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Merge pull request #2850 from akohlmey/lammps-gather-bonds

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Implement lammps_gather_bonds() into the C-library interface and the Python module
This commit is contained in:
Axel Kohlmeyer
2021-07-27 11:30:19 -04:00
committed by GitHub
parent dab884fd1f a4ffffad33
commit 8838fbc1c3
14 changed files with 740 additions and 2 deletions
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6
doc/src/Library_scatter.rst
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@ -17,6 +17,7 @@ It documents the following functions:
- :cpp:func:`lammps_gather_atoms_subset`
- :cpp:func:`lammps_scatter_atoms`
- :cpp:func:`lammps_scatter_atoms_subset`
- :cpp:func:`lammps_gather_bonds`
- :cpp:func:`lammps_gather`
- :cpp:func:`lammps_gather_concat`
- :cpp:func:`lammps_gather_subset`
@ -51,6 +52,11 @@ It documents the following functions:
-----------------------
.. doxygenfunction:: lammps_gather_bonds
:project: progguide
-----------------------
.. doxygenfunction:: lammps_gather
:project: progguide

45
python/lammps/core.py
View File

@ -201,6 +201,9 @@ class lammps(object):
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_scatter_atoms_subset.restype = None
self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_bonds.restype = None
self.lib.lammps_gather.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather.restype = None
@ -1206,6 +1209,32 @@ class lammps(object):
with ExceptionCheck(self):
self.lib.lammps_scatter_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
# -------------------------------------------------------------------------
def gather_bonds(self):
"""Retrieve global list of bonds
This is a wrapper around the :cpp:func:`lammps_gather_bonds`
function of the C-library interface.
This function returns a tuple with the number of bonds and a
flat list of ctypes integer values with the bond type, bond atom1,
bond atom2 for each bond.
.. versionadded:: 28Jul2021
:return: a tuple with the number of bonds and a list of c_int or c_long
:rtype: (int, 3*nbonds*c_tagint)
"""
nbonds = self.extract_global("nbonds")
with ExceptionCheck(self):
data = ((3*nbonds)*self.c_tagint)()
self.lib.lammps_gather_bonds(self.lmp,data)
return nbonds,data
# -------------------------------------------------------------------------
# return vector of atom/compute/fix properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
@ -1752,6 +1781,8 @@ class lammps(object):
- x is a 2d NumPy array of doubles of the coordinates of the local atoms
- f is a 2d NumPy array of doubles of the forces on the local atoms that will be added
.. versionchanged:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param callback: Python function that will be called from fix external
@ -1782,6 +1813,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
@ -1800,6 +1833,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: potential energy value to be added by fix external
@ -1817,6 +1852,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: list of 6 floating point numbers with the virial to be added by fix external
@ -1835,6 +1872,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: list of potential energy values for local atoms to be added by fix external
@ -1856,6 +1895,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param vatom: list of natoms lists with 6 floating point numbers to be added by fix external
@ -1886,6 +1927,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param length: length of the global vector
@ -1902,6 +1945,8 @@ class lammps(object):
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param idx: 1-based index of the value in the global vector

24
python/lammps/numpy_wrapper.py
View File

@ -248,6 +248,24 @@ class numpy_wrapper:
# -------------------------------------------------------------------------
def gather_bonds(self):
"""Retrieve global list of bonds as NumPy array
This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: 28Jul2021
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nbonds,3)
"""
import numpy as np
nbonds, value = self.lmp.gather_bonds()
return np.ctypeslib.as_array(value).reshape(nbonds,3)
# -------------------------------------------------------------------------
def fix_external_get_force(self, fix_id):
"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
@ -256,6 +274,8 @@ class numpy_wrapper:
method. It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` pointer.
.. versionchanged:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
@ -276,6 +296,8 @@ class numpy_wrapper:
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy
@ -301,6 +323,8 @@ class numpy_wrapper:
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy

