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# Source code for ase.io.castep

    # -*- coding: utf-8 -*-
    """This module defines I/O routines with CASTEP files.
    The key idea is that all function accept or return  atoms objects.
    CASTEP specific parameters will be returned through the <atoms>.calc
    attribute.
    """
    import os
    import re
    import warnings
    import numpy as np
    from copy import deepcopy

    import ase

    from ase.parallel import paropen
    from ase.spacegroup import Spacegroup
    from ase.geometry.cell import cellpar_to_cell
    from ase.constraints import FixAtoms, FixedPlane, FixedLine, FixCartesian

    # independent unit management included here:
    # When high accuracy is required, this allows to easily pin down
    # unit conversion factors from different "unit definition systems"
    # (CODATA1986 for ase-3.6.0.2515 vs CODATA2002 for CASTEP 5.01).
    #
    # ase.units in in ase-3.6.0.2515 is based on CODATA1986
    import ase.units
    units_ase = {
        'hbar': ase.units._hbar * ase.units.J,
        'Eh': ase.units.Hartree,
        'kB': ase.units.kB,
        'a0': ase.units.Bohr,
        't0': ase.units._hbar * ase.units.J / ase.units.Hartree,
        'c': ase.units._c,
        'me': ase.units._me / ase.units._amu,
        'Pascal': 1.0 / ase.units.Pascal}

    # CODATA1986 (included herein for the sake of completeness)
    # taken from
    #    http://physics.nist.gov/cuu/Archive/1986RMP.pdf
    units_CODATA1986 = {
        'hbar': 6.5821220E-16,      # eVs
        'Eh': 27.2113961,           # eV
        'kB': 8.617385E-5,          # eV/K
        'a0': 0.529177249,          # A
        'c': 299792458,             # m/s
        'e': 1.60217733E-19,        # C
        'me': 5.485799110E-4}       # u

    # CODATA2002: default in CASTEP 5.01
    # (-> check in more recent CASTEP in case of numerical discrepancies?!)
    # taken from
    #    http://physics.nist.gov/cuu/Document/all_2002.pdf
    units_CODATA2002 = {
        'hbar': 6.58211915E-16,     # eVs
        'Eh': 27.2113845,           # eV
        'kB': 8.617343E-5,          # eV/K
        'a0': 0.5291772108,         # A
        'c': 299792458,             # m/s
        'e': 1.60217653E-19,        # C
        'me': 5.4857990945E-4}      # u

    # (common) derived entries
    for d in (units_CODATA1986, units_CODATA2002):
        d['t0'] = d['hbar'] / d['Eh']     # s
        d['Pascal'] = d['e'] * 1E30       # Pa

    __all__ = [
        # routines for the generic io function
        'read_castep',
        'read_castep_castep',
        'read_castep_castep_old',
        'read_cell',
        'read_castep_cell',
        'read_geom',
        'read_castep_geom',
        'read_phonon',
        'read_castep_phonon',
        # additional reads that still need to be wrapped
        'read_md',
        'read_param',
        'read_seed',
        # write that is already wrapped
        'write_castep_cell',
        # param write - in principle only necessary in junction with the calculator
        'write_param']

    def write_freeform(fd, outputobj):
        """
        Prints out to a given file a CastepInputFile or derived class, such as
        CastepCell or CastepParam.
        """

        options = outputobj._options

        # Some keywords, if present, are printed in this order
        preferred_order = ['lattice_cart', 'lattice_abc',
                           'positions_frac', 'positions_abs',
                           'species_pot', 'symmetry_ops',   # CELL file
                           'task', 'cut_off_energy'         # PARAM file
                           ]

        keys = outputobj.get_attr_dict().keys()
        # This sorts only the ones in preferred_order and leaves the rest
        # untouched
        keys = sorted(keys, key=lambda x: preferred_order.index(x)
                      if x in preferred_order
                      else len(preferred_order))

        for kw in keys:
            opt = options[kw]
            if opt.type.lower() == 'block':
                fd.write('%BLOCK {0}\n{1}\n%ENDBLOCK {0}\n\n'.format(
                         kw.upper(),
                         opt.value.strip('\n')))
            else:
                fd.write('{0}: {1}\n'.format(kw.upper(), opt.value))

    def write_cell(filename, atoms, positions_frac=False, castep_cell=None,
                   force_write=False):
        """
        Wrapper function for the more generic write() functionality.

        Note that this is function is intended to maintain backwards-compatibility
        only.
        """
        from ase.io import write

        write(filename, atoms, positions_frac=positions_frac,
              castep_cell=castep_cell, force_write=force_write)

    def write_castep_cell(fd, atoms, positions_frac=False, force_write=False,
                          precision=6, magnetic_moments=None,
                          castep_cell=None):
        """
        This CASTEP export function write minimal information to
        a .cell file. If the atoms object is a trajectory, it will
        take the last image.

        Note that function has been altered in order to require a filedescriptor
        rather than a filename. This allows to use the more generic write()
        function from formats.py

        Note that the "force_write" keywords has no effect currently.

