Merge branch 'develop' into fortran-expansion
This commit is contained in:
Axel Kohlmeyer
7
.github/ISSUE_TEMPLATE/help_request.md
vendored
7
.github/ISSUE_TEMPLATE/help_request.md
vendored
@ -1,6 +1,6 @@
|
||||
---
|
||||
name: Request for Help
|
||||
about: "Don't post help requests here, email the lammps-users mailing list"
|
||||
about: "Don't post help requests here, post in the LAMMPS forum"
|
||||
title: ""
|
||||
labels: invalid
|
||||
assignees: ''
|
||||
@ -8,8 +8,9 @@ assignees: ''
|
||||
---
|
||||
|
||||
Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
|
||||
Instead send an e-mail to the lammps-users mailing list.
|
||||
Instead, you can post to the LAMMPS category in the Materials Science Community
|
||||
Discourse forum at: https://matsci.org/lammps/
|
||||
|
||||
This issue tracker is for tracking LAMMPS development related issues only.
|
||||
|
||||
Thanks for your cooperation.
|
||||
Thank you in advance for your cooperation.
|
||||
|
||||
@ -2,12 +2,13 @@ LAMMPS Library Interfaces
|
||||
*************************
|
||||
|
||||
As described on the :doc:`library interface to LAMMPS <Howto_library>`
|
||||
page, LAMMPS can be built as a library (static or shared), so that
|
||||
it can be called by another code, used in a :doc:`coupled manner
|
||||
page, LAMMPS can be built as a library (static or shared), so that it
|
||||
can be called by another code, used in a :doc:`coupled manner
|
||||
<Howto_couple>` with other codes, or driven through a :doc:`Python
|
||||
script <Python_head>`. Even the LAMMPS standalone executable is
|
||||
essentially a thin wrapper on top of the LAMMPS library, creating a
|
||||
LAMMPS instance, processing input and then existing.
|
||||
script <Python_head>`. The LAMMPS standalone executable itself is
|
||||
essentially a thin wrapper on top of the LAMMPS library, which creates a
|
||||
LAMMPS instance, passes the input for processing to that instance, and
|
||||
then exits.
|
||||
|
||||
Most of the APIs described below are based on C language wrapper
|
||||
functions in the files ``src/library.h`` and ``src/library.cpp``, but
|
||||
@ -87,6 +88,18 @@ run LAMMPS in serial mode.
|
||||
message retrieved <lammps_get_last_error_message>`. We thus
|
||||
recommend enabling C++ exceptions when using the library interface,
|
||||
|
||||
.. admonition:: Using the C library interface as a plugin
|
||||
:class: note
|
||||
|
||||
Rather than including the C library directly and link to the LAMMPS
|
||||
library at compile time, you can use the ``liblammpsplugin.h`` header
|
||||
file and the ``liblammpsplugin.c`` C code in the
|
||||
``examples/COUPLE/plugin`` folder for an interface to LAMMPS that is
|
||||
largely identical to the regular library interface, only that it will
|
||||
load a LAMMPS shared library file at runtime. This can be useful for
|
||||
applications where the interface to LAMMPS would be an optional
|
||||
feature.
|
||||
|
||||
.. warning::
|
||||
|
||||
No checks are made on the arguments of the function calls of the C
|
||||
@ -163,5 +176,3 @@ The following links provide some examples and references to the C++ API.
