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lammps-gran-kokkos/python/lammps/core.py
Richard Berger 990c07a133 bugfix: correctly build argv when using Python interface
2023-11-10 11:47:04 -05:00

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# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# https://www.lammps.org/ Sandia National Laboratories
# LAMMPS Development team: developers@lammps.org
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
#
# See the README file in the top-level LAMMPS directory.
# -------------------------------------------------------------------------
# Python wrapper for the LAMMPS library via ctypes
# for python2/3 compatibility
from __future__ import print_function
import os
import sys
from ctypes import * # lgtm [py/polluting-import]
from os.path import dirname,abspath,join
from inspect import getsourcefile
from .constants import * # lgtm [py/polluting-import]
from .data import * # lgtm [py/polluting-import]
# -------------------------------------------------------------------------
class MPIAbortException(Exception):
def __init__(self, message):
self.message = message
def __str__(self):
return repr(self.message)
# -------------------------------------------------------------------------
class ExceptionCheck:
"""Utility class to rethrow LAMMPS C++ exceptions as Python exceptions"""
def __init__(self, lmp):
self.lmp = lmp
def __enter__(self):
pass
def __exit__(self, exc_type, exc_value, traceback):
if self.lmp.has_exceptions and self.lmp.lib.lammps_has_error(self.lmp.lmp):
raise self.lmp._lammps_exception
# -------------------------------------------------------------------------
class lammps(object):
"""Create an instance of the LAMMPS Python class.
.. _mpi4py_docs: https://mpi4py.readthedocs.io/
This is a Python wrapper class that exposes the LAMMPS C-library
interface to Python. It either requires that LAMMPS has been compiled
as shared library which is then dynamically loaded via the ctypes
Python module or that this module called from a Python function that
is called from a Python interpreter embedded into a LAMMPS executable,
for example through the :doc:`python invoke <python>` command.
When the class is instantiated it calls the :cpp:func:`lammps_open`
function of the LAMMPS C-library interface, which in
turn will create an instance of the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>`
C++ class. The handle to this C++ class is stored internally
and automatically passed to the calls to the C library interface.
:param name: "machine" name of the shared LAMMPS library ("mpi" loads ``liblammps_mpi.so``, "" loads ``liblammps.so``)
:type name: string
:param cmdargs: list of command line arguments to be passed to the :cpp:func:`lammps_open` function. The executable name is automatically added.
:type cmdargs: list
:param ptr: pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.
:type ptr: pointer
:param comm: MPI communicator (as provided by `mpi4py <mpi4py_docs_>`_). ``None`` means use ``MPI_COMM_WORLD`` implicitly.
:type comm: MPI_Comm
"""
# -------------------------------------------------------------------------
# create an instance of LAMMPS
def __init__(self,name='',cmdargs=None,ptr=None,comm=None):
self.comm = comm
self.opened = 0
# determine module file location
modpath = dirname(abspath(getsourcefile(lambda:0)))
# for windows installers the shared library is in a different folder
winpath = abspath(os.path.join(modpath,'..','..','bin'))
# allow override for running tests on Windows
if (os.environ.get("LAMMPSDLLPATH")):
winpath = os.environ.get("LAMMPSDLLPATH")
self.lib = None
self.lmp = None
# if a pointer to a LAMMPS object is handed in
# when being called from a Python interpreter
# embedded into a LAMMPS executable, all library
# symbols should already be available so we do not
# load a shared object.
try:
if ptr is not None: self.lib = CDLL("",RTLD_GLOBAL)
except OSError:
self.lib = None
# load liblammps.so unless name is given
# if name = "g++", load liblammps_g++.so
# try loading the LAMMPS shared object from the location
# of the lammps package with an absolute path,
# so that LD_LIBRARY_PATH does not need to be set for regular install
# fall back to loading with a relative path,
# typically requires LD_LIBRARY_PATH to be set appropriately
# guess shared library extension based on OS, if not inferred from actual file
if any([f.startswith('liblammps') and f.endswith('.dylib')
for f in os.listdir(modpath)]):
lib_ext = ".dylib"
elif any([f.startswith('liblammps') and f.endswith('.dll')
for f in os.listdir(modpath)]):
lib_ext = ".dll"
elif os.path.exists(winpath) and any([f.startswith('liblammps') and f.endswith('.dll')
for f in os.listdir(winpath)]):
lib_ext = ".dll"
modpath = winpath
elif any([f.startswith('liblammps') and f.endswith('.so')
for f in os.listdir(modpath)]):
lib_ext = ".so"
else:
import platform
if platform.system() == "Darwin":
lib_ext = ".dylib"
elif platform.system() == "Windows":
lib_ext = ".dll"
else:
lib_ext = ".so"
if not self.lib:
if name:
libpath = join(modpath,"liblammps_%s" % name + lib_ext)
else:
libpath = join(modpath,"liblammps" + lib_ext)
if not os.path.isfile(libpath):
if name:
libpath = "liblammps_%s" % name + lib_ext
else:
libpath = "liblammps" + lib_ext
self.lib = CDLL(libpath,RTLD_GLOBAL)
# declare all argument and return types for all library methods here.
# exceptions are where the arguments depend on certain conditions and
# then are defined where the functions are used.
self.lib.lammps_extract_setting.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_setting.restype = c_int
# set default types
# needed in later declarations
self.c_bigint = get_ctypes_int(self.extract_setting("bigint"))
self.c_tagint = get_ctypes_int(self.extract_setting("tagint"))
self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
self.lib.lammps_open.restype = c_void_p
self.lib.lammps_open_no_mpi.restype = c_void_p
self.lib.lammps_close.argtypes = [c_void_p]
self.lib.lammps_flush_buffers.argtypes = [c_void_p]
self.lib.lammps_free.argtypes = [c_void_p]
self.lib.lammps_error.argtypes = [c_void_p, c_int, c_char_p]
self.lib.lammps_file.argtypes = [c_void_p, c_char_p]
self.lib.lammps_file.restype = None
self.lib.lammps_command.argtypes = [c_void_p, c_char_p]
self.lib.lammps_command.restype = c_char_p
self.lib.lammps_commands_list.restype = None
self.lib.lammps_commands_string.argtypes = [c_void_p, c_char_p]
self.lib.lammps_commands_string.restype = None
self.lib.lammps_get_natoms.argtypes = [c_void_p]
self.lib.lammps_get_natoms.restype = c_double
self.lib.lammps_extract_box.argtypes = \
[c_void_p,POINTER(c_double),POINTER(c_double),
POINTER(c_double),POINTER(c_double),POINTER(c_double),
POINTER(c_int),POINTER(c_int)]
self.lib.lammps_extract_box.restype = None
self.lib.lammps_reset_box.argtypes = \
[c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
self.lib.lammps_reset_box.restype = None
self.lib.lammps_gather_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.restype = None
self.lib.lammps_gather_atoms_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.restype = None
self.lib.lammps_gather_atoms_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_atoms_subset.restype = None
self.lib.lammps_scatter_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.restype = None
self.lib.lammps_scatter_atoms_subset.argtypes = \
[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_angles.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_angles.restype = None
self.lib.lammps_gather_dihedrals.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_dihedrals.restype = None
self.lib.lammps_gather_impropers.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_impropers.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
self.lib.lammps_gather_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_concat.restype = None
self.lib.lammps_gather_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_subset.restype = None
self.lib.lammps_scatter.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter.restype = None
self.lib.lammps_scatter_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_scatter_subset.restype = None
self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int]
self.lib.lammps_find_pair_neighlist.restype = c_int
self.lib.lammps_find_fix_neighlist.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_find_fix_neighlist.restype = c_int
self.lib.lammps_find_compute_neighlist.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_find_compute_neighlist.restype = c_int
self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int]
self.lib.lammps_neighlist_num_elements.restype = c_int
