Source code for scm.plams.trajectories.xyzhistoryfile

#!/usr/bin/env python

import numpy
from ..tools.periodic_table import PT
from ..mol.molecule import Molecule
from ..mol.atom import Atom
from ..core.settings import Settings
from .xyzfile import XYZTrajectoryFile
from .xyzfile import data_from_xyzcomment

__all__ = ['XYZHistoryFile']

[docs]class XYZHistoryFile (XYZTrajectoryFile) : """ Class representing an XYZ file containing a molecular simulation history with varying numbers of atoms An instance of this class has the following attributes: * ``file_object`` -- A Python :py:class:`file` object, referring to the actual XYZ file * ``position`` -- The frame to which the cursor is currently pointing in the XYZ file * ``mode`` -- Designates whether the file is in read or write mode ('r' or 'w') * ``elements`` -- The elements of the atoms in the system at the current frame An |XYZHistoryFile| object behaves very similar to a regular file object. It has read and write methods (:meth:`read_next` and :meth:`write_next`) that read and write from/to the position of the cursor in the ``file_object`` attribute. If the file is in read mode, an additional method :meth:`read_frame` can be used that moves the cursor to any frame in the file and reads from there. The amount of information stored in memory is kept to a minimum, as only information from the current frame is ever stored. Reading and writing to and from the files can be done as follows:: >>> from scm.plams import XYZHistoryFile >>> xyz = XYZHistoryFile('old.xyz') >>> mol = xyz.get_plamsmol() >>> xyzout = XYZHistoryFile('new.xyz',mode='w') >>> for i in range(xyz.get_length()) : >>> crd,cell = xyz.read_frame(i,molecule=mol) >>> xyzout.write_next(molecule=mol) The above script reads information from the XYZ file ``old.xyz`` into the |Molecule| object ``mol`` in a step-by-step manner. The |Molecule| object is then passed to the :meth:`write_next` method of the new |XYZHistoryFile| object corresponding to the new xyz file ``new.xyz``. The exact same result can also be achieved by iterating over the instance as a callable >>> xyz = XYZHistoryFile('old.xyz') >>> mol = xyz.get_plamsmol() >>> xyzout = XYZHistoryFile('new.xyz',mode='w') >>> for crd,cell in xyz(mol) : >>> xyzout.write_next(molecule=mol) This procedure requires all coordinate information to be passed to and from the |Molecule| object for each frame, which can be time-consuming. It is therefore also possible to bypass the |Molecule| object when reading through the frames:: >>> xyz = XYZHistoryFile('old.xyz') >>> xyzout = XYZHistoryFile('new.xyz',mode='w') >>> for crd,cell in xyz : >>> xyzout.write_next(coords=crd,elements=xyz.elements) By default the write mode will create a minimal version of the XYZ file, containing only elements and coordinates. Additional information can be written to the file by supplying additional arguments to the :meth:`write_next` method. The additional keywords `step` and `energy` trigger the writing of a remark containing the molecule name, the step number, the energy, and the lattice vectors. >>> mol = Molecule('singleframe.xyz') >>> xyzout = XYZHistoryFile('new.xyz',mode='w') >>> xyzout.set_name('MyMol') >>> xyzout.write_next(molecule=mol, step=0, energy=5.) """
[docs] def __init__ (self, filename, mode='r', fileobject=None, ntap=None) : """ Initiates an XYZHistoryFile object * ``filename`` -- The path to the XYZ file * ``mode`` -- The mode in which to open the XYZ file ('r' or 'w') * ``fileobject`` -- Optionally, a file object can be passed instead (filename needs to be set to None) * ``ntap`` -- If the file is in write mode, the number of atoms can be passed here """ XYZTrajectoryFile.__init__(self,filename,mode,fileobject,ntap) self.input_elements = self.elements[:]
def _is_endoffile (self) : """ If the end of file is reached, return coords and cell as None """ end = False line = self.file_object.readline() if len(line) == 0 : end = True return end nats = int(line.split()[0]) for i in range(nats+1) : line = self.file_object.readline() if len(line) == 0 : end = True break return end def _read_coordinates (self, molecule) : """ Read the coordinates at current step """ # Find the number of atoms line = self.file_object.readline() if len(line) == 0 : return None, None # End of file is reached nats = int(line.split()[0]) line = self.file_object.readline() # Handle the comment line cell = None historydata = data_from_xyzcomment(line) if 'Lattice' in historydata : cell = historydata['Lattice'] del historydata['Lattice'] if self.include_historydata : self.historydata = historydata # Read coordinates and elements coords = [] elements = [] for i in range(nats) : line = self.file_object.readline() words = line.split() coords.append([float(w) for w in words[1:4]]) elements.append(words[0]) # If the elements changed, update the molecule if elements != self.elements : self.elements = elements self.coords = numpy.array(coords) # Rebuild the molecule (bonds will disappear for now) if isinstance(molecule,Molecule) : for at in reversed(molecule.atoms) : molecule.delete_atom(at) molecule.properties = Settings() for el in elements : atom = Atom(PT.get_atomic_number(el)) molecule.add_atom(atom) else : self.coords[:] = coords # Assign the data to the molecule object if isinstance(molecule,Molecule) : self._set_plamsmol(self.coords,cell,molecule,bonds=None) return coords, cell
[docs] def write_next (self,coords=None,molecule=None,elements=None,cell=[0.,0.,0.],conect=None,historydata=None) : """ Write frame to next position in trajectory file * ``coords`` -- A list or numpy array of (``ntap``,3) containing the system coordinates * ``molecule`` -- A molecule object to read the molecular data from * ``elements`` -- The element symbols of the atoms in the system * ``cell`` -- A set of lattice vectors or cell diameters * ``energy`` -- An energy value to be written to the remark line * ``conect`` -- A dictionary containing connectivity info (not used) * ``historydata`` -- A dictionary containing additional variables to be written to the comment line The ``historydata`` dictionary can contain for example: ('Step','Energy'), the frame number and the energy respectively .. note:: Either ``coords`` and ``elements`` or ``molecule`` are mandatory arguments """ if isinstance(molecule,Molecule) : coords, cell, elements = self._read_plamsmol(molecule)[:3] self.elements = elements cell = self._convert_cell(cell) self._write_moldata(coords, cell, historydata) self.position += 1