|
||||
:maxdepth: 1
|
||||
|
||||
Cplusplus
|
||||
|
||||
|
||||
|
||||
@ -112,7 +112,7 @@ requests to compute `gamma`, as shown in example below:
|
||||
compute max_pace_gamma all reduce max f_pace_gamma
|
||||
variable dump_skip equal "c_max_pace_gamma < 5"
|
||||
|
||||
dump pace_dump all custom 20 extrapolative_structures.dump id x y z f_pace_gamma
|
||||
dump pace_dump all custom 20 extrapolative_structures.dump id type x y z f_pace_gamma
|
||||
dump_modify pace_dump skip v_dump_skip
|
||||
|
||||
variable max_pace_gamma equal c_max_pace_gamma
|
||||
|
||||
1
examples/COUPLE/plugin/.gitignore
vendored
Normal file
1
examples/COUPLE/plugin/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
/build
|
||||
47
examples/COUPLE/plugin/CMakeLists.txt
Normal file
47
examples/COUPLE/plugin/CMakeLists.txt
Normal file
@ -0,0 +1,47 @@
|
||||
##########################################
|
||||
# CMake build system for coupling to the LAMMPS library
|
||||
# where the library is loaded dynamically at runtime.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
|
||||
"Please remove CMakeCache.txt and CMakeFiles first.")
|
||||
endif()
|
||||
|
||||
project(liblammpsplugin VERSION 1.0 LANGUAGES C)
|
||||
|
||||
# by default, install into $HOME/.local (not /usr/local),
|
||||
# so that no root access (and sudo) is needed
|
||||
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
|
||||
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
|
||||
endif()
|
||||
|
||||
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
|
||||
# and prints lots of pointless warnings about "unsafe" functions
|
||||
if(MSVC)
|
||||
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
|
||||
if(LAMMPS_EXCEPTIONS)
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
endif()
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
find_package(MPI REQUIRED)
|
||||
# do not include the (obsolete) MPI C++ bindings which makes
|
||||
# for leaner object files and avoids namespace conflicts
|
||||
set(MPI_CXX_SKIP_MPICXX TRUE)
|
||||
|
||||
##########################
|
||||
|
||||
add_executable(simple-plugin simple.c liblammpsplugin.c)
|
||||
target_link_libraries(simple-plugin PRIVATE MPI::MPI_C)
|
||||
target_compile_definitions(simple-plugin PRIVATE LAMMPS_LIB_MPI)
|
||||
|
||||
# link with -ldl or equivalent for plugin loading; except on Windows
|
||||
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
|
||||
target_link_libraries(simple-plugin PRIVATE ${CMAKE_DL_LIBS})
|
||||
endif()
|
||||
@ -11,32 +11,39 @@ liblammpsplugin.c is the LAMMPS library plugin loader
|
||||
You can then build the driver executable codes with a compile line
|
||||
like below.
|
||||
|
||||
mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
|
||||
mpicc -c -O -Wall -g simple.c
|
||||
mpicc simple.o liblammpsplugin.o -ldl -o simpleC
|
||||
mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g liblammpsplugin.c
|
||||
mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g simple.c
|
||||
mpicc simple.o liblammpsplugin.o -ldl -o simple-plugin
|
||||
|
||||
or using the provided CMake file with:
|
||||
|
||||
mkdir build
|
||||
cd build
|
||||
cmake ../
|
||||
cmake --build .
|
||||
|
||||
You also need to build LAMMPS as a shared library
|
||||
(see examples/COUPLE/README), e.g.
|
||||
(see examples/COUPLE/README), e.g.
|
||||
|
||||
cd $HOME/lammps/src
|
||||
make mode=shlib mpi
|
||||
|
||||
or
|
||||
or
|
||||
|
||||
cd $HOME/lammps
|
||||
mkdir build-shared
|
||||
cd build-shared
|
||||
cmake -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on ../cmake
|
||||
cmake -D BUILD_MPI=on -D BUILD_SHARED_LIBS=on ../cmake
|
||||
make
|
||||
|
||||
You then run simpleC on a parallel machine
|
||||
You then run simple-plugin on a parallel machine
|
||||
on some number of processors Q with 3 arguments:
|
||||
|
||||
% mpirun -np Q simpleC P in.lj $HOME/lammps/src/liblammps.so
|
||||
% mpirun -np Q simple-plugin P in.lj $HOME/lammps/src/liblammps.so
|
||||
|
||||
or
|
||||
|
||||
% mpirun -np Q simpleC P in.lj $HOME/lammps/build-shared/liblammps.so
|
||||
% mpirun -np Q simple-plugin P in.lj $HOME/lammps/build-shared/liblammps.so
|
||||
|
||||
P is the number of procs you want LAMMPS to run on (must be <= Q) and
|
||||
in.lj is a LAMMPS input script and the last argument is the path to
|
||||
|
||||
@ -18,10 +18,29 @@
|
||||
a LAMMPS plugin to some other software.
