Chimie Théorique » QMX

from ase.atoms import Atom, Atoms

from ase.calculators.singlepoint import SinglePointCalculator

def read_gpaw_text(fileobj, index=-1):

    if isinstance(fileobj, str):

        fileobj = open(fileobj)

    def index_startswith(lines, string):

        for i, line in enumerate(lines):

            if line.startswith(string):

                return i

        raise ValueError

    lines = fileobj.readlines()

    images = []

    while True:

        try:

            i = lines.index('Unit Cell:\n')

        except ValueError:

            pass

        else:

            cell = []

            pbc = []

            for line in lines[i + 3:i + 6]:

                words = line.split()

                if len(words) == 5:  # old format

                    cell.append(float(words[2]))

                    pbc.append(words[1] == 'yes')

                else:                # new format with GUC

                    cell.append([float(word) for word in words[3:6]])

                    pbc.append(words[2] == 'yes')

        try:

            i = lines.index('Positions:\n')

        except ValueError:

            break

        atoms = Atoms(cell=cell, pbc=pbc)

        for line in lines[i + 1:]:

            words = line.split()

            if len(words) != 5:

                break

            n, symbol, x, y, z = words

            symbol = symbol.split('.')[0]

            atoms.append(Atom(symbol, [float(x), float(y), float(z)]))

        lines = lines[i + 5:]

        try:

            i = lines.index('-------------------------\n')

        except ValueError:

            e = None

        else:

            line = lines[i + 9]

            assert line.startswith('Zero Kelvin:')

            e = float(line.split()[-1])

        try:

            ii = index_startswith(lines, 'Total Charge:')

        except ValueError:

            q = None

        else:

            q = float(lines[ii].split()[2])

        try:

            ii = lines.index('Forces in eV/Ang:\n')

        except ValueError:

            f = None

        else:

            f = []

            for i in range(ii + 1, ii + 1 + len(atoms)):

                try:

                    x, y, z = lines[i].split()[-3:]

                    f.append((float(x), float(y), float(z)))

                except (ValueError, IndexError), m:

                    raise IOError('Malformed GPAW log file: %s' % m)

        if len(images) > 0 and e is None:

            break

        if e is not None or f is not None:

            atoms.set_calculator(SinglePointCalculator(e, f, None, None, atoms)) ### Fixme magmoms

        if q is not None:

            n = len(atoms)

            atoms.set_charges([q / n] * n)

        images.append(atoms)

        lines = lines[i:]

    if len(images) == 0:

        raise IOError('Corrupted GPAW-text file!')

    return images[index]