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 test_read_lattice_vecors(self):
test_in = 'OUTCAR.21'
parser = Parser(test_in)
test_lattice = np.array([
[10.546640000, 0.000000000, 0.000000000],
[0.000000000, 10.546640000, 0.000000000],
[0.000000000, 0.000000000, 10.546640000]
])
self.assertTrue(
np.array_equal(parser.find_lattice_vectors(), test_lattice), 'lattice vectors do not match'
)
def test_warn_not_cubic(self):
import sys
from io import StringIO
warn_message = '*************WARNING*************\nThe given lattice vectors\n' \
'[[10. 0. 0. ]\n [ 0. 10.54664 0. ]\n' \
' [ 0. 0. 10.54664]]\n' \
'do not constitute a simple basic lattice.\n' \
'The programm wont work correctly'
wrong_parser = Parser('test_data/wrong_data_outcar.21')
saved_stdout = sys.stdout
try:
out = StringIO()
sys.stdout = out
wrong_parser.find_lattice_vectors()
output = out.getvalue().strip()
self.assertEqual(output, warn_message, 'Warning message is not correct')
finally:
sys.stdout = saved_stdout
def load_data(u_conf: dict, stepsize=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)
'''
if stepsize == 0:
stepsize = int(input("Stepsize for prediction? (integer): -> "))
# 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, forces) for (energy, position, forces) in parser
.build_configurations(stepsize)
]
return (len(configurations), parser.find_ion_nr(), lattice_vectors, configurations)
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_file_opening(self):
correct_path = 'OUTCAR.21'
correct_parser = Parser(correct_path)
self.assertEqual(correct_parser.filepath, correct_path)
self.assertIsNotNone(correct_parser.outcar_content)
def test_ion_nrs(self):
test_in = 'OUTCAR.21'
parser = Parser(test_in)
nr_ions = parser.find_ion_nr()
self.assertIsInstance(nr_ions, int, 'ions should have type int')
self.assertEqual(nr_ions, 64, f'nr of ions should be 64, is {nr_ions}')
def test_file_not_opening(self):
wrong_path = 'mydata.21'
with self.assertRaises(ValueError):
Parser(wrong_path)