|
||||
*/
|
||||
|
||||
#include "library.h"
|
||||
#include "liblammpsplugin.h"
|
||||
#include <stdlib.h>
|
||||
|
||||
#if defined(_WIN32)
|
||||
|
||||
#ifndef WIN32_LEAN_AND_MEAN
|
||||
#define WIN32_LEAN_AND_MEAN
|
||||
#endif
|
||||
|
||||
#if defined(_WIN32_WINNT)
|
||||
#undef _WIN32_WINNT
|
||||
#endif
|
||||
|
||||
// target Windows version is windows 7 and later
|
||||
#define _WIN32_WINNT _WIN32_WINNT_WIN7
|
||||
#define PSAPI_VERSION 2
|
||||
|
||||
#include <windows.h>
|
||||
#else
|
||||
#include <dlfcn.h>
|
||||
#endif
|
||||
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
{
|
||||
@ -29,14 +48,29 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
void *handle;
|
||||
|
||||
if (lib == NULL) return NULL;
|
||||
|
||||
#ifdef _WIN32
|
||||
handle = (void *) LoadLibrary(lib);
|
||||
#else
|
||||
handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);
|
||||
#endif
|
||||
if (handle == NULL) return NULL;
|
||||
|
||||
lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));
|
||||
lmp->handle = handle;
|
||||
|
||||
#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
|
||||
#ifdef _WIN32
|
||||
#define ADDSYM(symbol) *(void **) (&lmp->symbol) = (void *) GetProcAddress((HINSTANCE) handle, "lammps_" #symbol)
|
||||
#else
|
||||
#define ADDSYM(symbol) *(void **) (&lmp->symbol) = dlsym(handle,"lammps_" #symbol)
|
||||
#endif
|
||||
|
||||
#if defined(LAMMPS_LIB_MPI)
|
||||
ADDSYM(open);
|
||||
#else
|
||||
lmp->open = NULL;
|
||||
#endif
|
||||
|
||||
ADDSYM(open_no_mpi);
|
||||
ADDSYM(open_fortran);
|
||||
ADDSYM(close);
|
||||
@ -46,6 +80,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(kokkos_finalize);
|
||||
ADDSYM(python_finalize);
|
||||
|
||||
ADDSYM(error);
|
||||
|
||||
ADDSYM(file);
|
||||
ADDSYM(command);
|
||||
ADDSYM(commands_list);
|
||||
@ -70,6 +106,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(extract_compute);
|
||||
ADDSYM(extract_fix);
|
||||
ADDSYM(extract_variable);
|
||||
ADDSYM(extract_variable_datatype);
|
||||
ADDSYM(set_variable);
|
||||
|
||||
ADDSYM(gather_atoms);
|
||||
@ -77,8 +114,15 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(gather_atoms_subset);
|
||||
ADDSYM(scatter_atoms);
|
||||
ADDSYM(scatter_atoms_subset);
|
||||
|
||||
ADDSYM(gather_bonds);
|
||||
|
||||
ADDSYM(gather);
|
||||
ADDSYM(gather_concat);
|
||||
ADDSYM(gather_subset);
|
||||
ADDSYM(scatter);
|
||||
ADDSYM(scatter_subset);
|
||||
|
||||
ADDSYM(create_atoms);
|
||||
|
||||
ADDSYM(find_pair_neighlist);
|
||||
@ -116,6 +160,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(plugin_count);
|
||||
ADDSYM(plugin_name);
|
||||
|
||||
ADDSYM(encode_image_flags);
|
||||
ADDSYM(decode_image_flags);
|
||||
|
||||
ADDSYM(set_fix_external_callback);
|
||||
ADDSYM(fix_external_get_force);
|
||||
ADDSYM(fix_external_set_energy_global);
|
||||
@ -125,6 +172,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(fix_external_set_vector_length);
|
||||
ADDSYM(fix_external_set_vector);
|
||||
|
||||
ADDSYM(flush_buffers);
|
||||
|
||||
ADDSYM(free);
|
||||
|
||||
ADDSYM(is_running);
|
||||
@ -139,6 +188,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
lmp->has_error = NULL;
|
||||
