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Merge branch 'master' into kim-simulator-models

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# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
This commit is contained in:
Axel Kohlmeyer
2019-07-29 20:43:10 -04:00
parent c03e9c9711 2e6850835f
commit 6833d6def6
1474 changed files with 3992 additions and 5934 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
cmake/CMakeLists.txt
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@ -497,10 +497,44 @@ if(BUILD_LIB)
if(LAMMPS_DEPS) if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS}) add_dependencies(lammps ${LAMMPS_DEPS})
endif() endif()
set(LAMMPS_CXX_HEADERS
angle.h
atom.h
bond.h
citeme.h
comm.h
compute.h
dihedral.h
domain.h
error.h
fix.h
force.h
group.h
improper.h
input.h
kspace.h
lammps.h
lattice.h
lmppython.h
memory.h
modify.h
neighbor.h
neigh_list.h
output.h
pair.h
pointers.h
region.h
timer.h
universe.h
update.h
variable.h)
list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/)
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
@ -551,11 +585,11 @@ include(Documentation)
############################################################################### ###############################################################################
# Install potential and force field files in data directory # Install potential and force field files in data directory
############################################################################### ###############################################################################
set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR}) install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
if(BUILD_TOOLS)
set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files) install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR}) endif()
configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)

4
cmake/etc/profile.d/lammps.csh.in
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@ -1,4 +1,4 @@
# set environment for LAMMPS and msi2lmp executables # set environment for LAMMPS and msi2lmp executables
# to find potential and force field files # to find potential and force field files
if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@ if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files

4
cmake/etc/profile.d/lammps.sh.in
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@ -1,5 +1,5 @@
# set environment for LAMMPS and msi2lmp executables # set environment for LAMMPS and msi2lmp executables
# to find potential and force field files # to find potential and force field files
LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@} MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
export LAMMPS_POTENTIALS MSI2LMP_LIBRARY export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

133
doc/include-file-conventions.md Normal file
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@ -0,0 +1,133 @@
# Outline of include file conventions in LAMMPS
This purpose of this document is to provide a point of reference
for LAMMPS developers and contributors as to what include files
and definitions to put where into LAMMPS source.
Last change 2019-07-05
## Table of Contents
* [Motivation](#motivation)
* [Rules](#rules)
* [Tools](#tools)
* [Legacy Code](#legacy-code)
## Motivation
The conventions outlined in this document are supposed to help make
maintenance of the LAMMPS software easier. By trying to achieve
consistency across files contributed by different developers, it will
become easier for the code maintainers to modify and adjust files and,
overall, the chance for errors or portability issues will be reduced.
The rules employed are supposed to minimize naming conflicts and
simplify dependencies between files and thus speed up compilation. They
may, as well, make otherwise hidden dependencies visible.
## Rules
Below are the various rules that are applied. Not all are enforced
strictly and automatically. If there are no significant side effects,
exceptions may be possible for cases where a full compliance to the
rules may require a large effort compared to the benefit.
### Core Files Versus Package Files
All rules listed below are most strictly observed for core LAMMPS files,
which are the files that are not part of a package, and the files of the
packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of
the spectrum are USER packages and legacy packages that predate these
rules and thus may not be fully compliant. Also, new contributions
will be checked more closely, while existing code will be incrementally
adapted to the rules as time and required effort permits.
### System Versus Local Header Files
All system- or library-provided include files are included with angular
brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
include files provided with LAMMPS are included with double quotes
(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
For headers declaring functions of the C-library, the corresponding
C++ versions should be included (examples: `#include <cstdlib>` or
`#include <cctypes>`). However, these includes are limited to those defined
in the C++98 standard. Some files thus must use the older style until
the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
or `#include <inttypes.h>` versus `#include <cinttypes>`).
### C++ Standard Compliance
LAMMPS core files currently correspond to the C++98 standard. Files
requiring C++11 or later are only permitted in (optional) packages
and particularly packages that are not part of the list of commonly
used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
Since using both at the same time can cause problems, iostreams should
be avoided where possible.
### Lean Header Files
Header files will typically contain the definition of a (single) class.
These header files should have as few include statements as possible.
This is particularly important for classes that implement a "style" and
thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
all be included in the auto-generated `"some_style.h"` files which
results in a high potential for direct or indirect symbol name clashes.
In the ideal case, the header would only include one file defining the
parent class. That would typically be either `#include "pointers.h"` for
the `Pointers` class, or a header of a class derived from it like
`#include "pair.h"` for the `Pair` class and so on. References to other
classes inside the class should be make through pointers, for which forward
declarations (inside the `LAMMPS_NS` or the new class' namespace) can
be employed. The full definition will then be included into the corresponding
implementation file. In the given example from above, the header file
would be called `some_name.h` and the implementation `some_name.cpp` (all
lower case with underscores, while the class itself would be in camel case
and no underscores `SomeName`, and the style name with lower case names separated by
a forward slash).
### Implementation Files
In the implementation files (typically, those would have the same base name
as the corresponding header with a .cpp extension instead of .h) include
statements should follow the "include what you use" principle.
### Order of Include Statements
Include files should be included in this order:
* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
* mpi.h
* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
* LAMMPS local headers (preferably in alphabetical order)
### Special Cases and Exceptions
#### pointers.h
The `pointer.h` header file also includes `cstdio` and `lmptype.h`
(and through it `stdint.h`, `intttypes.h`, and `climits`).
This means any header including `pointers.h` can assume that `FILE`,
`NULL`, `INT_MAX` are defined.
## Tools
The [Include What You Use tool](https://include-what-you-use.org/)
can be used to provide supporting information about compliance with
the rules listed here. There are some limitations and the IWYU tool
may give incorrect advice. The tools is activated by setting the
CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
path of the `include-what-you-use` command. When activated, the
tool will be run after each compilation and provide suggestions for
which include files should be added or removed.
## Legacy Code
A lot of code predates the application of the rules in this document
and the rules themselves are a moving target. So there are going to be
significant chunks of code that do not fully comply. This applies
for example to the USER-REAXC, or the USER-ATC package. The LAMMPS
developers are dedicated to make an effort to improve the compliance
and welcome volunteers wanting to help with the process.

10
doc/src/Build_cmake.txt
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@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up repeated compilation ccache (= Compiler Cache) software may speed up repeated compilation
even more. even more.
After compilation, you can optionally copy the LAMMPS executable and After compilation, you may optionally install the LAMMPS executable into
library into your system folders (by default under $HOME/.local) with: your system with:
make install # optional, copy LAMMPS executable & library elsewhere :pre make install # optional, copy LAMMPS executable & library elsewhere :pre
This will install the lammps executable and library (if requested), some
tools (if configured) and additional files like library API headers,
manpages, potential and force field files. The location of the installation
tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
to $\{HOME\}/.local
:line :line
There are 3 variants of CMake: a command-line version (cmake), a text mode There are 3 variants of CMake: a command-line version (cmake), a text mode

10
doc/src/Errors_warnings.txt
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@ -129,6 +129,16 @@ Self-explanatory. :dd
Self-explanatory. :dd Self-explanatory. :dd
{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt
The communication cutoff defaults to the maximum of what is inferred from
pair and bond styles (will be zero, if none are defined) and what is specified
via "comm_modify cutoff"_comm_modify.html (defaults to 0.0). If this results
to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
incorrect periodic images of atoms in interaction lists. To avoid, either use
"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify
cutoff"_comm_modify.html. :dd
{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
Self-explanatory. :dd Self-explanatory. :dd

24
doc/src/Speed_kokkos.txt
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@ -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 the discussion for the "GPU package"_Speed_gpu.html for details of how
to check and do this. to check and do this.
NOTE: Kokkos with CUDA currently implicitly assumes that the MPI NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
library is CUDA-aware and has support for GPU-direct. This is not is CUDA-aware. This is not always the case, especially when using
always the case, especially when using pre-compiled MPI libraries pre-compiled MPI libraries provided by a Linux distribution. This is not
provided by a Linux distribution. This is not a problem when using a problem when using only a single GPU with a single MPI rank. When
only a single GPU and a single MPI rank on a desktop. When running running with multiple MPI ranks, you may see segmentation faults without
with multiple MPI ranks, you may see segmentation faults without CUDA-aware MPI support. These can be avoided by adding the flags "-pk
GPU-direct support. These can be avoided by adding the flags "-pk kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or using the command "package kokkos cuda/aware off"_package.html in the
by using the command "package kokkos gpu/direct off"_package.html in input file.
the input file.
[Building LAMMPS with the KOKKOS package:] [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 speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
is recommended in this scenario. is recommended in this scenario.
Using a CUDA-aware MPI library with Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
support for GPU-direct is highly recommended. GPU-direct use can be avoided by using "-pk kokkos cuda/aware no"_package.html. As above for
avoided by using "-pk kokkos gpu/direct no"_package.html. As above for
multi-core CPUs (and no GPU), if N is the number of physical cores/node, 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. then the number of MPI tasks/node should not exceed N.

