Uncomment example code

Spin-Chemistry-Labs · Mar 21, 2024 · 59093c5 · 59093c5
1 parent c3dfc94
commit 59093c5
Showing 1 changed file with 26 additions and 19 deletions.
diff --git a/examples/semiclassical_micelles.py b/examples/semiclassical_micelles.py
@@ -19,7 +19,12 @@
 )
 from radicalpy.relaxation import SingletTripletDephasing
 from radicalpy.simulation import Basis, SemiclassicalSimulation, State
-from radicalpy.utils import autocorrelation, Bhalf_fit, is_fast_run, read_trajectory_files
+from radicalpy.utils import (
+    Bhalf_fit,
+    autocorrelation,
+    is_fast_run,
+    read_trajectory_files,
+)
 
 
 def main(
@@ -31,24 +36,26 @@ def main(
     trp = Molecule.all_nuclei("tryptophan_cation")
     sim = SemiclassicalSimulation([flavin, trp], basis=Basis.ZEEMAN)
 
-    # trajectory_data = read_trajectory_files("./examples/data/md_fad_trp_aot", scale=1e-10)
-    # trajectory_ts = (
-    #     np.linspace(0, len(trajectory_data), len(trajectory_data)) * 5e-12 * 1e9
-    # )
-    # j = exchange_interaction_in_solution_MC(trajectory_data[:, 1], J0=5)
-    #
-    # plot_exchange_interaction_in_solution(trajectory_ts, trajectory_data, j)
-    #
-    # acf_j = autocorrelation(j, factor=1)
-    # zero_point_crossing_j = np.where(np.diff(np.sign(acf_j)))[0][0]
-    # t_j_max = max(trajectory_ts[:zero_point_crossing_j]) * 1e-9
-    # t_j = np.linspace(5e-12, t_j_max, zero_point_crossing_j)
-    #
-    # acf_j_fit = autocorrelation_fit(t_j, j, 5e-12, t_j_max)
-    # plot_autocorrelation_fit(t_j, acf_j, acf_j_fit, zero_point_crossing_j)
-    #
-    # kstd = k_STD(-j, acf_j_fit["tau_c"])
-    kstd = 11681368.059456564
+    trajectory_data = read_trajectory_files(
+        "./examples/data/md_fad_trp_aot", scale=1e-10
+    )
+    trajectory_ts = (
+        np.linspace(0, len(trajectory_data), len(trajectory_data)) * 5e-12 * 1e9
+    )
+    j = exchange_interaction_in_solution_MC(trajectory_data[:, 1], J0=5)
+
+    plot_exchange_interaction_in_solution(trajectory_ts, trajectory_data, j)
+
+    acf_j = autocorrelation(j, factor=1)
+    zero_point_crossing_j = np.where(np.diff(np.sign(acf_j)))[0][0]
+    t_j_max = max(trajectory_ts[:zero_point_crossing_j]) * 1e-9
+    t_j = np.linspace(5e-12, t_j_max, zero_point_crossing_j)
+
+    acf_j_fit = autocorrelation_fit(t_j, j, 5e-12, t_j_max)
+    plot_autocorrelation_fit(t_j, acf_j, acf_j_fit, zero_point_crossing_j)
+
+    kstd = k_STD(-j, acf_j_fit["tau_c"])
+    # kstd = 11681368.059456564
     triplet_excited_state_quenching_rate = 5e6
     recombination_rate = 8e6
     free_radical_escape_rate = 5e5