def __init__(self, mode, lattice_vectors, name=None, sigma=1.0, offs=0.0):
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:
globals.msg.error(
"cv.lamellar: List of supplied latice vectors is empty.\n")
raise RuntimeEror('Error creating collective variable.')
if type(mode) != type(dict()):
globals.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,
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 = _metadynamics.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]))
if not globals.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.LamellarOrderParameter(
globals.system_definition, cpp_mode, cpp_lattice_vectors, offs,
suffix)
else:
self.cpp_force = _metadynamics.LamellarOrderParameterGPU(
globals.system_definition, cpp_mode, cpp_lattice_vectors, offs,
suffix)
globals.system.addCompute(self.cpp_force, self.force_name)
def __init__(self, qstar, mode, nx, ny=None, nz=None, name=None,sigma=1.0,zero_modes=None):
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()):
globals.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, globals.system_definition.getParticleData().getNTypes()):
t = globals.system_definition.getParticleData().getNameByType(i)
if t not in mode.keys():
globals.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:
globals.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 globals.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.OrderParameterMesh(globals.system_definition, nx,ny,nz,qstar, cpp_mode, cpp_zero_modes)
else:
self.cpp_force = _metadynamics.OrderParameterMeshGPU(globals.system_definition, nx,ny,nz,qstar, cpp_mode, cpp_zero_modes)
globals.system.addCompute(self.cpp_force, self.force_name)
def __init__(self, mode, lattice_vectors, name=None,sigma=1.0,offs=0.0):
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:
globals.msg.error("cv.lamellar: List of supplied latice vectors is empty.\n")
raise RuntimeEror('Error creating collective variable.')
if type(mode) != type(dict()):
globals.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, 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 = _metadynamics.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]))
if not globals.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.LamellarOrderParameter(globals.system_definition, cpp_mode, cpp_lattice_vectors, offs,suffix)
else:
self.cpp_force = _metadynamics.LamellarOrderParameterGPU(globals.system_definition, cpp_mode, cpp_lattice_vectors, offs, suffix)
globals.system.addCompute(self.cpp_force, self.force_name)
def __init__(self,
qstar,
mode,
nx,
ny=None,
nz=None,
name=None,
sigma=1.0,
zero_modes=None):
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()):
globals.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,
globals.system_definition.getParticleData().getNTypes()):
t = globals.system_definition.getParticleData().getNameByType(i)
if t not in mode.keys():
globals.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:
globals.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 globals.exec_conf.isCUDAEnabled():
self.cpp_force = _metadynamics.OrderParameterMesh(
globals.system_definition, nx, ny, nz, qstar, cpp_mode,
cpp_zero_modes)
else:
self.cpp_force = _metadynamics.OrderParameterMeshGPU(
globals.system_definition, nx, ny, nz, qstar, cpp_mode,
cpp_zero_modes)
globals.system.addCompute(self.cpp_force, self.force_name)