10
doc/src/angle_table.txt
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@ -143,6 +143,16 @@ instructions on how to use the accelerated styles effectively.
:line :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:] [Restrictions:]
This angle style can only be used if LAMMPS was built with the This angle style can only be used if LAMMPS was built with the

10
doc/src/bond_table.txt
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@ -140,6 +140,16 @@ instructions on how to use the accelerated styles effectively.
:line :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:] [Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE This bond style can only be used if LAMMPS was built with the MOLECULE

12
doc/src/comm_modify.txt
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@ -69,9 +69,15 @@ processors. By default the ghost cutoff = neighbor cutoff = pairwise
force cutoff + neighbor skin. See the "neighbor"_neighbor.html command force cutoff + neighbor skin. See the "neighbor"_neighbor.html command
for more information about the skin distance. If the specified Rcut is for more information about the skin distance. If the specified Rcut is
greater than the neighbor cutoff, then extra ghost atoms will be acquired. greater than the neighbor cutoff, then extra ghost atoms will be acquired.
If the provided cutoff is smaller, the provided value will be ignored If the provided cutoff is smaller, the provided value will be ignored,
and the ghost cutoff is set to the neighbor cutoff. Specifying a the ghost cutoff is set to the neighbor cutoff and a warning will be
cutoff value of 0.0 will reset any previous value to the default. printed. Specifying a cutoff value of 0.0 will reset any previous value
to the default. If bonded interactions exist and equilibrium bond length
information is available, then also a heuristic based on that bond length
is computed. It is used as communication cutoff, if there is no pair
style present and no {comm_modify cutoff} command used. Otherwise a
warning is printed, if this bond based estimate is larger than the
communication cutoff used. A
The {cutoff/multi} option is equivalent to {cutoff}, but applies to The {cutoff/multi} option is equivalent to {cutoff}, but applies to
communication mode {multi} instead. Since in this case the communication communication mode {multi} instead. Since in this case the communication

10
doc/src/dihedral_table.txt
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@ -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 See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively. 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:] [Restrictions:]
This dihedral style can only be used if LAMMPS was built with the This dihedral style can only be used if LAMMPS was built with the

10
doc/src/dihedral_table_cut.txt
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@ -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 potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword. 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:] [Restrictions:]
This dihedral style can only be used if LAMMPS was built with the This dihedral style can only be used if LAMMPS was built with the

48
doc/src/fix_bond_react.txt
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@ -24,7 +24,7 @@ common_keyword = {stabilization} :l
{stabilization} values = {no} or {yes} {group-ID} {xmax} {stabilization} values = {no} or {yes} {group-ID} {xmax}
{no} = no reaction site stabilization {no} = no reaction site stabilization
{yes} = perform reaction site stabilization {yes} = perform reaction site stabilization
{group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
{xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre
react = mandatory argument indicating new reaction specification :l react = mandatory argument indicating new reaction specification :l
react-ID = user-assigned name for the reaction :l react-ID = user-assigned name for the reaction :l
@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l
[Examples:] [Examples:]
For unabridged example scripts and files, see examples/USER/misc/bond_react.
molecule mol1 pre_reacted_topology.txt molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt molecule mol2 post_reacted_topology.txt
fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
@ -106,6 +108,20 @@ involved in any new reactions. The {xmax} value keyword should
typically be set to the maximum distance that non-reacting atoms move typically be set to the maximum distance that non-reacting atoms move
during the simulation. during the simulation.
Fix bond/react creates and maintains two important dynamic groups of
atoms when using the {stabilization} keyword. The first group contains
all atoms currently involved in a reaction; this group is
automatically thermostatted by an internally-created
"nve/limit"_fix_nve_limit.html integrator. The second group contains
all atoms currently not involved in a reaction. This group should be
used by a thermostat in order to time integrate the system. The name
of this group of non-reacting atoms is created by appending '_REACT'
to the group-ID argument of the {stabilization} keyword, as shown in
the second example above.
NOTE: When using reaction stabilization, you should generally not have
a separate thermostat which acts on the 'all' group.
The group-ID set using the {stabilization} keyword can be an existing The group-ID set using the {stabilization} keyword can be an existing
static group or a previously-unused group-ID. It cannot be specified static group or a previously-unused group-ID. It cannot be specified
as 'all'. If the group-ID is previously unused, the fix bond/react as 'all'. If the group-ID is previously unused, the fix bond/react
@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic
group is named by appending '_REACT' to the group-ID, e.g. group is named by appending '_REACT' to the group-ID, e.g.
nvt_grp_REACT. By specifying an existing group, you may thermostat nvt_grp_REACT. By specifying an existing group, you may thermostat
constant-topology parts of your system separately. The dynamic group constant-topology parts of your system separately. The dynamic group
contains only non-reacting atoms at a given timestep, and therefore contains only atoms not involved in a reaction at a given timestep,
should be used by a subsequent system-wide time integrator such as and therefore should be used by a subsequent system-wide time
nvt, npt, or nve, as shown in the second example above. The time integrator such as nvt, npt, or nve, as shown in the second example
integration command should be placed after the fix bond/react command above (full examples can be found at examples/USER/misc/bond_react).
due to the internal dynamic grouping performed by fix bond/react. The time integration command should be placed after the fix bond/react
command due to the internal dynamic grouping performed by fix
bond/react.
NOTE: If the group-ID is an existing static group, react-group-IDs NOTE: If the group-ID is an existing static group, react-group-IDs
should also be specified as this static group, or a subset. should also be specified as this static group, or a subset.
NOTE: If the group-ID is previously unused, the internally-created
group applies to all atoms in the system, i.e. you should generally
not have a separate thermostat which acts on the 'all' group, or any
other group.
The following comments pertain to each {react} argument (in other The following comments pertain to each {react} argument (in other
words, can be customized for each reaction, or reaction step): words, can be customized for each reaction, or reaction step):
@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction
by-products, this feature can be used to remove specific topologies, by-products, this feature can be used to remove specific topologies,
such as small rings, that may be otherwise indistinguishable. such as small rings, that may be otherwise indistinguishable.
Also, it may be beneficial to ensure reacting atoms are at a certain Optionally, you can enforce additional behaviors on reacting atoms.
temperature before being released to the overall thermostat. For this, For example, it may be beneficial to force reacting atoms to remain at
you can use the internally-created dynamic group named a certain temperature. For this, you can use the internally-created
"bond_react_MASTER_group." For example, adding the following command dynamic group named "bond_react_MASTER_group", which consists of all
would thermostat the group of all atoms currently involved in a atoms currently involved in a reaction. For example, adding the
reaction: following command would add an additional thermostat to the group of
all currently-reacting atoms:
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre

28
doc/src/package.txt
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@ -64,7 +64,7 @@ args = arguments specific to the style :l
{no_affinity} values = none {no_affinity} values = none
{kokkos} args = keyword value ... {kokkos} args = keyword value ...
zero or more keyword/value pairs may be appended 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} {neigh} value = {full} or {half}
full = full neighbor list full = full neighbor list
half = half neighbor list built in thread-safe manner 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 no = perform communication pack/unpack in non-KOKKOS mode
host = perform pack/unpack on host (e.g. with OpenMP threading) host = perform pack/unpack on host (e.g. with OpenMP threading)
device = perform pack/unpack on device (e.g. on GPU) device = perform pack/unpack on device (e.g. on GPU)
{gpu/direct} = {off} or {on} {cuda/aware} = {off} or {on}
off = do not use GPU-direct off = do not use CUDA-aware MPI
on = use GPU-direct (default) on = use CUDA-aware MPI (default)
{omp} args = Nthreads keyword value ... {omp} args = Nthreads keyword value ...
Nthread = # of OpenMP threads to associate with each MPI process Nthread = # of OpenMP threads to associate with each MPI process
zero or more keyword/value pairs may be appended 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 performing the exchange pack/unpack on the host CPU can give speedup
since it reduces the number of CUDA kernel launches. 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 this keyword is set to {on}, buffers in GPU memory are passed directly
through MPI send/receive calls. This reduces overhead of first copying 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 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 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 {cuda/aware} 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 set to {off} while any of the {comm}
keywords are set to {device}, the value for these {comm} keywords will keywords are set to {device}, the value for these {comm} keywords will
be automatically changed to {host}. This setting has no effect if not 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 running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
versions), Mvapich2 1.9 (or later), and CrayMPI. 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 :line
@ -641,8 +643,8 @@ switch"_Run_options.html.
For the KOKKOS package, the option defaults for GPUs are neigh = full, For the KOKKOS package, the option defaults for GPUs are neigh = full,
neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
value, comm = device, gpu/direct = on. When LAMMPS can safely detect value, comm = device, cuda/aware = on. When LAMMPS can safely detect
that GPU-direct is not available, the default value of gpu/direct 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 = 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 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 option neigh/thread = on when there are 16K atoms or less on an MPI

