git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

@@ -0,0 +1,121 @@
+"""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 ""