def __init__( self,
mc,
ln_gamma,
q_factor,
r0,
q0,
drift_period,
symmetry = []
):
import math
import numpy
hoomd.util.print_status_line();
# initialize base class
_compute.__init__(self);
if type(r0) == numpy.ndarray:
self.lattice_positions = r0.tolist();
else:
self.lattice_positions = list(r0);
if type(q0) == numpy.ndarray:
self.lattice_orientations = q0.tolist();
else:
self.lattice_orientations = list(q0);
self.mc = mc;
self.q_factor = q_factor;
self.trans_spring_const = math.exp(ln_gamma);
self.rotat_spring_const = self.q_factor*self.trans_spring_const;
self.lattice = lattice_field( self.mc,
position = self.lattice_positions,
orientation = self.lattice_orientations,
k = self.trans_spring_const,
q = self.rotat_spring_const,
symmetry=symmetry);
self.remove_drift = hoomd.hpmc.update.remove_drift(self.mc, self.lattice, period=drift_period);
def __init__(self,
mc,
ln_gamma,
q_factor,
r0,
q0,
drift_period,
symmetry=[]):
import math
import numpy
hoomd.util.print_status_line()
# initialize base class
_compute.__init__(self)
if type(r0) == numpy.ndarray:
self.lattice_positions = r0.tolist()
else:
self.lattice_positions = list(r0)
if type(q0) == numpy.ndarray:
self.lattice_orientations = q0.tolist()
else:
self.lattice_orientations = list(q0)
self.mc = mc
self.q_factor = q_factor
self.trans_spring_const = math.exp(ln_gamma)
self.rotat_spring_const = self.q_factor * self.trans_spring_const
self.lattice = lattice_field(self.mc,
position=self.lattice_positions,
orientation=self.lattice_orientations,
k=self.trans_spring_const,
q=self.rotat_spring_const,
symmetry=symmetry)
self.remove_drift = hoomd.hpmc.update.remove_drift(self.mc,
self.lattice,
period=drift_period)
def __init__(self):
_compute.__init__(self);
self.cpp_compute = None;
def __init__(self):
_compute.__init__(self)
self.cpp_compute = None
def __init__(self, mc, seed, suffix='', test_type=None, nsample=None):
# initialize base class
_compute.__init__(self);
# create the c++ mirror class
cl = _hoomd.CellList(hoomd.context.current.system_definition);
hoomd.context.current.system.addCompute(cl, "auto_cl3")
cls = None;
if not hoomd.context.current.device.cpp_exec_conf.isCUDAEnabled():
if isinstance(mc, integrate.sphere):
cls = _hpmc.ComputeFreeVolumeSphere;
elif isinstance(mc, integrate.convex_polygon):
cls = _hpmc.ComputeFreeVolumeConvexPolygon;
elif isinstance(mc, integrate.simple_polygon):
cls = _hpmc.ComputeFreeVolumeSimplePolygon;
elif isinstance(mc, integrate.convex_polyhedron):
cls = _hpmc.ComputeFreeVolumeConvexPolyhedron;
elif isinstance(mc, integrate.convex_spheropolyhedron):
cls = _hpmc.ComputeFreeVolumeSpheropolyhedron;
elif isinstance(mc, integrate.ellipsoid):
cls = _hpmc.ComputeFreeVolumeEllipsoid;
elif isinstance(mc, integrate.convex_spheropolygon):
cls =_hpmc.ComputeFreeVolumeSpheropolygon;
elif isinstance(mc, integrate.faceted_ellipsoid):
cls =_hpmc.ComputeFreeVolumeFacetedEllipsoid;
elif isinstance(mc, integrate.polyhedron):
cls =_hpmc.ComputeFreeVolumePolyhedron;
elif isinstance(mc, integrate.sphinx):
cls =_hpmc.ComputeFreeVolumeSphinx;
elif isinstance(mc, integrate.convex_spheropolyhedron_union):
cls = _hpmc.ComputeFreeVolumeConvexPolyhedronUnion
elif isinstance(mc, integrate.faceted_ellipsoid_union):
cls = _hpmc.ComputeFreeVolumeFacetedEllipsoidUnion
elif isinstance(mc, integrate.sphere_union):
cls = _hpmc.ComputeFreeVolumeSphereUnion;
else:
hoomd.context.current.device.cpp_msg.error("compute.free_volume: Unsupported integrator.\n");
raise RuntimeError("Error initializing compute.free_volume");
else:
if isinstance(mc, integrate.sphere):
cls = _hpmc.ComputeFreeVolumeGPUSphere;
elif isinstance(mc, integrate.convex_polygon):
cls = _hpmc.ComputeFreeVolumeGPUConvexPolygon;
elif isinstance(mc, integrate.simple_polygon):
cls = _hpmc.ComputeFreeVolumeGPUSimplePolygon;
elif isinstance(mc, integrate.convex_polyhedron):
cls = _hpmc.ComputeFreeVolumeGPUConvexPolyhedron;
elif isinstance(mc, integrate.convex_spheropolyhedron):
cls = _hpmc.ComputeFreeVolumeGPUSpheropolyhedron;
elif isinstance(mc, integrate.ellipsoid):
cls = _hpmc.ComputeFreeVolumeGPUEllipsoid;
elif isinstance(mc, integrate.convex_spheropolygon):
cls =_hpmc.ComputeFreeVolumeGPUSpheropolygon;
elif isinstance(mc, integrate.faceted_ellipsoid):
cls =_hpmc.ComputeFreeVolumeGPUFacetedEllipsoid;
