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lammps.py
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Sat, Jul 6, 19:56

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 wrapper on LAMMPS library via ctypes
import types
from ctypes import *
LMPINT = 0
LMPDOUBLE = 1
LMPIPTR = 2
LMPDPTR = 3
LMPDPTRPTR = 4
class lammps:
def __init__(self,args=None):
# attempt to load parallel library first, serial library next
# could provide caller a flag to choose which library to load
try:
self.lib = CDLL("_lammps.so")
except:
try:
self.lib = CDLL("_lammps_serial.so")
except:
raise OSError,"Could not load LAMMPS dynamic library"
# create an instance of LAMMPS
# don't know how to pass an MPI communicator from PyPar
# no_mpi call lets LAMMPS use MPI_COMM_WORLD
# cargs = array of C strings from args
if args:
args.insert(0,"lammps.py")
narg = len(args)
cargs = (c_char_p*narg)(*args)
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)
def __del__(self):
if self.lmp: self.lib.lammps_close(self.lmp)
def close(self):
self.lib.lammps_close(self.lmp)
self.lmp = None
def file(self,file):
self.lib.lammps_file(self.lmp,file)
def command(self,cmd):
self.lib.lammps_command(self.lmp,cmd)
def extract_global(self,name,type):
if type == LMPDOUBLE:
self.lib.lammps_extract_global.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_global(self.lmp,name)
return ptr[0]
if type == LMPINT:
self.lib.lammps_extract_global.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_global(self.lmp,name)
return ptr[0]
return None
def extract_atom(self,name,type):
if type == LMPDPTRPTR:
self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
ptr = self.lib.lammps_extract_atom(self.lmp,name)
return ptr
if type == LMPDPTR:
self.lib.lammps_extract_atom.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_atom(self.lmp,name)
return ptr
if type == LMPIPTR:
self.lib.lammps_extract_atom.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_atom(self.lmp,name)
return ptr
return None
def extract_compute(self,id,style,type):
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]
elif type == 1:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr
elif 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
# 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 type == 0:
if style > 0: return None
self.lib.lammps_extract_fix.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_bix(self.lmp,id,style,type,i,j)
result = ptr[0]
self.lib.lammps_free(ptr)
return result
elif type == 1:
self.lib.lammps_extract_fix.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr
elif type == 2:
self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr
return None
# 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 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")
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 xrange(nlocal): result[i] = ptr[i]
self.lib.lammps_free(ptr)
return result
return None
def get_natoms(self):
return self.lib.lammps_get_natoms(self.lmp)
def get_coords(self):
nlen = 3 * self.lib.lammps_get_natoms(self.lmp)
coords = (c_double*nlen)()
self.lib.lammps_get_coords(self.lmp,coords)
return coords
# assume coords is an array of c_double, as created by get_coords()
# could check if it is some other Python object and create c_double array?
# constructor for c_double array can take an arg to use to fill it?
def put_coords(self,coords):
self.lib.lammps_put_coords(self.lmp,coords)

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