4075885785

Build Type

push

github

Committed by Shyue Ping Ong

Commit Message

Merge branch 'master' of github.com:materialsproject/pymatgen

Run Details

96 of 96 new or added lines in 27 files covered. (100.0%)

81013 of 102710 relevant lines covered (78.88%)

0.79 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

14.89

/pymatgen/command_line/gulp_caller.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

"""
Interface with command line GULP.
http://projects.ivec.org
WARNING: you need to have GULP installed on your system.
"""

from __future__ import annotations

import os
import re
import subprocess

from monty.tempfile import ScratchDir

from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table import Element
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

__author__ = "Bharat Medasani, Wenhao Sun"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Bharat Medasani"
__email__ = "bkmedasani@lbl.gov,wenhao@mit.edu"
__status__ = "Production"
__date__ = "Jun 22, 2013M"

_anions = set(map(Element, ["O", "S", "F", "Cl", "Br", "N", "P"]))
_cations = set(
    map(
        Element,
        [
            "Li",
            "Na",
            "K",  # alkali metals
            "Be",
            "Mg",
            "Ca",  # alkaline metals
            "Al",
            "Sc",
            "Ti",
            "V",
            "Cr",
            "Mn",
            "Fe",
            "Co",
            "Ni",
            "Cu",
            "Zn",
            "Ge",
            "As",
            "Y",
            "Zr",
            "Nb",
            "Mo",
            "Tc",
            "Ru",
            "Rh",
            "Pd",
            "Ag",
            "Cd",
            "In",
            "Sn",
            "Sb",
            "Hf",
            "Ta",
            "W",
            "Re",
            "Os",
            "Ir",
            "Pt",
            "Au",
            "Hg",
            "Tl",
            "Pb",
            "Bi",
            "La",
            "Ce",
            "Pr",
            "Nd",
            "Pm",
            "Sm",
            "Eu",
            "Gd",
            "Tb",
            "Dy",
            "Ho",
            "Er",
            "Tm",
            "Yb",
            "Lu",
        ],
    )
)
_gulp_kw = {
    # Control of calculation type
    "angle",
    "bond",
    "cosmo",
    "cosmic",
    "cost",
    "defect",
    "distance",
    "eem",
    "efg",
    "fit",
    "free_energy",
    "gasteiger",
    "genetic",
    "gradients",
    "md",
    "montecarlo",
    "noautobond",
    "noenergy",
    "optimise",
    "pot",
    "predict",
    "preserve_Q",
    "property",
    "phonon",
    "qeq",
    "qbond",
    "single",
    "sm",
    "static_first",
    "torsion",
    "transition_state",
    # Geometric variable specification
    "breathe",
    "bulk_noopt",
    "cellonly",
    "conp",
    "conv",
    "isotropic",
    "orthorhombic",
    "nobreathe",
    "noflgs",
    "shell",
    "unfix",
    # Algorithm
    "c6",
    "dipole",
    "fbfgs",
    "fix_molecule",
    "full",
    "hill",
    "kfull",
    "marvinSE",
    "madelung",
    "minimum_image",
    "molecule",
    "molmec",
    "molq",
    "newda",
    "noanisotropic_2b",
    "nod2sym",
    "nodsymmetry",
    "noelectrostatics",
    "noexclude",
    "nofcentral",
    "nofirst_point",
    "noksymmetry",
    "nolist_md",
    "nomcediff",
    "nonanal",
    "noquicksearch",
    "noreal",
    "norecip",
    "norepulsive",
    "nosasinitevery",
    "nosderv",
    "nozeropt",
    "numerical",
    "qiter",
    "qok",
    "spatial",
    "storevectors",
    "nomolecularinternalke",
    "voight",
    "zsisa",
    # Optimisation method
    "conjugate",
    "dfp",
    "lbfgs",
    "numdiag",
    "positive",
    "rfo",
    "unit",
    # Output control
    "average",
    "broaden_dos",
    "cartesian",
    "compare",
    "conserved",
    "dcharge",
    "dynamical_matrix",
    "eigenvectors",
    "global",
    "hessian",
    "hexagonal",
    "intensity",
    "linmin",
    "meanke",
    "nodensity_out",
    "nodpsym",
    "nofirst_point",
    "nofrequency",
    "nokpoints",
    "operators",
    "outcon",
    "prt_eam",
    "prt_two",
    "prt_regi_before",
    "qsas",
    "restore",
    "save",
    "terse",
    # Structure control
    "full",
    "hexagonal",
    "lower_symmetry",
    "nosymmetry",
    # PDF control
    "PDF",
    "PDFcut",
    "PDFbelow",
    "PDFkeep",
    "coreinfo",
    "nowidth",
    "nopartial",
    # Miscellaneous
    "nomodcoord",
    "oldunits",
    "zero_potential",
}


