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Merge branch 'master' into fft

This commit is contained in:
Stan Moore 2019-07-29 14:05:46 -06:00 committed by GitHub
parent 2ec743abb7 35cee904d7
commit 4874fcc32a
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GPG Key ID: 4AEE18F83AFDEB23
846 changed files with 53187 additions and 10820 deletions
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29
cmake/CMakeLists.txt
View File

@ -37,7 +37,7 @@ include(PreventInSourceBuilds)
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
#release comes with -O3 by default
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
@ -106,6 +106,8 @@ if(BUILD_LIB)
endif()
endif()
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
if(NOT BUILD_EXE AND NOT BUILD_LIB)
message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
endif()
@ -222,6 +224,9 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
if(CMAKE_GENERATOR STREQUAL "Ninja")
status(FATAL_ERROR "Cannot build internal linear algebra library with Ninja build tool due to lack for Fortran support")
endif()
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
@ -298,6 +303,7 @@ include(Packages/USER-QUIP)
include(Packages/USER-QMMM)
include(Packages/USER-VTK)
include(Packages/KIM)
include(Packages/LATTE)
include(Packages/MESSAGE)
include(Packages/MSCG)
include(Packages/COMPRESS)
@ -517,6 +523,19 @@ if(BUILD_EXE)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
endif()
if(BUILD_TOOLS)
add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
# ninja-build currently does not support fortran. thus we skip building this tool
if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
enable_language(C)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
@ -525,7 +544,6 @@ if(BUILD_EXE)
target_link_libraries(msi2lmp m)
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
endif()
include(Documentation)
@ -655,5 +673,10 @@ if(PKG_KOKKOS)
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
endif()
if(PKG_KSPACE)
message(STATUS "Using ${FFT} as FFT")
message(STATUS "Using ${FFT} as primary FFT library")
if(FFT_SINGLE)
message(STATUS "Using single precision FFTs")
else()
message(STATUS "Using double precision FFTs")
endif()
endif()

3
cmake/Modules/Packages/KIM.cmake
View File

@ -13,6 +13,9 @@ if(PKG_KIM)
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
if(DOWNLOAD_KIM)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
endif()
message(STATUS "KIM-API download requested - we will build our own")
enable_language(C)
enable_language(Fortran)

28
cmake/Modules/Packages/KSPACE.cmake
View File

@ -1,5 +1,5 @@
if(PKG_KSPACE)
option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
set(FFTW "FFTW3")
if(FFT_SINGLE)
set(FFTW "FFTW3F")
@ -7,26 +7,30 @@ if(PKG_KSPACE)
endif()
find_package(${FFTW} QUIET)
if(${FFTW}_FOUND)
set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
else()
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
endif()
set(FFT_VALUES KISS ${FFTW} MKL CUFFT)
set(FFT_VALUES KISS FFTW MKL CUFFT)
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
validate_option(FFT FFT_VALUES)
string(TOUPPER ${FFT} FFT)
if(NOT FFT STREQUAL "KISS")
find_package(${FFT} REQUIRED)
if(NOT FFT STREQUAL "FFTW3F")
add_definitions(-DFFT_FFTW)
else()
add_definitions(-DFFT_${FFT})
endif()
include_directories(${${FFT}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
if(FFT STREQUAL "FFTW3")
find_package(${FFTW} REQUIRED)
add_definitions(-DFFT_FFTW3)
include_directories(${${FFTW}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
elseif(FFT STREQUAL "MKL")
find_package(MKL REQUIRED)
add_definitions(-DFFT_MKL)
include_directories(${MKL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
else()
# last option is KISSFFT
add_definitions(-DFFT_KISS)
endif()
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
set(FFT_PACK_VALUES array pointer memcpy)
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

3
cmake/Modules/Packages/LATTE.cmake
View File

@ -11,6 +11,9 @@ if(PKG_LATTE)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
endif()
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
endif()
message(STATUS "LATTE download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build

3
cmake/Modules/Packages/MSCG.cmake
View File

@ -11,6 +11,9 @@ if(PKG_MSCG)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
endif()
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
endif()
include(ExternalProject)
if(NOT LAPACK_FOUND)
set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")

3
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -17,6 +17,9 @@ if(PKG_USER-PLUMED)
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
endif()
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})

3
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -13,6 +13,9 @@ if(PKG_USER-SCAFACOS)
endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
endif()
message(STATUS "ScaFaCoS download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(scafacos_build

3
cmake/Modules/Packages/VORONOI.cmake
View File

@ -7,6 +7,9 @@ if(PKG_VORONOI)
endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO)
if(CMAKE_GENERATOR STREQUAL "Ninja")
message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
endif()
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "5 June 2019" "2019-06-05"
.TH LAMMPS "19 July 2019" "2019-07-19"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

16
doc/src/Build_cmake.txt
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@ -32,10 +32,18 @@ cmake \[options ...\] ../cmake # configuration with (command-line) cmake
make # compilation :pre
The cmake command will detect available features, enable selected
packages and options, and will generate the build environment. The make
command will then compile and link LAMMPS, producing (by default) an
executable called "lmp" and a library called "liblammps.a" in the
"build" folder.
packages and options, and will generate the build environment. By default
this build environment will be created for "Unix Makefiles" on most
platforms and particularly on Linux. However, alternate build tools
(e.g. Ninja) and support files for Integrated Development Environments
(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
selected via the "-G" command line flag. For the rest of the documentation
we will assume that the build environment is generated for makefiles
and thus the make command will be used to compile and link LAMMPS as
indicated above, producing (by default) an executable called "lmp" and
a library called "liblammps.a" in the "build" folder. When generating
a build environment for the "Ninja" build tool, the build command would
be "ninja" instead of "make".
If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local

