genal.shell

用Visuanl C++开发的遗传算法程序

# This is a shell script to operate a global search on the basis
# of genetic algorithms
# Operates on an HP under POSIX (NOT csh)

rm genetic.log
touch genetic.log


echo >> genetic.log
echo >> genetic.log
echo "       -----------------------------------------------" >> genetic.log
echo "       -----------------------------------------------" >> genetic.log
echo "                     GENETIC ALGORITHMS" >> genetic.log
echo "                      author: R. Doell" >> genetic.log
echo "            version 2.0   creation date: 08/29/95" >> genetic.log
echo "       -----------------------------------------------" >> genetic.log
echo "       -----------------------------------------------" >> genetic.log
echo >> genetic.log
echo >> genetic.log

# cc  new in v1.1: for different chromosomes with identical bitcode
# cc               the iv curves are not recalculated
# cc  v1.1 hardly faster than v1.0 ---> stay with v1.0

# new in v1.5: number of best parents surviving can be set in file 'control'

# new in v1.6: search stops as soon as parameters are determined within 0.05 A

# new in v2.0: selection criterion moved from 'select' to 'crossover'


# ======================================================================



echo "   -------------------------------------------------------" >> genetic.log
echo "    generate random starting population ....." >> genetic.log
echo "   -------------------------------------------------------" >> genetic.log

# execute program 'sconf.exe' with input file 'control'.
# the output file 'population' contains the starting population coded as
# 1's and 0's. output file 'bithelp' contains the number of bits to describe
# one chromosome.

sconf.exe

# cp prot PROT
read word1 word2 < error
if [ $word1 = error ]
   then
        echo " genal.shell aborted due to error in 'sconf.exe'"
        exit
fi
rm error

echo "       ..... and calculate fitness for every chromosome" >> genetic.log
echo "   -------------------------------------------------------" >> genetic.log
echo >> genetic.log



# translate digital code of population back to 'real' parameters
# execute program 'transl.exe' with input 'control' and 'population'
# and output 'popw'

transl.exe

# cat prot >> PROT
# cat popw >> PROT



# get number of parameters from file 'control'
#          typeset -i nparam
#          grep nparam control | read nparam rest
           grep nparam control > temp
           read nparam rest < temp
           rm temp
           echo $nparam >> genetic.log

# get number of chromosomes from file 'control'
#          typeset -i nindiv
#          grep nindiv control | read nindiv rest
           grep nindiv control > temp
           read nindiv rest < temp
           rm temp
           echo $nindiv >> genetic.log

# =====================================================================
# initialize loop over chromosomes
#          typeset -i indivc
indivc=1

while [ "$indivc" -le "$nindiv" ]
   do
#    file 'helpfile' contains the number of parameters and the number of the
#    presently treated chromosome
   echo $nparam > helpfile
   echo $indivc >> helpfile


#    execute program 'fitness.exe' with input files 'helpfile', 'bithelp',
#    'popw' and 'population'. the output file 'fithelp' contains the fitness
#    of the presently treated chromosome (with number indivc).


#  calculate fitness (= r-factor) for the chromosomes

#    fitness1.exe extracts needed information from file 'popw' and writes
#    it to file 'ivhelp'
#   fitness1.exe
#    iv.exe calculates iv curves and writes them to file 'intens'
#   iv.exe < inir110 > /dev/null
#    rfacga.exe calculates respective r-factor and writes it to file 'rhelp'
#   rfacga.exe < intens > /dev/null
#    fitness2.exe converts results into proper format


echo $indivc > temp
pop=0
echo $pop >> temp

#  convert.exe needs to be written to take
#  "popw" and writes it into a format for whatever means you have 
#  for calculating and R-factor or figure of merit (in this case "sref")
#  the output ("phase.log" in this case) hold the R-factor which is written to the
#  file "rhelp".  The "fitness2.exe" can be run without changes. 
   
