Detailed pyFastChem module description¶

By using the library PyBind11, FastChem can be called directly
within Python. This requires the compilation of FastChem’s
Python wrapper that is located in the file
python/fastchem_python_wrapper.cpp. pyFastChem currently only
links to the long double C++ version of FastChem.
As described here, when using the
CMake approach, pyFastChem will be automatically compiled when
cmake is configured with the corresponding option. If the
configuration and compilation is successful, a module file should be
present in the python/ folder that contains the Python module
which acts as a wrapper between Python and the C++ version of
FastChem. The file should be named pyfastchem.cpython-xxxx,
where xxxx will be a combination of your Python version and
operating system.
If pyFastChem has been built using the setup.py script or
installed via PyPI, then the module will be located in your normal
Python module library path. It, thus, can be accessed from everywhere
on your system like any other standard Python package. The location
and additional module information can be obtained via

pip show pyfastchem

Depending on your Python installation, pip might need to be replaced by pip3.

A description of the module is given here. Besides the pyFastChem module, we also provide several example Python scripts that show how to call FastChem from within Python for several different scenarios. We discuss the examples here.

The pyFastChem module provides access to the FastChem object class as well as additional constants used within FastChem. They are essentially identical to their C++ counterparts discussed here.

To include the pyFastChem module in your Python project, just import it using

import pyfastchem

This provides access to the FastChem object class as well as the input and output structures and additional pre-defined constants used by FastChem.

pyFastChem constants¶

The pyFastChem module contains a number of pre-defined constants. This includes the constant pyfastchem.FASTCHEM_UNKNOWN_SPECIES of type int that is returned by some pyFastChem methods when a chemical species is not found.

The chemistry calculation can also return several output flags of type int defined as constants in the pyFastChem module:

pyfastchem.FASTCHEM_SUCCESS: Indicates that the calculation has been successful, i.e. that the chemistry iterations converged.
pyfastchem.FASTCHEM_NO_CONVERGENCE: Indicates that the calculation was not successful, i.e. that the chemistry did not converge within the allowed maximum number of iterations steps given in the config file or set manually via the setParameter method together with the nbIterationsChem parameter (see here). One way to solve such a problem is to increase the maximum number of iteration steps.
pyfastchem.FASTCHEM_INITIALIZATION_FAILED: Indicates that something went wrong during reading one of the input files. To find the source of the problem, one can set the verbose level in the config file or manually via setVerboseLevel (see here) to a higher value and look at the terminal output.
pyfastchem.FASTCHEM_IS_BUSY: The chemistry calculations of FastChem can only be called once for each object class instance. Attempting to start a new calculation while another is still running will result in FastChem returning this flag.
pyfastchem.FASTCHEM_WRONG_INPUT_VALUES: FastChem returns this flag if some input values are wrong. Currently, this refers to the temperature and pressure vectors in the input structure not having the same size (see here for details on the input structure).
pyfastchem.FASTCHEM_PHASE_RULE_VIOLATION: FastChem returns this flag if condensation is used and the system violates the phase rule. This happens when the number of elements contained in condensates equals the total number of elements. In this case, the gas phase lacks a degree of freedom to yield the correct gas pressure. Such a system cannot be solved as there has always to be at least one incondensable element in the gas phase (see the section about the phase rule in Paper III).

In addition to these flags, the pyFastChem module also includes a constant string array pyfastchem.FASTCHEM_MSG that contains string expressions for each of these flags. Using this array with any of the aforementioned flags pyfastchen.FASTCHEM_MSG[flag] returns a string with a description of the corresponding flag’s meaning. For example,

pyfastchem.FASTCHEM_MSG[pyfastchem.FASTCHEM_NO_CONVERGENCE]

will return the string "convergence failed".

pyFastChem constructor¶

Since FastChem is written as an object class, an instance of that class (i.e. an object) needs to be created before FastChem can be used. This is done by calling the constructor of the FastChem class that is contained within the pyFastChem module. There are three main ways to call the constructor and create an object.

