run_tests.py

"""
This is a module for unit testing the CP2K parser. The unit tests are run with
a custom backend that outputs the results directly into native python object for
easier and faster analysis.
"""
import os
import unittest
import logging
import numpy as np
from cp2kparser import CP2KParser
from nomadtoolkit import Analyzer
from nomadcore.unit_conversion.unit_conversion import convert_unit


#===============================================================================
def get_results(folder, metainfo_to_keep=None):
    """Get the given result from the calculation in the given folder by using
    the Analyzer in the nomadtoolkit package. Tries to optimize the parsing by
    giving the metainfo_to_keep argument.

    Args:
        folder: The folder relative to the directory of this script where the
        parsed calculation resides.
        metaname: The quantity to extract.
    """
    dirname = os.path.dirname(__file__)
    folder = os.path.join(dirname, folder)
    parser = CP2KParser(folder, metainfo_to_keep)
    analyzer = Analyzer(parser)
    results = analyzer.parse()
    return results


#===============================================================================
def get_result(folder, metaname):
    results = get_results(folder, metaname)
    result = results[metaname]
    return result


#===============================================================================
class TestXCFunctional(unittest.TestCase):
    """Tests that the XC functionals can be properly parsed.
    """

    def test_pade(self):
        xc = get_result("XC_functional/pade", "XC_functional")
        self.assertEqual(xc, "LDA_XC_TETER93")

    def test_lda(self):
        xc = get_result("XC_functional/lda", "XC_functional")
        self.assertEqual(xc, "LDA_XC_TETER93")

    def test_becke88(self):
        xc = get_result("XC_functional/becke88", "XC_functional")
        self.assertEqual(xc, "GGA_X_B88")

    def test_blyp(self):
        xc = get_result("XC_functional/blyp", "XC_functional")
        self.assertEqual(xc, "GGA_C_LYP_GGA_X_B88")


#===============================================================================
class TestEnergyForce(unittest.TestCase):
    """Tests for a CP2K calculation with RUN_TYPE ENERGY_FORCE.
    """

    def setUp(self):
        self.results = get_results("energy_force", "section_run")

    def test_energy_total_scf_iteration(self):
        energy_total = self.results["energy_total_scf_iteration"]
        expected_result = convert_unit(np.array(-32.2320848878), "hartree")
        self.assertTrue(np.array_equal(energy_total[0], expected_result))

    def test_energy_total(self):
        energy_total = self.results["energy_total"]
        expected_result = convert_unit(np.array(-31.297885372811063), "hartree")
        self.assertTrue(np.array_equal(energy_total, expected_result))

    def test_atom_forces(self):
        atomic_forces = self.results["atom_forces"]
        expected_result = convert_unit(
            np.array([
                [0.00000000, 0.00000000, 0.00000000],
                [0.00000000, 0.00000001, 0.00000001],
                [0.00000001, 0.00000001, 0.00000000],
                [0.00000001, 0.00000000, 0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
            ]),
            "forceAu"
        )
        self.assertTrue(np.array_equal(atomic_forces, expected_result))

    def test_atom_label(self):
        atom_labels = self.results["atom_label"]
        expected_labels = np.array(8*["Si"])
        self.assertTrue(np.array_equal(atom_labels, expected_labels))

    def test_simulation_cell(self):
        cell = self.results["simulation_cell"]
        n_vectors = cell.shape[0]
        n_dim = cell.shape[1]
        self.assertEqual(n_vectors, 3)
        self.assertEqual(n_dim, 3)
        expected_cell = convert_unit(np.array([[5.431, 0, 0], [0, 5.431, 0], [0, 0, 5.431]]), "angstrom")
        self.assertTrue(np.array_equal(cell, expected_cell))

    def test_number_of_atoms(self):
        n_atoms = self.results["number_of_atoms"]
        self.assertEqual(n_atoms, 8)

    def test_atom_position(self):
        atom_position = self.results["atom_position"]
        expected_position = convert_unit(np.array([4.073023, 4.073023, 1.357674]), "angstrom")
        self.assertTrue(np.array_equal(atom_position[-1, :], expected_position))

    def test_cp2k_filenames(self):
        input_filename = self.results["cp2k_input_filename"]
        expected_input = "si_bulk8.inp"
        self.assertTrue(input_filename, expected_input)

        bs_filename = self.results["cp2k_basis_set_filename"]
        expected_bs = "../BASIS_SET"
        self.assertEqual(bs_filename, expected_bs)

        geminal_filename = self.results["cp2k_geminal_filename"]
        expected_geminal = "BASIS_GEMINAL"
        self.assertEqual(geminal_filename, expected_geminal)

        potential_filename = self.results["cp2k_potential_filename"]
        expected_potential = "../GTH_POTENTIALS"
        self.assertEqual(potential_filename, expected_potential)

        mm_potential_filename = self.results["cp2k_mm_potential_filename"]
        expected_mm_potential = "MM_POTENTIAL"
        self.assertEqual(mm_potential_filename, expected_mm_potential)

        coordinate_filename = self.results["cp2k_coordinate_filename"]
        expected_coordinate = "__STD_INPUT__"
        self.assertEqual(coordinate_filename, expected_coordinate)

#===============================================================================
if __name__ == '__main__':
    pass
    logger = logging.getLogger("cp2kparser")
    logger.setLevel(logging.ERROR)

    suites = []
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
    alltests = unittest.TestSuite(suites)
    unittest.TextTestRunner(verbosity=0).run(alltests)