def __init__(self, init, beads, nm, cell, fcomponents, ensemble=None, motion=None, prefix=""):
"""Initialises System class.
Args:
init: A class to deal with initializing the system.
beads: A beads object giving the atom positions.
cell: A cell object giving the system box.
fcomponents: A list of force components that are active for each
replica of the system.
bcomponents: A list of force components that are considered as bias, and act on each
replica of the system.
ensemble: An ensemble object giving the objects necessary for
producing the correct ensemble.
nm: A class dealing with path NM operations.
prefix: A string used to differentiate the output files of different
systems.
"""
info(" # Initializing system object ", verbosity.low)
self.prefix = prefix
self.init = init
self.ensemble = ensemble
self.motion = motion
self.beads = beads
self.cell = cell
self.nm = nm
self.fcomp = fcomponents
self.forces = Forces()
self.properties = Properties()
self.trajs = Trajectories()
def __init__(self,
beads,
cell,
forces,
ensemble,
prng,
outputs,
nm,
init,
step=0,
tsteps=1000,
ttime=0):
"""Initialises Simulation class.
Args:
beads: A beads object giving the atom positions.
cell: A cell object giving the system box.
forces: A forcefield object giving the force calculator for each
replica of the system.
ensemble: An ensemble object giving the objects necessary for
producing the correct ensemble.
prng: A random number object.
outputs: A list of output objects.
nm: A class dealing with path NM operations.
init: A class to deal with initializing the simulation object.
step: An optional integer giving the current simulation time step.
Defaults to 0.
tsteps: An optional integer giving the total number of steps. Defaults
to 1000.
ttime: The simulation running time. Used on restart, to keep a
cumulative total.
"""
info(" # Initializing simulation object ", verbosity.low)
self.prng = prng
self.ensemble = ensemble
self.beads = beads
self.cell = cell
self.nm = nm
# initialize the configuration of the system
self.init = init
init.init_stage1(self)
self.flist = forces
self.forces = Forces()
self.outputs = outputs
dset(self, "step", depend_value(name="step", value=step))
self.tsteps = tsteps
self.ttime = ttime
self.properties = Properties()
self.trajs = Trajectories()
self.chk = None
self.rollback = True
import sys
from optparse import OptionParser
src_dir = ".."
sys.path.append(src_dir)
from ipi.engine.properties import Properties, Trajectories, help_latex
__all__ = ['help_list', 'list_objects']
list_objects = {'property_list': Properties(),
'trajectory_list': Trajectories()}
usage = "usage: python %prog [options]"
parser = OptionParser(usage=usage)
parser.add_option("-o", action="store", dest="prefix", help="Prefix for the output files", default="help")
parser.add_option("-i", action="store", dest="opt", help="Root object for the help files. Options: ['property_list', 'trajectory_list']", default='property_list')
parser.add_option("-r", action="store_true", dest="ref", default=False, help="If false, this creates a stand-alone document.")
(options, args) = parser.parse_args()
if options.opt not in list_objects:
raise ValueError("Option " + options.opt + " is not a viable tag name")
def help_list(option='property_list', prefix="help", standalone=True):
"""Writes the help file.
# i-PI Copyright (C) 2014-2015 i-PI developers
# See the "licenses" directory for full license information.
import sys
from optparse import OptionParser
src_dir = ".."
sys.path.append(src_dir)
from ipi.engine.properties import Properties, Trajectories, help_latex
__all__ = ['help_list', 'list_objects']
list_objects = {
'property_list': Properties(),
'trajectory_list': Trajectories()
}
usage = "usage: python %prog [options]"
parser = OptionParser(usage=usage)
parser.add_option("-o",
action="store",
dest="prefix",
help="Prefix for the output files",
default="help")
parser.add_option(
"-i",
action="store",
dest="opt",
help=
# This file is part of i-PI.
# i-PI Copyright (C) 2014-2015 i-PI developers
# See the "licenses" directory for full license information.
import sys
from optparse import OptionParser
from ipi.engine.properties import Properties, Trajectories, help_latex
src_dir = ".."
sys.path.append(src_dir)
__all__ = ["help_list", "list_objects"]
list_objects = {
"property_list": Properties(),
"trajectory_list": Trajectories()
}
usage = "usage: python %prog [options]"
parser = OptionParser(usage=usage)
parser.add_option(
"-o",
action="store",
dest="prefix",
help="Prefix for the output files",
default="help",
)
parser.add_option(
"-i",
action="store",
