AutoMapper is a package of tools designed to automate the creation of files required for the LAMMPS command fix bond/react. The tools allow the user to convert LAMMPS input files into molecule format files and an automatically generated a map file of a reaction. AutoMapper will reduce these files to the smallest possible partial structure without any additional user input. AutoMapper should work with any valid LAMMPS input file, though was designed to work with Moltemplate output files so users may find it easier to use these packages together. AutoMapper is completely forcefield independant so users are free to use any forcefield they wish. Any problems encountered while using AutoMapper should be raised in the Issues section where they will be addressed as quickly as possible. For a full tutorial and annotated walkthrough, see the manual. An in depth overview of how AutoMapper works can be found in the journal article in Computational Materials Science. If you use AutoMapper in your research, please cite this work in your publications.
AutoMapper was originally built for LAMMPS versions 29Oct20 but is being updated for new versions of REACTER. It has the capability to handle create atoms and should work with new type ID strings: both of these features were added in the 29Sept21 version. The depreciation warning caused by using Bonding IDs instead of Initiator IDs can be ignored for now.
AutoMapper is now being maintained by Molydyn as part of our efforts to make computational chemistry more accessible, and help drive materials discovery through simulation. More details can be found on our website, where you can try out Atlas, our sister tool to AutoMapper, designed to be the simplest way of setting up a LAMMPS simulation.
All tools are accessible through AutoMapper.py. They are:
clean: Unify the types (e.g. Atom, Bond, Angle, etc.) between two or more files and remove unused coefficients.molecule: Convert a LAMMPS input file to the LAMMPS molecule file format.map: Create pre- and post-bond molecule files and a map file, the full requirements for usingbond/react.
AutoMapper.py can be called from the command line with arguments for user control. It is recommended to put this downloaded repository on your PATH so that AutoMapper.py can be called from your modelling directories. Use AutoMapper.py -h for a full description of the arguments or see the manual for more details. A full Example Workflow is available within the repository which walks through the use of AutoMapper within a Linux environment.
Below are command line examples for the different tools.
AutoMapper.py . clean pre-reaction.data post-reaction.data --coeff_file system.in.settings
AutoMapper.py . molecule cleanedpre-reaction.data --save_name pre- --ba 1 4
AutoMapper.py . map cleanedpre-reaction.data cleanedpost-reaction.data --save_name pre-molecule.data post-molecule.data --ba 2 5 3 7 --da 1 8 1 8 --ebt H H C C N O O
AutoMapper requires Python 3.6+ and the third party Python module natsort to run.
These tools have been built for the LAMMPS atom style 'full'; results with other atom styles may vary.
For the clean tool pair coefficients must be defined with numbers and not use wildcards (*).