def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
type=Path,
default=Path("momentum_distribution.h5"),
help="path to the momentum_distribution file",
)
parser.add_argument("--colorbar", type=bool)
add_argparse_2d_args(parser)
add_argparse_save_arg(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
times, momenta, density = read_momentum_distribution_hdf5(
args.path,
"momentum_distribution",
)
average_momentum = numpy.zeros_like(times)
for i, _ in enumerate(average_momentum):
average_momentum[i] = numpy.sum(momenta * density[i])
Y, X = numpy.meshgrid(momenta, times)
mesh = ax.pcolormesh(X, Y, density)
plt.plot(times, average_momentum)
apply_2d_args(ax, figure, args)
handle_saving(figure, args)
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
type=Path,
default="propagate.h5/output",
help="path to the output file",
)
add_argparse_2d_args(parser)
add_argparse_save_arg(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
time, _, energy, _ = read_output(args.path)
plot_energy(ax, time, energy)
system = units.get_default_unit_system()
ax.set_xlabel(system.get_time_unit().format_label("t"))
ax.set_ylabel(system.get_length_unit().format_label("x"))
apply_2d_args(ax, figure, args)
handle_saving(figure, args)
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path", nargs=2, help="path to the output file")
add_argparse_2d_args(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
time1, _, energy1, _ = read_output(args.path[0])
time2, _, energy2, _ = read_output(args.path[1])
if time1.shape != time2.shape:
raise ValueError("different number of time points")
if not numpy.allclose(time1, time2):
raise ValueError("different time points")
plot_energy_diff(ax, time1, energy1, energy2)
system = units.get_default_unit_system()
ax.set_xlabel(system.get_time_unit().format_label("t"))
ax.set_ylabel(system.get_energy_unit().format_label(r"\Delta E"))
apply_2d_args(ax, figure, args)
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path", nargs=2, help="path to the natpop file")
parser.add_argument("-n", "--node", type=int, default=1, help="node")
parser.add_argument("-d",
"--dof",
type=int,
default=1,
help="degree of freedom")
add_argparse_2d_args(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
time1, natpop1 = read_natpop(args.path[0], node=args.node, dof=args.dof)
time2, natpop2 = read_natpop(args.path[1], node=args.node, dof=args.dof)
if time1.shape != time2.shape:
raise ValueError("number of time points differs")
if not numpy.allclose(time1, time2):
raise ValueError("time points differ")
entropy1 = compute_entropy(natpop1)
entropy2 = compute_entropy(natpop2)
plot_entropy_diff(ax, time1, entropy1, entropy2)
system = units.get_default_unit_system()
ax.set_xlabel(system.get_time_unit().format_label("t"))
apply_2d_args(ax, figure, args)
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
type=Path,
default=Path("propagate.h5/natpop"),
help="path to the natpop file",
)
parser.add_argument("-n", "--node", type=int, default=1, help="node")
parser.add_argument("-d",
"--dof",
type=int,
default=1,
help="degree of freedom")
add_argparse_2d_args(parser)
add_argparse_save_arg(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
time, natpop = read_natpop(args.path, node=args.node, dof=args.dof)
plot_natpop(ax, time, natpop)
try:
ax.set_xlabel(
units.get_default_unit_system().get_time_unit().format_label("t"))
except units.MissingUnitError:
ax.set_xlabel("$t$")
apply_2d_args(ax, figure, args)
handle_saving(figure, args)
if not args.output:
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path", help="path to the dmat file")
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
app = QtWidgets.QApplication(sys.argv)
DmatSlider(*inout.read_dmat_spfrep(args.path), args)
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path", help="path to the dmat file")
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
app = QtWidgets.QApplication(sys.argv)
data = read_dmat_spfrep_hdf5(args.path, "dmat_spfrep")
gui = Gui(data, 0, len(data[0]) - 1)
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
type=Path,
default=Path("propagate.h5/gpop"),
help="path to the gpop file",
)
parser.add_argument("-d",
"--dof",
type=int,
default=1,
help="degree of freedom")
parser.add_argument(
"--momentum",
action="store_true",
help="whether to transform to momentum space",
)
parser.add_argument("--logz", action="store_true")
parser.add_argument("--zmin", type=float)
