def bind(self, simul):
"""Binds output proxy to simulation object.
Args:
simul: A simulation object to be bound.
"""
self.simul = simul
import ipi.inputs.simulation as isimulation
self.status = isimulation.InputSimulation()
self.status.store(simul)
def load_from_xml(fn_input,
custom_verbosity=None,
request_banner=False,
read_only=False):
"""Load an XML input file and return a `Simulation` object.
Arguments:
fn_input (str): Name of the input file.
custom_verbosity (str): If not `None`, overrides the verbosity
specified by the input file.
request_banner (bool): Whether to print the i-PI banner,
if verbosity is higher than 'quiet'.
"""
# parse the file
xmlrestart = xml_parse_file(open(fn_input))
# prepare the simulation input object
input_simulation = isimulation.InputSimulation()
# check the input and partition it appropriately
input_simulation.parse(xmlrestart.fields[0][1])
# override verbosity if requested
if custom_verbosity is None:
# Get from the input file
custom_verbosity = input_simulation.verbosity.fetch()
input_simulation.verbosity.value = custom_verbosity
# print banner if not suppressed and simulation verbose enough
if request_banner and input_simulation.verbosity.value != "quiet":
banner()
# create the simulation object
simulation = input_simulation.fetch()
# pipe between the components of the simulation
simulation.bind(read_only)
# echo the input file if verbose enough
if verbosity.level > 0:
print(" # i-PI loaded input file: ", fn_input)
if verbosity.level > 1:
print(" --- begin input file content ---")
ifile = open(fn_input, "r")
for line in ifile.readlines():
print(line, end=" ")
print(" --- end input file content ---")
ifile.close()
return simulation
src_dir = "../"
sys.path.append(src_dir)
from ipi.inputs import barostats, cell, simulation, system, \
ensembles, thermostats, forcefields, forces, atoms, beads, \
prng, initializer, normalmodes, outputs, motion, smotion
time.sleep(1)
__all__ = ['help', 'objects']
objects = {
'barostats': barostats.InputBaro(),
'cell': cell.InputCell(),
'simulation': simulation.InputSimulation(),
'smotion': smotion.smotion.InputSmotion(),
'remd': smotion.remd.InputReplicaExchange(),
'meta': smotion.metad.InputMetaDyn(),
'system': system.InputSystem(),
'ensembles': ensembles.InputEnsemble(),
'motion': motion.motion.InputMotion(),
'dynamics': motion.dynamics.InputDynamics(),
'alchemy': motion.alchemy.InputAlchemy(),
'instanton': motion.instanton.InputInst(),
'phonons': motion.phonons.InputDynMatrix(),
'geop': motion.geop.InputGeop(),
'neb': motion.neb.InputNEB(),
'thermostats': thermostats.InputThermo(),
'forcefield': forcefields.InputForceField(),
'ffsocket': forcefields.InputFFSocket(),
outputs,
motion,
smotion,
)
src_dir = "../"
sys.path.append(src_dir)
time.sleep(1)
__all__ = ["help", "objects"]
objects = {
"barostats": barostats.InputBaro(),
"cell": cell.InputCell(),
"simulation": simulation.InputSimulation(),
"smotion": smotion.smotion.InputSmotion(),
"remd": smotion.remd.InputReplicaExchange(),
"meta": smotion.metad.InputMetaDyn(),
"system": system.InputSystem(),
"ensembles": ensembles.InputEnsemble(),
"motion": motion.motion.InputMotion(),
"dynamics": motion.dynamics.InputDynamics(),
"t_ramp": motion.ramp.InputTemperatureRamp(),
"p_ramp": motion.ramp.InputPressureRamp(),
"alchemy": motion.alchemy.InputAlchemy(),
"planetary": motion.planetary.InputPlanetary(),
"atomswap": motion.atomswap.InputAtomSwap(),
"instanton": motion.instanton.InputInst(),
"phonons": motion.phonons.InputDynMatrix(),
"geop": motion.geop.InputGeop(),
