def test_lindblad():
mesolver = Lindblad_solver(H, c_ops=[sz.astype(complex)])
Nt = 800
dt = 0.5
import time
start_time = time.time()
# L = mesolver.liouvillian()
t0 = -10 / au2fs
result = mesolver.evolve(rho0,
dt=dt,
Nt=Nt,
e_ops=[H1],
return_result=True,
t0=t0)
#corr = mesolver.correlation_3op_2t(rho0, [sz, sz, sz], dt, Nt, Ntau=Nt)
# print(result.observables)
import proplot as plt
fig, ax = plt.subplots()
times = np.arange(Nt) * dt + t0
ax.plot(times, result.observables[:, 0])
ax.format(ylabel='Coherence')
print('Execution time = {} s'.format(time.time() - start_time))
fig, ax = plt.subplots()
ax.plot(times, pulse.field(times))
ax.set_ylabel('E(t)')
return
def plot_reaction_rate_burning_rate(df_rate):
fig, ax = pplot.subplots(aspect=(4, 3), axwidth=4)
c1 = pplot.scale_luminance('cerulean', 0.5)
c2 = pplot.scale_luminance('red', 0.5)
df_rate.sort_values(by="time", inplace=True)
lns1 = ax.plot(df_rate["time"],
df_rate["vol_averaged_reaction_rate"],
color=c1,
label="Reaction rate")
max_rate = df_rate["vol_averaged_reaction_rate"].max()
ax.format(xlabel="Time (s)",
ylabel="Volume-Averaged coke reaction rate (kg/m$^3$/s)",
ycolor=c1,
ylim=(-1, max_rate * 1.1))
ax2 = ax.twinx()
lns2 = ax2.plot(df_rate["time"],
df_rate["burning_fraction"] * 100,
color=c2,
linestyle="--",
label="Conversion")
ax2.format(xlabel="Time (s)",
ylabel="Conversion (%)",
ycolor=c2,
ylim=(-1, 100))
lns = lns1 + lns2
labs = [l.get_label() for l in lns]
ax.legend(lns, labs, loc="upper right", fancybox=True)
return ax, ax2, fig
def test_sesolver():
s0, sx, sy, sz = pauli()
H = (-0.05) * sz - 0. * sx
solver = SESolver(H)
Nt = 1000
dt = 4
psi0 = (basis(2, 0) + basis(2, 1)) / np.sqrt(2)
start_time = time.time()
result = solver.evolve(psi0, dt=dt, Nt=Nt, e_ops=[sx])
print("--- %s seconds ---" % (time.time() - start_time))
start_time = time.time()
times = np.arange(Nt) * dt
r = _ode_solver(H, psi0, dt=dt, Nt=Nt, nout=2, e_ops=[sx])
print("--- %s seconds ---" % (time.time() - start_time))
# test correlation functions
# corr = solver.correlation_3p_1t(psi0=psi0, oplist=[s0, sx, sx],
# dt=0.05, Nt=Nt)
#
# times = np.arange(Nt)
#
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.plot(times, result.observables[:, 0])
ax.plot(r.times, r.observables[:, 0], '--')
# ax.plot(times, corr.real)
plt.show()
def Plot_MaxTemperature_OutletO2ConcHistory(df_combined):
fig, ax = pplot.subplots(aspect=(4, 3), axwidth=4)
lns1 = ax.plot(df_combined["Time"],
df_combined["max"],
color=c1,
label="Max Point Temperature",
linestyle="-")
lns2 = ax.plot(df_combined["Time"],
df_combined["Transverse_Tmax"],
color=c1,
label="Max Transversely Averaged Temperature",
linestyle="--")
ax.format(xlabel="Time (s)", ylabel="Temperature (K)", ycolor=c1)
ax2 = ax.twinx()
lns3 = ax2.plot(df_combined["Time"],
df_combined["O2ConcAtOutlet"],
color=c2,
linestyle="-.",
label="O$_2$ Molar Concentration at outlet")
max_O2 = df_combined["O2ConcAtOutlet"].max()
ax2.format(ylabel="O$_2$ mole concentration At Outlet (mol/m$^3$)",
ycolor=c2)
lns = lns1 + lns2 + lns3
labs = [l.get_label() for l in lns]
ax.legend(lns, labs, loc="upper right", ncol=1, fancybox=True)
# fig.tight_layout()
return ax, ax2, fig
def linear_absorption(omegas, transition_energies, dip, output=None, \
gamma=1./au2ev, normalize=False):
'''
SOS for linear absorption signal S = 2 pi |mu_{fg}|^2 delta(omega - omega_{fg}).
The delta function is replaced with a Lorentzian function.
Parameters
----------
omegas : 1d array
the frequency range for the signal
transition_energies : TYPE
DESCRIPTION.
edip : 1d array
transtion dipole moment
output : TYPE, optional
DESCRIPTION. The default is None.
gamma : float, optional
Lifetime broadening. The default is 1./au2ev.
normalize : TYPE, optional
Normalize the maximum intensity of the signal as 1. The default is False.
