Quick Reference

Calculations

Calculation	Function	Required args
Saturation pressure	`calculate_saturation_pressure()`	`sample`, `temperature`
Dissolved volatiles	`calculate_dissolved_volatiles()`	`sample`, `temperature`, `pressure`, `X_fluid`
Equilibrium fluid	`calculate_equilibrium_fluid_comp()`	`sample`, `temperature`, `pressure`
Isobars & isopleths	`calculate_isobars_and_isopleths()`	`sample`, `temperature`, `pressure_list`, `isopleth_list`
Degassing path	`calculate_degassing_path()`	`sample`, `temperature`
Liquid density	`calculate_liquid_density()`	`sample`, `temperature`, `pressure`
Liquid viscosity	`calculate_liquid_viscosity()`	`sample`, `temperature`

Tip

Single sample: v.calculate_*(...).result — append .result to get values.

Batch: myfile.calculate_*(...) — called on a BatchFile object, no .result needed.

Models

Use v.get_model_names() to print a list of all models.

Mixed	`MagmaSat` (default), `ShishkinaIdealMixing`, `Dixon`, `IaconoMarziano`, `Liu`
H2O	`ShishkinaWater`, `DixonWater`, `IaconoMarzianoWater`, `MooreWater`, `LiuWater`,
CO2	`ShishkinaCarbon`, `DixonCarbon`, `IaconoMarzianoCarbon`, `AllisonCarbon`, `AllisonCarbon_sunset`, `AllisonCarbon_sfvf`, `AllisonCarbon_erebus`, `AllisonCarbon_vesuvius`, `AllisonCarbon_etna`, `AllisonCarbon_stromboli`, `LiuCarbon`

Arguments

Argument	Type	Description
`sample`	Sample	A `Sample` object. Required for single-sample calculations; omit for batch.
`temperature`	float or str	Temperature in degrees C. Pass a column name (str) for batch calculations.
`pressure`	float or str	Pressure in bars. Pass a column name (str) for batch calculations.
`X_fluid`	float or str	Mole fraction of CO2 in the fluid (0 to 1). Pass a column name (str) for batch.
`model`	str	Model name. Default: `'MagmaSat'`. See `v.get_model_names()`.
`verbose`	bool	Return extra values (single-sample only). Default: `False`.
`print_status`	bool	Print progress (batch only). Default: `False`.

Sample

Task	Syntax
Create manually	`v.Sample({'SiO2': 77.3, 'Al2O3': 12.6, ...})`
With normalization	`v.Sample({...}, default_normalization='standard')`
With input units	`v.Sample({...}, units='mol_oxides')`
With output units	`v.Sample({...}, default_units='mol_oxides')`
Extract from file	`myfile.get_sample_composition('SampleName', asSampleClass=True)`
Get composition	`my_sample.get_composition()`
Get normalized	`my_sample.get_composition(normalization='standard')`
Update composition	`my_sample.change_composition(new_comp)`

BatchFile

Task	Syntax
Import CSV or Excel file	`v.BatchFile('file.extension')`
Specific sheet (name)	`v.BatchFile('file.xlsx', sheet_name="Sheet2")`
Specific sheet (index)	`v.BatchFile('file.xlsx', sheet_name=0)`
With normalization	`v.BatchFile('file.xlsx', default_normalization='standard')`
Specify input units (default is wt% oxides)	`v.BatchFile('file.xlsx', units='mol_oxides')`
Specify output units (default is wt% oxides)	`v.BatchFile('file.xlsx', default_units='mol_oxides')`
From DataFrame	`v.BatchFile(filename=None, dataframe=my_df)`
Get all data	`myfile.get_data()`
Get normalized data	`myfile.get_data(normalization='standard')`
Extract one sample (defaults to return as dict, pass `asSampleClass=True` to return as Sample() object.)	`myfile.get_sample_composition('Label', asSampleClass=True)`

Normalization

Value	Description
`"none"` (default)	No normalization is applied.
`"standard"`	Normalizes all oxides (including volatiles) to 100 wt%.
`"fixedvolatiles"`	Normalizes to 100 wt%, but H2O and CO2 stay fixed while other oxides are reduced proportionally.
`"additionalvolatiles"`	Normalizes non-volatile oxides to 100 wt%. Original H2O and CO2 are added on top, so the total may exceed 100%.

See normalization examples below

Units

Value	Description
`"wtpt_oxides"` (default)	Weight percent oxides.
`"mol_oxides"`	Mol fraction oxides.
`"mol_cations"`	Mol fraction cations.
`"mol_singleO"`	Mol fraction on a single-oxygen basis.

units vs default_units

units tells VESIcal what your input data are in.

default_units tells VESIcal what units to return data in.

See units examples below

Saving

Method	Description
save_results()	Save any VESIcal objects, DataFrames, dicts, or scalars to CSV or Excel with flexible output modes.
save_excel()*	Save to a `.xlsx` file with one sheet per calculation.
save_csv()*	Save to one CSV file per calculation.

