isotopes/std isotopes/std

isotopes/std isotopes/std#

Description#

isotopes transform: legacy two-isotopologue isotopic ratio transform.

This is an earlier, simpler version of the conc2ratio / ratio2conc pair, restricted to exactly two isotopologues (one signature and one reference species).

Given a signature δ-value and a total concentration, the forward pass computes:

\[ \begin{align}\begin{aligned}a = \left(1 + \frac{\delta}{1000}\right) R_{std}\\[iso_1] = \frac{C_{tot}}{1 + a}, \quad [iso_2] = \frac{C_{tot} \cdot a}{1 + a}\end{aligned}\end{align} \]

The adjoint propagates isotopologue sensitivities back to δ and total concentration sensitivities.

The transform also exposes native2obsvect and obsvect2native functions for converting between the model’s native representation and the observation vector format used by the legacy isotope pipeline.

Note

For new applications, prefer conc2ratio / ratio2conc which handle an arbitrary number of isotopologues.

YAML arguments#

The following arguments are used to configure the plugin. pyCIF will return an exception at the initialization if mandatory arguments are not specified, or if any argument does not fit accepted values or type:

Optional arguments#

parameter : str, optional

Parameter name on which the transform works on

component : str, optional

Component name on which the transform works on

orig_parameter_plg : Plugin, optional

Plugin object on which the transform works on

orig_component_plg : Plugin, optional

Corresponding component object on which the transform works on

successor : str, optional

Name of the successor transform

precursor : str, optional

Name of the precursor transform

YAML template#

Please find below a template for a YAML configuration:

 1transform:
 2  plugin:
 3    name: isotopes
 4    version: std
 5    type: transform
 6
 7  # Optional arguments
 8  parameter: XXXXX  # str
 9  component: XXXXX  # str
10  orig_parameter_plg: XXXXX  # Plugin
11  orig_component_plg: XXXXX  # Plugin
12  successor: XXXXX  # str
13  precursor: XXXXX  # str

See also

API reference (functions & code)