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

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/pymatgen/io/fiesta.py

"""
This module implements input and output for Fiesta (http://perso.neel.cnrs.fr/xavier.blase/fiesta/index.html).

and

-Nwchem2Fiesta class: to create the input files needed for a Fiesta run
-Fiesta_run: run gw_fiesta and bse_fiesta
-Localised Basis set reader
"""

from __future__ import annotations

import os
import re
import shutil
import subprocess
from string import Template

from monty.io import zopen
from monty.json import MSONable

from pymatgen.core.structure import Molecule

__author__ = "ndardenne"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__email__ = "n.dardenne@uclouvain.be"
__date__ = "24/5/15"


class Nwchem2Fiesta(MSONable):
    """
    To run NWCHEM2FIESTA inside python:

    If nwchem.nw is the input, nwchem.out the output, and structure.movecs the
    "movecs" file, the syntax to run NWCHEM2FIESTA is: NWCHEM2FIESTA
    nwchem.nw  nwchem.nwout  structure.movecs > log_n2f
    """

    def __init__(self, folder, filename="nwchem", log_file="log_n2f"):
        """
        folder: where are stored the nwchem
        filename: name of nwchem files read by NWCHEM2FIESTA (filename.nw, filename.nwout and filename.movecs)
        logfile: logfile of NWCHEM2FIESTA

        the run method launches NWCHEM2FIESTA
        """
        self.folder = folder
        self.filename = filename
        self.log_file = log_file

        self._NWCHEM2FIESTA_cmd = "NWCHEM2FIESTA"
        self._nwcheminput_fn = filename + ".nw"
        self._nwchemoutput_fn = filename + ".nwout"
        self._nwchemmovecs_fn = filename + ".movecs"

    def run(self):
        """
        Performs actual NWCHEM2FIESTA run
        """
        init_folder = os.getcwd()
        os.chdir(self.folder)

        with zopen(self.log_file, "w") as fout:
            subprocess.call(
                [
                    self._NWCHEM2FIESTA_cmd,
                    self._nwcheminput_fn,
                    self._nwchemoutput_fn,
                    self._nwchemmovecs_fn,
                ],
                stdout=fout,
            )

        os.chdir(init_folder)

    def as_dict(self):
        """
        :return: MSONable dict
        """
        return {
            "@module": type(self).__module__,
            "@class": type(self).__name__,
            "filename": self.filename,
            "folder": self.folder,
        }

    @classmethod
    def from_dict(cls, d):
        """
        :param d: Dict representation.
        :return: Nwchem2Fiesta
        """
        return cls(folder=d["folder"], filename=d["filename"])


class FiestaRun(MSONable):
    """
    To run FIESTA inside python:
        if grid is [x,x] then bse runs
        if grid is [x,x,y] the fiesta(gw) runs
        otherwise it breaks
    """

    def __init__(
        self, folder: str | None = None, grid: tuple[int, int, int] = (2, 2, 2), log_file: str = "log"
    ) -> None:
        """
        Args:
            folder: Folder to look for runs.
            grid:
            log_file: logfile of Fiesta
        """
        self.folder = folder or os.getcwd()
        self.log_file = log_file
        self.grid = grid

    def run(self):
        """
        Performs FIESTA (gw) run.
        """
        if len(self.grid) == 3:
            self.mpi_procs = self.grid[0] * self.grid[1] * self.grid[2]
            self._gw_run()
        elif len(self.grid) == 2:
            self.mpi_procs = self.grid[0] * self.grid[1]
            self.bse_run()
        else:
            raise ValueError("Wrong grid size: must be [nrow, ncolumn, nslice] for gw of [nrow, nslice] for bse")

    def _gw_run(self):
        """
        Performs FIESTA (gw) run
        """
        if self.folder != os.getcwd():
            init_folder = os.getcwd()
            os.chdir(self.folder)

        with zopen(self.log_file, "w") as fout:
            subprocess.call(
                [
                    "mpirun",
                    "-n",
                    str(self.mpi_procs),
                    "fiesta",
                    str(self.grid[0]),
                    str(self.grid[1]),
                    str(self.grid[2]),
                ],
                stdout=fout,
            )

