Fixed maxfev argument in minimize function

PyEIS/PyEIS_Advanced_tools.py

@@ -12,142 +12,167 @@
 import numpy as np
 
 from scipy.constants import codata
-F = codata.physical_constants['Faraday constant'][0]
-qe = codata.physical_constants['elementary charge'][0]
-R = codata.physical_constants['molar gas constant'][0]
-kB = codata.physical_constants['Boltzmann constant'][0]
-kB_eV = codata.physical_constants['Boltzmann constant in eV/K'][0]
-N_A = codata.physical_constants['Avogadro constant'][0]
+
+F = codata.physical_constants["Faraday constant"][0]
+qe = codata.physical_constants["elementary charge"][0]
+R = codata.physical_constants["molar gas constant"][0]
+kB = codata.physical_constants["Boltzmann constant"][0]
+kB_eV = codata.physical_constants["Boltzmann constant in eV/K"][0]
+N_A = codata.physical_constants["Avogadro constant"][0]
 F, R, qe, kB, kB_eV, N_A
 
 ### Normalization of constant phase elements
 ##
 #
-def norm_nonFara_Q_C(Rs, Q, n, L='none'):
-    '''
+def norm_nonFara_Q_C(Rs, Q, n, L="none"):
+    """
     Normalziation of a non-faradaic interfacial capacitance (Blocking Electrode)
-    
+
     Following Brug and Hirschorn's normalization of distribtuion of relaxation times
     Ref.:
         - G.J.Brug et al., J.Electroanal. Chem. Interfacial Electrochem., 176, 275 (1984)
-    
+
     Kristian B. Knudsen (kknu@berkeley.edu || kristianbknudsen@gmail.com)
-    
+
     Inputs
     ------------------
     Q = Constant phase element [s^n/ohm]
     n = Exponent of CPE [-]
     Rs = Series Resistance [ohm]
-    
+
     Optional Inputs
     ------------------
     L = Thickness/length of electrode, used in Porous Electrode Theory [cm]
-    
+
     Returns
     ------------------
     C_eff = normalized capacitance for a non-faradaic electrode [s/ohm = F]
-    '''
-    if L == 'none':
-        C_eff = (Q * Rs**(1-n))**(1/n)
+    """
+    if L == "none":
+        C_eff = (Q * Rs ** (1 - n)) ** (1 / n)
     else:
-        C_eff = ((Q*L) * Rs**(1-n))**(1/n)
+        C_eff = ((Q * L) * Rs ** (1 - n)) ** (1 / n)
     return C_eff
 
-def norm_Fara_Q_C(Rs, Rct, n, Q='none', fs='none', L='none'):
-    '''
+
+def norm_Fara_Q_C(Rs, Rct, n, Q="none", fs="none", L="none"):
+    """
     Normalziation of a faradaic interfacial capacitance (Blocking Electrode)
-    
+
     Contains option to use summit frequency (fs) instead of CPE (Q) - valueable for outputs of fits
-    
+
     Following Brug and Hirschorn's normalization of distribtuion of relaxation times
     Ref.:
         - G.J.Brug et al., J.Electroanal. Chem. Interfacial Electrochem., 176, 275 (1984)
         - B.Hirschorn, et al., ElectrochimicaActa, 55, 6218 (2010)
-    
+
     Kristian B. Knudsen (kknu@berkeley.edu || kristianbknudsen@gmail.com)
-    
+
     Inputs
     ----------
     n = Exponent of CPE [-]
     Rs = Series Resistance [ohm]
     Rct = Charge Transfer Resistance [ohm]
-    
+
     Optional Inputs
     ------------------
     Q = Constant phase element [s^n/ohm]
     fs = summit frequencey of fitted spectra [Hz]
-    
+
     Returns
     ----------
     C_eff = normalized capacitance for a faradaic electrode [s/ohm = F]
-    '''
-    if Q == 'none':
-        if L == 'none':
-            Q = (1/(Rct*(2*np.pi*fs)**n))
-            C_eff = Q**(1/n) * ((Rs*Rct)/(Rs*Rct))**((1-n)/n)
-        if L != 'none':
+    """
+    if Q == "none":
+        if L == "none":
+            Q = 1 / (Rct * (2 * np.pi * fs) ** n)
+            C_eff = Q ** (1 / n) * ((Rs * Rct) / (Rs * Rct)) ** ((1 - n) / n)
+        if L != "none":
             Rct_norm = Rct / L
-            Q = (1/(Rct_norm*(2*np.pi*fs)**n))
-            C_eff = Q**(1/n) * ((Rs*Rct_norm)/(Rs*Rct_norm))**((1-n)/n)
-    if fs == 'none':
-        C_eff = Q**(1/n) * ((Rs*Rct)/(Rs*Rct))**((1-n)/n)
+            Q = 1 / (Rct_norm * (2 * np.pi * fs) ** n)
+            C_eff = Q ** (1 / n) * ((Rs * Rct_norm) / (Rs * Rct_norm)) ** ((1 - n) / n)
+    if fs == "none":
+        C_eff = Q ** (1 / n) * ((Rs * Rct) / (Rs * Rct)) ** ((1 - n) / n)
     return C_eff
 