Returns
-------
signal : 1d array
linear absorption signal at omegas
'''
signal = 0.0
for j, transition_energy in enumerate(transition_energies):
signal += dip[j]**2 * lorentzian(omegas - transition_energy, gamma)
if normalize:
signal /= max(signal)
if output is not None:
fig, ax = plt.subplots(figsize=(4, 3))
ax.plot(omegas * au2ev, signal)
#scale = 1./np.sum(dip**2)
for j, transition_energy in enumerate(transition_energies):
ax.axvline(transition_energy * au2ev, 0., dip[j]**2, color='grey')
ax.set_xlim(min(omegas) * au2ev, max(omegas) * au2ev)
ax.set_xlabel('Energy (keV)')
ax.set_ylabel('Absorption')
#ax.set_yscale('log')
# ax.set_ylim(0, 1)
# fig.subplots_adjust(wspace=0, hspace=0, bottom=0.15, \
# left=0.17, top=0.96, right=0.96)
fig.savefig(output, dpi=1200, transparent=True)
return signal
def plot_bamf_p(bAmfClr, bAmfCld, output_fig_dir):
'''plot bAmf at each pressure level'''
for p_index in range(bAmfClr.shape[0]):
f, axs = plot.subplots(ncols=2)
x, y = np.meshgrid(bAmfClr.x, bAmfClr.y)
m1 = axs[0].pcolormesh(y, x, bAmfClr[p_index, ...], levels=256)
m2 = axs[1].pcolormesh(y, x, bAmfCld[p_index, ...], levels=256)
axs[0].colorbar(m1, loc='r', label='bAmfClr')
axs[1].colorbar(m2, loc='r', label='bAmfCld')
# save figure
output_name = os.path.join(output_fig_dir, f'bAmf_layer{p_index}.png')
logging.info(f'Saving bAmf to {output_name}')
f.savefig(output_name)
def relative(name, dir_):
"""
Plots relative time comparisons.
"""
cats, nlats, sizes, tables = runtimes(name, dir_)
inco, = np.where(np.array([cat.lower() for cat in cats]) == 'nco')
inco = inco[0]
f, ax = plot.subplots(axwidth=2.5,
aspect=(2, 3),
legend='b',
span=False,
share=1)
hs = []
ic, xc = 0, 0 # make xarray lines different shades of same color
ref = np.array([table[inco][3] for table in tables])
for i in idxs:
if i == inco:
continue
cat = cats[i]
if 'xarray' in cat.lower():
color = xcolors[xc]
xc += 1
else:
# color = f'C{ic}'
color = ocolors[ic]
ic += 1
times = [table[i][3]
for table in tables] # 4th cell contains 'real' time
hs += ax.plot(sizes,
np.array(times) / ref,
color=color,
marker='o',
markersize=6,
label=cat,
lw=1)
ax.format(xlabel='file size (MB)',
ylabel='ratio',
gridminor=True,
ylim=(0.1, 3),
yscale='log',
yformatter='scalar',
xlim=(min(sizes), max(sizes)),
xscale='log',
xformatter='scalar',
suptitle=f'{name.title()} benchmark relative to NCO')
f.bpanel.legend(hs, ncols=2, order='F')
return f
def plot_all_stations(
df,
df_diff,
ncols=2,
days_smooth_gps=30,
ylim=None,
share=False,
figsize=(10, 10),
outname=None,
drop_na_insar=True,
):
import proplot as pplt
nplots = len(df_diff.index)
# fig, axes = plt.subplots(
fig, axes = pplt.subplots(
nrows=int(np.ceil(nplots / ncols)),
ncols=ncols,
# refwidth=1,
# refheight=1,
figsize=figsize,
sharex=share,
sharey=share,
# figsize=(4 * ncols, nplots)
)
# axes = axes.ravel()
for idx, n in enumerate(df_diff.index):
# ax = axes.ravel()[idx]
ax = axes[idx]
gps_col, insar_col = f"{n}_gps", f"{n}_insar"
# curdf = df[[]] # .dropna()
ax.plot(df.index, df[gps_col], marker="o", ms=1, alpha=0.3)
_plot_smoothed(ax, df, gps_col, days_smooth_gps, "-")
insar_df = df[[insar_col
]].dropna() if drop_na_insar else df[[insar_col]]
ax.plot(insar_df.index, insar_df[insar_col], marker="o", ms=1)
# print(df[insar_col].dropna())
# ax.legend()
# ax.grid()
ax.set_title(n)
axes.format(grid=True, ylim=ylim, ylabel="cm")
