483.1401 0 1059.31 150706.14 -157946.06 534.37576 15617.028 200.84816 300.11638 1.9100302
|
||||
1220 78.119883 -3799.6824 882.65153 -4682.3339 1488.5302 0 1036.1696 150739.15 -157946.19 155.57627 15628.242 197.53922 295.16257 1.8974641
|
||||
1240 79.419663 -3800.7533 911.18613 -4711.9394 1475.5968 0 1005.3229 150752.61 -157945.47 -457.64009 15638.953 203.92533 304.69739 1.9733514
|
||||
1260 80.721954 -3763.5149 950.12041 -4713.6353 1441.6787 0 964.69517 150825.9 -157945.91 -604.24646 15647.017 212.6389 317.74138 2.0086447
|
||||
1280 82.018768 -3770.742 937.09634 -4707.8384 1445.4659 0 949.37244 150842.61 -157945.28 -993.94783 15650.702 209.72409 313.39122 1.9703726
|
||||
1300 83.314893 -3777.4899 904.34062 -4681.8306 1435.5873 0 967.49755 150860.85 -157945.76 -640.04936 15648.293 202.39329 302.46077 1.8535337
|
||||
1320 84.617907 -3766.6204 885.81908 -4652.4395 1416.0678 0 971.89494 150906.86 -157947.27 -366.46049 15641.654 198.24813 296.26647 1.8149522
|
||||
1340 85.931152 -3774.8032 919.58694 -4694.3901 1425.1776 0 939.16654 150887.07 -157945.81 -950.33698 15631.589 205.80544 307.5014 2.0019282
|
||||
1360 87.242691 -3787.4243 922.65238 -4710.0767 1430.1028 0 964.01827 150842.71 -157946.91 -767.13405 15614.998 206.4915 308.53756 1.9863831
|
||||
1380 88.556261 -3792.754 900.77391 -4693.5279 1420.8035 0 953.09514 150878.52 -157945.95 -1072.9667 15593.378 201.59505 301.19366 1.9946415
|
||||
1400 89.868914 -3772.1032 910.85489 -4682.9581 1401.9732 0 959.20659 150901.09 -157945.23 -640.48972 15566.828 203.85119 304.58411 1.9776581
|
||||
1420 91.085535 -3782.5246 898.64718 -4681.1718 1436.1885 0 1010.9254 150817.16 -157945.45 -21.80524 15536.721 201.11908 300.5555 1.8440133
|
||||
1440 92.406331 -3775.4206 919.73488 -4695.1554 1446.1057 0 1018.1835 150785.23 -157944.68 46.810177 15507.157 205.83855 307.4904 2.123189
|
||||
1460 93.732761 -3757.7457 938.91361 -4696.6593 1451.5945 0 1008.6517 150787.38 -157944.28 -175.88589 15478.297 210.13079 313.97065 2.030827
|
||||
1480 95.057074 -3776.8625 933.4271 -4710.2896 1469.7064 0 1033.8521 150731.34 -157945.19 171.44717 15450.004 208.9029 312.19981 1.8912834
|
||||
1500 96.391192 -3764.5196 945.12068 -4709.6403 1483.0898 0 1052.3029 150699.59 -157944.62 431.18844 15423.716 211.51995 316.14058 1.85565
|
||||
1520 97.721669 -3760.514 960.29952 -4720.8136 1507.6965 0 1068.2902 150648.96 -157945.76 714.27148 15402.108 214.917 321.14587 2.0294443
|
||||
1540 99.056402 -3787.9932 950.73472 -4738.728 1514.4781 0 1058.2368 150635.29 -157946.73 547.92963 15384.955 212.77638 318.01984 1.8639142
|
||||
1560 100.30064 -3822.5612 921.12091 -4743.6821 1519.8628 0 1084.8337 150596.5 -157944.88 479.4088 15370.571 206.14875 308.02344 1.987069
|
||||
1580 101.63827 -3832.4207 936.50822 -4768.9289 1562.5808 0 1124.0034 150490.87 -157946.38 833.06708 15360.019 209.59246 313.15266 2.0528778
|
||||
1600 102.98354 -3862.3688 922.42346 -4784.7923 1571.2038 0 1110.9988 150479.2 -157946.19 674.29885 15354.399 206.44026 308.48417 1.9395764
|
||||
1620 104.32562 -3863.8731 946.37539 -4810.2485 1562.9498 0 1094.323 150478.98 -157946.5 -224.35579 15352.811 211.80075 316.51174 1.9551706
|
||||
1640 105.66368 -3834.5163 952.04367 -4786.5599 1536.5144 0 1078.6783 150544.66 -157946.41 -30.565669 15352.152 213.06933 318.41145 1.9589345
|
||||
1660 107.00124 -3859.131 892.31028 -4751.4413 1515.0462 0 1076.4059 150603.91 -157946.81 227.01045 15352.058 199.70087 298.41871 1.8658052
|
||||
1680 108.2363 -3858.2995 918.6578 -4776.9573 1533.9319 0 1064.9106 150570.69 -157946.49 335.15388 15352.595 205.5975 307.20976 1.9617869
|
||||
1700 109.5659 -3850.0817 929.25672 -4779.3384 1552.5519 0 1094.2161 150519.21 -157945.31 393.76719 15353.331 207.96956 310.72982 2.0330981
|
||||
1720 110.90017 -3890.603 917.87519 -4808.4781 1566.3302 0 1075.6092 150495.91 -157946.33 -76.371955 15355.997 205.42235 306.92393 2.0083539
|
||||
1740 112.13829 -3891.5259 936.37478 -4827.9007 1568.2195 0 1085.8514 150464.14 -157946.11 0.9297943 15358.36 209.5626 313.09836 2.0719603
|
||||
1760 113.46951 -3881.0244 903.38798 -4784.4124 1524.2547 0 1079.0557 150557.47 -157945.19 192.41461 15360.098 202.18008 302.05776 2.0203699
|
||||
1780 114.81068 -3885.7248 910.74799 -4796.4728 1532.8732 0 1055.4583 150560.36 -157945.17 -530.84683 15362.305 203.82727 304.58876 1.8966227
|
||||
1800 116.14689 -3907.0506 885.50025 -4792.5508 1533.7624 0 1068.2841 150550.77 -157945.37 240.13827 15362.751 198.17677 296.0834 1.9671724
|
||||
1820 117.48197 -3898.1244 894.18625 -4792.3107 1521.378 0 1059.1428 150574.05 -157946.88 34.574046 15361.495 200.12072 298.96924 2.0234207
|
||||
1840 118.82815 -3874.3766 895.94028 -4770.3169 1523.7865 0 1077.7882 150573.72 -157945.61 324.16201 15359.092 200.51327 299.59285 1.9530985
|
||||
1860 120.06522 -3892.2617 891.17198 -4783.4337 1526.1544 0 1091.1167 150543.11 -157943.82 574.32363 15357.261 199.44612 297.92332 2.0928308
|
||||
1880 121.40834 -3906.8943 911.93286 -4818.8271 1552.4086 0 1113.1993 150462.35 -157946.79 279.12422 15356.96 204.09245 304.90059 2.0679776
|
||||
1900 122.76151 -3922.7591 879.82965 -4802.5888 1550.6607 0 1108.3657 150485.77 -157947.38 356.47291 15359.386 196.90768 294.18644 1.9563556
|
||||
1920 124.11267 -3960.2437 869.21003 -4829.4537 1521.5339 0 1036.9974 150558.9 -157946.89 -839.29936 15362.76 194.53099 290.66184 1.8802157
|
||||
1940 125.45713 -3954.661 876.75754 -4831.4186 1506.7448 0 1007.0383 150601.14 -157946.34 -1316.6937 15361.338 196.22014 293.17781 1.9123591
|
||||
1960 126.70769 -3938.7558 876.41976 -4815.1756 1481.7627 0 996.84388 150652.15 -157945.93 -887.63902 15352.095 196.14454 293.08662 1.8680915
|
||||
1980 128.05176 -3911.4383 894.43818 -4805.8765 1516.4382 0 1037.517 150585.32 -157945.15 -176.75144 15336.185 200.1771 299.12472 1.8815139
|
||||
2000 129.4091 -3920.2641 888.06919 -4808.3333 1495.9942 0 1040.703 150601.72 -157946.75 -243.72475 15316.676 198.75171 296.94612 1.9653682
|
||||
Loop time of 129.409 on 1 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Pair time (%) = 109.108 (84.3128)
|
||||
Bond time (%) = 0.0499372 (0.0385887)
|
||||
Kspce time (%) = 3.30969 (2.55754)
|
||||
Neigh time (%) = 9.70209 (7.49723)
|
||||
Comm time (%) = 0.829103 (0.640684)
|
||||
Outpt time (%) = 0.00999022 (0.00771987)
|
||||
Other time (%) = 6.39989 (4.94547)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21780 ave 21780 max 21780 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.34087e+06 ave 2.34087e+06 max 2.34087e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2340869
|
||||
Ave neighs/atom = 936.348
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 6
|
||||
|
||||
|
|
@ -1,230 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
comm_modify vel yes
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 14
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
|
||||
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
|
||||
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
|
||||
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix NVE DRUDES nve
|
||||
|
||||
