Merge branch 'master' into parse-logical-keyword
This commit is contained in:
Axel Kohlmeyer
@ -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)
|
||||
|
||||
|
||||
@ -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 ${CUDA_REQUEST_PIC}
|
||||
|
||||
@ -38,7 +38,7 @@ if(DOWNLOAD_QUIP)
|
||||
set(temp "${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")
|
||||
|
||||
@ -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 ] },
|
||||
]
|
||||
|
||||
@ -24,6 +24,7 @@ set(ALL_PACKAGES
|
||||
DRUDE
|
||||
EFF
|
||||
EXTRA-COMPUTE
|
||||
EXTRA-DUMP
|
||||
EXTRA-FIX
|
||||
EXTRA-MOLECULE
|
||||
EXTRA-PAIR
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -209,6 +209,9 @@ Convenience functions
|
||||
.. doxygenfunction:: date2num
|
||||
:project: progguide
|
||||
|
||||
.. doxygenfunction:: current_date
|
||||
:project: progguide
|
||||
|
||||
Customized standard functions
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
|
||||
@ -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)
|
||||
|
||||
@ -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>`_
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -8,9 +8,8 @@ fix brownian command
|
||||
fix brownian/sphere command
|
||||
===========================
|
||||
|
||||
fix brownian/sphere command
|
||||
===========================
|
||||
|
||||
fix brownian/asphere command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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:
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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')]
|
||||
|
||||
@ -2441,6 +2441,7 @@ packings
|
||||
padua
|
||||
Padua
|
||||
pafi
|
||||
PairIJ
|
||||
palegoldenrod
|
||||
palegreen
|
||||
paleturquoise
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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();
|
||||
}
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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(); }
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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,",");
|
||||
@ -992,10 +992,8 @@ int DeviceT::compile_kernels() {
|
||||
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()))
|
||||
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);
|
||||
}
|
||||
|
||||
|
||||
@ -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 &);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
@ -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]);
|
||||
|
||||
@ -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) {
|
||||
|
||||
@ -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;
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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,
|
||||
|
||||
@ -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:
|
||||
|
||||
@ -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);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -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);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -39,7 +39,6 @@
|
||||
#include <cstring>
|
||||
#include <map>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
||||
@ -37,7 +37,6 @@
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include <vector>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
@ -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) {
|
||||
|
||||
|
||||
@ -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);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -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;
|
||||
}
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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"
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -14,7 +14,6 @@
|
||||
#include "atom_vec_oxdna.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -17,8 +17,6 @@
|
||||
|
||||
#include "pair_oxrna2_excv.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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"
|
||||
|
||||
|
||||
@ -25,7 +25,6 @@
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
@ -25,7 +25,6 @@
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
@ -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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -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;
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
////////////////////////////////////////////////////////////////////////
|
||||
|
||||
@ -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"
|
||||
|
||||
@ -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);
|
||||
|
||||
@ -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
|
||||
@ -58,8 +55,7 @@ void DumpAtomGZ::openfile()
|
||||
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);
|
||||
@ -109,9 +105,7 @@ void DumpAtomGZ::write_header(bigint ndump)
|
||||
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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -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
|
||||
@ -66,8 +61,7 @@ void DumpAtomZstd::openfile()
|
||||
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);
|
||||
@ -117,9 +111,7 @@ void DumpAtomZstd::write_header(bigint ndump)
|
||||
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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -198,9 +188,12 @@ int DumpAtomZstd::modify_param(int narg, char **arg)
|
||||
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[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");
|
||||
|
||||
@ -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
|
||||
@ -60,8 +57,7 @@ void DumpCFGGZ::openfile()
|
||||
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);
|
||||
@ -111,8 +107,10 @@ 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);
|
||||
@ -127,8 +125,7 @@ void DumpCFGGZ::write_header(bigint n)
|
||||
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]);
|
||||
for (int i = 0; i < nfield - 5; i++) header += fmt::format("auxiliary[{}] = {}\n", i, auxname[i]);
|
||||
|
||||
writer.write(header.c_str(), header.length());
|
||||
}
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -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
|
||||
@ -68,8 +63,7 @@ void DumpCFGZstd::openfile()