self.lib.lammps_neighlist_element_neighbors.argtypes = \
[c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
self.lib.lammps_neighlist_element_neighbors.restype = None
self.lib.lammps_is_running.argtypes = [c_void_p]
self.lib.lammps_is_running.restype = c_int
self.lib.lammps_force_timeout.argtypes = [c_void_p]
self.lib.lammps_has_error.argtypes = [c_void_p]
self.lib.lammps_has_error.restype = c_int
self.lib.lammps_get_last_error_message.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_get_last_error_message.restype = c_int
self.lib.lammps_extract_global.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_global_datatype.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_global_datatype.restype = c_int
self.lib.lammps_extract_compute.argtypes = [c_void_p, c_char_p, c_int, c_int]
self.lib.lammps_get_thermo.argtypes = [c_void_p, c_char_p]
self.lib.lammps_get_thermo.restype = c_double
self.lib.lammps_last_thermo.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_last_thermo.restype = c_void_p
self.lib.lammps_encode_image_flags.restype = self.c_imageint
self.lib.lammps_config_has_package.argtypes = [c_char_p]
self.lib.lammps_config_package_name.argtypes = [c_int, c_char_p, c_int]
self.lib.lammps_config_accelerator.argtypes = [c_char_p, c_char_p, c_char_p]
self.lib.lammps_set_variable.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_has_style.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_style_count.argtypes = [c_void_p, c_char_p]
self.lib.lammps_style_name.argtypes = [c_void_p, c_char_p, c_int, c_char_p, c_int]
self.lib.lammps_has_id.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_id_count.argtypes = [c_void_p, c_char_p]
self.lib.lammps_id_name.argtypes = [c_void_p, c_char_p, c_int, c_char_p, c_int]
self.lib.lammps_plugin_count.argtypes = [ ]
self.lib.lammps_plugin_name.argtypes = [c_int, c_char_p, c_char_p, c_int]
self.lib.lammps_version.argtypes = [c_void_p]
self.lib.lammps_get_os_info.argtypes = [c_char_p, c_int]
self.lib.lammps_get_gpu_device_info.argtypes = [c_char_p, c_int]
self.lib.lammps_get_mpi_comm.argtypes = [c_void_p]
self.lib.lammps_decode_image_flags.argtypes = [self.c_imageint, POINTER(c_int*3)]
self.lib.lammps_extract_atom.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_atom_datatype.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_atom_datatype.restype = c_int
self.lib.lammps_extract_fix.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int, c_int]
self.lib.lammps_extract_variable.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_extract_variable_datatype.argtypes = [c_void_p, c_char_p]
self.lib.lammps_extract_variable_datatype.restype = c_int
self.lib.lammps_fix_external_get_force.argtypes = [c_void_p, c_char_p]
self.lib.lammps_fix_external_get_force.restype = POINTER(POINTER(c_double))
self.lib.lammps_fix_external_set_energy_global.argtypes = [c_void_p, c_char_p, c_double]
self.lib.lammps_fix_external_set_virial_global.argtypes = [c_void_p, c_char_p, POINTER(c_double)]
self.lib.lammps_fix_external_set_energy_peratom.argtypes = [c_void_p, c_char_p, POINTER(c_double)]
self.lib.lammps_fix_external_set_virial_peratom.argtypes = [c_void_p, c_char_p, POINTER(POINTER(c_double))]
self.lib.lammps_fix_external_set_vector_length.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_fix_external_set_vector.argtypes = [c_void_p, c_char_p, c_int, c_double]
# detect if Python is using a version of mpi4py that can pass communicators
# only needed if LAMMPS has been compiled with MPI support.
self.has_mpi4py = False
if self.has_mpi_support:
try:
from mpi4py import __version__ as mpi4py_version
# tested to work with mpi4py versions 2 and 3
self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
except ImportError:
# ignore failing import
pass
# if no ptr provided, create an instance of LAMMPS
# we can pass an MPI communicator from mpi4py v2.0.0 and later
# no_mpi call lets LAMMPS use MPI_COMM_WORLD
# cargs = array of C strings from args
# if ptr, then are embedding Python in LAMMPS input script
# ptr is the desired instance of LAMMPS
# just convert it to ctypes ptr and store in self.lmp
if ptr is None:
# with mpi4py v2+, we can pass MPI communicators to LAMMPS
# need to adjust for type of MPI communicator object
# allow for int (like MPICH) or void* (like OpenMPI)
if self.has_mpi_support and self.has_mpi4py:
from mpi4py import MPI
self.MPI = MPI
if comm is not None:
if not self.has_mpi_support:
raise Exception('LAMMPS not compiled with real MPI library')
if not self.has_mpi4py:
raise Exception('Python mpi4py version is not 2 or 3')
if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int):
MPI_Comm = c_int
else:
MPI_Comm = c_void_p
# Detect whether LAMMPS and mpi4py definitely use different MPI libs
if sizeof(MPI_Comm) != self.lib.lammps_config_has_mpi_support():
raise Exception('Inconsistent MPI library in LAMMPS and mpi4py')
narg = 0
cargs = None
if cmdargs is not None:
cmdargs.insert(0,"lammps")
narg = len(cmdargs)
for i in range(narg):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*(narg+1))(*cmdargs)
cargs[narg] = None
self.lib.lammps_open.argtypes = [c_int, c_char_p*(narg+1), MPI_Comm, c_void_p]
else:
self.lib.lammps_open.argtypes = [c_int, c_char_p, MPI_Comm, c_void_p]
self.opened = 1
comm_ptr = self.MPI._addressof(comm)
comm_val = MPI_Comm.from_address(comm_ptr)
self.lmp = c_void_p(self.lib.lammps_open(narg,cargs,comm_val,None))
else:
if self.has_mpi4py and self.has_mpi_support:
self.comm = self.MPI.COMM_WORLD
self.opened = 1
if cmdargs is not None:
cmdargs.insert(0,"lammps")
narg = len(cmdargs)
for i in range(narg):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*(narg+1))(*cmdargs)
cargs[narg] = None
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*(narg+1), c_void_p]
self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))
else:
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p, c_void_p]
self.lmp = c_void_p(self.lib.lammps_open_no_mpi(0,None,None))
else:
# magic to convert ptr to ctypes ptr
if sys.version_info >= (3, 0):
# Python 3 (uses PyCapsule API)
pythonapi.PyCapsule_GetPointer.restype = c_void_p
pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
self.lmp = c_void_p(pythonapi.PyCapsule_GetPointer(ptr, None))
else:
# Python 2 (uses PyCObject API)
pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
# check if library initilialization failed
if not self.lmp:
raise(RuntimeError("Failed to initialize LAMMPS object"))
# optional numpy support (lazy loading)
self._numpy = None
self._installed_packages = None
self._available_styles = None
# check if liblammps version matches the installed python module version
# but not for in-place usage, i.e. when the version is 0
import lammps
if lammps.__version__ > 0 and lammps.__version__ != self.lib.lammps_version(self.lmp):
raise(AttributeError("LAMMPS Python module installed for LAMMPS version %d, but shared library is version %d" \
% (lammps.__version__, self.lib.lammps_version(self.lmp))))
# add way to insert Python callback for fix external
self.callback = {}
self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
self.lib.lammps_set_fix_external_callback.restype = None
# -------------------------------------------------------------------------
# shut-down LAMMPS instance
def __del__(self):
self.close()
# -------------------------------------------------------------------------
# context manager implementation
def __enter__(self):
return self
def __exit__(self, ex_type, ex_value, ex_traceback):
self.close()
# -------------------------------------------------------------------------
@property
def numpy(self):
""" Return object to access numpy versions of API
It provides alternative implementations of API functions that
return numpy arrays instead of ctypes pointers. If numpy is not installed,
accessing this property will lead to an ImportError.
:return: instance of numpy wrapper object
:rtype: numpy_wrapper
"""
if not self._numpy:
from .numpy_wrapper import numpy_wrapper
self._numpy = numpy_wrapper(self)
return self._numpy
# -------------------------------------------------------------------------
def close(self):
"""Explicitly delete a LAMMPS instance through the C-library interface.
This is a wrapper around the :cpp:func:`lammps_close` function of the C-library interface.
"""
if self.lmp and self.opened:
self.lib.lammps_close(self.lmp)
self.lmp = None
self.opened = 0
# -------------------------------------------------------------------------
def finalize(self):
"""Shut down the MPI communication and Kokkos environment (if active) through the
library interface by calling :cpp:func:`lammps_mpi_finalize` and
:cpp:func:`lammps_kokkos_finalize`.
