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This commit is contained in:
Axel Kohlmeyer
2018-04-19 18:30:51 -04:00
parent f1ee46cc64
commit 164537cf37
1 changed files with 25 additions and 25 deletions
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50
python/lammps.py
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@ -5,7 +5,7 @@
# #
# Copyright (2003) Sandia Corporation. Under the terms of Contract # Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under # certain rights in this software. This software is distributed under
# the GNU General Public License. # the GNU General Public License.
# #
# See the README file in the top-level LAMMPS directory. # See the README file in the top-level LAMMPS directory.
@ -37,7 +37,7 @@ def get_ctypes_int(size):
return c_int32 return c_int32
elif size == 8: elif size == 8:
return c_int64 return c_int64
return c_int return c_int
class MPIAbortException(Exception): class MPIAbortException(Exception):
def __init__(self, message): def __init__(self, message):
@ -47,7 +47,7 @@ class MPIAbortException(Exception):
return repr(self.message) return repr(self.message)
class lammps(object): class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator # detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py = False has_mpi4py = False
@ -71,7 +71,7 @@ class lammps(object):
# if a pointer to a LAMMPS object is handed in, # if a pointer to a LAMMPS object is handed in,
# all symbols should already be available # all symbols should already be available
try: try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL) if ptr: self.lib = CDLL("",RTLD_GLOBAL)
except: except:
@ -84,7 +84,7 @@ class lammps(object):
# so that LD_LIBRARY_PATH does not need to be set for regular install # so that LD_LIBRARY_PATH does not need to be set for regular install
# fall back to loading with a relative path, # fall back to loading with a relative path,
# typically requires LD_LIBRARY_PATH to be set appropriately # typically requires LD_LIBRARY_PATH to be set appropriately
if not self.lib: if not self.lib:
try: try:
if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL) if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
@ -110,15 +110,15 @@ class lammps(object):
self.lib.lammps_gather_atoms.argtypes = \ self.lib.lammps_gather_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p] [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.restype = None
self.lib.lammps_gather_atoms_concat.argtypes = \ self.lib.lammps_gather_atoms_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p] [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_concat.restype = None
self.lib.lammps_gather_atoms_subset.argtypes = \ 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] [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_gather_atoms_subset.restype = None
self.lib.lammps_scatter_atoms.argtypes = \ self.lib.lammps_scatter_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p] [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.restype = None
@ -137,7 +137,7 @@ class lammps(object):
# just convert it to ctypes ptr and store in self.lmp # just convert it to ctypes ptr and store in self.lmp
if not ptr: if not ptr:
# with mpi4py v2, can pass MPI communicator to LAMMPS # with mpi4py v2, can pass MPI communicator to LAMMPS
# need to adjust for type of MPI communicator object # need to adjust for type of MPI communicator object
# allow for int (like MPICH) or void* (like OpenMPI) # allow for int (like MPICH) or void* (like OpenMPI)
@ -211,7 +211,7 @@ class lammps(object):
self.c_imageint = get_ctypes_int(self.extract_setting("imageint")) self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
# shut-down LAMMPS instance # shut-down LAMMPS instance
def __del__(self): def __del__(self):
if self.lmp and self.opened: if self.lmp and self.opened:
self.lib.lammps_close(self.lmp) self.lib.lammps_close(self.lmp)
@ -230,7 +230,7 @@ class lammps(object):
self.lib.lammps_file(self.lmp,file) self.lib.lammps_file(self.lmp,file)
# send a single command # send a single command
def command(self,cmd): def command(self,cmd):
if cmd: cmd = cmd.encode() if cmd: cmd = cmd.encode()
self.lib.lammps_command(self.lmp,cmd) self.lib.lammps_command(self.lmp,cmd)
@ -250,13 +250,13 @@ class lammps(object):
cmds = [x.encode() for x in cmdlist if type(x) is str] cmds = [x.encode() for x in cmdlist if type(x) is str]
args = (c_char_p * len(cmdlist))(*cmds) args = (c_char_p * len(cmdlist))(*cmds)