|
||||
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);
|
||||
@ -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);
|
||||
@ -123,8 +115,10 @@ 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);
|
||||
@ -139,8 +133,7 @@ void DumpCFGZstd::write_header(bigint n)
|
||||
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]);
|
||||
for (int i = 0; i < nfield - 5; i++) header += fmt::format("auxiliary[{}] = {}\n", i, auxname[i]);
|
||||
|
||||
writer.write(header.c_str(), header.length());
|
||||
}
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -242,9 +233,12 @@ int DumpCFGZstd::modify_param(int narg, char **arg)
|
||||
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[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");
|
||||
|
||||
@ -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
|
||||
@ -58,8 +55,7 @@ void DumpCustomGZ::openfile()
|
||||
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);
|
||||
@ -107,9 +103,7 @@ void DumpCustomGZ::write_header(bigint ndump)
|
||||
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);
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -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"
|
||||
|
||||
|
||||
@ -28,7 +28,6 @@ DumpStyle(custom/zstd,DumpCustomZstd);
|
||||
|
||||
#include "dump_custom.h"
|
||||
#include "zstd_file_writer.h"
|
||||
#include <stdio.h>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
|
||||
@ -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
|
||||
@ -58,8 +55,7 @@ void DumpLocalGZ::openfile()
|
||||
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);
|
||||
@ -107,9 +103,7 @@ void DumpLocalGZ::write_header(bigint ndump)
|
||||
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);
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -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
|
||||
@ -65,8 +61,7 @@ void DumpLocalZstd::openfile()
|
||||
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);
|
||||
@ -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);
|
||||
@ -118,9 +111,7 @@ void DumpLocalZstd::write_header(bigint ndump)
|
||||
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);
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -201,9 +190,12 @@ int DumpLocalZstd::modify_param(int narg, char **arg)
|
||||
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[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");
|
||||
|
||||
@ -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
|
||||
@ -58,8 +54,7 @@ void DumpXYZGZ::openfile()
|
||||
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);
|
||||
@ -117,8 +112,8 @@ 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])],
|
||||
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);
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -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
|
||||
@ -65,8 +60,7 @@ void DumpXYZZstd::openfile()
|
||||
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);
|
||||
@ -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);
|
||||
@ -128,8 +120,8 @@ 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])],
|
||||
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);
|
||||
@ -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(); }
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -166,9 +156,12 @@ int DumpXYZZstd::modify_param(int narg, char **arg)
|
||||
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[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");
|
||||
|
||||
@ -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();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -50,8 +45,7 @@ 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));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -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;
|
||||
}
|
||||
|
||||
@ -20,7 +20,6 @@
|
||||
|
||||
#include "file_writer.h"
|
||||
|
||||
#include <exception>
|
||||
#include <string>
|
||||
#include <zlib.h>
|
||||
|
||||
|
||||
@ -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];
|
||||
@ -38,7 +34,7 @@ ZstdFileWriter::ZstdFileWriter() : FileWriter(),
|
||||
|
||||
ZstdFileWriter::~ZstdFileWriter()
|
||||
{
|
||||
close();
|
||||
ZstdFileWriter::close();
|
||||
|
||||
delete[] out_buffer;
|
||||
out_buffer = nullptr;
|
||||
@ -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();
|
||||
|
||||
@ -114,7 +108,7 @@ void ZstdFileWriter::flush()
|
||||
|
||||
void ZstdFileWriter::close()
|
||||
{
|
||||
if (!isopen()) return;
|
||||
if (!ZstdFileWriter::isopen()) return;
|
||||
|
||||
size_t remaining;
|
||||
ZSTD_inBuffer input = {nullptr, 0, 0};
|
||||
@ -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;
|
||||
}
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
|
||||
@ -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[] =
|
||||
|
||||
@ -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");
|
||||
|
||||
|
||||
@ -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);
|
||||
}
|
||||
|
||||
|
||||
@ -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"
|
||||
|
||||
@ -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()
|
||||
}
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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);
|
||||
}
|
||||
|
||||
@ -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"
|
||||
|
||||
@ -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;
|
||||
}
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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;
|
||||
}
|
||||
|
||||
@ -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>
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -31,7 +31,6 @@
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <ctime>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -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();
|
||||
|
||||
|
||||
@ -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);
|
||||
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -24,6 +24,7 @@
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_deform.h"
|
||||
#include "fix_drude.h"
|
||||
#include "force.h"
|
||||
#include "irregular.h"
|
||||
#include "kspace.h"
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user