def test_pseudoprojector(self):
print("TEST PSEUDO")
sys.stdout.flush()
# test ps projections
wf = Wavefunction.from_directory(".")
basis = Wavefunction.from_directory(".")
pr = Projector(wf, basis, method="pseudo")
res = pr.single_band_projection(6)
assert res.shape[0] == basis.nband * basis.nspin * basis.nwk
res = pr.defect_band_analysis(4, 10, False)
assert len(res.keys()) == 15
def test_desymmetrization(self):
print("TEST DESYM")
sys.stdout.flush()
# test ae projections
wf1 = Wavefunction.from_directory(".", False)
basis = Wavefunction.from_directory("nosym", False)
pr = Projector(wf1, basis, unsym_wf=True, unsym_basis=True)
test_vals = {}
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
print("CHECK_VALS", v, c)
test_vals[b] = (v, c)
for b in range(wf1.nband // 2):
if b < 6:
assert_almost_equal(test_vals[b][0], 1, decimal=3)
assert_almost_equal(test_vals[b][1], 0, decimal=7)
else:
assert_almost_equal(test_vals[b][0], 0, decimal=7)
assert_almost_equal(test_vals[b][1], 1, decimal=3)
def test_projector(self):
print("TEST PROJ")
sys.stdout.flush()
# test ae projections
wf1 = Wavefunction.from_directory('.', False)
basis = Wavefunction.from_directory('.', False)
pr = Projector(wf1, basis)
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
generator = Projector.setup_multiple_projections('.', ['.', '.'])
for wf_dir, wf in generator:
wf.defect_band_analysis(4, 10, spinpol=True)
wf1 = Wavefunction.from_directory('.', False)
basis = Wavefunction.from_directory('.', False)
pr = Projector(wf1, basis, 'aug_recip')
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
wf1 = Wavefunction.from_directory('.', False)
basis = Wavefunction.from_directory('.', False)
pr = Projector(wf1, basis, 'realspace')
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
def test_projector_gz(self):
print("TEST PROJGZ")
sys.stdout.flush()
# test ae projections
wf1 = Wavefunction.from_files("CONTCAR", "WAVECAR2.gz", "POTCAR",
"vasprun.xml", False)
basis = Wavefunction.from_directory(".", False)
pr = Projector(wf1, basis)
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
generator = Projector.setup_multiple_projections(".", [".", "."])
for wf_dir, wf in generator:
wf.defect_band_analysis(4, 10, spinpol=True)
def test_flip_spin(self):
wf = Wavefunction.from_directory('.', False)
basis = Wavefunction.from_directory('.', False)
pr = Projector(wf, basis)
for b in range(wf.nband):
res = pr.single_band_projection(b, flip_spin=True)
res = np.abs(res)**2
print(b, res)
for br in range(basis.nband):
expected = 1 if b == br else 0
decimal = 4 if b == br else 8
for k in range(basis.nspin * basis.nwk):
assert_almost_equal(np.sum(
res[br * basis.nwk * basis.nspin + k]),
expected,
decimal=decimal)
pr = Projector(wf, basis, method='aug_recip')
for b in range(wf.nband):
res = pr.single_band_projection(b, flip_spin=True)
res = np.abs(res)**2
print(b, res)
for br in range(basis.nband):
expected = 1 if b == br else 0
decimal = 4 if b == br else 8
for k in range(basis.nspin * basis.nwk):
assert_almost_equal(np.sum(
res[br * basis.nwk * basis.nspin + k]),
expected,
decimal=decimal)
def main(band_indice, defect_ind, dir_init, dir_final):
from pawpyseed.core.projector import Wavefunction, Projector # also imports the wavefunction module
wf_list = []
overlap_list = []
wf_basis = Wavefunction.from_directory(dir_init, setup_projectors=False)
kpt_len = len(wf_basis.kpts)
for dir_name in ["{}".format(_) for _ in dir_final]:
wf_trap = Wavefunction.from_directory(dir_name, setup_projectors=False)
pr = Projector(wf_trap, wf_basis)
result = pr.single_band_projection(band_num=defect_ind)
# result = result.reshape((kpt_len, int(len(result)/kpt_len)))
result = result.reshape((int(len(result) / kpt_len), kpt_len))
result = result[:, 0]
overlap_list.append(result[band_indice])
print("\n\n\n")
print("=================================")
print("----------- Overlaps ------------")
print("=================================")
print(np.abs(np.array(overlap_list)))
def test_offsite(self):
Projector = DummyProjector
print("TEST OFFSITE")
sys.stdout.flush()
wf1 = Wavefunction.from_directory("nosym", False)
basis = Wavefunction.from_directory("nosym", False)
print("ENCUT", wf1.encut, basis.encut)
pr = Projector(wf1, basis)
test_vals = {}
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
print("CHECK_VALS", v, c)
test_vals[b] = (v, c)
for b in range(wf1.nband // 2):
if b < 6:
assert_almost_equal(test_vals[b][0], 1, decimal=2)
assert_almost_equal(test_vals[b][1], 0, decimal=4)
else:
assert_almost_equal(test_vals[b][0], 0, decimal=4)
assert_almost_equal(test_vals[b][1], 1, decimal=2)
generator = Projector.setup_multiple_projections(".", [".", "."])