lmp->get_last_error_message = NULL;
|
||||
#endif
|
||||
|
||||
ADDSYM(python_api_version);
|
||||
return lmp;
|
||||
}
|
||||
|
||||
@ -147,7 +198,11 @@ int liblammpsplugin_release(liblammpsplugin_t *lmp)
|
||||
if (lmp == NULL) return 1;
|
||||
if (lmp->handle == NULL) return 2;
|
||||
|
||||
#ifdef _WIN32
|
||||
FreeLibrary((HINSTANCE) handle);
|
||||
#else
|
||||
dlclose(lmp->handle);
|
||||
#endif
|
||||
free((void *)lmp);
|
||||
return 0;
|
||||
}
|
||||
|
||||
@ -28,11 +28,71 @@
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
#if defined(LAMMPS_LIB_MPI)
|
||||
#include <mpi.h>
|
||||
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
|
||||
#include <inttypes.h> /* for int64_t */
|
||||
#endif
|
||||
|
||||
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
|
||||
#include <stdint.h> /* for int64_t */
|
||||
#endif
|
||||
|
||||
/* The following must be kept in sync with the equivalent constants in
|
||||
* python/lammps/constants.py, fortran/lammps.f90, tools/swig/lammps.i,
|
||||
* and examples/COUPLE/plugin/liblammpsplugin.h */
|
||||
|
||||
/* Data type constants for extracting data from atoms, computes and fixes */
|
||||
|
||||
enum _LMP_DATATYPE_CONST {
|
||||
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
|
||||
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
|
||||
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
|
||||
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
|
||||
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
|
||||
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
|
||||
LAMMPS_STRING = 6 /*!< C-String */
|
||||
};
|
||||
|
||||
/* Style constants for extracting data from computes and fixes. */
|
||||
|
||||
enum _LMP_STYLE_CONST {
|
||||
LMP_STYLE_GLOBAL = 0, /*!< return global data */
|
||||
LMP_STYLE_ATOM = 1, /*!< return per-atom data */
|
||||
LMP_STYLE_LOCAL = 2 /*!< return local data */
|
||||
};
|
||||
|
||||
/* Type and size constants for extracting data from computes and fixes. */
|
||||
|
||||
enum _LMP_TYPE_CONST {
|
||||
LMP_TYPE_SCALAR = 0, /*!< return scalar */
|
||||
LMP_TYPE_VECTOR = 1, /*!< return vector */
|
||||
LMP_TYPE_ARRAY = 2, /*!< return array */
|
||||
LMP_SIZE_VECTOR = 3, /*!< return length of vector */
|
||||
LMP_SIZE_ROWS = 4, /*!< return number of rows */
|
||||
LMP_SIZE_COLS = 5 /*!< return number of columns */
|
||||
};
|
||||
|
||||
/* Error codes to select the suitable function in the Error class */
|
||||
|
||||
enum _LMP_ERROR_CONST {
|
||||
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
|
||||
LMP_ERROR_ONE = 1, /*!< called from one MPI rank */
|
||||
LMP_ERROR_ALL = 2, /*!< called from all MPI ranks */
|
||||
LMP_ERROR_WORLD = 4, /*!< error on Comm::world */
|
||||
LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
|
||||
};
|
||||
|
||||
/** Variable style constants for extracting data from variables.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
|
||||
* fortran/lammps.f90, and tools/swig/lammps.i */
|
||||
|
||||
enum _LMP_VAR_CONST {
|
||||
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
|
||||
LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
|
||||
LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */
|