*these will be deprecated in the next major release.

Examples

Setup

import VESIcal as v

Create a Sample

my_sample = v.Sample({'SiO2': 77.3, 'TiO2': 0.08, ... })

class VESIcal.sample_class.Sample(composition, units='wtpt_oxides', default_normalization='none', default_units='wtpt_oxides')[source]: The sample class stores compositional information for samples, and contains methods for normalization and other compositional calculations.

Extract a sample from an imported file:

extracted_sample = myfile.get_sample_composition('SampleOne', asSampleClass=True)

Import an Excel or CSV File

myfile = v.BatchFile('path/to/your/file.xlsx')

# specific sheet by name
myfile = v.BatchFile('path/to/your/file.xlsx', sheet_name="NameOfYourSheet")

# specific sheet by index (0-based)
myfile = v.BatchFile('path/to/your/file.xlsx', sheet_name=0)

class VESIcal.batchfile.BatchFile(filename, sheet_name=0, file_type='excel', units='wtpt_oxides', label='Label', default_normalization='none', default_units='wtpt_oxides', dataframe=None, **kwargs)[source]

A batch file with sample names and oxide compositions

Variables:

filename (str) – Path to the batch file, e.g., “my_file.xlsx”. This always needs to be passed, even if the user is passing a pandas DataFrame rather than an batch file. If passing a DataFrame, filename should be set to None. File can be excel file (.xlsx) or .csv.
sheet_name (str) –
OPTIONAL. For Excel files. Default value is 0 which gets the first sheet in the batch spreadsheet file. This implements the pandas. read_excel() sheet_name parameter. But functionality to read in more than one sheet at a time (e.g., pandas.read_excel(sheet_name=None)) is not yet imlpemented in VESIcal. From the pandas 1.0.4 documentation:

Available cases: - Defaults to 0: 1st sheet as a DataFrame - 1: 2nd sheet as a DataFrame - “Sheet1”: Load sheet with name “Sheet1”
file_type (str) – OPTIONAL. Default is ‘excel’, which denotes that passed file has extension .xlsx. Other option is ‘csv’, which denotes that the passed file has extension .csv.
units (str) – OPTIONAL. Default is ‘wtpt_oxides’. String defining whether the oxide composition is given in wt percent (“wtpt_oxides”, which is the default), mole oxides (mol_oxides) or mole cations (mol_cations).
default_normalization (None or str) –
The type of normalization to apply to the data by default. One of: - None (no normalization) - ‘standard’ (default): Normalizes an input composition to 100%. - ‘fixedvolatiles’: Normalizes major element oxides to 100 wt%,

including volatiles. The volatile wt% will remain fixed, whilst the other major element oxides are reduced proportionally so that the total is 100 wt%.
- ’additionalvolatiles’: Normalises major element oxide wt% to 100%, assuming it is volatile-free. If H2O or CO2 are passed to the function, their un-normalized values will be retained in addition to the normalized non-volatile oxides, summing to >100%.
str (default_units) – The type of composition to return by default, one of: - wtpt_oxides (default) - mol_oxides - mol_cations
label (str) – OPTIONAL. Default is ‘Label’. Name of the column within the passed file referring to sample names.
dataframe (pandas DataFrame) – OPTIONAL. Default is None in which case this argument is ignored. This argument is used when the user wishes to turn a pandas DataFrame into an BatchFile object, for example when user data is already in python rather than being imported from a file. In this case set dataframe equal to the dataframe object being passed in. If using this option, pass None to filename.

Normalization

On import:

my_sample = v.Sample({...}, default_normalization='standard')
myfile = v.BatchFile('file.xlsx', default_normalization='standard')

On existing data:

normed = mysample.get_composition(normalization="standard")
mysample.change_composition(normed)

Normalize an entire BatchFile:

my_normed_data = myfile.get_data(normalization="standard")
myNewData = v.BatchFile(filename=None, dataframe=my_normed_data)

Units

# input is mol fraction oxides, output as mol fraction oxides
my_sample = v.Sample({...}, units='mol_oxides', default_units='mol_oxides')

# input is wt% (default), convert output to mol fraction oxides
myfile = v.BatchFile('file.xlsx', default_units='mol_oxides')

Tips and Tricks

Pull arguments from a file:

myfile.calculate_dissolved_volatiles(
    temperature="MyTemps",    # column name in your file
    pressure="SomePs",        # column name in your file
    X_fluid=0.35              # single value applied to all samples
).result

Choose a model:

v.get_model_names()  # list all available models

v.calculate_saturation_pressure(
    sample=my_sample, temperature=900,
    model='ShishkinaIdealMixing'
).result

Dissolved Volatile Concentrations

v.calculate_dissolved_volatiles(sample, temperature, pressure, X_fluid)

# single sample
v.calculate_dissolved_volatiles(
    sample=my_sample, temperature=1000, pressure=2000, X_fluid=0.5
).result

# batch
myfile.calculate_dissolved_volatiles(temperature=1000, pressure=2000, X_fluid=0.5)

Equilibrium Fluid Compositions

v.calculate_equilibrium_fluid_comp(sample, temperature, pressure)

# single sample
v.calculate_equilibrium_fluid_comp(
    sample=my_sample, temperature=1000, pressure=2000
).result

# batch
myfile.calculate_equilibrium_fluid_comp(temperature=1000, pressure=2000)

Saturation Pressures

v.calculate_saturation_pressure(sample, temperature)

# single sample
v.calculate_saturation_pressure(sample=my_sample, temperature=1000).result

# batch
myfile.calculate_saturation_pressure(temperature=1000)

Isobars and Isopleths

v.calculate_isobars_and_isopleths(sample, temperature, pressure_list, isopleth_list)

Single-sample only.

