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Merge branch 'master' into multi-config-support

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This commit is contained in:
Axel Kohlmeyer
2021-09-20 20:42:03 -04:00
parent daa39d680c 8d8c710982
commit fe64649e49
414 changed files with 2160 additions and 2577 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
cmake/Modules/OpenCLLoader.cmake
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@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

7
cmake/Modules/Packages/GPU.cmake
View File

@ -71,6 +71,11 @@ if(GPU_API STREQUAL "CUDA")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Untested CUDA Toolkit version. Use at your own risk")
else()
# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
@ -107,8 +112,6 @@ if(GPU_API STREQUAL "CUDA")
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}

2
cmake/Modules/Packages/ML-QUIP.cmake
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@ -38,7 +38,7 @@ if(DOWNLOAD_QUIP)
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n")
set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
message(STATUS "QUIP download via git requested - we will build our own")

25
cmake/iwyu/iwyu-extra-map.imp
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@ -1,7 +1,28 @@
[
{ include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
{ include: [ "<bits/exception.h>", public, "<exception>", public ] },
{ include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
{ include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
{ include: [ "@<(cell|c_loops|container).hh>", private, "<voro++.hh>", public ] },
{ include: [ "@\"atom_vec_.*.h\"", public, "\"style_atom.h\"", public ] },
{ include: [ "@\"body_.*.h\"", public, "\"style_body.h\"", public ] },
{ include: [ "@\"compute_.*.h\"", public, "\"style_compute.h\"", public ] },
{ include: [ "@\"fix_.*.h\"", public, "\"style_fix.h\"", public ] },
{ include: [ "@\"dump_.*.h\"", public, "\"style_dump.h\"", public ] },
{ include: [ "@\"min_.*.h\"", public, "\"style_minimize.h\"", public ] },
{ include: [ "@\"reader_.*.h\"", public, "\"style_reader.h\"", public ] },
{ include: [ "@\"region_.*.h\"", public, "\"style_region.h\"", public ] },
{ include: [ "@\"pair_.*.h\"", public, "\"style_pair.h\"", public ] },
{ include: [ "@\"angle_.*.h\"", public, "\"style_angle.h\"", public ] },
{ include: [ "@\"bond_.*.h\"", public, "\"style_bond.h\"", public ] },
{ include: [ "@\"dihedral_.*.h\"", public, "\"style_dihedral.h\"", public ] },
{ include: [ "@\"improper_.*.h\"", public, "\"style_improper.h\"", public ] },
{ include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
{ include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
{ include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
{ include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
{ include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
{ include: [ "<float.h>", public, "<cfloat>", public ] },
{ include: [ "<limits.h>", public, "<climits>", public ] },
{ include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
]

1
cmake/presets/most.cmake
View File

@ -24,6 +24,7 @@ set(ALL_PACKAGES
DRUDE
EFF
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
EXTRA-MOLECULE
EXTRA-PAIR

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "31 August 2021" "2021-08-31"
.TH LAMMPS "20 September 2021" "2021-09-20"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

13
doc/src/Build_development.rst
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@ -58,13 +58,16 @@ Report missing and unneeded '#include' statements (CMake only)
The conventions for how and when to use and order include statements in
LAMMPS are documented in :doc:`Modify_style`. To assist with following
these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
This is still under development and for large and complex projects like LAMMPS
This tool is still under development and for large and complex projects like LAMMPS
there are some false positives, so suggested changes need to be verified manually.
It is recommended to use at least version 0.14, which has much fewer incorrect
reports than earlier versions.
It is recommended to use at least version 0.16, which has much fewer incorrect
reports than earlier versions. To install the IWYU toolkit, you need to have
the clang compiler **and** its development package installed. Download the IWYU
version that matches the version of the clang compiler, configure, build, and
install it.
The necessary steps to generate the report can be enabled via a
CMake variable:
The necessary steps to generate the report can be enabled via a CMake variable
during CMake configuration.
.. code-block:: bash

3
doc/src/Developer_utils.rst
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@ -203,6 +203,9 @@ Convenience functions
.. doxygenfunction:: date2num
:project: progguide
.. doxygenfunction:: current_date
:project: progguide
Customized standard functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

3
doc/src/Errors_debug.rst
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@ -40,11 +40,10 @@ We use it to show how to identify the origin of a segmentation fault.
After recompiling LAMMPS and running the input you should get something like this:
.. code-block:
.. code-block::
$ ./lmp -in in.melt
LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)

10
doc/src/Errors_messages.rst
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@ -7879,19 +7879,19 @@ keyword to allow for additional bonds to be formed
*Unexpected end of -reorder file*
Self-explanatory.
*Unexpected empty line in AngleCoeffs section*
*Unexpected empty line in Angle Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in BondCoeffs section*
*Unexpected empty line in Bond Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in DihedralCoeffs section*
*Unexpected empty line in Dihedral Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in ImproperCoeffs section*
*Unexpected empty line in Improper Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected empty line in PairCoeffs section*
*Unexpected empty line in Pair Coeffs section*
Read a blank line where there should be coefficient data.
*Unexpected end of custom file*

2
doc/src/Intro_website.rst
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@ -26,7 +26,7 @@ available online are listed below.
* `Tutorials <https://www.lammps.org/tutorials.html>`_
* `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
* `Other software usable with LAMMPS <https://www.lammps.org/external.html>`_
* `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
* `Benchmark performance <https://www.lammps.org/bench.html>`_

4
doc/src/Modify_contribute.rst
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@ -115,8 +115,8 @@ External contributions
If you prefer to do so, you can also develop and support your add-on
feature **without** having it included in the LAMMPS distribution, for
example as a download from a website of your own. See the `Offsite
LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page
example as a download from a website of your own. See the `External
LAMMPS packages and tools <https://www.lammps.org/external.html>`_ page
of the LAMMPS website for examples of groups that do this. We are happy
to advertise your package and website from that page. Simply email the
`developers <https://www.lammps.org/authors.html>`_ with info about your

29
doc/src/Modify_style.rst
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@ -305,19 +305,22 @@ you are uncertain, please ask.
FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg`
convenience function where possible.
- header files should only include the absolute minimum number of
include files and **must not** contain any ``using`` statements;
rather the include statements should be put into the corresponding
implementation files. For implementation files, the
"include-what-you-use" principle should be employed. However, when
including the ``pointers.h`` header (or one of the base classes
derived from it) certain headers will be included and thus need to be
specified. These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`,
`string`, `utils.h`, `fmt/format.h`, `climits`, `cinttypes`. This also
means any header can assume that `FILE`, `NULL`, and `INT_MAX` are
defined.
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not** contain
any ``using`` statements. Typically that would be only the header for
the base class. Instead any include statements should be put into the
corresponding implementation files and forward declarations be used.
For implementation files, the "include what you use" principle should
be employed. However, there is the notable exception that when the
``pointers.h`` header is included (or one of the base classes derived
from it) certain headers will always be included and thus do not need
to be explicitly specified.
These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`,
`vector`, `fmt/format.h`, `climits`, `cinttypes`.
This also means any such file can assume that `FILE`, `NULL`, and
`INT_MAX` are defined.
- header files that define a new LAMMPS style (i.e. that have a
- Header files that define a new LAMMPS style (i.e. that have a
``SomeStyle(some/name,SomeName);`` macro in them) should only use the
include file for the base class and otherwise use forward declarations
and pointers; when interfacing to a library use the PIMPL (pointer
@ -325,7 +328,7 @@ you are uncertain, please ask.
that contains all library specific data (and thus requires the library
header) but use a forward declaration and define the struct only in
the implementation file. This is a **strict** requirement since this
is where type clashes between packages and hard to fine bugs have
is where type clashes between packages and hard to find bugs have
regularly manifested in the past.
- Please use clang-format only to reformat files that you have

2
doc/src/Tools.rst
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@ -7,7 +7,7 @@ steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <https://www.lammps.org/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
* `External LAMMPS packages & tools <https://www.lammps.org/external.html>`_
* `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at

5
doc/src/fix_brownian.rst
View File

@ -8,9 +8,8 @@ fix brownian command
fix brownian/sphere command
===========================
fix brownian/sphere command
===========================
fix brownian/asphere command
============================
Syntax
""""""

2
doc/src/package.rst
View File

@ -27,7 +27,7 @@ Syntax
on = set Newton pairwise flag on (currently not allowed)
*pair/only* = *off* or *on*
off = apply "gpu" suffix to all available styles in the GPU package (default)
on - apply "gpu" suffix only pair styles
on = apply "gpu" suffix only pair styles
*binsize* value = size
size = bin size for neighbor list construction (distance units)
*split* = fraction

48
doc/src/pair_hybrid.rst
View File

@ -198,8 +198,8 @@ same:
Coefficients must be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as described above, or in the
data file read by the :doc:`read_data <read_data>` commands, or by
mixing as described below.
"Pair Coeffs" or "PairIJ Coeffs" section of the data file read by the
:doc:`read_data <read_data>` command, or by mixing as described below.
For all of the *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles,
every atom type pair I,J (where I <= J) must be assigned to at least one
@ -208,14 +208,21 @@ examples above, or in the data file read by the :doc:`read_data
<read_data>`, or by mixing as described below. Also all sub-styles
must be used at least once in a :doc:`pair_coeff <pair_coeff>` command.
.. note::
LAMMPS never performs mixing of parameters from different sub-styles,
**even** if they use the same type of coefficients, e.g. contain
a Lennard-Jones potential variant. Those parameters must be provided
explicitly.
If you want there to be no interactions between a particular pair of
atom types, you have 3 choices. You can assign the type pair to some
sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
atom types, you have 3 choices. You can assign the pair of atom types
to some sub-style and use the :doc:`neigh_modify exclude type <neigh_modify>`
command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ
potential). Or, for *hybrid*, *hybrid/overlay*, or *hybrid/scaled*
simulations, you can use this form of the pair_coeff command in your
input script:
input script or the "PairIJ Coeffs" section of your data file:
.. code-block:: LAMMPS
@ -238,19 +245,20 @@ styles with different requirements.
----------
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying weightings that change the strength of pairwise
interactions between pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology, as normally set by the
:doc:`special_bonds <special_bonds>` command. Different weights can be
assigned to different pair hybrid sub-styles via the :doc:`pair_modify
special <pair_modify>` command. This allows multiple force fields to be
used in a model of a hybrid system, however, there is no consistent
approach to determine parameters automatically for the interactions
between the two force fields, this is only recommended when particles
Different force fields (e.g. CHARMM vs. AMBER) may have different rules
for applying exclusions or weights that change the strength of pairwise
non-bonded interactions between pairs of atoms that are also 1-2, 1-3,
and 1-4 neighbors in the molecular bond topology. This is normally a
global setting defined the :doc:`special_bonds <special_bonds>` command.
However, different weights can be assigned to different hybrid
sub-styles via the :doc:`pair_modify special <pair_modify>` command.
This allows multiple force fields to be used in a model of a hybrid
system, however, there is no consistent approach to determine parameters
automatically for the interactions **between** atoms of the two force
fields, thus this approach this is only recommended when particles
described by the different force fields do not mix.
Here is an example for mixing CHARMM and AMBER: The global *amber*
Here is an example for combining CHARMM and AMBER: The global *amber*
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:
@ -260,7 +268,7 @@ then overrides them with 0.0 only for CHARMM:
pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
The this input achieves the same effect:
This input achieves the same effect:
.. code-block:: LAMMPS
@ -270,9 +278,9 @@ The this input achieves the same effect:
pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
Here is an example for combining Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where - for the
Tersoff part of the system - the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:

2
doc/src/read_data.rst
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@ -619,7 +619,7 @@ of analysis.
* - bond
- atom-ID molecule-ID atom-type x y z
* - charge
- atom-type q x y z
- atom-ID atom-type q x y z
* - dipole
- atom-ID atom-type q x y z mux muy muz
* - dpd

1
doc/utils/sphinx-config/conf.py.in
View File

@ -418,6 +418,7 @@ html_context['current_version'] = os.environ.get('LAMMPS_WEBSITE_BUILD_VERSION',
html_context['git_commit'] = git_commit
html_context['versions'] = [
('latest', 'https://docs.lammps.org/latest/'),
('stable', 'https://docs.lammps.org/stable/'),
(version, 'https://docs.lammps.org/')
]
html_context['downloads'] = [('PDF', 'Manual.pdf')]

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

@ -2440,6 +2440,7 @@ packings
padua
Padua
pafi
PairIJ
palegoldenrod
palegreen
paleturquoise

6
examples/COUPLE/lammps_quest/README
View File

@ -1,3 +1,9 @@
IMPORTANT NOTE: This example has not been updated since 2014,
so it is not likely to work anymore out of the box. There have
been changes to LAMMPS and its library interface that would need
to be applied. Please see the manual for the documentation of
the library interface.
This directory has an application that runs classical MD via LAMMPS,
but uses quantum forces calculated by the Quest DFT (density
functional) code in place of the usual classical MD forces calculated

6
examples/COUPLE/lammps_spparks/README
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@ -1,3 +1,9 @@
IMPORTANT NOTE: This example has not been updated since 2013,
so it is not likely to work anymore out of the box. There have
been changes to LAMMPS and its library interface that would need
to be applied. Please see the manual for the documentation of
the library interface.
This directory has an application that models grain growth in the
presence of strain.