||||
LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
|
||||
};
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
@ -49,7 +109,11 @@ struct _liblammpsplugin {
|
||||
int abiversion;
|
||||
int has_exceptions;
|
||||
void *handle;
|
||||
#if defined(LAMMPS_LIB_MPI)
|
||||
void *(*open)(int, char **, MPI_Comm, void **);
|
||||
#else
|
||||
void *open;
|
||||
#endif
|
||||
void *(*open_no_mpi)(int, char **, void **);
|
||||
void *(*open_fortran)(int, char **, void **, int);
|
||||
void (*close)(void *);
|
||||
@ -59,13 +123,15 @@ struct _liblammpsplugin {
|
||||
void (*kokkos_finalize)();
|
||||
void (*python_finalize)();
|
||||
|
||||
void (*error)(void *, int, const char *);
|
||||
|
||||
void (*file)(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 *);
|
||||
double (*get_thermo)(void *, const char *);
|
||||
|
||||
void (*extract_box)(void *, double *, double *,
|
||||
double *, double *, double *, int *, int *);
|
||||
@ -78,12 +144,13 @@ struct _liblammpsplugin {
|
||||
int *(*extract_global_datatype)(void *, const char *);
|
||||
void *(*extract_global)(void *, const char *);
|
||||
|
||||
void *(*extract_atom_datatype)(void *, const char *);
|
||||
int *(*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 (*extract_variable_datatype)(void *, const char *);
|
||||
int (*set_variable)(void *, char *, char *);
|
||||
|
||||
void (*gather_atoms)(void *, char *, int, int, void *);
|
||||
@ -93,22 +160,26 @@ struct _liblammpsplugin {
|
||||
void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
|
||||
|
||||
void (*gather_bonds)(void *, void *);
|
||||
|
||||
// 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
|
||||
|
||||
void (*gather)(void *, char *, int, int, void *);
|
||||
void (*gather_concat)(void *, char *, int, int, void *);
|
||||
void (*gather_subset)(void *, char *, int, int, int, int *,void *);
|
||||
void (*scatter)(void *, char *, int, int, void *);
|
||||
void (*scatter_subset)(void *, char *, int, int, int, int *, void *);
|
||||
|
||||
/* lammps_create_atoms() takes tagint and imageint as args
|
||||
* the 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);
|
||||
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);
|
||||
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 (*find_compute_neighlist)(void *, const char *, int);
|
||||
int (*neighlist_num_elements)(void *, int);
|
||||
void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
|
||||
|
||||
@ -141,8 +212,16 @@ struct _liblammpsplugin {
|
||||
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 *);
|
||||
#if !defined(LAMMPS_BIGBIG)
|
||||
int (*encode_image_flags)(int, int, int);
|
||||
void (*decode_image_flags)(int, int *);
|
||||
#else
|
||||
int64_t (*encode_image_flags)(int, int, int);
|
||||
void (*decode_image_flags)(int64_t, int *);
|
||||
#endif
|
||||
|
||||
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void *);
|
||||
double **(*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 *);
|
||||
@ -150,6 +229,8 @@ struct _liblammpsplugin {
|
||||
void (*fix_external_set_vector_length)(void *, const char *, int);
|
||||
void (*fix_external_set_vector)(void *, const char *, int, double);
|
||||
|
||||
