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Merge branch 'master' into fix-external-python-support

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Axel Kohlmeyer 2021-07-22 23:09:54 -04:00
parent c8cc5ecb9f 320f7da91a
commit ff7f2e78a1
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1
.gitignore vendored
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@ -46,5 +46,6 @@ Thumbs.db
/CMakeFiles/
/Testing
/Makefile
/Testing
/cmake_install.cmake
/lmp

71
cmake/Modules/Packages/ML-QUIP.cmake
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@ -1,3 +1,70 @@
enable_language(Fortran)
find_package(QUIP REQUIRED)
target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
find_package(QUIP QUIET)
if(QUIP_FOUND)
set(DOWNLOAD_QUIP_DEFAULT OFF)
else()
set(DOWNLOAD_QUIP_DEFAULT ON)
endif()
option(DOWNLOAD_QUIP "Download the QUIP library instead of using an already installed one" ${DOWNLOAD_QUIP_DEFAULT})
if(DOWNLOAD_QUIP)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
set(temp "F77 = ${CMAKE_Fortran_COMPILER}\nF90 = ${CMAKE_Fortran_COMPILER}\nF95 = ${CMAKE_Fortran_COMPILER}\n")
set(temp "${temp}CC=${CMAKE_C_COMPILER}\nCPLUSPLUS=${CMAKE_CXX_COMPILER}\nLINKER=${CMAKE_Fortran_COMPILER}\n")
if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
else()
message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
endif()
set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
set(temp "${temp}MATH_LINKOPTS=")
foreach(flag ${BLAS_LIBRARIES})
set(temp "${temp} ${flag}")
endforeach()
foreach(flag ${LAPACK_LIBRARIES})
set(temp "${temp} ${flag}")
endforeach()
set(temp "${temp}\n")
set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n")
file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
message(STATUS "QUIP download via git requested - we will build our own")
# QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
# The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
include(ExternalProject)
ExternalProject_Add(quip_build
GIT_REPOSITORY "https://github.com/libAtoms/QUIP/"
GIT_TAG origin/public
GIT_SHALLOW YES
GIT_PROGRESS YES
PATCH_COMMAND cp ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
BUILD_COMMAND env QUIP_ARCH=lammps make libquip
INSTALL_COMMAND ""
BUILD_IN_SOURCE YES
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
)
ExternalProject_get_property(quip_build SOURCE_DIR)
add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::QUIP PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
add_dependencies(LAMMPS::QUIP quip_build)
else()
find_package(QUIP REQUIRED)
target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
endif()

18
cmake/Modules/Packages/OPENMP.cmake
View File

@ -25,15 +25,15 @@
endif()
if(PKG_REAXFF)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_forces_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
endif()
target_sources(lammps PRIVATE ${OPENMP_SOURCES})

51
doc/src/Build_extras.rst
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@ -31,36 +31,36 @@ This is the list of packages that may require additional steps.
.. table_from_list::
:columns: 6
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MESSAGE <message>`
* :ref:`ML-IAP <mliap>`
* :ref:`MSCG <mscg>`
* :ref:`OPT <opt>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`VORONOI <voronoi>`
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COMPRESS <compress>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`INTEL <intel>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MESONT <mesont>`
* :ref:`MOLFILE <molfile>`
* :ref:`NETCDF <netcdf>`
* :ref:`MESSAGE <message>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`PLUMED <plumed>`
* :ref:`OPENMP <openmp>`
* :ref:`QMMM <qmmm>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`
* :ref:`PLUMED <plumed>`
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`MACHDYN <machdyn>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
----------
@ -1857,8 +1857,8 @@ ML-QUIP package
To build with this package, you must download and build the QUIP
library. It can be obtained from GitHub. For support of GAP
potentials, additional files with specific licensing conditions need
to be downloaded and configured. See step 1 and step 1.1 in the
``lib/quip/README`` file for details on how to do this.
to be downloaded and configured. The automatic download will from
within CMake will download the non-commercial use version.
.. tabs::
@ -1866,11 +1866,14 @@ to be downloaded and configured. See step 1 and step 1.1 in the
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
CMake will **not** download and build the QUIP library. But once you have
done that, a CMake build of LAMMPS with ``-D PKG_ML-QUIP=yes`` should
work. Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
.. tab:: Traditional make

1
doc/src/Commands_compute.rst
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@ -72,6 +72,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
* :doc:`heat/flux <compute_heat_flux>`
* :doc:`heat/flux/tally <compute_tally>`
* :doc:`heat/flux/virial/tally <compute_tally>`
* :doc:`hexorder/atom <compute_hexorder_atom>`
* :doc:`hma <compute_hma>`
* :doc:`improper <compute_improper>`

7
doc/src/Commands_fix.rst
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@ -157,6 +157,7 @@ OPT.
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`pair/tracker <fix_pair_tracker>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
@ -178,14 +179,14 @@ OPT.
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
* :doc:`qeq/reax (ko) <fix_qeq_reax>`
* :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
* :doc:`qeq/shielded <fix_qeq>`
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`rattle <fix_shake>`
* :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
* :doc:`reax/c/species (k) <fix_reaxc_species>`
* :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rhok <fix_rhok>`

3
doc/src/Commands_pair.rst
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@ -235,7 +235,7 @@ OPT.
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`rann <pair_rann>`
* :doc:`reax/c (ko) <pair_reaxc>`
* :doc:`reaxff (ko) <pair_reaxff>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
@ -273,6 +273,7 @@ OPT.
* :doc:`tip4p/cut (o) <pair_coul>`
* :doc:`tip4p/long (o) <pair_coul>`
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tracker <pair_tracker>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`vashishta (gko) <pair_vashishta>`

4
doc/src/Errors_warnings.rst
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@ -514,7 +514,7 @@ This will most likely cause errors in kinetic fluctuations.
will integrate the body motion, but it would be more efficient to use
fix rigid.
*Not using real units with pair reax*
*Not using real units with pair reaxff*
This is most likely an error, unless you have created your own ReaxFF
parameter file in a different set of units.
@ -805,5 +805,3 @@ This will most likely cause errors in kinetic fluctuations.
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.
*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
Self-explanatory.

2
doc/src/Examples.rst
View File

@ -150,6 +150,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| threebody | regression test input for a variety of manybody potentials |
+-------------+------------------------------------------------------------------+
| tracker | track interactions in LJ melt |
+-------------+------------------------------------------------------------------+
| vashishta | use of the Vashishta potential |
+-------------+------------------------------------------------------------------+
| voronoi | Voronoi tesselation via compute voronoi/atom command |

8
doc/src/Packages_details.rst
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@ -2274,10 +2274,10 @@ for monitoring molecules as bonds are created and destroyed.
* src/REAXFF: filenames -> commands
* src/REAXFF/README
* :doc:`pair_style reax/c <pair_reaxc>`
* :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
* :doc:`fix reax/c/species <fix_reaxc_species>`
* examples/reax
* :doc:`pair_style reaxff <pair_reaxff>`
* :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
* :doc:`fix reaxff/species <fix_reaxff_species>`
* examples/reaxff
----------

2
doc/src/Packages_list.rst
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@ -370,7 +370,7 @@ whether an extra library is needed to build and use the package:
- no
* - :ref:`REAXFF <PKG-REAXFF>`
- ReaxFF potential (C/C++)
- :doc:`pair_style reaxc <pair_reaxc>`
- :doc:`pair_style reaxff <pair_reaxff>`
- reax
- no
* - :ref:`REPLICA <PKG-REPLICA>`

15
doc/src/Tools.rst
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@ -76,7 +76,6 @@ Post-processing tools
* :ref:`phonon <phonon>`
* :ref:`pymol_asphere <pymol>`
* :ref:`python <pythontools>`
* :ref:`reax <reax_tool>`
* :ref:`replica <replica>`
* :ref:`smd <smd>`
* :ref:`spin <spin>`
@ -947,20 +946,6 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
----------
.. _reax_tool:
reax tool
--------------------------
The reax sub-directory contains stand-alone codes that can
post-process the output of the :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
command from a LAMMPS simulation using :doc:`ReaxFF <pair_reaxc>`. See
the README.txt file for more info.
These tools were written by Aidan Thompson at Sandia.
----------
.. _smd:
smd tool

7
doc/src/bond_oxdna.rst
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@ -84,6 +84,13 @@ commands:
the bond topology in the data file. The first (second) atom in a bond definition
is understood to point towards the 3'-end (5'-end) of the strand.
.. warning::
If data files are produced with :doc:`write_data <write_data>`, then the
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
Otherwise the data files will not have the same 3'-to-5' polarity as the
initial data file. This limitation does not apply to binary restart files
produced with :doc:`write_restart <write_restart>`.
Example input and data files for DNA and RNA duplexes can be found in
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python

11
doc/src/compute.rst
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@ -208,7 +208,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`event/displace <compute_event_displace>` - detect event on atom displacement
* :doc:`fabric <compute_fabric>` - calculates fabric tensors from pair interactions
* :doc:`fep <compute_fep>` -
* :doc:`force/tally <compute_tally>` -
* :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
* :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
* :doc:`global/atom <compute_global_atom>` -
* :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
@ -217,7 +217,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`gyration/shape <compute_gyration_shape>` - shape parameters from gyration tensor
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` - shape parameters from gyration tensor for each chunk
* :doc:`heat/flux <compute_heat_flux>` - heat flux through a group of atoms
* :doc:`heat/flux/tally <compute_tally>` -
* :doc:`heat/flux/tally <compute_tally>` - heat flux through a group of atoms via the tally callback mechanism
* :doc:`heat/flux/virial/tally <compute_tally>` - virial heat flux between two groups via the tally callback mechanism
* :doc:`hexorder/atom <compute_hexorder_atom>` - bond orientational order parameter q6
* :doc:`hma <compute_hma>` - harmonically mapped averaging for atomic crystals
* :doc:`improper <compute_improper>` - energy of each improper sub-style
@ -240,8 +241,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`pe <compute_pe>` - potential energy
* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies
* :doc:`pe/mol/tally <compute_tally>` -
* :doc:`pe/tally <compute_tally>` -
* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
* :doc:`pressure/cylinder <compute_pressure_cylinder>` - pressure tensor in cylindrical coordinates
@ -289,7 +290,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
* :doc:`stress/tally <compute_tally>` -
* :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
* :doc:`temp <compute_temp>` - temperature of group of atoms
* :doc:`temp/asphere <compute_temp_asphere>` - temperature of aspherical particles

5
doc/src/compute_pair.rst
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@ -24,7 +24,7 @@ Examples
compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair tersoff 2 epair
compute 1 all pair reax/c
compute 1 all pair reaxff
Description
"""""""""""
@ -64,7 +64,8 @@ is stored as a global scalar.
:doc:`pair_modify <pair_modify>` command.
Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into 14 components is tallied by the :doc:`pair_style reax/c <pair_reaxc>` command. These values (1 or more)
potential energy into 14 components is tallied by the
:doc:`pair_style reaxff <pair_reaxff>` command. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
:doc:`individual pair styles <pair_style>` for info on these values.

96
doc/src/compute_tally.rst
View File

@ -1,5 +1,6 @@
.. index:: compute force/tally
.. index:: compute heat/flux/tally
.. index:: compute heat/flux/virial/tally
.. index:: compute pe/tally
.. index:: compute pe/mol/tally
.. index:: compute stress/tally
@ -10,6 +11,9 @@ compute force/tally command
compute heat/flux/tally command
===============================
compute heat/flux/virial/tally command
======================================
compute pe/tally command
========================
@ -27,7 +31,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -38,13 +42,17 @@ Examples
compute 1 lower force/tally upper
compute 1 left pe/tally right
compute 1 lower stress/tally lower
compute 1 subregion heat/flux/tally all
compute 1 liquid heat/flux/virial/tally solid
Description
"""""""""""
Define a computation that calculates properties between two groups of
atoms by accumulating them from pairwise non-bonded computations. The
two groups can be the same. This is similar to :doc:`compute group/group <compute_group_group>` only that the data is
atoms by accumulating them from pairwise non-bonded computations.
Except for *heat/flux/virial/tally*, the two groups can be the same.
This is similar to :doc:`compute group/group <compute_group_group>`
only that the data is
accumulated directly during the non-bonded force computation. The
computes *force/tally*\ , *pe/tally*\ , *stress/tally*\ , and
*heat/flux/tally* are primarily provided as example how to program
@ -57,6 +65,76 @@ the based classes of LAMMPS.
----------
Compute *heat/flux/tally* obtains the heat flux
(strictly speaking, heat flow) inside the first group,
which is the sum of the convective contribution
due to atoms in the first group and the virial contribution
due to interaction between the first and second groups:
.. math::
\mathbf{Q}= \sum_{i \in \text{group 1}} e_i \mathbf{v}_i + \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{\substack{j \in \text{group 2} \\ j \neq i } } \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij}
When the second group in *heat/flux/tally* is set to "all",
the resulting values will be identical
to that obtained by :doc:`compute heat/flux <compute_heat_flux>`,
provided only pairwise interactions exist.
Compute *heat/flux/virial/tally* obtains the total virial heat flux
(strictly speaking, heat flow) into the first group due to interaction
with the second group, and is defined as:
.. math::
Q = \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{j \in \text{group 2}} \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right)
Although, the *heat/flux/virial/tally* compute
does not include the convective term,
it can be used to obtain the total heat flux over control surfaces,
when there are no particles crossing over,
such as is often in solid-solid and solid-liquid interfaces.
This would be identical to the method of planes method.
Note that the *heat/flux/virial/tally* compute is distinctly different
from the *heat/flux* and *heat/flux/tally* computes,
that are essentially volume averaging methods.
The following example demonstrates the difference:
.. code-block:: LAMMPS
# System with only pairwise interactions.
# Non-periodic boundaries in the x direction.
# Has LeftLiquid and RightWall groups along x direction.
# Heat flux over the solid-liquid interface
compute hflow_hfvt LeftLiquid heat/flux/virial/tally RightWall
variable hflux_hfvt equal c_hflow_hfvt/(ly*lz)
# x component of approximate heat flux vector inside the liquid region,
# two approaches.
#
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
compute hflow_hf LeftLiquid heat/flux myKE myPE myStress
variable hflux_hf equal c_hflow_hf[1]/${volLiq}
#
compute hflow_hft LeftLiquid heat/flux/tally all
variable hflux_hft equal c_hflow_hft[1]/${volLiq}
# Pressure over the solid-liquid interface, three approaches.
#
compute force_gg RightWall group/group LeftLiquid
variable press_gg equal c_force_gg[1]/(ly*lz)
#
compute force_ft RightWall force/tally LeftLiquid
compute rforce_ft RightWall reduce sum c_force_ft[1]
variable press_ft equal c_rforce_ft/(ly*lz)
#
compute rforce_hfvt all reduce sum c_hflow_hfvt[1]
variable press_hfvt equal -c_rforce_hfvt/(ly*lz)
----------
The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
@ -83,7 +161,17 @@ magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).
individual atom). As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).
Both the scalar and vector values calculated by this compute are
"extensive".

12
doc/src/dump_modify.rst
View File

@ -66,7 +66,7 @@ Syntax
*unwrap* arg = *yes* or *no*
* these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header*
.. parsed-literal::
@ -113,6 +113,9 @@ Syntax
rate = target bitrate for movie in kbps
*framerate* arg = fps
fps = frames per second for movie
*header* arg = *yes* or *no*
*yes* to write the header
*no* to not write the header
* these keywords apply only to the */gz* and */zstd* dump styles
* keyword = *compression_level*
@ -977,6 +980,13 @@ images less frequently.
----------
The *header* keyword toggles whether the dump file will include a header.
Excluding a header will reduce the size of the dump file for fixes such as
:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
typically written to the header.
----------
The COMPRESS package offers both GZ and Zstd compression variants of styles
atom, custom, local, cfg, and xyz. When using these styles the compression
level can be controlled by the :code:`compression_level` parameter. File names

3
doc/src/dump_netcdf.rst
View File

@ -73,6 +73,9 @@ NETCDF package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` doc page for
more info.
The *netcdf* and *netcdf/mpiio* dump styles currently cannot dump
string properties or properties from variables.
----------
Related commands

7
doc/src/fix.rst
View File

@ -300,6 +300,7 @@ accelerated styles exist.
* :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
* :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
* :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
* :doc:`pair/tracker <fix_pair_tracker>` - track properties of pairwise interactions
* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
* :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
@ -321,14 +322,14 @@ accelerated styles exist.
* :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
* :doc:`qeq/reax <fix_qeq_reax>` - charge equilibration for ReaxFF potential
* :doc:`qeq/reaxff <fix_qeq_reaxff>` - charge equilibration for ReaxFF potential
* :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method
* :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
* :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
* :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
* :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
* :doc:`reax/c/bonds <fix_reaxc_bonds>` - write out ReaxFF bond information
* :doc:`reax/c/species <fix_reaxc_species>` - write out ReaxFF molecule information
* :doc:`reaxff/bonds <fix_reaxff_bonds>` - write out ReaxFF bond information
* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
* :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems

2
doc/src/fix_adapt.rst
View File

@ -186,7 +186,7 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`reax/c <pair_reaxc>` | chi, eta, gamma | type global |
| :doc:`reaxff <pair_reaxff>` | chi, eta, gamma | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`snap <pair_snap>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+

2
doc/src/fix_gcmc.rst
View File

@ -374,7 +374,7 @@ in the context of NVT dynamics.
has been reached.
With some pair_styles, such as :doc:`Buckingham <pair_buck>`,
:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxc>`, two
:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxff>`, two
atoms placed close to each other may have an arbitrary large, negative
potential energy due to the functional form of the potential. While
these unphysical configurations are inaccessible to typical dynamical

4
doc/src/fix_oneway.rst
View File

@ -50,7 +50,9 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
none
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""