20
examples/COUPLE/multiple/multiple.cpp
View File

@ -28,13 +28,9 @@
#include <cstdlib>
#include <cstring>
#include "lammps.h" // these are LAMMPS include files
#include "input.h"
#include "atom.h"
#define LAMMPS_LIB_MPI // to make lammps_open() visible
#include "library.h"
using namespace LAMMPS_NS;
int main(int narg, char **arg)
{
// setup MPI and various communicators
@ -74,7 +70,7 @@ int main(int narg, char **arg)
char str1[32],str2[32],str3[32];
char **lmparg = new char*[8];
lmparg[0] = NULL; // required placeholder for program name
lmparg[0] = (char *) "LAMMPS"; // required placeholder for program name
lmparg[1] = (char *) "-screen";
sprintf(str1,"screen.%d",instance);
lmparg[2] = str1;
@ -86,13 +82,9 @@ int main(int narg, char **arg)
sprintf(str3,"%g",temperature + instance*tdelta);
lmparg[7] = str3;
// open N instances of LAMMPS
// either of these methods will work
// create N instances of LAMMPS
LAMMPS *lmp = new LAMMPS(8,lmparg,comm_lammps);
//LAMMPS *lmp;
//lammps_open(8,lmparg,comm_lammps,(void **) &lmp);
void *lmp = lammps_open(8,lmparg,comm_lammps,NULL);
delete [] lmparg;
@ -103,7 +95,7 @@ int main(int narg, char **arg)
// query final temperature and print result for each instance
double *ptr = (double *)
lammps_extract_compute(lmp,(char *) "thermo_temp",0,0);
lammps_extract_compute(lmp,"thermo_temp",LMP_STYLE_GLOBAL,LMP_TYPE_SCALAR);
double finaltemp = *ptr;
double *temps = new double[ninstance];
@ -125,7 +117,7 @@ int main(int narg, char **arg)
// delete LAMMPS instances
delete lmp;
lammps_close(lmp);
// close down MPI

2
examples/COUPLE/plugin/README
View File

@ -13,7 +13,7 @@ like below.
mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
mpicc -c -O -Wall -g simple.c
mpicc simple.o liblammsplugin.o -ldl -o simpleC
mpicc simple.o liblammpsplugin.o -ldl -o simpleC
You also need to build LAMMPS as a shared library
(see examples/COUPLE/README), e.g.

82
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -38,44 +38,98 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
ADDSYM(open);
ADDSYM(open_no_mpi);
ADDSYM(open_fortran);
ADDSYM(close);
ADDSYM(version);
ADDSYM(mpi_init);
ADDSYM(mpi_finalize);
ADDSYM(kokkos_finalize);
ADDSYM(python_finalize);
ADDSYM(file);
ADDSYM(command);
ADDSYM(commands_list);
ADDSYM(commands_string);
ADDSYM(free);
ADDSYM(extract_setting);
ADDSYM(extract_global);
ADDSYM(get_natoms);
ADDSYM(get_thermo);
ADDSYM(extract_box);
ADDSYM(reset_box);
ADDSYM(memory_usage);
ADDSYM(get_mpi_comm);
ADDSYM(extract_setting);
ADDSYM(extract_global_datatype);
ADDSYM(extract_global);
ADDSYM(extract_atom_datatype);
ADDSYM(extract_atom);
ADDSYM(extract_compute);
ADDSYM(extract_fix);
ADDSYM(extract_variable);
ADDSYM(get_thermo);
ADDSYM(get_natoms);
ADDSYM(set_variable);
ADDSYM(reset_box);
ADDSYM(gather_atoms);
ADDSYM(gather_atoms_concat);
ADDSYM(gather_atoms_subset);
ADDSYM(scatter_atoms);
ADDSYM(scatter_atoms_subset);
ADDSYM(gather_bonds);
ADDSYM(set_fix_external_callback);
ADDSYM(create_atoms);
ADDSYM(config_has_package);
ADDSYM(config_package_count);
ADDSYM(config_package_name);
ADDSYM(find_pair_neighlist);
ADDSYM(find_fix_neighlist);
ADDSYM(find_compute_neighlist);
ADDSYM(neighlist_num_elements);
ADDSYM(neighlist_element_neighbors);
ADDSYM(version);
ADDSYM(get_os_info);
ADDSYM(config_has_mpi_support);
ADDSYM(config_has_gzip_support);
ADDSYM(config_has_png_support);
ADDSYM(config_has_jpeg_support);
ADDSYM(config_has_ffmpeg_support);
ADDSYM(config_has_exceptions);
ADDSYM(create_atoms);
ADDSYM(config_has_package);
ADDSYM(config_package_count);
ADDSYM(config_package_name);
ADDSYM(config_accelerator);
ADDSYM(has_gpu_device);
ADDSYM(get_gpu_device_info);
ADDSYM(has_style);
ADDSYM(style_count);
ADDSYM(style_name);
ADDSYM(has_id);
ADDSYM(id_count);
ADDSYM(id_name);
ADDSYM(plugin_count);
ADDSYM(plugin_name);
ADDSYM(set_fix_external_callback);
ADDSYM(fix_external_get_force);
ADDSYM(fix_external_set_energy_global);
ADDSYM(fix_external_set_energy_peratom);
ADDSYM(fix_external_set_virial_global);
ADDSYM(fix_external_set_virial_peratom);
ADDSYM(fix_external_set_vector_length);
ADDSYM(fix_external_set_vector);
ADDSYM(free);
ADDSYM(is_running);
ADDSYM(force_timeout);
#ifdef LAMMPS_EXCEPTIONS
lmp->has_exceptions = 1;
ADDSYM(has_error);

128
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -39,75 +39,121 @@ extern "C" {
#if defined(LAMMPS_BIGBIG)
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
#elif defined(LAMMPS_SMALLBIG)
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
#else
#elif defined(LAMMPS_SMALLSMALL)
typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
#else
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
#endif
struct _liblammpsplugin {
int abiversion;
int has_exceptions;
void *handle;
void (*open)(int, char **, MPI_Comm, void **);
void (*open_no_mpi)(int, char **, void **);
void *(*open)(int, char **, MPI_Comm, void **);
void *(*open_no_mpi)(int, char **, void **);
void *(*open_fortran)(int, char **, void **, int);
void (*close)(void *);
int (*version)(void *);
void (*mpi_init)();
void (*mpi_finalize)();
void (*kokkos_finalize)();
void (*python_finalize)();
void (*file)(void *, char *);
char *(*command)(void *, char *);
void (*commands_list)(void *, int, char **);
void (*commands_string)(void *, char *);
void (*free)(void *);
int (*extract_setting)(void *, char *);
void *(*extract_global)(void *, char *);
char *(*command)(void *, const char *);
void (*commands_list)(void *, int, const char **);
void (*commands_string)(void *, const char *);
double (*get_natoms)(void *);
double (*get_thermo)(void *, char *);
void (*extract_box)(void *, double *, double *,
double *, double *, double *, int *, int *);
void *(*extract_atom)(void *, char *);
void *(*extract_compute)(void *, char *, int, int);
void *(*extract_fix)(void *, char *, int, int, int, int);
void *(*extract_variable)(void *, char *, char *);
double (*get_thermo)(void *, char *);
int (*get_natoms)(void *);
int (*set_variable)(void *, char *, char *);
void (*reset_box)(void *, double *, double *, double, double, double);
void (*memory_usage)(void *, double *);
int (*get_mpi_comm)(void *);
int (*extract_setting)(void *, const char *);
int *(*extract_global_datatype)(void *, const char *);
void *(*extract_global)(void *, const char *);
void *(*extract_atom_datatype)(void *, const char *);
void *(*extract_atom)(void *, const char *);
void *(*extract_compute)(void *, const char *, int, int);
void *(*extract_fix)(void *, const char *, int, int, int, int);
void *(*extract_variable)(void *, const char *, char *);
int (*set_variable)(void *, char *, char *);
void (*gather_atoms)(void *, char *, int, int, void *);
void (*gather_atoms_concat)(void *, char *, int, int, void *);
void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);
void (*scatter_atoms)(void *, char *, int, int, void *);
void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
void (*set_fix_external_callback)(void *, char *, FixExternalFnPtr, void*);
void (*gather_bonds)(void *, void *);
int (*config_has_package)(char * package_name);
int (*config_package_count)();
int (*config_package_name)(int index, char * buffer, int max_size);
// lammps_create_atoms() takes tagint and imageint as args
// ifdef insures they are compatible with rest of LAMMPS
// caller must match to how LAMMPS library is built
#ifndef LAMMPS_BIGBIG
void (*create_atoms)(void *, int, int *, int *, double *,
double *, int *, int);
#else
void (*create_atoms)(void *, int, int64_t *, int *, double *,
double *, int64_t *, int);
#endif
int (*find_pair_neighlist)(void *, const char *, int, int, int);
int (*find_fix_neighlist)(void *, const char *, int);
int (*find_compute_neighlist)(void *, char *, int);
int (*neighlist_num_elements)(void *, int);
void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
int (*version)(void *);
void (*get_os_info)(char *, int);
int (*config_has_mpi_support)();
int (*config_has_gzip_support)();
int (*config_has_png_support)();
int (*config_has_jpeg_support)();
int (*config_has_ffmpeg_support)();
int (*config_has_exceptions)();
int (*find_pair_neighlist)(void* ptr, char * style, int exact, int nsub, int request);
int (*find_fix_neighlist)(void* ptr, char * id, int request);
int (*find_compute_neighlist)(void* ptr, char * id, int request);
int (*neighlist_num_elements)(void* ptr, int idx);
void (*neighlist_element_neighbors)(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
int (*config_has_package)(const char *);
int (*config_package_count)();
int (*config_package_name)(int, char *, int);
// lammps_create_atoms() takes tagint and imageint as args
// ifdef insures they are compatible with rest of LAMMPS
// caller must match to how LAMMPS library is built
int (*config_accelerator)(const char *, const char *, const char *);
int (*has_gpu_device)();
void (*get_gpu_device_info)(char *, int);
#ifdef LAMMPS_BIGBIG
void (*create_atoms)(void *, int, int64_t *, int *,
double *, double *, int64_t *, int);
#else
void (*create_atoms)(void *, int, int *, int *,
double *, double *, int *, int);
#endif
int (*has_style)(void *, const char *, const char *);
int (*style_count)(void *, const char *);
int (*style_name)(void *, const char *, int, char *, int);
int (*has_id)(void *, const char *, const char *);
int (*id_count)(void *, const char *);
int (*id_name)(void *, const char *, int, char *, int);
int (*plugin_count)();
int (*plugin_name)(int, char *, char *, int);
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*);
void (*fix_external_get_force)(void *, const char *);
void (*fix_external_set_energy_global)(void *, const char *, double);
void (*fix_external_set_energy_peratom)(void *, const char *, double *);
void (*fix_external_set_virial_global)(void *, const char *, double *);
void (*fix_external_set_virial_peratom)(void *, const char *, double **);
void (*fix_external_set_vector_length)(void *, const char *, int);
void (*fix_external_set_vector)(void *, const char *, int, double);
void (*free)(void *);
void (*is_running)(void *);
void (*force_timeout)(void *);
int (*has_error)(void *);
int (*get_last_error_message)(void *, char *, int);

