Fix old rate equations

examples/kinetics_cryptochrome.py

@@ -3,7 +3,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from radicalpy.classical import RateEquations
+from radicalpy.classical import Rate, RateEquations
 
 
 def main():
@@ -106,10 +106,10 @@ def main():
         "S": 1,
     }
     time = np.linspace(0, 100e-6, 500)
-
-    result_off = RateEquations({**base, **off}, time, initial_states)
-    result_on = RateEquations({**base, **on}, time, initial_states)
-
+    re_off = RateEquations({**base, **off})
+    re_on = RateEquations({**base, **on})
+    result_off = re_off.time_evolution(time, initial_states)
+    result_on = re_on.time_evolution(time, initial_states)
     fluor_field_off = result_off["A-D"]
     fluor_field_on = result_on["A-D"]
     fluor_delta_A = fluor_field_on - fluor_field_off
@@ -128,9 +128,9 @@ def main():
     axs[1].plot(time * scale, rp_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)
@@ -148,9 +148,9 @@ def main():
     axs[1].plot(time * scale, fluor_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[1].set_xlabel(r"Time ($\mu s$)", 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)

examples/kinetics_fad.py

@@ -107,8 +107,10 @@ def main():
     }
     time = np.linspace(0, 6e-6, 200)
 
-    result_off = RateEquations({**base, **off}, time, initial_states)
-    result_on = RateEquations({**base, **on}, time, initial_states)
+    re_off = RateEquations({**base, **off})
+    re_on = RateEquations({**base, **on})
+    result_off = re_off.time_evolution(time, initial_states)
+    result_on = re_on.time_evolution(time, initial_states)
     fac = 0.07
 
     keys = ["S", "T+/-", "T0", "Quencher"] + 2 * ["T*+/-", "T*0"]

examples/kinetics_simple.py

@@ -46,8 +46,10 @@ def main():
     initial_states = {Tp: 1 / 3, T0: 1 / 3, Tm: 1 / 3}
     time = np.linspace(0, 1e-6, 10000)
 
-    result_off = RateEquations(off, time, initial_states)
-    result_on = RateEquations(on, time, initial_states)
+    re_off = RateEquations(off)
+    re_on = RateEquations(on)
+    result_off = re_off.time_evolution(time, initial_states)
+    result_on = re_on.time_evolution(time, initial_states)
 
     keys = [S, Tp, T0, Tm]
     rp_field_off = result_off[keys]
@@ -65,9 +67,9 @@ def main():
     axs[1].plot(time * scale, rp_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)

radicalpy/classical.py

@@ -126,7 +126,7 @@ def check_initial_states(self, initial_states: dict):
 
     def _construct_matrix(self):
         tmp = [
-            (v.value, self.indices[i], self.indices[j])
+            (v.value if isinstance(v, Rate) else v, self.indices[i], self.indices[j])
             for i, d in self.rate_equations.items()
             for j, v in d.items()
         ]