def test_dos_construction_from_frequencies(self):
""" Test that we can make sensible phonon DOS's and free
energy calculations from frequency and qpoint data, and that
it agrees with CASTEP's calculated values.
"""
fname = REAL_PATH + "data/castep_files/CuP-thermo-test.castep"
doc, _ = castep2dict(fname, db=False)
dos = VibrationalDOS(doc)
backup_eigs = np.copy(dos.eigs)
self.assertAlmostEqual(dos.zpe,
doc["thermo_zero_point_energy"] /
doc["num_atoms"],
places=4)
np.testing.assert_array_equal(
dos.eigs,
backup_eigs,
err_msg="Eigenvalues were changed by some function")
self.assertAlmostEqual(
dos.vibrational_free_energy(1000),
doc["thermo_free_energy"][1000.0] / doc["num_atoms"],
places=4,
)
np.testing.assert_array_equal(
dos.eigs,
backup_eigs,
err_msg="Eigenvalues were changed by some function")
self.assertEqual(dos.compute_free_energy(0.0), dos.zpe)
def test_failed_make_from_castep(self):
""" Tests that an error is raised when trying to create
a Spectral object from a castep file that contains no
spectral data.
"""
fname = REAL_PATH + "data/castep_files/KP-castep17.castep"
doc, s = castep2dict(fname, db=False)
with self.assertRaises(RuntimeError):
ElectronicDispersion(doc)
with self.assertRaises(RuntimeError):
ElectronicDispersion(**doc)
with self.assertRaises(RuntimeError):
ElectronicDOS(doc)
with self.assertRaises(RuntimeError):
ElectronicDOS(**doc)
with self.assertRaises(RuntimeError):
VibrationalDOS(doc)
with self.assertRaises(RuntimeError):
VibrationalDOS(**doc)
with self.assertRaises(RuntimeError):
VibrationalDispersion(doc)
with self.assertRaises(RuntimeError):
VibrationalDispersion(**doc)
def test_td_hull_plot(self):
from matador.hull.hull_temperature import TemperatureDependentHull
from matador.scrapers import castep2dict
cursor, s = castep2dict(REAL_PATH +
"data/castep_phonon_files/*.castep",
db=False)
td_hull = TemperatureDependentHull(cursor=cursor,
energy_key="total_energy_per_atom")
td_hull.plot_hull(plot_fname="td_hull", png=True)
self.assertTrue(os.path.isfile("td_hull.png"))
def test_doc2pmg(self):
from matador.scrapers import castep2dict
doc, s = castep2dict(REAL_PATH +
"data/castep_files/KP-castep17.castep",
as_model=True)
pmg_structure = doc.pmg_structure
self.assertEqual(pmg_structure.formula, "K7 P2")
np.testing.assert_array_almost_equal(pmg_structure.lattice.matrix,
doc.lattice_cart,
decimal=16)
for ind, site in enumerate(doc):
np.testing.assert_array_almost_equal(
site.coords, pmg_structure[ind].frac_coords, decimal=16)
self.assertEqual(site.species, pmg_structure[ind].species_string)
self.assertDictEqual(pmg_structure.info["matador"], doc._data)
def test_beef_hull_plot(self):
""" Test plotting BEEF hull. """
from matador.hull import EnsembleHull
from matador.scrapers import castep2dict
expected_file = "KP_beef_hull.svg"
cursor, s = castep2dict(REAL_PATH + "data/beef_files/*.castep",
db=False)
self.assertEqual(len(s), 0)
beef_hull = EnsembleHull(
cursor,
"_beef",
elements=["K", "P"],
num_samples=10,
energy_key="total_energy_per_atom",
parameter_key="thetas",
)
beef_hull.plot_hull(svg=True)
self.assertTrue(os.path.isfile(expected_file))
def test_doc2ase(self):
from matador.scrapers import castep2dict
doc, s = castep2dict(REAL_PATH +
"data/castep_files/KP-castep17.castep",
as_model=True)
ase_atoms = doc.ase_atoms
np.testing.assert_array_almost_equal(ase_atoms.cell.array,
doc.lattice_cart,
decimal=16)
np.testing.assert_array_almost_equal(doc.positions_frac,
ase_atoms.get_scaled_positions(),
decimal=12)
for ind, site in enumerate(doc):
np.testing.assert_array_almost_equal(site.coords_cartesian,
ase_atoms[ind].position,
decimal=12)
self.assertEqual(site.species, ase_atoms[ind].symbol)
self.assertDictEqual(ase_atoms.info["matador"], doc._data)
def get_equation_of_state(seed, plot=False):
""" Extract E(V) data from CASTEP files and perform
fits for the equation of state and bulk moduli.
Parameters:
seed (str/dict): filename or scraped dictionary to fit.
Keyword arguments:
plot (bool): plot the fitted EoS.
"""
if isinstance(seed, dict):
results = seed
else:
from matador.scrapers import castep2dict
results, success = castep2dict(seed, intermediates=True, db=False)
if not success:
raise RuntimeError(results)
volumes = []
energies = []
for snapshot in results['intermediates']:
volumes.append(snapshot['cell_volume'])
energies.append(snapshot['total_energy'])
volumes.append(results['cell_volume'])
energies.append(results['total_energy'])
volumes = np.asarray(volumes)
energies = np.asarray(energies)
if len(volumes) < 3:
raise RuntimeError('Seed {} does not contain enough energies vs volumes to fit a bulk modulus')
energies = energies[np.argsort(volumes)]
volumes = np.sort(volumes)
E_0 = np.min(energies)
V_0 = volumes[np.argmin(energies)]
types_of_fit = EquationOfState.__subclasses__()
results['eos'] = []
results['summary'] = []
probes_all = []
curves = []
labels = []
for eos_type in types_of_fit:
eos = eos_type(E_0, V_0)
eos.fit(volumes, energies)
results['summary'].append(eos_type.__name__ + '\n')
results['summary'].append('fitting parameters = {d[0]:.6f}, {d[1]:.6f}\n'.format(d=eos.fit_parameters))
results['summary'].append('rrrmsd = {:10.10f} %\n'.format(eos.rrmsd))
results['summary'].append('bulk modulus = {d[0]:.6f} +/- {d[1]:.6f} GPa\n'
.format(d=(eos.bulk_modulus, eos.bulk_modulus_err)))
results['summary'].append(80*'-' + '\n')
probes = np.linspace(min(volumes), max(volumes), num=100)
fitted_curve = eos.evaluate(probes, *eos.popt)
results['eos'].append(eos)
probes_all.append(probes)
curves.append(fitted_curve)
name = eos_type.__name__.replace('EOS', '')
label = '-'.join(re.findall('[A-Z][^A-Z]*', name))
label += " {eos.bulk_modulus:3.1f}±{eos.bulk_modulus_err:3.1f} GPa"
labels.append(label)
if plot:
try:
plot_volume_curve(probes_all, labels, curves, volumes, energies, seed)
except Exception:
print("There was a problem making the bulk modulus plot.")
return results