2
doc/src/Commands_all.txt
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@ -50,11 +50,11 @@ An alphabetic list of all general LAMMPS commands.
"dump"_dump.html,
"dump adios"_dump_adios.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"dump movie"_dump_image.html,
"dump netcdf"_dump_netcdf.html,
"dump netcdf/mpiio"_dump_netcdf.html,
"dump vtk"_dump_vtk.html,
"dump_modify"_dump_modify.html,
"dynamical_matrix"_dynamical_matrix.html,
"echo"_echo.html,
"fix"_fix.html,

2
doc/src/Commands_pair.txt
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@ -222,6 +222,8 @@ OPT.
"sph/rhosum"_pair_sph_rhosum.html,
"sph/taitwater"_pair_sph_taitwater.html,
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
"spin/dipole/cut"_pair_spin_dipole.html,
"spin/dipole/long"_pair_spin_dipole.html,
"spin/dmi"_pair_spin_dmi.html,
"spin/exchange"_pair_spin_exchange.html,
"spin/magelec"_pair_spin_magelec.html,

15
doc/src/Eqs/angle_class2_p6.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
$$
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

15
doc/src/Eqs/angle_cosine_buck6d.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
$$
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

15
doc/src/Eqs/improper_inversion_harmonic.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K \left(\theta - \theta_0\right)^2
$$
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

18
doc/src/Eqs/pair_agni.tex Normal file
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@ -0,0 +1,18 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
\begin{eqnarray*}
F_i^u & = & \sum_t^{N_t}\alpha_t \cdot \exp\left[-\frac{\left(d_{i,t}^u\right)^2}{2l^2}\right] \\
d_{i,t}^u & = & \left|\left| V_i^u(\eta) - V_t^u(\eta) \right|\right| \\
V_i^u(\eta) & = & \sum_{j \neq i}\frac{r^u_{ij}}{r_{ij}} \cdot e^{-\left(\frac{r_{ij}}{\eta} \right)^2} \cdot f_d\left(r_{ij}\right) \\
f_d\left(r_{ij}\right) & = & \frac{1}{2} \left[\cos\left(\frac{\pi r_{ij}}{R_c}\right) + 1 \right]
\end{eqnarray*}
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

1
doc/src/Eqs/pair_buck6d.txt → doc/src/Eqs/pair_buck6d.tex
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@ -1,6 +1,7 @@
\documentclass[12pt]{article}
\begin{document}
\pagestyle{empty}
\begin{eqnarray*}
E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\

15
doc/src/Eqs/pair_coul_gauss.tex Normal file
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@ -0,0 +1,15 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
$$
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

5
doc/src/Errors_messages.txt
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@ -5890,6 +5890,11 @@ The element names in the ADP file do not match those requested. :dd
The element names in the EAM file do not match those requested. :dd
{Incorrect format of ... section in data file} :dt
Number or type of values per line in the given section of the data file
is not consistent with the requirements for this section. :dd
{Incorrect format in COMB potential file} :dt
Incorrect number of words per line in the potential file. :dd

31
doc/src/Install_linux.txt
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@ -15,7 +15,8 @@ Binaries are available for different versions of Linux:
"Pre-built Fedora Linux executables"_#fedora
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
"Pre-built OpenSuse Linux executables"_#opensuse
"Gentoo Linux executable"_#gentoo :all(b)
"Gentoo Linux executable"_#gentoo
"Arch Linux build-script"_#arch :all(b)
:line
@ -168,3 +169,31 @@ for details.
Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up
this Gentoo capability.
:line
Archlinux build-script :h4,link(arch)
LAMMPS is available via Arch's unofficial Arch User repository (AUR).
There are three scripts available, named lammps, lammps-beta and lammps-git.
They respectively package the stable, patch and git releases.
To install, you will need to have the git package installed. You may use
any of the above names in-place of lammps.
$ git clone https://aur.archlinux.org/lammps.git :pre
$ cd lammps :pre
$ makepkg -s :pre
# makepkg -i :pre
To update, you may repeat the above, or change into the cloned directory,
and execute the following, after which, if there are any changes, you may
use makepkg as above.
$ git pull :pre
Alternatively, you may use an AUR helper to install these packages.
Note that the AUR provides build-scripts that download the source and
the build the package on your machine.

