Hello everyone,
I am new to the field of LAMMPS and MD simulation in general. Can anyone suggest a reliable open source software for building geometry other than LAMMPS and Material Studio? My eventual goal is to simulate tobermorite/jennite layer of structure with water layer in the middle. Currently, I am trying to build layers of graphite and water in one simulation box. I am using topotools in VMD to build the geometry but I couldn't control the number of atoms and also do not know how to merge to simulation box together.
Any help will be appreciated.
Hi Vinay,
I know we can build geometry with LAMMPS but It is quite a hassle when we want to build a complex system such as cement phases with water in the interlayer. That's why I was trying to find a tool which can be used to define only the structure of the system. Then we can read the structure file in LAMMPS for the simulation.
I recommend the python.ASE package. It has much better capabilities for building complex slabs than the built-in LAMMPS functions. It is however more of a scripting tool rather than a fancy WYSWIG editor, although you can display your system. It can save to .pdb which can be converted via topotools writelammpsdata to LAMMPS compatible files. If you are familiar with scripting (python knowledge not really needed) you could give it a try.
https://wiki.fysik.dtu.dk/ase/
I use with topotools the packmol package (http://www.ime.unicamp.br/~martinez/packmol/). You can see the possibilities in the input examples section.
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