Source code for

"""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
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
from ase.utils import atoms_to_spglib_cell

# 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- vs CODATA2002 for CASTEP 5.01).
# ase.units in in ase- 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
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
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
    # additional reads that still need to be wrapped
    # write that is already wrapped
    # param write - in principle only necessary in junction with the calculator

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(
            fd.write('{0}: {1}\n'.format(kw.upper(), opt.value))

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

    Note that this is function is intended to maintain backwards-compatibility
    from import write

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

[docs]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 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: warnings.warn('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.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('masses'): from import atomic_masses masses = atoms.get_array('masses') custom_masses = {} for i, species in enumerate(elems): custom_mass = masses[i] # build record of different masses for each species if species not in custom_masses.keys(): # build dictionary of positions of all species with # same name and mass value ideally there should only # be one mass per species custom_masses[species] = {custom_mass: [i]} # if multiple masses found for a species elif custom_mass not in custom_masses[species].keys(): # if custom species were already manually defined raise an error if atoms.has('castep_custom_species'): raise ValueError( "Could not write custom mass block for {0}. \n" "Custom mass was set ({1}), but an inconsistent set of " "castep_custom_species already defines " "({2}) for {0}. \n" "If using both features, ensure that " "each species type in " "atoms.arrays['castep_custom_species'] " "has consistent mass values and that each atom " "with non-standard " "mass belongs to a custom species type." "".format( species, custom_mass, list( custom_masses[species].keys())[0])) # append mass to create custom species later else: custom_masses[species][custom_mass] = [i] else: custom_masses[species][custom_mass].append(i) # create species_mass block mass_block = [] for el, mass_dict in custom_masses.items(): # ignore mass record that match defaults default = mass_dict.pop(atomic_masses[atoms.get_array( 'numbers')[list(elems).index(el)]], None) if mass_dict: # no custom species need to be created if len(mass_dict) == 1 and not default: mass_block.append('{0} {1}'.format( el, list(mass_dict.keys())[0])) # for each custom mass, create new species and change names to # match in 'elems' list else: warnings.warn( 'Custom mass specified for ' 'standard species {0}, creating custom species' .format(el)) for i, vals in enumerate(mass_dict.items()): mass_val, idxs = vals custom_species_name = "{0}:{1}".format(el, i) warnings.warn( 'Creating custom species {0} with mass {1}'.format( custom_species_name, str(mass_dict))) for idx in idxs: elems[idx] = custom_species_name mass_block.append('{0} {1}'.format( custom_species_name, mass_val)) setattr(cell, 'species_mass', mass_block) 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): warnings.warn( 'Warning: you have constraints in your atoms, that are ' 'not supported by the CASTEP ase interface') break species_indices = atoms.symbols.species_indices() if isinstance(constr, FixAtoms): for i in constr.index: try: symbol = atoms.get_chemical_symbols()[i] nis = species_indices[i] + 1 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 = species_indices[n] + 1 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 = species_indices[n] + 1 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 = species_indices[n] + 1 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 import read return read(filename, index=index, format='castep-cell')
[docs]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 warnings.warn( 'read_cell: Warning - Was not able to validate CASTEP input. ' 'This may be due to a non-existing ' '"castep_keywords.json" ' 'file or a non-existing CASTEP installation. ' '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 = [line.split() for line 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 = [line.split() for line 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 = [line.split() for line in lines] if 'scaled' not 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])] # read in custom species mass if 'species_mass' in celldict: spec_list = custom_species if custom_species else aargs['symbols'] aargs['masses'] = [None for _ in spec_list] lines = celldict.pop('species_mass')[0].split('\n') line_tokens = [line.split() for line in lines] if len(line_tokens[0]) == 1: if line_tokens[0][0].lower() not in ('amu', 'u'): raise ValueError( "unit specifier '{0}' in %BLOCK SPECIES_MASS " "not recognised".format( line_tokens[0][0].lower())) line_tokens = line_tokens[1:] for tokens in line_tokens: token_pos_list = [i for i, x in enumerate( spec_list) if x == tokens[0]] if len(token_pos_list) == 0: warnings.warn( 'read_cell: Warning - ignoring unused ' 'species mass {0} in %BLOCK SPECIES_MASS'.format( tokens[0])) for idx in token_pos_list: aargs['masses'][idx] = tokens[1] # Now on to the species potentials... if 'species_pot' in celldict: lines = celldict.pop('species_pot')[0].split('\n') line_tokens = [line.split() for line 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 = [line.split() for line 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 = [line.split() for line 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 as e: raise RuntimeError( 'Problem setting calc.cell.%s = %s: %s' % (k, val, e)) # 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: 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_to_spglib_cell(atoms)) atoms_spg = Spacegroup(int(symmd['number']))['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 = [] index_dict = atoms.symbols.indices() for (species, nic), value in raw_constraints.items(): absolute_nr = index_dict[species][nic - 1] if len(value) == 3: # Check if they are linearly independent if np.linalg.det(value) == 0: warnings.warn( '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: warnings.warn( '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: warnings.warn('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 import read return read(filename, index=index, format='castep-castep')
[docs]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 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? warnings.warn('WARNING: {0} Using fallback .castep reader...'.format(e)) # Fall back on the old method return read_castep_castep_old(fd, index) # 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 Left in for future reference and backwards compatibility needs, as well as a fallback for when 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 =[[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.calc = 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 import read return read(filename, index=index, format='castep-geom', units=units)
[docs]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 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.calc = 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 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)
[docs]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 import read return read(filename, index=index, format='castep-md', full_output=full_output, return_scalars=return_scalars, units=units)
[docs]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.calc = SinglePointCalculator( atoms=atoms, energy=Epot, forces=forces) else: atoms.calc = 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() for line in lines: m = 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: warnings.warn(' Set optional argument ' '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\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._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 warnings.warn( 'Corresponding *.castep file not found. ' '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)