Source code for pymatgen.core.trajectory

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from pymatgen.core.structure import Structure, Lattice
from import Xdatcar, Vasprun
from monty.json import MSONable
from fnmatch import fnmatch
import numpy as np
import warnings
import os

This module provides classes used to define a MD trajectory.

__author__ = "Eric Sivonxay, Shyam Dwaraknath"
__version__ = "0.0"
__date__ = "Jan 25, 2019"

[docs]class Trajectory(MSONable): """ Trajectory object that stores structural information related to a MD simulation. Provides basic functions such as slicing trajectory or obtaining displacements. """ def __init__(self, lattice, species, frac_coords, time_step=2, site_properties=None, constant_lattice=True, coords_are_displacement=False, base_positions=None): """ Create a trajectory object Args: lattice: The lattice as any 2D array. Each row should correspond to a lattice vector. E.g., [[10,0,0], [20,10,0], [0,0,30]] specifies a lattice with lattice vectors [10,0,0], [20,10,0] and [0,0,30]. species: List of species on each site. Can take in flexible input, including: i. A sequence of element / specie specified either as string symbols, e.g. ["Li", "Fe2+", "P", ...] or atomic numbers, e.g., (3, 56, ...) or actual Element or Specie objects. ii. List of dict of elements/species and occupancies, e.g., [{"Fe" : 0.5, "Mn":0.5}, ...]. This allows the setup of disordered structures. frac_coords (MxNx3 array): list of fractional coordinates of each species time_step (int, float): Timestep of simulation in femtoseconds. Defaults to 2fs. site_properties (list): Properties associated with the sites as a list of dicts of sequences, e.g., [{"magmom":[5,5,5,5]}, {"magmom":[5,5,5,5]}]. The sequences have to be the same length as the atomic species and fractional_coords. Number of supplied dicts should match number of frames in trajectory Defaults to None for no properties. constant_lattice (bool): Whether the lattice changes during the simulation, such as in an NPT MD simulation. coords_are_displacement (bool): Whether supplied coordinates are given in displacements (True) or positions (False) base_positions (Nx3 array): The starting positions of all atoms in trajectory. Used to reconstruct positions when converting from displacements to positions. Only needs to be specified if coords_are_displacement=True. Defaults to first index of frac_coords if coords_are_displacement=False. """ # To support from_dict and as_dict if isinstance(frac_coords, list): frac_coords = np.array(frac_coords) if isinstance(lattice, list): lattice = np.array(lattice) self.frac_coords = frac_coords if coords_are_displacement: if base_positions is None: warnings.warn( "Without providing an array of starting positions, the positions for each time step will not be available") self.base_positions = base_positions else: self.base_positions = frac_coords[0] self.coords_are_displacement = coords_are_displacement if not constant_lattice and np.shape(lattice) == (3, 3): self.lattice = [lattice for i in range(self.frac_coords.shape[0])] else: self.lattice = lattice self.constant_lattice = constant_lattice self.species = species self.site_properties = site_properties self.time_step = time_step
[docs] def get_structure(self, i): """ Returns structure at specified index Args: i (int): Index of structure Returns: (Structure) pymatgen structure object """ return self[i]
[docs] def to_positions(self): """ Converts fractional coordinates of trajectory into positions """ if self.coords_are_displacement: cumulative_displacements = np.cumsum(self.frac_coords, axis=0) positions = self.base_positions + cumulative_displacements self.frac_coords = positions self.coords_are_displacement = False return
[docs] def to_displacements(self): """ Converts position coordinates of trajectory into displacements between consecutive frames """ if not self.coords_are_displacement: displacements = np.subtract(self.frac_coords, np.roll(self.frac_coords, 1, axis=0)) displacements[0] = np.zeros(np.shape(self.frac_coords[0])) # Deal with PBC displacements = [np.subtract(item, np.round(item)) for item in displacements] self.frac_coords = displacements self.coords_are_displacement = True return
[docs] def extend(self, trajectory): """ Concatenate another trajectory Args: trajectory (Trajectory): Trajectory to add """ if self.time_step != trajectory.time_step: raise ValueError('Trajectory not extended: Time steps of trajectories is incompatible') if len(self.species) != len(trajectory.species) and self.species != trajectory.species: raise ValueError('Trajectory not extended: species in trajectory do not match') self.to_positions() trajectory.to_positions() self.frac_coords = np.concatenate((self.frac_coords, trajectory.frac_coords), axis=0) self.lattice, self.constant_lattice = self._combine_attribute(self.lattice, trajectory.lattice, self.frac_coords.shape[0], trajectory.frac_coords.shape[0]) self.site_properties = self._combine_attribute(self.site_properties, trajectory.site_properties, self.frac_coords.shape[0], trajectory.frac_coords.shape[0])