225
examples/COUPLE/plugin/log.simple.plugin.1
View File

@ -1,9 +1,12 @@
LAMMPS (18 Feb 2020)
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
LAMMPS (31 Aug 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
1 by 1 by 1 MPI processor grid
Created 256 atoms
create_atoms CPU = 0.000297844 secs
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
create_atoms CPU = 0.001 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
@ -14,108 +17,108 @@ Neighbor list info ...
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
Loop time of 0.00164276 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00239712 on 1 procs for 10 steps with 256 atoms
Performance: 2629719.113 tau/day, 6087.313 timesteps/s
93.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1802163.347 tau/day, 4171.674 timesteps/s
97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014956 | 0.0014956 | 0.0014956 | 0.0 | 91.04
Pair | 0.0020572 | 0.0020572 | 0.0020572 | 0.0 | 85.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.045e-05 | 8.045e-05 | 8.045e-05 | 0.0 | 4.90
Output | 1.1399e-05 | 1.1399e-05 | 1.1399e-05 | 0.0 | 0.69
Modify | 3.7431e-05 | 3.7431e-05 | 3.7431e-05 | 0.0 | 2.28
Other | | 1.789e-05 | | | 1.09
Comm | 0.00018731 | 0.00018731 | 0.00018731 | 0.0 | 7.81
Output | 4.478e-05 | 4.478e-05 | 4.478e-05 | 0.0 | 1.87
Modify | 6.3637e-05 | 6.3637e-05 | 6.3637e-05 | 0.0 | 2.65
Other | | 4.419e-05 | | | 1.84
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9984 ave 9984 max 9984 min
Neighs: 9984.00 ave 9984 max 9984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 39
Ave neighs/atom = 39.000000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 10
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
Loop time of 0.00199768 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00329271 on 1 procs for 10 steps with 256 atoms
Performance: 2162504.180 tau/day, 5005.797 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1311987.619 tau/day, 3037.008 timesteps/s
96.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018518 | 0.0018518 | 0.0018518 | 0.0 | 92.70
Pair | 0.0029015 | 0.0029015 | 0.0029015 | 0.0 | 88.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.9768e-05 | 7.9768e-05 | 7.9768e-05 | 0.0 | 3.99
Output | 1.1433e-05 | 1.1433e-05 | 1.1433e-05 | 0.0 | 0.57
Modify | 3.6904e-05 | 3.6904e-05 | 3.6904e-05 | 0.0 | 1.85
Other | | 1.773e-05 | | | 0.89
Comm | 0.00021807 | 0.00021807 | 0.00021807 | 0.0 | 6.62
Output | 4.9163e-05 | 4.9163e-05 | 4.9163e-05 | 0.0 | 1.49
Modify | 7.0573e-05 | 7.0573e-05 | 7.0573e-05 | 0.0 | 2.14
Other | | 5.339e-05 | | | 1.62
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9952 ave 9952 max 9952 min
Neighs: 9952.00 ave 9952 max 9952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9952
Ave neighs/atom = 38.875
Ave neighs/atom = 38.875000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 20
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
Loop time of 0.000304321 on 1 procs for 1 steps with 256 atoms
Loop time of 0.000638039 on 1 procs for 1 steps with 256 atoms
Performance: 1419553.695 tau/day, 3286.004 timesteps/s
98.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 677074.599 tau/day, 1567.302 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00027815 | 0.00027815 | 0.00027815 | 0.0 | 91.40
Pair | 0.00042876 | 0.00042876 | 0.00042876 | 0.0 | 67.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.321e-06 | 8.321e-06 | 8.321e-06 | 0.0 | 2.73
Output | 1.0513e-05 | 1.0513e-05 | 1.0513e-05 | 0.0 | 3.45
Modify | 3.968e-06 | 3.968e-06 | 3.968e-06 | 0.0 | 1.30
Other | | 3.365e-06 | | | 1.11
Comm | 5.2872e-05 | 5.2872e-05 | 5.2872e-05 | 0.0 | 8.29
Output | 0.00012218 | 0.00012218 | 0.00012218 | 0.0 | 19.15
Modify | 1.3762e-05 | 1.3762e-05 | 1.3762e-05 | 0.0 | 2.16
Other | | 2.047e-05 | | | 3.21
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9705 ave 9705 max 9705 min
Neighs: 9705.00 ave 9705 max 9705 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Force on 1 atom via extract_atom: 26.9581
@ -124,136 +127,136 @@ Setting up Verlet run ...
Unit style : lj
Current step : 21
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
Loop time of 0.00196027 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00281277 on 1 procs for 10 steps with 256 atoms
Performance: 2203779.175 tau/day, 5101.341 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1535852.558 tau/day, 3555.214 timesteps/s
92.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018146 | 0.0018146 | 0.0018146 | 0.0 | 92.57
Pair | 0.0024599 | 0.0024599 | 0.0024599 | 0.0 | 87.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.0268e-05 | 8.0268e-05 | 8.0268e-05 | 0.0 | 4.09
Output | 1.0973e-05 | 1.0973e-05 | 1.0973e-05 | 0.0 | 0.56
Modify | 3.6913e-05 | 3.6913e-05 | 3.6913e-05 | 0.0 | 1.88
Other | | 1.756e-05 | | | 0.90
Comm | 0.00020234 | 0.00020234 | 0.00020234 | 0.0 | 7.19
Output | 3.6436e-05 | 3.6436e-05 | 3.6436e-05 | 0.0 | 1.30
Modify | 6.7542e-05 | 6.7542e-05 | 6.7542e-05 | 0.0 | 2.40
Other | | 4.655e-05 | | | 1.65
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9688 ave 9688 max 9688 min
Neighs: 9688.00 ave 9688 max 9688 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9688
Ave neighs/atom = 37.8438
Ave neighs/atom = 37.843750
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 31
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
Loop time of 0.00433063 on 1 procs for 20 steps with 256 atoms
Loop time of 0.00560916 on 1 procs for 20 steps with 256 atoms
Performance: 1995088.941 tau/day, 4618.261 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1540338.414 tau/day, 3565.598 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035121 | 0.0035121 | 0.0035121 | 0.0 | 81.10
Neigh | 0.00050258 | 0.00050258 | 0.00050258 | 0.0 | 11.61
Comm | 0.00019444 | 0.00019444 | 0.00019444 | 0.0 | 4.49
Output | 1.2092e-05 | 1.2092e-05 | 1.2092e-05 | 0.0 | 0.28
Modify | 7.2917e-05 | 7.2917e-05 | 7.2917e-05 | 0.0 | 1.68
Other | | 3.647e-05 | | | 0.84
Pair | 0.0044403 | 0.0044403 | 0.0044403 | 0.0 | 79.16
Neigh | 0.00056186 | 0.00056186 | 0.00056186 | 0.0 | 10.02
Comm | 0.00036797 | 0.00036797 | 0.00036797 | 0.0 | 6.56
Output | 3.676e-05 | 3.676e-05 | 3.676e-05 | 0.0 | 0.66
Modify | 0.00011282 | 0.00011282 | 0.00011282 | 0.0 | 2.01
Other | | 8.943e-05 | | | 1.59
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1421 ave 1421 max 1421 min
Nghost: 1421.00 ave 1421 max 1421 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9700 ave 9700 max 9700 min
Neighs: 9700.00 ave 9700 max 9700 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 1
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 51
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
Loop time of 0.00196567 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00373815 on 1 procs for 10 steps with 256 atoms
Performance: 2197727.285 tau/day, 5087.332 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1155650.623 tau/day, 2675.117 timesteps/s
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018222 | 0.0018222 | 0.0018222 | 0.0 | 92.70
Pair | 0.0030908 | 0.0030908 | 0.0030908 | 0.0 | 82.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.8285e-05 | 7.8285e-05 | 7.8285e-05 | 0.0 | 3.98
Output | 1.0862e-05 | 1.0862e-05 | 1.0862e-05 | 0.0 | 0.55
Modify | 3.6719e-05 | 3.6719e-05 | 3.6719e-05 | 0.0 | 1.87
Other | | 1.764e-05 | | | 0.90
Comm | 0.00038189 | 0.00038189 | 0.00038189 | 0.0 | 10.22
Output | 4.1615e-05 | 4.1615e-05 | 4.1615e-05 | 0.0 | 1.11
Modify | 0.00013851 | 0.00013851 | 0.00013851 | 0.0 | 3.71
Other | | 8.533e-05 | | | 2.28
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1421 ave 1421 max 1421 min
Nghost: 1421.00 ave 1421 max 1421 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9700 ave 9700 max 9700 min
Neighs: 9700.00 ave 9700 max 9700 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
Unit style : lj
Current step : 61
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
Loop time of 0.00430528 on 1 procs for 20 steps with 256 atoms
Loop time of 0.00612177 on 1 procs for 20 steps with 256 atoms
Performance: 2006838.581 tau/day, 4645.460 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1411356.519 tau/day, 3267.029 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0034931 | 0.0034931 | 0.0034931 | 0.0 | 81.13
Neigh | 0.00050437 | 0.00050437 | 0.00050437 | 0.0 | 11.72
Comm | 0.0001868 | 0.0001868 | 0.0001868 | 0.0 | 4.34
Output | 1.1699e-05 | 1.1699e-05 | 1.1699e-05 | 0.0 | 0.27
Modify | 7.3308e-05 | 7.3308e-05 | 7.3308e-05 | 0.0 | 1.70
Other | | 3.604e-05 | | | 0.84
Pair | 0.0047211 | 0.0047211 | 0.0047211 | 0.0 | 77.12
Neigh | 0.00083088 | 0.00083088 | 0.00083088 | 0.0 | 13.57
Comm | 0.00032716 | 0.00032716 | 0.00032716 | 0.0 | 5.34
Output | 3.9891e-05 | 3.9891e-05 | 3.9891e-05 | 0.0 | 0.65
Modify | 0.00010926 | 0.00010926 | 0.00010926 | 0.0 | 1.78
Other | | 9.346e-05 | | | 1.53
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1405 ave 1405 max 1405 min
Nghost: 1405.00 ave 1405 max 1405 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9701 ave 9701 max 9701 min
Neighs: 9701.00 ave 9701 max 9701 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9701
Ave neighs/atom = 37.8945
Ave neighs/atom = 37.894531
Neighbor list builds = 1
Dangerous builds not checked
Deleted 256 atoms, new total = 0
@ -261,34 +264,34 @@ Setting up Verlet run ...
Unit style : lj
Current step : 81
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
Step Temp E_pair E_mol TotEng Press
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
Loop time of 0.00195843 on 1 procs for 10 steps with 256 atoms
Loop time of 0.00319065 on 1 procs for 10 steps with 256 atoms
Performance: 2205851.941 tau/day, 5106.139 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1353954.393 tau/day, 3134.154 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0018143 | 0.0018143 | 0.0018143 | 0.0 | 92.64
Pair | 0.0027828 | 0.0027828 | 0.0027828 | 0.0 | 87.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.8608e-05 | 7.8608e-05 | 7.8608e-05 | 0.0 | 4.01
Output | 1.0786e-05 | 1.0786e-05 | 1.0786e-05 | 0.0 | 0.55
Modify | 3.7106e-05 | 3.7106e-05 | 3.7106e-05 | 0.0 | 1.89
Other | | 1.762e-05 | | | 0.90
Comm | 0.00023286 | 0.00023286 | 0.00023286 | 0.0 | 7.30
Output | 4.0459e-05 | 4.0459e-05 | 4.0459e-05 | 0.0 | 1.27
Modify | 7.3576e-05 | 7.3576e-05 | 7.3576e-05 | 0.0 | 2.31
Other | | 6.094e-05 | | | 1.91
Nlocal: 256 ave 256 max 256 min
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431 ave 1431 max 1431 min
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9705 ave 9705 max 9705 min
Neighs: 9705.00 ave 9705 max 9705 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:00