if outname:
fig.savefig(outname)
return fig, axes
def plot_fig(values, ticks, title, filename):
NTA_lats = [-90, 90]
NTA_lons = [-180, 180]
gap_x, gap_y = 1, 1
levels = 11
map_lon = np.arange(-180, 180, gap_x)
map_lat = np.arange(-90, 90, gap_y)
Lon, Lat = np.meshgrid(map_lon, map_lat)
fig, axs = plot.subplots(nrows=1,
ncols=1,
aspect=2,
axwidth=4,
basemap=False,
proj='cyl') #proj_kw={'lon_0': 180})
m = axs[0, 0].contourf(map_lon,
map_lat,
values,
levels=ticks,
extend='both',
cmap='Spectral',
norm='segmented',
colorbar='r',
colorbar_kw={'ticks': ticks})
# axs[0,0].format(title='Cloud Top Temperature (Kelvin)')
axs.format(suptitle=title,
landcolor='mushroom',
facecolor='white',
land=False,
reso='med',
borders=True,
titleborder=True,
lonlabels='b',
latlabels='l',
coast=True,
latlines=30,
lonlines=60)
fig.savefig(filename, facecolor='white', dpi=300)
def plot_comp_s5p_chem(s5p, ds, output_fig_dir):
'''Plot the comparison between S5P TM5 and CHEM product'''
# load data
s5p_amfClr = s5p['air_mass_factor_clear']
s5p_amfCld = s5p['air_mass_factor_cloudy']
amfClr = ds['scdClr'] / ds['vcdGnd']
amfCld = ds['scdCld'] / ds['vcdGnd']
# crop the data to data valid domain which usually is the wrfchem domain
valid = ~amfClr.isnull()
amfClr = amfClr.where(valid, drop=True)
amfCld = amfCld.where(valid, drop=True)
s5p_amfClr = s5p_amfClr.where(valid, drop=True)
s5p_amfCld = s5p_amfCld.where(valid, drop=True)
# plot
f, axs = plot.subplots(nrows=3, ncols=2)
vmax = max(s5p_amfClr.max(), amfClr.max()).values
s5p_amfClr.plot(ax=axs[0], vmin=0, vmax=vmax)
amfClr.plot(ax=axs[1], vmin=0, vmax=vmax)
vmax = max(s5p_amfCld.max(), amfCld.max()).values
s5p_amfCld.plot(ax=axs[2], vmin=0, vmax=vmax)
amfCld.plot(ax=axs[3], vmin=0, vmax=vmax)
(s5p_amfClr / amfClr).plot(ax=axs[4], vmin=0)
(s5p_amfCld / amfCld).plot(ax=axs[5], vmin=0)
axs[0].format(title='S5P AMFClr')
axs[1].format(title='CHEM AMFClr')
axs[2].format(title='S5P AMFCld')
axs[3].format(title='CHEM AMFCld')
axs[4].format(title='AMFClr (S5P/CHEM)')
axs[5].format(title='AMFCld (S5P/CHEM)')
# save figure
output_name = os.path.join(output_fig_dir, 'comp_chem_tm5.png')
logging.info(f'Saving to {output_name}')
f.savefig(output_name)
def set_axis(file_list):
'''set the axis format'''
f, axs = plot.subplots(proj='eqc',
nrows=math.ceil((len(file_list)/4)),
ncols=4,
span=False,
share=3)
axs.format(abc=True,
abcloc='l',
abcstyle='(a)',
labels=True,
lonlines=lon_d,
latlines=lat_d,
lonlim=(extend[0], extend[1]),
latlim=(extend[2], extend[3]),
geogridlinewidth=1,
geogridcolor='w',
)
return axs, f
def set_axis(radar_list):
'''set the axis format'''
f, axs = plot.subplots(proj='eqc',
ncols=len(radar_list),
nrows=2,
span=False,
share=3)
axs.format(
rowlabels=['CRF', 'Flashrate'],
abc=True,
abcloc='l',
abcstyle='a)',
labels=True,
lonlines=lon_d,
latlines=lat_d,
lonlim=(extend[0], extend[1]),
latlim=(extend[2], extend[3]),
geogridlinewidth=1,
geogridcolor='w',
)
return axs, f
def cars(self, shift, omega1, t2=0., plt_signal=False, fname=None):
edip = self.edip_rms
E = self.eigvals()
S = sos.cars(E, edip, shift, omega1, t2=t2)
if not plt_signal:
return S
else:
fig, ax = plt.subplots()
ax.contourf(shift*au2wavenumber, omega1*au2ev, S.imag.T, lw=0.6,\
cmap='spectral')
ax.format(xlabel='Raman shift (cm$^{-1}$)',
ylabel=r'$\Omega_1$ (eV)')
fig.savefig(fname + '.pdf')
