Merge branch 'master' into mliappy3
This commit is contained in:
Richard Berger
@ -1,42 +1,42 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Installer script to install the LAMMPS python module and the corresponding
|
||||
Installer script to install the LAMMPS python package and the corresponding
|
||||
shared library into either the system-wide site-packages tree, or - failing
|
||||
that - into the corresponding user tree. Called from the 'install-python'
|
||||
build target in the conventional and CMake based build systems
|
||||
"""
|
||||
|
||||
# copy LAMMPS shared library and lammps.py to system dirs
|
||||
# copy LAMMPS shared library and lammps package to system dirs
|
||||
|
||||
from __future__ import print_function
|
||||
import sys,os,shutil
|
||||
from argparse import ArgumentParser
|
||||
|
||||
parser = ArgumentParser(prog='install.py',
|
||||
description='LAMMPS python module installer script')
|
||||
description='LAMMPS python package installer script')
|
||||
|
||||
parser.add_argument("-m", "--module", required=True,
|
||||
help="path to the source of the LAMMPS Python module")
|
||||
parser.add_argument("-p", "--package", required=True,
|
||||
help="path to the LAMMPS Python package")
|
||||
parser.add_argument("-l", "--lib", required=True,
|
||||
help="path to the compiled LAMMPS shared library")
|
||||
parser.add_argument("-v", "--version", required=True,
|
||||
help="path to the LAMMPS version.h header file")
|
||||
|
||||
parser.add_argument("-d","--dir",
|
||||
help="Legacy custom installation folder selection for module and library")
|
||||
help="Legacy custom installation folder selection for package and library")
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
# validate arguments and make paths absolute
|
||||
|
||||
if args.module:
|
||||
if not os.path.exists(args.module):
|
||||
print( "ERROR: LAMMPS module file %s does not exist" % args.module)
|
||||
if args.package:
|
||||
if not os.path.exists(args.package):
|
||||
print( "ERROR: LAMMPS package %s does not exist" % args.package)
|
||||
parser.print_help()
|
||||
sys.exit(1)
|
||||
else:
|
||||
args.module = os.path.abspath(args.module)
|
||||
args.package = os.path.abspath(args.package)
|
||||
|
||||
if args.lib:
|
||||
if not os.path.exists(args.lib):
|
||||
@ -66,9 +66,9 @@ if args.dir:
|
||||
# without any special processing or additional steps to that folder
|
||||
|
||||
if args.dir:
|
||||
print("Copying LAMMPS Python module to custom folder %s" % args.dir)
|
||||
print("Copying LAMMPS Python package to custom folder %s" % args.dir)
|
||||
try:
|
||||
shutil.copyfile(args.module, os.path.join(args.dir,'lammps.py'))
|
||||
shutil.copytree(args.package, os.path.join(args.dir,'lammps'))
|
||||
except shutil.Error:
|
||||
pass # fail silently
|
||||
|
||||
@ -81,15 +81,19 @@ if args.dir:
|
||||
sys.exit()
|
||||
|
||||
# extract version string from header
|
||||
fp = open(args.version,'r')
|
||||
txt=fp.read().split('"')[1].split()
|
||||
verstr=txt[0]+txt[1]+txt[2]
|
||||
fp.close()
|
||||
def get_lammps_version(header):
|
||||
with open(header, 'r') as f:
|
||||
line = f.readline()
|
||||
start_pos = line.find('"')+1
|
||||
end_pos = line.find('"', start_pos)
|
||||
return "".join(line[start_pos:end_pos].split())
|
||||
|
||||
print("Installing LAMMPS Python module version %s into site-packages folder" % verstr)
|
||||
verstr = get_lammps_version(args.version)
|
||||
|
||||
# we need to switch to the folder of the python module
|
||||
os.chdir(os.path.dirname(args.module))
|
||||
print("Installing LAMMPS Python package version %s into site-packages folder" % verstr)
|
||||
|
||||
# we need to switch to the folder of the python package
|
||||
os.chdir(os.path.dirname(args.package))
|
||||
|
||||
from distutils.core import setup
|
||||
from distutils.sysconfig import get_python_lib
|
||||
@ -103,10 +107,10 @@ try:
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "https://lammps.sandia.gov",
|
||||
description = "LAMMPS Molecular Dynamics Python module",
|
||||
description = "LAMMPS Molecular Dynamics Python package",
|
||||
license = "GPL",
|
||||
py_modules = ["lammps"],
|
||||
data_files = [(get_python_lib(), [args.lib])])
|
||||
packages=['lammps'],
|
||||
data_files = [(os.path.join(get_python_lib(), 'lammps'), [args.lib])])
|
||||
except:
|
||||
tryuser=True
|
||||
print ("Installation into global site-packages folder failed.\nTrying user folder %s now." % site.USER_SITE)
|
||||
@ -119,9 +123,9 @@ if tryuser:
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "https://lammps.sandia.gov",
|
||||
description = "LAMMPS Molecular Dynamics Python module",
|
||||
description = "LAMMPS Molecular Dynamics Python package",
|
||||
license = "GPL",
|
||||
py_modules = ["lammps"],
|
||||
data_files = [(site.USER_SITE, [args.lib])])
|
||||
packages=['lammps'],
|
||||
data_files = [(os.path.join(site.USER_SITE, 'lammps'), [args.lib])])
|
||||
except:
|
||||
print("Installation into user site package folder failed.")
|
||||
|
||||
4
python/lammps/__init__.py
Normal file
4
python/lammps/__init__.py
Normal file
@ -0,0 +1,4 @@
|
||||
from .constants import *
|
||||
from .core import *
|
||||
from .data import *
|
||||
from .pylammps import *
|
||||
49
python/lammps/constants.py
Normal file
49
python/lammps/constants.py
Normal file
@ -0,0 +1,49 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# 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.
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
from ctypes import c_int, c_int32, c_int64
|
||||
|
||||
# various symbolic constants to be used
|
||||
# in certain calls to select data formats
|
||||
LAMMPS_AUTODETECT = None
|
||||
LAMMPS_INT = 0
|
||||
LAMMPS_INT_2D = 1
|
||||
LAMMPS_DOUBLE = 2
|
||||
LAMMPS_DOUBLE_2D = 3
|
||||
LAMMPS_INT64 = 4
|
||||
LAMMPS_INT64_2D = 5
|
||||
LAMMPS_STRING = 6
|
||||
|
||||
# these must be kept in sync with the enums in library.h
|
||||
LMP_STYLE_GLOBAL = 0
|
||||
LMP_STYLE_ATOM = 1
|
||||
LMP_STYLE_LOCAL = 2
|
||||
|
||||
LMP_TYPE_SCALAR = 0
|
||||
LMP_TYPE_VECTOR = 1
|
||||
LMP_TYPE_ARRAY = 2
|
||||
LMP_SIZE_VECTOR = 3
|
||||
LMP_SIZE_ROWS = 4
|
||||
LMP_SIZE_COLS = 5
|
||||
|
||||
LMP_VAR_EQUAL = 0
|
||||
LMP_VAR_ATOM = 1
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def get_ctypes_int(size):
|
||||
if size == 4:
|
||||
return c_int32
|
||||
elif size == 8:
|
||||
return c_int64
|
||||
return c_int
|
||||
File diff suppressed because it is too large
Load Diff
73
python/lammps/data.py
Normal file
73
python/lammps/data.py
Normal file
@ -0,0 +1,73 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# 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.