elif isinstance(mc, integrate.polyhedron):
cls =_hpmc.ComputeFreeVolumeGPUPolyhedron;
elif isinstance(mc, integrate.sphinx):
cls =_hpmc.ComputeFreeVolumeGPUSphinx;
elif isinstance(mc, integrate.sphere_union):
cls = _hpmc.ComputeFreeVolumeGPUSphereUnion;
elif isinstance(mc, integrate.faceted_ellipsoid_union):
cls = _hpmc.ComputeFreeVolumeGPUFacetedEllipsoidUnion;
elif isinstance(mc, integrate.convex_spheropolyhedron_union):
cls = _hpmc.ComputeFreeVolumeGPUConvexPolyhedronUnion;
else:
hoomd.context.current.device.cpp_msg.error("compute.free_volume: Unsupported integrator.\n");
raise RuntimeError("Error initializing compute.free_volume");
if suffix is not '':
suffix = '_' + suffix
self.cpp_compute = cls(hoomd.context.current.system_definition,
mc.cpp_integrator,
cl,
seed,
suffix)
if test_type is not None:
itype = hoomd.context.current.system_definition.getParticleData().getTypeByName(test_type)
self.cpp_compute.setTestParticleType(itype)
if nsample is not None:
self.cpp_compute.setNumSamples(int(nsample))
hoomd.context.current.system.addCompute(self.cpp_compute, self.compute_name)
self.enabled = True
def __init__(self, mc, seed, suffix='', test_type=None, nsample=None):
hoomd.util.print_status_line();
# initialize base class
_compute.__init__(self);
# create the c++ mirror class
cl = _hoomd.CellList(hoomd.context.current.system_definition);
hoomd.context.current.system.addCompute(cl, "auto_cl3")
cls = None;
if not hoomd.context.exec_conf.isCUDAEnabled():
if isinstance(mc, integrate.sphere):
cls = _hpmc.ComputeFreeVolumeSphere;
elif isinstance(mc, integrate.convex_polygon):
cls = _hpmc.ComputeFreeVolumeConvexPolygon;
elif isinstance(mc, integrate.simple_polygon):
cls = _hpmc.ComputeFreeVolumeSimplePolygon;
elif isinstance(mc, integrate.convex_polyhedron):
cls = _hpmc.ComputeFreeVolumeConvexPolyhedron;
elif isinstance(mc, integrate.convex_spheropolyhedron):
cls = _hpmc.ComputeFreeVolumeSpheropolyhedron;
elif isinstance(mc, integrate.ellipsoid):
cls = _hpmc.ComputeFreeVolumeEllipsoid;
elif isinstance(mc, integrate.convex_spheropolygon):
cls =_hpmc.ComputeFreeVolumeSpheropolygon;
elif isinstance(mc, integrate.faceted_sphere):
cls =_hpmc.ComputeFreeVolumeFacetedSphere;
elif isinstance(mc, integrate.polyhedron):
cls =_hpmc.ComputeFreeVolumePolyhedron;
elif isinstance(mc, integrate.sphinx):
cls =_hpmc.ComputeFreeVolumeSphinx;
elif isinstance(mc, integrate.sphere_union):
cls = integrate._get_sized_entry('ComputeFreeVolumeSphereUnion', mc.capacity);
else:
hoomd.context.msg.error("compute.free_volume: Unsupported integrator.\n");
raise RuntimeError("Error initializing compute.free_volume");
else:
if isinstance(mc, integrate.sphere):
cls = _hpmc.ComputeFreeVolumeGPUSphere;
elif isinstance(mc, integrate.convex_polygon):
cls = _hpmc.ComputeFreeVolumeGPUConvexPolygon;
elif isinstance(mc, integrate.simple_polygon):
cls = _hpmc.ComputeFreeVolumeGPUSimplePolygon;
elif isinstance(mc, integrate.convex_polyhedron):
cls = _hpmc.ComputeFreeVolumeGPUConvexPolyhedron;
elif isinstance(mc, integrate.convex_spheropolyhedron):
cls = _hpmc.ComputeFreeVolumeGPUSpheropolyhedron;
elif isinstance(mc, integrate.ellipsoid):
cls = _hpmc.ComputeFreeVolumeGPUEllipsoid;
elif isinstance(mc, integrate.convex_spheropolygon):
cls =_hpmc.ComputeFreeVolumeGPUSpheropolygon;
elif isinstance(mc, integrate.faceted_sphere):
cls =_hpmc.ComputeFreeVolumeGPUFacetedSphere;
elif isinstance(mc, integrate.polyhedron):
cls =_hpmc.ComputeFreeVolumeGPUPolyhedron;
elif isinstance(mc, integrate.sphinx):
cls =_hpmc.ComputeFreeVolumeGPUSphinx;
elif isinstance(mc, integrate.sphere_union):
cls = integrate._get_sized_entry('ComputeFreeVolumeGPUSphereUnion', mc.capacity);
else:
hoomd.context.msg.error("compute.free_volume: Unsupported integrator.\n");
raise RuntimeError("Error initializing compute.free_volume");
if suffix is not '':
suffix = '_' + suffix
self.cpp_compute = cls(hoomd.context.current.system_definition,
mc.cpp_integrator,
cl,
seed,
suffix)
if test_type is not None:
itype = hoomd.context.current.system_definition.getParticleData().getTypeByName(test_type)
self.cpp_compute.setTestParticleType(itype)
if nsample is not None:
self.cpp_compute.setNumSamples(int(nsample))
hoomd.context.current.system.addCompute(self.cpp_compute, self.compute_name)
self.enabled = True