return S, fig, ax
# column share the same axis limits, scales, ticks, and labels. This is often
# convenient, but may be annoying for some users. To keep this feature turned off,
# simply :ref:`change the default settings <ug_rc>` with e.g.
# ``plot.rc.update(share=False, span=False)``. See :ref:`this section <ug_share>`
# for details.
# %%
# Generate sample data
import numpy as np
state = np.random.RandomState(51423)
data = 2 * (state.rand(100, 5) - 0.5).cumsum(axis=0)
# %%
# Single subplot
import proplot as plot
fig, ax = plot.subplots()
ax.plot(data, lw=2)
ax.format(suptitle='Single subplot', xlabel='x axis', ylabel='y axis')
# %%
# Simple subplot grid
import proplot as plot
fig, axs = plot.subplots(ncols=2)
axs[0].plot(data, lw=2)
axs[0].format(xticks=20, xtickminor=False)
axs.format(suptitle='Simple subplot grid',
title='Title',
xlabel='x axis',
ylabel='y axis')
# %%
data = fits.getdata("coadded_and_subtracted_cube.fits")
corrs = fits.getdata("correllelagrams.fits")
indices = range(39, 49)
dataframes = data[indices]
corrsframes = corrs[indices, 24:75, 24:75]
dataflat = np.hstack([fr for fr in dataframes])
corrsflat = np.hstack([fr for fr in corrsframes])
# recreate power stretch
a = 1000
corrspower = (a**corrsflat - 1) / a
fig, axs = plot.subplots(figsize=("510px", "140px"), nrows=2, hspace=0)
ymax = corrspower.shape[0]
ymid = ymax // 2
xmax = corrsflat.shape[1]
xmid = corrsframes.shape[-1] // 2
axs[0].imshow(dataflat,
cmap="inferno",
origin="lower",
extent=(-0.5, 509.5, -0.5, 50.5))
axs[0].format(xlim=(0, xmax), ylim=(0, ymax))
axs[1].imshow(corrspower, cmap="inferno", origin="lower")
axs[1].hlines(ymid, 0, xmax, color="white", ls="--", lw=0.2)
xs = range(xmid, corrsflat.shape[1], corrsframes.shape[-1])
axs[1].vlines(xs, 0, ymax, color="white", ls="--", lw=0.2)
ave_T_var_sumstar_nf[j] = st2.spatial_ave_xr(Tvar_sumstar_nf.sel(lon=slice(lonbounds_ave[0],lonbounds_ave[1])), lats=lats.sel(lat=slice(latbounds_ave[0],latbounds_ave[1])))
ave_T_var_lambdaQs[j] = st2.spatial_ave_xr(Tvar_lambdaQs.sel(lon=slice(lonbounds_ave[0],lonbounds_ave[1])), lats=lats.sel(lat=slice(latbounds_ave[0],latbounds_ave[1])))
ave_T_var_lambdaQr[j] = st2.spatial_ave_xr(Tvar_lambdaQr.sel(lon=slice(lonbounds_ave[0],lonbounds_ave[1])), lats=lats.sel(lat=slice(latbounds_ave[0],latbounds_ave[1])))
ave_T_var_lambdaQtot[j] = st2.spatial_ave_xr(Tvar_lambdaQtot.sel(lon=slice(lonbounds_ave[0],lonbounds_ave[1])), lats=lats.sel(lat=slice(latbounds_ave[0],latbounds_ave[1])))
# ave_T_var_lambdaQs[j] = st2.spatial_ave_xr(Tvar_Qs - Tvar_Qsstar, lats)
# ave_T_var_lambdaQr[j] = st2.spatial_ave_xr(Tvar_Qr - Tvar_Qrstar, lats)
print('T_var_sum', ave_T_var_sum[j])
print('T_var', ave_T_var[j])
fig, axs = plot.subplots(ncols=1, nrows=2, aspect=1.2, tight=True, share=False, hratios=(3,2))
#plot.subplots(ncols=2, nrows=3)
h1=axs[0].plot(Tns/12., ave_T_var_Qs, color='C2', label=r'$Q_s$', linewidth=2, zorder=5)
#plt.plot(Tns/12., ave_T_var_thf, color='C3', label=r'$THF$')
#plt.plot(Tns/12., ave_T_var_Rnet, color='C4', label=r'$R_{net}$')
h2=axs[0].plot(Tns/12., ave_T_var_Qr, color='C0', label=r'$Q_o$', linewidth=2, zorder=5)
#plt.plot(Tns/12., ave_T_var_Qek, color='C1', label=r'$Q_{ek}$')
h3=axs[0].plot(Tns/12., ave_T_var_sum, color='k', label=r'$\sigma^2_T$', linewidth=2, zorder=5)
#h4=axs[0].plot(Tns/12., ave_T_var, color='C5', label=r'$\sigma_T^2$')
axs[0].axhline(0, color='k', linewidth=1)
hs=[h1,h2,h3]
#Global/tropics
#axs[0].set_ylim(-0.1,0.6)
#axs[0].set_ylim(-0.1,0.48)
axs[0].set_ylim(-0.1,0.38)