def __iter__(self): for i in range(self.frac_coords.shape[0]): yield self[i] def __len__(self): return np.shape(self.frac_coords)[0] def __getitem__(self, frames): """ Gets a subset of the trajectory if a slice is given, if an int is given, return a structure Args: frames (int, slice): int or slice of trajectory to return Return: (Trajectory, Structure) Subset of trajectory """ if isinstance(frames, int) and frames < self.frac_coords.shape[0]: lattice = self.lattice if self.constant_lattice else self.lattice[frames] site_properties = self.site_properties[frames] if self.site_properties else None return Structure(Lattice(lattice), self.species, self.frac_coords[frames], site_properties=site_properties, to_unit_cell=True) if isinstance(frames, slice): frames = np.arange(frames.start, frames.stop, frames.step) elif not (isinstance(frames, list) or isinstance(frames, np.ndarray)): try: frames = np.asarray(frames) except: raise Exception('Given accessor is not of type int, slice, tuple, list, or array') if (isinstance(frames, list) or isinstance(frames, np.ndarray)) and \ (np.asarray([frames]) < self.frac_coords.shape[0]).all(): if self.constant_lattice: lattice = self.lattice else: lattice = self.lattice[frames, :] return Trajectory(lattice, self.species, self.frac_coords[frames, :], self.time_step, self.site_properties) else: warnings.warn('Some or all selected frames exceed trajectory length') return
[docs] def copy(self): return Trajectory(self.lattice, self.species, self.frac_coords, self.time_step, self.site_properties, self.constant_lattice, self.coords_are_displacement, self.base_positions)
[docs] @classmethod def from_structures(cls, structures, constant_lattice=True, **kwargs): """ Convenience constructor to obtain trajectory from a list of structures. Note: Assumes no atoms removed during simulation Args: structures (list): list of pymatgen Structure objects. constant_lattice (bool): Whether the lattice changes during the simulation, such as in an NPT MD simulation. True results in Returns: (Trajectory) """ frac_coords = [structure.frac_coords for structure in structures] if constant_lattice: lattice = structures[0].lattice.matrix else: lattice = [structure.lattice.matrix for structure in structures] site_properties = [structure.site_properties for structure in structures] return cls(lattice, structures[0].species, frac_coords, site_properties=site_properties, constant_lattice=constant_lattice, **kwargs)
[docs] @classmethod def from_file(cls, filename, constant_lattice=True, **kwargs): """ Convenience constructor to obtain trajectory from XDATCAR or vasprun.xml file Args: filename (str): The filename to read from. constant_lattice (bool): Whether the lattice changes during the simulation, such as in an NPT MD simulation. True results in Returns: (Trajectory) """ # TODO: Support other filetypes fname = os.path.basename(filename) if fnmatch(fname, "*XDATCAR*"): structures = Xdatcar(filename).structures elif fnmatch(fname, "vasprun*.xml*"): structures = Vasprun(filename).structures else: raise ValueError("Unsupported file") return cls.from_structures(structures, constant_lattice=constant_lattice, **kwargs)
[docs] def as_dict(self): d = {"@module": self.__class__.__module__, "@class": self.__class__.__name__, "species": self.species, "time_step": self.time_step, "site_properties": self.site_properties, "constant_lattice": self.constant_lattice, "coords_are_displacement": self.coords_are_displacement, "base_positions": self.base_positions} d["lattice"] = self.lattice.tolist() d["frac_coords"] = self.frac_coords.tolist() return d
@staticmethod def _combine_attribute(attr_1, attr_2, len_1, len_2): """ Helper function to combine trajectory properties such as site_properties or lattice """ if isinstance(attr_1, list) or isinstance(attr_2, list): attribute = np.concatenate((attr_1, attr_2), axis=0) attribute_changes = True else: if isinstance(attr_1, list) and isinstance(attr_2, list) and np.allclose(attr_1, attr_2): attribute = attr_1 attribute_changes = False else: attribute = [attr_1.copy()] * len_1 if type(attr_1) != list else attr_1.copy() attribute.extend([attr_2.copy()] * len_2 if type(attr_2 != list) else attr_2.copy()) attribute_changes = True return attribute, attribute_changes