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
################################################################################
|
||||
# LAMMPS data structures
|
||||
# Written by Richard Berger <richard.berger@temple.edu>
|
||||
################################################################################
|
||||
|
||||
class NeighList:
|
||||
"""This is a wrapper class that exposes the contents of a neighbor list.
|
||||
|
||||
It can be used like a regular Python list. Each element is a tuple of:
|
||||
|
||||
* the atom local index
|
||||
* its number of neighbors
|
||||
* and a pointer to an c_int array containing local atom indices of its
|
||||
neighbors
|
||||
|
||||
Internally it uses the lower-level LAMMPS C-library interface.
|
||||
|
||||
:param lmp: reference to instance of :py:class:`lammps`
|
||||
:type lmp: lammps
|
||||
:param idx: neighbor list index
|
||||
:type idx: int
|
||||
"""
|
||||
def __init__(self, lmp, idx):
|
||||
self.lmp = lmp
|
||||
self.idx = idx
|
||||
|
||||
def __str__(self):
|
||||
return "Neighbor List ({} atoms)".format(self.size)
|
||||
|
||||
def __repr__(self):
|
||||
return self.__str__()
|
||||
|
||||
@property
|
||||
def size(self):
|
||||
"""
|
||||
:return: number of elements in neighbor list
|
||||
"""
|
||||
return self.lmp.get_neighlist_size(self.idx)
|
||||
|
||||
def get(self, element):
|
||||
"""
|
||||
:return: tuple with atom local index, numpy array of neighbor local atom indices
|
||||
:rtype: (int, int, ctypes.POINTER(c_int))
|
||||
"""
|
||||
iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
|
||||
return iatom, numneigh, neighbors
|
||||
|
||||
# the methods below implement the iterator interface, so NeighList can be used like a regular Python list
|
||||
|
||||
def __getitem__(self, element):
|
||||
return self.get(element)
|
||||
|
||||
def __len__(self):
|
||||
return self.size
|
||||
|
||||
def __iter__(self):
|
||||
inum = self.size
|
||||
|
||||
for ii in range(inum):
|
||||
yield self.get(ii)
|
||||
338
python/lammps/numpy.py
Normal file
338
python/lammps/numpy.py
Normal file
@ -0,0 +1,338 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# 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.
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
################################################################################
|
||||
# NumPy additions
|
||||
# Written by Richard Berger <richard.berger@temple.edu>
|
||||
################################################################################
|
||||
|
||||
import warnings
|
||||
from ctypes import POINTER, c_double, c_int, c_int32, c_int64, cast
|
||||
|
||||
|
||||
from .constants import *
|
||||
from .data import NeighList
|
||||
|
||||
|
||||
class numpy_wrapper:
|
||||
"""lammps API NumPy Wrapper
|
||||
|
||||
This is a wrapper class that provides additional methods on top of an
|
||||
existing :py:class:`lammps` instance. The methods transform raw ctypes
|
||||
pointers into NumPy arrays, which give direct access to the
|
||||
original data while protecting against out-of-bounds accesses.
|
||||
|
||||
There is no need to explicitly instantiate this class. Each instance
|
||||
of :py:class:`lammps` has a :py:attr:`numpy <lammps.numpy>` property
|
||||
that returns an instance.
|
||||
|
||||
:param lmp: instance of the :py:class:`lammps` class
|
||||
:type lmp: lammps
|
||||
"""
|
||||
def __init__(self, lmp):
|
||||
self.lmp = lmp
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def _ctype_to_numpy_int(self, ctype_int):
|
||||
import numpy as np
|
||||
if ctype_int == c_int32:
|
||||
return np.int32
|
||||
elif ctype_int == c_int64:
|
||||
return np.int64
|
||||
return np.intc
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def extract_atom(self, name, dtype=LAMMPS_AUTODETECT, nelem=LAMMPS_AUTODETECT, dim=LAMMPS_AUTODETECT):
|
||||
"""Retrieve per-atom properties from LAMMPS as NumPy arrays
|
||||
|
||||
This is a wrapper around the :py:meth:`lammps.extract_atom()` method.
|
||||
It behaves the same as the original method, but returns NumPy arrays
|
||||
instead of ``ctypes`` pointers.
|
||||
|
||||
.. 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: type of the returned data (see :ref:`py_datatype_constants`)
|
||||
:type dtype: int, optional
|
||||
:param nelem: number of elements in array
|
||||
:type nelem: int, optional
|
||||
:param dim: dimension of each element
|
||||
:type dim: int, optional
|
||||
:return: requested data as NumPy array with direct access to C data or None
|
||||
:rtype: numpy.array or NoneType
|
||||
"""
|
||||
if dtype == LAMMPS_AUTODETECT:
|
||||
dtype = self.lmp.extract_atom_datatype(name)
|
||||
|
||||
if nelem == LAMMPS_AUTODETECT:
|
||||
if name == "mass":
|
||||
nelem = self.lmp.extract_global("ntypes") + 1
|
||||
else:
|
||||
nelem = self.lmp.extract_global("nlocal")
|
||||
if dim == LAMMPS_AUTODETECT:
|
||||
if dtype in (LAMMPS_INT_2D, LAMMPS_DOUBLE_2D, LAMMPS_INT64_2D):
|
||||
# TODO add other fields
|
||||
if name in ("x", "v", "f", "angmom", "torque", "csforce", "vforce"):
|
||||
dim = 3
|
||||
else:
|
||||
dim = 2
|
||||
else:
|
||||
dim = 1
|
||||
|
||||
raw_ptr = self.lmp.extract_atom(name, dtype)
|
||||
|
||||
if dtype in (LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D):
|
||||
return self.darray(raw_ptr, nelem, dim)
|
||||
elif dtype in (LAMMPS_INT, LAMMPS_INT_2D):
|
||||
return self.iarray(c_int32, raw_ptr, nelem, dim)
|
||||
elif dtype in (LAMMPS_INT64, LAMMPS_INT64_2D):
|
||||
return self.iarray(c_int64, raw_ptr, nelem, dim)
|
||||
return raw_ptr
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def extract_atom_iarray(self, name, nelem, dim=1):
|
||||
warnings.warn("deprecated, use extract_atom instead", DeprecationWarning)
|
||||
|
||||
if name in ['id', 'molecule']:
|
||||
c_int_type = self.lmp.c_tagint
|
||||
elif name in ['image']:
|
||||
c_int_type = self.lmp.c_imageint
|
||||
else:
|
||||
c_int_type = c_int
|
||||
|
||||
if dim == 1:
|
||||
raw_ptr = self.lmp.extract_atom(name, LAMMPS_INT)
|
||||
else:
|
||||
raw_ptr = self.lmp.extract_atom(name, LAMMPS_INT_2D)
|
||||
|
||||
return self.iarray(c_int_type, raw_ptr, nelem, dim)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def extract_atom_darray(self, name, nelem, dim=1):
|
||||
warnings.warn("deprecated, use extract_atom instead", DeprecationWarning)
|
||||
|
||||
if dim == 1:
|
||||
raw_ptr = self.lmp.extract_atom(name, LAMMPS_DOUBLE)
|
||||
else:
|
||||
raw_ptr = self.lmp.extract_atom(name, LAMMPS_DOUBLE_2D)
|
||||
|
||||
return self.darray(raw_ptr, nelem, dim)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def extract_compute(self, cid, style, type):
|
||||
"""Retrieve data from a LAMMPS compute
|
||||
|
||||
This is a wrapper around the
|
||||
:py:meth:`lammps.extract_compute() <lammps.lammps.extract_compute()>` method.