compute TEMP all temp/drude
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Memory usage per processor = 15.0906 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 0.47649789 2915.1578 4579.5774 -1664.4195 561.91893 0 600.76451 155095.13 -157922.23 27379.77 14058.574 1024.9188 1455.9194 160.86778
|
||||
40 0.97488093 1320.1721 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914
|
||||
60 1.4631288 284.06852 2671.4325 -2387.3639 575.54157 0 387.8792 154580.74 -157931.53 12104.741 15031.425 597.87207 886.98502 18.450413
|
||||
80 1.937151 -462.53017 2214.284 -2676.8142 560.36347 0 254.65245 154447.22 -157939.05 6285.2465 15651.216 495.56131 739.13811 7.4024411
|
||||
100 2.3922298 -965.19662 1839.831 -2805.0276 544.59528 0 115.80812 154469.59 -157935.02 2361.9397 16295.72 411.75795 615.12769 4.196977
|
||||
120 2.832803 -1316.6351 1649.585 -2966.2202 554.6664 0 50.928925 154365.49 -157937.3 -493.85523 16925.293 369.18052 552.0345 2.7331855
|
||||
140 3.2340388 -1590.9162 1440.6669 -3031.5831 526.07679 0 -24.44055 154404.35 -157937.57 -2586.2431 17517.285 322.42421 482.16117 2.297578
|
||||
160 3.6521859 -1742.3401 1326.8812 -3069.2213 539.49044 0 -43.846659 154369.1 -157933.96 -3549.2196 18059.707 296.95874 444.11026 2.0644677
|
||||
180 4.033325 -1895.1332 1224.1816 -3119.3148 555.27887 0 -18.261233 154275.94 -157932.27 -3762.2304 18545.518 273.97437 409.78413 1.806893
|
||||
200 4.4333398 -2004.4682 1176.8828 -3181.351 565.0443 0 0.21425471 154190.38 -157936.99 -4346.6036 18973.342 263.38879 393.94856 1.7400558
|
||||
220 4.8055639 -2094.1888 1098.3856 -3192.5744 592.45764 0 36.50238 154113.36 -157934.89 -4135.0794 19341.735 245.82095 367.67707 1.617053
|
||||
240 5.1688328 -2178.9829 1086.8322 -3265.8151 617.63697 0 96.836936 153957.27 -157937.56 -4121.5262 19651.8 243.23528 363.77401 1.6722646
|
||||
260 5.5313618 -2264.8265 1078.4348 -3343.2613 663.35817 0 167.76882 153763.13 -157937.52 -3799.3346 19907.052 241.35592 360.97385 1.6377289
|
||||
280 5.8937738 -2325.7764 1097.4356 -3423.212 717.74089 0 235.0127 153562.96 -157938.92 -3696.0526 20111.414 245.60833 367.31076 1.7042318
|
||||
300 6.254128 -2390.4932 1068.1054 -3458.5986 751.64681 0 295.31516 153435.34 -157940.9 -3512.2095 20268.754 239.04419 357.49427 1.665921
|
||||
320 6.6138928 -2455.1776 1041.7419 -3496.9195 765.8972 0 331.14997 153345 -157938.97 -3020.0674 20383.474 233.14397 348.62385 1.7179273
|
||||
340 6.9748628 -2536.9935 1050.7304 -3587.7239 793.64536 0 352.69908 153205.74 -157939.81 -3447.9127 20457.612 235.15562 351.6381 1.7214573
|
||||
360 7.3319299 -2603.5606 966.90943 -3570.47 819.14306 0 391.00909 153158.89 -157939.51 -3164.629 20490.764 216.39631 323.51872 1.7254892
|
||||
380 7.691319 -2594.787 1024.7927 -3619.5797 836.44816 0 434.32118 153047.12 -157937.47 -2902.9345 20485.923 229.35071 342.91482 1.7641915
|
||||
400 8.044276 -2647.3896 982.46478 -3629.8543 864.59805 0 479.08516 152963.5 -157937.04 -2535.9236 20447.668 219.87764 328.69587 1.8030508
|
||||
420 8.3971269 -2687.5263 1023.0437 -3710.57 928.04551 0 538.49845 152760.83 -157937.94 -2383.6292 20380.427 228.95928 342.31215 1.8044964
|
||||
440 8.753284 -2765.2192 999.28342 -3764.5026 966.26754 0 577.15359 152631.24 -157939.17 -2391.0923 20286.676 223.64168 334.34309 1.7947669
|
||||
460 9.1102748 -2806.7385 1004.2311 -3810.9696 996.86893 0 599.41867 152532.79 -157940.05 -2476.5754 20168.782 224.74899 335.97767 1.8475589
|
||||
480 9.471664 -2830.2582 1013.6925 -3843.9506 1009.5553 0 624.64584 152464.58 -157942.73 -2210.7254 20027.747 226.86645 339.14841 1.8588685
|
||||
500 9.8365009 -2865.4993 1024.473 -3889.9723 1017.2606 0 658.56598 152375.13 -157940.93 -2047.5735 19865.992 229.27916 342.78576 1.8103481
|
||||
520 10.207523 -2918.9299 973.10292 -3892.0328 1049.357 0 699.16951 152300.27 -157940.83 -1453.4121 19688.211 217.78243 325.51403 1.8799495
|
||||
540 10.583098 -2970.1121 925.84385 -3895.956 1077.9578 0 758.25478 152208.67 -157940.84 -821.19447 19499.417 207.20575 309.67486 1.8442683
|
||||
560 10.962813 -3008.9942 954.33133 -3963.3255 1114.7309 0 751.85274 152112.75 -157942.66 -1023.0801 19304.314 213.58131 319.23167 1.8463043
|
||||
580 11.351938 -3069.9822 951.38041 -4021.3626 1127.8186 0 765.20411 152027.82 -157942.2 -954.30565 19101.694 212.92089 318.20155 1.9391088
|
||||
600 11.74351 -3090.3867 973.25557 -4063.6423 1123.3487 0 744.86978 152009.46 -157941.32 -1226.2333 18891.444 217.81659 325.5949 1.8227604
|
||||
620 12.138507 -3114.2347 1002.2136 -4116.4483 1159.4812 0 766.24573 151899.05 -157941.23 -1406.6638 18672.922 224.29746 335.32178 1.8002314
|
||||
640 12.53874 -3160.3172 973.01388 -4133.3311 1181.5814 0 805.79135 151821.94 -157942.65 -1444.0821 18448.163 217.7625 325.51017 1.8464735
|
||||
660 12.945363 -3185.1871 975.57462 -4160.7618 1177.1798 0 795.84414 151809.59 -157943.38 -962.08053 18220.064 218.3356 326.36793 1.8252243
|
||||
680 13.358243 -3226.8034 977.21534 -4204.0187 1215.3088 0 862.3869 151662.05 -157943.76 -538.09214 17991.009 218.7028 326.90984 1.8513045
|
||||
700 13.774714 -3267.0358 979.72611 -4246.7619 1229.2873 0 878.80049 151588.58 -157943.43 -526.4724 17765.058 219.26471 327.74412 1.86738
|
||||
720 14.198356 -3275.0063 987.91851 -4262.9248 1260.2342 0 905.19546 151515.01 -157943.36 -285.51035 17544.004 221.09819 330.48021 1.8901628
|
||||
740 14.624448 -3298.9204 992.679 -4291.5994 1283.7665 0 917.78414 151449.24 -157942.39 351.98558 17329.448 222.1636 332.09658 1.843264
|
||||
760 15.05056 -3316.7113 1010.6458 -4327.3571 1296.6728 0 951.2091 151368.47 -157943.71 419.51796 17123.095 226.18459 338.07068 1.9518407
|
||||
780 15.504961 -3294.5707 1053.9493 -4348.52 1300.722 0 975.60682 151317.15 -157942 1040.7668 16927.715 235.87602 352.49204 2.1793007
|
||||
800 15.933704 -3363.0539 987.22337 -4350.2773 1325.1641 0 1013.664 151255.26 -157944.36 1462.6199 16747.7 220.94262 330.24432 1.8985721
|
||||
820 16.364414 -3437.2117 980.5397 -4417.7514 1350.8684 0 1029.953 151144.46 -157943.03 817.95684 16584.026 219.4468 327.9943 1.9129039
|
||||
840 16.799625 -3465.5868 981.23685 -4446.8236 1388.7125 0 1043.4314 151066.43 -157945.4 1366.0731 16434.707 219.60282 328.17006 2.0308095
|
||||
860 17.241996 -3460.2301 1020.3681 -4480.5981 1418.4709 0 1090.9207 150954.21 -157944.2 1450.0443 16300.524 228.36046 341.31823 2.0218282
|
||||
880 17.688347 -3499.5491 994.43799 -4493.9871 1444.4283 0 1113.276 150893.43 -157945.12 2227.6739 16183.439 222.55726 332.59403 2.0408296
|
||||
900 18.136371 -3526.9176 952.87144 -4479.789 1443.8422 0 1118.5107 150902.72 -157944.87 2220.1643 16085.505 213.25458 318.69359 1.9574553
|
||||
920 18.599828 -3545.2479 976.95271 -4522.2006 1443.4309 0 1118.3924 150859.69 -157943.71 2107.6215 16006.466 218.64402 326.75181 1.9926282
|
||||
940 19.064528 -3560.4406 994.62379 -4555.0644 1431.3624 0 1098.4902 150860.38 -157945.3 1495.9356 15944.46 222.59885 332.62316 2.0953461
|
||||
960 19.529192 -3590.569 964.78915 -4555.3582 1431.9284 0 1092.1793 150866.87 -157946.34 1559.1687 15897.003 215.92179 322.6406 2.0442546
|
||||
