""" 
This file is part of the Ru/H active learning example in AMS.

The most important things to modify/inspect are:
1) the TESTING_MODE (see below), and
2) the dft_settings() function.

"""

import copy
import matplotlib.pyplot as plt
import numpy as np
import os
import scm.plams as plams
from dataclasses import dataclass
from pathlib import Path
from pprint import pprint
from scm.libbase import Units
from scm.utils.conversions import plams_molecule_to_chemsys, chemsys_to_plams_molecule
from typing import List, Optional, Literal, Tuple, ClassVar, Sequence, Union
import importlib.metadata
import subprocess

ang2bohr = Units.get_factor("angstrom", "bohr")  # angstrom to bohr
bohr2ang = 1 / ang2bohr  # bohr to angstrom
rotation = "-85x,-5y,0z"  # plotting view in Jupyter notebook


TESTING_MODE = False  # set to True to use a custom M3GNet instead of DFT calculations for quick testing run-through


@dataclass
class QEKPointsConfig:
    """Class representing the K_Points input for Quantum ESPRESSO"""

    x: int = 1
    y: int = 1
    z: int = 1
    shift_x: bool = False
    shift_y: bool = False
    shift_z: bool = False

    def to_settings(self) -> plams.Settings:
        """Converts config to PLAMS Settings at the top level"""
        s = plams.Settings()
        if self.x == 1 and self.y == 1 and self.z == 1:
            s.input.QuantumEspresso.K_Points._h = "gamma"
            return s
        s.input.QuantumEspresso.K_Points._h = "automatic"
        s.input.QuantumEspresso.K_Points._1 = (
            f"{self.x} {self.y} {self.z} " f"{int(self.shift_x)} {int(self.shift_y)} {int(self.shift_z)}"
        )
        return s


###########################################
#### Calculation settings functions
###########################################


def dft_settings(kpoints: QEKPointsConfig = QEKPointsConfig(), conv_thr: float = 1e-6) -> plams.Settings:
    """Returns PLAMS Settings for Quantum ESPRESSO PBE-D3(BJ) with Gaussian Smearing

    kpoints will default to the Gamma point if not specified.
    """
    if TESTING_MODE:
        d = Path(os.path.expandvars("$AMSRESOURCES/MLPotential/M3GNet/RuH/engine.txt"))
        if not d.exists():
            raise FileNotFoundError(f"Couldn't find {d}. This file/directory was added in AMS2024.102.")
        plams.log(
            f"Warning: Using custom M3GNet potential from {d} and not DFT! "
            "Set TESTING_MODE = False in common_ru_h.py for running proper calculations."
        )
        s = plams.AMSJob.from_inputfile(str(d)).settings
        s.runscript.nproc = 1
        return s
    s = plams.Settings()
    s += kpoints.to_settings()
    s.input.QuantumEspresso.System.occupations = "smearing"
    s.input.QuantumEspresso.System.degauss = 0.015
    s.input.QuantumEspresso.Pseudopotentials.Family = "SSSP-Efficiency"
    s.input.QuantumEspresso.Pseudopotentials.Functional = "PBE"
    s.input.QuantumEspresso.System.dftd3_version = 4
    s.input.QuantumEspresso.System.vdw_corr = "Grimme-D3"
    s.input.QuantumEspresso.Electrons.conv_thr = conv_thr
    # delete the *.save, worker.*, and *.xml files since they are no longer needed
    # for parametrization jobs
    s.runscript.postamble_lines = ["rm -rf quantumespresso.save PESPoint*.save worker.* *.xml"]

    return s


def replay_settings(rkf: Union[str, os.PathLike], frames: Optional[List[int]] = None) -> plams.Settings:
    """Settings for AMS Replay jobs. Always sets Properties%Gradients = "Yes".

