Bjarne Kreitz

Species labeling in the output doesn't work properly

3

### Bug Description When generating mechanisms for surface reactions, there is a bug in the naming of the species in the output file. RMG used to replace the SMILES string...

adding resonance for adsorbates

12

### Motivation or Problem Adsorbate molecules can exhibit resonance similar to gas-phase molecules. For example, the bidentate adsorbate XCXC (where X is a surface site) has the following three configurations:...

update Pt111 library

11

**Update of the thermo library** The previous surfaceThermoPt111.py database was a mixture of VASP and QE calculations. The usage of different electronic structure codes with slightly different settings resulted in...

Remove reaction path degeneracy adjustments in surface families

7

**Description** In our last RMG-Cat meeting, we extensively discussed the concept of reaction path degeneracy and whether we should consider this for surface reactions, too. In the general catalysis community,...

Remove duplicate reaction family

2

**Update** The reaction family `Surface_Addition_Single_vdW` is the reverse reaction of `Surface_Dissociation_Beta_vdW`. There is no need to have both families. I removed the `Surface_Addition_Single_vdW` family since we have BEP rate rules...

**Issue** This is technically not an issue, but I want to start a discussion about reaction path degeneracy for heterogeneously catalyzed reactions. When RMG discovers a reaction and applies a...

Vd w bonds

10

### Motivation or Problem There are a couple of species that we currently cannot handle in RMG when generating mechanisms for heterogeneously catalyzed reactions, because we have no way to...

make adsorptionPt111 more flexible with lone pairs px

2

**Description** The nodes in the adsorption correction file adsorptionPt111.py were rather restrictive. In most nodes it was specified that the general`R` cannot have lone pairs `p0`. I didn't pay close...

Check for adsorbates in resonance structure generation

10

### Motivation or Problem @kirkbadger18 observed an issue when generating mechanisms with adsorbates that contain N atoms. RMG seems to generate species that have formal charges, although the reaction templates...

### Bug Description When generating a mechanism with RMG for a surface catalyzed reaction, RMG does not accurately convert the SMILES string of some species to the label. See the...