lammps.py
382de5034188lammm-devel

lammps.py
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			# ----------------------------------------------------------------------
			# 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.
			# -------------------------------------------------------------------------

			# Python wrappers on LAMMPS library via ctypes

			# for python3 compatibility

			from __future__ import print_function

			# imports for simple LAMMPS python wrapper module "lammps"

			import sys,traceback,types
			from ctypes import *
			from os.path import dirname,abspath,join
			from inspect import getsourcefile

			# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"

			from collections import namedtuple
			import os
			import select
			import re
			import sys

			def get_ctypes_int(size):
			if size == 4:
			return c_int32
			elif size == 8:
			return c_int64
			return c_int

			class MPIAbortException(Exception):
			def __init__(self, message):
			self.message = message

			def __str__(self):
			return repr(self.message)


			class lammps(object):

			# detect if Python is using version of mpi4py that can pass a communicator

			has_mpi4py_v2 = False
			try:
			from mpi4py import MPI
			from mpi4py import __version__ as mpi4py_version
			if mpi4py_version.split('.')[0] == '2':
			has_mpi4py_v2 = True
			except:
			pass

			# create instance of LAMMPS

			def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
			self.comm = comm
			self.opened = 0

			# determine module location

			modpath = dirname(abspath(getsourcefile(lambda:0)))
			self.lib = None

			# if a pointer to a LAMMPS object is handed in,
			# all symbols should already be available

			try:
			if ptr: self.lib = CDLL("",RTLD_GLOBAL)
			except:
			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 lammps.py 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

			if not self.lib:
			try:
			if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
			else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),
			RTLD_GLOBAL)
			except:
			if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
			else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)

			# if no ptr provided, create an instance of LAMMPS
			# don't know how to pass an MPI communicator from PyPar
			# but 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 not ptr:

			# with mpi4py v2, can pass MPI communicator to LAMMPS
			# need to adjust for type of MPI communicator object
			# allow for int (like MPICH) or void* (like OpenMPI)

			if lammps.has_mpi4py_v2 and comm != None:
			if lammps.MPI._sizeof(lammps.MPI.Comm) == sizeof(c_int):
			MPI_Comm = c_int
			else:
			MPI_Comm = c_void_p

			narg = 0
			cargs = 0
			if cmdargs:
			cmdargs.insert(0,"lammps.py")
			narg = len(cmdargs)
			for i in range(narg):
			if type(cmdargs[i]) is str:
			cmdargs[i] = cmdargs[i].encode()
			cargs = (c_char_pnarg)(cmdargs)
			self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
			MPI_Comm, c_void_p()]
			else:
			self.lib.lammps_open.argtypes = [c_int, c_int, \
			MPI_Comm, c_void_p()]

			self.lib.lammps_open.restype = None
			self.opened = 1
			self.lmp = c_void_p()
			comm_ptr = lammps.MPI._addressof(comm)
			comm_val = MPI_Comm.from_address(comm_ptr)
			self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))

			else:
			self.opened = 1
			if cmdargs:
			cmdargs.insert(0,"lammps.py")
			narg = len(cmdargs)
			for i in range(narg):
			if type(cmdargs[i]) is str:
			cmdargs[i] = cmdargs[i].encode()
			cargs = (c_char_pnarg)(cmdargs)
			self.lmp = c_void_p()
			self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
			else:
			self.lmp = c_void_p()
			self.lib.lammps_open_no_mpi(0,None,byref(self.lmp))
			# could use just this if LAMMPS lib interface supported it
			# self.lmp = self.lib.lammps_open_no_mpi(0,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))

			# optional numpy support (lazy loading)
			self._numpy = None

			# set default types
			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"))

			def __del__(self):
			if self.lmp and self.opened:
			self.lib.lammps_close(self.lmp)
			self.opened = 0

			def close(self):
			if self.opened: self.lib.lammps_close(self.lmp)
			self.lmp = None
			self.opened = 0

			def version(self):
			return self.lib.lammps_version(self.lmp)

			def file(self,file):
			if file: file = file.encode()
			self.lib.lammps_file(self.lmp,file)

