def __init__(self,
filename,
groups,
period,
header_prefix='',
r0_file=None,
overwrite=False,
phase=0):
hoomd.util.print_status_line()
# initialize base class
_analyzer.__init__(self)
# create the c++ mirror class
self.cpp_analyzer = _deprecated.MSDAnalyzer(
hoomd.context.current.system_definition, filename, header_prefix,
overwrite)
self.setupAnalyzer(period, phase)
# it is an error to specify no groups
if len(groups) == 0:
hoomd.context.msg.error(
'At least one group must be specified to analyze.msd\n')
raise RuntimeError('Error creating analyzer')
# set the group columns
for cur_group in groups:
self.cpp_analyzer.addColumn(cur_group.cpp_group, cur_group.name)
if r0_file is not None:
self.cpp_analyzer.setR0(r0_file)
def __init__(self,
mc,
filename,
xmax,
dx,
navg,
period,
overwrite=False,
phase=0):
hoomd.util.print_status_line()
# initialize base class
_analyzer.__init__(self)
# create the c++ mirror class
cls = None
if isinstance(mc, integrate.sphere):
cls = _hpmc.AnalyzerSDFSphere
elif isinstance(mc, integrate.convex_polygon):
cls = _hpmc.AnalyzerSDFConvexPolygon
elif isinstance(mc, integrate.simple_polygon):
cls = _hpmc.AnalyzerSDFSimplePolygon
elif isinstance(mc, integrate.convex_polyhedron):
cls = _hpmc.AnalyzerSDFConvexPolyhedron
elif isinstance(mc, integrate.convex_spheropolyhedron):
cls = _hpmc.AnalyzerSDFSpheropolyhedron
elif isinstance(mc, integrate.ellipsoid):
cls = _hpmc.AnalyzerSDFEllipsoid
elif isinstance(mc, integrate.convex_spheropolygon):
cls = _hpmc.AnalyzerSDFSpheropolygon
else:
hoomd.context.msg.error("analyze.sdf: Unsupported integrator.\n")
raise runtime_error("Error initializing analyze.sdf")
self.cpp_analyzer = cls(hoomd.context.current.system_definition,
mc.cpp_integrator, xmax, dx, navg, filename,
overwrite)
self.setupAnalyzer(period, phase)
# meta data
self.filename = filename
self.xmax = xmax
self.dx = dx
self.navg = navg
self.period = period
self.overwrite = overwrite
self.metadata_fields = [
'filename', 'xmax', 'dx', 'navg', 'period', 'overwrite'
]
def __init__(self, mc, filename, xmax, dx, navg, period, overwrite=False, phase=0):
hoomd.util.print_status_line();
# initialize base class
_analyzer.__init__(self);
# create the c++ mirror class
cls = None;
if isinstance(mc, integrate.sphere):
cls = _hpmc.AnalyzerSDFSphere;
elif isinstance(mc, integrate.convex_polygon):
cls = _hpmc.AnalyzerSDFConvexPolygon;
elif isinstance(mc, integrate.simple_polygon):
cls = _hpmc.AnalyzerSDFSimplePolygon;
elif isinstance(mc, integrate.convex_polyhedron):
cls = _hpmc.AnalyzerSDFConvexPolyhedron;
elif isinstance(mc, integrate.convex_spheropolyhedron):
cls = _hpmc.AnalyzerSDFSpheropolyhedron;
elif isinstance(mc, integrate.ellipsoid):
cls = _hpmc.AnalyzerSDFEllipsoid;
elif isinstance(mc, integrate.convex_spheropolygon):
cls =_hpmc.AnalyzerSDFSpheropolygon;
else:
hoomd.context.msg.error("analyze.sdf: Unsupported integrator.\n");
raise runtime_error("Error initializing analyze.sdf");
self.cpp_analyzer = cls(hoomd.context.current.system_definition,
mc.cpp_integrator,
xmax,
dx,
navg,
filename,
overwrite);
self.setupAnalyzer(period, phase);
# meta data
self.filename = filename
self.xmax = xmax
self.dx = dx
self.navg = navg
self.period = period
self.overwrite = overwrite
self.metadata_fields = ['filename', 'xmax', 'dx', 'navg', 'period', 'overwrite']
def __init__(self, filename, groups, period, header_prefix='', r0_file=None, overwrite=False, phase=0):
hoomd.util.print_status_line();
# initialize base class
_analyzer.__init__(self);
# create the c++ mirror class
self.cpp_analyzer = _deprecated.MSDAnalyzer(hoomd.context.current.system_definition, filename, header_prefix, overwrite);
self.setupAnalyzer(period, phase);
# it is an error to specify no groups
if len(groups) == 0:
hoomd.context.msg.error('At least one group must be specified to analyze.msd\n');
raise RuntimeError('Error creating analyzer');
# set the group columns
for cur_group in groups:
self.cpp_analyzer.addColumn(cur_group.cpp_group, cur_group.name);
if r0_file is not None:
self.cpp_analyzer.setR0(r0_file);