0
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="5 Jun 2019 version">
<META NAME="docnumber" CONTENT="19 Jul 2019 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
5 Jun 2019 version :c,h2
19 Jul 2019 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

BIN
doc/src/PDF/USER-CGDNA.pdf
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2
doc/src/Packages_details.txt
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@ -911,6 +911,8 @@ the usual manner via MD. Various pair, fix, and compute styles.
src/SPIN: filenames -> commands
"Howto spins"_Howto_spins.html
"pair_style spin/dipole/cut"_pair_spin_dipole.html
"pair_style spin/dipole/long"_pair_spin_dipole.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html

24
doc/src/Speed_kokkos.txt
View File

@ -46,16 +46,15 @@ software version 7.5 or later must be installed on your system. See
the discussion for the "GPU package"_Speed_gpu.html for details of how
to check and do this.
NOTE: Kokkos with CUDA currently implicitly assumes that the MPI
library is CUDA-aware and has support for GPU-direct. This is not
always the case, especially when using pre-compiled MPI libraries
provided by a Linux distribution. This is not a problem when using
only a single GPU and a single MPI rank on a desktop. When running
with multiple MPI ranks, you may see segmentation faults without
GPU-direct support. These can be avoided by adding the flags "-pk
kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or
by using the command "package kokkos gpu/direct off"_package.html in
the input file.
NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
is CUDA-aware. This is not always the case, especially when using
pre-compiled MPI libraries provided by a Linux distribution. This is not
a problem when using only a single GPU with a single MPI rank. When
running with multiple MPI ranks, you may see segmentation faults without
CUDA-aware MPI support. These can be avoided by adding the flags "-pk
kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
using the command "package kokkos cuda/aware off"_package.html in the
input file.
[Building LAMMPS with the KOKKOS package:]
@ -217,9 +216,8 @@ case, also packing/unpacking communication buffers on the host may give
speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
is recommended in this scenario.
Using a CUDA-aware MPI library with
support for GPU-direct is highly recommended. GPU-direct use can be
avoided by using "-pk kokkos gpu/direct no"_package.html. As above for
Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
avoided by using "-pk kokkos cuda/aware no"_package.html. As above for
multi-core CPUs (and no GPU), if N is the number of physical cores/node,
then the number of MPI tasks/node should not exceed N.

10
doc/src/angle_table.txt
View File

@ -143,6 +143,16 @@ instructions on how to use the accelerated styles effectively.
:line
[Restart info:]
This angle style writes the settings for the "angle_style table"
command to "binary restart files"_restart.html, so a angle_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
angle_coeff commands do need to be specified in the restart input
script.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the

10
doc/src/bond_table.txt
View File

@ -140,6 +140,16 @@ instructions on how to use the accelerated styles effectively.
:line
[Restart info:]
This bond style writes the settings for the "bond_style table"
command to "binary restart files"_restart.html, so a bond_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
bond_coeff commands do need to be specified in the restart input
script.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE

89
doc/src/compute.txt
View File

@ -171,42 +171,40 @@ The individual style names on the "Commands
compute"_Commands_compute.html doc page are followed by one or more of
(g,i,k,o,t) to indicate which accelerated styles exist.
"ackland/atom"_compute_ackland_atom.html -
"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation
"adf"_compute_adf.html - angular distribution function of triples of atoms
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle"_compute_angle.html -
"angle/local"_compute_angle_local.html -
"angle/local"_compute_bond_local.html - theta and energy of each angle
"angle"_compute_angle.html - energy of each angle sub-style
"angle/local"_compute_angle_local.html - theta and energy of each angle
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
"basal/atom"_compute_basal_atom.html -
"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
"body/local"_compute_body_local.html - attributes of body sub-particles
"bond"_compute_bond.html - values computed by a bond style
"bond"_compute_bond.html - energy of each bond sub-style
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"cnp/atom"_compute_cnp_atom.html -
"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom
"com"_compute_com.html - center-of-mass of group of atoms
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
"coord/atom"_compute_coord_atom.html - coordination number for each atom
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
"dihedral"_compute_dihedral.html -
"dihedral"_compute_dihedral.html - energy of each dihedral sub-style
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
"dipole/chunk"_compute_dipole_chunk.html -
"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk
"displace/atom"_compute_displace_atom.html - displacement of each atom
"dpd"_compute_dpd.html -
"dpd/atom"_compute_dpd_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html -
"entropy/atom"_compute_entropy_atom.html -
"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group
"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle
"event/displace"_compute_event_displace.html - detect event on atom displacement
"fep"_compute_fep.html -
"force/tally"_compute_tally.html -
@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
"heat/flux/tally"_compute_tally.html -
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
"improper"_compute_improper.html -
"improper"_compute_improper.html - energy of each improper sub-style
"improper/local"_compute_improper_local.html - angle of each improper
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
"ke"_compute_ke.html - translational kinetic energy
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
"ke/atom/eff"_compute_ke_atom_eff.html -
"ke/eff"_compute_ke_eff.html -
"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model
"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
"meso/e/atom"_compute_meso_e_atom.html -
"meso/rho/atom"_compute_meso_rho_atom.html -
"meso/t/atom"_compute_meso_t_atom.html -
"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
"msd"_compute_msd.html - mean-squared displacement of group of atoms
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of
"pe/tally"_compute_tally.html -
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
"pressure"_compute_pressure.html - total pressure and pressure tensor
"pressure/cylinder"_compute_pressure_cylinder.html -
"pressure/uef"_compute_pressure_uef.html -
"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
"ptm/atom"_compute_ptm_atom.html -
"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
"saed"_compute_saed.html -
"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes
"slice"_compute_slice.html - extract values from global vector or array
"smd/contact/radius"_compute_smd_contact_radius.html -
"smd/damage"_compute_smd_damage.html -
"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics
"smd/hourglass/error"_compute_smd_hourglass_error.html -
"smd/internal/energy"_compute_smd_internal_energy.html -
"smd/plastic/strain"_compute_smd_plastic_strain.html -
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
"smd/rho"_compute_smd_rho.html -
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics
"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics
"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics
"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
"smd/vol"_compute_smd_vol.html -
"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
"spin"_compute_spin.html -
"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"stress/mop"_compute_stress_mop.html -
"stress/mop/profile"_compute_stress_mop.html -
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
"stress/tally"_compute_tally.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/body"_compute_temp_body.html - temperature of body particles
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
"temp/cs"_compute_temp_cs.html -
"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
"temp/deform/eff"_compute_temp_deform_eff.html -
"temp/drude"_compute_temp_drude.html -
"temp/eff"_compute_temp_eff.html -
"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model
"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs
"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
"temp/region"_compute_temp_region.html - temperature of a region of atoms
"temp/region/eff"_compute_temp_region_eff.html -
"temp/rotate"_compute_temp_rotate.html -
"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model
"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
"temp/uef"_compute_temp_uef.html -
"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field
"ti"_compute_ti.html - thermodynamic integration free energy values
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
"xrd"_compute_xrd.html - :ul
"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul
[Restrictions:] none

