Fix some failing examples

Spin-Chemistry-Labs · Aug 16, 2024 · 91fe934 · 91fe934
1 parent 7d8c319
commit 91fe934
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Showing 4 changed files with 38 additions and 32 deletions.
diff --git a/examples/kinetics_fad.py b/examples/kinetics_fad.py
@@ -133,9 +133,9 @@ def main():
     axs[1].plot(time * scale, delta_delta_A, color="orange", linewidth=2)
     plt.xscale("linear")
     axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"])
-    axs[1].set_xlabel("Time ($\mu s$)", size=14)
-    axs[0].set_ylabel("$\Delta A$", size=14)
-    axs[1].set_ylabel("$\Delta \Delta A$", size=14)
+    axs[1].set_xlabel(r"Time ($\mu s$)", size=14)
+    axs[0].set_ylabel(r"$\Delta A$", size=14)
+    axs[1].set_ylabel(r"$\Delta \Delta A$", size=14)
     axs[0].tick_params(labelsize=14)
     axs[1].tick_params(labelsize=14)
     fig.set_size_inches(10, 5)
@@ -153,9 +153,9 @@ def main():
     axs[1].plot(time * scale, fluor_del_A, color="orange", linewidth=2)
     plt.xscale("linear")
     axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"])
-    axs[1].set_xlabel("Time ($\mu s$)", size=14)
-    axs[0].set_ylabel("$F$", size=14)
-    axs[1].set_ylabel("$\Delta F$", size=14)
+    axs[1].set_xlabel(r"Time ($\mu s$)", size=14)
+    axs[0].set_ylabel(r"$F$", size=14)
+    axs[1].set_ylabel(r"$\Delta F$", size=14)
     axs[0].tick_params(labelsize=14)
     axs[1].tick_params(labelsize=14)
     fig.set_size_inches(10, 5)

diff --git a/examples/kinetics_fad_semiclassical.py b/examples/kinetics_fad_semiclassical.py
@@ -8,14 +8,14 @@
 from radicalpy.plot import plot_3d_results, plot_bhalf_time
 from radicalpy.relaxation import RandomFields
 from radicalpy.simulation import Molecule, SemiclassicalSimulation
-from radicalpy.utils import Bhalf_fit
+from radicalpy.utils import Bhalf_fit, is_fast_run
 
 
-def main():
+def main(Bmax=30, dB=0.5, tmax=20e-6, dt=10e-9):
 
     # Parameters
-    time = np.arange(0, 20e-6, 10e-9)
-    Bs = np.arange(0, 30, 0.5)
+    time = np.arange(0, tmax, dt)
+    Bs = np.arange(0, Bmax, dB)
     num_samples = 400
     scale_factor = 10
     kr = 0  # 1.7e6  # radical pair relaxation rate
@@ -231,9 +231,9 @@ def main():
         rstride=1,
         cstride=1,
     )
-    ax.set_xlabel("$B_0$ / mT", size=18)
-    ax.set_ylabel("Time / $\mu s$", size=18)
-    ax.set_zlabel("$\Delta \Delta A$", size=18)
+    ax.set_xlabel(r"$B_0$ / mT", size=18)
+    ax.set_ylabel(r"Time / $\mu s$", size=18)
+    ax.set_zlabel(r"$\Delta \Delta A$", size=18)
     plt.tick_params(labelsize=14)
     fig.set_size_inches(10, 5)
     # plt.show()
@@ -271,8 +271,8 @@ def main():
             color="k",
             linewidth=2,
         )
-    plt.xlabel("Time / $\mu s$", size=18)
-    plt.ylabel("$B_{1/2}$ / mT", size=18)
+    plt.xlabel(r"Time / $\mu s$", size=18)
+    plt.ylabel(r"$B_{1/2}$ / mT", size=18)
     plt.tick_params(labelsize=14)
     plt.gcf().set_size_inches(10, 5)
     path = __file__[:-3] + f"_{1}.png"
@@ -293,9 +293,9 @@ def main():
         rstride=1,
         cstride=1,
     )
-    ax.set_xlabel("$B_0$ / mT", size=18)
-    ax.set_ylabel("Time / $\mu s$", size=18)
-    ax.set_zlabel("$\Delta \Delta A$", size=18)
+    ax.set_xlabel(r"$B_0$ / mT", size=18)
+    ax.set_ylabel(r"Time / $\mu s$", size=18)
+    ax.set_zlabel(r"$\Delta \Delta A$", size=18)
     plt.tick_params(labelsize=14)
     fig.set_size_inches(10, 5)
     # plt.show()
@@ -327,13 +327,16 @@ def main():
             color="k",
             linewidth=2,
         )
-    plt.xlabel("Time / $\mu s$", size=18)
-    plt.ylabel("$B_{1/2}$ / mT", size=18)
+    plt.xlabel(r"Time / $\mu s$", size=18)
+    plt.ylabel(r"$B_{1/2}$ / mT", size=18)
     plt.tick_params(labelsize=14)
     plt.gcf().set_size_inches(10, 5)
     path = __file__[:-3] + f"_{3}.png"
     plt.savefig(path, dpi=300)
 