124
doc/src/fix_pair_tracker.rst Normal file
View File

@ -0,0 +1,124 @@
.. index:: fix pair/tracker
fix pair/tracker command
========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID pair/tracker N attribute1 attribute2 ... keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* pair/tracker = style name of this fix command
* N = prepare data for output every this many timesteps
* one or more attributes may be appended
.. parsed-literal::
possible attributes = id1 id2 time/created time/broken time/total
rmin rave x y z
.. parsed-literal::
id1, id2 = IDs of the 2 atoms in each pair interaction
time/created = the time that the 2 atoms began interacting
time/broken = the time that the 2 atoms stopped interacting
time/total = the total time the 2 atoms interacted
r/min = the minimum radial distance between the 2 atoms during the interaction
r/ave = the average radial distance between the 2 atoms during the interaction
x, y, z = the center of mass position of the 2 atoms when they stopped interacting
* zero or more keyword/value pairs may be appended
* keyword = *time/min* or *type/include*
.. parsed-literal::
*time/min* value = T
T = minimum interaction time
*type/include* value = arg1 arg2
arg = separate lists of types (see below)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all pair/tracker 1000 id1 id2 time/min 100
fix 1 all pair/tracker 1000 time/created time/broken type/include 1 * type/include 2 3,4
Description
"""""""""""
Tracks properties of pairwise interactions between two atoms and records data
whenever the atoms move beyond the interaction cutoff.
Must be used in conjunction with :doc:`pair tracker <pair_tracker>`.
Data is accumulated over a span of *N* timesteps before being deleted.
The number of datums generated, aggregated across all processors, equals
the number of broken interactions. Interactions are only included if both
atoms are included in the specified fix group. Additional filters can be
applied using the *time/min* or *type/include* keywords described below.
.. note::
For extremely long-lived interactions, the calculation of *r/ave* may not be
correct due to double overflow.
The *time/min* keyword sets a minimum amount of time that an interaction must
persist to be included. This setting can be used to censor short-lived interactions.
The *type/include* keyword filters interactions based on the types of the two atoms.
Data is only saved for interactions between atoms with types in the two lists.
Each list consists of a series of type
ranges separated by commas. The range can be specified as a
single numeric value, or a wildcard asterisk can be used to specify a range
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
example, if M = the number of atom types, then an asterisk with no numeric
values means all types from 1 to M. A leading asterisk means all types
from 1 to n (inclusive). A trailing asterisk means all types from n to M
(inclusive). A middle asterisk means all types from m to n (inclusive).
Multiple *type/include* keywords may be added.
----------
Restart, fix_modify, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
Output info
"""""""""""
This compute calculates a local vector or local array depending on the
number of input values. The length of the vector or number of rows in
the array is the number of recorded, lost interactions. If a single input is
specified, a local vector is produced. If two or more inputs are
specified, a local array is produced where the number of columns = the
number of inputs. The vector or array can be accessed by any command
that uses local values from a compute as input. See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
options.
The vector or array values will be doubles that correspond to the
specified attribute.
Restrictions
""""""""""""
Must be used in conjunction with :doc:`pair style tracker <pair_tracker>`.
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair tracker <pair_tracker>`
Default
"""""""
none

6
doc/src/fix_plumed.rst
View File

@ -41,7 +41,7 @@ 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 :ref:`(PLUMED) <PLUMED>`.
A detailed discussion of the code can be found in :ref:`(Tribello) <Tribello>`.
There is an example input for using this package with LAMMPS in the
examples/PACKAGES/plumed directory.
@ -132,9 +132,9 @@ The default options are plumedfile = NULL and outfile = NULL
----------
.. _PLUMED:
.. _Tribello:
**(PLUMED)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Tribello)** G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
.. _plumeddocs: https://www.plumed.org/doc.html

41
doc/src/fix_qeq.rst
View File

@ -32,15 +32,16 @@ Syntax
* cutoff = global cutoff for charge-charge interactions (distance unit)
* tolerance = precision to which charges will be equilibrated
* maxiter = maximum iterations to perform charge equilibration
* qfile = a filename with QEq parameters or *coul/streitz* or *reax/c*
* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
* zero or more keyword/value pairs may be appended
* keyword = *alpha* or *qdamp* or *qstep*
* keyword = *alpha* or *qdamp* or *qstep* or *warn*
.. parsed-literal::
*alpha* value = Slater type orbital exponent (qeq/slater only)
*qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
Examples
""""""""
@ -90,19 +91,19 @@ on the current atom configuration), then remove the fix via the
The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
perform charge equilibration with the :doc:`COMB potential
<pair_comb>`. The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
<pair_comb>`. The :doc:`fix qeq/reaxff <fix_qeq_reaxff>` command can be
used to perform charge equilibration with the :doc:`ReaxFF force
field <pair_reaxc>`, although fix qeq/shielded yields the same
results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reax command will be
field <pair_reaxff>`, although fix qeq/shielded yields the same
results as fix qeq/reaxff if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reaxff command will be
deprecated.
The QEq method minimizes the electrostatic energy of the system (or
equalizes the derivative of energy with respect to charge of all the
atoms) by adjusting the partial charge on individual atoms based on
interactions with their neighbors within *cutoff*\ . It requires a few
parameters, in *metal* units, for each atom type which provided in a
file specified by *qfile*\ . The file has the following format
parameters in the appropriate units for each atom type which are read
from a file specified by *qfile*\ . The file has the following format
.. parsed-literal::
@ -112,7 +113,7 @@ file specified by *qfile*\ . The file has the following format
Ntype chi eta gamma zeta qcore
There have to be parameters given for every atom type. Wildcard entries
are possible using the same syntax as elsewhere in LAMMPS
are possible using the same type range syntax as for "coeff" commands
(i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
Empty lines or any text following the pound sign (#) are ignored.
Each line starts with the atom type followed by five parameters.
@ -126,6 +127,14 @@ entries per line are required.
* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
The fix qeq styles will print a warning if the charges are not
equilibrated within *tolerance* by *maxiter* steps, unless the
*warn* keyword is used with "no" as argument. This latter option
may be useful for testing and benchmarking purposes, as it allows
to use a fixed number of QEq iterations when *tolerance* is set
to a small enough value to always reach the *maxiter* limit. Turning
off warnings will avoid the excessive output in that case.
The *qeq/point* style describes partial charges on atoms as point
charges. Interaction between a pair of charged particles is 1/r,
which is the simplest description of the interaction between charges.
@ -141,11 +150,11 @@ interaction between a pair of charged particles. Interaction through
the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
field <vanDuin>` paper. The shielding accounts for charge overlap
between charged particles at small separation. This style is the same
as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
:doc:`pair_style reax/c <pair_reaxc>`. Only the *chi*\ , *eta*\ , and
as :doc:`fix qeq/reaxff <fix_qeq_reaxff>`, and can be used with
:doc:`pair_style reaxff <pair_reaxff>`. Only the *chi*\ , *eta*\ , and
*gamma* parameters from the *qfile* file are used. When using the string
*reax/c* as filename, these parameters are extracted directly from an
active *reax/c* pair style. This style solves partial charges on atoms
*reaxff* as filename, these parameters are extracted directly from an
active *reaxff* pair style. This style solves partial charges on atoms
via the matrix inversion method. A tolerance of 1.0e-6 is usually a
good number.
@ -221,15 +230,17 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
The qeq fixes are not compatible with the GPU and USER-INTEL packages.
Related commands
""""""""""""""""
:doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix qeq/comb <fix_qeq_comb>`
:doc:`fix qeq/reaxff <fix_qeq_reaxff>`, :doc:`fix qeq/comb <fix_qeq_comb>`
Default
"""""""
none
warn yes
----------

2
doc/src/fix_qeq_comb.rst
View File

@ -41,7 +41,7 @@ Perform charge equilibration (QeQ) in conjunction with the COMB
equilibration portion of the calculation using the so-called QEq
method, whereby the charge on each atom is adjusted to minimize the
energy of the system. This fix can only be used with the COMB
potential; see the :doc:`fix qeq/reax <fix_qeq_reax>` command for a QeQ
potential; see the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` command for a QeQ
calculation that can be used with any potential.
Only charges on the atoms in the specified group are equilibrated.

76
doc/src/fix_qeq_reax.rst → doc/src/fix_qeq_reaxff.rst
View File

@ -1,59 +1,61 @@
.. index:: fix qeq/reax
.. index:: fix qeq/reax/kk
.. index:: fix qeq/reax/omp
.. index:: fix qeq/reaxff
.. index:: fix qeq/reaxff/kk
.. index:: fix qeq/reaxff/omp
fix qeq/reax command
====================
fix qeq/reaxff command
======================
Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp*
Accelerator Variants: *qeq/reaxff/kk*, *qeq/reaxff/omp*
Syntax
""""""
.. parsed-literal::
fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args
fix ID group-ID qeq/reaxff Nevery cutlo cuthi tolerance params args
* ID, group-ID are documented in :doc:`fix <fix>` command
* qeq/reax = style name of this fix command
* qeq/reaxff = style name of this fix command
* Nevery = perform QEq every this many steps
* cutlo,cuthi = lo and hi cutoff for Taper radius
* tolerance = precision to which charges will be equilibrated
* params = reax/c or a filename
* params = reaxff or a filename
* one or more keywords or keyword/value pairs may be appended
.. parsed-literal::
keyword = *dual* or *maxiter*
*dual* = process S and T matrix in parallel (only for qeq/reax/omp)
keyword = *dual* or *maxiter* or *nowarn*
*dual* = process S and T matrix in parallel (only for qeq/reaxff/omp)
*maxiter* N = limit the number of iterations to *N*
*nowarn* = do not print a warning message if the maximum number of iterations was reached
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
Description
"""""""""""
Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe2>` and formulated in :ref:`(Nakano) <Nakano2>`. It is
typically used in conjunction with the ReaxFF force field model as
implemented in the :doc:`pair_style reax/c <pair_reaxc>` command, but
it can be used with any potential in LAMMPS, so long as it defines and
uses charges on each atom. The :doc:`fix qeq/comb <fix_qeq_comb>`
command should be used to perform charge equilibration with the :doc:`COMB potential <pair_comb>`. For more technical details about the
charge equilibration performed by fix qeq/reax, see the
Perform the charge equilibration (QEq) method as described in
:ref:`(Rappe and Goddard) <Rappe2>` and formulated in :ref:`(Nakano)
<Nakano2>`. It is typically used in conjunction with the ReaxFF force
field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. The :doc:`fix qeq/comb
<fix_qeq_comb>` command should be used to perform charge equilibration
with the :doc:`COMB potential <pair_comb>`. For more technical details
about the charge equilibration performed by fix qeq/reaxff, see the
:ref:`(Aktulga) <qeq-Aktulga>` paper.
The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It requires some parameters for each atom type.
If the *params* setting above is the word "reax/c", then these are
extracted from the :doc:`pair_style reax/c <pair_reaxc>` command and
If the *params* setting above is the word "reaxff", then these are
extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
the ReaxFF force field file it reads in. If a file name is specified
for *params*\ , then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
@ -74,17 +76,26 @@ of this fix are hard-coded to be A, eV, and electronic charge.
The optional *dual* keyword allows to perform the optimization
of the S and T matrices in parallel. This is only supported for
the *qeq/reax/omp* style. Otherwise they are processed separately.
the *qeq/reaxff/omp* style. Otherwise they are processed separately.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
The optional *nowarn* keyword silences the warning message printed
when the maximum number of iterations was reached. This can be
useful for comparing serial and parallel results where having the
same fixed number of QEq iterations is desired, which can be achieved
by using a very small tolerance and setting *maxiter* to the desired
number of iterations.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. No global scalar or vector or per-atom
quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`. No parameter of this fix can be used
with the *start/stop* keywords of the :doc:`run <run>` command.
No information about this fix is written to :doc:`binary restart files
<restart>`. This fix computes a global scalar (the number of
iterations) for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
This fix is invoked during :doc:`energy minimization <minimize>`.
@ -98,16 +109,17 @@ Restrictions
""""""""""""
This fix is part of the REAXFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
be used for periodic cell dimensions less than 10 angstroms.
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms.
Related commands
""""""""""""""""
:doc:`pair_style reax/c <pair_reaxc>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`
Default
"""""""

20
doc/src/fix_reaxc_bonds.rst → doc/src/fix_reaxff_bonds.rst
View File

@ -1,17 +1,17 @@
.. index:: fix reax/c/bonds
.. index:: fix reax/c/bonds/kk
.. index:: fix reaxff/bonds
.. index:: fix reaxff/bonds/kk
fix reax/c/bonds command
fix reaxff/bonds command
========================
Accelerator Variants: *reax/c/bonds/kk*
Accelerator Variants: *reaxff/bonds/kk*
Syntax
""""""
.. parsed-literal::
fix ID group-ID reaxc/bonds Nevery filename
fix ID group-ID reaxff/bonds Nevery filename
* ID, group-ID are documented in :doc:`fix <fix>` command
* reax/bonds = style name of this fix command
@ -23,17 +23,17 @@ Examples
.. code-block:: LAMMPS
fix 1 all reax/c/bonds 100 bonds.reaxc
fix 1 all reaxff/bonds 100 bonds.reaxff
Description
"""""""""""
Write out the bond information computed by the ReaxFF potential specified
by :doc:`pair_style reax/c <pair_reaxc>` in the exact same format as the
by :doc:`pair_style reaxff <pair_reaxff>` in the exact same format as the
original stand-alone ReaxFF code of Adri van Duin. The bond information
is written to *filename* on timesteps that are multiples of *Nevery*\ ,
including timestep 0. For time-averaged chemical species analysis,
please see the :doc:`fix reaxc/c/species <fix_reaxc_species>` command.
please see the :doc:`fix reaxff/species <fix_reaxff_species>` command.
The specified group-ID is ignored by this fix.
@ -76,7 +76,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
The fix reax/c/bonds command requires that the :doc:`pair_style reax/c <pair_reaxc>` is invoked. This fix is part of the
The fix reaxff/bonds command requires that the :doc:`pair_style reaxff <pair_reaxff>` is invoked. This fix is part of the
REAXFF package. It is only enabled if LAMMPS was built with that
package. See the :doc:`Build package <Build_package>` doc page for more
info.
@ -87,7 +87,7 @@ To write gzipped bond files, you must compile LAMMPS with the
Related commands
""""""""""""""""
:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/species <fix_reaxc_species>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/species <fix_reaxff_species>`
Default
"""""""

57
doc/src/fix_reaxc_species.rst → doc/src/fix_reaxff_species.rst
View File

@ -1,20 +1,20 @@
.. index:: fix reax/c/species
.. index:: fix reax/c/species/kk
.. index:: fix reaxff/species
.. index:: fix reaxff/species/kk
fix reax/c/species command
fix reaxff/species command
==========================
Accelerator Variants: *reax/c/species/kk*
Accelerator Variants: *reaxff/species/kk*
Syntax
""""""
.. parsed-literal::
fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ...
fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* reax/c/species = style name of this command
* reaxff/species = style name of this command
* Nevery = sample bond-order every this many timesteps
* Nrepeat = # of bond-order samples used for calculating averages
* Nfreq = calculate average bond-order every this many timesteps
@ -37,15 +37,15 @@ Examples
.. code-block:: LAMMPS
fix 1 all reax/c/species 10 10 100 species.out
fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
fix 1 all reaxff/species 10 10 100 species.out
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
Description
"""""""""""
Write out the chemical species information computed by the ReaxFF
potential specified by :doc:`pair_style reax/c <pair_reaxc>`.
potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
Bond-order values (either averaged or instantaneous, depending on
value of *Nrepeat*\ ) are used to determine chemical bonds. Every
*Nfreq* timesteps, chemical species information is written to
@ -73,7 +73,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must
match the number of LAMMPS atom types and each symbol must consist of
1 or 2 alphanumeric characters. Normally, these symbols should be
chosen to match the chemical identity of each LAMMPS atom type, as
specified using the :doc:`reax/c pair_coeff <pair_reaxc>` command and
specified using the :doc:`reaxff pair_coeff <pair_reaxff>` command and
the ReaxFF force field file.
The optional keyword *position* writes center-of-mass positions of
@ -115,12 +115,12 @@ average bond-order for the species analysis output on timestep 100.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
This fix computes both a global vector of length 2 and a per-atom
vector, either of which can be accessed by various :doc:`output commands <Howto_output>`. The values in the global vector are
"intensive".
This fix computes both a global vector of length 2 and a per-atom vector,
either of which can be accessed by various :doc:`output commands <Howto_output>`.
The values in the global vector are "intensive".
The 2 values in the global vector are as follows:
@ -134,7 +134,8 @@ will be the same and will be equal to the smallest atom ID of
any atom in the molecule.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command.
This fix is not invoked during :doc:`energy minimization <minimize>`.
----------
@ -145,26 +146,20 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
The "fix reax/c/species" currently only works with :doc:`pair_style reax/c <pair_reaxc>` and it requires that the :doc:`pair_style reax/c <pair_reaxc>` be invoked. This fix is part of the
REAXFF package. It is only enabled if LAMMPS was built with that
package. See the :doc:`Build package <Build_package>` doc page for more
info.
The "fix reaxff/species" requires that :doc:`pair_style reaxff <pair_reaxff>` is used.
This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that
package. See the :doc:`Build package <Build_package>` doc page for more info.
To write gzipped species files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
It should be possible to extend it to other reactive pair_styles (such as
:doc:`rebo <pair_airebo>`, :doc:`airebo <pair_airebo>`,
:doc:`comb <pair_comb>`, and :doc:`bop <pair_bop>`), but this has not yet been done.
To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option.
Related commands
""""""""""""""""
:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
Default
"""""""
The default values for bond-order cutoffs are 0.3 for all I-J pairs. The
default element symbols are C, H, O, N. Position files are not written
by default.
The default values for bond-order cutoffs are 0.3 for all I-J pairs.
The default element symbols are C, H, O, N.
Position files are not written by default.

