pymatgen.io.pwscf — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.pwscf

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    This module implements input and output processing from PWSCF.
    """

    import re

    from monty.io import zopen

    from monty.re import regrep
    from collections import defaultdict

    from pymatgen.core.periodic_table import Element
    from pymatgen.core.lattice import Lattice
    from pymatgen.core.structure import Structure
    from pymatgen.util.io_utils import clean_lines

    __author__ = "Shyue Ping Ong"
    __copyright__ = "Copyright 2012, The Materials Virtual Lab"
    __version__ = "0.1"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "ongsp@ucsd.edu"
    __date__ = "3/27/15"

    class PWInput:
        """
        Base input file class. Right now, only supports no symmetry and is
        very basic.
        """

        def __init__(self, structure, pseudo=None, control=None, system=None,
                     electrons=None, ions=None, cell=None, kpoints_mode="automatic",
                     kpoints_grid=(1, 1, 1), kpoints_shift=(0, 0, 0)):
            """
            Initializes a PWSCF input file.

            Args:
                structure (Structure): Input structure. For spin-polarized calculation,
                    properties (e.g. {"starting_magnetization": -0.5,
                    "pseudo": "Mn.pbe-sp-van.UPF"}) on each site is needed instead of
                    pseudo (dict).
                pseudo (dict): A dict of the pseudopotentials to use. Default to None.
                control (dict): Control parameters. Refer to official PWSCF doc
                    on supported parameters. Default to {"calculation": "scf"}
                system (dict): System parameters. Refer to official PWSCF doc
                    on supported parameters. Default to None, which means {}.
                electrons (dict): Electron parameters. Refer to official PWSCF doc
                    on supported parameters. Default to None, which means {}.
                ions (dict): Ions parameters. Refer to official PWSCF doc
                    on supported parameters. Default to None, which means {}.
                cell (dict): Cell parameters. Refer to official PWSCF doc
                    on supported parameters. Default to None, which means {}.
                kpoints_mode (str): Kpoints generation mode. Default to automatic.
                kpoints_grid (sequence): The kpoint grid. Default to (1, 1, 1).
                kpoints_shift (sequence): The shift for the kpoints. Defaults to
                    (0, 0, 0).
            """
            self.structure = structure
            sections = {}
            sections["control"] = control or {"calculation": "scf"}
            sections["system"] = system or {}
            sections["electrons"] = electrons or {}
            sections["ions"] = ions or {}
            sections["cell"] = cell or {}
            if pseudo is None:
                for site in structure:
                    try:
                        site.properties['pseudo']
                    except KeyError:
                        raise PWInputError("Missing %s in pseudo specification!"
                                           % site)
            else:
                for species in self.structure.composition.keys():
                    if species.symbol not in pseudo:
                        raise PWInputError("Missing %s in pseudo specification!"
                                           % species.symbol)
            self.pseudo = pseudo

            self.sections = sections
            self.kpoints_mode = kpoints_mode
            self.kpoints_grid = kpoints_grid
            self.kpoints_shift = kpoints_shift

        def __str__(self):
            out = []
            site_descriptions = {}

            if self.pseudo is not None:
                site_descriptions = self.pseudo
            else:
                c = 1
                for site in self.structure:
                    name = None
                    for k, v in site_descriptions.items():
                        if site.properties == v:
                            name = k

                    if name is None:
                        name = site.specie.symbol + str(c)
                        site_descriptions[name] = site.properties
                        c += 1

            def to_str(v):
                if isinstance(v, str):
                    return "'%s'" % v
                elif isinstance(v, float):
                    return "%s" % str(v).replace("e", "d")
                elif isinstance(v, bool):
                    if v:
                        return ".TRUE."
                    else:
                        return ".FALSE."
                return v

            for k1 in ["control", "system", "electrons", "ions", "cell"]:
                v1 = self.sections[k1]
                out.append("&%s" % k1.upper())
                sub = []
                for k2 in sorted(v1.keys()):
                    if isinstance(v1[k2], list):
                        n = 1
                        for l in v1[k2][:len(site_descriptions)]:
                            sub.append("  %s(%d) = %s" % (k2, n, to_str(v1[k2][n - 1])))
                            n += 1
                    else:
                        sub.append("  %s = %s" % (k2, to_str(v1[k2])))
                if k1 == "system":
                    if 'ibrav' not in self.sections[k1]:
                        sub.append("  ibrav = 0")
                    if 'nat' not in self.sections[k1]:
                        sub.append("  nat = %d" % len(self.structure))
                    if 'ntyp' not in self.sections[k1]:
                        sub.append("  ntyp = %d" % len(site_descriptions))
                sub.append("/")
                out.append(",\n".join(sub))

