def __init__(self, r_buff=0.4, check_period=1, d_max=None, dist_check=True, name=None, deterministic=False):
nlist.__init__(self)
if name is None:
self.name = "cell_nlist_%d" % cell.cur_id
cell.cur_id += 1
else:
self.name = name
# create the C++ mirror class
if not hoomd.context.current.device.cpp_exec_conf.isCUDAEnabled():
self.cpp_cl = _hoomd.CellList(hoomd.context.current.system_definition)
hoomd.context.current.system.addCompute(self.cpp_cl , self.name + "_cl")
self.cpp_nlist = _md.NeighborListBinned(hoomd.context.current.system_definition, 0.0, r_buff, self.cpp_cl )
else:
self.cpp_cl = _hoomd.CellListGPU(hoomd.context.current.system_definition)
hoomd.context.current.system.addCompute(self.cpp_cl , self.name + "_cl")
self.cpp_nlist = _md.NeighborListGPUBinned(hoomd.context.current.system_definition, 0.0, r_buff, self.cpp_cl )
self.cpp_nlist.setEvery(check_period, dist_check)
hoomd.context.current.system.addCompute(self.cpp_nlist, self.name)
self.cpp_cl.setSortCellList(deterministic)
# register this neighbor list with the context
hoomd.context.current.neighbor_lists += [self]
# save the user defined parameters
self.set_params(r_buff, check_period, d_max, dist_check)
def __init__(self, r_buff=0.4, check_period=1, d_max=None, dist_check=True, cell_width=None, name=None, deterministic=False):
hoomd.util.print_status_line()
# register the citation
c = hoomd.cite.article(cite_key='howard2016',
author=['M P Howard', 'J A Anderson', 'A Nikoubashman', 'S C Glotzer', 'A Z Panagiotopoulos'],
title='Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units',
journal='Computer Physics Communications',
volume=203,
pages='45--52',
month='Mar',
year='2016',
doi='10.1016/j.cpc.2016.02.003',
feature='stenciled neighbor lists')
hoomd.cite._ensure_global_bib().add(c)
nlist.__init__(self)
if name is None:
self.name = "stencil_nlist_%d" % stencil.cur_id
stencil.cur_id += 1
else:
self.name = name
# create the C++ mirror class
if not hoomd.context.exec_conf.isCUDAEnabled():
self.cpp_cl = _hoomd.CellList(hoomd.context.current.system_definition)
hoomd.context.current.system.addCompute(self.cpp_cl , self.name + "_cl")
cls = _hoomd.CellListStencil(hoomd.context.current.system_definition, self.cpp_cl)
hoomd.context.current.system.addCompute(cls, self.name + "_cls")
self.cpp_nlist = _md.NeighborListStencil(hoomd.context.current.system_definition, 0.0, r_buff, self.cpp_cl, cls)
else:
self.cpp_cl = _hoomd.CellListGPU(hoomd.context.current.system_definition)
hoomd.context.current.system.addCompute(self.cpp_cl , self.name + "_cl")
cls = _hoomd.CellListStencil(hoomd.context.current.system_definition, self.cpp_cl)
hoomd.context.current.system.addCompute(cls, self.name + "_cls")
self.cpp_nlist = _md.NeighborListGPUStencil(hoomd.context.current.system_definition, 0.0, r_buff, self.cpp_cl, cls)
self.cpp_nlist.setEvery(check_period, dist_check)
hoomd.context.current.system.addCompute(self.cpp_nlist, self.name)
self.cpp_cl.setSortCellList(deterministic)
# register this neighbor list with the context
hoomd.context.current.neighbor_lists += [self]
# save the user defined parameters
hoomd.util.quiet_status()
self.set_params(r_buff, check_period, d_max, dist_check)
self.set_cell_width(cell_width)
hoomd.util.unquiet_status()
def _attach(self):
integrator = self._simulation.operations.integrator
if not isinstance(integrator, integrate.HPMCIntegrator):
raise RuntimeError("The integrator must be an HPMC integrator.")
# Extract 'Shape' from '<hoomd.hpmc.integrate.Shape object>'
integrator_name = integrator.__class__.__name__
try:
if isinstance(self._simulation.device, hoomd.device.CPU):
cpp_cls = getattr(_hpmc, 'ComputeFreeVolume' + integrator_name)
else:
cpp_cls = getattr(
_hpmc, 'ComputeFreeVolume' + integrator_name + 'GPU')
except AttributeError:
raise RuntimeError("Unsupported integrator.")
cl = _hoomd.CellList(self._simulation.state._cpp_sys_def)
self._cpp_obj = cpp_cls(self._simulation.state._cpp_sys_def,
integrator._cpp_obj, cl)
super()._attach()
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