You cannot create or use any LAMMPS instances after this function is called
unless LAMMPS was compiled without MPI and without Kokkos support.
"""
self.close()
self.lib.lammps_kokkos_finalize()
self.lib.lammps_mpi_finalize()
# -------------------------------------------------------------------------
def error(self, error_type, error_text):
"""Forward error to the LAMMPS Error class.
.. versionadded:: 3Nov2022
This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
:param error_type:
:type error_type: int
:param error_text:
:type error_text: string
"""
if error_text: error_text = error_text.encode()
else: error_text = "(unknown error)".encode()
with ExceptionCheck(self):
self.lib.lammps_error(self.lmp, error_type, error_text)
# -------------------------------------------------------------------------
def version(self):
"""Return a numerical representation of the LAMMPS version in use.
This is a wrapper around the :cpp:func:`lammps_version` function of the C-library interface.
:return: version number
:rtype: int
"""
return self.lib.lammps_version(self.lmp)
# -------------------------------------------------------------------------
def get_os_info(self):
"""Return a string with information about the OS and compiler runtime
This is a wrapper around the :cpp:func:`lammps_get_os_info` function of the C-library interface.
:return: OS info string
:rtype: string
"""
sb = create_string_buffer(512)
self.lib.lammps_get_os_info(sb,512)
return sb.value.decode()
# -------------------------------------------------------------------------
def get_mpi_comm(self):
"""Get the MPI communicator in use by the current LAMMPS instance
This is a wrapper around the :cpp:func:`lammps_get_mpi_comm` function
of the C-library interface. It will return ``None`` if either the
LAMMPS library was compiled without MPI support or the mpi4py
Python module is not available.
:return: MPI communicator
:rtype: MPI_Comm
"""
if self.has_mpi4py and self.has_mpi_support:
from mpi4py import MPI
f_comm = self.lib.lammps_get_mpi_comm(self.lmp)
c_comm = MPI.Comm.f2py(f_comm)
return c_comm
else:
return None
# -------------------------------------------------------------------------
@property
def _lammps_exception(self):
sb = create_string_buffer(100)
error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
error_msg = sb.value.decode().strip()
if error_type == 2:
return MPIAbortException(error_msg)
return Exception(error_msg)
# -------------------------------------------------------------------------
def file(self, path):
"""Read LAMMPS commands from a file.
This is a wrapper around the :cpp:func:`lammps_file` function of the C-library interface.
It will open the file with the name/path `file` and process the LAMMPS commands line by line until
the end. The function will return when the end of the file is reached.
:param path: Name of the file/path with LAMMPS commands
:type path: string
"""
if path: path = path.encode()
else: return
with ExceptionCheck(self):
self.lib.lammps_file(self.lmp, path)
# -------------------------------------------------------------------------
def command(self,cmd):
"""Process a single LAMMPS input command from a string.
This is a wrapper around the :cpp:func:`lammps_command`
function of the C-library interface.
:param cmd: a single lammps command
:type cmd: string
"""
if cmd: cmd = cmd.encode()
else: return
with ExceptionCheck(self):
self.lib.lammps_command(self.lmp,cmd)
# -------------------------------------------------------------------------
def commands_list(self,cmdlist):
"""Process multiple LAMMPS input commands from a list of strings.
This is a wrapper around the
:cpp:func:`lammps_commands_list` function of
the C-library interface.
:param cmdlist: a single lammps command
:type cmdlist: list of strings
"""
cmds = [x.encode() for x in cmdlist if type(x) is str]
narg = len(cmdlist)
args = (c_char_p * narg)(*cmds)
self.lib.lammps_commands_list.argtypes = [c_void_p, c_int, c_char_p * narg]
with ExceptionCheck(self):
self.lib.lammps_commands_list(self.lmp,narg,args)
# -------------------------------------------------------------------------
def commands_string(self,multicmd):
"""Process a block of LAMMPS input commands from a string.
This is a wrapper around the
:cpp:func:`lammps_commands_string`
function of the C-library interface.
:param multicmd: text block of lammps commands
:type multicmd: string
"""
if type(multicmd) is str: multicmd = multicmd.encode()
with ExceptionCheck(self):
self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))
# -------------------------------------------------------------------------
def get_natoms(self):
"""Get the total number of atoms in the LAMMPS instance.
Will be precise up to 53-bit signed integer due to the
underlying :cpp:func:`lammps_get_natoms` function returning a double.
:return: number of atoms
:rtype: int
"""
return int(self.lib.lammps_get_natoms(self.lmp))
# -------------------------------------------------------------------------
def extract_box(self):
"""Extract simulation box parameters
This is a wrapper around the :cpp:func:`lammps_extract_box` function
of the C-library interface. Unlike in the C function, the result is
returned as a list.
:return: list of the extracted data: boxlo, boxhi, xy, yz, xz, periodicity, box_change
:rtype: [ 3*double, 3*double, double, double, 3*int, int]
"""
boxlo = (3*c_double)()
boxhi = (3*c_double)()
xy = c_double()
yz = c_double()
xz = c_double()
periodicity = (3*c_int)()
box_change = c_int()
with ExceptionCheck(self):
self.lib.lammps_extract_box(self.lmp,boxlo,boxhi,
byref(xy),byref(yz),byref(xz),
periodicity,byref(box_change))
boxlo = boxlo[:3]
boxhi = boxhi[:3]
xy = xy.value
yz = yz.value
xz = xz.value
periodicity = periodicity[:3]
box_change = box_change.value
return boxlo,boxhi,xy,yz,xz,periodicity,box_change
# -------------------------------------------------------------------------
def reset_box(self,boxlo,boxhi,xy,yz,xz):
"""Reset simulation box parameters
This is a wrapper around the :cpp:func:`lammps_reset_box` function
of the C-library interface.
:param boxlo: new lower box boundaries
:type boxlo: list of 3 floating point numbers
:param boxhi: new upper box boundaries
:type boxhi: list of 3 floating point numbers
:param xy: xy tilt factor
:type xy: float
:param yz: yz tilt factor
:type yz: float
:param xz: xz tilt factor
:type xz: float
"""
cboxlo = (3*c_double)(*boxlo)
cboxhi = (3*c_double)(*boxhi)
with ExceptionCheck(self):
self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz)
# -------------------------------------------------------------------------
def get_thermo(self,name):
"""Get current value of a thermo keyword
This is a wrapper around the :cpp:func:`lammps_get_thermo`
function of the C-library interface.
:param name: name of thermo keyword
:type name: string
:return: value of thermo keyword
:rtype: double or None
"""
if name: name = name.encode()
else: return None
with ExceptionCheck(self):
return self.lib.lammps_get_thermo(self.lmp,name)
# -------------------------------------------------------------------------
@property
def last_thermo_step(self):
""" Get the last timestep where thermodynamic data was computed
:return: the timestep or a negative number if there has not been any thermo output yet
:rtype: int
"""
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
return cast(ptr, POINTER(self.c_bigint)).contents.value
def last_thermo(self):
"""Get a dictionary of the last thermodynamic output
This is a wrapper around the :cpp:func:`lammps_last_thermo`
function of the C-library interface. It collects the cached thermo
data from the last timestep into a dictionary. The return value
is None, if there has not been any thermo output yet.
:return: a dictionary containing the last computed thermo output values
:rtype: dict or None
"""
rv = dict()
mystep = self.last_thermo_step
if mystep < 0:
return None
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("num".encode()), 0)
nfield = cast(ptr, POINTER(c_int)).contents.value
for i in range(nfield):
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("keyword".encode()), i)
kw = cast(ptr, c_char_p).value.decode()
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("type".encode()), i)
typ = cast(ptr, POINTER(c_int)).contents.value
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("data".encode()), i)
if typ == LAMMPS_DOUBLE:
val = cast(ptr, POINTER(c_double)).contents.value
elif typ == LAMMPS_INT:
val = cast(ptr, POINTER(c_int)).contents.value
elif typ == LAMMPS_INT64:
val = cast(ptr, POINTER(c_int64)).contents.value
else:
# we should not get here
raise TypeError("Unknown LAMMPS data type " + str(typ))
rv[kw] = val
return rv
# -------------------------------------------------------------------------
def extract_setting(self, name):
"""Query LAMMPS about global settings that can be expressed as an integer.