        if self.folder != os.getcwd():
            os.chdir(init_folder)

    def bse_run(self):
        """
        Performs BSE run
        """
        if self.folder != os.getcwd():
            init_folder = os.getcwd()
            os.chdir(self.folder)

        with zopen(self.log_file, "w") as fout:
            subprocess.call(
                [
                    "mpirun",
                    "-n",
                    str(self.mpi_procs),
                    "bse",
                    str(self.grid[0]),
                    str(self.grid[1]),
                ],
                stdout=fout,
            )

        if self.folder != os.getcwd():
            os.chdir(init_folder)

    def as_dict(self):
        """
        :return: MSONable dict
        """
        return {
            "@module": type(self).__module__,
            "@class": type(self).__name__,
            "log_file": self.log_file,
            "grid": self.grid,
            "folder": self.folder,
        }

    @classmethod
    def from_dict(cls, d):
        """
        :param d: Dict representation
        :return: FiestaRun
        """
        return cls(folder=d["folder"], grid=d["grid"], log_file=d["log_file"])


class BasisSetReader:
    """
    A basis set reader.
    Basis set are stored in data as a dict:
    :key l_zeta_ng for each nl orbitals which contain list of tuple (alpha, coef) for each of the ng gaussians
    in l_zeta orbital
    """

    def __init__(self, filename):
        """
        Args:
            filename: Filename to read.
        """
        self.filename = filename

        with zopen(filename) as f:
            basis_set = f.read()

        self.data = self._parse_file(basis_set)
        # compute the number of nlm orbitals per atom
        self.data.update(n_nlmo=self.set_n_nlmo())

    @staticmethod
    def _parse_file(input):
        lmax_nnlo_patt = re.compile(r"\s* (\d+) \s+ (\d+) \s+ \# .* ", re.VERBOSE)

        nl_orbital_patt = re.compile(r"\s* (\d+) \s+ (\d+) \s+ (\d+) \s+ \# .* ", re.VERBOSE)

        coef_alpha_patt = re.compile(r"\s* ([-\d.\D]+) \s+ ([-\d.\D]+) \s* ", re.VERBOSE)

        preamble = []
        basis_set = {}
        parse_preamble = False
        parse_lmax_nnlo = False
        parse_nl_orbital = False
        nnlo = None  # fix pylint E0601: Using variable 'nnlo' before assignment
        lmax = None

        for line in input.split("\n"):
            if parse_nl_orbital:
                m = nl_orbital_patt.search(line)
                n = coef_alpha_patt.search(line)
                if m:
                    l = m.group(1)
                    zeta = m.group(2)
                    ng = m.group(3)
                    basis_set[l + "_" + zeta + "_" + ng] = []
                elif n:
                    alpha = n.group(1)
                    coef = n.group(2)
                    basis_set[l + "_" + zeta + "_" + ng].append((alpha, coef))
            elif parse_lmax_nnlo:
                m = lmax_nnlo_patt.search(line)
                if m:
                    lmax = m.group(1)
                    nnlo = m.group(2)
                    parse_lmax_nnlo = False
                    parse_nl_orbital = True
            elif parse_preamble:
                preamble.append(line.strip())

            if line.find("</preamble>") != -1:
                parse_preamble = False
                parse_lmax_nnlo = True
            elif line.find("<preamble>") != -1:
                parse_preamble = True

        basis_set.update(lmax=lmax, n_nlo=nnlo, preamble=preamble)
        return basis_set

    def set_n_nlmo(self):
        """
        :return: the number of nlm orbitals for the basis set
        """
        nnlmo = 0

        data_tmp = self.data
        data_tmp.pop("lmax")
        data_tmp.pop("n_nlo")
        data_tmp.pop("preamble")

        for l_zeta_ng in data_tmp:
            l = l_zeta_ng.split("_")[0]
            nnlmo = nnlmo + (2 * int(l) + 1)

        return str(nnlmo)