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -1544,6 +1544,7 @@ Mandelli
Manh Manh
manifoldforce manifoldforce
Manolopoulos Manolopoulos
manpages
manybody manybody
MANYBODY MANYBODY
Maras Maras

2
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon → examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
View File

@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
fix 1 statted_grp_REACT nvt temp 300 300 100 fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

48
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized Normal file
View File

@ -0,0 +1,48 @@
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
# write_restart restart_longrun
# write_data restart_longrun.data

370
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
View File

@ -1,370 +0,0 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
100 274.25324 46.715512 0.0034851739 1 1
150 471.61579 31.321598 0.0034851739 1 1
200 362.87766 42.061118 0.0034851739 1 1
250 367.58058 65.303109 0.0034851739 1 1
300 372.38236 -52.421725 0.0034851739 1 1
350 297.69957 17.869945 0.0034851739 1 1
400 258.30433 49.19156 0.0034851739 1 1
450 253.34384 -5.8162637 0.0034851739 1 1
500 269.96465 -43.337517 0.0034851739 1 1
550 303.23718 10.180246 0.0034851739 1 1
600 329.59579 -48.97461 0.0034851739 1 1
650 350.42568 50.983183 0.0034851739 1 1
700 342.03272 35.43465 0.0034851739 1 1
750 269.23405 -41.873166 0.0034851739 1 1
800 245.15025 13.953092 0.0034851739 1 1
850 257.85421 -3.1492141 0.0034851739 1 1
900 316.15644 7.7798301 0.0034851739 1 1
950 299.9124 -15.77014 0.0034851739 1 1
1000 302.89968 -17.049693 0.0034851739 1 1
1050 308.91651 71.84632 0.0034851739 1 1
1100 348.43932 -18.742012 0.0034851739 1 1
1150 309.03036 50.536311 0.0034851739 1 1
1200 318.9761 -16.905746 0.0034851739 1 1
1250 320.42806 -0.057975092 0.0034851739 1 1
1300 289.7824 18.200772 0.0034851739 1 1
1350 284.79836 -9.1978427 0.0034851739 1 1
1400 325.43292 42.082833 0.0034851739 1 1
1450 261.5041 -37.823325 0.0034851739 1 1
1500 298.88723 -5.1647385 0.0034851739 1 1
1550 291.37403 -7.7764201 0.0034851739 1 1
1600 293.83475 22.2458 0.0034851739 1 1
1650 293.80611 24.202512 0.0034851739 1 1
1700 291.70205 -23.397884 0.0034851739 1 1
1750 292.32437 -10.671214 0.0034851739 1 1
1800 302.01367 -11.671025 0.0034851739 1 1
1850 322.1651 24.438331 0.0034851739 1 1
1900 310.45076 45.343592 0.0034851739 1 1
1950 325.91745 -19.847809 0.0034851739 1 1
2000 276.89662 63.387098 0.0034851739 1 1
2050 311.33783 -24.683247 0.0034851739 1 1
2100 346.2336 -27.526891 0.0034851739 1 1
2150 345.30604 -15.722411 0.0034851739 1 1
2200 346.7718 -17.857633 0.0034851739 1 1
2250 304.28676 -1.9965581 0.0034851739 1 1
2300 322.56372 -31.786868 0.0034851739 1 1
2350 282.64326 6.1982735 0.0034851739 1 1
2400 286.65759 -63.207781 0.0034851739 1 1
2450 257.05528 32.931491 0.0034851739 1 1
2500 283.64386 26.912373 0.0034851739 1 1
2550 299.54005 27.277039 0.0034851739 1 1
2600 283.92503 14.660972 0.0034851739 1 1
2650 321.93453 -18.977358 0.0034851739 1 1
2700 376.7189 31.826935 0.0034851739 1 1
2750 372.20075 -32.821697 0.0034851739 1 1
2800 361.40604 83.035183 0.0034851739 1 1
2850 332.27269 -23.927452 0.0034851739 1 1
2900 331.14638 -0.12328446 0.0034851739 1 1
2950 303.67489 -24.078857 0.0034851739 1 1
3000 311.40462 21.563537 0.0034851739 1 1
3050 284.72849 -23.849667 0.0034851739 1 1
3100 303.48477 39.347763 0.0034851739 1 1
3150 264.2739 -0.22299879 0.0034851739 1 1
3200 300.03351 31.545323 0.0034851739 1 1
3250 288.56663 5.7225228 0.0034851739 1 1
3300 200.13238 -31.239655 0.0034851739 1 1
3350 231.32512 16.631728 0.0034851739 1 1
3400 260.57402 2.1717992 0.0034851739 1 1
3450 301.47128 -42.210623 0.0034851739 1 1
3500 321.77414 40.074365 0.0034851739 1 1
3550 353.21858 28.387783 0.0034851739 1 1
3600 331.45989 -57.800858 0.0034851739 1 1
3650 303.88123 44.86596 0.0034851739 1 1
3700 329.73833 -0.80615652 0.0034851739 1 1
3750 297.55588 -0.49626039 0.0034851739 1 1
3800 286.38794 -10.010003 0.0034851739 1 1
3850 290.17417 -43.51187 0.0034851739 1 1
3900 247.88933 51.23735 0.0034851739 1 1
3950 332.31324 -18.194985 0.0034851739 1 1
4000 325.56802 18.402825 0.0034851739 1 1
4050 338.37593 36.430977 0.0034851739 1 1
4100 370.95478 39.290285 0.0034851739 1 1
4150 348.47859 -7.0779678 0.0034851739 1 1
4200 241.30632 -33.371788 0.0034851739 1 1
4250 242.17258 -9.986197 0.0034851739 1 1
4300 300.85311 -7.9244294 0.0034851739 1 1
4350 273.15684 -21.257283 0.0034851739 1 1
4400 305.77463 -5.8720722 0.0034851739 1 1
4450 314.97697 45.0373 0.0034851739 1 1
4500 310.77723 16.958773 0.0034851739 1 1
4550 302.1742 12.156862 0.0034851739 1 1
4600 319.74799 6.84889 0.0034851739 1 1
4650 270.86805 -13.767905 0.0034851739 1 1
