def set_params(self, T=None):
util.print_status_line();
self.check_initialization();
if T is not None:
T = variant._setup_variant_input(T);
self.cpp_updater.setT(T.cpp_variant);
def set_params(self, T=None):
util.print_status_line()
self.check_initialization()
# change the parameters
if T is not None:
# setup the variant inputs
T = variant._setup_variant_input(T)
self.cpp_force.setT(T.cpp_variant)
def __init__(self, Lx = None, Ly = None, Lz = None, xy = None, xz = None, yz = None, period = 1, L = None, phase=-1):
util.print_status_line();
# initialize base class
_updater.__init__(self);
self.metadata_fields = ['period']
if L is not None:
Lx = L;
Ly = L;
Lz = L;
if Lx is None and Ly is None and Lz is None and xy is None and xz is None and yz is None:
globals.msg.warning("update.box_resize: Ignoring request to setup updater without parameters\n")
return
box = globals.system_definition.getParticleData().getGlobalBox();
# setup arguments
if Lx is None:
Lx = box.getL().x;
if Ly is None:
Ly = box.getL().y;
if Lz is None:
Lz = box.getL().z;
if xy is None:
xy = box.getTiltFactorXY();
if xz is None:
xz = box.getTiltFactorXZ();
if yz is None:
yz = box.getTiltFactorYZ();
Lx = variant._setup_variant_input(Lx);
Ly = variant._setup_variant_input(Ly);
Lz = variant._setup_variant_input(Lz);
xy = variant._setup_variant_input(xy);
xz = variant._setup_variant_input(xz);
yz = variant._setup_variant_input(yz);
# store metadata
self.Lx = Lx
self.Ly = Ly
self.Lz = Lz
self.xy = xy
self.xz = xz
self.yz = yz
self.metadata_fields = ['Lx','Ly','Lz','xy','xz','yz']
# create the c++ mirror class
self.cpp_updater = hoomd.BoxResizeUpdater(globals.system_definition, Lx.cpp_variant, Ly.cpp_variant, Lz.cpp_variant,
xy.cpp_variant, xz.cpp_variant, yz.cpp_variant);
if period is None:
self.cpp_updater.update(globals.system.getCurrentTimeStep());
else:
self.setupUpdater(period, phase);
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, Lx=None, Ly=None, Lz=None, xy=None, xz=None, yz=None, period=1):
util.print_status_line()
# initialize base class
_updater.__init__(self)
if Lx is None and Ly is None and Lz is None and xy is None and xz is None and yz is None:
globals.msg.warning("update.box_resize: Ignoring request to setup updater without parameters\n")
return
# setup arguments
if Lx is None:
# use current box length in x-direction
Lx = globals.system_definition.getParticleData().getGlobalBox().getL().x
if Ly is None:
Ly = Lx
if Lz is None:
Lz = Lx
if xy is None:
xy = 0.0
if xz is None:
xz = 0.0
if yz is None:
yz = 0.0
Lx = variant._setup_variant_input(Lx)
Ly = variant._setup_variant_input(Ly)
Lz = variant._setup_variant_input(Lz)
xy = variant._setup_variant_input(xy)
xz = variant._setup_variant_input(xz)
yz = variant._setup_variant_input(yz)
# create the c++ mirror class
self.cpp_updater = hoomd.BoxResizeUpdater(
globals.system_definition,
Lx.cpp_variant,
Ly.cpp_variant,
Lz.cpp_variant,
xy.cpp_variant,
xz.cpp_variant,
yz.cpp_variant,
)
if period is None:
self.cpp_updater.update(globals.system.getCurrentTimeStep())
else:
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, Lx = None, Ly = None, Lz = None, xy = None, xz = None, yz = None, period = 1, L = None):
util.print_status_line();
# initialize base class
_updater.__init__(self);
if L is not None:
Lx = L;
Ly = L;
Lz = L;
if Lx is None and Ly is None and Lz is None and xy is None and xz is None and yz is None:
globals.msg.warning("update.box_resize: Ignoring request to setup updater without parameters\n")
return
box = globals.system_definition.getParticleData().getGlobalBox();