			# send a single command

			def command(self,cmd):
			if cmd: cmd = cmd.encode()
			self.lib.lammps_command(self.lmp,cmd)

			if self.uses_exceptions and self.lib.lammps_has_error(self.lmp):
			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:
			raise MPIAbortException(error_msg)
			raise Exception(error_msg)

			# send a list of commands

			def commands_list(self,cmdlist):
			cmds = [x.encode() for x in cmdlist if type(x) is str]
			args = (c_char_p * len(cmdlist))(*cmds)
			self.lib.lammps_commands_list(self.lmp,len(cmdlist),args)

			# send a string of commands

			def commands_string(self,multicmd):
			if type(multicmd) is str:
			multicmd = multicmd.encode()
			self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))

			# extract global info

			def extract_global(self,name,type):
			if name: name = name.encode()
			if type == 0:
			self.lib.lammps_extract_global.restype = POINTER(c_int)
			elif type == 1:
			self.lib.lammps_extract_global.restype = POINTER(c_double)
			else: return None
			ptr = self.lib.lammps_extract_global(self.lmp,name)
			return ptr[0]

			# extract per-atom info

			def extract_atom(self,name,type):
			if name: name = name.encode()
			if type == 0:
			self.lib.lammps_extract_atom.restype = POINTER(c_int)
			elif type == 1:
			self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int))
			elif type == 2:
			self.lib.lammps_extract_atom.restype = POINTER(c_double)
			elif type == 3:
			self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
			else: return None
			ptr = self.lib.lammps_extract_atom(self.lmp,name)
			return ptr

			# extract lammps type byte sizes

			def extract_setting(self, name):
			if name: name = name.encode()
			self.lib.lammps_extract_atom.restype = c_int
			return int(self.lib.lammps_extract_setting(self.lmp,name))

			@property
			def numpy(self):
			if not self._numpy:
			import numpy as np
			class LammpsNumpyWrapper:
			def __init__(self, lmp):
			self.lmp = lmp

			def extract_atom_iarray(self, name, nelem, dim=1):
			if dim == 1:
			tmp = self.lmp.extract_atom(name, 0)
			ptr = cast(tmp, POINTER(c_int * nelem))
			else:
			tmp = self.lmp.extract_atom(name, 1)
			ptr = cast(tmp[0], POINTER(c_int * nelem * dim))

			a = np.frombuffer(ptr.contents, dtype=np.intc)
			a.shape = (nelem, dim)
			return a

			def extract_atom_darray(self, name, nelem, dim=1):
			if dim == 1:
			tmp = self.lmp.extract_atom(name, 2)
			ptr = cast(tmp, POINTER(c_double * nelem))
			else:
			tmp = self.lmp.extract_atom(name, 3)
			ptr = cast(tmp[0], POINTER(c_double * nelem * dim))

			a = np.frombuffer(ptr.contents)
			a.shape = (nelem, dim)
			return a

			self._numpy = LammpsNumpyWrapper(self)
			return self._numpy

			# extract compute info

			def extract_compute(self,id,style,type):
			if id: id = id.encode()
			if type == 0:
			if style > 0: return None
			self.lib.lammps_extract_compute.restype = POINTER(c_double)
			ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
			return ptr[0]
			if type == 1:
			self.lib.lammps_extract_compute.restype = POINTER(c_double)
			ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
			return ptr
			if type == 2:
			self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
			ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
			return ptr
			return None

			# extract fix info
			# in case of global datum, free memory for 1 double via lammps_free()
			# double was allocated by library interface function

			def extract_fix(self,id,style,type,i=0,j=0):
			if id: id = id.encode()
			if style == 0:
			self.lib.lammps_extract_fix.restype = POINTER(c_double)
			ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
			result = ptr[0]
			self.lib.lammps_free(ptr)
			return result
			elif (style == 1) or (style == 2):
			if type == 1:
			self.lib.lammps_extract_fix.restype = POINTER(c_double)
			elif type == 2:
			self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
			else:
			return None
			ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
			return ptr
			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,type):
			if name: name = name.encode()
			if group: group = group.encode()
			if type == 0:
			self.lib.lammps_extract_variable.restype = POINTER(c_double)
			ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
			result = ptr[0]
			self.lib.lammps_free(ptr)
			return result
			if type == 1:
			self.lib.lammps_extract_global.restype = POINTER(c_int)
			nlocalptr = self.lib.lammps_extract_global(self.lmp,"nlocal".encode())
			nlocal = nlocalptr[0]
			result = (c_double*nlocal)()
			self.lib.lammps_extract_variable.restype = POINTER(c_double)
			ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
			for i in range(nlocal): result[i] = ptr[i]
			self.lib.lammps_free(ptr)
			return result
			return None

