Source code for

# Copyright (C) 2012, Jesper Friis, SINTEF
# (see accompanying license files for ASE).
"""Module to read and write atoms EON reactant.con files.

See for a description of EON.
import os
from warnings import warn
from glob import glob

import numpy as np

from ase.atoms import Atoms
from ase.constraints import FixAtoms
from ase.geometry import cellpar_to_cell, cell_to_cellpar
from ase.utils import writer

[docs]def read_eon(fileobj, index=-1): """Reads an EON reactant.con file. If *fileobj* is the name of a "states" directory created by EON, all the structures will be read.""" if isinstance(fileobj, str): if (os.path.isdir(fileobj)): return read_states(fileobj) else: fd = open(fileobj) else: fd = fileobj more_images_to_read = True images = [] first_line = fd.readline() while more_images_to_read: comment = first_line.strip() fd.readline() # 0.0000 TIME (??) cell_lengths = fd.readline().split() cell_angles = fd.readline().split() # Different order of angles in EON. cell_angles = [cell_angles[2], cell_angles[1], cell_angles[0]] cellpar = [float(x) for x in cell_lengths + cell_angles] fd.readline() # 0 0 (??) fd.readline() # 0 0 0 (??) ntypes = int(fd.readline()) # number of atom types natoms = [int(n) for n in fd.readline().split()] atommasses = [float(m) for m in fd.readline().split()] symbols = [] coords = [] masses = [] fixed = [] for n in range(ntypes): symbol = fd.readline().strip() symbols.extend([symbol] * natoms[n]) masses.extend([atommasses[n]] * natoms[n]) fd.readline() # Coordinates of Component n for i in range(natoms[n]): row = fd.readline().split() coords.append([float(x) for x in row[:3]]) fixed.append(bool(int(row[3]))) atoms = Atoms(symbols=symbols, positions=coords, masses=masses, cell=cellpar_to_cell(cellpar), constraint=FixAtoms(mask=fixed), info=dict(comment=comment)) images.append(atoms) first_line = fd.readline() if first_line == '': more_images_to_read = False if isinstance(fileobj, str): fd.close() if not index: return images else: return images[index]
def read_states(states_dir): """Read structures stored by EON in the states directory *states_dir*.""" subdirs = glob(os.path.join(states_dir, '[0123456789]*')) subdirs.sort(key=lambda d: int(os.path.basename(d))) images = [read_eon(os.path.join(subdir, 'reactant.con')) for subdir in subdirs] return images
[docs]@writer def write_eon(fileobj, images): """Writes structure to EON reactant.con file Multiple snapshots are allowed.""" if isinstance(images, Atoms): atoms = images elif len(images) == 1: atoms = images[0] else: raise ValueError('Can only write one configuration to EON ' 'reactant.con file') out = [] out.append('comment', 'Generated by ASE')) out.append('0.0000 TIME') # ?? a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.cell) out.append('%-10.6f %-10.6f %-10.6f' % (a, b, c)) out.append('%-10.6f %-10.6f %-10.6f' % (gamma, beta, alpha)) out.append('0 0') # ?? out.append('0 0 0') # ?? symbols = atoms.get_chemical_symbols() massdict = dict(list(zip(symbols, atoms.get_masses()))) atomtypes = sorted(massdict.keys()) atommasses = [massdict[at] for at in atomtypes] natoms = [symbols.count(at) for at in atomtypes] ntypes = len(atomtypes) out.append(str(ntypes)) out.append(' '.join([str(n) for n in natoms])) out.append(' '.join([str(n) for n in atommasses])) atom_id = 0 for n in range(ntypes): fixed = np.array([False] * len(atoms)) out.append(atomtypes[n]) out.append('Coordinates of Component %d' % (n + 1)) indices = [i for i, at in enumerate(symbols) if at == atomtypes[n]] a = atoms[indices] coords = a.positions for c in a.constraints: if not isinstance(c, FixAtoms): warn('Only FixAtoms constraints are supported by con files. ' 'Dropping %r', c) continue if c.index.dtype.kind == 'b': fixed = np.array(c.index, dtype=int) else: fixed = np.zeros((natoms[n], ), dtype=int) for i in c.index: fixed[i] = 1 for xyz, fix in zip(coords, fixed): out.append('%22.17f %22.17f %22.17f %d %4d' % (tuple(xyz) + (fix, atom_id))) atom_id += 1 fileobj.write('\n'.join(out)) fileobj.write('\n')