#############################
####   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

variable number file id.dat

label loopb
variable index uloop 8170
variable number2 equal next(number)

      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 'pe +1934998.63'

      group oxygen_vacancy id ${number2}
#      shell echo ${number}

      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.2248.xyz >> positions
      shell echo ${energy2} >> energy

      clear

next index 
jump STO.in loopb

#shell paste positions energy > partial.pdb
#shell wc -l positions > pdbconverter.inpt
#shell ~/bin/pdbconverter