def make_default(cls):
"""Used to make the default value of the outputs class for use when no
output is specified.
Needed since this is a fairly complicated default, with many mutable
objects, and the default has to be generated by a function that does not
use any mutable objects as arguments.
"""
return [
eoutputs.PropertyOutput(filename="i-pi.md",
stride=10,
outlist=[
"time", "step", "conserved",
"temperature", "potential",
"kinetic_cv"
]),
eoutputs.TrajectoryOutput(filename="i-pi.pos",
stride=100,
what="positions",
format="xyz"),
eoutputs.CheckpointOutput(filename="i-pi.checkpoint",
stride=1000,
overwrite=True)
]
def bind(self):
"""Calls the bind routines for all the objects in the simulation."""
if self.tsteps <= self.step:
raise ValueError(
"Simulation has already run for total_steps, will not even start. "
"Modify total_steps or step counter to continue.")
# initializes the output maker so it can be passed around to systems
f_start = (self.step == 0
) # special operations if we're starting from scratch
if f_start:
mode = "w"
else:
mode = "a"
self.output_maker = eoutputs.OutputMaker(self.outtemplate.prefix,
f_start)
for s in self.syslist:
# binds important computation engines
s.bind(self)
# start forcefields here so we avoid having a shitload of files printed
# out only to find the socket is busy or whatever prevented starting the threads
for k, f in self.fflist.iteritems():
f.start()
# Checks for repeated filenames.
filename_list = [x.filename for x in self.outtemplate]
if len(filename_list) > len(set(filename_list)):
raise ValueError(
"Output filenames are not unique. Modify filename attributes.")
self.outputs = []
for o in self.outtemplate:
o = deepcopy(o) # avoids overwriting the actual filename
if self.outtemplate.prefix != "":
o.filename = self.outtemplate.prefix + "." + o.filename
if type(
o
) is eoutputs.CheckpointOutput: # checkpoints are output per simulation
o.bind(self)
self.outputs.append(o)
else: # properties and trajectories are output per system
isys = 0
for s in self.syslist: # create multiple copies
no = deepcopy(o)
if s.prefix != "":
no.filename = s.prefix + "_" + no.filename
no.bind(s, mode)
self.outputs.append(no)
if f_start: # starting of simulation, print headers (if any)
no.print_header()
isys += 1
self.chk = eoutputs.CheckpointOutput("RESTART", 1, True, 0)
self.chk.bind(self)
if not self.smotion is None:
self.smotion.bind(self.syslist, self.prng, self.output_maker)
def bind(self):
"""Calls the bind routines for all the objects in the simulation."""
if self.tsteps <= self.step:
raise ValueError(
"Simulation has already run for total_steps, will not even start. "
"Modify total_steps or step counter to continue.")
for s in self.syslist:
# binds important computation engines
s.bind(self)
self.outputs = []
for o in self.outtemplate:
if type(
o
) is eoutputs.CheckpointOutput: # checkpoints are output per simulation
o.bind(self)
self.outputs.append(o)
else: # properties and trajectories are output per system
isys = 0
for s in self.syslist: # create multiple copies
no = deepcopy(o)
if s.prefix != "":
no.filename = s.prefix + "_" + no.filename
no.bind(s)
self.outputs.append(no)
isys += 1
self.chk = eoutputs.CheckpointOutput("RESTART", 1, True, 0)
self.chk.bind(self)
if self.mode == "paratemp":
self.paratemp.bind(self.syslist, self.prng)
softexit.register_function(self.paratemp.softexit)
def fetch(self):
"""Returns a CheckpointOutput object."""
step = super(InputCheckpoint, self).fetch()
return eoutputs.CheckpointOutput(self.filename.fetch(),
self.stride.fetch(),
self.overwrite.fetch(),
step=step)
def bind(self):
"""Calls the bind routines for all the objects in the simulation."""
if self.tsteps <= self.step:
raise ValueError(
"Simulation has already run for total_steps, will not even start. "
"Modify total_steps or step counter to continue.")
for s in self.syslist:
# binds important computation engines
s.bind(self)
# Checks for repeated filenames.
filename_list = [x.filename for x in self.outtemplate]
if len(filename_list) > len(set(filename_list)):
raise ValueError(
"Output filenames are not unique. Modify filename attributes.")
self.outputs = []
for o in self.outtemplate:
if type(
o
) is eoutputs.CheckpointOutput: # checkpoints are output per simulation
o.bind(self)
self.outputs.append(o)
else: # properties and trajectories are output per system
isys = 0
for s in self.syslist: # create multiple copies
no = deepcopy(o)
if s.prefix != "":
no.filename = s.prefix + "_" + no.filename
no.bind(s)
self.outputs.append(no)
isys += 1
self.chk = eoutputs.CheckpointOutput("RESTART", 1, True, 0)
self.chk.bind(self)
if not self.smotion is None:
self.smotion.bind(self.syslist, self.prng)