void (*flush_buffers)(void *);
|
||||
|
||||
void (*free)(void *);
|
||||
|
||||
void (*is_running)(void *);
|
||||
@ -157,6 +238,8 @@ struct _liblammpsplugin {
|
||||
|
||||
int (*has_error)(void *);
|
||||
int (*get_last_error_message)(void *, char *, int);
|
||||
|
||||
int (*python_api_version)();
|
||||
};
|
||||
|
||||
typedef struct _liblammpsplugin liblammpsplugin_t;
|
||||
|
||||
@ -19,10 +19,16 @@
|
||||
in.lammps = LAMMPS input script
|
||||
See README for compilation instructions */
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <mpi.h>
|
||||
|
||||
/* define so interface to lammps_open() is available,
|
||||
since we will run on split communicator */
|
||||
#define LAMMPS_LIB_MPI 1
|
||||
|
||||
#include "liblammpsplugin.h" /* this is the include for the plugin loader */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
@ -87,7 +93,13 @@ int main(int narg, char **arg)
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
|
||||
if (lammps == 1) {
|
||||
if (plugin->open == NULL) {
|
||||
printf("ERROR: liblammpsmpi.c must be compiled with -DLAMMPS_LIB_MPI=1 for this program\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,2);
|
||||
}
|
||||
lmp = plugin->open(0,NULL,comm_lammps,NULL);
|
||||
}
|
||||
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
@ -112,23 +124,23 @@ int main(int narg, char **arg)
|
||||
|
||||
int natoms = plugin->get_natoms(lmp);
|
||||
x = (double *) malloc(3*natoms*sizeof(double));
|
||||
plugin->gather_atoms(lmp,"x",1,3,x);
|
||||
plugin->gather_atoms(lmp,(char *)"x",1,3,x);
|
||||
v = (double *) malloc(3*natoms*sizeof(double));
|
||||
plugin->gather_atoms(lmp,"v",1,3,v);
|
||||
plugin->gather_atoms(lmp,(char *)"v",1,3,v);
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
plugin->scatter_atoms(lmp,"x",1,3,x);
|
||||
plugin->scatter_atoms(lmp,(char *)"x",1,3,x);
|
||||
|
||||
plugin->command(lmp,"run 1");
|
||||
}
|
||||
|
||||
// extract force on single atom two different ways
|
||||
/* extract force on single atom two different ways */
|
||||
|
||||
if (lammps == 1) {
|
||||
double **f = (double **) plugin->extract_atom(lmp,"f");
|
||||
printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
|
||||
|
||||
double *fx = (double *) plugin->extract_variable(lmp,"fx","all");
|
||||
double *fx = (double *) plugin->extract_variable(lmp,"fx",(char *)"all");
|
||||
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
|
||||
}
|
||||
|
||||
@ -160,7 +172,7 @@ int main(int narg, char **arg)
|
||||
if (v) free(v);
|
||||
if (type) free(type);
|
||||
|
||||
// close down LAMMPS
|
||||
/* close down LAMMPS */
|
||||
|
||||
if (lammps == 1) {
|
||||
plugin->close(lmp);
|
||||
|
||||
@ -1,17 +1,44 @@
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
project(simple CXX)
|
||||
|
||||
set(LAMMPS_SRC_DIRECTORY "" CACHE PATH "Path for lammps source")
|
||||
if(NOT LAMMPS_SRC_DIRECTORY STREQUAL "" AND EXISTS ${LAMMPS_SRC_DIRECTORY}/cmake/CMakeLists.txt)
|
||||
option(BUILD_LIB "Build LAMMPS library" ON)
|
||||
add_subdirectory(${LAMMPS_SRC_DIRECTORY}/cmake lammps)
|
||||
else()
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
|
||||
"Please remove CMakeCache.txt and CMakeFiles first.")
