#!/usr/bin/env python3

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# RMG - Reaction Mechanism Generator                                          #
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"""
This module contains unit tests of the :mod:`arkane.input` module.
"""

import os
import unittest

import rmgpy
from rmgpy.exceptions import InputError
from rmgpy.kinetics.tunneling import Eckart
from rmgpy.pdep.collision import SingleExponentialDown
from rmgpy.statmech.rotation import NonlinearRotor
from rmgpy.statmech.translation import IdealGasTranslation
from rmgpy.statmech.vibration import HarmonicOscillator
from rmgpy.thermo.nasa import NASAPolynomial, NASA
from rmgpy.transport import TransportData

from arkane.input import species, transitionState, reaction, SMILES, load_input_file, process_model_chemistry
from arkane.modelchem import LevelOfTheory, CompositeLevelOfTheory

################################################################################


class InputTest(unittest.TestCase):
    """
    Contains unit tests for the Arkane input module
    """

    def test_species(self):
        """
        Test loading a species from input file-like kew word arguments
        """
        label0 = 'CH2O'
        kwargs = {'E0': (28.69, 'kcal/mol'),
                  'structure': SMILES('C=O'),
                  'collisionModel': TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
                  'energyTransferModel': SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
                  'spinMultiplicity': 1,
                  'opticalIsomers': 1,
                  'modes': [HarmonicOscillator(frequencies=([1180, 1261, 1529, 1764, 2931, 2999], 'cm^-1')),
                            NonlinearRotor(rotationalConstant=([1.15498821005263, 1.3156969584727, 9.45570474524524],
                                                               "cm^-1"), symmetry=2, quantum=False),
                            IdealGasTranslation(mass=(30.0106, "g/mol")),
                            ]}

        spc0 = species(label0, **kwargs)
        self.assertEqual(spc0.label, 'CH2O')
        self.assertEqual(spc0.smiles, 'C=O')
        self.assertAlmostEqual(spc0.conformer.E0.value_si, 120038.96)
        self.assertEqual(spc0.conformer.spin_multiplicity, 1)
        self.assertEqual(spc0.conformer.optical_isomers, 1)
        self.assertEqual(len(spc0.conformer.modes), 3)
        self.assertIsInstance(spc0.transport_data, TransportData)
        self.assertIsInstance(spc0.energy_transfer_model, SingleExponentialDown)

    def test_species_atomic_nasa_polynomial(self):
        """
        Test loading a atom with NASA polynomials
        """
        label0 = "H(1)"
        kwargs = {"structure": SMILES('[H]'),
                  "thermo": NASA(polynomials=[
                      NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683], Tmin=(200, 'K'), Tmax=(1000, 'K')),
                      NASAPolynomial(coeffs=[2.5, 0, 0, 0, 0, 25473.7, -0.446683], Tmin=(1000, 'K'), Tmax=(6000, 'K'))],
                      Tmin=(200, 'K'), Tmax=(6000, 'K'), comment="""Thermo library: FFCM1(-)"""),
                  "energyTransferModel": SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'), T0=(300, 'K'), n=0.85)}
        spc0 = species(label0, **kwargs)
        self.assertEqual(spc0.label, label0)
        self.assertEqual(spc0.smiles, '[H]')
        self.assertTrue(spc0.has_statmech())
        self.assertEqual(spc0.thermo, kwargs['thermo'])