2
doc/src/compute_tally.txt
View File

@ -88,6 +88,8 @@ potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term. Also
bonded or Kspace interactions do not contribute to this compute.
The computes in this package are not compatible with dynamic groups.
[Related commands:]
{compute group/group}_compute_group_group.html, {compute

10
doc/src/dihedral_table.txt
View File

@ -191,6 +191,16 @@ switch"_Run_options.html when you invoke LAMMPS, or you can use the
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart info:]
This dihedral style writes the settings for the "dihedral_style table"
command to "binary restart files"_restart.html, so a dihedral_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
dihedral_coeff commands do need to be specified in the restart input
script.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the

10
doc/src/dihedral_table_cut.txt
View File

@ -189,6 +189,16 @@ Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword.
[Restart info:]
This dihedral style writes the settings for the "dihedral_style table/cut"
command to "binary restart files"_restart.html, so a dihedral_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
dihedral_coeff commands do need to be specified in the restart input
script.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the

3
doc/src/if.txt
View File

@ -57,8 +57,7 @@ Boolean expression is FALSE, then no commands are executed.
The syntax for Boolean expressions is described below.
Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
command, except an "include"_include.html command, which is not
allowed. If the command is more than one word, it must enclosed in
command. If the command is more than one word, it must enclosed in
quotes, so it will be treated as a single argument, as in the examples
above.

2
doc/src/improper_fourier.txt
View File

@ -27,7 +27,7 @@ The {fourier} improper style uses the following potential:
where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
:c,image(Eqs/umbrella.jpg)
:c,image(JPG/umbrella.jpg)
If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.

2
doc/src/improper_inversion_harmonic.txt
View File

@ -28,7 +28,7 @@ where K is the force constant and omega is the angle evaluated for
all three axis-plane combinations centered around the atom I. For
the IL axis and the IJK plane omega looks as follows:
:c,image(Eqs/umbrella.jpg)
:c,image(JPG/umbrella.jpg)
Note that the {inversion/harmonic} angle term evaluation differs to
the "improper_umbrella"_improper_umbrella.html due to the cyclic

2
doc/src/improper_umbrella.txt
View File

@ -29,7 +29,7 @@ commonly referred to as a classic inversion and used in the
where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
:c,image(Eqs/umbrella.jpg)
:c,image(JPG/umbrella.jpg)
If omega0 = 0 the potential term has a minimum for the planar
structure. Otherwise it has two minima at +/- omega0, with a barrier

1
doc/src/lammps.book
View File

@ -647,6 +647,7 @@ pair_sph_lj.html
pair_sph_rhosum.html
pair_sph_taitwater.html
pair_sph_taitwater_morris.html
pair_spin_dipole.html
pair_spin_dmi.html
pair_spin_exchange.html
pair_spin_magelec.html

