def __init__(self, file, type, nlist):
c = hoomd.cite.article(
cite_key='lin2017',
author=['L Yang', 'F Zhang', 'K M Ho', 'C Z Wang', 'A Travesset'],
title='Implementation of EAM and FS potentials in HOOMD-blue',
journal='Computer Physics Communications',
volume=0,
number=0,
pages='0--0',
year='2017',
doi='0',
feature='EAM')
hoomd.cite._ensure_global_bib().add(c)
hoomd.util.print_status_line()
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData(
).getDomainDecomposition():
hoomd.context.msg.error(
"pair.eam is not supported in multi-processor simulations.\n\n"
)
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
force._force.__init__(self)
# Translate type
if (type == 'Alloy'): type_of_file = 0
elif (type == 'FS'): type_of_file = 1
else: raise RuntimeError('Unknown EAM input file type')
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metal.EAMForceCompute(
hoomd.context.current.system_definition, file, type_of_file)
else:
self.cpp_force = _metal.EAMForceComputeGPU(
hoomd.context.current.system_definition, file, type_of_file)
#After load EAMForceCompute we know r_cut from EAM potential`s file. We need update neighbor list.
self.r_cut_new = self.cpp_force.get_r_cut()
self.nlist = nlist
self.nlist.subscribe(lambda: self.get_rcut())
self.nlist.update_rcut()
#Load neighbor list to compute.
self.cpp_force.set_neighbor_list(self.nlist.cpp_nlist)
if hoomd.context.exec_conf.isCUDAEnabled():
self.nlist.cpp_nlist.setStorageMode(
_md.NeighborList.storageMode.full)
hoomd.context.msg.notice(
2, "Set r_cut = " + str(self.r_cut_new) +
" from potential`s file '" + str(file) + "'.\n")
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
self.pair_coeff = hoomd.md.pair.coeff()
def __init__(self, file, type, nlist):
# Error out in MPI simulations
if (hoomd.version.mpi_enabled):
if hoomd.context.current.system_definition.getParticleData(
).getDomainDecomposition():
hoomd.context.current.device.cpp_msg.error(
"pair.eam is not supported in multi-processor simulations.\n\n"
)
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
force._force.__init__(self)
# Translate type
if (type == 'Alloy'):
type_of_file = 0
elif (type == 'FS'):
type_of_file = 1
else:
raise RuntimeError('Unknown EAM input file type')
# create the c++ mirror class
if not hoomd.context.current.device.cpp_exec_conf.isCUDAEnabled():
self.cpp_force = _metal.EAMForceCompute(
hoomd.context.current.system_definition, file, type_of_file)
else:
self.cpp_force = _metal.EAMForceComputeGPU(
hoomd.context.current.system_definition, file, type_of_file)
#After load EAMForceCompute we know r_cut from EAM potential`s file. We need update neighbor list.
self.r_cut_new = self.cpp_force.get_r_cut()
self.nlist = nlist
self.nlist.subscribe(lambda: self.get_rcut())
self.nlist.update_rcut()
#Load neighbor list to compute.
self.cpp_force.set_neighbor_list(self.nlist.cpp_nlist)
if hoomd.context.current.device.cpp_exec_conf.isCUDAEnabled():
self.nlist.cpp_nlist.setStorageMode(
_md.NeighborList.storageMode.full)
hoomd.context.current.device.cpp_msg.notice(
2, "Set r_cut = " + str(self.r_cut_new) +
" from potential`s file '" + str(file) + "'.\n")
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
self.pair_coeff = hoomd.md.pair.coeff()
def __init__(self, file, type, nlist):
c = hoomd.cite.article(
cite_key='morozov2011',
author=[
'I V Morozov', 'A M Kazennova', 'R G Bystryia', 'G E Normana',
'V V Pisareva', 'V V Stegailova'
],
title=
'Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs',
journal='Computer Physics Communications',
volume=182,
number=9,
pages='1974--1978',
year='2011',
doi='10.1016/j.cpc.2010.12.026',
feature='EAM')
hoomd.cite._ensure_global_bib().add(c)
hoomd.util.print_status_line()
# Error out in MPI simulations
if (_hoomd.is_MPI_available()):
if hoomd.context.current.system_definition.getParticleData(
).getDomainDecomposition():
hoomd.context.msg.error(
"pair.eam is not supported in multi-processor simulations.\n\n"
)
raise RuntimeError("Error setting up pair potential.")
# initialize the base class
force._force.__init__(self)
# Translate type
if (type == 'Alloy'): type_of_file = 0
elif (type == 'FS'): type_of_file = 1
else: raise RuntimeError('Unknown EAM input file type')
# create the c++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metal.EAMForceCompute(
hoomd.context.current.system_definition, file, type_of_file)
else:
self.cpp_force = _metal.EAMForceComputeGPU(
hoomd.context.current.system_definition, file, type_of_file)
#After load EAMForceCompute we know r_cut from EAM potential`s file. We need update neighbor list.
r_cut_new = self.cpp_force.get_r_cut()
self.nlist = nlist
self.nlist.subscribe(lambda: r_cut_new)
self.nlist.update_rcut()
#Load neighbor list to compute.
self.cpp_force.set_neighbor_list(self.nlist)
if hoomd.context.exec_conf.isCUDAEnabled():
self.nlist.setStorageMode(_md.NeighborList.storageMode.full)
hoomd.context.msg.notice(
2, "Set r_cut = " + str(r_cut_new) + " from potential`s file '" +
str(file) + "'.\n")
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
self.pair_coeff = coeff()