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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| import numpy | ||
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| class IonPair: | ||
| def __init__(self, q: float, a1: float, a2: float, s1: float = 1.0, s2: float = 1.0): | ||
| self.q = q | ||
| self.a1 = a1 | ||
| self.a2 = a2 | ||
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| self.mu = q * (a1 + a2) * s1 | ||
| self.a = (a1**3 + a2**3)**(1/3) * s2 | ||
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| @staticmethod | ||
| def _e_born_solvation(q: float, a: float, epsr: float, epsi: float = 1.0) -> float: | ||
| """Solvatation energy from Born theory""" | ||
| return q ** 2 / (2*a) * (1/epsr - 1/epsi) | ||
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| @staticmethod | ||
| def _e_coulomb(q1: float, q2: float, r: float, eps: float) -> float: | ||
| """Coulombic interaction between two charges in a given medium""" | ||
| return q1 * q2 / (r*eps) | ||
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| @staticmethod | ||
| def _e_coulomb2(q1: float, q2: float, mu: float, eps: float) -> float: | ||
| """Coulombic interaction / formation of a dipole""" | ||
| return q1 * q2 * numpy.abs(q1) / (eps * mu) | ||
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| @staticmethod | ||
| def _e_dipole_onsager(mu: float, a: float, epsr: float, epsi: float = 1.0) -> float: | ||
| """Solvatation energy of a dipole in a cavity, according to Onsager""" | ||
| return -3*(epsr-epsi)/((2*epsr+1)*(2*epsi+1))*mu**2/a**3 | ||
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| def e_born_solvation(self, epsr: float, epsi: float = 1.0) -> float: | ||
| return IonPair._e_born_solvation(self.q, self.a1, epsr, epsi) + IonPair._e_born_solvation(-self.q, self.a2, epsr, epsi) | ||
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| def e_coulomb(self, epsi: float = 1.0) -> float: | ||
| return IonPair._e_coulomb(self.q, -self.q, self.a1 + self.a2, epsi) | ||
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| def e_coulomb2(self, eps: float) -> float: | ||
| return IonPair._e_coulomb2(self.q, -self.q, self.mu, eps) | ||
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| def e_dipole_onsager(self, epsr, epsi: float = 1.0) -> float: | ||
| return IonPair._e_dipole_onsager(self.mu, self.a, epsr, epsi) | ||
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| def e_pair(self, epsr: float, epsi: float = 1.0) -> float: | ||
| return self.e_coulomb2(epsi) + self.e_dipole_onsager(epsr, epsi) - self.e_born_solvation(epsr, epsi) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| import pandas | ||
| import matplotlib.pyplot as plt | ||
| import numpy | ||
| import sys | ||
| import argparse | ||
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| from nitroxides.commons import AU_TO_ANG, AU_TO_EV, G_NME4, G_BF4, RADII_BF4, RADII_NME4, dG_DH_cplx_Kx1, AU_TO_KJMOL | ||
| from nitroxides.pairs import IonPair | ||
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| S1=1 | ||
| S2 = 1.5 | ||
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| def plot_r_Kx1(ax, data: pandas.DataFrame, family: str, solvent: str, epsilon_r: float, color: str, has_cation: bool = False, has_anion: bool = False): | ||
| subdata = data[(data['family'] == family) & (data['solvent'] == solvent) & (data['has_anion'] == has_anion) & (data['has_cation'] == has_cation)] | ||