parser.add_argument("--zmax", type=float)
parser.add_argument("--colorbar", action="store_true")
add_argparse_2d_args(parser)
add_argparse_save_arg(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
data = read_gpop(args.path, dof=args.dof)
if args.momentum:
data = transform_to_momentum_space(data)
mesh = plot_gpop(ax, *data, args.zmin, args.zmax, args.logz)
if args.colorbar:
figure.colorbar(mesh, ax=ax).solids.set_rasterized(True)
unitsys = units.get_default_unit_system()
try:
ax.set_xlabel(unitsys.get_time_unit().format_label("t"))
except units.MissingUnitError:
ax.set_xlabel("$t$")
try:
ax.set_ylabel(unitsys.get_length_unit().format_label("x"))
except units.MissingUnitError:
ax.set_ylabel("$x$")
apply_2d_args(ax, figure, args)
handle_saving(figure, args)
if not args.output:
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path",
type=Path,
nargs="+",
help="path to the output file")
parser.add_argument(
"--fft",
action="store_true",
help="whether to transform the signal to frequency space",
)
parser.add_argument("--xname", help="", default="time")
add_argparse_2d_args(parser)
add_argparse_save_arg(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
unitsys = mlxtk.units.get_default_unit_system()
for file in args.path:
name = file.stem
time, values = read_expval_hdf5(file, xname=args.xname)
if args.fft:
plot_expval(ax,
*mlxtk.tools.signal.fourier_transform(time, values),
label=name)
ax.set_xlabel(
(1 / unitsys.get_time_unit()).format_label(r"\omega"))
ax.set_ylabel(
mlxtk.units.ArbitraryUnit().format_label(
r"\mathrm{amplitude}"), )
else:
plot_expval(ax, time, values, label=name)
if args.xname == "time":
ax.set_xlabel(unitsys.get_time_unit().format_label("t"))
else:
ax.set_xlabel(args.xname)
if len(args.path) > 1:
ax.legend()
apply_2d_args(ax, figure, args)
handle_saving(figure, args)
if not args.output:
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
default="evec_dmat_dof1_spf",
help="path to the file containing the eigenvectors of the dmat",
)
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
app = QtWidgets.QApplication(sys.argv)
window = DmatEvecSlider(*inout.read_dmat_evecs_grid(args.path), args)
sys.exit(app.exec_())
del window
def main():
global MODFUNCS
parser = argparse.ArgumentParser()
parser.add_argument(
"scan_dir",
type=Path,
help="directory of the scan containing the file scan.pickle",
)
parser.add_argument(
"-f",
"--file",
type=Path,
default=Path("propagate") / "propagate.h5/natpop",
help="relative path within each simulation",
)
parser.add_argument("-d", "--dof", type=int, default=1, help="degree of freedom")
parser.add_argument("-n", "--node", type=int, default=1, help="node")
parser.add_argument(
"-e",
"--extension",
type=str,
default=".pdf",
help="file extensions for the plots",
)
parser.add_argument("-o", "--output", type=str, help="name of the output directory")
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
if not args.output:
args.output = f"natpop_{args.dof}_{args.node}"
def apply_args(fig: Figure, ax: Axes, parameters: Parameters):
del parameters
plot.apply_2d_args(ax, fig, args)
MODFUNCS = [apply_args] + MODFUNCS
load_scan(args.scan_dir).plot_foreach(
args.output,
partial(
plot_natpop,
file_path=args.file,
dof=args.dof,
node=args.node,
extension=args.extension,
),
)
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
type=str,
default="dmat2.h5/dmat2_gridrep",
help="path to the dmat file",
)
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
app = QtWidgets.QApplication(sys.argv)
data = read_dmat2_gridrep(args.path)
gui = Gui(data, 0, len(data[0]) - 1)
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="+",
default=["natpop"],
help="path to the natpop file",
)
parser.add_argument("-n", "--node", type=int, default=1, help="node")
parser.add_argument("-d",
"--dof",
type=int,
default=1,
help="degree of freedom")
parser.add_argument(
"--normalize",
action="store_true",
help="whether to normalize the entropy",
)
add_argparse_2d_args(parser)
add_argparse_save_arg(parser)
args = parser.parse_args()
labels = labels_from_paths(args.path)
figure, ax = plt.subplots(1, 1)
for path, label in zip(args.path, labels):
time, natpop = read_natpop(path, node=args.node, dof=args.dof)
try:
entropy = compute_entropy(natpop, args.normalize)
except ZeroDivisionError:
entropy = compute_entropy(natpop)
args.normalize = False
plot_entropy(ax, time, entropy, label=label, normalize=args.normalize)
system = units.get_default_unit_system()
