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Fix Mistake in convert_fO2_to_fe_partition #52

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Fix Mistake in convert_fO2_to_fe_partition #52

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201 changes: 95 additions & 106 deletions src/Thermobar/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4163,130 +4163,119 @@ def convert_fo2_to_fe_partition(*, liq_comps, T_K, P_kbar, model="Kress1991", f
liquid compositions with calculated Fe3Fet_Liq, FeO_Liq, Fe2O3_Liq, and XFe3Fe2.

'''
if any(liq_comps.columns=="Sample_ID_Liq"):
liq_comps_c=liq_comps.copy()
if any(liq_comps.columns == "Sample_ID_Liq"):
liq_comps_c = liq_comps.copy()

else:
liq_comps_c = liq_comps.copy()
liq_comps_c['Sample_ID_Liq'] = liq_comps_c.index

liq_comps_c=liq_comps.copy()
liq_comps_c['Sample_ID_Liq']=liq_comps_c.index
if isinstance(fo2, str):
fo2_int=fo2
if fo2_int=="NNO":
# Buffer position from frost (1991)
logfo2=(-24930/T_K) + 9.36 + 0.046 * ((P_kbar*1000)-1)/T_K+fo2_offset
fo2_int = fo2
if fo2_int == "NNO":
logfo2 = (-24930/T_K) + 9.36 + 0.046 * ((P_kbar*1000)-1) / T_K+fo2_offset

if fo2_int == "QFM":
logfo2_QFM_highT = (-25096.3 / T_K) + 8.735 + 0.11 * ((P_kbar * 1000)-1) / T_K
logfo2_QFM_lowT = (-26455.3 / T_K) + 10.344 + 0.092 * ((P_kbar * 1000)-1) / T_K
Cut_off_T = 573 + 273.15 + 0.025 * (P_kbar * 1000)

if fo2_int=="QFM":

# Buffer position from frost (1991)
logfo2_QFM_highT=(-25096.3/T_K) + 8.735 + 0.11 * ((P_kbar*1000)-1)/T_K
T_Choice='HighT Beta Qtz'

logfo2_QFM_lowT=(-26455.3/T_K) +10.344 + 0.092 * ((P_kbar*1000)-1)/T_K
T_Choice='Low T alpha Qtz'

Cut_off_T=573+273.15+0.025*(P_kbar*1000)

if isinstance(logfo2_QFM_lowT, float) or isinstance(logfo2_QFM_lowT, int):
if T_K<Cut_off_T:
logfo2_QFM=logfo2_QFM_lowT
if T_K>=Cut_off_T:
logfo2_QFM=logfo2_QFM_highT
if isinstance(logfo2_QFM_lowT, (float, int)): # Not sure what this is doing
if T_K < Cut_off_T:
logfo2_QFM = logfo2_QFM_lowT
elif T_K >= Cut_off_T:
logfo2_QFM = logfo2_QFM_highT

else:
logfo2_QFM=pd.Series(logfo2_QFM_highT)

T_K=pd.Series(T_K).fillna(0)
logfo2_QFM = pd.Series(logfo2_QFM_highT)

lowT = pd.Series(T_K)<Cut_off_T
# nanmask=np.isnan(T_K)
# final_mask=np.logical_or(lowT, nanmask)
# print(np.shape(lowT))
# print(sum(lowT))
# print(lowT)
T_K = pd.Series(T_K).fillna(0)

lowT = pd.Series(T_K) < Cut_off_T

if sum(lowT)>0:

logfo2_QFM.loc[lowT]=logfo2_QFM_lowT




logfo2=logfo2_QFM+logfo2_offset
if sum(lowT) > 0:
logfo2_QFM.loc[lowT] = logfo2_QFM_lowT

logfo2=logfo2_QFM + fo2_offset

fo2=10**logfo2




mol_frac_hyd_short=calculate_hydrous_mol_fractions_liquid(liq_comps_c)
mol_frac_hyd=pd.concat([mol_frac_hyd_short, liq_comps_c], axis=1)
To=1673.15

