def test_magres(self):
for _f in glob.glob(REAL_PATH + "data/magres_workflow/*"):
shutil.copy(_f, ".")
cell_dict, _ = cell2dict("Si.cell", db=False)
param_dict, _ = param2dict("Si.param", db=False)
_ = ComputeTask(
res="Si2.res",
ncores=NCORES,
nnodes=None,
node=None,
cell_dict=cell_dict,
param_dict=param_dict,
verbosity=VERBOSITY,
compute_dir="tmpier_tst",
workflow_kwargs={"final_elec_energy_tol": 1e-9},
)
self.assertTrue(os.path.isfile("completed/Si2.check"))
self.assertTrue(os.path.isfile("completed/Si2.bands"))
self.assertTrue(os.path.isfile("completed/Si2.castep"))
self.assertTrue(os.path.isfile("completed/Si2.magres"))
self.assertTrue(os.path.isfile("completed/Si2.cell_magres"))
self.assertTrue(os.path.isfile("completed/Si2.param_magres"))
self.assertTrue(os.path.isfile("completed/Si2.cell_scf"))
self.assertTrue(os.path.isfile("completed/Si2.param_scf"))
param, s = param2dict("completed/Si2.param_scf")
self.assertTrue(s, msg="Failed to read param file")
self.assertEqual(param["elec_energy_tol"], 1e-12)
param, s = param2dict("completed/Si2.param_magres")
self.assertEqual(param["elec_energy_tol"], 1e-12)
self.assertTrue(s, msg="Failed to read param file")
magres, s = magres2dict("completed/Si2.magres")
self.assertTrue(s, msg="Failed to read magres file")
a = 3.866895
np.testing.assert_array_almost_equal(magres["lattice_abc"],
np.array([[a, a, a], [60, 60,
60]]),
decimal=3)
np.testing.assert_array_almost_equal(magres["chemical_shielding_isos"],
np.array([129.577, 129.577]),
decimal=2)
self.assertTrue(os.path.isfile("completed/Si2.cell"))
self.assertTrue(os.path.isfile("completed/Si2.res"))
def test_bulk_mod(self):
for _f in glob.glob(REAL_PATH + "data/elastic_workflow/*"):
shutil.copy(_f, ".")
cell_dict, _ = cell2dict("bulk_mod.cell", db=False)
param_dict, _ = param2dict("bulk_mod.param", db=False)
_ = ComputeTask(
res="Si2.res",
ncores=NCORES,
nnodes=None,
node=None,
cell_dict=cell_dict,
param_dict=param_dict,
verbosity=VERBOSITY,
compute_dir="/tmp/scratch_test",
workflow_kwargs={
"plot": False,
"num_volumes": 5
},
)
self.assertFalse(os.path.isfile("completed/Si2.bib"))
self.assertTrue(os.path.isfile("completed/Si2.check"))
self.assertTrue(os.path.isfile("completed/Si2.bulk_mod.results"))
self.assertTrue(os.path.isfile("completed/Si2.bulk_mod.res"))
self.assertTrue(os.path.isfile("completed/Si2.bulk_mod.castep"))
with open("completed/Si2.bulk_mod.results", "r") as f:
flines = f.readlines()
B = []
for line in flines:
if "bulk modulus" in line:
B.append(float(line.split()[3]))
# check all computed bulk mods are between 88-92
self.assertEqual(len(B), 3)
self.assertTrue(all(abs(b - 90) < 2) for b in B)
self.assertFalse(os.path.isfile("completed/Si2.bulk_mod.pdf"))
self.assertTrue(os.path.isfile("completed/Si2.res"))
self.assertTrue(os.path.isfile("completed/Si2.geom"))
self.assertTrue(os.path.isfile("completed/Si2.castep"))
self.assertTrue(os.path.isfile("completed/Si2.bulk_mod.cell"))
self.assertFalse(os.path.exists("/tmp/scratch_test"))
self.assertFalse(os.path.exists("scratch_test_link"))
def test_phonon(self):
for _f in glob.glob(REAL_PATH + "data/phonon_workflow/*"):
shutil.copy(_f, ".")
cell_dict, _ = cell2dict("Si.cell", db=False)
param_dict, _ = param2dict("Si.param", db=False)
_ = ComputeTask(
res="Si2.res",
ncores=NCORES,
nnodes=None,
node=None,
cell_dict=cell_dict,
param_dict=param_dict,
verbosity=VERBOSITY,
compute_dir="tmpier_tst",
)
self.assertFalse(os.path.isfile("completed/Si2.bib"))
self.assertTrue(os.path.isfile("completed/Si2.check"))
self.assertTrue(os.path.isfile("completed/Si2.bands"))
self.assertTrue(os.path.isfile("completed/Si2.castep"))
self.assertTrue(os.path.isfile("completed/Si2.phonon"))
self.assertTrue(os.path.isfile("completed/Si2.phonon_dos"))
phon, s = phonon2dict("completed/Si2.phonon")
a = 2.7355124
np.testing.assert_array_almost_equal(phon["lattice_cart"],
np.array([[0, a, a], [a, 0, a],
[a, a, 0]]),
decimal=3)
a = 3.869
np.testing.assert_array_almost_equal(phon["lattice_abc"],
np.array([[a, a, a], [60, 60,
60]]),
decimal=3)
self.assertTrue(s, msg="Failed to read phonon file")
self.assertGreater(np.min(phon["eigenvalues_q"]), -0.05)
self.assertTrue(os.path.isfile("completed/Si2.cell"))
self.assertTrue(os.path.isfile("completed/Si2.res"))
def castep_rescaled_volume_scf(computer, calc_doc, seed, rescale=1):
""" Run a singleshot SCF calculation.
