forked from lijiext/lammps
138 lines
5.3 KiB
Python
138 lines
5.3 KiB
Python
"""Deals with creating the beads 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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InputBeads: Deals with creating the Beads 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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from ipi.engine.beads import *
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from ipi.engine.atoms import Atoms
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from ipi.utils.inputvalue import *
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from ipi.utils.depend import *
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from ipi.utils.units import *
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from ipi.inputs.atoms import *
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__all__ = ['InputBeads']
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class InputBeads(Input):
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"""Beads input class.
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Handles generating the appropriate beads 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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nbeads: An optional integer giving the number of beads. Defaults to 0.
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natoms: An optional integer giving the number of atoms. Defaults to 0.
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Fields:
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q: An optional array giving the bead positions. Defaults to an empty
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array with no elements.
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p: An optional array giving the bead momenta. Defaults to an empty
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array with no elements.
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m: An optional array giving the bead masses. Defaults to an empty array
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with no elements.
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names: An optional array giving the bead names. Defaults to an empty
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array with no elements.
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"""
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attribs = { "natoms" : (InputAttribute, {"dtype" : int, "default" : 0,
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"help" : "The number of atoms."}),
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"nbeads" : (InputAttribute, {"dtype" : int, "default" : 0,
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"help" : "The number of beads."})
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}
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fields={ "q" : (InputArray, {"dtype" : float,
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"default" : input_default(factory=np.zeros, args = (0,)),
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"help" : "The positions of the beads. In an array of size [nbeads, 3*natoms].",
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"dimension" : "length"}),
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"p" : (InputArray, {"dtype" : float,
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"default" : input_default(factory=np.zeros, args = (0,)),
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"help" : "The momenta of the beads. In an array of size [nbeads, 3*natoms].",
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"dimension" : "momentum"}),
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"m" : (InputArray, {"dtype" : float,
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"default" : input_default(factory=np.zeros, args = (0,)),
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"help" : "The masses of the atoms, in the format [m1, m2, ... ].",
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"dimension" : "mass"}),
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"names" : (InputArray, {"dtype" : str,
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"default" : input_default(factory=np.zeros, args=(0,), kwargs={'dtype': np.dtype('|S6')}),
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"help" : "The names of the atoms, in the format [name1, name2, ... ]."}) }
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default_help = "Describes the bead configurations in a path integral simulation."
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default_label = "BEADS"
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def store(self, beads):
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"""Takes a Beads instance and stores a minimal representation of it.
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Args:
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beads: A Beads object from which to initialise from.
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"""
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super(InputBeads,self).store()
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self.natoms.store(beads.natoms)
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self.nbeads.store(beads.nbeads)
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self.q.store(depstrip(beads.q))
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self.p.store(depstrip(beads.p))
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self.m.store(depstrip(beads.m))
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self.names.store(depstrip(beads.names))
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def fetch(self):
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"""Creates a beads object.
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Returns:
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A beads object of the appropriate type and with the appropriate
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properties given the attributes of the InputBeads object.
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"""
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super(InputBeads,self).fetch()
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beads = Beads(self.natoms.fetch(),self.nbeads.fetch())
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# tries to fill up with as much data as available and valid
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q = self.q.fetch()
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if (q.shape == (beads.nbeads,3*beads.natoms)):
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beads.q = q
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elif (beads.nbeads == 1 and q.shape == (3*beads.natoms,)):
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beads.q = q
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elif len(q) != 0:
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raise ValueError("Array shape mismatches for q in <beads> input.")
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p = self.p.fetch()
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if (p.shape == (beads.nbeads,3*beads.natoms)):
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beads.p = p
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elif (beads.nbeads == 1 and p.shape == (3*beads.natoms,)):
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beads.p = p
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elif len(p) != 0:
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raise ValueError("Array shape mismatches for p in <beads> input.")
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m = self.m.fetch()
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if (m.shape == (beads.natoms,)):
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beads.m = m
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elif len(m) != 0:
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raise ValueError("Array shape mismatches for m in <beads> input.")
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n = self.names.fetch()
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if (n.shape == (beads.natoms,)):
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beads.names = n
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elif len(n) != 0:
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raise ValueError("Array shape mismatches for names in <beads> input.")
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return beads
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