213
examples/COUPLE/plugin/log.simple.plugin.4
View File

@ -1,9 +1,12 @@
LAMMPS (18 Feb 2020)
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
LAMMPS (31 Aug 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
1 by 1 by 2 MPI processor grid
Created 256 atoms
create_atoms CPU = 0.000265157 secs
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
create_atoms CPU = 0.003 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
@ -14,7 +17,7 @@ Neighbor list info ...
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
@ -24,30 +27,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
Loop time of 0.00115264 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00330899 on 2 procs for 10 steps with 256 atoms
Performance: 3747912.946 tau/day, 8675.724 timesteps/s
94.5% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 1305535.501 tau/day, 3022.073 timesteps/s
75.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00074885 | 0.00075021 | 0.00075156 | 0.0 | 65.09
Pair | 0.0013522 | 0.0013813 | 0.0014104 | 0.1 | 41.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00031829 | 0.00031943 | 0.00032056 | 0.0 | 27.71
Output | 9.306e-06 | 2.6673e-05 | 4.4041e-05 | 0.0 | 2.31
Modify | 2.0684e-05 | 2.0891e-05 | 2.1098e-05 | 0.0 | 1.81
Other | | 3.544e-05 | | | 3.07
Comm | 0.00049139 | 0.00054241 | 0.00059342 | 0.0 | 16.39
Output | 3.6986e-05 | 0.00056588 | 0.0010948 | 0.0 | 17.10
Modify | 4.3909e-05 | 4.3924e-05 | 4.3939e-05 | 0.0 | 1.33
Other | | 0.0007755 | | | 23.44
Nlocal: 128 ave 128 max 128 min
Nlocal: 128.000 ave 128 max 128 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 1109 ave 1109 max 1109 min
Nghost: 1109.00 ave 1109 max 1109 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 4992 ave 4992 max 4992 min
Neighs: 4992.00 ave 4992 max 4992 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 39
Ave neighs/atom = 39.000000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -58,30 +61,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
Loop time of 0.00120443 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00648485 on 2 procs for 10 steps with 256 atoms
Performance: 3586761.860 tau/day, 8302.689 timesteps/s
95.5% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 666168.017 tau/day, 1542.056 timesteps/s
44.3% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00087798 | 0.00091359 | 0.0009492 | 0.0 | 75.85
Pair | 0.0022373 | 0.0024405 | 0.0026437 | 0.4 | 37.63
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016739 | 0.00020368 | 0.00023997 | 0.0 | 16.91
Output | 1.0124e-05 | 3.0513e-05 | 5.0901e-05 | 0.0 | 2.53
Modify | 1.89e-05 | 1.9812e-05 | 2.0725e-05 | 0.0 | 1.64
Other | | 3.683e-05 | | | 3.06
Comm | 0.0024446 | 0.0026464 | 0.0028481 | 0.4 | 40.81
Output | 3.9069e-05 | 0.00059734 | 0.0011556 | 0.0 | 9.21
Modify | 4.869e-05 | 4.912e-05 | 4.9551e-05 | 0.0 | 0.76
Other | | 0.0007515 | | | 11.59
Nlocal: 128 ave 134 max 122 min
Nlocal: 128.000 ave 134 max 122 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1115 max 1103 min
Nghost: 1109.00 ave 1115 max 1103 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4976 ave 5205 max 4747 min
Neighs: 4976.00 ave 5205 max 4747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9952
Ave neighs/atom = 38.875
Ave neighs/atom = 38.875000
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -92,34 +95,34 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
Loop time of 0.000206062 on 2 procs for 1 steps with 256 atoms
Loop time of 0.00128072 on 2 procs for 1 steps with 256 atoms
Performance: 2096456.406 tau/day, 4852.908 timesteps/s
94.1% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 337310.921 tau/day, 780.812 timesteps/s
60.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00012947 | 0.00013524 | 0.00014101 | 0.0 | 65.63
Pair | 0.00047351 | 0.00049064 | 0.00050777 | 0.0 | 38.31
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.858e-05 | 2.4113e-05 | 2.9647e-05 | 0.0 | 11.70
Output | 8.699e-06 | 2.4204e-05 | 3.9708e-05 | 0.0 | 11.75
Modify | 2.34e-06 | 2.3705e-06 | 2.401e-06 | 0.0 | 1.15
Other | | 2.013e-05 | | | 9.77
Comm | 7.6767e-05 | 9.3655e-05 | 0.00011054 | 0.0 | 7.31
Output | 5.4217e-05 | 0.00026297 | 0.00047172 | 0.0 | 20.53
Modify | 1.1554e-05 | 1.2026e-05 | 1.2498e-05 | 0.0 | 0.94
Other | | 0.0004214 | | | 32.91
Nlocal: 128 ave 135 max 121 min
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1116 max 1102 min
Nghost: 1109.00 ave 1116 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4852.5 ave 5106 max 4599 min
Neighs: 4852.50 ave 5106 max 4599 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Force on 1 atom via extract_atom: -18.109
Force on 1 atom via extract_variable: -18.109
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Force on 1 atom via extract_atom: -18.109
Force on 1 atom via extract_variable: -18.109
Force on 1 atom via extract_atom: 26.9581
Force on 1 atom via extract_variable: 26.9581
Setting up Verlet run ...
@ -130,30 +133,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
Loop time of 0.00119048 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00784933 on 2 procs for 10 steps with 256 atoms
Performance: 3628802.105 tau/day, 8400.005 timesteps/s
98.0% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 550365.761 tau/day, 1273.995 timesteps/s
59.6% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00085276 | 0.00089699 | 0.00094123 | 0.0 | 75.35
Pair | 0.0019235 | 0.0033403 | 0.0047572 | 2.5 | 42.56
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016896 | 0.00021444 | 0.00025992 | 0.0 | 18.01
Output | 9.413e-06 | 2.5939e-05 | 4.2465e-05 | 0.0 | 2.18
Modify | 1.8977e-05 | 2.0009e-05 | 2.1042e-05 | 0.0 | 1.68
Other | | 3.31e-05 | | | 2.78
Comm | 0.0016948 | 0.003118 | 0.0045411 | 2.5 | 39.72
Output | 3.6445e-05 | 0.00064636 | 0.0012563 | 0.0 | 8.23
Modify | 6.2842e-05 | 6.3209e-05 | 6.3577e-05 | 0.0 | 0.81
Other | | 0.0006814 | | | 8.68
Nlocal: 128 ave 135 max 121 min
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1116 max 1102 min
Nghost: 1109.00 ave 1116 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4844 ave 5096 max 4592 min
Neighs: 4844.00 ave 5096 max 4592 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9688
Ave neighs/atom = 37.8438
Ave neighs/atom = 37.843750
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -164,30 +167,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
Loop time of 0.00252603 on 2 procs for 20 steps with 256 atoms
Loop time of 0.00696051 on 2 procs for 20 steps with 256 atoms
Performance: 3420382.192 tau/day, 7917.551 timesteps/s
99.2% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 1241287.730 tau/day, 2873.351 timesteps/s
79.2% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016245 | 0.0017014 | 0.0017784 | 0.2 | 67.36
Neigh | 0.00025359 | 0.0002563 | 0.00025901 | 0.0 | 10.15
Comm | 0.00036863 | 0.00045124 | 0.00053385 | 0.0 | 17.86
Output | 9.839e-06 | 2.8031e-05 | 4.6223e-05 | 0.0 | 1.11
Modify | 3.7027e-05 | 3.9545e-05 | 4.2063e-05 | 0.0 | 1.57
Other | | 4.948e-05 | | | 1.96
Pair | 0.0028267 | 0.0036088 | 0.004391 | 1.3 | 51.85
Neigh | 0.00040272 | 0.00040989 | 0.00041707 | 0.0 | 5.89
Comm | 0.00081061 | 0.0015825 | 0.0023544 | 1.9 | 22.74
Output | 3.6006e-05 | 0.00062106 | 0.0012061 | 0.0 | 8.92
Modify | 6.8937e-05 | 7.1149e-05 | 7.336e-05 | 0.0 | 1.02
Other | | 0.0006671 | | | 9.58
Nlocal: 128 ave 132 max 124 min
Nlocal: 128.000 ave 132 max 124 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1100 ave 1101 max 1099 min
Nghost: 1100.00 ave 1101 max 1099 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4850 ave 4953 max 4747 min
Neighs: 4850.00 ave 4953 max 4747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 1
Dangerous builds not checked
Setting up Verlet run ...
@ -198,30 +201,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
Loop time of 0.00115444 on 2 procs for 10 steps with 256 atoms
Loop time of 0.00155862 on 2 procs for 10 steps with 256 atoms
Performance: 3742065.976 tau/day, 8662.190 timesteps/s
96.5% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 2771678.197 tau/day, 6415.922 timesteps/s
95.0% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00087346 | 0.00089311 | 0.00091275 | 0.0 | 77.36
Pair | 0.0012369 | 0.001266 | 0.001295 | 0.1 | 81.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016192 | 0.0001823 | 0.00020269 | 0.0 | 15.79
Output | 9.49e-06 | 2.6234e-05 | 4.2978e-05 | 0.0 | 2.27
Modify | 1.9095e-05 | 1.9843e-05 | 2.0591e-05 | 0.0 | 1.72
Other | | 3.296e-05 | | | 2.85
Comm | 0.00019462 | 0.00022315 | 0.00025169 | 0.0 | 14.32
Output | 2.0217e-05 | 2.1945e-05 | 2.3673e-05 | 0.0 | 1.41
Modify | 2.562e-05 | 2.5759e-05 | 2.5898e-05 | 0.0 | 1.65
Other | | 2.181e-05 | | | 1.40
Nlocal: 128 ave 132 max 124 min
Nlocal: 128.000 ave 132 max 124 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1100 ave 1101 max 1099 min
Nghost: 1100.00 ave 1101 max 1099 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4850 ave 4953 max 4747 min
Neighs: 4850.00 ave 4953 max 4747 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9700
Ave neighs/atom = 37.8906
Ave neighs/atom = 37.890625
Neighbor list builds = 0
Dangerous builds not checked
Setting up Verlet run ...
@ -232,30 +235,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
Loop time of 0.00244325 on 2 procs for 20 steps with 256 atoms
Loop time of 0.00351607 on 2 procs for 20 steps with 256 atoms
Performance: 3536279.919 tau/day, 8185.833 timesteps/s
99.0% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 2457288.612 tau/day, 5688.168 timesteps/s
97.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016916 | 0.0017038 | 0.001716 | 0.0 | 69.73
Neigh | 0.00025229 | 0.00025512 | 0.00025795 | 0.0 | 10.44
Comm | 0.00035772 | 0.00036918 | 0.00038064 | 0.0 | 15.11
Output | 1.0858e-05 | 2.7875e-05 | 4.4891e-05 | 0.0 | 1.14
Modify | 3.817e-05 | 3.9325e-05 | 4.048e-05 | 0.0 | 1.61
Other | | 4.796e-05 | | | 1.96
Pair | 0.0023896 | 0.0024147 | 0.0024397 | 0.1 | 68.67
Neigh | 0.00037331 | 0.00040456 | 0.0004358 | 0.0 | 11.51
Comm | 0.00050571 | 0.00051343 | 0.00052116 | 0.0 | 14.60
Output | 2.6424e-05 | 5.6547e-05 | 8.667e-05 | 0.0 | 1.61
Modify | 5.0287e-05 | 5.1071e-05 | 5.1856e-05 | 0.0 | 1.45
Other | | 7.58e-05 | | | 2.16
Nlocal: 128 ave 128 max 128 min
Nlocal: 128.000 ave 128 max 128 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 1088.5 ave 1092 max 1085 min
Nghost: 1088.50 ave 1092 max 1085 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4850.5 ave 4851 max 4850 min
Neighs: 4850.50 ave 4851 max 4850 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9701
Ave neighs/atom = 37.8945
Ave neighs/atom = 37.894531
Neighbor list builds = 1
Dangerous builds not checked
Deleted 256 atoms, new total = 0
@ -267,30 +270,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
Step Temp E_pair E_mol TotEng Press
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
Loop time of 0.00118092 on 2 procs for 10 steps with 256 atoms
Loop time of 0.0109747 on 2 procs for 10 steps with 256 atoms
Performance: 3658158.625 tau/day, 8467.960 timesteps/s
98.6% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 393631.731 tau/day, 911.185 timesteps/s
53.5% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0008476 | 0.00089265 | 0.00093771 | 0.0 | 75.59
Pair | 0.0012057 | 0.0012732 | 0.0013407 | 0.2 | 11.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016335 | 0.00020946 | 0.00025557 | 0.0 | 17.74
Output | 8.87e-06 | 2.5733e-05 | 4.2595e-05 | 0.0 | 2.18
Modify | 1.8755e-05 | 1.9814e-05 | 2.0872e-05 | 0.0 | 1.68
Other | | 3.326e-05 | | | 2.82
Comm | 0.00018882 | 0.00025686 | 0.00032489 | 0.0 | 2.34
Output | 2.1943e-05 | 0.0047067 | 0.0093915 | 6.8 | 42.89
Modify | 2.4614e-05 | 2.5439e-05 | 2.6264e-05 | 0.0 | 0.23
Other | | 0.004712 | | | 42.94
Nlocal: 128 ave 135 max 121 min
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1109 ave 1116 max 1102 min
Nghost: 1109.00 ave 1116 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 4852.5 ave 5106 max 4599 min
Neighs: 4852.50 ave 5106 max 4599 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 9705
Ave neighs/atom = 37.9102
Ave neighs/atom = 37.910156
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:00

7
examples/COUPLE/plugin/simple.c
View File

@ -87,7 +87,7 @@ int main(int narg, char **arg)
MPI_Abort(MPI_COMM_WORLD,1);
}
}
if (lammps == 1) plugin->open(0,NULL,comm_lammps,&lmp);
if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
while (1) {
if (me == 0) {
@ -139,7 +139,7 @@ int main(int narg, char **arg)
cmds[0] = (char *)"run 10";
cmds[1] = (char *)"run 20";
if (lammps == 1) plugin->commands_list(lmp,2,cmds);
if (lammps == 1) plugin->commands_list(lmp,2,(const char **)cmds);
/* delete all atoms
create_atoms() to create new ones with old coords, vels
@ -164,12 +164,13 @@ int main(int narg, char **arg)
if (lammps == 1) {
plugin->close(lmp);
MPI_Barrier(comm_lammps);
MPI_Comm_free(&comm_lammps);
liblammpsplugin_release(plugin);
}
/* close down MPI */
if (lammps == 1) MPI_Comm_free(&comm_lammps);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
}

21
lib/gpu/geryon/ocl_device.h
View File

@ -462,7 +462,6 @@ int UCL_Device::set_platform(int pid) {
_num_devices = 0;
for (int i=0; i<num_unpart; i++) {
cl_uint num_subdevices = 1;
cl_device_id *subdevice_list = device_list + i;
#ifdef CL_VERSION_1_2
cl_device_affinity_domain adomain;
@ -479,19 +478,21 @@ int UCL_Device::set_platform(int pid) {
CL_SAFE_CALL(clCreateSubDevices(device_list[i], props, 0, NULL,
&num_subdevices));
if (num_subdevices > 1) {
subdevice_list = new cl_device_id[num_subdevices];
cl_device_id *subdevice_list = new cl_device_id[num_subdevices];
CL_SAFE_CALL(clCreateSubDevices(device_list[i], props, num_subdevices,
subdevice_list, &num_subdevices));
for (int j=0; j<num_subdevices; j++) {
_cl_devices.push_back(device_list[i]);
add_properties(device_list[i]);
_num_devices++;
}
delete[] subdevice_list;
} else {
_cl_devices.push_back(device_list[i]);
add_properties(device_list[i]);
_num_devices++;
}
#endif
for (int j=0; j<num_subdevices; j++) {
_num_devices++;
_cl_devices.push_back(subdevice_list[j]);
add_properties(subdevice_list[j]);
}
if (num_subdevices > 1) delete[] subdevice_list;
} // for i
#endif

