def _main():
parser = argparse.ArgumentParser("Run postprocessing to set up Wannier90 calculation",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--subdir", type=str, default=None,
help="Subdirectory under work_base to run calculation")
parser.add_argument("--global_prefix", type=str, default="MoS2_WS2",
help="Prefix for calculation")
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)
if "qe_bands" in gconf:
qe_bands_dir = os.path.expandvars(gconf["qe_bands"])
qe_bands_path = os.path.join(qe_bands_dir, "bands.x")
else:
qe_bands_path = "bands.x"
calc = "pw_post"
prefix_groups = get_prefix_groups(base_path, args.global_prefix)
config = {"machine": "ls5", "cores": 24, "nodes": 1, "queue": "normal",
"hours": 8, "minutes": 0, "wannier": True, "project": "A-ph9",
"global_prefix": args.global_prefix, "max_jobs": 24,
"qe_bands": qe_bands_path}
submit_dgrid_pw_post(base_path, config, prefix_groups)
def _main():
parser = ArgumentParser("wfc cleanup")
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="System for which wannier/ .save directories will be removed")
parser.add_argument(
'--confirm',
action='store_true',
help="Must specify --confirm to confirm .save removal is desired")
args = parser.parse_args()
if not args.confirm:
return
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)
for prefix in prefixes:
save_path = os.path.join(work, prefix, "wannier",
"{}.save".format(prefix))
shutil.rmtree(save_path)
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
na, nb = 16, 16
num_dos = 1000
E_below_fermi, E_above_fermi = 3.0, 3.0
gaps = find_gaps(work, dps, E_below_fermi, E_above_fermi, num_dos, na, nb)
gap_plot_title = "Gaps [eV]"
gap_plot_name = "{}_gaps".format(args.global_prefix)
plot_d_vals(gap_plot_name, gap_plot_title, dps, gaps)
write_out_data["eV_overall_gap"] = gaps
with open("{}_plot_ds_data.json".format(args.global_prefix), 'w') as fp:
json.dump(write_out_data, fp)
def H_klat_Glat(dps, kGs):
'''Integrate by trapezoid method.
Lazy way to compute: for each region, compute each Hk at boundaries.
Avoid point storage scheme and possible high memory use
at cost of 4x runtime.
Trapezoid rule in 2D:
\int_{x1, x2} dx \int_{y1, y2} dy f(x,y) = (1/4)*(x2-x1)(y2-y1)
* (f(x1, y1) + f(x1, y2) + f(x2, y1) + f(x2, y2))
To avoid repeated unecessary loads of Hrs, and to avoid keeping all
Hrs in memory, compute integral values for each (k, G) pair
simultaneously.
'''
gconf = global_config()
work = os.path.expandvars(gconf["work_base"])
ds = []
for d, prefix in dps:
ds.append(d)
d_boundary_indices, delta_a, delta_b = trapezoid_d_regions(ds)
# Calculate integral over each region individually.
# region_integral_vals is a list (with indices corresponding to regions)
# whose elements are dicts {(k, G): region_integral_val, ...}
rint_args = []
for region_indices in d_boundary_indices:
rint_args.append([region_indices, delta_a, delta_b, kGs, work, dps])
with Pool() as p:
region_integral_vals = p.starmap(region_integral, rint_args)
