machin

analyses/plot_pot_exp.py

@@ -0,0 +1,96 @@
+import pandas
+import matplotlib.pyplot as plt
+import numpy
+import sys
+import pathlib
+import argparse
+
+from nitroxides.commons import dG_DH, AU_TO_ANG, LabelPositioner, AU_TO_EV, EPSILON_R, E_SHE
+
+LABELS = {'water': [], 'acetonitrile': []}
+POINTS_POSITION ={'water': [], 'acetonitrile': []}
+LABELS_KWARGS = {'water': [], 'acetonitrile': []}
+LABELS_PATH = {'water': pathlib.Path('pot_exp_water.pos'), 'acetonitrile': pathlib.Path('pot_exp_acetonitrile.pos')}
+
+def prepare_data(data: pandas.DataFrame, data_exp: pandas.DataFrame, solvent):
+    subdata = data[data['solvent'] == solvent]
+    subdata.insert(1, 'compound', [int(n.replace('mol_', '')) for n in subdata['name']])
+    subdata = subdata.join(data_exp[data_exp['E_ox_exp_{}'.format(solvent)].notnull()].set_index('compound'), on='compound', how='inner')
+
+    subdata['E_ox_exp_{}'.format(solvent)] /= 1000
+
+    dG_DH_ = dG_DH(subdata['z'] + 1, subdata['z'], subdata['r_ox'] / AU_TO_ANG, subdata['r_rad'] / AU_TO_ANG, EPSILON_R[solvent], 0.1) * AU_TO_EV
+    subdata.insert(1, 'E_ox_theo_{}'.format(solvent), subdata['E_ox'] - dG_DH_ - E_SHE[solvent])
+
+    return subdata[['compound', 'family', 'E_ox_theo_{}'.format(solvent), 'E_ox_exp_{}'.format(solvent)]]
+
+
+def plot_solv(ax, data: pandas.DataFrame, solvent: str, family: str, color: str):
+    subdata = data[data['family'] == family]
+    ax.plot(subdata['E_ox_theo_{}'.format(solvent)], subdata['E_ox_exp_{}'.format(solvent)], 'o', color=color, label=family.replace('Family.', ''))
+
+    for name, etheo, eexp in zip(subdata['compound'], subdata['E_ox_theo_{}'.format(solvent)], subdata['E_ox_exp_{}'.format(solvent)]):
+        LABELS[solvent].append(name)
+        POINTS_POSITION[solvent].append((etheo, eexp))
+        LABELS_KWARGS[solvent].append(dict(color=color, ha='center', va='center'))
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input', default='../data/Data_pot.csv')
+parser.add_argument('-i2', '--input2', default='../data/Data_pot_ox_exp.csv')
+parser.add_argument('-r', '--reposition-labels', action='store_true')
+parser.add_argument('-o', '--output', default='Data_pot_ox_exp.pdf')
+
+args = parser.parse_args()
+
+data = pandas.read_csv(args.input)
+data_exp = pandas.read_csv(args.input2)
+
+figure = plt.figure(figsize=(10, 5))
+ax1, ax2 = figure.subplots(1, 2)
+
+subdata_wa = prepare_data(data, data_exp, 'water')
+
+plot_solv(ax1, subdata_wa, 'water', 'Family.P6O', 'tab:blue')
+plot_solv(ax1, subdata_wa, 'water', 'Family.P5O', 'black')
+plot_solv(ax1, subdata_wa, 'water', 'Family.IIO', 'tab:green')
+plot_solv(ax1, subdata_wa, 'water', 'Family.APO', 'tab:red')
+
+positioner = LabelPositioner.from_file(
+    LABELS_PATH['water'], 
+    numpy.array(POINTS_POSITION['water']), 
+    LABELS['water'], 
+    labels_kwargs=LABELS_KWARGS['water']
+)
+
+if args.reposition_labels:
+    positioner.optimize(dx=1e-3, beta=1e5, krep=1, kspring=1000, c=0.05, b0=0.01)
+    positioner.save(LABELS_PATH['water'])
+
+positioner.add_labels(ax1)
+
+subdata_ac = prepare_data(data, data_exp, 'acetonitrile')
+
+plot_solv(ax2, subdata_ac, 'acetonitrile', 'Family.P6O', 'tab:blue')
+plot_solv(ax2, subdata_ac, 'acetonitrile', 'Family.P5O', 'black')
+plot_solv(ax2, subdata_ac, 'acetonitrile', 'Family.IIO', 'tab:green')
+plot_solv(ax2, subdata_ac, 'acetonitrile', 'Family.APO', 'tab:red')
+
+positioner = LabelPositioner.from_file(
+    LABELS_PATH['acetonitrile'], 
+    numpy.array(POINTS_POSITION['acetonitrile']), 
+    LABELS['acetonitrile'], 
+    labels_kwargs=LABELS_KWARGS['acetonitrile']
+)
+
+if args.reposition_labels:
+    positioner.optimize(dx=1e-3, beta=1e4, krep=1, kspring=1000, c=0.05, b0=0.01, scale=[0.3, 1])
+    positioner.save(LABELS_PATH['acetonitrile'])
+
+positioner.add_labels(ax2)
+
+ax2.legend()
+[ax.set_xlabel('Computed $E^0_{rel}(N^+|N^\\bullet)$ (V)') for ax in (ax1, ax2)]
+[ax.set_ylabel('Experimental $E^0_{rel}(N^+|N^\\bullet)$ (V)') for ax in (ax1, ax2)]
+
+plt.tight_layout()
+figure.savefig(args.output)