6
lib/gpu/geryon/ocl_timer.h
View File

@ -38,8 +38,10 @@ namespace ucl_opencl {
/// Class for timing OpenCL events
class UCL_Timer {
public:
inline UCL_Timer() : _total_time(0.0f), _initialized(false), has_measured_time(false) { }
inline UCL_Timer(UCL_Device &dev) : _total_time(0.0f), _initialized(false), has_measured_time(false)
inline UCL_Timer() : start_event(nullptr), stop_event(nullptr), _total_time(0.0f),
_initialized(false), has_measured_time(false) { }
inline UCL_Timer(UCL_Device &dev) : start_event(nullptr), stop_event(nullptr), _total_time(0.0f),
_initialized(false), has_measured_time(false)
{ init(dev); }
inline ~UCL_Timer() { clear(); }

5
lib/gpu/lal_answer.h
View File

@ -127,9 +127,8 @@ class Answer {
/// Add forces and torques from the GPU into a LAMMPS pointer
void get_answers(double **f, double **tor);
inline double get_answers(double **f, double **tor, double *eatom,
double **vatom, double *virial, double &ecoul,
int &error_flag_in) {
inline double get_answers(double **f, double **tor, double *eatom, double **vatom,
double *virial, double &ecoul, int &error_flag_in) {
double ta=MPI_Wtime();
time_answer.sync_stop();
_time_cpu_idle+=MPI_Wtime()-ta;

31
lib/gpu/lal_device.cpp
View File

@ -348,7 +348,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int ngpu,
}
template <class numtyp, class acctyp>
int DeviceT::set_ocl_params(std::string s_config, std::string extra_args) {
int DeviceT::set_ocl_params(std::string s_config, const std::string &extra_args) {
#ifdef USE_OPENCL
#include "lal_pre_ocl_config.h"
@ -368,7 +368,7 @@ int DeviceT::set_ocl_params(std::string s_config, std::string extra_args) {
int token_count=0;
std::string params[18];
char ocl_config[2048];
strcpy(ocl_config,s_config.c_str());
strncpy(ocl_config,s_config.c_str(),2047);
char *pch = strtok(ocl_config,",");
_ocl_config_name=pch;
pch = strtok(nullptr,",");
@ -984,18 +984,16 @@ int DeviceT::compile_kernels() {
_max_bio_shared_types=gpu_lib_data[17];
_pppm_max_spline=gpu_lib_data[18];
if (static_cast<size_t>(_block_pair)>gpu->group_size_dim(0) ||
static_cast<size_t>(_block_bio_pair)>gpu->group_size_dim(0) ||
static_cast<size_t>(_block_ellipse)>gpu->group_size_dim(0) ||
static_cast<size_t>(_pppm_block)>gpu->group_size_dim(0) ||
static_cast<size_t>(_block_nbor_build)>gpu->group_size_dim(0) ||
static_cast<size_t>(_block_cell_2d)>gpu->group_size_dim(0) ||
static_cast<size_t>(_block_cell_2d)>gpu->group_size_dim(1) ||
static_cast<size_t>(_block_cell_id)>gpu->group_size_dim(0) ||
static_cast<size_t>(_max_shared_types*_max_shared_types*
sizeof(numtyp)*17 > gpu->slm_size()) ||
static_cast<size_t>(_max_bio_shared_types*2*sizeof(numtyp) >
gpu->slm_size()))
if (static_cast<size_t>(_block_pair) > gpu->group_size_dim(0) ||
static_cast<size_t>(_block_bio_pair) > gpu->group_size_dim(0) ||
static_cast<size_t>(_block_ellipse) > gpu->group_size_dim(0) ||
static_cast<size_t>(_pppm_block) > gpu->group_size_dim(0) ||
static_cast<size_t>(_block_nbor_build) > gpu->group_size_dim(0) ||
static_cast<size_t>(_block_cell_2d) > gpu->group_size_dim(0) ||
static_cast<size_t>(_block_cell_2d) > gpu->group_size_dim(1) ||
static_cast<size_t>(_block_cell_id) > gpu->group_size_dim(0) ||
static_cast<size_t>(_max_shared_types*_max_shared_types*sizeof(numtyp)*17 > gpu->slm_size()) ||
static_cast<size_t>(_max_bio_shared_types*2*sizeof(numtyp) > gpu->slm_size()))
return -13;
if (_block_pair % _simd_size != 0 || _block_bio_pair % _simd_size != 0 ||
@ -1071,9 +1069,8 @@ void lmp_clear_device() {
global_device.clear_device();
}
double lmp_gpu_forces(double **f, double **tor, double *eatom,
double **vatom, double *virial, double &ecoul,
int &error_flag) {
double lmp_gpu_forces(double **f, double **tor, double *eatom, double **vatom,
double *virial, double &ecoul, int &error_flag) {
return global_device.fix_gpu(f,tor,eatom,vatom,virial,ecoul,error_flag);
}

10
lib/gpu/lal_device.h
View File

@ -163,17 +163,15 @@ class Device {
{ ans_queue.push(ans); }
/// Add "answers" (force,energies,etc.) into LAMMPS structures
inline double fix_gpu(double **f, double **tor, double *eatom,
double **vatom, double *virial, double &ecoul,
int &error_flag) {
inline double fix_gpu(double **f, double **tor, double *eatom, double **vatom,
double *virial, double &ecoul, int &error_flag) {
error_flag=0;
atom.data_unavail();
if (ans_queue.empty()==false) {
stop_host_timer();
double evdw=0.0;
while (ans_queue.empty()==false) {
evdw+=ans_queue.front()->get_answers(f,tor,eatom,vatom,virial,ecoul,
error_flag);
evdw += ans_queue.front()->get_answers(f,tor,eatom,vatom,virial,ecoul,error_flag);
ans_queue.pop();
}
return evdw;
@ -350,7 +348,7 @@ class Device {
int _data_in_estimate, _data_out_estimate;
std::string _ocl_config_name, _ocl_config_string, _ocl_compile_string;
int set_ocl_params(std::string, std::string);
int set_ocl_params(std::string, const std::string &);
};
}

4
lib/gpu/lal_neighbor.cpp
View File

@ -39,7 +39,7 @@ bool Neighbor::init(NeighborShared *shared, const int inum,
const int block_cell_2d, const int block_cell_id,
const int block_nbor_build, const int threads_per_atom,
const int simd_size, const bool time_device,
const std::string compile_flags, const bool ilist_map) {
const std::string &compile_flags, const bool ilist_map) {
clear();
_ilist_map = ilist_map;
@ -743,7 +743,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
mn = _max_nbors;
const numtyp i_cell_size=static_cast<numtyp>(1.0/_cell_size);
const int neigh_block=_block_cell_id;
const int GX=(int)ceil((float)nall/neigh_block);
const int GX=(int)ceil((double)nall/neigh_block);
const numtyp sublo0=static_cast<numtyp>(sublo[0]);
const numtyp sublo1=static_cast<numtyp>(sublo[1]);
const numtyp sublo2=static_cast<numtyp>(sublo[2]);

2
lib/gpu/lal_neighbor.h
View File

@ -71,7 +71,7 @@ class Neighbor {
const int block_cell_2d, const int block_cell_id,
const int block_nbor_build, const int threads_per_atom,
const int simd_size, const bool time_device,
const std::string compile_flags, const bool ilist_map);
const std::string &compile_flags, const bool ilist_map);
/// Set the cutoff+skin
inline void set_cutoff(const double cutoff) {

2
lib/gpu/lal_neighbor_shared.cpp
View File

@ -89,7 +89,7 @@ double NeighborShared::best_cell_size(const double subx, const double suby,
}
void NeighborShared::compile_kernels(UCL_Device &dev, const int gpu_nbor,
const std::string flags) {
const std::string &flags) {
if (_compiled)
return;

2
lib/gpu/lal_neighbor_shared.h
View File

@ -87,7 +87,7 @@ class NeighborShared {
/// Compile kernels for neighbor lists
void compile_kernels(UCL_Device &dev, const int gpu_nbor,
const std::string flags);
const std::string &flags);
// ----------------------------- Kernels
UCL_Program *nbor_program, *build_program;

16
lib/gpu/lal_pppm.cpp
View File

@ -54,7 +54,7 @@ int PPPMT::bytes_per_atom() const {
}
template <class numtyp, class acctyp, class grdtyp, class grdtyp4>
grdtyp * PPPMT::init(const int nlocal, const int nall, FILE *_screen,
grdtyp *PPPMT::init(const int nlocal, const int nall, FILE *_screen,
const int order, const int nxlo_out,
const int nylo_out, const int nzlo_out,
const int nxhi_out, const int nyhi_out,
@ -69,14 +69,14 @@ grdtyp * PPPMT::init(const int nlocal, const int nall, FILE *_screen,
flag=device->init(*ans,nlocal,nall);
if (flag!=0)
return 0;
return nullptr;
if (sizeof(grdtyp)==sizeof(double) && device->double_precision()==false) {
flag=-15;
return 0;
return nullptr;
}
if (device->ptx_arch()>0.0 && device->ptx_arch()<1.1) {
flag=-4;
return 0;
return nullptr;
}
ucl_device=device->gpu;
@ -168,7 +168,7 @@ grdtyp * PPPMT::init(const int nlocal, const int nall, FILE *_screen,
UCL_READ_WRITE)==UCL_SUCCESS);
if (!success) {
flag=-3;
return 0;
return nullptr;
}
error_flag.device.zero();
@ -342,13 +342,15 @@ void PPPMT::interp(const grdtyp qqrd2e_scale) {
vd_brick.update_device(true);
time_in.stop();
int ainum=this->ans->inum();
if (ainum==0)
return;
time_interp.start();
// Compute the block size and grid size to keep all cores busy
int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
int ainum=this->ans->inum();
k_interp.set_size(GX,BX);
k_interp.run(&atom->x, &atom->q, &ainum, &vd_brick, &d_rho_coeff,
&_npts_x, &_npts_yx, &_brick_x, &_brick_y, &_brick_z, &_delxinv,

13
python/lammps/numpy_wrapper.py
View File

@ -92,8 +92,12 @@ class numpy_wrapper:
if dim == LAMMPS_AUTODETECT:
if dtype in (LAMMPS_INT_2D, LAMMPS_DOUBLE_2D, LAMMPS_INT64_2D):
# TODO add other fields
if name in ("x", "v", "f", "angmom", "torque", "csforce", "vforce"):
if name in ("x", "v", "f", "x0", "omega", "angmom", "torque", "vforce", "vest"):
dim = 3
elif name == "smd_data_9":
dim = 9
elif name == "smd_stress":
dim = 6
else:
dim = 2
else:
@ -386,6 +390,9 @@ class numpy_wrapper:
# -------------------------------------------------------------------------
def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
if raw_ptr is None:
return None
import numpy as np
np_int_type = self._ctype_to_numpy_int(c_int_type)
@ -405,7 +412,11 @@ class numpy_wrapper:
# -------------------------------------------------------------------------
def darray(self, raw_ptr, nelem, dim=1):
if raw_ptr is None:
return None
import numpy as np
if dim == 1:
ptr = cast(raw_ptr, POINTER(c_double * nelem))
else:

3
src/ASPHERE/pair_line_lj.cpp
View File

@ -301,8 +301,7 @@ void PairLineLJ::compute(int eflag, int vflag)
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}

3
src/ASPHERE/pair_tri_lj.cpp
View File

@ -375,8 +375,7 @@ void PairTriLJ::compute(int eflag, int vflag)
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}

1
src/AWPMD/pair_awpmd_cut.cpp
View File

@ -39,7 +39,6 @@
#include <cstring>
#include <map>
#include <utility>
#include <vector>
using namespace LAMMPS_NS;

1
src/BOCS/fix_bocs.cpp
View File

@ -37,7 +37,6 @@
#include <cmath>
#include <cstring>
#include <vector>
using namespace LAMMPS_NS;
using namespace FixConst;

3
src/BODY/fix_wall_body_polygon.cpp
View File

@ -337,8 +337,7 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
num_contacts = 0;
facc[0] = facc[1] = facc[2] = 0;
vertex_against_wall(i, wall_pos, x, f, torque, side,
contact_list, num_contacts, facc);
vertex_against_wall(i, wall_pos, x, f, torque, side, contact_list, num_contacts, facc);
if (num_contacts >= 2) {

3
src/BODY/pair_body_nparticle.cpp
View File

@ -324,8 +324,7 @@ void PairBodyNparticle::compute(int eflag, int vflag)
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}

3
src/BODY/pair_body_rounded_polygon.cpp
View File

@ -207,8 +207,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
if (r > radi + radj + cut_inner) continue;
if (npi == 1 && npj == 1) {
sphere_against_sphere(i, j, delx, dely, delz, rsq,
k_nij, k_naij, x, v, f, evflag);
sphere_against_sphere(i, j, delx, dely, delz, rsq, k_nij, k_naij, x, v, f, evflag);
continue;
}

6
src/BROWNIAN/fix_brownian.cpp
View File

@ -20,17 +20,11 @@
#include "fix_brownian.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