class GulpIO:
    """
    To generate GULP input and process output
    """

    @staticmethod
    def keyword_line(*args):
        """
        Checks if the input args are proper gulp keywords and
        generates the 1st line of gulp input. Full keywords are expected.

        Args:
            args: 1st line keywords
        """
        # if len(list(filter(lambda x: x in _gulp_kw, args))) != len(args):
        #    raise GulpError("Wrong keywords given")
        gin = " ".join(args)
        gin += "\n"
        return gin

    @staticmethod
    def structure_lines(
        structure: Structure,
        cell_flg: bool = True,
        frac_flg: bool = True,
        anion_shell_flg: bool = True,
        cation_shell_flg: bool = False,
        symm_flg: bool = True,
    ):
        """
        Generates GULP input string corresponding to pymatgen structure.

        Args:
            structure: pymatgen Structure object
            cell_flg (default = True): Option to use lattice parameters.
            fractional_flg (default = True): If True, fractional coordinates
                are used. Else, Cartesian coordinates in Angstroms are used.
                ******
                GULP convention is to use fractional coordinates for periodic
                structures and Cartesian coordinates for non-periodic
                structures.
                ******
            anion_shell_flg (default = True): If True, anions are considered
                polarizable.
            cation_shell_flg (default = False): If True, cations are
                considered polarizable.
            symm_flg (default = True): If True, symmetry information is also
                written.

        Returns:
            string containing structure for GULP input
        """
        gin = ""
        if cell_flg:
            gin += "cell\n"
            lattice = structure.lattice
            alpha, beta, gamma = lattice.angles
            a, b, c = lattice.lengths
            lat_str = f"{a:6f} {b:6f} {c:6f} {alpha:6f} {beta:6f} {gamma:6f}"
            gin += lat_str + "\n"

        if frac_flg:
            gin += "frac\n"
            coord_attr = "frac_coords"
        else:
            gin += "cart\n"
            coord_attr = "coords"
        for site in structure.sites:
            coord = [str(i) for i in getattr(site, coord_attr)]
            specie = site.specie
            core_site_desc = specie.symbol + " core " + " ".join(coord) + "\n"
            gin += core_site_desc
            if (specie in _anions and anion_shell_flg) or (specie in _cations and cation_shell_flg):
                shel_site_desc = specie.symbol + " shel " + " ".join(coord) + "\n"
                gin += shel_site_desc
            else:
                pass

        if symm_flg:
            gin += "space\n"
            gin += str(SpacegroupAnalyzer(structure).get_space_group_number()) + "\n"
        return gin

    @staticmethod
    def specie_potential_lines(structure, potential, **kwargs):
        """
        Generates GULP input specie and potential string for pymatgen
        structure.

        Args:
            structure: pymatgen.core.structure.Structure object
            potential: String specifying the type of potential used
            kwargs: Additional parameters related to potential. For
                potential == "buckingham",
                anion_shell_flg (default = False):
                If True, anions are considered polarizable.
                anion_core_chrg=float
                anion_shell_chrg=float
                cation_shell_flg (default = False):
                If True, cations are considered polarizable.
                cation_core_chrg=float
                cation_shell_chrg=float

        Returns:
            string containing specie and potential specification for gulp
            input.
        """
        raise NotImplementedError("gulp_specie_potential not yet implemented.\nUse library_line instead")

    @staticmethod
    def library_line(file_name):
        """
        Specifies GULP library file to read species and potential parameters.
        If using library don't specify species and potential
        in the input file and vice versa. Make sure the elements of
        structure are in the library file.

