def _perform_common_init_tasks():
from hoomd_script import update
from hoomd_script import group
from hoomd_script import compute
# create the sorter
globals.sorter = update.sort()
# create the default compute.thermo on the all group
util._disable_status_lines = True
all = group.all()
compute._get_unique_thermo(group=all)
util._disable_status_lines = False
# set up Communicator, and register it with the System
if hoomd.is_MPI_available():
cpp_decomposition = globals.system_definition.getParticleData(
).getDomainDecomposition()
if cpp_decomposition is not None:
# create the c++ Communicator
if not globals.exec_conf.isCUDAEnabled():
cpp_communicator = hoomd.Communicator(
globals.system_definition, cpp_decomposition)
else:
cpp_communicator = hoomd.CommunicatorGPU(
globals.system_definition, cpp_decomposition)
# set Communicator in C++ System
globals.system.setCommunicator(cpp_communicator)
def __init__(self, filename, period, group=None, overwrite=False, unwrap_full=False, unwrap_rigid=False, angle_z=False, phase=-1):
util.print_status_line();
# initialize base class
analyze._analyzer.__init__(self);
# create the c++ mirror class
reported_period = period;
try:
reported_period = int(period);
except TypeError:
reported_period = 1;
if group is None:
util._disable_status_lines = True;
group = hs_group.all();
util._disable_status_lines = False;
self.cpp_analyzer = hoomd.DCDDumpWriter(globals.system_definition, filename, int(reported_period), group.cpp_group, overwrite);
self.cpp_analyzer.setUnwrapFull(unwrap_full);
self.cpp_analyzer.setUnwrapRigid(unwrap_rigid);
self.cpp_analyzer.setAngleZ(angle_z);
self.setupAnalyzer(period, phase);
# store metadata
self.filename = filename
self.period = period
self.group = group
self.metadata_fields = ['filename','period','group']
def _perform_common_init_tasks():
from hoomd_script import update;
from hoomd_script import group;
from hoomd_script import compute;
# create the sorter, using the evil import __main__ trick to provide the user with a default variable
import __main__;
__main__.sorter = update.sort();
# create the default compute.thermo on the all group
util._disable_status_lines = True;
all = group.all();
compute._get_unique_thermo(group=all);
util._disable_status_lines = False;
# set up Communicator, and register it with the System
if hoomd.is_MPI_available():
cpp_decomposition = globals.system_definition.getParticleData().getDomainDecomposition();
if cpp_decomposition is not None:
# create the c++ Communicator
if not globals.exec_conf.isCUDAEnabled():
cpp_communicator = hoomd.Communicator(globals.system_definition, cpp_decomposition)
else:
cpp_communicator = hoomd.CommunicatorGPU(globals.system_definition, cpp_decomposition)
# set Communicator in C++ System
globals.system.setCommunicator(cpp_communicator)
def __init__(self,
filename,
period,
group=None,
overwrite=False,
unwrap_full=False,
unwrap_rigid=False,
angle_z=False):
util.print_status_line()
# initialize base class
analyze._analyzer.__init__(self)
# create the c++ mirror class
reported_period = period
try:
reported_period = int(period)
except TypeError:
reported_period = 1
if group is None:
util._disable_status_lines = True
group = hs_group.all()
util._disable_status_lines = False
self.cpp_analyzer = hoomd.DCDDumpWriter(globals.system_definition,
filename, int(reported_period),
group.cpp_group, overwrite)
self.cpp_analyzer.setUnwrapFull(unwrap_full)
self.cpp_analyzer.setUnwrapRigid(unwrap_rigid)
self.cpp_analyzer.setAngleZ(angle_z)
self.setupAnalyzer(period)
def _perform_common_init_tasks():
from hoomd_script import update
from hoomd_script import group
from hoomd_script import compute
# create the sorter
globals.sorter = update.sort()
# create the default compute.thermo on the all group
util._disable_status_lines = True
all = group.all()
compute._get_unique_thermo(group=all)
util._disable_status_lines = False
# set up Communicator, and register it with the System
if hoomd.is_MPI_available():
cpp_decomposition = globals.system_definition.getParticleData().getDomainDecomposition()
if cpp_decomposition is not None:
# create the c++ Communicator
if not globals.exec_conf.isCUDAEnabled():
cpp_communicator = hoomd.Communicator(globals.system_definition, cpp_decomposition)
else:
cpp_communicator = hoomd.CommunicatorGPU(globals.system_definition, cpp_decomposition)
# set Communicator in C++ System
globals.system.setCommunicator(cpp_communicator)
def __init__(self,
filename,
period,
group=None,
overwrite=False,
offdiag=False):
util.print_status_line()
# initialize base class
analyze._analyzer.__init__(self)
# Find the dcd extension and construct new file names
end = filename.find('.dcd')
file_diag = filename[:end] + '.diag.dcd'
file_off = filename[:end] + '.off.dcd'
# create the c++ mirror class
reported_period = period
if type(period) != type(1):
reported_period = 1000
if group is None:
util._disable_status_lines = True
group = hs_group.all()
util._disable_status_lines = False
self.cpp_analyzer = _custom_analyzers_plugin.StressPerAtomDumpWriter(
globals.system_definition, file_diag, file_off,
int(reported_period), group.cpp_group, overwrite, offdiag)
self.setupAnalyzer(period)
def __init__(self, filename, period, group=None, overwrite=False, unwrap_full=False, unwrap_rigid=False):
util.print_status_line();
# initialize base class
analyze._analyzer.__init__(self);
# create the c++ mirror class
reported_period = period;
if type(period) != type(1):
reported_period = 1000;
if group is None:
util._disable_status_lines = True;
group = hs_group.all();
util._disable_status_lines = False;
self.cpp_analyzer = hoomd.DCDDumpWriter(globals.system_definition, filename, int(reported_period), group.cpp_group, overwrite);
self.cpp_analyzer.setUnwrapFull(unwrap_full);
self.cpp_analyzer.setUnwrapRigid(unwrap_rigid);
self.setupAnalyzer(period);
def __init__(self, filename, period, group=None, overwrite=False):
util.print_status_line()
# initialize base class
analyze._analyzer.__init__(self)
# create the c++ mirror class
reported_period = period
if type(period) != type(1):
reported_period = 1000
if group is None:
util._disable_status_lines = True
group = hs_group.all()
util._disable_status_lines = False
self.cpp_analyzer = _custom_analyzers_plugin.DCDVELDumpWriter(
globals.system_definition, filename, int(reported_period),
group.cpp_group, overwrite)
self.setupAnalyzer(period)