|
||||
endif()
|
||||
|
||||
project(couple-simple VERSION 1.0 LANGUAGES C CXX)
|
||||
|
||||
# by default, install into $HOME/.local (not /usr/local),
|
||||
# so that no root access (and sudo) is needed
|
||||
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
|
||||
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
|
||||
endif()
|
||||
|
||||
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
|
||||
# and prints lots of pointless warnings about "unsafe" functions
|
||||
if(MSVC)
|
||||
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
|
||||
if(LAMMPS_EXCEPTIONS)
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
endif()
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
find_package(MPI QUIET)
|
||||
# do not include the (obsolete) MPI C++ bindings which makes
|
||||
# for leaner object files and avoids namespace conflicts
|
||||
set(MPI_CXX_SKIP_MPICXX TRUE)
|
||||
|
||||
##########################
|
||||
|
||||
# build within LAMMPS build system
|
||||
if(NOT LAMMPS_SOURCE_DIR)
|
||||
find_package(LAMMPS REQUIRED)
|
||||
endif()
|
||||
|
||||
add_executable(simpleCC simple.cpp)
|
||||
target_link_libraries(simpleCC LAMMPS::lammps)
|
||||
|
||||
enable_language(C)
|
||||
add_executable(simpleC simple.c)
|
||||
target_link_libraries(simpleC LAMMPS::lammps)
|
||||
|
||||
@ -44,7 +44,8 @@ MODULE LIBLAMMPS
|
||||
! Data type constants for extracting data from global, atom, compute, and fix
|
||||
!
|
||||
! Must be kept in sync with the equivalent declarations in
|
||||
! src/library.h, python/lammps/constants.py, and tools/swig/lammps.i
|
||||
! src/library.h, python/lammps/constants.py, tools/swig/lammps.i,
|
||||
! and examples/COUPLE/plugin/liblammpsplugin.h
|
||||
!
|
||||
! These are NOT part of the API (the part the user sees)
|
||||
INTEGER(c_int), PARAMETER :: &
|
||||
|
||||
@ -22,8 +22,8 @@ LAMMPS_INT64 = 4
|
||||
LAMMPS_INT64_2D = 5
|
||||
LAMMPS_STRING = 6
|
||||
|
||||
# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i
|
||||
# and the constants in fortran/lammps.f90
|
||||
# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i,
|
||||
# examples/COUPLE/plugin/liblammpsplugin.h, and the constants in fortran/lammps.f90
|
||||
LMP_STYLE_GLOBAL = 0
|
||||
LMP_STYLE_ATOM = 1
|
||||
LMP_STYLE_LOCAL = 2
|
||||
|
||||
@ -240,15 +240,19 @@ void FixPair::post_force(int /*vflag*/)
|
||||
// extract pair style fields one by one
|
||||
// store their values in this fix
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
int icol = 0;
|
||||
int columns;
|
||||
|
||||
for (int ifield = 0; ifield < nfield; ifield++) {
|
||||
void *pvoid = pstyle->extract_peratom(fieldname[ifield],columns);
|
||||
if (pvoid == nullptr)
|
||||
error->all(FLERR,"Fix pair pair style cannot extract {}",fieldname[ifield]);
|
||||
|
||||
// Pair::extract_peratom() may return a null pointer if there are no atoms the sub-domain
|
||||
// so returning null is only an error if there are local atoms.