# Collect region integrals into totals.
integral_totals = []
for kG_i in range(len(kGs)):
integral_totals.append(None)
for region_list in region_integral_vals:
for kG_index, kG_val in enumerate(region_list):
if integral_totals[kG_index] is None:
integral_totals[kG_index] = kG_val
else:
integral_totals[kG_index] += kG_val
return integral_totals
def _main():
parser = argparse.ArgumentParser(
description="Plot TMD band structure result",
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,
default="MoS2_WS2",
help="Calculation global prefix")
parser.add_argument("--prefix",
type=str,
default=None,
help="If specified, plot bands for one prefix only")
parser.add_argument("--plot_evecs",
action='store_true',
help="Plot eigenvector components")
parser.add_argument("--minE",
type=float,
default=None,
help="Minimum energy to plot (not relative to E_F)")
parser.add_argument("--maxE",
type=float,
default=None,
help="Maximum energy to plot (not relative to E_F)")
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)
if args.prefix is None:
prefixes = get_prefixes(work, args.global_prefix)
for prefix in prefixes:
make_plot(work, prefix, args.plot_evecs, args.minE, args.maxE)
else:
make_plot(work, args.prefix, args.plot_evecs, args.minE, args.maxE)
def _main():
parser = argparse.ArgumentParser("Moire band structure")
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="Prefix for calculation")
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)
scf_0_path = os.path.join(work, prefixes[0], "wannier", "scf.out")
D = D_from_scf(scf_0_path)
D_2D = D[0:2, 0:2]
kpoints = [(0, 0), (1 / 2, 0), (1 / 3, 1 / 3), (0, 0)]
ks_per_interval = 10
ktildes = make_kpath(kpoints, ks_per_interval)
#ktildes = [(1/3, 1/3, 0)]
epsilon = 1 / 2
theta = 0.0
Gcut = 2
Gcut_cart = False
Hk_moires = moire_Hamiltonian(dps, ktildes, D_2D, epsilon, theta, Gcut,
Gcut_cart)
plot_Hk_moire(Hk_moires)
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("Analysis of H(k) symmetry")
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="Prefix for calculation")
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)
ordering = "2H"
if ordering == "2H":
d0_prefix = find_d_val(dps, (2 / 3, 1 / 3))
d1_prefix = find_d_val(dps, (0.0, 0.0))
d2_prefix = find_d_val(dps, (1 / 3, 2 / 3))
elif ordering == "2H_top":
d0_prefix = find_d_val(dps, (0.0, 0.0))
d1_prefix = find_d_val(dps, (1 / 3, 2 / 3))
d2_prefix = find_d_val(dps, (2 / 3, 1 / 3))
else:
raise ValueError("unrecognized ordering")
Ks = (("K0", (1 / 3, 1 / 3, 0.0)), ("K1", (-2 / 3, 1 / 3, 0.0)),
("K2", (1 / 3, -2 / 3, 0.0)))
for i_d, prefix in enumerate((d0_prefix, d1_prefix, d2_prefix)):
Hr = get_Hr(work, prefix)
# H(R = 0)
H0 = Hr[(0, 0, 0)][0] / Hr[(0, 0, 0)][1]
H0_vals = get_H_orbital_vals(H0, work, prefix)
# H(K)
Hk_vals = {}
for K_label, K in Ks:
HK = Hk_recip(K, Hr)
Hk_vals[K_label] = get_H_orbital_vals(HK, work, prefix)
print("i_d = {}, prefix = {}".format(str(i_d), prefix))
print("H(r = 0, 0, 0)[+,+] = {}".format(str(H0_vals["dp2_M_dp2_Mp"])))
print("H(r = 0, 0, 0)[-,-] = {}".format(str(H0_vals["dm2_M_dm2_Mp"])))
print("H(r = 0, 0, 0)[+,-] = {}".format(str(H0_vals["dp2_M_dm2_Mp"])))
print("H(r = 0, 0, 0)[-,+] = {}".format(str(H0_vals["dm2_M_dp2_Mp"])))
print("H(r = 0, 0, 0)[z2,z2] = {}".format(str(
H0_vals["dz2_M_dz2_Mp"])))
for K_label, K in Ks:
print("------------")
print("<d_+2^M|H({})|d_+2^M'> = {}".format(
K_label, str(Hk_vals[K_label]["dp2_M_dp2_Mp"])))
print("<d_-2^M|H({})|d_-2^M'> = {}".format(
K_label, str(Hk_vals[K_label]["dm2_M_dm2_Mp"])))
print("<d_+2^M|H({})|d_-2^M'> = {}".format(
K_label, str(Hk_vals[K_label]["dp2_M_dm2_Mp"])))
print("<d_-2^M|H({})|d_+2^M'> = {}".format(
K_label, str(Hk_vals[K_label]["dm2_M_dp2_Mp"])))
print("<d_z2^M|H({})|d_z2^M'> = {}".format(
K_label, str(Hk_vals[K_label]["dz2_M_dz2_Mp"])))
print("===================")
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",
type=float,
default=0.9,
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(
"--use_QE_evs",
action='store_true',
help=
"Use eigenvalues from QE instead of Wannier H(k); if set, spin_valence and spin_conduction act as if not specified."