|
||||
It behaves the same as the original method, but returns NumPy arrays
|
||||
instead of ``ctypes`` pointers.
|
||||
|
||||
:param id: compute ID
|
||||
:type id: string
|
||||
:param style: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
|
||||
:type style: int
|
||||
:param type: type of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
|
||||
:type type: int
|
||||
:return: requested data either as float, as NumPy array with direct access to C data, or None
|
||||
:rtype: float, numpy.array, or NoneType
|
||||
"""
|
||||
value = self.lmp.extract_compute(cid, style, type)
|
||||
|
||||
if style in (LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL):
|
||||
if type == LMP_TYPE_VECTOR:
|
||||
nrows = self.lmp.extract_compute(cid, style, LMP_SIZE_VECTOR)
|
||||
return self.darray(value, nrows)
|
||||
elif type == LMP_TYPE_ARRAY:
|
||||
nrows = self.lmp.extract_compute(cid, style, LMP_SIZE_ROWS)
|
||||
ncols = self.lmp.extract_compute(cid, style, LMP_SIZE_COLS)
|
||||
return self.darray(value, nrows, ncols)
|
||||
elif style == LMP_STYLE_ATOM:
|
||||
if type == LMP_TYPE_VECTOR:
|
||||
nlocal = self.lmp.extract_global("nlocal")
|
||||
return self.darray(value, nlocal)
|
||||
elif type == LMP_TYPE_ARRAY:
|
||||
nlocal = self.lmp.extract_global("nlocal")
|
||||
ncols = self.lmp.extract_compute(cid, style, LMP_SIZE_COLS)
|
||||
return self.darray(value, nlocal, ncols)
|
||||
return value
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def extract_fix(self, fid, style, type, nrow=0, ncol=0):
|
||||
"""Retrieve data from a LAMMPS fix
|
||||
|
||||
This is a wrapper around the :py:meth:`lammps.extract_fix() <lammps.lammps.extract_fix()>` method.
|
||||
It behaves the same as the original method, but returns NumPy arrays
|
||||
instead of ``ctypes`` pointers.
|
||||
|
||||
:param id: fix ID
|
||||
:type id: string
|
||||
:param style: style of the data retrieve (global, atom, or local), see :ref:`py_style_constants`
|
||||
:type style: int
|
||||
:param type: type or size of the returned data (scalar, vector, or array), see :ref:`py_type_constants`
|
||||
:type type: 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
|
||||
:rtype: integer or double value, pointer to 1d or 2d double array or None
|
||||
|
||||
"""
|
||||
value = self.lmp.extract_fix(fid, style, type, nrow, ncol)
|
||||
if style == LMP_STYLE_ATOM:
|
||||
if type == LMP_TYPE_VECTOR:
|
||||
nlocal = self.lmp.extract_global("nlocal")
|
||||
return self.darray(value, nlocal)
|
||||
elif type == LMP_TYPE_ARRAY:
|
||||
nlocal = self.lmp.extract_global("nlocal")
|
||||
ncols = self.lmp.extract_fix(fid, style, LMP_SIZE_COLS, 0, 0)
|
||||
return self.darray(value, nlocal, ncols)
|
||||
elif style == LMP_STYLE_LOCAL:
|
||||
if type == LMP_TYPE_VECTOR:
|
||||
nrows = self.lmp.extract_fix(fid, style, LMP_SIZE_ROWS, 0, 0)
|
||||
return self.darray(value, nrows)
|
||||
elif type == LMP_TYPE_ARRAY:
|
||||
nrows = self.lmp.extract_fix(fid, style, LMP_SIZE_ROWS, 0, 0)
|
||||
ncols = self.lmp.extract_fix(fid, style, LMP_SIZE_COLS, 0, 0)
|
||||
return self.darray(value, nrows, ncols)
|
||||
return value
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def extract_variable(self, name, group=None, vartype=LMP_VAR_EQUAL):
|
||||
""" Evaluate a LAMMPS variable and return its data
|
||||
|
||||
This function is a wrapper around the function
|
||||
:py:meth:`lammps.extract_variable() <lammps.lammps.extract_variable()>`
|
||||
method. It behaves the same as the original method, but returns NumPy arrays
|
||||
instead of ``ctypes`` pointers.
|
||||
|
||||
:param name: name of the variable to execute
|
||||
:type name: string
|
||||
:param group: name of group for atom-style variable (ignored for equal-style variables)
|
||||
:type group: string
|
||||
:param vartype: type of variable, see :ref:`py_vartype_constants`
|
||||
:type vartype: int
|
||||
:return: the requested data or None
|
||||
:rtype: c_double, numpy.array, or NoneType
|
||||
"""
|
||||
import numpy as np
|
||||
value = self.lmp.extract_variable(name, group, vartype)
|
||||
if vartype == LMP_VAR_ATOM:
|
||||
return np.ctypeslib.as_array(value)
|
||||
return value
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def get_neighlist(self, idx):
|
||||
"""Returns an instance of :class:`NumPyNeighList` which wraps access to the neighbor list with the given index
|
||||
|
||||
:param idx: index of neighbor list
|
||||
:type idx: int
|
||||
:return: an instance of :class:`NumPyNeighList` wrapping access to neighbor list data
|
||||
:rtype: NumPyNeighList
|
||||
"""
|
||||
if idx < 0:
|
||||
return None
|
||||
return NumPyNeighList(self.lmp, idx)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def get_neighlist_element_neighbors(self, idx, element):
|
||||
"""Return data of neighbor list entry
|
||||
|
||||
This function is a wrapper around the function
|
||||
:py:meth:`lammps.get_neighlist_element_neighbors() <lammps.lammps.get_neighlist_element_neighbors()>`
|
||||
method. It behaves the same as the original method, but returns a NumPy array containing the neighbors
|
||||
instead of a ``ctypes`` pointer.