4700 249.81731 -31.197487 0.0034851739 1 1
4750 285.86481 -9.8916364 0.0034851739 1 1
4800 233.98321 7.1338571 0.0034851739 1 1
4850 302.60551 49.262889 0.0034851739 1 1
4900 316.55056 34.663247 0.0034851739 1 1
4950 357.32741 11.583006 0.0034851739 1 1
5000 400.21045 -8.1781061 0.0034851739 1 1
5050 390.01845 -20.490275 0.0034851739 1 1
5100 378.84247 -41.328757 0.0034851739 1 1
5150 324.02038 -15.023862 0.0034851739 1 1
5200 262.08429 10.937354 0.0034851739 1 1
5250 255.75508 16.381455 0.0034851739 1 1
5300 277.84989 40.68232 0.0034851739 1 1
5350 302.92832 9.1989494 0.0034851739 1 1
5400 283.7196 -1.6584671 0.0034851739 1 1
5450 300.71266 -4.7030295 0.0034851739 1 1
5500 343.5499 -0.30550044 0.0034851739 1 1
5550 369.51271 21.691649 0.0034851739 1 1
5600 372.69789 -38.67994 0.0034851739 1 1
5650 327.41266 11.352137 0.0034851739 1 1
5700 278.98614 -23.827304 0.0034851739 1 1
5750 308.30054 -20.756187 0.0034851739 1 1
5800 341.45594 28.058441 0.0034851739 1 1
5850 322.97844 -10.731921 0.0034851739 1 1
5900 304.53591 32.825279 0.0034851739 1 1
5950 287.1752 -36.780091 0.0034851739 1 1
6000 296.52681 18.781896 0.0034851739 1 1
6050 314.25442 15.992829 0.0034851739 1 1
6100 313.86576 3.4342714 0.0034851739 1 1
6150 325.64196 32.392039 0.0034851739 1 1
6200 367.42931 -27.160706 0.0034851739 1 1
6250 369.30798 39.020934 0.0034851739 1 1
6300 328.92285 -23.175157 0.0034851739 1 1
6350 305.63077 4.9024453 0.0034851739 1 1
6400 241.70341 -13.676629 0.0034851739 1 1
6450 265.66717 2.40612 0.0034851739 1 1
6500 249.36037 13.420255 0.0034851739 1 1
6550 294.53814 10.853462 0.0034851739 1 1
6600 308.2025 18.995308 0.0034851739 1 1
6650 305.43797 -49.56785 0.0034851739 1 1
6700 320.27344 11.336281 0.0034851739 1 1
6750 321.78666 -23.463899 0.0034851739 1 1
6800 303.40388 7.6224553 0.0034851739 1 1
6850 297.18966 51.52256 0.0034851739 1 1
6900 284.18909 -8.4947203 0.0034851739 1 1
6950 331.03663 13.233655 0.0034851739 1 1
7000 311.37928 -43.265479 0.0034851739 1 1
7050 286.81661 -14.174683 0.0034851739 1 1
7100 302.84119 12.048954 0.0034851739 1 1
7150 297.19357 -43.111968 0.0034851739 1 1
7200 332.47359 26.048249 0.0034851739 1 1
7250 262.70677 41.176242 0.0034851739 1 1
7300 250.61405 -23.413982 0.0034851739 1 1
7350 296.91117 35.88133 0.0034851739 1 1
7400 245.09229 -13.447194 0.0034851739 1 1
7450 272.28131 -23.322585 0.0034851739 1 1
7500 209.04985 13.871239 0.0034851739 1 1
7550 255.00955 4.9325621 0.0034851739 1 1
7600 312.30937 -37.368274 0.0034851739 1 1
7650 305.65903 55.245496 0.0034851739 1 1
7700 325.09504 -18.347711 0.0034851739 1 1
7750 363.28282 -22.479686 0.0034851739 1 1
7800 350.17429 26.849547 0.0034851739 1 1
7850 271.70853 -17.764575 0.0034851739 1 1
7900 272.66484 -11.701967 0.0034851739 1 1
7950 298.60202 -12.765675 0.0034851739 1 1
8000 274.58852 49.641532 0.0034851739 1 1
8050 304.72347 -0.55414183 0.0034851739 1 1
8100 328.30757 -39.861301 0.0034851739 1 1
8150 406.67601 2.8999409 0.0034851739 1 1
8200 332.20083 -51.217399 0.0034851739 1 1
8250 354.50609 53.128769 0.0034851739 1 1
8300 337.2758 20.68562 0.0034851739 1 1
8350 361.89708 -54.185869 0.0034851739 1 1
8400 305.63496 24.058529 0.0034851739 1 1
8450 303.27461 4.304683 0.0034851739 1 1
8500 253.53694 -10.909021 0.0034851739 1 1
8550 277.03017 23.241479 0.0034851739 1 1
8600 291.41844 -22.240665 0.0034851739 1 1
8650 307.85368 31.919587 0.0034851739 1 1
8700 309.19724 0.53529642 0.0034851739 1 1
8750 354.6583 11.565515 0.0034851739 1 1
8800 329.78598 19.5996 0.0034851739 1 1
8850 240.79198 21.803515 0.0034851739 1 1
8900 318.40749 -59.816923 0.0034851739 1 1
8950 308.47211 -57.808635 0.0034851739 1 1
9000 271.51207 50.943482 0.0034851739 1 1
9050 249.4005 6.7529187 0.0034851739 1 1
9100 221.8772 47.196092 0.0034851739 1 1
9150 297.9351 4.0058184 0.0034851739 1 1
9200 274.85051 -24.774393 0.0034851739 1 1
9250 336.04757 5.3799028 0.0034851739 1 1
9300 380.44956 -22.389381 0.0034851739 1 1
9350 336.9824 23.050616 0.0034851739 1 1
9400 304.46425 32.530218 0.0034851739 1 1
9450 317.55591 -22.265425 0.0034851739 1 1
9500 323.70901 -7.0159787 0.0034851739 1 1
9550 316.07308 28.062131 0.0034851739 1 1
9600 262.74608 -0.78519192 0.0034851739 1 1
9650 271.55045 -21.430123 0.0034851739 1 1
9700 239.6022 14.483637 0.0034851739 1 1
9750 338.1437 -0.72765302 0.0034851739 1 1
9800 334.50189 19.495144 0.0034851739 1 1
9850 354.87554 19.272719 0.0034851739 1 1
9900 334.02141 -22.393457 0.0034851739 1 1
9950 293.63651 19.178873 0.0034851739 1 1
10000 319.81736 21.904414 0.0034851739 1 1
Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
Other | | 0.01666 | | | 0.90
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 823
Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

