def __init__(self, order_parameters, lattice_vectors, phases, interface_width, name):
# initialize the base class
force._force.__init__(self, name);
self.cpp_force = None;
cpp_order_parameters = hoomd.std_vector_scalar()
for l in order_parameters:
cpp_order_parameters.append(l)
cpp_lattice_vectors = _external.std_vector_int3()
for l in lattice_vectors:
if len(l) != 3:
globals.msg.error("List of input lattice vectors not a list of triples.\n")
raise RuntimeError('Error creating external ordering potential.')
cpp_lattice_vectors.append(hoomd.make_int3(l[0], l[1], l[2]))
cpp_phases = hoomd.std_vector_scalar()
for l in phases:
cpp_phases.append(l)
cpp_interface_width = float(interface_width)
if not globals.exec_conf.isCUDAEnabled():
self.cpp_force = _external.OrderingExternal(globals.system_definition, cpp_order_parameters, cpp_lattice_vectors, cpp_phases, cpp_interface_width, self.name)
else:
self.cpp_force = _external.OrderingExternalGPU(globals.system_definition, cpp_order_parameters, cpp_lattice_vectors, cpp_phases, cpp_interface_width, self.name)
globals.system.addCompute(self.cpp_force, self.force_name)
self.enabled = True;
def __init__(self, mode, lattice_vectors, name=None, sigma=1.0):
hoomd.util.print_status_line()
if name is not None:
name = "_" + name
suffix = name
else:
suffix = ""
_collective_variable.__init__(self, sigma, name)
if len(lattice_vectors) == 0:
hoomd.context.msg.error(
"cv.lamellar: List of supplied latice vectors is empty.\n")
raise RuntimeEror('Error creating collective variable.')
if type(mode) != type(dict()):
hoomd.context.msg.error(
"cv.lamellar: Mode amplitudes specified incorrectly.\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode = _hoomd.std_vector_scalar()
for i in range(
0,
hoomd.context.current.system_definition.getParticleData().
getNTypes()):
t = hoomd.context.current.system_definition.getParticleData(
).getNameByType(i)
if t not in mode.keys():
hoomd.context.msg.error(
"cv.lamellar: Missing mode amplitude for particle type " +
t + ".\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode.append(mode[t])
cpp_lattice_vectors = _metadynamics.std_vector_int3()
for l in lattice_vectors:
if len(l) != 3:
hoomd.context.msg.error(
"cv.lamellar: List of input lattice vectors not a list of triples.\n"
)
raise RuntimeError('Error creating collective variable.')
cpp_lattice_vectors.append(hoomd.make_int3(l[0], l[1], l[2]))
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.LamellarOrderParameter(
hoomd.context.current.system_definition, cpp_mode,
cpp_lattice_vectors, suffix)
else:
self.cpp_force = _metadynamics.LamellarOrderParameterGPU(
hoomd.context.current.system_definition, cpp_mode,
cpp_lattice_vectors, suffix)
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
def __init__(self, filename, mode, lattice_vectors, phases, grid, period=1, endtime=1, overwrite=False):
util.print_status_line();
# initialize base class
_analyzer.__init__(self);
if len(lattice_vectors) == 0:
globals.msg.error("analyze.sq: List of supplied latice vectors is empty.\n")
raise RuntimeEror('Error creating collective variable.')
if len(lattice_vectors) != len(phases):
globals.msg.error("analyze.sq: #phases is not equal to #lattice_vectors.\n")
raise RuntimeEror('Error creating collective variable.')
if type(mode) != type(dict()):
globals.msg.error("analyze.sq: Mode amplitudes specified incorrectly.\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode = hoomd.std_vector_scalar()
for i in range(0, globals.system_definition.getParticleData().getNTypes()):
t = globals.system_definition.getParticleData().getNameByType(i)
if t not in mode.keys():
globals.msg.error("cv.lamellar: Missing mode amplitude for particle type " + t + ".\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode.append(mode[t])
cpp_lattice_vectors = _CollectiveVariable_plugin.std_vector_int3()
for l in lattice_vectors:
if len(l) != 3:
globals.msg.error("cv.lamellar: List of input lattice vectors not a list of triples.\n")
raise RuntimeError('Error creating collective variable.')
