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_p*narg)(*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_p*narg)(*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 _ctype_to_numpy_int(self, ctype_int):
if ctype_int == c_int32:
return np.int32
elif ctype_int == c_int64:
return np.int64
return np.intc
def extract_atom_iarray(self, name, nelem, dim=1):
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
np_int_type = self._ctype_to_numpy_int(c_int_type)
if dim == 1:
tmp = self.lmp.extract_atom(name, 0)
ptr = cast(tmp, POINTER(c_int_type * nelem))
else:
tmp = self.lmp.extract_atom(name, 1)
ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
a = np.frombuffer(ptr.contents, dtype=np_int_type)
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 = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
elif type == 1:
data = ((count*natoms)*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
import sys, os, unittest
from lammps import lammps
has_mpi = False
has_mpi4py = False
has_exceptions = False
try:
from mpi4py import __version__ as mpi4py_version
# tested to work with mpi4py versions 2 and 3
has_mpi4py = mpi4py_version.split('.')[0] in ['2', '3']
except:
pass
try:
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine = os.environ['LAMMPS_MACHINE_NAME']
else:
machine = ""
lmp = lammps(name=machine)
has_mpi = lmp.has_mpi_support
has_exceptions = lmp.has_exceptions
lmp.close()
except:
pass
class PythonOpen(unittest.TestCase):
def setUp(self):
self.machine = None
if 'LAMMPS_MACHINE_NAME' in os.environ:
self.machine = os.environ['LAMMPS_MACHINE_NAME']
class lammps:
# 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):
# determine module location
modpath = dirname(abspath(getsourcefile(lambda:0)))
# load liblammps.so by default
# if name = "g++", load liblammps_g++.so
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:
type,value,tb = sys.exc_info()
traceback.print_exception(type,value,tb)
raise OSError,"Could not load LAMMPS dynamic library from %s" % modpath
# 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)
cargs = (c_char_p*narg)(*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)
cargs = (c_char_p*narg)(*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:
self.opened = 0
# magic to convert ptr to ctypes ptr
pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
def __del__(self):
if self.lmp and self.opened: self.lib.lammps_close(self.lmp)
def close(self):
if self.opened: self.lib.lammps_close(self.lmp)
self.lmp = None
def version(self):
return self.lib.lammps_version(self.lmp)
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 == 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]
def extract_atom(self,name,type):
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
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]
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
# 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 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
# 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
# set variable value
# value is converted to string
# returns 0 for success, -1 if failed
def set_variable(self,name,value):
return self.lib.lammps_set_variable(self.lmp,name,str(value))
# 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
def gather_atoms(self,name,type,count):
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
elif type == 1:
data = ((count*natoms)*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
# assume vector is of correct type and length, as created by gather_atoms()
def scatter_atoms(self,name,type,count,data):
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py = False
try:
from mpi4py import MPI
from mpi4py import __version__ as mpi4py_version
if mpi4py_version.split('.')[0] in ['2','3']: has_mpi4py = 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 any([f.startswith('liblammps') and f.endswith('.dylib') for f in os.listdir(modpath)]):
lib_ext = ".dylib"
else:
lib_ext = ".so"
if not self.lib:
try:
if not name: self.lib = CDLL(join(modpath,"liblammps" + lib_ext),RTLD_GLOBAL)
else: self.lib = CDLL(join(modpath,"liblammps_%s" % name + lib_ext),
RTLD_GLOBAL)
except:
if not name: self.lib = CDLL("liblammps" + lib_ext,RTLD_GLOBAL)
