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

2015/09/21 - Xin Chen (chenxin13@mails.tsinghua.edu.cn):

    NwOutput will read new kinds of data:

        1. normal hessian matrix.       ["hessian"]
        2. projected hessian matrix.    ["projected_hessian"]
        3. normal frequencies.          ["normal_frequencies"]

    For backward compatibility, the key for accessing the projected frequencies
    is still 'frequencies'.

2015/10/12 - Xin Chen
    NwOutput will read new kinds of data:

        1. forces.                      ["forces"]
"""

from __future__ import annotations

import os
import re
import warnings
from string import Template
from typing import TYPE_CHECKING

import numpy as np
from monty.io import zopen
from monty.json import MSONable
from pymatgen.analysis.excitation import ExcitationSpectrum
from pymatgen.core.structure import Molecule, Structure
from pymatgen.core.units import Energy, FloatWithUnit

if TYPE_CHECKING:
    from pathlib import Path
    from typing import ClassVar

    from typing_extensions import Self

NWCHEM_BASIS_LIBRARY = None
if os.getenv("NWCHEM_BASIS_LIBRARY"):
    NWCHEM_BASIS_LIBRARY = set(os.listdir(os.environ["NWCHEM_BASIS_LIBRARY"]))


class NwTask(MSONable):
    """Base task for Nwchem."""

    theories: ClassVar[dict[str, str]] = {
        "g3gn": "some description",
        "scf": "Hartree-Fock",
        "dft": "DFT",
        "esp": "ESP",
        "sodft": "Spin-Orbit DFT",
        "mp2": "MP2 using a semi-direct algorithm",
        "direct_mp2": "MP2 using a full-direct algorithm",
        "rimp2": "MP2 using the RI approximation",
        "ccsd": "Coupled-cluster single and double excitations",
        "ccsd(t)": "Coupled-cluster linearized triples approximation",
        "ccsd+t(ccsd)": "Fourth order triples contribution",
        "mcscf": "Multiconfiguration SCF",
        "selci": "Selected CI with perturbation correction",
        "md": "Classical molecular dynamics simulation",
        "pspw": "Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW",
        "band": "Pseudopotential plane-wave DFT for solids using NWPW",
        "tce": "Tensor Contraction Engine",
        "tddft": "Time Dependent DFT",
    }

    operations: ClassVar[dict[str, str]] = {
        "energy": "Evaluate the single point energy.",
        "gradient": "Evaluate the derivative of the energy with respect to nuclear coordinates.",
        "optimize": "Minimize the energy by varying the molecular structure.",
        "saddle": "Conduct a search for a transition state (or saddle point).",
        "hessian": "Compute second derivatives.",
        "frequencies": "Compute second derivatives and print out an analysis of molecular vibrations.",
        "freq": "Same as frequencies.",
        "vscf": "Compute anharmonic contributions to the vibrational modes.",
        "property": "Calculate the properties for the wave function.",
        "dynamics": "Perform classical molecular dynamics.",
        "thermodynamics": "Perform multi-configuration thermodynamic integration using classical MD.",
        "": "dummy",
    }

    def __init__(
        self,
        charge,
        spin_multiplicity,
        basis_set,
        basis_set_option="cartesian",
        title=None,
        theory="dft",
        operation="optimize",
        theory_directives=None,
        alternate_directives=None,
    ):
        """
        Very flexible arguments to support many types of potential setups.
        Users should use more friendly static methods unless they need the
        flexibility.

        Args:
            charge: Charge of the molecule. If None, charge on molecule is
                used. Defaults to None. This allows the input file to be set a
                charge independently from the molecule itself.
            spin_multiplicity: Spin multiplicity of molecule. Defaults to None,
                which means that the spin multiplicity is set to 1 if the
                molecule has no unpaired electrons and to 2 if there are
                unpaired electrons.
            basis_set: The basis set used for the task as a dict. e.g.
                {"C": "6-311++G**", "H": "6-31++G**"}.
            basis_set_option: cartesian (default) | spherical,
            title: Title for the task. Defaults to None, which means a title
                based on the theory and operation of the task is
                autogenerated.
            theory: The theory used for the task. Defaults to "dft".
            operation: The operation for the task. Defaults to "optimize".
            theory_directives: A dict of theory directives. For example,
                if you are running dft calculations, you may specify the
                exchange correlation functional using {"xc": "b3lyp"}.
            alternate_directives: A dict of alternate directives. For
                example, to perform cosmo calculations and dielectric
                constant of 78, you'd supply {'cosmo': {"dielectric": 78}}.
        """
        # Basic checks.
        if theory.lower() not in NwTask.theories:
            raise NwInputError(f"Invalid {theory=}")

