def get_pseudo_dir(soc, xc, pp):
if pp == 'nc':
if soc:
if xc == 'lda':
return os.path.join(_base_dir(), "pseudo", "lda_soc")
else:
return os.path.join(_base_dir(), "pseudo", "soc")
else:
if xc == 'lda':
return os.path.join(_base_dir(), "pseudo", "lda_no_soc")
else:
return os.path.join(_base_dir(), "pseudo", "no_soc")
elif pp == 'paw':
if soc and xc == 'lda':
return os.path.join(_base_dir(), "pseudo", "pslibrary_lda_soc_paw")
else:
raise ValueError("paw/non-soc not implemented")
def test_qe_config(self):
syms = ["WSe2", "WSe2", "WSe2"]
soc = True
vacuum_dist = 20.0 # Angstrom
D = 0.5 # V/nm
AB_stacking = True
xc = 'lda'
pp = 'nc'
db_path = os.path.join(_base_dir(), "c2dm.db")
db = ase.db.connect(db_path)
c_sep = get_c_sep(db, syms[0])
latvecs, at_syms, cartpos = make_cell(db, syms, c_sep, vacuum_dist,
AB_stacking)
system = Atoms(symbols=at_syms,
positions=cartpos,
cell=latvecs,
pbc=True)
system.center(axis=2)
wann_valence, num_wann = get_wann_valence(
system.get_chemical_symbols(), soc)
num_bands = get_num_bands(num_wann)
qe_config = make_qe_config(system, D, soc, num_bands, xc, pp)
#with open('test_build_qe_config_new.json', 'w') as fp:
# json.dump(qe_config, fp)
with open('test_build_qe_config.json', 'r') as fp:
qe_config_expected = json.load(fp)
check_qe_config(self, qe_config, qe_config_expected, soc, xc, pp)
prefix = 'test'
qe_input = build_qe(system, prefix, 'scf', qe_config)
#with open('test_build_qe_input_new', 'w') as fp:
# fp.write(qe_input)
with open('test_build_qe_input', 'r') as fp:
qe_input_expected = fp.read()
check_qe_input(self, qe_input, qe_input_expected, soc, xc, pp)
def test_cell_unshifted(self):
syms_bilayer = ["WSe2", "WSe2"]
syms_trilayer = ["WSe2", "WSe2", "WSe2"]
vacuum_dist = 20.0 # Angstrom
AB_stacking = True
db_path = os.path.join(_base_dir(), "c2dm.db")
db = ase.db.connect(db_path)
for syms in [syms_bilayer, syms_trilayer]:
c_sep = get_c_sep(db, syms[0])
layer_systems = [get_layer_system(db, sym, 'H') for sym in syms]
a = a_from_2H(layer_systems[0])
hs = [h_from_2H(layer_system) for layer_system in layer_systems]
for AB_stacking in [False, True]:
# layer_shifts = None should be the same as specifying
# a shift of (0.0, 0.0) for all layers.
latvecs_None, at_syms_None, cartpos_None = make_cell(
db,
syms,
c_sep,
vacuum_dist,
AB_stacking=AB_stacking,
layer_shifts=None)
shifts_zero = [(0.0, 0.0)] * len(syms)
latvecs_zero, at_syms_zero, cartpos_zero = make_cell(
db,
syms,
c_sep,
vacuum_dist,
AB_stacking=AB_stacking,
layer_shifts=shifts_zero)
self.assertTrue((latvecs_None == latvecs_zero).all())
self.assertEqual(at_syms_None, at_syms_zero)
for at_pos_None, at_pos_zero in zip(cartpos_None,
cartpos_zero):
assert ((at_pos_None == at_pos_zero).all())
self.assertEqual(at_syms_zero, ["Se", "W", "Se"] * len(syms))
# Should have the correct lattice constant.
eps = 1e-12
self.assertTrue(abs(np.linalg.norm(latvecs_None[0]) - a) < eps)
self.assertTrue(abs(np.linalg.norm(latvecs_None[1]) - a) < eps)
system = Atoms(symbols=at_syms_zero,
positions=cartpos_zero,
cell=latvecs_zero,
pbc=True)
system.center(axis=2)
A = (0.0, 0.0)
B = (1 / 3, 2 / 3)
latpos = system.get_scaled_positions()
for layer_index in range(len(syms)):