# `~proplot.ui.subplots`. This generates a `~proplot.axes.PolarAxes`
# instance. Its `~proplot.axes.PolarAxes.format` command permits
# polar-specific modifications like changing the central radius, the zero
# azimuth location, the radial and azimuthal limits, and the positive
# azimuthal direction. This projection can also be used to make sector plots
# and annular plots.
# %%
import proplot as plot
import numpy as np
N = 200
state = np.random.RandomState(51423)
x = np.linspace(0, 2 * np.pi, N)
y = 100 * (state.rand(N, 5) - 0.3).cumsum(axis=0) / N
plot.rc['axes.titlepad'] = '1em' # default matplotlib offset is incorrect
fig, axs = plot.subplots([[1, 1, 2, 2], [0, 3, 3, 0]], proj='polar')
axs.format(
suptitle='Polar axes demo',
linewidth=1,
ticklabelsize=9,
rlines=0.5,
rlim=(0, 19),
)
for i in range(5):
xi = x + i * 2 * np.pi / 5
axs.plot(xi, y[:, i], cycle='FlatUI', zorder=0, lw=3)
# Standard polar plot
axs[0].format(title='Normal plot',
thetaformatter='pi',
rlines=5,
# datasets with complex statistical distributions.
#
# In the below example, we create a new divering colormap and
# reconstruct the colormap from `this SciVisColor example
# <https://sciviscolor.org/media/filer_public/c7/27/c727e638-82eb-445b-bc96-e7b64c13efa2/colormoves.png>`__.
# We also save the results for future use by passing ``save=True`` to
# `~proplot.constructor.Colormap`.
# %%
import proplot as pplt
import numpy as np
state = np.random.RandomState(51423)
data = state.rand(30, 30).cumsum(axis=1)
# Generate figure
fig, axs = pplt.subplots([[0, 1, 1, 0], [2, 2, 3, 3]], refwidth=2.4, span=False)
axs.format(
xlabel='xlabel', ylabel='ylabel',
suptitle='Merging colormaps'
)
# Diverging colormap example
title1 = 'Diverging from sequential maps'
cmap1 = pplt.Colormap('Blues4_r', 'Reds3', name='Diverging', save=True)
# SciVisColor examples
title2 = 'SciVisColor example'
cmap2 = pplt.Colormap(
'Greens1_r', 'Oranges1', 'Blues1_r', 'Blues6',
ratios=(1, 3, 5, 10), name='SciVisColorUneven', save=True
)
def test_journal_subplots(journal):
"""Tests that subplots can be generated with journal specifications."""
f, axs = plot.subplots(journal=journal)
def plot_stats(data,
x_key,
x_label=None,
y_keys=None,
y_labels=None,
start_index=0,
save_filename=None):
"""
Generate time-series plots of stats specified by keys
Args:
data: [dict] containing data to be plotted. len of all values should be equal
data must include x_key as a valid key
x_key: [str] key for the x-axis (time varying component)
x_label: [str] corresponding label for the x_key, if not provided then the key is used
y_keys: [list of str] optional list of keys to plot, each should exist in data.keys()
If nothing is given, data.keys() will be used
y_labels: [list of str] optional list of labels, should be the same length as keys input
If nothing is given, y_keys will be used
start_index: [int] time offset for plotting data - default=0 will plot all data
save_filename: [str] containing the complete output filename.
Returns:
fig: matplotlib figure handle
"""
assert x_key in list(data.keys()), ('x_key=%s must be in data.keys()' %
x_key)
if x_label is None:
x_label = x_key
if y_keys is None:
y_keys = list(data.keys())
if 'epoch' in y_keys:
y_keys.remove('epoch')
if 'batch_step' in y_keys:
y_keys.remove('batch_step')
else:
assert all([y_key in list(data.keys()) for y_key in y_keys])
if y_labels is None:
y_labels = [' '.join(y_key.split('_')) for y_key in y_keys]
else:
assert len(y_labels) == len(y_keys), (
'The number of y_labels must match the number of y_keys')
num_y_keys = len(y_keys)
num_plots_y = int(np.ceil(np.sqrt(num_y_keys)))
num_plots_x = int(np.ceil(np.sqrt(num_y_keys)))
fig, axes = plot.subplots(nrows=num_plots_y,
ncols=num_plots_x,
sharex=False,
sharey=False)
key_idx = 0
for plot_id in np.ndindex((num_plots_y, num_plots_x)):
if key_idx < num_y_keys:
x_dat = data[x_key][start_index:]
y_dat = data[y_keys[key_idx]][start_index:]
if len(x_dat) == len(y_dat):
ax = axes[plot_id]
ax.plot(x_dat, y_dat)
ax.format(yticks=[
np.minimum(0.0, np.min(y_dat)),
np.maximum(0.0, np.max(y_dat))
],
ylabel=y_labels[key_idx])
key_idx += 1
else:
ax = clear_axis(axes[plot_id])
print(
'utils/plot_functions.py: WARNING: x and y for key %s must have same first dimensions but are %g and %g'
% (y_keys[key_idx], len(x_dat), len(y_dat)))
else:
ax = clear_axis(axes[plot_id])
axes.format(xlabel=x_label, suptitle='Stats per Batch')
if save_filename is not None:
fig.savefig(save_filename, transparent=True)
plot.close(fig)
return None
plot.show()
return fig
gcsmap = fs.get_mapper(pr_zarr)
dset = xr.open_zarr(gcsmap)
# %%
dset
# %% [markdown]
# ## Plot the first timestep
# %%
dset['time'][0]
# %%
fig, ax = plot.subplots(axwidth=4.5,
tight=True,
proj='robin',
proj_kw={'lon_0': 90},
figsize=(15, 10))
# format options
ax.format(
land=False,
coast=True,
innerborders=True,
borders=True,
labels=True,
geogridlinewidth=0,
)
map1 = ax.pcolormesh(dset['lon'],
dset['lat'],
dset['pr'][0, :, :] * 1.e3,
cmap='IceFire',
def photon_echo_t3(mol, omega1, omega2, t3, g_idx=[0], e_idx=None, f_idx=None,\
fname='2DES', plt_signal=False, separate=False):
"""
2D photon echo signal scanning omega1 and omega2 at detection time t3.