|
||||
|
||||
if ((pvoid == nullptr) && (nlocal > 0))
|
||||
error->one(FLERR, "Fix pair cannot extract property {} from pair style", fieldname[ifield]);
|
||||
|
||||
if (columns == 0) {
|
||||
double *pvector = (double *) pvoid;
|
||||
|
||||
@ -41,7 +41,7 @@
|
||||
/** Data type constants for extracting data from atoms, computes and fixes
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
|
||||
* fortran/lammps.f90, and tools/swig/lammps.i */
|
||||
* fortran/lammps.f90, tools/swig/lammps.i, examples/COUPLE/plugin/liblammpsplugin.h */
|
||||
|
||||
enum _LMP_DATATYPE_CONST {
|
||||
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
|
||||
@ -56,7 +56,7 @@ enum _LMP_DATATYPE_CONST {
|
||||
/** Style constants for extracting data from computes and fixes.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
|
||||
* fortran/lammps.f90, and tools/swig/lammps.i */
|
||||
* fortran/lammps.f90, tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
|
||||
|
||||
enum _LMP_STYLE_CONST {
|
||||
LMP_STYLE_GLOBAL = 0, /*!< return global data */
|
||||
@ -67,7 +67,7 @@ enum _LMP_STYLE_CONST {
|
||||
/** Type and size constants for extracting data from computes and fixes.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
|
||||
* fortran/lammps.f90, and tools/swig/lammps.i */
|
||||
* fortran/lammps.f90, tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
|
||||
|
||||
enum _LMP_TYPE_CONST {
|
||||
LMP_TYPE_SCALAR = 0, /*!< return scalar */
|
||||
@ -81,7 +81,7 @@ enum _LMP_TYPE_CONST {
|
||||
/** Error codes to select the suitable function in the Error class
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
|
||||
* fortran/lammps.f90, and tools/swig/lammps.i */
|
||||
* fortran/lammps.f90, tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
|
||||
|
||||
enum _LMP_ERROR_CONST {
|
||||
LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
|
||||
@ -94,7 +94,7 @@ enum _LMP_ERROR_CONST {
|
||||
/** Variable style constants for extracting data from variables.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
|
||||
* fortran/lammps.f90, and tools/swig/lammps.i */
|
||||
* fortran/lammps.f90, tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
|
||||
|
||||
enum _LMP_VAR_CONST {
|
||||
LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
|
||||
@ -260,15 +260,14 @@ void lammps_decode_image_flags(int64_t image, int *flags);
|
||||
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
|
||||
void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr,
|
||||
void *ptr);
|
||||
#elif defined(LAMMPS_SMALLBIG)
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
|
||||
void lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void *);
|
||||
#else
|
||||
typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
|
||||
void lammps_set_fix_external_callback(void *, const char *, FixExternalFnPtr, void *);
|
||||
#endif
|
||||
|
||||
void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalFnPtr funcptr,
|
||||
void *ptr);
|
||||
double **lammps_fix_external_get_force(void *handle, const char *id);
|
||||
void lammps_fix_external_set_energy_global(void *handle, const char *id, double eng);
|
||||
void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double *eng);
|
||||
|
||||
@ -71,3 +71,23 @@ add_executable(test_library_mpi test_library_mpi.cpp)
|
||||
target_link_libraries(test_library_mpi PRIVATE lammps GTest::GMock)
|
||||
target_compile_definitions(test_library_mpi PRIVATE ${TEST_CONFIG_DEFS})
|
||||
add_mpi_test(NAME LibraryMPI NUM_PROCS 4 COMMAND $<TARGET_FILE:test_library_mpi>)
|
||||
|
||||
# simple run tests for coupling to the LAMMPS library
|
||||
if(BUILD_MPI)
|
||||
if(BUILD_SHARED_LIBS)
|
||||
add_subdirectory(${LAMMPS_DIR}/examples/COUPLE/plugin ${CMAKE_BINARY_DIR}/build-couple)
|
||||
add_test(NAME RunCoupleSimplePlugin
|
||||
COMMAND $<TARGET_FILE:simple-plugin> 1 ${LAMMPS_DIR}/examples/COUPLE/plugin/in.lj $<TARGET_FILE:lammps>)
|
||||
set_tests_properties(RunCoupleSimplePlugin PROPERTIES
|
||||
ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2"
|
||||
PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?\\)")
|
||||
endif()
|
||||
add_subdirectory(${LAMMPS_DIR}/examples/COUPLE/simple ${CMAKE_BINARY_DIR}/build-simple)
|
||||
add_test(NAME RunCoupleSimpleC
|
||||
COMMAND $<TARGET_FILE:simpleC> 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj)
|
||||
add_test(NAME RunCoupleSimpleCC
|
||||
COMMAND $<TARGET_FILE:simpleCC> 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj)
|
||||
set_tests_properties(RunCoupleSimpleC RunCoupleSimpleCC PROPERTIES
|
||||
ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2"
|
||||
PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?\\)")
|
||||
endif()
|
||||
|
||||
Reference in New Issue
Block a user