)
parser.add_argument(
"--ev_width",
type=int,
default=8,
help="Number of characters per eigenvalue in QE bands.dat")
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)
K = (1 / 3, 1 / 3, 0.0)
Gamma = (0.0, 0.0, 0.0)
do_get_curvature_K, do_get_curvature_Gamma = True, False
write_gap_data(work, dps, args.threshold, args.spin_valence,
args.spin_conduction, args.use_QE_evs, args.ev_width, K,
"K", "$K$", do_get_curvature_K)
write_gap_data(work, dps, args.threshold, args.spin_valence,
args.spin_conduction, args.use_QE_evs, args.ev_width, Gamma,
"Gamma", "$\\Gamma$", do_get_curvature_Gamma)
def _main():
parser = argparse.ArgumentParser("Fourier components")
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="Prefix for calculation")
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)
soc = False
prefixes = get_prefixes(work, args.global_prefix)
ds = ds_from_prefixes(prefixes)
ds, prefixes = wrap_cell(ds, prefixes)
dps = sorted_d_group(ds, prefixes)
# Verify all Hr_orders are the same;
# after this, assume order is the same for all ds.
verify_Hr_orders_identical(work, prefixes)
atom_Hr_order = get_atom_order(work, prefixes[0])
orb_type = ("X2", "pz", "up", "X1p", "pz", "up")
i_sym, i_orbital, i_spin = orb_type[0], orb_type[1], orb_type[2]
j_sym, j_orbital, j_spin = orb_type[3], orb_type[4], orb_type[5]
i_index = orbital_index(atom_Hr_order, i_sym, i_orbital, i_spin, soc)
j_index = orbital_index(atom_Hr_order, j_sym, j_orbital, j_spin, soc)
Gs = []
num_Ga, num_Gb = 5, 5
for Ga in range(num_Ga):
for Gb in range(num_Gb):
G = (Ga, Gb)
Gs.append(G)
ks = [(1 / 3, 1 / 3, 0)]
kGs = list(itertools.product(ks, Gs))
all_H_vals = H_klat_Glat(dps, kGs)
Gas, Gbs = [], []
H_K_re_vals, H_K_im_vals = [], []
for kG_index, val in enumerate(all_H_vals):
k, G = kGs[kG_index]