        Args:
            file_name: Name of GULP library file

        Returns:
            GULP input string specifying library option
        """
        gulplib_set = "GULP_LIB" in os.environ

        def readable(f):
            return os.path.isfile(f) and os.access(f, os.R_OK)

        gin = ""
        dirpath, fname = os.path.split(file_name)
        if dirpath and readable(file_name):  # Full path specified
            gin = "library " + file_name
        else:
            fpath = os.path.join(os.getcwd(), file_name)  # Check current dir
            if readable(fpath):
                gin = "library " + fpath
            elif gulplib_set:  # Check the GULP_LIB path
                fpath = os.path.join(os.environ["GULP_LIB"], file_name)
                if readable(fpath):
                    gin = "library " + file_name
        if gin:
            return gin + "\n"
        raise GulpError("GULP Library not found")

    def buckingham_input(self, structure: Structure, keywords, library=None, uc=True, valence_dict=None):
        """
        Gets a GULP input for an oxide structure and buckingham potential
        from library.

        Args:
            structure: pymatgen.core.structure.Structure
            keywords: GULP first line keywords.
            library (Default=None): File containing the species and potential.
            uc (Default=True): Unit Cell Flag.
            valence_dict: {El: valence}
        """
        gin = self.keyword_line(*keywords)
        gin += self.structure_lines(structure, symm_flg=not uc)
        if not library:
            gin += self.buckingham_potential(structure, valence_dict)
        else:
            gin += self.library_line(library)
        return gin

    @staticmethod
    def buckingham_potential(structure, val_dict=None):
        """
        Generate species, buckingham, and spring options for an oxide structure
        using the parameters in default libraries.

        Ref:
            1. G.V. Lewis and C.R.A. Catlow, J. Phys. C: Solid State Phys.,
               18, 1149-1161 (1985)
            2. T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle,
               J. Mater Chem., 4, 831-837 (1994)

        Args:
            structure: pymatgen.core.structure.Structure
            val_dict (Needed if structure is not charge neutral): {El:valence}
                dict, where El is element.
        """
        if not val_dict:
            try:
                # If structure is oxidation state decorated, use that first.
                el = [site.specie.symbol for site in structure]
                valences = [site.specie.oxi_state for site in structure]
                val_dict = dict(zip(el, valences))
            except AttributeError:
                bv = BVAnalyzer()
                el = [site.specie.symbol for site in structure]
                valences = bv.get_valences(structure)
                val_dict = dict(zip(el, valences))

        # Try bush library first
        bpb = BuckinghamPotential("bush")
        bpl = BuckinghamPotential("lewis")
        gin = ""
        for key in val_dict:
            use_bush = True
            el = re.sub(r"[1-9,+,\-]", "", key)
            if el not in bpb.species_dict:
                use_bush = False
            elif val_dict[key] != bpb.species_dict[el]["oxi"]:
                use_bush = False
            if use_bush:
                gin += "species \n"
                gin += bpb.species_dict[el]["inp_str"]
                gin += "buckingham \n"
                gin += bpb.pot_dict[el]
                gin += "spring \n"
                gin += bpb.spring_dict[el]
                continue

            # Try lewis library next if element is not in bush
            # use_lewis = True
            if el != "O":  # For metals the key is "Metal_OxiState+"
                k = el + "_" + str(int(val_dict[key])) + "+"
                if k not in bpl.species_dict:
                    # use_lewis = False
                    raise GulpError(f"Element {k} not in library")
                gin += "species\n"
                gin += bpl.species_dict[k]
                gin += "buckingham\n"
                gin += bpl.pot_dict[k]
            else:
                gin += "species\n"
                k = "O_core"
                gin += bpl.species_dict[k]
                k = "O_shel"
                gin += bpl.species_dict[k]
                gin += "buckingham\n"
                gin += bpl.pot_dict[key]
                gin += "spring\n"
                gin += bpl.spring_dict[key]
        return gin

    def tersoff_input(self, structure: Structure, periodic=False, uc=True, *keywords):
        """
        Gets a GULP input with Tersoff potential for an oxide structure