980 19.991661 -3599.6592 986.56344 -4586.2227 1435.7543 0 1034.8682 150889.35 -157946.2 679.01087 15862.242 220.79492 330.01359 1.9307016
|
||||
1000 20.427668 -3634.9266 939.78172 -4574.7083 1424.4834 0 1022.664 150924.73 -157946.59 733.04572 15834.345 210.32508 314.30018 1.9584145
|
||||
1020 20.873712 -3669.298 934.76265 -4604.0606 1452.3 0 1016.3445 150873.46 -157946.16 143.60284 15811.749 209.2018 312.55492 2.0808526
|
||||
1040 21.319204 -3682.4175 935.86127 -4618.2788 1447.0344 0 1035.4526 150844.58 -157945.34 515.93558 15792.261 209.44767 312.98247 1.9790896
|
||||
1060 21.766855 -3704.0833 901.03929 -4605.1226 1476.4857 0 1067.779 150794.42 -157943.8 1092.0636 15777.267 201.65444 301.3325 1.8948719
|
||||
1080 22.214459 -3699.4923 921.66268 -4621.155 1475.7351 0 1079.7576 150767.2 -157943.85 1003.4205 15769.569 206.27 308.27973 1.8458618
|
||||
1100 22.662445 -3667.6761 957.47147 -4625.1476 1507.2355 0 1102.9252 150708.15 -157943.46 927.20789 15768.898 214.28408 320.17339 2.0742837
|
||||
1120 23.085055 -3668.1399 935.38917 -4603.5291 1507.3367 0 1080.9826 150753.9 -157945.75 810.87137 15775.175 209.34202 312.79082 2.0279075
|
||||
1140 23.534417 -3710.7149 937.22068 -4647.9356 1499.5413 0 1020.4759 150776.54 -157944.49 -138.27816 15786.277 209.75191 313.34734 2.1346658
|
||||
1160 23.985544 -3711.7493 900.74897 -4612.4983 1430.3269 0 990.84122 150911.11 -157944.78 8.4592568 15798.538 201.58947 301.24561 1.8661211
|
||||
1180 24.439474 -3729.7115 928.82825 -4658.5398 1435.7711 0 937.43508 150913.97 -157945.72 -905.33202 15809.125 207.87367 310.65722 1.8872897
|
||||
1200 24.895124 -3738.2838 909.79315 -4648.077 1436.4199 0 938.10918 150922.8 -157945.41 -1112.9968 15812.511 203.61357 304.28121 1.8714711
|
||||
1220 25.352201 -3757.8302 907.08742 -4664.9176 1424.1514 0 930.13653 150924.86 -157944.06 -1078.0621 15807.893 203.00803 303.40134 1.8521625
|
||||
1240 25.780748 -3778.5355 905.88168 -4684.4171 1453.9568 0 959.37689 150846.21 -157943.96 -975.25032 15795.393 202.73818 303.00695 1.778808
|
||||
1260 26.238145 -3773.7584 879.94641 -4653.7048 1473.5812 0 1002.67 150815.41 -157945.36 -360.58922 15776.466 196.93381 294.2433 1.9174557
|
||||
1280 26.696751 -3755.4956 904.13603 -4659.6316 1493.7103 0 1017.8327 150773.94 -157945.12 -256.88128 15755.525 202.3475 302.35592 1.9294965
|
||||
1300 27.158244 -3754.9246 903.51795 -4658.4425 1498.1329 0 1006.1786 150782.15 -157944.9 -455.2258 15732.436 202.20917 302.19365 1.8353806
|
||||
1320 27.619539 -3758.1232 913.25769 -4671.3808 1500.2049 0 1032.0703 150739.71 -157943.37 -251.62277 15706.775 204.38895 305.38485 1.9968111
|
||||
1340 28.079132 -3784.7481 937.61449 -4722.3626 1505.7439 0 993.46365 150723.27 -157944.84 -853.9871 15680.38 209.84005 313.60153 1.8911101
|
||||
1360 28.514251 -3808.7787 864.89279 -4673.6715 1475.0618 0 1009.2569 150785.65 -157943.64 -331.64382 15650.208 193.56478 289.20988 1.8929896
|
||||
1380 28.975972 -3798.7281 892.2622 -4690.9903 1465.561 0 993.58051 150793.83 -157943.96 -567.64508 15617.156 199.69011 298.39786 1.8757635
|
||||
1400 29.439238 -3807.9228 893.51775 -4701.4406 1459.3875 0 1000.4434 150784.38 -157945.65 -456.80001 15580.856 199.97111 298.79789 1.925086
|
||||
1420 29.904427 -3818.6783 890.66153 -4709.3398 1515.8208 0 1064.6851 150655.36 -157945.21 450.86768 15542.76 199.33188 297.83132 1.927452
|
||||
1440 30.368352 -3822.016 910.79285 -4732.8089 1539.2325 0 1076.0339 150597.99 -157946.07 429.02044 15506.302 203.83731 304.53724 2.0216852
|
||||
1460 30.835555 -3821.2117 931.47963 -4752.6914 1540.1582 0 1089.9477 150561.76 -157944.55 645.54716 15472.89 208.46705 311.56653 1.8487206
|
||||
1480 31.306455 -3838.255 920.25737 -4758.5124 1546.6509 0 1107.4468 150533.86 -157946.47 556.76352 15443.298 205.95549 307.74395 1.9637305
|
||||
1500 31.747528 -3839.4323 942.18813 -4781.6204 1557.1836 0 1105.7209 150502.68 -157947.21 535.34633 15417.723 210.86364 315.07463 2.0384198
|
||||
1520 32.218974 -3827.551 925.42642 -4752.9774 1555.4578 0 1097.174 150540.89 -157946.5 680.16246 15396 207.11233 309.42351 2.0793499
|
||||
1540 32.691924 -3836.1802 885.40721 -4721.5874 1558.3851 0 1144.6478 150521.13 -157945.75 1216.5367 15378.972 198.15595 296.02524 2.015983
|
||||
1560 33.164075 -3830.4342 955.31807 -4785.7523 1574.0464 0 1105.7294 150481.06 -157946.59 169.17645 15369.126 213.80214 319.4694 2.0400237
|
||||
1580 33.636497 -3808.4082 948.31996 -4756.7281 1556.8058 0 1079.1205 150552.4 -157945.06 603.87966 15363.124 212.23595 317.13706 2.0112224
|
||||
1600 34.111529 -3835.9681 925.63461 -4761.6027 1575.0508 0 1091.3896 150517.16 -157945.2 356.94873 15359.871 207.15893 309.60148 1.8514712
|
||||
1620 34.558112 -3865.8357 866.45292 -4732.2886 1577.3357 0 1137.1716 150497.63 -157944.43 945.81112 15359.844 193.91394 289.72922 1.8926829
|
||||
1640 35.029171 -3849.5025 884.49282 -4733.9954 1547.0606 0 1101.4292 150561.92 -157944.41 703.96326 15365.598 197.95131 295.76038 1.913597
|
||||
1660 35.495665 -3861.3162 906.62112 -4767.9373 1547.2773 0 1074.8986 150555.48 -157945.6 46.512723 15375.298 202.90367 303.1667 1.9573677
|
||||
1680 35.959871 -3857.7679 907.8657 -4765.6336 1547.7327 0 1089.3299 150543.52 -157946.22 383.48079 15386.165 203.18221 303.5736 2.0202069
|
||||
1700 36.428885 -3869.0902 891.82145 -4760.9117 1512.1728 0 1012.6239 150658.31 -157944.02 -488.95961 15397.869 199.59147 298.24425 1.8990607
|
||||
1720 36.903833 -3870.4685 893.82411 -4764.2926 1485.7646 0 989.27762 150706.25 -157945.59 -542.70653 15406.338 200.03967 298.80302 2.1113341
|
||||
1740 37.380529 -3847.3408 893.93384 -4741.2746 1509.8117 0 1031.6641 150663.04 -157945.79 -307.1162 15410.521 200.06423 298.90093 2.0090208
|
||||
1760 37.827319 -3840.438 868.84851 -4709.2865 1474.404 0 1018.599 150744.2 -157946.49 -276.44721 15412.838 194.45008 290.51398 1.9203414
|
||||
1780 38.297568 -3842.0322 910.50606 -4752.5383 1494.2187 0 1002.3762 150696.05 -157945.18 -585.57252 15412.983 203.77313 304.47127 1.9624414
|
||||
1800 38.76671 -3861.9431 881.98228 -4743.9254 1471.6721 0 978.01808 150752.55 -157946.17 -711.07254 15409.636 197.38944 294.90206 1.9749925
|
||||
1820 39.233968 -3890.8613 856.10452 -4746.9658 1505.1405 0 991.9875 150701.72 -157945.82 -509.17282 15401.428 191.59795 286.24213 1.9311068
|
||||
1840 39.704207 -3860.2881 907.57785 -4767.866 1492.5264 0 999.80677 150685.45 -157945.65 -697.50098 15387.414 203.11779 303.52338 1.9123566
|
||||
1860 40.174673 -3879.0681 938.58496 -4817.653 1532.9628 0 1046.6919 150550.41 -157947.72 -311.83188 15369.15 210.05724 313.84514 2.0580305
|
||||
1880 40.646746 -3871.1182 925.64972 -4796.7679 1531.6363 0 1064.5321 150553.96 -157946.9 136.0161 15350.638 207.16231 309.48972 2.0957912
|
||||
1900 41.120691 -3868.9005 949.1652 -4818.0657 1593.1686 0 1150.4095 150384.01 -157945.65 753.94006 15333.301 212.42512 317.39691 2.0615952
|
||||
1920 41.59464 -3868.6343 954.03473 -4822.669 1610.5603 0 1192.2159 150320.88 -157946.33 1209.5547 15321.106 213.51493 319.06152 2.011006
|
||||
1940 42.037294 -3884.0548 926.13369 -4810.1885 1595.5448 0 1167.6153 150372.25 -157945.6 1289.8018 15318.433 207.27062 309.70304 1.9619634