|
||||
|
||||
:param element: neighbor list index
|
||||
:type element: int
|
||||
:param element: neighbor list element index
|
||||
:type element: int
|
||||
:return: tuple with atom local index and numpy array of neighbor local atom indices
|
||||
:rtype: (int, numpy.array)
|
||||
"""
|
||||
iatom, numneigh, c_neighbors = self.lmp.get_neighlist_element_neighbors(idx, element)
|
||||
neighbors = self.iarray(c_int, c_neighbors, numneigh, 1)
|
||||
return iatom, neighbors
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
|
||||
import numpy as np
|
||||
np_int_type = self._ctype_to_numpy_int(c_int_type)
|
||||
|
||||
if dim == 1:
|
||||
ptr = cast(raw_ptr, POINTER(c_int_type * nelem))
|
||||
else:
|
||||
ptr = cast(raw_ptr[0], POINTER(c_int_type * nelem * dim))
|
||||
|
||||
a = np.frombuffer(ptr.contents, dtype=np_int_type)
|
||||
a.shape = (nelem, dim)
|
||||
return a
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def darray(self, raw_ptr, nelem, dim=1):
|
||||
import numpy as np
|
||||
if dim == 1:
|
||||
ptr = cast(raw_ptr, POINTER(c_double * nelem))
|
||||
else:
|
||||
ptr = cast(raw_ptr[0], POINTER(c_double * nelem * dim))
|
||||
|
||||
a = np.frombuffer(ptr.contents)
|
||||
a.shape = (nelem, dim)
|
||||
return a
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class NumPyNeighList(NeighList):
|
||||
"""This is a wrapper class that exposes the contents of a neighbor list.
|
||||
|
||||
It can be used like a regular Python list. Each element is a tuple of:
|
||||
|
||||
* the atom local index
|
||||
* a NumPy array containing the local atom indices of its neighbors
|
||||
|
||||
Internally it uses the lower-level LAMMPS C-library interface.
|
||||
|
||||
:param lmp: reference to instance of :py:class:`lammps`
|
||||
:type lmp: lammps
|
||||
:param idx: neighbor list index
|
||||
:type idx: int
|
||||
"""
|
||||
def __init__(self, lmp, idx):
|
||||
super(NumPyNeighList, self).__init__(lmp, idx)
|
||||
|
||||
def get(self, element):
|
||||
"""
|
||||
:return: tuple with atom local index, numpy array of neighbor local atom indices
|
||||
:rtype: (int, numpy.array)
|
||||
"""
|
||||
iatom, neighbors = self.lmp.numpy.get_neighlist_element_neighbors(self.idx, element)
|
||||
return iatom, neighbors
|
||||
861
python/lammps/pylammps.py
Normal file
861
python/lammps/pylammps.py
Normal file
@ -0,0 +1,861 @@
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# 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.
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
################################################################################
|
||||
# Alternative Python Wrapper
|
||||
# Written by Richard Berger <richard.berger@temple.edu>
|
||||
################################################################################
|
||||
|
||||
# for python2/3 compatibility
|
||||
|
||||
from __future__ import print_function
|
||||
|
||||
import os
|
||||
import re
|
||||
import select
|
||||
import sys
|
||||
from collections import namedtuple
|
||||
|
||||
from .core import lammps
|
||||
|
||||
|
||||
class OutputCapture(object):
|
||||
""" Utility class to capture LAMMPS library output """
|
||||
|
||||
def __init__(self):
|
||||
self.stdout_pipe_read, self.stdout_pipe_write = os.pipe()
|
||||
self.stdout_fd = 1
|
||||
|
||||
def __enter__(self):
|
||||
self.stdout = os.dup(self.stdout_fd)
|
||||
os.dup2(self.stdout_pipe_write, self.stdout_fd)
|
||||
return self
|
||||
|
||||
def __exit__(self, type, value, tracebac):
|
||||
os.dup2(self.stdout, self.stdout_fd)
|
||||
os.close(self.stdout)
|
||||
os.close(self.stdout_pipe_read)
|
||||
os.close(self.stdout_pipe_write)
|
||||
|
||||
# check if we have more to read from the pipe
|
||||
def more_data(self, pipe):
|
||||
r, _, _ = select.select([pipe], [], [], 0)
|
||||
return bool(r)
|
||||
|
||||
# read the whole pipe
|
||||
def read_pipe(self, pipe):
|
||||
out = ""
|
||||
while self.more_data(pipe):
|
||||
out += os.read(pipe, 1024).decode()
|
||||
return out
|
||||
|
||||
@property
|
||||
def output(self):
|
||||
return self.read_pipe(self.stdout_pipe_read)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class Variable(object):
|
||||
def __init__(self, pylammps_instance, name, style, definition):
|
||||
self._pylmp = pylammps_instance
|
||||
self.name = name
|
||||
self.style = style
|
||||
self.definition = definition.split()
|
||||
|
||||
@property
|
||||
def value(self):
|
||||
if self.style == 'atom':
|
||||
return list(self._pylmp.lmp.extract_variable(self.name, "all", 1))
|
||||
else:
|
||||
value = self._pylmp.lmp_print('"${%s}"' % self.name).strip()
|
||||
try:
|
||||
return float(value)
|
||||
except ValueError:
|
||||
return value
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class AtomList(object):
|
||||
"""
|
||||
A dynamic list of atoms that returns either an :py:class:`Atom` or
|
||||
:py:class:`Atom2D` instance for each atom. Instances are only allocated
|
||||
when accessed.
|
||||
|
||||
:ivar natoms: total number of atoms
|
||||
:ivar dimensions: number of dimensions in system
|
||||
"""
|
||||
def __init__(self, pylammps_instance):
|
||||
self._pylmp = pylammps_instance
|
||||
self.natoms = self._pylmp.system.natoms
|
||||
self.dimensions = self._pylmp.system.dimensions
|
||||
self._loaded = {}
|
||||
|
||||
def __getitem__(self, index):
|
||||
"""
|
||||
Return Atom with given local index
|
||||
|
||||
:param index: Local index of atom
|
||||
:type index: int
|
||||
:rtype: Atom or Atom2D
|
||||
"""
|
||||
if index not in self._loaded:
|
||||
if self.dimensions == 2:
|
||||
atom = Atom2D(self._pylmp, index + 1)
|
||||
else:
|
||||
atom = Atom(self._pylmp, index + 1)
|
||||
self._loaded[index] = atom
|
||||
return self._loaded[index]
|
||||
|
||||
def __len__(self):
|
||||
return self.natoms
|
||||
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class Atom(object):
|
||||
"""
|
||||
A wrapper class then represents a single atom inside of LAMMPS
|
||||
|
||||
It provides access to properties of the atom and allows you to change some of them.