7
src/BROWNIAN/fix_brownian_asphere.cpp
View File

@ -21,17 +21,10 @@
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

5
src/BROWNIAN/fix_brownian_base.cpp
View File

@ -17,15 +17,12 @@
Contributing author: Sam Cameron (University of Bristol)
------------------------------------------------------------------------- */
#include "fix_brownian.h"
#include "fix_brownian_base.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"

5
src/BROWNIAN/fix_brownian_sphere.cpp
View File

@ -20,17 +20,12 @@
#include "fix_brownian_sphere.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

5
src/BROWNIAN/fix_propel_self.cpp
View File

@ -23,14 +23,11 @@
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;

1
src/CG-DNA/atom_vec_oxdna.cpp
View File

@ -14,7 +14,6 @@
#include "atom_vec_oxdna.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"

2
src/CG-DNA/pair_oxdna_stk.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_oxdna.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -30,7 +29,6 @@
#include <cmath>
#include <cstring>
#include <utility>
using namespace LAMMPS_NS;
using namespace MFOxdna;

2
src/CG-DNA/pair_oxrna2_excv.cpp
View File

@ -17,8 +17,6 @@
#include "pair_oxrna2_excv.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------

2
src/CG-DNA/pair_oxrna2_stk.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_oxdna.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@ -31,7 +30,6 @@
#include <cmath>
#include <cstring>
#include <utility>
using namespace LAMMPS_NS;
using namespace MathConst;

8
src/CG-SDK/pair_lj_sdk_coul_msm.cpp
View File

@ -18,13 +18,15 @@
------------------------------------------------------------------------- */
#include "pair_lj_sdk_coul_msm.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "error.h"
#include "force.h"
#include "kspace.h"
#include "neigh_list.h"
#include "error.h"
#include <cmath>
#include <cstring>
#include "lj_sdk_common.h"

1
src/CLASS2/dihedral_class2.cpp
View File

@ -25,7 +25,6 @@
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "update.h"
#include <cmath>
#include <cstring>

1
src/CLASS2/improper_class2.cpp
View File

@ -25,7 +25,6 @@
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "update.h"
#include <cmath>
#include <cstring>

3
src/CLASS2/pair_lj_class2.cpp
View File

@ -397,8 +397,7 @@ void PairLJClass2::compute_outer(int eflag, int vflag)
fpair = factor_lj*forcelj*r2inv;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

3
src/COLLOID/fix_wall_colloid.cpp
View File

@ -18,10 +18,11 @@
#include "fix_wall_colloid.h"
#include <cmath>
#include "atom.h"
#include "error.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace FixConst;

13
src/COLVARS/colvarproxy_lammps.cpp
View File

@ -10,13 +10,6 @@
#include "colvarproxy_lammps.h"
#include <mpi.h>
#include <sys/stat.h>
#include <cerrno>
#include <cstring>
#include <iostream>
#include <memory>
#include <string>
#include "lammps.h"
#include "error.h"
@ -26,6 +19,12 @@
#include "colvarmodule.h"
#include "colvarproxy.h"
#include <sys/stat.h>
#include <cerrno>
#include <cstring>
#include <iostream>
#include <memory>
#define HASH_FAIL -1
////////////////////////////////////////////////////////////////////////

5
src/COLVARS/colvarproxy_lammps.h
View File

@ -12,11 +12,6 @@
#include "colvarproxy_lammps_version.h" // IWYU pragma: export
#include <cstddef>
#include <mpi.h>
#include <string>
#include <vector>
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvartypes.h"

3
src/COLVARS/fix_colvars.cpp
View File

@ -44,7 +44,6 @@
#include <cstring>
#include <iostream>
#include <memory>
#include <vector>
static const char colvars_pub[] =
"fix colvars command:\n\n"
@ -1000,7 +999,7 @@ double FixColvars::compute_scalar()
/* ---------------------------------------------------------------------- */
/* local memory usage. approximately. */
double FixColvars::memory_usage(void)
double FixColvars::memory_usage()
{
double bytes = (double) (num_coords * (2*sizeof(int)+3*sizeof(double)));
bytes += (double)(double) (nmax*size_one) + sizeof(this);

60
src/COMPRESS/dump_atom_gz.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -12,27 +11,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "domain.h"
#include "dump_atom_gz.h"
#include "domain.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) :
DumpAtom(lmp, narg, arg)
DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump atom/gz only writes compressed files");
if (!compressed) error->all(FLERR, "Dump atom/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpAtomGZ::~DumpAtomGZ()
{
}
DumpAtomGZ::~DumpAtomGZ() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -55,16 +52,15 @@ void DumpAtomGZ::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -94,7 +90,7 @@ void DumpAtomGZ::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
/* ---------------------------------------------------------------------- */
@ -106,12 +102,10 @@ void DumpAtomGZ::write_header(bigint ndump)
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
}
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@ -145,14 +139,14 @@ void DumpAtomGZ::write_data(int n, double *mybuf)
for (int i = 0; i < n; i++) {
int written = 0;
if (image_flag == 1) {
written = snprintf(vbuffer, VBUFFER_SIZE, format,
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
written = snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4],
static_cast<int>(mybuf[m + 5]), static_cast<int>(mybuf[m + 6]),
static_cast<int>(mybuf[m + 7]));
} else {
written = snprintf(vbuffer, VBUFFER_SIZE, format,
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
written =
snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
}
if (written > 0) {
writer.write(vbuffer, written);
@ -174,9 +168,7 @@ void DumpAtomGZ::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -188,14 +180,14 @@ int DumpAtomGZ::modify_param(int narg, char **arg)
int consumed = DumpAtom::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

71
src/COMPRESS/dump_atom_zstd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,6 +18,7 @@
#ifdef LAMMPS_ZSTD
#include "domain.h"
#include "dump_atom_zstd.h"
#include "error.h"
#include "file_writer.h"
@ -26,21 +26,16 @@
#include <cstring>
using namespace LAMMPS_NS;
DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) :
DumpAtom(lmp, narg, arg)
DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump atom/zstd only writes compressed files");
if (!compressed) error->all(FLERR, "Dump atom/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpAtomZstd::~DumpAtomZstd()
{
}
DumpAtomZstd::~DumpAtomZstd() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -63,16 +58,15 @@ void DumpAtomZstd::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -102,7 +96,7 @@ void DumpAtomZstd::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
/* ---------------------------------------------------------------------- */
@ -114,12 +108,10 @@ void DumpAtomZstd::write_header(bigint ndump)
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
}
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@ -153,14 +145,14 @@ void DumpAtomZstd::write_data(int n, double *mybuf)
for (int i = 0; i < n; i++) {
int written = 0;
if (image_flag == 1) {
written = snprintf(vbuffer, VBUFFER_SIZE, format,
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
written = snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4],
static_cast<int>(mybuf[m + 5]), static_cast<int>(mybuf[m + 6]),
static_cast<int>(mybuf[m + 7]));
} else {
written = snprintf(vbuffer, VBUFFER_SIZE, format,
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
written =
snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
}
if (written > 0) {
writer.write(vbuffer, written);
@ -182,9 +174,7 @@ void DumpAtomZstd::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -196,20 +186,23 @@ int DumpAtomZstd::modify_param(int narg, char **arg)
int consumed = DumpAtom::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "checksum") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
if (strcmp(arg[1], "yes") == 0)
writer.setChecksum(true);
else if (strcmp(arg[1], "no") == 0)
writer.setChecksum(false);
else
error->all(FLERR, "Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
} else if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

73
src/COMPRESS/dump_cfg_gz.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -12,10 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "dump_cfg_gz.h"
#include "atom.h"
#include "domain.h"
#include "dump_cfg_gz.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
@ -23,18 +24,14 @@
using namespace LAMMPS_NS;
#define UNWRAPEXPAND 10.0
DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) :
DumpCFG(lmp, narg, arg)
DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump cfg/gz only writes compressed files");
if (!compressed) error->all(FLERR, "Dump cfg/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCFGGZ::~DumpCFGGZ()
{
}
DumpCFGGZ::~DumpCFGGZ() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -57,16 +54,15 @@ void DumpCFGGZ::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -96,7 +92,7 @@ void DumpCFGGZ::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
/* ---------------------------------------------------------------------- */
@ -111,24 +107,25 @@ void DumpCFGGZ::write_header(bigint n)
// so molecules are not split across periodic box boundaries
double scale = 1.0;
if (atom->peri_flag) scale = atom->pdscale;
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
if (atom->peri_flag)
scale = atom->pdscale;
else if (unwrapflag == 1)
scale = UNWRAPEXPAND;
std::string header = fmt::format("Number of particles = {}\n", n);
header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale);
header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd);
header += fmt::format("H0(1,1) = {0:g} A\n", domain->xprd);
header += fmt::format("H0(1,2) = 0 A \n");
header += fmt::format("H0(1,3) = 0 A \n");
header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy);
header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd);
header += fmt::format("H0(2,1) = {0:g} A \n", domain->xy);
header += fmt::format("H0(2,2) = {0:g} A\n", domain->yprd);
header += fmt::format("H0(2,3) = 0 A \n");
header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz);
header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz);
header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd);
header += fmt::format("H0(3,1) = {0:g} A \n", domain->xz);
header += fmt::format("H0(3,2) = {0:g} A \n", domain->yz);
header += fmt::format("H0(3,3) = {0:g} A\n", domain->zprd);
header += fmt::format(".NO_VELOCITY.\n");
header += fmt::format("entry_count = {}\n",nfield-2);
for (int i = 0; i < nfield-5; i++)
header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]);
header += fmt::format("entry_count = {}\n", nfield - 2);
for (int i = 0; i < nfield - 5; i++) header += fmt::format("auxiliary[{}] = {}\n", i, auxname[i]);
writer.write(header.c_str(), header.length());
}
@ -153,13 +150,13 @@ void DumpCFGGZ::write_data(int n, double *mybuf)
written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
} else if (j >= 2) {
if (vtype[j] == Dump::INT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
else if (vtype[j] == Dump::DOUBLE)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
else if (vtype[j] == Dump::STRING)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
else if (vtype[j] == Dump::BIGINT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
}
if (written > 0) {
writer.write(vbuffer, written);
@ -180,17 +177,17 @@ void DumpCFGGZ::write_data(int n, double *mybuf)
} else if (j == 1) {
written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
} else if (j >= 2 && j <= 4) {
double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
double unwrap_coord = (mybuf[m] - 0.5) / UNWRAPEXPAND + 0.5;
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord);
} else if (j >= 5) {
if (vtype[j] == Dump::INT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
else if (vtype[j] == Dump::DOUBLE)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
else if (vtype[j] == Dump::STRING)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
else if (vtype[j] == Dump::BIGINT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
}
if (written > 0) {
writer.write(vbuffer, written);
@ -214,9 +211,7 @@ void DumpCFGGZ::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -228,14 +223,14 @@ int DumpCFGGZ::modify_param(int narg, char **arg)
int consumed = DumpCFG::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

90
src/COMPRESS/dump_cfg_zstd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -18,10 +17,12 @@
#ifdef LAMMPS_ZSTD
#include "dump_cfg_zstd.h"
#include "atom.h"
#include "domain.h"
#include "dump_cfg_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
@ -29,20 +30,14 @@
using namespace LAMMPS_NS;
#define UNWRAPEXPAND 10.0
DumpCFGZstd::DumpCFGZstd(LAMMPS *lmp, int narg, char **arg) :
DumpCFG(lmp, narg, arg)
DumpCFGZstd::DumpCFGZstd(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump cfg/zstd only writes compressed files");
if (!compressed) error->all(FLERR, "Dump cfg/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCFGZstd::~DumpCFGZstd()
{
}
DumpCFGZstd::~DumpCFGZstd() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -65,16 +60,15 @@ void DumpCFGZstd::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -95,9 +89,7 @@ void DumpCFGZstd::openfile()
// each proc with filewriter = 1 opens a file
if (filewriter) {
if (append_flag) {
error->one(FLERR, "dump cfg/zstd currently doesn't support append");
}
if (append_flag) { error->one(FLERR, "dump cfg/zstd currently doesn't support append"); }
try {
writer.open(filecurrent);
@ -108,7 +100,7 @@ void DumpCFGZstd::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
/* ---------------------------------------------------------------------- */
@ -123,24 +115,25 @@ void DumpCFGZstd::write_header(bigint n)
// so molecules are not split across periodic box boundaries
double scale = 1.0;
if (atom->peri_flag) scale = atom->pdscale;
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
if (atom->peri_flag)
scale = atom->pdscale;
else if (unwrapflag == 1)
scale = UNWRAPEXPAND;
std::string header = fmt::format("Number of particles = {}\n", n);
header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale);
header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd);
header += fmt::format("H0(1,1) = {0:g} A\n", domain->xprd);
header += fmt::format("H0(1,2) = 0 A \n");
header += fmt::format("H0(1,3) = 0 A \n");
header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy);
header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd);
header += fmt::format("H0(2,1) = {0:g} A \n", domain->xy);
header += fmt::format("H0(2,2) = {0:g} A\n", domain->yprd);
header += fmt::format("H0(2,3) = 0 A \n");
header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz);
header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz);
header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd);
header += fmt::format("H0(3,1) = {0:g} A \n", domain->xz);
header += fmt::format("H0(3,2) = {0:g} A \n", domain->yz);
header += fmt::format("H0(3,3) = {0:g} A\n", domain->zprd);
header += fmt::format(".NO_VELOCITY.\n");
header += fmt::format("entry_count = {}\n",nfield-2);
for (int i = 0; i < nfield-5; i++)
header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]);
header += fmt::format("entry_count = {}\n", nfield - 2);
for (int i = 0; i < nfield - 5; i++) header += fmt::format("auxiliary[{}] = {}\n", i, auxname[i]);
writer.write(header.c_str(), header.length());
}
@ -165,13 +158,13 @@ void DumpCFGZstd::write_data(int n, double *mybuf)
written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
} else if (j >= 2) {
if (vtype[j] == Dump::INT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
else if (vtype[j] == Dump::DOUBLE)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
else if (vtype[j] == Dump::STRING)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
else if (vtype[j] == Dump::BIGINT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
}
if (written > 0) {
writer.write(vbuffer, written);
@ -192,17 +185,17 @@ void DumpCFGZstd::write_data(int n, double *mybuf)
} else if (j == 1) {
written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
} else if (j >= 2 && j <= 4) {
double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
double unwrap_coord = (mybuf[m] - 0.5) / UNWRAPEXPAND + 0.5;
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord);
} else if (j >= 5) {
if (vtype[j] == Dump::INT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
else if (vtype[j] == Dump::DOUBLE)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
else if (vtype[j] == Dump::STRING)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
else if (vtype[j] == Dump::BIGINT)
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
}
if (written > 0) {
writer.write(vbuffer, written);
@ -226,9 +219,7 @@ void DumpCFGZstd::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -240,14 +231,17 @@ int DumpCFGZstd::modify_param(int narg, char **arg)
int consumed = DumpCFG::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "checksum") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
if (strcmp(arg[1], "yes") == 0)
writer.setChecksum(true);
else if (strcmp(arg[1], "no") == 0)
writer.setChecksum(false);
else
error->all(FLERR, "Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
} else if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;

50
src/COMPRESS/dump_custom_gz.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -12,27 +11,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "domain.h"
#include "dump_custom_gz.h"
#include "domain.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump custom/gz only writes compressed files");
if (!compressed) error->all(FLERR, "Dump custom/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCustomGZ::~DumpCustomGZ()
{
}
DumpCustomGZ::~DumpCustomGZ() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -55,16 +52,15 @@ void DumpCustomGZ::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -94,7 +90,7 @@ void DumpCustomGZ::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
void DumpCustomGZ::write_header(bigint ndump)
@ -104,12 +100,10 @@ void DumpCustomGZ::write_header(bigint ndump)
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
}
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@ -144,13 +138,13 @@ void DumpCustomGZ::write_data(int n, double *mybuf)
for (int j = 0; j < nfield; j++) {
int written = 0;
if (vtype[j] == Dump::INT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
} else if (vtype[j] == Dump::DOUBLE) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
} else if (vtype[j] == Dump::STRING) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
} else if (vtype[j] == Dump::BIGINT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
}
if (written > 0) {
@ -174,9 +168,7 @@ void DumpCustomGZ::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -188,14 +180,14 @@ int DumpCustomGZ::modify_param(int narg, char **arg)
int consumed = DumpCustom::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

4
src/COMPRESS/dump_custom_zstd.cpp
View File

@ -18,8 +18,10 @@
#ifdef LAMMPS_ZSTD
#include "domain.h"
#include "dump_custom_zstd.h"
#include "file_writer.h"
#include "domain.h"
#include "error.h"
#include "update.h"

1
src/COMPRESS/dump_custom_zstd.h
View File

@ -28,7 +28,6 @@ DumpStyle(custom/zstd,DumpCustomZstd);
#include "dump_custom.h"
#include "zstd_file_writer.h"
#include <stdio.h>
namespace LAMMPS_NS {

52
src/COMPRESS/dump_local_gz.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -12,27 +11,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "domain.h"
#include "dump_local_gz.h"
#include "domain.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
DumpLocal(lmp, narg, arg)
DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump local/gz only writes compressed files");
if (!compressed) error->all(FLERR, "Dump local/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpLocalGZ::~DumpLocalGZ()
{
}
DumpLocalGZ::~DumpLocalGZ() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -55,16 +52,15 @@ void DumpLocalGZ::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -94,7 +90,7 @@ void DumpLocalGZ::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
void DumpLocalGZ::write_header(bigint ndump)
@ -104,12 +100,10 @@ void DumpLocalGZ::write_header(bigint ndump)
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
}
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump);
@ -135,7 +129,7 @@ void DumpLocalGZ::write_header(bigint ndump)
void DumpLocalGZ::write_data(int n, double *mybuf)
{
if (buffer_flag == 1) {
writer.write(mybuf, sizeof(char)*n);
writer.write(mybuf, sizeof(char) * n);
} else {
constexpr size_t VBUFFER_SIZE = 256;
char vbuffer[VBUFFER_SIZE];
@ -144,11 +138,11 @@ void DumpLocalGZ::write_data(int n, double *mybuf)
for (int j = 0; j < size_one; j++) {
int written = 0;
if (vtype[j] == Dump::INT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
} else if (vtype[j] == Dump::DOUBLE) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
} else if (vtype[j] == Dump::BIGINT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
} else {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
}
@ -174,9 +168,7 @@ void DumpLocalGZ::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -188,14 +180,14 @@ int DumpLocalGZ::modify_param(int narg, char **arg)
int consumed = DumpLocal::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

70
src/COMPRESS/dump_local_zstd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -18,28 +17,25 @@
#ifdef LAMMPS_ZSTD
#include "domain.h"
#include "dump_local_zstd.h"
#include "domain.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) :
DumpLocal(lmp, narg, arg)
DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump local/zstd only writes compressed files");
if (!compressed) error->all(FLERR, "Dump local/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpLocalZstd::~DumpLocalZstd()
{
}
DumpLocalZstd::~DumpLocalZstd() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -62,16 +58,15 @@ void DumpLocalZstd::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -92,9 +87,7 @@ void DumpLocalZstd::openfile()
// each proc with filewriter = 1 opens a file
if (filewriter) {
if (append_flag) {
error->one(FLERR, "dump cfg/zstd currently doesn't support append");
}
if (append_flag) { error->one(FLERR, "dump cfg/zstd currently doesn't support append"); }
try {
writer.open(filecurrent);
@ -105,7 +98,7 @@ void DumpLocalZstd::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
void DumpLocalZstd::write_header(bigint ndump)
@ -115,12 +108,10 @@ void DumpLocalZstd::write_header(bigint ndump)
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
}
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump);
@ -146,7 +137,7 @@ void DumpLocalZstd::write_header(bigint ndump)
void DumpLocalZstd::write_data(int n, double *mybuf)
{
if (buffer_flag == 1) {
writer.write(mybuf, sizeof(char)*n);
writer.write(mybuf, sizeof(char) * n);
} else {
constexpr size_t VBUFFER_SIZE = 256;
char vbuffer[VBUFFER_SIZE];
@ -155,11 +146,11 @@ void DumpLocalZstd::write_data(int n, double *mybuf)
for (int j = 0; j < size_one; j++) {
int written = 0;
if (vtype[j] == Dump::INT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int>(mybuf[m]));
} else if (vtype[j] == Dump::DOUBLE) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
} else if (vtype[j] == Dump::BIGINT) {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint>(mybuf[m]));
} else {
written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
}
@ -185,9 +176,7 @@ void DumpLocalZstd::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -199,20 +188,23 @@ int DumpLocalZstd::modify_param(int narg, char **arg)
int consumed = DumpLocal::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "checksum") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
if (strcmp(arg[1], "yes") == 0)
writer.setChecksum(true);
else if (strcmp(arg[1], "no") == 0)
writer.setChecksum(false);
else
error->all(FLERR, "Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
} else if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

45
src/COMPRESS/dump_xyz_gz.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,26 +12,23 @@
------------------------------------------------------------------------- */
#include "dump_xyz_gz.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) :
DumpXYZ(lmp, narg, arg)
DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : DumpXYZ(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump xyz/gz only writes compressed files");
if (!compressed) error->all(FLERR, "Dump xyz/gz only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpXYZGZ::~DumpXYZGZ()
{
}
DumpXYZGZ::~DumpXYZGZ() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -55,16 +51,15 @@ void DumpXYZGZ::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -94,7 +89,7 @@ void DumpXYZGZ::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
void DumpXYZGZ::write_header(bigint ndump)
@ -117,9 +112,9 @@ void DumpXYZGZ::write_data(int n, double *mybuf)
char vbuffer[VBUFFER_SIZE];
int m = 0;
for (int i = 0; i < n; i++) {
int written = snprintf(vbuffer, VBUFFER_SIZE, format,
typenames[static_cast<int> (mybuf[m+1])],
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
int written =
snprintf(vbuffer, VBUFFER_SIZE, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
if (written > 0) {
writer.write(vbuffer, written);
} else if (written < 0) {
@ -139,9 +134,7 @@ void DumpXYZGZ::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -153,14 +146,14 @@ int DumpXYZGZ::modify_param(int narg, char **arg)
int consumed = DumpXYZ::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

63
src/COMPRESS/dump_xyz_zstd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,27 +18,23 @@
#ifdef LAMMPS_ZSTD
#include "dump_xyz_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) :
DumpXYZ(lmp, narg, arg)
DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) : DumpXYZ(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump xyz/zstd only writes compressed files");
if (!compressed) error->all(FLERR, "Dump xyz/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpXYZZstd::~DumpXYZZstd()
{
}
DumpXYZZstd::~DumpXYZZstd() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -62,16 +57,15 @@ void DumpXYZZstd::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -92,9 +86,7 @@ void DumpXYZZstd::openfile()
// each proc with filewriter = 1 opens a file
if (filewriter) {
if (append_flag) {
error->one(FLERR, "dump cfg/zstd currently doesn't support append");
}
if (append_flag) { error->one(FLERR, "dump cfg/zstd currently doesn't support append"); }
try {
writer.open(filecurrent);
@ -105,7 +97,7 @@ void DumpXYZZstd::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
void DumpXYZZstd::write_header(bigint ndump)
@ -128,9 +120,9 @@ void DumpXYZZstd::write_data(int n, double *mybuf)
char vbuffer[VBUFFER_SIZE];
int m = 0;
for (int i = 0; i < n; i++) {
int written = snprintf(vbuffer, VBUFFER_SIZE, format,
typenames[static_cast<int> (mybuf[m+1])],
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
int written =
snprintf(vbuffer, VBUFFER_SIZE, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
if (written > 0) {
writer.write(vbuffer, written);
} else if (written < 0) {
@ -150,9 +142,7 @@ void DumpXYZZstd::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -164,20 +154,23 @@ int DumpXYZZstd::modify_param(int narg, char **arg)
int consumed = DumpXYZ::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "checksum") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
if (strcmp(arg[1], "yes") == 0)
writer.setChecksum(true);
else if (strcmp(arg[1], "no") == 0)
writer.setChecksum(false);
else
error->all(FLERR, "Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
} else if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;

21
src/COMPRESS/gz_file_writer.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -17,22 +16,18 @@
------------------------------------------------------------------------- */
#include "gz_file_writer.h"
#include <stdio.h>
#include "fmt/format.h"
#include <cstdio>
using namespace LAMMPS_NS;
GzFileWriter::GzFileWriter() : FileWriter(),
compression_level(Z_BEST_COMPRESSION),
gzFp(nullptr)
{
}
GzFileWriter::GzFileWriter() : FileWriter(), compression_level(Z_BEST_COMPRESSION), gzFp(nullptr) {}
/* ---------------------------------------------------------------------- */
GzFileWriter::~GzFileWriter()
{
close();
GzFileWriter::close();
}
/* ---------------------------------------------------------------------- */
@ -50,13 +45,12 @@ void GzFileWriter::open(const std::string &path, bool append)
gzFp = gzopen(path.c_str(), mode.c_str());
if (gzFp == nullptr)
throw FileWriterException(fmt::format("Could not open file '{}'", path));
if (gzFp == nullptr) throw FileWriterException(fmt::format("Could not open file '{}'", path));
}
/* ---------------------------------------------------------------------- */
size_t GzFileWriter::write(const void * buffer, size_t length)
size_t GzFileWriter::write(const void *buffer, size_t length)
{
if (!isopen()) return 0;
@ -76,7 +70,7 @@ void GzFileWriter::flush()
void GzFileWriter::close()
{
if (!isopen()) return;
if (!GzFileWriter::isopen()) return;
gzclose(gzFp);
gzFp = nullptr;
@ -100,7 +94,8 @@ void GzFileWriter::setCompressionLevel(int level)
const int max_level = Z_BEST_COMPRESSION;
if (level < min_level || level > max_level)
throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
throw FileWriterException(
fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
compression_level = level;
}