|
||||
1960 42.507917 -3889.403 953.52537 -4842.9284 1598.8799 0 1116.9498 150388.89 -157947.65 327.93587 15323.804 213.40093 318.9112 1.9579466
|
||||
1980 42.973861 -3911.0951 911.40927 -4822.5043 1553.4244 0 1085.4519 150485.64 -157947.02 169.14591 15332.113 203.97527 304.77814 1.9637281
|
||||
2000 43.43889 -3892.0279 902.31728 -4794.3452 1534.2125 0 1088.703 150530.25 -157947.51 473.37009 15341.654 201.94046 301.71557 1.9929295
|
||||
Loop time of 43.4389 on 4 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Pair time (%) = 30.8131 (70.9343)
|
||||
Bond time (%) = 0.0167851 (0.0386406)
|
||||
Kspce time (%) = 2.78529 (6.41196)
|
||||
Neigh time (%) = 2.7229 (6.26835)
|
||||
Comm time (%) = 2.36382 (5.4417)
|
||||
Outpt time (%) = 0.00704503 (0.0162182)
|
||||
Other time (%) = 4.72998 (10.8888)
|
||||
|
||||
Nlocal: 625 ave 641 max 600 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 13465.2 ave 13518 max 13362 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 585334 ave 608376 max 546210 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 2341334
|
||||
Ave neighs/atom = 936.534
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 7
|
||||
|
||||
|
|
@ -1,236 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 14
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
comm_modify vel yes
|
||||
compute TATOM ATOMS temp/com
|
||||
compute TEMP all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix_modify RIGID temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
|
||||
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 1 100.0
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3375 1000
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Memory usage per processor = 24.8361 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 1.5779378 3742.6839 5338.7884 -1596.1045 567.30749 0 662.23765 155098.36 -157924.01 31679.424 13979.574 1194.8318 1690.2246 201.65659
|
||||
40 3.2595179 2752.8331 4407.7651 -1654.932 793.00135 0 870.33079 154593.76 -157912.03 27394.571 14278.56 986.46688 1450.7477 55.932382
|
||||
60 4.9160559 1995.591 3982.0372 -1986.4462 660.67737 0 750.60932 154536.67 -157934.4 22230.527 14691.401 891.1881 1315.7324 40.317107
|
||||
80 6.5368109 1376.4607 3451.5429 -2075.0822 617.73899 0 606.3673 154625.69 -157924.88 17342.36 15201.343 772.46238 1147.1933 21.455584
|
||||
100 8.1206679 885.61474 3037.6308 -2152.0161 536.23281 0 448.92334 154793.04 -157930.22 13263.15 15783.251 679.82802 1011.6854 14.7536
|
||||
120 9.6622779 487.58833 2926.9844 -2439.396 534.45257 0 332.92672 154624.58 -157931.35 8680.1072 16409.225 655.06511 977.0118 9.8615914
|
||||
140 11.151044 159.92993 2531.0941 -2371.1641 507.26614 0 248.61605 154802.7 -157929.75 6399.7614 17052.819 566.46405 845.55948 7.1402545
|
||||
160 12.594065 -100.92554 2408.1685 -2509.0941 490.99513 0 134.36067 154800.59 -157935.04 3836.8939 17698.15 538.95306 805.19219 5.3968881
|
||||
180 13.99897 -313.40437 2221.7416 -2535.1459 469.97779 0 75.805558 154853.24 -157934.17 1959.0151 18334.826 497.23032 743.14066 4.4151864
|
||||
200 15.366489 -490.94535 2067.2605 -2558.2059 455.16264 0 77.545085 154841.14 -157932.06 1193.2843 18956.449 462.65715 691.7234 3.5993432
|
||||
220 16.600555 -642.90899 1962.7268 -2605.6358 481.409 0 64.82886 154779.27 -157931.14 257.97318 19559.017 439.26229 657.06726 2.7738353
|
||||
240 17.905356 -770.44499 1795.759 -2566.204 467.25833 0 68.82314 154829.98 -157932.26 19.366424 20139.417 401.89456 601.24562 2.3886434
|
||||
260 19.179106 -878.63388 1752.9497 -2631.5836 476.38325 0 71.933328 154747.16 -157927.06 -779.27927 20696.165 392.31375 587.06527 2.0260796
|
||||
280 20.338816 -971.86313 1649.5511 -2621.4143 473.83718 0 58.460942 154779.6 -157933.32 -1008.6839 21226.44 369.17293 552.5314 1.7176302
|
||||
300 21.569212 -1057.5245 1580.9766 -2638.5012 480.33124 0 92.042617 154721.84 -157932.72 -1273.0871 21728.981 353.82581 529.63244 1.5049172
|
||||
320 22.749114 -1132.8131 1507.0527 -2639.8658 477.51281 0 107.39942 154707.48 -157932.26 -1098.1682 22203.702 337.28149 504.90539 1.3591193
|
||||
340 23.866651 -1199.4814 1495.1233 -2694.6047 479.99745 0 106.51864 154656.08 -157937.2 -1429.2857 22652.428 334.61166 500.95977 1.2462004
|
||||
360 25.082959 -1264.8469 1440.8985 -2705.7454 491.71868 0 107.29672 154624.8 -157929.57 -1584.3973 23073.056 322.47604 482.79111 1.2009575
|
||||
380 26.115491 -1323.6479 1376.047 -2699.695 497.4857 0 130.64748 154603.75 -157931.58 -1822.0261 23465.375 307.96215 461.10877 1.0530068
|
||||
400 27.098619 -1373.3921 1374.977 -2748.3691 504.29487 0 124.46131 154555.55 -157932.67 -2021.5919 23828.229 307.72267 460.78429 0.98399317
|
||||
420 28.070089 -1426.0355 1375.3813 -2801.4168 515.478 0 142.00079 154473.71 -157932.61 -2208.8244 24160.02 307.81316 460.97813 0.86759754
|
||||
440 29.088747 -1476.2448 1329.2669 -2805.5117 535.72651 0 196.6858 154393.5 -157931.42 -1618.3009 24460.675 297.49266 445.47247 0.93805929
|
||||
460 30.039555 -1527.7744 1320.4118 -2848.1861 568.66085 0 263.35802 154252.43 -157932.64 -1494.5444 24734.828 295.51087 442.54962 0.84234766
|
||||
480 30.98472 -1576.2009 1300.9323 -2877.1332 594.86236 0 314.31593 154144.87 -157931.19 -1089.6762 24985.934 291.15132 436.02273 0.82622001
|
||||
500 31.921181 -1626.4788 1317.6697 -2944.1486 623.62396 0 334.61944 154026.32 -157928.71 -1168.0859 25218.234 294.89719 441.63818 0.82542904
|
||||
520 32.850868 -1678.487 1262.6568 -2941.1438 633.47682 0 363.44379 153992.91 -157930.98 -1163.3304 25431.978 282.58518 423.21273 0.76490406
|
||||
540 33.831238 -1726.1374 1271.5003 -2997.6376 640.74261 0 345.52688 153948.98 -157932.89 -1537.3705 25626.826 284.56437 426.19842 0.72713952
|
||||
560 34.751061 -1771.2597 1269.233 -3040.4927 644.30805 0 317.8435 153929.28 -157931.92 -1722.5181 25799.253 284.05695 425.41542 0.77189915
|
||||
580 35.665466 -1815.0265 1246.413 -3061.4395 683.24088 0 371.72686 153815.69 -157932.1 -1494.5382 25947.498 278.94979 417.73291 0.82565978
|
||||
600 36.573731 -1858.3541 1196.3137 -3054.6678 696.06741 0 437.52527 153744.09 -157932.35 -954.95797 26075.526 267.73745 400.95599 0.76490653
|
||||
620 37.479106 -1899.6548 1179.8195 -3079.4743 696.68256 0 400.17078 153755.86 -157932.18 -1545.546 26187.542 264.04602 395.42296 0.76404516
|
||||
640 38.439799 -1936.5953 1175.0129 -3111.6082 690.67817 0 392.53009 153736.67 -157931.49 -1651.1722 26278.598 262.97029 393.82361 0.73771389
|
||||
660 39.342719 -1974.4946 1176.582 -3151.0766 687.10898 0 368.78109 153725.56 -157932.53 -1642.1352 26346.954 263.32147 394.35652 0.72471807
|
||||
680 40.233007 -2011.9427 1170.7634 -3182.7062 704.7553 0 376.83243 153670.03 -157934.32 -1891.1355 26391.697 262.01926 392.39338 0.74699214
|
||||
700 41.124436 -2051.0351 1135.0688 -3186.1039 725.49013 0 408.02789 153612.64 -157932.26 -1554.558 26411.443 254.03072 380.39243 0.79925352
|
||||
720 42.014817 -2087.2728 1127.2712 -3214.544 747.73788 0 483.80639 153486.98 -157933.07 -1246.9189 26409.313 252.28561 377.77086 0.81053421
|
||||
