Visualization challenge LAMMPS

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LAMMPS -visualization challenge dataset-running free energy perturbation (FEP)using LAMMPS

We uploaded a trajectory file obtained from LAMMPS calculation, you can see a coordinate file, (included data.lmp file), dump.lammpstrj file, a molecular dynamics trajectory (can be loaded in VMD directly). In addition to a picture you can make an animated file for submission.

Challenge:

To win a visualization competition, we would like you to make an aesthetically pleasing and scientifically meaningful picture or animation. You can use one single plot or combine multiple plots using your favorite tools.

Theoretical details must READ and understand before running Calculations

Free Energy perturbation (FEP) using LAMMPS -How LAMMPS Calculate FEP

http://lammps.sandia.gov/doc/compute_fep.html

For general theory, look at wikipedia page

https://en.wikipedia.org/wiki/Free_energy_perturbation

For original github example (this package is installed in LAMMPS as a USER package)

https://github.com/agiliopadua/compute_fep

For example directory

https://github.com/agiliopadua/compute_fep/tree/master/examples/USER/fep/CH4hyd/fep10

A guide to better visualization

http://lammps.sandia.gov/tutorials/italy14/VMD_Visualization_Scripting_TopoTools.pdf

Things to remember

Free energy perturbation is not a single calculation, it is the difference between two calculations, we added two input LAMMPS files here, but only one used for calculation. An accopanied python script is also present "fep.py" taken from github repository reffered above.

The free-energy profiles can be observed by plotting the values in the third column (fep10.lmp) of the results files. The Python script, fep.py can be used to calculate the free-energy differences (T=300 K)

fep.py 300 < fep01.lmp 
fep.py 300 < fep10.lmp

VMD models


Model New Results

Software Used

LAMMPS

LAMMPSlogo.png

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis.



Using LAMMPS on Kogence

Using LAMMPS on Kogence

You can either fork and modify an existing LAMMPS public project or alternatively you can also start from scratch and create a new LAMMPS project.

  • In order to fork an existing project
    • Make sure you fist click "Copy" button to create a personal copy to modify.
    • Then click Settings -> Machine to choose a machine and
    • Click Settings -> Software and choose LAMMPS from the dropdown menu. In the empty text box, type the name of the input script.
  • In order to create a new project from scratch
    • Click on Model Library -> My Models
    • Click on + button on top left corner. Provide name and short description for your new project.
    • Click on + button again in the next project screen and either create or upload an existing LAMMPS input file.
    • Click Settings -> Software and choose LAMMPS from the dropdown menu. In the empty text box, type the name of the input script.
  • Access to command terminal with installed LAMPPS environment
    • Click Settings -> Software and choose LAMMPS from the dropdown menu. In the empty text box, type "xterm" (without quotes).

To see detailed step-by-step instructions on how to use LAMMPS on Kogence free cloud supercomputing platform [click here].

LAMMPS Versions on Kogence

  • 11 Aug, 2017 (runs with only MPI threads and no openMP threads even on single node)
  • 31 Mar, 2017 (runs with openMP threads on single node)

For more details see LAMMPS .