def get_dataset_color(dataset,depth=None):
"""Set the colors to ensure a uniform scheme for each dataset """
dataset=string.lower(dataset)
d={}
d["dai"]=cm.Blues(.5)
d["tree"]=cm.summer(.3)
d["cru"]=cm.Blues(.9)
#models
d["picontrol"]=cm.Purples(.8)
d["h85"]="k"
d["tree_noise"]=cm.PiYG(.2)
#Soil moisture
d["merra2"]={}
d["merra2"]["30cm"]=cm.copper(.3)
d["merra2"]["2m"]=cm.copper(.3)
d["gleam"]={}
d["gleam"]["30cm"]=cm.Reds(.3)
d["gleam"]["2m"]=cm.Reds(.7)
if depth is None:
return d[dataset]
else:
return d[dataset][depth]
def four_Vm_traces(data,
ax,
tzoom=[1000, 2000],
Tbar=50,
Vshift=30,
vpeak=-42,
vbottom=-80):
t = np.arange(int(data['tstop'] / data['dt'])) * data['dt']
cond = (t > tzoom[0]) & (t < tzoom[1])
## excitatory traces:
for i in range(3):
ax.plot(t[cond],
data['VMS_RecExc'][i][cond] + Vshift * i,
color=copper(i / 3 / 1.5),
lw=1)
# adding spikes
for i in range(3):
tspikes = data['tRASTER_RecExc'][np.argwhere(
data['iRASTER_RecExc'] == i).flatten()]
for ts in tspikes[(tspikes > tzoom[0]) & (tspikes < tzoom[1])]:
ax.plot([ts, ts],
Vshift * i + np.array([-50, vpeak]),
'--',
color=copper(i / 3 / 1.5),
lw=1)
# ## inhibitory trace:
cond = (t > tzoom[0]) & (t < tzoom[1])
ax.plot(t[cond], data['VMS_RecInh'][0][cond] + Vshift * 3, color=Red, lw=1)
tspikes = data['tRASTER_RecInh'][np.argwhere(
data['iRASTER_RecInh'] == 0).flatten()]
for ts in tspikes[(tspikes > tzoom[0]) & (tspikes < tzoom[1])]:
ax.plot([ts, ts],
Vshift * 3 + np.array([-53, vpeak]),
'--',
color=Red,
lw=1)
ax.plot(tzoom[0] * np.ones(2), [-50, -40], lw=5, color='gray')
ax.annotate('10mV', (-0.1, .4),
rotation=90,
fontsize=14,
xycoords='axes fraction')
ax.plot([tzoom[0], tzoom[0] + Tbar], [-75, -75], lw=5, color='gray')
ax.annotate(str(Tbar) + ' ms', (0.1, -0.1),
fontsize=14,
xycoords='axes fraction')
set_plot(ax, [], xticks=[], yticks=[])
def plot_profiles():
fnames = [
"chgl_10_00000001000.tsv", "chgl_10_00000005000.tsv",
"chgl_10_00000010000.tsv", "chgl_10_00000030000.tsv",
"chgl_10_00000040000.tsv", "chgl_10_00000050000.tsv"
]
times = list(range(len(fnames)))
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
folder = "data/almgsi_ch500K_run3"
folder = "data/almgsi_ch500K_run_truncnorm"
times = np.array(times, dtype=np.float64)
times -= np.min(times)
times /= np.max(times)
times = times.tolist()
for t, fname in zip(times, fnames):
full_fname = folder + "/" + fname
freq, prof = fft(full_fname)
print(np.mean(prof))
ax.plot(freq,
prof / np.sum(prof),
drawstyle='steps',
color=cm.copper(t))
ax.set_yscale('log')
ax.set_xlabel("Frequency (nm \${-1}\$)")
ax.set_ylabel("Occurence probability")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
plt.show()
def setup_figure():
fig=plt.figure(1)
plt.clf()
ax = fig.add_subplot(1,1,1)
ax.set_xlim([-rho-1,rho+1])
ax.set_ylim([-rho-1,rho+1])
ax.set_aspect('equal')
cells=[]
springs=[]
borders=[]
for i in range(0,N):
c = plt.Circle((-0,0),0.5,color=cm.copper(0))
cells.append(ax.add_artist(c))
if plot_springs:
for i in range(0,len(pairs)):
springs += ax.plot([], [], color=cm.spectral(0))
if plot_voronoi:
for i in range(0, pairs2.shape[0]):
borders += ax.plot([], [], color='k')
ang_mom = ax.add_patch(FancyArrowPatch((0,0),(1,1),ec='r', fc='r', zorder=0, arrowstyle=u'simple,head_width=20, head_length=10'))
return(fig,cells,springs,borders,ang_mom)
def first():
filename = "scatter.txt"
file = open(filename, "r")
tmp = []
x = []
y = []
for line in file:
tmp.append(line)
for word in tmp[0].split():
x.append(float(word))
for word in tmp[1].split():
y.append(float(word))
file.close
plt.axes(polar=True)
data = []
for num in y:
data.append((num+5)*20)
clr = cm.copper(data)
plt.scatter(x, y, 10, y)
plt.show()
def get_colors(self, qty):
qty = np.power(qty / qty.max(), 1.0 / CONTRAST)
if COLORMAP == 0:
rgba = cm.gray(qty, alpha=ALPHA)
elif COLORMAP == 1:
rgba = cm.afmhot(qty, alpha=ALPHA)
elif COLORMAP == 2:
rgba = cm.hot(qty, alpha=ALPHA)
elif COLORMAP == 3:
rgba = cm.gist_heat(qty, alpha=ALPHA)
elif COLORMAP == 4:
rgba = cm.copper(qty, alpha=ALPHA)
elif COLORMAP == 5:
rgba = cm.gnuplot2(qty, alpha=ALPHA)
elif COLORMAP == 6:
rgba = cm.gnuplot(qty, alpha=ALPHA)
elif COLORMAP == 7:
rgba = cm.gist_stern(qty, alpha=ALPHA)
elif COLORMAP == 8:
rgba = cm.gist_earth(qty, alpha=ALPHA)
elif COLORMAP == 9:
rgba = cm.spectral(qty, alpha=ALPHA)
return rgba
def distributions(self, number_of_agents, row_agents, col_agents, row_strategies, col_strategies,plot):
self.row_strategies_distribution = self.proportion_classified_strategies(row_agents, row_strategies)
for rs in range(len(row_strategies)):
self.row_accumulated_strategies[rs].append(self.row_strategies_distribution[rs])
self.col_strategies_distribution = self.proportion_classified_strategies(col_agents, col_strategies)
for cs in range(len(col_strategies)):
self.col_accumulated_strategies[cs].append(self.col_strategies_distribution[cs])
self.total_strategies_per_generation = self.total_classified_strategies(row_agents, row_strategies, col_agents, col_strategies)
for sh in range(len(self.strategies_history)):
self.strategies_history[sh].append(self.total_strategies_per_generation[sh])
print "\n Row players' strategy distribution:"
print "\t", self.row_strategies_distribution
print "\n Column players' strategy distribution:"
print "\t", self.col_strategies_distribution
ga.kill_agents(env.row_agents, env.number_of_agents, env.number_of_row_agents, env.row_strategies)
ga.kill_agents(env.col_agents, env.number_of_agents, env.number_of_col_agents, env.col_strategies)
print "Row agents eliminated", (number_of_agents / 2) - len(env.col_agents)
print "Col agents eliminated", (number_of_agents / 2) - len(env.row_agents)
ga.reproduce_agents(env.row_agents, env.number_of_agents, env.number_of_row_agents, env.row_strategies)
ga.reproduce_agents(env.col_agents, env.number_of_agents, env.number_of_col_agents, env.col_strategies)
if plot==True:
for k in range(len(env.row_strategies)):
c = cm.copper((k + 1) / len(env.row_strategies))
pl.plot(self.row_accumulated_strategies[k], color=c, label="Row strategies: %s" % (k + 1))
for k in range(len(env.col_strategies)):
c = cm.winter((k + 1) / len(env.row_strategies))
pl.plot(self.col_accumulated_strategies[k], color=c, label="Col strategies: %s" % (k + 1))
pl.draw()
def get_colors(self, qty):
qty = np.power(qty / qty.max(), 1.0 / CONTRAST)
if COLORMAP == 0:
rgba = cm.gray(qty, alpha=ALPHA)
elif COLORMAP == 1:
rgba = cm.afmhot(qty, alpha=ALPHA)
elif COLORMAP == 2:
rgba = cm.hot(qty, alpha=ALPHA)
elif COLORMAP == 3:
rgba = cm.gist_heat(qty, alpha=ALPHA)
elif COLORMAP == 4:
rgba = cm.copper(qty, alpha=ALPHA)
elif COLORMAP == 5:
rgba = cm.gnuplot2(qty, alpha=ALPHA)
elif COLORMAP == 6:
rgba = cm.gnuplot(qty, alpha=ALPHA)
elif COLORMAP == 7:
rgba = cm.gist_stern(qty, alpha=ALPHA)
elif COLORMAP == 8:
rgba = cm.gist_earth(qty, alpha=ALPHA)
elif COLORMAP == 9:
rgba = cm.spectral(qty, alpha=ALPHA)
return rgba
def plt_bw(ground_truth, predicted, loss, rows, ymax=None):
"""Plot windows and color encode by loss"""
if ymax is None:
ymax = np.max(ground_truth[rows])
lossmax = np.max(loss[rows])
bg = "#ffffff"
n = rows.size
plt.figure(figsize=(20, n * 2))
for i, k in enumerate(rows):
# display original
ax = plt.subplot(n * 2, 1, i * 2 + 1)
ax.set_facecolor("#888888")
plt.bar(np.arange(ground_truth[k].size), ground_truth[k], color=bg)
plt.ylim(0, ymax)
ax.get_xaxis().set_visible(False)
c = rgba_to_hex(copper((lossmax - loss[k]) / lossmax))
# display reconstruction
ax = plt.subplot(n * 2, 1, i * 2 + 2)
ax.set_facecolor(c)
plt.bar(np.arange(predicted[k].size), predicted[k], color=bg)
plt.ylim(0, ymax)
ax.get_xaxis().set_visible(False)
plt.show()
def plot_global_reion_runs(zs, data):
