outer join of pandas df generated from for loop

If you want to extend the frame iteratively then concat should actually work. This

df1 = pd.DataFrame(columns = ["Al", "Si", "K", "Th"], data = [[1,2,3,4]])
df2 = pd.DataFrame(columns = ["W", "Cu"], data = [[5,6]])
df = pd.concat([df1, df2], axis='rows')
df.fillna(0, inplace=True)

gives you

    Al   Si    K   Th    W   Cu
0  1.0  2.0  3.0  4.0  0.0  0.0
0  0.0  0.0  0.0  0.0  5.0  6.0

Just a suggestion: Wouldn’t you be better off if you do the creation of the underlying data with basic Python only?

Something like

import re
import pandas as pd

re_comps = re.compile(r'([A-Z][a-z]?)([0-9]*)')

formulas = ("NaAlSiO2", "WCu2")
elements = {element for formula in formulas
                    for element, _ in re_comps.findall(formula)}
perc_dict = {key: len(formulas) * [None] for key in elements.union({'Formula'})}
for i, formula in enumerate(formulas):
    perc_dict['Formula'][i] = formula
    total_weight = molecular_w_calc(formula)
    for element, count in re_comps.findall(formula):
        count = 1 if count == '' else int(count)
        perc_dict[element][i] = (Element_mass[element] * 100 * count) / total_weight

and only then Pandas

perc_df = pd.DataFrame(perc_dict)
perc_df.set_index('Formula', drop=True, inplace=True)
perc_df.sort_index(axis='columns', inplace=True)

The structure of the resulting perc_df looks like (the values are obviously wrong, since I didn’t have the Element_mass dictionary and molecular_w_calc function):

           Al   Cu   Na    O   Si    W
Formula                               
NaAlSiO2  1.0  NaN  1.0  2.0  1.0  NaN
WCu2      NaN  2.0  NaN  NaN  NaN  1.0

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