    def infos_on_basis_set(self):
        """
        infos on the basis set as in Fiesta log
        """
        o = []
        o.append("=========================================")
        o.append("Reading basis set:")
        o.append("")
        o.append(f" Basis set for {self.filename} atom ")
        o.append(f" Maximum angular momentum = {self.data['lmax']}")
        o.append(f" Number of atomics orbitals = {self.data['n_nlo']}")
        o.append(f" Number of nlm orbitals = {self.data['n_nlmo']}")
        o.append("=========================================")

        return str(0)


class FiestaInput(MSONable):
    """
    Input File for Fiesta called "cell.in" by default (mandatory in Fiesta for now)
    """

    def __init__(
        self,
        mol,
        correlation_grid: dict[str, str] | None = None,
        Exc_DFT_option: dict[str, str] | None = None,
        COHSEX_options: dict[str, str] | None = None,
        GW_options: dict[str, str] | None = None,
        BSE_TDDFT_options: dict[str, str] | None = None,
    ):
        """
        :param mol: pymatgen mol
        :param correlation_grid: dict
        :param Exc_DFT_option: dict
        :param COHSEX_options: dict
        :param GW_options: dict
        :param BSE_TDDFT_options: dict
        """
        self._mol = mol
        self.correlation_grid = correlation_grid or {"dE_grid": "0.500", "n_grid": "14"}
        self.Exc_DFT_option = Exc_DFT_option or {"rdVxcpsi": "1"}
        self.COHSEX_options = COHSEX_options or {
            "eigMethod": "C",
            "mix_cohsex": "0.500",
            "nc_cohsex": "0",
            "nit_cohsex": "0",
            "nv_cohsex": "0",
            "resMethod": "V",
            "scf_cohsex_wf": "0",
        }
        self.GW_options = GW_options or {"nc_corr": "10", "nit_gw": "3", "nv_corr": "10"}
        self.BSE_TDDFT_options = BSE_TDDFT_options or {
            "do_bse": "1",
            "do_tddft": "0",
            "nc_bse": "382",
            "nit_bse": "50",
            "npsi_bse": "1",
            "nv_bse": "21",
        }

    def set_auxiliary_basis_set(self, folder, auxiliary_folder, auxiliary_basis_set_type="aug_cc_pvtz"):
        """
        copy in the desired folder the needed auxiliary basis set "X2.ion" where X is a specie.
        :param auxiliary_folder: folder where the auxiliary basis sets are stored
        :param auxiliary_basis_set_type: type of basis set (string to be found in the extension of the file name; must
            be in lower case). ex: C2.ion_aug_cc_pvtz_RI_Weigend find "aug_cc_pvtz"
        """
        list_files = os.listdir(auxiliary_folder)

        for specie in self._mol.symbol_set:
            for file in list_files:
                if file.upper().find(specie.upper() + "2") != -1 and file.lower().find(auxiliary_basis_set_type) != -1:
                    shutil.copyfile(auxiliary_folder + "/" + file, folder + "/" + specie + "2.ion")

    def set_GW_options(self, nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5):
        """
        Set parameters in cell.in for a GW computation
        :param nv__band: number of valence bands to correct with GW
        :param nc_band: number of conduction bands to correct with GW
        :param n_iteration: number of iteration
        :param n_grid and dE_grid:: number of points and spacing in eV for correlation grid
        """
        self.GW_options.update(nv_corr=nv_band, nc_corr=nc_band, nit_gw=n_iteration)
        self.correlation_grid.update(dE_grid=dE_grid, n_grid=n_grid)