370
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
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@ -1,370 +0,0 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
100 274.25324 46.715512 0.0034851739 1 1
150 471.61579 31.321598 0.0034851739 1 1
200 362.87766 42.061118 0.0034851739 1 1
250 367.58058 65.303109 0.0034851739 1 1
300 372.38236 -52.421725 0.0034851739 1 1
350 297.69957 17.869945 0.0034851739 1 1
400 258.30433 49.19156 0.0034851739 1 1
450 253.34384 -5.8162637 0.0034851739 1 1
500 269.96465 -43.337517 0.0034851739 1 1
550 303.23718 10.180246 0.0034851739 1 1
600 329.59579 -48.97461 0.0034851739 1 1
650 350.42568 50.983183 0.0034851739 1 1
700 342.03272 35.43465 0.0034851739 1 1
750 269.23405 -41.873166 0.0034851739 1 1
800 245.15025 13.953092 0.0034851739 1 1
850 257.85421 -3.1492141 0.0034851739 1 1
900 316.15644 7.7798301 0.0034851739 1 1
950 299.9124 -15.77014 0.0034851739 1 1
1000 302.89968 -17.049693 0.0034851739 1 1
1050 308.91651 71.84632 0.0034851739 1 1
1100 348.43932 -18.742012 0.0034851739 1 1
1150 309.03036 50.536311 0.0034851739 1 1
1200 318.9761 -16.905746 0.0034851739 1 1
1250 320.42806 -0.057975092 0.0034851739 1 1
1300 289.7824 18.200772 0.0034851739 1 1
1350 284.79836 -9.1978427 0.0034851739 1 1
1400 325.43292 42.082833 0.0034851739 1 1
1450 261.5041 -37.823325 0.0034851739 1 1
1500 298.88723 -5.1647385 0.0034851739 1 1
1550 291.37403 -7.7764201 0.0034851739 1 1
1600 293.83475 22.2458 0.0034851739 1 1
1650 293.80611 24.202512 0.0034851739 1 1
1700 291.70205 -23.397884 0.0034851739 1 1
1750 292.32437 -10.671214 0.0034851739 1 1
1800 302.01367 -11.671025 0.0034851739 1 1
1850 322.1651 24.438331 0.0034851739 1 1
1900 310.45076 45.343592 0.0034851739 1 1
1950 325.91745 -19.847809 0.0034851739 1 1
2000 276.89662 63.387098 0.0034851739 1 1
2050 311.33783 -24.683247 0.0034851739 1 1
2100 346.2336 -27.526891 0.0034851739 1 1
2150 345.30604 -15.722411 0.0034851739 1 1
2200 346.7718 -17.857633 0.0034851739 1 1
2250 304.28676 -1.9965581 0.0034851739 1 1
2300 322.56372 -31.786868 0.0034851739 1 1
2350 282.64326 6.1982735 0.0034851739 1 1
2400 286.65759 -63.207781 0.0034851739 1 1
2450 257.05528 32.931491 0.0034851739 1 1
2500 283.64386 26.912373 0.0034851739 1 1
2550 299.54005 27.277039 0.0034851739 1 1
2600 283.92503 14.660972 0.0034851739 1 1
2650 321.93453 -18.977358 0.0034851739 1 1
2700 376.7189 31.826935 0.0034851739 1 1
2750 372.20075 -32.821697 0.0034851739 1 1
2800 361.40604 83.035183 0.0034851739 1 1
2850 332.27269 -23.927452 0.0034851739 1 1
2900 331.14638 -0.12328446 0.0034851739 1 1
2950 303.67489 -24.078857 0.0034851739 1 1
3000 311.40462 21.563537 0.0034851739 1 1
3050 284.72849 -23.849667 0.0034851739 1 1
3100 303.48477 39.347763 0.0034851739 1 1
3150 264.2739 -0.22299878 0.0034851739 1 1
3200 300.03351 31.545323 0.0034851739 1 1
3250 288.56663 5.7225229 0.0034851739 1 1
3300 200.13238 -31.239655 0.0034851739 1 1
3350 231.32512 16.631728 0.0034851739 1 1
3400 260.57402 2.1717992 0.0034851739 1 1
3450 301.47128 -42.210623 0.0034851739 1 1
3500 321.77414 40.074365 0.0034851739 1 1
3550 353.21858 28.387783 0.0034851739 1 1
3600 331.45989 -57.800858 0.0034851739 1 1
3650 303.88123 44.86596 0.0034851739 1 1
3700 329.73833 -0.8061567 0.0034851739 1 1
3750 297.55588 -0.49626022 0.0034851739 1 1
3800 286.38794 -10.010003 0.0034851739 1 1
3850 290.17417 -43.51187 0.0034851739 1 1
3900 247.88933 51.23735 0.0034851739 1 1
3950 332.31324 -18.194985 0.0034851739 1 1
4000 325.56802 18.402825 0.0034851739 1 1
4050 338.37594 36.430977 0.0034851739 1 1
4100 370.95478 39.290285 0.0034851739 1 1
4150 348.47859 -7.0779683 0.0034851739 1 1
4200 241.30632 -33.371789 0.0034851739 1 1
4250 242.17258 -9.9861962 0.0034851739 1 1
4300 300.85311 -7.924429 0.0034851739 1 1
4350 273.15684 -21.257282 0.0034851739 1 1
4400 305.77464 -5.8720712 0.0034851739 1 1
4450 314.97697 45.037299 0.0034851739 1 1
4500 310.77723 16.958771 0.0034851739 1 1
4550 302.17421 12.156862 0.0034851739 1 1
4600 319.74799 6.8488914 0.0034851739 1 1
4650 270.86805 -13.767907 0.0034851739 1 1
4700 249.81731 -31.197484 0.0034851739 1 1
4750 285.86481 -9.8916332 0.0034851739 1 1
4800 233.98321 7.1338518 0.0034851739 1 1
4850 302.60551 49.262886 0.0034851739 1 1
4900 316.55055 34.663238 0.0034851739 1 1
4950 357.32741 11.583013 0.0034851739 1 1
5000 400.21044 -8.1780861 0.0034851739 1 1
5050 390.01845 -20.490268 0.0034851739 1 1
5100 378.84249 -41.328772 0.0034851739 1 1
5150 324.02039 -15.023852 0.0034851739 1 1
5200 262.08427 10.937367 0.0034851739 1 1
5250 255.75506 16.381495 0.0034851739 1 1
5300 277.84991 40.682283 0.0034851739 1 1
5350 302.92834 9.1989644 0.0034851739 1 1
5400 283.71964 -1.6583895 0.0034851739 1 1
5450 300.71261 -4.703054 0.0034851739 1 1
5500 343.54987 -0.30546396 0.0034851739 1 1
5550 369.51272 21.691639 0.0034851739 1 1
5600 372.69786 -38.679919 0.0034851739 1 1
5650 327.41256 11.352201 0.0034851739 1 1
5700 278.9861 -23.82728 0.0034851739 1 1
5750 308.30037 -20.756238 0.0034851739 1 1
5800 341.4559 28.058314 0.0034851739 1 1
5850 322.9786 -10.731862 0.0034851739 1 1
5900 304.53598 32.825105 0.0034851739 1 1
5950 287.17515 -36.780057 0.0034851739 1 1
6000 296.52688 18.782156 0.0034851739 1 1
6050 314.25411 15.99272 0.0034851739 1 1
6100 313.86572 3.4344108 0.0034851739 1 1
6150 325.64197 32.39212 0.0034851739 1 1
6200 367.4298 -27.161154 0.0034851739 1 1
6250 369.30937 39.020881 0.0034851739 1 1
6300 328.92245 -23.175612 0.0034851739 1 1
6350 305.6293 4.9011587 0.0034851739 1 1
6400 241.70456 -13.675247 0.0034851739 1 1
6450 265.66574 2.4049735 0.0034851739 1 1
6500 249.3592 13.420453 0.0034851739 1 1
6550 294.5367 10.856753 0.0034851739 1 1
6600 308.20246 18.992923 0.0034851739 1 1
6650 305.43756 -49.57151 0.0034851739 1 1
6700 320.27395 11.339101 0.0034851739 1 1
6750 321.7875 -23.463361 0.0034851739 1 1
6800 303.40316 7.6256997 0.0034851739 1 1
6850 297.18652 51.52186 0.0034851739 1 1
6900 284.19084 -8.496294 0.0034851739 1 1
6950 331.04173 13.227745 0.0034851739 1 1
7000 311.38027 -43.26105 0.0034851739 1 1
7050 286.82046 -14.171194 0.0034851739 1 1
7100 302.81691 12.058085 0.0034851739 1 1
7150 297.18018 -43.110658 0.0034851739 1 1
7200 332.46131 26.051496 0.0034851739 1 1
7250 262.72288 41.161451 0.0034851739 1 1
7300 250.62739 -23.440907 0.0034851739 1 1
7350 296.92141 35.869216 0.0034851739 1 1
7400 245.06807 -13.467896 0.0034851739 1 1
7450 272.2659 -23.292836 0.0034851739 1 1
7500 209.05776 13.888665 0.0034851739 1 1
7550 255.03716 4.9662624 0.0034851739 1 1
7600 312.26011 -37.350427 0.0034851739 1 1
7650 305.5823 55.208039 0.0034851739 1 1
7700 325.13382 -18.370791 0.0034851739 1 1
7750 363.24898 -22.473126 0.0034851739 1 1
7800 350.19254 26.792307 0.0034851739 1 1
7850 271.76418 -17.843445 0.0034851739 1 1
7900 272.70301 -11.709349 0.0034851739 1 1
7950 298.5993 -12.736235 0.0034851739 1 1
8000 274.52611 49.657345 0.0034851739 1 1
8050 304.73711 -0.52485689 0.0034851739 1 1
8100 328.29239 -39.901891 0.0034851739 1 1
8150 406.52096 2.8669076 0.0034851739 1 1
8200 332.17309 -51.168754 0.0034851739 1 1
8250 354.68419 53.003157 0.0034851739 1 1
8300 337.28934 20.766408 0.0034851739 1 1
8350 361.81133 -54.159227 0.0034851739 1 1
8400 305.59597 24.011667 0.0034851739 1 1
8450 303.25823 4.423341 0.0034851739 1 1
8500 253.50747 -11.026949 0.0034851739 1 1
8550 277.13504 23.204625 0.0034851739 1 1
8600 291.40211 -22.253861 0.0034851739 1 1
8650 307.93765 32.14162 0.0034851739 1 1
8700 309.1529 0.36279434 0.0034851739 1 1
8750 355.10326 11.677219 0.0034851739 1 1
8800 330.21328 19.235269 0.0034851739 1 1
8850 241.29109 21.707386 0.0034851739 1 1
8900 319.15363 -60.010115 0.0034851739 1 1
8950 308.88552 -57.637014 0.0034851739 1 1
9000 272.22373 51.15837 0.0034851739 1 1
9050 248.84947 7.3390565 0.0034851739 1 1
9100 221.91564 48.387079 0.0034851739 1 1
9150 298.03506 2.9058639 0.0034851739 1 1
9200 274.25114 -24.597819 0.0034851739 1 1
9250 334.08373 5.1079577 0.0034851739 1 1
9300 383.07285 -23.274763 0.0034851739 1 1
9350 335.00581 20.94212 0.0034851739 1 1
9400 309.23862 34.074744 0.0034851739 1 1
9450 312.62262 -28.468057 0.0034851739 1 1
9500 324.54274 2.851136 0.0034851739 1 1
9550 313.32781 22.468182 0.0034851739 1 1
9600 269.04372 4.064934 0.0034851739 1 1
9650 270.98476 -21.520127 0.0034851739 1 1
9700 236.8736 16.250728 0.0034851739 1 1
9750 333.94686 1.6864148 0.0034851739 1 1
9800 330.91875 12.150018 0.0034851739 1 1
9850 343.8603 25.338853 0.0034851739 1 1
9900 330.93364 -28.292992 0.0034851739 1 1
9950 291.25518 25.795948 0.0034851739 1 1
10000 319.25565 25.323846 0.0034851739 1 1
Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
Other | | 0.02359 | | | 0.66
Nlocal: 11 ave 44 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 33 ave 44 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 205.75 ave 823 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 823
Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

