def plot(covIndex):
figR, ax = plt.subplots(nrows=1, ncols=2, figsize=(5,3.5))
figR.subplots_adjust(top=0.88,left=0.15,right=0.9,bottom=0.15, wspace=0.1)
plotAx(ax[0], min0energy, covIndex, x0indexes)
plotAx(ax[1], min1energy, covIndex, x1indexes)
ax[0].plot(x, np.ones(len(x))*60, ":", color="gray")
ax[0].annotate(r"", xy=(60,60), xytext=(65,max0energy), xycoords="data",arrowprops=dict(arrowstyle="-", edgecolor='gray'))
ax[0].annotate(r"", xy=(58,0), xytext=(67,0), xycoords="data",arrowprops=dict(arrowstyle="-", edgecolor='gray'))
# post
ax[0].set_xlabel(r"$1/k_BT$")#, size=14)
ax[1].set_xlabel(r"$1/k_BT$")#, size=14)
ax[0].set_ylabel(r"Energy $(meV)$")#, size=14)
ax[labelIndex].annotate(r"$\epsilon^{R}_\alpha=\omega^{R}_\alpha(E^k_\alpha+E^M_\alpha)$", xy=(0.25,0.3), xycoords="axes fraction")
ax[1].yaxis.tick_right()
#inf.smallerFont(ax[0], 14)
#inf.smallerFont(ax[1], 14)
ax[0].set_ylim(0, max0energy)
ax[0].set_xlim(x0min, x0max)
ax[1].set_ylim(0,60)
ax[1].set_xlim(x1min, x1max)
ax02 = mp.setY2TemperatureLabels(ax[0],kb, majors=majors0)
ax12 = mp.setY2TemperatureLabels(ax[1],kb, majors=majors1)
ax[0].legend(loc="best", prop={'size':9})
ax[1].legend(loc="best", prop={'size':9})
plt.savefig("plotResume/resume"+str(covIndex)+"_{:5f}".format(coverages[covIndex])+".svg")
plt.close(figR)
def plotManyTotalRates(axarr, index, d, latSize, annotate=True):
kb = 8.617332e-5
totalRateM, totalRateE, temperatures, coverages, totalRateH = d
cm = plt.get_cmap('tab20c')
if os.getcwd()[-4:] == "CuNi":
color = [cm(0 / 20), cm(1 / 20), cm(2 / 20)]
marker = ["o", "2", "^"]
label = "Cu/Ni"
else:
color = [cm(4 / 20), cm(5 / 20), cm(6 / 20)]
marker = ["d", "+", "s"]
label = "Ni/Cu"
axarr.plot(1 / kb / temperatures,
totalRateE[index],
"-",
marker=marker[0],
ms=7,
label=label + r": $R_e = N_e/T$",
color=color[0])
axarr.plot(1 / kb / temperatures,
totalRateH[index],
":",
marker=marker[2],
ms=7,
label=label + r": $R_d = N_d/T$",
color=color[2],
markerfacecolor="None")
axarr.plot(1 / kb / temperatures,
totalRateM[index],
marker=marker[1],
ms=7,
ls="",
label=label +
r": $R_e' = \sum_{\alpha \in \{e\}} m_\alpha k_\alpha$",
color=color[1])
if annotate:
#axarr.annotate(r"$\epsilon^{R}_\alpha=\omega^{R}_\alpha(E^k_\alpha+E^M_\alpha)$", xy=(0.47,0.1), xycoords="axes fraction")
axarr.annotate(r"$\theta =$" + str(np.round(coverages[index], 1)),
xy=(0.1, 0.57),
xycoords="axes fraction")
axarr.set_ylabel("Total rate per site")
axarr.set_xlabel(r"$1/k_BT$")
mp.setY2TemperatureLabels(axarr, kb)
else:
axarr.plot(1 / kb / temperatures,
np.ones(len(temperatures)) * coverages[index],
"--",
label=r"$R_a$" + " " + r"$(R = R_a + R_d)$",
color=cm(9 / 20))
axarr.set_yscale("log")
#axarr.set_ylim(3e-2,1e3)
axarr.legend(loc="best", prop={'size': 8})
def flush(self, omegaSumTof):
if not self.showPlot:
return
if self.one:
self.axarr[1].legend(bbox_to_anchor=(1.05, 1),
loc=2,
borderaxespad=0.)