4
doc/src/kim_commands.rst
View File

@ -372,9 +372,9 @@ the *kim interactions* command executes the following LAMMPS input commands:
.. code-block:: LAMMPS
pair_style reax/c lmp_control safezone 2.0 mincap 100
pair_style reaxff lmp_control safezone 2.0 mincap 100
pair_coeff * * ffield.reax.rdx C H N O
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
fix reaxqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq
.. note::

3
doc/src/package.rst
View File

@ -448,7 +448,8 @@ does not require atomic operations in the calculation of pair forces. For
that reason, *full* is the default setting for GPUs. However, when
running on CPUs, a *half* neighbor list is the default because it are
often faster, just as it is for non-accelerated pair styles. Similarly,
the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`.
the *neigh/qeq* keyword determines how neighbor lists are built for
:doc:`fix qeq/reaxff/kk <fix_qeq_reaxff>`.
If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
threads only over atoms. However, for small systems, this may not expose

6
doc/src/pair_granular.rst
View File

@ -665,12 +665,6 @@ then LAMMPS will use that cutoff for the specified atom type
combination, and automatically set pairwise cutoffs for the remaining
atom types.
If two particles are moving away from each other while in contact, there
is a possibility that the particles could experience an effective attractive
force due to damping. If the *limit_damping* keyword is used, this option
will zero out the normal component of the force if there is an effective
attractive force. This keyword cannot be used with the JKR or DMT models.
----------
.. include:: accel_styles.rst

118
doc/src/pair_reaxc.rst → doc/src/pair_reaxff.rst
View File

@ -1,18 +1,18 @@
.. index:: pair_style reax/c
.. index:: pair_style reax/c/kk
.. index:: pair_style reax/c/omp
.. index:: pair_style reaxff
.. index:: pair_style reaxff/kk
.. index:: pair_style reaxff/omp
pair_style reax/c command
pair_style reaxff command
=========================
Accelerator Variants: *reax/c/kk*, *reax/c/omp*
Accelerator Variants: *reaxff/kk*, *reaxff/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style reax/c cfile keyword value
pair_style reaxff cfile keyword value
* cfile = NULL or name of a control file
* zero or more keyword/value pairs may be appended
@ -20,7 +20,7 @@ Syntax
.. parsed-literal::
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff fix
*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
*safezone* = factor used for array allocation
@ -32,37 +32,38 @@ Examples
.. code-block:: LAMMPS
pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100
pair_style reaxff NULL
pair_style reaxff controlfile checkqeq no
pair_style reaxff NULL lgvdw yes
pair_style reaxff NULL safezone 1.6 mincap 100
pair_coeff * * ffield.reax C H O N
Description
"""""""""""
Style *reax/c* computes the ReaxFF potential of van Duin, Goddard and
Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: :ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the :ref:`(Aktulga) <Aktulga>` paper. The *reax/c* style was initially
implemented as a stand-alone C code and is now integrated into LAMMPS
as a package.
supplemental information of the following paper:
:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`. The version integrated
into LAMMPS matches the version of ReaxFF From Summer 2010. For more
technical details about the pair reaxff implementation of ReaxFF, see
the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
implemented as a stand-alone C code and is now converted to C++ and
integrated into LAMMPS as a package.
The *reax/c/kk* style is a Kokkos version of the ReaxFF potential that
is derived from the *reax/c* style. The Kokkos version can run on GPUs
The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
is derived from the *reaxff* style. The Kokkos version can run on GPUs
and can also use OpenMP multithreading. For more information about the
Kokkos package, see :doc:`Packages details <Packages_details>` and
:doc:`Speed kokkos <Speed_kokkos>` doc pages. One important
consideration when using the *reax/c/kk* style is the choice of either
consideration when using the *reaxff/kk* style is the choice of either
half or full neighbor lists. This setting can be changed using the
Kokkos :doc:`package <package>` command.
The *reax/c* style differs from the (obsolete) "pair_style reax"
The *reaxff* style differs from the (obsolete) "pair_style reax"
command in the implementation details. The *reax* style was a
Fortran library, linked to LAMMPS. The *reax* style has been removed
from LAMMPS after the 12 December 2018 version.
@ -73,7 +74,7 @@ documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N.
The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of *pair_style reax/c* potential
Duin. We have tested the accuracy of *pair_style reaxff* potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
@ -102,10 +103,11 @@ control variable. The format of the control file is described below.
The LAMMPS default values for the ReaxFF global parameters
correspond to those used by Adri van Duin's stand-alone serial
code. If these are changed by setting control variables in the control
file, the results from LAMMPS and the serial code will not agree.
code. If these are changed by setting control variables in the
control file, the results from LAMMPS and the serial code will
not agree.
Examples using *pair_style reax/c* are provided in the examples/reax
Examples using *pair_style reaxff* are provided in the examples/reax
sub-directory.
Use of this pair style requires that a charge be defined for every
@ -115,25 +117,28 @@ charges.
The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that the :doc:`fix qeq/reax <fix_qeq_reax>` command be used with *pair_style reax/c*
when simulating a ReaxFF model, to equilibrate charge each timestep.
Using the keyword *checkqeq* with the value *no*
turns off the check for *fix qeq/reax*\ ,
allowing a simulation to be run without charge equilibration.
In this case, the static charges you
assign to each atom will be used for computing the electrostatic
interactions in the system.
See the :doc:`fix qeq/reax <fix_qeq_reax>` command for details.
Therefore, by default, LAMMPS requires that either the
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
:doc:`fix qeq/shielded <fix_qeq>` command be used with
*pair_style reaxff* when simulating a ReaxFF model, to equilibrate
the charges each timestep.
Using the keyword *checkqeq* with the value *no* turns off the check
for the QEq fixes, allowing a simulation to be run without charge
equilibration. In this case, the static charges you assign to each
atom will be used for computing the electrostatic interactions in
the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
:doc:`fix qeq/shielded <fix_qeq>` command documentation for more details.
Using the optional keyword *lgvdw* with the value *yes* turns on the
low-gradient correction of the ReaxFF/C for long-range London
Dispersion, as described in the :ref:`(Liu) <Liu_2011>` paper. Force field
file *ffield.reax.lg* is designed for this correction, and is trained
for several energetic materials (see "Liu"). When using lg-correction,
recommended value for parameter *thb* is 0.01, which can be set in the
low-gradient correction of ReaxFF for long-range London Dispersion,
as described in the :ref:`(Liu) <Liu_2011>` paper. The bundled force
field file *ffield.reax.lg* is designed for this correction, and is
trained for several energetic materials (see "Liu"). When using *lgvdw yes*,
the recommended value for parameter *thb* is 0.01, which can be set in the
control file. Note: Force field files are different for the original
or lg corrected pair styles, using wrong ffield file generates an
error message.
or lg corrected pair styles, using the wrong ffield file generates an
error.
Using the optional keyword *enobonds* with the value *yes*\ , the energy
of atoms with no bonds (i.e. isolated atoms) is included in the total
@ -144,7 +149,7 @@ discontinuities in the potential energy when the bonding of an atom
drops to zero.
Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used
for allocating reax/c arrays. Increasing these values can avoid memory
for allocating reaxff arrays. Increasing these values can avoid memory
problems, such as segmentation faults and bondchk failed errors, that
could occur under certain conditions. These keywords are not used by
the Kokkos version, which instead uses a more robust memory allocation
@ -158,7 +163,8 @@ equilibration contributions which are stored in the thermo variable
:doc:`thermo <thermo>` command.
This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 14.
energy into sub-categories, which can be accessed via the
:doc:`compute pair <compute_pair>` command as a vector of values of length 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the original FORTRAN ReaxFF
code):
@ -183,14 +189,14 @@ headings) the following commands could be included in an input script:
.. code-block:: LAMMPS
compute reax all pair reax/c
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
[...]
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea [...] v_eqeq
Only a single pair_coeff command is used with the *reax/c* style which
Only a single pair_coeff command is used with the *reaxff* style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
@ -209,7 +215,7 @@ to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when the *reax/c* style is used as part
performed. This can be used when the *reaxff* style is used as part
of the *hybrid* pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
@ -241,7 +247,7 @@ brief description of their use and default values.
*simulation_name*
Output files produced by *pair_style reax/c* carry
Output files produced by *pair_style reaxff* carry
this name + extensions specific to their contents. Partial energies
are reported with a ".pot" extension, while the trajectory file has
".trj" extension.
@ -286,8 +292,7 @@ brief description of their use and default values.
to be considered in three body interactions. (default value = 0.00001)
*write_freq*
Frequency of writes into the trajectory file. (default
value = 0)
Frequency of writes into the trajectory file. (default value = 0)
*traj_title*
Title of the trajectory - not the name of the trajectory file.
@ -315,7 +320,8 @@ Mixing, shift, table, tail correction, restart, rRESPA info
This pair style does not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
This pair style does not write its information to :doc:`binary restart files <restart>`,
since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
@ -333,18 +339,20 @@ Restrictions
""""""""""""
This pair style is part of the REAXFF package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.
The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real :doc:`units <units>`. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
directory are parameterized for *real* :doc:`units <units>`. You can use
the ReaxFF pair style with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation does not use "real" units.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`, :doc:`fix reax/c/species <fix_reaxc_species>`
:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix reaxff/bonds <fix_reaxff_bonds>`, :doc:`fix reaxff/species <fix_reaxff_species>`
Default
"""""""

3
doc/src/pair_style.rst
View File

@ -299,7 +299,7 @@ accelerated styles exist.
* :doc:`python <pair_python>` -
* :doc:`quip <pair_quip>` -
* :doc:`rann <pair_rann>` -
* :doc:`reax/c <pair_reaxc>` - ReaxFF potential in C
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
@ -338,6 +338,7 @@ accelerated styles exist.
* :doc:`tip4p/cut <pair_coul>` - Coulomb for TIP4P water w/out LJ
* :doc:`tip4p/long <pair_coul>` - long-range Coulomb for TIP4P water w/out LJ
* :doc:`tip4p/long/soft <pair_fep_soft>` -
* :doc:`tracker <pair_tracker>` - monitor information about pairwise interactions
* :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
* :doc:`ufm <pair_ufm>` -
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential

97
doc/src/pair_tracker.rst Normal file
View File

@ -0,0 +1,97 @@
.. index:: pair_style tracker
pair_style tracker command
==========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style tracker keyword
* zero or more keyword/arg pairs may be appended
* keyword = *finite*
.. parsed-literal::
*finite* value = none
pair style uses atomic diameters to identify contacts
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay tracker ...
pair_coeff 1 1 tracker 2.0
pair_style hybrid/overlay tracker finite ...
pair_coeff * * tracker
fix 1 all pair/tracker 1000 time/created time/broken
dump 1 all local 1000 dump.local f_1[1] f_1[2]
dump_modify 1 write_header no
Description
"""""""""""
Style *tracker* monitors information about pairwise interactions.
It does not calculate any forces on atoms.
:doc:`Pair hybrid/overlay <pair_hybrid>` can be used to combine this pair
style with another pair style. Style *tracker* must be used in conjunction
with about :doc:`fix pair_tracker <fix_pair_tracker>` which contains
information on what data can be output.
If the *finite* keyword is not defined, the following coefficients must be
defined for each pair of atom types via the :doc:`pair_coeff <pair_coeff>`
command as in the examples above, or in the data file or restart files
read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cutoff (distance units)
If the *finite* keyword is defined, no coefficients may be defined.
Interaction cutoffs are alternatively calculated based on the
diameter of finite particles.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the cutoff coefficient and cutoff
distance for this pair style can be mixed. The cutoff is always mixed via a
*geometric* rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is *geometric*\ . See the
"pair_modify" command for details.
This pair style writes its information to :doc:`binary restart files <restart>`, so
pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
The :doc:`pair_modify <pair_modify>` shift, table, and tail options
are not relevant for this pair style.
----------
Restrictions
""""""""""""
A corresponding :doc:`fix pair_tracker <fix_pair_tracker>` must be defined
to use this pair style.
This pair style is currently incompatible with granular pair styles that extend
beyond the contact (e.g. JKR and DMT).
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`fix pair_tracker <fix_pair_tracker>`
Default
"""""""
none

55
doc/utils/check-styles.py
View File

@ -254,40 +254,27 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index)
skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c')
counter = 0
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",
command,'Command',suffix=False)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",
compute,'Compute',suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",
compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",
fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=True)
counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",
fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False)
counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",
pair,'Pair',skip=('meam/c','lj/sf'),suffix=True)
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",
pair,'Pair',skip=('meam/c','lj/sf'),suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",
bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",
bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",
angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",
angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",
dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",
dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",
improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",
improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",
kspace,'KSpace',suffix=True)
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=False)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",fix,'Fix',skip=skip_fix,suffix=True)
counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",fix,'Fix',skip=skip_fix,suffix=False)
counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair,'Pair',skip=skip_pair,suffix=True)
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
if counter:
print(f"Found {counter} issue(s) with style lists")
@ -295,13 +282,13 @@ if counter:
counter = 0
counter += check_style_index("compute", compute, index["compute"])
counter += check_style_index("fix", fix, index["fix"], skip=['python'])
counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf'])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
if counter:
print(f"Found {counter} issue(s) with style index")

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -1132,6 +1132,7 @@ Germano
gerolf
Gerolf
Gershgorin
getter
gettimeofday
gewald
Gezelter
@ -2743,6 +2744,7 @@ reamin
reax
REAXFF
ReaxFF
reaxff
rebo
recursing
Ree

8
examples/PACKAGES/cgdna/README
View File

@ -72,6 +72,14 @@ between two individual nucleotides can be established.
/******************************************************************************/
/examples/oxDNA2/dsring:
This example uses a dsDNA ring of 74 base pairs. The bonds which close the ring
are (in 3' to 5' direction) between nucleotide 74 and 1 and between nucleotide
148 and 75, respectively.
/******************************************************************************/
/examples/oxRNA2/duplex2
This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or

3
examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1
View File

@ -7,7 +7,7 @@ units lj
dimension 3
newton off
newton on
boundary p p p
@ -67,3 +67,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

1170
examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1
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1170
examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.4
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1171
examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.1 Normal file
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1171
examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.2Jul21.duplex1.g++.4 Normal file
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File diff suppressed because it is too large Load Diff

3
examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2
View File

@ -7,7 +7,7 @@ units lj
dimension 3
newton off
newton on
boundary p p p
@ -67,3 +67,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

1172
examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1
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1172
examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.4
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1173
examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.1 Normal file
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1173
examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.2Jul21.duplex2.g++.4 Normal file
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622
examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring Normal file
View File