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LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000181113 secs
read_data CPU = 0.0251833 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
87.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13
Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01
Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70
Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60
Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74
Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80
Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64
Other | | 0.001306 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 740 ave 740 max 740 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000178751 secs
read_data CPU = 0.0385782 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
Other | | 0.0008281 | | | 0.31
Nlocal: 11 ave 21 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 32.5 ave 43 max 23 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 185 ave 376 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 Normal file
View File

@ -0,0 +1,147 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000217102 secs
read_data CPU = 0.00630778 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
91.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17
Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42
Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78
Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61
Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74
Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98
Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91
Other | | 0.001336 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 818 ave 818 max 818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 Normal file
View File

@ -0,0 +1,147 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000163256 secs
read_data CPU = 0.0244579 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
Other | | 0.0007123 | | | 0.28
Nlocal: 11 ave 29 max 0 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 25 ave 31 max 12 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 204.5 ave 443 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

2
lib/poems/system.h
View File

@ -15,7 +15,6 @@
* CONTACT: anderk5@rpi.edu * * CONTACT: anderk5@rpi.edu *
*_________________________________________________________________________*/ *_________________________________________________________________________*/
#ifndef SYSTEM_H #ifndef SYSTEM_H
#define SYSTEM_H #define SYSTEM_H
@ -31,7 +30,6 @@
#include "workspace.h" #include "workspace.h"
#include "matrixfun.h" #include "matrixfun.h"
#include "onsolver.h" #include "onsolver.h"
#include "system.h"
#include "inertialframe.h" #include "inertialframe.h"
#include "rigidbody.h" #include "rigidbody.h"
#include "revolutejoint.h" #include "revolutejoint.h"

3
src/ASPHERE/compute_erotate_asphere.cpp
View File

@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <mpi.h>
#include "compute_erotate_asphere.h" #include "compute_erotate_asphere.h"
#include <mpi.h>
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
@ -20,7 +20,6 @@
#include "atom_vec_tri.h" #include "atom_vec_tri.h"
#include "update.h" #include "update.h"
#include "force.h" #include "force.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

3
src/ASPHERE/compute_temp_asphere.cpp
View File

@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL) Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "compute_temp_asphere.h"
#include <mpi.h> #include <mpi.h>
#include <cstring> #include <cstring>
#include "compute_temp_asphere.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
@ -26,7 +26,6 @@
#include "domain.h" #include "domain.h"
#include "modify.h" #include "modify.h"
#include "group.h" #include "group.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

7
src/ASPHERE/fix_nh_asphere.cpp
View File

@ -15,15 +15,10 @@
Contributing author: Mike Brown (SNL) Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include <cstdlib>
#include <cmath>
#include "math_extra.h"
#include "fix_nh_asphere.h" #include "fix_nh_asphere.h"
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
#include "group.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

2
src/ASPHERE/fix_nph_asphere.cpp
View File

@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include "fix_nph_asphere.h" #include "fix_nph_asphere.h"
#include <cstring>
#include "modify.h" #include "modify.h"
#include "error.h" #include "error.h"

2
src/ASPHERE/fix_npt_asphere.cpp
View File

@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include "fix_npt_asphere.h" #include "fix_npt_asphere.h"
#include <cstring>
#include "modify.h" #include "modify.h"
#include "error.h" #include "error.h"

6
src/ASPHERE/fix_nve_asphere.cpp
View File

@ -15,16 +15,10 @@
Contributing author: Mike Brown (SNL) Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstring>
#include "fix_nve_asphere.h" #include "fix_nve_asphere.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

6
src/ASPHERE/fix_nve_asphere_noforce.cpp
View File

@ -11,16 +11,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstring>
#include <cstdlib>
#include "fix_nve_asphere_noforce.h" #include "fix_nve_asphere_noforce.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
#include "group.h"
#include "update.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

3
src/ASPHERE/fix_nve_line.cpp
View File

@ -11,9 +11,6 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstring>
#include "fix_nve_line.h" #include "fix_nve_line.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_line.h" #include "atom_vec_line.h"

3
src/ASPHERE/fix_nve_tri.cpp
View File

@ -11,9 +11,6 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstring>
#include "fix_nve_tri.h" #include "fix_nve_tri.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"

2
src/ASPHERE/fix_nvt_asphere.cpp
View File

@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include "fix_nvt_asphere.h" #include "fix_nvt_asphere.h"
#include <cstring>
#include "group.h" #include "group.h"
#include "modify.h" #include "modify.h"
#include "error.h" #include "error.h"

7
src/ASPHERE/pair_gayberne.cpp
View File

@ -15,11 +15,9 @@
Contributing author: Mike Brown (SNL) Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_gayberne.h" #include "pair_gayberne.h"
#include <mpi.h>
#include <cmath>
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
@ -27,7 +25,6 @@
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "integrate.h"
#include "citeme.h" #include "citeme.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"

5
src/ASPHERE/pair_line_lj.cpp
View File

@ -11,11 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_line_lj.h" #include "pair_line_lj.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "atom_vec_line.h" #include "atom_vec_line.h"
#include "force.h" #include "force.h"

7
src/ASPHERE/pair_resquared.cpp
View File

@ -15,11 +15,9 @@
Contributing author: Mike Brown (SNL) Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_resquared.h" #include "pair_resquared.h"
#include <mpi.h>
#include <cmath>
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
@ -27,7 +25,6 @@
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "integrate.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"

5
src/ASPHERE/pair_tri_lj.cpp
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@ -11,11 +11,8 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_tri_lj.h" #include "pair_tri_lj.h"
#include <cmath>
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_tri.h" #include "atom_vec_tri.h"

4
src/BODY/body_nparticle.cpp
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@ -11,8 +11,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstdlib>
#include "body_nparticle.h" #include "body_nparticle.h"
#include <cstring>
#include <cstdlib>
#include "my_pool_chunk.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "atom.h" #include "atom.h"

4
src/BODY/body_rounded_polygon.cpp
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@ -15,8 +15,10 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstdlib>
#include "body_rounded_polygon.h" #include "body_rounded_polygon.h"
#include <cmath>
#include <cstring>
#include "my_pool_chunk.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "atom.h" #include "atom.h"
#include "force.h" #include "force.h"

6
src/BODY/body_rounded_polyhedron.cpp
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@ -15,12 +15,14 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstdlib>
#include "body_rounded_polyhedron.h" #include "body_rounded_polyhedron.h"
#include <cmath>
#include <cstring>
#include <cstdlib>
#include "my_pool_chunk.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "atom.h" #include "atom.h"
#include "force.h" #include "force.h"
#include "domain.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"

6
src/BODY/compute_body_local.cpp
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@ -11,16 +11,14 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstring>
#include "compute_body_local.h" #include "compute_body_local.h"
#include <mpi.h>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "body.h" #include "body.h"
#include "update.h" #include "update.h"
#include "domain.h"
#include "force.h" #include "force.h"
#include "bond.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"

3
src/BODY/compute_temp_body.cpp
View File

@ -16,9 +16,9 @@
based on ComputeTempAsphere based on ComputeTempAsphere
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "compute_temp_body.h"
#include <mpi.h> #include <mpi.h>
#include <cstring> #include <cstring>
#include "compute_temp_body.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
@ -27,7 +27,6 @@
#include "domain.h" #include "domain.h"
#include "modify.h" #include "modify.h"
#include "group.h" #include "group.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

7
src/BODY/fix_nh_body.cpp
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@ -16,15 +16,10 @@
based on FixNHAsphere based on FixNHAsphere
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include <cstdlib>
#include <cmath>
#include "math_extra.h"
#include "fix_nh_body.h" #include "fix_nh_body.h"
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "group.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

2
src/BODY/fix_nph_body.cpp
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@ -15,8 +15,8 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include "fix_nph_body.h" #include "fix_nph_body.h"
#include <cstring>
#include "modify.h" #include "modify.h"
#include "error.h" #include "error.h"

2
src/BODY/fix_npt_body.cpp
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@ -15,8 +15,8 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include "fix_npt_body.h" #include "fix_npt_body.h"
#include <cstring>
#include "modify.h" #include "modify.h"
#include "error.h" #include "error.h"

6
src/BODY/fix_nve_body.cpp
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@ -11,16 +11,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstring>
#include "fix_nve_body.h" #include "fix_nve_body.h"
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