        if operation.lower() not in NwTask.operations:
            raise NwInputError(f"Invalid {operation=}")
        self.charge = charge
        self.spin_multiplicity = spin_multiplicity
        self.title = title if title is not None else f"{theory} {operation}"
        self.theory = theory

        self.basis_set = basis_set or {}
        if NWCHEM_BASIS_LIBRARY is not None:
            for b in set(self.basis_set.values()):
                if re.sub(r"\*", "s", b.lower()) not in NWCHEM_BASIS_LIBRARY:
                    warnings.warn(f"Basis set {b} not in NWCHEM_BASIS_LIBRARY")

        self.basis_set_option = basis_set_option

        self.operation = operation
        self.theory_directives = theory_directives or {}
        self.alternate_directives = alternate_directives or {}

    def __str__(self):
        bset_spec = []
        for el, bset in sorted(self.basis_set.items(), key=lambda x: x[0]):
            bset_spec.append(f' {el} library "{bset}"')
        theory_spec = []
        if self.theory_directives:
            theory_spec.append(f"{self.theory}")
            for k in sorted(self.theory_directives):
                theory_spec.append(f" {k} {self.theory_directives[k]}")
            theory_spec.append("end")
        for k in sorted(self.alternate_directives):
            theory_spec.append(k)
            for k2 in sorted(self.alternate_directives[k]):
                theory_spec.append(f" {k2} {self.alternate_directives[k][k2]}")
            theory_spec.append("end")

        t = Template(
            """title "$title"
charge $charge
basis $basis_set_option
$bset_spec
end
$theory_spec
"""
        )

        output = t.substitute(
            title=self.title,
            charge=int(self.charge),
            spinmult=self.spin_multiplicity,
            basis_set_option=self.basis_set_option,
            bset_spec="\n".join(bset_spec),
            theory_spec="\n".join(theory_spec),
            theory=self.theory,
        )

        if self.operation is not None:
            output += f"task {self.theory} {self.operation}"
        return output

    def as_dict(self):
        """Get MSONable dict."""
        return {
            "@module": type(self).__module__,
            "@class": type(self).__name__,
            "charge": self.charge,
            "spin_multiplicity": self.spin_multiplicity,
            "title": self.title,
            "theory": self.theory,
            "operation": self.operation,
            "basis_set": self.basis_set,
            "basis_set_option": self.basis_set_option,
            "theory_directives": self.theory_directives,
            "alternate_directives": self.alternate_directives,
        }

    @classmethod
    def from_dict(cls, dct: dict) -> Self:
        """
        Args:
            dct (dict): Dict representation.

        Returns:
            NwTask
        """
        return cls(
            charge=dct["charge"],
            spin_multiplicity=dct["spin_multiplicity"],
            title=dct["title"],
            theory=dct["theory"],
            operation=dct["operation"],
            basis_set=dct["basis_set"],
            basis_set_option=dct["basis_set_option"],
            theory_directives=dct["theory_directives"],
            alternate_directives=dct["alternate_directives"],
        )

    @classmethod
    def from_molecule(
        cls,
        mol,
        theory,
        charge=None,
        spin_multiplicity=None,
        basis_set="6-31g",
        basis_set_option="cartesian",
        title=None,
        operation="optimize",
        theory_directives=None,
        alternate_directives=None,
    ) -> Self:
        """
        Very flexible arguments to support many types of potential setups.
        Users should use more friendly static methods unless they need the
        flexibility.

