Minerals

petropandas.minerals

Mineral

Base Mineral class to store mineral structure and endmembers calculation

Attributes:

Name	Type	Description
noxy	int	number of oxygens
ncat	int	number of cations
needsFe	str	"Fe2" for only FeO oxide needed, "Fe3" for both FeO and Fe2O3 oxide needed, None for no Fe needed
structure	tuple	structural formula definition. Iterable collection of tuples (name, ncat, list of cations) e.g. ("T", 4, ["Si{4+}", "Al{3+}"]). Tuples are ordered in population order.
has_structure	bool	True when structure is defined
has_endmembers	bool	True when endmembers method is defined

calculate(cations, force=False)

Calculate structural formula from cations p.f.u

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Name	Type	Description
StrucForm	StrucForm	structural formula

apfu(cations, force=False)

Calculate mineral atom p.f.u based on site occupancies

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry(cations, force=False)

Calculate average missfit of populated and ideal cations on sites

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
floating	pandas.Series: average missfit

Feldspar

Feldspar with 3 endmembers

calculate(cations, force=False)

Calculate structural formula from cations p.f.u

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Name	Type	Description
StrucForm	StrucForm	structural formula

apfu(cations, force=False)

Calculate mineral atom p.f.u based on site occupancies

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry(cations, force=False)

Calculate average missfit of populated and ideal cations on sites

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
floating	pandas.Series: average missfit

Garnet

Garnet using Fe2 and Fe3 with 6 endmembers

calculate(cations, force=False)

Calculate structural formula from cations p.f.u

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Name	Type	Description
StrucForm	StrucForm	structural formula

apfu(cations, force=False)

Calculate mineral atom p.f.u based on site occupancies

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry(cations, force=False)

Calculate average missfit of populated and ideal cations on sites

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
floating	pandas.Series: average missfit

Garnet_Fe2

Garnet using total Fe with 4 endmembers

calculate(cations, force=False)

Calculate structural formula from cations p.f.u

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Name	Type	Description
StrucForm	StrucForm	structural formula

apfu(cations, force=False)

Calculate mineral atom p.f.u based on site occupancies

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry(cations, force=False)

Calculate average missfit of populated and ideal cations on sites

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
floating	pandas.Series: average missfit

Pyroxene

Pyroxene

calculate(cations, force=False)

Calculate structural formula from cations p.f.u

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Name	Type	Description
StrucForm	StrucForm	structural formula

apfu(cations, force=False)

Calculate mineral atom p.f.u based on site occupancies

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry(cations, force=False)

Calculate average missfit of populated and ideal cations on sites

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
floating	pandas.Series: average missfit

Pyroxene_Fe2

Simple Pyroxene using total Fe with 3 endmembers

calculate(cations, force=False)

Calculate structural formula from cations p.f.u

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Name	Type	Description
StrucForm	StrucForm	structural formula

apfu(cations, force=False)

Calculate mineral atom p.f.u based on site occupancies

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry(cations, force=False)

Calculate average missfit of populated and ideal cations on sites

Parameters:

Name	Type	Description	Default
cations	Series	cations p.f.u	required

Returns:

Type	Description
floating	pandas.Series: average missfit

StrucForm

Class to manipulate mineral structural formula

Parameters:

Name	Type	Description	Default
mineral	Mineral	mineral instance	required

Attributes:

Name	Type	Description
mineral	Mineral	mineral instance
sites	list	list of sites
reminder	Series	remainder after site population or empty

apfu property

Calculate mineral atom p.f.u based on site occupancies

Returns:

Type	Description
Series	pandas.Series: atoms p.f.u

check_stechiometry property

Calculate average missfit of populated and ideal cations on sites

get(atom)

Get total number of given atom in structure

Parameters:

Name	Type	Description	Default
atom	str	atom name	required

site(name)

Get site by name

Parameters:

Name	Type	Description	Default
name	str	site name	required

Site

Class to store mineral site information

Parameters:

Name	Type	Description	Default
name	str	name of site	required
ncat	int	ideal number of cations	required
candidates	list	list of cations in population order	required

Attributes:

Name	Type	Description
name	str	name of site
ncat	int	ideal number of cations
candidates	list	list of cations in population order
atoms	dict	populated atoms
free	float	remaining space in site, i.e. Ideal - Occupied

add(atom, amount, force=False)

Add atom to site

Parameters:

Name	Type	Description	Default
atom	str	cation name	required
amount	float	number of attoms to add	required
force	bool	If False atoms are added up to ideal occupancy. When True full amount is added. Default False	False

get(atom, fraction=False)

Get number of given atom on site

Parameters:

Name	Type	Description	Default
atom	str	atom name	required