else: self.lib = CDLL("liblammps_%s" % name + lib_ext,RTLD_GLOBAL)
# define ctypes API for each library method
# NOTE: should add one of these for each lib function
self.lib.lammps_extract_box.argtypes = \
[c_void_p,POINTER(c_double),POINTER(c_double),
POINTER(c_double),POINTER(c_double),POINTER(c_double),
POINTER(c_int),POINTER(c_int)]
self.lib.lammps_extract_box.restype = None
self.lib.lammps_reset_box.argtypes = \
[c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
self.lib.lammps_reset_box.restype = None
self.lib.lammps_gather_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.restype = None
self.lib.lammps_gather_atoms_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.restype = None
self.lib.lammps_gather_atoms_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_atoms_subset.restype = None
self.lib.lammps_scatter_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.restype = None
self.lib.lammps_scatter_atoms_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_scatter_atoms_subset.restype = None
# 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 comm:
if not lammps.has_mpi4py:
raise Exception('Python mpi4py version is not 2 or 3')
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_p*narg)(*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:
if lammps.has_mpi4py:
from mpi4py import MPI
self.comm = MPI.COMM_WORLD
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_p*narg)(*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"))
self._installed_packages = None
# add way to insert Python callback for fix external
self.callback = {}
self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
self.lib.lammps_set_fix_external_callback.restype = None
# shut-down LAMMPS instance
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.has_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 lammps type byte sizes
def extract_setting(self, name):
if name: name = name.encode()
self.lib.lammps_extract_setting.restype = c_int
return int(self.lib.lammps_extract_setting(self.lmp,name))
# 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 global info
def extract_box(self):
boxlo = (3*c_double)()
boxhi = (3*c_double)()
xy = c_double()
yz = c_double()
xz = c_double()
periodicity = (3*c_int)()
box_change = c_int()
self.lib.lammps_extract_box(self.lmp,boxlo,boxhi,
byref(xy),byref(yz),byref(xz),
periodicity,byref(box_change))
boxlo = boxlo[:3]
boxhi = boxhi[:3]
xy = xy.value
yz = yz.value
xz = xz.value
periodicity = periodicity[:3]
box_change = box_change.value
return boxlo,boxhi,xy,yz,xz,periodicity,box_change
# extract per-atom info
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
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
@property
def numpy(self):
if not self._numpy:
import numpy as np
class LammpsNumpyWrapper:
def __init__(self, lmp):
self.lmp = lmp
def _ctype_to_numpy_int(self, ctype_int):
if ctype_int == c_int32:
return np.int32
elif ctype_int == c_int64:
return np.int64
return np.intc
def extract_atom_iarray(self, name, nelem, dim=1):
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
np_int_type = self._ctype_to_numpy_int(c_int_type)
if dim == 1:
tmp = self.lmp.extract_atom(name, 0)
ptr = cast(tmp, POINTER(c_int_type * nelem))
else:
tmp = self.lmp.extract_atom(name, 1)
ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
a = np.frombuffer(ptr.contents, dtype=np_int_type)
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:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr[0]
else if style == 1:
return None
else if style == 2:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
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
# 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)
# 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)
# reset simulation box size
def reset_box(self,boxlo,boxhi,xy,yz,xz):
cboxlo = (3*c_double)(*boxlo)
cboxhi = (3*c_double)(*boxhi)
self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz)
# return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def gather_atoms(self,name,type,count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
elif type == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
else: return None
return data