2
src/BODY/fix_nvt_body.cpp
View File

@ -15,8 +15,8 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cstring>
#include "fix_nvt_body.h" #include "fix_nvt_body.h"
#include <cstring>
#include "group.h" #include "group.h"
#include "modify.h" #include "modify.h"
#include "error.h" #include "error.h"

8
src/BODY/fix_wall_body_polygon.cpp
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@ -15,19 +15,15 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "fix_wall_body_polygon.h" #include "fix_wall_body_polygon.h"
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "body_rounded_polygon.h" #include "body_rounded_polygon.h"
#include "domain.h" #include "domain.h"
#include "update.h" #include "update.h"
#include "force.h" #include "force.h"
#include "pair.h"
#include "modify.h"
#include "respa.h"
#include "math_const.h" #include "math_const.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"

8
src/BODY/fix_wall_body_polyhedron.cpp
View File

@ -15,19 +15,15 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "fix_wall_body_polyhedron.h" #include "fix_wall_body_polyhedron.h"
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "body_rounded_polyhedron.h" #include "body_rounded_polyhedron.h"
#include "domain.h" #include "domain.h"
#include "update.h" #include "update.h"
#include "force.h" #include "force.h"
#include "pair.h"
#include "modify.h"
#include "respa.h"
#include "math_const.h" #include "math_const.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"

6
src/BODY/pair_body_nparticle.cpp
View File

@ -11,11 +11,9 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_body_nparticle.h" #include "pair_body_nparticle.h"
#include <cmath>
#include <cstring>
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"

7
src/BODY/pair_body_rounded_polygon.cpp
View File

@ -18,11 +18,10 @@
the contact history for friction forces. the contact history for friction forces.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_body_rounded_polygon.h" #include "pair_body_rounded_polygon.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "math_extra.h" #include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"

9
src/BODY/pair_body_rounded_polyhedron.cpp
View File

@ -20,12 +20,10 @@
the contact history for friction forces. the contact history for friction forces.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_body_rounded_polyhedron.h" #include "pair_body_rounded_polyhedron.h"
#include "math_extra.h" #include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "body_rounded_polyhedron.h" #include "body_rounded_polyhedron.h"
@ -41,7 +39,6 @@
#include "math_const.h" #include "math_const.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathExtra;
using namespace MathConst; using namespace MathConst;
#define DELTA 10000 #define DELTA 10000

4
src/CLASS2/angle_class2.cpp
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@ -15,10 +15,10 @@
Contributing author: Eric Simon (Cray) Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "angle_class2.h"
#include <mpi.h>
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
#include <cstdlib>
#include "angle_class2.h"
#include "atom.h" #include "atom.h"
#include "neighbor.h" #include "neighbor.h"
#include "domain.h" #include "domain.h"

1
src/CLASS2/angle_class2.h
View File

@ -20,7 +20,6 @@ AngleStyle(class2,AngleClass2)
#ifndef LMP_ANGLE_CLASS2_H #ifndef LMP_ANGLE_CLASS2_H
#define LMP_ANGLE_CLASS2_H #define LMP_ANGLE_CLASS2_H
#include <cstdio>
#include "angle.h" #include "angle.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {

5
src/CLASS2/bond_class2.cpp
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@ -15,12 +15,11 @@
Contributing author: Eric Simon (Cray) Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include "bond_class2.h" #include "bond_class2.h"
#include <mpi.h>
#include <cmath>
#include "atom.h" #include "atom.h"
#include "neighbor.h" #include "neighbor.h"
#include "domain.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"

1
src/CLASS2/bond_class2.h
View File

@ -20,7 +20,6 @@ BondStyle(class2,BondClass2)
#ifndef LMP_BOND_CLASS2_H #ifndef LMP_BOND_CLASS2_H
#define LMP_BOND_CLASS2_H #define LMP_BOND_CLASS2_H
#include <cstdio>
#include "bond.h" #include "bond.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {

5
src/CLASS2/dihedral_class2.cpp
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@ -15,14 +15,13 @@
Contributing author: Eric Simon (Cray) Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "dihedral_class2.h"
#include <mpi.h>
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
#include <cstdlib>
#include "dihedral_class2.h"
#include "atom.h" #include "atom.h"
#include "neighbor.h" #include "neighbor.h"
#include "update.h" #include "update.h"
#include "domain.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"

1
src/CLASS2/dihedral_class2.h
View File

@ -20,7 +20,6 @@ DihedralStyle(class2,DihedralClass2)
#ifndef LMP_DIHEDRAL_CLASS2_H #ifndef LMP_DIHEDRAL_CLASS2_H
#define LMP_DIHEDRAL_CLASS2_H #define LMP_DIHEDRAL_CLASS2_H
#include <cstdio>
#include "dihedral.h" #include "dihedral.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {

5
src/CLASS2/improper_class2.cpp
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@ -15,14 +15,13 @@
Contributing author: Eric Simon (Cray) Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "improper_class2.h"
#include <mpi.h>
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
#include <cstdlib>
#include "improper_class2.h"
#include "atom.h" #include "atom.h"
#include "neighbor.h" #include "neighbor.h"
#include "update.h" #include "update.h"
#include "domain.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"

1
src/CLASS2/improper_class2.h
View File

@ -20,7 +20,6 @@ ImproperStyle(class2,ImproperClass2)
#ifndef LMP_IMPROPER_CLASS2_H #ifndef LMP_IMPROPER_CLASS2_H
#define LMP_IMPROPER_CLASS2_H #define LMP_IMPROPER_CLASS2_H
#include <cstdio>
#include "improper.h" #include "improper.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {

8
src/CLASS2/pair_lj_class2.cpp
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@ -9,11 +9,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lj_class2.h" #include "pair_lj_class2.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
@ -21,7 +20,6 @@
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h" #include "neigh_request.h"
#include "update.h" #include "update.h"
#include "integrate.h"
#include "respa.h" #include "respa.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"

7
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -11,11 +11,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lj_class2_coul_cut.h" #include "pair_lj_class2_coul_cut.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"

8
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -11,17 +11,15 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lj_class2_coul_long.h" #include "pair_lj_class2_coul_long.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "kspace.h" #include "kspace.h"
#include "update.h" #include "update.h"
#include "integrate.h"
#include "respa.h" #include "respa.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"

6
src/COLLOID/fix_wall_colloid.cpp
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@ -15,13 +15,11 @@
Contributing authors: Jeremy Lechman (SNL) Contributing authors: Jeremy Lechman (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstring>
#include "fix_wall_colloid.h" #include "fix_wall_colloid.h"
#include <mpi.h>
#include <cmath>
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "update.h"
#include "respa.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

10
src/COLLOID/pair_brownian.cpp
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@ -15,23 +15,19 @@
Contributing authors: Amit Kumar and Michael Bybee (UIUC) Contributing authors: Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_brownian.h" #include "pair_brownian.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
#include "domain.h" #include "domain.h"
#include "update.h" #include "update.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "fix_deform.h"
#include "fix_wall.h" #include "fix_wall.h"
#include "input.h" #include "input.h"
#include "variable.h" #include "variable.h"

11
src/COLLOID/pair_brownian_poly.cpp
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@ -16,14 +16,11 @@
Dave Heine (Corning), polydispersity Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_brownian_poly.h" #include "pair_brownian_poly.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
@ -32,14 +29,12 @@
#include "update.h" #include "update.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "fix_deform.h"
#include "fix_wall.h" #include "fix_wall.h"
#include "input.h" #include "input.h"
#include "variable.h" #include "variable.h"
#include "random_mars.h" #include "random_mars.h"
#include "math_const.h" #include "math_const.h"
#include "math_special.h" #include "math_special.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

7
src/COLLOID/pair_colloid.cpp
View File

@ -15,15 +15,12 @@
Contributing author: Pieter in 't Veld (SNL) Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_colloid.h" #include "pair_colloid.h"
#include <mpi.h>
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "math_special.h" #include "math_special.h"
#include "memory.h" #include "memory.h"

10
src/COLLOID/pair_lubricate.cpp
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@ -16,18 +16,15 @@
Amit Kumar and Michael Bybee (UIUC) Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lubricate.h" #include "pair_lubricate.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
#include "domain.h" #include "domain.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
@ -35,7 +32,6 @@
#include "fix_wall.h" #include "fix_wall.h"
#include "input.h" #include "input.h"
#include "variable.h" #include "variable.h"
#include "random_mars.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"

