
from glob import glob
import math
import os
import shutil
import sys
import subprocess
import time

from datetime import datetime
from uuid import uuid4
from string import Template
from pathlib import Path

from htsohm.simulation.raspa import write_mol_file, write_mixing_rules
from htsohm.simulation.raspa import write_pseudo_atoms, write_force_field
from htsohm.simulation.templates import load_and_subs_template
from htsohm.db import VoidFraction
from htsohm.void_fraction import calculate_void_fraction
from htsohm.slog import slog

def write_raspa_file(filename, material, simulation_config):
    """Writes RASPA input file for calculating helium void fraction.

    Args:
        filename (str): path to input file.
        material_id (str): uuid for material.

    Writes RASPA input-file.

    """

    # Load simulation parameters from config
    unit_cells = material.structure.minimum_unit_cells(simulation_config['cutoff'])
    values = {
            "Cutoff"                 : simulation_config['cutoff'],
            "NumberOfCycles"         : simulation_config["simulation_cycles"],
            "FrameworkName"          : material.uuid,
            "ExternalTemperature"    : simulation_config["temperature"],
            "MoleculeName"           : simulation_config["adsorbate"],
            "UnitCell"               : " ".join(map(str, unit_cells))}

    # Load template and replace values
    input_data = load_and_subs_template("input_file_templates/void_fraction.input", values)

    # Write simulation input-file
    with open(filename, "w") as raspa_input_file:
        raspa_input_file.write(input_data)

def write_output_files(material, simulation_config, output_dir):
    # Write simulation input-files
    # RASPA input-file
    filename = os.path.join(output_dir, "void_fraction.input")
    write_raspa_file(filename, material, simulation_config)
    # Pseudomaterial mol-file
    write_mol_file(material, output_dir)
    # Lennard-Jones parameters, force_field_mixing_rules.def
    write_mixing_rules(material.structure, output_dir)
    # Pseudoatom definitions, pseudo_atoms.def (placeholder values)
    write_pseudo_atoms(material.structure, output_dir)
    # Overwritten interactions, force_field.def (none overwritten by default)
    write_force_field(output_dir)

def parse_output(output_file, material, void_fraction):
    """Parse output file for void fraction data.

    Args:
        output_file (str): path to simulation output file.
        material: material that was simulated
        void_fraction: current void fraction object. This gets modified to include the result data.

    Returns:
        nothing
    """

    with open(output_file) as origin:
        for line in origin:
            if not "Average Widom Rosenbluth-weight:" in line:
                continue
            void_fraction.void_fraction = float(line.split()[4])


def run(material, simulation_config, config):
    """Runs void fraction simulation.

    Args:
        material (Material): material record.

    Returns:
        results (dict): void fraction simulation results.

    """
    output_dir = "output_{}_{}".format(material.uuid, uuid4())
    slog("Output directory : {}".format(output_dir))
    os.makedirs(output_dir, exist_ok=True)

    write_output_files(material, simulation_config, output_dir)

    # Run simulations
    slog("Probe            : {}".format(simulation_config["adsorbate"]))
    if "do_geo" in simulation_config:
        slog("Probe radius [geo]: {}".format(simulation_config["probe_radius"]))
    slog("Temperature      : {}".format(simulation_config["temperature"]))

    void_fraction = VoidFraction()
    void_fraction.adsorbate = simulation_config["adsorbate"]
    void_fraction.temperature = simulation_config["temperature"]

    if "do_raspa" in simulation_config and simulation_config["do_raspa"]:
        tbegin = time.perf_counter()
        process = subprocess.run(["simulate", "-i", "./void_fraction.input"], check=True, cwd=output_dir, capture_output=True, text=True)

        data_files = glob(os.path.join(output_dir, "Output", "System_0", "*.data"))
        if len(data_files) != 1:
            raise Exception("ERROR: There should only be one data file in the output directory for %s. Check code!" % output_dir)
        output_file = data_files[0]

        # Parse output
        parse_output(output_file, material, void_fraction)
        slog("RASPA void fraction simulation time: %5.2f seconds" % (time.perf_counter() - tbegin))
        slog("RASPA VOID FRACTION : {}".format(void_fraction.void_fraction))
        if material.parent:
            slog("(parent VOID FRACTION : {})".format(material.parent.void_fraction[0].void_fraction))


    # run geometric void fraction
    if "do_geo" in simulation_config and simulation_config["do_geo"]:
        tbegin = time.perf_counter()
        atoms = [(a.x * material.structure.a, a.y * material.structure.b, a.z * material.structure.c, a.atom_types.sigma) for a in material.structure.atom_sites]
        box = (material.structure.a, material.structure.b, material.structure.c)
        void_fraction.void_fraction_geo = calculate_void_fraction(atoms, box, probe_r=simulation_config["probe_radius"])
        slog("GEOMETRIC void fraction: %f" % void_fraction.void_fraction_geo)
        slog("GEOMETRIC void fraction simulation time: %5.2f   seconds" % (time.perf_counter() - tbegin))
    if "do_zeo" in simulation_config:
        pass
        # run zeo void fraction here

    material.void_fraction.append(void_fraction)

    if not config['keep_configs']:
        shutil.rmtree(output_dir, ignore_errors=True)
    sys.stdout.flush()


from glob import glob
import math
import os
import shutil
import sys
import subprocess
import time

from datetime import datetime
from uuid import uuid4
from string import Template
from pathlib import Path

from htsohm.simulation.raspa import write_mol_file, write_mixing_rules
from htsohm.simulation.raspa import write_pseudo_atoms, write_force_field
from htsohm.simulation.templates import load_and_subs_template
from htsohm.db import VoidFraction
from htsohm.void_fraction import calculate_void_fraction
from htsohm.slog import slog

def write_raspa_file(filename, material, simulation_config):
    """Writes RASPA input file for calculating helium void fraction.