# Take data (e.g. from get_global_reion_runs) and plot.
nzeta = zs.shape[0]
ntvir = zs.shape[1]
nmfp = zs.shape[2]
plt.figure('Global runs')
plt.clf()
plt.subplot(131)
colors = iter(cm.copper(np.linspace(0, 1, nzeta)))
for i in xrange(nzeta):
plt.plot(zs[i, ntvir / 2, nmfp / 2, :], data[i, ntvir / 2, nmfp / 2, :], color=next(colors))
plt.subplot(132)
colors = iter(cm.copper(np.linspace(0, 1, ntvir)))
for i in xrange(ntvir):
plt.plot(zs[nzeta / 2, i, nmfp / 2, :], data[nzeta / 2, i, nmfp / 2, :], color=next(colors))
plt.subplot(133)
colors = iter(cm.copper(np.linspace(0, 1, nmfp)))
for i in xrange(nmfp):
plt.plot(zs[nzeta / 2, ntvir / 2, i, :], data[nzeta / 2, ntvir / 2, i, :], color=next(colors))
def animate_system(positions: pd.DataFrame,
steps: int = 10,
size: int = 100) -> int:
"""
Creates an interactive plot to visualize the positions of the
moons at each step
"""
velocities = pd.DataFrame({
'x': [0] * len(positions),
'y': [0] * len(positions),
'z': [0] * len(positions)
})
# Create empty plot
fig = plt.figure(figsize=(7, 7))
ax = fig.add_subplot(111, projection='3d')
x, y, z = [], [], []
colors = cm.copper(4)
sc = ax.scatter(x, y, z, s=size)
# Compute all positions
step_pos = []
for i in range(steps):
# Apply gravity
velocities = update_velocity(positions, velocities)
# Apply velocity
positions = positions + velocities
step_pos.append(positions)
# Set plot limits
allx = [i for sl in [list(p['x']) for p in step_pos] for i in sl]
ally = [i for sl in [list(p['y']) for p in step_pos] for i in sl]
allz = [i for sl in [list(p['z']) for p in step_pos] for i in sl]
ax.set_xlim3d(min(allx), max(allx))
ax.set_ylim3d(min(ally), max(ally))
ax.set_zlim3d(min(allz), max(allz))
# Animation
def animate(i):
pos = step_pos[i]
sc._offsets3d = (pos['x'].values, pos['y'].values, pos['z'].values)
ani = matplotlib.animation.FuncAnimation(fig,
animate,
frames=steps,
interval=200,
repeat=False)
return ani
def get_colors(color_c=3, color_step=100):
cmap_colors = np.vstack((
cm.Oranges(np.linspace(0.4, 1, color_step)),
cm.Reds(np.linspace(0.4, 1, color_step)),
cm.Greys(np.linspace(0.4, 1, color_step)),
cm.Purples(np.linspace(0.4, 1, color_step)),
cm.Blues(np.linspace(0.4, 1, color_step)),
cm.Greens(np.linspace(0.4, 1, color_step)),
cm.pink(np.linspace(0.4, 1, color_step)),
cm.copper(np.linspace(0.4, 1, color_step)),
))
return cmap_colors[np.arange(color_c * color_step) % (color_step * 8)]
def soilmoisture_fingerprints(mask, name=None, fortalk=False):
Fingerprints = {}
depths = ["pdsi", "30cm", "2m"]
if fortalk:
letters = ["", "", ""]
else:
letters = ["(a): ", "(b): ", "(c): "]
pcs = []
pclabels = []
for depth in depths:
i = depths.index(depth)
if fortalk:
plt.figure()
else:
plt.subplot(2, 2, i + 1)
sm = soilmoisture(depth, mask=mask)
solver = Eof(MV.average(sm, axis=0), weights='area')
Fingerprints[depth] = solver
fac = da.get_orientation(solver)
if name is None:
m = b.landplot(fac * solver.eofs()[0], vmin=-.1, vmax=.1)
plt.colorbar(orientation='horizontal', label='EOF loading')
else:
m = b.plot_regional(fac * solver.eofs()[0],
name,
vmin=-.1,
vmax=.1)
m.drawcountries()
m.drawcoastlines(color='gray')
if depth is not "pdsi":
plt.title(letters[i] + depth + " fingerprint")
else:
plt.title(letters[i] + " PDSI fingerprint")
pcs += [fac * solver.pcs()[:, 0]]
if fortalk:
plt.figure()
else:
plt.subplot(2, 2, 4)
for i in range(3):
if depths[i] == "pdsi":
label = "PDSI"
else:
label = depths[i]
time_plot(pcs[i], label=label, lw=3, color=cm.copper(i / 2.))
plt.legend(loc=0)
plt.title("(d): Principal Components")
plt.xlabel("Time")
plt.ylabel("Temporal amplitude")
plt.xlim(1900, 2100)
return Fingerprints
def analyze_scan(Model, smooth=10, filename=None):
F_aff, seeds, Model, DATA = get_scan(Model, filename=filename)
fig1, ax1 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
fig2, ax2 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
for i in range(len(F_aff)):
TRACES = []
for j in range(len(seeds)):
data = DATA[i * len(seeds) + j]
# TRACES.append(data['POP_ACT_RecExc'])
TRACES.append(
gaussian_smoothing(data['POP_ACT_RecExc'],
int(smooth / data['dt'])))
mean = np.array(TRACES).mean(axis=0)
std = np.array(TRACES).std(axis=0)
# smoothing
cond = data['t'] > 350
ax1.plot(data['t'][cond],
mean[cond],
color=cm.copper(i / len(F_aff)),
lw=2)
ax1.fill_between(data['t'][cond],
mean[cond] - std[cond],
mean[cond] + std[cond],
color=cm.copper(i / len(F_aff)),
alpha=.5)
ax2.plot(data['t'][cond],
data['faff'][cond],
color=cm.copper(i / len(F_aff)))
set_plot(ax1, xlabel='time (ms)', ylabel='rate (Hz)')
set_plot(ax2, xlabel='time (ms)', ylabel='rate (Hz)')
# put_list_of_figs_to_svg_fig([fig1, fig2])
return fig1, fig2
def animate(f):
global pairs, pairs2
# load data
F=F_vs_t[f]
r=r_vs_t[f]
n=n_vs_t[f]
p=(rho+0.9)*p_angular[f]/np.sqrt(np.sum(p_angular[f]**2))
ang_mom.set_positions((0, 0), (p[x_plane], p[y_plane]))
if update_nn:
pairs = simforces.get_all_pairs(getDelaunayTrianglesOnSphere(r)+1)
for i in range(0,N):
#j=indsort[i]
c=int((r[z_plane,i]+1)/2*256)
cells[i].center=(r[x_plane,i],r[y_plane,i])
cells[i].set_facecolor(cm.copper(c))
cells[i].set_zorder(r[z_plane,i])
if plot_springs:
for i in range(0,len(pairs)):
i1 = pairs[i,0] - 1
i2 = pairs[i,1] - 1
if (r[z_plane,i1] > 0) and (r[z_plane,i2] > 0):
dist = np.sqrt(np.sum((r[:,i1]- r[:,i2])**2))
c=int((dist-1)*128)
springs[i].set_data([r[x_plane,i1], r[x_plane,i2]], [r[y_plane,i1], r[y_plane,i2]])
springs[i].set_color(cm.spectral(c))
else:
springs[i].set_data([], [])
if plot_voronoi:
list_, baricenters, out_polygon_dict, pairs2, all_areas = getVoronoiOnSphere(r)
b = rho*baricenters
for i in range(0,len(pairs2)):
i1 = pairs2[i,0]
i2 = pairs2[i,1]
if (b[z_plane,i1] > 0) and (b[z_plane,i2] > 0):
borders[i].set_data([b[x_plane,i1], b[x_plane,i2]], [b[y_plane,i1], b[y_plane,i2]])
else:
borders[i].set_data([], [])
if f == 20:
fig.savefig('test.png')
return (cells,springs,borders,ang_mom)
def run(self, plot=False, stack=False):
if plot==True:
pl.ion()
pl.ylim(0, 1)
pl.xlabel("Generations")
pl.ylabel("Probability")
for k in range(len(env.row_strategies)):
c = cm.copper((k + 1) / len(env.row_strategies))
pl.plot(self.row_accumulated_strategies[k], color=c, label="Row strategies: %s" % (k + 1))
for k in range(len(env.col_strategies)):
c = cm.winter((k + 1) / len(env.row_strategies))
pl.plot(self.col_accumulated_strategies[k], color=c, label="Col strategies: %s" % (k + 1))
#pl.legend(bbox_to_anchor=(0.7, 0.85), loc=2, prop={'size':7})
pl.legend(loc=2, prop={'size':7})
pl.draw()
self.generations_passing(ga.generations, ga.rounds_per_generation, env.number_of_agents, env.row_agents, env.col_agents, plot, stack)
def not_used05():
jet = cm.get_cmap(
'jet'
) # <matplotlib.colors.LinearSegmentedColormap object at 0x000002D606451E80>
print(jet(0))
print(jet(127))
print(jet(255))
print(jet(2550))
print('-' * 50)
# 색상을 표현하는 다양한 방법
print(jet([0, 255]))
print(jet(range(0, 5, 2)))
print(jet(np.linspace(0.3, 0.7, 5)))
print('-' * 50)
print(cm.jet(0))
print(cm.copper(0))
L = 32
datamaker0 = fs.SuperRegistration(np.zeros((2, L, L)), deg=deg)
datamaker0.shifts = np.array([3 * np.random.randn(2)])
shifts = datamaker0.shifts
fdata = datamaker0.model
fdata /= fdata.std()
data = fdata + 0.05 * np.random.randn(*fdata.shape)
reg = SuperRegistration(data, 16)
#print(reg.fit(iprint=2, delta=1E-4))
evd, bias = [], []
fig, ax = plt.subplots(1, 2, sharex=True)
order = list(range(10, 25))
nlist = list(range(2, 9, 2)) # [2]
colors = copper(Normalize()(nlist))
shifts = np.random.randn(max(nlist) - 1, 2)
datalist = []
biases = []
evidences = []
# This sequence plots the evidence as a function of complexity as a
# function of the number of images
for n, c in zip(nlist, colors):
dm = fs.SuperRegistration(np.zeros((n, L, L)), deg)
dm.coef = datamaker0.coef
dm.shifts = shifts[:n - 1]
data = dm.model / dm.model.std()
data += 0.05 * np.random.randn(*data.shape)
def get_stability_condition(plot_results=True):
current_factors = [0.6, 0.7, 0.8, 0.9, 1.0]
colors = cm.copper(np.linspace(0.0, 1.0, len(current_factors)))
# Get profiles
dat = np.loadtxt(os.path.join('input_profiles.dat'))
# Modify and plot input profiles
r = dat[:, 0]
R = dat[:, 1]
j_phi = dat[:, 2]
B_z = dat[:, 3]
B_theta = dat[:, 4]
psi_n = dat[:, 5]
r_to_psin = interpolate.interp1d(r, psi_n)
psin_to_r = interpolate.interp1d(r, psi_n)
q = r * B_z / (R * B_theta)
q[0] = q[1]
if plot_results:
fig, ax = plt.subplots(2, 2, figsize=(10, 10), sharex=True)
ax[0, 0].plot(r, B_z, c='k')
ax[0, 0].set_ylabel('$B_{\phi}$ [T]', fontsize=fontsize)
ax[1, 0].plot(r, B_theta, c='k')
ax[1, 0].set_ylabel('$B_{\\theta}$ [T]', fontsize=fontsize)
for i, factor in enumerate(current_factors[::-1]):
linestyle = '--' if i > 0 else '-'
ax[0, 1].plot(r, factor * j_phi * 1e-3, linestyle=linestyle, c=colors[i])
ax[0, 1].set_ylabel('$j_{\phi}$ [kA]', fontsize=fontsize)
ax[1, 1].plot(r, q, c='k')
ax[1, 1].set_ylabel('q', fontsize=fontsize)
ax[1, 1].set_xlabel('r [m]', fontsize=fontsize)
ax[1, 0].set_xlabel('r [m]', fontsize=fontsize)
ax[0, 0].set_xlim([0.0, 1.0])
fig.tight_layout()
plt.savefig('input_profiles')
plt.show()
plt.figure()
for epsilon in [1e-12, 1e-8, 1e-6, 1e-4]:
r_max = r[-1]
deltas = list()
alphas = list()
for factor in current_factors:
j_phi_sim = j_phi * factor
solver = TearingModeSolver(m, r, r_max, B_theta, B_z, j_phi_sim, q, num_pts, delta=epsilon)
solver.find_delta(plot_output=False)
deltas.append(solver.delta)
alphas.append(1 - factor)
plt.plot(alphas, deltas, label="$\epsilon$={}".format(epsilon))
np.savetxt('deltas_{}.dat'.format(epsilon), np.stack((alphas, deltas), axis=-1))
plt.grid(linestyle='--')
plt.ylabel('$\Delta\'$', fontsize=fontsize)
plt.xlabel('$\\alpha$', fontsize=fontsize)
plt.legend()
plt.xlim([0.0, 1.0])
plt.savefig('current_stability_{}'.format(m))
plt.show()
def main():
args = parse_args()
q_mean, p_mean, Q, P, W = prepare_data(args)
no_steps = Q.shape[0]
q_min = Q[:, 0, 0].min()
q_max = Q[:, 0, -1].max()
p_min = P[:, 0, 0].min()
p_max = P[:, -1, 0].max()
if args.vmin[-1] == "%":
W_min = numpy.percentile(W[:], float(args.vmin[:-1]))
else:
W_min = float(args.vmin)
if args.vmax[-1] == "%":
W_max = numpy.percentile(W[:], 100. - float(args.vmax[:-1]))
else:
W_max = float(args.vmax)
midpoint = 1 - W_max / (W_max + abs(W_min))
cmap = shifted_color_map(cm.coolwarm, midpoint=midpoint, name="shifted")
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_xlim(q_min, q_max)
ax.set_ylim(p_min, p_max)
ax.set_xlabel("q")
ax.set_ylabel("p")
if args.visualization == "polished":
shading = "gouraud"
else:
shading = "flat"
quad = QuadContainer(
ax.pcolormesh(Q[0],
P[0],
W[0],
vmin=W_min,
vmax=W_max,
cmap=cmap,
shading=shading))
ax.set_aspect("equal")
if args.track:
ax.set_color_cycle(
[cm.copper(1. * i / (no_steps - 1)) for i in range(no_steps - 1)])
for i in range(no_steps - 1):
ax.plot(q_mean[i:i + 2], p_mean[i:i + 2], alpha=.3)
cb = fig.colorbar(quad.quad)
cb.set_label("Quasiprobability Density")
cb.solids.set_rasterized(True)
if args.visualization == "polished":
ax.set_axis_bgcolor(cb.to_rgba(0.))