@ -0,0 +1,622 @@
LAMMPS data file via write_data, version 2 Jul 2021
148 atoms
4 atom types
148 bonds
1 bond types
148 ellipsoids
0 100 xlo xhi
0 100 ylo yhi
0 100 zlo zhi
Masses
1 3.1575
2 3.1575
3 3.1575
4 3.1575
Atoms # hybrid
1 1 24.4563103076585 24.545468489552267 25.008405986404544 1 1 3.7269849963023267 0 0 0
2 4 24.529799925849524 24.236299729034574 25.438869726984304 1 1 3.7269849963023267 0 0 0
3 3 24.837268545282573 23.98498105692614 25.841653825869834 1 1 3.7269849963023267 0 0 0
4 2 25.160243408748546 23.990448143707216 26.252262907702004 1 1 3.7269849963023267 0 0 0
5 1 25.511800888983288 24.20297091581725 26.46953407064928 1 1 3.7269849963023267 0 0 0
6 2 25.746069731378416 24.53734405670471 26.70776555674676 1 1 3.7269849963023267 0 0 0
7 3 25.808044471759384 24.911661509909727 27.06389642784591 1 1 3.7269849963023267 0 0 0
8 2 25.702150220414598 25.16021735315657 27.552609445175545 1 1 3.7269849963023267 0 0 0
9 4 25.86583558481563 25.223272838133713 28.134182300485513 1 1 3.7269849963023267 0 0 0
10 2 25.80332921740182 25.045832983472046 28.610009845867623 1 1 3.7269849963023267 0 0 0
11 3 25.910927625439783 24.67877553909445 29.01481046441401 1 1 3.7269849963023267 0 0 0
12 2 26.258738827371122 24.424202368909146 29.31202041427481 1 1 3.7269849963023267 0 0 0
13 2 26.685861178879446 24.203670648569435 29.53932592988526 1 1 3.7269849963023267 0 0 0
14 1 27.213655907159712 24.05889335581843 29.529355686667273 1 1 3.7269849963023267 0 0 0
15 2 27.732458381354213 24.12301887416258 29.465296878682626 1 1 3.7269849963023267 0 0 0
16 3 28.176435469098767 24.39188111290902 29.295132944313664 1 1 3.7269849963023267 0 0 0
17 1 28.526140016035093 24.71780561439453 29.306758099194106 1 1 3.7269849963023267 0 0 0
18 4 28.81297070371788 25.156085631242032 29.41241337896862 1 1 3.7269849963023267 0 0 0
19 2 29.207268942683253 25.464359514737925 29.764217600427827 1 1 3.7269849963023267 0 0 0
20 4 29.513927400101824 25.6118524234793 30.245210919346164 1 1 3.7269849963023267 0 0 0
21 2 30.003254698861596 25.548164315889366 30.532777142800704 1 1 3.7269849963023267 0 0 0
22 3 30.48018822794972 25.262106981177638 30.605441832922853 1 1 3.7269849963023267 0 0 0
23 1 30.892907579242564 24.96400488333011 30.400187079758883 1 1 3.7269849963023267 0 0 0
24 1 31.272921417837917 24.75606240152481 30.084591571801752 1 1 3.7269849963023267 0 0 0
25 2 31.45980735195335 24.678047303787324 29.516918385152074 1 1 3.7269849963023267 0 0 0
26 3 31.706752399918585 24.760376327238674 29.084205170613252 1 1 3.7269849963023267 0 0 0
27 1 31.825883349902693 25.019554534293842 28.71228151368503 1 1 3.7269849963023267 0 0 0
28 4 32.03386829513462 25.369633243002873 28.451125390816088 1 1 3.7269849963023267 0 0 0
29 3 32.53689331378325 25.61089652717825 28.295900822185594 1 1 3.7269849963023267 0 0 0
30 2 33.06271263659326 25.774152791508687 28.273746725064125 1 1 3.7269849963023267 0 0 0
31 4 33.52142887694454 25.601797466727078 28.11055235018921 1 1 3.7269849963023267 0 0 0
32 2 33.91568709239206 25.283711279253097 27.8909943443993 1 1 3.7269849963023267 0 0 0
33 1 34.177641179115845 25.004593725832265 27.451561879204412 1 1 3.7269849963023267 0 0 0
34 4 34.208626385427706 24.707495330231843 27.048442321724874 1 1 3.7269849963023267 0 0 0
35 2 34.082012453158825 24.505795567094143 26.61473051581215 1 1 3.7269849963023267 0 0 0
36 4 33.949520365838396 24.526137035750864 26.16790391788176 1 1 3.7269849963023267 0 0 0
37 2 33.92476566121366 24.592689183725792 25.626516502507826 1 1 3.7269849963023267 0 0 0
38 4 33.85225391322309 24.960947839094587 25.26017383231366 1 1 3.7269849963023267 0 0 0
39 3 34.11228837744851 25.35347319831364 24.942278784477317 1 1 3.7269849963023267 0 0 0
40 1 34.36033208544573 25.757747127699123 24.601914493641434 1 1 3.7269849963023267 0 0 0
41 4 34.68447265108969 25.75281386419404 24.241508437854133 1 1 3.7269849963023267 0 0 0
42 2 34.79269490735618 25.623672790695387 23.678538924804666 1 1 3.7269849963023267 0 0 0
43 1 34.753741466077045 25.337233303593457 23.16601298167167 1 1 3.7269849963023267 0 0 0
44 4 34.59181548863591 24.986079417371133 22.755301708206787 1 1 3.7269849963023267 0 0 0
45 4 34.40879419362997 24.630898502963813 22.55999758905835 1 1 3.7269849963023267 0 0 0
46 2 33.90877081260677 24.454255308291586 22.480370414000724 1 1 3.7269849963023267 0 0 0
47 3 33.389994748568355 24.448033629140625 22.400237534903862 1 1 3.7269849963023267 0 0 0
48 3 32.92270356937016 24.68336387187774 22.32934654102368 1 1 3.7269849963023267 0 0 0
49 1 32.45576642621448 24.99545345297995 22.22583331074809 1 1 3.7269849963023267 0 0 0
50 4 32.18015654347581 25.250534381556076 21.872483225748145 1 1 3.7269849963023267 0 0 0
51 2 31.963112737103277 25.40181159513097 21.39874463404153 1 1 3.7269849963023267 0 0 0
52 2 31.677804642093392 25.364851924896104 20.875873168885278 1 1 3.7269849963023267 0 0 0
53 3 31.39441653928761 25.115305865863796 20.473551707902534 1 1 3.7269849963023267 0 0 0
54 2 30.920751116009413 24.90955329317796 20.247774626492223 1 1 3.7269849963023267 0 0 0
55 2 30.433930757552503 24.49259165599716 20.285516091786025 1 1 3.7269849963023267 0 0 0
56 1 29.927593328854318 24.417379016374497 20.44729306614509 1 1 3.7269849963023267 0 0 0
57 1 29.468689211209185 24.356983174590244 20.73481874763059 1 1 3.7269849963023267 0 0 0
58 4 29.05647892922904 24.518592766825268 21.008770793972737 1 1 3.7269849963023267 0 0 0
59 3 28.71710307148458 24.823751059656175 21.267189817160382 1 1 3.7269849963023267 0 0 0
60 2 28.475966743694585 25.270452656180346 21.345694213935065 1 1 3.7269849963023267 0 0 0
61 3 28.13628879031047 25.66658729399272 21.21785093681449 1 1 3.7269849963023267 0 0 0
62 2 27.601021447013018 25.768855335649704 21.03779448055474 1 1 3.7269849963023267 0 0 0
63 2 27.00931772523695 25.617172753906647 20.911648911662837 1 1 3.7269849963023267 0 0 0
64 1 26.55519195243888 25.359523630164194 20.975378082063024 1 1 3.7269849963023267 0 0 0
65 4 26.273989173217412 24.94557093741794 21.304033513543096 1 1 3.7269849963023267 0 0 0
66 2 26.221914749013006 24.585776360115993 21.63789003190145 1 1 3.7269849963023267 0 0 0
67 4 26.193438361250763 24.376750813571793 22.050097162808477 1 1 3.7269849963023267 0 0 0
68 3 26.201324065482883 24.325450386461092 22.606452770336915 1 1 3.7269849963023267 0 0 0
69 4 26.17471898214314 24.575749724802375 23.091585548564353 1 1 3.7269849963023267 0 0 0
70 2 26.02335082849493 24.908257401252587 23.529107108416536 1 1 3.7269849963023267 0 0 0
71 3 25.651267664730547 25.192079918693462 23.831752862227333 1 1 3.7269849963023267 0 0 0
72 2 25.217003840349953 25.339279875756237 24.059449373495085 1 1 3.7269849963023267 0 0 0
73 3 24.821858366366477 25.32373878201269 24.349325228837248 1 1 3.7269849963023267 0 0 0
74 2 24.52371941046921 25.002103481686692 24.640726114051727 1 1 3.7269849963023267 0 0 0
75 3 25.598009016668964 24.518873693595243 24.91882101447603 2 1 3.7269849963023267 0 0 0
76 2 25.427238756513358 24.301007582224713 24.44316375014865 2 1 3.7269849963023267 0 0 0
77 3 25.064917226893478 24.1744996693387 24.04114053737127 2 1 3.7269849963023267 0 0 0
78 2 24.935835560058162 24.310630170294576 23.497873361870962 2 1 3.7269849963023267 0 0 0
79 3 24.947052458805103 24.604993171264848 23.080111757564428 2 1 3.7269849963023267 0 0 0
80 1 25.108221368921303 24.93987851339803 22.78466627575098 2 1 3.7269849963023267 0 0 0
81 2 25.567029051298007 25.336883558925546 22.613483665009124 2 1 3.7269849963023267 0 0 0
82 1 25.977933802261195 25.494884341698153 22.361177765359677 2 1 3.7269849963023267 0 0 0
83 3 26.51585409198948 25.56882274198199 22.270702612866675 2 1 3.7269849963023267 0 0 0
84 1 26.898094042158256 25.43126923497678 22.136142593902736 2 1 3.7269849963023267 0 0 0
85 4 27.2282338544016 25.03939058206712 21.975004266020655 2 1 3.7269849963023267 0 0 0
86 3 27.45312307645279 24.76234771560634 21.573973110116803 2 1 3.7269849963023267 0 0 0
87 3 27.601433385556053 24.56156448386474 21.121284432422822 2 1 3.7269849963023267 0 0 0
88 2 27.887087703479907 24.639659406696175 20.647423041744478 2 1 3.7269849963023267 0 0 0
89 3 28.261596261597024 24.878830990697377 20.262074903970543 2 1 3.7269849963023267 0 0 0
90 2 28.669247681666896 25.241598582808898 20.13595769437227 2 1 3.7269849963023267 0 0 0
91 1 29.162947101827424 25.46126020981763 20.29119476534042 2 1 3.7269849963023267 0 0 0
92 4 29.626827720432082 25.569578560516256 20.521043387351114 2 1 3.7269849963023267 0 0 0
93 4 29.94106479726571 25.46437861463676 20.945812440078498 2 1 3.7269849963023267 0 0 0
94 3 30.29025124351676 25.13135267765501 21.293123410503096 2 1 3.7269849963023267 0 0 0
95 3 30.69726706273153 24.79296975393911 21.37843871066455 2 1 3.7269849963023267 0 0 0
96 2 31.065205835301647 24.466654538309413 21.38217937265794 2 1 3.7269849963023267 0 0 0
97 3 31.47949349145455 24.235044344783937 21.207303357880345 2 1 3.7269849963023267 0 0 0
98 3 32.0141851785801 24.199047010891896 21.144063603619387 2 1 3.7269849963023267 0 0 0
99 1 32.531553756690144 24.430680075450717 21.057107964598707 2 1 3.7269849963023267 0 0 0
100 4 32.98962179526399 24.778596160926984 21.144383998305358 2 1 3.7269849963023267 0 0 0
101 2 33.412089437390414 25.16978981992855 21.366097445928173 2 1 3.7269849963023267 0 0 0
102 2 33.64688673923798 25.416880152326826 21.80823145369244 2 1 3.7269849963023267 0 0 0
103 3 33.73260009980956 25.581799927882354 22.284949811529895 2 1 3.7269849963023267 0 0 0
104 1 33.71190505788351 25.621797401531534 22.839310166247465 2 1 3.7269849963023267 0 0 0
105 1 33.57308722698115 25.405379008714707 23.245158668130212 2 1 3.7269849963023267 0 0 0
106 4 33.690827355981554 25.10089414752484 23.595216498164593 2 1 3.7269849963023267 0 0 0
107 3 34.01115578964591 24.78647396522056 23.89598110848665 2 1 3.7269849963023267 0 0 0
108 1 34.484013716732484 24.626220866364136 24.174215444712242 2 1 3.7269849963023267 0 0 0
109 4 34.990266640570965 24.69448985833302 24.562811124280305 2 1 3.7269849963023267 0 0 0
110 2 35.145896903493316 24.793241326024813 25.04385957026009 2 1 3.7269849963023267 0 0 0
111 1 35.06860532892695 25.048723590439906 25.570332580544218 2 1 3.7269849963023267 0 0 0
112 3 34.935175985993084 25.335540132080055 26.006545003503096 2 1 3.7269849963023267 0 0 0
113 1 34.49657428034769 25.607489233067064 26.123731584378923 2 1 3.7269849963023267 0 0 0
114 3 34.0132432396664 25.732289222865404 26.321416792125166 2 1 3.7269849963023267 0 0 0
115 1 33.58776734894964 25.62064953889948 26.688539619472973 2 1 3.7269849963023267 0 0 0
116 4 33.15654425248354 25.338672553764333 26.826329665315537 2 1 3.7269849963023267 0 0 0
117 3 32.9076504056509 24.991331214323903 27.228446976881234 2 1 3.7269849963023267 0 0 0
118 1 32.9297689116334 24.632517190191024 27.681355827816688 2 1 3.7269849963023267 0 0 0
119 3 33.00216450637092 24.55541285047072 28.22302417752094 2 1 3.7269849963023267 0 0 0
120 2 32.9420586075282 24.60559201752168 28.777865869642905 2 1 3.7269849963023267 0 0 0
121 1 32.83738319038634 24.94702033575836 29.307330619456266 2 1 3.7269849963023267 0 0 0
122 4 32.57977335421255 25.328020610731436 29.570214128887336 2 1 3.7269849963023267 0 0 0
123 2 32.17061122190304 25.708023527353955 29.63983317809503 2 1 3.7269849963023267 0 0 0
124 3 31.636567367502767 25.872024842140746 29.617831484163407 2 1 3.7269849963023267 0 0 0
125 4 31.132545834345493 25.788771465761464 29.473140927527755 2 1 3.7269849963023267 0 0 0
126 4 30.66416343932506 25.546908667108468 29.387529102708452 2 1 3.7269849963023267 0 0 0
127 2 30.33924138958816 25.185314142044398 29.432101524801457 2 1 3.7269849963023267 0 0 0
128 3 30.21851533734297 24.75102015597501 29.680917821332173 2 1 3.7269849963023267 0 0 0
129 1 29.83055401261429 24.475918281129495 29.97162814225401 2 1 3.7269849963023267 0 0 0
130 3 29.249485560956284 24.357720612933235 30.18837063610894 2 1 3.7269849963023267 0 0 0
131 1 28.781676718751342 24.49568907629974 30.44184869682069 2 1 3.7269849963023267 0 0 0
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123 0.23810161605704377 -0.11946357658421103 0.0053425918702379 -0.26507085311347767 -0.005060520073985519 -0.028794675468980298
124 0.3312048487900394 0.26189741666863997 -0.10964110515509969 0.1544616897402785 -0.23337971316705755 0.10244776357671773
125 -0.20606377334048767 -0.2480013884660967 0.0503364492363312 -0.2245111582587185 -0.21456054582014408 0.2050630976792822
126 -0.03552739269815303 0.1691039422819466 -0.07802319703580368 -0.4323743483104413 0.18256530801905368 0.18628686436697428
127 -0.20029656593994563 0.32983545343079457 -0.2070512488410065 0.019326899103251225 0.027644495282593218 0.442626348526685
128 0.08491008750400077 0.1035215229851968 -0.1739408713288041 0.27470989108566846 -0.24402446279772083 0.07443846420743241
129 -0.08830853934911108 -0.26734530364104053 -0.1988201363520286 -0.06923156954944658 -0.02189796001542307 -0.1338797245794809
130 0.20981215982263213 0.13488162846156487 -0.03943887942626307 -0.011593722599637339 -0.6890299572253064 0.1790251091910087
131 0.07652601338116555 -0.19283772018282666 -0.2776397161982535 0.24663050117341062 0.044069318144154775 0.2747329718398644
132 0.06005147641503129 0.2830757435240006 0.44875979576568403 0.13517880915103314 0.11908709936381356 0.5021295927265543
133 -0.023103333857207493 -0.20854066459336754 0.12433937928122553 0.07532809593947921 0.006567418488669447 0.005099910874471501
134 -0.19768408467989063 0.07010969542764198 -0.20904359061206418 0.3500450579217665 0.2621319675031076 0.05700557921808894
135 -0.15495059768685077 -0.19368431486198104 -0.12813393686867544 -0.005681639055833594 0.36877138324218484 -0.11103137477367178
136 0.14611337822004258 0.07560160260606268 0.09033752786956158 0.45086630093824887 -0.0540905457830462 0.35712304127420874
137 -0.006832587008219201 0.10626881118619334 0.23727231793522738 -0.23670719085338437 0.15102882182810315 -0.18569984864833494
138 0.0367287542741905 0.2260961629741195 0.061837966953977974 0.24931042513512916 0.21197461409518875 -0.33336511048900325
139 -0.07349205704521018 -0.05634613320016501 -0.504982154096888 0.1436392338796232 0.15906028117556678 -0.019355526701785235
140 -0.3030520336145537 -0.09599950732226913 0.06438387924367373 -0.14946707336004578 -0.3965545748060501 -0.18379582563170568
141 -0.24908521126941452 -0.19982821516723162 0.0074328635453094405 -0.14962181978906317 -0.07272114881413824 0.16246832274161657
142 0.17835016534905518 -0.013889886430521995 -0.03882561392387829 0.09373150575976509 0.027511161845731512 -0.09158102178193173
143 -0.018236845831437268 0.10323283487519967 0.3004315866605606 -0.2507354481152932 0.05050127009326096 -0.2300087204030466
144 -0.044410313090765555 -0.4573359137793594 0.09495183962234632 0.09635470152905644 0.09803237993644494 -0.34402426898911387
145 0.2821400944928483 0.11836361011832264 0.1696408065684072 0.33048216564352206 -0.29139537671087906 -0.037084369809477505
146 -0.18244194711837852 0.08624974326226817 -0.006779741723387931 -0.0687522501302224 0.03106090508494657 0.035844399389801454
147 0.1794175506420554 -0.0852079364441406 0.21416128313592545 0.1329441722287453 -0.0010388729930562906 0.05954056910834935
148 -0.24523838476169282 0.07566025581718214 -0.10739416751806342 0.46725839193497026 0.04242428905379958 0.1432137106005151
Bonds
1 1 1 2
2 1 74 1
3 1 2 3
4 1 3 4
5 1 4 5
6 1 5 6
7 1 6 7
8 1 7 8
9 1 8 9
10 1 9 10
11 1 10 11
12 1 11 12
13 1 12 13
14 1 13 14
15 1 14 15
16 1 15 16
17 1 16 17
18 1 17 18
19 1 18 19
20 1 19 20
21 1 20 21
22 1 21 22
23 1 22 23
24 1 23 24
25 1 24 25
26 1 25 26
27 1 26 27
28 1 27 28
29 1 28 29
30 1 29 30
31 1 30 31
32 1 31 32
33 1 32 33
34 1 33 34
35 1 34 35
36 1 35 36
37 1 36 37
38 1 37 38
39 1 38 39
40 1 39 40
41 1 40 41
42 1 41 42
43 1 42 43
44 1 43 44
45 1 44 45
46 1 45 46
47 1 46 47
48 1 47 48
49 1 48 49
50 1 49 50
51 1 50 51
52 1 51 52
53 1 52 53
54 1 53 54
55 1 54 55
56 1 55 56
57 1 56 57
58 1 57 58
59 1 58 59
60 1 59 60
61 1 60 61
62 1 61 62
63 1 62 63
64 1 63 64
65 1 64 65
66 1 65 66
67 1 66 67
68 1 67 68
69 1 68 69
70 1 69 70
71 1 70 71
72 1 71 72
73 1 72 73
74 1 73 74
75 1 75 76
76 1 148 75
77 1 76 77
78 1 77 78
79 1 78 79
80 1 79 80
81 1 80 81
82 1 81 82
83 1 82 83
84 1 83 84
85 1 84 85
86 1 85 86
87 1 86 87
88 1 87 88
89 1 88 89
90 1 89 90
91 1 90 91
92 1 91 92
93 1 92 93
94 1 93 94
95 1 94 95
96 1 95 96
97 1 96 97
98 1 97 98
99 1 98 99
100 1 99 100
101 1 100 101
102 1 101 102
103 1 102 103
104 1 103 104
105 1 104 105
106 1 105 106
107 1 106 107
108 1 107 108
109 1 108 109
110 1 109 110
111 1 110 111
112 1 111 112
113 1 112 113
114 1 113 114
115 1 114 115
116 1 115 116
117 1 116 117
118 1 117 118
119 1 118 119
120 1 119 120
121 1 120 121
122 1 121 122
123 1 122 123
124 1 123 124
125 1 124 125
126 1 125 126
127 1 126 127
128 1 127 128
129 1 128 129
130 1 129 130
131 1 130 131
132 1 131 132
133 1 132 133
134 1 133 134
135 1 134 135
136 1 135 136
137 1 136 137
138 1 137 138
139 1 138 139
140 1 139 140
141 1 140 141
142 1 141 142
143 1 142 143
144 1 143 144
145 1 144 145
146 1 145 146
147 1 146 147
148 1 147 148
Ellipsoids
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9828541875306525 0.12879706731240614 -0.10093645894201106 0.08497524793392826
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9076319099077714 0.14371009860279324 -0.0061127301821370696 0.3943530882425885
3 1.173984503142341 1.173984503142341 1.173984503142341 0.7156666230136304 0.13639947227633528 0.03941894579775276 0.6838586223622523
4 1.173984503142341 1.173984503142341 1.173984503142341 0.551483876992997 0.0945081114480617 0.05507676463033448 0.826982648116119
5 1.173984503142341 1.173984503142341 1.173984503142341 0.24878195093628586 0.25477295141293216 0.17560035853168876 0.9178032459085236
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.09814576590180418 0.2630252745002951 0.0750862666667879 0.9568422890777962
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.36099905322484027 0.20576958877633506 0.05427501922331751 0.9079607822994866
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.7222470672351088 0.18134561062508855 -0.07603445152283007 0.6630925316718025
9 1.173984503142341 1.173984503142341 1.173984503142341 0.7207213859113211 -0.081618921713485 0.2444656792207328 -0.6435336566113217
10 1.173984503142341 1.173984503142341 1.173984503142341 0.9121007124750514 -0.01217119606138896 0.2913039145765659 -0.2882120428457281
11 1.173984503142341 1.173984503142341 1.173984503142341 0.953249593652999 0.05081512321641071 0.29695596119287027 -0.0234561839375449
12 1.173984503142341 1.173984503142341 1.173984503142341 0.893216854716605 0.19782387032700505 0.32197381347668597 0.2436436541638224