        Args:
            mol: Input molecule
            charge: Charge of the molecule. If None, charge on molecule is
                used. Defaults to None. This allows the input file to be set a
                charge independently from the molecule itself.
            spin_multiplicity: Spin multiplicity of molecule. Defaults to None,
                which means that the spin multiplicity is set to 1 if the
                molecule has no unpaired electrons and to 2 if there are
                unpaired electrons.
            basis_set: The basis set to be used as string or a dict. e.g.
                {"C": "6-311++G**", "H": "6-31++G**"} or "6-31G". If string,
                same basis set is used for all elements.
            basis_set_option: cartesian (default) | spherical,
            title: Title for the task. Defaults to None, which means a title
                based on the theory and operation of the task is
                autogenerated.
            theory: The theory used for the task. Defaults to "dft".
            operation: The operation for the task. Defaults to "optimize".
            theory_directives: A dict of theory directives. For example,
                if you are running dft calculations, you may specify the
                exchange correlation functional using {"xc": "b3lyp"}.
            alternate_directives: A dict of alternate directives. For
                example, to perform cosmo calculations with DFT, you'd supply
                {'cosmo': "cosmo"}.
        """
        formula = re.sub(r"\s", "", mol.formula)
        title = title if title is not None else f"{formula} {theory} {operation}"

        charge = charge if charge is not None else mol.charge
        n_electrons = -charge + mol.charge + mol.nelectrons
        if spin_multiplicity is not None:
            if (n_electrons + spin_multiplicity) % 2 != 1:
                raise ValueError(f"{charge=} and {spin_multiplicity=} is not possible for this molecule")
        elif charge == mol.charge:
            spin_multiplicity = mol.spin_multiplicity
        else:
            spin_multiplicity = 1 if n_electrons % 2 == 0 else 2

        elements = set(mol.composition.get_el_amt_dict())
        if isinstance(basis_set, str):
            basis_set = dict.fromkeys(elements, basis_set)

        return cls(
            charge,
            spin_multiplicity,
            basis_set,
            basis_set_option=basis_set_option,
            title=title,
            theory=theory,
            operation=operation,
            theory_directives=theory_directives,
            alternate_directives=alternate_directives,
        )

    @classmethod
    def dft_task(cls, mol, xc="b3lyp", **kwargs):
        """
        A class method for quickly creating DFT tasks with optional
        cosmo parameter .

        Args:
            mol: Input molecule
            xc: Exchange correlation to use.
            kwargs: Any of the other kwargs supported by NwTask. Note the
                theory is always "dft" for a dft task.
        """
        t = NwTask.from_molecule(mol, theory="dft", **kwargs)
        t.theory_directives.update({"xc": xc, "mult": t.spin_multiplicity})
        return t

    @classmethod
    def esp_task(cls, mol, **kwargs):
        """
        A class method for quickly creating ESP tasks with RESP
        charge fitting.

        Args:
            mol: Input molecule
            kwargs: Any of the other kwargs supported by NwTask. Note the
                theory is always "dft" for a dft task.
        """
        return NwTask.from_molecule(mol, theory="esp", **kwargs)


class NwInput(MSONable):
    """
    An object representing a Nwchem input file, which is essentially a list
    of tasks on a particular molecule.
    """

    def __init__(
        self,
        mol,
        tasks,
        directives=None,
        geometry_options=("units", "angstroms"),
        symmetry_options=None,
        memory_options=None,
    ):
        """
        Args:
            mol: Input molecule. If molecule is a single string, it is used as a
                direct input to the geometry section of the Gaussian input
                file.
            tasks: List of NwTasks.
            directives: List of root level directives as tuple. e.g.
                [("start", "water"), ("print", "high")]
            geometry_options: Additional list of options to be supplied to the
                geometry. e.g. ["units", "angstroms", "noautoz"]. Defaults to
                ("units", "angstroms").
            symmetry_options: Addition list of option to be supplied to the
                symmetry. E.g. ["c1"] to turn off the symmetry
            memory_options: Memory controlling options. str.
                E.g "total 1000 mb stack 400 mb".
        """
        self._mol = mol
        self.directives = directives if directives is not None else []
        self.tasks = tasks
        self.geometry_options = geometry_options
        self.symmetry_options = symmetry_options
        self.memory_options = memory_options