Parameters:
computer (:obj:`ComputeTask`): the object that will be calling CASTEP.
calc_doc (dict): the structure to run on.
seed (str): root filename of structure.
Keyword arguments:
rescale (float): amount to rescale volume by.
"""
assert rescale > 0
LOG.info('Performing CASTEP SCF on volume rescaled by {:.2f}.'.format(
rescale**3))
scf_doc = copy.deepcopy(calc_doc)
# get relaxed cell from previous step
fname = f"completed/{seed}-out.cell"
if not os.path.isfile(fname):
raise RuntimeError(f"Could not find relaxed geometry in {fname}.")
relaxed_cell, s = cell2dict(fname, positions=True, lattice=True)
scf_doc["lattice_cart"] = relaxed_cell["lattice_cart"]
scf_doc["positions_frac"] = relaxed_cell["positions_frac"]
LOG.debug("Found equilibrium geometry: {scf_doc['lattice_cart']}")
for i in range(3):
for k in range(3):
scf_doc['lattice_cart'][i][k] *= rescale
scf_doc['task'] = 'singlepoint'
bulk_mod_seed = seed + '.bulk_mod'
computer.seed = bulk_mod_seed
return computer.run_castep_singleshot(scf_doc,
bulk_mod_seed,
keep=True,
intermediate=True)
def test_full_spectral(self):
for _f in glob.glob(REAL_PATH + "data/spectral_workflow/*"):
shutil.copy(_f, ".")
cell_dict, _ = cell2dict("Si.cell")
param_dict, _ = param2dict("Si.param", db=False)
_ = ComputeTask(
res="Si2.res",
ncores=NCORES,
nnodes=None,
node=None,
cell_dict=cell_dict,
param_dict=param_dict,
verbosity=VERBOSITY,
compute_dir=None,
)
self.assertFalse(os.path.isfile("completed/Si2.bib"))
self.assertTrue(os.path.isfile("completed/Si2.check"))
self.assertTrue(os.path.isfile("completed/Si2-out.cell_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2-out.cell_dos"))
self.assertTrue(os.path.isfile("completed/Si2-out.cell_scf"))
self.assertTrue(os.path.isfile("completed/Si2.adaptive.agr"))
self.assertTrue(os.path.isfile("completed/Si2.adaptive.dat"))
self.assertTrue(os.path.isfile("completed/Si2.bands"))
self.assertTrue(os.path.isfile("completed/Si2.bands_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2.bands_dos"))
self.assertTrue(os.path.isfile("completed/Si2.castep"))
self.assertTrue(os.path.isfile("completed/Si2.castep_bin"))
self.assertTrue(os.path.isfile("completed/Si2.castep_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2.castep_dos"))
self.assertTrue(os.path.isfile("completed/Si2.castep_scf"))
self.assertTrue(os.path.isfile("completed/Si2.cell"))
self.assertTrue(os.path.isfile("completed/Si2.cell_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2.cell_dos"))
self.assertTrue(os.path.isfile("completed/Si2.cell_scf"))
self.assertTrue(os.path.isfile("completed/Si2.cst_esp"))
self.assertTrue(os.path.isfile("completed/Si2.dome_bin"))
self.assertTrue(os.path.isfile("completed/Si2.dome_bin_broadening"))
self.assertTrue(os.path.isfile("completed/Si2.dome_bin_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2.dome_bin_dos"))
self.assertTrue(os.path.isfile("completed/Si2.dome_bin_pdos"))
self.assertTrue(os.path.isfile("completed/Si2.odi"))
self.assertTrue(os.path.isfile("completed/Si2.odi_broadening"))
self.assertTrue(os.path.isfile("completed/Si2.odi_pdis"))
self.assertTrue(os.path.isfile("completed/Si2.odi_pdos"))
self.assertTrue(os.path.isfile("completed/Si2.odo"))
self.assertTrue(os.path.isfile("completed/Si2.odo_broadening"))
self.assertTrue(os.path.isfile("completed/Si2.odo_pdis"))
self.assertTrue(os.path.isfile("completed/Si2.odo_pdos"))
self.assertTrue(os.path.isfile("completed/Si2.param"))
self.assertTrue(os.path.isfile("completed/Si2.param_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2.param_dos"))
self.assertTrue(os.path.isfile("completed/Si2.param_scf"))
self.assertTrue(os.path.isfile("completed/Si2.pdis.dat"))
self.assertTrue(os.path.isfile("completed/Si2.pdos.dat"))
self.assertTrue(os.path.isfile("completed/Si2.pdos_bin"))
self.assertTrue(os.path.isfile("completed/Si2.pdos_bin_broadening"))
self.assertTrue(os.path.isfile("completed/Si2.pdos_bin_dispersion"))
self.assertTrue(os.path.isfile("completed/Si2.pdos_bin_dos"))
self.assertTrue(os.path.isfile("completed/Si2.pdos_bin_pdis"))
self.assertTrue(os.path.isfile("completed/Si2.pdos_bin_pdos"))
self.assertTrue(os.path.isfile("completed/Si2.res"))