|
||||
"""
|
||||
def __init__(self, pylammps_instance, index):
|
||||
self._pylmp = pylammps_instance
|
||||
self.index = index
|
||||
|
||||
@property
|
||||
def id(self):
|
||||
"""
|
||||
Return the atom ID
|
||||
|
||||
:type: int
|
||||
"""
|
||||
return int(self._pylmp.eval("id[%d]" % self.index))
|
||||
|
||||
@property
|
||||
def type(self):
|
||||
"""
|
||||
Return the atom type
|
||||
|
||||
:type: int
|
||||
"""
|
||||
return int(self._pylmp.eval("type[%d]" % self.index))
|
||||
|
||||
@property
|
||||
def mol(self):
|
||||
"""
|
||||
Return the atom molecule index
|
||||
|
||||
:type: int
|
||||
"""
|
||||
return self._pylmp.eval("mol[%d]" % self.index)
|
||||
|
||||
@property
|
||||
def mass(self):
|
||||
"""
|
||||
Return the atom mass
|
||||
|
||||
:type: float
|
||||
"""
|
||||
return self._pylmp.eval("mass[%d]" % self.index)
|
||||
|
||||
@property
|
||||
def position(self):
|
||||
"""
|
||||
:getter: Return position of atom
|
||||
:setter: Set position of atom
|
||||
:type: tuple (float, float, float)
|
||||
"""
|
||||
return (self._pylmp.eval("x[%d]" % self.index),
|
||||
self._pylmp.eval("y[%d]" % self.index),
|
||||
self._pylmp.eval("z[%d]" % self.index))
|
||||
|
||||
@position.setter
|
||||
def position(self, value):
|
||||
"""
|
||||
:getter: Return velocity of atom
|
||||
:setter: Set velocity of atom
|
||||
:type: tuple (float, float, float)
|
||||
"""
|
||||
self._pylmp.set("atom", self.index, "x", value[0])
|
||||
self._pylmp.set("atom", self.index, "y", value[1])
|
||||
self._pylmp.set("atom", self.index, "z", value[2])
|
||||
|
||||
@property
|
||||
def velocity(self):
|
||||
return (self._pylmp.eval("vx[%d]" % self.index),
|
||||
self._pylmp.eval("vy[%d]" % self.index),
|
||||
self._pylmp.eval("vz[%d]" % self.index))
|
||||
|
||||
@velocity.setter
|
||||
def velocity(self, value):
|
||||
self._pylmp.set("atom", self.index, "vx", value[0])
|
||||
self._pylmp.set("atom", self.index, "vy", value[1])
|
||||
self._pylmp.set("atom", self.index, "vz", value[2])
|
||||
|
||||
@property
|
||||
def force(self):
|
||||
"""
|
||||
Return the total force acting on the atom
|
||||
|
||||
:type: tuple (float, float, float)
|
||||
"""
|
||||
return (self._pylmp.eval("fx[%d]" % self.index),
|
||||
self._pylmp.eval("fy[%d]" % self.index),
|
||||
self._pylmp.eval("fz[%d]" % self.index))
|
||||
|
||||
@property
|
||||
def charge(self):
|
||||
"""
|
||||
Return the atom charge
|
||||
|
||||
:type: float
|
||||
"""
|
||||
return self._pylmp.eval("q[%d]" % self.index)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class Atom2D(Atom):
|
||||
"""
|
||||
A wrapper class then represents a single 2D atom inside of LAMMPS
|
||||
|
||||
Inherits all properties from the :py:class:`Atom` class, but returns 2D versions
|
||||
of position, velocity, and force.
|
||||
|
||||
It provides access to properties of the atom and allows you to change some of them.
|
||||
"""
|
||||
def __init__(self, pylammps_instance, index):
|
||||
super(Atom2D, self).__init__(pylammps_instance, index)
|
||||
|
||||
@property
|
||||
def position(self):
|
||||
"""
|
||||
:getter: Return position of atom
|
||||
:setter: Set position of atom
|
||||
:type: tuple (float, float)
|
||||
"""
|
||||
return (self._pylmp.eval("x[%d]" % self.index),
|
||||
self._pylmp.eval("y[%d]" % self.index))
|
||||
|
||||
@position.setter
|
||||
def position(self, value):
|
||||
self._pylmp.set("atom", self.index, "x", value[0])
|
||||
self._pylmp.set("atom", self.index, "y", value[1])
|
||||
|
||||
@property
|
||||
def velocity(self):
|
||||
"""
|
||||
:getter: Return velocity of atom
|
||||
:setter: Set velocity of atom
|
||||
:type: tuple (float, float)
|
||||
"""
|
||||
return (self._pylmp.eval("vx[%d]" % self.index),
|
||||
self._pylmp.eval("vy[%d]" % self.index))
|
||||
|
||||
@velocity.setter
|
||||
def velocity(self, value):
|
||||
self._pylmp.set("atom", self.index, "vx", value[0])
|
||||
self._pylmp.set("atom", self.index, "vy", value[1])
|
||||
|
||||
@property
|
||||
def force(self):
|
||||
"""
|
||||
Return the total force acting on the atom
|
||||
|
||||
:type: tuple (float, float)
|
||||
"""
|
||||
return (self._pylmp.eval("fx[%d]" % self.index),
|
||||
self._pylmp.eval("fy[%d]" % self.index))
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class variable_set:
|
||||
def __init__(self, name, variable_dict):
|
||||
self._name = name
|
||||
array_pattern = re.compile(r"(?P<arr>.+)\[(?P<index>[0-9]+)\]")
|
||||
|
||||
for key, value in variable_dict.items():
|
||||
m = array_pattern.match(key)
|
||||
if m:
|
||||
g = m.groupdict()
|
||||
varname = g['arr']
|
||||
idx = int(g['index'])
|
||||
if varname not in self.__dict__:
|
||||
self.__dict__[varname] = {}
|
||||
self.__dict__[varname][idx] = value
|
||||
else:
|
||||
self.__dict__[key] = value
|
||||
|
||||
def __str__(self):
|
||||
return "{}({})".format(self._name, ','.join(["{}={}".format(k, self.__dict__[k]) for k in self.__dict__.keys() if not k.startswith('_')]))
|
||||
|
||||
def __repr__(self):
|
||||
return self.__str__()
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
def get_thermo_data(output):
|
||||
""" traverse output of runs and extract thermo data columns """
|
||||
if isinstance(output, str):
|
||||
lines = output.splitlines()
|
||||
else:
|
||||
lines = output
|
||||
|
||||
runs = []
|
||||
columns = []
|
||||
in_run = False
|
||||
current_run = {}
|
||||
|
||||
for line in lines:
|
||||
if line.startswith("Per MPI rank memory allocation"):
|
||||
in_run = True
|
||||
elif in_run and len(columns) == 0:
|
||||
# first line after memory usage are column names
|
||||
columns = line.split()
|
||||
|
||||
current_run = {}
|
||||
|
||||
for col in columns:
|
||||
current_run[col] = []
|
||||
|
||||
elif line.startswith("Loop time of "):
|
||||
in_run = False
|
||||
columns = None
|
||||
thermo_data = variable_set('ThermoData', current_run)
|
||||
r = {'thermo' : thermo_data }
|
||||
runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
|
||||
elif in_run and len(columns) > 0:
|
||||
items = line.split()
|
||||
# Convert thermo output and store it.
|
||||
# It must have the same number of columns and
|
||||
# all of them must be convertible to floats.
|
||||
# Otherwise we ignore the line
|
||||
if len(items) == len(columns):
|
||||
try:
|
||||
values = [float(x) for x in items]
|
||||
for i, col in enumerate(columns):
|
||||
current_run[col].append(values[i])
|
||||
except ValueError:
|
||||
pass
|
||||
|
||||
return runs
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
class PyLammps(object):
|
||||
"""
|
||||
This is a Python wrapper class around the lower-level
|
||||
:py:class:`lammps` class, exposing a more Python-like,
|
||||
object-oriented interface for prototyping system inside of IPython and
|
||||
Jupyter notebooks.
