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FENE Dimer : Mango-Selm data files and LAMMPS scripts

This is a tutorial from a previous version. For current and additional examples, see GitHub: mango-selm

Quick Start:

  • This example can be found in ./USER-SELM/example/FENE_Dimer/ of the package.
  • Quick start is to use ./run.sh, visualization using VMD with ./vis_vmd.sh

Details: To setup simulations directly in LAMMPS to use the Mango-Selm package the command "fix SELM paramFile.SELM_params" is called in the LAMMPS script. The file paramFile.SELM_params can be considered the "master file" playing for the SELM package a role coordinating the package behavior analogous to the LAMMPS script. All of the SELM package settings are controlled through XML files of the form *.SELM_* . These give the settings for the Eulerian degrees of freedom (solvent fluid), the Lagrangian degrees of freedom (particles), and how they are coupled.

The FENE dimer example files can be found below

  • FENE_Dimer.LAMMPS_script
  • FENE_Dimer.SELM_params
  • FENE_Dimer.LAMMPS_read_data
  • Particles.SELM_Lagrangian
  • LAMMPS_SHEAR_QUASI_STEADY1_FFTW3.SELM_Integrator
  • LAMMPS_SHEAR_UNIFORM1_FFTW3.SELM_Eulerian
  • CouplingOp.SELM_CouplingOperator

To perform simulations with the SELM Fluctuating Hydrodynamics thermostat the simulation is run with the command

"./lmp_XXX -in FENE_Dimer.LAMMPS_script"

Replace ./lmp_XXX with your name for the LAMMPS compiled binary.

The results can be visualized in VMD or other packages using the DCD file output or VTK files. See the visualization files and auxiliary scripts provided in the example directory.

The complete set of scripts and data files for the FENE Dimer example can be found in "USER-SELM/example/FENE_Dimer/". See downloads page.

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Page last modified on May 18, 2021, at 07:06 pm


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