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beads.py
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Sat, Jun 22, 22:59

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

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