git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

@@ -0,0 +1,107 @@
+"""Deals with creating the barostat 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:
+   InputBaro: Deals with creating the Barostat object from a file, and
+      writing the checkpoints.
+"""
+
+import numpy as np
+import ipi.engine.thermostats
+from ipi.engine.barostats import *
+from ipi.utils.inputvalue import *
+from ipi.inputs.thermostats import *
+
+__all__ = ['InputBaro']
+
+class InputBaro(Input):
+   """Barostat input class.
+
+   Handles generating the appropriate barostat 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 type of barostat used. Defaults to
+         'rigid'.
+
+   Fields:
+      thermostat: A thermostat object giving the cell thermostat.
+      tau: The time constant associated with the dynamics of the piston.
+      p: The conjugate momentum to the volume degree of freedom.
+   """
+
+   attribs={ "mode": (InputAttribute, {"dtype"    : str,
+                                   "default" : "dummy",
+                                   "help"     : """The type of barostat.  Currently, only a 'isotropic' barostat is implemented, that combines
+                                   ideas from the Bussi-Zykova-Parrinello barostat for classical MD with ideas from the
+                                   Martyna-Hughes-Tuckerman centroid barostat for PIMD; see Ceriotti, More, Manolopoulos, Comp. Phys. Comm. 2013 for
+                                   implementation details.""",
+                                   "options"  : ["dummy", "isotropic"]}) }
+   fields={ "thermostat": (InputThermo, {"default" : input_default(factory=ipi.engine.thermostats.Thermostat),
+                                         "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."}),
+            "tau": (InputValue, {"default" : 1.0,
+                                  "dtype" : float,
+                                  "dimension" : "time",
+                                  "help"    : "The time constant associated with the dynamics of the piston."}),
+            "p": (InputArray, {  "dtype"     : float,
+                                 "default"   : input_default(factory=np.zeros, args = (0,)),
+                                 "help"      : "Momentum (or momenta) of the piston.",
+                                 "dimension" : "momentum" })
+           }
+
+   default_help = "Simulates an external pressure bath."
+   default_label = "BAROSTAT"
+
+   def store(self, baro):
+      """Takes a barostat instance and stores a minimal representation of it.
+
+      Args:
+         baro: A barostat object.
+      """
+
+      super(InputBaro,self).store(baro)
+      self.thermostat.store(baro.thermostat)
+      self.tau.store(baro.tau)
+      if type(baro) is BaroBZP:
+         self.mode.store("isotropic")
+         self.p.store(baro.p)
+      elif type(baro) is Barostat:
+         self.mode.store("dummy")
+      else:
+         raise TypeError("The type " + type(baro).__name__ + " is not a valid barostat type")
+
+
+   def fetch(self):
+      """Creates a barostat object.
+
+      Returns:
+         A barostat object of the appropriate type and with the appropriate
+         thermostat given the attributes of the InputBaro object.
+      """
+
+      super(InputBaro,self).fetch()
+      if self.mode.fetch() == "isotropic":
+         baro = BaroBZP(thermostat=self.thermostat.fetch(), tau=self.tau.fetch())
+         if self.p._explicit: baro.p = self.p.fetch()
+      elif self.mode.fetch() == "dummy":
+         baro = Barostat(thermostat=self.thermostat.fetch(), tau=self.tau.fetch())
+      else:
+         raise ValueError(self.mode.fetch() + " is not a valid mode of barostat")
+
+      return baro