        Arguments:

            positions_frac: boolean. If true, positions are printed as fractional
                            rather than absolute. Default is false.
            castep_cell: if provided, overrides the existing CastepCell object in
                         the Atoms calculator
            precision: number of digits to which lattice and positions are printed
            magnetic_moments: if None, no SPIN values are initialised.
                              If 'initial', the values from
                              get_initial_magnetic_moments() are used.
                              If 'calculated', the values from
                              get_magnetic_moments() are used.
                              If an array of the same length as the atoms object,
                              its contents will be used as magnetic moments.
        """

        if atoms is None:
            print('Atoms object not initialized')
            return False
        if isinstance(atoms, list):
            if len(atoms) > 1:
                atoms = atoms[-1]

        # Header
        fd.write('#######################################################\n')
        fd.write('#CASTEP cell file: %s\n' % fd.name)
        fd.write('#Created using the Atomic Simulation Environment (ASE)#\n')
        fd.write('#######################################################\n\n')

        # To write this we simply use the existing Castep calculator, or create
        # one
        from ase.calculators.castep import Castep, CastepCell

        try:
            has_cell = isinstance(atoms.calc.cell, CastepCell)
        except AttributeError:
            has_cell = False

        if has_cell:
            cell = deepcopy(atoms.calc.cell)
        else:
            cell = Castep(keyword_tolerance=2).cell

        # Write lattice
        fformat = '%{0}.{1}f'.format(precision + 3, precision)
        cell_block_format = ' '.join([fformat] * 3)
        cell.lattice_cart = [cell_block_format % tuple(line)
                             for line in atoms.get_cell()]

        if positions_frac:
            pos_keyword = 'positions_frac'
            positions = atoms.get_scaled_positions()
        else:
            pos_keyword = 'positions_abs'
            positions = atoms.get_positions()

        if atoms.has('castep_custom_species'):
            elems = atoms.get_array('castep_custom_species')
        else:
            elems = atoms.get_chemical_symbols()

        if atoms.has('castep_labels'):
            labels = atoms.get_array('castep_labels')
        else:
            labels = ['NULL'] * len(elems)

        if str(magnetic_moments).lower() == 'initial':
            magmoms = atoms.get_initial_magnetic_moments()
        elif str(magnetic_moments).lower() == 'calculated':
            magmoms = atoms.get_magnetic_moments()
        elif np.array(magnetic_moments).shape == (len(elems),):
            magmoms = np.array(magnetic_moments)
        else:
            magmoms = [0] * len(elems)

        pos_block = []
        pos_block_format = '%s ' + cell_block_format

        for i, el in enumerate(elems):
            xyz = positions[i]
            line = pos_block_format % tuple([el] + list(xyz))
            # ADD other keywords if necessary
            if magmoms[i] != 0:
                line += ' SPIN={0} '.format(magmoms[i])
            if labels[i].strip() not in ('NULL', ''):
                line += ' LABEL={0} '.format(labels[i])
            pos_block.append(line)

        setattr(cell, pos_keyword, pos_block)

        constraints = atoms.constraints
        if len(constraints):
            _supported_constraints = (FixAtoms, FixedPlane, FixedLine,
                                      FixCartesian)

            constr_block = []

            for constr in constraints:
                if not isinstance(constr, _supported_constraints):
                    print('Warning: you have constraints in your atoms, that are')
                    print('         not supported by the CASTEP ase interface')
                    break
                if isinstance(constr, FixAtoms):
                    for i in constr.index:

                        try:
                            symbol = atoms.get_chemical_symbols()[i]
                            nis = atoms.calc._get_number_in_species(i)
                        except KeyError:
                            raise UserWarning('Unrecognized index in'
                                              + ' constraint %s' % constr)
                        for j in range(3):
                            l = '%6d %3s %3d   ' % (len(constr_block) + 1,
                                                    symbol,
                                                    nis)
                            l += ['1 0 0', '0 1 0', '0 0 1'][j]
                            constr_block += [l]

                elif isinstance(constr, FixCartesian):
                    n = constr.a
                    symbol = atoms.get_chemical_symbols()[n]
                    nis = atoms.calc._get_number_in_species(n)

                    for i, m in enumerate(constr.mask):
                        if m == 1:
                            continue
                        l = '%6d %3s %3d   ' % (len(constr_block) + 1, symbol, nis)
                        l += ' '.join(['1' if j == i else '0' for j in range(3)])
                        constr_block += [l]

                elif isinstance(constr, FixedPlane):
                    n = constr.a
                    symbol = atoms.get_chemical_symbols()[n]
                    nis = atoms.calc._get_number_in_species(n)

                    l = '%6d %3s %3d   ' % (len(constr_block) + 1, symbol, nis)
                    l += ' '.join([str(d) for d in constr.dir])
                    constr_block += [l]

                elif isinstance(constr, FixedLine):
                    n = constr.a
                    symbol = atoms.get_chemical_symbols()[n]
                    nis = atoms.calc._get_number_in_species(n)

                    direction = constr.dir
                    ((i1, v1), (i2, v2)) = sorted(enumerate(direction),
                                                  key=lambda x: abs(x[1]),
                                                  reverse=True)[:2]
                    n1 = np.zeros(3)
                    n1[i2] = v1
                    n1[i1] = -v2
                    n1 = n1 / np.linalg.norm(n1)

                    n2 = np.cross(direction, n1)

                    l1 = '%6d %3s %3d   %f %f %f' % (len(constr_block) + 1,
                                                     symbol, nis,
                                                     n1[0], n1[1], n1[2])
                    l2 = '%6d %3s %3d   %f %f %f' % (len(constr_block) + 2,
                                                     symbol, nis,
                                                     n2[0], n2[1], n2[2])

                    constr_block += [l1, l2]

            cell.ionic_constraints = constr_block

        write_freeform(fd, cell)

        return True

    def read_freeform(fd):
        """
        Read a CASTEP freeform file (the basic format of .cell and .param files)
        and return keyword-value pairs as a dict (values are strings for single
        keywords and lists of strings for blocks).
        """

        from ase.calculators.castep import CastepInputFile

        inputobj = CastepInputFile(keyword_tolerance=2)

        filelines = fd.readlines()

        keyw = None
        read_block = False
        block_lines = None

        for i, l in enumerate(filelines):

