git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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tools/i-pi/ipi/inputs/ensembles.py
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185
tools/i-pi/ipi/inputs/ensembles.py
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"""Deals with creating the ensembles class.
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Copyright (C) 2013, Joshua More and Michele Ceriotti
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http.//www.gnu.org/licenses/>.
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Classes:
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InputEnsemble: Deals with creating the Ensemble object from a file, and
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writing the checkpoints.
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"""
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import numpy as np
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import ipi.engine.thermostats
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import ipi.engine.initializer
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import ipi.engine.barostats
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from ipi.engine.ensembles import *
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from ipi.utils.inputvalue import *
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from ipi.inputs.barostats import *
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from ipi.inputs.thermostats import *
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from ipi.inputs.initializer import *
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from ipi.utils.units import *
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__all__ = ['InputEnsemble']
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class InputEnsemble(Input):
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"""Ensemble input class.
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Handles generating the appropriate ensemble class from the xml input file,
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and generating the xml checkpoint tags and data from an instance of the
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object.
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Attributes:
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mode: An optional string giving the mode of ensemble to be simulated.
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Defaults to 'unknown'.
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Fields:
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thermostat: The thermostat to be used for constant temperature dynamics.
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barostat: The barostat to be used for constant pressure or stress
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dynamics.
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timestep: An optional float giving the size of the timestep in atomic
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units. Defaults to 1.0.
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temperature: An optional float giving the temperature in Kelvin. Defaults
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to 1.0.
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pressure: An optional float giving the external pressure in atomic units.
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Defaults to 1.0.
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fixcom: An optional boolean which decides whether the centre of mass
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motion will be constrained or not. Defaults to False.
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replay_file: An optional string that gives an input file name to get
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a trajectory to be re-run.
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"""
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attribs={"mode" : (InputAttribute, {"dtype" : str,
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"help" : "The ensemble that will be sampled during the simulation. 'replay' means that a simulation is restarted from a previous simulation.",
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"options" : ['nve', 'nvt', 'npt', 'replay']}) }
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fields={"thermostat" : (InputThermo, {"default" : input_default(factory=ipi.engine.thermostats.Thermostat),
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"help" : "The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature."} ),
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"barostat" : (InputBaro, {"default" : input_default(factory=ipi.engine.barostats.Barostat),
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"help" : InputBaro.default_help}),
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"timestep": (InputValue, {"dtype" : float,
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"default" : 1.0,
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"help" : "The time step.",
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"dimension" : "time"}),
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"temperature" : (InputValue, {"dtype" : float,
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"default" : 1.0,
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"help" : "The temperature of the system.",
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"dimension" : "temperature"}),
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"pressure" : (InputValue, {"dtype" : float,
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"default" : 1.0,
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"help" : "The external pressure.",
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"dimension" : "pressure"}),
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"fixcom": (InputValue, {"dtype" : bool,
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"default" : True,
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"help" : "This describes whether the centre of mass of the particles is fixed."}),
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"replay_file": (InputInitFile, {"default" : input_default(factory=ipi.engine.initializer.InitBase),
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"help" : "This describes the location to read a trajectory file from."})
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}
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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."
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default_label = "ENSEMBLE"
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def store(self, ens):
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"""Takes an ensemble instance and stores a minimal representation of it.
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Args:
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ens: An ensemble object.
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"""
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super(InputEnsemble,self).store(ens)
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if type(ens) is ReplayEnsemble:
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self.mode.store("rerun")
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tens = 0
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elif type(ens) is NVEEnsemble:
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self.mode.store("nve")
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tens = 1
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elif type(ens) is NVTEnsemble:
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self.mode.store("nvt")
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tens = 2
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elif type(ens) is NPTEnsemble:
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self.mode.store("npt")
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tens = 3
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self.timestep.store(ens.dt)
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self.temperature.store(ens.temp)
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if tens == 0:
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self.replay_file.store(ens.intraj)
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if tens > 1:
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self.thermostat.store(ens.thermostat)
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self.fixcom.store(ens.fixcom)
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if tens > 2:
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self.barostat.store(ens.barostat)
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if tens == 3:
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self.pressure.store(ens.pext)
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def fetch(self):
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"""Creates an ensemble object.
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Returns:
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An ensemble object of the appropriate mode and with the appropriate
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objects given the attributes of the InputEnsemble object.
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"""
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super(InputEnsemble,self).fetch()
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if self.mode.fetch() == "nve" :
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ens = NVEEnsemble(dt=self.timestep.fetch(),
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temp=self.temperature.fetch(), fixcom=self.fixcom.fetch())
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elif self.mode.fetch() == "nvt" :
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ens = NVTEnsemble(dt=self.timestep.fetch(),
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temp=self.temperature.fetch(), thermostat=self.thermostat.fetch(), fixcom=self.fixcom.fetch())
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elif self.mode.fetch() == "npt" :
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ens = NPTEnsemble(dt=self.timestep.fetch(),
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temp=self.temperature.fetch(), thermostat=self.thermostat.fetch(), fixcom=self.fixcom.fetch(),
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pext=self.pressure.fetch(), barostat=self.barostat.fetch() )
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elif self.mode.fetch() == "replay":
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ens = ReplayEnsemble(dt=self.timestep.fetch(),
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temp=self.temperature.fetch(),fixcom=False,intraj=self.replay_file.fetch() )
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else:
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raise ValueError("'" + self.mode.fetch() + "' is not a supported ensemble mode.")
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return ens
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def check(self):
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"""Function that deals with optional arguments.
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Makes sure that if the ensemble requires a thermostat or barostat that
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they have been defined by the user and not given the default values.
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"""
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super(InputEnsemble,self).check()
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if self.mode.fetch() == "nvt":
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if self.thermostat._explicit == False:
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raise ValueError("No thermostat tag supplied for NVT simulation")
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if self.mode.fetch() == "npt":
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if self.thermostat._explicit == False:
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raise ValueError("No thermostat tag supplied for NPT simulation")
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if self.barostat._explicit == False:
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raise ValueError("No barostat tag supplied for NPT simulation")
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if self.barostat.thermostat._explicit == False:
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raise ValueError("No thermostat tag supplied in barostat for NPT simulation")
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if self.timestep.fetch() <= 0:
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raise ValueError("Non-positive timestep specified.")
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if self.temperature.fetch() <= 0:
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raise ValueError("Non-positive temperature specified.")
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if self.mode.fetch() == "npt":
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if not self.pressure._explicit:
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raise ValueError("Pressure should be supplied for constant pressure simulation")
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if self.mode.fetch() == "npt" or self.mode.fetch() == "nvt":
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if not self.temperature._explicit:
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raise ValueError("Temperature should be supplied for constant temperature simulation")
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