if model=="Kress1991":
ln_XFe2FeO3_XFeO=((0.196*np.log(fo2))+(11492/T_K)-6.675+((-2.243*mol_frac_hyd['Al2O3_Liq_mol_frac_hyd'])+(-1.828*mol_frac_hyd['FeOt_Liq_mol_frac_hyd'])
+(3.201*mol_frac_hyd['CaO_Liq_mol_frac_hyd'])+(5.854*mol_frac_hyd['Na2O_Liq_mol_frac_hyd'])+(6.215*mol_frac_hyd['K2O_Liq_mol_frac_hyd']))
-3.36*(1-(To/T_K) - np.log(T_K/To)) -0.000000701*((P_kbar*100000000)/T_K)
+ -0.000000000154*(((T_K-1673)*(P_kbar*100000000))/T_K) + 0.0000000000000000385*((P_kbar*100000000)**2/T_K))
#print(ln_XFe2FeO3_XFeO)
#print(fo2)

if model=="Put2016_eq6b":
ln_XFe2FeO3_XFeO=(-6.53+10813.8/T_K + 0.19*np.log(fo2)+ 12.4*(mol_frac_hyd['Na2O_Liq_mol_frac_hyd']
+mol_frac_hyd['K2O_Liq_mol_frac_hyd'])
-3.44*(mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']/(mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']+mol_frac_hyd['SiO2_Liq_mol_frac_hyd']))
+4.15*mol_frac_hyd['CaO_Liq_mol_frac_hyd'])

X_Fe2O3_X_FeO=np.exp(ln_XFe2FeO3_XFeO)
X_Fe2O3=X_Fe2O3_X_FeO*mol_frac_hyd['FeOt_Liq_mol_frac_hyd']/(2*X_Fe2O3_X_FeO+1)
mol_frac_hyd_short = calculate_hydrous_mol_fractions_liquid(liq_comps_c)
mol_frac_hyd = pd.concat([mol_frac_hyd_short, liq_comps_c], axis=1)
To = 1673.15

if model == "Kress1991":
ln_XFe2FeO3_XFeO = (
(0.196*np.log(fo2)) + (11492/T_K) - 6.675
+ ((-2.243*mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']) + (-1.828*mol_frac_hyd['FeOt_Liq_mol_frac_hyd'])
+ (3.201*mol_frac_hyd['CaO_Liq_mol_frac_hyd'])
+ (5.854*mol_frac_hyd['Na2O_Liq_mol_frac_hyd'])
+ (6.215*mol_frac_hyd['K2O_Liq_mol_frac_hyd']))
- 3.36*(1-(To/T_K) - np.log(T_K/To)) - 7.01E-07*((P_kbar*1E8)/T_K)
- 1.54E-10 * (((T_K-1673)*(P_kbar*1E8))/T_K) + 3.85E-17*((P_kbar*1E8)**2/T_K)
)

if model == "Put2016_eq6b":
ln_XFe2FeO3_XFeO = (
- 6.53 + 10813.8/T_K + 0.19*np.log(fo2) + 12.4*(mol_frac_hyd['Na2O_Liq_mol_frac_hyd']
+ mol_frac_hyd['K2O_Liq_mol_frac_hyd'])
- 3.44*(mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']/(mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']+mol_frac_hyd['SiO2_Liq_mol_frac_hyd']))
+ 4.15*mol_frac_hyd['CaO_Liq_mol_frac_hyd'])

X_Fe2O3_X_FeO = np.exp(ln_XFe2FeO3_XFeO)
X_Fe2O3 = X_Fe2O3_X_FeO * mol_frac_hyd['FeOt_Liq_mol_frac_hyd']/(2*X_Fe2O3_X_FeO+1)

#X_FeO=mol_frac_hyd['FeOt_Liq_mol_frac_hyd']/(2*X_Fe2O3_X_FeO+1) Kayla's way
X_FeO=mol_frac_hyd['FeOt_Liq_mol_frac_hyd']-2*X_Fe2O3
Sum_all_mol_frac_hyd=(mol_frac_hyd['SiO2_Liq_mol_frac_hyd']+mol_frac_hyd['TiO2_Liq_mol_frac_hyd']+mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']+mol_frac_hyd['MnO_Liq_mol_frac_hyd']
+mol_frac_hyd['MgO_Liq_mol_frac_hyd']+mol_frac_hyd['CaO_Liq_mol_frac_hyd']+mol_frac_hyd['Na2O_Liq_mol_frac_hyd']+mol_frac_hyd['K2O_Liq_mol_frac_hyd']
+mol_frac_hyd['P2O5_Liq_mol_frac_hyd']+X_FeO+X_Fe2O3)