 
 if __name__ == "__main__":
-    main()
+    if is_fast_run():
+        main(Bmax=10, dB=2, tmax=10e-6, dt=1e-6)
+    else:
+        main()
diff --git a/examples/kinetics_fad_semiclassical_wavelength.py b/examples/kinetics_fad_semiclassical_wavelength.py
@@ -11,14 +11,14 @@
 from radicalpy.plot import plot_3d_results, plot_bhalf_time, plot_general
 from radicalpy.relaxation import RandomFields, SingletTripletDephasing
 from radicalpy.simulation import Basis, Molecule, SemiclassicalSimulation
-from radicalpy.utils import Bhalf_fit
+from radicalpy.utils import Bhalf_fit, is_fast_run
 
 
-def main():
+def main(Bmax=30, dB=0.5, tmax=10e-6, dt=10e-9):
 
     # Parameters
-    time = np.arange(0, 10e-6, 10e-9)
-    Bs = np.arange(0, 30, 0.5)
+    time = np.arange(0, tmax, dt)
+    Bs = np.arange(0, Bmax, dB)
     num_samples = 200
     scale_factor = 1  # 4e-1
     kr = 7e7  # 1.7e6  # radical pair relaxation rate
@@ -700,7 +700,7 @@ def main():
     plot_3d_results(
         groundstate_wavelength,
         results["Bs"],
-        mary_groundstate[250, :, :],
+        mary_groundstate[len(mary_groundstate) // 4, :, :],
         xlabel,
         ylabel,
         zlabel,
@@ -731,7 +731,7 @@ def main():
     plot_3d_results(
         emission_wavelength,
         results["Bs"],
-        mary_emission[250, :, :],
+        mary_emission[len(mary_emission) // 4, :, :],
         xlabel,
         ylabel,
         zlabel,
@@ -762,7 +762,7 @@ def main():
     plot_3d_results(
         wavelength,
         results["Bs"],
-        mary[250, :, :],
+        mary[len(mary) // 4, :, :],
         xlabel,
         ylabel,
         zlabel,
@@ -774,4 +774,7 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    if is_fast_run():
+        main(Bmax=10, dB=2, tmax=10e-6, dt=1e-6)
+    else:
+        main()
diff --git a/examples/kinetics_flavin_quencher.py b/examples/kinetics_flavin_quencher.py
@@ -161,8 +161,8 @@ def main():
     plt.xscale("linear")
     axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"])
     axs[1].set_xlabel("Time ($ns$)", size=14)
-    axs[0].set_ylabel("$\Delta A$", size=14)
-    axs[1].set_ylabel("$\Delta \Delta A$", size=14)
+    axs[0].set_ylabel(r"$\Delta A$", size=14)
+    axs[1].set_ylabel(r"$\Delta \Delta A$", size=14)
     axs[0].tick_params(labelsize=14)
     axs[1].tick_params(labelsize=14)
     fig.set_size_inches(10, 5)
@@ -182,7 +182,7 @@ def main():
     axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"])
     axs[1].set_xlabel("Time ($ms$)", size=14)
     axs[0].set_ylabel("$F$", size=14)
-    axs[1].set_ylabel("$\Delta F$", size=14)
+    axs[1].set_ylabel(r"$\Delta F$", size=14)
     axs[0].tick_params(labelsize=14)
     axs[1].tick_params(labelsize=14)
     fig.set_size_inches(10, 5)