13 1.173984503142341 1.173984503142341 1.173984503142341 0.7804220903358083 0.3075288797089802 0.40715287039611386 0.3613777652111879
14 1.173984503142341 1.173984503142341 1.173984503142341 0.6203605365073518 0.3741569541553062 0.35408302093722205 0.5914258978819795
15 1.173984503142341 1.173984503142341 1.173984503142341 0.3960444020645081 0.5102735688288697 0.4358052977828721 0.6267722544691949
16 1.173984503142341 1.173984503142341 1.173984503142341 0.13777757932263526 0.6041124653901045 0.23900745590897193 0.7476235040554876
17 1.173984503142341 1.173984503142341 1.173984503142341 -0.14487300744864823 0.6140449381421356 0.15150134965763856 0.7609257300858729
18 1.173984503142341 1.173984503142341 1.173984503142341 -0.3344250731601342 0.6010892081702673 -0.017846433649279014 0.7256260325188738
19 1.173984503142341 1.173984503142341 1.173984503142341 -0.5074640025256208 0.5175428589716987 -0.22947810189520476 0.6495917764401355
20 1.173984503142341 1.173984503142341 1.173984503142341 0.6927772486705646 -0.40626836540518185 0.4423107744840648 -0.3992078127626656
21 1.173984503142341 1.173984503142341 1.173984503142341 0.6829206576647326 -0.27522098535816325 0.6168603801346256 -0.27812956688100604
22 1.173984503142341 1.173984503142341 1.173984503142341 0.6788549938954256 0.033964180979933575 0.7308067787169422 -0.06264011378478199
23 1.173984503142341 1.173984503142341 1.173984503142341 0.5999805514844269 0.2793954015736318 0.7386615340865574 0.12783069068438008
24 1.173984503142341 1.173984503142341 1.173984503142341 0.4418314756383255 0.5057611588638139 0.7228215888566917 0.16284823610552174
25 1.173984503142341 1.173984503142341 1.173984503142341 0.3141779374831782 0.7142758691047312 0.539765722838384 0.31584041993110096
26 1.173984503142341 1.173984503142341 1.173984503142341 0.13009402904433304 0.8026224209437359 0.4188011593597563 0.40432459970221063
27 1.173984503142341 1.173984503142341 1.173984503142341 0.015395939306808548 0.9125609417624169 0.11793521250895517 0.3912630550831749
28 1.173984503142341 1.173984503142341 1.173984503142341 0.020389821926513313 0.8930600411816652 -0.2308403071738297 0.3856692502524667
29 1.173984503142341 1.173984503142341 1.173984503142341 -0.19829980450156168 0.789544960878009 -0.45297996531610585 0.3634626436224299
30 1.173984503142341 1.173984503142341 1.173984503142341 -0.29878991597718874 0.6265110900381559 -0.6619230912649768 0.28295982297804007
31 1.173984503142341 1.173984503142341 1.173984503142341 0.3240360642338418 -0.36827828790860756 0.8343565738846102 -0.2514375456181544
32 1.173984503142341 1.173984503142341 1.173984503142341 0.32014650617553997 -0.05971181117410955 0.9438400245399936 -0.05573797867026355
33 1.173984503142341 1.173984503142341 1.173984503142341 0.24982350857997523 0.1590081591159326 0.9549704885538687 -0.01832991779955874
34 1.173984503142341 1.173984503142341 1.173984503142341 0.16999266129422064 0.3749550480019231 0.9099327896340427 -0.05033413784692161
35 1.173984503142341 1.173984503142341 1.173984503142341 0.19340334476340248 0.6890998585251199 0.6972337573677242 0.040020229907810456
36 1.173984503142341 1.173984503142341 1.173984503142341 0.1612116171856501 0.859720290458655 0.48091314403740787 0.06011975174706676
37 1.173984503142341 1.173984503142341 1.173984503142341 0.009261495255550381 0.9402304673687385 0.3245385528799807 0.10274055008497525
38 1.173984503142341 1.173984503142341 1.173984503142341 -0.178489162453817 0.9806521854786103 0.005310303981292909 0.08021664836046656
39 1.173984503142341 1.173984503142341 1.173984503142341 -0.1288029405461015 0.9602840555925231 -0.21902557887358792 0.11529150393911712
40 1.173984503142341 1.173984503142341 1.173984503142341 -0.04731791323035676 0.8474709401996229 -0.5273646012711862 0.037955209534064525
41 1.173984503142341 1.173984503142341 1.173984503142341 -0.022651622917573347 0.5565011565487459 -0.8295791934725275 -0.03989647223225978
42 1.173984503142341 1.173984503142341 1.173984503142341 -0.13596774829773478 -0.40509299019424533 0.9040951590175422 0.004938031933284807
43 1.173984503142341 1.173984503142341 1.173984503142341 -0.23079724764482035 -0.14600108158768343 0.957686102648897 -0.09084956492998986
44 1.173984503142341 1.173984503142341 1.173984503142341 -0.24753675871742536 0.17224891940889686 0.9383869011016502 -0.16877762495953091
45 1.173984503142341 1.173984503142341 1.173984503142341 -0.2811167754571826 0.35162969585761844 0.8297679896375197 -0.32987118534443655
46 1.173984503142341 1.173984503142341 1.173984503142341 -0.26615049812015845 0.5992229988318759 0.625822287547174 -0.422424164117712
47 1.173984503142341 1.173984503142341 1.173984503142341 -0.26520515010155843 0.7417880533852412 0.3692915113072771 -0.49299137101062096
48 1.173984503142341 1.173984503142341 1.173984503142341 -0.16226711788695447 0.8323801954647086 0.1174686480853541 -0.5167336928900556
49 1.173984503142341 1.173984503142341 1.173984503142341 -0.04572661296718043 0.8408693531665875 -0.11047316886003926 -0.5278669214241181
50 1.173984503142341 1.173984503142341 1.173984503142341 0.19411685314820926 0.7587839226558699 -0.3585937241690634 -0.5079135231802451
51 1.173984503142341 1.173984503142341 1.173984503142341 0.2884389061686524 0.6577064384331197 -0.5877305498173151 -0.3725560884796933
52 1.173984503142341 1.173984503142341 1.173984503142341 -0.40417504294512524 -0.5007922981141542 0.722387900683145 0.2529927464502668
53 1.173984503142341 1.173984503142341 1.173984503142341 0.487705221455796 0.2123778745642691 -0.8387806766732518 -0.11613023637226708
54 1.173984503142341 1.173984503142341 1.173984503142341 0.6413097692721371 -0.008544696549571698 -0.7672266752769908 0.0034636311017504627
55 1.173984503142341 1.173984503142341 1.173984503142341 0.6030429100152689 -0.25373110064689114 -0.7459977158111821 0.12428670584311194
56 1.173984503142341 1.173984503142341 1.173984503142341 0.5864519496083405 -0.372875091537276 -0.6178931881796406 0.36775846001532553
57 1.173984503142341 1.173984503142341 1.173984503142341 -0.48911574896863785 0.5441144354000708 0.4276113192775303 -0.5308990722593522
58 1.173984503142341 1.173984503142341 1.173984503142341 -0.4417465957365199 0.6181565224178451 0.16076362948117487 -0.6299980272854125
59 1.173984503142341 1.173984503142341 1.173984503142341 -0.28308904114546696 0.6664475020761871 -0.017606380786631723 -0.6894913611607815
60 1.173984503142341 1.173984503142341 1.173984503142341 -0.04343392830476409 0.6249932397866798 -0.2350918967721212 -0.7431209485440797
61 1.173984503142341 1.173984503142341 1.173984503142341 0.3001051086276221 0.5396150277384395 -0.35255590439280615 -0.7031762793867672
62 1.173984503142341 1.173984503142341 1.173984503142341 0.556986262583898 0.4368102678055262 -0.5133240400778073 -0.4852437769932583
63 1.173984503142341 1.173984503142341 1.173984503142341 0.795279938190695 0.19986687104396691 -0.4327075609483636 -0.3746294442093639
64 1.173984503142341 1.173984503142341 1.173984503142341 0.8774746414896595 0.14848167889587988 -0.4429894517950587 -0.10840567408197696
65 1.173984503142341 1.173984503142341 1.173984503142341 0.9026256675673767 0.09862023274988396 -0.3935312309258709 0.14378499305169315
66 1.173984503142341 1.173984503142341 1.173984503142341 0.7992966483039178 0.0008565776883433751 -0.3722117248777941 0.4717865684271695
67 1.173984503142341 1.173984503142341 1.173984503142341 0.5936072962961377 -0.03652051284490529 -0.2825637892972656 0.7526316063676206
68 1.173984503142341 1.173984503142341 1.173984503142341 0.43644057731838104 -0.13786664664361545 -0.15590190259912107 0.8753325122370452
69 1.173984503142341 1.173984503142341 1.173984503142341 0.14188152802643034 -0.12788407699426005 0.012864675110957144 0.9815038435943596
70 1.173984503142341 1.173984503142341 1.173984503142341 -0.17011699210314196 -0.1964455848932923 0.08682166929707971 0.9617335072223387
71 1.173984503142341 1.173984503142341 1.173984503142341 -0.38329053167753524 -0.1996467474595419 0.09852206601835616 0.8963944148992972
72 1.173984503142341 1.173984503142341 1.173984503142341 0.6594122085000511 0.160793297137392 -0.16758115116995345 -0.7150088199800926
73 1.173984503142341 1.173984503142341 1.173984503142341 0.8512883171626583 0.18060232735097068 -0.17245589356555377 -0.4614650205511664
74 1.173984503142341 1.173984503142341 1.173984503142341 0.9616314641817232 0.12709468738918034 -0.12391907222748418 -0.20917918412557554
75 1.173984503142341 1.173984503142341 1.173984503142341 0.11151873278872049 0.1669724888151189 0.9775349714635312 -0.06410257234991716
76 1.173984503142341 1.173984503142341 1.173984503142341 0.002211126817898623 0.5521186363105357 0.8337434054774612 0.0056618176970950045
77 1.173984503142341 1.173984503142341 1.173984503142341 0.07044943717430134 0.7729866626831493 0.6298061627604926 0.029541385625851832
78 1.173984503142341 1.173984503142341 1.173984503142341 -0.010806653246459833 0.9027252443710524 0.411417996086784 0.1253219131547623
79 1.173984503142341 1.173984503142341 1.173984503142341 -0.06940131778729772 0.9746360030066041 0.11360573819677272 0.17989401041019523
80 1.173984503142341 1.173984503142341 1.173984503142341 -0.20000556212707324 0.9595560965524266 -0.15823100448109342 0.11921754027075034
81 1.173984503142341 1.173984503142341 1.173984503142341 -0.26251769804085484 0.8226181738157728 -0.4903553171765896 0.11804855458657725
82 1.173984503142341 1.173984503142341 1.173984503142341 -0.3837234853374367 0.6543399037804607 -0.6234720263018537 0.1894154416623109
83 1.173984503142341 1.173984503142341 1.173984503142341 0.3855852781915845 -0.47229630772423525 0.7839693435947087 -0.11684288277706342
84 1.173984503142341 1.173984503142341 1.173984503142341 0.46002037442553534 -0.1407678919113547 0.866403276034954 -0.1338320551890411
85 1.173984503142341 1.173984503142341 1.173984503142341 0.48887603366012683 0.1731127982177676 0.8530376609375365 0.05795629239499309
86 1.173984503142341 1.173984503142341 1.173984503142341 0.43899101160689896 0.3758967470065976 0.8089928976311329 0.1073266923956608
87 1.173984503142341 1.173984503142341 1.173984503142341 0.3553143558383719 0.6425723574078863 0.5903209324805503 0.33522182313466425
88 1.173984503142341 1.173984503142341 1.173984503142341 0.2536540111199051 0.7421214888111948 0.45155240831127663 0.42545947049716176
89 1.173984503142341 1.173984503142341 1.173984503142341 0.15382396432141013 0.7505310904822217 0.14263847154124493 0.6266542401168209
90 1.173984503142341 1.173984503142341 1.173984503142341 -0.16810175118036055 0.7288374808427736 -0.10080598156099228 0.6560303970475613
91 1.173984503142341 1.173984503142341 1.173984503142341 -0.2831885739735942 0.643948067209743 -0.26839675685463915 0.6581020431646983
92 1.173984503142341 1.173984503142341 1.173984503142341 -0.4831024117054533 0.453267716115057 -0.42739397992663336 0.6152193293896797
93 1.173984503142341 1.173984503142341 1.173984503142341 0.6770118192914993 -0.21059755897505428 0.4910911741276808 -0.5060959626269103
94 1.173984503142341 1.173984503142341 1.173984503142341 0.7442670171743097 -0.08947621534664056 0.6143775419962679 -0.2461723987865454
95 1.173984503142341 1.173984503142341 1.173984503142341 0.7666665318729418 0.12269014310665635 0.6290675727017766 -0.03799403460385277
96 1.173984503142341 1.173984503142341 1.173984503142341 0.7171919647397696 0.27392119614493066 0.6165739462155079 0.17446900258634976
97 1.173984503142341 1.173984503142341 1.173984503142341 0.6242311603419127 0.43977982483754113 0.46478542263682826 0.4482227961944326
98 1.173984503142341 1.173984503142341 1.173984503142341 0.42790222650129595 0.5250655697375166 0.4214312365282337 0.6029938183014272
99 1.173984503142341 1.173984503142341 1.173984503142341 0.2468582232791126 0.49224626821105333 0.30309532857077576 0.7777453637472519
100 1.173984503142341 1.173984503142341 1.173984503142341 -0.03380456035420594 0.5634460183047242 0.08545990308043122 0.8210252378101995
101 1.173984503142341 1.173984503142341 1.173984503142341 -0.26750916515001516 0.4857064004847054 0.009320517332115886 0.8321305588942125
102 1.173984503142341 1.173984503142341 1.173984503142341 -0.543656333310932 0.3668193234682623 -0.09381801460790738 0.7490524382953638
103 1.173984503142341 1.173984503142341 1.173984503142341 0.7108784431095552 -0.3004632412363646 0.2190205688208185 -0.5969955361820375
104 1.173984503142341 1.173984503142341 1.173984503142341 0.8734231811131953 -0.14399683070372168 0.19737468070828412 -0.4212363883340244
105 1.173984503142341 1.173984503142341 1.173984503142341 0.9684624161954964 -0.105190045875246 0.17391545136610614 -0.14411460176424984
106 1.173984503142341 1.173984503142341 1.173984503142341 0.9799304485597246 0.037984124779449666 0.14105544742949488 0.13563510976418097
107 1.173984503142341 1.173984503142341 1.173984503142341 0.8816175546504624 0.20405639480623733 0.14071717244217888 0.40163435168159917
108 1.173984503142341 1.173984503142341 1.173984503142341 0.6668815181201708 0.2184913756962591 0.13935946384415568 0.6986483374152993
109 1.173984503142341 1.173984503142341 1.173984503142341 0.49523667831069 0.06959764035843413 0.04878276823652622 0.8645906791282876
110 1.173984503142341 1.173984503142341 1.173984503142341 0.2207732329238526 -0.06373893139772668 0.037699540120053256 0.9725097803741426
111 1.173984503142341 1.173984503142341 1.173984503142341 -0.032729617987676665 -0.18237738709355036 0.08976233597699147 0.9785754870337106
112 1.173984503142341 1.173984503142341 1.173984503142341 -0.15032793635914565 -0.23367266896015637 0.20496632388946223 0.9385027444830824
113 1.173984503142341 1.173984503142341 1.173984503142341 0.5098818708103572 0.17022830741237596 -0.2655328085989286 -0.8003343855739379
114 1.173984503142341 1.173984503142341 1.173984503142341 0.7386002630722802 0.13150233806957554 -0.2899184849443961 -0.5942424240655826
115 1.173984503142341 1.173984503142341 1.173984503142341 0.8183885516845668 0.21176889551544467 -0.29030250974778893 -0.44846244680902864
116 1.173984503142341 1.173984503142341 1.173984503142341 0.9430612626489262 0.10580295822334976 -0.2990836107868347 -0.09995090135116472
117 1.173984503142341 1.173984503142341 1.173984503142341 0.9613379941508746 0.03141943836189481 -0.22153618567675704 0.16051105360936818
118 1.173984503142341 1.173984503142341 1.173984503142341 0.8625667911488177 0.009442517727487543 -0.19942173035959687 0.46488745210704746
119 1.173984503142341 1.173984503142341 1.173984503142341 0.7259073589630057 -0.13376476050843852 -0.17209740381142 0.6523403855740064
120 1.173984503142341 1.173984503142341 1.173984503142341 0.5281310594886722 -0.2846679630342966 -0.07506778574311505 0.7964964296021063
121 1.173984503142341 1.173984503142341 1.173984503142341 0.24241907358145395 -0.3683073657243024 0.039055584363879806 0.8966924436210727
122 1.173984503142341 1.173984503142341 1.173984503142341 -0.044981165612273756 -0.40529534424684105 0.1971478516389492 0.8915408589998233
123 1.173984503142341 1.173984503142341 1.173984503142341 -0.3495232584251298 -0.40209106895373176 0.34714827984449365 0.7717799789373487
124 1.173984503142341 1.173984503142341 1.173984503142341 0.5344020410886484 0.3826673897545711 -0.38492167218812157 -0.6479316581080214
125 1.173984503142341 1.173984503142341 1.173984503142341 0.7053269695515239 0.29260497262472956 -0.500965349977395 -0.40734495718073077
126 1.173984503142341 1.173984503142341 1.173984503142341 0.7696439701870998 0.21424045744249637 -0.5824916559487316 -0.1498421045620125
127 1.173984503142341 1.173984503142341 1.173984503142341 0.7423816103336222 0.1139330316098165 -0.6216492250908265 0.22235343462746351
128 1.173984503142341 1.173984503142341 1.173984503142341 0.5887700508646756 -0.08843642096111673 -0.6840133892265956 0.4214908184185525
129 1.173984503142341 1.173984503142341 1.173984503142341 0.453096146271983 -0.38728607571982976 -0.6241259420947486 0.5051536263270361
130 1.173984503142341 1.173984503142341 1.173984503142341 -0.4409693358675804 0.53279196704852 0.4417418096721996 -0.5714393565905346
131 1.173984503142341 1.173984503142341 1.173984503142341 -0.18566644236274712 0.6770317752573873 0.25184635469644123 -0.6661301382600142
132 1.173984503142341 1.173984503142341 1.173984503142341 0.015608637060561658 0.7425789407541207 -0.020406929491472138 -0.6692656008090734
133 1.173984503142341 1.173984503142341 1.173984503142341 0.08018393872270876 0.7828265827838332 -0.23834222384166942 -0.5691625967964753
134 1.173984503142341 1.173984503142341 1.173984503142341 0.13194668226893702 0.7589329168513657 -0.46681103776605365 -0.43439424003717964
135 1.173984503142341 1.173984503142341 1.173984503142341 0.23078479216727615 0.7124321296591045 -0.5847273355040361 -0.31188585002858094
136 1.173984503142341 1.173984503142341 1.173984503142341 -0.25136284638005546 -0.45701375225575186 0.841389844073701 0.14148597103058816
137 1.173984503142341 1.173984503142341 1.173984503142341 -0.33882629405552384 -0.365928882584538 0.8652581637618377 0.05119673222505744
138 1.173984503142341 1.173984503142341 1.173984503142341 -0.3901032217728516 -0.04271905647523107 0.919195929073709 -0.03276282269018462
139 1.173984503142341 1.173984503142341 1.173984503142341 -0.3503464321192356 0.2164507057056595 0.8846466649907219 -0.21864754199770353
140 1.173984503142341 1.173984503142341 1.173984503142341 -0.2714234139641493 0.5100075547669219 0.7525252671110235 -0.3161128703362045
141 1.173984503142341 1.173984503142341 1.173984503142341 -0.18623801902606954 0.7425995746707363 0.5393607888180064 -0.35064399531961904
142 1.173984503142341 1.173984503142341 1.173984503142341 -0.20986530401416495 0.8687694482447833 0.31310815046609125 -0.3211845047308489
143 1.173984503142341 1.173984503142341 1.173984503142341 -0.1354858154681459 0.9418151150282347 0.014007263864675714 -0.3072973795370049
144 1.173984503142341 1.173984503142341 1.173984503142341 -0.09121534676964865 0.942226022288734 -0.27543028841845296 -0.16741576884323378
145 1.173984503142341 1.173984503142341 1.173984503142341 -0.07761809459687324 0.8625267258049417 -0.49537475942792236 -0.06802151413402847
146 1.173984503142341 1.173984503142341 1.173984503142341 -0.07853628249634757 0.6763776292711046 -0.7295609015799718 -0.06392375019562685
147 1.173984503142341 1.173984503142341 1.173984503142341 0.18414802295685903 -0.34920401662445405 0.9187682994180332 0.0032973320918147885
148 1.173984503142341 1.173984503142341 1.173984503142341 0.13019081328575915 -0.1370605858009623 0.9781659097238085 -0.08634929652338917

