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Add note about uncertainty to simulate.py documentation
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mliu49 committed Jun 4, 2019
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9 changes: 6 additions & 3 deletions documentation/source/users/rmg/modules/simulate.rst
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.. _simulate:

***********************************
Simulation and Sensitivity Analysis
***********************************
***********************************************
Simulation and Sensitivity/Uncertainty Analysis
***********************************************

For sensitivity analysis, RMG-Py must be compiled with the DASPK solver, which is done by default but has
some dependency restrictions. (See :ref:`License Restrictions on Dependencies <dependenciesRestrictions>` for more details.)
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the sensitivity analysis is conducted for. Sensitivities to thermo of individual species is also saved as semi normalized sensitivities
dln(C_i)/d(G_j) where the units are given in 1/(kcal mol-1). The sensitivityThreshold is set to some value so that only
sensitivities for dln(C_i)/dln(k_j) > sensitivityThreshold or dlnC_i/d(G_j) > sensitivityThreshold are saved to this file.

Uncertainty analysis can also be requested via input file options. For more details, see :ref:`uncertaintyanalysis`.
The results of the analysis will be printed in the ``simulate.log`` file which is generated.

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