Source code for pyiron.vasp.structure

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

from collections import OrderedDict
import numpy as np
from pyiron.atomistics.structure.atoms import Atoms
import warnings

__author__ = "Sudarsan Surendralal"
__copyright__ = (
    "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Sudarsan Surendralal"
__email__ = "surendralal@mpie.de"
__status__ = "production"
__date__ = "Sep 1, 2017"


[docs]def read_atoms( filename="CONTCAR", return_velocities=False, species_list=None, species_from_potcar=False, ): """ Routine to read structural static from a POSCAR type file Args: filename (str): Input filename return_velocities (bool): True if the predictor corrector velocities are read (only from MD output) species_list (list/numpy.ndarray): A list of the species (if not present in the POSCAR file or a POTCAR in the same directory) species_from_potcar (bool): True if the species list should be read from the POTCAR file in the same directory Returns: pyiron.atomistics.structure.atoms.Atoms: The generated structure object """ directory = "/".join(filename.split("/")[0:-1]) potcar_file = "/".join([directory, "POTCAR"]) if (species_list is None) and species_from_potcar: species_list = get_species_list_from_potcar(potcar_file) file_string = list() with open(filename) as f: for line in f: line = line.strip() file_string.append(line) return atoms_from_string( file_string, read_velocities=return_velocities, species_list=species_list )
[docs]def get_species_list_from_potcar(filename="POTCAR"): """ Generates the species list from a POTCAR type file Args: filename (str): Input filename Returns: list: A list of species symbols """ trigger = "VRHFIN =" species_list = list() with open(filename) as potcar_file: lines = potcar_file.readlines() for line in lines: line = line.strip() if trigger in line: str_1 = line.split(trigger) str_2 = str_1[-1].split(":") species_list.append(str_2[0].replace(" ", "")) return species_list
[docs]def write_poscar(structure, filename="POSCAR", write_species=True, cartesian=True): """ Writes a POSCAR type file from a structure object Args: structure (pyiron.atomistics.structure.atoms.Atoms): The structure instance to be written to the POSCAR format filename (str): Output filename write_species (bool): True if the species should be written to the file cartesian (bool): True if the positions are written in Cartesian coordinates """ endline = "\n" with open(filename, "w") as f: selec_dyn = False f.write("Poscar file generated with pyiron" + endline) f.write("1.0" + endline) for a_i in structure.get_cell(): x, y, z = a_i f.write("{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + endline) atom_numbers = structure.get_number_species_atoms() if write_species: f.write(" ".join(atom_numbers.keys()) + endline) num_str = [str(val) for val in atom_numbers.values()] f.write(" ".join(num_str)) f.write(endline) if "selective_dynamics" in structure.get_tags(): selec_dyn = True f.write("Selective dynamics" + endline) sorted_coords = list() selec_dyn_lst = list() for species in atom_numbers.keys(): indices = structure.select_index(species) for i in indices: if cartesian: sorted_coords.append(structure.positions[i]) else: sorted_coords.append(structure.get_scaled_positions()[i]) if selec_dyn: selec_dyn_lst.append(structure.selective_dynamics[i]) if cartesian: f.write("Cartesian" + endline) else: f.write("Direct" + endline) if selec_dyn: for i, vec in enumerate(sorted_coords): x, y, z = vec sd_string = " ".join(["T" if sd else "F" for sd in selec_dyn_lst[i]]) f.write( "{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + " " + sd_string + endline ) else: for i, vec in enumerate(sorted_coords): x, y, z = vec f.write("{0:.15f} {1:.15f} {2:.15f}".format(x, y, z) + endline)