def gather_atoms_concat(self,name,type,count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
elif type == 1:
data = ((count*natoms)*c_double)()
self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data)
else: return None
return data
def gather_atoms_subset(self,name,type,count,ndata,ids):
if name: name = name.encode()
if type == 0:
data = ((count*ndata)*c_int)()
self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
elif type == 1:
data = ((count*ndata)*c_double)()
self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data)
else: return None
return data
# scatter vector of atom properties across procs
# 2 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def scatter_atoms(self,name,type,count,data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
def scatter_atoms_subset(self,name,type,count,ndata,ids,data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,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 has_exceptions(self):
""" Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """
return self.lib.lammps_config_has_exceptions() != 0
@property
def has_gzip_support(self):
return self.lib.lammps_config_has_gzip_support() != 0
@property
def has_png_support(self):
return self.lib.lammps_config_has_png_support() != 0
@property
def has_jpeg_support(self):
return self.lib.lammps_config_has_jpeg_support() != 0
@property
def has_ffmpeg_support(self):
return self.lib.lammps_config_has_ffmpeg_support() != 0
@property
def installed_packages(self):
if self._installed_packages is None:
self._installed_packages = []
npackages = self.lib.lammps_config_package_count()
sb = create_string_buffer(100)
for idx in range(npackages):
self.lib.lammps_config_package_name(idx, sb, 100)
self._installed_packages.append(sb.value.decode())
return self._installed_packages
def set_fix_external_callback(self, fix_name, callback, caller=None):
import numpy as np
def _ctype_to_numpy_int(ctype_int):
if ctype_int == c_int32:
return np.int32
elif ctype_int == c_int64:
return np.int64
return np.intc
def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
if cast(caller_ptr,POINTER(py_object)).contents:
pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
else:
pyCallerObj = None
tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
tag.shape = (nlocal)
xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
x = np.frombuffer(xptr.contents)
x.shape = (nlocal, 3)
fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
f = np.frombuffer(fptr.contents)
f.shape = (nlocal, 3)
callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
cFunc = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
cCaller = cast(pointer(py_object(caller)), c_void_p)
self.callback[fix_name] = { 'function': cFunc, 'caller': caller }
self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller)
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_p*narg)(*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_p*narg)(*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
pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
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)
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)
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]
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
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
# 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
# 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,str(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
def gather_atoms(self,name,type,count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count*natoms)*c_int)()
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
elif type == 1:
data = ((count*natoms)*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
# assume vector is of correct type and length, as created by gather_atoms()
def scatter_atoms(self,name,type,count,data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
@property
def uses_exceptions(self):
try:
if self.lib.lammps_has_error:
return True
except(AttributeError):
return False
class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py = False
try:
from mpi4py import MPI
from mpi4py import __version__ as mpi4py_version
if mpi4py_version.split('.')[0] in ['2', '3']: has_mpi4py = True
