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A Python-based tool to automatically generate LAMMPS configurations and input files for polymer-solvent systems with optional crosslinking and crowding effects.
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33
commits
Refactor file handling: extract LAMMPS input and XYZ writing functions into separate modules
d54c95cView on GitHubBegan the extraction of file writers from the ParticleSystem class into separate functions.
912e614View on GitHubFixed max random seed for langevin. Added the possibility to generate random initial velocities for the atoms (disabled by default)
5d6ddb4View on GitHubFixed random generator. Selected random seed for Langevin thermostat
8650e33View on GitHubAdded the possibility to change the mass of the spheres. Slightly modified json structure
297ee1bView on GitHubAdded the possibility to choose restart file frequency. Fixed the naming of new lamppstrj files if restarting a simulation. Moved restart files in restarts folder
42d8fe4View on GitHubMerged addColloids and addSolvent functions into a generic addSpheres function.
a65d923View on GitHubMoved the generation of the input file in the ParticleSystem class. Defined functions for generate_polymers and generate_input, together with main functions. Created main.py to run the tool with one terminal command
62197dbView on GitHubAdded argparse to parse parameter file name from comand line.
ac98baeView on GitHubFixed minor error on atomList for patches. Minor change on generate_input
e28c414View on GitHubUpdated Particle System class, moved the system creation from generate_polymers.py into the particle system class.
52fff05View on GitHubAdded .gitignore. Separated saveXYZ function in another file. Started the implementation of ParticleSystem.
64796d8View on GitHub