72
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variable number equal 5
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
variable rhos equal 0.2
units lj
dimension 3
newton on
boundary p p p
atom_style hybrid bond ellipsoid oxdna
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.dsring
set atom * mass 3.1575
group all type 1 4
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
special_bonds lj 0 1 1
# oxDNA2 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 seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 seqdep 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 seqdep 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 seqdep 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 ${T} ${rhos} 0.815
# NVE ensemble
fix 1 all nve/asphere
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
timestep 1e-5
#comm_style tiled
fix 3 all balance 1000 1.03 shift xyz 10 1.03
comm_modify cutoff 3.8
compute quat all property/atom quatw quati quatj quatk
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
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump_modify out sort id
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
run 100000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

281
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LAMMPS (2 Jul 2021)
variable number equal 5
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
variable rhos equal 0.2
units lj
dimension 3
newton on
boundary p p p
atom_style hybrid bond ellipsoid oxdna
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157)
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.dsring
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
148 atoms
reading velocities ...
148 velocities
scanning bonds ...
1 = max bonds/atom
148 ellipsoids
reading bonds ...
148 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
set atom * mass 3.1575
Setting atom values ...
148 settings made for mass
group all type 1 4
148 atoms in group all
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
special_bonds lj 0 1 1
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
# oxDNA2 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 seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 seqdep 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 seqdep 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 seqdep 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 ${T} ${rhos} 0.815
pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
# NVE ensemble
fix 1 all nve/asphere
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
timestep 1e-5
#comm_style tiled
fix 3 all balance 1000 1.03 shift xyz 10 1.03
comm_modify cutoff 3.8
compute quat all property/atom quatw quati quatj quatk
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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump_modify out sort id
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6389877
ghost atom cutoff = 5.6389877
binsize = 2.8194939, bins = 36 36 36
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889
Per MPI rank memory allocation (min/avg/max) = 9.601 | 9.601 | 9.601 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000
1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183
2000 ekin = 20.585620972069 | erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104
3000 ekin = 20.6239332104642 | erot = 21.5529389082728 | epot = -222.947572771312 | etot = -180.770700652575
4000 ekin = 20.6395549184482 | erot = 21.6854113323895 | epot = -223.095666904229 | etot = -180.770700653391
5000 ekin = 20.6295551742564 | erot = 21.7809539301805 | epot = -223.181209757876 | etot = -180.770700653439
6000 ekin = 20.5959625511847 | erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045
7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517716 | etot = -180.770700652122
8000 ekin = 20.4774701419092 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943
9000 ekin = 20.4074566554238 | erot = 21.8097283692398 | epot = -222.987885674261 | etot = -180.770700649597
10000 ekin = 20.3427303660296 | erot = 21.7629575866663 | epot = -222.876388600948 | etot = -180.770700648253
11000 ekin = 20.2927407149577 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189
12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286
13000 ekin = 20.2733920359447 | erot = 21.6092715397932 | epot = -222.653364221616 | etot = -180.770700645878
14000 ekin = 20.319652478907 | erot = 21.558663097499 | epot = -222.649016222075 | etot = -180.770700645669
15000 ekin = 20.4104009374291 | erot = 21.5031572556304 | epot = -222.684258838857 | etot = -180.770700645798
16000 ekin = 20.5472869005793 | erot = 21.4346177247038 | epot = -222.752605272036 | etot = -180.770700646753
17000 ekin = 20.7266657908775 | erot = 21.3426631585214 | epot = -222.840029597232 | etot = -180.770700647833
18000 ekin = 20.9417612759981 | erot = 21.2178611180923 | epot = -222.930323042997 | etot = -180.770700648907
19000 ekin = 21.1819308659399 | erot = 21.0532289630289 | epot = -223.00586047892 | etot = -180.770700649951
20000 ekin = 21.4358169889477 | erot = 20.8473069564703 | epot = -223.053824595387 | etot = -180.770700649969
21000 ekin = 21.6968513751 | erot = 20.6066744652581 | epot = -223.074226489837 | etot = -180.770700649478
22000 ekin = 21.9614458442786 | erot = 20.3429420444505 | epot = -223.07508853737 | etot = -180.770700648641
23000 ekin = 22.2276099755705 | erot = 20.0703385165238 | epot = -223.068649139875 | etot = -180.77070064778
24000 ekin = 22.4935893196675 | erot = 19.802067172166 | epot = -223.066357139276 | etot = -180.770700647443
25000 ekin = 22.7566064548228 | erot = 19.5464828008836 | epot = -223.073789902975 | etot = -180.770700647269
26000 ekin = 23.0126717548399 | erot = 19.3065017718462 | epot = -223.089874174571 | etot = -180.770700647885
27000 ekin = 23.2550417060594 | erot = 19.0797753474567 | epot = -223.105517701932 | etot = -180.770700648416
28000 ekin = 23.4774329734805 | erot = 18.8646197299574 | epot = -223.112753352067 | etot = -180.770700648629
29000 ekin = 23.6747927720663 | erot = 18.6628653411825 | epot = -223.108358761693 | etot = -180.770700648445
30000 ekin = 23.8432321400247 | erot = 18.4812216983637 | epot = -223.095154486375 | etot = -180.770700647986
31000 ekin = 23.9793041752229 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647145
32000 ekin = 24.0810246040235 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646295
33000 ekin = 24.1468986449398 | erot = 18.1820705445406 | epot = -223.09966983514 | etot = -180.770700645659
34000 ekin = 24.1756615132863 | erot = 18.2103812210172 | epot = -223.156743379607 | etot = -180.770700645303
35000 ekin = 24.1663193894652 | erot = 18.3185351073568 | epot = -223.255555142089 | etot = -180.770700645267
36000 ekin = 24.1167205812964 | erot = 18.5091649894187 | epot = -223.396586216223 | etot = -180.770700645508
37000 ekin = 24.0274860006135 | erot = 18.7785134320989 | epot = -223.576700078937 | etot = -180.770700646225
38000 ekin = 23.8991479078985 | erot = 19.1166063146995 | epot = -223.78645486989 | etot = -180.770700647292
39000 ekin = 23.7326911853236 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648763
40000 ekin = 23.5294223072121 | erot = 19.9254673141826 | epot = -224.225590272292 | etot = -180.770700650897
41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045567 | etot = -180.770700653371
42000 ekin = 23.0154529235024 | erot = 20.7165619564844 | epot = -224.502715535761 | etot = -180.770700655774
43000 ekin = 22.7111536814278 | erot = 21.0163895622227 | epot = -224.498243901357 | etot = -180.770700657707
44000 ekin = 22.3710575806356 | erot = 21.2060371289779 | epot = -224.347795365752 | etot = -180.770700656139
45000 ekin = 22.0515843162889 | erot = 21.2588026881767 | epot = -224.08108764689 | etot = -180.770700642424
46000 ekin = 21.7855632553132 | erot = 21.2036013766601 | epot = -223.75986526006 | etot = -180.770700628087
47000 ekin = 21.5167766971454 | erot = 21.0656367023669 | epot = -223.353114011014 | etot = -180.770700611502
48000 ekin = 21.4540196107332 | erot = 20.8430832424325 | epot = -223.067803499524 | etot = -180.770700646358
49000 ekin = 21.3647564765273 | erot = 20.5521507191689 | epot = -222.68760781692 | etot = -180.770700621224
50000 ekin = 21.3125768184616 | erot = 20.2526464671335 | epot = -222.335923904309 | etot = -180.770700618713
51000 ekin = 21.2949924810833 | erot = 19.9798421626046 | epot = -222.045535260403 | etot = -180.770700616715
52000 ekin = 21.313714424968 | erot = 19.762769134369 | epot = -221.847184173962 | etot = -180.770700614625
53000 ekin = 21.3664076685101 | erot = 19.6202359856903 | epot = -221.757344279694 | etot = -180.770700625493
54000 ekin = 21.4214245524056 | erot = 19.5588232319504 | epot = -221.750948393747 | etot = -180.770700609391
55000 ekin = 21.5995673396088 | erot = 19.5805214885682 | epot = -221.950789453583 | etot = -180.770700625406
56000 ekin = 21.7643125668302 | erot = 19.6816042107783 | epot = -222.216617401428 | etot = -180.77070062382
57000 ekin = 21.922130908444 | erot = 19.8499880475958 | epot = -222.542819582063 | etot = -180.770700626024
58000 ekin = 22.0666093644387 | erot = 20.0713856445721 | epot = -222.908695636277 | etot = -180.770700627266
59000 ekin = 22.1910921687945 | erot = 20.3284024096015 | epot = -223.290195207095 | etot = -180.770700628699
60000 ekin = 22.2920682490233 | erot = 20.6003319531545 | epot = -223.663100832376 | etot = -180.770700630198
61000 ekin = 22.3680528265786 | erot = 20.8645614198866 | epot = -224.003314878046 | etot = -180.77070063158
62000 ekin = 22.4198570332631 | erot = 21.0983714926633 | epot = -224.288929158679 | etot = -180.770700632752
63000 ekin = 22.450080073992 | erot = 21.28155214409 | epot = -224.502332851296 | etot = -180.770700633215
64000 ekin = 22.4634052763983 | erot = 21.3990470998282 | epot = -224.633153009903 | etot = -180.770700633676
65000 ekin = 22.4639885390964 | erot = 21.4413332838528 | epot = -224.676022456447 | etot = -180.770700633498
66000 ekin = 22.4559522488544 | erot = 21.4074154510867 | epot = -224.634068332758 | etot = -180.770700632817
67000 ekin = 22.4417384097826 | erot = 21.3051580893564 | epot = -224.517597130738 | etot = -180.770700631599
68000 ekin = 22.421878544646 | erot = 21.1490017805243 | epot = -224.34158095606 | etot = -180.77070063089
69000 ekin = 22.3954651199576 | erot = 20.9555571676358 | epot = -224.121722917263 | etot = -180.770700629669
70000 ekin = 22.3613349801193 | erot = 20.7433545871758 | epot = -223.875390195706 | etot = -180.770700628411
71000 ekin = 22.3171019087139 | erot = 20.5301141425049 | epot = -223.617916679045 | etot = -180.770700627826
72000 ekin = 22.2595195485147 | erot = 20.3296309382964 | epot = -223.359851114099 | etot = -180.770700627288
73000 ekin = 22.1869461213877 | erot = 20.1521902584588 | epot = -223.109837006429 | etot = -180.770700626583
74000 ekin = 22.0990935565683 | erot = 20.0059494138149 | epot = -222.875743596756 | etot = -180.770700626373
75000 ekin = 21.9959491639282 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795
76000 ekin = 21.8806005890445 | erot = 19.828424336326 | epot = -222.479725550679 | etot = -180.770700625308
77000 ekin = 21.7590261899809 | erot = 19.8043252195864 | epot = -222.334052034216 | etot = -180.770700624649
78000 ekin = 21.6392419839503 | erot = 19.8262630279236 | epot = -222.236205635986 | etot = -180.770700624113
79000 ekin = 21.5302317519716 | erot = 19.8938812521576 | epot = -222.194813627769 | etot = -180.77070062364
80000 ekin = 21.4402276725657 | erot = 20.0060100278943 | epot = -222.216938324074 | etot = -180.770700623614
81000 ekin = 21.3741486759855 | erot = 20.158514479161 | epot = -222.303363779439 | etot = -180.770700624292
82000 ekin = 21.3325013763505 | erot = 20.3431413542724 | epot = -222.44634335588 | etot = -180.770700625257
83000 ekin = 21.3128808684037 | erot = 20.548330990772 | epot = -222.631912485779 | etot = -180.770700626604
84000 ekin = 21.310766170793 | erot = 20.7607919785174 | epot = -222.842258777119 | etot = -180.770700627809
85000 ekin = 21.3216301567277 | erot = 20.9678418539246 | epot = -223.060172639485 | etot = -180.770700628833
86000 ekin = 21.3400295156723 | erot = 21.1566564817957 | epot = -223.267386627523 | etot = -180.770700630055
87000 ekin = 21.3617783036992 | erot = 21.3170902458394 | epot = -223.449569179882 | etot = -180.770700630344
88000 ekin = 21.3873913218409 | erot = 21.445443991042 | epot = -223.603535942848 | etot = -180.770700629965
89000 ekin = 21.421574069399 | erot = 21.5439953706456 | epot = -223.736270068948 | etot = -180.770700628904
90000 ekin = 21.4723781618091 | erot = 21.6216769093347 | epot = -223.86475569847 | etot = -180.770700627326
91000 ekin = 21.549406625472 | erot = 21.6927202486463 | epot = -224.012827499723 | etot = -180.770700625604
92000 ekin = 21.6619209347597 | erot = 21.7730744493012 | epot = -224.205696008348 | etot = -180.770700624287
93000 ekin = 21.8158778641472 | erot = 21.8756732628048 | epot = -224.462251750825 | etot = -180.770700623873
94000 ekin = 22.0110275730997 | erot = 22.0060799403022 | epot = -224.787808138196 | etot = -180.770700624794
95000 ekin = 22.2387555838384 | erot = 22.1596167137192 | epot = -225.16907292429 | etot = -180.770700626733
96000 ekin = 22.4832444899361 | erot = 22.3220202374401 | epot = -225.575965356875 | etot = -180.770700629499
97000 ekin = 22.7237276202693 | erot = 22.4720556690122 | epot = -225.966483921719 | etot = -180.770700632437
98000 ekin = 22.9377647716041 | erot = 22.5858660312277 | epot = -226.294331437118 | etot = -180.770700634287
99000 ekin = 23.1071231637237 | erot = 22.6457411046184 | epot = -226.523564904806 | etot = -180.770700636464
100000 ekin = 23.2156001924311 | erot = 22.6390310936006 | epot = -226.625331923822 | etot = -180.770700637791
100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000
Loop time of 83.9672 on 1 procs for 100000 steps with 148 atoms
Performance: 1028.974 tau/day, 1190.942 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 80.885 | 80.885 | 80.885 | 0.0 | 96.33
Bond | 0.94789 | 0.94789 | 0.94789 | 0.0 | 1.13
Neigh | 0.011589 | 0.011589 | 0.011589 | 0.0 | 0.01
Comm | 0.045979 | 0.045979 | 0.045979 | 0.0 | 0.05
Output | 0.11973 | 0.11973 | 0.11973 | 0.0 | 0.14
Modify | 1.8641 | 1.8641 | 1.8641 | 0.0 | 2.22
Other | | 0.09239 | | | 0.11
Nlocal: 148.000 ave 148 max 148 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4199.00 ave 4199 max 4199 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4199
Ave neighs/atom = 28.371622
Ave special neighs/atom = 6.0000000
Neighbor list builds = 100
Dangerous builds = 0
write_data last_config.${number}.* nocoeff
write_data last_config.5.* nocoeff
System init for write_data ...
#write_restart last_config.${number}.*
Total wall time: 0:01:23

