Main Model#

class peridoxia.main.ModelRun(initial_assemblage: Assemblage | None = None, melting: bool = True, melting_method: str = 'fractional', potential_temperature_C: float = 1350, P_range_GPa: list[float] = [4, 0.1], P_step: float = -0.01, gt_out_P_range_GPa: list[float] = [3.0, 2.799], label: str = 'Model Run', color: str = 'k', gt_out_rxn_wts: dict = {'gt__pyx_pyxTs': 2, 'gt_olv__spl_pyx': 1}, debug: int = 0, run_model=True)#

This is the main class for running the model.

Parameters:

initial_assemblagedata_struct.Assemblage | None, optional: Initial composition, which must be given as an Assemblage object. See Data Structures for creating an Assemblage from a set of modes/phase compositions. By default None.
meltingbool, optional: If ‘melting’ is set to False, system remains subsolidus. Otherwise, melting proceeds according to P-T-F parametrization. By default True.
melting_methodstr, optional: By default, model performs fractional melting. If melting_method is set to ‘batch’, batch/equilibrium melting will be performed instead. NOTE: batch melting is not extensively tested. By default ‘fractional’.
potential_temperature_Cfloat, optional: Potential temperature for the system, in Celsius. By default 1350.
P_range_GPalist[float], optional: Pressure range for model run, in Gigapascals. If melting is allowed to proceed, model will stop automatically at cpx-out. By default [4,0.1].
P_stepfloat, optional: Pressure interval for each model run step, in Gigapascals. By default -0.01.
gt_out_P_range_GPalist[float], optional: Pressure range of gt-out reactions, in Gigapascals. Default value is from Robinson and Wood (1998).Garnet-out is not currently compositionally dependent. This will be coming in later versions of the model. By default [2.8+0.2,2.8-0.001].
labelstr, optional: Descriptive label for model run. By default ‘Model Run’.
colorstr, optional: Color for plotting model run. By default ‘k’.
gt_out_rxn_wts_type_, optional: Relative amount of the two categories of gt-out reactions. By default {‘gt_olv__spl_pyx’:1, ‘gt__pyx_pyxTs’:2}.
debugint, optional: Can set to 0, 1, or 2 for levels of output. By default 0.
run_modelbool, optional: If set to True, initializing the system will also run the model. If set to False, an empty ModelRun object is created (useful for loading data files). By default True.

Attributes:

FFM: Returns the value of the FFM buffer for each assemblage in the ModelRun object; FFM formulation is the first three terms of the fayalite-ferrosilite-magnetite buffer as compiled by Davis et al.
G_cont_to_fO2: Returns the Gibbs Free Energy contribution to fO2 for each assemblage in the ModelRun object.
PGPa: Returns P (in GPa) for each assemblage in the ModelRun object.
Pbar: Returns P (in bar) for each assemblage in the ModelRun object.
QFM: Returns the value of the QFM buffer for each assemblage in the ModelRun object; QFM formulation is that of Frost (1991).
TC: Returns T (in C) for each assemblage in the ModelRun object.
TK: Returns T (in K) for each assemblage in the ModelRun object.
TK_olv_spl: Returns T (in K) from olivine and spinel compositions using the Li et al., 1995 thermometer for each assemblage in the ModelRun object; This should return the same value as TK, since this is a partitioning constraint.
agg_liq: Returns aggregated liquid phase history object; User can call all PhaseHistory and LiquidHistory attributes on ModelRun.agg_liq object.
color: Returns the color for plotting the ModelRun object
cpx: Returns clinopyroxene phase history object; User can call all PhaseHistory and ClinopyroxeneHistory attributes on ModelRun.cpx object.
gt: Returns garnet phase history object; User can call all PhaseHistory and GarnetHistory attributes on ModelRun.gt object.
initial_assemblage: Returns the initial assemblage.
input_arguments: Returns a dictionary of all input arguments; this dictionary can be used directly as an input argument to ModelRun in order to re-create a run.
label: Returns the label for the ModelRun object.
liq: Returns incremental liquid phase history object; User can call all PhaseHistory and LiquidHistory attributes on ModelRun.liq object.
logfO2_abs: Returns the absolute logfO2 value of the assemblage, not normalized to any buffer.
logfO2_dFFM: Returns logfO2 relative to FFM buffer; FFM formulation is the first three terms of the fayalite-ferrosilite-magnetite buffer as compiled by Davis et al.
logfO2_dQFM: Returns logfO2 relative to QFM buffer; QFM formulation is that of Frost (1991).
olv: Returns olivine phase history object; User can call all PhaseHistory and OlivineHistory attributes on ModelRun.olv object.
opx: Returns orthopyroxene phase history object; User can call all PhaseHistory and OrthopyroxeneHistory attributes on ModelRun.opx object.
pot_TC: Returns the potential temperature (in C) at which the model run was performed.
pot_TK: Returns the potential temperature (in K) at which the model run was performed.
spl: Returns spinel phase history object; User can call all PhaseHistory and SpinelHistory attributes on ModelRun.spl object.
sys: Returns system (residual solid phases + incremental liquid) phase history object; User can call all PhaseHistory and SystemHistory attributes on ModelRun.sys object.

