#!/bin/bash
#
# 1_PESscan.bash, a bash script for generating input files for calculating PESs.
#
# Any problems, drop a line.  damian@somewhereville.com, www.somewhereville.com
#
#
# usage ./1_PESscan.bash $1 $2 $3 $4 $5 $6
# as in...
# usage ./1_PESscan.bash Kdiphenylmethanide gjf g03 100 25 25
# 
# $1 = name of the input file template (no extension)
# $2 = name of the file extension (gjf for Gaussian, inp for GAMESS, etc.)
# $3 = command line executable (g03 for Gaussian, gms... for GAMESS
# $4 = decimal increments for the X axis (100 = unit, no decimals)
# $5 = decimal increments for the Y axis (100 = unit, no decimals)
# $6 = decimal increments for the Z axis (100 = unit, no decimals)
# 
# the script does a sweep from MINX to MAXX, MINY to MAXY, MINZ to MAXZ and is written around
# a bash limitation of doing decimals in names (unless someone shows me otherwise)
#


# define the maxima and minima here
# define the maxima and minima here
# define the maxima and minima here
# define the maxima and minima here
# 
# modify these numbers to match the range of the sweeps.
# 
# if this is for a planar molecule, then the plane should be aligned along two axes.
# for instance, if scanning with a vertical height of X, the molecule should be along
# X=0 for all atoms (again, assumed planar)
#
# negative values work fine, too.
#


MINX=2
MAXX=5
MINY=0
MAXY=5
MINZ=0
MAXZ=5


#
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
#

for((X=$MINX; X<=$MAXX-1; X++)) ; do

for((x=0; x<100; x++)) ; do

if [ "$x" = 0 ]; then
Xx=$X.$x'00000'
else
Xx=$X.$x'0000'
fi
x=$x+$4-1


for((Y=$MINY; Y<=$MAXY-1; Y++)) ; do

for((y=0; y<100; y++)) ; do

if [ "$y" = 0 ]; then
Yy=$Y.$y'00000'
else
Yy=$Y.$y'0000'
fi
y=$y+$5-1


for((Z=$MINZ; Z<=$MAXZ-1; Z++)) ; do

for((z=0; z<100; z++)) ; do

if [ "$z" = 0 ]; then
Zz=$Z.$z'00000'
else
Zz=$Z.$z'0000'
fi
z=$z+$6-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done
done
done

#
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
# this section hits all of the cases that AREN'T at maximum values of X, Y, Z
#




#
# This section hits all cases where the X is at its maximum (except the final maximim)
# This section hits all cases where the X is at its maximum (except the final maximim)
# This section hits all cases where the X is at its maximum (except the final maximim)
# This section hits all cases where the X is at its maximum (except the final maximim)
#

for((X=$MAXX; X<=$MAXX; X++)) ; do

Xx=$X.'000000'

for((Y=$MINY; Y<=$MAXY-1; Y++)) ; do

for((y=0; y<100; y++)) ; do

if [ "$y" = 0 ]; then
Yy=$Y.$y'00000'
else
Yy=$Y.$y'0000'
fi
y=$y+$5-1


for((Z=$MINZ; Z<=$MAXZ-1; Z++)) ; do

for((z=0; z<100; z++)) ; do

if [ "$z" = 0 ]; then
Zz=$Z.$z'00000'
else
Zz=$Z.$z'0000'
fi
z=$z+$6-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done
done

#
# This section hits all cases where the X is at its maximum (except the final maximim)
# This section hits all cases where the X is at its maximum (except the final maximim)
# This section hits all cases where the X is at its maximum (except the final maximim)
# This section hits all cases where the X is at its maximum (except the final maximim)
#




#
# This section hits all cases where the Y is at its maximum (except the final maximim)
# This section hits all cases where the Y is at its maximum (except the final maximim)
# This section hits all cases where the Y is at its maximum (except the final maximim)
# This section hits all cases where the Y is at its maximum (except the final maximim)
#

for((Y=$MAXY; Y<=$MAXY; Y++)) ; do

Yy=$Y.'000000'

for((X=$MINX; X<=$MAXX-1; X++)) ; do

for((x=0; x<100; x++)) ; do

if [ "$x" = 0 ]; then
Xx=$X.$x'00000'
else
Xx=$X.$x'0000'
fi
x=$x+$4-1


for((Z=$MINZ; Z<=$MAXZ-1; Z++)) ; do

for((z=0; z<100; z++)) ; do

if [ "$z" = 0 ]; then
Zz=$Z.$z'00000'
else
Zz=$Z.$z'0000'
fi
z=$z+$6-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done
done

#
# This section hits all cases where the Y is at its maximum (except the final maximim)
# This section hits all cases where the Y is at its maximum (except the final maximim)
# This section hits all cases where the Y is at its maximum (except the final maximim)
# This section hits all cases where the Y is at its maximum (except the final maximim)
#