    :param rkf: Path to ams.rkf file from which to extract frames
    :type rkf: os.PathLike
    :param frames: Which frames (indexing starts with 1) to replay. For details, see the AMS Replay documentation.
    :type frames: Optional[List[int]], optional
    :raises FileNotFoundError: If the ams.rkf file does not exist.
    :return: Returns PLAMS Settings object at the top level.
    :rtype: plams.Settings
    """
    s = plams.Settings()
    s.input.ams.Task = "Replay"
    s.input.ams.Properties.Gradients = "Yes"
    rkf = Path(rkf).resolve()
    if not rkf.exists():
        raise FileNotFoundError(f"{rkf} does not exist")
    s.input.ams.Replay.File = str(rkf)
    if frames:
        s.input.ams.Replay.Frames = " ".join(str(x) for x in frames)
    return s


def m3gnet_up_settings() -> plams.Settings:
    """Returns PLAMS Settings for the M3GNet Universal Potential"""
    s = plams.Settings()
    s.input.MLPotential.Model = "M3GNet-UP-2022"
    s.runscript.nproc = 1  # always run AMS Driver in serial for MLPotential
    return s


def lattice_optimization_settings() -> plams.Settings:
    """Returns PLAMS settings for lattice optimization"""
    s = plams.Settings()
    s.input.ams.Task = "GeometryOptimization"
    s.input.ams.GeometryOptimization.OptimizeLattice = "Yes"
    return s


def constraints_settings(constrained_atoms: Optional[Union[int, Sequence[int]]] = None) -> plams.Settings:
    """Sets settings.input.ams.Constraints.Atom. Returns Settings at top level"""
    s = plams.Settings()
    if constrained_atoms is None:
        return s
    if isinstance(constrained_atoms, int):
        s.input.ams.Constraints.Atom = [constrained_atoms]
    else:
        s.input.ams.Constraints.Atom = list(constrained_atoms)

    return s


def pesscan_settings(
    scan_coordinates: Sequence["SingleScanCoordinate"],
    n_points=10,
) -> plams.Settings:
    s = plams.Settings()
    s.input.ams.Task = "PESScan"
    # fix at least 1 Ru atom in place to prevent the entire slab from diffusing
    s.input.ams.PESScan.ScanCoordinate = [plams.Settings()]
    s.input.ams.PESScan.ScanCoordinate[0].nPoints = n_points
    s.input.ams.PESScan.ScanCoordinate[0] += scan_coordinate_list_to_settings(scan_coordinates)
    s.input.ams.PESScan.CalcPropertiesAtPESPoints = "Yes"

    return s


###########################################
##### General structure functions #########
###########################################


def slice_slab(
    bulk: plams.Molecule,
    miller: Tuple[int, int, int],
    thickness: float = 7.0,
    cell_z: float = 15.0,
    ref_atom: int = 0,
) -> plams.Molecule:
    """Returns a slab cut out from the bulk crystal.

    :param bulk: The bulk crystal
    :type bulk: plams.Molecule
    :param miller: Miller indices. For hexagonal crystals with 4 indices, do not specify the third index.
    :type miller: Tuple[int, int, int]
    :param thickness: Approximate thickness of slab (angstrom), defaults to 7.0
    :type thickness: float, optional
    :param cell_z: Lattice parameter in the surface normal direction (angstrom), defaults to 15.0
    :type cell_z: float, optional
    :param ref_atom: Reference atom index (0-based), defaults to 0
    :type ref_atom: int, optional
    :return: Returns a slab (3D periodicity with a vacuum gap)
    :rtype: plams.Molecule
    """
    bulk_ucs = plams_molecule_to_chemsys(bulk)
    slab = copy.copy(bulk_ucs)  # create a copy
    slab.slice_thickness(
        ref_atom=ref_atom,
        top=(cell_z / 2 + thickness / 2) * ang2bohr,  # bohr
        bottom=(cell_z / 2 - thickness / 2) * ang2bohr,  # bohr
        miller=np.array(miller),  # 1, 0, -1, 0 (third index ignored for hexagonal cell)
        translate=0.0,
    )
    lattice_with_gap = np.concatenate((slab.lattice.vectors, np.transpose([[0, 0, cell_z * ang2bohr]])), axis=1)
    slab.lattice.vectors = lattice_with_gap

    # slab.supercell([3, 2])  # create a 3x2 supercell
    slab.map_atoms([0, 0, 0])  # maps atoms into the 0..1 0..1 unit cell

    return chemsys_to_plams_molecule(slab)


def add_adsorbate(
    slab: plams.Molecule,
    symbol: str = "H",
    frac_x: float = 0.0,
    frac_y: float = 0.0,
    delta_z: float = 2.0,
) -> plams.Molecule:
    """
    Adds an atom with given fractional xy coordinates on top of the slab, with a distance of delta_z (angstrom).

