# 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 collections import defaultdict

from monty.io import zopen
from monty.re import regrep

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


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 str(species) not in pseudo:
                    raise PWInputError("Missing %s in pseudo specification!" % species)
        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
            if isinstance(v, float):
                return "%s" % str(v).replace("e", "d")
            if isinstance(v, bool):
                if v:
                    return ".TRUE."
                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(f"  {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(f"  {k}  {Element(e).atomic_mass:.4f} {p}")

        out.append("ATOMIC_POSITIONS crystal")
        if self.pseudo is not None:
            for site in self.structure:
                out.append(f"  {site.specie} {site.a:.6f} {site.b:.6f} {site.c:.6f}")
        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(f"  {name} {site.a:.6f} {site.b:.6f} {site.c:.6f}")

        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"  {vec[0]:f} {vec[1]:f} {vec[2]:f}")
        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())
            if "ATOMIC_SPECIES" in line:
                return ("pseudo",)
            if "K_POINTS" in line:
                return "kpoints", line.split("{")[1][:-1]
            if "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:
                return "structure", line.split("{")[1][:-1]
            if line == "/":
                return None
            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":
                            v.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,
        )

    @staticmethod
    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)
            return int(numstr)

        try:
            if key in bool_keys:
                if val.lower() == ".true.":
                    return True
                if val.lower() == ".false.":
                    return False
                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"]