Methods

`get_data_table`([method, full_table])	Returns a Pandas dataframe with run results.
`load_model_run_from_file`(file[, sheet_name, ...])	Loads output from a previous model run.
`plot`([x, y])	Plots ModelRun attributes.
`save_data_table`([file_name, data_table, method])	Saves a single model run.
`test_run`()	Runs a simple test to ensure everything is installed and functioning properly.

classmethod load_model_run_from_file(file: str, sheet_name: str = 'Sheet1', label: str = 'model_run', color: str = 'k', pot_TC=None)#

Loads output from a previous model run.

See Files and Templates for template file
Current included phases: [‘olv’, ‘opx’, ‘cpx’, ‘spl’, ‘gt’, ‘liq’, ‘agg_liq’]
Current included oxides: [‘SiO2’, ‘Al2O3’, ‘Fe2O3’, ‘Cr2O3’, ‘FeO’, ‘MgO’, ‘CaO’]
File expects columns: T°C, P (GPa), olv_mass, olv_SiO2, … , opx_mass, opx_SiO2, … , etc… (in any order)
Extra columns are added to a dictionary, stored in [model_run].extras

NOTE: This method can be used to load results from other models, such as pMELTS. However, be aware that only the phases/oxides included in this model will be directly considered– other phases/oxides (e.g., plagioclase or Na2O) will be ignored when loading data and creating assemblages. Thus, when calculating properties for pMELTS runs with a wider set of phases/oxides, you will get a different answer here than calculated directly on the pMELTS results. If you wish to plot or otherwise use results that rely on a wider set of phases/oxides, you must externally calculate these fields, add them as columns to your input spreadsheet, and access them through the [model_run].extras dictionary method.

Parameters:

filestr: The path/name of the file to load, e.g. ‘input_file.xlsx’.
sheet_namestr, optional: The Excel sheet to load, by default ‘Sheet1’.
labelstr, optional: A descriptive label for the model run, by default ‘model_run’.
colorstr, optional: The color to use when plotting the model run, by default ‘k’.
pot_TC: float, optional: The potential temperature of the model run, in Celsius, by default None.