            # Strip all comments, aka anything after a hash
            l = re.split(r'[#!;]', l, 1)[0].strip()

            if l == '':
                # Empty line... skip
                continue

            lsplit = re.split(r'\s*[:=]*\s+', l, 1)

            if read_block:
                if lsplit[0].lower() == '%endblock':
                    if len(lsplit) == 1 or lsplit[1].lower() != keyw:
                        raise ValueError('Out of place end of block at '
                                         'line %i in freeform file' % i + 1)
                    else:
                        read_block = False
                        inputobj.__setattr__(keyw, block_lines)
                else:
                    block_lines += [l]
            else:
                # Check the first word

                # Is it a block?
                read_block = (lsplit[0].lower() == '%block')
                if read_block:
                    if len(lsplit) == 1:
                        raise ValueError(('Unrecognizable block at line %i '
                                          'in io freeform file') % i + 1)
                    else:
                        keyw = lsplit[1].lower()
                else:
                    keyw = lsplit[0].lower()

                # Now save the value
                if read_block:
                    block_lines = []
                else:
                    inputobj.__setattr__(keyw, ' '.join(lsplit[1:]))

        return inputobj.get_attr_dict(types=True)

    def read_cell(filename, index=None):
        """
        Wrapper function for the more generic read() functionality.

        Note that this is function is intended to maintain backwards-compatibility
        only.
        """
        from ase.io import read
        return read(filename, index=index, format='castep-cell')

    def read_castep_cell(fd, index=None, calculator_args={}, find_spg=False,
                         units=units_CODATA2002):
        """Read a .cell file and return an atoms object.
        Any value found that does not fit the atoms API
        will be stored in the atoms.calc attribute.

        By default, the Castep calculator will be tolerant and in the absence of a
        castep_keywords.json file it will just accept all keywords that aren't
        automatically parsed.
        """

        from ase.calculators.castep import Castep

        cell_units = {  # Units specifiers for CASTEP
            'bohr': units_CODATA2002['a0'],
            'ang': 1.0,
            'm': 1e10,
            'cm': 1e8,
            'nm': 10,
            'pm': 1e-2
        }

        calc = Castep(**calculator_args)

        if calc.cell.castep_version == 0 and calc._kw_tol < 3:
            # No valid castep_keywords.json was found
            print('read_cell: Warning - Was not able to validate CASTEP input.')
            print('           This may be due to a non-existing '
                  '"castep_keywords.json"')
            print('           file or a non-existing CASTEP installation.')
            print('           Parsing will go on but keywords will not be '
                  'validated and may cause problems if incorrect during a CASTEP '
                  'run.')

        celldict = read_freeform(fd)

        def parse_blockunit(line_tokens, blockname):
            u = 1.0
            if len(line_tokens[0]) == 1:
                usymb = line_tokens[0][0].lower()
                u = cell_units.get(usymb, 1)
                if usymb not in cell_units:
                    warnings.warn(('read_cell: Warning - ignoring invalid '
                                   'unit specifier in %BLOCK {0} '
                                   '(assuming Angstrom instead)'
                                   ).format(blockname))
                line_tokens = line_tokens[1:]
            return u, line_tokens

        # Arguments to pass to the Atoms object at the end
        aargs = {
            'pbc': True
        }

        # Start by looking for the lattice
        lat_keywords = [w in celldict for w in ('lattice_cart', 'lattice_abc')]
        if all(lat_keywords):
            warnings.warn('read_cell: Warning - two lattice blocks present in the'
                          ' same file. LATTICE_ABC will be ignored')
        elif not any(lat_keywords):
            raise ValueError('Cell file must contain at least one between '
                             'LATTICE_ABC and LATTICE_CART')

        if 'lattice_abc' in celldict:

            lines = celldict.pop('lattice_abc')[0].split('\n')
            line_tokens = [l.split() for l in lines]

            u, line_tokens = parse_blockunit(line_tokens, 'lattice_abc')

            if len(line_tokens) != 2:
                warnings.warn('read_cell: Warning - ignoring additional '
                              'lines in invalid %BLOCK LATTICE_ABC')

            abc = [float(p) * u for p in line_tokens[0][:3]]
            angles = [float(phi) for phi in line_tokens[1][:3]]

            aargs['cell'] = cellpar_to_cell(abc + angles)

        if 'lattice_cart' in celldict:

            lines = celldict.pop('lattice_cart')[0].split('\n')
            line_tokens = [l.split() for l in lines]

            u, line_tokens = parse_blockunit(line_tokens, 'lattice_cart')

            if len(line_tokens) != 3:
                warnings.warn('read_cell: Warning - ignoring more than '
                              'three lattice vectors in invalid %BLOCK '
                              'LATTICE_CART')

            aargs['cell'] = [[float(x) * u for x in lt[:3]] for lt in line_tokens]

        # Now move on to the positions
        pos_keywords = [w in celldict
                        for w in ('positions_abs', 'positions_frac')]

        if all(pos_keywords):
            warnings.warn('read_cell: Warning - two lattice blocks present in the'
                          ' same file. POSITIONS_FRAC will be ignored')
            del celldict['positions_frac']
        elif not any(pos_keywords):
            raise ValueError('Cell file must contain at least one between '
                             'POSITIONS_FRAC and POSITIONS_ABS')

        aargs['symbols'] = []
        pos_type = 'positions'
        pos_block = celldict.pop('positions_abs', [None])[0]
        if pos_block is None:
            pos_type = 'scaled_positions'
            pos_block = celldict.pop('positions_frac', [None])[0]
        aargs[pos_type] = []

        lines = pos_block.split('\n')
        line_tokens = [l.split() for l in lines]

        if not 'scaled' in pos_type:
            u, line_tokens = parse_blockunit(line_tokens, 'positions_abs')
        else:
            u = 1.0