7
src/COLLOID/pair_lubricateU.cpp
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@ -15,25 +15,20 @@
Contributing authors: Amit Kumar and Michael Bybee (UIUC) Contributing authors: Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_lubricateU.h"
#include <mpi.h> #include <mpi.h>
#include <cmath> #include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_lubricateU.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
#include "domain.h" #include "domain.h"
#include "update.h" #include "update.h"
#include "math_const.h" #include "math_const.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "fix_deform.h"
#include "fix_wall.h" #include "fix_wall.h"
#include "input.h" #include "input.h"
#include "variable.h" #include "variable.h"

7
src/COLLOID/pair_lubricateU_poly.cpp
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@ -17,24 +17,19 @@
Dave Heine (Corning), polydispersity Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_lubricateU_poly.h"
#include <mpi.h> #include <mpi.h>
#include <cmath> #include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_lubricateU_poly.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h" #include "neigh_request.h"
#include "domain.h" #include "domain.h"
#include "update.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "fix_deform.h"
#include "fix_wall.h" #include "fix_wall.h"
#include "input.h" #include "input.h"
#include "variable.h" #include "variable.h"

10
src/COLLOID/pair_lubricate_poly.cpp
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@ -17,13 +17,11 @@
Dave Heine (Corning), polydispersity Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lubricate_poly.h" #include "pair_lubricate_poly.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h" #include "neighbor.h"
@ -33,8 +31,6 @@
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "fix_deform.h" #include "fix_deform.h"
#include "memory.h"
#include "random_mars.h"
#include "fix_wall.h" #include "fix_wall.h"
#include "input.h" #include "input.h"
#include "variable.h" #include "variable.h"

5
src/COLLOID/pair_yukawa_colloid.cpp
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@ -15,16 +15,13 @@
Contributing authors: Randy Schunk (Sandia) Contributing authors: Randy Schunk (Sandia)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include "pair_yukawa_colloid.h" #include "pair_yukawa_colloid.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "force.h" #include "force.h"
#include "comm.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "memory.h"
#include "error.h" #include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

1
src/COMPRESS/dump_xyz_gz.cpp
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@ -12,7 +12,6 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "dump_xyz_gz.h" #include "dump_xyz_gz.h"
#include "domain.h"
#include "error.h" #include "error.h"
#include "update.h" #include "update.h"

7
src/CORESHELL/compute_temp_cs.cpp
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@ -16,11 +16,9 @@
(hendrik.heenen at mytum.com) (hendrik.heenen at mytum.com)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <mpi.h>
#include <cstdlib>
#include <cstring>
#include <cmath>
#include "compute_temp_cs.h" #include "compute_temp_cs.h"
#include <mpi.h>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "domain.h" #include "domain.h"
@ -28,7 +26,6 @@
#include "force.h" #include "force.h"
#include "group.h" #include "group.h"
#include "modify.h" #include "modify.h"
#include "fix.h"
#include "fix_store.h" #include "fix_store.h"
#include "comm.h" #include "comm.h"
#include "memory.h" #include "memory.h"

8
src/CORESHELL/pair_born_coul_dsf_cs.cpp
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@ -16,19 +16,13 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006) References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_born_coul_dsf_cs.h" #include "pair_born_coul_dsf_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h"
#include "error.h"
#include "math_special.h" #include "math_special.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

12
src/CORESHELL/pair_born_coul_long_cs.cpp
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@ -15,23 +15,13 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_born_coul_long_cs.h" #include "pair_born_coul_long_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h"
#include "force.h" #include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917 #define EWALD_F 1.12837917
#define EWALD_P 9.95473818e-1 #define EWALD_P 9.95473818e-1

10
src/CORESHELL/pair_born_coul_wolf_cs.cpp
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@ -12,24 +12,16 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_born_coul_wolf_cs.h" #include "pair_born_coul_wolf_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "math_const.h" #include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst; using namespace MathConst;
using namespace MathSpecial;
#define EPSILON 1.0e-20 #define EPSILON 1.0e-20

12
src/CORESHELL/pair_buck_coul_long_cs.cpp
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@ -15,23 +15,13 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_buck_coul_long_cs.h" #include "pair_buck_coul_long_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h"
#include "force.h" #include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917 #define EWALD_F 1.12837917
#define EWALD_P 9.95473818e-1 #define EWALD_P 9.95473818e-1

13
src/CORESHELL/pair_coul_long_cs.cpp
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@ -15,22 +15,11 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_coul_long_cs.h" #include "pair_coul_long_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h"
#include "force.h" #include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

11
src/CORESHELL/pair_coul_wolf_cs.cpp
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@ -11,25 +11,16 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_coul_wolf_cs.h" #include "pair_coul_wolf_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h" #include "force.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "math_const.h" #include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst; using namespace MathConst;
using namespace MathSpecial;
#define EPSILON 1.0e-20 #define EPSILON 1.0e-20

16
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
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@ -15,27 +15,13 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lj_cut_coul_long_cs.h" #include "pair_lj_cut_coul_long_cs.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h"
#include "force.h" #include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917 #define EWALD_F 1.12837917
#define EWALD_P 9.95473818e-1 #define EWALD_P 9.95473818e-1

4
src/DIPOLE/atom_vec_dipole.cpp
View File

@ -11,13 +11,11 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include "atom_vec_dipole.h" #include "atom_vec_dipole.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "domain.h" #include "domain.h"
#include "force.h"
#include "modify.h" #include "modify.h"
#include "fix.h" #include "fix.h"
#include "memory.h" #include "memory.h"

6
src/DIPOLE/pair_lj_cut_dipole_cut.cpp
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@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "pair_lj_cut_dipole_cut.h" #include "pair_lj_cut_dipole_cut.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"

7
src/DIPOLE/pair_lj_cut_dipole_long.cpp
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@ -11,11 +11,10 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_lj_cut_dipole_long.h" #include "pair_lj_cut_dipole_long.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "neighbor.h" #include "neighbor.h"

8
src/DIPOLE/pair_lj_long_dipole_long.cpp
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@ -15,23 +15,19 @@
Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia) Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_lj_long_dipole_long.h"
#include <mpi.h>
#include <cmath> #include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring> #include <cstring>
#include "math_const.h" #include "math_const.h"
#include "math_vector.h" #include "math_vector.h"
#include "pair_lj_long_dipole_long.h"
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "neigh_request.h"
#include "force.h" #include "force.h"
#include "kspace.h" #include "kspace.h"
#include "update.h" #include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"

2
src/GPU/fix_gpu.cpp
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@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_gpu.h"
#include <cstring> #include <cstring>
#include <cstdlib> #include <cstdlib>
#include "fix_gpu.h"
#include "atom.h" #include "atom.h"
#include "force.h" #include "force.h"
#include "pair.h" #include "pair.h"

2
src/GPU/pair_beck_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_beck_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_beck_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_born_coul_long_cs_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (Northwestern) Contributing author: Trung Dac Nguyen (Northwestern)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_born_coul_long_cs_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_born_coul_long_cs_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_born_coul_long_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_born_coul_long_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_born_coul_long_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_born_coul_wolf_cs_gpu.cpp
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@ -15,11 +15,11 @@
Contributing authors: Trung Dac Nguyen (Northwestern) Contributing authors: Trung Dac Nguyen (Northwestern)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_born_coul_wolf_cs_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_born_coul_wolf_cs_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_born_coul_wolf_gpu.cpp
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@ -15,11 +15,11 @@
Contributing authors: Trung Dac Nguyen (ORNL) Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_born_coul_wolf_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_born_coul_wolf_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_born_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_born_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_born_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_buck_coul_cut_gpu.cpp
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@ -15,11 +15,11 @@
Contributing authors: Trung Dac Nguyen (ORNL) Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_buck_coul_cut_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_buck_coul_cut_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_buck_coul_long_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_buck_coul_long_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_buck_coul_long_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_buck_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_buck_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_buck_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_colloid_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_colloid_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_colloid_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_coul_cut_gpu.cpp
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@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen Contributing author: Trung Dac Nguyen
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_coul_cut_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_coul_cut_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_coul_debye_gpu.cpp
View File

@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ndtrung@umich.edu) Contributing author: Trung Dac Nguyen (ndtrung@umich.edu)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_coul_debye_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_coul_debye_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

2
src/GPU/pair_coul_dsf_gpu.cpp
View File

@ -15,11 +15,11 @@
Contributing author: Trung Dac Nguyen (ORNL) Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_coul_dsf_gpu.h"
#include <cmath> #include <cmath>
#include <cstdio> #include <cstdio>
#include <cstdlib> #include <cstdlib>
#include <cstring> #include <cstring>
#include "pair_coul_dsf_gpu.h"
#include "atom.h" #include "atom.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "comm.h" #include "comm.h"

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