        Args:
            structure: pymatgen.core.structure.Structure
            periodic (Default=False): Flag denoting whether periodic
                boundary conditions are used
            library (Default=None): File containing the species and potential.
            uc (Default=True): Unit Cell Flag.
            keywords: GULP first line keywords.
        """
        # gin="static noelectrostatics \n "
        gin = self.keyword_line(*keywords)
        gin += self.structure_lines(
            structure,
            cell_flg=periodic,
            frac_flg=periodic,
            anion_shell_flg=False,
            cation_shell_flg=False,
            symm_flg=not uc,
        )
        gin += self.tersoff_potential(structure)
        return gin

    @staticmethod
    def tersoff_potential(structure):
        """
        Generate the species, tersoff potential lines for an oxide structure

        Args:
            structure: pymatgen.core.structure.Structure
        """
        bv = BVAnalyzer()
        el = [site.specie.symbol for site in structure]
        valences = bv.get_valences(structure)
        el_val_dict = dict(zip(el, valences))

        gin = "species \n"
        qerfstring = "qerfc\n"

        for key, value in el_val_dict.items():
            if key != "O" and value % 1 != 0:
                raise SystemError("Oxide has mixed valence on metal")
            specie_string = key + " core " + str(value) + "\n"
            gin += specie_string
            qerfstring += key + " " + key + " 0.6000 10.0000 \n"

        gin += "# noelectrostatics \n Morse \n"
        met_oxi_ters = TersoffPotential().data
        for key, value in el_val_dict.items():
            if key != "O":
                metal = key + "(" + str(int(value)) + ")"
                ters_pot_str = met_oxi_ters[metal]
                gin += ters_pot_str

        gin += qerfstring
        return gin

    @staticmethod
    def get_energy(gout):
        """
        Args:
            gout ():

        Returns:
            Energy
        """
        energy = None
        for line in gout.split("\n"):
            if "Total lattice energy" in line and "eV" in line:
                energy = line.split()
            elif "Non-primitive unit cell" in line and "eV" in line:
                energy = line.split()
        if energy:
            return float(energy[4])
        raise GulpError("Energy not found in Gulp output")

    @staticmethod
    def get_relaxed_structure(gout):
        """
        Args:
            gout ():

        Returns:
            (Structure) relaxed structure.
        """
        # Find the structure lines
        structure_lines = []
        cell_param_lines = []
        output_lines = gout.split("\n")
        no_lines = len(output_lines)
        i = 0
        # Compute the input lattice parameters
        while i < no_lines:
            line = output_lines[i]
            if "Full cell parameters" in line:
                i += 2
                line = output_lines[i]
                a = float(line.split()[8])
                alpha = float(line.split()[11])
                line = output_lines[i + 1]
                b = float(line.split()[8])
                beta = float(line.split()[11])
                line = output_lines[i + 2]
                c = float(line.split()[8])
                gamma = float(line.split()[11])
                i += 3
                break
            if "Cell parameters" in line:
                i += 2
                line = output_lines[i]
                a = float(line.split()[2])
                alpha = float(line.split()[5])
                line = output_lines[i + 1]
                b = float(line.split()[2])
                beta = float(line.split()[5])
                line = output_lines[i + 2]
                c = float(line.split()[2])
                gamma = float(line.split()[5])
                i += 3
                break
            i += 1

        while i < no_lines:
            line = output_lines[i]
            if "Final fractional coordinates of atoms" in line:
                # read the site coordinates in the following lines
                i += 6
                line = output_lines[i]
                while line[0:2] != "--":
                    structure_lines.append(line)
                    i += 1
                    line = output_lines[i]
                    # read the cell parameters
                i += 9
                line = output_lines[i]
                if "Final cell parameters" in line:
                    i += 3
                    for del_i in range(6):
                        line = output_lines[i + del_i]
                        cell_param_lines.append(line)

                break
            i += 1

        # Process the structure lines
        if structure_lines:
            sp = []
            coords = []
            for line in structure_lines:
                fields = line.split()
                if fields[2] == "c":
                    sp.append(fields[1])
                    coords.append(list(float(x) for x in fields[3:6]))
        else:
            raise OSError("No structure found")