|
||||
|
||||
It either creates its own instance of :py:class:`lammps` or can be
|
||||
initialized with an existing instance. The arguments are the same of the
|
||||
lower-level interface. The original interface can still be accessed via
|
||||
:py:attr:`PyLammps.lmp`.
|
||||
|
||||
: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
|
||||
|
||||
:ivar lmp: instance of original LAMMPS Python interface
|
||||
:vartype lmp: :py:class:`lammps`
|
||||
|
||||
:ivar runs: list of completed runs, each storing the thermo output
|
||||
:vartype run: list
|
||||
"""
|
||||
|
||||
def __init__(self, name="", cmdargs=None, ptr=None, comm=None):
|
||||
self.has_echo = False
|
||||
|
||||
if cmdargs:
|
||||
if '-echo' in cmdargs:
|
||||
idx = cmdargs.index('-echo')
|
||||
# ensures that echo line is ignored during output capture
|
||||
self.has_echo = idx+1 < len(cmdargs) and cmdargs[idx+1] in ('screen', 'both')
|
||||
|
||||
if ptr:
|
||||
if isinstance(ptr,PyLammps):
|
||||
self.lmp = ptr.lmp
|
||||
elif isinstance(ptr,lammps):
|
||||
self.lmp = ptr
|
||||
else:
|
||||
self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=ptr,comm=comm)
|
||||
else:
|
||||
self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=None,comm=comm)
|
||||
print("LAMMPS output is captured by PyLammps wrapper")
|
||||
self._cmd_history = []
|
||||
self.runs = []
|
||||
|
||||
def __del__(self):
|
||||
if self.lmp: self.lmp.close()
|
||||
self.lmp = None
|
||||
|
||||
def close(self):
|
||||
"""Explicitly delete a LAMMPS instance
|
||||
|
||||
This is a wrapper around the :py:meth:`lammps.close` of the Python interface.
|
||||
"""
|
||||
if self.lmp: self.lmp.close()
|
||||
self.lmp = None
|
||||
|
||||
def version(self):
|
||||
"""Return a numerical representation of the LAMMPS version in use.
|
||||
|
||||
This is a wrapper around the :py:meth:`lammps.version` function of the Python interface.
|
||||
|
||||
:return: version number
|
||||
:rtype: int
|
||||
"""
|
||||
return self.lmp.version()
|
||||
|
||||
def file(self, file):
|
||||
"""Read LAMMPS commands from a file.
|
||||
|
||||
This is a wrapper around the :py:meth:`lammps.file` function of the Python interface.
|
||||
|
||||
:param path: Name of the file/path with LAMMPS commands
|
||||
:type path: string
|
||||
"""
|
||||
self.lmp.file(file)
|
||||
|
||||
def write_script(self, filepath):
|
||||
"""
|
||||
Write LAMMPS script file containing all commands executed up until now
|
||||
|
||||
:param filepath: path to script file that should be written
|
||||
:type filepath: string
|
||||
"""
|
||||
with open(filepath, "w") as f:
|
||||
for cmd in self._cmd_history:
|
||||
print(cmd, file=f)
|
||||
|
||||
def command(self, cmd):
|
||||
"""
|
||||
Execute LAMMPS command
|
||||
|
||||
All commands executed will be stored in a command history which can be
|
||||
written to a file using :py:meth:`PyLammps.write_script()`
|
||||
|
||||
:param cmd: command string that should be executed
|
||||
:type: cmd: string
|
||||
"""
|
||||
self.lmp.command(cmd)
|
||||
self._cmd_history.append(cmd)
|
||||
|
||||
def run(self, *args, **kwargs):
|
||||
"""
|
||||
Execute LAMMPS run command with given arguments
|
||||
|
||||
All thermo output during the run is captured and saved as new entry in
|
||||
:py:attr:`PyLammps.runs`. The latest run can be retrieved by
|
||||
:py:attr:`PyLammps.last_run`.
|
||||
"""
|
||||
output = self.__getattr__('run')(*args, **kwargs)
|
||||
|
||||
comm = self.lmp.get_mpi_comm()
|
||||
if comm:
|
||||
output = self.lmp.comm.bcast(output, root=0)
|
||||
|
||||
self.runs += get_thermo_data(output)
|
||||
return output
|
||||
|
||||
@property
|
||||
def last_run(self):
|
||||
"""
|
||||
Return data produced of last completed run command
|
||||
|
||||
:getter: Returns an object containing information about the last run command
|
||||
:type: dict
|
||||
"""
|
||||
if len(self.runs) > 0:
|
||||
return self.runs[-1]
|
||||
return None
|
||||
|
||||
@property
|
||||
def atoms(self):
|
||||
"""
|
||||
All atoms of this LAMMPS instance
|
||||
|
||||
:getter: Returns a list of atoms currently in the system
|
||||
:type: AtomList
|
||||
"""
|
||||
return AtomList(self)
|
||||
|
||||
@property
|
||||
def system(self):
|
||||
"""
|
||||
The system state of this LAMMPS instance
|
||||
|
||||
:getter: Returns an object with properties storing the current system state
|
||||
:type: namedtuple
|
||||
"""
|
||||
output = self.info("system")
|
||||
d = self._parse_info_system(output)
|
||||
return namedtuple('System', d.keys())(*d.values())
|
||||
|
||||
@property
|
||||
def communication(self):
|
||||
"""
|
||||
The communication state of this LAMMPS instance
|
||||
|
||||
:getter: Returns an object with properties storing the current communication state
|
||||
:type: namedtuple
|
||||
"""
|
||||
output = self.info("communication")
|
||||
d = self._parse_info_communication(output)
|
||||
return namedtuple('Communication', d.keys())(*d.values())
|
||||
|
||||
@property
|
||||
def computes(self):
|
||||
"""
|
||||
The list of active computes of this LAMMPS instance
|
||||
|
||||
:getter: Returns a list of computes that are currently active in this LAMMPS instance
|
||||
:type: list
|
||||
"""
|
||||
output = self.info("computes")
|
||||
return self._parse_element_list(output)
|
||||
|
||||
@property
|
||||
def dumps(self):
|
||||
"""
|
||||
The list of active dumps of this LAMMPS instance
|
||||
|
||||
:getter: Returns a list of dumps that are currently active in this LAMMPS instance
|
||||
:type: list
|
||||
"""
|
||||
output = self.info("dumps")
|
||||
return self._parse_element_list(output)
|
||||
|
||||
@property
|
||||
def fixes(self):
|
||||
"""
|
||||
The list of active fixes of this LAMMPS instance
|
||||
|
||||
:getter: Returns a list of fixes that are currently active in this LAMMPS instance
|
||||
:type: list
|
||||
"""
|
||||
output = self.info("fixes")
|
||||
return self._parse_element_list(output)
|
||||
|
||||
@property
|
||||
def groups(self):
|
||||
"""
|
||||
The list of active atom groups of this LAMMPS instance
|
||||
|
||||
:getter: Returns a list of atom groups that are currently active in this LAMMPS instance
|
||||
:type: list
|
||||
"""
|
||||
output = self.info("groups")
|
||||
return self._parse_groups(output)
|
||||
|
||||
@property
|
||||
def variables(self):
|
||||
"""
|
||||
Returns a dictionary of all variables defined in the current LAMMPS instance
|
||||
|
||||
:getter: Returns a dictionary of all variables that are defined in this LAMMPS instance
|
||||
:type: dict
|
||||
"""
|
||||
output = self.info("variables")
|
||||
vars = {}
|
||||
for v in self._parse_element_list(output):
