tools/i-pi/ipi/inputs/barostats.py

   1 """Deals with creating the barostat class.
   2
   3 Copyright (C) 2013, Joshua More and Michele Ceriotti
   4
   5 This program is free software: you can redistribute it and/or modify
   6 it under the terms of the GNU General Public License as published by
   7 the Free Software Foundation, either version 3 of the License, or
   8 (at your option) any later version.
   9
  10 This program is distributed in the hope that it will be useful,
  11 but WITHOUT ANY WARRANTY; without even the implied warranty of
  12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  13 GNU General Public License for more details.
  14
  15 You should have received a copy of the GNU General Public License
  16 along with this program. If not, see <http.//www.gnu.org/licenses/>.
  17
  18
  19 Classes:
  20    InputBaro: Deals with creating the Barostat object from a file, and
  21       writing the checkpoints.
  22 """
  23
  24 import numpy as np
  25 import ipi.engine.thermostats
  26 from ipi.engine.barostats import *
  27 from ipi.utils.inputvalue import *
  28 from ipi.inputs.thermostats import *
  29
  30 __all__ = ['InputBaro']
  31
  32 class InputBaro(Input):
  33    """Barostat input class.
  34
  35    Handles generating the appropriate barostat class from the xml input file,
  36    and generating the xml checkpoint tags and data from an
  37    instance of the object.
  38
  39    Attributes:
  40       mode: An optional string giving the type of barostat used. Defaults to
  41          'rigid'.
  42
  43    Fields:
  44       thermostat: A thermostat object giving the cell thermostat.
  45       tau: The time constant associated with the dynamics of the piston.
  46       p: The conjugate momentum to the volume degree of freedom.
  47    """
  48
  49    attribs={ "mode": (InputAttribute, {"dtype"    : str,
  50                                    "default" : "dummy",
  51                                    "help"     : """The type of barostat.  Currently, only a 'isotropic' barostat is implemented, that combines
  52                                    ideas from the Bussi-Zykova-Parrinello barostat for classical MD with ideas from the
  53                                    Martyna-Hughes-Tuckerman centroid barostat for PIMD; see Ceriotti, More, Manolopoulos, Comp. Phys. Comm. 2013 for
  54                                    implementation details.""",
  55                                    "options"  : ["dummy", "isotropic"]}) }
  56    fields={ "thermostat": (InputThermo, {"default" : input_default(factory=ipi.engine.thermostats.Thermostat),
  57                                          "help"    : "The thermostat for the cell. Keeps the cell velocity distribution at the correct temperature. Note that the 'pile_l', 'pile_g', 'nm_gle' and 'nm_gle_g' options will not work for this thermostat."}),
  58             "tau": (InputValue, {"default" : 1.0,
  59                                   "dtype" : float,
  60                                   "dimension" : "time",
  61                                   "help"    : "The time constant associated with the dynamics of the piston."}),
  62             "p": (InputArray, {  "dtype"     : float,
  63                                  "default"   : input_default(factory=np.zeros, args = (0,)),
  64                                  "help"      : "Momentum (or momenta) of the piston.",
  65                                  "dimension" : "momentum" })
  66            }
  67
  68    default_help = "Simulates an external pressure bath."
  69    default_label = "BAROSTAT"
  70
  71    def store(self, baro):
  72       """Takes a barostat instance and stores a minimal representation of it.
  73
  74       Args:
  75          baro: A barostat object.
  76       """
  77
  78       super(InputBaro,self).store(baro)
  79       self.thermostat.store(baro.thermostat)
  80       self.tau.store(baro.tau)
  81       if type(baro) is BaroBZP:
  82          self.mode.store("isotropic")
  83          self.p.store(baro.p)
  84       elif type(baro) is Barostat:
  85          self.mode.store("dummy")
  86       else:
  87          raise TypeError("The type " + type(baro).__name__ + " is not a valid barostat type")
  88
  89
  90    def fetch(self):
  91       """Creates a barostat object.
  92
  93       Returns:
  94          A barostat object of the appropriate type and with the appropriate
  95          thermostat given the attributes of the InputBaro object.
  96       """
  97
  98       super(InputBaro,self).fetch()
  99       if self.mode.fetch() == "isotropic":
 100          baro = BaroBZP(thermostat=self.thermostat.fetch(), tau=self.tau.fetch())
 101          if self.p._explicit: baro.p = self.p.fetch()
 102       elif self.mode.fetch() == "dummy":
 103          baro = Barostat(thermostat=self.thermostat.fetch(), tau=self.tau.fetch())
 104       else:
 105          raise ValueError(self.mode.fetch() + " is not a valid mode of barostat")
 106
 107       return baro