    @staticmethod
    def make_FULL_BSE_Densities_folder(folder):
        """
        mkdir "FULL_BSE_Densities" folder (needed for bse run) in the desired folder
        """
        if os.path.exists(folder + "/FULL_BSE_Densities"):
            return "FULL_BSE_Densities folder already exists"

        os.makedirs(folder + "/FULL_BSE_Densities")
        return "makedirs FULL_BSE_Densities folder"

    def set_BSE_options(self, n_excitations=10, nit_bse=200):
        """
        Set parameters in cell.in for a BSE computation
        :param nv_bse: number of valence bands
        :param nc_bse: number of conduction bands
        :param n_excitations: number of excitations
        :param nit_bse: number of iterations
        """
        self.BSE_TDDFT_options.update(npsi_bse=n_excitations, nit_bse=nit_bse)

    def dump_BSE_data_in_GW_run(self, BSE_dump=True):
        """
        :param BSE_dump: boolean
        :return: set the "do_bse" variable to one in cell.in
        """
        if BSE_dump:
            self.BSE_TDDFT_options.update(do_bse=1, do_tddft=0)
        else:
            self.BSE_TDDFT_options.update(do_bse=0, do_tddft=0)

    def dump_TDDFT_data_in_GW_run(self, TDDFT_dump=True):
        """
        :param TDDFT_dump: boolean
        :return: set the do_tddft variable to one in cell.in
        """
        if TDDFT_dump:
            self.BSE_TDDFT_options.update(do_bse=0, do_tddft=1)
        else:
            self.BSE_TDDFT_options.update(do_bse=0, do_tddft=0)

    @property
    def infos_on_system(self):
        """
        Returns infos on initial parameters as in the log file of Fiesta
        """
        o = []
        o.append("=========================================")
        o.append("Reading infos on system:")
        o.append("")
        o.append(
            f" Number of atoms = {self._mol.composition.num_atoms} ; number of species = {len(self._mol.symbol_set)}"
        )
        o.append(f" Number of valence bands = {int(self._mol.nelectrons / 2)}")
        o.append(
            f" Sigma grid specs: n_grid = {self.correlation_grid['n_grid']} ;  "
            f"dE_grid = {self.correlation_grid['dE_grid']} (eV)"
        )
        if int(self.Exc_DFT_option["rdVxcpsi"]) == 1:
            o.append(" Exchange and correlation energy read from Vxcpsi.mat")
        elif int(self.Exc_DFT_option["rdVxcpsi"]) == 0:
            o.append(" Exchange and correlation energy re-computed")

        if self.COHSEX_options["eigMethod"] == "C":
            o.append(
                f" Correcting  {self.COHSEX_options['nv_cohsex']} valence bands and  "
                f"{self.COHSEX_options['nc_cohsex']} conduction bands at COHSEX level"
            )
            o.append(f" Performing   {self.COHSEX_options['nit_cohsex']} diagonal COHSEX iterations")
        elif self.COHSEX_options["eigMethod"] == "HF":
            o.append(
                f" Correcting  {self.COHSEX_options['nv_cohsex']} valence bands and  "
                f"{self.COHSEX_options['nc_cohsex']} conduction bands at HF level"
            )
            o.append(f" Performing   {self.COHSEX_options['nit_cohsex']} diagonal HF iterations")

        o.append(f" Using resolution of identity : {self.COHSEX_options['resMethod']}")
        o.append(
            f" Correcting  {self.GW_options['nv_corr']} valence bands and "
            f"{self.GW_options['nc_corr']} conduction bands at GW level"
        )
        o.append(f" Performing   {self.GW_options['nit_gw']} GW iterations")

        if int(self.BSE_TDDFT_options["do_bse"]) == 1:
            o.append(" Dumping data for BSE treatment")

        if int(self.BSE_TDDFT_options["do_tddft"]) == 1:
            o.append(" Dumping data for TD-DFT treatment")
        o.append("")
        o.append(" Atoms in cell cartesian A:")
        symbols = []
        for syb in self._mol.symbol_set:
            symbols.append(syb)

        for site in self._mol:
            o.append(f" {site.x} {site.y} {site.z} {int(symbols.index(site.specie.symbol)) + 1}")

        o.append("=========================================")

        return str(o)