Fe2O3_unnorm=X_Fe2O3*159.6
FeO_unnorm=X_FeO*71.844
Sum_All_mol=(mol_frac_hyd['SiO2_Liq_mol_frac_hyd']*60.0843+mol_frac_hyd['TiO2_Liq_mol_frac_hyd']*79.8788
+mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']*101.961+mol_frac_hyd['MnO_Liq_mol_frac_hyd']*70.9375
+mol_frac_hyd['MgO_Liq_mol_frac_hyd']*40.3044+mol_frac_hyd['CaO_Liq_mol_frac_hyd']*56.0774+mol_frac_hyd['Na2O_Liq_mol_frac_hyd']*61.9789+mol_frac_hyd['K2O_Liq_mol_frac_hyd']*94.196
+mol_frac_hyd['P2O5_Liq_mol_frac_hyd']*141.937+X_Fe2O3*159.6+X_FeO*71.844)
New_Fe2O3_wt=(100*X_Fe2O3*159.6)/Sum_All_mol
New_FeO_wt=(100*X_FeO*71.844)/Sum_All_mol

New_Oxide_out_nonorm=liq_comps.copy()
New_Oxide_out_nonorm['FeO_Liq']=New_FeO_wt
New_Oxide_out_nonorm['Fe2O3_Liq']=New_Fe2O3_wt
New_Oxide_out_nonorm['XFe3Fe2']=X_Fe2O3_X_FeO
New_Oxide_out_nonorm['Fe3Fet_Liq']=New_Fe2O3_wt*0.8998/(New_FeO_wt+New_Fe2O3_wt*0.8998)


New_Oxide_out_norm=pd.DataFrame(data={'SiO2_Liq': 100*mol_frac_hyd['SiO2_Liq_mol_frac_hyd']*60.084/Sum_All_mol,
'TiO2_Liq': 100*mol_frac_hyd['TiO2_Liq_mol_frac_hyd']*79.8788/Sum_All_mol,
'Al2O3_Liq':100*mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']*101.961/Sum_All_mol,
'Fe2O3_Liq': (100*X_Fe2O3*159.6)/Sum_All_mol,
'FeO_Liq': (100*X_FeO*71.844)/Sum_All_mol,
'MnO_Liq': 100*mol_frac_hyd['MnO_Liq_mol_frac_hyd']*70.9375/Sum_All_mol,
'MgO_Liq': 100*mol_frac_hyd['MgO_Liq_mol_frac_hyd']*40.3044/Sum_All_mol,
'CaO_Liq': 100*mol_frac_hyd['CaO_Liq_mol_frac_hyd']*56.0774/Sum_All_mol,
'Na2O_Liq': 100*mol_frac_hyd['Na2O_Liq_mol_frac_hyd']*61.9789/Sum_All_mol,
'K2O_Liq': 100*mol_frac_hyd['K2O_Liq_mol_frac_hyd']*94.196/Sum_All_mol,
'P2O5_Liq': 100*mol_frac_hyd['P2O5_Liq_mol_frac_hyd']*141.937/Sum_All_mol,
})
Old_Sum=(100/liq_comps_c.drop(['Sample_ID_Liq'], axis=1).sum(axis=1))
New_Oxide_out_New_old_total=New_Oxide_out_norm.div(Old_Sum, axis=0)
New_Oxide_out_New_old_total['Fe3Fet_Liq']=(New_Oxide_out_norm['Fe2O3_Liq']*0.8998/(New_Oxide_out_norm['FeO_Liq']+New_Oxide_out_norm['Fe2O3_Liq']*0.8998)).fillna(0)



if renorm==False:
New_Oxide_out_nonorm['ln_XFe2FeO3_XFeO']=ln_XFe2FeO3_XFeO
X_FeO = mol_frac_hyd['FeOt_Liq_mol_frac_hyd']-2*X_Fe2O3
# Sum_all_mol_frac_hyd=(mol_frac_hyd['SiO2_Liq_mol_frac_hyd']+mol_frac_hyd['TiO2_Liq_mol_frac_hyd']+mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']+mol_frac_hyd['MnO_Liq_mol_frac_hyd']
# +mol_frac_hyd['MgO_Liq_mol_frac_hyd']+mol_frac_hyd['CaO_Liq_mol_frac_hyd']+mol_frac_hyd['Na2O_Liq_mol_frac_hyd']+mol_frac_hyd['K2O_Liq_mol_frac_hyd']
# +mol_frac_hyd['P2O5_Liq_mol_frac_hyd']+X_FeO+X_Fe2O3)