            out.append("ATOMIC_SPECIES")
            for k, v in sorted(site_descriptions.items(), key=lambda i: i[0]):
                e = re.match(r"[A-Z][a-z]?", k).group(0)
                if self.pseudo is not None:
                    p = v
                else:
                    p = v['pseudo']
                out.append("  %s  %.4f %s" % (k, Element(e).atomic_mass, p))

            out.append("ATOMIC_POSITIONS crystal")
            if self.pseudo is not None:
                for site in self.structure:
                    out.append("  %s %.6f %.6f %.6f" % (site.specie.symbol, site.a,
                                                        site.b, site.c))
            else:
                for site in self.structure:
                    name = None
                    for k, v in sorted(site_descriptions.items(),
                                       key=lambda i: i[0]):
                        if v == site.properties:
                            name = k
                    out.append("  %s %.6f %.6f %.6f" % (name, site.a, site.b, site.c))

            out.append("K_POINTS %s" % self.kpoints_mode)
            kpt_str = ["%s" % i for i in self.kpoints_grid]
            kpt_str.extend(["%s" % i for i in self.kpoints_shift])
            out.append("  %s" % " ".join(kpt_str))
            out.append("CELL_PARAMETERS angstrom")
            for vec in self.structure.lattice.matrix:
                out.append("  %f %f %f" % (vec[0], vec[1], vec[2]))
            return "\n".join(out)

        def as_dict(self):
            """
            Create a dictionary representation of a PWInput object

            Returns:
                dict
            """
            pwinput_dict = {'structure': self.structure.as_dict(),
                            'pseudo': self.pseudo,
                            'sections': self.sections,
                            'kpoints_mode': self.kpoints_mode,
                            'kpoints_grid': self.kpoints_grid,
                            'kpoints_shift': self.kpoints_shift}
            return pwinput_dict

        @classmethod
        def from_dict(cls, pwinput_dict):
            """
            Load a PWInput object from a dictionary.

            Args:
                pwinput_dict (dict): dictionary with PWInput data

            Returns:
                PWInput object
            """
            pwinput = cls(structure=Structure.from_dict(pwinput_dict['structure']),
                          pseudo=pwinput_dict['pseudo'],
                          control=pwinput_dict['sections']['control'],
                          system=pwinput_dict['sections']['system'],
                          electrons=pwinput_dict['sections']['electrons'],
                          ions=pwinput_dict['sections']['ions'],
                          cell=pwinput_dict['sections']['cell'],
                          kpoints_mode=pwinput_dict['kpoints_mode'],
                          kpoints_grid=pwinput_dict['kpoints_grid'],
                          kpoints_shift=pwinput_dict['kpoints_shift'])
            return pwinput

        def write_file(self, filename):
            """
            Write the PWSCF input file.

            Args:
                filename (str): The string filename to output to.
            """
            with open(filename, "w") as f:
                f.write(self.__str__())

        @staticmethod
        def from_file(filename):
            """
            Reads an PWInput object from a file.

            Args:
                filename (str): Filename for file

            Returns:
                PWInput object
            """
            with zopen(filename, "rt") as f:
                return PWInput.from_string(f.read())

        @staticmethod
        def from_string(string):
            """
            Reads an PWInput object from a string.

            Args:
                string (str): PWInput string

            Returns:
                PWInput object
            """
            lines = list(clean_lines(string.splitlines()))

            def input_mode(line):
                if line[0] == "&":
                    return ("sections", line[1:].lower())
                elif "ATOMIC_SPECIES" in line:
                    return ("pseudo",)
                elif "K_POINTS" in line:
                    return ("kpoints", line.split("{")[1][:-1])
                elif "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:
                    return ("structure", line.split("{")[1][:-1])
                elif line == "/":
                    return None
                else:
                    return mode

            sections = {"control": {}, "system": {}, "electrons": {},
                        "ions": {}, "cell": {}}
            pseudo = {}
            pseudo_index = 0
            lattice = []
            species = []
            coords = []
            structure = None
            site_properties = {"pseudo": []}
            mode = None
            for line in lines:
                mode = input_mode(line)
                if mode is None:
                    pass
                elif mode[0] == "sections":
                    section = mode[1]
                    m = re.match(r'(\w+)\(?(\d*?)\)?\s*=\s*(.*)', line)
                    if m:
                        key = m.group(1).strip()
                        key_ = m.group(2).strip()
                        val = m.group(3).strip()
                        if key_ != "":
                            if sections[section].get(key, None) is None:
                                val_ = [0.0] * 20  # MAX NTYP DEFINITION
                                val_[int(key_) - 1] = PWInput.proc_val(key, val)
                                sections[section][key] = val_