281
examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 Normal file
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LAMMPS (2 Jul 2021)
variable number equal 5
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
variable rhos equal 0.2
units lj
dimension 3
newton on
boundary p p p
atom_style hybrid bond ellipsoid oxdna
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:157)
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.dsring
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000)
1 by 2 by 2 MPI processor grid
reading atoms ...
148 atoms
reading velocities ...
148 velocities
scanning bonds ...
1 = max bonds/atom
148 ellipsoids
reading bonds ...
148 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds
set atom * mass 3.1575
Setting atom values ...
148 settings made for mass
group all type 1 4
148 atoms in group all
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
special_bonds lj 0 1 1
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000 seconds
# oxDNA2 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 seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 seqdep 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 seqdep 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 seqdep 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 ${T} ${rhos} 0.815
pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
# NVE ensemble
fix 1 all nve/asphere
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
timestep 1e-5
#comm_style tiled
fix 3 all balance 1000 1.03 shift xyz 10 1.03
comm_modify cutoff 3.8
compute quat all property/atom quatw quati quatj quatk
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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
dump_modify out sort id
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6389877
ghost atom cutoff = 5.6389877
binsize = 2.8194939, bins = 36 36 36
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889
Per MPI rank memory allocation (min/avg/max) = 9.383 | 9.432 | 9.506 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000
1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183
2000 ekin = 20.585620972069 | erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104
3000 ekin = 20.6239332104643 | erot = 21.5529389082727 | epot = -222.947572771312 | etot = -180.770700652575
4000 ekin = 20.6395549184482 | erot = 21.6854113323894 | epot = -223.095666904229 | etot = -180.770700653391
5000 ekin = 20.6295551742564 | erot = 21.7809539301804 | epot = -223.181209757876 | etot = -180.770700653439
6000 ekin = 20.5959625511847 | erot = 21.8369756530726 | epot = -223.203638857302 | etot = -180.770700653045
7000 ekin = 20.5431034482069 | erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652123
8000 ekin = 20.4774701419093 | erot = 21.8437134145373 | epot = -223.09188420739 | etot = -180.770700650943
9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649598
10000 ekin = 20.3427303660297 | erot = 21.7629575866662 | epot = -222.876388600949 | etot = -180.770700648253
11000 ekin = 20.2927407149578 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.77070064719
12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383222 | etot = -180.770700646287
13000 ekin = 20.2733920359447 | erot = 21.6092715397933 | epot = -222.653364221617 | etot = -180.770700645879
14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.77070064567
15000 ekin = 20.410400937429 | erot = 21.5031572556307 | epot = -222.684258838858 | etot = -180.770700645799
16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272037 | etot = -180.770700646753
17000 ekin = 20.7266657908773 | erot = 21.3426631585218 | epot = -222.840029597232 | etot = -180.770700647833
18000 ekin = 20.9417612759978 | erot = 21.2178611180927 | epot = -222.930323042998 | etot = -180.770700648907
19000 ekin = 21.1819308659396 | erot = 21.0532289630294 | epot = -223.005860478921 | etot = -180.770700649952
20000 ekin = 21.4358169889472 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.77070064997
21000 ekin = 21.6968513750995 | erot = 20.6066744652585 | epot = -223.074226489837 | etot = -180.770700649479
22000 ekin = 21.9614458442779 | erot = 20.3429420444508 | epot = -223.075088537371 | etot = -180.770700648642
23000 ekin = 22.2276099755697 | erot = 20.070338516524 | epot = -223.068649139875 | etot = -180.770700647781
24000 ekin = 22.4935893196667 | erot = 19.8020671721661 | epot = -223.066357139277 | etot = -180.770700647444
25000 ekin = 22.756606454822 | erot = 19.5464828008836 | epot = -223.073789902976 | etot = -180.77070064727
26000 ekin = 23.0126717548391 | erot = 19.3065017718461 | epot = -223.089874174572 | etot = -180.770700647887
27000 ekin = 23.2550417060586 | erot = 19.0797753474566 | epot = -223.105517701932 | etot = -180.770700648417
28000 ekin = 23.4774329734797 | erot = 18.8646197299572 | epot = -223.112753352067 | etot = -180.77070064863
29000 ekin = 23.6747927720654 | erot = 18.6628653411822 | epot = -223.108358761694 | etot = -180.770700648446
30000 ekin = 23.8432321400238 | erot = 18.4812216983633 | epot = -223.095154486375 | etot = -180.770700647988
31000 ekin = 23.979304175222 | erot = 18.3307845334015 | epot = -223.08078935577 | etot = -180.770700647146
32000 ekin = 24.0810246040226 | erot = 18.2261577055998 | epot = -223.077882955919 | etot = -180.770700646297
33000 ekin = 24.1468986449389 | erot = 18.1820705445401 | epot = -223.09966983514 | etot = -180.770700645661
34000 ekin = 24.1756615132855 | erot = 18.2103812210167 | epot = -223.156743379607 | etot = -180.770700645304
35000 ekin = 24.1663193894644 | erot = 18.3185351073563 | epot = -223.255555142089 | etot = -180.770700645269
36000 ekin = 24.1167205812957 | erot = 18.5091649894184 | epot = -223.396586216223 | etot = -180.770700645509
37000 ekin = 24.0274860006128 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646226
38000 ekin = 23.8991479078978 | erot = 19.1166063146994 | epot = -223.786454869891 | etot = -180.770700647293
39000 ekin = 23.7326911853231 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648764
40000 ekin = 23.5294223072117 | erot = 19.9254673141828 | epot = -224.225590272293 | etot = -180.770700650899
41000 ekin = 23.289939614139 | erot = 20.3408097780563 | epot = -224.401450045568 | etot = -180.770700653372
42000 ekin = 23.0154529235022 | erot = 20.7165619564848 | epot = -224.502715535762 | etot = -180.770700655775
43000 ekin = 22.7111536814277 | erot = 21.0163895622231 | epot = -224.498243901359 | etot = -180.770700657708
44000 ekin = 22.3710575806355 | erot = 21.2060371289783 | epot = -224.347795365754 | etot = -180.77070065614
45000 ekin = 22.0515843162889 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425
46000 ekin = 21.7855632553133 | erot = 21.20360137666 | epot = -223.759865260062 | etot = -180.770700628089
47000 ekin = 21.5167766971456 | erot = 21.0656367023667 | epot = -223.353114011016 | etot = -180.770700611503
48000 ekin = 21.4540196107333 | erot = 20.8430832424321 | epot = -223.067803499525 | etot = -180.77070064636
49000 ekin = 21.3647564765274 | erot = 20.5521507191682 | epot = -222.687607816922 | etot = -180.770700621226
50000 ekin = 21.3125768184617 | erot = 20.2526464671325 | epot = -222.33592390431 | etot = -180.770700618715
51000 ekin = 21.2949924810834 | erot = 19.9798421626035 | epot = -222.045535260404 | etot = -180.770700616717
52000 ekin = 21.3137144249679 | erot = 19.7627691343679 | epot = -221.847184173963 | etot = -180.770700614627
53000 ekin = 21.3664076685099 | erot = 19.6202359856891 | epot = -221.757344279695 | etot = -180.770700625496
54000 ekin = 21.4214245524052 | erot = 19.5588232319492 | epot = -221.750948393748 | etot = -180.770700609393
55000 ekin = 21.5995673396082 | erot = 19.580521488567 | epot = -221.950789453583 | etot = -180.770700625408
56000 ekin = 21.7643125668294 | erot = 19.681604210777 | epot = -222.216617401429 | etot = -180.770700623823
57000 ekin = 21.922130908443 | erot = 19.8499880475945 | epot = -222.542819582064 | etot = -180.770700626026
58000 ekin = 22.0666093644375 | erot = 20.0713856445709 | epot = -222.908695636278 | etot = -180.770700627269
59000 ekin = 22.1910921687932 | erot = 20.3284024096003 | epot = -223.290195207095 | etot = -180.770700628702
60000 ekin = 22.2920682490219 | erot = 20.6003319531534 | epot = -223.663100832376 | etot = -180.770700630201
61000 ekin = 22.3680528265772 | erot = 20.8645614198856 | epot = -224.003314878046 | etot = -180.770700631583
62000 ekin = 22.4198570332617 | erot = 21.0983714926625 | epot = -224.288929158679 | etot = -180.770700632755
63000 ekin = 22.4500800739905 | erot = 21.2815521440892 | epot = -224.502332851297 | etot = -180.770700633217
64000 ekin = 22.4634052763968 | erot = 21.3990470998276 | epot = -224.633153009904 | etot = -180.770700633679
65000 ekin = 22.463988539095 | erot = 21.4413332838523 | epot = -224.676022456448 | etot = -180.770700633501
66000 ekin = 22.4559522488531 | erot = 21.4074154510864 | epot = -224.634068332759 | etot = -180.770700632819
67000 ekin = 22.4417384097814 | erot = 21.3051580893563 | epot = -224.517597130739 | etot = -180.770700631601
68000 ekin = 22.4218785446449 | erot = 21.1490017805243 | epot = -224.341580956061 | etot = -180.770700630892
69000 ekin = 22.3954651199567 | erot = 20.9555571676359 | epot = -224.121722917264 | etot = -180.770700629671
70000 ekin = 22.3613349801186 | erot = 20.743354587176 | epot = -223.875390195707 | etot = -180.770700628413
71000 ekin = 22.3171019087134 | erot = 20.5301141425052 | epot = -223.617916679047 | etot = -180.770700627829
72000 ekin = 22.2595195485144 | erot = 20.3296309382966 | epot = -223.3598511141 | etot = -180.77070062729
73000 ekin = 22.1869461213875 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626585
74000 ekin = 22.0990935565682 | erot = 20.0059494138151 | epot = -222.875743596758 | etot = -180.770700626375
75000 ekin = 21.9959491639282 | erot = 19.8965902063257 | epot = -222.663239996051 | etot = -180.770700625797
76000 ekin = 21.8806005890446 | erot = 19.8284243363261 | epot = -222.479725550681 | etot = -180.77070062531
77000 ekin = 21.759026189981 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.770700624651
78000 ekin = 21.6392419839505 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114
79000 ekin = 21.5302317519718 | erot = 19.8938812521574 | epot = -222.19481362777 | etot = -180.770700623641
80000 ekin = 21.4402276725659 | erot = 20.0060100278939 | epot = -222.216938324075 | etot = -180.770700623615
81000 ekin = 21.3741486759857 | erot = 20.1585144791605 | epot = -222.303363779439 | etot = -180.770700624293
82000 ekin = 21.3325013763506 | erot = 20.3431413542717 | epot = -222.446343355881 | etot = -180.770700625259
83000 ekin = 21.3128808684039 | erot = 20.5483309907712 | epot = -222.63191248578 | etot = -180.770700626605
84000 ekin = 21.3107661707932 | erot = 20.7607919785166 | epot = -222.842258777119 | etot = -180.77070062781
85000 ekin = 21.3216301567279 | erot = 20.9678418539237 | epot = -223.060172639486 | etot = -180.770700628834
86000 ekin = 21.3400295156725 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630057
87000 ekin = 21.3617783036995 | erot = 21.3170902458388 | epot = -223.449569179883 | etot = -180.770700630345
88000 ekin = 21.3873913218413 | erot = 21.4454439910414 | epot = -223.603535942849 | etot = -180.770700629967
89000 ekin = 21.4215740693994 | erot = 21.5439953706451 | epot = -223.73627006895 | etot = -180.770700628906
90000 ekin = 21.4723781618096 | erot = 21.6216769093343 | epot = -223.864755698472 | etot = -180.770700627328
91000 ekin = 21.5494066254725 | erot = 21.6927202486459 | epot = -224.012827499725 | etot = -180.770700625606
92000 ekin = 21.6619209347601 | erot = 21.7730744493007 | epot = -224.20569600835 | etot = -180.77070062429
93000 ekin = 21.8158778641474 | erot = 21.8756732628043 | epot = -224.462251750827 | etot = -180.770700623875
94000 ekin = 22.0110275730999 | erot = 22.0060799403016 | epot = -224.787808138198 | etot = -180.770700624796
95000 ekin = 22.2387555838384 | erot = 22.1596167137185 | epot = -225.169072924291 | etot = -180.770700626735
96000 ekin = 22.4832444899359 | erot = 22.3220202374394 | epot = -225.575965356876 | etot = -180.770700629501
97000 ekin = 22.7237276202691 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632439
98000 ekin = 22.9377647716038 | erot = 22.5858660312271 | epot = -226.294331437119 | etot = -180.770700634288
99000 ekin = 23.1071231637233 | erot = 22.645741104618 | epot = -226.523564904806 | etot = -180.770700636465
100000 ekin = 23.2156001924307 | erot = 22.6390310936004 | epot = -226.625331923823 | etot = -180.770700637791
100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000
Loop time of 28.0802 on 4 procs for 100000 steps with 148 atoms
Performance: 3076.899 tau/day, 3561.226 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.209 | 21.356 | 25.248 | 81.3 | 76.05
Bond | 0.26072 | 0.26526 | 0.27015 | 0.9 | 0.94
Neigh | 0.005772 | 0.0058625 | 0.005932 | 0.1 | 0.02
Comm | 1.7227 | 5.6246 | 10.79 | 158.9 | 20.03
Output | 0.043943 | 0.046855 | 0.048664 | 0.9 | 0.17
Modify | 0.54715 | 0.55336 | 0.55902 | 0.7 | 1.97
Other | | 0.2279 | | | 0.81
Nlocal: 37.0000 ave 38 max 36 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 111.000 ave 112 max 110 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1049.75 ave 1270 max 757 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 4199
Ave neighs/atom = 28.371622
Ave special neighs/atom = 6.0000000
Neighbor list builds = 100
Dangerous builds = 0
write_data last_config.${number}.* nocoeff
write_data last_config.5.* nocoeff
System init for write_data ...
#write_restart last_config.${number}.*
Total wall time: 0:00:28

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newton on
boundary p p p
@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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boundary p p p
@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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@ -84,3 +84,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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run 1000000
write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/test.sh Executable file
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@ -0,0 +1,232 @@
#! /bin/bash
DATE='2Jul21'
LMPDIR=/Users/ohenrich/Work/code/lammps
SRCDIR=$LMPDIR/src
EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples
if [ $# -eq 1 ] && [ $1 = run ]; then
echo '# Compiling executable in' $SRCDIR
cd $SRCDIR
make clean-all
make -j8 mpi
######################################################
echo '# Running oxDNA duplex1 test'
cd $EXDIR/oxDNA/duplex1
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex1 .
cp ../data.duplex1 .
mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.1
grep etot log.$DATE.duplex1.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.4
grep etot log.$DATE.duplex1.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxDNA duplex2 test'
cd $EXDIR/oxDNA/duplex2
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex2 .
cp ../data.duplex2 .
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.1
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.4
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxDNA2 duplex1 test'
cd $EXDIR/oxDNA2/duplex1
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex1 .
cp ../data.duplex1 .
mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.1
grep etot log.$DATE.duplex1.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
mv log.lammps log.$DATE.duplex1.g++.4
grep etot log.$DATE.duplex1.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxDNA2 duplex2 test'
cd $EXDIR/oxDNA2/duplex2
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex2 .
cp ../data.duplex2 .
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.1
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.4
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxDNA2 duplex3 test'
cd $EXDIR/oxDNA2/duplex3
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex3 .
cp ../data.duplex3 .
mpirun -np 1 ./lmp_mpi < in.duplex3 > /dev/null
mv log.lammps log.$DATE.duplex3.g++.1
grep etot log.$DATE.duplex3.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex3 > /dev/null
mv log.lammps log.$DATE.duplex3.g++.4
grep etot log.$DATE.duplex3.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxDNA2 unique_bp test'
cd $EXDIR/oxDNA2/unique_bp
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex4.4type .
cp ../in.duplex4.8type .
cp ../data.duplex4.4type .
cp ../data.duplex4.8type .
mpirun -np 1 ./lmp_mpi < in.duplex4.4type > /dev/null
mv log.lammps log.$DATE.duplex4.4type.g++.1
grep etot log.$DATE.duplex4.4type.g++.1 > e_test.dat
grep etot ../log*4type*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex4.4type > /dev/null
mv log.lammps log.$DATE.duplex4.4type.g++.4
grep etot log.$DATE.duplex4.4type.g++.4 > e_test.dat
grep etot ../log*4type*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 1 ./lmp_mpi < in.duplex4.8type > /dev/null
mv log.lammps log.$DATE.duplex4.8type.g++.1
grep etot log.$DATE.duplex4.8type.g++.1 > e_test.dat
grep etot ../log*8type*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex4.8type > /dev/null
mv log.lammps log.$DATE.duplex4.8type.g++.4
grep etot log.$DATE.duplex4.8type.g++.4 > e_test.dat
grep etot ../log*8type*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxDNA2 dsring test'
cd $EXDIR/oxDNA2/dsring
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.dsring .
cp ../data.dsring .
mpirun -np 1 ./lmp_mpi < in.dsring > /dev/null
mv log.lammps log.$DATE.dsring.g++.1
grep etot log.$DATE.dsring.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.dsring > /dev/null
mv log.lammps log.$DATE.dsring.g++.4
grep etot log.$DATE.dsring.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
######################################################
echo '# Running oxRNA2 duplex2 test'
cd $EXDIR/oxRNA2/duplex2
mkdir test
cd test
cp $SRCDIR/lmp_mpi .
cp ../in.duplex2 .
cp ../data.duplex2 .
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.1
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
grep etot ../log*1 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
mv log.lammps log.$DATE.duplex2.g++.4
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
grep etot ../log*4 > e_old.dat
ndiff -relerr 1e-8 e_test.dat e_old.dat
######################################################
echo '# Done'
elif [ $# -eq 1 ] && [ $1 = clean ]; then
echo '# Deleting test directories'
rm -rf $EXDIR/oxDNA/duplex1/test
rm -rf $EXDIR/oxDNA/duplex2/test
rm -rf $EXDIR/oxDNA2/duplex1/test
rm -rf $EXDIR/oxDNA2/duplex2/test
rm -rf $EXDIR/oxDNA2/duplex3/test
rm -rf $EXDIR/oxDNA2/unique_bp/test
rm -rf $EXDIR/oxDNA2/dsring/test
rm -rf $EXDIR/oxRNA2/duplex2/test
echo '# Done'
else
echo '# Usage:'
echo '# ./test.sh run ... to run test suite'
echo '# ./test.sh clean ... to delete test directories'
fi