no_digits = int(ceil(log10(no_steps)) + 1)
title_string = "Wigner Function at step {:{width}}/{:{width}}"
title = ax.set_title(title_string.format(0, no_steps, width=no_digits))
ax.grid(True)
if args.output:
fig.savefig(args.output + "_thumb.pdf")
def animate(i):
title.set_text(title_string.format(i, no_steps, width=no_digits))
quad.update_quad(
ax.pcolormesh(Q[i],
P[i],
W[i],
vmin=W_min,
vmax=W_max,
cmap=cmap,
shading=shading))
ax.grid(True)
return quad.quad,
ani = FuncAnimation(fig,
animate,
no_steps,
interval=100,
repeat_delay=1000)
if args.output:
print("Saving movie to {}. This may take a couple of minutes.".format(
args.output))
ani.save(args.output + ".mp4",
fps=10,
extra_args=['-vcodec', 'libx264'])
pyplot.show()
def get_stability_condition(plot_results=True):
current_factors = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.65, 0.675, 0.6875, 0.7, 0.8, 0.9, 1.0]
colors = cm.copper(np.linspace(0.0, 1.0, len(current_factors)))
# Get profiles
dat = np.loadtxt(os.path.join('input_profiles.dat'))
# Modify and plot input profiles
r = dat[:, 0]
R = dat[:, 1]
j_phi = dat[:, 2]
B_z = dat[:, 3]
B_theta = dat[:, 4]
psi_n = dat[:, 5]
r_to_psin = interpolate.interp1d(r, psi_n)
psin_to_r = interpolate.interp1d(r, psi_n)
q = r * B_z / (R * B_theta)
q[0] = q[1]
if plot_results:
fig, ax = plt.subplots(2, 2, figsize=(10, 10), sharex=True)
ax[0, 0].plot(r, B_z, c='k')
ax[0, 0].set_ylabel('$B_{\phi}$ [T]', fontsize=fontsize)
ax[1, 0].plot(r, B_theta, c='k')
ax[1, 0].set_ylabel('$B_{\\theta}$ [T]', fontsize=fontsize)
for i, factor in enumerate(current_factors[::-1]):
linestyle = '--' if i > 0 else '-'
ax[0, 1].plot(r, factor * j_phi * 1e-3, linestyle=linestyle, c=colors[i])
ax[0, 1].set_ylabel('$j_{\phi}$ [kA]', fontsize=fontsize)
ax[1, 1].plot(r, q, c='k')
ax[1, 1].set_ylabel('q', fontsize=fontsize)
ax[1, 1].set_xlabel('r [m]', fontsize=fontsize)
ax[1, 0].set_xlabel('r [m]', fontsize=fontsize)
ax[0, 0].set_xlim([0.0, 1.0])
fig.tight_layout()
plt.savefig('input_profiles')
plt.show()
r_max = r[-1]
deltas = list()
gammas = list()
alphas = list()
if os.path.exists(data_output):
alphas = 1 - np.asarray(current_factors)
deltas = np.loadtxt(data_output)
gammas = np.loadtxt(gamma_output)
else:
for factor in current_factors:
j_phi_sim = j_phi * factor
solver = TearingModeSolver(m, r, r_max, B_theta, B_z, j_phi_sim, q, num_pts, delta=1e-12)
solver.find_delta(plot_output=False)
solver.get_gamma()
# Transform to psi_norm for comparison with JOREK
psin_lower = r_to_psin(solver.r_lower)
psin_upper = r_to_psin(solver.r_upper)
if plot_results:
fig, ax = plt.subplots(2, sharex=True)
ax[0].plot(psin_lower, solver.psi_sol_lower[:, 0], label='solution from axis')
ax[0].plot(psin_upper, solver.psi_sol_upper[:, 0], label='solution from boundary')
# Plot comparison solution if it exists
validation_file = 'flux_validation_vc_{}.csv'.format(factor)
if os.path.exists(validation_file):
flux_validation = np.loadtxt(validation_file, delimiter=',')
flux_validation[:, 1] /= np.max(flux_validation[:, 1])
flux_validation[:, 1] *= np.max(solver.psi_sol_lower[:, 0])
ax[0].plot(flux_validation[:, 0], flux_validation[:, 1], linestyle='--', label='JOREK')
ax[0].set_ylabel('$\Psi_1$', fontsize=fontsize)
ax[0].legend()
ax[0].set_xlim([0.0, 1.0])
ax[1].plot(psin_lower, solver.psi_sol_lower[:, 1])
ax[1].plot(psin_upper, solver.psi_sol_upper[:, 1])
ax[1].set_ylabel('$\\frac{\partial \Psi_1}{\partial r}$', fontsize=fontsize)
ax[1].set_xlabel('$\hat \Psi$', fontsize=fontsize)
plt.show()
deltas.append(solver.delta)
gammas.append(solver.gamma)
alphas.append(1 - factor)
np.savetxt(data_output, np.asarray(deltas))
np.savetxt(gamma_output, np.asarray(gammas))
alphas = np.asarray(alphas)
deltas = np.asarray(deltas)
gammas = np.asarray(gammas)
# Plot gammas
gammas_jor = np.asarray([0.000112257, 7.25606e-5, 3.87257e-5, 2.29265e-5, 1.50064e-5, 6.86054e-6, 2.586e-6])
gammas_jor /= 6.4836e-7
alphas_jor = [0.0, 0.1, 0.2, 0.25, 0.275, 0.3, 0.3125]
eta = 1e-7 * 1.9382
rho = 1e20 * 2 * 1.673 * 1e-27
gammas *= eta ** 0.6 / rho ** 0.2
fig, ax = plt.subplots(1)
ax.plot(alphas, gammas, label='Linear $\Delta\'$')
ax.scatter(alphas, gammas)
ax.plot(alphas_jor, gammas_jor, label='JOREK $\Delta\'$')
ax.scatter(alphas_jor, gammas_jor)
plt.savefig('current_stability_gammas_{}'.format(m))
ax.set_ylabel('$\gamma\ [s^{-1}]$', fontsize=fontsize)
ax.set_xlabel('$\\alpha$', fontsize=fontsize)
plt.show()
alphas_jor_8 = [0.0, 0.1, 0.2, 0.3]
gammas_8 = np.asarray([41.701, 25.616, 12.98966, 2.5974])
gammas_9 = np.asarray([6.809, 4.0393, 1.99651, 0.46058])
# Plot deltas
solver = TearingModeSolver(m, r, r_max, B_theta, B_z, j_phi, q, num_pts, delta=1e-12)
deltas_jor = gammas_jor / 0.55 / (eta / PhysicalConstants.mu_0) ** 0.6
deltas_jor /= (m * solver.r_to_B_theta(solver.r_instability) / np.sqrt(PhysicalConstants.mu_0 * rho)) ** 0.4
deltas_jor /= (solver.r_to_q_deriv(solver.r_instability) / (solver.r_instability * solver.r_to_q(solver.r_instability))) ** 0.4
deltas_jor = deltas_jor ** (5.0 / 4.0)
deltas_jor_8 = gammas_8 / 0.55 / (eta * 0.1 / PhysicalConstants.mu_0) ** 0.6
deltas_jor_8 /= (m * solver.r_to_B_theta(solver.r_instability) / np.sqrt(PhysicalConstants.mu_0 * rho)) ** 0.4
deltas_jor_8 /= (solver.r_to_q_deriv(solver.r_instability) / (solver.r_instability * solver.r_to_q(solver.r_instability))) ** 0.4
deltas_jor_8 = deltas_jor_8 ** (5.0 / 4.0)
deltas_jor_9 = gammas_9 / 0.55 / (eta * 0.01 / PhysicalConstants.mu_0) ** 0.6
deltas_jor_9 /= (m * solver.r_to_B_theta(solver.r_instability) / np.sqrt(PhysicalConstants.mu_0 * rho)) ** 0.4
deltas_jor_9 /= (solver.r_to_q_deriv(solver.r_instability) / (solver.r_instability * solver.r_to_q(solver.r_instability))) ** 0.4
deltas_jor_9 = deltas_jor_9 ** (5.0 / 4.0)
scaling = 1.05
fig, ax = plt.subplots(1)
ax.plot(alphas, deltas, label='Linear $\Delta\'$')
ax.scatter(alphas, deltas)
ax.plot(alphas_jor, deltas_jor, label='JOREK $\Delta\'$')
ax.scatter(alphas_jor, deltas_jor)
ax.plot(alphas_jor_8, deltas_jor_8, label='JOREK $\Delta\' for $\eta=10^{-8}$')
ax.scatter(alphas_jor_8, deltas_jor_8)
ax.plot(alphas_jor_8, deltas_jor_9, label='JOREK $\Delta\'$ for $\eta=10^{-9}$')
ax.scatter(alphas_jor_8, deltas_jor_9)
ax.axhline(0.0, c='k', linestyle='--')
ax.axvline(0.346, linestyle='--', color='grey', label='Linear stability boundary')
ax.axvline(0.3125, linestyle='--', color='g', label='JOREK stability boundary')
ax.axvline(0.325, linestyle='--', color='g')
ax.fill_betweenx(scaling * deltas, 0.3125, 0.325, facecolor='green', alpha=0.2)
ax.set_ylabel('$\Delta\'$', fontsize=fontsize)
ax.set_xlabel('$\\alpha$', fontsize=fontsize)
ax.set_xlim([0.0, 1.0])
ax.set_ylim([scaling * min(deltas), scaling * max(deltas)])
ax.grid(linestyle='--')
ax.legend()
plt.savefig('current_stability_deltas_{}'.format(m))
plt.show()
"params_dam_nilc.yml",
"params_dam_wfixed.yml",
"params_dam_tinker10.yml",
# "params_wnarrow_ns.yml",
# "params_masked.yml"
]
sci = [r"$\mathrm{2MPZ}$"] + \
[r"$\mathrm{WI \times SC}$ - $\mathrm{%d}$" % i for i in range(1, 6)]
lbls = [
"Fiducial", "NILC", "Fixed $w_z$", "Tinker 2010",
r"$\langle N_s \rangle$ independent"
"tSZ-masked"
]
colours = ["k", "grey", "r", "brown", "orange"]
col = [copper(i) for i in np.linspace(0, 1, len(sci))]
fmts = ["o", "o", "v", "s", "*", "d"]
p = ParamRun(param_yml[0])
#temp = [chan(paryml, diff=True, error_type="hpercentile", chains=False, b_hydro=0.5*np.ones([1,6]))
# for paryml in param_yml]
#pars = [t[0] for t in temp]
#data = np.array([[p["b_hydro"] for p in par] for par in pars])
#data = [d.T for d in data]
print("HI")
BF = [chan(fname).get_best_fit("b_hydro") for fname in param_yml]
print("Best fits OK")
widths = chan(param_yml[0]).get_best_fit("width")
widths = np.hstack((widths["width"][:, 0]))
dz, dN = [[] for i in range(2)]
def excess(temps):
ref_energies = {"Al": -3.73667187, "Mg": -1.59090625}
if (temps == "all"):
db = connect(mc_db_name)
all_temps = []
for row in db.select(converged=1):
if (row.temperature not in all_temps):
all_temps.append(row.temperature)
temps = all_temps
res = get_free_energies()
try:
for key, value in res.iteritems():
F = np.array(value["free_energy"])
plt_set = False
for i in range(1, len(F)):
if (F[i] < F[i - 1]):
print(value["temperature"][i])
plt_set = True
F -= F[0]
if (plt_set):
print(key)
plt.plot(value["temperature"], F)
plt.show()
for key, value in res.iteritems():
E = np.array(value["internal_energy"])
E -= E[0]
plt.plot(value["temperature"], E)
plt.show()
except Exception as exc:
print(str(exc))
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
markers = ["o", "x", "^", "v", "d"]
colors = [
'#b2182b', '#ef8a62', '#fddbc7', '#f7f7f7', '#d1e5f0', '#67a9cf',
'#2166ac'
]
fig_entropy = plt.figure()
ax_entropy = fig_entropy.add_subplot(1, 1, 1)
fig_mg_weighted = plt.figure()
ax_mg_weighted = fig_mg_weighted.add_subplot(1, 1, 1)
fig_F = plt.figure()
ax_F = fig_F.add_subplot(1, 1, 1)
Tmin = np.min(temps)
Tmax = np.max(temps)
print("Min temp: {}, Max temp: {}".format(Tmin, Tmax))
all_excess = []
all_concs = []
all_temps = []
for count, T in enumerate(temps):
excess = []
concs = []
entropy = []
free_eng = []
temperature = None
for key, entry in res.iteritems():
if ("Mg" in entry["conc"].keys()):
mg_conc = entry["conc"]["Mg"]
else:
mg_conc = 0.0
concs.append(mg_conc)
diff = np.abs(entry["temperature"] - T)
indx = np.argmin(diff)
if (diff[indx] > 1.0):
print(
"Warning! Difference {}. Temperature might not be simulated!"