Returns:

ModelRun object: A ModelRun object with the assemblage information at each step.

classmethod test_run()#: Runs a simple test to ensure everything is installed and functioning properly.

property input_arguments: dict#: Returns a dictionary of all input arguments; this dictionary can be used directly as an input argument to ModelRun in order to re-create a run.

property initial_assemblage: Assemblage#: Returns the initial assemblage.

property label: str#: Returns the label for the ModelRun object.

property color: str#: Returns the color for plotting the ModelRun object

property pot_TK: float#: Returns the potential temperature (in K) at which the model run was performed.

property pot_TC: float#: Returns the potential temperature (in C) at which the model run was performed.

property TC: ndarray#: Returns T (in C) for each assemblage in the ModelRun object.

property TK: ndarray#: Returns T (in K) for each assemblage in the ModelRun object.

property TK_olv_spl: ndarray#: Returns T (in K) from olivine and spinel compositions using the Li et al., 1995 thermometer for each assemblage in the ModelRun object; This should return the same value as TK, since this is a partitioning constraint.

property PGPa: ndarray#: Returns P (in GPa) for each assemblage in the ModelRun object.

property Pbar: ndarray#: Returns P (in bar) for each assemblage in the ModelRun object.

property G_cont_to_fO2: ndarray#: Returns the Gibbs Free Energy contribution to fO2 for each assemblage in the ModelRun object.

property logfO2_abs: ndarray#: Returns the absolute logfO2 value of the assemblage, not normalized to any buffer.

property FFM: ndarray#: Returns the value of the FFM buffer for each assemblage in the ModelRun object; FFM formulation is the first three terms of the fayalite-ferrosilite-magnetite buffer as compiled by Davis et al. (2017).

property QFM: ndarray#: Returns the value of the QFM buffer for each assemblage in the ModelRun object; QFM formulation is that of Frost (1991).

property logfO2_dFFM: ndarray#: Returns logfO2 relative to FFM buffer; FFM formulation is the first three terms of the fayalite-ferrosilite-magnetite buffer as compiled by Davis et al. (2017).

property logfO2_dQFM: ndarray#: Returns logfO2 relative to QFM buffer; QFM formulation is that of Frost (1991).

property olv#: Returns olivine phase history object; User can call all PhaseHistory and OlivineHistory attributes on ModelRun.olv object.

property opx#: Returns orthopyroxene phase history object; User can call all PhaseHistory and OrthopyroxeneHistory attributes on ModelRun.opx object.

property cpx#: Returns clinopyroxene phase history object; User can call all PhaseHistory and ClinopyroxeneHistory attributes on ModelRun.cpx object.

property spl#: Returns spinel phase history object; User can call all PhaseHistory and SpinelHistory attributes on ModelRun.spl object.

property gt#: Returns garnet phase history object; User can call all PhaseHistory and GarnetHistory attributes on ModelRun.gt object.

property liq#: Returns incremental liquid phase history object; User can call all PhaseHistory and LiquidHistory attributes on ModelRun.liq object.

property agg_liq#: Returns aggregated liquid phase history object; User can call all PhaseHistory and LiquidHistory attributes on ModelRun.agg_liq object.

property sys#: Returns system (residual solid phases + incremental liquid) phase history object; User can call all PhaseHistory and SystemHistory attributes on ModelRun.sys object.

get_data_table(method: str = 'standard', full_table: bool = True) → DataFrame#

Returns a Pandas dataframe with run results.

Parameters:

methodstr, optional: Standard method returns P/T/fO2 and phase masses/oxide wt%. Compact method returns P/T/extensive endmembers. By default ‘standard’.
full_tablebool, optional: full_table=True will display the entire table (all rows and columns). By default True.

Returns:

pd.DataFrame: A Pandas dataframe with run results.

save_data_table(file_name='model_output.xlsx', data_table: DataFrame | None = None, method='standard')#

Saves a single model run. To save a set of model runs, use save_data_tables() function in plotting_and_saving module.

Parameters:

file_namestr, optional: The path/file name to save the file to, by default ‘model_output.xlsx’.
data_tablepd.DataFrame | None, optional: The data table to save. By default will use “get_data_table” method, but can be used to save other tables as well (e.g., if you have modified the columns of the table). By default None.
methodstr, optional: See “get_data_table”. By default ‘standard’.

plot(x: str = 'PGPa', y: str = 'logfO2_dFFM')#

Plots ModelRun attributes.

