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Updates and additions to Pt(111) adsorption correction tree#717

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kirkbadger18 wants to merge 7 commits intoReactionMechanismGenerator:mainfrom
kirkbadger18:NOx_adscor_data
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Updates and additions to Pt(111) adsorption correction tree#717
kirkbadger18 wants to merge 7 commits intoReactionMechanismGenerator:mainfrom
kirkbadger18:NOx_adscor_data

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@kirkbadger18
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I have taken the thermodynamics data from the new and existing species in the Pt(111) thermodynamics library and updated the adsorption corrections for Pt(111). The new workflow was used as described here. To build these adsorption corrections I used the data and python scripts in the following folder:

thermo_PR_data.zip

There are 4 sources of changes to existing nodes.

  1. I got rid of the nodes which were so descriptive that they could only describe one species that we already have in the thermolibrary (*CO, *N, *C, *O).
  2. The higher level nodes now average over some of the nitrogen species, so they will change
  3. The previous script for computing the gas phase enthalpy and constant pressure heat capacity treated the enthalpy as equal to the internal energy, and it treated the constant pressure heat capacity as equal to the constant volume heat capacity, I have changed this by adding RT and R to get to the right value.
  4. The old scripts had a bug where they struggled to identify species being linear, so some linear species like HCO had their enthalpy change by RT and also due to not assigning it as linear before.

In addition to the changes to existing nodes, new nodes were added to handle new types of chemistry in the new nitrogen species. The new trees can be visualized by the following images:
thermo_tree_bidentate_N
thermo_tree_monodentate_N
thermo_tree_vdW

…istry and to resolve bugs in computing the values previously
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