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| if has_anion: | ||
| dG_DH = dG_DH_cplx_Kx1(subdata['z'] + 1, subdata['z'], -1, subdata['r_A'] / AU_TO_ANG, subdata['r_AX'] / AU_TO_ANG, RADII_BF4[solvent] / AU_TO_ANG, epsilon_r) # K_01 | ||
| dG = (subdata['G_cplx'] - G_BF4[solvent] + dG_DH) * AU_TO_EV | ||
| dGp = IonPair( | ||
| q=1, | ||
| a1=subdata['r_A'] / AU_TO_ANG, | ||
| a2=RADII_BF4[solvent] / AU_TO_ANG, | ||
| s1=subdata['d_OX'] / (subdata['r_A'] + RADII_BF4[solvent]), | ||
| s2=subdata['r_AX']/(subdata['r_A'] **3 + RADII_BF4[solvent]**3)**(1/3) | ||
| ).e_pair(epsilon_r) | ||
| else: | ||
| dG_DH = dG_DH_cplx_Kx1(subdata['z'] - 1, subdata['z'], 1, subdata['r_A'] / AU_TO_ANG, subdata['r_AX'] / AU_TO_ANG, RADII_NME4[solvent] / AU_TO_ANG, epsilon_r) # K_21 | ||
| dG = (subdata['G_cplx'] - G_NME4[solvent] + dG_DH) * AU_TO_EV | ||
| dGp = IonPair( | ||
| q=-1, | ||
| a1=subdata['r_A'] / AU_TO_ANG, | ||
| a2=RADII_NME4[solvent] / AU_TO_ANG, | ||
| s1=subdata['d_OX'] / (subdata['r_A'] + RADII_NME4[solvent]), | ||
| s2=subdata['r_AX']/(subdata['r_A'] **3 + RADII_NME4[solvent]**3)**(1/3) | ||
| ).e_pair(epsilon_r) | ||
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| ax.plot(dGp, dG, 'o', color=color, label=family.replace('Family.', '')) | ||
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| parser = argparse.ArgumentParser() | ||
| parser.add_argument('-i', '--input', default='../data/Data_cplx_Kx1.csv') | ||
| parser.add_argument('-o', '--output', default='Data_cplx_r_Kx1.pdf') | ||
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| args = parser.parse_args() | ||
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| data = pandas.read_csv(args.input) | ||
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| figure = plt.figure(figsize=(8, 6)) | ||
| ax1, ax2 = figure.subplots(2, 1, sharey=True) | ||
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| plot_r_Kx1(ax1, data, 'Family.AMO', 'acetonitrile', 35.,'tab:pink', has_anion=True) | ||
| plot_r_Kx1(ax1, data, 'Family.P6O', 'acetonitrile', 35.,'tab:blue', has_anion=True) | ||
| plot_r_Kx1(ax1, data, 'Family.P5O', 'acetonitrile', 35., 'black', has_anion=True) | ||
| plot_r_Kx1(ax1, data, 'Family.IIO', 'acetonitrile', 35., 'tab:green', has_anion=True) | ||
| plot_r_Kx1(ax1, data, 'Family.APO', 'acetonitrile', 35., 'tab:red', has_anion=True) | ||
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| ax1.legend(ncols=5) | ||
| # ax1.text(38, 1, "Water", fontsize=18) | ||
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| plot_r_Kx1(ax2, data, 'Family.AMO', 'acetonitrile', 35.,'tab:pink', has_cation=True) | ||
| plot_r_Kx1(ax2, data, 'Family.P6O', 'acetonitrile', 35.,'tab:blue', has_cation=True) | ||
| plot_r_Kx1(ax2, data, 'Family.P5O', 'acetonitrile', 35., 'black', has_cation=True) | ||
| plot_r_Kx1(ax2, data, 'Family.IIO', 'acetonitrile', 35., 'tab:green', has_cation=True) | ||
| plot_r_Kx1(ax2, data, 'Family.APO', 'acetonitrile', 35., 'tab:red', has_cation=True) | ||
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| #ax2.text(38, -2, "Acetonitrile", fontsize=18) | ||
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| [ax.set_ylabel('$\\Delta G^\\star_{pair}$ (eV)') for ax in [ax1, ax2]] | ||
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| # ax2.set_xlabel('$d$ (Å)') | ||
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| plt.tight_layout() | ||
| figure.savefig(args.output) |
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