def step(self):
"""Does one simulation time step."""
self.ptime = self.ttime = 0
self.qtime = -time.time()
try:
if (self.intraj.mode == "xyz"):
for b in self.beads:
myatoms = read_xyz(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units,
1.0)
b.q[:] = myatoms.q
elif (self.intraj.mode == "pdb"):
for b in self.beads:
myatoms, mycell = read_pdb(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units,
1.0)
mycell.h *= unit_to_internal("length", self.intraj.units,
1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif (self.intraj.mode == "chk"
or self.intraj.mode == "checkpoint"):
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
self.qtime += time.time()
def init_chk(filename):
"""Reads an checkpoint file and returns the data contained in it.
Args:
filename: A string giving the name of the checkpoint file to be read from.
Returns:
A Beads object, Cell object and Thermostat object as read from the
checkpoint file.
"""
# reads configuration from a checkpoint file
rfile = open(filename, "r")
xmlchk = xml_parse_file(rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
rcell = simchk.cell.fetch()
rbeads = simchk.beads.fetch()
rthermo = simchk.ensemble.thermostat.fetch()
return (rbeads, rcell, rthermo)
def init_chk(filename):
"""Reads an checkpoint file and returns the data contained in it.
Args:
filename: A string giving the name of the checkpoint file to be read from.
Returns:
A Beads object, Cell object and Thermostat object as read from the
checkpoint file.
"""
# reads configuration from a checkpoint file
rfile = open(filename,"r")
xmlchk = xml_parse_file(rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
rcell = simchk.cell.fetch()
rbeads = simchk.beads.fetch()
rthermo = simchk.ensemble.thermostat.fetch()
return (rbeads, rcell, rthermo)
def step(self):
"""Does one simulation time step."""
self.ptime = self.ttime = 0
self.qtime = -time.time()
try:
if self.intraj.mode == "xyz":
for b in self.beads:
myatoms = read_xyz(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units, 1.0)
b.q[:] = myatoms.q
elif self.intraj.mode == "pdb":
for b in self.beads:
myatoms, mycell = read_pdb(self.rfile)
myatoms.q *= unit_to_internal("length", self.intraj.units, 1.0)
mycell.h *= unit_to_internal("length", self.intraj.units, 1.0)
b.q[:] = myatoms.q
self.cell.h[:] = mycell.h
elif self.intraj.mode == "chk" or self.intraj.mode == "checkpoint":
# reads configuration from a checkpoint file
xmlchk = xml_parse_file(self.rfile) # Parses the file.
from ipi.inputs.simulation import InputSimulation
simchk = InputSimulation()
simchk.parse(xmlchk.fields[0][1])
mycell = simchk.cell.fetch()
mybeads = simchk.beads.fetch()
self.cell.h[:] = mycell.h
self.beads.q[:] = mybeads.q
softexit.trigger(" # Read single checkpoint")
except EOFError:
softexit.trigger(" # Finished reading re-run trajectory")
self.qtime += time.time()