genal_pop.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)
#
PATH=$PATH:/usr/local/phasing/Genetic/LBL/bin:/usr/local/phasing/bin
export PATH


rm genetic.log fitfile elite solutions
touch genetic.log


echo >> genetic.log
echo "       -----------------------------------------------" >> genetic.log
echo "                     GENETIC ALGORITHMS" >> genetic.log
echo "               Authors: R. Doell, LBL" >> genetic.log
echo "               E. Landree, C. Collazo, L. D. Marks, NU" >> genetic.log
echo "               Acta Crystallographica B 53, 916-922 (1997)"  >> genetic.log
echo "               Version 4.0   creation date: 07/08/98" >> genetic.log
echo "       -----------------------------------------------" >> genetic.log
echo >> genetic.log


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

# execute program 'sconf2.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.  This uses the number of children to start.

sconf2.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'

transl2.exe

# get number of parameters from file 'control'
           grep nparam control > temp
           read nparam rest < temp
           rm temp

# get number of chromosomes from file 'control'
           grep nindiv control > temp
           read nindiv rest < temp
           rm temp

# get number of children from file 'control'
           grep nchild control > temp
           read nchild rest < temp
           rm temp


# get tension for cross.f from 'control'
           grep tension control > temp
           read tension rest < temp
           rm temp


# =====================================================================
# initialize loop over chromosomes
# Control file
# Number of parameters
    echo $nparam > sref.control
# Number of members for this population
    echo $nchild >> sref.control
# Which population ?
    echo "0" >> sref.control
# Total number of bits
    read totbits < bithelp
    echo $totbits >> sref.control
#
   xrefs_pop10 phase.tmpl rn.d single.at junk junk2 < phase.cnt > phase.log

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

# file 'fitfile' contains all chromosomes with fitness and binary code
# Sort, removing duplicates of a given FOM value
    sort -u -n -o store fitfile
    mv store fitfile


# count total number of investigated chromosomes
ncount=$nchild


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



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


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

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

# 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 - NO
           

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 > temp
   read bf rest < temp
   rm temp
   
   
   echo "   --> highest fitness: \c" >> genetic.log
   echo $bf >> genetic.log

   echo " --> average fitness of population $popc :\c" >> genetic.log
   read var1 var2 < helpfile2
   echo $var1 >> genetic.log

   echo "     number of chromosomes investigated up to now: $ncount" >> genetic.log
   echo >> genetic.log

   echo " --> average fitness of population $popc :\c"
   echo $var1
   
   stat >> 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


#    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'

#    increase counter for total number of investigated chromosomes
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

 
# 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

if [ -r elite ]
then
cat elite > fitfile
fi

# =====================================================================
# initialize loop over chromosomes
# Control file
# Number of parameters
    echo $nparam > sref.control
# Number of members for this population
    echo $nchild >> sref.control
# Which population ?
    echo $popc >> sref.control
# Total number of bits
    read totbits < bithelp
    echo $totbits >> sref.control
#
 xrefs_pop10 phase.tmpl rn.d single.at junk junk2 < phase.cnt > phase.log
# =====================================================================


# create new 'fitfile' from which next parents are chosen
grep nindiv control > temp ; read nindiv rest < temp ; rm temp
# CHANGED
#    sort -u -n -o store fitfile
# Sort, removing duplicates of a given FOM value
    sort -u -n -o store fitfile
     head -$nindiv store > fitfile
     
# update solutions and elite files (Chris -- April 10)
# CHANGED
#	sort -o solutions.tmp -n fitfile solutions
# Sort, removing duplicates of a given FOM value
	sort -u -o solutions.tmp -n fitfile solutions
	
#instead of Keeper.exe
           grep nsurv control > temp
           read nsurv rest < temp
           rm temp
# Changed only for every other cycle
if [ -r elite ]
	then
		rm elite
		echo "Note: Removing elite " >> genetic.log
	else
 		uniq solutions.tmp temp2  
		head -$nsurv temp2  > elite
fi

           grep nsave keep.control > temp
           read nsave rest < temp
           rm temp
           uniq solutions.tmp temp2  
           head -$nsave temp2 > solutions
           rm temp2
#     rm solutions.tmp		



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

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 " --> 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

echo " --> average fitness of (final) population $fpop :\c" 
cat helpfile2 
   stat >> genetic.log


# delete files not needed any more
     rm helpfile bithelp fitfile
     rm store popw helpfile2
     rm prot helpfile3 lpop
     rm population random.hold
     rm solutions.tmp junk* sref.control elite