def _perform_common_init_tasks():
from hoomd_script import update
from hoomd_script import group
from hoomd_script import compute
# create the sorter
globals.sorter = update.sort()
# create the default compute.thermo on the all group
util._disable_status_lines = True
all = group.all()
compute._get_unique_thermo(group=all)
util._disable_status_lines = False
# set up Communicator, and register it with the System
if hoomd.is_MPI_available():
cpp_decomposition = globals.system_definition.getParticleData(
).getDomainDecomposition()
if cpp_decomposition is not None:
# create the c++ Communicator
if not globals.exec_conf.isCUDAEnabled():
cpp_communicator = hoomd.Communicator(
globals.system_definition, cpp_decomposition)
else:
cpp_communicator = hoomd.CommunicatorGPU(
globals.system_definition, cpp_decomposition)
# set Communicator in C++ System
globals.system.setCommunicator(cpp_communicator)
def _perform_common_init_tasks():
from hoomd_script import update
from hoomd_script import group
from hoomd_script import compute
# create the sorter
globals.sorter = update.sort()
# create the default compute.thermo on the all group
util._disable_status_lines = True
all = group.all()
compute._get_unique_thermo(group=all)
util._disable_status_lines = False
# set up Communicator, and register it with the System
if hoomd.is_MPI_available():
cpp_decomposition = globals.system_definition.getParticleData().getDomainDecomposition()
if cpp_decomposition is not None:
# create the c++ Communicator
if not globals.exec_conf.isCUDAEnabled():
cpp_communicator = hoomd.Communicator(globals.system_definition, cpp_decomposition)
else:
cpp_communicator = hoomd.CommunicatorGPU(globals.system_definition, cpp_decomposition)
# set Communicator in C++ System
globals.system.setCommunicator(cpp_communicator)
def _perform_common_init_tasks():
from hoomd_script import update;
from hoomd_script import group;
from hoomd_script import compute;
# create the sorter, using the evil import __main__ trick to provide the user with a default variable
import __main__;
__main__.sorter = update.sort();
# create the default compute.thermo on the all group
util._disable_status_lines = True;
all = group.all();
compute._get_unique_thermo(group=all);
util._disable_status_lines = False;
# set up Communicator, and register it with the System
if hoomd.is_MPI_available():
cpp_decomposition = globals.system_definition.getParticleData().getDomainDecomposition();
if cpp_decomposition is not None:
# create the c++ Communicator
if not globals.exec_conf.isCUDAEnabled():
cpp_communicator = hoomd.Communicator(globals.system_definition, cpp_decomposition)
else:
cpp_communicator = hoomd.CommunicatorGPU(globals.system_definition, cpp_decomposition)
# set Communicator in C++ System
globals.system.setCommunicator(cpp_communicator)
def __init__(self, T, period=1):
util.print_status_line();
# initialize base class
_updater.__init__(self);
# setup the variant inputs
T = variant._setup_variant_input(T);
# create the compute thermo
thermo = compute._get_unique_thermo(group=globals.group_all);
# create the c++ mirror class
self.cpp_updater = hoomd.TempRescaleUpdater(globals.system_definition, thermo.cpp_compute, T.cpp_variant);
self.setupUpdater(period);
def __init__(self, group, P, tau, bk, mode, dt, period=1):
util.print_status_line();
# initialize base class
_updater.__init__(self);
# setup the variant inputs
P = variant._setup_variant_input(P);
# create the compute thermo
thermo_all = compute._get_unique_thermo(group=globals.group_all);
# Get deltaT
deltaT = dt;
# initialize the reflected c++ class
if not globals.exec_conf.isCUDAEnabled():
if (mode == "isotropic"):
cpp_mode = _custom_updaters.PressBerendsenUpdater.integrationMode.isotropic;
elif (mode == "anisotropic"):
cpp_mode = _custom_updaters.PressBerendsenUpdater.integrationMode.anisotropic;
elif (mode == "semi-isotropic"):
