VolFe 0.2__py3-none-any.whl

VolFe/import_files.py

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+# import_data.py
+
+import pandas as pd
+
+# loads species.csv, models.csv, and user setup file
+def import_files(filename):
+    species = pd.read_csv("species.csv", index_col = [0]) # attributes of the different species used in the system
+    models = pd.read_csv("models.csv", index_col = [0]) # model options
+    setup = pd.read_csv(filename) # csv for initial conditions of the system - typically inputs.csv
+    return species, models, setup

VolFe/isotopes.py

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+# isotopes.py
+
+import pandas as pd
+import numpy as np
+
+import VolFe.melt_gas as mg
+import VolFe.calculations as c
+
+######################
+### delta notation ###
+######################
+
+def delta_standards(standard,isotope,element):
+    if element == "S":
+        if standard == "VCDT":
+            if isotope == 34:
+                reference = 1/22.6436 # 34S/32S Ding et al. (2001)
+    elif element == "C":
+        if standard == "VPBD":
+            if isotope == 13:
+                reference = 0.01123720 # 13C/12C International Atomic Energy Agency (1995)
+    elif element == "H":
+        if standard == "VSMOW":
+            if isotope == 2:
+                reference = 155.76/1.e6 # 2H/1H Hagemann et al. (1970)
+    return reference
+ 
+def ratio2delta(standard,isotope,ratio,element):
+    reference = delta_standard(standard,isotope,element)
+    d = ((ratio - reference)/reference)*1000.
+    return d
+
+def delta2ratio(standard,isotope,d):
+    reference = delta_standard(standard,isotope,element)
+    ratio = ((d/1000.)*reference) + reference
+    return ratio
+
+# newton raphson solver
+def newton_raphson(x0,constants,e1,step,eqs,deriv,maxiter=1000):
+
+    def dx(x,eqs):
+        f_ = eqs(x,constants)
+        result =(abs(0-f_))
+        return result
+    
+    def nr(x0,eqs,deriv):
+        f_ = eqs(x0,constants)
+        df_ = deriv
+        x0 = x0 - step*(f_/df_)
+        return x0
+    
+    # create results table
+    results = pd.DataFrame([["guessx","diff","step"]])  
+    results.to_csv('results_nr_isotopes.csv', index=False, header=False)
+    diff = dx(x0,eqs)
+    results1 = pd.DataFrame([[x0,diff,step]]) 
+    results = results.append(results1, ignore_index=True)
+    results.to_csv('results_nr_isotopes.csv', index=False, header=False) 
+    
+    delta1 = dx(x0,eqs)
+    results = pd.DataFrame([["guessx","diff","step"]])  
+    results.to_csv('results_nr_isotopes.csv', index=False, header=False)
+    results1 = pd.DataFrame([[x0,delta1,step]]) 
+    results = results.append(results1, ignore_index=True)
+    results.to_csv('results_nr_isotopes.csv', index=False, header=False) 
+    
+    while delta1 > e1:
+        guessx = x0
+        f_ = eqs(x0,constants)
+        df_ = deriv(x0,constants)
+        x0 = x0 - step*(f_/df_)
+        #while x0 < 0.:
+        #    step = step/10.
+        #    x0 = x0 - step*(f_/df_)
+        delta1 = dx(x0,eqs)      
+        results1 = pd.DataFrame([[x0,delta1,step]])
+        results = results.append(results1, ignore_index=True)
+        results.to_csv('results_nr_isotopes.csv', index=False, header=False) 
+    return x0  
+
+# two isotopes, two species
+def i2s2(element,PT,R_i,melt_wf):
+    if element == "S":
+        knowns = i2s2_S_melt(PT,R_i,melt_wf)
+    a, x, L = knowns # a = fractionation factor A-B, x = mole fraction of S in B, L = mole fraction of light isotope total 
+    A = a - 1.
+    B = (1. - a)*(L + x) - 1.
+    C = a*x*L
+    l_b = (-B - ((B**2) - (4.*A*C))**0.5)/(2.*A)
+    h_b = x - l_b
+    R_b = h_b/l_b
+    R_a = a*R_b
+    return R_a, R_b