.format(diff[indx]))
excess.append(entry["internal_energy"][indx] -
ref_energies["Al"] * entry["conc"]["Al"] -
ref_energies["Mg"] * entry["conc"]["Mg"])
free_eng.append(entry["free_energy"][indx] -
ref_energies["Al"] * entry["conc"]["Al"] -
ref_energies["Mg"] * entry["conc"]["Mg"])
if (temperature is None):
temperature = entry["temperature"][indx]
#excess[-1] += entry["TS"][indx]
entropy.append(entry["entropy"][indx])
#excess.append( entry["free_energy"][indx]+entry["TS"][indx] )
#excess.append( entry["free_energy"][indx] )
concs += [0.0, 1.0]
excess += [0.0, 0.0]
entropy += [0.0, 0.0]
free_eng += [0.0, 0.0]
srt_indx = np.argsort(concs)
concs = [concs[indx] for indx in srt_indx]
excess = np.array([excess[indx] for indx in srt_indx])
entropy = np.array([entropy[indx] for indx in srt_indx])
free_eng = np.array([free_eng[indx] for indx in srt_indx])
all_excess.append(excess)
all_concs.append(concs)
mapped_temp = float(temperature - Tmin) / (Tmax - Tmin)
print(mapped_temp)
all_temps.append(temperature)
ax.plot(concs,
excess * mol / kJ,
marker=markers[count % len(markers)],
label="{}K".format(temperature),
mfc="none",
color=cm.copper(mapped_temp),
lw=2)
ax_entropy.plot(concs,
1000.0 * entropy * mol / kJ,
marker=markers[count % len(markers)],
label="{}K".format(temperature),
color=cm.copper(mapped_temp),
lw=2,
mfc="none")
ax_F.plot(concs,
free_eng * mol / kJ,
marker=markers[count % len(markers)],
label="{}K".format(temperature),
mfc="none",
color=cm.copper(mapped_temp),
lw=2)
ax_mg_weighted.plot(concs, (excess / concs) * mol / kJ,
marker=markers[count % len(markers)],
color=cm.copper(mapped_temp),
lw=2,
mfc="none")
ax.legend(frameon=False)
ax.set_xlabel("Mg concentration")
ax.set_ylabel("Enthalpy of formation (kJ/mol)")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax_entropy.set_xlabel("Mg concentration")
ax_entropy.set_ylabel("Entropy (J/K mol)")
ax_entropy.spines["right"].set_visible(False)
ax_entropy.spines["top"].set_visible(False)
fig_info = plt.figure()
Z = [[0, 0], [0, 0]]
#temp_info = [np.min(T),np.max(T)]
ax_info = fig_info.add_subplot(1, 1, 1)
temp_info = np.linspace(np.min(temps), np.max(temps), 256)
Cb_info = ax_info.contourf(Z, temp_info, cmap="copper")
cbar = fig.colorbar(Cb_info,
orientation="horizontal",
ticks=[100, 300, 500, 700])
cbar.ax.xaxis.set_ticks_position("top")
cbar.ax.set_xticklabels([100, 300, 500, 700])
cbar.ax.xaxis.set_label_position("top")
#cbar.ax.tick_params(axis='x',direction='in',labeltop='on')
cbar.set_label("Temperature (K)")
cbar2 = fig_entropy.colorbar(Cb_info,
orientation="horizontal",
ticks=[100, 300, 500, 700])
cbar2.ax.xaxis.set_ticks_position("top")
cbar2.ax.set_xticklabels([100, 300, 500, 700])
cbar2.ax.xaxis.set_label_position("top")
cbar2.set_label("Temperature (K)")
all_maxima, all_minima = find_extremal_points(all_concs,
all_excess,
show_plot=False)
ax_F.set_ylabel("Free Energy of Formation (kJ/mol)")
all_data = []
for temp, maxima, minima in zip(all_temps, all_maxima, all_minima):
all_data.append({
"temperature": temp,
"maxima": maxima,
"minima": minima
})
with open("data/extremal_points.json", 'w') as outfile:
json.dump(all_data, outfile, indent=2, separators=(",", ":"))
plt.show()
hist_dat.append([apc.loc['resp'].drop('v4', level='layer_label').loc[layer]
for layer in layers_to_examine] + [apc.loc['resp'].loc['v4'],])
#hist_dat.append([apc.loc['resp'].drop('v4', level='layer_label').loc[layer]
# for layer in layers_to_examine])
hist_dat_leg.append({'title':'CN resp', 'labels':layers_to_examine,
'fontsize':'xx-small' , 'frameon':True, 'loc':4,'markerscale':100})
for leg in hist_dat_leg:
leg['fontsize'] = fs
leg['labelspacing'] = 0
for i, ax_ind in enumerate(hist_pos):
ax = ax_list[ax_ind]
if not (ax_ind==hist_pos[-1]):
colors = ['g','r','b','m','c', 'k', '0.5']
else:
colors = cm.copper(np.linspace(0,1,len(hist_dat[i])))
colors[-1] = [1, 0, 0, 0]
for apc_vals, color in zip(hist_dat[i], colors):
x = apc_vals.dropna().values
y_c, bins_c = d_hist(ax, np.sqrt(x), cumulative=True, color=color, alpha=0.75, lw=2)
bins_c = np.concatenate([apc_vals.dropna().values for apc_vals in hist_dat[i]]).ravel()
beautify(ax, spines_to_remove=['top','right'])
ax.set_xticks([0,0.5,1])
ax.set_xticklabels([0,0.5,1], fontsize=10)
ax.spines['left'].set_bounds(0,1)
ax.set_xlim(0,1)
ax.set_yticks([0, 0.5, 1])
ax.set_yticklabels([0, 0.5, 1], fontsize=10)
ax.set_ylim(0,1.1)
if not (ax_ind==hist_pos[-1]):
from PIL import Image
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import cm
im = Image.open('../data/grenouille.jpg')
rouge, vert, bleu = im.split()
z = np.array(rouge)
z = np.uint8(cm.copper(z) * 255)
im2 = Image.fromarray(z)
im2.save("grenouille_saved.jpg")
import matplotlib.pyplot as plt
from matplotlib import cm
with open('bars.txt') as f:
lines = f.readlines()
x = [float(i) for i in lines[0].split()]
y = [float(i) for i in lines[1].split()]
color = cm.copper(y)
fig = plt.figure()
ax = fig.add_subplot(111)
rects = ax.bar(x, y, color=color)
for rect in rects:
height = rect.get_height()
ax.text(rect.get_x() + rect.get_width() / 2.,
1.005 * height,
'%.2f' % float(height),
ha='center',
va='bottom')
plt.show()
def main():
T = np.array([
10000, 9000, 8000, 7000, 6000, 5000, 4000, 3000, 2000, 1000, 800, 700,
600, 500, 400, 375, 350, 325, 300, 275, 250, 225, 200, 175, 150
])
mg_concs = []
enthalpies = []
free_energy = []
ref_energies = {"Al": -3.73667187, "Mg": -1.59090625}
temps = []
concs = []
filenames = glob.glob("data/mfa217/*")
ignore_indx = []
for i, filename in enumerate(filenames):
with open(filename, 'r') as infile:
data = json.load(infile)
mg_concs.append(data["conc"]["Mg"])
concs.append(data["conc"])
print(data["conc"], filename)
enthalpies.append(
np.array(data["internal_energy"]) / data["natoms"] -
ref_energies["Mg"] * data["conc"]["Mg"] -
ref_energies["Al"] * data["conc"]["Al"])
free_energy.append(
np.array(data["free_energy"]) / data["natoms"] -
ref_energies["Mg"] * data["conc"]["Mg"] -
ref_energies["Al"] * data["conc"]["Al"])
try:
temps.append(data["temperature"])
except Exception as exc:
ignore_indx.append(i)
print("Error occured in {}. Message: {}".format(
filename, str(exc)))
if (save_free_eng):
res = {}
i = 0
for indx in range(len(filenames)):
if (indx in ignore_indx):
continue
res[filenames[i]] = {}
res[filenames[i]]["conc"] = concs[i]
res[filenames[i]]["free_energy"] = free_energy[i].tolist()
res[filenames[i]]["temperature"] = temps[i]
i += 1
with open(free_eng_file, 'w') as outfile:
json.dump(res, outfile, indent=2, separators=(",", ":"))
print("Free energies written to {}".format(free_eng_file))
figH = plt.figure()
axH = figH.add_subplot(1, 1, 1)
figF = plt.figure()
axF = figF.add_subplot(1, 1, 1)
figS = plt.figure()
axS = figS.add_subplot(1, 1, 1)
Tmax = 800
Tmin = 150
print(len(temps[0]))
print(len(enthalpies[0]))
for i in range(len(enthalpies[0])):
try:
T = temps[0][i]
if (T > Tmax):
continue
srt_indx = np.argsort(mg_concs)
H = [enthalpies[j][i] for j in range(len(enthalpies))]
F = [free_energy[j][i] for j in range(len(free_energy))]
srt_mg = [mg_concs[indx] for indx in srt_indx]
H = np.array([H[indx] for indx in srt_indx])
F = np.array([F[indx] for indx in srt_indx])
mapped_T = float(T - Tmin) / (Tmax - Tmin)
S = (H - F) / T
axH.plot(srt_mg,
H * mol / kJ,
marker="x",
color=cm.copper(mapped_T))
axF.plot(srt_mg,
F * mol / kJ,
marker="o",
color=cm.copper(mapped_T))
axS.plot(srt_mg,
1E6 * S * mol / kJ,
marker="o",
color=cm.copper(mapped_T))
except Exception as exc:
print(str(exc))
axH.set_xlabel("Mg concentration")
axH.set_ylabel("Enthalpy of Formation (kJ/mol)")
axF.set_xlabel("Mg concentration")
axF.set_ylabel("Free Energy of Formation (kJ/mol)")
axS.set_xlabel("Mg concentration")
axS.set_ylabel("Entropy (mJ/K mol)")
axH.spines["right"].set_visible(False)
axH.spines["top"].set_visible(False)
axF.spines["right"].set_visible(False)
axF.spines["top"].set_visible(False)
axS.spines["right"].set_visible(False)
axS.spines["top"].set_visible(False)
plt.show()
if pltcolor:
plt.figure(1)
plt.plot(t, en, label=runname)
plt.figure(2)
plt.plot(t, hdiss + hdissz, label=runname)
plt.figure(3)
plt.plot(t, enz, label=runname)
plt.figure(4)
plt.plot(t, diss + dissz, label=runname)
else:
plt.figure(1)
plt.plot(t,
en,
label=r"$\Omega = %.3f$" % omegas[runname],
color=cm.copper(cscale(omegas[runname], omegas)))
plt.figure(2)
plt.plot(t,
hdiss + hdissz,
label=r"$\Omega = %.3f$" % omegas[runname],
color=cm.copper(cscale(omegas[runname], omegas)))
plt.figure(3)
plt.plot(t,
enz,
label=r"$\Omega = %.3f$" % omegas[runname],
color=cm.copper(cscale(omegas[runname], omegas)))
plt.figure(4)
plt.plot(t,
def get_stability_condition(plot_results=True):
current_factors = [
0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.65, 0.675, 0.6875, 0.7, 0.8, 0.9,
1.0, 1.1, 1.2, 1.3
]
colors = cm.copper(np.linspace(0.0, 1.0, len(current_factors)))
# Get profiles
dat = np.loadtxt(os.path.join('input_profiles.dat'))
# Modify and plot input profiles
r = dat[:, 0]
R = dat[:, 1]
j_phi = dat[:, 2]
B_z = dat[:, 3]
B_theta = dat[:, 4]
psi_n = dat[:, 5]
r_to_psin = interpolate.interp1d(r, psi_n)
psin_to_r = interpolate.interp1d(r, psi_n)
q = r * B_z / (R * B_theta)
q[0] = q[1]
if plot_results:
fig, ax = plt.subplots(2, 2, figsize=(10, 10), sharex=True)
ax[0, 0].plot(r, B_z, c='k')
ax[0, 0].set_ylabel('$B_{\phi}$ [T]', fontsize=fontsize)
ax[1, 0].plot(r, B_theta, c='k')
ax[1, 0].set_ylabel('$B_{\\theta}$ [T]', fontsize=fontsize)
for i, factor in enumerate(current_factors[::-1]):
linestyle = '--' if i > 0 else '-'
ax[0, 1].plot(r,
factor * j_phi * 1e-3,
linestyle=linestyle,
c=colors[i])
ax[0, 1].set_ylabel('$j_{p}$ [kA]', fontsize=fontsize)
ax[1, 1].plot(r, q, c='k')