    @property
    def molecule(self):
        """
        Returns molecule associated with this FiestaInput.
        """
        return self._mol

    def __str__(self):
        symbols = []
        for syb in self._mol.symbol_set:
            symbols.append(syb)

        geometry = []
        for site in self._mol:
            geometry.append(f" {site.x} {site.y} {site.z} {int(symbols.index(site.specie.symbol)) + 1}")

        t = Template(
            """# number of atoms and species
   $nat    $nsp
# number of valence bands
    $nvbands
# number of points and spacing in eV for correlation grid
    $n_grid    $dE_grid
# relire=1 ou recalculer=0 Exc DFT
    $rdVxcpsi
# number of COHSEX corrected occp and unoccp bands: C=COHSEX  H=HF
    $nv_cohsex    $nc_cohsex   $eigMethod
# number of COHSEX iter, scf on wfns, mixing coeff; V=RI-V  I=RI-D
    $nit_cohsex   $resMethod       $scf_cohsex_wf       $mix_cohsex
# number of GW corrected occp and unoccp bands
   $nv_corr   $nc_corr
# number of GW iterations
    $nit_gw
# dumping for BSE and TDDFT
    $do_bse    $do_tddft
# number of occp. and virtual bands of BSE: nocore and up to 40 eVs
    $nv_bse   $nc_bse
# number of excitations needed and number of iterations
    $npsi_bse   $nit_bse
# list of symbols in order
$symbols
# scaling factor
    1.000
# atoms x,y,z cartesian .. will be multiplied by scale
$geometry
            """
        )

        return t.substitute(
            nat=int(self._mol.composition.num_atoms),
            nsp=len(self._mol.symbol_set),
            nvbands=int(self._mol.nelectrons / 2),
            n_grid=self.correlation_grid["n_grid"],
            dE_grid=self.correlation_grid["dE_grid"],
            rdVxcpsi=self.Exc_DFT_option["rdVxcpsi"],
            nv_cohsex=self.COHSEX_options["nv_cohsex"],
            nc_cohsex=self.COHSEX_options["nc_cohsex"],
            eigMethod=self.COHSEX_options["eigMethod"],
            nit_cohsex=self.COHSEX_options["nit_cohsex"],
            resMethod=self.COHSEX_options["resMethod"],
            scf_cohsex_wf=self.COHSEX_options["scf_cohsex_wf"],
            mix_cohsex=self.COHSEX_options["mix_cohsex"],
            nv_corr=self.GW_options["nv_corr"],
            nc_corr=self.GW_options["nc_corr"],
            nit_gw=self.GW_options["nit_gw"],
            do_bse=self.BSE_TDDFT_options["do_bse"],
            do_tddft=self.BSE_TDDFT_options["do_tddft"],
            nv_bse=self.BSE_TDDFT_options["nv_bse"],
            nc_bse=self.BSE_TDDFT_options["nc_bse"],
            npsi_bse=self.BSE_TDDFT_options["npsi_bse"],
            nit_bse=self.BSE_TDDFT_options["nit_bse"],
            symbols="\n".join(symbols),
            geometry="\n".join(geometry),
        )

    def write_file(self, filename):
        """
        Write FiestaInput to a file
        :param filename: Filename
        """
        with zopen(filename, "w") as f:
            f.write(str(self))

    def as_dict(self):
        """
        :return: MSONable dict
        """
        return {
            "mol": self._mol.as_dict(),
            "correlation_grid": self.correlation_grid,
            "Exc_DFT_option": self.Exc_DFT_option,
            "COHSEX_options": self.COHSEX_options,
            "GW_options": self.GW_options,
            "BSE_TDDFT_options": self.BSE_TDDFT_options,
        }

    @classmethod
    def from_dict(cls, d):
        """
        :param d: Dict representation
        :return: FiestaInput
        """
        return cls(
            Molecule.from_dict(d["mol"]),
            correlation_grid=d["correlation_grid"],
            Exc_DFT_option=d["Exc_DFT_option"],
            COHSEX_options=d["geometry_options"],
            GW_options=d["symmetry_options"],
            BSE_TDDFT_options=d["memory_options"],
        )

    @classmethod
    def from_string(cls, string_input):
        """
        Read an FiestaInput from a string. Currently tested to work with
        files generated from this class itself.