    @property
    def molecule(self):
        """Molecule associated with this GaussianInput."""
        return self._mol

    def __str__(self):
        out = []
        if self.memory_options:
            out.append(f"memory {self.memory_options}")
        for d in self.directives:
            out.append(f"{d[0]} {d[1]}")
        out.append("geometry " + " ".join(self.geometry_options))
        if self.symmetry_options:
            out.append(" symmetry " + " ".join(self.symmetry_options))
        for site in self._mol:
            out.append(f" {site.specie.symbol} {site.x} {site.y} {site.z}")
        out.append("end\n")
        for task in self.tasks:
            out.extend((str(task), ""))
        return "\n".join(out)

    def write_file(self, filename):
        """
        Args:
            filename (str): Filename.
        """
        with zopen(filename, mode="w") as file:
            file.write(str(self))

    def as_dict(self):
        """Get MSONable dict."""
        return {
            "mol": self._mol.as_dict(),
            "tasks": [task.as_dict() for task in self.tasks],
            "directives": [list(task) for task in self.directives],
            "geometry_options": list(self.geometry_options),
            "symmetry_options": self.symmetry_options,
            "memory_options": self.memory_options,
        }

    @classmethod
    def from_dict(cls, dct: dict) -> Self:
        """
        Args:
            dct (dict): Dict representation.

        Returns:
            NwInput
        """
        return cls(
            Molecule.from_dict(dct["mol"]),
            tasks=[NwTask.from_dict(dt) for dt in dct["tasks"]],
            directives=[tuple(li) for li in dct["directives"]],
            geometry_options=dct["geometry_options"],
            symmetry_options=dct["symmetry_options"],
            memory_options=dct["memory_options"],
        )

    @classmethod
    def from_str(cls, string_input: str) -> Self:
        """
        Read an NwInput from a string. Currently tested to work with
        files generated from this class itself.

        Args:
            string_input: string_input to parse.

        Returns:
            NwInput object
        """
        directives = []
        tasks = []
        charge = spin_multiplicity = title = basis_set = None
        basis_set_option = None
        mol = None
        theory_directives: dict[str, dict[str, str]] = {}
        geom_options = symmetry_options = memory_options = None

        lines = string_input.strip().split("\n")
        while len(lines) > 0:
            line = lines.pop(0).strip()
            if line == "":
                continue

            tokens = line.split()
            if tokens[0].lower() == "geometry":
                geom_options = tokens[1:]
                line = lines.pop(0).strip()
                tokens = line.split()
                if tokens[0].lower() == "symmetry":
                    symmetry_options = tokens[1:]
                    line = lines.pop(0).strip()
                # Parse geometry
                species = []
                coords = []
                while line.lower() != "end":
                    tokens = line.split()
                    species.append(tokens[0])
                    coords.append([float(i) for i in tokens[1:]])
                    line = lines.pop(0).strip()
                mol = Molecule(species, coords)
            elif tokens[0].lower() == "charge":
                charge = int(tokens[1])
            elif tokens[0].lower() == "title":
                title = line[5:].strip().strip('"')
            elif tokens[0].lower() == "basis":
                # Parse basis sets
                line = lines.pop(0).strip()
                basis_set = {}
                while line.lower() != "end":
                    tokens = line.split()
                    basis_set[tokens[0]] = tokens[-1].strip('"')
                    line = lines.pop(0).strip()
            elif tokens[0].lower() in NwTask.theories:
                # read the basis_set_option
                if len(tokens) > 1:
                    basis_set_option = tokens[1]
                # Parse theory directives.
                theory = tokens[0].lower()
                line = lines.pop(0).strip()
                theory_directives[theory] = {}
                while line.lower() != "end":
                    tokens = line.split()
                    theory_directives[theory][tokens[0]] = tokens[-1]
                    if tokens[0] == "mult":
                        spin_multiplicity = float(tokens[1])
                    line = lines.pop(0).strip()
            elif tokens[0].lower() == "task":
                tasks.append(
                    NwTask(
                        charge=charge,
                        spin_multiplicity=spin_multiplicity,
                        title=title,
                        theory=tokens[1],
                        operation=tokens[2],
                        basis_set=basis_set,
                        basis_set_option=basis_set_option,
                        theory_directives=theory_directives.get(tokens[1]),
                    )
                )
            elif tokens[0].lower() == "memory":
                memory_options = " ".join(tokens[1:])
            else:
                directives.append(line.strip().split())

        return cls(
            mol,
            tasks=tasks,
            directives=directives,
            geometry_options=geom_options,
            symmetry_options=symmetry_options,
            memory_options=memory_options,
        )

    @classmethod
    def from_file(cls, filename: str | Path) -> Self:
        """
        Read an NwInput from a file. Currently tested to work with
        files generated from this class itself.