# Atoms should have the correct in-plane positions.
layer_pos = latpos[3 * layer_index:3 * layer_index + 3]
if AB_stacking:
if layer_index % 2 == 0:
self.assertTrue(has_pos_seq(layer_pos, [A, B, A]))
else:
self.assertTrue(has_pos_seq(layer_pos, [B, A, B]))
else:
self.assertTrue(has_pos_seq(layer_pos, [A, B, A]))
# Atoms should have the correct vertical positions.
h = hs[layer_index]
layer_cartpos = cartpos_zero[3 *
layer_index:3 * layer_index +
3]
zs = [layer_cartpos[i][2] for i in range(3)]
self.assertTrue(abs(zs[2] - zs[0] - h) < eps)
self.assertTrue(abs(zs[2] - zs[1] - h / 2) < eps)
if layer_index != 0:
z_below = cartpos_zero[3 * layer_index - 1][2]
self.assertTrue(abs(zs[0] - z_below - c_sep) < eps)
def test_cell_shifted(self):
syms_bilayer = ["WSe2", "WSe2"]
syms_trilayer = ["WSe2", "WSe2", "WSe2"]
vacuum_dist = 20.0 # Angstrom
AB_stacking = True
db_path = os.path.join(_base_dir(), "c2dm.db")
db = ase.db.connect(db_path)
for syms in [syms_bilayer, syms_trilayer]:
c_sep = get_c_sep(db, syms[0])
shifts_zero = [(0.0, 0.0)] * len(syms)
num_shifts_l2 = 3
all_shifts_nonzero = make_layer_shifts(len(syms), num_shifts_l2)
for AB_stacking in [False, True]:
for layer_shifts in all_shifts_nonzero:
latvecs_zero, at_syms_zero, cartpos_zero = make_cell(
db,
syms,
c_sep,
vacuum_dist,
AB_stacking=AB_stacking,
layer_shifts=shifts_zero)
latvecs_shift, at_syms_shift, cartpos_shift = make_cell(
db,
syms,
c_sep,
vacuum_dist,
AB_stacking=AB_stacking,
layer_shifts=layer_shifts)
self.assertTrue((latvecs_zero == latvecs_shift).all())
self.assertEqual(at_syms_zero, at_syms_shift)
system_zero = Atoms(symbols=at_syms_zero,
positions=cartpos_zero,
cell=latvecs_zero,
pbc=True)
system_zero.center(axis=2)
system_shift = Atoms(symbols=at_syms_shift,
positions=cartpos_shift,
cell=latvecs_shift,
pbc=True)
system_shift.center(axis=2)
latpos_zero = system_zero.get_scaled_positions()
latpos_shift = system_shift.get_scaled_positions()
for layer_index in range(len(syms)):
# Atoms should have the correct in-plane positions.
layer_pos_zero = latpos_zero[3 * layer_index:3 *
layer_index + 3]
layer_pos_shift = latpos_shift[3 * layer_index:3 *
layer_index + 3]
self.assertTrue(
has_pos_shift(layer_pos_zero, layer_pos_shift,
layer_shifts[layer_index]))
# Atoms should have the correct vertical positions.
eps = 1e-12
for i in range(3):
self.assertTrue(
abs(layer_pos_zero[i][2] -
layer_pos_shift[i][2]) < eps)
def _main():
parser = argparse.ArgumentParser(
"Build and run calculation over various TMD stacks",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--run",
action="store_true",
help="Run calculation after making inputs")
parser.add_argument("--subdir",
type=str,
default=None,
help="Subdirectory under work_base to run calculation")
parser.add_argument("--stacking",
type=str,
default="AB",
help="Stacking mode: 'AB' (2H) or 'AA' (1H)")
parser.add_argument("--D",
type=float,
default=None,
help="Displacement field (default: no field)")
parser.add_argument("--xc",
type=str,
default="lda",
help="Exchange-correlation functional (lda or pbe)")
parser.add_argument("--pp",
type=str,
default="nc",
help="Pseudopotential type ('nc' or 'paw')")
args = parser.parse_args()
soc = True
all_syms = get_all_syms()
AB_stacking = get_stacking(args.stacking)
vacuum_dist = 20.0 # Angstrom
db_path = os.path.join(_base_dir(), "c2dm.db")
db = ase.db.connect(db_path)
prefixes = []
for syms in all_syms:
p = set_up_calculation(db, args.subdir, syms, AB_stacking, soc,
vacuum_dist, args.D, args.xc, args.pp)
prefixes.append(p)
global_prefix = "alignment"
machine = "stampede2"
num_nodes = 2
num_cores = num_nodes * mpi_procs_per_node(machine)
queue_config = {
"machine": machine,
"nodes": num_nodes,
"cores": num_cores,
"queue": "normal",
"hours": 12,
"minutes": 0,
"wannier": True,
"project": "A-ph9",