+
 def Theta(E, E0, n, T=298.15, F=F, R=R):
-    '''
+    """
     See explantion in C_redox_Estep_semiinfinite()
     Kristian B. Knudsen (kknu@berkeley.edu || Kristianbknudsen@gmail.com)
-    '''
-    return np.exp(((n*F)/(R*T))*(E-E0))
+    """
+    return np.exp(((n * F) / (R * T)) * (E - E0))
+
 
 def Varsigma(D_ox, D_red):
-    '''
+    """
     See explantion in C_redox_Estep_semiinfinite()
     Kristian B. Knudsen (kknu@berkeley.edu || Kristianbknudsen@gmail.com)
-    '''
-    return (D_ox/D_red)**(1/2)
+    """
+    return (D_ox / D_red) ** (1 / 2)
+
 
 def C_redox_Estep_semiinfinite(E, E0, n, C_ox, D_ox, D_red, T=298.15, R=R, F=F):
-    '''
-    The concentration at the electrode surface (x=0) as a function of potential following Nernst eq. 
+    """
+    The concentration at the electrode surface (x=0) as a function of potential following Nernst eq.
     during semi-infinite linear diffusion (Macro disk electrode)
-    
+
     O + ne- --> R
-    
+
     Ref: Bard A.J., Faulkner L. R., ISBN: 0-471-04372-9 (2001) "Electrochemical methods: Fundamentals and applications". New York: Wiley.
 
     Author: Kristian B. Knudsen (kknu@berkeley.edu || Kristianbknudsen@gmail.com)
-    
+
     returns
     ----------
     [0] = C_red at x=0
     [1] = C_ox at x=0
-    '''
-    C_red0 = C_ox * (Varsigma(D_ox=D_ox, D_red=D_red)/(1+(Varsigma(D_ox=D_ox, D_red=D_red)*Theta(E=E, E0=E0, n=n, T=T, F=F, R=R))))
-    C_ox0 = C_ox * ((Varsigma(D_ox=D_ox, D_red=D_red)*Theta(E=E, E0=E0, n=n, T=T, F=F, R=R))/(1+(Varsigma(D_ox=D_ox, D_red=D_red)*Theta(E=E, E0=E0, n=n, T=T, F=F, R=R))))
+    """
+    C_red0 = C_ox * (
+        Varsigma(D_ox=D_ox, D_red=D_red)
+        / (
+            1
+            + (Varsigma(D_ox=D_ox, D_red=D_red) * Theta(E=E, E0=E0, n=n, T=T, F=F, R=R))
+        )
+    )
+    C_ox0 = C_ox * (
+        (Varsigma(D_ox=D_ox, D_red=D_red) * Theta(E=E, E0=E0, n=n, T=T, F=F, R=R))
+        / (
+            1
+            + (Varsigma(D_ox=D_ox, D_red=D_red) * Theta(E=E, E0=E0, n=n, T=T, F=F, R=R))
+        )
+    )
     return C_red0, C_ox0
 
+
 def C_redox_Estep_semihemisperhical(E, E0, n, C_ox, D_ox, D_red, T=298.15, R=R, F=F):
-    '''
-    The concentration at the electrode surface (x=0) as a function of potential following Nernst eq. 
+    """
+    The concentration at the electrode surface (x=0) as a function of potential following Nernst eq.
     during semi-infinite hemispherical diffusion (Micro disk electrode)
 
     O + ne- --> R
-    
+
     Note: This equation applies only for a reversible system with rapid kinetics
-    
+
     Ref: Bard A.J., Faulkner L. R., ISBN: 0-471-04372-9 (2001) "Electrochemical methods: Fundamentals and applications". New York: Wiley.
 
     Author: Kristian B. Knudsen (kknu@berkeley.edu || Kristianbknudsen@gmail.com)
-    
+
     returns
     ----------
     [0] = C_red at x=0
     [1] = C_ox at x=0
-    '''
-    C_red0 = C_ox * ((Varsigma(D_ox, D_red)**2)/(1+Varsigma(D_ox, D_red)**2 * Theta(E, E0, n, T, F, R)))
-    C_ox0 = C_ox * (1- (1/(1+Varsigma(D_ox, D_red)**2 * Theta(E, E0, n, T, F, R))))
+    """
+    C_red0 = C_ox * (
+        (Varsigma(D_ox, D_red) ** 2)
+        / (1 + Varsigma(D_ox, D_red) ** 2 * Theta(E, E0, n, T, F, R))
+    )
+    C_ox0 = C_ox * (
+        1 - (1 / (1 + Varsigma(D_ox, D_red) ** 2 * Theta(E, E0, n, T, F, R)))
+    )
     return C_red0, C_ox0
+
+
 #
-#print()
-#print('---> EIS Advanced Tools Loaded (v. 0.0.2 - 06/15/18)')
+# print()
+# print('---> EIS Advanced Tools Loaded (v. 0.0.2 - 06/15/18)')