   ./convert.exe
   read match < match
   if [ $match -le 0 ]
   then
#    sref phase.run single.d single.at junk junk2 < phase.cnt > phase.log
     ./black_box.exe number_x
    
#   Non-complex R-factor
#    grep R-factor phase.log > temp2
#    read rest1 rest2 rest3 rest4 rfact < temp2

#   Complex R-factor
#    grep complex phase.log > temp2
#    read rest1 rest2 rest3 rest4 rest5 rfact < temp2
    
    read rfact < box_out
    rm box_out

    echo $rfact > rhelp
    addnew.exe
#    rm temp2
   fi
   
   fitness2.exe
   rm temp
   rm match
   cat fithelp >> fitfile



# end loop over chromosomes
# let indivc=indivc+1
indivc=`expr $indivc + 1`
done

# =====================================================================

# file 'fitfile' contains all chromosomes with fitness and binary code
   cat fitfile | sort -n > store
   mv store fitfile
#   echo "initial fitfile after sorting:" >> PROT
#   echo "fitness:         code:" >> PROT
#   cat fitfile >> PROT


# count total number of investigated chromosomes
#   typeset -i ncount
#   let ncount=nindiv
ncount=$nindiv


# =====================================================================
# initialize loop over populations



# get number of new children from file 'control'
#          typeset -i nchild
#          grep nchild control | read nchild rest
           grep nchild control > temp
           read nchild rest < temp
           rm temp


# get maximum number of populations from file 'control'
#          typeset -i npop
#          grep npop control | read npop rest
           grep npop control > temp
           read npop rest < temp
           rm temp

# get number of surviving parents from file 'control'
#          typeset -i nsurv
#          grep nsurv control | read nsurv rest
           grep nsurv control > temp
           read nsurv rest < temp
           rm temp
           echo $nsurv >> keep.control

# get tension from file 'control'
           grep tension control > temp
           read tension rest < temp
           rm temp

# make sure nindiv is set to correct value (Chris -- March 24)          
           grep nindiv control > temp
           read nindiv rest < temp
           rm temp
           
# initialize solutions and elite files (Chris -- April 10)
	   cp fitfile solutions
	   touch elite
           
           
# cc         preset some help variables
# cc                 flag=nomatch
# cc                 typeset -i cmatch
# cc                 cmatch=0
# cc                 typeset -i nchrom

popc=1
echo $popc
#    calculate average fitness of present population
#    input files: 'helpfile', 'fitfile'
#    output file containing value of average fitness: 'helpfile2'

while [ "$popc" -lt "$npop" ]
do 

#   echo $nparam > helpfile
#   echo $nindiv >> helpfile

   avfit.exe
   
#   head -1 fitfile | read bf rest
   head -1 fitfile > temp
   read bf rest < temp
   rm temp
   
   echo "   --> highest fitness: \c" >> genetic.log
   echo $bf >> genetic.log
   echo "       achieved for:    \c" >> genetic.log
   echo $rest >> genetic.log
   echo "       parameter(s):    \c" >> genetic.log
#   head -1 fitfile | 1transl.exe

   echo " --> average fitness of population $popc :\c" >> genetic.log
   cat helpfile2 >> genetic.log
   echo "     number of chromosomes investigated up to now: $ncount" >> genetic.log
   echo >> genetic.log

echo >> genetic.log
echo " ---------------------------------------------------------" >> genetic.log
echo "  perform crossover and mutation in population $popc ....." >> genetic.log
echo " ---------------------------------------------------------" >> genetic.log

#    crossover: input files: 'bithelp', 'control' and 'fitfile'
#               output file: 'lpop' (containing new large population)
   echo $nindiv >> bithelp
   grep idum control >> bithelp

   cross.exe tension
#  cross_share.exe tension

#    mutation: input files 'bithelp', 'control' and 'lpop'
#              output: 'mpop' (containing mutated population)

   mutate.exe


echo "        ..... and calculate fitness for every child of it" >> genetic.log
echo " ---------------------------------------------------------" >> genetic.log

#    translate digital code of child population back to 'real' parameters
#    execute program 'ltransl.exe' with input 'control' and 'mpop'
#    cat prot >> PROT
#    cat popw >> PROT

#    increase counter for total number of investigated chromosomes
#   let ncount=ncount+nchild
ncount=`expr $ncount + $nchild`

# =====================================================================
   mv mpop population
   
# translate mutated children to real parameters to go into the file popw
# Chris -- March 24
rm popw
transl.exe

#    initialize loop over chromosomes
   
indivc=1 
 
# get number of parameters from file 'control'
# To make sure nparam is set correctly (Chris -- March 24)
           grep nparam control > temp
           read nparam rest < temp
           rm temp
           
           
           
# let nsurv chromosomes with best fitness 'survive'
           cat elite > fitfile


while [ "$indivc" -le "$nchild" ]
do
#       file 'helpfile' contains the number of parameters and the number of the
#       presently treated chromosome
      echo $nparam > helpfile
      echo $indivc >> helpfile

