Dear all
I hope this message finds you well. I am currently working on molecular dynamics simulations using LAMMPS and have encountered an issue related to setting up bond interactions. I have consulted the paper and found the appropriate bond_style (harmonic) and the required parameters for each bond. However, I am facing difficulties in determining the correct order (as illustrated in the diagram below, labeled as 1, 2, 3).
I would like to inquire if there are any specific rules or guidelines for setting the order of bonds in LAMMPS. Currently, my workaround involves exporting a data file from MS software and manually arranging the bonds in the desired order, which doesn't seem ideal.
Any advice or guidance on establishing the correct bond order in LAMMPS would be greatly appreciated. Thank you for your time and assistance.
Best reards
Lin Jinghua
I always do it by starting from one side of the structure and move to the next bond and so on. I don’t see problem as long as you are named your atoms correctly and you linked them to the right type.
There is no straitforward way. You can do in in any order you like as long as the bond parameters mach with the bonds of the structure. A really nice new feature of LAMMPS (version 2022 and newer) is the capability of giving bond types (like 1, 2, 3 etc.) a name so you keep track what is what within a simulation and a forcefield. Im pasting a link to the corellated documentation
https://docs.lammps.org/Howto_type_labels.html
https://docs.lammps.org/read_data.html
Hope this helped!
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