# setup arguments
if Lx is None:
Lx = box.getL().x;
if Ly is None:
Ly = box.getL().y;
if Lz is None:
Lz = box.getL().z;
if xy is None:
xy = box.getTiltFactorXY();
if xz is None:
xz = box.getTiltFactorXZ();
if yz is None:
yz = box.getTiltFactorYZ();
Lx = variant._setup_variant_input(Lx);
Ly = variant._setup_variant_input(Ly);
Lz = variant._setup_variant_input(Lz);
xy = variant._setup_variant_input(xy);
xz = variant._setup_variant_input(xz);
yz = variant._setup_variant_input(yz);
# create the c++ mirror class
self.cpp_updater = hoomd.BoxResizeUpdater(globals.system_definition, Lx.cpp_variant, Ly.cpp_variant, Lz.cpp_variant,
xy.cpp_variant, xz.cpp_variant, yz.cpp_variant);
if period is None:
self.cpp_updater.update(globals.system.getCurrentTimeStep());
else:
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']
def __init__(self, r_cut, T, seed=1, name=None):
util.print_status_line()
# tell the base class how we operate
# initialize the base class
pair.pair.__init__(self, r_cut, name)
# update the neighbor list
neighbor_list = pair._update_global_nlist(r_cut)
neighbor_list.subscribe(lambda: self.log * self.get_max_rcut())
# create the c++ mirror class
if globals.exec_conf.isCUDAEnabled():
self.cpp_force = _custom_pair_potentials.PotentialPairLoweThermoLowe(
globals.system_definition, neighbor_list.cpp_nlist, self.name)
self.cpp_class = _custom_pair_potentials.PotentialPairLoweThermoLowe
else:
neighbor_list.cpp_nlist.setStorageMode(
hoomd.NeighborList.storageMode.full)
self.cpp_force = _custom_pair_potentials.PotentialPairLoweThermoLoweGPU(
globals.system_definition, neighbor_list.cpp_nlist, self.name)
self.cpp_class = _custom_pair_potentials.PotentialPairLoweThermoLoweGPU
self.cpp_force.setBlockSize(
tune._get_optimal_block_size('pair.dpd'))
globals.system.addCompute(self.cpp_force, self.force_name)
# setup the coefficent options
self.required_coeffs = ['A', 'gamma']
# set the seed for dpd thermostat
self.cpp_force.setSeed(seed)
# set the temperature
# setup the variant inputs
T = variant._setup_variant_input(T)
self.cpp_force.setT(T.cpp_variant)
def __init__(self,
Lx=None,
Ly=None,
Lz=None,
xy=None,
xz=None,
yz=None,
period=1,
L=None,
phase=-1):
util.print_status_line()
# initialize base class
_updater.__init__(self)
self.metadata_fields = ['period']
if L is not None:
Lx = L
Ly = L
Lz = L
if Lx is None and Ly is None and Lz is None and xy is None and xz is None and yz is None:
globals.msg.warning(
"update.box_resize: Ignoring request to setup updater without parameters\n"
)
return
box = globals.system_definition.getParticleData().getGlobalBox()
# setup arguments
if Lx is None:
Lx = box.getL().x
if Ly is None:
Ly = box.getL().y
if Lz is None:
Lz = box.getL().z
if xy is None:
xy = box.getTiltFactorXY()
if xz is None:
xz = box.getTiltFactorXZ()
if yz is None:
yz = box.getTiltFactorYZ()
Lx = variant._setup_variant_input(Lx)
Ly = variant._setup_variant_input(Ly)
Lz = variant._setup_variant_input(Lz)
xy = variant._setup_variant_input(xy)
xz = variant._setup_variant_input(xz)
yz = variant._setup_variant_input(yz)
# store metadata
self.Lx = Lx
self.Ly = Ly
self.Lz = Lz
self.xy = xy
self.xz = xz
self.yz = yz
self.metadata_fields = ['Lx', 'Ly', 'Lz', 'xy', 'xz', 'yz']
# create the c++ mirror class
self.cpp_updater = hoomd.BoxResizeUpdater(
globals.system_definition, Lx.cpp_variant, Ly.cpp_variant,
Lz.cpp_variant, xy.cpp_variant, xz.cpp_variant, yz.cpp_variant)
if period is None:
self.cpp_updater.update(globals.system.getCurrentTimeStep())
else:
self.setupUpdater(period, phase)