28
doc/src/package.txt
View File

@ -64,7 +64,7 @@ args = arguments specific to the style :l
{no_affinity} values = none
{kokkos} args = keyword value ...
zero or more keyword/value pairs may be appended
keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct}
keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware}
{neigh} value = {full} or {half}
full = full neighbor list
half = half neighbor list built in thread-safe manner
@ -87,9 +87,9 @@ args = arguments specific to the style :l
no = perform communication pack/unpack in non-KOKKOS mode
host = perform pack/unpack on host (e.g. with OpenMP threading)
device = perform pack/unpack on device (e.g. on GPU)
{gpu/direct} = {off} or {on}
off = do not use GPU-direct
on = use GPU-direct (default)
{cuda/aware} = {off} or {on}
off = do not use CUDA-aware MPI
on = use CUDA-aware MPI (default)
{omp} args = Nthreads keyword value ...
Nthread = # of OpenMP threads to associate with each MPI process
zero or more keyword/value pairs may be appended
@ -520,19 +520,21 @@ pack/unpack communicated data. When running small systems on a GPU,
performing the exchange pack/unpack on the host CPU can give speedup
since it reduces the number of CUDA kernel launches.
The {gpu/direct} keyword chooses whether GPU-direct will be used. When
The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When
this keyword is set to {on}, buffers in GPU memory are passed directly
through MPI send/receive calls. This reduces overhead of first copying
the data to the host CPU. However GPU-direct is not supported on all
the data to the host CPU. However CUDA-aware MPI is not supported on all
systems, which can lead to segmentation faults and would require using a
value of {off}. If LAMMPS can safely detect that GPU-direct is not
value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not
available (currently only possible with OpenMPI v2.0.0 or later), then
the {gpu/direct} keyword is automatically set to {off} by default. When
the {gpu/direct} keyword is set to {off} while any of the {comm}
the {cuda/aware} keyword is automatically set to {off} by default. When
the {cuda/aware} keyword is set to {off} while any of the {comm}
keywords are set to {device}, the value for these {comm} keywords will
be automatically changed to {host}. This setting has no effect if not
running on GPUs. GPU-direct is available for OpenMPI 1.8 (or later
versions), Mvapich2 1.9 (or later), and CrayMPI.
running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment
variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
flag is used.
:line
@ -641,8 +643,8 @@ switch"_Run_options.html.
For the KOKKOS package, the option defaults for GPUs are neigh = full,
neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
value, comm = device, gpu/direct = on. When LAMMPS can safely detect
that GPU-direct is not available, the default value of gpu/direct
value, comm = device, cuda/aware = on. When LAMMPS can safely detect
that CUDA-aware MPI is not available, the default value of cuda/aware
becomes "off". For CPUs or Xeon Phis, the option defaults are neigh =
half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
option neigh/thread = on when there are 16K atoms or less on an MPI

2
doc/src/pair_class2.txt
View File

@ -155,7 +155,7 @@ All of the lj/class2 pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
Only the {lj/class2} pair style support the use of the
Only the {lj/class2} and {lj/class2/coul/long} pair styles support the use of the
{inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.

2
doc/src/pair_hbond_dreiding.txt
View File

@ -46,7 +46,7 @@ Here, {r} is the radial distance between the donor (D) and acceptor
(A) atoms and {theta} is the bond angle between the acceptor, the
hydrogen (H) and the donor atoms:
:c,image(Eqs/dreiding_hbond.jpg)
:c,image(JPG/dreiding_hbond.jpg)
These 3-body interactions can be defined for pairs of acceptor and
donor atoms, based on atom types. For each donor/acceptor atom pair,

3
doc/src/pair_meamc.txt
View File

@ -147,7 +147,8 @@ asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
parameters are the standard beta parameters). The rozero parameter is
parameters are the standard beta parameters). Note that only parameters
normalized to t0 = 1.0 are supported. The rozero parameter is
an element-dependent density scaling that weights the reference
background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
is typically 1.0 for single-element systems. The ibar parameter

10
doc/src/pair_modify.txt
View File

@ -13,7 +13,8 @@ pair_modify command :h3
pair_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
{pair} values = sub-style N {special} which wt1 wt2 wt3
or sub-style N {compute/tally} flag
sub-style = sub-style of "pair hybrid"_pair_hybrid.html
@ -33,7 +34,8 @@ keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or
{tabinner/disp} value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
{tail} value = {yes} or {no}
{compute} value = {yes} or {no} :pre
{compute} value = {yes} or {no}
{nofdotr} :pre
:ule
[Examples:]
@ -212,6 +214,10 @@ a pair style will not work, because the
"kspace_style"_kspace_style.html command requires a Kspace-compatible
pair style be defined.
The {nofdotr} keyword allows to disable an optimization that computes
the global stress tensor from the total forces and atom positions rather
than from summing forces between individual pairs of atoms.
:line
The {special} keyword allows to override the 1-2, 1-3, and 1-4

8
doc/src/pair_oxdna.txt
View File

@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
args = list of arguments for these particular styles :ul
{oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = temperature-independent coefficient in stacking strength
kappa = coefficient of linear temperature dependence in stacking strength
{oxdna/hbond} args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond 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 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -62,7 +64,7 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

12
doc/src/pair_oxdna2.txt
View File

@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
args = list of arguments for these particular styles :ul
{oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
{oxdna/hbond} args = seq eps 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
xi = temperature-independent coefficient in stacking strength
kappa = coefficient of linear temperature dependence in stacking strength
{oxdna2/hbond} args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
{oxdna2/dh} args = T rhos qeff
@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul
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 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond 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
@ -68,8 +70,8 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
the temperature coefficients have to be matched to the one used in the fix.

6
doc/src/pair_spin_dipole.txt
View File

@ -81,9 +81,3 @@ currently supported.
"fix nve/spin"_fix_nve_spin.html
[Default:] none
:line
:link(Allen2)
[(Allen)] Allen and Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.