This is a wrapper around the :cpp:func:`lammps_extract_setting`
function of the C-library interface. Its documentation includes
a list of the supported keywords.
:param name: name of the setting
:type name: string
:return: value of the setting
:rtype: int
"""
if name: name = name.encode()
else: return None
return int(self.lib.lammps_extract_setting(self.lmp,name))
# -------------------------------------------------------------------------
# extract global info datatype
def extract_global_datatype(self, name):
"""Retrieve global property datatype from LAMMPS
This is a wrapper around the :cpp:func:`lammps_extract_global_datatype`
function of the C-library interface. Its documentation includes a
list of the supported keywords.
This function returns ``None`` if the keyword is not
recognized. Otherwise it will return a positive integer value that
corresponds to one of the :ref:`data type <py_datatype_constants>`
constants define in the :py:mod:`lammps` module.
:param name: name of the property
:type name: string
:return: data type of global property, see :ref:`py_datatype_constants`
:rtype: int
"""
if name: name = name.encode()
else: return None
return self.lib.lammps_extract_global_datatype(self.lmp, name)
# -------------------------------------------------------------------------
# extract global info
def extract_global(self, name, dtype=LAMMPS_AUTODETECT):
"""Query LAMMPS about global settings of different types.
This is a wrapper around the :cpp:func:`lammps_extract_global` function
of the C-library interface. Since there are no pointers in Python, this
method will - unlike the C function - return the value or a list of
values. The :cpp:func:`lammps_extract_global` documentation includes a
list of the supported keywords and their data types.
Since Python needs to know the data type to be able to interpret
the result, by default, this function will try to auto-detect the data type
by asking the library. You can also force a specific data type. For that
purpose the :py:mod:`lammps` module contains :ref:`data type <py_datatype_constants>`
constants. This function returns ``None`` if either the keyword is not recognized,
or an invalid data type constant is used.
:param name: name of the property
:type name: string
:param dtype: data type of the returned data (see :ref:`py_datatype_constants`)
:type dtype: int, optional
:return: value of the property or list of values or None
:rtype: int, float, list, or NoneType
"""
if dtype == LAMMPS_AUTODETECT:
dtype = self.extract_global_datatype(name)
# set length of vector for items that are not a scalar
vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3,
'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3,
'special_lj':4, 'special_coul':4 }
if name in vec_dict:
veclen = vec_dict[name]
elif name == 'respa_dt':
veclen = self.extract_global('respa_levels',LAMMPS_INT)
else:
veclen = 1
if name: name = name.encode()
else: return None
if dtype == LAMMPS_INT:
self.lib.lammps_extract_global.restype = POINTER(c_int32)
target_type = int
elif dtype == LAMMPS_INT64:
self.lib.lammps_extract_global.restype = POINTER(c_int64)
target_type = int
elif dtype == LAMMPS_DOUBLE:
self.lib.lammps_extract_global.restype = POINTER(c_double)
target_type = float
elif dtype == LAMMPS_STRING:
self.lib.lammps_extract_global.restype = c_char_p
target_type = str
else:
target_type = None
ptr = self.lib.lammps_extract_global(self.lmp, name)
if ptr:
if dtype == LAMMPS_STRING:
return ptr.decode('utf-8')
if veclen > 1:
result = []
for i in range(0,veclen):
result.append(target_type(ptr[i]))
return result
else: return target_type(ptr[0])
return None
# -------------------------------------------------------------------------
# extract per-atom info datatype
def extract_atom_datatype(self, name):
"""Retrieve per-atom property datatype from LAMMPS
This is a wrapper around the :cpp:func:`lammps_extract_atom_datatype`
function of the C-library interface. Its documentation includes a
list of the supported keywords.
This function returns ``None`` if the keyword is not
recognized. Otherwise it will return an integer value that
corresponds to one of the :ref:`data type <py_datatype_constants>` constants
defined in the :py:mod:`lammps` module.
:param name: name of the property
:type name: string
:return: data type of per-atom property (see :ref:`py_datatype_constants`)
:rtype: int
"""
if name: name = name.encode()
else: return None
return self.lib.lammps_extract_atom_datatype(self.lmp, name)
# -------------------------------------------------------------------------
# extract per-atom info
def extract_atom(self, name, dtype=LAMMPS_AUTODETECT):
"""Retrieve per-atom properties from LAMMPS
This is a wrapper around the :cpp:func:`lammps_extract_atom`
function of the C-library interface. Its documentation includes a
list of the supported keywords and their data types.
Since Python needs to know the data type to be able to interpret
the result, by default, this function will try to auto-detect the data type
by asking the library. You can also force a specific data type by setting ``dtype``
to one of the :ref:`data type <py_datatype_constants>` constants defined in the
:py:mod:`lammps` module.
This function returns ``None`` if either the keyword is not
recognized, or an invalid data type constant is used.
.. note::
While the returned arrays of per-atom data are dimensioned
for the range [0:nmax] - as is the underlying storage -
the data is usually only valid for the range of [0:nlocal],
unless the property of interest is also updated for ghost
atoms. In some cases, this depends on a LAMMPS setting, see
for example :doc:`comm_modify vel yes <comm_modify>`.
:param name: name of the property
:type name: string
:param dtype: data type of the returned data (see :ref:`py_datatype_constants`)
:type dtype: int, optional
:return: requested data or ``None``
:rtype: ctypes.POINTER(ctypes.c_int32), ctypes.POINTER(ctypes.POINTER(ctypes.c_int32)),
ctypes.POINTER(ctypes.c_int64), ctypes.POINTER(ctypes.POINTER(ctypes.c_int64)),
ctypes.POINTER(ctypes.c_double), ctypes.POINTER(ctypes.POINTER(ctypes.c_double)),
or NoneType
"""
if dtype == LAMMPS_AUTODETECT:
dtype = self.extract_atom_datatype(name)
if name: name = name.encode()
else: return None
if dtype == LAMMPS_INT:
self.lib.lammps_extract_atom.restype = POINTER(c_int32)
elif dtype == LAMMPS_INT_2D:
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int32))
elif dtype == LAMMPS_DOUBLE:
self.lib.lammps_extract_atom.restype = POINTER(c_double)
elif dtype == LAMMPS_DOUBLE_2D:
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
elif dtype == LAMMPS_INT64:
self.lib.lammps_extract_atom.restype = POINTER(c_int64)
elif dtype == LAMMPS_INT64_2D:
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int64))
else: return None
ptr = self.lib.lammps_extract_atom(self.lmp, name)
if ptr: return ptr
else: return None
# -------------------------------------------------------------------------
def extract_compute(self,cid,cstyle,ctype):
"""Retrieve data from a LAMMPS compute
This is a wrapper around the :cpp:func:`lammps_extract_compute`
function of the C-library interface.
This function returns ``None`` if either the compute id is not
recognized, or an invalid combination of :ref:`cstyle <py_style_constants>`
and :ref:`ctype <py_type_constants>` constants is used. The
names and functionality of the constants are the same as for
the corresponding C-library function. For requests to return
a scalar or a size, the value is returned, otherwise a pointer.
:param cid: compute ID
:type cid: string
:param cstyle: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
:type cstyle: int
:param ctype: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
:type ctype: int
:return: requested data as scalar, pointer to 1d or 2d double array, or None
:rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType
"""
if cid: cid = cid.encode()
else: return None
if ctype == LMP_TYPE_SCALAR:
if cstyle == LMP_STYLE_GLOBAL:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr[0]
elif cstyle == LMP_STYLE_ATOM:
return None
elif cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr[0]
elif ctype == LMP_TYPE_VECTOR:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr
elif ctype == LMP_TYPE_ARRAY:
self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr
elif ctype == LMP_SIZE_COLS:
if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr[0]
elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS:
if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr[0]
return None
# -------------------------------------------------------------------------
# extract fix info
# in case of global data, free memory for 1 double via lammps_free()
# double was allocated by library interface function
def extract_fix(self,fid,fstyle,ftype,nrow=0,ncol=0):
"""Retrieve data from a LAMMPS fix
This is a wrapper around the :cpp:func:`lammps_extract_fix`
function of the C-library interface.