    Returns a new plams.Molecule
    """
    surface_lattice = np.array(slab.lattice)[:2, :2]
    x, y = frac_x * surface_lattice[0] + frac_y * surface_lattice[1]
    max_z = np.max(slab.as_array()[:, 2])
    z = max_z + delta_z
    ret = slab.copy()
    ret.add_atom(plams.Atom(symbol=symbol, coords=(x, y, z)))
    return ret


def get_bottom_atom_index(mol: plams.Molecule) -> int:
    """Returns 1-based index of the atom with the smallest z coordinate"""

    return int(np.argmin(mol.as_array()[:, 2])) + 1


##########################################################
##### Functions and classes for PES Scan coordinates #####
##########################################################


@dataclass
class SingleScanCoordinate:
    key: ClassVar[str] = "MustBeOverridden"


@dataclass
class CartesianScanCoordinate(SingleScanCoordinate):
    """
    Small helper class for data inside a cartesian coordinate in the PESScan task.

    Multiple cartesian scan coordinates can be combined into a single PESScan scan coordinate.
    """

    key: ClassVar[str] = "Coordinate"

    atom: int  # first atom has index 1
    coordinate: Literal["x", "y", "z"]
    start: float  # starting coordinate in angstrom
    end: float  # final coordinate in angstrom

    def __str__(self) -> str:
        """Returns a string in the AMS input format"""
        return f"{self.atom} {self.coordinate} {self.start:.4f} {self.end:.4f}"


@dataclass
class CellVolumeScalingRangeScanCoordinate(SingleScanCoordinate):
    """
    Small helper class for data inside a cell volume scaling range coordinate in the PESScan task.
    """

    key: ClassVar[str] = "CellVolumeScalingRange"

    start: float  # starting coordinate in angstrom
    end: float  # final coordinate in angstrom

    def __str__(self) -> str:
        """Returns a string in the AMS input format"""
        return f"{self.start} {self.end}"


@dataclass
class DistanceScanCoordinate(SingleScanCoordinate):
    """
    Small helper class for data inside a distance coordinate in the PESScan task.
    """

    key: ClassVar[str] = "Distance"

    atom1: int  # first atom has index 1
    atom2: int  # first atom has index 1
    start: float  # starting coordinate in angstrom
    end: float  # final coordinate in angstrom

    def __str__(self) -> str:
        """Returns a string in the AMS input format"""
        return f"{self.atom1} {self.atom2} {self.start:.4f} {self.end:.4f}"


def scan_coordinate_list_to_settings(scan_coordinates: Sequence[SingleScanCoordinate]) -> plams.Settings:
    """
    Return value is not at the top level.

    Example: s.input.ams.PESScan.ScanCoordinate[0] = scan_coordinate_list_to_settings([sc1, sc2])
    """
    s = plams.Settings()
    for x in scan_coordinates:
        if x.key not in s:
            s[x.key] = []
        s[x.key].append(str(x))

    return s


def get_surface_diffusion_scan_coordinates(
    slab: plams.Molecule,
    atom_index: int,
) -> List[CartesianScanCoordinate]:
    """Cause the atom with index ``atom_index`` (1-based) to diffuse to the top right corner of the unit cell.

    :param slab: Slab including adsorbate
    :type slab: plams.Molecule
    :param atom_index: One-based atom index, defaults to None
    :type atom_index: Optional[int], optional
    :return: List of CartesianScanCoordinate that can be used for PES Scans
    :rtype: List[CartesianScanCoordinate]
    """
    orig_x, orig_y = slab[atom_index].coords[0], slab[atom_index].coords[1]
    lattice = np.array(slab.lattice)
    target_xy = np.round(lattice[0, :2] + lattice[1, :2], decimals=4)
    target_x, target_y = target_xy
    print(
        f"Atom {atom_index} will diffuse from "
        f"(x, y) = {orig_x}, {orig_y} to {target_x}, {target_y} "
        "with the z coordinate optimized"
    )
    return [
        CartesianScanCoordinate(atom=atom_index, coordinate="x", start=orig_x, end=target_x),
        CartesianScanCoordinate(atom=atom_index, coordinate="y", start=orig_y, end=target_y),
    ]


def get_bulk_diffusion_scan_coordinates(
    slab: plams.Molecule, atom_index: int, delta_z: float = 2.0
) -> List[CartesianScanCoordinate]:
    """Cause the atom with index ``atom_index`` (1-based) to diffuse through the slab.