        Args:
            filename: Filename to parse.

        Returns:
            NwInput object
        """
        with zopen(filename) as file:
            return cls.from_str(file.read())


class NwInputError(Exception):
    """Error class for NwInput."""


class NwOutput:
    """
    A Nwchem output file parser. Very basic for now - supports only dft and
    only parses energies and geometries. Please note that Nwchem typically
    outputs energies in either au or kJ/mol. All energies are converted to
    eV in the parser.
    """

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

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

        chunks = re.split(r"NWChem Input Module", data)
        if re.search(r"CITATION", chunks[-1]):
            chunks.pop()
        preamble = chunks.pop(0)

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

    def parse_tddft(self):
        """
        Parses TDDFT roots. Adapted from nw_spectrum.py script.

        Returns:
            dict[str, list]: A dict of the form {"singlet": [dict, ...], "triplet": [dict, ...]} where
                each sub-dict is of the form {"energy": float, "osc_strength": float}.
        """
        start_tag = "Convergence criterion met"
        end_tag = "Excited state energy"
        singlet_tag = "singlet excited"
        triplet_tag = "triplet excited"
        state = "singlet"
        inside = False  # true when we are inside output block

        lines = self.raw.split("\n")

        roots = {"singlet": [], "triplet": []}

        while lines:
            line = lines.pop(0).strip()

            if start_tag in line:
                inside = True

            elif end_tag in line:
                inside = False

            elif singlet_tag in line:
                state = "singlet"

            elif triplet_tag in line:
                state = "triplet"

            elif inside and "Root" in line and "eV" in line:
                tokens = line.split()
                roots[state].append({"energy": float(tokens[-2])})

            elif inside and "Dipole Oscillator Strength" in line:
                osc = float(line.split()[-1])
                roots[state][-1]["osc_strength"] = osc

        return roots

    def get_excitation_spectrum(self, width=0.1, npoints=2000):
        """Generate an excitation spectra from the singlet roots of TDDFT calculations.

        Args:
            width (float): Width for Gaussian smearing.
            npoints (int): Number of energy points. More points => smoother
                curve.

        Returns:
            ExcitationSpectrum: can be plotted using pymatgen.vis.plotters.SpectrumPlotter.
        """
        roots = self.parse_tddft()
        data = roots["singlet"]
        en = np.array([d["energy"] for d in data])
        osc = np.array([d["osc_strength"] for d in data])

        epad = 20.0 * width
        emin = en[0] - epad
        emax = en[-1] + epad
        de = (emax - emin) / npoints

        # Use width of at least two grid points
        if width < 2 * de:
            width = 2 * de

        energies = [emin + ie * de for ie in range(npoints)]

        cutoff = 20.0 * width
        gamma = 0.5 * width
        gamma_sqrd = gamma * gamma

        de = (energies[-1] - energies[0]) / (len(energies) - 1)
        prefac = gamma / np.pi * de

        x = []
        y = []
        for energy in energies:
            xx0 = energy - en
            stot = osc / (xx0 * xx0 + gamma_sqrd)
            t = np.sum(stot[np.abs(xx0) <= cutoff])
            x.append(energy)
            y.append(t * prefac)
        return ExcitationSpectrum(x, y)

    @staticmethod
    def _parse_preamble(preamble):
        info = {}
        for line in preamble.split("\n"):
            tokens = line.split("=")
            if len(tokens) > 1:
                info[tokens[0].strip()] = tokens[-1].strip()
        return info

    def __iter__(self):
        return iter(self.data)

    def __getitem__(self, ind):
        return self.data[ind]

    def __len__(self):
        return len(self.data)

