/PyScripts

Primary LanguagePythonMIT LicenseMIT

PyScripts

  1. lammpsdata2xyz.py: it can convert the lammps data file to .xyz or .lammpstrj files
  • command example:
lammpsdata2xyz.py xxx.data
  • Here, there should be a "# element" behind every mass in lammpsdata
  1. msi2clayff.py: it can convert the obtained hydroxylated SiO2 lammps data from msi2lmp.exe tool to lammps data with clayff force fields
  • command example:
msi2clayff.py xxx.data
  1. png2tif.py: it can convert the png to tif
  • command example:
png2tif.py png_name tif_name fig_quality
  1. outputTraj_N_Frame.py: it can out put the lammpstrj file, any frame
  • command example:
outputTraj_N_Frame.py  ./xxx.lammpstrj 0 10 ./output.lammpstrj
outputTraj_N_Frame.py  ./xxx.xyz 0 10 ./output.xyz
  1. sort_trj.py: it can sort lammpstrj file, according to the "id, mol, or type"
  • command example:
sort_trj.py  ./xxx.lammpstrj "id"
sort_trj.py  ./xxx.lammpstrj "mol"
sort_trj.py  ./xxx.lammpstrj "type"
  1. pdb2xyz.py: it can convert the pdbfile to xyzfile
pdb2xyz.py ./xxx.pdb
pdb2xyz.py ./xxx.pdb xxx.xyz
  1. figures to gif file
fig2gif.py [figs_path] [gif_file] [duration]
fig2gif.py ./2d/ output.gif 1
  1. convert lammpstrj file to a trjfile of meet HTR
to_HTR_lammpstrj.py -h
to_HTR_lammpstrj.py -i input.lammpstrj -o output_HTR.lammpstrj -fr 1 2
  1. combine files to a file
combine_files.py ./temp/ traj_npt_dissociation_330_1.lammpstrj

Dependencies

pip install -r requirements.txt

make scripts to read

bash ./scripts/chmod.sh