2. Stoichiometry calculation and ternary plot of apatite

pyAp allows users to calculate the stoichiometry and mole fractions of components in apatite using functions ApStoic.py and ApStoic_Ketcham.py.

The stoichiometry calculation method was adapted from Ketcham (2015) https://doi.org/10.2138/am-2015-5171

The results can be plotted in the F-Cl-OH ternary diagram by calling functions in ApThernary.py. See an example below.

Import releavant modules and data

Import modules

import matplotlib.pyplot as plt, pandas as pd, math
from pyAp.ApStoic import stoi_
from pyAp import ApTernary
from pyAp.ApStoic_Ketcham import stoi_ketcham

Import data

data = pd.read_excel('data_ap_major_volatile.xlsx')

Stoichiometry calculation

Use assume_oxy=26 for F- or Cl-apatite; assume_oxy=25 for OH-apatite. The default is 26 if no values are assigned.

results_stoi = stoi_(data,assume_oxy = 26)
results_stoi

	SI	TI	AL	FE	CA	MG	MN	K	NA	P	S	C	XF	XCL	XOH	CE	SR	stoi,(Ca/P-5/3)/(5/3)*100%	sample
0	0.017412	0.013097	0.020520	0.014561	10.072936	0.025958	0.014746	0.022210	0.033756	5.895973	0.026133	0.002377	0.825950	0.073766	0.100284	0.012748	0.010095	3.656599	Ap1
1	0.017514	0.013175	0.020641	0.014647	10.132331	0.026111	0.014833	0.022341	0.033955	5.930739	0.026287	0.002391	0.692350	0.059361	0.248289	0.012823	0.010155	3.656599	Ap2
2	0.017419	0.013103	0.020528	0.014567	10.077123	0.025968	0.014752	0.022219	0.033770	5.898424	0.026144	0.002378	0.771207	0.118075	0.110718	0.012753	0.010100	3.656599	Ap3

Use an oxygen number between 25 and 26 using stoi_ketcham() function in module ApStoic_Ketcham.py

results_ketc = stoi_ketcham(data)

The calculated oxygen number should fall between 25 and 26

results_ketc['OXYGEN NUMBER']

0    25.896121
1    25.744319
2    25.885361
Name: OXYGEN NUMBER, dtype: float64

Plot apatite on F-Cl-OH ternary diagram

Plot F-Cl-OH mole fractions calculated above

# set up a figure for ternary plot
fig1 = plt.figure()
fig1.set_size_inches(7, 6)

# plot ternary (w/o data)
ApTernary.ternary(fig1)

for idx, value in results_stoi.iterrows():

    x_f = value['XF']
    x_cl = value['XCL']
    x = (x_f + x_cl/2) * 100
    y = x_cl*math.sqrt(3)*50

    if x > 100:
        x = 100
    if y > math.sqrt(3)*50:
        y = math.sqrt(3)*50

    plt.plot(x,y,'o',label=value['sample'])

plt.legend(loc='best')
plt.show()

Plot apatite F-Cl-OH mole fractions from files

load data

df = pd.read_excel('data_calc_water.xlsx')

plot ternary

fig2 = plt.figure()
fig2.set_size_inches(7, 6)

# plot ternary (w/o data)
ApTernary.ternary(fig2)
for idx, value in df.iterrows():

    x_f = value['XF']
    x_cl = value['XCL']
    x = (x_f + x_cl/2) * 100
    y = x_cl*math.sqrt(3)*50

    if x > 100:
        x = 100
    if y > math.sqrt(3)*50:
        y = math.sqrt(3)*50

    plt.plot(x,y,'o',label=value['sample'])

plt.legend(loc='best')
plt.show()