# Fe2O3_unnorm=X_Fe2O3*159.6
# FeO_unnorm=X_FeO*71.844
Sum_All_mol = (
mol_frac_hyd['SiO2_Liq_mol_frac_hyd']*60.0843 + mol_frac_hyd['TiO2_Liq_mol_frac_hyd']*79.8788 +
+ mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']*101.961 + mol_frac_hyd['MnO_Liq_mol_frac_hyd']*70.9375
+ mol_frac_hyd['MgO_Liq_mol_frac_hyd']*40.3044 + mol_frac_hyd['CaO_Liq_mol_frac_hyd']*56.0774
+ mol_frac_hyd['Na2O_Liq_mol_frac_hyd']*61.9789 + mol_frac_hyd['K2O_Liq_mol_frac_hyd']*94.196
+ mol_frac_hyd['P2O5_Liq_mol_frac_hyd']*141.937 + X_Fe2O3*159.6 + X_FeO*71.844
)
New_Fe2O3_wt = (100*X_Fe2O3*159.6) / Sum_All_mol
New_FeO_wt = (100*X_FeO*71.844) / Sum_All_mol

New_Oxide_out_nonorm = liq_comps.copy()
New_Oxide_out_nonorm.update({
'FeO_Liq': New_FeO_wt,
'Fe2O3_Liq': New_Fe2O3_wt,
'XFe3Fe2': X_Fe2O3_X_FeO,
'Fe3Fet_Liq': New_Fe2O3_wt*0.8998 / (New_FeO_wt + New_Fe2O3_wt*0.8998)
})

New_Oxide_out_norm = pd.DataFrame(data={
'SiO2_Liq': 100*mol_frac_hyd['SiO2_Liq_mol_frac_hyd']*60.084 / Sum_All_mol,
'TiO2_Liq': 100*mol_frac_hyd['TiO2_Liq_mol_frac_hyd']*79.8788 / Sum_All_mol,
'Al2O3_Liq': 100*mol_frac_hyd['Al2O3_Liq_mol_frac_hyd']*101.961 / Sum_All_mol,
'Fe2O3_Liq': (100*X_Fe2O3*159.6) / Sum_All_mol,
'FeO_Liq': (100*X_FeO*71.844) / Sum_All_mol,
'MnO_Liq': 100*mol_frac_hyd['MnO_Liq_mol_frac_hyd']*70.9375 / Sum_All_mol,
'MgO_Liq': 100*mol_frac_hyd['MgO_Liq_mol_frac_hyd']*40.3044 / Sum_All_mol,
'CaO_Liq': 100*mol_frac_hyd['CaO_Liq_mol_frac_hyd']*56.0774 / Sum_All_mol,
'Na2O_Liq': 100*mol_frac_hyd['Na2O_Liq_mol_frac_hyd']*61.9789 / Sum_All_mol,
'K2O_Liq': 100*mol_frac_hyd['K2O_Liq_mol_frac_hyd']*94.196 / Sum_All_mol,
'P2O5_Liq': 100*mol_frac_hyd['P2O5_Liq_mol_frac_hyd']*141.937 / Sum_All_mol,
})
Old_Sum = 100 / liq_comps_c.drop(['Sample_ID_Liq'], axis=1).sum(axis=1)
New_Oxide_out_New_old_total = New_Oxide_out_norm.div(Old_Sum, axis=0)
New_Oxide_out_New_old_total['Fe3Fet_Liq'] = (
New_Oxide_out_norm['Fe2O3_Liq'] * 0.8998 / (New_Oxide_out_norm['FeO_Liq'] + New_Oxide_out_norm['Fe2O3_Liq']*0.8998)
).fillna(0)

if renorm == False:
New_Oxide_out_nonorm['ln_XFe2FeO3_XFeO'] = ln_XFe2FeO3_XFeO
return New_Oxide_out_nonorm

else:
New_Oxide_out_New_old_total['ln_XFe2FeO3_XFeO']=ln_XFe2FeO3_XFeO
New_Oxide_out_New_old_total['ln_XFe2FeO3_XFeO'] = ln_XFe2FeO3_XFeO
return New_Oxide_out_New_old_total

## Need some functions for calculating mole proportions with Fe partition
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