2
doc/src/pair_style.txt
View File

@ -284,6 +284,8 @@ accelerated styles exist.
"sph/rhosum"_pair_sph_rhosum.html -
"sph/taitwater"_pair_sph_taitwater.html -
"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
"spin/dipole/cut"_pair_spin_dipole.html -
"spin/dipole/long"_pair_spin_dipole.html -
"spin/dmi"_pair_spin_dmi.html -
"spin/exchange"_pair_spin_exchange.html -
"spin/magelec"_pair_spin_magelec.html -

1
doc/src/pairs.txt
View File

@ -105,6 +105,7 @@ Pair Styles :h1
pair_sph_rhosum
pair_sph_taitwater
pair_sph_taitwater_morris
pair_spin_dipole
pair_spin_dmi
pair_spin_exchange
pair_spin_magelec

3
doc/src/read_data.txt
View File

@ -565,6 +565,7 @@ molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z
sphere: atom-ID atom-type diameter density x y z
spin: atom-ID atom-type sp x y z spx spy spz
template: atom-ID molecule-ID template-index template-atom atom-type x y z
tri: atom-ID molecule-ID atom-type triangleflag density x y z
wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
@ -595,6 +596,8 @@ mux,muy,muz = components of dipole moment of atom (dipole units)
q = charge on atom (charge units)
rho = density (need units) for SPH particles
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
sp = norm of magnetic spin of atom (in number of Bohr magnetons)
spx,spy,spz = components of magnetic spin of atom (adim normalized vector)
template-atom = which atom within a template molecule the atom is
template-index = which molecule within the molecule template the atom is part of
theta = internal temperature of a DPD particle

13
doc/utils/sphinx-config/_themes/lammps_theme/static/css/theme.css
View File

@ -5092,4 +5092,17 @@ span[id*='MathJax-Span'] {
src: local("Roboto Slab Bold"), local("RobotoSlab-Bold"), url(../fonts/RobotoSlab-Bold.ttf) format("truetype");
}
.codeblock, pre.literal-block, .rst-content .literal-block, .rst-content pre.literal-block, div[class^='highlight'] {
font-size: 12px;
line-height: 1.5;
display: block;
overflow: auto;
color: #404040;
padding: 12px 12px;
}
.codeblock,div[class^='highlight'] {
padding: 0;
}
/*# sourceMappingURL=theme.css.map */

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -101,6 +101,7 @@ api
Appl
Apu
arccos
Archlinux
arcsin
arg
args
@ -1520,6 +1521,7 @@ Magdeburg
magelec
Maginn
magneton
magnetons
mainboard
mainboards
makefile
@ -1527,6 +1529,7 @@ Makefile
makefiles
Makefiles
makelist
makepkg
Makse
malloc
Malolepsza

11
examples/USER/cgdna/README
View File

@ -22,6 +22,17 @@ A - C - G - T - A - C - G - T
| | | | | | | |
T - G - C - A T - G - C - A
/examples/duplex3:
This is basically the duplex1 run with sequence-dependent stacking
and hydrogen-bonding strengths enabled and both nucleotide mass and
moment of inertia set to the value of the standalone implementation
of oxDNA (M = I = 1). To achieve this, the masses can be set directly
in the input and data file, whereas the moment of inertia is set via
the diameter of the ellipsoid in the data file and has a value of 3.16227766.
The change of mass and moment of inertia allows direct comparision of
e.g. trajectory data, energies or time-dependent observables on a per-timestep
basis until numerical noise causes deviations at later simulation times.
/util:
This directory contains a simple python setup tool which creates
single straight or helical DNA strands, DNA duplexes or arrays of DNA

2
examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1
View File

@ -32,7 +32,7 @@ Atoms
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
# Atom-ID, translational, rotational velocity
# Atom-ID, translational velocity, angular momentum
Velocities
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

9
examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
View File

@ -1,6 +1,7 @@
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
timestep 1e-5
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
run 1000000
#write_restart config.${number}.*

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172
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@ -1,172 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
Performance: 60875.649 tau/day, 70457.927 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
Other | | 0.002982 | | | 2.10
Nlocal: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 43 ave 43 max 43 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43
Ave neighs/atom = 4.3
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

172
examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4
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@ -1,172 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
Performance: 64220.659 tau/day, 74329.466 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
Other | | 0.05989 | | | 44.52
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 7.5 ave 10 max 5 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 17.5 ave 33 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 70
Ave neighs/atom = 7
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2
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@ -38,7 +38,7 @@ Atoms
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
# Atom-ID, translational, rotational velocity
# Atom-ID, translational velocity, angular momentum
Velocities
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

9
examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
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@ -1,6 +1,7 @@
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
timestep 1e-5
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
run 1000000
#write_restart config.${number}.*

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@ -1,172 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
Performance: 29234.801 tau/day, 33836.575 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
Other | | 0.003813 | | | 1.29
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 88 ave 88 max 88 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 88
Ave neighs/atom = 5.5
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

172
examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4
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@ -1,172 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
Performance: 34303.820 tau/day, 39703.495 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
Other | | 0.1208 | | | 47.96
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 9 ave 10 max 8 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 34.5 ave 67 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 138
Ave neighs/atom = 8.625
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1
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@ -32,7 +32,7 @@ Atoms
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
# Atom-ID, translational, rotational velocity
# Atom-ID, translational velocity, angular momentum
Velocities
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

11
examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
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@ -1,6 +1,7 @@
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
@ -30,19 +31,19 @@ bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
timestep 1e-5
@ -73,6 +74,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
run 1000000
#write_restart config.${number}.*