#       execute program 'fitness.exe'

#       calculate fitness (= r-factor) for the chromosomes


# cc      skip computation of fitness if another chromosome has the same bitcode
# cc       
# cc             let nhelp=nchild+1-indivc
# cc             tail -$nhelp population | read help1 help2 rest
# cc             let i=1
# cc             while [ "$i" -lt "$indivc" ]
# cc                do
# cc                tail -$i fitfile | read help3 help4 rest
# cc                if test "$help2" = "$help4"
# cc                   then
# cc                   tail -$i fitfile | head -1 > fithelp
# cc                   let i=i+nchild
# cc                   flag=match
# cc                fi
# cc                let i=i+1
# cc             done
# cc   
# cc           
# cc             if test "$flag" = match
# cc                then
# cc                let cmatch=cmatch+1
# cc                flag=nomatch
# cc             else

#          fitness1.exe extracts needed information from file 'popw' and
#          writes it to file 'ivhelp'
#        fitness1.exe
#          iv.exe calculates iv curves and writes them to file 'intens'
#        iv.exe < inir110 > /dev/null
#         rfacga.exe calculates r-factor and writes it to file 'rhelp'
#       rfacga.exe < intens > /dev/null
#          fitness2.exe converts results into proper format

echo $indivc > temp
echo $popc >> temp

#  convert.exe needs to be written to take
#  "popw" and writes it into a format for whatever means you have 
#  for calculating and R-factor or figure of merit (in this case "sref")
#  the output ("phase.log" in this case) hold the R-factor which is written to the
#  file "rhelp".  The "fitness2.exe" can be run without changes. 
      
   ./convert.exe
   read match < match
   if [ $match -le 0 ]
   then
#    sref phase.run single.d single.at junk junk2 < phase.cnt > phase.log
     ./black_box.exe number_x
    
#   Non-complex R-factor
#    grep R-factor phase.log > temp2
#    read rest1 rest2 rest3 rest4 rfact < temp2

#   Complex R-factor
#    grep complex phase.log > temp2
#    read rest1 rest2 rest3 rest4 rest5 rfact < temp2
    
    read rfact < box_out
    rm box_out

    echo $rfact > rhelp
    addnew.exe
#    rm temp2
   fi

         fitness2.exe
   
   rm temp
   rm match

# cc             fi

      cat fithelp >> fitfile

#    end loop over chromosomes
#   let indivc=indivc+1
indivc=`expr $indivc + 1`
 
done

# =====================================================================

# CC#    create file 'children': number of children, number of chromosomes
# CC#    in a parents' population and file 'fitfile'
# CC
# CC   echo "$((nsurv+nchild))        number of children" > children
# CC   echo "$nindiv        number of parent chromosomes" >> children
# CC   cat fitfile | sort -n >> children
# CC   rm fitfile
# CC   grep nselec control >> children
# CC   grep nsurv control >> children
# CC
# CC#    echo >> PROT
# CC#    echo "children:" >> PROT
# CC#    cat children >> PROT
# CC#    echo >> PROT
# CC

# CC#    select new parents from file 'children'
# CC   select.exe
# CC   cat fitfile | sort -n > store
# CC   mv store fitfile


# create new 'fitfile' from which next parents are chosen
     cat fitfile | sort -n > store
     head -$nindiv store > fitfile
     
# update solutions and elite files (Chris -- April 10)
     cp solutions solutions.tmp
     rm solutions
     rm elite
     keeper.exe
     rm solutions.tmp


#   echo " fitfile" >> PROT
#   echo >> PROT
#   cat fitfile >> PROT
#   echo >> PROT
#   echo >> PROT


# end loop over populations
# let popc=popc+1
 popc=`expr $popc + 1`
 echo population = $popc

done

# =====================================================================


# final output


# calculate average fitness of final population
echo $nparam > helpfile
echo $nindiv >> helpfile
avfit.exe

echo >> genetic.log
head -1 fitfile | read bf rest
echo "   --> highest fitness in last population:  \c" >> genetic.log
echo $bf >> genetic.log
echo "       achieved for:     \c" >> genetic.log
echo $rest >> genetic.log
echo "       parameter(s):     \c" >> genetic.log
head -1 fitfile | 1transl.exe
echo " --> average fitness of (final) population $fpop :\c" >> genetic.log
cat helpfile2 >> genetic.log
echo "     total number of chromosomes investigated: $ncount" >> genetic.log
echo >> genetic.log


# delete files not needed any more
     rm helpfile
     rm fithelp
     rm bithelp
     rm fitfile
     rm store
     rm popw
     rm prot
     rm helpfile2
     rm lpop
     rm population
     rm rhelp
     rm ab16in
     rm ab16out
     rm solutions.tmp

exit 0