ax[1, 1].set_ylabel('q', fontsize=fontsize)
ax[1, 1].set_xlabel('r [m]', fontsize=fontsize)
ax[1, 0].set_xlabel('r [m]', fontsize=fontsize)
ax[0, 0].set_xlim([0.0, 1.0])
fig.tight_layout()
plt.savefig('input_profiles')
plt.show()
r_max = r[-1]
deltas = list()
gammas = list()
alphas = list()
current = np.zeros((len(current_factors), 3))
if os.path.exists(data_output):
alphas = 1 - np.asarray(current_factors)
deltas = np.loadtxt(data_output)
gammas = np.loadtxt(gamma_output)
for i, factor in enumerate(current_factors):
j_phi_sim = j_phi * (1 - factor)
solver = TearingModeSolver(m,
r,
r_max,
B_theta,
B_z,
j_phi_sim,
q,
num_pts,
delta=1e-12)
current[i, 0] = factor
current[i, 1] = solver.r_to_j_phi(solver.r_instability)
current[i, 2] = solver.r_to_j_phi_deriv(solver.r_instability)
np.savetxt('instability_currents.dat',
current,
header='Alpha\t\tJ [A]\t\tdJ_dr [A/m]')
else:
for factor in current_factors:
j_phi_sim = j_phi * factor
solver = TearingModeSolver(m,
r,
r_max,
B_theta,
B_z,
j_phi_sim,
q,
num_pts,
delta=1e-12)
solver.find_delta(plot_output=False)
solver.get_gamma()
# Transform to psi_norm for comparison with JOREK
psin_lower = r_to_psin(solver.r_lower)
psin_upper = r_to_psin(solver.r_upper)
if plot_results:
fig, ax = plt.subplots(2, sharex=True)
ax[0].plot(psin_lower,
solver.psi_sol_lower[:, 0],
label='solution from axis')
ax[0].plot(psin_upper,
solver.psi_sol_upper[:, 0],
label='solution from boundary')
# Plot comparison solution if it exists
validation_file = 'flux_validation_vc_{}.csv'.format(factor)
if os.path.exists(validation_file):
flux_validation = np.loadtxt(validation_file)
flux_validation[:, 1] /= np.max(flux_validation[:, 1])
flux_validation[:, 1] *= np.max(solver.psi_sol_lower[:, 0])
ax[0].plot(flux_validation[:, 0],
flux_validation[:, 1],
linestyle='--',
label='JOREK')
ax[0].set_ylabel('$\Psi_1$', fontsize=fontsize)
ax[0].legend()
ax[0].set_xlim([0.0, 1.0])
ax[1].plot(psin_lower, solver.psi_sol_lower[:, 1])
ax[1].plot(psin_upper, solver.psi_sol_upper[:, 1])
ax[1].set_ylabel('$\\frac{\partial \Psi_1}{\partial r}$',
fontsize=fontsize)
ax[1].set_xlabel('$\hat \Psi$', fontsize=fontsize)
plt.show()
deltas.append(solver.delta)
gammas.append(solver.gamma)
alphas.append(1 - factor)
alphas = np.stack(
(np.asarray(alphas[::-1]), np.asarray(deltas[::-1]))).transpose()
gammas = np.stack(
(np.asarray(alphas[::-1]), np.asarray(gammas[::-1]))).transpose()
np.savetxt(data_output, alphas)
np.savetxt(gamma_output, gammas)
# Load JOREK gammas
alphas_jor = [
-0.3, -0.2, -0.1, 0.0, 0.1, 0.2, 0.25, 0.275, 0.3, 0.3125, 0.325,
0.3375
]
gammas_jor = np.asarray([
0.000305073, 0.000216954, 0.000154881, 0.000110055, 7.14455e-5,
3.94265e-5, 2.48401e-5, 1.77428e-5, 1.0663e-5, 7.15803e-6, 3.77522e-6,
9.28732e-7
])
gammas_jor /= 6.4836e-7
np.savetxt(
'gammas_jor_vs_alpha.dat',
np.stack((np.asarray(alphas_jor), np.asarray(gammas_jor))).transpose())
alphas_jor_8 = [0.0, 0.1, 0.2, 0.3]
gammas_8 = np.asarray([41.701, 25.616, 12.98966, 2.5974])
gammas_9 = np.asarray([6.809, 4.0393, 1.99651, 0.46058])
# Load tm1 data
tm1_data = np.loadtxt('gammas_tm1_vs_alpha.dat')
# Multiply normalised solver gamma by density and resistivity
eta = 1e-7 * 1.9382
rho = 1e20 * 2 * 1.673 * 1e-27
gammas[:, 1] *= eta**0.6 / rho**0.2
np.savetxt('gammas_vs_alpha_si.dat', gammas)
# Plot gammas
fig, ax = plt.subplots(2, sharex=True)
ax[0].plot(gammas[:, 0], gammas[:, 1], label='Linear')
ax[0].scatter(gammas[:, 0], gammas[:, 1])
ax[0].plot(alphas_jor, gammas_jor, label='JOREK')
ax[0].scatter(alphas_jor, gammas_jor)
ax[0].plot(tm1_data[:, 0], tm1_data[:, 1], label='TM1')
ax[0].scatter(tm1_data[:, 0], tm1_data[:, 1])
ax[0].set_ylabel('$\gamma\ [s^{-1}]$', fontsize=fontsize)
ax[0].set_xlim([0.0, 1.0])
ax[0].set_ylim([0.0, 250.0])
ax[0].legend()
gammas_interp = interpolate.interp1d(gammas[:, 0], gammas[:, 1])
gammas_tm1_interp = interpolate.interp1d(tm1_data[:, 0], tm1_data[:, 1])
ax[1].plot(alphas_jor,
100 * np.abs(gammas_jor - gammas_interp(alphas_jor)) /
gammas_interp(alphas_jor),
label='JOREK vs. Linear',
c='orange')
ax[1].scatter(alphas_jor,
100 * np.abs(gammas_jor - gammas_interp(alphas_jor)) /
gammas_interp(alphas_jor),
c='orange')
ax[1].plot(tm1_data[:, 0],
100 * np.abs(tm1_data[:, 1] - gammas_interp(tm1_data[:, 0])) /
gammas_interp(tm1_data[:, 0]),
label='TM1 vs. Linear',
c='g')
ax[1].scatter(tm1_data[:, 0],
100 *
np.abs(tm1_data[:, 1] - gammas_interp(tm1_data[:, 0])) /
gammas_interp(tm1_data[:, 0]),
c='g')
skipped_index_low = 3
skipped_index_high = -3
ax[1].plot(
alphas_jor[skipped_index_low:skipped_index_high],
100 * np.abs(gammas_jor[skipped_index_low:skipped_index_high] -
gammas_tm1_interp(
alphas_jor[skipped_index_low:skipped_index_high])) /
gammas_tm1_interp(alphas_jor[skipped_index_low:skipped_index_high]),
label='TM1 vs. JOREK',
c='r')
ax[1].scatter(
alphas_jor[skipped_index_low:skipped_index_high],
100 * np.abs(gammas_jor[skipped_index_low:skipped_index_high] -
gammas_tm1_interp(
alphas_jor[skipped_index_low:skipped_index_high])) /
gammas_tm1_interp(alphas_jor[skipped_index_low:skipped_index_high]),
c='r')
ax[1].set_ylabel('Relative difference $[\%]$', fontsize=fontsize)
ax[1].set_xlabel('$\\alpha$', fontsize=fontsize)
ax[1].set_xlim([0.0, 0.4])
plt.savefig('current_stability_gammas_{}'.format(m))
plt.show()
# Get equivalent JOREK and TM1 delta
solver = TearingModeSolver(m,
r,
r_max,
B_theta,
B_z,
j_phi,
q,
num_pts,
delta=1e-12)
deltas_jor = gammas_jor / 0.55 / (eta / PhysicalConstants.mu_0)**0.6
deltas_jor /= (m * solver.r_to_B_theta(solver.r_instability) /
np.sqrt(PhysicalConstants.mu_0 * rho))**0.4
deltas_jor /= (
solver.r_to_q_deriv(solver.r_instability) /
(solver.r_instability * solver.r_to_q(solver.r_instability)))**0.4
deltas_jor = deltas_jor**(5.0 / 4.0)
deltas_jor_8 = gammas_8 / 0.55 / (eta * 0.1 / PhysicalConstants.mu_0)**0.6
deltas_jor_8 /= (m * solver.r_to_B_theta(solver.r_instability) /
np.sqrt(PhysicalConstants.mu_0 * rho))**0.4
deltas_jor_8 /= (
solver.r_to_q_deriv(solver.r_instability) /
(solver.r_instability * solver.r_to_q(solver.r_instability)))**0.4
deltas_jor_8 = deltas_jor_8**(5.0 / 4.0)
deltas_jor_9 = gammas_9 / 0.55 / (eta * 0.01 / PhysicalConstants.mu_0)**0.6
deltas_jor_9 /= (m * solver.r_to_B_theta(solver.r_instability) /
np.sqrt(PhysicalConstants.mu_0 * rho))**0.4
deltas_jor_9 /= (
solver.r_to_q_deriv(solver.r_instability) /
(solver.r_instability * solver.r_to_q(solver.r_instability)))**0.4
deltas_jor_9 = deltas_jor_9**(5.0 / 4.0)
deltas_tm1 = tm1_data[:, 1] / 0.55 / (eta / PhysicalConstants.mu_0)**0.6
deltas_tm1 /= (m * solver.r_to_B_theta(solver.r_instability) /
np.sqrt(PhysicalConstants.mu_0 * rho))**0.4
deltas_tm1 /= (
solver.r_to_q_deriv(solver.r_instability) /
(solver.r_instability * solver.r_to_q(solver.r_instability)))**0.4
deltas_tm1 = deltas_tm1**(5.0 / 4.0)
# Plot equivalent gammas
scaling = 1.05 # Factor to improve plot
fig, ax = plt.subplots(1)
ax.plot(deltas[:, 0], deltas[:, 1], label='Linear')
ax.scatter(deltas[:, 0], deltas[:, 1])
ax.plot(alphas_jor, deltas_jor, label='JOREK')
ax.scatter(alphas_jor, deltas_jor)
# ax.plot(alphas_jor_8, deltas_jor_8, label='JOREK $\Delta\'$ for $\eta=10^{-8}$')
# ax.scatter(alphas_jor_8, deltas_jor_8)
# ax.plot(alphas_jor_8, deltas_jor_9, label='JOREK $\Delta\'$ for $\eta=10^{-9}$')
# ax.scatter(alphas_jor_8, deltas_jor_9)
ax.plot(tm1_data[:, 0], deltas_tm1, label='TM1')
ax.scatter(tm1_data[:, 0], deltas_tm1)
ax.axhline(0.0, c='k', linestyle='--')
ax.axvline(0.358,
linestyle='--',
color='grey',
label='Linear stability boundary')
ax.axvline(0.3375,
linestyle='--',
color='g',
label='JOREK stability boundary')
ax.axvline(0.35, linestyle='--', color='g')
ax.fill_betweenx(scaling * deltas[:, 1],
0.3375,
0.35,
facecolor='green',
alpha=0.2)
ax.set_ylabel('$\Delta\'$', fontsize=fontsize)
ax.set_xlabel('$\\alpha$', fontsize=fontsize)
ax.set_xlim([0.0, 1.0])
ax.set_ylim([scaling * min(deltas[:, 1]), 22.0])
ax.grid(linestyle='--')
ax.legend()
plt.savefig('current_stability_deltas_{}'.format(m))
plt.show()
def enthalpy_form():
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
markers = ["o", "x", "^", "v", "d"]
all_data = []
folder = "data/mc_hcp"
for conc in concs:
new_data = {}
fname = "{}/thermo_{}.csv".format(folder, conc)
T, conc, H_form = np.loadtxt(fname,
delimiter=",",
unpack=True,
usecols=(0, 2, 3))
new_data["T"] = T[1:]
new_data["H"] = H_form[1:]
new_data["conc"] = conc[1:]
all_data.append(new_data)
n_temps = len(all_data[0]["T"])
Tmax = np.max(all_data[0]["T"])
Tmin = np.min(all_data[0]["T"])
for i in range(n_temps):
T = all_data[0]["T"][i]
form = []
conc = []
for dset in all_data:
form.append(dset["H"][i])
conc.append(dset["conc"][i])
srt_indx = np.argsort(conc)
conc = [conc[indx] for indx in srt_indx]
form = [form[indx] for indx in srt_indx]
conc.append(1.0)
form.append(0.0)
mapped_temp = (T - Tmin) / (Tmax - Tmin)
ax.plot(conc,
form,
marker=markers[i % len(markers)],
color=cm.copper(mapped_temp),
label="{}K".format(T))
ax.set_xlabel("Mg concentration")
ax.set_ylabel("Enthalpy of formation (kJ/mol)")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
#ax.legend()
Z = [[0, 0], [0, 0]]
fig_info = plt.figure()
#temp_info = [np.min(T),np.max(T)]
ax_info = fig_info.add_subplot(1, 1, 1)
temp_info = np.linspace(Tmin, Tmax, 256)
Cb_info = ax_info.contourf(Z, temp_info, cmap="copper")
cbar = fig.colorbar(Cb_info,
orientation="horizontal",
ticks=[100, 300, 500, 700])
cbar.ax.xaxis.set_ticks_position("top")
cbar.ax.set_xticklabels([100, 300, 500, 700])
cbar.ax.xaxis.set_label_position("top")
#cbar.ax.tick_params(axis='x',direction='in',labeltop='on')
cbar.set_label("Temperature (K)")
def get_random_plot(name, direc):
"""
Random plot generation method.