"global_prefix": global_prefix,
"max_jobs": 6,
"outer_min": -10.0,
"outer_max": 5.0,
"inner_min": -8.0,
"inner_max": 3.0,
"subdir": args.subdir,
"qe_bands": _global_config()['qe_bands']
}
_write_queuefiles(_get_base_path(args.subdir), prefixes, queue_config)
def _main():
parser = argparse.ArgumentParser(
"Build and run calculation over displacement field values",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--run",
action="store_true",
help="Run calculation after making inputs")
parser.add_argument("--subdir",
type=str,
default=None,
help="Subdirectory under work_base to run calculation")
parser.add_argument(
"--syms",
type=str,
default="WSe2;WSe2;WSe2",
help=
"Semicolon-separated list of atomic composition of layers. Format example: WSe2;MoSe2;MoS2"
)
parser.add_argument("--stacking",
type=str,
default="AB",
help="Stacking mode: 'AB' (2H) or 'AA' (1H)")
parser.add_argument("--minD",
type=float,
default=0.01,
help="Minimum displacement field in V/nm")
parser.add_argument("--maxD",
type=float,
default=0.5,
help="Maximum displacement field in V/nm")
parser.add_argument(
"--numD",
type=int,
default=10,
help=
"Number of displacement field steps. Set to 0 to not use displacement field."
)
parser.add_argument(
"--shifts_l2",
type=int,
default=None,
help=
"Number of interlayer shifts to include for second layer: if specified, include\
calculations with second layer shifts tiling the unit cell.")
parser.add_argument(
"--interlayer_relax",
action="store_true",
help="Relax in the out-of-plane direction before performing scf")
parser.add_argument("--no_soc",
action="store_true",
help="Turn off spin-orbit coupling")
parser.add_argument("--xc",
type=str,
default="lda",
help="Exchange-correlation functional (lda or pbe)")
parser.add_argument("--pp",
type=str,
default="nc",
help="Pseudopotential type ('nc' or 'paw')")
args = parser.parse_args()
syms = _extract_syms(args.syms)
global_prefix = "_".join(syms)
print("Generating inputs for {} system {}.".format(num_layers_label(syms),
syms))
soc = not args.no_soc
db_path = os.path.join(_base_dir(), "c2dm.db")
db = ase.db.connect(db_path)
# Choose separation between layers as if the system was a bulk system
# where all layers are the same as the first layer here.
# TODO -- is there a better strategy for this?
c_sep = get_c_sep(db, syms[0])
vacuum_dist = 20.0 # Angstrom
if args.stacking == 'AB':
AB_stacking = True
elif args.stacking == 'AA':
AB_stacking = False
else:
raise ValueError("unrecognized value for argument 'stacking'")
if args.numD == 0:
Ds = [None]
else:
Ds = np.linspace(args.minD, args.maxD, args.numD)
if args.shifts_l2 is None:
all_layer_shifts = [None]
else:
num_layers = len(syms)
all_layer_shifts = make_layer_shifts(num_layers, args.shifts_l2)
prefixes = []
for layer_shifts in all_layer_shifts:
prefixes.extend(
make_system_at_shift(global_prefix, args.subdir, db, syms, c_sep,
vacuum_dist, AB_stacking, soc,
args.interlayer_relax, args.xc, args.pp, Ds,
layer_shifts))
machine = "stampede2"
num_nodes = 1
num_cores = num_nodes * mpi_procs_per_node(machine)
queue_config = {
"machine": machine,
"cores": num_cores,
"nodes": num_nodes,
"queue": "normal",
"hours": 12,
"minutes": 0,
"wannier": True,
"project": "A-ph9",
"global_prefix": global_prefix,
"max_jobs": 1,
"relax": args.interlayer_relax,
"outer_min": -10.0,
"outer_max": 6.0,
"inner_min": -8.0,
"inner_max": 3.0,
"subdir": args.subdir,
"qe_bands": _global_config()['qe_bands']
}
print(
"Generating queuefiles for machine {} on {} nodes and {} jobs with max runtime {} hours."
.format(machine, num_nodes, queue_config["max_jobs"],
queue_config["hours"]))
base_path = _get_base_path(args.subdir)
prefix_groups = _write_queuefiles(base_path, prefixes, queue_config)
if args.run:
calc_name = "wan_setup"
submit_pw(base_path, queue_config, prefix_groups, calc_name)