        if cell_param_lines:
            a = float(cell_param_lines[0].split()[1])
            b = float(cell_param_lines[1].split()[1])
            c = float(cell_param_lines[2].split()[1])
            alpha = float(cell_param_lines[3].split()[1])
            beta = float(cell_param_lines[4].split()[1])
            gamma = float(cell_param_lines[5].split()[1])
        latt = Lattice.from_parameters(a, b, c, alpha, beta, gamma)

        return Structure(latt, sp, coords)


class GulpCaller:
    """
    Class to run gulp from commandline
    """

    def __init__(self, cmd="gulp"):
        """
        Initialize with the executable if not in the standard path

        Args:
            cmd: Command. Defaults to gulp.
        """

        def is_exe(f) -> bool:
            return os.path.isfile(f) and os.access(f, os.X_OK)

        fpath, fname = os.path.split(cmd)
        if fpath:
            if is_exe(cmd):
                self._gulp_cmd = cmd
                return
        else:
            for path in os.environ["PATH"].split(os.pathsep):
                path = path.strip('"')
                file = os.path.join(path, cmd)
                if is_exe(file):
                    self._gulp_cmd = file
                    return
        raise GulpError("Executable not found")

    def run(self, gin):
        """
        Run GULP using the gin as input

        Args:
            gin: GULP input string

        Returns:
            gout: GULP output string
        """
        with ScratchDir("."):
            with subprocess.Popen(
                self._gulp_cmd,
                stdout=subprocess.PIPE,
                stdin=subprocess.PIPE,
                stderr=subprocess.PIPE,
            ) as p:
                out, err = p.communicate(bytearray(gin, "utf-8"))
            out = out.decode("utf-8")
            err = err.decode("utf-8")

            if "Error" in err or "error" in err:
                print(gin)
                print("----output_0---------")
                print(out)
                print("----End of output_0------\n\n\n")
                print("----output_1--------")
                print(out)
                print("----End of output_1------")
                raise GulpError(err)

            # We may not need this
            if "ERROR" in out:
                raise GulpError(out)

            # Sometimes optimisation may fail to reach convergence
            conv_err_string = "Conditions for a minimum have not been satisfied"
            if conv_err_string in out:
                raise GulpConvergenceError()

            gout = ""
            for line in out.split("\n"):
                gout = gout + line + "\n"
            return gout


def get_energy_tersoff(structure, gulp_cmd="gulp"):
    """
    Compute the energy of a structure using Tersoff potential.

    Args:
        structure: pymatgen.core.structure.Structure
        gulp_cmd: GULP command if not in standard place
    """
    gio = GulpIO()
    gc = GulpCaller(gulp_cmd)
    gin = gio.tersoff_input(structure)
    gout = gc.run(gin)
    return gio.get_energy(gout)


def get_energy_buckingham(structure, gulp_cmd="gulp", keywords=("optimise", "conp", "qok"), valence_dict=None):
    """
    Compute the energy of a structure using Buckingham potential.

    Args:
        structure: pymatgen.core.structure.Structure
        gulp_cmd: GULP command if not in standard place
        keywords: GULP first line keywords
        valence_dict: {El: valence}. Needed if the structure is not charge
            neutral.
    """
    gio = GulpIO()
    gc = GulpCaller(gulp_cmd)
    gin = gio.buckingham_input(structure, keywords, valence_dict=valence_dict)
    gout = gc.run(gin)
    return gio.get_energy(gout)


def get_energy_relax_structure_buckingham(structure, gulp_cmd="gulp", keywords=("optimise", "conp"), valence_dict=None):
    """
    Relax a structure and compute the energy using Buckingham potential.