Inputs:
name: (string) name of the plot which will be saved.
Outputs:
ax : (matplotlib obj) Matplotlib object of the axes of the plot
fig : (matplotlib obj) Matplotlib object of the figure of the plot
x, y : (list, list) Actuall x and y coordinates of the points.
s : (list) sizes of the points.
categories : (list) categories of the points.
tick_size : (list) Tick size on the plot. [width, length]
axes_x_pos, axes_y_pos: (float, float) Position of the labels of the axis.
"""
# PLOT STYLE
style = random.choice(styles)
plt.style.use(style)
# POINT DISTRIBUTION
distribution = random.choice(point_dist)
# RESOLUTION AND TICK SIZE
dpi = int(dpi_min + np.random.rand(1)[0] * (dpi_max - dpi_min))
figsize = (figsize_min + np.random.rand(2) *
(figsize_max - figsize_min)).astype(int)
tick_size = [(tick_size_width_min + np.random.rand(1)[0] *
(tick_size_width_max - tick_size_width_min)),
(tick_size_length_min + np.random.rand(1)[0] *
(tick_size_length_max - tick_size_length_min))]
tick_size.sort()
fig, ax = plt.subplots(figsize=figsize, dpi=dpi)
# ACTUAL POINTS
points_nb = int(points_nb_min + (np.random.rand(1)[0]**1.5) *
(points_nb_max - points_nb_min))
#print points_nb
x_scale = int(x_min_top + np.random.rand(1)[0] * (x_max_top - x_min_top))
#print x_scale
y_scale = int(y_min_top + np.random.rand(1)[0] * (y_max_top - y_min_top))
#print y_scale
x_scale_range = x_scale + int(np.random.rand(1)[0] * x_scale_range_max)
#print x_scale_range
y_scale_range = y_scale + int(np.random.rand(1)[0] * y_scale_range_max)
#print y_scale_range
x_min = (-np.random.rand(1)[0] + np.random.rand(1)[0]) * 10**(x_scale)
x_max = (-np.random.rand(1)[0] +
np.random.rand(1)[0]) * 10**(x_scale_range)
x_min, x_max = min(x_min, x_max), max(x_min, x_max)
y_min = (-np.random.rand(1)[0] + np.random.rand(1)[0]) * 10**(y_scale)
y_max = (-np.random.rand(1)[0] +
np.random.rand(1)[0]) * 10**(y_scale_range)
y_min, y_max = min(y_min, y_max), max(y_min, y_max)
if distribution == 'uniform':
x = x_min + np.random.rand(points_nb) * (x_max - x_min)
y = y_min + np.random.rand(points_nb) * (y_max - y_min)
elif distribution == 'linear':
x = x_min + np.random.rand(points_nb) * (x_max - x_min)
y = x * (max(y_max, -y_min) / (max(x_max, -x_min))) * random.choice(
[-1.0, 1.0]) + (y_min + np.random.rand(points_nb) *
(y_max - y_min)) * np.random.rand(1)[0] / 2.0
elif distribution == 'quadratic':
x = x_min + np.random.rand(points_nb) * (x_max - x_min)
y = x**2 * (1.0 / (max(x_max, -x_min)))**2 * max(
y_max, -y_min) * random.choice(
[-1.0, 1.0]) + (y_min + np.random.rand(points_nb) *
(y_max - y_min)) * np.random.rand(1)[0] / 2.0
# POINTS VARIATION
nb_points_var = 1 + int(np.random.rand(1)[0] * max_points_variations)
nb_points_var_colors = 1 + int(np.random.rand(1)[0] * nb_points_var)
nb_points_var_markers = 1 + int(
np.random.rand(1)[0] * (nb_points_var - nb_points_var_colors))
nb_points_var_size = max(
1, 1 + nb_points_var - nb_points_var_colors - nb_points_var_markers)
rand_color_number = np.random.rand(1)[0]
if rand_color_number <= 0.5:
colors = cm.rainbow(np.random.rand(nb_points_var_colors))
elif rand_color_number > 0.5 and rand_color_number <= 0.7:
colors = cm.gnuplot(np.random.rand(nb_points_var_colors))
elif rand_color_number > 0.7 and rand_color_number <= 0.8:
colors = cm.copper(np.random.rand(nb_points_var_colors))
else:
colors = cm.gray(np.linspace(0, 0.6, nb_points_var_colors))
s_set = (size_points_min + np.random.rand(nb_points_var_size) *
(size_points_max - size_points_min))**2
markers_subset = list(np.random.choice(markers,
size=nb_points_var_markers))
markers_empty = np.random.rand(1)[0] > 0.75
markers_empty_ratio = random.choice([0.0, 0.5, 0.7])
# BUILDING THE PLOT
s = []
categories = []
cat_dict = {}
index_cat = 0
for _x, _y, in zip(x, y):
s_ = random.choice(s_set)
c_ = random.choice(colors)
m_ = random.choice(markers_subset)
if m_ in markers_with_full and markers_empty:
e_ = np.random.rand(1)[0] > markers_empty_ratio
else:
e_ = False
cat = [s_, c_, m_, e_]
if cat_in_dict(cat, cat_dict) is False:
cat_dict[index_cat] = cat
index_cat += 1
categories.append(cat_in_dict(cat, cat_dict))
s.append(s_)
if e_:
plt.scatter(_x, _y, s=s_, color=c_, marker=m_, facecolors='none')
else:
plt.scatter(_x, _y, s=s_, color=c_, marker=m_)
# PAD BETWEEN TICKS AND LABELS
#labs = [item.get_text() for item in ax.get_xticklabels()]
#print labs
pad_x = max(tick_size[1] + 0.5,
int(pad_min + np.random.rand(1)[0] * (pad_max - pad_min)))
pad_y = max(tick_size[1] + 0.5,
int(pad_min + np.random.rand(1)[0] * (pad_max - pad_min)))
direction_ticks_x = random.choice(direction_ticks)
direction_ticks_y = random.choice(direction_ticks)
# NON-DEFAULT TICKS PROB, WITH THRESHOLD OF 0.6
weid_ticks_prob = np.random.rand(1)[0]
# TICKS STYLE AND LOCATION (X AXIS)
if np.random.rand(1)[0] > 0.5:
axes_x_pos = 1
ax.xaxis.tick_top()
ax.xaxis.set_label_position("top")
if weid_ticks_prob > 0.6:
ax.xaxis.set_tick_params(width=tick_size[0],
length=tick_size[1],
color='black',
pad=pad_x,
direction=direction_ticks_x,
bottom=np.random.rand(1)[0] > 0.5,
top=True)
else:
ax.xaxis.set_tick_params(bottom=np.random.rand(1)[0] > 0.5,
top=True)
if np.random.rand(1)[0] > 0.5:
ax.spines['bottom'].set_visible(False)
ax.xaxis.set_tick_params(bottom=False)
if np.random.rand(1)[0] > 0.5:
axes_x_pos = np.random.rand(1)[0]
ax.spines['top'].set_position(('axes', axes_x_pos))
else:
axes_x_pos = 0
if weid_ticks_prob > 0.6:
ax.xaxis.set_tick_params(width=tick_size[0],
length=tick_size[1],
color='black',
pad=pad_x,
direction=direction_ticks_x,
bottom=True,
top=np.random.rand(1)[0] > 0.5)
else:
ax.xaxis.set_tick_params(bottom=True,
top=np.random.rand(1)[0] > 0.5)
if np.random.rand(1)[0] > 0.5:
ax.spines['top'].set_visible(False)
ax.xaxis.set_tick_params(top=False)
if np.random.rand(1)[0] > 0.5:
axes_x_pos = np.random.rand(1)[0]
ax.spines['bottom'].set_position(('axes', axes_x_pos))
# TICKS STYLE AND LOCATION (Y AXIS)
if np.random.rand(1)[0] > 0.5:
axes_y_pos = 1
ax.yaxis.tick_right()
ax.yaxis.set_label_position("right")
if weid_ticks_prob > 0.6:
ax.yaxis.set_tick_params(width=tick_size[0],
length=tick_size[1],
color='black',
pad=pad_y,
direction=direction_ticks_y,
left=np.random.rand(1)[0] > 0.5,
right=True)
else:
ax.yaxis.set_tick_params(left=np.random.rand(1)[0] > 0.5,
right=True)
if np.random.rand(1)[0] > 0.5:
ax.spines['left'].set_visible(False)
ax.yaxis.set_tick_params(left=False)
if np.random.rand(1)[0] > 0.5:
axes_y_pos = np.random.rand(1)[0]
ax.spines['right'].set_position(('axes', axes_y_pos))
else:
axes_y_pos = 0
if weid_ticks_prob > 0.6:
ax.yaxis.set_tick_params(width=tick_size[0],
length=tick_size[1],
color='black',
pad=pad_y,
direction=direction_ticks_y,
left=True,
right=np.random.rand(1)[0] > 0.5)
else:
ax.yaxis.set_tick_params(left=True,
right=np.random.rand(1)[0] > 0.5)
if np.random.rand(1)[0] > 0.5:
ax.spines['right'].set_visible(False)
ax.yaxis.set_tick_params(right=False)
if np.random.rand(1)[0] > 0.5:
axes_y_pos = np.random.rand(1)[0]
ax.spines['left'].set_position(('axes', axes_y_pos))
# LABEL ROTATION
if np.random.rand(1)[0] > 0.77:
plt.xticks(rotation=int(np.random.rand(1)[0] * 90))
if np.random.rand(1)[0] > 0.77:
plt.yticks(rotation=int(np.random.rand(1)[0] * 90))
# SUB-TICKs
if weid_ticks_prob > 0.6:
color_subtick = random.choice(color_subtick_list)
length_subtick = 0.75 * np.random.rand(1)[0] * tick_size[1]
if np.random.rand(1)[0] > 0.7:
minorLocator = AutoMinorLocator()
ax.xaxis.set_minor_locator(minorLocator)
ax.xaxis.set_tick_params(which='minor',
length=length_subtick,
direction=direction_ticks_x,
color=color_subtick,
bottom=ax.spines['bottom'].get_visible(),
top=ax.spines['top'].get_visible())
if np.random.rand(1)[0] > 0.7:
minorLocator = AutoMinorLocator()
ax.yaxis.set_minor_locator(minorLocator)
ax.yaxis.set_tick_params(which='minor',
length=length_subtick,
direction=direction_ticks_y,
color=color_subtick,
left=ax.spines['left'].get_visible(),
right=ax.spines['right'].get_visible())
# FONT AND SIZE FOR LABELS (tick labels, axes labels and title)
font = random.choice(font_list)
size_ticks = int(tick_label_size_min + np.random.rand(1)[0] *
(tick_label_size_max - tick_label_size_min))
size_axes = int(axes_label_size_min + np.random.rand(1)[0] *
(axes_label_size_max - axes_label_size_min))
size_title = int(title_size_min + np.random.rand(1)[0] *
(title_size_max - title_size_min))
ticks_font = font_manager.FontProperties(fname=font,
style='normal',
size=size_ticks,
weight='normal',
stretch='normal')
axes_font = font_manager.FontProperties(fname=font,
style='normal',
size=size_axes,
weight='normal',
stretch='normal')
title_font = font_manager.FontProperties(fname=font,
style='normal',