except:
pass
# create instance of LAMMPS
#<<<<<<< master
# def __init__(self, infile, label="", mesh=100., dmtol=0.001, \
#=======
def __init__(self, infile, label="", \
constraints=[], tdir="./", lunit="Ang", eunit="eV", md2ang=0.06466, \
name="", cmdargs=args.split(), 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)
# define ctypes API for each library method
# NOTE: should add one of these for each lib function
self.lib.lammps_extract_box.argtypes = \
[c_void_p, POINTER(c_double), POINTER(c_double),
POINTER(c_double), POINTER(c_double), POINTER(c_double),
POINTER(c_int), POINTER(c_int)]
self.lib.lammps_extract_box.restype = None
self.lib.lammps_reset_box.argtypes = \
[c_void_p, POINTER(c_double), POINTER(c_double), c_double, c_double, c_double]
self.lib.lammps_reset_box.restype = None
self.lib.lammps_gather_atoms.argtypes = \
[c_void_p, c_char_p, c_int, c_int, c_void_p]
self.lib.lammps_gather_atoms.restype = None
self.lib.lammps_gather_atoms_concat.argtypes = \
[c_void_p, c_char_p, c_int, c_int, c_void_p]
self.lib.lammps_gather_atoms_concat.restype = None
self.lib.lammps_gather_atoms_subset.argtypes = \
[c_void_p, c_char_p, c_int, c_int, c_int, POINTER(c_int), c_void_p]
self.lib.lammps_gather_atoms_subset.restype = None
self.lib.lammps_scatter_atoms.argtypes = \
[c_void_p, c_char_p, c_int, c_int, c_void_p]
self.lib.lammps_scatter_atoms.restype = None
self.lib.lammps_scatter_atoms_subset.argtypes = \
[c_void_p, c_char_p, c_int, c_int, c_int, POINTER(c_int), c_void_p]
self.lib.lammps_scatter_atoms_subset.restype = None
# 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 comm:
if not lammps.has_mpi4py:
raise Exception('Python mpi4py version is not 2 or 3')
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_p * narg)(*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:
if lammps.has_mpi4py:
from mpi4py import MPI
self.comm = MPI.COMM_WORLD
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_p * narg)(*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"))
self._installed_packages = None
self.infile = infile
self.md2ang = md2ang
self.constraints = constraints
self.label = label
self.lunit = lunit
self.eunit = eunit
#start lammps
self.start()
def start(self, np=1):
print("lammps launched")
#todo:better to set the unit to metals here again
self.command("units metal")
lines = open(self.infile, 'r').readlines()
for line in lines:
self.command(line)
self.type = N.array(self.gather_atoms("type", 0, 1))
#self.mass = N.array(self.gather_atoms("mass",1,1))
self.mass = self.extract_atom("mass", 2)
self.els = []
for type in self.type:
self.els.append(self.mass[type])
self.xyz = self.gather_atoms("x", 1, 3)
self.newxyz = self.gather_atoms("x", 1, 3)
self.conv = self.md2ang * N.array(
[3 * [1.0 / N.sqrt(mass)] for mass in self.els]).flatten()
self.number = self.get_natoms()
#<<<<<<< Updated upstream
#<<<<<<< master
#=======
# #conversion factor from eV/Ang (force from lammps)
# #to the intermal unit of MD
# #todo
# #self.els = self.extract_atom("mass",2)
# self.els = self.gather_atoms("mass",1,1)
# print("self.els:",self.els[1])
# #self.conv = self.md2ang*N.array([3*[1.0/N.sqrt(AtomicMassTable[a])]\
# # for a in self.els]).flatten()
# self.conv = 1.
#>>>>>>> master
#=======
#conversion factor from eV/Ang (force from lammps)
#to the intermal unit of MD
#todo
#self.els = self.extract_atom("mass",2)
#self.els = self.gather_atoms("mass",1,1)
#print("self.els:",self.els[1])
#self.conv = self.md2ang*N.array([3*[1.0/N.sqrt(AtomicMassTable[a])]\
# for a in self.els]).flatten()
#self.conv = 1.
self.type = N.array(self.gather_atoms("type", 0, 1))
#self.mass = N.array(self.gather_atoms("mass",1,1))
self.mass = self.extract_atom("mass", 2)
self.els = []
for type in self.type:
self.els.append(self.mass[type])
self.xyz = self.gather_atoms("x", 1, 3)
self.newxyz = self.gather_atoms("x", 1, 3)
self.conv = self.md2ang * N.array(
[3 * [1.0 / N.sqrt(mass)] for mass in self.els]).flatten()
self.axyz = []
for i, a in enumerate(self.els):
self.axyz.append([
get_atomname(a), self.xyz[i * 3], self.xyz[i * 3 + 1],
self.xyz[i * 3 + 2]
])
#print(self.conv.shape)
self.initforce()
def quit(self):
self.close()
print("Quit lammps!")