        Args:
            string_input: string_input to parse.
        Returns:
            FiestaInput object
        """
        correlation_grid = {}
        Exc_DFT_option = {}
        COHSEX_options = {}
        GW_options = {}
        BSE_TDDFT_options = {}

        lines = string_input.strip().split("\n")

        # number of atoms and species
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        nat = toks[0]
        nsp = toks[1]
        # number of valence bands
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()

        # correlation_grid
        # number of points and spacing in eV for correlation grid
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        correlation_grid["n_grid"] = toks[0]
        correlation_grid["dE_grid"] = toks[1]

        # Exc DFT
        # relire=1 ou recalculer=0 Exc DFT
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        Exc_DFT_option["rdVxcpsi"] = toks[0]

        # COHSEX
        # number of COHSEX corrected occp and unoccp bands: C=COHSEX  H=HF
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        COHSEX_options["nv_cohsex"] = toks[0]
        COHSEX_options["nc_cohsex"] = toks[1]
        COHSEX_options["eigMethod"] = toks[2]
        # number of COHSEX iter, scf on wfns, mixing coeff; V=RI-V  I=RI-D
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        COHSEX_options["nit_cohsex"] = toks[0]
        COHSEX_options["resMethod"] = toks[1]
        COHSEX_options["scf_cohsex_wf"] = toks[2]
        COHSEX_options["mix_cohsex"] = toks[3]

        # GW
        # number of GW corrected occp and unoccp bands
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        GW_options["nv_corr"] = toks[0]
        GW_options["nc_corr"] = toks[1]
        # number of GW iterations
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        GW_options["nit_gw"] = toks[0]

        # BSE
        # dumping for BSE and TDDFT
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        BSE_TDDFT_options["do_bse"] = toks[0]
        BSE_TDDFT_options["do_tddft"] = toks[1]
        # number of occp. and virtual bands of BSE: nocore and up to 40 eVs
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        BSE_TDDFT_options["nv_bse"] = toks[0]
        BSE_TDDFT_options["nc_bse"] = toks[1]
        # number of excitations needed and number of iterations
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        BSE_TDDFT_options["npsi_bse"] = toks[0]
        BSE_TDDFT_options["nit_bse"] = toks[1]

        # Molecule
        # list of symbols in order
        lines.pop(0)
        atname = []
        i = int(nsp)
        while i != 0:
            l = lines.pop(0).strip()
            toks = l.split()
            atname.append(toks[0])
            i -= 1

        # scaling factor
        lines.pop(0)
        l = lines.pop(0).strip()
        toks = l.split()
        # atoms x,y,z cartesian .. will be multiplied by scale
        lines.pop(0)
        # Parse geometry
        species = []
        coords = []
        i = int(nat)
        while i != 0:
            l = lines.pop(0).strip()
            toks = l.split()
            coords.append([float(j) for j in toks[0:3]])
            species.append(atname[int(toks[3]) - 1])
            i -= 1

        mol = Molecule(species, coords)

        return FiestaInput(
            mol=mol,
            correlation_grid=correlation_grid,
            Exc_DFT_option=Exc_DFT_option,
            COHSEX_options=COHSEX_options,
            GW_options=GW_options,
            BSE_TDDFT_options=BSE_TDDFT_options,
        )

    @classmethod
    def from_file(cls, filename):
        """
        Read an Fiesta input from a file. Currently tested to work with
        files generated from this class itself.

        Args:
            filename: Filename to parse.

        Returns:
            FiestaInput object
        """
        with zopen(filename) as f:
            return cls.from_string(f.read())


class FiestaOutput:
    """
    A Fiesta output file parser.

    All energies are in eV.
    """

    def __init__(self, filename):
        """
        Args:
            filename: Filename to read.
        """
        self.filename = filename

        with zopen(filename) as f:
            data = f.read()

        chunks = re.split(r"GW Driver iteration", data)

