Source code for

This module contains functionality for reading and writing an ASE
Atoms object in V_Sim 3.5+ ascii format.


import numpy as np
from ase.utils import reader, writer

[docs]@reader def read_v_sim(fd): """Import V_Sim input file. Reads cell, atom positions, etc. from v_sim ascii file. V_sim format is specified here: """ from ase import Atoms, units from ase.geometry import cellpar_to_cell import re # Read comment: fd.readline() line = fd.readline() + ' ' + fd.readline() box = line.split() for i in range(len(box)): box[i] = float(box[i]) keywords = [] positions = [] symbols = [] unit = 1.0 re_comment = re.compile(r'^\s*[#!]') re_node = re.compile(r'^\s*\S+\s+\S+\s+\S+\s+\S+') while True: line = fd.readline() if line == '': break # EOF p = re_comment.match(line) if p is not None: # remove comment character at the beginning of line line = line[p.end():].replace(',', ' ').lower() if line[:8] == "keyword:": keywords.extend(line[8:].split()) elif re_node.match(line): unit = 1.0 if not ("reduced" in keywords): if (("bohr" in keywords) or ("bohrd0" in keywords) or ("atomic" in keywords) or ("atomicd0" in keywords)): unit = units.Bohr fields = line.split() positions.append([unit * float(fields[0]), unit * float(fields[1]), unit * float(fields[2])]) symbols.append(fields[3]) # create atoms object based on the information if "angdeg" in keywords: cell = cellpar_to_cell(box) else: unit = 1.0 if (("bohr" in keywords) or ("bohrd0" in keywords) or ("atomic" in keywords) or ("atomicd0" in keywords)): unit = units.Bohr cell = np.zeros((3, 3)) cell.flat[[0, 3, 4, 6, 7, 8]] = box[:6] cell *= unit if "reduced" in keywords: atoms = Atoms(cell=cell, scaled_positions=positions) else: atoms = Atoms(cell=cell, positions=positions) if "periodic" in keywords: atoms.pbc = [True, True, True] elif "freebc" in keywords: atoms.pbc = [False, False, False] elif "surface" in keywords: atoms.pbc = [True, False, True] else: # default is periodic boundary conditions atoms.pbc = [True, True, True] atoms.set_chemical_symbols(symbols) return atoms
[docs]@writer def write_v_sim(fd, atoms): """Write V_Sim input file. Writes the atom positions and unit cell. V_sim format is specified here: """ from ase.geometry import cellpar_to_cell, cell_to_cellpar # Convert the lattice vectors to triangular matrix by converting # to and from a set of lengths and angles cell = cellpar_to_cell(cell_to_cellpar(atoms.cell)) dxx = cell[0, 0] dyx, dyy = cell[1, 0:2] dzx, dzy, dzz = cell[2, 0:3] fd.write('===== v_sim input file created using the' ' Atomic Simulation Environment (ASE) ====\n') fd.write('{0} {1} {2}\n'.format(dxx, dyx, dyy)) fd.write('{0} {1} {2}\n'.format(dzx, dzy, dzz)) # Use v_sim 3.5 keywords to indicate scaled positions, etc. fd.write('#keyword: reduced\n') fd.write('#keyword: angstroem\n') if np.all(atoms.pbc): fd.write('#keyword: periodic\n') elif not np.any(atoms.pbc): fd.write('#keyword: freeBC\n') elif np.array_equiv(atoms.pbc, [True, False, True]): fd.write('#keyword: surface\n') else: raise Exception( 'Only supported boundary conditions are full PBC,' ' no periodic boundary, and surface which is free in y direction' ' (i.e. Atoms.pbc = [True, False, True]).') # Add atoms (scaled positions) for position, symbol in zip(atoms.get_scaled_positions(), atoms.get_chemical_symbols()): fd.write('{0} {1} {2} {3}\n'.format( position[0], position[1], position[2], symbol))