1
src/COMPRESS/gz_file_writer.h
View File

@ -20,7 +20,6 @@
#include "file_writer.h"
#include <exception>
#include <string>
#include <zlib.h>

40
src/COMPRESS/zstd_file_writer.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,16 +18,13 @@
#ifdef LAMMPS_ZSTD
#include "zstd_file_writer.h"
#include <stdio.h>
#include "fmt/format.h"
#include <cstdio>
using namespace LAMMPS_NS;
ZstdFileWriter::ZstdFileWriter() : FileWriter(),
compression_level(0),
checksum_flag(1),
cctx(nullptr),
fp(nullptr)
ZstdFileWriter::ZstdFileWriter() :
FileWriter(), compression_level(0), checksum_flag(1), cctx(nullptr), fp(nullptr)
{
out_buffer_size = ZSTD_CStreamOutSize();
out_buffer = new char[out_buffer_size];
@ -38,9 +34,9 @@ ZstdFileWriter::ZstdFileWriter() : FileWriter(),
ZstdFileWriter::~ZstdFileWriter()
{
close();
ZstdFileWriter::close();
delete [] out_buffer;
delete[] out_buffer;
out_buffer = nullptr;
out_buffer_size = 0;
}
@ -57,9 +53,7 @@ void ZstdFileWriter::open(const std::string &path, bool append)
fp = fopen(path.c_str(), "wb");
}
if (!fp) {
throw FileWriterException(fmt::format("Could not open file '{}'", path));
}
if (!fp) { throw FileWriterException(fmt::format("Could not open file '{}'", path)); }
cctx = ZSTD_createCCtx();
@ -75,15 +69,15 @@ void ZstdFileWriter::open(const std::string &path, bool append)
/* ---------------------------------------------------------------------- */
size_t ZstdFileWriter::write(const void * buffer, size_t length)
size_t ZstdFileWriter::write(const void *buffer, size_t length)
{
if (!isopen()) return 0;
ZSTD_inBuffer input = { buffer, length, 0 };
ZSTD_inBuffer input = {buffer, length, 0};
ZSTD_EndDirective mode = ZSTD_e_continue;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
ZSTD_outBuffer output = {out_buffer, out_buffer_size, 0};
ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, fp);
} while (input.pos < input.size);
@ -98,11 +92,11 @@ void ZstdFileWriter::flush()
if (!isopen()) return;
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_inBuffer input = {nullptr, 0, 0};
ZSTD_EndDirective mode = ZSTD_e_flush;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
ZSTD_outBuffer output = {out_buffer, out_buffer_size, 0};
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, fp);
} while (remaining);
@ -114,14 +108,14 @@ void ZstdFileWriter::flush()
void ZstdFileWriter::close()
{
if (!isopen()) return;
if (!ZstdFileWriter::isopen()) return;
size_t remaining;
ZSTD_inBuffer input = { nullptr, 0, 0 };
ZSTD_inBuffer input = {nullptr, 0, 0};
ZSTD_EndDirective mode = ZSTD_e_end;
do {
ZSTD_outBuffer output = { out_buffer, out_buffer_size, 0 };
ZSTD_outBuffer output = {out_buffer, out_buffer_size, 0};
remaining = ZSTD_compressStream2(cctx, &output, &input, mode);
fwrite(out_buffer, sizeof(char), output.pos, fp);
} while (remaining);
@ -150,7 +144,8 @@ void ZstdFileWriter::setCompressionLevel(int level)
const int max_level = ZSTD_maxCLevel();
if (level < min_level || level > max_level)
throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
throw FileWriterException(
fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
compression_level = level;
}
@ -159,8 +154,7 @@ void ZstdFileWriter::setCompressionLevel(int level)
void ZstdFileWriter::setChecksum(bool enabled)
{
if (isopen())
throw FileWriterException("Checksum flag can not be changed while file is open");
if (isopen()) throw FileWriterException("Checksum flag can not be changed while file is open");
checksum_flag = enabled ? 1 : 0;
}

7
src/CORESHELL/pair_born_coul_dsf_cs.cpp
View File

@ -18,13 +18,14 @@
------------------------------------------------------------------------- */
#include "pair_born_coul_dsf_cs.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "math_const.h"
#include "math_special.h"
#include "neigh_list.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;

7
src/CORESHELL/pair_born_coul_wolf_cs.cpp
View File

@ -14,12 +14,13 @@
#include "pair_born_coul_wolf_cs.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "math_const.h"
#include "neigh_list.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;

5
src/CORESHELL/pair_coul_wolf_cs.cpp
View File

@ -13,13 +13,14 @@
------------------------------------------------------------------------- */
#include "pair_coul_wolf_cs.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "math_const.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;

3
src/DIELECTRIC/atom_vec_dielectric.cpp
View File

@ -17,6 +17,9 @@
#include "atom.h"
#include "citeme.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_user_dielectric_package[] =

4
src/DIELECTRIC/compute_efield_atom.cpp
View File

@ -33,12 +33,14 @@
#include "pppm_dielectric.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeEfieldAtom::ComputeEfieldAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), efield(NULL)
Compute(lmp, narg, arg), efield(nullptr)
{
if (narg < 3) error->all(FLERR,"Illegal compute efield/atom command");

11
src/DIELECTRIC/fix_polarize_bem_gmres.cpp
View File

@ -41,11 +41,9 @@
#include "comm.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "msm_dielectric.h"
#include "pair_coul_cut_dielectric.h"
#include "pair_coul_long_dielectric.h"
@ -54,7 +52,6 @@
#include "pair_lj_cut_coul_msm_dielectric.h"
#include "pppm_dielectric.h"
#include "random_park.h"
#include "timer.h"
#include "update.h"
#include <cmath>
@ -69,8 +66,8 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), q_backup(NULL), c(NULL), g(NULL), h(NULL), r(NULL), s(NULL), v(NULL),
y(NULL)
Fix(lmp, narg, arg), q_backup(nullptr), c(nullptr), g(nullptr), h(nullptr), r(nullptr), s(nullptr), v(nullptr),
y(nullptr)
{
if (narg < 5) error->all(FLERR, "Illegal fix polarize/bem/gmres command");
@ -110,7 +107,7 @@ FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *lmp, int narg, char **arg) :
if (atom->torque_flag) torqueflag = 1;
if (atom->avec->forceclearflag) extraflag = 1;
grow_arrays(atom->nmax);
FixPolarizeBEMGMRES::grow_arrays(atom->nmax);
atom->add_callback(0); // to ensure to work with atom->sort()
// output the residual and actual number of iterations
@ -133,7 +130,7 @@ FixPolarizeBEMGMRES::~FixPolarizeBEMGMRES()
memory->destroy(mat2tag);
memory->destroy(tag2mat);
if (allocated) deallocate();
if (allocated) FixPolarizeBEMGMRES::deallocate();
atom->delete_callback(id, 0);
}

1
src/DIELECTRIC/fix_polarize_bem_icc.cpp
View File

@ -33,7 +33,6 @@
#include "group.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
#include "msm_dielectric.h"
#include "pair_coul_cut_dielectric.h"
#include "pair_coul_long_dielectric.h"

6
src/DIELECTRIC/fix_polarize_functional.cpp
View File

@ -33,13 +33,11 @@
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "math_const.h"
#include "math_extra.h"
#include "math_special.h"
#include "memory.h"
#include "modify.h"
#include "msm_dielectric.h"
#include "neigh_list.h"
#include "neigh_request.h"
@ -50,8 +48,6 @@
#include "pair_lj_cut_coul_long_dielectric.h"
#include "pair_lj_cut_coul_msm_dielectric.h"
#include "pppm_dielectric.h"
#include "random_park.h"
#include "timer.h"
#include "update.h"
#include <cmath>
@ -131,7 +127,7 @@ FixPolarizeFunctional::FixPolarizeFunctional(LAMMPS *lmp, int narg, char **arg)
cg_r = cg_p = cg_Ap = nullptr;
cg_A = nullptr;
grow_arrays(atom->nmax);
FixPolarizeFunctional::grow_arrays(atom->nmax);
atom->add_callback(0); // to ensure to work with atom->sort()
}

6
src/DIELECTRIC/msm_dielectric.cpp
View File

@ -23,15 +23,9 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include <cstring>
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;

2
src/DIELECTRIC/pair_coul_cut_dielectric.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
@ -29,7 +28,6 @@
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

6
src/DIELECTRIC/pair_coul_long_dielectric.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "kspace.h"
@ -30,7 +29,6 @@
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -221,10 +219,10 @@ void PairCoulLongDielectric::init_style()
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL) error->all(FLERR, "Pair style requires a KSpace style");
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables(cut_coul, NULL);
if (ncoultablebits) init_tables(cut_coul, nullptr);
}

1
src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"

6
src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
@ -29,7 +28,6 @@
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -40,8 +38,8 @@ using namespace MathConst;
PairLJCutCoulDebyeDielectric::PairLJCutCoulDebyeDielectric(LAMMPS *lmp) : PairLJCutCoulDebye(lmp)
{
efield = NULL;
epot = NULL;
efield = nullptr;
epot = nullptr;
nmax = 0;
}

3
src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp
View File

@ -19,7 +19,6 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "kspace.h"
@ -257,7 +256,7 @@ void PairLJCutCoulLongDielectric::init_style()
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL) error->all(FLERR, "Pair style requires a KSpace style");
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables

7
src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp
View File

@ -19,10 +19,8 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "integrate.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
@ -31,6 +29,7 @@
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -365,7 +364,7 @@ void PairLJCutCoulMSMDielectric::init_style()
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL) error->all(FLERR, "Pair style requires a KSpace style");
if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
@ -382,5 +381,5 @@ void *PairLJCutCoulMSMDielectric::extract(const char *str, int &dim)
dim = 2;
if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
if (strcmp(str, "sigma") == 0) return (void *) sigma;
return NULL;
return nullptr;
}

5
src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp
View File

@ -19,19 +19,14 @@
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "integrate.h"
#include "kspace.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>

4
src/DIELECTRIC/pppm_dielectric.cpp
View File

@ -23,15 +23,11 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fft3d_wrap.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include "remap_wrap.h"
#include <cmath>

7
src/DIELECTRIC/pppm_disp_dielectric.cpp
View File

@ -21,21 +21,14 @@
#include "angle.h"
#include "atom.h"
#include "atom_vec_dielectric.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fft3d_wrap.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include "remap_wrap.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

1
src/DPD-MESO/pair_edpd.cpp
View File

@ -31,7 +31,6 @@
#include "update.h"
#include <cmath>
#include <ctime>
#include <cstring>
using namespace LAMMPS_NS;

5
src/DPD-REACT/fix_rx.cpp
View File

@ -34,7 +34,6 @@
#include <cfloat> // DBL_EPSILON
#include <cmath>
#include <cstring>
#include <vector> // std::vector<>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -59,7 +58,7 @@ namespace /* anonymous */
{
typedef double TimerType;
TimerType getTimeStamp(void) { return MPI_Wtime(); }
TimerType getTimeStamp() { return MPI_Wtime(); }
double getElapsedTime( const TimerType &t0, const TimerType &t1) { return t1-t0; }
} // end namespace
@ -1246,7 +1245,7 @@ int FixRX::rkf45_h0 (const int neq, const double t, const double /*t_stop*/,
return (iter + 1);
}
void FixRX::odeDiagnostics(void)
void FixRX::odeDiagnostics()
{
TimerType timer_start = getTimeStamp();

2
src/DPD-SMOOTH/fix_meso_move.cpp
View File

@ -224,7 +224,7 @@ FixMesoMove::FixMesoMove (LAMMPS *lmp, int narg, char **arg) :
// perform initial allocation of atom-based array
// register with Atom class
grow_arrays(atom->nmax);
FixMesoMove::grow_arrays(atom->nmax);
atom->add_callback(Atom::GROW);
atom->add_callback(Atom::RESTART);

6
src/DRUDE/fix_drude.cpp
View File

@ -25,7 +25,6 @@
#include <cstring>
#include <map>
#include <set>
#include <vector>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -55,7 +54,7 @@ FixDrude::FixDrude(LAMMPS *lmp, int narg, char **arg) :
}
drudeid = nullptr;
grow_arrays(atom->nmax);
FixDrude::grow_arrays(atom->nmax);
atom->add_callback(Atom::GROW);
atom->add_callback(Atom::RESTART);
atom->add_callback(Atom::BORDER);
@ -516,7 +515,8 @@ void FixDrude::ring_copy_drude(int size, char *cbuf, void *ptr) {
* ----------------------------------------------------------------------*/
void FixDrude::set_arrays(int i) {
if (drudetype[atom->type[i]] != NOPOL_TYPE) {
if (atom->nspecial[i] ==0) error->all(FLERR, "Polarizable atoms cannot be inserted with special lists info from the molecule template");
if (atom->nspecial[i] == nullptr)
error->all(FLERR, "Polarizable atoms cannot be inserted with special lists info from the molecule template");
drudeid[i] = atom->special[i][0]; // Drude partner should be at first place in the special list
} else {
drudeid[i] = 0;

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