			# set variable value
			# value is converted to string
			# returns 0 for success, -1 if failed

			def set_variable(self,name,value):
			if name: name = name.encode()
			if value: value = str(value).encode()
			return self.lib.lammps_set_variable(self.lmp,name,value)

			# return current value of thermo keyword

			def get_thermo(self,name):
			if name: name = name.encode()
			self.lib.lammps_get_thermo.restype = c_double
			return self.lib.lammps_get_thermo(self.lmp,name)

			# return total number of atoms in system

			def get_natoms(self):
			return self.lib.lammps_get_natoms(self.lmp)

			# return vector of atom properties gathered across procs, ordered by atom ID
			# 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: how could we insure are converting to correct Python type
			# e.g. for Python list or NumPy, etc
			# ditto for extact_atom() above

			def gather_atoms(self,name,type,count):
			if name: name = name.encode()
			natoms = self.lib.lammps_get_natoms(self.lmp)
			if type == 0:
			data = ((countnatoms)c_int)()
			self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
			elif type == 1:
			data = ((countnatoms)c_double)()
			self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
			else: return None
			return data

			# scatter vector of atom properties across procs, ordered by atom ID
			# 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: how could we insure are passing correct type to LAMMPS
			# e.g. for Python list or NumPy, etc

			def scatter_atoms(self,name,type,count,data):
			if name: name = name.encode()
			self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)

			# 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 insure 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,image=None,shrinkexceed=False):
			if id:
			id_lmp = (c_int * n)()
			id_lmp[:] = id
			else:
			id_lmp = id

			if image:
			image_lmp = (c_int * n)()
			image_lmp[:] = image
			else:
			image_lmp = image

			type_lmp = (c_int * n)()
			type_lmp[:] = type
			self.lib.lammps_create_atoms(self.lmp,n,id_lmp,type_lmp,x,v,image_lmp,shrinkexceed)


			@property
			def uses_exceptions(self):
			""" Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """
			try:
			if self.lib.lammps_has_error:
			return True
			except(AttributeError):
			return False

			# -------------------------------------------------------------------------
			# -------------------------------------------------------------------------
			# -------------------------------------------------------------------------

			################################################################################
			# Alternative Python Wrapper
			# Written by Richard Berger <richard.berger@temple.edu>
			################################################################################

			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, lammps_wrapper_instance, name, style, definition):
			self.wrapper = lammps_wrapper_instance
			self.name = name
			self.style = style
			self.definition = definition.split()

			@property
			def value(self):
			if self.style == 'atom':
			return list(self.wrapper.lmp.extract_variable(self.name, "all", 1))
			else:
			value = self.wrapper.lmp_print('"${%s}"' % self.name).strip()
			try:
			return float(value)
			except ValueError:
			return value


			class AtomList(object):
			def __init__(self, lammps_wrapper_instance):
			self.lmp = lammps_wrapper_instance
			self.natoms = self.lmp.system.natoms
			self.dimensions = self.lmp.system.dimensions

			def __getitem__(self, index):
			if self.dimensions == 2:
			return Atom2D(self.lmp, index + 1)
			return Atom(self.lmp, index + 1)


			class Atom(object):
			def __init__(self, lammps_wrapper_instance, index):
			self.lmp = lammps_wrapper_instance
			self.index = index

			@property
			def id(self):
			return int(self.lmp.eval("id[%d]" % self.index))

			@property
			def type(self):
			return int(self.lmp.eval("type[%d]" % self.index))

			@property
			def mol(self):
			return self.lmp.eval("mol[%d]" % self.index)

			@property
			def mass(self):
			return self.lmp.eval("mass[%d]" % self.index)

			@property
			def position(self):
			return (self.lmp.eval("x[%d]" % self.index),
			self.lmp.eval("y[%d]" % self.index),
			self.lmp.eval("z[%d]" % self.index))