    :param slab: _description_
    :type slab: plams.Molecule
    :param atom_index: _description_
    :type atom_index: int
    :return: _description_
    :rtype: List[CartesianScanCoordinate]
    """
    target_z = np.min(slab.as_array()[:, 2]) - delta_z
    orig_z = slab[atom_index].coords[2]
    print(
        f"Atom {atom_index} will diffuse from "
        f"z = {orig_z:.4f} to {target_z:.4f} "
        "with the x and y coordinates optimized"
    )
    return [CartesianScanCoordinate(atom=atom_index, coordinate="z", start=orig_z, end=target_z)]


def get_surface_bond_scan_coordinates(
    slab: plams.Molecule, atom_index: int, start: Optional[float] = None, end: float = 1.2
) -> List[DistanceScanCoordinate]:
    """Cause the atom with index ``atom_index`` (1-based)
    to move towards its nearest neighbor until the distance is ``target_length.

    start: float
        If None will use the current distance

    end: float
        Target distance (angstrom)
    """

    ase_atoms = plams.toASE(slab)
    distance_matrix = ase_atoms.get_all_distances(mic=True)
    row = distance_matrix[atom_index - 1, :]
    row[atom_index - 1] = 1e10
    min_d = np.min(row)
    min_i = int(np.argmin(row) + 1)

    start = start or min_d

    return [DistanceScanCoordinate(atom1=atom_index, atom2=min_i, start=start, end=end)]


########
## Plotting functions
########


def plot_pesscan(job: plams.AMSJob, title: Optional[str] = None, ax=None) -> plt.Axes:
    """Plots a PESScan finished PESScan job. If multiple scan coordinates only uses the first one on the x axis."""
    if ax is None:
        fig, ax = plt.subplots()

    r = job.results.get_pesscan_results()

    ax.plot(r["RaveledPESCoords"][0], r["PES"])
    ax.set_xlabel(f"{r['RaveledScanCoords'][0]} ({r['RaveledUnits'][0]})")
    ax.set_ylabel("Energy (Ha)")
    ax.ticklabel_format(useOffset=False)
    ax.set_title(title or str(job.name))

    return ax


#######
## Check that correct versions of packages are installed
#######


def run_amspackages_check(package: str) -> subprocess.CompletedProcess:
    x = subprocess.run(
        ["sh", os.path.expandvars("$AMSBIN/amspackages"), "-v", "check", package], stdout=subprocess.PIPE, text=True
    )
    return x


def get_qe_version_and_build() -> Tuple[Union[str, None], Union[int, None]]:
    x = run_amspackages_check("qe")
    print(x.stdout.strip())
    if x.returncode != 0:
        return None, None

    try:
        version_number = x.stdout.split("v[")[1].split("]")[0]
        build_number = int(x.stdout.split("build:")[1].split()[0])
    except (KeyError, IndexError, TypeError):
        return None, None

    return version_number, build_number


def check_qe_installation():
    if TESTING_MODE:
        return True

    min_build = 115
    msg = f"QE must be at least version 7.1, build {min_build}. Install or update through the AMS package manager."

    version_number, build_number = get_qe_version_and_build()

    assert version_number is not None, msg
    assert build_number is not None, msg

    assert version_number >= "7.1", msg

    if version_number == "7.1":
        assert build_number >= min_build, msg


def check_m3gnet_installation():
    x = run_amspackages_check("m3gnet")
    print(x.stdout.strip())
    assert x.returncode == 0, f"m3gnet is not installed. Install it through the AMS package manager."


def get_ams_version() -> str:
    return importlib.metadata.version("scm")


def check_ams_installation(min_version="2024.102"):
    ams_version = get_ams_version()
    print(f"Current AMS version: {ams_version}")
    assert ams_version >= min_version, f"AMS version must be at least {min_version}"


def check_installation(ref_dir: Optional[Union[Path, str]] = None):
    check_ams_installation()
    check_m3gnet_installation()
    check_qe_installation()
    if ref_dir:
        assert Path(ref_dir).exists(), f"{ref_dir} must exist in the current working directory."