cpp_lattice_vectors.append(hoomd.make_int3(l[0], l[1], l[2]))
cpp_phases = _CollectiveVariable_plugin.std_vector_scalar()
for l in phases:
cpp_phases.append(l)
cpp_grid = _CollectiveVariable_plugin.std_vector_uint()
for l in grid:
cpp_grid.append(l)
# initialize the reflected c++ class
if not globals.exec_conf.isCUDAEnabled():
self.cpp_analyzer = _CollectiveVariable_plugin.CollectiveVariable(globals.system_definition, cpp_mode, cpp_lattice_vectors, cpp_phases, cpp_grid, endtime, filename, overwrite);
else:
self.cpp_analyzer = _CollectiveVariable_plugin.CollectiveVariableGPU(globals.system_definition, cpp_mode, cpp_lattice_vectors, cpp_phases, cpp_grid, endtime,filename, overwrite);
self.setupAnalyzer(period)
def __init__(self, mode, nx, ny=None, nz=None, name=None, sigma=1.0, zero_modes=None):
hoomd.util.print_status_line()
if name is not None:
name = "_" + name
suffix = name
else:
suffix = ""
if ny is None:
ny = nx
if nz is None:
nz = nx
_collective_variable.__init__(self, sigma, name)
if type(mode) != type(dict()):
hoomd.context.msg.error("cv.mesh: Mode amplitudes specified incorrectly.\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode = _hoomd.std_vector_scalar()
for i in range(0, hoomd.context.current.system_definition.getParticleData().getNTypes()):
t = hoomd.context.current.system_definition.getParticleData().getNameByType(i)
if t not in mode.keys():
hoomd.context.msg.error("cv.mesh: Missing mode amplitude for particle type " + t + ".\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode.append(mode[t])
cpp_zero_modes = _metadynamics.std_vector_int3()
if zero_modes is not None:
for l in zero_modes:
if len(l) != 3:
hoomd.context.msg.error("cv.lamellar: List of modes to zero not a list of triples.\n")
raise RuntimeError('Error creating collective variable.')
cpp_zero_modes.append(hoomd.make_int3(l[0], l[1], l[2]))
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.OrderParameterMesh(
hoomd.context.current.system_definition, nx, ny, nz, cpp_mode, cpp_zero_modes)
else:
self.cpp_force = _metadynamics.OrderParameterMeshGPU(
hoomd.context.current.system_definition, nx, ny, nz, cpp_mode, cpp_zero_modes)
hoomd.context.current.system.addCompute(self.cpp_force, self.force_name)
def __init__(self, mode, lattice_vectors, name=None, sigma=1.0):
hoomd.util.print_status_line()
if name is not None:
name = "_" + name
suffix = name
else:
suffix = ""
_collective_variable.__init__(self, sigma, name)
if len(lattice_vectors) == 0:
hoomd.context.msg.error("cv.lamellar: List of supplied latice vectors is empty.\n")
raise RuntimeEror('Error creating collective variable.')
if type(mode) != type(dict()):
hoomd.context.msg.error("cv.lamellar: Mode amplitudes specified incorrectly.\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode = _hoomd.std_vector_scalar()
for i in range(0, hoomd.context.current.system_definition.getParticleData().getNTypes()):
t = hoomd.context.current.system_definition.getParticleData().getNameByType(i)
if t not in mode.keys():
hoomd.context.msg.error("cv.lamellar: Missing mode amplitude for particle type " + t + ".\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode.append(mode[t])
cpp_lattice_vectors = _metadynamics.std_vector_int3()
for l in lattice_vectors:
if len(l) != 3:
hoomd.context.msg.error("cv.lamellar: List of input lattice vectors not a list of triples.\n")
raise RuntimeError('Error creating collective variable.')
cpp_lattice_vectors.append(hoomd.make_int3(l[0], l[1], l[2]))
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.LamellarOrderParameter(
hoomd.context.current.system_definition, cpp_mode, cpp_lattice_vectors, suffix)
else:
self.cpp_force = _metadynamics.LamellarOrderParameterGPU(
hoomd.context.current.system_definition, cpp_mode, cpp_lattice_vectors, suffix)
hoomd.context.current.system.addCompute(self.cpp_force, self.force_name)
def __init__(self, order_parameters, lattice_vectors, phases,
interface_width, name):
# initialize the base class
force._force.__init__(self, name)
self.cpp_force = None
cpp_order_parameters = hoomd.std_vector_scalar()
for l in order_parameters:
cpp_order_parameters.append(l)
cpp_lattice_vectors = _external.std_vector_int3()
for l in lattice_vectors:
if len(l) != 3:
globals.msg.error(
"List of input lattice vectors not a list of triples.\n")
raise RuntimeError(
'Error creating external ordering potential.')