        # Here we extract all the possible additional info
        # These are marked by their type

        add_info = {
            'SPIN': (float, 0.0),   # (type, default)
            'MAGMOM': (float, 0.0),
            'LABEL': (str, 'NULL')
        }
        add_info_arrays = dict((k, []) for k in add_info)

        def parse_info(raw_info):

            re_keys = (r'({0})\s*[=:\s]{{1}}\s'
                       r'*([^\s]*)').format('|'.join(add_info.keys()))
            # Capture all info groups
            info = re.findall(re_keys, raw_info)
            info = {g[0]: add_info[g[0]][0](g[1]) for g in info}
            return info

        # Array for custom species (a CASTEP special thing)
        # Usually left unused
        custom_species = None

        for tokens in line_tokens:
            # Now, process the whole 'species' thing
            spec_custom = tokens[0].split(':', 1)
            elem = spec_custom[0]
            if len(spec_custom) > 1 and custom_species is None:
                # Add it to the custom info!
                custom_species = list(aargs['symbols'])
            if custom_species is not None:
                custom_species.append(tokens[0])
            aargs['symbols'].append(elem)
            aargs[pos_type].append([float(p) * u for p in tokens[1:4]])
            # Now for the additional information
            info = ' '.join(tokens[4:])
            info = parse_info(info)
            for k in add_info:
                add_info_arrays[k] += [info.get(k, add_info[k][1])]

        # Now on to the species potentials...
        if 'species_pot' in celldict:
            lines = celldict.pop('species_pot')[0].split('\n')
            line_tokens = [l.split() for l in lines]

            for tokens in line_tokens:
                if len(tokens) == 1:
                    # It's a library
                    all_spec = (set(custom_species) if custom_species is not None
                                else set(aargs['symbols']))
                    for s in all_spec:
                        calc.cell.species_pot = (s, tokens[0])
                else:
                    calc.cell.species_pot = tuple(tokens[:2])

        # Ionic constraints
        raw_constraints = {}

        if 'ionic_constraints' in celldict:
            lines = celldict.pop('ionic_constraints')[0].split('\n')
            line_tokens = [l.split() for l in lines]

            for tokens in line_tokens:
                if not len(tokens) == 6:
                    continue
                _, species, nic, x, y, z = tokens
                # convert xyz to floats
                x = float(x)
                y = float(y)
                z = float(z)

                nic = int(nic)
                if (species, nic) not in raw_constraints:
                    raw_constraints[(species, nic)] = []
                raw_constraints[(species, nic)].append(np.array(
                                                       [x, y, z]))

        # Symmetry operations
        if 'symmetry_ops' in celldict:
            lines = celldict.pop('symmetry_ops')[0].split('\n')
            line_tokens = [l.split() for l in lines]

            # Read them in blocks of four
            blocks = np.array(line_tokens).astype(float)
            if (len(blocks.shape) != 2 or blocks.shape[1] != 3
                    or blocks.shape[0] % 4 != 0):
                warnings.warn('Warning: could not parse SYMMETRY_OPS'
                              ' block properly, skipping')
            else:
                blocks = blocks.reshape((-1, 4, 3))
                rotations = blocks[:, :3]
                translations = blocks[:, 3]

                # Regardless of whether we recognize them, store these
                calc.cell.symmetry_ops = (rotations, translations)

        # Anything else that remains, just add it to the cell object:
        for k, (val, otype) in celldict.items():
            try:
                if otype == 'block':
                    val = val.split('\n')  # Avoids a bug for one-line blocks
                calc.cell.__setattr__(k, val)
            except Exception:
                raise RuntimeError('Problem setting calc.cell.%s = %s' % (k, val))

        # Get the relevant additional info
        aargs['magmoms'] = np.array(add_info_arrays['SPIN'])
        # SPIN or MAGMOM are alternative keywords
        aargs['magmoms'] = np.where(aargs['magmoms'] != 0,
                                    aargs['magmoms'],
                                    add_info_arrays['MAGMOM'])
        labels = np.array(add_info_arrays['LABEL'])

        aargs['calculator'] = calc

        atoms = ase.Atoms(**aargs)

        # Spacegroup...
        if find_spg:
            # Try importing spglib
            try:
                import spglib
            except ImportError:
                try:
                    from pyspglib import spglib
                except ImportError:
                    # spglib is not present
                    warnings.warn('spglib not found installed on this system - '
                                  'automatic spacegroup detection is not possible')
                    spglib = None

            if spglib is not None:
                symmd = spglib.get_symmetry_dataset(atoms)
                atoms_spg = Spacegroup(int(symmd['number']))
                atoms.info['spacegroup'] = atoms_spg

        atoms.new_array('castep_labels', labels)
        if custom_species is not None:
            atoms.new_array('castep_custom_species', np.array(custom_species))

        fixed_atoms = []
        constraints = []
        for (species, nic), value in raw_constraints.items():
            absolute_nr = atoms.calc._get_absolute_number(species, nic)
            if len(value) == 3:
                # Check if they are linearly independent
                if np.linalg.det(value) == 0:
                    print('Error: Found linearly dependent constraints attached '
                          'to atoms %s' % (absolute_nr))
                    continue
                fixed_atoms.append(absolute_nr)
            elif len(value) == 2:
                direction = np.cross(value[0], value[1])
                # Check if they are linearly independent
                if np.linalg.norm(direction) == 0:
                    print('Error: Found linearly dependent constraints attached '
                          'to atoms %s' % (absolute_nr))
                    continue
                constraint = ase.constraints.FixedLine(
                    a=absolute_nr,
                    direction=direction)
                constraints.append(constraint)
            elif len(value) == 1:
                constraint = ase.constraints.FixedPlane(
                    a=absolute_nr,
                    direction=np.array(value[0], dtype=np.float32))
                constraints.append(constraint)
            else:
                print('Error: Found %s statements attached to atoms %s'
                      % (len(value), absolute_nr))

        # we need to sort the fixed atoms list in order not to raise an assertion
        # error in FixAtoms
        if fixed_atoms:
            constraints.append(
                ase.constraints.FixAtoms(indices=sorted(fixed_atoms)))
        if constraints:
            atoms.set_constraint(constraints)

        atoms.calc.atoms = atoms
        atoms.calc.push_oldstate()

        return atoms

    def read_castep(filename, index=None):
        """
        Wrapper function for the more generic read() functionality.

        Note that this is function is intended to maintain backwards-compatibility
        only.
        """
        from ase.io import read
        return read(filename, index=index, format='castep-castep')

    def read_castep_castep(fd, index=None):
        """
        Reads a .castep file and returns an atoms  object.
        The calculator information will be stored in the calc attribute.

        There is no use of the "index" argument as of now, it is just inserted for
        convenience to comply with the generic "read()" in ase.io

        Please note that this routine will return an atom ordering as found
        within the castep file. This means that the species will be ordered by
        ascending atomic numbers. The atoms witin a species are ordered as given
        in the original cell file.

        Note: This routine returns a single atoms_object only, the last
        configuration in the file. Yet, if you want to parse an MD run, use the
        novel function `read_md()`
        """

        from ase.calculators.castep import Castep

        try:
            calc = Castep()
        except Exception as e:
            # No CASTEP keywords found?
            print('WARNING:\n{0}\nUsing fallback .castep reader...'.format(e))
            # Fall back on the old method
            return read_castep_castep_old(fd, index)

        calc.read(castep_file=fd)

        # now we trick the calculator instance such that we can savely extract
        # energies and forces from this atom. Basically what we do is to trick the
        # internal routine calculation_required() to always return False such that
        # we do not need to re-run a CASTEP calculation.
        #
        # Probably we can solve this with a flag to the read() routine at some
        # point, but for the moment I do not want to change too much in there.
        calc._old_atoms = calc.atoms
        calc._old_param = calc.param
        calc._old_cell = calc.cell

        return [calc.atoms]  # Returning in the form of a list for next()

    def read_castep_castep_old(fd, index=None):
        """
        DEPRECATED
        Now replaced by ase.calculators.castep.Castep.read(). Left in for future
        reference and backwards compatibility needs, as well as a fallback for
        when castep_keywords.py can't be created.

        Reads a .castep file and returns an atoms  object.
        The calculator information will be stored in the calc attribute.
        If more than one SCF step is found, a list of all steps
        will be stored in the traj attribute.

        Note that the index argument has no effect as of now.

        Please note that this routine will return an atom ordering as found
        within the castep file. This means that the species will be ordered by
        ascending atomic numbers. The atoms witin a species are ordered as given
        in the original cell file.
        """
        from ase.calculators.singlepoint import SinglePointCalculator

        lines = fd.readlines()

        traj = []
        energy_total = None
        energy_0K = None
        for i, line in enumerate(lines):
            if 'NB est. 0K energy' in line:
                energy_0K = float(line.split()[6])
            # support also for dispersion correction
            elif 'NB dispersion corrected est. 0K energy*' in line:
                energy_0K = float(line.split()[-2])
            elif 'Final energy, E' in line:
                energy_total = float(line.split()[4])
            elif 'Dispersion corrected final energy' in line:
                pass
                # dispcorr_energy_total = float(line.split()[-2])
                # sedc_apply = True
            elif 'Dispersion corrected final free energy' in line:
                pass  # dispcorr_energy_free = float(line.split()[-2])
            elif 'dispersion corrected est. 0K energy' in line:
                pass  # dispcorr_energy_0K = float(line.split()[-2])
            elif 'Unit Cell' in line:
                cell = [x.split()[0:3] for x in lines[i + 3:i + 6]]
                cell = np.array([[float(col) for col in row] for row in cell])
            elif 'Cell Contents' in line:
                geom_starts = i
                start_found = False
                for j, jline in enumerate(lines[geom_starts:]):
                    if jline.find('xxxxx') > 0 and start_found:
                        geom_stop = j + geom_starts
                        break
                    if jline.find('xxxx') > 0 and not start_found:
                        geom_start = j + geom_starts + 4
                        start_found = True
                species = [line.split()[1] for line in lines[geom_start:geom_stop]]
                geom = np.dot(np.array([[float(col) for col in line.split()[3:6]]
                                        for line in lines[geom_start:geom_stop]]),
                              cell)
            elif 'Writing model to' in line:
                atoms = ase.Atoms(
                    cell=cell,
                    pbc=True,
                    positions=geom,
                    symbols=''.join(species))
                # take 0K energy where available, else total energy
                if energy_0K:
                    energy = energy_0K
                else:
                    energy = energy_total
                # generate a minimal single-point calculator
                sp_calc = SinglePointCalculator(atoms=atoms,
                                                energy=energy,
                                                forces=None,
                                                magmoms=None,
                                                stress=None)
                atoms.set_calculator(sp_calc)
                traj.append(atoms)
        if index is None:
            return traj
        else:
            return traj[index]

    def read_geom(filename, index=':', units=units_CODATA2002):
        """
        Wrapper function for the more generic read() functionality.

        Note that this is function is intended to maintain backwards-compatibility
        only. Keyword arguments will be passed to read_castep_geom().
        """
        from ase.io import read
        return read(filename, index=index, format='castep-geom', units=units)

    def read_castep_geom(fd, index=None, units=units_CODATA2002):
        """Reads a .geom file produced by the CASTEP GeometryOptimization task and
        returns an atoms  object.
        The information about total free energy and forces of each atom for every
        relaxation step will be stored for further analysis especially in a
        single-point calculator.
        Note that everything in the .geom file is in atomic units, which has
        been conversed to commonly used unit angstrom(length) and eV (energy).

        Note that the index argument has no effect as of now.

        Contribution by Wei-Bing Zhang. Thanks!

        Routine now accepts a filedescriptor in order to out-source the gz and
        bz2 handling to formats.py. Note that there is a fallback routine
        read_geom() that behaves like previous versions did.
        """
        from ase.calculators.singlepoint import SinglePointCalculator

        # fd is closed by embracing read() routine
        txt = fd.readlines()

        traj = []

        Hartree = units['Eh']
        Bohr = units['a0']

        # Yeah, we know that...
        # print('N.B.: Energy in .geom file is not 0K extrapolated.')
        for i, line in enumerate(txt):
            if line.find('<-- E') > 0:
                start_found = True
                energy = float(line.split()[0]) * Hartree
                cell = [x.split()[0:3] for x in txt[i + 1:i + 4]]
                cell = np.array([[float(col) * Bohr for col in row] for row in
                                 cell])
            if line.find('<-- R') > 0 and start_found:
                start_found = False
                geom_start = i
                for i, line in enumerate(txt[geom_start:]):
                    if line.find('<-- F') > 0:
                        geom_stop = i + geom_start
                        break
                species = [line.split()[0] for line in
                           txt[geom_start:geom_stop]]
                geom = np.array([[float(col) * Bohr for col in
                                  line.split()[2:5]] for line in
                                 txt[geom_start:geom_stop]])
                forces = np.array([[float(col) * Hartree / Bohr for col in
                                    line.split()[2:5]] for line in
                                   txt[geom_stop:geom_stop
                                       + (geom_stop - geom_start)]])
                image = ase.Atoms(species, geom, cell=cell, pbc=True)
                image.set_calculator(
                    SinglePointCalculator(atoms=image, energy=energy,
                                          forces=forces))
                traj.append(image)

        if index is None:
            return traj
        else:
            return traj[index]

    def read_phonon(filename, index=None, read_vib_data=False,
                    gamma_only=True, frequency_factor=None,
                    units=units_CODATA2002):
        """
        Wrapper function for the more generic read() functionality.

        Note that this is function is intended to maintain backwards-compatibility
        only. For documentation see read_castep_phonon().
        """
        from ase.io import read

        if read_vib_data:
            full_output = True
        else:
            full_output = False

        return read(filename, index=index, format='castep-phonon',
                    full_output=full_output, read_vib_data=read_vib_data,
                    gamma_only=gamma_only, frequency_factor=frequency_factor,
                    units=units)

    def read_castep_phonon(fd, index=None, read_vib_data=False,
                           gamma_only=True, frequency_factor=None,
                           units=units_CODATA2002):
        """
        Reads a .phonon file written by a CASTEP Phonon task and returns an atoms
        object, as well as the calculated vibrational data if requested.

        Note that the index argument has no effect as of now.
        """

        # fd is closed by embracing read() routine
        lines = fd.readlines()

        atoms = None
        cell = []
        N = Nb = Nq = 0
        scaled_positions = []
        symbols = []
        masses = []

        # header
        l = 0
        while l < len(lines):

            line = lines[l]

            if 'Number of ions' in line:
                N = int(line.split()[3])
            elif 'Number of branches' in line:
                Nb = int(line.split()[3])
            elif 'Number of wavevectors'in line:
                Nq = int(line.split()[3])
            elif 'Unit cell vectors (A)' in line:
                for ll in range(3):
                    l += 1
                    fields = lines[l].split()
                    cell.append([float(x) for x in fields[0:3]])
            elif 'Fractional Co-ordinates' in line:
                for ll in range(N):
                    l += 1
                    fields = lines[l].split()
                    scaled_positions.append([float(x) for x in fields[1:4]])
                    symbols.append(fields[4])
                    masses.append(float(fields[5]))
            elif 'END header' in line:
                l += 1
                atoms = ase.Atoms(symbols=symbols,
                                  scaled_positions=scaled_positions,
                                  cell=cell)
                break

            l += 1

        # Eigenmodes and -vectors
        if frequency_factor is None:
            Kayser_to_eV = 1E2 * 2 * np.pi * units['hbar'] * units['c']
        # N.B. "fixed default" unit for frequencies in .phonon files is "cm-1"
        # (i.e. the latter is unaffected by the internal unit conversion system of
        # CASTEP!) set conversion factor to convert therefrom to eV by default for
        # now
        frequency_factor = Kayser_to_eV
        qpoints = []
        weights = []
        frequencies = []
        displacements = []
        for nq in range(Nq):
            fields = lines[l].split()
            qpoints.append([float(x) for x in fields[2:5]])
            weights.append(float(fields[5]))
        freqs = []
        for ll in range(Nb):
            l += 1
            fields = lines[l].split()
            freqs.append(frequency_factor * float(fields[1]))
        frequencies.append(np.array(freqs))

        # skip the two Phonon Eigenvectors header lines
        l += 2

        # generate a list of displacements with a structure that is identical to
        # what is stored internally in the Vibrations class (see in
        # ase.vibrations.Vibrations.modes):
        #      np.array(displacements).shape == (Nb,3*N)

        disps = []
        for ll in range(Nb):
            disp_coords = []
            for lll in range(N):
                l += 1
                fields = lines[l].split()
                disp_x = float(fields[2]) + float(fields[3]) * 1.0j
                disp_y = float(fields[4]) + float(fields[5]) * 1.0j
                disp_z = float(fields[6]) + float(fields[7]) * 1.0j
                disp_coords.extend([disp_x, disp_y, disp_z])
            disps.append(np.array(disp_coords))
        displacements.append(np.array(disps))

        if read_vib_data:
            if gamma_only:
                vibdata = [frequencies[0], displacements[0]]
            else:
                vibdata = [qpoints, weights, frequencies, displacements]
            return vibdata, atoms
        else:
            return atoms

    def read_md(filename, index=None, return_scalars=False,
                units=units_CODATA2002):
        """Wrapper function for the more generic read() functionality.

        Note that this function is intended to maintain backwards-compatibility
        only. For documentation see read_castep_md()
        """
        if return_scalars:
            full_output = True
        else:
            full_output = False

        from ase.io import read
        return read(filename, index=index, format='castep-md',
                    full_output=full_output, return_scalars=return_scalars,
                    units=units)

    def read_castep_md(fd, index=None, return_scalars=False,
                       units=units_CODATA2002):
        """Reads a .md file written by a CASTEP MolecularDynamics task
        and returns the trajectory stored therein as a list of atoms object.

        Note that the index argument has no effect as of now."""

        from ase.calculators.singlepoint import SinglePointCalculator

        factors = {
            't': units['t0'] * 1E15,     # fs
            'E': units['Eh'],            # eV
            'T': units['Eh'] / units['kB'],
            'P': units['Eh'] / units['a0']**3 * units['Pascal'],
            'h': units['a0'],
            'hv': units['a0'] / units['t0'],
            'S': units['Eh'] / units['a0']**3,
            'R': units['a0'],
            'V': np.sqrt(units['Eh'] / units['me']),
            'F': units['Eh'] / units['a0']}

        # fd is closed by embracing read() routine
        lines = fd.readlines()

        l = 0
        while 'END header' not in lines[l]:
            l += 1
        l_end_header = l
        lines = lines[l_end_header + 1:]
        times = []
        energies = []
        temperatures = []
        pressures = []
        traj = []

        # Initialization
        time = None
        Epot = None
        Ekin = None
        EH = None
        temperature = None
        pressure = None
        symbols = None
        positions = None
        cell = None
        velocities = None
        symbols = []
        positions = []
        velocities = []
        forces = []
        cell = np.eye(3)
        cell_velocities = []
        stress = []

        for (l, line) in enumerate(lines):
            fields = line.split()
            if len(fields) == 0:
                if l != 0:
                    times.append(time)
                    energies.append([Epot, EH, Ekin])
                    temperatures.append(temperature)
                    pressures.append(pressure)
                    atoms = ase.Atoms(symbols=symbols,
                                      positions=positions,
                                      cell=cell)
                    atoms.set_velocities(velocities)
                    if len(stress) == 0:
                        atoms.set_calculator(
                            SinglePointCalculator(atoms=atoms, energy=Epot,
                                                  forces=forces))
                    else:
                        atoms.set_calculator(
                            SinglePointCalculator(atoms=atoms, energy=Epot,
                                                  forces=forces, stress=stress))
                    traj.append(atoms)
                symbols = []
                positions = []
                velocities = []
                forces = []
                cell = []
                cell_velocities = []
                stress = []
                continue
            if len(fields) == 1:
                time = factors['t'] * float(fields[0])
                continue

            if fields[-1] == 'E':
                E = [float(x) for x in fields[0:3]]
                Epot, EH, Ekin = [factors['E'] * Ei for Ei in E]
                continue

            if fields[-1] == 'T':
                temperature = factors['T'] * float(fields[0])
                continue

            # only printed in case of variable cell calculation or calculate_stress
            # explicitly requested
            if fields[-1] == 'P':
                pressure = factors['P'] * float(fields[0])
                continue
            if fields[-1] == 'h':
                h = [float(x) for x in fields[0:3]]
                cell.append([factors['h'] * hi for hi in h])
                continue

            # only printed in case of variable cell calculation
            if fields[-1] == 'hv':
                hv = [float(x) for x in fields[0:3]]
                cell_velocities.append([factors['hv'] * hvi for hvi in hv])
                continue

            # only printed in case of variable cell calculation
            if fields[-1] == 'S':
                S = [float(x) for x in fields[0:3]]
                stress.append([factors['S'] * Si for Si in S])
                continue
            if fields[-1] == 'R':
                symbols.append(fields[0])
                R = [float(x) for x in fields[2:5]]
                positions.append([factors['R'] * Ri for Ri in R])
                continue
            if fields[-1] == 'V':
                V = [float(x) for x in fields[2:5]]
                velocities.append([factors['V'] * Vi for Vi in V])
                continue
            if fields[-1] == 'F':
                F = [float(x) for x in fields[2:5]]
                forces.append([factors['F'] * Fi for Fi in F])
                continue

        if index is None:
            pass
        else:
            traj = traj[index]

        if return_scalars:
            data = [times, energies, temperatures, pressures]
            return data, traj
        else:
            return traj

    # Routines that only the calculator requires

    def read_param(filename='', calc=None, fd=None, get_interface_options=False):

        if fd is None:
            if filename == '':
                raise ValueError('One between filename and fd must be provided')
            fd = open(filename)
        elif filename:
            warnings.warn('Filestream used to read param, file name will be '
                          'ignored')

        # If necessary, get the interface options
        if get_interface_options:
            int_opts = {}
            optre = re.compile(r'# ASE_INTERFACE ([^\s]+) : ([^\s]+)')

            lines = fd.readlines()
            fd.seek(0)

            for l in lines:
                m = optre.search(l)
                if m:
                    int_opts[m.groups()[0]] = m.groups()[1]

        data = read_freeform(fd)

        if calc is None:
            from ase.calculators.castep import Castep
            calc = Castep(check_castep_version=False, keyword_tolerance=2)

        for kw, (val, otype) in data.items():
            if otype == 'block':
                val = val.split('\n')  # Avoids a bug for one-line blocks
            calc.param.__setattr__(kw, val)

        if not get_interface_options:
            return calc
        else:
            return calc, int_opts

    def write_param(filename, param, check_checkfile=False,
                    force_write=False,
                    interface_options=None):
        """Writes a CastepParam object to a CASTEP .param file

        Parameters:
            filename: the location of the file to write to. If it
            exists it will be overwritten without warning. If it
            doesn't it will be created.
            param: a CastepParam instance
            check_checkfile : if set to True, write_param will
            only write continuation or reuse statement
            if a restart file exists in the same directory
        """
        if os.path.isfile(filename) and not force_write:
            print('ase.io.castep.write_param: Set optional argument')
            print('force_write=True to overwrite %s.' % filename)
            return False

        out = paropen(filename, 'w')
        out.write('#######################################################\n')
        out.write('#CASTEP param file: %s\n' % filename)
        out.write('#Created using the Atomic Simulation Environment (ASE)#\n')
        if interface_options is not None:
            out.write('# Internal settings of the calculator\n')
            out.write('# This can be switched off by settings\n')
            out.write('# calc._export_settings = False\n')
            out.write('# If stated, this will be automatically processed\n')
            out.write('# by ase.io.castep.read_seed()\n')
            for option, value in sorted(interface_options.items()):
                out.write('# ASE_INTERFACE %s : %s\n' % (option, value))
        out.write('#######################################################\n\n')

        if check_checkfile:
            param = deepcopy(param)  # To avoid modifying the parent one
            for checktype in ['continuation', 'reuse']:
                opt = getattr(param, checktype)
                if opt and opt.value:
                    fname = opt.value
                    if fname == 'default':
                        fname = os.path.splitext(filename)[0] + '.check'
                    if not (os.path.exists(fname) or
                            # CASTEP also understands relative path names, hence
                            # also check relative to the param file directory
                            os.path.exists(
                        os.path.join(os.path.dirname(filename),
                                     opt.value))):
                        opt.clear()

        write_freeform(out, param)

        out.close()

    def read_seed(seed, new_seed=None, ignore_internal_keys=False):
        """A wrapper around the CASTEP Calculator in conjunction with
        read_cell and read_param. Basically this can be used to reuse
        a previous calculation which results in a triple of
        cell/param/castep file. The label of the calculation if pre-
        fixed with `copy_of_` and everything else will be recycled as
        much as possible from the addressed calculation.

        Please note that this routine will return an atoms ordering as specified
        in the cell file! It will thus undo the potential reordering internally
        done by castep.
        """

        directory = os.path.abspath(os.path.dirname(seed))
        seed = os.path.basename(seed)

        paramfile = os.path.join(directory, '%s.param' % seed)
        cellfile = os.path.join(directory, '%s.cell' % seed)
        castepfile = os.path.join(directory, '%s.castep' % seed)
        checkfile = os.path.join(directory, '%s.check' % seed)

        atoms = read_cell(cellfile)
        atoms.calc._directory = directory
        atoms.calc._rename_existing_dir = False
        atoms.calc._castep_pp_path = directory
        atoms.calc.merge_param(paramfile,
                               ignore_internal_keys=ignore_internal_keys)
        if new_seed is None:
            atoms.calc._label = 'copy_of_%s' % seed
        else:
            atoms.calc._label = str(new_seed)
        if os.path.isfile(castepfile):
            # _set_atoms needs to be True here
            # but we set it right back to False
            # atoms.calc._set_atoms = False
            # BUGFIX: I do not see a reason to do that!
            atoms.calc.read(castepfile)
            # atoms.calc._set_atoms = False

            # if here is a check file, we also want to re-use this information
            if os.path.isfile(checkfile):
                atoms.calc._check_file = os.path.basename(checkfile)

            # sync the top-level object with the
            # one attached to the calculator
            atoms = atoms.calc.atoms
        else:
            # There are cases where we only want to restore a calculator/atoms
            # setting without a castep file...
            pass
            # No print statement required in these cases
            print('Corresponding *.castep file not found.')
            print('Atoms object will be restored from *.cell and *.param only.')
        atoms.calc.push_oldstate()

        return atoms

    def read_bands(filename='', fd=None, units=units_CODATA2002):
        """Read Castep.bands file to kpoints, weights and eigenvalues

        Args:
            filename (str):
                path to seedname.bands file
            fd (fd):
                file descriptor for open bands file
            units (dict):
                Conversion factors for atomic units

        Returns:
            (tuple):
                (kpts, weights, eigenvalues, efermi)

                Where ``kpts`` and ``weights`` are 1d numpy arrays, eigenvalues
                is an array of shape (spin, kpts, nbands) and efermi is a float
        """

        Hartree = units['Eh']

        if fd is None:
            if filename == '':
                raise ValueError('One between filename and fd must be provided')
            fd = open(filename)
        elif filename:
            warnings.warn('Filestream used to read param, file name will be '
                          'ignored')

        nkpts, nspin, _, nbands, efermi = [t(fd.readline().split()[-1]) for t in
                                           [int, int, float, int, float]]

        kpts, weights = np.zeros((nkpts, 3)), np.zeros(nkpts)
        eigenvalues = np.zeros((nspin, nkpts, nbands))

        # Skip unit cell
        for _ in range(4):
            fd.readline()

        def _kptline_to_i_k_wt(line):
            line = line.split()
            line = [int(line[1])] + list(map(float, line[2:]))
            return (line[0] - 1, line[1:4], line[4])

        # CASTEP often writes these out-of-order, so check index and write directly
        # to the correct row
        for kpt_line in range(nkpts):
            i_kpt, kpt, wt = _kptline_to_i_k_wt(fd.readline())
            kpts[i_kpt,:], weights[i_kpt] = kpt, wt
            for spin in range(nspin):
                fd.readline()  # Skip 'Spin component N' line
                eigenvalues[spin, i_kpt, :] = [float(fd.readline())
                                               for _ in range(nbands)]

        return (kpts, weights, eigenvalues * Hartree, efermi * Hartree)

Documentation v: 3.19.0

Versions
  3.20.0b1 (development)
  3.19.0 (latest stable)