127
src/library.cpp
View File

@ -367,7 +367,7 @@ must be explicitly shut down after any LAMMPS instance using it is
closed (to release associated resources).
After calling this function no Kokkos functionality may be used.
.. versionadded:: TBD
.. versionadded:: 2Jul2021
\endverbatim */
@ -2686,6 +2686,115 @@ void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count,
END_CAPTURE
}
/** Gather type and constituent atom info for all bonds
*
\verbatim embed:rst
This function copies the list of all bonds into a buffer provided by
the calling code. The buffer will be filled with bond type, bond atom 1,
bond atom 2 for each bond. Thus the buffer has to be allocated to the
dimension of 3 times the **total** number of bonds times the size of
the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
whether they are stored in 32-bit or 64-bit integers, respectively.
This size depends on the compile time settings used when compiling
the LAMMPS library and can be queried by calling
:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** bonds
in the system.
.. versionadded:: 28Jul2021
Below is a brief C code demonstrating accessing this collected bond information.
.. code-block:: c
#include <stdio.h>
#include <stdlib.h>
#include <inttypes.h>
#include "library.h"
int main(int argc, char **argv)
{
int tagintsize;
int64_t i, nbonds;
void *handle, *bonds;
handle = lammps_open_no_mpi(0, NULL, NULL);
lammps_file(handle, "in.some_input");
tagintsize = lammps_extract_setting(handle, "tagint");
if (tagintsize == 4)
nbonds = *(int32_t *)lammps_extract_global(handle, "nbonds");
else
nbonds = *(int64_t *)lammps_extract_global(handle, "nbonds");
bonds = malloc(nbonds * 3 * tagintsize);
lammps_gather_bonds(handle, bonds);
if (lammps_extract_setting(handle, "world_rank") == 0) {
if (tagintsize == 4) {
int32_t *bonds_real = (int32_t *)bonds;
for (i = 0; i < nbonds; ++i) {
printf("bond % 4ld: type = %d, atoms: % 4d % 4d\n",i,
bonds_real[3*i], bonds_real[3*i+1], bonds_real[3*i+2]);
}
} else {
int64_t *bonds_real = (int64_t *)bonds;
for (i = 0; i < nbonds; ++i) {
printf("bond % 4ld: type = %ld, atoms: % 4ld % 4ld\n",i,
bonds_real[3*i], bonds_real[3*i+1], bonds_real[3*i+2]);
}
}
}
lammps_close(handle);
lammps_mpi_finalize();
free(bonds);
return 0;
}
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param data pointer to data to copy the result to */
void lammps_gather_bonds(void *handle, void *data)
{
LAMMPS *lmp = (LAMMPS *)handle;
BEGIN_CAPTURE {
void *val = lammps_extract_global(handle,"nbonds");
bigint nbonds = *(bigint *)val;
// no bonds
if (nbonds == 0) return;
// count per MPI rank bonds, determine offsets and allocate local buffers
int localbonds = lmp->atom->avec->pack_bond(nullptr);
int nprocs = lmp->comm->nprocs;
int *bufsizes = new int[nprocs];
int *bufoffsets = new int[nprocs];
MPI_Allgather(&localbonds, 1, MPI_INT, bufsizes, 1, MPI_INT, lmp->world);
bufoffsets[0] = 0;
bufsizes[0] *= 3; // 3 items per bond: type, atom1, atom2
for (int i = 1; i < nprocs; ++i) {
bufoffsets[i] = bufoffsets[i-1] + bufsizes[i-1];
bufsizes[i] *= 3; // 3 items per bond: type, atom1, atom2
}
tagint **bonds;
lmp->memory->create(bonds, localbonds, 3, "library:gather_bonds:localbonds");
lmp->atom->avec->pack_bond(bonds);
MPI_Allgatherv(&bonds[0][0], 3*localbonds, MPI_LMP_TAGINT, data, bufsizes,
bufoffsets, MPI_LMP_TAGINT, lmp->world);
lmp->memory->destroy(bonds);
delete[] bufsizes;
delete[] bufoffsets;
}
END_CAPTURE
}
/* ----------------------------------------------------------------------
Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France)
gather the named atom-based entity for all atoms
@ -4836,6 +4945,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionchanged:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -4899,6 +5010,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -4947,6 +5060,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -4996,6 +5111,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5045,6 +5162,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5097,6 +5216,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5142,6 +5263,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5196,6 +5319,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.