Extra argument	Description
`pressure_list`	List of pressures (bars) at which to calculate isobars.
`isopleth_list`	List of X_fluid values at which to calculate isopleths.

isobars, isopleths = v.calculate_isobars_and_isopleths(
    sample=my_sample,
    temperature=1000,
    pressure_list=[500, 1000, 2000],
    isopleth_list=[0.25, 0.5, 0.75]
).result

fig, ax = v.plot(isobars=isobars, isopleths=isopleths)
v.show()

For custom plotting, get smoothed data as a DataFrame:

smoothed = v.vplot.smooth_isobars_and_isopleths(isobars=isobars, isopleths=isopleths)

Degassing Paths

v.calculate_degassing_path(sample, temperature)

Single-sample only.

Extra argument	Description
`init_vapor`	Initial percent of exsolved fluid (e.g., `2.0` for 2%). Default: `0.0`.
`fractionate_vapor`	Fraction of fluid removed at each step. `0.0` = closed (default), `1.0` = fully open, `0.2` = 20% removed per step.

# closed system (default)
closed = v.calculate_degassing_path(sample=my_sample, temperature=1000).result

# closed system with 2% initial fluid
init = v.calculate_degassing_path(sample=my_sample, temperature=1000, init_vapor=2.0).result

# fully open system
opened = v.calculate_degassing_path(sample=my_sample, temperature=1000, fractionate_vapor=1.0).result

# partially open (20% removed per step)
partial = v.calculate_degassing_path(sample=my_sample, temperature=1000, fractionate_vapor=0.2).result

fig, ax = v.plot(
    degassing_paths=[closed, init, opened, partial],
    degassing_path_labels=["Closed", "2% Initial Fluid", "Open", "Partly Open"]
)
v.show()

Liquid Density

v.calculate_liquid_density(sample, temperature, pressure)

# single sample
v.calculate_liquid_density(sample=my_sample, temperature=1000, pressure=2000).result

# batch
myfile.calculate_liquid_density(temperature=1000, pressure=2000)

Liquid Viscosity

v.calculate_liquid_viscosity(sample, temperature)

# single sample
v.calculate_liquid_viscosity(sample=my_sample, temperature=1000).result

# batch
myfile.calculate_liquid_viscosity(temperature=1000)

Save Results (General Purpose)

v.save_results(filename, obj, filetype="csv", mode="single_sheet", descriptions=None)

Save any combination of VESIcal objects, DataFrames, dicts, or scalars to CSV or Excel. Supports Sample, Calculate, and BatchFile objects, as well as pandas DataFrames/Series, dictionaries, lists, and scalar values.

Argument	Description
`filename`	Base filename. Extension is added or replaced automatically. For `multi_file` mode, index suffixes are appended (e.g., `output_1.csv`, `output_2.csv`).
`obj`	Data to save: a single object or a list of objects.
`filetype`	`"csv"` (default) or `"excel"`
`mode`	`"single_sheet"` (default): all data in one file/sheet. `"multi_sheet"`: each object on its own Excel sheet (Excel only). `"multi_file"`: each object in a separate file.
`descriptions`	Optional list of string labels added as a `Description` column.

# Save a single calculation result
v.save_results("satP.csv", satP)

# Save a list of mixed types to Excel, one sheet per item
v.save_results("results.xlsx", [mysample, satP, dissolved],
    filetype="excel", mode="multi_sheet",
    descriptions=["Sample", "Saturation Pressure", "Dissolved Volatiles"])

# Save each item to its own CSV file
v.save_results("output", [satP, dissolved],
    filetype="csv", mode="multi_file")

Old save methods

These will be deprecated in next major release.

Save to Excel

dissolved = myfile.calculate_dissolved_volatiles(temperature=900, pressure=1000, X_fluid=0.5)
SatP = myfile.calculate_saturation_pressure(temperature=900)

myfile.save_excel("myoutput.xlsx", calculations=[dissolved, SatP])

# with custom sheet names
myfile.save_excel("myoutput.xlsx",
    calculations=[dissolved, SatP],
    sheet_names=["Dissolved", "Saturation Pressures"]
)

Save to CSV

myfile.save_csv(
    filename=["my_dissolved_output.csv", "my_SatP_output.csv"],
    calculations=[dissolved, SatP]
)