ax.set_xlabel(system.get_time_unit().format_label("t"))
apply_2d_args(ax, figure, args)
if len(args.path) > 1:
ax.legend()
handle_saving(figure, args)
if not args.output:
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"scan_dir",
type=str,
help="directory of the scan containing the file scan.pickle",
)
parser.add_argument(
"-f",
"--file",
type=Path,
default=Path("propagate") / "output",
help="relative path within each simulation",
)
parser.add_argument(
"-e",
"--extension",
type=str,
default=".pdf",
help="file extensions for the plots",
)
parser.add_argument(
"-o",
"--output",
type=Path,
default="energy",
help="name of the output directory",
)
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
def apply_args(fig: Figure, ax: Axes, parameters: Parameters):
del parameters
plot.apply_2d_args(ax, fig, args)
load_scan(args.scan_dir).plot_foreach(
args.output,
partial(
plot_energy,
file_path=args.file,
modfunc=apply_args,
extension=args.extension,
),
)
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"scan_dir",
type=Path,
help="directory of the scan containing the file scan.pickle",
)
parser.add_argument(
"expval",
type=Path,
help="relative path to expval within each simulation",
)
parser.add_argument(
"-e",
"--extension",
type=str,
default=".pdf",
help="file extensions for the plots",
)
parser.add_argument("-o",
"--output",
type=str,
help="name of the output directory")
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
if not args.output:
args.output = "_".join(args.expval.with_suffix("").parts)
def apply_args(fig: Figure, ax: Axes, parameters: Parameters):
del parameters
plot.apply_2d_args(ax, fig, args)
load_scan(args.scan_dir).plot_foreach(
args.output,
partial(
plot_expval,
file_path=args.expval,
modfunc=apply_args,
extension=args.extension,
),
)
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path_natpop",
nargs="?",
default="natpop",
help="path to the natpop file",
)
parser.add_argument(
"path_evals",
nargs="?",
default="eval_dmat_dof1",
help="path to the file containing the dmat eigenvalues",
)
parser.add_argument("-n", "--node", type=int, default=1, help="node")
parser.add_argument("-d",
"--dof",
type=int,
default=1,
help="degree of freedom")
add_argparse_2d_args(parser)
args = parser.parse_args()
figure, ax = plt.subplots(1, 1)
time, natpop = read_natpop(args.path_natpop, node=args.node, dof=args.dof)
time2, evals = read_dmat_evals(args.path_evals)
if not numpy.allclose(time, time2):
raise RuntimeError("time points do not match")
for natpop, value in zip(natpop.T, evals.T):
plt.plot(time, natpop - value)
system = units.get_default_unit_system()
ax.set_xlabel(system.get_time_unit().format_label("t"))
apply_2d_args(ax, figure, args)
plt.show()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path",
nargs="?",
default="psi",
help="path to psi file")
parser.add_argument(
"gpop",
nargs="?",
default="gpop",
help="path to a gpop file in order to determin the grid",
)
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
times, spfs = inout.read_spfs(args.path)
_, grid, _ = inout.read_gpop(args.gpop, dof=1)
app = QtWidgets.QApplication(sys.argv)
window = DmatEvecSlider(times, grid, spfs, args)
assert window
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"path",
nargs="?",
default="propagate.h5/gpop",
help="path to the gpop file",
)
parser.add_argument("-d", "--dof", type=int, default=1, help="degree of freedom")
parser.add_argument(
"--momentum",
action="store_true",
help="transform to momentum space",
)
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
app = QtWidgets.QApplication(sys.argv)
data = read_gpop(args.path, args.dof)
if args.momentum:
data = transform_to_momentum_space(data)
gui = Gui(data, 0, len(data[0]) - 1, plot_args=args)
sys.exit(app.exec_())
def main():
parser = argparse.ArgumentParser()
parser.add_argument("path_psi", nargs="?", help="path to psi file")
parser.add_argument(
"path_norbs",
nargs="?",
help="path to file with natural orbitals",
)
plot.add_argparse_2d_args(parser)
args = parser.parse_args()
times, spfs = inout.read_spfs(args.path_psi)
_, grid, norbs = inout.read_dmat_evecs_grid(args.path_norbs)
weights = numpy.sqrt(dvr.add_harmdvr(225, 0.0, 0.3).get_weights())
for i in range(norbs.shape[0]):
for j in range(norbs.shape[1]):
norbs[i][j] *= weights
app = QtWidgets.QApplication(sys.argv)
window = DmatEvecSlider(times, grid, numpy.abs(spfs) - numpy.abs(norbs), args)
assert window
sys.exit(app.exec_())