2
src/library.h
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@ -152,6 +152,8 @@ void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *d
void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count, int ndata, int *ids,
void *data);
void lammps_gather_bonds(void *handle, void *data);
void lammps_gather(void *handle, char *name, int type, int count, void *data);
void lammps_gather_concat(void *handle, char *name, int type, int count, void *data);
void lammps_gather_subset(void *handle, char *name, int type, int count, int ndata, int *ids,

2
tools/swig/lammps.i
View File

@ -91,6 +91,7 @@ extern void lammps_gather_atoms_concat(void *, char *, int, int, void *);
extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
extern void lammps_scatter_atoms(void *, char *, int, int, void *);
extern void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
extern void lammps_gather_bonds(void *handle, void *data);
extern void lammps_gather(void *, char *, int, int, void *);
extern void lammps_gather_concat(void *, char *, int, int, void *);
extern void lammps_gather_subset(void *, char *, int, int, int, int *, void *);
@ -225,6 +226,7 @@ extern void lammps_gather_atoms_concat(void *, char *, int, int, void *);
extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
extern void lammps_scatter_atoms(void *, char *, int, int, void *);
extern void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
extern void lammps_gather_bonds(void *handle, void *data);
extern void lammps_gather(void *, char *, int, int, void *);
extern void lammps_gather_concat(void *, char *, int, int, void *);
extern void lammps_gather_subset(void *, char *, int, int, int, int *, void *);

6
unittest/c-library/CMakeLists.txt
View File

@ -17,6 +17,12 @@ target_compile_definitions(test_library_properties PRIVATE -DTEST_INPUT_FOLDER=$
add_test(LibraryProperties test_library_properties)
set_tests_properties(LibraryProperties PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
add_executable(test_library_scatter_gather test_library_scatter_gather.cpp test_main.cpp)
target_link_libraries(test_library_scatter_gather PRIVATE lammps GTest::GTest GTest::GMock)
target_compile_definitions(test_library_scatter_gather PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
add_test(LibraryScatterGather test_library_scatter_gather)
set_tests_properties(LibraryScatterGather PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
set(TEST_CONFIG_DEFS "-DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR};-DLAMMPS_${LAMMPS_SIZES}")
set(PKG_COUNT 0)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})

2
unittest/c-library/test_library_external.cpp
View File

@ -1,4 +1,4 @@
// unit tests creating LAMMPS instances via the library interface
// unit tests for interfacing with fix external via the library interface
#include "library.h"

133
unittest/c-library/test_library_scatter_gather.cpp Normal file
View File

@ -0,0 +1,133 @@
// unit tests for testing scatter/gather operations through the library interface
#include "lammps.h"
#include "library.h"
#include "lmptype.h"
#include <string>
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "test_main.h"
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
using ::LAMMPS_NS::bigint;
using ::LAMMPS_NS::tagint;
using ::testing::HasSubstr;
using ::testing::StartsWith;
class GatherProperties : public ::testing::Test {
protected:
void *lmp;
std::string INPUT_DIR = STRINGIFY(TEST_INPUT_FOLDER);
GatherProperties(){};
~GatherProperties() override{};
void SetUp() override
{
const char *args[] = {"LAMMPS_test", "-log", "none",
"-echo", "screen", "-nocite",
"-var", "input_dir", STRINGIFY(TEST_INPUT_FOLDER)};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
lmp = lammps_open_no_mpi(argc, argv, NULL);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
EXPECT_THAT(output, StartsWith("LAMMPS ("));
}
void TearDown() override
{
::testing::internal::CaptureStdout();
lammps_close(lmp);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_THAT(output, HasSubstr("Total wall time:"));
if (verbose) std::cout << output;
lmp = nullptr;
}
};
TEST_F(GatherProperties, gather_bonds_newton_on)
{
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
std::string input = INPUT_DIR + PATH_SEP + "in.fourmol";
if (!verbose) ::testing::internal::CaptureStdout();
lammps_command(lmp, "newton on on");
lammps_file(lmp, input.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
bigint nbonds = *(bigint *)lammps_extract_global(lmp, "nbonds");
EXPECT_EQ(nbonds, 24);
tagint *bonds = new tagint[3 * nbonds];
lammps_gather_bonds(lmp, bonds);
#define CHECK_BOND(idx, type, atom1, atom2) \
if (((bonds[3 * idx + 1] == atom1) && (bonds[3 * idx + 2] == atom2)) || \
((bonds[3 * idx + 1] == atom2) && (bonds[3 * idx + 2] == atom1))) { \
EXPECT_EQ(bonds[3 * idx], type); \
++count; \
}
// check validity of a few bonds by comparing the bond type and counting the matches.
int count = 0;
for (bigint i = 0; i < nbonds; ++i) {
CHECK_BOND(i, 5, 1, 2);
CHECK_BOND(i, 3, 1, 3);
CHECK_BOND(i, 2, 3, 4);
CHECK_BOND(i, 2, 3, 5);
CHECK_BOND(i, 1, 3, 6);
CHECK_BOND(i, 3, 6, 8);
CHECK_BOND(i, 4, 6, 7);
CHECK_BOND(i, 5, 8, 9);
CHECK_BOND(i, 5, 27, 28);
CHECK_BOND(i, 5, 27, 29);
}
EXPECT_EQ(count, 10);
delete[] bonds;
};
TEST_F(GatherProperties, gather_bonds_newton_off)
{
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
std::string input = INPUT_DIR + PATH_SEP + "in.fourmol";
if (!verbose) ::testing::internal::CaptureStdout();
lammps_command(lmp, "newton off off");
lammps_file(lmp, input.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
bigint nbonds = *(bigint *)lammps_extract_global(lmp, "nbonds");
EXPECT_EQ(nbonds, 24);
tagint *bonds = new tagint[3 * nbonds];
lammps_gather_bonds(lmp, bonds);
#define CHECK_BOND(idx, type, atom1, atom2) \
if (((bonds[3 * idx + 1] == atom1) && (bonds[3 * idx + 2] == atom2)) || \
((bonds[3 * idx + 1] == atom2) && (bonds[3 * idx + 2] == atom1))) { \
EXPECT_EQ(bonds[3 * idx], type); \
++count; \
}
// check validity of a few bonds by comparing the bond type and counting the matches.
int count = 0;
for (bigint i = 0; i < nbonds; ++i) {
CHECK_BOND(i, 5, 1, 2);
CHECK_BOND(i, 3, 1, 3);
CHECK_BOND(i, 2, 3, 4);
CHECK_BOND(i, 2, 3, 5);
CHECK_BOND(i, 1, 3, 6);
CHECK_BOND(i, 3, 6, 8);
CHECK_BOND(i, 4, 6, 7);
CHECK_BOND(i, 5, 8, 9);
CHECK_BOND(i, 5, 27, 28);
CHECK_BOND(i, 5, 27, 29);
}
EXPECT_EQ(count, 10);
delete[] bonds;
};

7
unittest/python/CMakeLists.txt
View File

@ -29,6 +29,7 @@ if(Python_EXECUTABLE)
# prepare to augment the environment so that the LAMMPS python module and the shared library is found.
set(PYTHON_TEST_ENVIRONMENT PYTHONPATH=${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH})
list(APPEND PYTHON_TEST_ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
list(APPEND PYTHON_TEST_ENVIRONMENT "TEST_INPUT_DIR=${CMAKE_CURRENT_SOURCE_DIR}")
if(APPLE)
list(APPEND PYTHON_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:$ENV{DYLD_LIBRARY_PATH};LAMMPS_CMAKE_CACHE=${CMAKE_BINARY_DIR}/CMakeCache.txt")
else()
@ -90,6 +91,12 @@ if(Python_EXECUTABLE)
COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-fix-external.py -v
WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
set_tests_properties(PythonFixExternal PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
add_test(NAME PythonScatterGather
COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-scatter-gather.py -v
WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
set_tests_properties(PythonScatterGather PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
else()
message(STATUS "Skipping Tests for the LAMMPS Python Module: no suitable Python interpreter")
endif()

210
unittest/python/data.fourmol Normal file
View File

@ -0,0 +1,210 @@
LAMMPS data file via write_data, version 5 May 2020, timestep = 0
29 atoms
5 atom types
24 bonds
5 bond types
30 angles
4 angle types
31 dihedrals
5 dihedral types
2 impropers
2 improper types
-6.024572 8.975428 xlo xhi
-7.692866 7.307134 ylo yhi
-8.086924 6.913076 zlo zhi
Masses
1 12.0107
2 4.00794
3 14.0067
4 15.9994
5 15.9994
Pair Coeffs # zero
1
2
3
4
5
Bond Coeffs # zero
1 1.5
2 1.1
3 1.3
4 1.2
5 1
Angle Coeffs # zero
1 110.1
2 111
3 120
4 108.5
Atoms # full
10 2 1 7.0000000000000007e-02 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01 0 0 0
11 2 2 8.9999999999999997e-02 1.7929780509347666e+00 -1.9871047540768743e+00 -1.8840626643185674e+00 0 0 0
12 2 1 -2.7000000000000002e-01 3.0030247876861225e+00 -4.8923319967572748e-01 -1.6188658531537248e+00 0 0 0
13 2 2 8.9999999999999997e-02 4.0447273787895934e+00 -9.0131998547446246e-01 -1.6384447268320836e+00 0 0 0
14 2 2 8.9999999999999997e-02 2.6033152817257075e+00 -4.0789761505963579e-01 -2.6554413538823063e+00 0 0 0
2 1 2 3.1000000000000000e-01 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 0 0 0
3 1 1 -2.0000000000000000e-02 -6.9435377880558602e-01 1.2440473127136711e+00 -6.2233801468892025e-01 0 0 0
4 1 2 8.9999999999999997e-02 -1.5771614164685133e+00 1.4915333140468066e+00 -1.2487126845040522e+00 0 0 0
6 1 1 5.1000000000000001e-01 2.9412607937706009e-01 2.2719282656652909e-01 -1.2843094067857870e+00 0 0 0
7 1 4 -5.1000000000000001e-01 3.4019871062879609e-01 -9.1277350075786561e-03 -2.4633113224304561e+00 0 0 0
19 3 2 4.2359999999999998e-01 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 0 0 0
15 2 2 8.9999999999999997e-02 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 0 0 0
18 3 4 -8.4719999999999995e-01 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 0 0 0
20 3 2 4.2359999999999998e-01 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 0 0 0
8 2 3 -4.6999999999999997e-01 1.1641187171852805e+00 -4.8375305955385234e-01 -6.7659823767368688e-01 0 0 0
9 2 2 3.1000000000000000e-01 1.3777459838125838e+00 -2.5366338669522998e-01 2.6877644730326306e-01 0 0 0
16 2 1 5.1000000000000001e-01 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 0 0 0
17 2 4 -5.1000000000000001e-01 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 0 0 0
1 1 3 -4.6999999999999997e-01 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 0 0 0
5 1 2 8.9999999999999997e-02 -8.9501761359359255e-01 9.3568128743071344e-01 4.0227731871484346e-01 0 0 0
21 4 5 -8.4719999999999995e-01 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00 0 0 0
22 4 2 4.2359999999999998e-01 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00 0 0 0
23 4 2 4.2359999999999998e-01 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00 0 0 0
24 5 5 -8.4719999999999995e-01 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00 0 0 0
25 5 2 4.2359999999999998e-01 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00 0 0 0
26 5 2 4.2359999999999998e-01 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00 0 0 0
27 6 5 -8.4719999999999995e-01 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 0 0 0
28 6 2 4.2359999999999998e-01 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 0 0 0
29 6 2 4.2359999999999998e-01 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 0 0 0
Velocities
1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04
2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03
3 -1.2736791029204805e-03 1.6108674226414498e-03 -3.3618185901550799e-04
4 -9.2828595122009308e-04 -1.2537885319521818e-03 -4.1204974953432108e-03
5 -1.1800848061603740e-03 7.5424401975844038e-04 6.9023177964912290e-05
6 -3.0914004879905335e-04 1.2755385764678133e-03 7.9574303350202582e-04
7 -1.1037894966874103e-04 -7.6764845099077425e-04 -7.7217630460203659e-04
8 3.9060281273221989e-04 -8.1444231918053418e-04 1.5134641148324972e-04
9 1.2475530960659720e-03 -2.6608454451432528e-03 1.1117602907112732e-03
10 4.5008983776042893e-04 4.9530197647538077e-04 -2.3336234361093645e-04
11 -3.6977669078869707e-04 -1.5289071951960539e-03 -2.9176389881837113e-03
12 1.0850834530183159e-03 -6.4965897903201833e-04 -1.2971152622619948e-03
13 4.0754559196230639e-03 3.5043502394946119e-03 -7.8324487687854666e-04
14 -1.3837220448746613e-04 -4.0656048637594394e-03 -3.9333461173944500e-03
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04
18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03
21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04
22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03
23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03
24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04
25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03
26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
Bonds
1 5 1 2
2 3 1 3
3 2 3 4
4 2 3 5
5 1 3 6
6 3 6 8
7 4 6 7
8 5 8 9
9 3 8 10
10 2 10 11
11 1 10 12
12 1 10 16
13 2 12 13
14 2 12 14
15 2 12 15
16 4 16 17
17 5 18 19
18 5 18 20
19 5 21 22
20 5 21 23
21 5 24 25
22 5 24 26
23 5 27 28
24 5 27 29
Angles
1 4 2 1 3
2 4 1 3 5
3 4 1 3 4
4 4 1 3 6
5 4 4 3 5
6 2 5 3 6
7 2 4 3 6
8 3 3 6 7
9 3 3 6 8
10 3 7 6 8
11 2 6 8 9
12 2 9 8 10
13 3 6 8 10
14 2 8 10 11
15 3 8 10 16
16 2 11 10 12
17 1 12 10 16
18 1 8 10 12
19 2 11 10 16
20 2 10 12 15
21 2 10 12 14
22 2 10 12 13
23 4 13 12 15
24 4 13 12 14
25 4 14 12 15
26 4 10 16 17
27 1 19 18 20
28 1 22 21 23
29 1 25 24 26
30 1 28 27 29
Dihedrals
1 2 2 1 3 6
2 2 2 1 3 4
3 3 2 1 3 5
4 1 1 3 6 8
5 1 1 3 6 7
6 5 4 3 6 8
7 5 4 3 6 7
8 5 5 3 6 8
9 5 5 3 6 7
10 4 3 6 8 9
11 3 3 6 8 10
12 3 7 6 8 9
13 4 7 6 8 10
14 2 6 8 10 12
15 2 6 8 10 16
16 2 6 8 10 11
17 2 9 8 10 12
18 4 9 8 10 16
19 5 9 8 10 11
20 5 8 10 12 13
21 1 8 10 12 14
22 5 8 10 12 15
23 4 8 10 16 17
24 5 11 10 12 13
25 5 11 10 12 14
26 5 11 10 12 15
27 2 11 10 16 17
28 2 12 10 16 17
29 5 16 10 12 13
30 5 16 10 12 14
31 5 16 10 12 15
Impropers
1 1 6 3 8 7
2 2 8 6 10 9