Parameters:

xstr, optional: A string representing the assemblage or phase attribute to plot on the x axis, by default ‘PGPa’.
ystr, optional: A string representing the assemblage or phase attribute to plot on the x axis, by default ‘logfO2_dFFM’.

class peridoxia.main.PhaseHistory(model_run: ModelRun, phs_str: str, name: str, color: str)#

Class for returning properties of individual phases for each assemblage in a ModelRun object.

By default, the ModelRun class creates PhaseHistory objects for olv, opx, cpx, spl, gt, liq, agg_liq, and sys.

The methods and properties listed here can be called for each of those phase objects, e.g. “[ModelRunObject].olv.mass”.
Each PhaseHistory object also has phase-specific properties, which are listed in the [Phase]History subclasses below.
For instance, the OlivineHistory subclass has a Fo_num property, allowing the user to call [ModelRunObject].olv.Fo_num.
See Tutorial for more information.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
phs_strstr: The phase string representing the phase type: ‘olv’, ‘opx’, ‘cpx’, ‘gt’, ‘spl’, ‘liq’, ‘sys’. This tells PhaseHistory which type of object to create.
namestr: The name of the phase instance. Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type string.
colorstr: The color for plotting the phase.

Attributes:

Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

property phs_obj_list: list#: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.

property phs_str: str#: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc. (but not ‘agg_liq’, which is a Liquid phase object).

property name: str#: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.

property ext_end_mol: ndarray#: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.

property mass: ndarray#: Returns an array of masses for the given phase for each assemblage in the ModelRun object.

property oxides: ndarray#: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.

property oxide_order: ndarray#: Returns an array of strings representing the order of oxides when returned by the model.

property mol_cat: ndarray#: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.

property Fe3_Al: ndarray#: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.

property Fe3_tFe: ndarray#: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.

property Cr_num: ndarray#: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.

property Mg_num: ndarray#: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.

class peridoxia.main.OlivineHistory(model_run: ModelRun, name: str = 'olv', color: str = 'springgreen')#

Class for olivine properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the olivine-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘olv’.
colorstr, optional: The color for plotting the phase, by default ‘springgreen’.

Attributes:

Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Fo_num: Returns an array of Fo# values (100*Mg/(Mg+Fe2+)) in olivine for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
fO2_cont: Returns an array of fO2 contributions (-12*log(1-Mg_num) - 2620*(Mg_num)^2/T) in olivine for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

property Fo_num: ndarray#: Returns an array of Fo# values (100*Mg/(Mg+Fe2+)) in olivine for each assemblage in the ModelRun object.

property fO2_cont: ndarray#: Returns an array of fO2 contributions (-12*log(1-Mg_num) - 2620*(Mg_num)^2/T) in olivine for each assemblage in the ModelRun object.

class peridoxia.main.OrthopyroxeneHistory(model_run: ModelRun, name: str = 'opx', color: str = 'darkolivegreen')#

Class for orthopyroxene properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the orthopyroxene-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘opx’.
colorstr, optional: The color for plotting the phase, by default ‘darkolivegreen’.

Attributes:

Al_per_6_O: Returns an array of total Al per 6 Oxygen in orthopyroxene for each assemblage in the ModelRun object.
Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
Ts_per_6_O: Returns an array of Al_VI+Cr_VI per 6 Oxygen as a proxy for Ts per 6 Oxygen in orthopyroxene for each assemblage in the ModelRun object.
XM1XM2: Returns an array of (X_Fe2+)_M1*(X_Fe3+)_M2 in orthopyroxene for each assemblage in the ModelRun object; Gives slightly different result than original XM1XM2 calculator because it takes Fe3+ vs Fe2+ into account (differences are on the order of 0.01 log units contribution to fO2).
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
fO2_cont: Returns an array of fO2 contributions (3*log(XM1XM2)) in orthopyroxene for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

property Ts_per_6_O: ndarray#: Returns an array of Al_VI+Cr_VI per 6 Oxygen as a proxy for Ts per 6 Oxygen in orthopyroxene for each assemblage in the ModelRun object.

