def rattle_calc(self, atoms, calc):
try:
os.remove('checkpoints.db')
except OSError:
pass
orig_atoms = atoms.copy()
# first do a couple of calculations
np.random.seed(0)
atoms.rattle()
cp_calc_1 = CheckpointCalculator(calc)
atoms.set_calculator(cp_calc_1)
e11 = atoms.get_potential_energy()
f11 = atoms.get_forces()
atoms.rattle()
e12 = atoms.get_potential_energy()
f12 = atoms.get_forces()
# then re-read them from checkpoint file
atoms = orig_atoms
np.random.seed(0)
atoms.rattle()
cp_calc_2 = CheckpointCalculator(calc)
atoms.set_calculator(cp_calc_2)
e21 = atoms.get_potential_energy()
f21 = atoms.get_forces()
atoms.rattle()
e22 = atoms.get_potential_energy()
f22 = atoms.get_forces()
self.assertAlmostEqual(e11, e21)
self.assertAlmostEqual(e12, e22)
self.assert_(np.abs(f11 - f21).max() < 1e-5)
self.assert_(np.abs(f12 - f22).max() < 1e-5)
def rattle_calc(atoms, calc):
try:
os.remove('checkpoints.db')
except OSError:
pass
orig_atoms = atoms.copy()
# first do a couple of calculations
np.random.seed(0)
atoms.rattle()
cp_calc_1 = CheckpointCalculator(calc)
atoms.calc = cp_calc_1
e11 = atoms.get_potential_energy()
f11 = atoms.get_forces()
atoms.rattle()
e12 = atoms.get_potential_energy()
f12 = atoms.get_forces()
# then re-read them from checkpoint file
atoms = orig_atoms
np.random.seed(0)
atoms.rattle()
cp_calc_2 = CheckpointCalculator(calc)
atoms.calc = cp_calc_2
e21 = atoms.get_potential_energy()
f21 = atoms.get_forces()
atoms.rattle()
e22 = atoms.get_potential_energy()
f22 = atoms.get_forces()
assert e11 == e21
assert e12 == e22
assert(np.abs(f11 - f21).max() < 1e-5)
assert(np.abs(f12 - f22).max() < 1e-5)
sys.stdout.write(open(test_file).read())
print('=' * 60)
import model # import and run the current model
# adapt model to test, e.g. to set output directory name
if hasattr(model, 'start'):
model.start(test_name)
# create a checkpoint file for this specific (model, test) combination
if ('GAP_TESTER_CHECKPOINT' in os.environ
and os.environ['GAP_TESTER_CHECKPOINT'] != "") or not hasattr(
model, 'no_checkpoint') or not model.no_checkpoint:
checkpoint_file = run_root + '.db'
print('Using checkpoint file', checkpoint_file)
model.calculator = CheckpointCalculator(model.calculator,
db=checkpoint_file)
import test # import and run the current test
print('=' * 60)
print('Property calculation output:')
print('')
# serialise results in machine readable JSON format
json_file = open(json_file_name, 'w')
json.dump(test.properties, json_file)
json_file.close()
print('')
print('Summary of computed properties:')
print(test.properties)