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