property Al_per_6_O: ndarray#: Returns an array of total Al per 6 Oxygen in orthopyroxene for each assemblage in the ModelRun object.

property XM1XM2: ndarray#: Returns an array of (X_Fe2+)_M1*(X_Fe3+)_M2 in orthopyroxene for each assemblage in the ModelRun object; Gives slightly different result than original XM1XM2 calculator because it takes Fe3+ vs Fe2+ into account (differences are on the order of 0.01 log units contribution to fO2).

property fO2_cont: ndarray#: Returns an array of fO2 contributions (3*log(XM1XM2)) in orthopyroxene for each assemblage in the ModelRun object.

class peridoxia.main.ClinopyroxeneHistory(model_run: ModelRun, name: str = 'cpx', color: str = 'green')#

Class for clinopyroxene properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the clinopyroxene-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘cpx’.
colorstr, optional: The color for plotting the phase, by default ‘green’.

Attributes:

Al_per_6_O: Returns an array of total Al per 6 Oxygen in clinopyroxene for each assemblage in the ModelRun object.
Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
Ts_per_6_O: Returns an array of Al_VI+Cr_VI per 6 Oxygen as a proxy for Ts per 6 Oxygen in clinopyroxene for each assemblage in the ModelRun object.
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

property Ts_per_6_O: ndarray#: Returns an array of Al_VI+Cr_VI per 6 Oxygen as a proxy for Ts per 6 Oxygen in clinopyroxene for each assemblage in the ModelRun object.

property Al_per_6_O: ndarray#: Returns an array of total Al per 6 Oxygen in clinopyroxene for each assemblage in the ModelRun object.

class peridoxia.main.SpinelHistory(model_run: ModelRun, name: str = 'spl', color: str = 'black')#

Class for spinel properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the spinel-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘spl’.
colorstr, optional: The color for plotting the phase, by default ‘black’.

Attributes:

Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
aFe3O4: Returns an array of magnetite activity in spinel for each assemblage in the ModelRun object; Magnetite activity is calculated via the ThermoEngine python package (enki-portal.org) using the spinel activity models of Sack and Ghiorso (1991ab).
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
fO2_cont: Returns an array of fO2 contributions (2*log(aFe3O4)) in spinel for each assemblage in the ModelRun object; Magnetite activity is calculated via the ThermoEngine python package (enki-portal.org) using the spinel activity models of Sack and Ghiorso (1991ab).
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

property aFe3O4: ndarray#: Returns an array of magnetite activity in spinel for each assemblage in the ModelRun object; Magnetite activity is calculated via the ThermoEngine python package (enki-portal.org) using the spinel activity models of Sack and Ghiorso (1991ab).

property fO2_cont: ndarray#: Returns an array of fO2 contributions (2*log(aFe3O4)) in spinel for each assemblage in the ModelRun object; Magnetite activity is calculated via the ThermoEngine python package (enki-portal.org) using the spinel activity models of Sack and Ghiorso (1991ab).

class peridoxia.main.GarnetHistory(model_run: ModelRun, name: str = 'gt', color: str = 'purple')#

Class for garnet properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the garnet-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘gt’.
colorstr, optional: The color for plotting the phase, by default ‘purple’.

Attributes:

Ca_mass_ratio: Returns an array of Ca-garnet/Fe-Mg-garnet mass ratios for each assemblage in the ModelRun object.
Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

property Ca_mass_ratio: ndarray#: Returns an array of Ca-garnet/Fe-Mg-garnet mass ratios for each assemblage in the ModelRun object.

class peridoxia.main.LiquidHistory(model_run: ModelRun, name: str = 'liq', color: str = 'red')#

Class for liquid properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the liquid-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘liq’.
colorstr, optional: The color for plotting the phase, by default ‘red’.