[docs]def atoms_from_string(string, read_velocities=False, species_list=None): """ Routine to convert a string list read from a input/output structure file and convert into Atoms instance Args: string (list): A list of strings (lines) read from the POSCAR/CONTCAR/CHGCAR/LOCPOT file read_velocities (bool): True if the velocities from a CONTCAR file should be read (predictor corrector) species_list (list/numpy.ndarray): A list of species of the atoms Returns: pyiron.atomistics.structure.atoms.Atoms: The required structure object """ string = [s.strip() for s in string] string_lower = [s.lower() for s in string] atoms_dict = dict() atoms_dict["first_line"] = string[0] # del string[0] atoms_dict["selective_dynamics"] = False atoms_dict["relative"] = False if "direct" in string_lower or "d" in string_lower: atoms_dict["relative"] = True atoms_dict["scaling_factor"] = float(string[1]) unscaled_cell = list() for i in [2, 3, 4]: vec = list() for j in range(3): vec.append(float(string[i].split()[j])) unscaled_cell.append(vec) if atoms_dict["scaling_factor"] > 0.0: atoms_dict["cell"] = np.array(unscaled_cell) * atoms_dict["scaling_factor"] else: atoms_dict["cell"] = np.array(unscaled_cell) * ( (-atoms_dict["scaling_factor"]) ** (1.0 / 3.0) ) if "selective dynamics" in string_lower: atoms_dict["selective_dynamics"] = True no_of_species = len(string[5].split()) species_dict = OrderedDict() position_index = 7 if atoms_dict["selective_dynamics"]: position_index += 1 for i in range(no_of_species): species_dict["species_" + str(i)] = dict() try: species_dict["species_" + str(i)]["count"] = int(string[5].split()[i]) except ValueError: species_dict["species_" + str(i)]["species"] = string[5].split()[i] species_dict["species_" + str(i)]["count"] = int(string[6].split()[i]) atoms_dict["species_dict"] = species_dict if "species" in atoms_dict["species_dict"]["species_0"].keys(): position_index += 1 positions = list() selective_dynamics = list() n_atoms = sum( [ atoms_dict["species_dict"][key]["count"] for key in atoms_dict["species_dict"].keys() ] ) try: for i in range(position_index, position_index + n_atoms): string_list = np.array(string[i].split()) positions.append([float(val) for val in string_list[0:3]]) if atoms_dict["selective_dynamics"]: selective_dynamics.append(["T" in val for val in string_list[3:6]]) except (ValueError, IndexError): raise AssertionError( "The number of positions given does not match the number of atoms" ) atoms_dict["positions"] = np.array(positions) if not atoms_dict["relative"]: if atoms_dict["scaling_factor"] > 0.0: atoms_dict["positions"] *= atoms_dict["scaling_factor"] else: atoms_dict["positions"] *= (-atoms_dict["scaling_factor"]) ** (1.0 / 3.0) velocities = list() try: atoms = _dict_to_atoms(atoms_dict, species_list=species_list) except ValueError: atoms = _dict_to_atoms(atoms_dict, read_from_first_line=True) if atoms_dict["selective_dynamics"]: selective_dynamics = np.array(selective_dynamics) unique_sel_dyn, inverse, counts = np.unique( selective_dynamics, axis=0, return_counts=True, return_inverse=True ) count_index = np.argmax(counts) atoms.add_tag(selective_dynamics=unique_sel_dyn.tolist()[count_index]) is_not_majority = np.arange(len(unique_sel_dyn), dtype=int) != count_index for i, val in enumerate(unique_sel_dyn): if is_not_majority[i]: for key in np.argwhere(inverse == i).flatten(): atoms.selective_dynamics[int(key)] = val.tolist() if read_velocities: velocity_index = position_index + n_atoms + 1 for i in range(velocity_index, velocity_index + n_atoms): try: velocities.append([float(val) for val in string[i].split()[0:3]]) except IndexError: break if not (len(velocities) == n_atoms): warnings.warn( "The velocities are either not available or they are incomplete/corrupted. Returning empty " "list instead", UserWarning, ) return atoms, list() return atoms, velocities else: return atoms