cpp_mode = _custom_updaters.PressBerendsenUpdater.integrationMode.semi_isotropic;
elif (mode == "uniaxial"):
cpp_mode = _custom_updaters.PressBerendsenUpdater.integrationMode.one_dimensional;
else:
print >> sys.stderr, "\n***Error! Invalid mode\n";
raise RuntimeError("Error changing parameters in update.press_berendsen");
self.cpp_updater = _custom_updaters.PressBerendsenUpdater(globals.system_definition, group.cpp_group, thermo_all.cpp_compute, tau, P.cpp_variant, bk, deltaT, cpp_mode);
else:
if (mode == "isotropic"):
cpp_mode = _custom_updaters.PressBerendsenUpdaterGPU.integrationMode.isotropic;
elif (mode == "anisotropic"):
cpp_mode = _custom_updaters.PressBerendsenUpdaterGPU.integrationMode.anisotropic;
elif (mode == "semi-isotropic"):
cpp_mode = _custom_updaters.PressBerendsenUpdaterGPU.integrationMode.semi_isotropic;
elif (mode == "uniaxial"):
cpp_mode = _custom_updaters.PressBerendsenUpdaterGPU.integrationMode.one_dimensional;
else:
print >> sys.stderr, "\n***Error! Invalid mode\n";
raise RuntimeError("Error changing parameters in update.press_berendsen");
self.cpp_updater = _custom_updaters.PressBerendsenUpdaterGPU(globals.system_definition, group.cpp_group, thermo_all.cpp_compute, tau, P.cpp_variant, bk, deltaT, cpp_mode);
self.setupUpdater(period);
def __init__(self, T, period=1):
util.print_status_line()
# Error out in MPI simulations
if hoomd.is_MPI_available():
if globals.system_definition.getParticleData().getDomainDecomposition():
globals.msg.error("update.rescale_temp not supported in multi-processor simulations.\n\n")
raise RuntimeError("Error setting up updater.")
# initialize base class
_updater.__init__(self)
# setup the variant inputs
T = variant._setup_variant_input(T)
# create the compute thermo
thermo = compute._get_unique_thermo(group=globals.group_all)
# create the c++ mirror class
self.cpp_updater = hoomd.TempRescaleUpdater(globals.system_definition, thermo.cpp_compute, T.cpp_variant)
self.setupUpdater(period)
def __init__(self, T, period=1):
util.print_status_line();
# Error out in MPI simulations
if (hoomd.is_MPI_available()):
if globals.system_definition.getParticleData().getDomainDecomposition():
globals.msg.error("update.rescale_temp not supported in multi-processor simulations.\n\n")
raise RuntimeError("Error setting up updater.")
# initialize base class
_updater.__init__(self);
# setup the variant inputs
T = variant._setup_variant_input(T);
# create the compute thermo
thermo = compute._get_unique_thermo(group=globals.group_all);
# create the c++ mirror class
self.cpp_updater = hoomd.TempRescaleUpdater(globals.system_definition, thermo.cpp_compute, T.cpp_variant);
self.setupUpdater(period);
def __init__(self, group, T, tau, dt, period=1):
util.print_status_line();
# initialize base class
_updater.__init__(self);
# setup the variant inputs
T = variant._setup_variant_input(T);
# create the compute thermo
thermo = compute._get_unique_thermo(group = group);
# Get deltaT
deltaT = dt;
# initialize the reflected c++ class
if not globals.exec_conf.isCUDAEnabled():
self.cpp_updater = _custom_updaters.TempBerendsenUpdater(globals.system_definition,group.cpp_group,thermo.cpp_compute,tau,T.cpp_variant,deltaT);
else:
self.cpp_updater = _custom_updaters.TempBerendsenUpdaterGPU(globals.system_definition,group.cpp_group,thermo.cpp_compute,tau,T.cpp_variant,deltaT);
self.setupUpdater(period);
def __init__(self, T, period=1, phase=-1):
util.print_status_line()
# initialize base class
_updater.__init__(self)
# setup the variant inputs
T = variant._setup_variant_input(T)
# create the compute thermo
thermo = compute._get_unique_thermo(group=globals.group_all)
# create the c++ mirror class
self.cpp_updater = hoomd.TempRescaleUpdater(globals.system_definition,
thermo.cpp_compute,
T.cpp_variant)
self.setupUpdater(period, phase)
# store metadta
self.T = T
self.period = period
self.metadata_fields = ['T', 'period']
