Source code for Chempy.making_abundances

import numpy as np



def mass_fraction_to_abundances(cube, solar_abundances):
	'''
	calculating the abundances in dex from mass fractions

	INPUT:
	
	   cube = cube table instance
	
	   solar_abundances = solar abundance table instance

	OUTPUT:
	
	   abundances
	
	   element_names
	
	   element_numbers
	'''
	element_names = list(set(solar_abundances['Symbol']).intersection(cube.dtype.names))
	element_number = []
	element_masses = []
	for item in element_names:
		element_number.append(int(solar_abundances['Number'][np.where(solar_abundances['Symbol']==item)]))
		element_masses.append(solar_abundances['Mass'][np.where(solar_abundances['Symbol']==item)])
	
	sorted_index = np.argsort(np.array(element_number))
	element_number = [element_number[i] for i in sorted_index]
	element_masses = [element_masses[i] for i in sorted_index]
	element_names = [element_names[i] for i in sorted_index]

	base = np.zeros(len(cube))
	list_of_arrays = []
	for i in range(len(element_names)):
		list_of_arrays.append(base)

	cube_abundances = np.core.records.fromarrays(list_of_arrays,names=element_names)

	for i,item in enumerate(element_names):
		cube_abundances[item] = np.divide(cube[item],float(element_masses[i]))

	normalisation = np.copy(cube_abundances['H'])

	for i,item in enumerate(element_names):
		cube_abundances[item] = np.divide(cube_abundances[item],normalisation)
	
	for i,item in enumerate(element_names):
		#cube_abundances[item] = np.log10(cube_abundances[item]) + 12.
		# supressing the warnings
		assert cube_abundances[item].all() >= 0.
		with np.errstate(invalid = 'ignore', divide = 'ignore'):
			cube_abundances[item] = np.where(cube_abundances[item] == 0. , -np.inf, np.log10(cube_abundances[item]) + 12.)

	for i,item in enumerate(element_names):
		cube_abundances[item] -= solar_abundances['photospheric'][np.where(solar_abundances['Symbol']==item)] 

	return (cube_abundances,element_names,element_number)

def abundance_to_mass_fraction(all_elements,all_masses,all_abundances,abundances,symbols):
	'''
	Calculating mass fractions from abundances.

	INPUT:
	
	   all_elements = list of all elements from solar abundance instance
	
	   all_masses = list of corresponding masses from solar abundances
	
	   all_abundances = solar abundances (not needed)
	
	   abundances = the abundances
	
	   symbols = a list of the elemental symbols corresponding to the abundances

	OUTPUT:
	
	   the fractions as an array
	'''
	fractions = []
	for i,item in enumerate(symbols):
		fractions.append(abundances[i])
		fractions[i] -= 12
		fractions[i] = np.power(10,fractions[i])
		fractions[i] *= all_masses[np.where(all_elements == item)]
	tmp = sum(fractions)
	for i,item in enumerate(symbols):
		fractions[i] /= tmp
	return np.hstack(fractions)

def abundance_to_mass_fraction_normed_to_solar(all_elements,all_masses,all_abundances,abundances,symbols):
	'''
	Calculating mass fractions normed to solar from abundances.

	INPUT:
	   
	   all_elements = list of all elements from solar abundance instance
	
	   all_masses = list of corresponding masses from solar abundances
	
	   all_abundances = solar abundances (not needed)
	
	   abundances = the abundances
	
	   symbols = a list of the elemental symbols corresponding to the abundances

	OUTPUT:
	
	   the fractions as an array
	'''
	fractions = []
	for i,item in enumerate(symbols):
		fractions.append(abundances[i] + all_abundances[np.where(all_elements == item)])
		fractions[i] -= 12
		fractions[i] = np.power(10,fractions[i])
		fractions[i] *= all_masses[np.where(all_elements == item)]
	tmp = sum(fractions)
	for i,item in enumerate(symbols):
		fractions[i] /= tmp
	return np.hstack(fractions)