                                site_properties[key] = []
                            else:
                                sections[section][key][int(key_) - 1] = PWInput.proc_val(key, val)
                        else:
                            sections[section][key] = PWInput.proc_val(key, val)

                elif mode[0] == "pseudo":
                    m = re.match(r'(\w+)\s+(\d*.\d*)\s+(.*)', line)
                    if m:
                        pseudo[m.group(1).strip()] = {}
                        pseudo[m.group(1).strip()]["index"] = pseudo_index
                        pseudo[m.group(1).strip()]["pseudopot"] = m.group(3).strip()
                        pseudo_index += 1
                elif mode[0] == "kpoints":
                    m = re.match(r'(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)', line)
                    if m:
                        kpoints_grid = (int(m.group(1)), int(m.group(2)), int(m.group(3)))
                        kpoints_shift = (int(m.group(4)), int(m.group(5)), int(m.group(6)))
                    else:
                        kpoints_mode = mode[1]
                elif mode[0] == "structure":
                    m_l = re.match(r'(-?\d+\.?\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
                    m_p = re.match(r'(\w+)\s+(-?\d+\.\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
                    if m_l:
                        lattice += [float(m_l.group(1)), float(m_l.group(2)), float(m_l.group(3))]
                    elif m_p:
                        site_properties["pseudo"].append(pseudo[m_p.group(1)]["pseudopot"])
                        species += [pseudo[m_p.group(1)]["pseudopot"].split(".")[0]]
                        coords += [[float(m_p.group(2)), float(m_p.group(3)), float(m_p.group(4))]]

                        for k, v in site_properties.items():
                            if k != "pseudo":
                                site_properties[k].append(sections['system'][k][pseudo[m_p.group(1)]["index"]])
                    if mode[1] == "angstrom":
                        coords_are_cartesian = True
                    elif mode[1] == "crystal":
                        coords_are_cartesian = False

            structure = Structure(Lattice(lattice), species, coords,
                                  coords_are_cartesian=coords_are_cartesian,
                                  site_properties=site_properties)
            return PWInput(structure=structure, control=sections["control"],
                           system=sections["system"], electrons=sections["electrons"],
                           ions=sections["ions"], cell=sections["cell"], kpoints_mode=kpoints_mode,
                           kpoints_grid=kpoints_grid, kpoints_shift=kpoints_shift)

        def proc_val(key, val):
            """
            Static helper method to convert PWINPUT parameters to proper type, e.g.,
            integers, floats, etc.

            Args:
                key: PWINPUT parameter key
                val: Actual value of PWINPUT parameter.
            """
            float_keys = ('etot_conv_thr', 'forc_conv_thr', 'conv_thr', 'Hubbard_U', 'Hubbard_J0', 'defauss',
                          'starting_magnetization',)

            int_keys = ('nstep', 'iprint', 'nberrycyc', 'gdir', 'nppstr', 'ibrav', 'nat', 'ntyp', 'nbnd', 'nr1',
                        'nr2', 'nr3', 'nr1s', 'nr2s', 'nr3s', 'nspin', 'nqx1', 'nqx2', 'nqx3', 'lda_plus_u_kind',
                        'edir', 'report', 'esm_nfit', 'space_group', 'origin_choice', 'electron_maxstep',
                        'mixing_ndim', 'mixing_fixed_ns', 'ortho_para', 'diago_cg_maxiter', 'diago_david_ndim',
                        'nraise', 'bfgs_ndim', 'if_pos', 'nks', 'nk1', 'nk2', 'nk3', 'sk1', 'sk2', 'sk3', 'nconstr')

            bool_keys = ('wf_collect', 'tstress', 'tprnfor', 'lkpoint_dir', 'tefield', 'dipfield', 'lelfield',
                         'lorbm', 'lberry', 'lfcpopt', 'monopole', 'nosym', 'nosym_evc', 'noinv', 'no_t_rev',
                         'force_symmorphic', 'use_all_frac', 'one_atom_occupations', 'starting_spin_angle',
                         'noncolin', 'x_gamma_extrapolation', 'lda_plus_u', 'lspinorb', 'london',
                         'ts_vdw_isolated', 'xdm', 'uniqueb', 'rhombohedral', 'realxz', 'block',
                         'scf_must_converge', 'adaptive_thr', 'diago_full_acc', 'tqr', 'remove_rigid_rot',
                         'refold_pos')