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@ -1,178 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
Performance: 57828.835 tau/day, 66931.522 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
Other | | 0.004268 | | | 2.86
Nlocal: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45
Ave neighs/atom = 4.5
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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@ -1,178 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
Performance: 59247.054 tau/day, 68572.979 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
Other | | 0.06674 | | | 45.76
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 7.5 ave 10 max 5 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 18.5 ave 35 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 74
Ave neighs/atom = 7.4
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2
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@ -38,7 +38,7 @@ Atoms
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
# Atom-ID, translational, rotational velocity
# Atom-ID, translational velocity, angular momentum
Velocities
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

12
examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
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@ -1,7 +1,7 @@
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
dimension 3
@ -30,19 +30,19 @@ bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
timestep 1e-5
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
run 1000000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
Performance: 26356.746 tau/day, 30505.493 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
Other | | 0.003398 | | | 1.04
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 116 ave 116 max 116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 116
Ave neighs/atom = 7.25
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
Performance: 29625.313 tau/day, 34288.557 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
Other | | 0.139 | | | 47.65
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11 ave 14 max 8 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 46 ave 89 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 184
Ave neighs/atom = 11.5
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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@ -0,0 +1,73 @@
# LAMMPS data file
10 atoms
10 ellipsoids
8 bonds
4 atom types
1 bond types
# System size
-20.000000 20.000000 xlo xhi
-20.000000 20.000000 ylo yhi
-20.000000 20.000000 zlo zhi
Masses
1 1.0
2 1.0
3 1.0
4 1.0
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
Atoms
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
# Atom-ID, translational velocity, angular momentum
Velocities
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
# Atom-ID, shape, quaternion
Ellipsoids
1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
# Bond topology
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 6 7
6 1 7 8
7 1 8 9
8 1 9 10

79
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@ -0,0 +1,79 @@
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex3
set atom * mass 1.0
group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond 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} 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
#write_restart config.${number}.*

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1
examples/USER/misc/kolmogorov_crespi_full/CH.rebo Symbolic link
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@ -0,0 +1 @@
../../../../potentials/CH.rebo

2
examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
View File

@ -18,7 +18,7 @@ group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * rebo CH.rebo NULL C # chemical
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings

51
examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1 → examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (8 Mar 2018)
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000353813 secs
read_data CPU = 0.0043292 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
@ -32,8 +35,8 @@ group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * rebo CH.rebo NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings
@ -92,32 +95,32 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms
0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393292 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
900 -5025.3984547937 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 103.724 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.833 ns/day, 28.812 hours/ns, 9.641 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 | 155.99 | 155.99 | 155.99 | 0.0 | 99.90
Bond | 0.00075769 | 0.00075769 | 0.00075769 | 0.0 | 0.00
Pair | 103.59 | 103.59 | 103.59 | 0.0 | 99.87
Bond | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.084217 | 0.084217 | 0.084217 | 0.0 | 0.05
Output | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.00
Modify | 0.034797 | 0.034797 | 0.034797 | 0.0 | 0.02
Other | | 0.02838 | | | 0.02
Comm | 0.082476 | 0.082476 | 0.082476 | 0.0 | 0.08
Output | 0.0010884 | 0.0010884 | 0.0010884 | 0.0 | 0.00
Modify | 0.032938 | 0.032938 | 0.032938 | 0.0 | 0.03
Other | | 0.01749 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -133,4 +136,4 @@ Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:36
Total wall time: 0:01:43

51
examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4 → examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (8 Mar 2018)
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000187874 secs
read_data CPU = 0.00234103 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
@ -32,8 +35,8 @@ group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * rebo CH.rebo NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings
@ -92,32 +95,32 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms
0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393291 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
900 -5025.3984547938 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 33.7338 on 4 procs for 1000 steps with 1360 atoms
Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 2.561 ns/day, 9.370 hours/ns, 29.644 timesteps/s
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 39.928 | 40.992 | 42.377 | 15.8 | 96.36
Bond | 0.0003643 | 0.00043392 | 0.00048113 | 0.0 | 0.00
Pair | 30.833 | 31.356 | 32.18 | 9.1 | 92.95
Bond | 0.00026059 | 0.00029182 | 0.00031185 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.12253 | 1.5076 | 2.5698 | 82.1 | 3.54
Output | 0.0012577 | 0.0013637 | 0.0016453 | 0.4 | 0.00
Modify | 0.010833 | 0.012247 | 0.013317 | 0.9 | 0.03
Other | | 0.02864 | | | 0.07
Comm | 1.443 | 2.2722 | 2.8091 | 34.3 | 6.74
Output | 0.00068855 | 0.00095087 | 0.0017185 | 0.0 | 0.00
Modify | 0.010187 | 0.011709 | 0.015284 | 1.9 | 0.03
Other | | 0.09241 | | | 0.27
Nlocal: 340 ave 344 max 334 min
Histogram: 1 0 0 0 0 0 1 0 1 1
@ -133,4 +136,4 @@ Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:42
Total wall time: 0:00:33

4
lib/gpu/lal_answer.cpp
View File

@ -15,7 +15,7 @@
#include "lal_answer.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define AnswerT Answer<numtyp,acctyp>
template <class numtyp, class acctyp>
@ -311,4 +311,4 @@ void AnswerT::cq(const int cq_index) {
}
template class Answer<PRECISION,ACC_PRECISION>;
}