        # preamble: everything before the first GW Driver iteration
        chunks.pop(0)

        # self.job_info = self._parse_preamble(preamble)
        self.data = [self._parse_job(c) for c in chunks]

    @staticmethod
    def _parse_job(output):
        GW_BANDS_results_patt = re.compile(
            r"^<it.*  \| \s+ (\D+\d*) \s+ \| \s+ ([-\d.]+) \s+ ([-\d.]+) \s+ ([-\d.]+) \s+ \| "
            r" \s+ ([-\d.]+) \s+ ([-\d.]+) \s+ ([-\d.]+) \s+ \|"
            r" \s+ ([-\d.]+) \s+ ([-\d.]+) \s+ ",
            re.VERBOSE,
        )

        GW_GAPS_results_patt = re.compile(
            r"^<it.*  \| \s+ Egap_KS \s+ = \s+ ([-\d.]+) \s+ \| \s+ Egap_QP \s+ = \s+ ([-\d.]+) \s+ \| "
            r" \s+ Egap_QP \s+ = \s+ ([-\d.]+) \s+ \|",
            re.VERBOSE,
        )

        end_patt = re.compile(r"\s*program returned normally\s*")

        total_time_patt = re.compile(r"\s*total \s+ time: \s+  ([\d.]+) .*", re.VERBOSE)

        GW_results = {}
        parse_gw_results = False
        parse_total_time = False

        for l in output.split("\n"):
            if parse_total_time:
                m = end_patt.search(l)
                if m:
                    GW_results.update(end_normally=True)

                m = total_time_patt.search(l)
                if m:
                    GW_results.update(total_time=m.group(1))

            if parse_gw_results:
                if l.find("Dumping eigen energies") != -1:
                    parse_total_time = True
                    parse_gw_results = False
                    continue

                m = GW_BANDS_results_patt.search(l)
                if m:
                    d = {}
                    d.update(
                        band=m.group(1).strip(),
                        eKS=m.group(2),
                        eXX=m.group(3),
                        eQP_old=m.group(4),
                        z=m.group(5),
                        sigma_c_Linear=m.group(6),
                        eQP_Linear=m.group(7),
                        sigma_c_SCF=m.group(8),
                        eQP_SCF=m.group(9),
                    )
                    GW_results[m.group(1).strip()] = d

                n = GW_GAPS_results_patt.search(l)
                if n:
                    d = {}
                    d.update(
                        Egap_KS=n.group(1),
                        Egap_QP_Linear=n.group(2),
                        Egap_QP_SCF=n.group(3),
                    )
                    GW_results["Gaps"] = d

            if l.find("GW Results") != -1:
                parse_gw_results = True

        return GW_results


class BSEOutput:
    """
    A bse output file parser. The start...

    All energies are in eV.
    """

    def __init__(self, filename):
        """
        Args:
            filename: Filename to read.
        """
        self.filename = filename

        with zopen(filename) as f:
            log_bse = f.read()

        # self.job_info = self._parse_preamble(preamble)
        self.exiton = self._parse_job(log_bse)

    @staticmethod
    def _parse_job(output):
        BSE_exitons_patt = re.compile(
            r"^exiton \s+ (\d+)  : \s+  ([\d.]+) \( \s+ ([-\d.]+) \) \s+ \| .*  ",
            re.VERBOSE,
        )

        end_patt = re.compile(r"\s*program returned normally\s*")

        total_time_patt = re.compile(r"\s*total \s+ time: \s+  ([\d.]+) .*", re.VERBOSE)

        BSE_results = {}
        parse_BSE_results = False
        parse_total_time = False

        for l in output.split("\n"):
            if parse_total_time:
                m = end_patt.search(l)
                if m:
                    BSE_results.update(end_normally=True)

                m = total_time_patt.search(l)
                if m:
                    BSE_results.update(total_time=m.group(1))

            if parse_BSE_results:
                if l.find("FULL BSE main valence -> conduction transitions weight:") != -1:
                    parse_total_time = True
                    parse_BSE_results = False
                    continue

                m = BSE_exitons_patt.search(l)
                if m:
                    d = {}
                    d.update(bse_eig=m.group(2), osc_strength=m.group(3))
                    BSE_results[str(m.group(1).strip())] = d

            if l.find("FULL BSE eig.(eV), osc. strength and dipoles:") != -1:
                parse_BSE_results = True

        return BSE_results

materialsproject / pymatgen / 4075885785

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