This function returns ``None`` if either the fix id is not
recognized, or an invalid combination of :ref:`fstyle <py_style_constants>`
and :ref:`ftype <py_type_constants>` constants is used. The
names and functionality of the constants are the same as for
the corresponding C-library function. For requests to return
a scalar or a size, the value is returned, also when accessing
global vectors or arrays, otherwise a pointer.
:param fid: fix ID
:type fid: string
:param fstyle: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
:type fstyle: int
:param ftype: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
:type ftype: int
:param nrow: index of global vector element or row index of global array element
:type nrow: int
:param ncol: column index of global array element
:type ncol: int
:return: requested data or None
:rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType
"""
if fid: fid = fid.encode()
else: return None
if fstyle == LMP_STYLE_GLOBAL:
if ftype in (LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
self.lib.lammps_extract_fix.restype = POINTER(c_double)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
result = ptr[0]
self.lib.lammps_free(ptr)
return result
elif ftype in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
self.lib.lammps_extract_fix.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
return ptr[0]
else:
return None
elif fstyle == LMP_STYLE_ATOM:
if ftype == LMP_TYPE_VECTOR:
self.lib.lammps_extract_fix.restype = POINTER(c_double)
elif ftype == LMP_TYPE_ARRAY:
self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
elif ftype == LMP_SIZE_COLS:
self.lib.lammps_extract_fix.restype = POINTER(c_int)
else:
return None
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
if ftype == LMP_SIZE_COLS:
return ptr[0]
else:
return ptr
elif fstyle == LMP_STYLE_LOCAL:
if ftype == LMP_TYPE_VECTOR:
self.lib.lammps_extract_fix.restype = POINTER(c_double)
elif ftype == LMP_TYPE_ARRAY:
self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
elif ftype in (LMP_TYPE_SCALAR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
self.lib.lammps_extract_fix.restype = POINTER(c_int)
else:
return None
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_fix(self.lmp,fid,fstyle,ftype,nrow,ncol)
if ftype in (LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
return ptr
else:
return ptr[0]
else:
return None
# -------------------------------------------------------------------------
# extract variable info
# free memory for 1 double or 1 vector of doubles via lammps_free()
# for vector, must copy nlocal returned values to local c_double vector
# memory was allocated by library interface function
def extract_variable(self, name, group=None, vartype=None):
""" Evaluate a LAMMPS variable and return its data
This function is a wrapper around the function
:cpp:func:`lammps_extract_variable` of the C library interface,
evaluates variable name and returns a copy of the computed data.
The memory temporarily allocated by the C-interface is deleted
after the data is copied to a Python variable or list.
The variable must be either an equal-style (or equivalent)
variable or an atom-style variable. The variable type can be
provided as the ``vartype`` parameter, which may be one of several
constants: ``LMP_VAR_EQUAL``, ``LMP_VAR_ATOM``, ``LMP_VAR_VECTOR``,
or ``LMP_VAR_STRING``. If omitted or ``None``, LAMMPS will determine its
value for you based on a call to
:cpp:func:`lammps_extract_variable_datatype` from the C library interface.
The group parameter is only used for atom-style variables and defaults to
the group "all".
:param name: name of the variable to execute
:type name: string
:param group: name of group for atom-style variable
:type group: string, only for atom-style variables
:param vartype: type of variable, see :ref:`py_vartype_constants`
:type vartype: int
:return: the requested data
:rtype: c_double, (c_double), or NoneType
"""
if name: name = name.encode()
else: return None
if group: group = group.encode()
if vartype is None :
vartype = self.lib.lammps_extract_variable_datatype(self.lmp, name)
if vartype == LMP_VAR_EQUAL:
self.lib.lammps_extract_variable.restype = POINTER(c_double)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
if ptr: result = ptr[0]
else: return None
self.lib.lammps_free(ptr)
return result
elif vartype == LMP_VAR_ATOM:
nlocal = self.extract_global("nlocal")
result = (c_double*nlocal)()
self.lib.lammps_extract_variable.restype = POINTER(c_double)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
if ptr:
for i in range(nlocal): result[i] = ptr[i]
self.lib.lammps_free(ptr)
else: return None
return result
elif vartype == LMP_VAR_VECTOR :
nvector = 0
self.lib.lammps_extract_variable.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_variable(self.lmp,name,
'LMP_SIZE_VECTOR'.encode())
if ptr :
nvector = ptr[0]
self.lib.lammps_free(ptr)
else :
return None
self.lib.lammps_extract_variable.restype = POINTER(c_double)
result = (c_double*nvector)()
values = self.lib.lammps_extract_variable(self.lmp,name,group)
if values :
for i in range(nvector) :
result[i] = values[i]
# do NOT free the values pointer (points to internal vector data)
return result
else :
return None
elif vartype == LMP_VAR_STRING :
self.lib.lammps_extract_variable.restype = c_char_p
with ExceptionCheck(self) :
ptr = self.lib.lammps_extract_variable(self.lmp, name, group)
return ptr.decode('utf-8')
return None
# -------------------------------------------------------------------------
def flush_buffers(self):
"""Flush output buffers
This is a wrapper around the :cpp:func:`lammps_flush_buffers`
function of the C-library interface.
"""
self.lib.lammps_flush_buffers(self.lmp)
# -------------------------------------------------------------------------
def set_variable(self,name,value):
"""Set a new value for a LAMMPS string style variable
This is a wrapper around the :cpp:func:`lammps_set_variable`
function of the C-library interface.
:param name: name of the variable
:type name: string
:param value: new variable value
:type value: any. will be converted to a string
:return: either 0 on success or -1 on failure
:rtype: int
"""
if name: name = name.encode()
else: return -1
if value: value = str(value).encode()
else: return -1
with ExceptionCheck(self):
return self.lib.lammps_set_variable(self.lmp,name,value)
# -------------------------------------------------------------------------
# return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# dtype = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def gather_atoms(self,name,dtype,count):
if name: name = name.encode()
natoms = self.get_natoms()
with ExceptionCheck(self):
if dtype == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,dtype,count,data)
elif dtype == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms(self.lmp,name,dtype,count,data)
else:
return None
return data
# -------------------------------------------------------------------------
def gather_atoms_concat(self,name,dtype,count):
if name: name = name.encode()
natoms = self.get_natoms()
with ExceptionCheck(self):
if dtype == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,dtype,count,data)
elif dtype == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,dtype,count,data)
else:
return None
return data
def gather_atoms_subset(self,name,dtype,count,ndata,ids):
if name: name = name.encode()
with ExceptionCheck(self):
if dtype == 0:
data = ((count*ndata)*c_int)()
self.lib.lammps_gather_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
elif dtype == 1:
data = ((count*ndata)*c_double)()
self.lib.lammps_gather_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
else:
return None
return data
# -------------------------------------------------------------------------
# scatter vector of atom properties across procs
# 2 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def scatter_atoms(self,name,dtype,count,data):
if name: name = name.encode()
with ExceptionCheck(self):
self.lib.lammps_scatter_atoms(self.lmp,name,dtype,count,data)
# -------------------------------------------------------------------------
def scatter_atoms_subset(self,name,dtype,count,ndata,ids,data):
if name: name = name.encode()
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
.. versionadded:: 28Jul2021
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.
: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
# -------------------------------------------------------------------------
def gather_angles(self):
"""Retrieve global list of angles
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_angles`
function of the C-library interface.
This function returns a tuple with the number of angles and a
flat list of ctypes integer values with the angle type, angle atom1,
angle atom2, angle atom3 for each angle.
