Part of the package is a set of small tools that help with preparing input for post-processing. What they do is to parse output files and prepare intput files according to this format. If you understand the format (and it is not particularly complicated), it is easy to generate a parsing script for any code. The minimal requirements are positions, forces and energies. Other quantities are there mostly for reference, and can safely be set to zero.
The scripts process_outcar.py and process_outcar_5.3.py are used to extract information from VASP OUTCAR files. The usage is straightforward:
process_outcar_5.3.py OUTCAR
This will create the relevant input files. Alternatively, is you used some statistical sampling method and have many VASP simulations that need to be stitched together, use
process_outcar_5.3.py *OUTCAR
That is, the script takes any number of OUTCARs as argument. The script assumes you have used ISIF = 2, since without it forces don't get written.
Get Antoine to send me his script.
LAMMPS does not write anything by default. To get usable output, I make sure to add the following to the input file:
units metal variable st equal step variable tm equal step variable Et equal etotal-v_baseline variable Ep equal pe-v_baseline variable Ek equal ke variable tmp equal temp variable pr equal press/10000 variable sxx equal pxx/10000 variable syy equal pyy/10000 variable szz equal pzz/10000 variable sxy equal pxy/10000 variable sxz equal pxz/10000 variable syz equal pyz/10000 fix statdump all print 100 "${st} ${tm} ${Et} ${Ep} ${Ek} ${tmp} ${pr} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" screen no file dump.stat dump posdump all custom 100 dump.positions xs ys zs dump forcedump all custom 100 dump.forces fx fy fz dump_modify posdump format "%20.15e %20.15e %20.15e" dump_modify forcedump format "%20.15e %20.15e %20.15e"
The frequency of the dumps and so on can of course be adjusted. Make sure you use generate structure to create the LAMMPS cell file, since it will also create structure input files in the format TDEP needs. These dump files are not exactly the correct format. A small script can rearrange it to the correct format:
#!/bin/bash # figure out how many atoms there are na=`head -n 4 dump.forces | tail -n 1` # remove the header from the stat file grep -v '^#' dump.stat > infile.stat # figure out how many timesteps there are nt=`wc -l infile.stat | awk '{print $1}'` # create the positions and force files [ -f infile.forces ] && rm infile.forces [ -f infile.positions ] && rm infile.positions for t in `seq 1 ${nt}` do nl=$(( ${na}+9)) nll=$(( ${nl}*${t} )) echo "t ${t} ${nl} ${nll}" head -n ${nll} dump.forces | tail -n ${na} >> infile.forces head -n ${nll} dump.positions | tail -n ${na} >> infile.positions done
There are probably far better ways of doing this, happy to take any suggestions.