pyfastchem.FastChem(str element_abundance_file,
                    str gas_species_data_file,
                    int verbose_level)

This constructor requires three parameters: the locations of the element abundance and gas phase species data files, as well as the verbose level. All other options and parameters within FastChem will be set to their default values but can be later changed by using the appropriate methods described here. The default maximum number of chemistry iterations is 3000, the number of Newton, bisection and Nelder-Mead method iterations is 3000, and the default accuracy of the of Newton method and the chemistry iterations is set to \(10^{-4}\). This constructor will not read in any condensate data. Trying to use an object created via this method for a calculation using condensation will result in an error message.

pyfastchem.FastChem(str element_abundance_file,
                    str gas_species_data_file,
                    str condensate_species_data_file,
                    int verbose_level)

This constructor requires four parameters: the locations of the element abundance and gas phase species data files, the condensate data file, as well as the verbose level. All other options and parameters within FastChem will be set to their default values but can be later changed by using the appropriate methods described here. The default maximum number of chemistry iterations is 3000, the number of Newton, bisection and Nelder-Mead method iterations is 3000, and the default accuracy of the of Newton method and the chemistry iterations is set to \(10^{-4}\). Note that instead of a location for the condensate data, a str containing 'none' can be used here as well. In that case, no condensate data will be read in and trying to use the object for a calculation using condensation will result in an error message.

pyfastchem.FastChem(str parameter_file,
                    int intial_verbose_level)

The constructor requires two different arguments: the location of the parameter file and the initial verbose level. The latter one will be replaced by the corresponding value read in from the parameter file. The structure of this parameter file is discussed here. All of parameter values read in from the file can also be adjusted during runtime by using the methods listed here.

pyFastChem input and output structures¶

Running a FastChem chemistry calculation requires input and output data structures, resembling those of the C++ version. In Python they are represented as classes rather than a C++struct.

Input structure¶

The original C++ struct translated by PyBind11 has the following structure in Python:

class FastChemInput:
    temperature: list[float] = []
    pressure: list[float] = []

    equilibrium_condensation = False
    rainout_condensation = False

The input class contains the following variables:

temperature: An array of float numbers that describe the temperature in K.
pressure: An array of float numbers that describe the pressure in bar.
equilibrium_condensation: A bool parameter that enables the calculation of equilibrium condensation. Its default value is False.
rainout_condensation: A bool parameter that enables the calculation of condensation via the rainout approximation. Its default value is False. Note that when the flag rainout_condensation is set to True, the value of the parameter equilibrium_condensation is ignored.

An input structure, in the example here called input_data, can be defined from the pyFastChem module in the following way:

input_data = pyfastchem.FastChemInput()

The two input arrays for temperature and pressure need to have the same length. The PyBind11 library allows normal Python lists or NumPy arrays to be used here. For example, a NumPy array for the pressure could be defined using NumPy’s logspace function:

input_data.pressure = np.logspace(-6, 1, num=1000)

Both of these input variables need to be an array-type variable, even if only a single temperature-pressure point is going to be calculated.

Output structure¶

The original C++ output struct translated by PyBind11 has the following structure in Python:

class FastChemOutput:
    number_densities: list[list[float]]
    total_element_density: list[float]
    mean_molecular_weight: list[float]

    number_densities_cond: list[list[float]]
    element_cond_degree: list[list[float]]

    element_conserved: list[list[int]]
    nb_chemistry_iterations: list[int]
    nb_cond_iterations: list[int]
    nb_iterations: list[int]
    fastchem_flag: list[int]