+
+def i2s2_S_melt(PT,R_i,melt_wf):
+    a = (1./mg.alpha_SO2_SO4(PT))*mg.alpha_H2S_S(PT)*mg.alpha_gas("S","SO2","H2S",PT) # SO4-S2-
+    x = 1.-melt_wf["S6ST"] # mole fraction of S as S2- in the melt
+    R_i_ = 1./R_i["S"] # 32S/34S
+    L = R_i_/(R_i_ + 1.) # mole fraction of 32S
+    return a, x, L
+
+def i2s6_S_alphas(PT): # all alphas against S2- in the melt
+    a_b = mg.alpha_H2S_S(PT) # H2S-S
+    a_c = (1./mg.alpha_SO2_SO4(PT))*mg.alpha_H2S_S(PT)*mg.alpha_gas("S","SO2","H2S",PT) # SO4-S 
+    a_d = mg.alpha_H2S_S(PT)*mg.alpha_gas("S","S2","H2S",PT) # S2-S
+    a_e = mg.alpha_H2S_S(PT)*mg.alpha_gas("S","SO2","H2S",PT) # SO2-S
+    a_f = mg.alpha_H2S_S(PT)*mg.alpha_gas("S","OCS","H2S",PT) # OCS-S
+    return a_b, a_c, a_d, a_e, a_f
+
+def i2s6(element,PT,R,melt_wf,gas_mf,species,nr_step,nr_tol,guessx): # species distribution is mole fraction of S in each species
+    
+    if element == "S":
+        a_b, a_c, a_d, a_e, a_f = i2s6_S_alphas(PT)
+        species_distribution = c.mf_S_species(melt_wf,gas_mf,species)
+        T_a = species_distribution["S2-"]
+        T_b = species_distribution["H2S"]
+        T_c = species_distribution["SO42-"]
+        T_d = species_distribution["S2"]
+        T_e = species_distribution["SO2"]
+        T_f = species_distribution["OCS"]
+        R_i = R["S"]
+        
+    constants = a_b, a_c, a_d, a_e, a_f, T_a, T_b, T_c, T_d, T_e, T_f, R_i
+   
+    def isotope_distribution(l_a, constants):
+        a_b, a_c, a_d, a_e, a_f, T_a, T_b, T_c, T_d, T_e, T_f, R_i = constants
+        R_a = (T_a - l_a)/l_a # 34S/32S
+        R_b = a_b*R_a
+        R_c = a_c*R_a
+        R_d = a_d*R_a
+        R_e = a_e*R_a
+        R_f = a_f*R_a
+        return R_a, R_b, R_c, R_d, R_e, R_f
+    
+    def av_m_g(element,l_a,constants):
+        
+        a_b, a_c, a_d, a_e, a_f, T_a, T_b, T_c, T_d, T_e, T_f, R_i = constants
+        R_a, R_b, R_c, R_d, R_e, R_f = isotope_distribution(l_a, constants)
+        
+        # heavy/total isotope ratio
+        R_a_ = R_a/(R_a + 1.)
+        R_b_ = R_b/(R_b + 1.)
+        R_c_ = R_c/(R_c + 1.)
+        R_d_ = R_d/(R_d + 1.)
+        R_e_ = R_e/(R_e + 1.)
+        R_f_ = R_f/(R_f + 1.)
+        
+        if element == "S":
+            h_m = R_a_*T_a + R_c_*T_c # 34S melt (S2- + SO42-)
+            l_m = (1. - R_a_)*T_a + (1. - R_c_)*T_c
+            h_g = R_b_*T_b + R_d_*T_d + R_e_*T_e + R_f_*T_f # 34S gas (H2S + S2 + SO2 + OCS)
+            l_g = (1. - R_b_)*T_b + (1. - R_d_)*T_d + (1. - R_e_)*T_e + (1. - R_f_)*T_f # 34S gas (H2S + S2 + SO2 + OCS)
+   
+        R_m = h_m/l_m
+        R_g = h_g/l_g
+        return R_m, R_g
+            
+    def f(l_a, constants):
+        a_b, a_c, a_d, a_e, a_f, T_a, T_b, T_c, T_d, T_e, T_f, R_i = constants
+        R_a = (T_a/l_a) - 1.
+        l_b = T_b/(1.+a_b*R_a)
+        l_c = T_c/(1.+a_c*R_a)
+        l_d = T_d/(1.+a_d*R_a)
+        l_e = T_e/(1.+a_e*R_a)
+        l_f = T_f/(1.+a_f*R_a)
+        total = l_a + l_b + l_c + l_d + l_e + l_f
+        R_i_ = 1./R_i
+        l_t = (R_i_/(R_i_ + 1.))
+        return l_t - total
+    
+    def df(l_a, constants):
+        a_b, a_c, a_d, a_e, a_f, T_a, T_b, T_c, T_d, T_e, T_f, R_i = constants
+        R_i_ = 1./R_i
+        l_t = (R_i_/(R_i_ + 1.))
+        result = -T_a*T_b*a_b/(l_a**2*(a_b*(T_a/l_a - 1.0) + 1.0)**2) - T_a*T_c*a_c/(l_a**2*(a_c*(T_a/l_a - 1.0) + 1.0)**2) - T_a*T_d*a_d/(l_a**2*(a_d*(T_a/l_a - 1.0) + 1.0)**2) - T_a*T_f*a_f/(l_a**2*(a_f*(T_a/l_a - 1.0) + 1.0)**2) - 1.
+        return result
+    
+    l_a = newton_raphson(guessx,constants,nr_tol,nr_step,f,df)
+    result1 = isotope_distribution(l_a, constants)
+    result2 = av_m_g(element,l_a,constants)
+    return result1, result2