:return: a tuple with the number of angles and a list of c_int or c_long
:rtype: (int, 4*nangles*c_tagint)
"""
nangles = self.extract_global("nangles")
with ExceptionCheck(self):
data = ((4*nangles)*self.c_tagint)()
self.lib.lammps_gather_angles(self.lmp,data)
return nangles,data
# -------------------------------------------------------------------------
def gather_dihedrals(self):
"""Retrieve global list of dihedrals
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_dihedrals`
function of the C-library interface.
This function returns a tuple with the number of dihedrals and a
flat list of ctypes integer values with the dihedral type, dihedral atom1,
dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.
:return: a tuple with the number of dihedrals and a list of c_int or c_long
:rtype: (int, 5*ndihedrals*c_tagint)
"""
ndihedrals = self.extract_global("ndihedrals")
with ExceptionCheck(self):
data = ((5*ndihedrals)*self.c_tagint)()
self.lib.lammps_gather_dihedrals(self.lmp,data)
return ndihedrals,data
# -------------------------------------------------------------------------
def gather_impropers(self):
"""Retrieve global list of impropers
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_impropers`
function of the C-library interface.
This function returns a tuple with the number of impropers and a
flat list of ctypes integer values with the improper type, improper atom1,
improper atom2, improper atom3, improper atom4 for each improper.
:return: a tuple with the number of impropers and a list of c_int or c_long
:rtype: (int, 5*nimpropers*c_tagint)
"""
nimpropers = self.extract_global("nimpropers")
with ExceptionCheck(self):
data = ((5*nimpropers)*self.c_tagint)()
self.lib.lammps_gather_impropers(self.lmp,data)
return nimpropers,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()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def gather(self,name,dtype,count):
if name: name = name.encode()
natoms = self.get_natoms()
with ExceptionCheck(self):
if dtype == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather(self.lmp,name,dtype,count,data)
elif dtype == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather(self.lmp,name,dtype,count,data)
else:
return None
return data
def gather_concat(self,name,dtype,count):
if name: name = name.encode()
natoms = self.get_natoms()
with ExceptionCheck(self):
if dtype == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_concat(self.lmp,name,dtype,count,data)
elif dtype == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_concat(self.lmp,name,dtype,count,data)
else:
return None
return data
def gather_subset(self,name,dtype,count,ndata,ids):
if name: name = name.encode()
with ExceptionCheck(self):
if dtype == 0:
data = ((count*ndata)*c_int)()
self.lib.lammps_gather_subset(self.lmp,name,dtype,count,ndata,ids,data)
elif dtype == 1:
data = ((count*ndata)*c_double)()
self.lib.lammps_gather_subset(self.lmp,name,dtype,count,ndata,ids,data)
else:
return None
return data
# scatter vector of atom/compute/fix properties across procs
# 2 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to ensure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def scatter(self,name,dtype,count,data):
if name: name = name.encode()
with ExceptionCheck(self):
self.lib.lammps_scatter(self.lmp,name,dtype,count,data)
def scatter_subset(self,name,dtype,count,ndata,ids,data):
if name: name = name.encode()
with ExceptionCheck(self):
self.lib.lammps_scatter_subset(self.lmp,name,dtype,count,ndata,ids,data)
# -------------------------------------------------------------------------
def encode_image_flags(self,ix,iy,iz):
""" convert 3 integers with image flags for x-, y-, and z-direction
into a single integer like it is used internally in LAMMPS
This method is a wrapper around the :cpp:func:`lammps_encode_image_flags`
function of library interface.
:param ix: x-direction image flag
:type ix: int
:param iy: y-direction image flag
:type iy: int
:param iz: z-direction image flag
:type iz: int
:return: encoded image flags
:rtype: lammps.c_imageint
"""
return self.lib.lammps_encode_image_flags(ix,iy,iz)
# -------------------------------------------------------------------------
def decode_image_flags(self,image):
""" Convert encoded image flag integer into list of three regular integers.
This method is a wrapper around the :cpp:func:`lammps_decode_image_flags`
function of library interface.
:param image: encoded image flags
:type image: lammps.c_imageint
:return: list of three image flags in x-, y-, and z- direction
:rtype: list of 3 int
"""
flags = (c_int*3)()
self.lib.lammps_decode_image_flags(image,byref(flags))
return [int(i) for i in flags]
# -------------------------------------------------------------------------
# create N atoms on all procs
# N = global number of atoms
# id = ID of each atom (optional, can be None)
# type = type of each atom (1 to Ntypes) (required)
# x = coords of each atom as (N,3) array (required)
# v = velocity of each atom as (N,3) array (optional, can be None)
# NOTE: how could we ensure are passing correct type to LAMMPS
# e.g. for Python list or NumPy, etc
# ditto for gather_atoms() above
def create_atoms(self,n,id,type,x,v=None,image=None,shrinkexceed=False):
"""
Create N atoms from list of coordinates and properties
This function is a wrapper around the :cpp:func:`lammps_create_atoms`
function of the C-library interface, and the behavior is similar except
that the *v*, *image*, and *shrinkexceed* arguments are optional and
default to *None*, *None*, and *False*, respectively. With *None* being
equivalent to a ``NULL`` pointer in C.
The lists of coordinates, types, atom IDs, velocities, image flags can
be provided in any format that may be converted into the required
internal data types. Also the list may contain more than *N* entries,
but not fewer. In the latter case, the function will return without
attempting to create atoms. You may use the :py:func:`encode_image_flags
<lammps.encode_image_flags>` method to properly combine three integers
with image flags into a single integer.
:param n: number of atoms for which data is provided
:type n: int
:param id: list of atom IDs with at least n elements or None
:type id: list of lammps.tagint
:param type: list of atom types
:type type: list of int
:param x: list of coordinates for x-, y-, and z (flat list of 3n entries)
:type x: list of float
:param v: list of velocities for x-, y-, and z (flat list of 3n entries) or None (optional)
:type v: list of float
:param image: list of encoded image flags (optional)
:type image: list of lammps.imageint
:param shrinkexceed: whether to expand shrink-wrap boundaries if atoms are outside the box (optional)
:type shrinkexceed: bool
:return: number of atoms created. 0 if insufficient or invalid data
:rtype: int
"""
if id is not None:
id_lmp = (self.c_tagint*n)()
try:
id_lmp[:] = id[0:n]
except ValueError:
return 0
else:
id_lmp = None
type_lmp = (c_int*n)()
try:
type_lmp[:] = type[0:n]
except ValueError:
return 0
three_n = 3*n
x_lmp = (c_double*three_n)()
try:
x_lmp[:] = x[0:three_n]
except ValueError:
return 0
if v is not None:
v_lmp = (c_double*(three_n))()
try:
v_lmp[:] = v[0:three_n]
except ValueError:
return 0
else:
v_lmp = None
if image is not None:
img_lmp = (self.c_imageint*n)()
try:
img_lmp[:] = image[0:n]
except ValueError:
return 0
else:
img_lmp = None
if shrinkexceed:
se_lmp = 1
else:
se_lmp = 0
self.lib.lammps_create_atoms.argtypes = [c_void_p, c_int, POINTER(self.c_tagint*n),
POINTER(c_int*n), POINTER(c_double*three_n),
POINTER(c_double*three_n),
POINTER(self.c_imageint*n), c_int]
with ExceptionCheck(self):
return self.lib.lammps_create_atoms(self.lmp, n, id_lmp, type_lmp, x_lmp, v_lmp, img_lmp, se_lmp)
# -------------------------------------------------------------------------
@property
def has_mpi_support(self):
""" Report whether the LAMMPS shared library was compiled with a
real MPI library or in serial.
This is a wrapper around the :cpp:func:`lammps_config_has_mpi_support`
function of the library interface.
:return: False when compiled with MPI STUBS, otherwise True
:rtype: bool
"""
return self.lib.lammps_config_has_mpi_support() != 0
# -------------------------------------------------------------------------
@property
def is_running(self):
""" Report whether being called from a function during a run or a minimization
.. versionadded:: 9Oct2020
Various LAMMPS commands must not be called during an ongoing
run or minimization. This property allows to check for that.
This is a wrapper around the :cpp:func:`lammps_is_running`
function of the library interface.