ax2 = mp.setY2TemperatureLabels(self.axarr[1],
8.617332e-5,
majors=np.array(
[25, 50, 75, 100, 200, 1000]))
self.__smallerFont(ax2, 10)
else:
self.__smallerFont(self.axarr[0], 8)
self.__smallerFont(self.axarr[1], 14)
self.__putLabels()
self.fig.savefig("../../../plot" + str(self.moment) + "_" +
str(self.prod) + self.out)
plt.close(self.fig)
except FileNotFoundError:
pass
os.getcwd()
rate = 0
try:
totalRate = getTotalRate()
except ZeroDivisionError:
totalRate = 0
print(f, totalRate[-1])
x.append(f)
y.append(totalRate[-100])
os.chdir(workingPath)
i += 1
p = inf.getInputParameters(glob.glob("*/output*")[0])
fig, ax = plt.subplots(1, 1, sharey=True, figsize=(5, 3.5))
fig.subplots_adjust(top=0.85,
bottom=0.15,
left=0.15,
right=0.95,
hspace=0.25,
wspace=0.35)
plot(x, y, p, ax, "total rate", "x")
#labels=[r"$R_a$ (adsorption)", r"$R_d$ (desorption)", r"$R_r$ (reaction)", r"$R_h$ (diffusion)", "NO", "N2", "TOF"]
#markers=["o", "+","x","1","s","d","h","v"]
#for i in range(0,len(y2[0])):
# plot(x, y2[:,i], p, ax, labels[i], markers[i+1])
mp.setY2TemperatureLabels(ax, kb)
fig.savefig("totalRate.pdf") #, bbox_inches='tight')
def plotResume(self, concerted, covIndex, cov):
#cm = plt.get_cmap('prism')
x = list(reversed(1 / self.kb / concerted.temperatures))
if covIndex == 0: # save temporary data
shape = np.shape(concerted.epsilon)
np.savetxt("shape.txt", shape)
np.savetxt("x_index.txt", x)
np.savetxt(
"epsilon.txt",
concerted.epsilon.reshape(shape[0] * shape[1] * shape[2]))
np.savetxt(
"lastOmegas.txt",
concerted.lastOmegas.reshape(shape[0] * shape[1] * shape[2]))
np.savetxt("targetE.txt",
concerted.tgt.reshape(shape[1] * shape[0]))
np.savetxt("rcomptE.txt",
concerted.rct.reshape(shape[1] * shape[0]))
figR, ax = plt.subplots(1, figsize=(5, 3.5))
if concerted.total:
rl = "R"
else:
rl = "TOF"
figR.subplots_adjust(top=0.88, left=0.15, right=0.95, bottom=0.15)
tgt = concerted.tgt[:, covIndex]
rct = concerted.rct[:, covIndex]
ax.plot(x,
tgt * 1000,
marker="o",
label=r"$E^{" + rl + r"}_{app}$",
color="red")
ax.plot(x,
rct * 1000,
"--",
label=r"$\sum \epsilon^{" + rl + r"}_\alpha$",
color="green")
for i, a in enumerate(range(concerted.minAlfa, concerted.maxAlfa - 1)):
#if any(abs(concerted.epsilon[-1,::-1,i]) > 0.0001): # 0.1meV
if any(concerted.omega[covIndex, :, i] > 0.01):
#ax.plot(x, epsilon[-1,::-1,i], label=labelAlfa[a], color=cm(abs(i/20)), marker=markers[i%8])
ax.fill_between(x,
concerted.lastOmegas[covIndex, :, i] * 1000,
label=concerted.labelAlfa[a],
color=self.cm(a % 20 / (19)))
# ax2 = ax.twinx()
# ax2.plot(x, err, label="Relative error")
#ax.set_ylim(0,0.03)
#ax.set_xlim(20,30)
labels = [item for item in ax.get_xticklabels()]
ax.plot(x,
abs(np.array(tgt) - np.array(rct)) * 1000,
label="Absolute error",
color="black")
if cov == 0.100002:
maxIndex = np.argmax(abs(np.array(tgt) - np.array(rct)))
print("Maximum error at 0.1:",
max(abs(np.array(tgt) - np.array(rct)) * 1000),
"at temperature", 1 / self.kb / x[maxIndex])
ax.legend(loc="best", prop={'size': 9})
#ax.set_xticklabels(labels)
ax.set_xlabel(r"$1/k_BT$", size=14)
ax.set_ylabel(r"Energy $(meV)$", size=14)
#ax.set_yscale("log")
#ax.set_xscale("log")
ax2 = mp.setY2TemperatureLabels(ax, self.kb)
inf.smallerFont(ax2, 12)
ax.annotate(r"$\epsilon^{" + rl + r"}_\alpha=\omega^{" + rl +
r"}_\alpha(E^k_\alpha+E^M_\alpha)$",
xy=(0.2, 0.4),
xycoords="axes fraction")
inf.smallerFont(ax, 14)
ax.set_ylim(1e-2, 100)
#ax.set_xlim(30,510)
#ax.set_yscale("log")
plt.savefig("multiplicitiesResume" + concerted.ext +
"{:5f}".format(cov) + self.out) #, bbox_inches='tight')
ax.set_xlim(12, 30)
ax.set_ylim(1e-1, 210)
#ax.set_yscale("log")
#ax2 = mp.setY2TemperatureLabels(ax,self.kb)
plt.savefig("multiplicitiesResume" + concerted.ext +
"{:5f}".format(cov) + "high" +
self.out) #, bbox_inches='tight')
plt.close(figR)