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ensembles.py
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Wed, Jul 17, 23:37

ensembles.py
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"""Deals with creating the ensembles class.
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/>.
Classes:
InputEnsemble: Deals with creating the Ensemble object from a file, and
writing the checkpoints.
"""
import numpy as np
import ipi.engine.thermostats
import ipi.engine.initializer
import ipi.engine.barostats
from ipi.engine.ensembles import *
from ipi.utils.inputvalue import *
from ipi.inputs.barostats import *
from ipi.inputs.thermostats import *
from ipi.inputs.initializer import *
from ipi.utils.units import *
__all__ = ['InputEnsemble']
class InputEnsemble(Input):
"""Ensemble input class.
Handles generating the appropriate ensemble class from the xml input file,
and generating the xml checkpoint tags and data from an instance of the
object.
Attributes:
mode: An optional string giving the mode of ensemble to be simulated.
Defaults to 'unknown'.
Fields:
thermostat: The thermostat to be used for constant temperature dynamics.
barostat: The barostat to be used for constant pressure or stress
dynamics.
timestep: An optional float giving the size of the timestep in atomic
units. Defaults to 1.0.
temperature: An optional float giving the temperature in Kelvin. Defaults
to 1.0.
pressure: An optional float giving the external pressure in atomic units.
Defaults to 1.0.
fixcom: An optional boolean which decides whether the centre of mass
motion will be constrained or not. Defaults to False.
replay_file: An optional string that gives an input file name to get
a trajectory to be re-run.
"""
attribs={"mode" : (InputAttribute, {"dtype" : str,
"help" : "The ensemble that will be sampled during the simulation. 'replay' means that a simulation is restarted from a previous simulation.",
"options" : ['nve', 'nvt', 'npt', 'replay']}) }
fields={"thermostat" : (InputThermo, {"default" : input_default(factory=ipi.engine.thermostats.Thermostat),
"help" : "The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature."} ),
"barostat" : (InputBaro, {"default" : input_default(factory=ipi.engine.barostats.Barostat),
"help" : InputBaro.default_help}),
"timestep": (InputValue, {"dtype" : float,
"default" : 1.0,
"help" : "The time step.",
"dimension" : "time"}),
"temperature" : (InputValue, {"dtype" : float,
"default" : 1.0,
"help" : "The temperature of the system.",
"dimension" : "temperature"}),
"pressure" : (InputValue, {"dtype" : float,
"default" : 1.0,
"help" : "The external pressure.",
"dimension" : "pressure"}),
"fixcom": (InputValue, {"dtype" : bool,
"default" : True,
"help" : "This describes whether the centre of mass of the particles is fixed."}),
"replay_file": (InputInitFile, {"default" : input_default(factory=ipi.engine.initializer.InitBase),
"help" : "This describes the location to read a trajectory file from."})
}
default_help = "Holds all the information that is ensemble specific, such as the temperature and the external pressure, and the thermostats and barostats that control it."
default_label = "ENSEMBLE"
def store(self, ens):
"""Takes an ensemble instance and stores a minimal representation of it.
Args:
ens: An ensemble object.
"""
super(InputEnsemble,self).store(ens)
if type(ens) is ReplayEnsemble:
self.mode.store("rerun")
tens = 0
elif type(ens) is NVEEnsemble:
self.mode.store("nve")
tens = 1
elif type(ens) is NVTEnsemble:
self.mode.store("nvt")
tens = 2
elif type(ens) is NPTEnsemble:
self.mode.store("npt")
tens = 3
self.timestep.store(ens.dt)
self.temperature.store(ens.temp)
if tens == 0:
self.replay_file.store(ens.intraj)
if tens > 1:
self.thermostat.store(ens.thermostat)
self.fixcom.store(ens.fixcom)
if tens > 2:
self.barostat.store(ens.barostat)
if tens == 3:
self.pressure.store(ens.pext)
def fetch(self):
"""Creates an ensemble object.
Returns:
An ensemble object of the appropriate mode and with the appropriate
objects given the attributes of the InputEnsemble object.
"""
super(InputEnsemble,self).fetch()
if self.mode.fetch() == "nve" :
ens = NVEEnsemble(dt=self.timestep.fetch(),
temp=self.temperature.fetch(), fixcom=self.fixcom.fetch())
elif self.mode.fetch() == "nvt" :
ens = NVTEnsemble(dt=self.timestep.fetch(),
temp=self.temperature.fetch(), thermostat=self.thermostat.fetch(), fixcom=self.fixcom.fetch())
elif self.mode.fetch() == "npt" :
ens = NPTEnsemble(dt=self.timestep.fetch(),
temp=self.temperature.fetch(), thermostat=self.thermostat.fetch(), fixcom=self.fixcom.fetch(),
pext=self.pressure.fetch(), barostat=self.barostat.fetch() )
elif self.mode.fetch() == "replay":
ens = ReplayEnsemble(dt=self.timestep.fetch(),
temp=self.temperature.fetch(),fixcom=False,intraj=self.replay_file.fetch() )
else:
raise ValueError("'" + self.mode.fetch() + "' is not a supported ensemble mode.")
return ens
def check(self):
"""Function that deals with optional arguments.
Makes sure that if the ensemble requires a thermostat or barostat that
they have been defined by the user and not given the default values.
"""
super(InputEnsemble,self).check()
if self.mode.fetch() == "nvt":
if self.thermostat._explicit == False:
raise ValueError("No thermostat tag supplied for NVT simulation")
if self.mode.fetch() == "npt":
if self.thermostat._explicit == False:
raise ValueError("No thermostat tag supplied for NPT simulation")
if self.barostat._explicit == False:
raise ValueError("No barostat tag supplied for NPT simulation")
if self.barostat.thermostat._explicit == False:
raise ValueError("No thermostat tag supplied in barostat for NPT simulation")
if self.timestep.fetch() <= 0:
raise ValueError("Non-positive timestep specified.")
if self.temperature.fetch() <= 0:
raise ValueError("Non-positive temperature specified.")
if self.mode.fetch() == "npt":
if not self.pressure._explicit:
raise ValueError("Pressure should be supplied for constant pressure simulation")
if self.mode.fetch() == "npt" or self.mode.fetch() == "nvt":
if not self.temperature._explicit:
raise ValueError("Temperature should be supplied for constant temperature simulation")

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