for wf_dir, wf in generator:
wf.defect_band_analysis(4, 10, spinpol=True)
wf1 = Wavefunction.from_directory("nosym", False)
basis = Wavefunction.from_directory("nosym", False)
print("ENCUT", wf1.encut, basis.encut)
pr = Projector(wf1, basis, "aug_recip")
test_vals = {}
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
print("CHECK_VALS", v, c)
test_vals[b] = (v, c)
for b in range(wf1.nband // 2):
if b < 6:
assert_almost_equal(test_vals[b][0], 1, decimal=2)
assert_almost_equal(test_vals[b][1], 0, decimal=4)
else:
assert_almost_equal(test_vals[b][0], 0, decimal=4)
assert_almost_equal(test_vals[b][1], 1, decimal=2)
def test_projector(self):
print("TEST PROJ")
sys.stdout.flush()
# test ae projections
wf1 = Wavefunction.from_directory(".", False)
basis = Wavefunction.from_directory(".", False)
pr = Projector(wf1, basis)
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
generator = Projector.setup_multiple_projections(".", [".", "."])
for wf_dir, wf in generator:
wf.defect_band_analysis(4, 10, spinpol=True)
wf1 = Wavefunction.from_directory(".", False)
basis = Wavefunction.from_directory(".", False)
pr = Projector(wf1, basis, "aug_recip")
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
wf1 = Wavefunction.from_directory(".", False)
basis = Wavefunction.from_directory(".", False)
pr = Projector(wf1, basis, "realspace")
for b in range(wf1.nband):
v, c = pr.proportion_conduction(b)
if b < 6:
assert_almost_equal(v, 1, decimal=4)
assert_almost_equal(c, 0, decimal=8)
else:
assert_almost_equal(v, 0, decimal=8)
assert_almost_equal(c, 1, decimal=4)
with assert_raises(ValueError):
pr.proportion_conduction(100)
pr.proportion_conduction(-1)
def run_pawpy(self):
"""
Container for running pawpyseed on all defects in this workflow
"""
vbm = None
bulk_dirs, wf_dirs = [], []
bulk_sizes, wf_sizes = [], []
for sc_size, bulk_fw in self.bulk_fw_sets.items():
launch_dir = bulk_fw.launches[-1].launch_dir
bulk_sizes.append(sc_size)
bulk_dirs.append(launch_dir)
if not vbm:
# need to check different filenames
vr = Vasprun(os.path.join(launch_dir, "vasprun.xml"))
vbm = vr.eigenvalue_band_properties[2]
print("\twill use vbm value of ", vbm)
for sc_size, size_set in self.dwo.defect_fw_sets.items():
for fw in size_set:
wf_sizes.append(sc_size)
wf_dirs.append(fw.launches[-1].launch_dir)
projector_list, bases = Projector.setup_bases(bulk_dirs, wf_dirs, True)
num_proj_els = bases[0].num_proj_els
store_all_data = {}
basis_sets = {}
for i, sc_size in enumerate(bulk_sizes):
basis_sets[sc_size] = bases[i]
# for each defect, in a given supercell size
for sc_size, size_set in self.dwo.defect_fw_sets.items():
for fw in size_set:
try:
launch_dir = fw.launches[-1].launch_dir
print(f"start parsing of {fw.name} wavefunction")
# setup file path,
print("\tsetting up files")
self._setup_file_for_parsing(launch_dir)
# find band number which is at VBM and iniitalize band_dict and find spin polarization
print("\tinitializing band_dict")
band_dict, spinpol = self._get_vbm_band_dict(
launch_dir, vbm)
# setup defect wavefunction
print("\tmerging wf from dir")
wf = Wavefunction.from_atomate_directory(
launch_dir, setup_projectors=False)
# loop over band projections around band edge and store results
print("\tperforming projections")
pr = Projector(
wf,
basis_sets[sc_size],
projector_list=projector_list,
unsym_wf=True,
)
for bandnum in band_dict.keys():
v, c = pr.proportion_conduction(bandnum,
spinpol=spinpol)
band_dict[bandnum]["VB_projection"] = v[:]
band_dict[bandnum]["CB_projection"] = c[:]
print(bandnum, band_dict[bandnum])
# then tear down file path
print("\ttear down files")
rmtree(os.path.join(launch_dir, "kyle_file"))
# release defect memory
pr.wf.free_all()
store_all_data[fw.fw_id] = band_dict
except Exception as e:
print(
"___&*$#&(*#@&$)(*&@#)($----\n--> ERROR OCCURED. "
"Skipping this defect.\n-------------^#$^*&^#$&*^#@^$#-------------"
)
print(repr(e))
# now release all bulk basis memory
for bulk_basis in basis_sets.values():
bulk_basis.free_all()
Projector.free_projector_list(projector_list, num_proj_els)
return store_all_data
def setup(self):
os.chdir(os.path.join(MODULE_DIR, '../../../test_files'))
generator = Projector.setup_multiple_projections('.', ['.', '.'])
self.bes = BasisExpansion.makeit(generator)
def setup(self):
os.chdir(os.path.join(MODULE_DIR, '../../../test_files'))
generator = Projector.setup_multiple_projections('.', ['.', '.'])
self.bcs = BulkCharacter.makeit(generator)