qGA

#!/bin/bash

##  Basics: Number of nodes, processors per node (ppn), and walltime (hhh:mm:ss)
#PBS -l nodes=4:ppn=8
#PBS -l walltime=20:00:00
#PBS -N GA_Mo-adatom-4O
#PBS -A cnm29902

## File names for stdout and stderr.  If not set here, the defaults
## are <JOBNAME>.o<JOBNUM> and <JOBNAME>.e<JOBNUM>
#PBS -o vasp.out
#PBS -e err.out

## send mail at begin, end, abort, or never (b, e, a, n)
#PBS -m a

# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR

# count allocated cores
NPROCS=`wc -l < $PBS_NODEFILE`

# start MPI job over default interconnect

here=`pwd`
Npop=10 # Number of individuals in population
Nfit=10  # Number of fittest individuals
NG=4    # Number of generations to run
NO=4    # Number of oxygen atoms
H=0.20  # Height of oxygen atoms, in reduced coordinates
M=0.2   # Mutate rate
minD=1.5  # Minimum distance between atoms, in angstroms


# Run initial batch 
# DAN NOTE: POTENTIAL PARALLELIZATION POINT  
  g=0
  mkdir $here/G$g

  for n in `seq 1 $Npop`
  do
    mkdir $here/G$g/S$n
    cd $here/G$g/S$n
    cp $here/INCAR .
    cp $here/KPOINTS .
    cp $here/POTCAR .
    D=1
    while [ $D -gt 0 ]; do  # Keep making random POSCARs until minimum distance requirements are satisfied
      sed -n '1,5p' $here/POSCAR > POSCAR
      NAtoms=`sed -n '6p' $here/POSCAR`
      echo $NO $NAtoms >> POSCAR
      echo Selective Dynamics >> POSCAR
      echo Direct >> POSCAR
      for m in `seq 1 $NO`
      do 
        X=`echo $RANDOM | awk '{ printf "%20.14f", $1/32767 }'`
        Y=`echo $RANDOM | awk '{ printf "%20.14f", $1/32767 }'`
        echo $X $Y $H T T F >> POSCAR
      done
      sed -n '9,$p' $here/POSCAR >> POSCAR
      D=`convasp -dist $minD < POSCAR  | sed -n '6,$p' | sed '/^[0-9]/d' | wc | awk '{ print $1 }'`
    done
    # Run calculations
    mpirun -machinefile $PBS_NODEFILE -np $NPROCS vasp
    rm CHG
    mkdir FixedZ
    cp * FixedZ
    # Allow O z coordinate, and top Pt/Mo atoms to relax
    mv CONTCAR POSCAR
    sed -i '10,13s/F/T/' POSCAR  # O
    sed -i '14s/F/T/g' POSCAR    # Mo
    sed -i '17,19s/F/T/g' POSCAR # Pt
    mpirun -machinefile $PBS_NODEFILE -np $NPROCS vasp
    rm CHG
  done

# Evolve
# DAN NOTE: POTENTIAL PARALLELIZATION POINT
  dE=1000
  while [ $g -lt $NG ]; do

  # fittest individuals in all generations

    # check all energies
    for i in `seq 0 $g`
    do
      for n in `seq 1 $Npop`
      do
        cd $here/G$i/S$n
        E=`grep "free  e" OUTCAR | tail -n 1 | awk '{ print $5 }'`
        D=`grep -c "Total CPU" OUTCAR`
        echo $i $n $E $D  >> $here/Results$g.txt
      done
    done
    cat $here/Results$g.txt | sort -n -k3 | head -$Nfit > $here/BestG$g.txt
    EBest=`head -1 $here/BestG$g.txt | awk '{ print $3 }'`

    # create parent POSCARs in new generation
    mkdir $here/G$((g+1))
    for n in `seq 1 $Nfit`
    do
      ig=`sed -n "$n p" $here/BestG$g.txt | awk '{ print $1 }'`
      is=`sed -n "$n p" $here/BestG$g.txt | awk '{ print $2 }'`
      cat $here/G$ig/S$is/CONTCAR | sed '/O/d' > $here/TMP
      convasp -incell < $here/TMP > $here/G$((g+1))/CONTCAR$n
    done
    g=$((g+1))

  # create offsprings
    for n in `seq 1 $Npop`
    do
      mkdir $here/G$g/S$n  
      cd $here/G$g/S$n

      D=1
     while [ $D -gt 0 ]; do  # Keep making POSCARs from previous generation until minimum distance requirements are satisfied

        # choose parents
        P1=`echo $RANDOM $Nfit | awk '{ printf "%d", $1/32767*$2+1 }'` 
        P2=$P1
        while [ $P1 -eq $P2 ]; do
          P2=`echo $RANDOM $Nfit | awk '{ printf "%d", $1/32767*$2+1 }'`  
        done

        # choose x or y 
        XorY=`echo $RANDOM | awk '{ printf "%d", $1/32767*2+1 }'`
        echo $P1 $P2 $XorY > LOG
 
        # combine parents
        O1=`sed -n '9,10p' $here/G$g/CONTCAR$P1 | sort -n -k$XorY | sed -n '1p' | awk '{ print $1, $2, $3 }'`
        O2=`sed -n '9,10p' $here/G$g/CONTCAR$P2 | sort -n -k$XorY | sed -n '2p' | awk '{ print $1, $2, $3 }'`
        # mutate
        MN=`echo $M 32767 | awk '{ printf "%d", $1*$2 }'`
        S=`echo $RANDOM`
        if [ $S -lt $MN ]; then
          x1=`echo $RANDOM | awk '{ print $1/32767 }'`
          y1=`echo $RANDOM | awk '{ print $1/32767 }'`
          x2=`echo $RANDOM | awk '{ print $1/32767 }'`
          y2=`echo $RANDOM | awk '{ print $1/32767 }'`
          O1=`echo $O1 $x1 $y1 | awk '{ print $1+$4, $2+$5, $3 }'`
          O2=`echo $O2 $x2 $y2 | awk '{ print $1+$4, $2+$5, $3 }'`
        fi
        sed -n '1,8p' $here/G$g/CONTCAR1 > POSCAR
        echo $O1 T T F >> POSCAR
        echo $O2 T T F >> POSCAR
        sed -n '11,$p' $here/G$g/CONTCAR1 >> POSCAR
        D=`convasp -dist $minD < POSCAR  | sed -n '6,$p' | sed '/^[0-9]/d' | wc | awk '{ print $1 }'`
      done
      # run calculations
      cp $here/INCAR .
      cp $here/POTCAR .
      cp $here/KPOINTS .
      mpirun -machinefile $PBS_NODEFILE -np $NPROCS vasp
      rm CHG
      mkdir FixedZ
      cp * FixedZ
      # Allow O z coordinate, and top Pt/Mo atoms to relax
      mv CONTCAR POSCAR
      sed -i '10,13s/F/T/' POSCAR  # O
      sed -i '14s/F/T/g' POSCAR    # Mo
      sed -i '17,19s/F/T/g' POSCAR # Pt
      mpirun -machinefile $PBS_NODEFILE -np $NPROCS vasp
      rm CHG
    done

    # Compare energies
    for n in `seq 1 $Npop`
    do
      cd $here/G$g/S$n
      E=`grep "free  e" OUTCAR | tail -n 1 | awk '{ print $5 }'`
      echo $n $E  >> $here/G$g/Energies.txt
    done
    ENew=`cat $here/G$g/Energies.txt | sort -n -k2 | head -1 | awk '{ print $2 }'`
    dE=`echo $ENew $EBest | awk '{ printf "%d", ($1-$2)*1000 }'`
 
  done