    @staticmethod
    def _parse_job(output):
        energy_patt = re.compile(r"Total \w+ energy\s+=\s+([.\-\d]+)")
        energy_gas_patt = re.compile(r"gas phase energy\s+=\s+([.\-\d]+)")
        energy_sol_patt = re.compile(r"sol phase energy\s+=\s+([.\-\d]+)")
        coord_patt = re.compile(r"\d+\s+(\w+)\s+[.\-\d]+\s+([.\-\d]+)\s+([.\-\d]+)\s+([.\-\d]+)")
        lat_vector_patt = re.compile(r"a[123]=<\s+([.\-\d]+)\s+([.\-\d]+)\s+([.\-\d]+)\s+>")
        corrections_patt = re.compile(r"([\w\-]+ correction to \w+)\s+=\s+([.\-\d]+)")
        preamble_patt = re.compile(
            r"(No. of atoms|No. of electrons|SCF calculation type|Charge|Spin multiplicity)\s*:\s*(\S+)"
        )
        force_patt = re.compile(r"\s+(\d+)\s+(\w+)" + 6 * r"\s+([0-9\.\-]+)")

        time_patt = re.compile(r"\s+ Task \s+ times \s+ cpu: \s+   ([.\d]+)s .+ ", re.VERBOSE)

        error_defs = {
            "calculations not reaching convergence": "Bad convergence",
            "Calculation failed to converge": "Bad convergence",
            "geom_binvr: #indep variables incorrect": "autoz error",
            "dft optimize failed": "Geometry optimization failed",
        }

        def fort2py(x):
            return x.replace("D", "e")

        def isfloatstring(in_str):
            return in_str.find(".") == -1

        parse_hess = False
        parse_proj_hess = False
        hessian = projected_hessian = None
        parse_force = False
        all_forces = []
        forces = []

        data = {}
        energies = []
        frequencies = normal_frequencies = None
        corrections = {}
        molecules = []
        structures = []
        species = []
        coords = []
        lattice = []
        errors = []
        basis_set = {}
        bset_header = []
        parse_geom = False
        parse_freq = False
        parse_bset = False
        parse_projected_freq = False
        job_type = ""
        parse_time = False
        time = 0

        for line in output.split("\n"):
            for e, v in error_defs.items():
                if line.find(e) != -1:
                    errors.append(v)
            if parse_time and (match := time_patt.search(line)):
                time = match[1]
                parse_time = False
            if parse_geom:
                if line.strip() == "Atomic Mass":
                    if lattice:
                        structures.append(Structure(lattice, species, coords, coords_are_cartesian=True))
                    else:
                        molecules.append(Molecule(species, coords))
                    species = []
                    coords = []
                    lattice = []
                    parse_geom = False
                else:
                    if match := coord_patt.search(line):
                        species.append(match[1].capitalize())
                        coords.append([float(match[2]), float(match[3]), float(match[4])])

                    if match := lat_vector_patt.search(line):
                        lattice.append([float(match[1]), float(match[2]), float(match[3])])

            if parse_force:
                if match := force_patt.search(line):
                    forces.extend(map(float, match.groups()[5:]))
                elif len(forces) > 0:
                    all_forces.append(forces)
                    forces = []
                    parse_force = False

            elif parse_freq:
                if len(line.strip()) == 0:
                    if len(normal_frequencies[-1][1]) == 0:
                        continue
                    parse_freq = False
                else:
                    vibs = [float(vib) for vib in line.strip().split()[1:]]
                    n_vibs = len(vibs)
                    for mode, dis in zip(normal_frequencies[-n_vibs:], vibs):
                        mode[1].append(dis)

            elif parse_projected_freq:
                if len(line.strip()) == 0:
                    if len(frequencies[-1][1]) == 0:
                        continue
                    parse_projected_freq = False
                else:
                    vibs = [float(vib) for vib in line.strip().split()[1:]]
                    n_vibs = len(vibs)
                    for mode, dis in zip(frequencies[-n_vibs:], vibs):
                        mode[1].append(dis)

            elif parse_bset:
                if line.strip() == "":
                    parse_bset = False
                else:
                    tokens = line.split()
                    if tokens[0] != "Tag" and not re.match(r"-+", tokens[0]):
                        basis_set[tokens[0]] = dict(zip(bset_header[1:], tokens[1:]))
                    elif tokens[0] == "Tag":
                        bset_header = tokens
                        bset_header.pop(4)
                        bset_header = [h.lower() for h in bset_header]

            elif parse_hess:
                if line.strip() == "":
                    continue
                if len(hessian) > 0 and line.find("----------") != -1:
                    parse_hess = False
                    continue
                tokens = line.strip().split()
                if len(tokens) > 1:
                    try:
                        row = int(tokens[0])
                    except Exception:
                        continue
                    if isfloatstring(tokens[1]):
                        continue
                    vals = [float(fort2py(x)) for x in tokens[1:]]
                    if len(hessian) < row:
                        hessian.append(vals)
                    else:
                        hessian[row - 1].extend(vals)

