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[lammps-users] fix_bond/react

From: Jacob Gissinger <Jacob.Gissinger@...780...>
Date: Thu, 19 Apr 2018 10:06:56 -0600

Dear Jake,

Thank you very much, the example files now run. From the examples it is fairly clear how to setup the molecule templates and the reaction map files, I only have a few questions to ask concerning setting up a new type of reaction. Is there maybe documentation explaining the work of these files?

yes, you can currently find the doc page at /doc/src/fix_bond_react.txt (in the pull request)

also, I would definitely be interested in feedback about the clarity of the doc page

In case not, let me just list the couple of questions I have:

- What is the role of the equivalences section in the map file?

this relates each atom in the pre-reacted template to its corresponding atom in the post-reacted template (using template IDs). in my experience of modifying molecule templates, 'atom 1' of the pre-reacted template usually corresponds to 'atom 1' of the post-reacted template, but this might not always be the case
- In the data template, what is the purpose of the Coords section, and what configuration is expected to be given using the coordinate values?

bond/react ignores the 'coords' section of molecule template files
- In case of reaction, is there a way to output or access the IDs of the atoms that have reacted?

no, but this could be an interesting feature request. what would be your use for this? currently, you could dump the bond topology or atom types and search for changes

Thank you in advance and regards, Mark.