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

   1 """Deals with creating the beads 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    InputBeads: Deals with creating the Beads object from a file, and
  21       writing the checkpoints.
  22 """
  23
  24 import numpy as np
  25 from ipi.engine.beads import *
  26 from ipi.engine.atoms import Atoms
  27 from ipi.utils.inputvalue import *
  28 from ipi.utils.depend import *
  29 from ipi.utils.units import *
  30 from ipi.inputs.atoms import *
  31
  32 __all__ = ['InputBeads']
  33
  34 class InputBeads(Input):
  35    """Beads input class.
  36
  37    Handles generating the appropriate beads class from the xml input file,
  38    and generating the xml checkpoint tags and data from an instance of the
  39    object.
  40
  41    Attributes:
  42       nbeads: An optional integer giving the number of beads. Defaults to 0.
  43       natoms: An optional integer giving the number of atoms. Defaults to 0.
  44
  45    Fields:
  46       q: An optional array giving the bead positions. Defaults to an empty
  47          array with no elements.
  48       p: An optional array giving the bead momenta. Defaults to an empty
  49          array with no elements.
  50       m: An optional array giving the bead masses. Defaults to an empty array
  51          with no elements.
  52       names: An optional array giving the bead names. Defaults to an empty
  53          array with no elements.
  54    """
  55
  56    attribs = { "natoms"  : (InputAttribute, {"dtype" : int,  "default"   : 0,
  57                                              "help"  : "The number of atoms."}),
  58                "nbeads"  : (InputAttribute, {"dtype" : int,  "default"   : 0,
  59                                              "help"  : "The number of beads."})
  60             }
  61    fields={ "q"     : (InputArray, {"dtype"     : float,
  62                                     "default"   : input_default(factory=np.zeros, args = (0,)),
  63                                     "help"      : "The positions of the beads. In an array of size [nbeads, 3*natoms].",
  64                                     "dimension" : "length"}),
  65             "p"     : (InputArray, {"dtype"     : float,
  66                                     "default"   : input_default(factory=np.zeros, args = (0,)),
  67                                     "help"      : "The momenta of the beads. In an array of size [nbeads, 3*natoms].",
  68                                     "dimension" : "momentum"}),
  69             "m"     : (InputArray, {"dtype"     : float,
  70                                     "default"   : input_default(factory=np.zeros, args = (0,)),
  71                                     "help"      : "The masses of the atoms, in the format [m1, m2, ... ].",
  72                                     "dimension" : "mass"}),
  73             "names" : (InputArray, {"dtype"     : str,
  74                                     "default"   : input_default(factory=np.zeros, args=(0,), kwargs={'dtype': np.dtype('|S6')}),
  75                                     "help"      : "The names of the atoms, in the format [name1, name2, ... ]."})  }
  76
  77    default_help = "Describes the bead configurations in a path integral simulation."
  78    default_label = "BEADS"
  79
  80
  81    def store(self, beads):
  82       """Takes a Beads instance and stores a minimal representation of it.
  83
  84       Args:
  85          beads: A Beads object from which to initialise from.
  86       """
  87
  88       super(InputBeads,self).store()
  89       self.natoms.store(beads.natoms)
  90       self.nbeads.store(beads.nbeads)
  91
  92       self.q.store(depstrip(beads.q))
  93       self.p.store(depstrip(beads.p))
  94       self.m.store(depstrip(beads.m))
  95       self.names.store(depstrip(beads.names))
  96
  97    def fetch(self):
  98       """Creates a beads object.
  99
 100       Returns:
 101          A beads object of the appropriate type and with the appropriate
 102          properties given the attributes of the InputBeads object.
 103       """
 104
 105       super(InputBeads,self).fetch()
 106       beads = Beads(self.natoms.fetch(),self.nbeads.fetch())
 107
 108       # tries to fill up with as much data as available and valid
 109       q = self.q.fetch()
 110       if (q.shape == (beads.nbeads,3*beads.natoms)):
 111          beads.q = q
 112       elif (beads.nbeads == 1 and q.shape == (3*beads.natoms,)):
 113          beads.q = q
 114       elif len(q) != 0:
 115          raise ValueError("Array shape mismatches for q in <beads> input.")
 116
 117       p = self.p.fetch()
 118       if (p.shape == (beads.nbeads,3*beads.natoms)):
 119          beads.p = p
 120       elif (beads.nbeads == 1 and p.shape == (3*beads.natoms,)):
 121          beads.p = p
 122       elif len(p) != 0:
 123          raise ValueError("Array shape mismatches for p in <beads> input.")
 124
 125       m = self.m.fetch()
 126       if (m.shape == (beads.natoms,)):
 127          beads.m = m
 128       elif len(m) != 0:
 129          raise ValueError("Array shape mismatches for m in <beads> input.")
 130
 131       n = self.names.fetch()
 132       if (n.shape == (beads.natoms,)):
 133          beads.names = n
 134       elif len(n) != 0:
 135          raise ValueError("Array shape mismatches for names in <beads> input.")
 136
 137       return beads