size=size_title,
weight='normal',
stretch='normal')
# TEXTS FOR AXIS LABELS AND TITLE
label_x_length = int(axes_label_length_min + np.random.rand(1)[0] *
(axes_label_length_max - axes_label_length_min))
#print label_x_length
label_y_length = int(axes_label_length_min + np.random.rand(1)[0] *
(axes_label_length_max - axes_label_length_min))
title_length = int(title_length_min + np.random.rand(1)[0] *
(title_length_max - title_length_min))
x_label = ("".join([
random.choice(string.ascii_letters + ' ')
for i in range(label_x_length)
])).strip()
#print x_label
y_label = ("".join([
random.choice(string.ascii_letters + ' ')
for i in range(label_y_length)
])).strip()
title = ("".join([
random.choice(string.ascii_letters + ' ')
for i in range(title_length)
])).strip()
plt.xlabel(x_label, fontproperties=axes_font)
plt.ylabel(y_label, fontproperties=axes_font, color='black')
if axes_x_pos == 1:
plt.title(title, fontproperties=title_font, color='black', y=1.1)
else:
plt.title(title, fontproperties=title_font, color='black')
for label in ax.get_xticklabels():
label.set_fontproperties(ticks_font)
for label in ax.get_yticklabels():
label.set_fontproperties(ticks_font)
# GRID
if np.random.rand(1)[0] > 0.7:
plt.grid(b=True,
which='major',
color=random.choice(color_grid),
linestyle=random.choice(linestyles))
# AXIS LIMITS
xmin = min(x)
xmax = max(x)
deltax = 0.05 * abs(xmax - xmin)
plt.xlim(xmin - deltax, xmax + deltax)
ymin = min(y)
ymax = max(y)
deltay = 0.05 * abs(ymax - ymin)
plt.ylim(ymin - deltay, ymax + deltay)
# BACKGROUND AND PATCH COLORS
if np.random.rand(1)[0] > 0.75:
color_bg = (1 - colorbg_transparant_max
) + colorbg_transparant_max * np.random.rand(3)
ax.set_axis_bgcolor(color_bg)
if np.random.rand(1)[0] > 0.75:
color_bg = (1 - colorbg_transparant_max
) + colorbg_transparant_max * np.random.rand(3)
fig.patch.set_facecolor(color_bg)
# MAKE SURE THE PLOT FITS INSIDE THE FIGURES
try:
plt.tight_layout()
plt.savefig("./data/{}/".format(direc) + name,
dpi='figure',
facecolor=fig.get_facecolor())
except RuntimeError:
pass
return ax, fig, x, y, s, categories, tick_size, axes_x_pos, axes_y_pos
def main():
''' set paths & parameters '''
# Parse information from the command line
parser = argparse.ArgumentParser(prog='LES_CP')
parser.add_argument("casename")
parser.add_argument("path_root")
parser.add_argument("path1")
parser.add_argument("path2")
parser.add_argument("path_out")
parser.add_argument("--tmin")
parser.add_argument("--tmax")
parser.add_argument("--kmax")
parser.add_argument("--everysecond")
args = parser.parse_args()
set_input_parameters(args)
# ic_arr, jc_arr = define_geometry(nml)
if args.everysecond:
every_second = args.everysecond
else:
every_second = True
print('every_second', every_second)
file_name = 'stats_radial_averaged.nc'
file1 = nc.Dataset(os.path.join(path1, 'data_analysis', file_name))
file2 = nc.Dataset(os.path.join(path2, 'data_analysis', file_name))
dx1 = file1.groups['dimensions'].dimensions['dx'].size
dx2 = file2.groups['dimensions'].dimensions['dx'].size
dz1 = file1.groups['dimensions'].dimensions['dz'].size
dz2 = file2.groups['dimensions'].dimensions['dz'].size
if dx1 < dx2: # want to have file2 higher resolution
file_aux = file2
file2 = file1
file1 = file_aux
del file_aux
print('dx: ', dx1_nml[0], dx2_nml[0], dx1)
print('dz: ', dx1_nml[2], dx2_nml[2], dz1)
print('nx: ', nx1[0], nx2[0])
print('nz: ', nx1[2], nx2[2])
grp_stats1 = file1.groups['stats'].variables
grp_stats2 = file2.groups['stats'].variables
time1 = file1.groups['timeseries'].variables['time'][:]
time2 = file2.groups['timeseries'].variables['time'][:]
print('times: ')
print time1
print time2
nt = np.minimum(len(time1), len(time2))
time1 = time1[:nt]
time2 = time2[:nt]
if len(time1) != len(time2):
time1 = time1[:nt]
time2 = time2[:nt]
if time1.any() != time2.any():
print 'problem with times'
sys.exit()
r1 = file1.groups['stats'].variables['r'][:]
r2 = file2.groups['stats'].variables['r'][:]
ri1 = file1.groups['stats'].variables['ri'][:]
ri2 = file2.groups['stats'].variables['ri'][:]
try:
krange1 = file1.groups['dimensions'].variables['krange'][:]
krange2 = file2.groups['dimensions'].variables['krange'][:]
except:
krange1 = np.arange(kmax)
krange2 = np.arange(kmax)
print ''
print 'kranges:'
print krange1
print krange2
if dz1 > dz2:
print 'dz1 > dz2'
dz12 = np.double(dz1) / dz2
kmax_ = np.int(
np.minimum(np.int(np.round(kmax / dz12)),
len(krange2) / dz12))
krange1 = krange1[:kmax_]
krange2 = krange2[0::np.int(dz12)]
elif dz1 < dz2:
print 'dz1 < dz2'
dz12 = np.double(dz2) / dz1
kmax_ = np.int(np.round(kmax / dz12))
krange1 = krange1[0::2]
krange2 = krange2[:kmax_]
else:
dz12 = 1.
kmax_ = kmax
print('')
print 'dz: ', dz1, dz2, dz12
print 'kmax: ', kmax, kmax_
print krange1
print krange2
print 'zranges:'
print krange1 * dz1
print krange2 * dz2
var_list = ['w', 'v_rad', 's']
ncol = len(var_list)
rmax = 8e3
irmax1 = np.where(r1 == rmax)[0]
irmax2 = np.where(r2 == rmax)[0]
# irmax1 = -1
# irmax2 = -1
print ''
print r1[-1], r2[-1]
print 'irmax: ', irmax1, irmax2
print 'rmax', r1[irmax1], r2[irmax2]
print ''
for k0 in range(kmax_):
k1 = krange1[k0]
k2 = krange2[k0]
print('z1, z2: ', k1 * dz1, k2 * dz2)
fig_name = 'radial_average_z' + str(k1 * dz1) + '.png'
fig, axes = plt.subplots(1, ncol, sharey='none', figsize=(7 * ncol, 5))
for i, ax in enumerate(axes):
var1 = grp_stats1[var_list[i]][:, :, :]
var2 = grp_stats2[var_list[i]][:, :, :]
if var_list[i] == 'w':
ax.set_ylim(
-6,
np.maximum(np.amax(var1[:, :, k0]), np.amax(var2[:, :,
k0])))
if every_second == True:
for it, t0 in enumerate(time1[1::2]):
# print('- t='+str(t0))
count_color = 2 * np.double(it) / len(time1)
if it == 0:
ax.plot(r1[:irmax1],
var1[2 * it + 1, :irmax1, k1],
color=cm.copper(count_color),
linewidth=3,
label='t=' + str(t0) + ', dx=' + str(dx1))
else:
ax.plot(r1[:irmax1],
var1[2 * it + 1, :irmax1, k1],
color=cm.copper(count_color),
linewidth=3,
label='t=' + str(t0))
for it, t0 in enumerate(time1[1::2]):
#print('t=' + str(t0))
count_color = 2 * np.double(it) / len(time1)
if it == 0:
ax.plot(r2[:irmax2],
var2[2 * it + 1, :irmax2, k2],
'-',
color=cm.jet(count_color),
linewidth=3,
label='dx=' + str(dx2))
else:
# ax.plot(r2[:irmax2], )
ax.plot(r2[:irmax2],
var2[2 * it + 1, :irmax2, k2],
'-',
color=cm.jet(count_color),
linewidth=2,
label='dx=' + str(dx2))
else:
for it, t0 in enumerate(time1):
print('t=' + str(t0))
count_color = np.double(it) / len(time1)
if it == 0:
ax.plot(r1[:irmax1],
var1[it, :irmax1, k1],
color=cm.copper(count_color),
linewidth=3,
label='t=' + str(t0) + ', dx=' + str(dx1))
else:
ax.plot(r1[:irmax1],
var1[it, :irmax1, k1],
color=cm.copper(count_color),
linewidth=3,
label='t=' + str(t0))
for it, t0 in enumerate(time1):
print('t=' + str(t0))
count_color = np.double(it) / len(time1)
if it == 0:
ax.plot(r2[:irmax2],
var2[it, :irmax2, k2],
'-',
color=cm.jet(count_color),
linewidth=2,
label='dx=' + str(dx2))
else:
ax.plot(r2[:irmax2],
var2[it, :irmax2, k2],
'-',
color=cm.jet(count_color),
linewidth=2,
label='dx=' + str(dx2))
ax.set_title(var_list[i])
ax.set_xlabel('radius r [m]')
ax.set_ylabel(var_list[i])
axes[2].legend(loc='upper center',
bbox_to_anchor=(1.15, 0.8),
fancybox=True,
ncol=2,
fontsize=8)
# plt.tight_layout()
plt.subplots_adjust(bottom=0.12,
right=.9,
left=0.04,
top=0.9,
wspace=0.15)
fig.suptitle('Radially averaged variables (k=' + str(k0) + ')')
fig.savefig(os.path.join(path_out_figs, fig_name))
plt.close(fig)
file1.close()
file2.close()
return
def few_Vm_fig(SET_OF_DATA,
pop_key='Exc',
tspace=200.,
tzoom=[200, np.inf],
VMS1=np.arange(3),
VMS2=None,
Tbar=100,
Vbar=10,
Vshift=30,
vpeak=-42,
vbottom=-80):
fig, ax = plt.subplots(figsize=(5 * len(SET_OF_DATA), 5))
# plt.subplots_adjust(left=.15, bottom=.1, right=.99)
if VMS2 is None:
VMS2 = VMS1 # ID of cells
t0 = 0
for k, data in enumerate(SET_OF_DATA):
VMS = [VMS1, VMS2][k]
t = np.arange(int(data['tstop'] / data['dt'])) * data['dt']
cond = (t > tzoom[0]) & (t < tzoom[1])
for i, j in enumerate(VMS):
ax.plot(t[cond]+t0, data['VMS_'+str(pop_key)][j][cond]+Vshift*i,\
color=copper(i/len(VMS)/1.5), lw=1)
ax.plot(t[cond] + t0,
0 * t[cond] + -70 + Vshift * i,
':',
color=copper(i / len(VMS) / 1.5),
lw=1)
ax.plot([t[cond][0] + t0], [-70 + Vshift * i],
'>',
color=copper(i / len(VMS) / 1.5))
# adding spikes
for i, j in enumerate(VMS):
tspikes = data['tRASTER_' + str(pop_key)][np.argwhere(
data['iRASTER_' + str(pop_key)] == j).flatten()]
cond = (tspikes > tzoom[0]) & (tspikes < tzoom[1])
for ts in tspikes[cond]:
ax.plot([ts + t0, ts + t0],
Vshift * i + np.array([-50, vpeak]),
'--',
color=copper(i / len(VMS) / 1.5),
lw=1)
t0 = tspace + tzoom[1] - tzoom[0]