It has the following variables:

number_densities: The two-dimensional array contains the number densities in of all gas phase species (elements, molecules, ions) as float numbers. The first dimension refers to the temperature-pressure grid and has the same size as the temperature and pressure arrays of the input structure. The second dimension refers to the number of species and has a length of getGasSpeciesNumber() (see here).
total_element_density: One-dimensional array of float numbers that contains the total number density of all atoms \(j\), i.e. \(n_\mathrm{tot} = \sum_j \left( n_j + \sum_i \nu_{ij} n_i + \sum_c \nu_{cj} n_c \right)\), summed over their atomic number densities, as well as the ones contained in all other molecules/ions \(j\) and condensates \(c\). This quantity is usually only a diagnostic output and not relevant for other calculations. The dimension of the array is equal to that of the input temperature and pressure vectors.
mean_molecular_weight: One-dimensional array of float numbers. Contains the mean molecular weight of the mixture in units of the unified atomic mass unit. For all practical purposes, this can also be converted into units of g/mol. The dimension of the array is equal to that of the input temperature and pressure vectors.
number_densities_cond: The two-dimensional array contains the fictitious number densities in of all condensate species as float numbers. The first dimension refers to the temperature-pressure grid and has the same size as the temperature and pressure arrays of the input structure. The second dimension refers to the number of species and has a length of getCondSpeciesNumber() (see here).
element_cond_degree: The two-dimensional array contains the degree of condensation for all elements. The first dimension refers to the temperature-pressure grid and has the same size as the temperature and pressure vectors of the input structure. The second dimension refers to the number of elements and has a length of getElementNumber() (see here).
element_conserved: The two-dimensional array of int numbers contains information on the state of element conservation. A value of 0 indicates that element conservation is not fulfilled, whereas a value of 1 means that the element has been conserved. The first dimension refers to the temperature-pressure grid and has the same size as the temperature and pressure vectors of the input structure. The second dimension refers to the number of elements and has a length of getElementNumber() (see here).
nb_chemistry_iterations: One-dimensional array of int numbers. Contains the total number of chemistry iterations that were required to solve the system for each temperature-pressure point. The dimension of the array is equal to that of the input temperature and pressure vectors.
nb_cond_iterations: One-dimensional array of int numbers. Contains the total number of condensate calculation iterations that were required for each temperature-pressure point. The dimension of the array is equal to that of the input temperature and pressure vectors.
nb_iterations: One-dimensional array of int numbers. Contains the total number of coupled condensation-gas phase chemistry calculation iterations that were required to solve the system for each temperature-pressure point. The dimension of the vector is equal to that of the input temperature and pressure vectors.
fastchem_flag: One-dimensional array of int numbers. Contains flags that give information on potential issues of the chemistry calculation for each temperature-pressure point. The set of potential values is stated here. A string message for each corresponding flag can also be obtained from the constant pyfastchem.FASTCHEM_MSG vector of strings, via pyfastchem.FASTCHEM_MSG[flag]. The dimension of the array is equal to that of the input temperature and pressure vectors.

The output structure from the pyFastChem module, in the example here called output_data, can be defined in the following way:

output_data = pyfastchem.FastChemOutput()

The arrays of the output structure don’t need to be pre-allocated. This will be done internally within FastChem when running the chemistry calculations. If the arrays already contain data, their contents will be overwritten. The arrays from the output structure can also be easily converted to more practical NumPy arrays by using, for example:

number_densities = np.array(output_data.number_densities)

pyFastChem functions¶

The pyFastChem object returned from pyfastchem.FastChem() has several methods that allow to interact with FastChem. These methods are equivalent to those of the C++ object class discussed here.

However, note that some methods listed below officially require an unsigned int parameter variable in their original C++ version. Since this data type doesn’t exist in Python, PyBind11 will convert the supplied int value to its unsigned integer version for C++. Even though the parameter is defined as an int value for Python, only positive numbers, including 0, are accepted as valid input. Using a negative value will result in an error message from PyBind11.

int calcDensities(pyfastchem.FastChemInput() input,
                  pyfastchem.FastChemOutput() output)

Starts a chemistry calculation with the provided pyfastchem.FastChemInput() and pyfastchem.FastChemOutput() structures. Returns an int value that represents the highest value from the flag vector within the pyfastchem.FastChemOutput() structure.

setParameter(str param_name,
             param_type param_value)

