def _main():
parser = argparse.ArgumentParser("Calculation of gaps",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--subdir", type=str, default=None,
help="Subdirectory under work_base where calculation was run")
parser.add_argument("--threshold_K", type=float, default=0.9,
help="Threshold for deciding if a state is dominated by one layer")
parser.add_argument("--threshold_Gamma", type=float, default=0.6,
help="Threshold for deciding if a state is dominated by one layer")
parser.add_argument("--spin_valence", type=str, default=None,
help="Set 'up' or 'down' to choose valence band spin type; closest to E_F is used if not set")
parser.add_argument("--spin_conduction", type=str, default=None,
help="Set 'up' or 'down' to choose conduction band spin type; closest to E_F is used if not set")
parser.add_argument("--D", type=float, default=None,
help="Perpendicular electric field value [V/nm]")
parser.add_argument('global_prefix', type=str,
help="Calculation name")
args = parser.parse_args()
gconf = _global_config()
work = os.path.expandvars(gconf["work_base"])
if args.subdir is not None:
work = os.path.join(work, args.subdir)
prefixes = get_prefixes(work, args.global_prefix)
if args.D is not None:
prefixes = filter_to_D(prefixes, args.D)
ds = ds_from_prefixes(prefixes)
ds, prefixes = wrap_cell(ds, prefixes)
dps = sorted_d_group(ds, prefixes)
K = (1/3, 1/3, 0.0)
layer_labels = ["bot.", "top"]
relax_data = get_relax_data(work, dps)
plot_relax_data(relax_data, dps)
gap_data_K = get_gap_data(work, dps, args.threshold_K, args.spin_valence, args.spin_conduction,
K, "K")
plot_gap_data(gap_data_K, dps, "K", "$K$", layer_labels)
Gamma = (0.0, 0.0, 0.0)
gap_data_Gamma = get_gap_data(work, dps, args.threshold_Gamma, args.spin_valence, args.spin_conduction,
Gamma, "Gamma", use_curvature=False)
plot_gap_data(gap_data_Gamma, dps, "Gamma", r"$\Gamma$", layer_labels, use_curvature=False)
def _main():
parser = argparse.ArgumentParser(
"Find calculations with missing files.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
"--subdir",
type=str,
default=None,
help="Subdirectory under work_base where calculation has been run")
parser.add_argument("--global_prefix",
type=str,
default="WSe2_WSe2_WSe2",
help="Prefix for calculation")
parser.add_argument(
"--depth",
type=int,
default=1,
help="How many subdirectories to search inside each calculation.")
parser.add_argument(
"missing_pattern",
type=str,
help=
"Regular expression pattern identifying files to search for. Report calculations where no file matches the pattern."
)
args = parser.parse_args()
gconf = _global_config()
base_path = os.path.expandvars(gconf["work_base"])
if args.subdir is not None:
base_path = os.path.join(base_path, args.subdir)
prefixes = get_prefixes(base_path, args.global_prefix)
missing_pattern_re = re.compile(args.missing_pattern)
missing = []
for prefix in prefixes:
in_dir = os.path.join(base_path, prefix)
if find_pattern(in_dir, missing_pattern_re, args.depth) is None:
missing.append(prefix)
for missing_prefix in missing:
print(missing_prefix)
def _main():
parser = argparse.ArgumentParser(description="Plot various quantities as function of displacement")
parser.add_argument("--subdir", type=str, default=None,
help="Subdirectory under work_base where calculation was run")
parser.add_argument('--global_prefix', type=str, default="MoS2_WS2",
help="Calculation global prefix")
args = parser.parse_args()
gconf = _global_config()
work = os.path.expandvars(gconf["work_base"])
if args.subdir is not None:
work = os.path.join(work, args.subdir)
prefixes = get_prefixes(work, args.global_prefix)
ds = ds_from_prefixes(prefixes)
ds, prefixes = wrap_cell(ds, prefixes)
dps = sorted_d_group(ds, prefixes)
write_out_data = {"_ds": []}
for d, prefix in dps:
write_out_data["_ds"].append(d)
energies = get_energies(work, dps)
energies_rel_meV = energies_relative_to(energies, dps, (0.0, 0.0))
E_title = "$\\Delta E$ [meV]"
E_plot_name = "{}_energies".format(args.global_prefix)
plot_d_vals(E_plot_name, E_title, dps, energies_rel_meV)
write_out_data["meV_relative_total_energy"] = energies_rel_meV
soc = True
Hk_vals = extract_Hk_vals(work, dps, soc)
for label, this_vals in Hk_vals.items():
title = label
plot_name = "{}_{}".format(args.global_prefix, label)
plot_d_vals(plot_name, title, dps, this_vals)
write_out_data["eV_{}".format(label)] = this_vals
def _main():
parser = argparse.ArgumentParser(
"Calculate optical matrix elements",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
"--subdir",
type=str,
default=None,
help="Subdirectory under work_base where calculation was run")
parser.add_argument('global_prefix', type=str, help="Calculation name")
args = parser.parse_args()
gconf = _global_config()
work = os.path.expandvars(gconf["work_base"])
if args.subdir is not None:
work = os.path.join(work, args.subdir)
prefixes = get_prefixes(work, args.global_prefix)
ds = ds_from_prefixes(prefixes)
ds, prefixes = wrap_cell(ds, prefixes)
dps = sorted_d_group(ds, prefixes)
write_optical_data(work, dps)
def _main():
parser = argparse.ArgumentParser(
"Report band extrema and their layer / spin weights",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
"--subdir",
type=str,
default=None,
help="Subdirectory under work_base where calculation was run")
parser.add_argument(
"--num_layers",
type=int,
default=2,
help=
"Number of layers in system (determines number of band extrema to consider)"
)
parser.add_argument("--D",
type=float,
default=None,
help="Perpendicular electric field value [V/nm]")
parser.add_argument('global_prefix', type=str, help="Calculation name")
args = parser.parse_args()
gconf = _global_config()
work = os.path.expandvars(gconf["work_base"])
if args.subdir is not None:
work = os.path.join(work, args.subdir)
prefixes = get_prefixes(work, args.global_prefix)
if args.D is not None:
prefixes = filter_to_D(prefixes, args.D)
ds = ds_from_prefixes(prefixes)
ds, prefixes = wrap_cell(ds, prefixes)
dps = sorted_d_group(ds, prefixes)
K = (1 / 3, 1 / 3, 0.0)
layer_labels = ["bot.", "top"]
relax_data = get_relax_data(work, dps)
plot_relax_data(relax_data, dps)
K_num_valence_bands = args.num_layers
K_num_conduction_bands = 2 * args.num_layers
Gamma_num_valence_bands = 2
Gamma_num_conduction_bands = 4
extrema_data_K = get_extrema_data(work, dps, K, "K", args.num_layers,
K_num_valence_bands,
K_num_conduction_bands)
plot_extrema_data(extrema_data_K, dps, "K", "$K$", layer_labels)
Gamma = (0.0, 0.0, 0.0)
extrema_data_Gamma = get_extrema_data(work, dps, Gamma, "Gamma",
args.num_layers,
Gamma_num_valence_bands,
Gamma_num_conduction_bands)
plot_extrema_data(extrema_data_Gamma, dps, "Gamma", r"$\Gamma$",
layer_labels)