            elif parse_proj_hess:
                if line.strip() == "":
                    continue
                nat3 = len(hessian)
                tokens = line.strip().split()
                if len(tokens) > 1:
                    try:
                        row = int(tokens[0])
                    except Exception:
                        continue
                    if isfloatstring(tokens[1]):
                        continue
                    vals = [float(fort2py(x)) for x in tokens[1:]]
                    if len(projected_hessian) < row:
                        projected_hessian.append(vals)
                    else:
                        projected_hessian[row - 1].extend(vals)
                    if len(projected_hessian[-1]) == nat3:
                        parse_proj_hess = False

            else:
                if match := energy_patt.search(line):
                    energies.append(Energy(match[1], "Ha").to("eV"))
                    parse_time = True
                    continue

                if match := energy_gas_patt.search(line):
                    cosmo_scf_energy = energies[-1]
                    energies[-1] = {}
                    energies[-1]["cosmo scf"] = cosmo_scf_energy
                    energies[-1].update({"gas phase": Energy(match[1], "Ha").to("eV")})

                if match := energy_sol_patt.search(line):
                    energies[-1].update({"sol phase": Energy(match[1], "Ha").to("eV")})

                if match := preamble_patt.search(line):
                    try:
                        val = int(match[2])
                    except ValueError:
                        val = match[2]
                    k = match[1].replace("No. of ", "n").replace(" ", "_")
                    data[k.lower()] = val
                elif line.find('Geometry "geometry"') != -1:
                    parse_geom = True
                elif line.find('Summary of "ao basis"') != -1:
                    parse_bset = True
                elif line.find("P.Frequency") != -1:
                    parse_projected_freq = True
                    if frequencies is None:
                        frequencies = []
                    tokens = line.strip().split()[1:]
                    frequencies.extend([(float(freq), []) for freq in tokens])

                elif line.find("Frequency") != -1:
                    tokens = line.strip().split()
                    if len(tokens) > 1 and tokens[0] == "Frequency":
                        parse_freq = True
                        if normal_frequencies is None:
                            normal_frequencies = []
                        normal_frequencies.extend([(float(freq), []) for freq in line.strip().split()[1:]])

                elif line.find("MASS-WEIGHTED NUCLEAR HESSIAN") != -1:
                    parse_hess = True
                    if not hessian:
                        hessian = []
                elif line.find("MASS-WEIGHTED PROJECTED HESSIAN") != -1:
                    parse_proj_hess = True
                    if not projected_hessian:
                        projected_hessian = []

                elif line.find("atom               coordinates                        gradient") != -1:
                    parse_force = True

                elif job_type == "" and line.strip().startswith("NWChem"):
                    job_type = line.strip()
                    if job_type == "NWChem DFT Module" and "COSMO solvation results" in output:
                        job_type += " COSMO"
                elif match := corrections_patt.search(line):
                    corrections[match[1]] = FloatWithUnit(match[2], "kJ mol^-1").to("eV atom^-1")

        if frequencies:
            for _freq, mode in frequencies:
                mode[:] = zip(*[iter(mode)] * 3)
        if normal_frequencies:
            for _freq, mode in normal_frequencies:
                mode[:] = zip(*[iter(mode)] * 3)
        if hessian:
            len_hess = len(hessian)
            for ii in range(len_hess):
                for jj in range(ii + 1, len_hess):
                    hessian[ii].append(hessian[jj][ii])
        if projected_hessian:
            len_hess = len(projected_hessian)
            for ii in range(len_hess):
                for jj in range(ii + 1, len_hess):
                    projected_hessian[ii].append(projected_hessian[jj][ii])

        data.update(
            {
                "job_type": job_type,
                "energies": energies,
                "corrections": corrections,
                "molecules": molecules,
                "structures": structures,
                "basis_set": basis_set,
                "errors": errors,
                "has_error": len(errors) > 0,
                "frequencies": frequencies,
                "normal_frequencies": normal_frequencies,
                "hessian": hessian,
                "projected_hessian": projected_hessian,
                "forces": all_forces,
                "task_time": time,
            }
        )

        return data
