# LAMMPS workflow
LAMMPS [home](https://lammps.sandia.gov/)
LAMMPS script [explanations](https://lammps.sandia.gov/doc/Examples.html) (example input scripts available in install directory)
### Creation of initial geometry files ([Avogadro](https://avogadro.cc/))
### Generation of geometry for LAMMPS script
- generate supercell from basic `.cif` crystal file using [*supercell*](https://orex.github.io/supercell/) software
- *supercell* [documentation](https://orex.github.io/supercell/doc/supercell_man.html#section_5)
- run input example:
`supercell -i input.cif -v 2 -s 2x2x2 -o output`
- generate `.xyz` file from `.cif` file generated by *supercell* using *cif2xyz*
- *cif2xyz* GitHub [repository](https://github.com/JJPPeters/CIF2XYZ/blob/master/main.cpp)
- run input example:
`cif2xyz input.cif -z angle_x,angle_y,angle_z -d dimension_x,dimension_y,dimension_z -o output`
- generate system and initial positions for *LAMMPS* script using [*packmol*](http://m3g.iqm.unicamp.br/packmol/download.shtml) software
- *packmol* [User's guide](http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml#radii)
- generate system in either `.xyz` or `.pdb` file format (other supported but not suitable)
- `.xyz` file (only positions, no bonds, unlimited system size)
- `.pdb` file (positions + bonds, 9,999 atoms system limit)
- input file [example](https://github.com/Fercik86/LAMMPS_NWChem_workflows/blob/LAMMPS/packmol/builder_example.int)
- run input example:
`packmol < packmol.inp`
- (optional) generate odd shaped models
- using *cutter.py* script
- cuts out along the specified axis or plane
- keeps/removes file either over or under axis/plane
### Visualizing generated system using [*OVITO*](https://www.ovito.org/) sotfware
Visualization done to check wheter the system was generated correctly and can be used as input geometry in *LAMMPS* script
### Generate *LAMMPS* input geometry .dat file using *OVITO* and *"swapper"*
- Import file to be exported to `.dat`
- Export to `.dat` using: `File > Export File > LAMMPS Data File` (Atom style **full** recommended)
- Use *"swapper"* to differentiate same atoms in different molecules (instructions on use in the script beginning)
### Writing *LAMMPS* input script
Any text editor can be used to edit *LAMMPS* input scripts.
[*Notepad++*](https://notepad-plus-plus.org/) is a better alternative to the default Notepad.
[*Visual Studio Code*](https://code.visualstudio.com/) is the recommended option.
[*LAMMPS* extentsion](https://marketplace.visualstudio.com/items?itemName=ThFriedrich.lammps&utm_source=VSCode.pro&utm_campaign=AhmadAwais) for VS Code makes writting *LAMMPS* scripts much easier thanks to the syntax highlighting, hover explanations, offline documentation and more.
### *LAMMPS* script example
(TBA)
((there are no easy examples))
### Running *LAMMPS* on Windows
Running in serial mode (1 core)

lmp_serial < in.file
--> will run in the console  

Running with MPI (multi-core)

mpiexec -n 4 lmp_mpi -in input.lmp -pk omp 2 -sf omp
--> will run in the console (4 cores, omp hyperthreading)  

### Visualizing results
- *LAMMPS* output file
- text editor
- `.lammpstrj` file
- *OVITO* [link](https://www.ovito.org/)
### Processing of results
- Calculating Diffusion coefficients via MSD (mean square displacement) from `.lammpstrj` file
- using *"bestScript"* [link](https://github.com/ErikPitko/lammps-parser)
- calculation of x_MSD, y_MSD, z_MSD, combined_MSD of each selected atom type
- MSDs are plotted against time
- Diffusion coefficient is obtained as slope of initial linear part of the diffusion curve
- Based on the work of David Keffer [ref](http://www.utkstair.org/clausius/docs/che548/pdf/selfD.pdf)
- Visualising trajectories from `.lammpstrj` file
- using *"bestScript"* [link](https://github.com/ErikPitko/lammps-parser)
- generation of coordinates in each timestep for each selected atom type
- Coordinates are plotted against time to obtain 3D trajectory
- [script](https://github.com/Fercik86/LAMMPS_NWChem_workflows/blob/LAMMPS/OriginPro_scripts/origin_scripts.txt) for *OriginPro* to change columns to X1 Y1 Z1; X2 Y2 Z2;...

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