Sets an internal FastChem parameter. Depending on the parameter, the variable type param_type can either be an int, a bool, or a float value. A list of parameters and their types can be found here. The C++double types listed there should be replaced by Python float values, while unsigned int are used as int. PyBind11 often converts the Python bool type to an integer value rather than a C++bool type. Setting a boolean parameter will then result in an error message. In such a case, instead of using a simple True as parameter value, an explicit conversion has to be done instead, for example via np.bool_(True).

int getGasSpeciesNumber()

Returns the total number of gas phase species (atoms, ions, molecules) as int value.

int getElementNumber()

Returns the total number of elements as int value.

int getMoleculeNumber()

Returns the total number of molecules and ions (anything other than elements) as int value.

int getCondSpeciesNumber()

Returns the total number of condensate species as int value.

str getGasSpeciesName(int species_index)

Returns the name of a gas phase species with int index species_index as str; returns empty string if species does not exist.

str getGasSpeciesSymbol(int species_index)

Returns the symbol of an element or the formula of a molecule/ion with int index species_index as str; returns empty string if species does not exist

int getGasSpeciesIndex(str symbol)

Returns the index of a gas phase species (element/molecule/ion) with str symbol/formula symbol as int; returns the constant pyfastchem.FASTCHEM_UNKOWN_SPECIES if species does not exist.

str getElementName(int species_index)

Returns the name of an element with int index species_index as str; returns empty string if species does not exist.

str getElementSymbol(int species_index)

Returns the symbol of an element with int index species_index as str; returns empty string if species does not exist

int getElementIndex(str symbol)

Returns the index of an element with str symbol/formula symbol as int; returns the constant pyfastchem.FASTCHEM_UNKOWN_SPECIES if species does not exist.

str getCondSpeciesName(int species_index)

Returns the name of a condensate species with int index species_index as str; returns empty string if species does not exist.

str getCondSpeciesSymbol(int species_index)

Returns the formula of a condensate with int index species_index as str; returns empty string if species does not exist

int getCondSpeciesIndex(str symbol)

Returns the index of a condensate species with str symbol/formula symbol as int; returns the constant pyfastchem.FASTCHEM_UNKOWN_SPECIES if species does not exist.

float getElementAbundance(int species_index)

Returns the abundance of an element with int index species_index as float; returns 0 if the element does not exist

float [] getElementAbundance()

Returns the abundances of all elements as an array of float values; array has a length of getElementNumber()

setElementAbundances(float [] abundances)

Sets the abundances of all elements; the abundances are supplied as an array of float values, where the array has to have a size of getElementNumber(); if this is not the case, FastChem will print an error message and leave the element abundances unchanged

float getGasSpeciesWeight(int species_index)

Returns the weight of a gas phase species with int index species_index as float; returns 0 if species does not exist; for an element this refers to the atomic weight

float getElementWeight(int species_index)

Returns the atomic weight of an element with int index species_index as float; returns 0 if species does not exist

float getCondSpeciesWeight(int species_index)

Returns the weight of a condensate species with int index species_index as float; returns 0 if species does not exist

str convertToHillNotation(str formula)

Converts a chemical formula to the Hill notation that is used for the gas-phase species in FastChem. For example, H2O would be returned as H2O1. The conversion can also treat formulas with brackets, for example, Na(OH)2 or ions, such as Fe+ or Fe++. The latter two would be returned as Fe1+ and Fe1++, respectively. Higher ionsation stages are supported via ^, even though they are currently not included in the standard FastChem data files. For example, Fe^3+ would be returned as Fe1^3+.

int [] getGasSpeciesStoichiometry(int species_index)

Returns a vector with the stoichiometric coefficients of a gas-phase species with int index species_index ; array has a length of getElementNumber()

int [] getCondSpeciesStoichiometry(int species_index)

Returns a vector with the stoichiometric coefficients of a condensed-phase species with int index species_index ; array has a length of getElementNumber()

setVerboseLevel(int level)

Sets the verbose level of FastChem, i.e. the amount of text output in the terminal. A value of 0 will result in FastChem being almost silent, whereas a value of 4 would provide a lot of debug output. A value larger than 4 will be interpreted as 4. This value will overwrite the one from the FastChem config file.