# Only one k used.
# TODO - check k?
H_K_re_vals.append(val[i_index, j_index].real)
H_K_im_vals.append(val[i_index, j_index].imag)
Gas.append(float(G[0]))
Gbs.append(float(G[1]))
plt.scatter(Gas,
Gbs,
c=H_K_re_vals,
cmap='viridis',
s=50,
edgecolors="none")
plt.colorbar()
plt.savefig("G_K_re.png", bbox_inches='tight', dpi=500)
plt.clf()
plt.scatter(Gas,
Gbs,
c=H_K_im_vals,
cmap='viridis',
s=50,
edgecolors="none")
plt.colorbar()
plt.savefig("G_K_im.png", bbox_inches='tight', dpi=500)
plt.clf()
def _main():
parser = argparse.ArgumentParser(
"Build and run calculation on grid of d's",
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("--symA",
type=str,
default="MoS2",
help="Atomic composition of bottom layer")
parser.add_argument("--symB",
type=str,
default="WS2",
help="Atomic composition of top layer")
parser.add_argument("--monolayer",
action="store_true",
help="Use monolayer system instead of bilayer")
parser.add_argument(
"--ordering",
type=str,
default="2H",
help="Ordering of atoms: '2H' -> BAB/ABA; '2H_top' -> BAB/BAB")
parser.add_argument(
"--c_sep",
type=float,
default=None,
help=
"Separation between layers (use value from bilayer of symA if not specified)"
)
parser.add_argument("--soc",
action="store_true",
help="Use spin-orbit coupling")
parser.add_argument("--xc",
type=str,
default="lda",
help="Exchange-correlation functional (lda or pbe)")
parser.add_argument("--num_d_a",
type=int,
default=3,
help="Number of d's (shifts) along the a-axis")
parser.add_argument("--num_d_b",
type=int,
default=3,
help="Number of d's (shifts) along the b-axis")
parser.add_argument("--pp",
type=str,
default="nc",
help="Pseudopotential type ('nc' or 'paw')")
parser.add_argument(
"--iprelax",
action="store_true",
help="Vary in-plane lattice constant to search for lowest energy")
parser.add_argument("--bands_only",
action="store_true",
help="Run only scf and bands calc")
args = parser.parse_args()
symA, symB = args.symA, args.symB
if args.monolayer:
symB = None
tmd_base = _base_dir()
db_path = os.path.join(tmd_base, "c2dm.db")
gconf = global_config()
if not args.monolayer:
c_bulk_values = {"MoS2": 12.296, "MoSe2": 12.939}
c_bulk = c_bulk_values[symA]
else:
c_bulk = None
dgrid = dgrid_inputs(db_path,
symA,
symB,
c_bulk,
args.num_d_a,
args.num_d_b,
c_sep=args.c_sep,
soc=args.soc,
xc=args.xc,
ordering=args.ordering,
iprelax=args.iprelax,
pp=args.pp,
bands_only=args.bands_only)
base_path = os.path.expandvars(gconf["work_base"])
if args.subdir is not None:
base_path = os.path.join(base_path, args.subdir)
# Recompiled QE to increase precision in bands.dat output file.
# (The hard-coded default is 3 decimal places (1 meV) which is too small
# for gap variation on the scale of 10 meV).
#
# Starting with QE 5.4.0,
# in PP/src/bands.f90 changed:
# Line 470: 10f8.3 --> 10f13.8
# Line 476: 10f8.3 --> 10f13.8
#
# To compile QE on LS5, need to specify mpich scalapack.
# With module 'espresso/5.4.0' loaded, compile with:
# ./configure SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
# make pp
if "qe_bands" in gconf:
qe_bands_dir = os.path.expandvars(gconf["qe_bands"])
qe_bands_path = os.path.join(qe_bands_dir, "bands.x")
else:
qe_bands_path = "bands.x"
write_dgrid(base_path, dgrid)
#config = {"machine": "__local__", "wannier": True}
#config = {"machine": "__local__", "wannier": True, "__local_mpi_cmd__": "mpirun"}
if symA is not None and symB is not None:
global_prefix = "{}_{}".format(symA, symB)
elif symB is None:
global_prefix = symA
elif symA is None:
global_prefix = symB
else:
raise ValueError("symA and symB are None")
num_nodes = 1
num_cores = 24 * num_nodes
config = {
"machine": "ls5",
"cores": num_cores,
"nodes": num_nodes,
"queue": "normal",
"hours": 4,
"minutes": 0,
"wannier": True,
"project": "A-ph9",
"global_prefix": global_prefix,
"max_jobs": 24,
"outer_min": -10.0,
"outer_max": 7.0,
"inner_min": -8.0,
"inner_max": 3.0,
"subdir": args.subdir,
"iprelax": args.iprelax,
"bands_only": args.bands_only,
"qe_bands": qe_bands_path
}
prefix_groups = write_dgrid_queuefiles(base_path, dgrid, config)
if args.run:
if not args.iprelax and not args.bands_only:
calc_name = "wan_setup"
else:
calc_name = "bands_only"
submit_dgrid_pw(base_path, config, prefix_groups, calc_name)