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atoms.py
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atoms.py
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"""Deals with creating the atoms 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/>.
Generates an atoms class either from a set of positions and momenta.
This class is only used if no beads tag is present in the xml file.
Classes:
InputAtoms: Deals with creating the Atoms object from a file, and
writing the checkpoints.
"""
import numpy as np
from ipi.engine.atoms import *
from ipi.utils.inputvalue import *
from ipi.utils.depend import *
from ipi.utils.units import unit_to_internal
__all__ = ['InputAtoms']
class InputAtoms(Input):
"""Atoms input class.
Handles generating the appropriate atoms class from the xml input file,
and generating the xml checkpoint tags and data from an instance of the
object.
Attributes:
natoms: An optional integer giving the number of atoms. Defaults to 0.
q: An optional array giving the atom positions. Defaults to an empty
array with no elements.
p: An optional array giving the atom momenta. Defaults to an empty
array with no elements.
m: An optional array giving the atom masses. Defaults to an empty
array with no elements.
names: An optional array giving the atom names. Defaults to an empty
array with no elements
"""
fields={ "natoms" : (InputValue, {"dtype" : int,
"default" : 0,
"help" : "The number of atoms." }),
"q" : (InputArray, {"dtype" : float,
"default" : input_default(factory=np.zeros, args=(0,)),
"help" : "The positions of the atoms, in the format [x1, y1, z1, x2, ... ].",
"dimension" : "length" }),
"p" : (InputArray, {"dtype" : float,
"default" : input_default(factory=np.zeros, args=(0,)),
"help" : "The momenta of the atoms, in the format [px1, py1, pz1, px2, ... ].",
"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 = "Deals with a single replica of the system or classical simulations."
default_label = "ATOMS"
def store(self, atoms):
"""Takes an Atoms instance and stores a minimal representation of it.
Args:
atoms: An Atoms object from which to initialise from.
filename: An optional string giving a filename to take the atom
positions from. Defaults to ''.
"""
super(InputAtoms,self).store()
self.natoms.store(atoms.natoms)
self.q.store(depstrip(atoms.q))
self.p.store(depstrip(atoms.p))
self.m.store(depstrip(atoms.m))
self.names.store(depstrip(atoms.names))
def fetch(self):
"""Creates an atoms object.
Returns:
An atoms object of the appropriate type and with the appropriate
properties given the attributes of the InputAtoms object.
"""
super(InputAtoms,self).fetch()
atoms = Atoms(self.natoms.fetch())
atoms.q = self.q.fetch()
atoms.p = self.p.fetch()
atoms.m = self.m.fetch()
atoms.names = self.names.fetch()
return atoms
def write(self, name="", indent=""):
"""Overloads Input write() function so that nothing is written if
no atoms are present. This occurs if the beads object has been specified,
so that the classical atoms object is not initialized.
Returns:
A string giving the appropriate xml tags for the checkpoint file.
"""
if self.natoms.fetch() > 0:
return super(InputAtoms,self).write(name=name,indent=indent)
else:
return ""

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