def test_read_pos_force_energy(self):
test_in = 'OUTCAR.21'
g_pos = np.array([2.26725, 2.36995, 0.06367])
g_force = np.array([-0.171492, -0.290427, -1.773642])
g_energy = -306.41169589
parser = Parser(test_in)
self.assertIsNotNone(parser.build_configurations(1000), 'does not build iterator')
nr_of_configs = len(list(parser.build_configurations(1000)))
self.assertEqual(nr_of_configs, 1, 'does not return at least one config')
nr_of_configs = len(list(parser.build_configurations(1)))
self.assertEqual(nr_of_configs, 1000, 'does not return the correct number of configs')
for energy, position, force in parser.build_configurations(1000):
self.assertTrue(np.array_equal(position[0], g_pos), 'returns wrong position')
self.assertTrue(np.array_equal(force[0], g_force), 'returns wrong force')
self.assertEqual(energy, g_energy, 'returns wrong energy')
def test_offset(self):
test_in = 'OUTCAR.21'
ref_pos = np.array([2.23782, 2.37638, 0.06997])
ref_force = np.array([-0.130492, -0.307476, -1.951215])
ref_energy = -306.56723878
parser = Parser(test_in)
for energy, pos, force in parser.build_configurations(10000,1):
self.assertEqual(energy, ref_energy)
self.assertTrue(np.array_equal(ref_pos, pos[0]))
self.assertTrue(np.array_equal(ref_force, force[0]))
def load_data(u_conf: dict, offset=0) -> (int, int, np.array, list):
'''
Loads the data from the file specified in u_conf and returns the parameters of the
simulation as (N_conf, N_ion, lattice vectors, list of configurations).
'''
# load parser and save nr of ions and lattice vectors
parser = Parser(u_conf['file_in'])
lattice_vectors = parser.find_lattice_vectors()
lat_consts = np.diag(lattice_vectors.dot(lattice_vectors.T))
# check if lattice constant is bigger than 2 rcut
if any(np.greater(2 * u_conf["cutoff"], lat_consts)):
raise ValueError(
'Cutoff cannot be bigger than half the lattice constants')
# build the configurations from the parser
configurations = [
Configuration(position, energy, force)
for (energy, position,
force) in parser.build_configurations(u_conf['stepsize'], offset)
]
return (len(configurations), parser.find_ion_nr(), lattice_vectors,
configurations)