25
unittest/python/in.fourmol Normal file
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@ -0,0 +1,25 @@
variable units index real
variable input_dir index .
variable data_file index ${input_dir}/data.fourmol
variable pair_style index 'zero 8.0'
variable bond_style index zero
variable angle_style index zero
variable dihedral_style index zero
variable improper_style index zero
atom_style full
atom_modify map array
neigh_modify delay 2 every 2 check no
units ${units}
timestep 0.1
pair_style ${pair_style}
bond_style ${bond_style}
angle_style ${angle_style}
dihedral_style ${dihedral_style}
improper_style ${improper_style}
read_data ${data_file}
dihedral_coeff *
improper_coeff *

63
unittest/python/python-numpy.py
View File

@ -15,6 +15,17 @@ try:
except:
pass
has_full=False
try:
machine=None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
lmp=lammps(name=machine)
has_full = lmp.has_style("atom","full")
lmp.close()
except:
pass
try:
import numpy
NUMPY_INSTALLED = True
@ -32,6 +43,14 @@ class PythonNumpy(unittest.TestCase):
def tearDown(self):
del self.lmp
def checkBond(self, vals, btype, batom1, batom2):
if ((vals[1] == batom1 and vals[2] == batom2)
or (vals[1] == batom2 and vals[2] == batom1)):
self.assertEqual(vals[0], btype)
return 1
else:
return 0
def testLammpsPointer(self):
self.assertEqual(type(self.lmp.lmp), c_void_p)
@ -148,6 +167,50 @@ class PythonNumpy(unittest.TestCase):
self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all())
self.assertEqual(len(v), 2)
@unittest.skipIf(not has_full,"Gather bonds test")
def testGatherBond_newton_on(self):
self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
self.lmp.command("newton on on")
self.lmp.file("in.fourmol")
self.lmp.command("run 0 post no")
bonds = self.lmp.numpy.gather_bonds()
self.assertEqual(len(bonds),24)
count = 0
for bond in bonds:
count += self.checkBond(bond, 5, 1, 2)
count += self.checkBond(bond, 3, 1, 3)
count += self.checkBond(bond, 2, 3, 4)
count += self.checkBond(bond, 2, 3, 5)
count += self.checkBond(bond, 1, 6, 3)
count += self.checkBond(bond, 3, 6, 8)
count += self.checkBond(bond, 4, 6, 7)
count += self.checkBond(bond, 5, 8, 9)
count += self.checkBond(bond, 5, 27, 28)
count += self.checkBond(bond, 5, 29, 27)
self.assertEqual(count,10)
@unittest.skipIf(not has_full,"Gather bonds test")
def testGatherBond_newton_off(self):
self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
self.lmp.command("newton off off")
self.lmp.file("in.fourmol")
self.lmp.command("run 0 post no")
bonds = self.lmp.numpy.gather_bonds()
self.assertEqual(len(bonds),24)
count = 0
for bond in bonds:
count += self.checkBond(bond, 5, 1, 2)
count += self.checkBond(bond, 3, 1, 3)
count += self.checkBond(bond, 2, 3, 4)
count += self.checkBond(bond, 2, 3, 5)
count += self.checkBond(bond, 1, 6, 3)
count += self.checkBond(bond, 3, 6, 8)
count += self.checkBond(bond, 4, 6, 7)
count += self.checkBond(bond, 5, 8, 9)
count += self.checkBond(bond, 5, 27, 28)
count += self.checkBond(bond, 5, 29, 27)
self.assertEqual(count,10)
def testNeighborListSimple(self):
self.lmp.commands_string("""
units lj

90
unittest/python/python-scatter-gather.py Normal file
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@ -0,0 +1,90 @@
import sys,os,unittest
from lammps import lammps
has_full=False
try:
machine=None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
lmp=lammps(name=machine)
has_full = lmp.has_style("atom","full")
lmp.close()
except:
pass
class PythonGather(unittest.TestCase):
def setUp(self):
machine=None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
self.lmp=lammps(name=machine,
cmdargs=['-nocite',
'-log','none',
'-echo','screen'])
self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
# clean up temporary files
def tearDown(self):
self.lmp.close()
# bond data comparison
def checkBond(self, vals, btype, batom1, batom2):
if ((vals[1] == batom1 and vals[2] == batom2)
or (vals[1] == batom2 and vals[2] == batom1)):
self.assertEqual(vals[0], btype)
return 1
else:
return 0
##############################
@unittest.skipIf(not has_full, "Gather_bonds test")
def testGatherBond_newton_on(self):
"""Test gather_bonds() with newton on"""
self.lmp.command("newton on on")
self.lmp.file("in.fourmol")
self.lmp.command("run 0 post no")
nbonds, bonds = self.lmp.gather_bonds()
self.assertEqual(nbonds, 24)
self.assertEqual(len(bonds), 3*24)
count = 0;
for i in range(0,nbonds):
count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2)
count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3)
count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4)
count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5)
count += self.checkBond(bonds[3*i:3*i+3], 1, 6, 3)
count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8)
count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7)
count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9)
count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28)
count += self.checkBond(bonds[3*i:3*i+3], 5, 29, 27)
self.assertEqual(count,10)
@unittest.skipIf(not has_full, "Gather_bonds test")
def testGatherBond_newton_off(self):
"""Test gather_bonds() with newton off"""
self.lmp.command("newton off off")
self.lmp.file("in.fourmol")
self.lmp.command("run 0 post no")
nbonds, bonds = self.lmp.gather_bonds()
self.assertEqual(nbonds, 24)
self.assertEqual(len(bonds), 3*24)
count = 0;
for i in range(0,nbonds):
count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2)
count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3)
count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4)
count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5)
count += self.checkBond(bonds[3*i:3*i+3], 1, 3, 6)
count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8)
count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7)
count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9)
count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28)
count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 29)
self.assertEqual(count,10)
##############################
if __name__ == "__main__":
unittest.main()