    def test_species_polyatomic_nasa_polynomial(self):
        """
        Test loading a species with NASA polynomials
        """
        label0 = "benzyl"
        kwargs = {"structure": SMILES('[c]1ccccc1'),
                  "thermo": NASA(polynomials=[NASAPolynomial(
                      coeffs=[2.78632, 0.00784632, 7.97887e-05, -1.11617e-07, 4.39429e-11, 39695, 11.5114],
                      Tmin=(100, 'K'), Tmax=(943.73, 'K')),
                      NASAPolynomial(
                          coeffs=[13.2455, 0.0115667, -2.49996e-06, 4.66496e-10, -4.12376e-14,
                                  35581.1, -49.6793], Tmin=(943.73, 'K'), Tmax=(5000, 'K'))],
                      Tmin=(100, 'K'), Tmax=(5000, 'K'),
                      comment="""Thermo library: Fulvene_H + radical(CbJ)"""),
                  "energyTransferModel": SingleExponentialDown(alpha0=(3.5886, 'kJ/mol'), T0=(300, 'K'), n=0.85)}
        spc0 = species(label0, **kwargs)
        self.assertEqual(spc0.label, label0)
        self.assertTrue(spc0.has_statmech())
        self.assertEqual(spc0.thermo, kwargs['thermo'])

    def test_transition_state(self):
        """
        Test loading a transition state from input file-like kew word arguments
        """
        label0 = 'TS1'
        kwargs = {'E0': (39.95, 'kcal/mol'),
                  'spinMultiplicity': 2,
                  'opticalIsomers': 1,
                  'frequency': (-1934, 'cm^-1'),
                  'modes': [HarmonicOscillator(frequencies=([792, 987, 1136, 1142, 1482, 2441, 3096, 3183], 'cm^-1')),
                            NonlinearRotor(rotationalConstant=([0.928, 0.962, 5.807], "cm^-1"), symmetry=1,
                                           quantum=False),
                            IdealGasTranslation(mass=(31.01843, "g/mol"))]}

        ts0 = transitionState(label0, **kwargs)
        self.assertEqual(ts0.label, 'TS1')
        self.assertAlmostEqual(ts0.conformer.E0.value_si, 167150.8)
        self.assertEqual(ts0.conformer.spin_multiplicity, 2)
        self.assertEqual(ts0.conformer.optical_isomers, 1)
        self.assertEqual(ts0.frequency.value_si, -1934.0)
        self.assertEqual(len(ts0.conformer.modes), 3)

    def test_reaction(self):
        """
        Test loading a reaction from input file-like kew word arguments
        """

        species(
            label='methoxy',
            structure=SMILES('C[O]'),
            E0=(9.44, 'kcal/mol'),
            modes=[
                HarmonicOscillator(frequencies=([758, 960, 1106, 1393, 1403, 1518, 2940, 3019, 3065], 'cm^-1')),
                NonlinearRotor(rotationalConstant=([0.916, 0.921, 5.251], "cm^-1"), symmetry=3, quantum=False),
                IdealGasTranslation(mass=(31.01843, "g/mol"))],
            spinMultiplicity=2,
            opticalIsomers=1,
            molecularWeight=(31.01843, 'amu'),
            collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
            energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95))

        species(
            label='formaldehyde',
            E0=(28.69, 'kcal/mol'),
            molecularWeight=(30.0106, "g/mol"),
            collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
            energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
            spinMultiplicity=1,
            opticalIsomers=1,
            modes=[HarmonicOscillator(frequencies=([1180, 1261, 1529, 1764, 2931, 2999], 'cm^-1')),
                   NonlinearRotor(rotationalConstant=([1.15498821005263, 1.3156969584727, 9.45570474524524], "cm^-1"),
                                  symmetry=2, quantum=False),
                   IdealGasTranslation(mass=(30.0106, "g/mol"))])

        species(
            label='H',
            E0=(0.000, 'kcal/mol'),
            molecularWeight=(1.00783, "g/mol"),
            collisionModel=TransportData(sigma=(3.69e-10, 'm'), epsilon=(4.0, 'kJ/mol')),
            energyTransferModel=SingleExponentialDown(alpha0=(0.956, 'kJ/mol'), T0=(300, 'K'), n=0.95),
            modes=[IdealGasTranslation(mass=(1.00783, "g/mol"))],
            spinMultiplicity=2,
            opticalIsomers=1)