#
# This section hits all cases where the Z is at its maximum (except the final maximim)
# This section hits all cases where the Z is at its maximum (except the final maximim)
# This section hits all cases where the Z is at its maximum (except the final maximim)
# This section hits all cases where the Z is at its maximum (except the final maximim)
#

for((Z=$MAXZ; Z<=$MAXZ; Z++)) ; do

Zz=$Z.'000000'


for((X=$MINX; X<=$MAXX-1; X++)) ; do

for((x=0; x<100; x++)) ; do

if [ "$x" = 0 ]; then
Xx=$X.$x'00000'
else
Xx=$X.$x'0000'
fi
x=$x+$4-1


for((Y=$MINY; Y<=$MAXY-1; Y++)) ; do

for((y=0; y<100; y++)) ; do

if [ "$y" = 0 ]; then
Yy=$Y.$y'00000'
else
Yy=$Y.$y'0000'
fi
y=$y+$5-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done
done

#
# This section hits all cases where the Z is at its maximum (except the final maximim)
# This section hits all cases where the Z is at its maximum (except the final maximim)
# This section hits all cases where the Z is at its maximum (except the final maximim)
# This section hits all cases where the Z is at its maximum (except the final maximim)
#




#
# This section gets the maximum X, Y and all remaining values of Z
# This section gets the maximum X, Y and all remaining values of Z
# This section gets the maximum X, Y and all remaining values of Z
# This section gets the maximum X, Y and all remaining values of Z
#

for((X=$MAXX; X<=$MAXX; X++)) ; do

Xx=$X.'000000'

for((Y=$MINY; Y<=$MAXY; Y++)) ; do

Yy=$Y.'000000'


for((Z=$MINZ; Z<=$MAXZ-1; Z++)) ; do

for((z=0; z<100; z++)) ; do

if [ "$z" = 0 ]; then
Zz=$Z.$z'00000'
else
Zz=$Z.$z'0000'
fi
z=$z+$6-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done

#
# This section gets the maximum X, Y and all remaining values of Z
# This section gets the maximum X, Y and all remaining values of Z
# This section gets the maximum X, Y and all remaining values of Z
# This section gets the maximum X, Y and all remaining values of Z
#




#
# This section gets the maximum X, Z and all remaining values of Y
# This section gets the maximum X, Z and all remaining values of Y
# This section gets the maximum X, Z and all remaining values of Y
# This section gets the maximum X, Z and all remaining values of Y
#

for((Z=$MAXZ; Z<=$MAXZ; Z++)) ; do

Zz=$Z.'000000'

for((X=$MINX; X<=$MAXX; X++)) ; do

Xx=$X.'000000'


for((Y=$MINY; Y<=$MAXY-1; Y++)) ; do

for((y=0; y<100; y++)) ; do

if [ "$y" = 0 ]; then
Yy=$Y.$y'00000'
else
Yy=$Y.$y'0000'
fi
y=$y+$5-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done

#
# This section gets the maximum X, Z and all remaining values of Y
# This section gets the maximum X, Z and all remaining values of Y
# This section gets the maximum X, Z and all remaining values of Y
# This section gets the maximum X, Z and all remaining values of Y
#




#
# This section gets the maximum Y, Z and all remaining values of X
# This section gets the maximum Y, Z and all remaining values of X
# This section gets the maximum Y, Z and all remaining values of X
# This section gets the maximum Y, Z and all remaining values of X
#

for((Z=$MAXZ; Z<=$MAXZ; Z++)) ; do

Zz=$Z.'000000'

for((Y=$MINY; Y<=$MAXY; Y++)) ; do

Yy=$Y.'000000'


for((X=$MINX; X<=$MAXX-1; X++)) ; do

for((x=0; x<100; x++)) ; do

if [ "$x" = 0 ]; then
Xx=$X.$x'00000'
else
Xx=$X.$x'0000'
fi
x=$x+$4-1

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done
done

#
# This section gets the maximum Y, Z and all remaining values of X
# This section gets the maximum Y, Z and all remaining values of X
# This section gets the maximum Y, Z and all remaining values of X
# This section gets the maximum Y, Z and all remaining values of X
#





#
# This section gets the last integer positions in the grid
# This section gets the last integer positions in the grid
# This section gets the last integer positions in the grid
# This section gets the last integer positions in the grid
#

for((Z=$MINZ; Z<=$MAXZ; Z++)) ; do

Zz=$Z.'000000'

for((X=$MINX; X<=$MAXX; X++)) ; do

Xx=$X.'000000'

for((Y=$MINY; Y<=$MAXY; Y++)) ; do

Yy=$Y.'000000'

sed "s/REPLACEX/$Xx/g;s/REPLACEY/$Yy/g;s/REPLACEZ/$Zz/g" $1.$2 > $1'_X_'$Xx'_Y_'$Yy'_Z_'$Zz'.'$2
done
done
done

#
# This section gets the last integer positions in the grid
# This section gets the last integer positions in the grid
# This section gets the last integer positions in the grid
# This section gets the last integer positions in the grid
#




#
# This section makes the batch file
# This section makes the batch file
# This section makes the batch file
# This section makes the batch file
#
# if you defines $3 correctly, the batch file should contain all the info to execute the
# scan files.  The final batch name will be 4_batchscript.bat.
#

ls $1_*.$2 > 4_batch.batch
sed "s/$1/$3 $1/g" 4_batch.batch > 4_batchscript.bat
rm 4_batch.batch