|
||||
vars[v['name']] = Variable(self, v['name'], v['style'], v['def'])
|
||||
return vars
|
||||
|
||||
def eval(self, expr):
|
||||
"""
|
||||
Evaluate expression
|
||||
|
||||
:param expr: the expression string that should be evaluated inside of LAMMPS
|
||||
:type expr: string
|
||||
|
||||
:return: the value of the evaluated expression
|
||||
:rtype: float if numeric, string otherwise
|
||||
"""
|
||||
value = self.lmp_print('"$(%s)"' % expr).strip()
|
||||
try:
|
||||
return float(value)
|
||||
except ValueError:
|
||||
return value
|
||||
|
||||
def _split_values(self, line):
|
||||
return [x.strip() for x in line.split(',')]
|
||||
|
||||
def _get_pair(self, value):
|
||||
return [x.strip() for x in value.split('=')]
|
||||
|
||||
def _parse_info_system(self, output):
|
||||
lines = output[6:-2]
|
||||
system = {}
|
||||
|
||||
for line in lines:
|
||||
if line.startswith("Units"):
|
||||
system['units'] = self._get_pair(line)[1]
|
||||
elif line.startswith("Atom style"):
|
||||
system['atom_style'] = self._get_pair(line)[1]
|
||||
elif line.startswith("Atom map"):
|
||||
system['atom_map'] = self._get_pair(line)[1]
|
||||
elif line.startswith("Atoms"):
|
||||
parts = self._split_values(line)
|
||||
system['natoms'] = int(self._get_pair(parts[0])[1])
|
||||
system['ntypes'] = int(self._get_pair(parts[1])[1])
|
||||
system['style'] = self._get_pair(parts[2])[1]
|
||||
elif line.startswith("Kspace style"):
|
||||
system['kspace_style'] = self._get_pair(line)[1]
|
||||
elif line.startswith("Dimensions"):
|
||||
system['dimensions'] = int(self._get_pair(line)[1])
|
||||
elif line.startswith("Orthogonal box"):
|
||||
system['orthogonal_box'] = [float(x) for x in self._get_pair(line)[1].split('x')]
|
||||
elif line.startswith("Boundaries"):
|
||||
system['boundaries'] = self._get_pair(line)[1]
|
||||
elif line.startswith("xlo"):
|
||||
keys, values = [self._split_values(x) for x in self._get_pair(line)]
|
||||
for key, value in zip(keys, values):
|
||||
system[key] = float(value)
|
||||
elif line.startswith("ylo"):
|
||||
keys, values = [self._split_values(x) for x in self._get_pair(line)]
|
||||
for key, value in zip(keys, values):
|
||||
system[key] = float(value)
|
||||
elif line.startswith("zlo"):
|
||||
keys, values = [self._split_values(x) for x in self._get_pair(line)]
|
||||
for key, value in zip(keys, values):
|
||||
system[key] = float(value)
|
||||
elif line.startswith("Molecule type"):
|
||||
system['molecule_type'] = self._get_pair(line)[1]
|
||||
elif line.startswith("Bonds"):
|
||||
parts = self._split_values(line)
|
||||
system['nbonds'] = int(self._get_pair(parts[0])[1])
|
||||
system['nbondtypes'] = int(self._get_pair(parts[1])[1])
|
||||
system['bond_style'] = self._get_pair(parts[2])[1]
|
||||
elif line.startswith("Angles"):
|
||||
parts = self._split_values(line)
|
||||
system['nangles'] = int(self._get_pair(parts[0])[1])
|
||||
system['nangletypes'] = int(self._get_pair(parts[1])[1])
|
||||
system['angle_style'] = self._get_pair(parts[2])[1]
|
||||
elif line.startswith("Dihedrals"):
|
||||
parts = self._split_values(line)
|
||||
system['ndihedrals'] = int(self._get_pair(parts[0])[1])
|
||||
system['ndihedraltypes'] = int(self._get_pair(parts[1])[1])
|
||||
system['dihedral_style'] = self._get_pair(parts[2])[1]
|
||||
elif line.startswith("Impropers"):
|
||||
parts = self._split_values(line)
|
||||
system['nimpropers'] = int(self._get_pair(parts[0])[1])
|
||||
system['nimpropertypes'] = int(self._get_pair(parts[1])[1])
|
||||
system['improper_style'] = self._get_pair(parts[2])[1]
|
||||
|
||||
return system
|
||||
|
||||
def _parse_info_communication(self, output):
|
||||
lines = output[6:-3]
|
||||
comm = {}
|
||||
|
||||
for line in lines:
|
||||
if line.startswith("MPI library"):
|
||||
comm['mpi_version'] = line.split(':')[1].strip()
|
||||
elif line.startswith("Comm style"):
|
||||
parts = self._split_values(line)
|
||||
comm['comm_style'] = self._get_pair(parts[0])[1]
|
||||
comm['comm_layout'] = self._get_pair(parts[1])[1]
|
||||
elif line.startswith("Processor grid"):
|
||||
comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
|
||||
elif line.startswith("Communicate velocities for ghost atoms"):
|
||||
comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
|
||||
elif line.startswith("Nprocs"):
|
||||
parts = self._split_values(line)
|
||||
comm['nprocs'] = int(self._get_pair(parts[0])[1])
|
||||
comm['nthreads'] = int(self._get_pair(parts[1])[1])
|
||||
return comm
|
||||
|
||||
def _parse_element_list(self, output):
|
||||
lines = output[6:-3]
|
||||
elements = []
|
||||
|
||||
for line in lines:
|
||||
element_info = self._split_values(line.split(':')[1].strip())
|
||||
element = {'name': element_info[0]}
|
||||
for key, value in [self._get_pair(x) for x in element_info[1:]]:
|
||||
element[key] = value
|
||||
elements.append(element)
|
||||
return elements
|
||||
|
||||
def _parse_groups(self, output):
|
||||
lines = output[6:-3]
|
||||
groups = []
|
||||
group_pattern = re.compile(r"(?P<name>.+) \((?P<type>.+)\)")
|
||||
|
||||
for line in lines:
|
||||
m = group_pattern.match(line.split(':')[1].strip())
|
||||
group = {'name': m.group('name'), 'type': m.group('type')}
|
||||
groups.append(group)
|
||||
return groups
|
||||
|
||||
def lmp_print(self, s):
|
||||
""" needed for Python2 compatibility, since print is a reserved keyword """
|
||||
return self.__getattr__("print")(s)
|
||||
|
||||
def __dir__(self):
|
||||
return ['angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'atom_style',
|
||||
'bond_coeff', 'bond_style', 'boundary', 'change_box', 'communicate', 'compute',
|
||||
'create_atoms', 'create_box', 'delete_atoms', 'delete_bonds', 'dielectric',
|
||||
'dihedral_coeff', 'dihedral_style', 'dimension', 'dump', 'fix', 'fix_modify',
|
||||
'group', 'improper_coeff', 'improper_style', 'include', 'kspace_modify',
|
||||
'kspace_style', 'lattice', 'mass', 'minimize', 'min_style', 'neighbor',
|
||||
'neigh_modify', 'newton', 'nthreads', 'pair_coeff', 'pair_modify',
|
||||
'pair_style', 'processors', 'read', 'read_data', 'read_restart', 'region',
|
||||
'replicate', 'reset_timestep', 'restart', 'run', 'run_style', 'thermo',
|
||||
'thermo_modify', 'thermo_style', 'timestep', 'undump', 'unfix', 'units',
|
||||
'variable', 'velocity', 'write_restart']
|
||||
|
||||
def __getattr__(self, name):
|
||||
"""
|
||||
This method is where the Python 'magic' happens. If a method is not
|
||||
defined by the class PyLammps, it assumes it is a LAMMPS command. It takes
|
||||
all the arguments, concatinates them to a single string, and executes it using
|
||||
:py:meth:`lammps.PyLammps.command()`.