ax.plot([tzoom[0], tzoom[0] + Tbar],
ax.get_ylim()[0] * np.ones(2),
lw=5,
color='gray')
ax.annotate(str(Tbar) + 'ms', (tzoom[0], .9 * ax.get_ylim()[0]),
fontsize=14)
ax.plot(tzoom[1] * np.ones(2), [-60, -60 + Vbar], lw=5, color='gray')
ax.annotate(str(Vbar) + 'mV', (tzoom[1], -60), fontsize=14)
ax.annotate('-70mV', (tzoom[1], -70), fontsize=14)
set_plot(ax, [], xticks=[], yticks=[])
c = plt.axes([.5, .5, .01, .2])
cmap = mpl.colors.ListedColormap(copper(np.linspace(0, 1 / 1.5,
len(VMS1))))
cb = mpl.colorbar.ColorbarBase(c, cmap=cmap, orientation='vertical')
cb.set_label('Cell ID', fontsize=12)
cb.set_ticks([])
return fig
import numpy as np
import scipy as sp
from matplotlib.widgets import Slider
from matplotlib.colors import Normalize
from matplotlib import cm
import matplotlib.pyplot as pl
sizes = np.array([128, 256, 512, 1024, 2048])
data = -np.array([np.loadtxt("./df-hist-raw-%i.txt" % i) for i in sizes])
dev = np.array([91.0 / 48 - d.mean() for d in data])
std = np.array([d.std() for d in data])
colors = cm.copper(Normalize()(np.arange(len(dev))))
x, y = [], []
for t in data:
ty, tx = np.histogram(t, bins=24, normed=True)
x.append((tx[1:] + tx[:-1]) / 2)
y.append(ty)
x = np.array(x).T
y = np.array(y).T
def rescale(sizes, xs, ys, dfc, tau):
return (dfc - xs) * sizes ** tau, ys * sizes ** -tau
def plotall():
"""
Note: to save, use dpi=300 to match other plots
"""
import numpy as np
import scipy as sp
from matplotlib.widgets import Slider
from matplotlib.colors import Normalize
from matplotlib import cm
import matplotlib.pyplot as pl
sizes = np.array([128, 256, 512, 1024, 2048])
data = -np.array([np.loadtxt("./df-hist-raw-%i.txt" % i) for i in sizes])
dev = np.array([91. / 48 - d.mean() for d in data])
std = np.array([d.std() for d in data])
colors = cm.copper(Normalize()(np.arange(len(dev))))
x, y = [], []
for t in data:
ty, tx = np.histogram(t, bins=24, normed=True)
x.append((tx[1:] + tx[:-1]) / 2)
y.append(ty)
x = np.array(x).T
y = np.array(y).T
def rescale(sizes, xs, ys, dfc, tau):
return (dfc - xs) * sizes**tau, ys * sizes**-tau
def plotall():
"""
Note: to save, use dpi=300 to match other plots
"""
def plot_frequency_statistics():
folder = "data/almgsi_ch500K_run_truncnorm/postproc"
folder = "/work/sophus/almgsi_ch500K_run2/postproc"
fnames = [
"chgl_50_frequency_statistics.csv", "chgl_40_frequency_statistics.csv",
"chgl_30_frequency_statistics.csv", "chgl_20_frequency_statistics.csv",
"chgl_10_frequency_statistics.csv"
]
fnames = [folder + "/" + f for f in fnames]
concs = [0.5, 0.4, 0.3, 0.2, 0.1]
orig_concs = deepcopy(concs)
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
freqs = []
profiles = []
markers = ['o', 'd', 'v', '^', 'h', 'p']
concs = np.array(concs)
concs -= np.min(concs)
concs /= np.max(concs)
col = 1
if col == 2:
print("Plotting second moment of distribution")
elif col == 1:
print("Plotting first moment of distribution")
else:
raise ValueError("col has to be 1 or 2")
for i, fname in enumerate(fnames):
data = np.loadtxt(fname, delimiter=",")
freqs.append(data[:, 0])
profiles.append(data[:, col])
ax.plot(data[:, 0],
data[:, col],
markers[i],
mfc="none",
color=cm.copper(concs[i]),
ms=8,
markeredgewidth=1.5,
label="{}%".format(int(100 * orig_concs[i])))
# Fit a linear line to beginning
slope, interscept, _, _, _ = linregress(np.log(freqs[0][:12]),
np.log(profiles[0][:12]))
print("Slope (exponent)", slope)
freq_fit = np.logspace(-1.5, 3, 10)
ax.plot(freq_fit,
np.exp(interscept) * freq_fit**slope,
ls='--',
color="#5d5C61")
ax.set_xscale("log")
ax.set_yscale("log", basey=2)
ax.set_xlabel("Dimensionless time")
ax.set_ylabel("Frequency (nm\$^{-1}\$)")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.legend(frameon=False)
plt.show()
def get_stability_condition(plot_results=True):
current_factors = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
colors = cm.copper(np.linspace(0.0, 1.0, len(current_factors)))
# Get profiles
dat = np.loadtxt(os.path.join('input_profiles.dat'))
# Modify and plot input profiles
r = dat[:, 0]
R = dat[:, 1]
j_phi = dat[:, 2]
B_z = dat[:, 3]
B_theta = dat[:, 4]
psi_n = dat[:, 5]
r_to_psin = interpolate.interp1d(r, psi_n)
psin_to_r = interpolate.interp1d(r, psi_n)
q = r * B_z / (R * B_theta)
q[0] = q[1]
if plot_results:
fig, ax = plt.subplots(2, 2, figsize=(10, 10), sharex=True)
ax[0, 0].plot(r, B_z, c='k')
ax[0, 0].set_ylabel('$B_{\phi}$ [T]', fontsize=fontsize)
ax[1, 0].plot(r, B_theta, c='k')
ax[1, 0].set_ylabel('$B_{\\theta}$ [T]', fontsize=fontsize)
for i, factor in enumerate(current_factors[::-1]):
linestyle = '--' if i > 0 else '-'
ax[0, 1].plot(r,
factor * j_phi * 1e-3,
linestyle=linestyle,
c=colors[i])
ax[0, 1].set_ylabel('$j_{\phi}$ [kA]', fontsize=fontsize)
ax[1, 1].plot(r, q, c='k')
ax[1, 1].set_ylabel('q', fontsize=fontsize)
ax[1, 1].set_xlabel('r [m]', fontsize=fontsize)
ax[1, 0].set_xlabel('r [m]', fontsize=fontsize)
ax[0, 0].set_xlim([0.0, 1.0])
fig.tight_layout()
plt.savefig('input_profiles')
plt.show()
r_max = r[-1]
deltas = list()
alphas = list()
for factor in current_factors:
j_phi_sim = j_phi * factor
solver = TearingModeSolver(m,
r,
r_max,
B_theta,
B_z,
j_phi_sim,
q,
num_pts,
delta=1e-12)
solver.find_delta(plot_output=False)
psin_lower = r_to_psin(solver.r_lower)
psin_upper = r_to_psin(solver.r_upper)
if plot_results:
fig, ax = plt.subplots(2, sharex=True)
ax[0].plot(psin_lower,
solver.psi_sol_lower[:, 0],
label='solution from axis')
ax[0].plot(psin_upper,
solver.psi_sol_upper[:, 0],
label='solution from boundary')
# Plot comparison solution if it exists
validation_file = 'flux_validation_vc_{}.csv'.format(factor)
if os.path.exists(validation_file):
flux_validation = np.loadtxt(validation_file, delimiter=',')
flux_validation[:, 1] /= np.max(flux_validation[:, 1])
flux_validation[:, 1] *= np.max(solver.psi_sol_lower[:, 0])
ax[0].plot(flux_validation[:, 0],
flux_validation[:, 1],
linestyle='--',
label='JOREK')
ax[0].set_ylabel('$\Psi_1$', fontsize=fontsize)
ax[0].legend()
ax[0].set_xlim([0.0, 1.0])
ax[1].plot(psin_lower, solver.psi_sol_lower[:, 1])
ax[1].plot(psin_upper, solver.psi_sol_upper[:, 1])
ax[1].set_ylabel('$\\frac{\partial \Psi_1}{\partial r}$',
fontsize=fontsize)
ax[1].set_xlabel('$\hat \Psi$', fontsize=fontsize)
plt.show()
deltas.append(solver.delta)
alphas.append(1 - factor)
np.savetxt('deltas', np.asarray(deltas))
plt.figure()
plt.plot(alphas, deltas)
plt.axvline(0.346,
linestyle='--',
color='grey',
label='Linear stability boundary')
plt.axvline(0.25,
linestyle='--',
color='g',
label='JOREK stability boundary')
plt.grid(linestyle='--')
plt.ylabel('$\Delta\'$', fontsize=fontsize)
plt.xlabel('$\\alpha$', fontsize=fontsize)
plt.legend()
plt.xlim([0.0, 1.0])
plt.savefig('current_stability_{}'.format(m))
plt.show()
def main():
args = parse_args()
q_mean, p_mean, Q, P, W = prepare_data(args)
no_steps = Q.shape[0]
q_min = Q[:,0,0].min()
q_max = Q[:,0,-1].max()
p_min = P[:,0,0].min()
p_max = P[:,-1,0].max()
if args.vmin[-1]=="%":
W_min = numpy.percentile(W[:], float(args.vmin[:-1]))
else:
W_min = float(args.vmin)
if args.vmax[-1]=="%":
W_max = numpy.percentile(W[:], 100.-float(args.vmax[:-1]))
else:
W_max = float(args.vmax)
midpoint = 1 - W_max/(W_max + abs(W_min))
cmap = shifted_color_map(cm.coolwarm, midpoint=midpoint, name="shifted")
fig = pyplot.figure()
ax = fig.add_subplot(1,1,1)
ax.set_xlim(q_min, q_max)
ax.set_ylim(p_min, p_max)
ax.set_xlabel("q")
ax.set_ylabel("p")
if args.visualization=="polished":
shading="gouraud"
else:
shading="flat"
quad = QuadContainer(ax.pcolormesh(Q[0], P[0], W[0],
vmin=W_min, vmax=W_max,
cmap=cmap,
shading=shading))
ax.set_aspect("equal")
if args.track:
ax.set_color_cycle([cm.copper(1.*i/(no_steps-1)) for i in range(no_steps-1)])
for i in range(no_steps-1):
ax.plot(q_mean[i:i+2],p_mean[i:i+2], alpha=.3)
cb = fig.colorbar(quad.quad)
cb.set_label("Quasiprobability Density")
cb.solids.set_rasterized(True)
if args.visualization=="polished":
ax.set_axis_bgcolor(cb.to_rgba(0.))
no_digits = int(ceil(log10(no_steps))+1)
title_string = "Wigner Function at step {:{width}}/{:{width}}"
title = ax.set_title(title_string.format(0, no_steps, width=no_digits))
ax.grid(True)
if args.output:
fig.savefig(args.output+"_thumb.pdf")
def animate(i):
title.set_text(title_string.format(i, no_steps, width=no_digits))
quad.update_quad(ax.pcolormesh(Q[i], P[i], W[i],
vmin=W_min, vmax=W_max,
cmap=cmap,
shading=shading))
ax.grid(True)
return quad.quad,
ani = FuncAnimation(fig, animate, no_steps, interval=100, repeat_delay=1000)
if args.output:
print("Saving movie to {}. This may take a couple of minutes.".format(args.output))
ani.save(args.output+".mp4", fps=10, extra_args=['-vcodec', 'libx264'])
pyplot.show()