        transitionState(
            label='TS3',
            E0=(34.1, 'kcal/mol'),
            spinMultiplicity=2,
            opticalIsomers=1,
            frequency=(-967, 'cm^-1'),
            modes=[HarmonicOscillator(frequencies=([466, 581, 1169, 1242, 1499, 1659, 2933, 3000], 'cm^-1')),
                   NonlinearRotor(rotationalConstant=([0.970, 1.029, 3.717], "cm^-1"), symmetry=1, quantum=False),
                   IdealGasTranslation(mass=(31.01843, "g/mol"))])

        reactants = ['formaldehyde', 'H']
        products = ['methoxy']
        tunneling = 'Eckart'

        rxn = reaction('CH2O+H=Methoxy', reactants, products, 'TS3', tunneling=tunneling)
        self.assertEqual(rxn.label, 'CH2O+H=Methoxy')
        self.assertEqual(len(rxn.reactants), 2)
        self.assertEqual(len(rxn.products), 1)
        self.assertAlmostEqual(rxn.reactants[0].conformer.E0.value_si, 0)
        self.assertAlmostEqual(rxn.reactants[1].conformer.E0.value_si, 120038.96)
        self.assertAlmostEqual(rxn.products[0].conformer.E0.value_si, 39496.96)
        self.assertAlmostEqual(rxn.transition_state.conformer.E0.value_si, 142674.4)
        self.assertAlmostEqual(rxn.transition_state.frequency.value_si, -967.0)
        self.assertIsInstance(rxn.transition_state.tunneling, Eckart)

    def test_load_input_file(self):
        """Test loading an Arkane input file"""
        path = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)), 'examples', 'arkane', 'networks',
                            'acetyl+O2', 'input.py')
        job_list, reaction_dict, species_dict, transition_state_dict, network_dict, model_chemistry \
            = load_input_file(path)

        self.assertEqual(len(job_list), 1)

        self.assertEqual(len(reaction_dict), 5)
        self.assertTrue('entrance1' in reaction_dict)
        self.assertTrue('exit2' in reaction_dict)

        self.assertEqual(len(species_dict), 9)
        self.assertTrue('acetyl' in species_dict)
        self.assertTrue('hydroperoxyl' in species_dict)

        self.assertEqual(len(transition_state_dict), 5)
        self.assertTrue('entrance1' in transition_state_dict)
        self.assertTrue('isom1' in transition_state_dict)

        self.assertEqual(len(network_dict), 1)
        self.assertTrue('acetyl + O2' in network_dict)

        self.assertIsNone(model_chemistry)

    def test_process_model_chemistry(self):
        """
        Test processing the model chemistry to derive the sp and freq levels
        """
        mc = 'ccsd(t)-f12a/aug-cc-pvtz//b3lyp/6-311++g(3df,3pd)'
        lot = process_model_chemistry(mc)
        self.assertIsInstance(lot, CompositeLevelOfTheory)
        self.assertEqual(lot.energy, LevelOfTheory('ccsd(t)-f12a', 'aug-cc-pvtz'))
        self.assertEqual(lot.freq, LevelOfTheory('b3lyp', '6-311++g(3df,3pd)'))

        mc = 'b3lyp-d3/def2-tzvp'
        lot = process_model_chemistry(mc)
        self.assertIsInstance(lot, LevelOfTheory)
        self.assertEqual(lot, LevelOfTheory('b3lyp-d3', 'def2-tzvp'))

        mc = 'cbs-qb3'
        lot = process_model_chemistry(mc)
        self.assertIsInstance(lot, LevelOfTheory)
        self.assertEqual(lot, LevelOfTheory('cbs-qb3'))

        mc = LevelOfTheory('test')
        lot = process_model_chemistry(mc)
        self.assertIs(mc, lot)

        with self.assertRaises(InputError):
            process_model_chemistry('CCSD(T)-F12a/aug-cc-pVTZ//CCSD(T)-F12a/aug-cc-pVTZ//B3LYP/6-311++G(3df,3pd)')

################################################################################


if __name__ == '__main__':
    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