    Args:
        filename (str): path to input file.
        material_id (str): uuid for material.

    Writes RASPA input-file.

    """

    # Load simulation parameters from config
    unit_cells = material.structure.minimum_unit_cells(simulation_config['cutoff'])
    values = {
            "Cutoff"                 : simulation_config['cutoff'],
            "NumberOfCycles"         : simulation_config["simulation_cycles"],
            "FrameworkName"          : material.uuid,
            "ExternalTemperature"    : simulation_config["temperature"],
            "MoleculeName"           : simulation_config["adsorbate"],
            "UnitCell"               : " ".join(map(str, unit_cells))}

    # Load template and replace values
    input_data = load_and_subs_template("input_file_templates/void_fraction.input", values)

    # Write simulation input-file
    with open(filename, "w") as raspa_input_file:
        raspa_input_file.write(input_data)

def write_output_files(material, simulation_config, output_dir):
    # Write simulation input-files
    # RASPA input-file
    filename = os.path.join(output_dir, "void_fraction.input")
    write_raspa_file(filename, material, simulation_config)
    # Pseudomaterial mol-file
    write_mol_file(material, output_dir)
    # Lennard-Jones parameters, force_field_mixing_rules.def
    write_mixing_rules(material.structure, output_dir)
    # Pseudoatom definitions, pseudo_atoms.def (placeholder values)
    write_pseudo_atoms(material.structure, output_dir)
    # Overwritten interactions, force_field.def (none overwritten by default)
    write_force_field(output_dir)

def parse_output(output_file, material, void_fraction):
    """Parse output file for void fraction data.

    Args:
        output_file (str): path to simulation output file.
        material: material that was simulated
        void_fraction: current void fraction object. This gets modified to include the result data.

    Returns:
        nothing
    """

    with open(output_file) as origin:
        for line in origin:
            if not "Average Widom Rosenbluth-weight:" in line:
                continue
            void_fraction.void_fraction = float(line.split()[4])


def run(material, simulation_config, config):
    """Runs void fraction simulation.

    Args:
        material (Material): material record.

    Returns:
        results (dict): void fraction simulation results.

    """
    output_dir = "output_{}_{}".format(material.uuid, uuid4())
    slog("Output directory : {}".format(output_dir))
    os.makedirs(output_dir, exist_ok=True)

    write_output_files(material, simulation_config, output_dir)

    # Run simulations
    slog("Probe            : {}".format(simulation_config["adsorbate"]))
    if "do_geo" in simulation_config:
        slog("Probe radius [geo]: {}".format(simulation_config["probe_radius"]))
    slog("Temperature      : {}".format(simulation_config["temperature"]))

    void_fraction = VoidFraction()
    void_fraction.adsorbate = simulation_config["adsorbate"]
    void_fraction.temperature = simulation_config["temperature"]

    if "do_raspa" in simulation_config and simulation_config["do_raspa"]:
        tbegin = time.perf_counter()
        process = subprocess.run(["simulate", "-i", "./void_fraction.input"], check=True, cwd=output_dir, capture_output=True, text=True)

        data_files = glob(os.path.join(output_dir, "Output", "System_0", "*.data"))
        if len(data_files) != 1:
            raise Exception("ERROR: There should only be one data file in the output directory for %s. Check code!" % output_dir)
        output_file = data_files[0]

        # Parse output
        parse_output(output_file, material, void_fraction)
        slog("RASPA void fraction simulation time: %5.2f seconds" % (time.perf_counter() - tbegin))
        slog("RASPA VOID FRACTION : {}".format(void_fraction.void_fraction))
        if material.parent:
            slog("(parent VOID FRACTION : {})".format(material.parent.void_fraction[0].void_fraction))


    # run geometric void fraction
    if "do_geo" in simulation_config and simulation_config["do_geo"]:
        tbegin = time.perf_counter()
        atoms = [(a.x * material.structure.a, a.y * material.structure.b, a.z * material.structure.c, a.atom_types.sigma) for a in material.structure.atom_sites]
        box = (material.structure.a, material.structure.b, material.structure.c)
        void_fraction.void_fraction_geo = calculate_void_fraction(atoms, box, probe_r=simulation_config["probe_radius"])
        slog("GEOMETRIC void fraction: %f" % void_fraction.void_fraction_geo)
        slog("GEOMETRIC void fraction simulation time: %5.2f   seconds" % (time.perf_counter() - tbegin))
    if "do_zeo" in simulation_config:
        pass
        # run zeo void fraction here

    material.void_fraction.append(void_fraction)

    if not config['keep_configs']:
        shutil.rmtree(output_dir, ignore_errors=True)
    sys.stdout.flush()

Writes RASPA input file for calculating helium void fraction.      Args:         filename (str): path to input file.         material_id (str): uuid for material.      Writes RASPA input-file. # Load simulation parameters from config # Load template and replace values # Write simulation input-file # Write simulation input-files # RASPA input-file # Pseudomaterial mol-file # Lennard-Jones parameters, force_field_mixing_rules.def # Pseudoatom definitions, pseudo_atoms.def (placeholder values) # Overwritten interactions, force_field.def (none overwritten by default) Parse output file for void fraction data.      Args:         output_file (str): path to simulation output file.         material: material that was simulated         void_fraction: current void fraction object. This gets modified to include the result data.      Returns:         nothing Runs void fraction simulation.      Args:         material (Material): material record.      Returns:         results (dict): void fraction simulation results. # Run simulations # Parse output # run geometric void fraction # run zeo void fraction here