The current implementation only applies for a single ground state.
For a manifold of g states, the ground state bleaching neglected here has to be considered.
Parameters
----------
evals : ndarray
eigenvalues of system.
edip : ndarray
electric dipole matrix.
omega1 : TYPE
DESCRIPTION.
omega3 : TYPE
DESCRIPTION.
tau2 : TYPE
DESCRIPTION.
g_idx : TYPE
DESCRIPTION.
e_idx : TYPE
DESCRIPTION.
gamma : TYPE
DESCRIPTION.
separate: bool
separate the ladder diagrams
Returns
-------
TYPE
DESCRIPTION.
"""
E = mol.eigvals()
edip = mol.edip_rms
gamma = mol.gamma
dephasing = mol.dephasing
if gamma is None:
raise ValueError('Please set the decay constants gamma first.')
N = mol.nstates
if e_idx is None: e_idx = range(1, N)
if f_idx is None: f_idx = range(1, N)
# gsb = _GSB(evals, edip, omega1, omega3, t2, g_idx, e_idx, gamma)
se = _SE(E,
edip,
-omega1,
omega2,
t3,
g_idx,
e_idx,
gamma,
dephasing=dephasing)
esa = _ESA(E, edip, -omega1, omega2, t3, g_idx, e_idx, f_idx, \
gamma, dephasing=dephasing)
S = se + esa
if plt_signal == True:
# make plots
fig, ax = plt.subplots(refaspect=2)
im = ax.contourf(
omega1 * au2ev,
omega2 * au2ev,
S.real / abs(S).max(), #interpolation='bilinear',
cmap=cm.RdBu,
lw=0.6,
origin='lower') #-abs(SPE).max())
ax.set_xlabel(r'$-\Omega_1$ (eV)')
ax.set_ylabel(r'$\Omega_2$ (eV)')
if separate:
np.savez(fname, omega1, omega2, se, esa)
return se, esa
else:
np.savez(fname, omega1, omega2, S)
return S
def benchmark(name, dir_, ncols=3, ymin=0.1, ymax=50, server='uriah'):
"""
Plots benchmark result summaries.
"""
cats, nlats, sizes, tables, fname = runtimes(name, dir_, server=server)
plot.rc.cycle = 'colorblind10'
server = {
'uriah': 'macbook',
'cheyenne4': 'supercomputer',
'monde': 'server'
}.get(server, server)
f, axs = plot.subplots(axwidth=2.5,
ncols=2,
aspect=(2, 3),
legend='b',
span=False,
share=1)
nxarray = len([cat for cat in cats if 'xarray' in cat.lower()])
xcolors = plot.colors('greys', nxarray, left=0.3)
ocolors = [
color for i, color in enumerate(plot.colors('colorblind10'))
if i not in (5, 7)
]
idxs = np.argsort(cats) # use alphabetical order
for ax, scale in zip(axs, ('linear', 'log')):
hs = []
ic, xc = 0, 0 # make xarray lines different shades of same color
for i in idxs:
cat = cats[i]
if 'xarray' in cat.lower():
color = xcolors[xc]
xc += 1
else:
# color = f'C{ic}'
color = ocolors[ic]
ic += 1
times = [table[i][3]
for table in tables] # 4th cell contains 'real' time
hs += ax.plot(sizes,
times,
color=color,
marker='o',
markersize=6,
label=cat,
lw=1)
# hs += [ax.scatter(sizes, times, color=[color], label=cat)]
ax.format(
xlabel='file size (MB)',
ylabel='time (seconds)',
gridminor=True,
# ax.format(xlabel='latitude count', ylabel='time (seconds)',
ylim=(0, ymax) if scale == 'linear' else (ymin, ymax),
yscale=scale,
yformatter='scalar',
xlim=(min(sizes), max(sizes)),
xscale=scale,
xformatter='scalar',
title=f'{scale.title()} scale',
suptitle=f'{name.title()} benchmark on {server}')
f.bpanel.legend(hs, ncols=ncols, order='F')
f.save(fname)
return f
def npbytes_to_str(var):
return (bytes(var).decode("utf-8"))
# read data
ds = xr.open_dataset('../output_files/wrfchemi_00z_d01')
# take 06 UTC and 24 MOZCART species as an example
t = 6
# get info of time
Times = ds['Times']
time_str = datetime.strptime("".join(npbytes_to_str(Times[t].values)),
"%Y-%m-%d_%H:%M:%S").strftime("%Y-%m-%d_%H:%M:%S")
# get keys except "Times"
species = ds.drop_vars('Times')
# plot
f, axs = plot.subplots(tight=True, share=0,
nrows=6, ncols=4,
)
axs.format(suptitle=time_str+' nearest')
for index, key in enumerate(species):
m = axs[index].pcolormesh(ds[key][t, 0, ...], levels=256, cmap='Fire')
axs[index].format(title=ds[key].attrs['description'])
axs[index].colorbar(m, loc='r',
label=ds[key].attrs['units'],
tickminor=False)
f.savefig('../emission_example.png')