740 42.908141 -2122.8783 1145.0602 -3267.9385 791.69089 0 545.96341 153327.46 -157933.05 -1064.8488 26390.224 256.26683 383.71741 0.85313379
|
||||
760 43.799068 -2155.8658 1189.0654 -3344.9312 789.63603 0 492.27945 153309.89 -157936.74 -1502.4138 26356.52 266.11528 398.4847 0.84422302
|
||||
780 44.690825 -2197.1759 1166.0016 -3363.1774 813.89866 0 521.14986 153239.56 -157937.79 -1316.1431 26304.488 260.95354 390.75511 0.82849551
|
||||
800 45.65434 -2236.6034 1147.1342 -3383.7376 858.77647 0 581.50775 153111.46 -157935.49 -1059.9568 26235.547 256.73099 384.3699 0.93971538
|
||||
820 46.655089 -2273.5686 1128.3309 -3401.8996 876.66305 0 635.8842 153020.42 -157934.87 -522.03009 26154.47 252.52277 378.09253 0.87820184
|
||||
840 47.581215 -2310.5392 1107.1453 -3417.6845 906.73 0 663.59923 152946.29 -157934.31 -660.73299 26066.561 247.78139 370.96848 0.9116362
|
||||
860 48.461532 -2342.7319 1130.0857 -3472.8176 942.10066 0 680.8635 152839.09 -157934.87 -541.95751 25971.767 252.91551 378.61448 1.0117334
|
||||
880 49.348792 -2377.0856 1100.1359 -3477.2215 941.37588 0 700.77054 152814.73 -157934.1 -443.18233 25871.504 246.21267 368.56741 1.0107473
|
||||
900 50.240716 -2408.6694 1120.4615 -3529.131 953.77939 0 683.49952 152768.93 -157935.34 -805.27426 25765.603 250.76159 375.35036 1.0825367
|
||||
920 51.130132 -2442.8312 1111.7289 -3554.56 950.77289 0 674.01395 152754.6 -157933.95 -905.29746 25651.192 248.80721 372.46424 0.9955159
|
||||
940 52.02236 -2475.7651 1083.1001 -3558.8652 929.08218 0 652.94438 152792.16 -157933.05 -788.57962 25527.175 242.40003 362.8243 1.0666862
|
||||
960 52.924057 -2508.9913 1065.8755 -3574.8668 958.92048 0 698.81111 152699.64 -157932.24 -628.47136 25394.225 238.54512 356.97396 1.2103698
|
||||
980 53.828788 -2536.4577 1080.5323 -3616.99 965.47688 0 709.51639 152642.64 -157934.62 -711.96055 25254.689 241.82535 361.89287 1.2066617
|
||||
1000 54.736123 -2567.3495 1049.6524 -3617.0019 961.00327 0 711.26219 152645.74 -157935.01 -767.44539 25108.887 234.91437 351.52221 1.2288643
|
||||
1020 55.707224 -2595.1206 1073.4918 -3668.6124 974.79134 0 682.20149 152609.52 -157935.12 -1086.5823 24955.503 240.24966 359.53972 1.1890491
|
||||
1040 56.677394 -2626.5258 1072.5969 -3699.1227 1013.3934 0 711.73335 152511.92 -157936.17 -993.59976 24792.452 240.04939 359.23966 1.1887504
|
||||
1060 57.582305 -2655.4118 1059.0687 -3714.4806 1011.7018 0 747.43846 152460.24 -157933.86 -555.51961 24621.133 237.02176 354.6316 1.3280226
|
||||
1080 58.451085 -2684.3286 1093.9034 -3778.232 1041.5624 0 765.98574 152348.29 -157934.07 -993.29607 24444.559 244.81782 366.39031 1.183205
|
||||
1100 59.320593 -2716.1558 1073.5935 -3789.7493 1046.6309 0 741.4524 152358.32 -157936.15 -1031.9439 24260.537 240.27243 359.559 1.2187426
|
||||
1120 60.197434 -2748.4358 1043.9493 -3792.3851 1050.7685 0 732.61894 152361.65 -157937.42 -1173.2273 24068.431 233.638 349.62448 1.1977845
|
||||
1140 61.088693 -2777.1545 1036.6106 -3813.7651 1060.884 0 757.21086 152307.36 -157939.22 -1043.4335 23867.228 231.99557 347.17994 1.1628589
|
||||
1160 62.010573 -2805.5456 1027.0164 -3832.5621 1057.9262 0 777.84714 152269.56 -157937.89 -729.25379 23659.194 229.84839 343.97766 1.1301417
|
||||
1180 62.973114 -2832.7144 1030.8608 -3863.5752 1084.2376 0 767.80175 152221.94 -157937.56 -1365.8515 23446.354 230.70875 345.24169 1.1814637
|
||||
1200 63.943778 -2860.0062 1032.0824 -3892.0886 1078.2587 0 781.38106 152185.86 -157937.59 -1050.1069 23225.033 230.98216 345.65138 1.1817665
|
||||
1220 64.923382 -2887.3006 1026.4756 -3913.7762 1073.1543 0 809.51178 152141.13 -157937.57 -956.1976 22997.996 229.72734 343.81693 1.0887098
|
||||
1240 65.912183 -2912.0696 1020.0729 -3932.1425 1095.3889 0 826.297 152085.57 -157939.4 -534.84968 22767.897 228.2944 341.63565 1.15531
|
||||
1260 66.908861 -2938.0025 1009.7902 -3947.7927 1120.1948 0 846.76965 152025.28 -157940.04 -581.84084 22538.229 225.99312 338.22714 1.0731061
|
||||
1280 67.970707 -2960.3724 1046.6347 -4007.0071 1144.3297 0 866.43256 151921.62 -157939.39 -368.35961 22310.088 234.239 350.59018 1.0681573
|
||||
1300 68.984941 -2983.8905 1039.0599 -4022.9504 1162.4788 0 878.40157 151876.66 -157940.49 -408.4644 22085.613 232.54373 348.07145 1.0232144
|
||||
1320 70.043952 -3009.5808 969.8918 -3979.4726 1186.5907 0 935.08613 151836.22 -157937.36 431.8242 21865.457 217.06378 324.88371 0.98977725
|
||||
1340 71.117119 -3028.1057 1016.1027 -4044.2084 1215.7197 0 933.65661 151744.63 -157938.22 -118.90908 21653.612 227.40587 340.39676 0.96927182
|
||||
1360 72.19871 -3048.8293 986.21586 -4035.0452 1231.0917 0 974.10814 151697.47 -157937.72 485.3122 21448.458 220.71713 330.39668 0.91660237
|
||||
1380 73.289545 -3067.6975 1046.3647 -4114.0622 1252.358 0 948.20869 151626.66 -157941.29 -131.77945 21251.912 234.17856 350.55699 0.95332826
|
||||
1400 74.389534 -3091.6437 1003.804 -4095.4478 1223.2343 0 914.21639 151708.69 -157941.59 -228.59592 21060.319 224.6534 336.27611 0.95868112
|
||||
1420 75.496459 -3117.9845 1017.2871 -4135.2716 1252.8701 0 934.95412 151617.13 -157940.22 -328.62774 20872.161 227.67095 340.80959 0.93833238
|
||||
1440 76.611495 -3137.2342 990.73612 -4127.9703 1224.5861 0 925.81135 151661.05 -157939.42 -23.294916 20687.614 221.72878 331.93708 0.86871384
|
||||
1460 77.73649 -3159.4947 1040.535 -4200.0297 1218.936 0 881.92261 151636.87 -157937.75 -581.29505 20507.346 232.87387 348.59778 0.96029886
|
||||
1480 78.872562 -3183.8273 1037.9432 -4221.7705 1246.5207 0 908.21966 151561.59 -157938.1 -884.42345 20328.04 232.29381 347.7323 0.95226246
|
||||
1500 80.110645 -3206.5826 1008.5663 -4215.1489 1236.8936 0 929.15034 151558.28 -157939.47 -91.502556 20149.349 225.7192 337.88949 0.92718943
|
||||
1520 81.168804 -3228.1152 994.3422 -4222.4574 1276.2214 0 948.25706 151492.45 -157939.39 -262.49453 19974.554 222.53583 333.16141 0.83959152
|
||||
1540 82.328931 -3248.9878 997.70762 -4246.6954 1273.2453 0 944.04689 151475.31 -157939.3 -310.12487 19802.717 223.28901 334.28865 0.84316615
|
||||
1560 83.500822 -3268.9264 1001.6639 -4270.5903 1283.2174 0 972.25539 151413.47 -157939.53 -368.92162 19633.499 224.17444 335.57814 0.91870789
|
||||
1580 84.681217 -3289.8506 972.05937 -4261.9099 1290.892 0 995.40503 151394.08 -157942.29 309.3174 19467.313 217.54888 325.64947 0.91261747
|
||||
1600 85.872982 -3306.0485 999.0593 -4305.1078 1336.2852 0 1018.2817 151281.27 -157940.94 78.176324 19307.332 223.59152 334.68976 0.94786237
|
||||
1620 87.166941 -3323.911 1023.7518 -4347.6628 1346.5659 0 1012.0297 151235.76 -157942.02 401.58054 19152.885 229.11774 342.98696 0.92107142
|
||||
1640 88.373719 -3346.3201 1013.0953 -4359.4153 1368.3551 0 1038.3633 151174.74 -157940.87 115.49888 19004.339 226.7328 339.39185 0.96123977
|
||||
1660 89.588199 -3366.6764 980.18808 -4346.8645 1385.5623 0 1066.3348 151143.21 -157941.97 785.51107 18860.969 219.3681 328.38652 0.89253119
|
||||
1680 90.812635 -3382.4343 999.75094 -4382.1852 1367.9173 0 1045.8848 151142.33 -157938.32 549.73441 18726.008 223.74631 334.953 0.88544944
|
||||