    Args:
        structure: pymatgen.core.structure.Structure
        gulp_cmd: GULP command if not in standard place
        keywords: GULP first line keywords
        valence_dict: {El: valence}. Needed if the structure is not charge
            neutral.
    """
    gio = GulpIO()
    gc = GulpCaller(gulp_cmd)
    gin = gio.buckingham_input(structure, keywords, valence_dict=valence_dict)
    gout = gc.run(gin)
    energy = gio.get_energy(gout)
    relax_structure = gio.get_relaxed_structure(gout)
    return energy, relax_structure


class GulpError(Exception):
    """
    Exception class for GULP.
    Raised when the GULP gives an error
    """

    def __init__(self, msg):
        """
        Args:
            msg (str): Message
        """
        self.msg = msg

    def __str__(self):
        return "GulpError : " + self.msg


class GulpConvergenceError(Exception):
    """
    Exception class for GULP.
    Raised when proper convergence is not reached in Mott-Littleton
    defect energy optimisation procedure in GULP
    """

    def __init__(self, msg=""):
        """
        Args:
            msg (str): Message
        """
        self.msg = msg

    def __str__(self):
        return self.msg


class BuckinghamPotential:
    """
    Generate the Buckingham Potential Table from the bush.lib and lewis.lib.

    Ref:
    T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle,  J. Mater Chem.,
    4, 831-837 (1994).
    G.V. Lewis and C.R.A. Catlow, J. Phys. C: Solid State Phys., 18,
    1149-1161 (1985)
    """

    def __init__(self, bush_lewis_flag):
        """
        Args:
            bush_lewis_flag (str): Flag for using Bush or Lewis potential.
        """
        assert bush_lewis_flag in {"bush", "lewis"}
        pot_file = "bush.lib" if bush_lewis_flag == "bush" else "lewis.lib"
        with open(os.path.join(os.environ["GULP_LIB"], pot_file)) as f:
            # In lewis.lib there is no shell for cation
            species_dict, pot_dict, spring_dict = {}, {}, {}
            sp_flg, pot_flg, spring_flg = False, False, False
            for row in f:
                if row[0] == "#":
                    continue
                if row.split()[0] == "species":
                    sp_flg, pot_flg, spring_flg = True, False, False
                    continue
                if row.split()[0] == "buckingham":
                    sp_flg, pot_flg, spring_flg = False, True, False
                    continue
                if row.split()[0] == "spring":
                    sp_flg, pot_flg, spring_flg = False, False, True
                    continue

                elmnt = row.split()[0]
                if sp_flg:
                    if bush_lewis_flag == "bush":
                        if elmnt not in species_dict:
                            species_dict[elmnt] = {"inp_str": "", "oxi": 0}
                        species_dict[elmnt]["inp_str"] += row
                        species_dict[elmnt]["oxi"] += float(row.split()[2])
                    elif bush_lewis_flag == "lewis":
                        if elmnt == "O":
                            if row.split()[1] == "core":
                                species_dict["O_core"] = row
                            if row.split()[1] == "shel":
                                species_dict["O_shel"] = row
                        else:
                            metal = elmnt.split("_")[0]
                            # oxi_state = metaloxi.split('_')[1][0]
                            species_dict[elmnt] = metal + " core " + row.split()[2] + "\n"
                    continue

                if pot_flg:
                    if bush_lewis_flag == "bush":
                        pot_dict[elmnt] = row
                    elif bush_lewis_flag == "lewis":
                        if elmnt == "O":
                            pot_dict["O"] = row
                        else:
                            metal = elmnt.split("_")[0]
                            # oxi_state = metaloxi.split('_')[1][0]
                            pot_dict[elmnt] = metal + " " + " ".join(row.split()[1:]) + "\n"
                    continue

                if spring_flg:
                    spring_dict[elmnt] = row

            if bush_lewis_flag == "bush":
                # Fill the null keys in spring dict with empty strings
                for key in pot_dict:
                    if key not in spring_dict:
                        spring_dict[key] = ""

            self.species_dict = species_dict
            self.pot_dict = pot_dict
            self.spring_dict = spring_dict


class TersoffPotential:
    """
    Generate Tersoff Potential Table from "OxideTersoffPotentialentials" file
    """

    def __init__(self):
        """
        Init TersoffPotential
        """
        module_dir = os.path.dirname(os.path.abspath(__file__))
        with open(os.path.join(module_dir, "OxideTersoffPotentials")) as f:
            data = {}
            for row in f:
                metaloxi = row.split()[0]
                line = row.split(")")
                data[metaloxi] = line[1]
        self.data = data

materialsproject / pymatgen / 4075885785

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous