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Molecular Dynamics Simulations LAMMPS Input Scripts

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Molecular Dynamics simulation input files

Required packages:

Simulation template files:

  • header.LAMMPS: contains unit conversions and constants, atomic data and simulation state parameters
  • system.in.groups: contains solid and fluid group definitions (based on type) as well as the partitioning of the solid into upper and lower surfaces. It also contains a description of the dynamic pump group (in case of NEMD simulation)
  • system.in.init: contains the initialization setup (pair_style and atom_style for LAMMPS)
  • system.in.loadUpper: stores the forces on the upper and lower wall before loading, also performs the loading on the upper wall, with the barostat described here (Tribol Lett (2010) 39:49–61)
  • system.in.settings: contains the force field parameters for the fluid as well as LJ parameters for the solid
  • system.in.run: contains the simulation instructions (equilibration, NEMD, etc.) as well as writing the thermodynamic output and the NetCDF trajectory.
  • system.in.virial: samples the virial pressure calculation (along with the Voronoi volumes) during the simulation.

Workflow:

  1. Initialize: Run the python module initialize_walls (located in home/tools/md) in equilib/data/moltemp with the positional arguments.

  2. Equilibrate: The equilibration is performed by submitting as a batch job in the equilib.

  3. Load: The output LAMMPS data file data.nvt from the equilibration step equilib/out is copied to the input of the loading load/blocks.

  4. Flow: Now the final part in the MD calculation is to induce a flow on the atoms/molecules. This is performed either by simulating a pressure gradient or shearing or both.

  5. Post Processing: The trajectories file format is based on the NetCDF (Network Common Data Form) developed by Unidata. The NetCDF trajectories can be analysed at any stage of the simulation process by netCDF4 which is a Python interface to the netCDF C library.

  6. Plotting

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