1700 92.044767 -3400.8462 996.00209 -4396.8483 1351.6629 0 1019.0394 151174.27 -157941.83 32.327852 18598.28 222.90731 333.67893 0.91827006
|
||||
1720 93.284649 -3418.3313 989.38116 -4407.7125 1347.9882 0 1026.3475 151161.41 -157943.46 700.69172 18474.978 221.42553 331.45637 0.92100955
|
||||
1740 94.538928 -3435.1347 964.16624 -4399.301 1357.6456 0 1051.1466 151135.74 -157943.84 477.68306 18358.2 215.78238 322.997 0.92157841
|
||||
1760 95.90276 -3452.4681 996.08241 -4448.5506 1365.9896 0 1001.3994 151128.36 -157944.3 -77.655143 18246.618 222.92529 333.72093 0.88815023
|
||||
1780 97.200704 -3470.0186 947.16368 -4417.1823 1357.1769 0 1006.9477 151162.27 -157943.57 100.19368 18137.3 211.97718 317.3159 0.87577473
|
||||
1800 98.461648 -3484.6818 988.75293 -4473.4348 1367.5971 0 995.1924 151106.14 -157942.36 -208.37477 18030.204 221.28494 331.23294 0.94635825
|
||||
1820 99.729642 -3503.5324 959.4974 -4463.0298 1386.9033 0 1035.1867 151057.26 -157942.38 196.09637 17924.392 214.73749 321.44422 0.89454363
|
||||
1840 101.00392 -3518.4137 985.10207 -4503.5157 1425.227 0 1062.1927 150951.14 -157942.08 189.40933 17821.795 220.46787 330.02248 0.91769756
|
||||
1860 102.28783 -3531.6076 978.71334 -4510.3209 1447.6145 0 1081.8026 150905.2 -157944.94 369.13672 17723.495 219.03805 327.84302 0.99005655
|
||||
1880 103.57975 -3546.6803 982.10151 -4528.7818 1416.6032 0 1040.8725 150959.42 -157945.68 206.83653 17629.384 219.79633 328.97668 0.9960403
|
||||
1900 104.81168 -3563.7438 961.75306 -4525.4969 1426.2883 0 1055.2567 150936.42 -157943.46 223.06115 17537.856 215.24231 322.15829 0.97986655
|
||||
1920 106.04042 -3579.7815 953.8957 -4533.6772 1420.242 0 1053.3469 150938.67 -157945.93 264.48404 17448.909 213.48382 319.52979 0.96489929
|
||||
1940 107.27692 -3592.4628 995.11883 -4587.5816 1434.5738 0 1036.2736 150885.59 -157944.02 -203.71783 17362.885 222.70964 333.32982 1.0238542
|
||||
1960 108.52049 -3607.1225 959.8186 -4566.9411 1454.811 0 1091.6157 150830.59 -157943.96 412.09226 17278.194 214.80937 321.46995 1.0586113
|
||||
1980 109.76987 -3621.5836 950.82575 -4572.4094 1481.3655 0 1148.5036 150742.3 -157944.58 1156.6083 17197.362 212.79675 318.42806 1.1085537
|
||||
2000 111.02457 -3632.4321 939.77229 -4572.2044 1484.3457 0 1154.0077 150733.65 -157944.21 1008.3019 17124.028 210.32297 314.7467 1.0548599
|
||||
Loop time of 111.025 on 1 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Pair time (%) = 87.5509 (78.8572)
|
||||
Bond time (%) = 0.0493031 (0.0444073)
|
||||
Kspce time (%) = 3.35179 (3.01896)
|
||||
Neigh time (%) = 9.36055 (8.43106)
|
||||
Comm time (%) = 0.69479 (0.625798)
|
||||
Outpt time (%) = 0.0108259 (0.00975088)
|
||||
Other time (%) = 10.0064 (9.01281)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 20348 ave 20348 max 20348 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.09326e+06 ave 2.09326e+06 max 2.09326e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2093261
|
||||
Ave neighs/atom = 837.304
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 120
|
||||
Dangerous builds = 16
|
||||
|
||||
|
|
@ -1,236 +0,0 @@
|
|||
LAMMPS (8 Jul 2015)
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
kspace_style pppm 1.0e-3
|
||||
|
||||
read_data data.swm4-ndp
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2500 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
2000 bonds
|
||||
reading angles ...
|
||||
500 angles
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
3 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 0.210939 3.183950 # ODw ODw
|
||||
pair_coeff * 2* 0.000000 0.0
|
||||
|
||||
group ATOMS type 1:3
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1
|
||||
500 atoms in group CORES
|
||||
group DRUDES type 4
|
||||
500 atoms in group DRUDES
|
||||
|
||||
variable TK equal 300.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
fix DRUDE all drude C N N D
|
||||
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 300 12345
|
||||
velocity DRUDES create ${TDK} 12345
|
||||
velocity DRUDES create 1 12345
|
||||
|
||||
delete_bonds ATOMS multi
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
master list distance cutoff = 14
|
||||
2000 total bonds, 500 turned on, 1500 turned off
|
||||
500 total angles, 0 turned on, 500 turned off
|
||||
0 total dihedrals, 0 turned on, 0 turned off
|
||||
0 total impropers, 0 turned on, 0 turned off
|
||||
|
||||
comm_modify vel yes
|
||||
compute TATOM ATOMS temp/com
|
||||
compute TEMP all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500
|
||||
fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500
|
||||
500 rigid bodies with 2000 atoms
|
||||
0.832099 = max distance from body owner to body atom
|
||||
fix_modify RIGID temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395)
|
||||
fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 ${TDK} 100.0
|
||||
fix NVT DRUDES nvt temp 1 1 100.0
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
|
||||
thermo 20
|
||||
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.217457
|
||||
grid = 10 10 10
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.197288
|
||||
estimated relative force accuracy = 0.000594128
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1500 300
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 4
|
||||
New max number of 1-2 to 1-4 neighbors: 4 (+0)
|
||||
Memory usage per processor = 15.0906 Mbytes
|
||||
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2]
|
||||
0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785
|
||||
20 0.60629702 3742.7991 5338.7966 -1595.9975 567.29055 0 662.23349 155098.48 -157924 31679.046 13979.575 1194.8336 1690.2267 201.65776
|
||||
40 1.2431891 2752.9388 4407.9332 -1654.9944 792.86725 0 870.27523 154593.92 -157912.06 27392.302 14278.564 986.5045 1450.7624 56.079837
|
||||
60 1.875339 1995.9775 3980.851 -1984.8735 660.64216 0 750.43214 154538.47 -157934.42 22242.676 14691.413 890.92262 1315.3403 40.305321
|
||||
80 2.471236 1377.1261 3449.7879 -2072.6618 617.64243 0 605.75693 154628.63 -157924.69 17345.214 15201.397 772.06962 1146.6088 21.44718
|
||||
100 3.0357449 886.38995 3038.4108 -2152.0208 537.89929 0 450.99962 154789.13 -157930.05 13299.227 15783.335 680.00257 1011.6773 15.016231
|
||||
120 3.585844 488.055 2928.1336 -2440.0786 536.23164 0 334.88597 154620.05 -157931.25 8694.3472 16409.509 655.3223 977.40122 9.8538294
|
||||
140 4.117424 160.14918 2538.5116 -2378.3624 509.19396 0 249.89205 154793.34 -157930.79 6363.1137 17053.486 568.1241 847.92526 7.2744139
|
||||
160 4.6321139 -103.57595 2403.1613 -2506.7372 494.69822 0 144.07174 154790.83 -157936.34 4017.2005 17699.095 537.83243 803.44775 5.3901399
|
||||
180 5.126441 -315.61252 2216.7944 -2532.4069 477.29447 0 80.852363 154842.41 -157932.96 1958.1627 18336.716 496.12314 741.4685 4.440167
|
||||
200 5.6090059 -490.61276 2058.9074 -2549.5202 470.23217 0 80.799455 154831.63 -157932.18 1260.1943 18960.132 460.78771 688.92684 3.5878733
|
||||
220 6.0495639 -644.09355 2001.1189 -2645.2125 494.11524 0 53.071997 154741.65 -157934.05 -16.373549 19564.819 447.85452 669.94663 2.7746068
|
||||