cpp_lattice_vectors.append(hoomd.make_int3(l[0], l[1], l[2]))
cpp_phases = hoomd.std_vector_scalar()
for l in phases:
cpp_phases.append(l)
cpp_interface_width = float(interface_width)
if not globals.exec_conf.isCUDAEnabled():
self.cpp_force = _external.OrderingExternal(
globals.system_definition, cpp_order_parameters,
cpp_lattice_vectors, cpp_phases, cpp_interface_width,
self.name)
else:
self.cpp_force = _external.OrderingExternalGPU(
globals.system_definition, cpp_order_parameters,
cpp_lattice_vectors, cpp_phases, cpp_interface_width,
self.name)
globals.system.addCompute(self.cpp_force, self.force_name)
self.enabled = True
def __init__(self, filename_sq, filename_vh, mode, lattice_vectors, period=1, vanhove_endtime=1, overwrite=False):
util.print_status_line();
# initialize base class
_analyzer.__init__(self);
if len(lattice_vectors) == 0:
globals.msg.error("analyze.sq: List of supplied latice vectors is empty.\n")
raise RuntimeEror('Error creating collective variable.')
if type(mode) != type(dict()):
globals.msg.error("analyze.sq: Mode amplitudes specified incorrectly.\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode = hoomd.std_vector_scalar()
for i in range(0, globals.system_definition.getParticleData().getNTypes()):
t = globals.system_definition.getParticleData().getNameByType(i)
if t not in mode.keys():
globals.msg.error("cv.lamellar: Missing mode amplitude for particle type " + t + ".\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode.append(mode[t])
cpp_lattice_vectors = _sq_plugin.std_vector_int3()
for l in lattice_vectors:
if len(l) != 3:
globals.msg.error("cv.lamellar: List of input lattice vectors not a list of triples.\n")
raise RuntimeError('Error creating collective variable.')
cpp_lattice_vectors.append(hoomd.make_int3(l[0], l[1], l[2]))
# initialize the reflected c++ class
if not globals.exec_conf.isCUDAEnabled():
self.cpp_analyzer = _sq_plugin.StructureFactor(globals.system_definition, cpp_mode, cpp_lattice_vectors, vanhove_endtime, filename_sq, filename_vh, overwrite);
else:
self.cpp_analyzer = _sq_plugin.StructureFactorGPU(globals.system_definition, cpp_mode, cpp_lattice_vectors, vanhove_endtime, filename_sq, filename_vh, overwrite);
self.setupAnalyzer(period)
def __init__(self,
mode,
nx,
ny=None,
nz=None,
name=None,
sigma=1.0,
zero_modes=None):
hoomd.util.print_status_line()
if name is not None:
name = "_" + name
suffix = name
else:
suffix = ""
if ny is None:
ny = nx
if nz is None:
nz = nx
_collective_variable.__init__(self, sigma, name)
if type(mode) != type(dict()):
hoomd.context.msg.error(
"cv.mesh: Mode amplitudes specified incorrectly.\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode = _hoomd.std_vector_scalar()
for i in range(
0,
hoomd.context.current.system_definition.getParticleData().
getNTypes()):
t = hoomd.context.current.system_definition.getParticleData(
).getNameByType(i)
if t not in mode.keys():
hoomd.context.msg.error(
"cv.mesh: Missing mode amplitude for particle type " + t +
".\n")
raise RuntimeEror('Error creating collective variable.')
cpp_mode.append(mode[t])
cpp_zero_modes = _metadynamics.std_vector_int3()
if zero_modes is not None:
for l in zero_modes:
if len(l) != 3:
hoomd.context.msg.error(
"cv.lamellar: List of modes to zero not a list of triples.\n"
)
raise RuntimeError('Error creating collective variable.')
cpp_zero_modes.append(hoomd.make_int3(l[0], l[1], l[2]))
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.OrderParameterMesh(
hoomd.context.current.system_definition, nx, ny, nz, cpp_mode,
cpp_zero_modes)
else:
self.cpp_force = _metadynamics.OrderParameterMeshGPU(
hoomd.context.current.system_definition, nx, ny, nz, cpp_mode,
cpp_zero_modes)
hoomd.context.current.system.addCompute(self.cpp_force,
self.force_name)