def newx(self, q):
for i in range(3 * self.number):
self.newxyz[i] = self.xyz[i] + self.conv[i] * q[i]
return self.newxyz
def absforce(self, q):
self.scatter_atoms("x", 1, 3, self.newx(q))
self.command("run 1")
return self.conv * N.array(self.gather_atoms("f", 1, 3))
def initforce(self):
print("Calculate zero displacement force")
extq = N.zeros(3 * self.number)
self.f0 = self.absforce(extq)
#print(self.f0)
def force(self, q):
f = self.absforce(q) - self.f0
return f
#----------------------------------------------------------------------
# send a single command
def command(self, cmd):
if cmd: cmd = cmd.encode()
self.lib.lammps_command(self.lmp, cmd)
if self.has_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 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))
# 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 global info
def extract_box(self):
boxlo = (3 * c_double)()
boxhi = (3 * c_double)()
xy = c_double()
yz = c_double()
xz = c_double()
periodicity = (3 * c_int)()
box_change = c_int()
self.lib.lammps_extract_box(self.lmp, boxlo, boxhi, byref(xy),
byref(yz), byref(xz), periodicity,
byref(box_change))
boxlo = boxlo[:3]
boxhi = boxhi[:3]
xy = xy.value
yz = yz.value
xz = xz.value
periodicity = periodicity[:3]
box_change = box_change.value
return boxlo, boxhi, xy, yz, xz, periodicity, box_change
# extract per-atom info
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
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
# shut-down LAMMPS instance
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)
@property
def numpy(self):
if not self._numpy:
import numpy as np
class LammpsNumpyWrapper:
def __init__(self, lmp):
self.lmp = lmp
def _ctype_to_numpy_int(self, ctype_int):
if ctype_int == c_int32:
return np.int32
elif ctype_int == c_int64:
return np.int64
return np.intc
def extract_atom_iarray(self, name, nelem, dim=1):
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
np_int_type = self._ctype_to_numpy_int(c_int_type)
if dim == 1:
tmp = self.lmp.extract_atom(name, 0)
ptr = cast(tmp, POINTER(c_int_type * nelem))
else:
tmp = self.lmp.extract_atom(name, 1)
ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
a = np.frombuffer(ptr.contents, dtype=np_int_type)
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:
if style == 0:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_compute(self.lmp, id, style,
type)
return ptr[0]
else:
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
# 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)
# 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)
# reset simulation box size
def reset_box(self, boxlo, boxhi, xy, yz, xz):
cboxlo = (3 * c_double)(*boxlo)
cboxhi = (3 * c_double)(*boxhi)
self.lib.lammps_reset_box(self.lmp, cboxlo, cboxhi, xy, yz, xz)
# return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def gather_atoms(self, name, type, count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count * natoms) * c_int)()
self.lib.lammps_gather_atoms(self.lmp, name, type, count, data)
elif type == 1:
data = ((count * natoms) * c_double)()
self.lib.lammps_gather_atoms(self.lmp, name, type, count, data)
else:
return None
return data
def gather_atoms_concat(self, name, type, count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
if type == 0:
data = ((count * natoms) * c_int)()
self.lib.lammps_gather_atoms_concat(self.lmp, name, type, count,
data)
elif type == 1:
data = ((count * natoms) * c_double)()
self.lib.lammps_gather_atoms_concat(self.lmp, name, type, count,
data)
else:
return None
return data
def gather_atoms_subset(self, name, type, count, ndata, ids):
if name: name = name.encode()
if type == 0:
data = ((count * ndata) * c_int)()
self.lib.lammps_gather_atoms_subset(self.lmp, name, type, count,
ndata, ids, data)
elif type == 1:
data = ((count * ndata) * c_double)()
self.lib.lammps_gather_atoms_subset(self.lmp, name, type, count,
ndata, ids, data)
else:
return None
return data
# scatter vector of atom properties across procs
# 2 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
# type = 0 for integer values, 1 for double values
# count = number of per-atom valus, 1 for type or charge, 3 for x or f
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
def scatter_atoms(self, name, type, count, data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp, name, type, count, data)
def scatter_atoms_subset(self, name, type, count, ndata, ids, data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms_subset(self.lmp, name, type, count,
ndata, ids, 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 has_exceptions(self):
""" Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """
return self.lib.lammps_config_has_exceptions() != 0
@property
def has_gzip_support(self):
return self.lib.lammps_config_has_gzip_support() != 0
@property
def has_png_support(self):
return self.lib.lammps_config_has_png_support() != 0
@property
def has_jpeg_support(self):
return self.lib.lammps_config_has_jpeg_support() != 0
@property
def has_ffmpeg_support(self):
return self.lib.lammps_config_has_ffmpeg_support() != 0
@property
def installed_packages(self): #
if self._installed_packages is None:
self._installed_packages = []
npackages = self.lib.lammps_config_package_count()
sb = create_string_buffer(100)
for idx in range(npackages):
self.lib.lammps_config_package_name(idx, sb, 100)
self._installed_packages.append(sb.value.decode())
return self._installed_packages