Attributes:

Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

Methods

`fO2_Borisov_2018`([pressure_term])	Returns an array of logfO2 (absolute) values in liquid for each assemblage in the ModelRun object; Uses the Borisov et al. (2018) formulation (Table 2); Pressure term options are: 'None', 'KC1991', 'Zhang2017'.
`fO2_Hirschmann_2022`([pressure_term])	Returns an array of logfO2 (absolute) values in liquid for each assemblage in the ModelRun object; Uses the Hirschmann et al. (2022) formulation (Eq 21); Pressure term options are: 'None', 'KC1991', 'Zhang2017', and 'Deng2020'.
`fO2_Kress_and_Carmichael_1991`()	Returns an array of logfO2 (absolute) values in liquid for each assemblage in the ModelRun object; Uses the Kress and Carmichael (1991) formulation.

fO2_Kress_and_Carmichael_1991() → ndarray#: Returns an array of logfO2 (absolute) values in liquid for each assemblage in the ModelRun object; Uses the Kress and Carmichael (1991) formulation.

fO2_Borisov_2018(pressure_term: str = 'None') → ndarray#: Returns an array of logfO2 (absolute) values in liquid for each assemblage in the ModelRun object; Uses the Borisov et al. (2018) formulation (Table 2); Pressure term options are: ‘None’, ‘KC1991’, ‘Zhang2017’.

fO2_Hirschmann_2022(pressure_term: str = 'None') → ndarray#: Returns an array of logfO2 (absolute) values in liquid for each assemblage in the ModelRun object; Uses the Hirschmann et al. (2022) formulation (Eq 21); Pressure term options are: ‘None’, ‘KC1991’, ‘Zhang2017’, and ‘Deng2020’.

class peridoxia.main.SystemHistory(model_run: ModelRun, name: str = 'sys', color: str = 'grey')#

Class for system properties over the course of a model run. Inherits from PhaseHistory, so all PhaseHistory properties can be accessed in addition to the system-specific properties indicated here.

Parameters:

model_runModelRun: The ModelRun object from which to load the phase data.
namestr, optional: The name of the phase instance, by default ‘sys’.
colorstr, optional: The color for plotting the phase, by default ‘grey’.

Attributes:

Cr_num: Returns an array of Cr# values (Cr/(Cr+Al)) for the given phase for each assemblage in the ModelRun object.
Fe3_Al: Returns an array of Fe3/Al ratios for the given phase for each assemblage in the ModelRun object.
Fe3_tFe: Returns an array of Fe3+/tFe ratios for the given phase for each assemblage in the ModelRun object.
Mg_num: Returns an array of Mg# values (Mg/(Mg+Fe2+)) for the given phase for each assemblage in the ModelRun object.
ext_end_mol: Returns an array of extensive endmember moles for the given phase for each assemblage in the ModelRun object.
mass: Returns an array of masses for the given phase for each assemblage in the ModelRun object.
mol_cat: Returns an array of cation moles (per 100 g of oxides) for the given phase for each assemblage in the ModelRun object; Cation order is same as oxide order, and can be retrieved by calling [self].oxide_order.
name: Returns the name of the phase, which represents the name of the phase instance; Often the same as the phase string, but may be different– e.g., for the aggregated liquid, ‘agg_liq’ would be the name, whereas ‘liq’ would be the phase type.
oxide_order: Returns an array of strings representing the order of oxides when returned by the model.
oxides: Returns an array of oxides, normalized to 100 wt%, for the given phase for each assemblage in the ModelRun object; Oxide order can be retrieved by calling [self].oxide_order.
phs_obj_list: Returns a list of Phase objectes for the given phase for each assemblage in the ModelRun object.
phs_str: Returns the phase string, which represents the type of phase: e.g., ‘olv’, ‘opx’, ‘liq’, ‘sys’, etc.

Main Model#

This Page