:return: True when called during a run otherwise false
:rtype: bool
"""
return self.lib.lammps_is_running(self.lmp) == 1
# -------------------------------------------------------------------------
def force_timeout(self):
""" Trigger an immediate timeout, i.e. a "soft stop" of a run.
.. versionadded:: 9Oct2020
This function allows to cleanly stop an ongoing run or minimization
at the next loop iteration.
This is a wrapper around the :cpp:func:`lammps_force_timeout`
function of the library interface.
"""
self.lib.lammps_force_timeout(self.lmp)
# -------------------------------------------------------------------------
@property
def has_exceptions(self):
""" Report whether the LAMMPS shared library was compiled with C++
exceptions handling enabled
This is a wrapper around the :cpp:func:`lammps_config_has_exceptions`
function of the library interface.
:return: state of C++ exception support
:rtype: bool
"""
return self.lib.lammps_config_has_exceptions() != 0
# -------------------------------------------------------------------------
@property
def has_gzip_support(self):
""" Report whether the LAMMPS shared library was compiled with support
for reading and writing compressed files through ``gzip``.
This is a wrapper around the :cpp:func:`lammps_config_has_gzip_support`
function of the library interface.
:return: state of gzip support
:rtype: bool
"""
return self.lib.lammps_config_has_gzip_support() != 0
# -------------------------------------------------------------------------
@property
def has_png_support(self):
""" Report whether the LAMMPS shared library was compiled with support
for writing images in PNG format.
This is a wrapper around the :cpp:func:`lammps_config_has_png_support`
function of the library interface.
:return: state of PNG support
:rtype: bool
"""
return self.lib.lammps_config_has_png_support() != 0
# -------------------------------------------------------------------------
@property
def has_jpeg_support(self):
""" Report whether the LAMMPS shared library was compiled with support
for writing images in JPEG format.
This is a wrapper around the :cpp:func:`lammps_config_has_jpeg_support`
function of the library interface.
:return: state of JPEG support
:rtype: bool
"""
return self.lib.lammps_config_has_jpeg_support() != 0
# -------------------------------------------------------------------------
@property
def has_ffmpeg_support(self):
""" State of support for writing movies with ``ffmpeg`` in the LAMMPS shared library
This is a wrapper around the :cpp:func:`lammps_config_has_ffmpeg_support`
function of the library interface.
:return: state of ffmpeg support
:rtype: bool
"""
return self.lib.lammps_config_has_ffmpeg_support() != 0
# -------------------------------------------------------------------------
def has_package(self, name):
""" Report if the named package has been enabled in the LAMMPS shared library.
.. versionadded:: 3Nov2022
This is a wrapper around the :cpp:func:`lammps_config_has_package`
function of the library interface.
:param name: name of the package
:type name: string
:return: state of package availability
:rtype: bool
"""
return self.lib.lammps_config_has_package(name.encode()) != 0
# -------------------------------------------------------------------------
@property
def accelerator_config(self):
""" Return table with available accelerator configuration settings.
This is a wrapper around the :cpp:func:`lammps_config_accelerator`
function of the library interface which loops over all known packages
and categories and returns enabled features as a nested dictionary
with all enabled settings as list of strings.
:return: nested dictionary with all known enabled settings as list of strings
:rtype: dictionary
"""
result = {}
for p in ['GPU', 'KOKKOS', 'INTEL', 'OPENMP']:
result[p] = {}
c = 'api'
result[p][c] = []
for s in ['cuda', 'hip', 'phi', 'pthreads', 'opencl', 'openmp', 'serial']:
if self.lib.lammps_config_accelerator(p.encode(),c.encode(),s.encode()):
result[p][c].append(s)
c = 'precision'
result[p][c] = []
for s in ['double', 'mixed', 'single']:
if self.lib.lammps_config_accelerator(p.encode(),c.encode(),s.encode()):
result[p][c].append(s)
return result
# -------------------------------------------------------------------------
@property
def has_gpu_device(self):
""" Availability of GPU package compatible device
This is a wrapper around the :cpp:func:`lammps_has_gpu_device`
function of the C library interface.
:return: True if a GPU package compatible device is present, otherwise False
:rtype: bool
"""
return self.lib.lammps_has_gpu_device() != 0
# -------------------------------------------------------------------------
def get_gpu_device_info(self):
"""Return a string with detailed information about any devices that are
usable by the GPU package.
This is a wrapper around the :cpp:func:`lammps_get_gpu_device_info`
function of the C-library interface.
:return: GPU device info string
:rtype: string
"""
sb = create_string_buffer(8192)
self.lib.lammps_get_gpu_device_info(sb,8192)
return sb.value.decode()
# -------------------------------------------------------------------------
@property
def installed_packages(self):
""" List of the names of enabled packages in the LAMMPS shared library
This is a wrapper around the functions :cpp:func:`lammps_config_package_count`
and :cpp:func`lammps_config_package_name` of the library interface.
:return
"""
if self._installed_packages is None:
self._installed_packages = []
npackages = self.lib.lammps_config_package_count()
sb = create_string_buffer(100)
for idx in range(npackages):
self.lib.lammps_config_package_name(idx, sb, 100)
self._installed_packages.append(sb.value.decode())
return self._installed_packages
# -------------------------------------------------------------------------
def has_style(self, category, name):
"""Returns whether a given style name is available in a given category
This is a wrapper around the function :cpp:func:`lammps_has_style`
of the library interface.
:param category: name of category
:type category: string
:param name: name of the style
:type name: string
:return: true if style is available in given category
:rtype: bool
"""
return self.lib.lammps_has_style(self.lmp, category.encode(), name.encode()) != 0
# -------------------------------------------------------------------------
def available_styles(self, category):
"""Returns a list of styles available for a given category
This is a wrapper around the functions :cpp:func:`lammps_style_count()`
and :cpp:func:`lammps_style_name()` of the library interface.
:param category: name of category
:type category: string
:return: list of style names in given category
:rtype: list
"""
if self._available_styles is None:
self._available_styles = {}
if category not in self._available_styles:
self._available_styles[category] = []
with ExceptionCheck(self):
nstyles = self.lib.lammps_style_count(self.lmp, category.encode())
sb = create_string_buffer(100)
for idx in range(nstyles):
with ExceptionCheck(self):
self.lib.lammps_style_name(self.lmp, category.encode(), idx, sb, 100)
self._available_styles[category].append(sb.value.decode())
return self._available_styles[category]
# -------------------------------------------------------------------------
def has_id(self, category, name):
"""Returns whether a given ID name is available in a given category
.. versionadded:: 9Oct2020
This is a wrapper around the function :cpp:func:`lammps_has_id`
of the library interface.
:param category: name of category
:type category: string
:param name: name of the ID
:type name: string
:return: true if ID is available in given category
:rtype: bool
"""
return self.lib.lammps_has_id(self.lmp, category.encode(), name.encode()) != 0
# -------------------------------------------------------------------------
def available_ids(self, category):
"""Returns a list of IDs available for a given category
.. versionadded:: 9Oct2020
This is a wrapper around the functions :cpp:func:`lammps_id_count()`
and :cpp:func:`lammps_id_name()` of the library interface.
:param category: name of category
:type category: string
:return: list of id names in given category
:rtype: list
"""
categories = ['compute','dump','fix','group','molecule','region','variable']
available_ids = []
if category in categories:
num = self.lib.lammps_id_count(self.lmp, category.encode())
sb = create_string_buffer(100)
for idx in range(num):
self.lib.lammps_id_name(self.lmp, category.encode(), idx, sb, 100)
available_ids.append(sb.value.decode())
return available_ids
# -------------------------------------------------------------------------
def available_plugins(self, category):
"""Returns a list of plugins available for a given category
.. versionadded:: 10Mar2021
This is a wrapper around the functions :cpp:func:`lammps_plugin_count()`
and :cpp:func:`lammps_plugin_name()` of the library interface.
:return: list of style/name pairs of loaded plugins
:rtype: list
"""
available_plugins = []
num = self.lib.lammps_plugin_count(self.lmp)
sty = create_string_buffer(100)
nam = create_string_buffer(100)
for idx in range(num):
self.lib.lammps_plugin_name(idx, sty, nam, 100)
available_plugins.append([sty.value.decode(), nam.value.decode()])
return available_plugins
# -------------------------------------------------------------------------
def set_fix_external_callback(self, fix_id, callback, caller=None):
"""Set the callback function for a fix external instance with a given fix ID.