self.lib.lammps_commands_list(self.lmp,len(cmdlist),args) self.lib.lammps_commands_list(self.lmp,len(cmdlist),args)
# send a string of commands # send a string of commands
def commands_string(self,multicmd): def commands_string(self,multicmd):
if type(multicmd) is str: multicmd = multicmd.encode() if type(multicmd) is str: multicmd = multicmd.encode()
self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd)) self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))
# extract lammps type byte sizes # extract lammps type byte sizes
def extract_setting(self, name): def extract_setting(self, name):
@ -265,7 +265,7 @@ class lammps(object):
return int(self.lib.lammps_extract_setting(self.lmp,name)) return int(self.lib.lammps_extract_setting(self.lmp,name))
# extract global info # extract global info
def extract_global(self,name,type): def extract_global(self,name,type):
if name: name = name.encode() if name: name = name.encode()
if type == 0: if type == 0:
@ -277,7 +277,7 @@ class lammps(object):
return ptr[0] return ptr[0]
# extract global info # extract global info
def extract_box(self): def extract_box(self):
boxlo = (3*c_double)() boxlo = (3*c_double)()
boxhi = (3*c_double)() boxhi = (3*c_double)()
@ -286,11 +286,11 @@ class lammps(object):
xz = c_double() xz = c_double()
periodicity = (3*c_int)() periodicity = (3*c_int)()
box_change = c_int() box_change = c_int()
self.lib.lammps_extract_box(self.lmp,boxlo,boxhi, self.lib.lammps_extract_box(self.lmp,boxlo,boxhi,
byref(xy),byref(yz),byref(xz), byref(xy),byref(yz),byref(xz),
periodicity,byref(box_change)) periodicity,byref(box_change))
boxlo = boxlo[:3] boxlo = boxlo[:3]
boxhi = boxhi[:3] boxhi = boxhi[:3]
xy = xy.value xy = xy.value
@ -298,9 +298,9 @@ class lammps(object):
xz = xz.value xz = xz.value
periodicity = periodicity[:3] periodicity = periodicity[:3]
box_change = box_change.value box_change = box_change.value
return boxlo,boxhi,xy,yz,xz,periodicity,box_change return boxlo,boxhi,xy,yz,xz,periodicity,box_change
# extract per-atom info # extract per-atom info
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
@ -318,7 +318,7 @@ class lammps(object):
else: return None else: return None
ptr = self.lib.lammps_extract_atom(self.lmp,name) ptr = self.lib.lammps_extract_atom(self.lmp,name)
return ptr return ptr
@property @property
def numpy(self): def numpy(self):
if not self._numpy: if not self._numpy:
@ -371,7 +371,7 @@ class lammps(object):
return self._numpy return self._numpy
# extract compute info # extract compute info
def extract_compute(self,id,style,type): def extract_compute(self,id,style,type):
if id: id = id.encode() if id: id = id.encode()
if type == 0: if type == 0:
@ -466,7 +466,7 @@ class lammps(object):
cboxlo = (3*c_double)(*boxlo) cboxlo = (3*c_double)(*boxlo)
cboxhi = (3*c_double)(*boxhi) cboxhi = (3*c_double)(*boxhi)
self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz) self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz)
# return vector of atom properties gathered across procs # return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp # 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract() # name = atom property recognized by LAMMPS in atom->extract()
@ -475,7 +475,7 @@ class lammps(object):
# returned data is a 1d vector - doc how it is ordered? # returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
def gather_atoms(self,name,type,count): def gather_atoms(self,name,type,count):
if name: name = name.encode() if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp) natoms = self.lib.lammps_get_natoms(self.lmp)
@ -487,7 +487,7 @@ class lammps(object):
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
else: return None else: return None
return data return data
def gather_atoms_concat(self,name,type,count): def gather_atoms_concat(self,name,type,count):
if name: name = name.encode() if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp) natoms = self.lib.lammps_get_natoms(self.lmp)
@ -519,7 +519,7 @@ class lammps(object):
# assume data is of correct type and length, as created by gather_atoms() # assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to insure are converting to/from correct Python type # NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes # e.g. for Python list or NumPy or ctypes
def scatter_atoms(self,name,type,count,data): def scatter_atoms(self,name,type,count,data):
if name: name = name.encode() if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)