240 6.5042329 -773.76581 1911.0759 -2684.8417 491.56501 0 36.579309 154722.88 -157935.86 -773.18555 20144.755 427.70271 639.97688 2.2989541
|
||||
260 6.9512041 -886.818 1719.7038 -2606.5218 462.97731 0 47.595907 154814.45 -157931.55 -696.23419 20696.487 384.87324 575.96351 1.9229602
|
||||
280 7.3921249 -983.57561 1659.2167 -2642.7923 476.06924 0 65.542713 154749.27 -157933.68 -1099.4208 21220.613 371.3361 555.78067 1.7042918
|
||||
300 7.8054619 -1069.4015 1531.598 -2600.9995 487.38132 0 130.06616 154709.03 -157927.47 -548.86446 21717.521 342.77477 513.11788 1.4030219
|
||||
320 8.2272029 -1144.9139 1562.933 -2707.8469 509.00464 0 127.16899 154591.31 -157935.33 -1516.7077 22190.692 349.78761 523.61225 1.4145866
|
||||
340 8.6145689 -1216.4369 1511.7737 -2728.2106 518.42214 0 144.71934 154541.92 -157933.27 -1345.493 22636.556 338.33806 506.55234 1.2328234
|
||||
360 9.0159991 -1279.8637 1435.4044 -2715.2681 525.01973 0 153.83119 154536.21 -157930.33 -1447.797 23056.471 321.24646 480.9789 1.1390786
|
||||
380 9.4004741 -1340.2241 1391.5909 -2731.815 536.93555 0 180.52081 154483.31 -157932.58 -1315.0222 23450.141 311.4409 466.34776 1.004293
|
||||
400 9.7971771 -1398.7544 1401.1636 -2799.918 547.12264 0 190.99461 154394.23 -157932.27 -1686.7786 23818.238 313.5833 469.59825 0.92621346
|
||||
420 10.175245 -1450.5676 1355.0166 -2805.5842 555.43355 0 178.57277 154392.99 -157932.58 -1948.3006 24158.665 303.2555 454.12588 0.90821389
|
||||
440 10.550016 -1501.2755 1336.6037 -2837.8792 573.29095 0 195.76657 154324.78 -157931.72 -1845.698 24470.004 299.13465 447.99648 0.8127319
|
||||
460 10.93798 -1551.1246 1327.3311 -2878.4557 580.57019 0 206.92238 154267.88 -157933.83 -2059.7154 24752.911 297.05944 444.88976 0.80466605
|
||||
480 11.304226 -1597.9166 1280.274 -2878.1906 596.27629 0 247.5201 154210.94 -157932.93 -1714.1239 25006.108 286.52794 429.10945 0.79188456
|
||||
500 11.66949 -1645.4221 1303.9947 -2949.4168 620.22431 0 275.42964 154086.38 -157931.45 -1833.6239 25232.592 291.83668 437.06941 0.78754301
|
||||
520 12.030775 -1692.7733 1261.2365 -2954.0098 639.32812 0 295.13753 154045.85 -157934.32 -1715.0443 25432.412 282.26732 422.73896 0.75950535
|
||||
540 12.389967 -1739.3602 1247.1301 -2986.4903 666.88476 0 341.37591 153937.16 -157931.91 -1556.9492 25607.225 279.11027 418.00746 0.75767537
|
||||
560 12.765452 -1783.4916 1212.3647 -2995.8563 669.09681 0 366.501 153899.16 -157930.62 -1543.0147 25758.368 271.3297 406.37068 0.70509124
|
||||
580 13.122579 -1824.6061 1200.7205 -3025.3267 699.41498 0 409.47507 153794.95 -157929.16 -1053.8519 25887.592 268.72372 402.43012 0.77346975
|
||||
600 13.47702 -1864.0982 1206.4231 -3070.5213 726.9912 0 439.25863 153695.5 -157932.27 -1130.6737 26000.4 269.99996 404.33899 0.78190692
|
||||
620 13.82937 -1902.6883 1167.061 -3069.7493 741.54351 0 453.21801 153667.95 -157932.46 -921.61026 26097.341 261.19065 391.14672 0.7561126
|
||||
640 14.180362 -1941.2814 1168.4808 -3109.7622 758.6291 0 484.81029 153578.39 -157931.59 -1084.6877 26180.233 261.50841 391.64626 0.70968727
|
||||
660 14.527615 -1977.9114 1159.1979 -3137.1094 746.51288 0 452.2958 153598.59 -157934.51 -1424.6628 26247.07 259.43088 388.52145 0.73088365
|
||||
680 14.875155 -2015.8231 1149.125 -3164.9481 730.41157 0 417.95266 153620.83 -157934.15 -1485.3138 26293.983 257.17653 385.144 0.72723522
|
||||
700 15.22063 -2052.4439 1175.9011 -3228.345 735.43016 0 393.72125 153577.95 -157935.44 -1936.2883 26318.916 263.16908 394.10321 0.77446426
|
||||
720 15.565813 -2092.4868 1137.4051 -3229.892 739.27374 0 431.22089 153537.92 -157938.3 -1669.6367 26318.64 254.5536 381.18868 0.77432854
|
||||
740 15.926298 -2128.2671 1117.2535 -3245.5206 763.39303 0 451.2336 153475.75 -157935.89 -1554.5185 26294.984 250.04362 374.42691 0.77695221
|
||||
760 16.273413 -2164.5578 1132.9117 -3297.4695 791.93983 0 493.17297 153351.43 -157934.01 -1464.3621 26250.086 253.54797 379.63211 0.87260304
|
||||
780 16.620524 -2201.7367 1138.2941 -3340.0308 832.89022 0 542.69718 153217.14 -157932.76 -1185.0268 26186.538 254.75255 381.43046 0.88724559
|
||||
800 16.968419 -2236.9734 1127.0464 -3364.0197 849.94855 0 579.03844 153137.36 -157930.36 -957.1991 26107.922 252.23529 377.65702 0.8873688
|
||||
820 17.320858 -2274.0191 1152.6791 -3426.6982 878.53555 0 605.98285 153020.89 -157932.1 -1004.5494 26016.264 257.97196 386.24526 0.90940959
|
||||
840 17.671788 -2312.5555 1157.6702 -3470.2257 915.53242 0 653.69994 152892.11 -157931.56 -793.45868 25912.528 259.08897 387.88866 0.97141875
|
||||
860 18.021136 -2351.0088 1136.5124 -3487.5212 921.37408 0 665.09396 152857.19 -157931.18 -528.38134 25800.163 254.35382 380.78143 0.98986969
|
||||
880 18.370286 -2387.3364 1155.2826 -3542.619 934.02359 0 660.06761 152795.05 -157931.76 -775.58796 25681.702 258.55463 386.99987 1.1470186
|
||||
900 18.737898 -2425.9324 1151.5543 -3577.4867 936.00838 0 670.95003 152749.78 -157934.22 -883.49007 25555.357 257.72021 385.72656 1.1920669
|
||||
920 19.09607 -2461.264 1119.906 -3581.17 931.8496 0 682.4928 152739.5 -157935.01 -890.93067 25420.635 250.63726 375.12148 1.1675653
|
||||
940 19.45002 -2496.7293 1081.4763 -3578.2056 971.61744 0 731.21429 152653.33 -157934.36 -483.6151 25277.795 242.03662 362.20568 1.2144341
|
||||
960 19.805087 -2527.097 1111.841 -3638.938 964.7058 0 704.68407 152623.89 -157932.22 -841.64397 25129.524 248.8323 372.33505 1.3291216
|
||||
980 20.160533 -2560.1354 1096.9132 -3657.0486 954.19645 0 693.42648 152627.51 -157932.19 -949.1276 24974.275 245.49142 367.3853 1.2126954
|
||||
1000 20.518917 -2592.9079 1053.7186 -3646.6266 959.23242 0 684.31399 152644.74 -157934.91 -869.15319 24811.035 235.8244 352.90011 1.2013298
|
||||
1020 20.849072 -2623.091 1066.4493 -3689.5404 998.09604 0 709.32917 152535.4 -157932.37 -881.38225 24640.265 238.67355 357.17132 1.2006706
|
||||
1040 21.194962 -2652.822 1083.618 -3736.44 1011.32 0 727.70427 152458.99 -157934.45 -815.2175 24461.841 242.51594 362.90994 1.2429114
|
||||
1060 21.530151 -2683.6347 1074.3994 -3758.0341 1029.3659 0 763.93884 152381.4 -157932.73 -616.78933 24277.069 240.45279 359.82116 1.235143
|
||||
1080 21.868091 -2715.2991 1094.3032 -3809.6022 1068.1764 0 785.28284 152272.57 -157935.63 -541.23611 24088.232 244.9073 366.48583 1.2604348
|
||||
1100 22.209137 -2747.0371 1066.1644 -3813.2016 1080.2369 0 833.94072 152208.13 -157935.51 -217.98411 23897.246 238.60979 357.0619 1.2283546
|
||||
1120 22.551618 -2774.9066 1084.3361 -3859.2427 1113.055 0 847.43384 152114.69 -157934.42 -77.787494 23707.475 242.67665 363.13214 1.2803322
|
||||
1140 22.899431 -2803.21 1072.4113 -3875.6213 1090.9217 0 807.02034 152161.17 -157934.73 -668.47773 23520.606 240.00786 359.14316 1.2572349
|
||||
1160 23.252016 -2834.8697 1052.5943 -3887.464 1096.5034 0 789.77107 152162.88 -157936.62 -589.78074 23331.777 235.57277 352.55512 1.1369148
|
||||
1180 23.609597 -2863.7817 1031.8109 -3895.5926 1087.1932 0 789.79657 152165.44 -157938.03 -586.94333 23140.391 230.92139 345.60929 1.0837566
|
||||
1200 23.970129 -2891.3631 1042.111 -3933.4741 1093.7082 0 775.83298 152136.1 -157939.12 -1109.7168 22947.229 233.22659 349.07035 1.0726257