            def smart_int_or_float(numstr):
                if numstr.find(".") != -1 or numstr.lower().find("e") != -1:
                    return float(numstr)
                else:
                    return int(numstr)

            try:
                if key in bool_keys:
                    if val.lower() == ".true.":
                        return True
                    elif val.lower() == ".false.":
                        return False
                    else:
                        raise ValueError(key + " should be a boolean type!")

                if key in float_keys:
                    return float(re.search(r"^-?\d*\.?\d*d?-?\d*", val.lower()).group(0).replace("d", "e"))

                if key in int_keys:
                    return int(re.match(r"^-?[0-9]+", val).group(0))

            except ValueError:
                pass

            try:
                val = val.replace("d", "e")
                return smart_int_or_float(val)
            except ValueError:
                pass

            if "true" in val.lower():
                return True
            if "false" in val.lower():
                return False

            m = re.match(r"^[\"|'](.+)[\"|']$", val)
            if m:
                return m.group(1)

    class PWInputError(BaseException):
        """
        Error for PWInput
        """
        pass

    class PWOutput:
        """
        Parser for PWSCF output file.
        """
        patterns = {
            "energies": r'total energy\s+=\s+([\d\.\-]+)\sRy',
            "ecut": r'kinetic\-energy cutoff\s+=\s+([\d\.\-]+)\s+Ry',
            "lattice_type": r'bravais\-lattice index\s+=\s+(\d+)',
            "celldm1": r"celldm\(1\)=\s+([\d\.]+)\s",
            "celldm2": r"celldm\(2\)=\s+([\d\.]+)\s",
            "celldm3": r"celldm\(3\)=\s+([\d\.]+)\s",
            "celldm4": r"celldm\(4\)=\s+([\d\.]+)\s",
            "celldm5": r"celldm\(5\)=\s+([\d\.]+)\s",
            "celldm6": r"celldm\(6\)=\s+([\d\.]+)\s",
            "nkpts": r"number of k points=\s+([\d]+)"
        }

        def __init__(self, filename):
            """
            Args:
                filename (str): Filename
            """
            self.filename = filename
            self.data = defaultdict(list)
            self.read_pattern(PWOutput.patterns)
            for k, v in self.data.items():
                if k == "energies":
                    self.data[k] = [float(i[0][0]) for i in v]
                elif k in ["lattice_type", "nkpts"]:
                    self.data[k] = int(v[0][0][0])
                else:
                    self.data[k] = float(v[0][0][0])

        def read_pattern(self, patterns, reverse=False,
                         terminate_on_match=False, postprocess=str):
            r"""
            General pattern reading. Uses monty's regrep method. Takes the same
            arguments.

            Args:
                patterns (dict): A dict of patterns, e.g.,
                    {"energy": r"energy\\(sigma->0\\)\\s+=\\s+([\\d\\-.]+)"}.
                reverse (bool): Read files in reverse. Defaults to false. Useful for
                    large files, esp OUTCARs, especially when used with
                    terminate_on_match.
                terminate_on_match (bool): Whether to terminate when there is at
                    least one match in each key in pattern.
                postprocess (callable): A post processing function to convert all
                    matches. Defaults to str, i.e., no change.

            Renders accessible:
                Any attribute in patterns. For example,
                {"energy": r"energy\\(sigma->0\\)\\s+=\\s+([\\d\\-.]+)"} will set the
                value of self.data["energy"] = [[-1234], [-3453], ...], to the
                results from regex and postprocess. Note that the returned
                values are lists of lists, because you can grep multiple
                items on one line.
            """
            matches = regrep(self.filename, patterns, reverse=reverse,
                             terminate_on_match=terminate_on_match,
                             postprocess=postprocess)
            self.data.update(matches)

        def get_celldm(self, i):
            """
            Args:
                i (int): index

            Returns:
                Cell dimension along index
            """
            return self.data["celldm%d" % i]

        @property
        def final_energy(self):
            """
            Returns: Final energy
            """
            return self.data["energies"][-1]

        @property
        def lattice_type(self):
            """
            Returns: Lattice type.
            """
            return self.data["lattice_type"]