#############################
####   Initialization   #####
#############################

# bulk STO
units         metal   # Angstroms, femtoseconds, eV
atom_style    charge
boundary      p p p



###############################
###    Run a simulation    ####
###############################


shell rm -f energy.dat
shell rm -f energy
shell rm -f positions

label loopb
variable index loop 8207

      read_restart  restart_dislocation.*

      kspace_style     pppm 1e-4

      thermo         10 #Output every 10 steps thermodinamic quantities
      thermo_style   custom step temp vol press pe lx fmax atoms cpu

      set type 1 charge 1.84
      set type 3 charge -1.4

      variable energy equal 'pe'
      variable energy2 equal 'etotal +1934998.63'

      shell head -${index} id.dat > head.dat
      shell tail -1 head.dat > tail.dat
      variable number file tail.dat
      variable oxygen equal next(number)
      group oxygen_vacancy id ${oxygen}
      variable oxygen delete

      dump           1 oxygen_vacancy custom 1 test.*.xyz x y z

      run 0 

      undump         1


      delete_atoms group oxygen_vacancy
      set type 2 charge 2.3599463190
      minimize 0.0 0.05 1000 100000

      shell echo ${index} ${energy} >> energy.dat

      shell tail -1 test.2135.xyz >> positions
      shell echo ${energy2} >> energy

#      dump           2 all cfg 1 positions_${index}.*.cfg mass type xs ys zs 
#      dump_modify    2 element Mg Ti O
#     run 1

      clear

next index
jump STO.in loopb

shell paste positions energy > partial.pdb

shell wc -l positions > pdbconverter.inpt
shell ~/bin/pdbconverter