1
examples/PACKAGES/quip/gap_example.xml
View File

@ -1,3 +1,4 @@
<!-- DATE: 2015-02-20 UNITS: metal -->
<GAP_2015_2_20_0_10_54_35_765>
<Potential label="GAP_2015_2_20_0_10_54_35_765" init_args="Sum init_args_pot1={IP Glue} init_args_pot2={IP GAP label=GAP_2015_2_20_0_10_54_35_765}"/>
<Glue_params n_types="2">

1
examples/PACKAGES/quip/sw_example.xml
View File

@ -1,3 +1,4 @@
<!-- UNITS: metal DATE: 2015-02-24 CITATION: Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements. Ge and Si-Ge from Ethier and Lewis '92 -->
<SW_params n_types="3" label="PRB_31_plus_H_Ge">
<comment> Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements. Ge and Si-Ge from Ethier and Lewis '92 </comment>
<per_type_data type="1" atomic_num="1" />

2
examples/README
View File

@ -103,7 +103,7 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
qeq: use of QEQ package for charge equilibration
reax: RDX and TATB and several other models using ReaxFF
reaxff: RDX and TATB and several other models using ReaxFF
rerun: use of rerun and read_dump commands
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void

22
examples/qeq/buck.inc Normal file
View File

@ -0,0 +1,22 @@
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve

75
examples/qeq/in.qeq.buck
View File

@ -1,41 +1,68 @@
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
replicate 2 2 2
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot
thermo 10
timestep 0.0001
include buck.inc
velocity all create 300.0 1281937
fix 1 all nve
run 0 post no
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
write_restart qeq.restart
run 100
clear
print "Using fix qeq/point"
read_restart qeq.restart
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/shielded"
read_restart qeq.restart
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/slater"
read_restart qeq.restart
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/dynamic"
read_restart qeq.restart
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/fire"
read_restart qeq.restart
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
run 100

650
examples/qeq/log.20Apr21.qeq.buck.g++.1 Normal file
View File

@ -0,0 +1,650 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
read_data CPU = 0.009 seconds
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
velocity all create 300.0 1281937
run 0 post no
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.30705229
grid = 48 48 54
stencil order = 5
estimated absolute RMS force accuracy = 1.8909403e-05
estimated relative force accuracy = 1.3131854e-06
using double precision FFTW3
3d grid and FFT values/proc = 184525 124416
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Fix qeq CG convergence failed (4.357840257025601e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
WARNING: Fix qeq CG convergence failed (5.274094378414531e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
Per MPI rank memory allocation (min/avg/max) = 38.75 | 38.75 | 38.75 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10
Loop time of 1.66893e-06 on 1 procs for 0 steps with 1200 atoms
write_restart qeq.restart
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/point"
Using fix qeq/point
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/point, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3
10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8
20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8
30 -3568.22095 0.86767937 -0.43383969 0.000000000001 8
40 -3633.24956 0.87335551 -0.43667775 0.000000000000 8
50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8
60 -3784.36769 0.88402303 -0.44201151 -0.000000000000 8
70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8
80 -3965.29722 0.89431515 -0.44715757 -0.000000000001 8
90 -4048.36764 0.89698588 -0.44849294 0.000000000000 8
100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8
Loop time of 11.5935 on 1 procs for 100 steps with 1200 atoms
Performance: 0.075 ns/day, 322.041 hours/ns, 8.626 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 | 2.8257 | 2.8257 | 2.8257 | 0.0 | 24.37
Kspace | 1.2136 | 1.2136 | 1.2136 | 0.0 | 10.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015541 | 0.015541 | 0.015541 | 0.0 | 0.13
Output | 0.0014489 | 0.0014489 | 0.0014489 | 0.0 | 0.01
Modify | 7.5351 | 7.5351 | 7.5351 | 0.0 | 64.99
Other | | 0.00206 | | | 0.02
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/shielded"
Using fix qeq/shielded
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1
40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 7.93936 on 1 procs for 100 steps with 1200 atoms
Performance: 0.109 ns/day, 220.538 hours/ns, 12.595 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 | 2.8061 | 2.8061 | 2.8061 | 0.0 | 35.34
Kspace | 1.2176 | 1.2176 | 1.2176 | 0.0 | 15.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015528 | 0.015528 | 0.015528 | 0.0 | 0.20
Output | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 0.02
Modify | 3.8966 | 3.8966 | 3.8966 | 0.0 | 49.08
Other | | 0.002076 | | | 0.03
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/slater"
Using fix qeq/slater
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1
40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 7.9652 on 1 procs for 100 steps with 1200 atoms
Performance: 0.108 ns/day, 221.256 hours/ns, 12.555 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 | 2.809 | 2.809 | 2.809 | 0.0 | 35.27
Kspace | 1.2214 | 1.2214 | 1.2214 | 0.0 | 15.33
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015635 | 0.015635 | 0.015635 | 0.0 | 0.20
Output | 0.0014393 | 0.0014393 | 0.0014393 | 0.0 | 0.02
Modify | 3.9157 | 3.9157 | 3.9157 | 0.0 | 49.16
Other | | 0.002091 | | | 0.03
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/dynamic"
Using fix qeq/dynamic
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.38094 0.85231286 -0.42615643 0.000000000001 43
10 -3452.05217 0.85475894 -0.42737947 -0.000000000001 17
20 -3497.8643 0.85999180 -0.42999590 -0.000000000007 22
30 -3568.53169 0.86772479 -0.43386239 -0.000000000006 22
40 -3633.43753 0.87338291 -0.43669146 -0.000000000006 22
50 -3700.27953 0.87807632 -0.43903816 -0.000000000005 22
60 -3784.4004 0.88402822 -0.44201411 0.000000000002 17
70 -3877.73706 0.89012201 -0.44506100 0.000000000002 22
80 -3965.36111 0.89432486 -0.44716243 0.000000000008 17
90 -4048.57901 0.89701688 -0.44850844 -0.000000000004 22
100 -4118.62736 0.89718691 -0.44859346 -0.000000000026 17
Loop time of 18.5333 on 1 procs for 100 steps with 1200 atoms
Performance: 0.047 ns/day, 514.815 hours/ns, 5.396 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 | 2.8268 | 2.8268 | 2.8268 | 0.0 | 15.25
Kspace | 1.2138 | 1.2138 | 1.2138 | 0.0 | 6.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015407 | 0.015407 | 0.015407 | 0.0 | 0.08
Output | 0.0014303 | 0.0014303 | 0.0014303 | 0.0 | 0.01
Modify | 14.474 | 14.474 | 14.474 | 0.0 | 78.10
Other | | 0.001973 | | | 0.01
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/fire"
Using fix qeq/fire
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.06113 0.85226679 -0.42613339 0.000000000004 37
10 -3452.0494 0.85475813 -0.42737906 0.000000000001 10
20 -3497.83503 0.85998739 -0.42999370 0.000000000003 13
30 -3568.47507 0.86771599 -0.43385799 0.000000000004 13
40 -3633.35368 0.87337029 -0.43668514 0.000000000004 13
50 -3700.15601 0.87805847 -0.43902924 0.000000000005 13
60 -3784.32042 0.88401635 -0.44200818 0.000000000000 11
70 -3877.59818 0.89010162 -0.44505081 0.000000000000 13
80 -3965.28426 0.89431356 -0.44715678 0.000000000000 11
90 -4048.3338 0.89698069 -0.44849034 0.000000000001 13
100 -4118.63638 0.89718818 -0.44859409 0.000000000003 12
Loop time of 13.0492 on 1 procs for 100 steps with 1200 atoms
Performance: 0.066 ns/day, 362.479 hours/ns, 7.663 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 | 2.7996 | 2.7996 | 2.7996 | 0.0 | 21.45
Kspace | 1.2141 | 1.2141 | 1.2141 | 0.0 | 9.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015527 | 0.015527 | 0.015527 | 0.0 | 0.12
Output | 0.0014405 | 0.0014405 | 0.0014405 | 0.0 | 0.01
Modify | 9.0166 | 9.0166 | 9.0166 | 0.0 | 69.10
Other | | 0.001981 | | | 0.02
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00

650
examples/qeq/log.20Apr21.qeq.buck.g++.4 Normal file
View File

@ -0,0 +1,650 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
read_data CPU = 0.009 seconds
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
velocity all create 300.0 1281937
run 0 post no
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.30705229
grid = 48 48 54
stencil order = 5
estimated absolute RMS force accuracy = 1.8909403e-05
estimated relative force accuracy = 1.3131854e-06
using double precision FFTW3
3d grid and FFT values/proc = 57970 32256
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Fix qeq CG convergence failed (4.299911728887494e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
WARNING: Fix qeq CG convergence failed (5.273380778822746e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
Per MPI rank memory allocation (min/avg/max) = 14.97 | 15.02 | 15.08 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10
Loop time of 3.33786e-06 on 4 procs for 0 steps with 1200 atoms
write_restart qeq.restart
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/point"
Using fix qeq/point
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/point, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3
10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8
20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8
30 -3568.22095 0.86767937 -0.43383969 0.000000000000 8
40 -3633.24956 0.87335551 -0.43667775 -0.000000000000 8
50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8
60 -3784.36769 0.88402303 -0.44201151 0.000000000000 8
70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8
80 -3965.29722 0.89431515 -0.44715757 0.000000000000 8
90 -4048.36764 0.89698588 -0.44849294 -0.000000000000 8
100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8
Loop time of 3.30911 on 4 procs for 100 steps with 1200 atoms
Performance: 0.261 ns/day, 91.920 hours/ns, 30.220 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 | 0.67613 | 0.68904 | 0.71562 | 1.9 | 20.82
Kspace | 0.36056 | 0.3881 | 0.39892 | 2.6 | 11.73
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013339 | 0.017982 | 0.019974 | 2.0 | 0.54
Output | 0.0006721 | 0.00099713 | 0.0019572 | 0.0 | 0.03
Modify | 2.2109 | 2.211 | 2.211 | 0.0 | 66.81
Other | | 0.002041 | | | 0.06
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/shielded"
Using fix qeq/shielded
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.006 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1
40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 2.25559 on 4 procs for 100 steps with 1200 atoms
Performance: 0.383 ns/day, 62.655 hours/ns, 44.334 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67442 | 0.69181 | 0.70907 | 2.0 | 30.67
Kspace | 0.39381 | 0.41151 | 0.43023 | 2.6 | 18.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012851 | 0.01426 | 0.015146 | 0.7 | 0.63
Output | 0.00066686 | 0.00098681 | 0.0019395 | 0.0 | 0.04
Modify | 1.1349 | 1.135 | 1.135 | 0.0 | 50.32
Other | | 0.002035 | | | 0.09
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/slater"
Using fix qeq/slater
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.012 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1
40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 2.39249 on 4 procs for 100 steps with 1200 atoms
Performance: 0.361 ns/day, 66.458 hours/ns, 41.797 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.6751 | 0.70301 | 0.71919 | 2.1 | 29.38
Kspace | 0.45569 | 0.47315 | 0.49885 | 2.6 | 19.78
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012967 | 0.018681 | 0.020909 | 2.4 | 0.78
Output | 0.00066733 | 0.00099397 | 0.0019579 | 0.0 | 0.04
Modify | 1.1945 | 1.1946 | 1.1947 | 0.0 | 49.93
Other | | 0.002046 | | | 0.09
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/dynamic"
Using fix qeq/dynamic
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.002 seconds
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.38094 0.85231286 -0.42615643 -0.000000000001 43
10 -3452.05217 0.85475894 -0.42737947 -0.000000000003 17
20 -3497.8643 0.85999180 -0.42999590 0.000000000000 22
30 -3568.53169 0.86772479 -0.43386239 -0.000000000000 22
40 -3633.43753 0.87338291 -0.43669146 0.000000000006 22
50 -3700.27953 0.87807632 -0.43903816 0.000000000003 22
60 -3784.4004 0.88402822 -0.44201411 0.000000000009 17
70 -3877.73706 0.89012201 -0.44506100 0.000000000010 22
80 -3965.36111 0.89432486 -0.44716243 0.000000000011 17
90 -4048.57901 0.89701688 -0.44850844 0.000000000012 22
100 -4118.62736 0.89718691 -0.44859346 0.000000000013 17
Loop time of 5.27704 on 4 procs for 100 steps with 1200 atoms
Performance: 0.164 ns/day, 146.584 hours/ns, 18.950 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68437 | 0.69096 | 0.69826 | 0.7 | 13.09
Kspace | 0.38484 | 0.38941 | 0.39524 | 0.7 | 7.38
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012609 | 0.01529 | 0.016842 | 1.3 | 0.29
Output | 0.00067735 | 0.0010006 | 0.0019588 | 1.7 | 0.02
Modify | 4.1783 | 4.1783 | 4.1784 | 0.0 | 79.18
Other | | 0.002027 | | | 0.04
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/fire"
Using fix qeq/fire
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.05316 0.85226679 -0.42613339 0.000000000001 37
10 -3452.04937 0.85475813 -0.42737906 0.000000000001 10
20 -3497.83659 0.85998739 -0.42999370 0.000000000002 13
30 -3568.47793 0.86771599 -0.43385799 0.000000000002 13
40 -3633.35326 0.87337029 -0.43668514 0.000000000002 13
50 -3700.16079 0.87805847 -0.43902924 0.000000000000 13
60 -3784.31906 0.88401635 -0.44200818 -0.000000000001 11
70 -3877.60163 0.89010162 -0.44505081 -0.000000000000 13
80 -3965.28179 0.89431356 -0.44715678 0.000000000001 11
90 -4048.33861 0.89698069 -0.44849034 0.000000000001 13
100 -4118.63861 0.89718818 -0.44859409 0.000000000002 12
Loop time of 3.88026 on 4 procs for 100 steps with 1200 atoms
Performance: 0.223 ns/day, 107.785 hours/ns, 25.771 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68424 | 0.69912 | 0.73572 | 2.5 | 18.02
Kspace | 0.38093 | 0.41715 | 0.43168 | 3.2 | 10.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012711 | 0.013318 | 0.014003 | 0.4 | 0.34
Output | 0.00066566 | 0.00098735 | 0.0019317 | 0.0 | 0.03
Modify | 2.7477 | 2.7477 | 2.7477 | 0.0 | 70.81
Other | | 0.002004 | | | 0.05
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:17

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examples/qeq/log.27Nov18.qeq.buck.g++.1
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 1 by 1 MPI processor grid
9600 atoms
Time spent = 0.00114894 secs
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 8 8 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes
Step PotEng c_q1 c_q2 v_qtot S/CPU
0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0
10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877
20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179
30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643
40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341
50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127
60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762
70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546
80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079
90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419
100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001
Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms
Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 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 | 11.518 | 11.518 | 11.518 | 0.0 | 6.48
Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01
Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00
Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11
Other | | 0.007197 | | | 0.00
Nlocal: 9600 ave 9600 max 9600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22125 ave 22125 max 22125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.9408e+06 ave 2.9408e+06 max 2.9408e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:01

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examples/qeq/log.27Nov18.qeq.buck.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 2 by 2 MPI processor grid
9600 atoms
Time spent = 0.000675201 secs
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 8 8 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes
Step PotEng c_q1 c_q2 v_qtot S/CPU
0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0
10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312
20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316
30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335
40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139
50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263
60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722
70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406
80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813
90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145
100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486
Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms
Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 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 | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22
Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75
Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00
Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03
Other | | 0.01409 | | | 0.03
Nlocal: 2400 ave 2400 max 2400 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 11550 ave 11550 max 11550 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 735200 ave 740758 max 729642 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:49

1
examples/qeq/param.qeq1
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@ -1,3 +1,4 @@
# UNITS: real
1 5.3200 14.8732 1.0206 0.0 0.0
2 5.8678 14.0000 0.9000 0.0 0.0
3 8.5000 17.9978 1.0503 0.0 0.0

1
examples/qeq/param.qeq2
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@ -1,2 +1,3 @@
# UNITS: metal
1 0.00000 7.25028 0.01 0.772871 0.000000
2 11.26882 15.37920 0.01 0.243072 0.000000

52
examples/reax/in.reaxc.rdx
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@ -1,52 +0,0 @@
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

52
examples/reax/in.reaxc.rdx-shielded
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@ -1,52 +0,0 @@
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

55
examples/reax/in.reaxc.tatb
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@ -1,55 +0,0 @@
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25

55
examples/reax/in.reaxc.tatb-shielded
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@ -1,55 +0,0 @@
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25

116
examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1
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LAMMPS (4 Jan 2019)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.54 | 15.54 | 15.54 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79939 0 168.88404
10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512
30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749
40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085
50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995
60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414
70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648
80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464
90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914
100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951
Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms
Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.59308 | 0.59308 | 0.59308 | 0.0 | 90.21
Neigh | 0.020665 | 0.020665 | 0.020665 | 0.0 | 3.14
Comm | 0.0015757 | 0.0015757 | 0.0015757 | 0.0 | 0.24
Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.06
Modify | 0.04156 | 0.04156 | 0.04156 | 0.0 | 6.32
Other | | 0.000154 | | | 0.02
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1306 ave 1306 max 1306 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1306
Ave neighs/atom = 62.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

116
examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4
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LAMMPS (4 Jan 2019)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.62 | 12.08 | 13.84 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452
10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929
30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706
40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076
50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999
60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412
70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967
80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525
90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126
100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944
Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms
Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s
93.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53395 | 0.5352 | 0.53805 | 0.2 | 84.37
Neigh | 0.0088253 | 0.012023 | 0.016203 | 2.4 | 1.90
Comm | 0.0051677 | 0.0081 | 0.0093861 | 1.9 | 1.28
Output | 0.00049353 | 0.00054371 | 0.00058222 | 0.0 | 0.09
Modify | 0.074155 | 0.078299 | 0.081472 | 0.9 | 12.34
Other | | 0.0001715 | | | 0.03
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 326.5 ave 927 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1306
Ave neighs/atom = 62.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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