# dip[3, 3] = 1.
# dip[0, 3] = dip[3,0] = [0.5, 1, 0]
mol = Mol(H, dip)
mol.set_decay(gamma)
return mol
if __name__ == '__main__':
from lime.units import au2fs
from lime.style import subplots
fig, ax = plt.subplots(figsize=(4.2, 3.2))
E = np.array([0., 0.5, 1.1, 1.3]) / au2ev
gamma = [0, 0.002, 0.002, 0.002]
H = np.diag(E)
from lime.mol import Mol
from lime.optics import Biphoton
from matplotlib import cm
dip = np.zeros((len(E), len(E)))
dip[1, 2] = dip[2, 1] = 1.
dip[1, 3] = dip[3, 1] = 1.
dip[0, 1] = dip[1, 0] = 1.
dip[0, 3] = dip[3, 0] = 1
# %%
import proplot as pplt
import numpy as np
import pandas as pd
# Cycle that loops through 'dashes' Line2D property
cycle = pplt.Cycle(lw=3, dashes=[(1, 0.5), (1, 1.5), (3, 0.5), (3, 1.5)])
# Sample data
state = np.random.RandomState(51423)
data = (state.rand(20, 4) - 0.5).cumsum(axis=0)
data = pd.DataFrame(data, columns=pd.Index(['a', 'b', 'c', 'd'], name='label'))
# Plot data
fig, ax = pplt.subplots(refwidth=2.5, suptitle='Plot without color cycle')
obj = ax.plot(data,
cycle=cycle,
legend='ll',
legend_kw={
'ncols': 2,
'handlelength': 2.5
})
# %% [raw] raw_mimetype="text/restructuredtext"
# .. _ug_cycles_dl:
#
# Downloading color cycles
# ------------------------
#
# There are several interactive online tools for generating perceptually
def absorption(mol,
omegas,
plt_signal=False,
fname=None,
normalize=False,
scale=1.,
yscale=None):
'''
SOS for linear absorption signal S = 2 pi |mu_{fg}|^2 delta(omega - omega_{fg}).
The delta function is replaced with a Lorentzian function.
Parameters
----------
omegas : 1d array
detection frequency window for the signal
H : 2D array
Hamiltonian
edip : 2d array
electric dipole moment
output : TYPE, optional
DESCRIPTION. The default is None.
gamma : float, optional
Lifetime broadening. The default is 1./au2ev.
normalize : TYPE, optional
Normalize the maximum intensity of the signal as 1. The default is False.
Returns
-------
signal : 1d array
linear absorption signal at omegas
'''
edip = mol.edip_rms
gamma = mol.gamma
eigenergies = mol.eigvals()
# set the ground state energy to 0
eigenergies = eigenergies - eigenergies[0]
# assume the initial state is from the ground state 0
signal = 0.0
for j in range(1, mol.nstates):
e = eigenergies[j]
signal += abs(edip[j, 0])**2 * lorentzian(omegas - e, gamma[j])
if normalize:
signal /= max(signal)
if plt_signal:
fig, ax = plt.subplots(figsize=(4, 3))
ax.plot(omegas * au2ev, signal)
for j, e in enumerate(eigenergies):
ax.axvline(e * au2ev, 0., abs(edip[0, j])**2 * scale, color='grey')
ax.set_xlim(min(omegas) * au2ev, max(omegas) * au2ev)
ax.set_xlabel('Energy (eV)')
ax.set_ylabel('Absorption')
if yscale:
ax.set_yscale(yscale)
# ax.set_ylim(0, 1)
# fig.subplots_adjust(wspace=0, hspace=0, bottom=0.15, \
# left=0.17, top=0.96, right=0.96)
if fname is not None:
fig.savefig(fname, dpi=1200, transparent=True)
return signal, fig, ax
else:
