MDS

Happy New Year 2013!!! PACKMOL, Chunks, Molecules & LAMMPS

I found an embarrassing bug in PACKMOL. Actually, in the modifications I made to PACKMOL. How could this happen? Writing software is not glamorous and often thankless. At the best of times the user should get their work done and at the worst of times the user is ready to fire the programmer! Software is defined as "code, data and documentation maintained in a specific configuration." I have a software engineering book that explains this. Explicit requirements for software are code, data and documentation. The implicit requirement is the former are maintained in a specific configuration. Sadly, I lost configuration! I had fixed this problem a while back and lost the changes. I have been working behind the scenes to build a better infrastructure to prevent this. I will soon host all my source code on Dropbox. I will have a directory structure on Dropbox and point my development tools at Dropbox. Of course this sounds silly to many software engineers. Why didn't I just host my project on github and forget about Source Forge? Why am I not using state of the art development practices? I will change my evil ways once this project attracts additional software developers and collaboration becomes critical. As of this writing, the software is alpha and in need of additional developers who want to own this project.

Back to the bug I found. My modified PACKMOL reads and writes molecular machine part (MMP) files. This is a file format created by the NanoEngineer-1 molecular CAD application. I misplaced memory location of the molecule templates for all molecules after correctly processing the second molecule template. I also created a phantom molecule in the MMP file. I fixed this bug as well. Now the MMP file created by PACKMOL assigns a "chunk" to every molecule. What is a chunk? A chunk is a concept from NanoEngineer-1. It identifies one or more atoms. When you click on a chuck identifier inside the NE-1 CAD program the collection of atoms are highlighted in green. You can now move the entire chunk around on the screen. The funny thing is that the "mol" token is used in the MMP file to define a chunk. Someone must have originally wanted to make a chunk a molecule, but that did not happen completely. NanoEngineer-1 creates chunks willy-nilly. There can be one or more atoms in a chunk. A single molecule drawn in NanoEngineer-1 can contain many chunks as you create atoms as well as copy and paste existing atoms in order to save time drawing a molecule.

When using NanoEngineer-1 the user must enter "Chunks" mode by clicking the chunks button. Upon existing chunks mode one can see the tree of chunks down the left-hand-side of the application. Again, clicking on one or more will highlight the chunks in the canvas showing the chunks in the molecule drawn. Selecting more than one chunk is done by holding down the shift button and clicking on the chunks in the tree. Looking at the icon menubar one sees an icon of three green squares and a black arrow pointing to a single green rectangle. The tooltip tells you this is a chunk combiner tool. If you use this tool to combine chunks into a single chunk then all combined chunks will be highlighted. This is important in using LAMMPS!

LAMMPS has built into it the concept of a group-ID. This is a way to identify a group of atoms. For my purposes a group would be a molecule such as a water molecule floating around in a polymer matrix. LAMMPS also supports a full atom model. The model includes a molecule ID on every atom of a simulation.    The molecule-Id can be used as a group-ID. One can parse LAMMPS output files for specific molecules and use trajectory data to create a path a molecule travels over the course of a simulation. In order to get this molecule data to LAMMPS correctly from NanoEngineer-1 and PACKMOL you need to follow some simple rules:

1. Draw a single molecule per MMP file you create inside NanoEngineer-1. Once you have your single molecule completely drawn then combine the chunks into a single chunk.
2. Let PACKMOL create your initial MD cell from multiple MMP files. The MMP file processing in PACKMOL will uniquely identify all molecules created from the MMP files.
3. MSI2LMP reads and understands the chunks in the MMP file created by PACMOL and will assign unique molecule-IDs to all molecules when it creates the LAMMPS Geometry Input File.

I hope the fixes to PACKMOL and this discussion about chunks and molecules help you in creating successful MD cells. I have seen many downloads to date, but have not received many, three, comments back. Open source is about helping people be successful by making quality software. I look forward to comments, and feature suggestions. PACKMOL should create quality MD cells from many molecules now.