|
||||
|
||||
:param verbose: Print output of command
|
||||
:type verbose: bool
|
||||
:return: line or list of lines of output, None if no output
|
||||
:rtype: list or string
|
||||
"""
|
||||
def handler(*args, **kwargs):
|
||||
cmd_args = [name] + [str(x) for x in args]
|
||||
|
||||
with OutputCapture() as capture:
|
||||
cmd = ' '.join(cmd_args)
|
||||
self.command(cmd)
|
||||
output = capture.output
|
||||
|
||||
if 'verbose' in kwargs and kwargs['verbose']:
|
||||
print(output)
|
||||
|
||||
lines = output.splitlines()
|
||||
|
||||
if self.has_echo:
|
||||
lines = lines[1:]
|
||||
|
||||
if len(lines) > 1:
|
||||
return lines
|
||||
elif len(lines) == 1:
|
||||
return lines[0]
|
||||
return None
|
||||
|
||||
return handler
|
||||
|
||||
|
||||
class IPyLammps(PyLammps):
|
||||
"""
|
||||
IPython wrapper for LAMMPS which adds embedded graphics capabilities to PyLammmps interface
|
||||
|
||||
It either creates its own instance of :py:class:`lammps` or can be
|
||||
initialized with an existing instance. The arguments are the same of the
|
||||
lower-level interface. The original interface can still be accessed via
|
||||
:py:attr:`PyLammps.lmp`.
|
||||
|
||||
: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
|
||||
"""
|
||||
|
||||
def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
|
||||
super(IPyLammps, self).__init__(name=name,cmdargs=cmdargs,ptr=ptr,comm=comm)
|
||||
|
||||
def image(self, filename="snapshot.png", group="all", color="type", diameter="type",
|
||||
size=None, view=None, center=None, up=None, zoom=1.0, background_color="white"):
|
||||
""" Generate image using write_dump command and display it
|
||||
|
||||
See :doc:`dump image <dump_image>` for more information.
|
||||
|
||||
:param filename: Name of the image file that should be generated. The extension determines whether it is PNG or JPEG
|
||||
:type filename: string
|
||||
:param group: the group of atoms write_image should use
|
||||
:type group: string
|
||||
:param color: name of property used to determine color
|
||||
:type color: string
|
||||
:param diameter: name of property used to determine atom diameter
|
||||
:type diameter: string
|
||||
:param size: dimensions of image
|
||||
:type size: tuple (width, height)
|
||||
:param view: view parameters
|
||||
:type view: tuple (theta, phi)
|
||||
:param center: center parameters
|
||||
:type center: tuple (flag, center_x, center_y, center_z)
|
||||
:param up: vector pointing to up direction
|
||||
:type up: tuple (up_x, up_y, up_z)
|
||||
:param zoom: zoom factor
|
||||
:type zoom: float
|
||||
:param background_color: background color of scene
|
||||
:type background_color: string
|
||||
|
||||
:return: Image instance used to display image in notebook
|
||||
:rtype: :py:class:`IPython.core.display.Image`
|
||||
"""
|
||||
cmd_args = [group, "image", filename, color, diameter]
|
||||
|
||||
if size:
|
||||
width = size[0]
|
||||
height = size[1]
|
||||
cmd_args += ["size", width, height]
|
||||
|
||||
if view:
|
||||
theta = view[0]
|
||||
phi = view[1]
|
||||
cmd_args += ["view", theta, phi]
|
||||
|
||||
if center:
|
||||
flag = center[0]
|
||||
Cx = center[1]
|
||||
Cy = center[2]
|
||||
Cz = center[3]
|
||||
cmd_args += ["center", flag, Cx, Cy, Cz]
|
||||
|
||||
if up:
|
||||
Ux = up[0]
|
||||
Uy = up[1]
|
||||
Uz = up[2]
|
||||
cmd_args += ["up", Ux, Uy, Uz]
|
||||
|
||||
if zoom:
|
||||
cmd_args += ["zoom", zoom]
|
||||
|
||||
cmd_args.append("modify backcolor " + background_color)
|
||||
|
||||
self.write_dump(*cmd_args)
|
||||
from IPython.core.display import Image
|
||||
return Image(filename)
|
||||
|
||||
def video(self, filename):
|
||||
"""
|
||||
Load video from file
|
||||
|
||||
Can be used to visualize videos from :doc:`dump movie <dump_image>`.
|
||||
|
||||
:param filename: Path to video file
|
||||
:type filename: string
|
||||
:return: HTML Video Tag used by notebook to embed a video
|
||||
:rtype: :py:class:`IPython.display.HTML`
|
||||
"""
|
||||
from IPython.display import HTML
|
||||
return HTML("<video controls><source src=\"" + filename + "\"></video>")
|
||||
26
python/setup.py
Normal file
26
python/setup.py
Normal file
@ -0,0 +1,26 @@
|
||||
# this only installs the LAMMPS python package
|
||||
# it assumes the LAMMPS shared library is already installed
|
||||
from distutils.core import setup
|
||||
import os
|
||||
|
||||
LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
|
||||
LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
|
||||
LAMMPS_SOURCE_DIR = os.path.join(LAMMPS_DIR, 'src')
|
||||
|
||||
def get_lammps_version():
|
||||
with open(os.path.join(LAMMPS_SOURCE_DIR, 'version.h'), 'r') as f:
|
||||
line = f.readline()
|
||||
start_pos = line.find('"')+1
|
||||
end_pos = line.find('"', start_pos)
|
||||
return "".join(line[start_pos:end_pos].split())
|
||||
|
||||
setup(
|
||||
name = "lammps",
|
||||
version = get_lammps_version(),
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "https://lammps.sandia.gov",
|
||||
description = "LAMMPS Molecular Dynamics Python package",
|
||||
license = "GPL",
|
||||
packages=["lammps"]
|
||||
)
|
||||
Reference in New Issue
Block a user