This tool generates a data file for LAMMPS simulations of molecular systems starting with an atomistic structure.
- Accepts a wide range of input formats (e.g. CIF, PDB, XYZ)
- Works with periodic boundary conditions, even when covalent bonds cross boundariesThe tool uses OpenBabel to convert the initial files
- Sets up energy expression for Dreiding and PCFF force fields (including automatic bond recognition and atom typing)
- Assigns atomic changes using the Gasteiger method
Known bug: If resonance ring crosses the boundary, atoms will be incorrectly
Please be aware of the requirements specified below, before running struc2lammps. If ready to run, then follow the instructions:
- Specify the input arguments in input.args
- Initial structure (can be added in ./data/)
- If box parameters are not included in the initial structure please edit the box.txt file (include cell dimensions and angles)
- Bondscale parameter for connectivity identification (scaling sum of covalent radii of bonded atoms)
- Force field. Currently supporting Dreiding and PCFF
- run
python str2lmp.py - Just wait! You should see a LAMMPSDataFile.data once if finishes.
The data file provides pair coefficents in LJ (12/6) form but you will obtain a extra file with Buckingham potential (exp/6)
In order to sucesfully run struc2lammps and obtain a data file you must have:
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Properly installed OpenBabel with python bindings. Remember that struc2lammps only works with file formats currently supported by OpenBabel.
For more information about installing python bindings you can visit: https://openbabel.org/docs/dev/Installation/install.html#compile-bindings or https://pypi.org/project/openbabel/
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You also need to have installed OVITO. This is particularly important if your structure is not orthogonal. You will be prompted to specify the location of your OVITO’s Python interpreter. Information about where to find the ovitos script can be found here: https://ovito.org/manual/python/introduction/running.html
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LAMMPS must be installed (using executable
lmp)