def _dict_to_atoms(atoms_dict, species_list=None, read_from_first_line=False): """ Function to convert a generated dict into an structure object Args: atoms_dict (dict): Dictionary with the details (from string_to_atom) species_list (list/numpy.ndarray): List of species read_from_first_line (bool): True if we are to read the species information from the first line in the file Returns: pyiron.atomistics.structure.atoms.Atoms: The required structure object """ is_absolute = not (atoms_dict["relative"]) positions = atoms_dict["positions"] cell = atoms_dict["cell"] symbol = str() elements = list() el_list = list() for i, sp_key in enumerate(atoms_dict["species_dict"].keys()): if species_list is not None: try: el_list = np.array([species_list[i]]) el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"]) if isinstance(species_list[i], str): symbol += species_list[i] + str( atoms_dict["species_dict"][sp_key]["count"] ) else: symbol += species_list[i].Abbreviation + str( atoms_dict["species_dict"][sp_key]["count"] ) except IndexError: raise ValueError( "Number of species in the specified species list does not match that in the file" ) elif "species" in atoms_dict["species_dict"][sp_key].keys(): el_list = np.array([atoms_dict["species_dict"][sp_key]["species"]]) el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"]) symbol += atoms_dict["species_dict"][sp_key]["species"] symbol += str(atoms_dict["species_dict"][sp_key]["count"]) elif read_from_first_line: if not ( len(atoms_dict["first_line"].split()) == len(atoms_dict["species_dict"].keys()) ): raise AssertionError() el_list = np.array(atoms_dict["first_line"].split()[i]) el_list = np.tile(el_list, atoms_dict["species_dict"][sp_key]["count"]) symbol += atoms_dict["first_line"].split()[i] symbol += str(atoms_dict["species_dict"][sp_key]["count"]) elif species_list is None: raise ValueError( "Species list should be provided since pyiron can't detect species information" ) elements.append(el_list) elements_new = list() for ele in elements: for e in ele: elements_new.append(e) elements = elements_new if is_absolute: atoms = Atoms(elements, positions=positions, cell=cell, pbc=True) else: atoms = Atoms(elements, scaled_positions=positions, cell=cell, pbc=True) return atoms
[docs]def vasp_sorter(structure): """ Routine to sort the indices of a structure as it would be when written to a POSCAR file Args: structure (pyiron.atomistics.structure.atoms.Atoms): The structure whose indices need to be sorted Returns: list: A list of indices which is sorted by the corresponding species for writing to POSCAR """ atom_numbers = structure.get_number_species_atoms() sorted_indices = list() for species in atom_numbers.keys(): indices = structure.select_index(species) for i in indices: sorted_indices.append(i) return np.array(sorted_indices)
[docs]def manip_contcar(filename, new_filename, add_pos): """ Manipulate a CONTCAR/POSCAR file by adding something to the positions Args: filename (str): Filename/path of the input file new_filename (str): Filename/path of the output file add_pos (list/numpy.ndarray): Array of values to be added to the positions of the input """ actual_struct = read_atoms(filename) n = 0 direct = True with open(filename, "r") as f: lines = f.readlines() for line in lines: if "Direct" in line or "Cartesian" in line: direct = "Direct" in line break n += 1 pos_list = list() sd_list = list() if len(lines[n + 1].split()) == 6: for line in lines[n + 1 : n + 1 + len(actual_struct)]: pos_list.append([float(val) for val in line.split()[0:3]]) sd_list.append(["T" in val for val in line.split()[3:]]) else: for line in lines[n + 1 : n + 1 + len(actual_struct)]: pos_list.append([float(val) for val in line.split()[0:3]]) old_pos = np.array(pos_list) if direct: add_pos_rel = np.dot(add_pos, np.linalg.inv(actual_struct.cell)) new_pos = old_pos + add_pos_rel else: new_pos = old_pos + add_pos new_lines = lines new_pos_str = np.array(new_pos, dtype=str) if len(sd_list) > 0: bool_list = np.zeros_like(old_pos, dtype=str) bool_list[:] = "F" bool_list[np.array(sd_list)] = "T" for i, pos in enumerate(new_pos_str): linestr = np.append(pos, bool_list[i]) new_lines[n + 1 + i] = " ".join([str(val) for val in linestr]) + "\n" else: for i, pos in enumerate(new_pos_str): linestr = pos new_lines[n + 1 + i] = " ".join([str(val) for val in linestr]) + "\n" # Exclude predictor corrector positions if len(new_lines[n + len(new_pos_str) :]) >= 2 * len(new_pos_str): new_lines = new_lines[: n + 2 * (len(new_pos_str)) + 2] with open(new_filename, "w") as f: for new_line in new_lines: f.write(new_line)