return signal
# it every time ProPlot is imported, simply pass ``save=True`` to
# `~proplot.constructor.Cycle`. If you want to change the global property
# cycler, pass a *name* to the :rcraw:`cycle` setting or pass the result of
# `~proplot.constructor.Cycle` to the :rcraw:`axes.prop_cycle` setting (see
# the :ref:`configuration guide <ug_config>`).
# %%
import numpy as np
lw = 5
state = np.random.RandomState(51423)
data = (state.rand(12, 6) - 0.45).cumsum(axis=0)
kwargs = {'legend': 'b', 'labels': list('abcdef')}
# Modify the default color cycle
plot.rc.cycle = '538'
fig, axs = plot.subplots(ncols=3, axwidth=1.9)
axs.format(suptitle='Changing the color cycle')
ax = axs[0]
ax.plot(data, lw=lw, **kwargs)
ax.format(title='Global color cycle')
# Pass the cycle to a plotting command
ax = axs[1]
ax.plot(data, cycle='qual1', lw=lw, **kwargs)
ax.format(title='Local color cycle')
# As above but draw each line individually
# Note that the color cycle is not reset with each plot call
ax = axs[2]
labels = kwargs['labels']
for i in range(data.shape[1]):
def photon_echo(mol, pump, probe, t2=0., g_idx=[0], e_idx=None, f_idx=None, fname='signal', \
plt_signal=False, pol=None):
"""
Photon echo signal for a multi-level system using SOS expression.
Approximations:
1. decay are included phenomelogically
2. no population relaxation
Parameters
----------
mol : TYPE
DESCRIPTION.
pump : TYPE
Omega1, conjugate variable of t1
probe : TYPE
Omega3, conjugate variable of t3
t2 : TYPE
population time.
g_idx : TYPE
DESCRIPTION.
e_idx : TYPE
DESCRIPTION.
f_idx : TYPE
DESCRIPTION.
gamma : float
decay rates for excited states.
Raises
------
ValueError
DESCRIPTION.
Returns
-------
S : TYPE
DESCRIPTION.
"""
E = mol.eigvals()
dip = mol.edip_rms
gamma = mol.gamma
if gamma is None:
raise ValueError('Please set the decay constants gamma first.')
N = mol.nstates
if e_idx is None: e_idx = range(N)
if f_idx is None: f_idx = range(N)
# compute the signal
S = _photon_echo(E, dip, omega1=-pump, omega3=probe, t2=t2, g_idx=g_idx, e_idx=e_idx, f_idx=f_idx,\
gamma=gamma)
np.savez(fname, pump, probe, S)
if plt_signal == True:
# make plots
fig, ax = plt.subplots()
omega_min = min(pump) * au2ev
omega_max = max(pump) * au2ev
im = ax.contour(
S.real.T / abs(S).max(), #interpolation='bilinear',
cmap=cm.RdBu,
origin='lower',
extent=[omega_min, omega_max, omega_min, omega_max],
vmax=1,
vmin=-1) #-abs(SPE).max())
ax.plot(pump * au2ev, probe * au2ev, '--', lw=1, color='grey')
# ax.axhline(y=1.1, color='w', linestyle='--', linewidth=0.5, alpha=0.5)
# ax.axhline(y=0.9, color='w', linestyle='--', linewidth=0.5, alpha=0.5)
#
# ax.axvline(x=1.1, color='w', linestyle='--', linewidth=0.5, alpha=0.5)
# ax.axvline(x=0.9, color='w', linestyle='--', linewidth=0.5, alpha=0.5)
#im = ax.contour(SPE,
# origin='lower', extent=[0.8, omega_max, omega_min, omega_max],
# vmax=1, vmin=0) #-abs(SPE).max())
ax.set_xlabel(r'$-\Omega_1$ (eV)')
ax.set_ylabel(r'$\Omega_3$ (eV)')
#ax.set_title(r'$T_2 = $' + str(t2))
# plt.colorbar(im)
# fig.subplots_adjust(hspace=0.0,wspace=0.0,bottom=0.14,left=0.0,top=0.95,right=0.98)
return S
# cycle is used to style the input data. ProPlot iterates through property
# cycle properties when (1) making multiple calls to a plotting command, or (2)
# plotting successive columns of 2-dimensional input data. For more information
# on property cycles, see the :ref:`color cycles section <ug_cycles>` and `this
# matplotlib tutorial
# <https://matplotlib.org/tutorials/intermediate/color_cycle.html#sphx-glr-tutorials-intermediate-color-cycle-py>`__.
# %%
import proplot as plot
import numpy as np
state = np.random.RandomState(51423)
data1 = state.rand(6, 4)
data2 = state.rand(6, 4) * 1.5
with plot.rc.context({'lines.linewidth': 3}):
fig, axs = plot.subplots(ncols=2)
axs.format(xlabel='xlabel',
ylabel='ylabel',
suptitle='Local property cycles demo')
# Property cycles specific to datasets
axs[0].plot(data1, cycle='Reds', cycle_kw={'left': 0.3})
axs[0].plot(data2, cycle='Blues', cycle_kw={'left': 0.3})
axs[1].plot(data1 * data2,
cycle='black',
cycle_kw={'linestyle': ('-', '--', '-.', ':')})
# %% [raw] raw_mimetype="text/restructuredtext"
# .. _ug_1dstd:
#
# Standardized arguments