Optionally also set a reference to the calling object.
This is a wrapper around the :cpp:func:`lammps_set_fix_external_callback` function
of the C-library interface. However this is set up to call a Python function with
the following arguments.
.. code-block: python
def func(object, ntimestep, nlocal, tag, x, f):
- object is the value of the "caller" argument
- ntimestep is the current timestep
- nlocal is the number of local atoms on the current MPI process
- tag is a 1d NumPy array of integers representing the atom IDs of the local atoms
- 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
:type: function
:param caller: reference to some object passed to the callback function
:type: object, optional
"""
import numpy as np
def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1)
x = self.numpy.darray(x_ptr, nlocal, 3)
f = self.numpy.darray(fext_ptr, nlocal, 3)
callback(caller, ntimestep, nlocal, tag, x, f)
cFunc = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
cCaller = caller
self.callback[fix_id] = { 'function': cFunc, 'caller': caller }
with ExceptionCheck(self):
self.lib.lammps_set_fix_external_callback(self.lmp, fix_id.encode(), cFunc, cCaller)
# -------------------------------------------------------------------------
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.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
of the C-library interface.
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
:rtype: ctypes.POINTER(ctypes.POINTER(ctypes.double))
"""
with ExceptionCheck(self):
return self.lib.lammps_fix_external_get_force(self.lmp, fix_id.encode())
# -------------------------------------------------------------------------
def fix_external_set_energy_global(self, fix_id, eng):
"""Set the global energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function
of the C-library interface.
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: potential energy value to be added by fix external
:type: float
"""
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_energy_global(self.lmp, fix_id.encode(), eng)
# -------------------------------------------------------------------------
def fix_external_set_virial_global(self, fix_id, virial):
"""Set the global virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function
of the C-library interface.
: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
:type: float
"""
cvirial = (6*c_double)(*virial)
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_virial_global(self.lmp, fix_id.encode(), cvirial)
# -------------------------------------------------------------------------
def fix_external_set_energy_peratom(self, fix_id, eatom):
"""Set the per-atom energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
of the C-library interface.
: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
:type: float
"""
nlocal = self.extract_setting('nlocal')
if len(eatom) < nlocal:
raise Exception('per-atom energy list length must be at least nlocal')
ceatom = (nlocal*c_double)(*eatom)
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_energy_peratom(self.lmp, fix_id.encode(), ceatom)
# -------------------------------------------------------------------------
def fix_external_set_virial_peratom(self, fix_id, vatom):
"""Set the per-atom virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
of the C-library interface.
: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
:type: float
"""
# copy virial data to C compatible buffer
nlocal = self.extract_setting('nlocal')
if len(vatom) < nlocal:
raise Exception('per-atom virial first dimension must be at least nlocal')
if len(vatom[0]) != 6:
raise Exception('per-atom virial second dimension must be 6')
vbuf = (c_double * 6)
vptr = POINTER(c_double)
c_virial = (vptr * nlocal)()
for i in range(nlocal):
c_virial[i] = vbuf()
for j in range(6):
c_virial[i][j] = vatom[i][j]
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_virial_peratom(self.lmp, fix_id.encode(), c_virial)
# -------------------------------------------------------------------------
def fix_external_set_vector_length(self, fix_id, length):
"""Set the vector length for a global vector stored with fix external for analysis
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
of the C-library interface.
:param fix_id: Fix-ID of a fix external instance
:type: string
:param length: length of the global vector
:type: int
"""
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_vector_length(self.lmp, fix_id.encode(), length)
# -------------------------------------------------------------------------
def fix_external_set_vector(self, fix_id, idx, val):
"""Store a global vector value for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
of the C-library interface.
:param fix_id: Fix-ID of a fix external instance
:type: string
:param idx: 1-based index of the value in the global vector
:type: int
:param val: value to be stored in the global vector
:type: float
"""
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_vector(self.lmp, fix_id.encode(), idx, val)
# -------------------------------------------------------------------------
def get_neighlist(self, idx):
"""Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index
See :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>` if you want to use
NumPy arrays instead of ``c_int`` pointers.
:param idx: index of neighbor list
:type idx: int
:return: an instance of :class:`NeighList` wrapping access to neighbor list data
:rtype: NeighList
"""
if idx < 0:
return None
return NeighList(self, idx)
# -------------------------------------------------------------------------
def get_neighlist_size(self, idx):
"""Return the number of elements in neighbor list with the given index
:param idx: neighbor list index
:type idx: int
:return: number of elements in neighbor list with index idx
:rtype: int
"""
return self.lib.lammps_neighlist_num_elements(self.lmp, idx)
# -------------------------------------------------------------------------
def get_neighlist_element_neighbors(self, idx, element):
"""Return data of neighbor list entry
:param element: neighbor list index
:type element: int
:param element: neighbor list element index
:type element: int
:return: tuple with atom local index, number of neighbors and array of neighbor local atom indices
:rtype: (int, int, POINTER(c_int))
"""
c_iatom = c_int()
c_numneigh = c_int()
c_neighbors = POINTER(c_int)()
self.lib.lammps_neighlist_element_neighbors(self.lmp, idx, element, byref(c_iatom), byref(c_numneigh), byref(c_neighbors))
return c_iatom.value, c_numneigh.value, c_neighbors
# -------------------------------------------------------------------------
def find_pair_neighlist(self, style, exact=True, nsub=0, reqid=0):
"""Find neighbor list index of pair style neighbor list
Search for a neighbor list requested by a pair style instance that
matches "style". If exact is True, the pair style name must match
exactly. If exact is False, the pair style name is matched against
"style" as regular expression or sub-string. If the pair style is a
hybrid pair style, the style is instead matched against the hybrid
sub-styles. If the same pair style is used as sub-style multiple
types, you must set nsub to a value n > 0 which indicates the nth
instance of that sub-style to be used (same as for the pair_coeff
command). The default value of 0 will fail to match in that case.
Once the pair style instance has been identified, it may have
requested multiple neighbor lists. Those are uniquely identified by
a request ID > 0 as set by the pair style. Otherwise the request
ID is 0.
:param style: name of pair style that should be searched for
:type style: string
:param exact: controls whether style should match exactly or only must be contained in pair style name, defaults to True
:type exact: bool, optional
:param nsub: match nsub-th hybrid sub-style, defaults to 0
:type nsub: int, optional
:param reqid: list request id, > 0 in case there are more than one, defaults to 0
:type reqid: int, optional
:return: neighbor list index if found, otherwise -1
:rtype: int
"""
style = style.encode()
exact = int(exact)
idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, reqid)
return idx
# -------------------------------------------------------------------------
def find_fix_neighlist(self, fixid, reqid=0):
"""Find neighbor list index of fix neighbor list
The fix instance requesting the neighbor list is uniquely identified
by the fix ID. In case the fix has requested multiple neighbor
lists, those are uniquely identified by a request ID > 0 as set by
the fix. Otherwise the request ID is 0 (the default).
:param fixid: name of fix
:type fixid: string
:param reqid: id of neighbor list request, in case there are more than one request, defaults to 0
:type reqid: int, optional
:return: neighbor list index if found, otherwise -1
:rtype: int
"""
fixid = fixid.encode()
idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, reqid)
return idx
# -------------------------------------------------------------------------
def find_compute_neighlist(self, computeid, reqid=0):
"""Find neighbor list index of compute neighbor list
The compute instance requesting the neighbor list is uniquely
identified by the compute ID. In case the compute has requested
multiple neighbor lists, those are uniquely identified by a request
ID > 0 as set by the compute. Otherwise the request ID is 0 (the
default).
:param computeid: name of compute
:type computeid: string
:param reqid: index of neighbor list request, in case there are more than one request, defaults to 0
:type reqid: int, optional
:return: neighbor list index if found, otherwise -1
:rtype: int
"""
computeid = computeid.encode()
idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, reqid)
return idx
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