			@position.setter
			def position(self, value):
			self.lmp.set("atom", self.index, "x", value[0])
			self.lmp.set("atom", self.index, "y", value[1])
			self.lmp.set("atom", self.index, "z", value[2])

			@property
			def velocity(self):
			return (self.lmp.eval("vx[%d]" % self.index),
			self.lmp.eval("vy[%d]" % self.index),
			self.lmp.eval("vz[%d]" % self.index))

			@property
			def force(self):
			return (self.lmp.eval("fx[%d]" % self.index),
			self.lmp.eval("fy[%d]" % self.index),
			self.lmp.eval("fz[%d]" % self.index))

			@property
			def charge(self):
			return self.lmp.eval("q[%d]" % self.index)


			class Atom2D(Atom):
			def __init__(self, lammps_wrapper_instance, index):
			super(Atom2D, self).__init__(lammps_wrapper_instance, index)

			@property
			def position(self):
			return (self.lmp.eval("x[%d]" % self.index),
			self.lmp.eval("y[%d]" % self.index))

			@position.setter
			def position(self, value):
			self.lmp.set("atom", self.index, "x", value[0])
			self.lmp.set("atom", self.index, "y", value[1])

			@property
			def velocity(self):
			return (self.lmp.eval("vx[%d]" % self.index),
			self.lmp.eval("vy[%d]" % self.index))

			@property
			def force(self):
			return (self.lmp.eval("fx[%d]" % self.index),
			self.lmp.eval("fy[%d]" % self.index))


			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 = namedtuple('ThermoData', list(current_run.keys()))(*list(current_run.values()))
			r = {'thermo' : thermo_data }
			runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
			elif in_run and len(columns) > 0:
			values = [float(x) for x in line.split()]

			for i, col in enumerate(columns):
			current_run[col].append(values[i])
			return runs

			class PyLammps(object):
			"""
			More Python-like wrapper for LAMMPS (e.g., for iPython)
			See examples/ipython for usage
			"""

			def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
			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):
			if self.lmp: self.lmp.close()
			self.lmp = None

			def version(self):
			return self.lmp.version()

			def file(self,file):
			self.lmp.file(file)

			def write_script(self,filename):
			""" Write LAMMPS script file containing all commands executed up until now """
			with open(filename, "w") as f:
			for cmd in self._cmd_history:
			f.write("%s\n" % cmd)

			def command(self,cmd):
			self.lmp.command(cmd)
			self._cmd_history.append(cmd)

			def run(self, args, *kwargs):
			output = self.__getattr__('run')(args, *kwargs)
			self.runs += get_thermo_data(output)
			return output

			@property
			def last_run(self):
			if len(self.runs) > 0:
			return self.runs[-1]
			return None

			@property
			def atoms(self):
			return AtomList(self)

			@property
			def system(self):
			output = self.info("system")
			d = self._parse_info_system(output)
			return namedtuple('System', d.keys())(*d.values())

			@property
			def communication(self):
			output = self.info("communication")
			d = self._parse_info_communication(output)
			return namedtuple('Communication', d.keys())(*d.values())

			@property
			def computes(self):
			output = self.info("computes")
			return self._parse_element_list(output)

			@property
			def dumps(self):
			output = self.info("dumps")
			return self._parse_element_list(output)

			@property
			def fixes(self):
			output = self.info("fixes")
			return self._parse_element_list(output)

			@property
			def groups(self):
			output = self.info("groups")
			return self._parse_groups(output)

			@property
			def variables(self):
			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):
			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['nangletypes'] = 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):
			def handler(args, *kwargs):
			cmd_args = [name] + [str(x) for x in args]

			with OutputCapture() as capture:
			self.command(' '.join(cmd_args))
			output = capture.output

			if 'verbose' in kwargs and kwargs['verbose']:
			print(output)

			lines = output.splitlines()

			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
			"""

			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):
			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 white")

			self.write_dump(*cmd_args)
			from IPython.core.display import Image
			return Image('snapshot.png')

			def video(self, filename):
			from IPython.display import HTML
			return HTML("<video controls><source src=\"" + filename + "\"></video>")

lammps/python/lammps.py382de5034188lammm-devel

lammps.pyView Options

lammps/python/lammps.py
382de5034188lammm-devel

lammps.py
View Options