Can anyone recommend a very basic book for someone who wants to understand LAMMPS molecular dynamics starting from scratch (material science and mechanical engineering perspective)?
There’s actually a section on the website with some:
https://www.lammps.org/books.html
I think the Allen and Tildesley one is certainly the most famous, but I own these two and found them helpful:
Understanding Molecular Simulation by Frenkel and Smit
Molecular Dynamics with Deterministic and Stochastic Numerical Methods by Leimkuhler and Matthews
Thank You
The search button is also helpful. Not to replace the books, but to show you that this questions has been asked countless times.
Some comments on this:
- There is just “molecular dynamics”. Whether you use LAMMPS or some other MD software, the physics and results are the same, only the way how you enter data and settings is different. So you need to distinguish between learning how to use as specific MD simulation software (in your case LAMMPS) for which you first and foremost have to revert to the manual and examples, and learning how to apply the MD methodology in general for which you need to look at text books, take classes, and practice with an experienced practitioner. You will learn best, if you had some training in classical mechanics and statistical thermodynamics. The latter is especially where people trained in engineering are struggling.
- From looking at your posts over the last few days, my recommendation is that you should first look for a book or similar that teaches you how to search the web, the forum archives, and the published literature to find answers and explanations to questions covering problems similar to those of your inquiries. Questions for recommended text books on MD have been asked and answered several times, for example, but also other issues that you have raised.
- I would also recommend to have a look at materials with suggestions how to ask for help in a more effective way. A classic document for that is this How To Ask Questions The Smart Way. While this focuses on software development, a lot is transferable to MD which is somewhere between pure software development and pure science. Your way of asking for help is not making it easy to help you and thus is wasting your energy and that of the people responding. If you don’t change your ways quickly, you will find that your questions will be responded to slowly or not at all.
- From looking at the types of problems you are struggling with, it seems to me that they can not so much addressed with text book knowledge (even though you will need this to master the topic sufficiently), but rather requires the in-person tutoring from an experienced practitioner in MD simulations. As far as I can tell a lot of your problems are of rather practical nature and a sign of bad planning and thus you are not likely to find much help in text books. Rather than approaching your goal in steps and slowly build your skills in MD simulations, you seem to be eager to jump ahead and immediately implement the full system. Unless you are an extremely gifted genius, this approach will lead to doom and insurmountable problems. Remember: to solve a problem properly, you first have to understand it. The the solution will be obvious or you can ask a well qualified question. Just adding or changing some command so that the symptoms disappear will not guarantee that the problem is solved.