4
lib/gpu/lal_atom.cpp
View File

@ -15,7 +15,7 @@
#include "lal_atom.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define AtomT Atom<numtyp,acctyp>
template <class numtyp, class acctyp>
@ -349,4 +349,4 @@ void AtomT::compile_kernels(UCL_Device &dev) {
#endif
template class Atom<PRECISION,ACC_PRECISION>;
}

5
lib/gpu/lal_base_atomic.cpp
View File

@ -14,7 +14,8 @@
***************************************************************************/
#include "lal_base_atomic.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BaseAtomicT BaseAtomic<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
@ -285,4 +286,4 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str,
}
template class BaseAtomic<PRECISION,ACC_PRECISION>;
}

4
lib/gpu/lal_base_charge.cpp
View File

@ -15,7 +15,7 @@
***************************************************************************/
#include "lal_base_charge.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BaseChargeT BaseCharge<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
@ -302,4 +302,4 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str,
}
template class BaseCharge<PRECISION,ACC_PRECISION>;
}

4
lib/gpu/lal_base_dipole.cpp
View File

@ -15,7 +15,7 @@
***************************************************************************/
#include "lal_base_dipole.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BaseDipoleT BaseDipole<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
@ -311,4 +311,4 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str,
}
template class BaseDipole<PRECISION,ACC_PRECISION>;
}

4
lib/gpu/lal_base_dpd.cpp
View File

@ -15,7 +15,7 @@
***************************************************************************/
#include "lal_base_dpd.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BaseDPDT BaseDPD<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
@ -308,4 +308,4 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str,
}
template class BaseDPD<PRECISION,ACC_PRECISION>;
}

4
lib/gpu/lal_base_ellipsoid.cpp
View File

@ -15,7 +15,7 @@
#include "lal_base_ellipsoid.h"
#include <cstdlib>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#if defined(USE_OPENCL)
#include "ellipsoid_nbor_cl.h"
@ -488,4 +488,4 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev,
}
template class BaseEllipsoid<PRECISION,ACC_PRECISION>;
}

4
lib/gpu/lal_base_three.cpp
View File

@ -14,7 +14,7 @@
***************************************************************************/
#include "lal_base_three.h"
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BaseThreeT BaseThree<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
@ -397,4 +397,4 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str,
}
template class BaseThree<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_beck.cpp
View File

@ -23,7 +23,7 @@ const char *beck=0;
#include "lal_beck.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BeckT Beck<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -150,3 +150,4 @@ void BeckT::loop(const bool _eflag, const bool _vflag) {
}
template class Beck<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_born.cpp
View File

@ -23,7 +23,7 @@ const char *born=0;
#include "lal_born.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BornT Born<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -179,3 +179,4 @@ void BornT::loop(const bool _eflag, const bool _vflag) {
}
template class Born<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_born_coul_long.cpp
View File

@ -23,7 +23,7 @@ const char *born_coul_long=0;
#include "lal_born_coul_long.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BornCoulLongT BornCoulLong<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -173,3 +173,4 @@ void BornCoulLongT::loop(const bool _eflag, const bool _vflag) {
}
template class BornCoulLong<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_born_coul_long_cs.cpp
View File

@ -23,7 +23,7 @@ const char *born_coul_long_cs=0;
#include "lal_born_coul_long_cs.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BornCoulLongCST BornCoulLongCS<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -93,3 +93,4 @@ int BornCoulLongCST::init(const int ntypes, double **host_cutsq, double **host_r
}
template class BornCoulLongCS<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_born_coul_wolf.cpp
View File

@ -23,7 +23,7 @@ const char *born_coul_wolf=0;
#include "lal_born_coul_wolf.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BornCoulWolfT BornCoulWolf<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -174,3 +174,4 @@ void BornCoulWolfT::loop(const bool _eflag, const bool _vflag) {
}
template class BornCoulWolf<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_born_coul_wolf_cs.cpp
View File

@ -23,7 +23,7 @@ const char *born_coul_wolf_cs=0;
#include "lal_born_coul_wolf_cs.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BornCoulWolfCST BornCoulWolfCS<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -95,3 +95,4 @@ int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_r
}
template class BornCoulWolfCS<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_buck.cpp
View File

@ -23,7 +23,7 @@ const char *buck=0;
#include "lal_buck.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BuckT Buck<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -168,3 +168,4 @@ void BuckT::loop(const bool _eflag, const bool _vflag) {
}
template class Buck<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_buck_coul.cpp
View File

@ -23,7 +23,7 @@ const char *buck_coul=0;
#include "lal_buck_coul.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BuckCoulT BuckCoul<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -161,3 +161,4 @@ void BuckCoulT::loop(const bool _eflag, const bool _vflag) {
}
template class BuckCoul<PRECISION,ACC_PRECISION>;
}

3
lib/gpu/lal_buck_coul_long.cpp
View File

@ -23,7 +23,7 @@ const char *buck_coul_long=0;
#include "lal_buck_coul_long.h"
#include <cassert>
using namespace LAMMPS_AL;
namespace LAMMPS_AL {
#define BuckCoulLongT BuckCoulLong<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> device;
@ -166,3 +166,4 @@ void BuckCoulLongT::loop(const bool _eflag, const bool _vflag) {
}
template class BuckCoulLong<PRECISION,ACC_PRECISION>;
}

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