|
||||
1220 24.3333 -2919.3393 1043.3795 -3962.7187 1095.6802 0 760.56643 152121.29 -157940.25 -1189.6331 22748.747 233.51046 349.50414 1.0560945
|
||||
1240 24.699158 -2942.4201 1015.5889 -3958.009 1114.7861 0 821.20595 152042.69 -157936.69 -581.49954 22545.116 227.29088 340.1868 1.0444581
|
||||
1260 25.06694 -2965.9906 1011.5209 -3977.5115 1137.3984 0 850.69736 151972.34 -157937.95 -557.09399 22340.759 226.38045 338.85243 0.98374803
|
||||
1280 25.506043 -2989.5484 1016.7798 -4006.3282 1160.9102 0 882.24024 151890.5 -157939.98 -93.844073 22136.859 227.55742 340.60408 1.0089629
|
||||
1300 25.885481 -3011.5964 1043.7628 -4055.3592 1184.2311 0 891.6381 151808.85 -157940.08 -307.32007 21936.757 233.59626 349.6133 1.0504806
|
||||
1320 26.286564 -3035.1132 1037.5333 -4072.6466 1179.597 0 903.59052 151784.33 -157940.16 -91.53774 21739.794 232.20209 347.62923 0.8833997
|
||||
1340 26.707803 -3061.1043 1034.7198 -4095.8241 1231.5568 0 955.77666 151655.57 -157938.72 53.261099 21546.978 231.57242 346.58931 1.0307605
|
||||
1360 27.133179 -3085.252 983.77833 -4069.0303 1230.971 0 968.86383 151669.63 -157938.5 197.66951 21360.266 220.17161 329.49241 1.002352
|
||||
1380 27.554558 -3101.9696 1037.9918 -4139.9614 1216.6215 0 897.01691 151685.79 -157939.39 -392.64446 21180.32 232.3047 347.61632 1.0380526
|
||||
1400 27.956349 -3124.8379 1003.328 -4128.1659 1199.4883 0 863.54306 151748.07 -157939.27 -548.32584 21003.378 224.54686 336.16828 0.85494391
|
||||
1420 28.361482 -3146.8927 1020.9417 -4167.8344 1210.319 0 850.57584 151710.13 -157938.86 -1093.8532 20825.938 228.48885 342.04449 0.9178739
|
||||
1440 28.768238 -3170.6554 993.33274 -4163.9882 1239.5959 0 893.87046 151642.2 -157939.65 -436.10089 20645.122 222.30991 332.79717 0.88336557
|
||||
1460 29.177687 -3191.0873 980.2106 -4171.2979 1257.3639 0 955.42122 151554.27 -157938.35 -139.1763 20465.429 219.37314 328.30589 0.99602014
|
||||
1480 29.586943 -3208.4185 993.92387 -4202.3424 1243.9183 0 936.28667 151555.9 -157938.45 -261.1948 20289.512 222.4422 333.01034 0.85071989
|
||||
1500 29.995233 -3229.0775 1028.0284 -4257.1059 1272.6443 0 960.80911 151449.75 -157940.31 -307.25416 20116.744 230.07487 344.43881 0.88683413
|
||||
1520 30.435761 -3250.8294 998.11977 -4248.9491 1282.1976 0 990.08774 151419.81 -157941.05 64.772936 19947.298 223.38125 334.38841 0.90320757
|
||||
1540 30.853458 -3268.3168 1004.1599 -4272.4768 1299.4164 0 987.20608 151381.91 -157941.01 -80.22578 19782.738 224.73305 336.30685 1.007422
|
||||
1560 31.279241 -3289.0826 966.08591 -4255.1685 1287.1272 0 982.95309 151416.22 -157941.47 198.4371 19622.918 216.21201 323.54353 0.99939162
|
||||
1580 31.708028 -3306.2125 979.26815 -4285.4807 1288.5111 0 952.23769 151415.68 -157941.91 -206.26434 19467.717 219.16222 328.0518 0.90689318
|
||||
1600 32.140092 -3325.1219 984.21128 -4309.3331 1308.258 0 963.95207 151360.81 -157942.35 -284.04656 19314.766 220.2685 329.66568 0.9610293
|
||||
1620 32.5727 -3340.9024 1013.5306 -4354.433 1318.1025 0 944.3489 151325.17 -157942.05 -653.005 19163.698 226.83023 339.47468 1.0097397
|
||||
1640 32.982791 -3360.2312 974.13546 -4334.3667 1312.594 0 986.63361 151308.68 -157942.28 343.78235 19013.496 218.01352 326.28924 0.99083786
|
||||
1660 33.419277 -3375.6484 982.60503 -4358.2535 1345.3148 0 970.47388 151266.28 -157940.32 -374.81541 18867.836 219.90902 329.06869 1.0301828
|
||||
1680 33.858902 -3394.428 981.74052 -4376.1685 1319.3919 0 955.09161 151289.81 -157940.47 -162.3498 18724.14 219.71554 328.81202 0.99514477
|
||||
1700 34.30191 -3412.8462 973.87976 -4386.7259 1341.294 0 965.41854 151248.54 -157941.98 -351.70824 18582.062 217.95629 326.03525 1.1973975
|
||||
1720 34.776698 -3429.9352 986.76909 -4416.7043 1362.6752 0 1013.2358 151149.58 -157942.2 37.299904 18441.349 220.84095 330.4706 1.0534043
|
||||
1740 35.222457 -3446.5561 971.25044 -4417.8065 1381.6012 0 1046.8608 151096.61 -157942.88 336.29665 18304.289 217.36784 325.28479 1.0839935
|
||||
1760 35.644247 -3463.1798 999.75562 -4462.9354 1395.5442 0 1012.1296 151070.28 -157940.88 -252.71902 18172.322 223.74736 334.82695 1.1205298
|
||||
1780 36.095301 -3481.5453 991.5153 -4473.0606 1403.686 0 1029.7008 151037.13 -157943.57 -108.73918 18043.082 221.90316 332.00846 1.1669904
|
||||
1800 36.548801 -3496.9886 965.33662 -4462.3252 1390.3088 0 1050.6761 151040.12 -157943.43 539.62368 17917.488 216.04432 323.23991 1.1447201
|
||||
1820 37.00671 -3510.113 991.32596 -4501.439 1392.0482 0 1034.7898 151015.68 -157943.96 152.36115 17797.781 221.86078 332.04409 1.050451
|
||||
1840 37.465953 -3528.9352 974.95032 -4503.8855 1387.6457 0 1012.5199 151036.63 -157940.68 -250.11127 17681.765 218.19588 326.4633 1.104675
|
||||
1860 37.926741 -3545.3967 970.46573 -4515.8624 1391.3683 0 1035.1551 151000.11 -157942.49 -218.15781 17567.52 217.19222 325.05524 1.0190724
|
||||
1880 38.391252 -3561.7398 933.83134 -4495.5711 1404.458 0 1032.7156 151010.9 -157943.64 -1.9885562 17454.833 208.99337 312.70412 1.1301542
|
||||
1900 38.856336 -3574.6165 984.6503 -4559.2668 1422.0814 0 1060.3245 150900.79 -157942.46 190.15103 17344.24 220.36676 329.66505 1.2027369
|
||||
1920 39.32352 -3589.0687 963.85062 -4552.9193 1427.8662 0 1075.6986 150887.22 -157943.7 506.81653 17237.394 215.71175 322.81523 1.0733524
|
||||
1940 39.79544 -3604.8214 970.89136 -4575.7128 1416.926 0 1037.9197 150913.56 -157944.12 -60.261935 17135.412 217.28748 325.12481 1.144127
|
||||
1960 40.270815 -3620.548 963.48434 -4584.0323 1401.1546 0 1016.5609 150941.43 -157943.17 -388.03612 17035.264 215.62977 322.67138 1.1152888
|
||||
1980 40.749353 -3638.3971 977.90456 -4616.3017 1415.5473 0 1009.486 150904.71 -157946.04 -640.67547 16934.97 218.85705 327.48198 1.1614525
|
||||
2000 41.229238 -3654.2588 957.08437 -4611.3432 1418.1059 0 1031.2688 150883.23 -157943.95 -595.60403 16834.098 214.19745 320.55039 1.0631632
|
||||
Loop time of 41.2293 on 4 procs for 2000 steps with 2500 atoms
|
||||
|
||||
Pair time (%) = 23.5391 (57.0932)
|
||||
Bond time (%) = 0.0153775 (0.0372976)
|
||||
Kspce time (%) = 3.17798 (7.70806)
|
||||
Neigh time (%) = 2.51543 (6.10108)
|
||||
Comm time (%) = 1.6585 (4.02262)
|
||||
Outpt time (%) = 0.00876421 (0.0212572)
|
||||
Other time (%) = 10.3141 (25.0165)
|
||||
|
||||
Nlocal: 625 ave 632 max 619 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 12577 ave 12644 max 12511 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 532752 ave 581561 max 492708 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2131009
|
||||
Ave neighs/atom = 852.404
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 120
|
||||
Dangerous builds = 16
|
||||
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Langevin)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 250 toluene system for drude polarizability example (Nose-Hoover)
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
improper_style opls
|
||||
ERROR: Unknown improper style opls (src/force.cpp:634)
|
||||
Last command: improper_style opls
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue