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simulation.py
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"""Contains the class that deals with the running of the simulation and
outputting the results.
Copyright (C) 2013, Joshua More and Michele Ceriotti
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http.//www.gnu.org/licenses/>.
The root class for the whole simulation. Contains references to all the top
level objects used in the simulation, and controls all the steps that are
not inherently system dependent, like the running of each time step,
choosing which properties to initialise, and which properties to output.
Classes:
Simulation: Deals with running the simulation and outputting the results.
"""
__all__ = ['Simulation']
import numpy as np
import os.path, sys, time
from ipi.utils.depend import *
from ipi.utils.units import *
from ipi.utils.prng import *
from ipi.utils.io import *
from ipi.utils.io.io_xml import *
from ipi.utils.messages import verbosity, info
from ipi.utils.softexit import softexit
from ipi.engine.atoms import *
from ipi.engine.cell import *
from ipi.engine.forces import Forces
from ipi.engine.beads import Beads
from ipi.engine.normalmodes import NormalModes
from ipi.engine.properties import Properties, Trajectories
from ipi.engine.outputs import CheckpointOutput
class Simulation(dobject):
"""Main simulation object.
Contains all the references and the main dynamics loop. Also handles the
initialisation and output.
Attributes:
beads: A beads object giving the atom positions.
cell: A cell object giving the system box.
prng: A random number generator object.
flist: A list of forcefield objects giving different ways to partially
calculate the forces.
forces: A Forces object for calculating the total force for all the
replicas.
ensemble: An ensemble object giving the objects necessary for producing
the correct ensemble.
tsteps: The total number of steps.
ttime: The wall clock time (in seconds).
format: A string specifying both the format and the extension of traj
output.
outputs: A list of output objects that should be printed during the run
nm: A helper object dealing with normal modes transformation
properties: A property object for dealing with property output.
trajs: A trajectory object for dealing with trajectory output.
chk: A checkpoint object for dealing with checkpoint output.
rollback: If set to true, the state of the simulation at the start
of the step will be output to a restart file rather than
the current state of the simulation. This is because we cannot
restart from half way through a step, only from the beginning of a
step, so this is necessary for the trajectory to be continuous.
Depend objects:
step: The current simulation step.
"""
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
def bind(self):
"""Calls the bind routines for all the objects in the simulation."""
# binds important computation engines
self.nm.bind(self.beads, self.ensemble)
self.forces.bind(self.beads, self.cell, self.flist)
self.ensemble.bind(self.beads, self.nm, self.cell, self.forces, self.prng)
self.init.init_stage2(self)
# binds output management objects
self.properties.bind(self)
self.trajs.bind(self)
for o in self.outputs:
o.bind(self)
self.chk = CheckpointOutput("RESTART", 1, True, 0)
self.chk.bind(self)
# registers the softexit routine
softexit.register(self.softexit)
def softexit(self):
"""Deals with a soft exit request.
Tries to ensure that a consistent restart checkpoint is
written out.
"""
if self.step < self.tsteps:
self.step += 1
if not self.rollback:
self.chk.store()
self.chk.write(store=False)
self.forces.stop()
def run(self):
"""Runs the simulation.
Does all the simulation steps, and outputs data to the appropriate files
when necessary. Also deals with starting and cleaning up the threads used
in the communication between the driver and the PIMD code.
"""
self.forces.run()
# prints inital configuration -- only if we are not restarting
if (self.step == 0):
self.step = -1
for o in self.outputs:
o.write()
self.step = 0
steptime = 0.0
simtime = time.time()
cstep = 0
tptime = 0.0
tqtime = 0.0
tttime = 0.0
ttot = 0.0
# main MD loop
for self.step in range(self.step,self.tsteps):
# stores the state before doing a step.
# this is a bit time-consuming but makes sure that we can honor soft
# exit requests without screwing the trajectory
steptime = -time.time()
self.chk.store()
self.ensemble.step()
for o in self.outputs:
o.write()
if os.path.exists("EXIT"): # soft-exit
self.rollback = False
softexit.trigger()
steptime += time.time()
ttot += steptime
tptime += self.ensemble.ptime
tqtime += self.ensemble.qtime
tttime += self.ensemble.ttime
cstep += 1
if verbosity.high or (verbosity.medium and self.step%100 == 0) or (verbosity.low and self.step%1000 == 0):
info(" # Average timings at MD step % 7d. t/step: %10.5e [p: %10.5e q: %10.5e t: %10.5e]" %
( self.step, ttot/cstep, tptime/cstep, tqtime/cstep, tttime/cstep ) )
cstep = 0
tptime = 0.0
tqtime = 0.0
tttime = 0.0
ttot = 0.0
info(" # MD diagnostics: V: %10.5e Kcv: %10.5e Ecns: %10.5e" %
(self.properties["potential"], self.properties["kinetic_cv"], self.properties["conserved"] ) )
if (self.ttime > 0 and time.time() - simtime > self.ttime):
info(" # Wall clock time expired! Bye bye!", verbosity.low )
break
info(" # Simulation ran successfully for the prescribed total_step! Bye bye!", verbosity.low )
self.rollback = False
softexit.trigger()

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