#!/bin/sh

#
# visualization script
# author: frank.zirkelbach@physik.uni-augsburg.de
#

# help function
draw_cyl() {
	cat >> temp.pov <<-EOF
cylinder {
<$1, $3, $2>, <$4, $6, $5>, 0.05
pigment { color White }
}
EOF
}
draw_bond() {
	cat >> temp.pov <<-EOF
cylinder {
<$1, $3, $2>, <$4, $6, $5>, $7
pigment { color Blue }
}
EOF
}

# defaults

lc=5.429
directory="doesnt_exist____for_sure"
width="640"
height="480"
radius="0.6"
x0="-0.6"; y0="-0.6"; z0="-0.6";
x1="0.6"; y1="0.6"; z1="0.6";
cx=""; cy=""; cz="";
lx="0"; ly="-100"; lz="100";
ortographic=""
bx0=""; by0=""; bz0="";
bx1=""; by1=""; bz1="";
bcr="0.1";
clx="0"; cly="0"; clz="0";
extra=0
displace=""
mirror=0
mx1=0; mx2=0; mx3=0;
my1=0; my2=0; my3=0;
mz1=0; mz2=0; mz3=0;
ab=0

# parse argv

while [ "$1" ]; do
	case "$1" in
		-d)		directory=$2;		shift 2;;
		-w)		width=$2;		shift 2;;
		-h)		height=$2;		shift 2;;
		-r)		radius=$2;		shift 2;;
		-nll)		x0=$2; y0=$3; z0=$4;	shift 4;;
		-fur)		x1=$2; y1=$3; z1=$4;	shift 4;;
		-c)		cx=$2; cy=$3; cz=$4;	shift 4;;
		-L)		clx=$2; cly=$3; clz=$4;	shift 4;;
		-l)		lx=$2; ly=$3; lz=$4;	shift 4;;
		-o)		ortographic=1;		shift 1;;
		-b)		bx0=$2; by0=$3; bz0=$4;
				bx1=$5; by1=$6; bz1=$7;	shift 7;;
		-B)		bcr=$2;			shift 2;;
		-C)		lc=$2;			shift 2;;
		-e)		extra=1; 		shift 1;;
		-D)		displace=$2;		shift 2;;
		-m)		mx1=$2; mx2=$3; mx3=$4;
				my1=$5; my2=$6; my3=$7;
				mz1=$8; mz2=$9; mz3=${10};
				mirror=1;		shift 10;;
		-A)		ab=$2;			shift 2;
				((cnt=1))
				while [ $cnt -le $ab ]; do
					anr[$cnt]=$1;	shift 1;
					((cnt+=1))
				done
				cutoff=$1;		shift 1;;
		*)
				echo "options:"
				echo "########"
				echo "directory to progress:"
				echo "  -d <directory> (mandatory)"
				echo "png dim:"
				echo "  -w <width>"
				echo "  -h <height>"
				echo "atom size:"
				echo "  -r <radius>"
				echo "  -B <bond cylinder radius>"
				echo "unit cell:"
				echo "  -C <lattice constant>"
				echo "  -m <dimX> <dimY> <dimZ> (mirror atoms)"
				echo "visualization volume:"
				echo "  -nll <x> <y> <z> (near lower left)"
				echo "  -fur <x> <y> <z> (far upper right)"
				echo "  -o (ortographic)"
				echo "bounding box:"
				echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
				echo "povray:"
				echo "  -c <x> <y> <z> (camera position)"
				echo "  -L <x> <y> <z> (camera look)"
				echo "  -l <x> <y> <z> (light source)"
				echo "bonds:"
				echo "  -ab <atom number> <cutoff> (auto bonds)"
				exit 1;;
	esac
done

# calculation from lattic eunits to angstroms

[ "$lc" = "sic" ] && lc=4.359
[ "$lc" = "si" ] && lc=5.480
[ "$lc" = "c" ] && lc=3.566

#offset=`echo 0.125 \* $lc | bc`
offset=0.0

x0=`echo $x0 \* $lc + $offset | bc`
y0=`echo $y0 \* $lc + $offset | bc`
z0=`echo $z0 \* $lc + $offset | bc`
x1=`echo $x1 \* $lc + $offset | bc`
y1=`echo $y1 \* $lc + $offset | bc`
z1=`echo $z1 \* $lc + $offset | bc`

mx1=`echo $mx1 \* $lc + $offset | bc`
my1=`echo $my1 \* $lc + $offset | bc`
mz1=`echo $mz1 \* $lc + $offset | bc`
mx2=`echo $mx2 \* $lc + $offset | bc`
my2=`echo $my2 \* $lc + $offset | bc`
mz2=`echo $mz2 \* $lc + $offset | bc`
mx3=`echo $mx3 \* $lc + $offset | bc`
my3=`echo $my3 \* $lc + $offset | bc`
mz3=`echo $mz3 \* $lc + $offset | bc`

clx=`echo $clx \* $lc + $offset | bc`
cly=`echo $cly \* $lc + $offset | bc`
clz=`echo $clz \* $lc + $offset | bc`

if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then
	cx=`echo $cx \* $lc + $offset | bc`
	cy=`echo $cy \* $lc + $offset | bc`
	cz=`echo $cz \* $lc + $offset | bc`
fi

if [ -n "$bx0" ]; then
	bx0=`echo $bx0 \* $lc + $offset | bc`
	by0=`echo $by0 \* $lc + $offset | bc`
	bz0=`echo $bz0 \* $lc + $offset | bc`
	bx1=`echo $bx1 \* $lc + $offset | bc`
	by1=`echo $by1 \* $lc + $offset | bc`
	bz1=`echo $bz1 \* $lc + $offset | bc`
fi

# povray command

POVRAY="povray -W${width} -H${height} -d" 

# convert options

COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf"
COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24"

# do it ...

if [ -d $directory ]; then
	filesource=$directory/atomic_conf_*.xyz
fi

if [ -f $directory ]; then
	filesource=$directory
fi

for file in $filesource; do

	cat > temp.pov <<-EOF
#include "colors.inc"
#include "textures.inc"
#include "shapes.inc"
#include "glass.inc"
#include "metals.inc"
#include "woods.inc"
#include "stones.inc"
EOF

	# meta info
	count=`grep '# \[P\]' $file | awk '{ print $3 }'`
	time=`grep '# \[P\]' $file | awk '{ print $4 }'`
	camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
	[ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"

	# atoms
#echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----"
	if [ -n "$x0" ]; then
		export x0 y0 z0 x1 y1 z1 radius extra
		export mx1 mx2 mx3
		export my1 my2 my3
		export mz1 mz2 mz3
		export mirror
		cat $file | grep -v '#' | awk '\
		BEGIN {
			x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
			x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
			mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
			mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
			my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
			mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
			mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
			radius=ENVIRON["radius"]; extra=ENVIRON["extra"];
			nx=0; ny=0; nz=0;
		}
		{
			if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
			   ($2<=x1)&&($3<=y1)&&($4<=z1)) {
				print "sphere { <"$2","$4","$3">, "radius" ";
				if(extra)
		print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
				else
		print "texture { pigment { color "$5" } ";
				print "finish { phong 1 metallic } } }";
			}

			if(mirror) {

			nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
			if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
			   (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
print "// translation: "$2/5.480" "$3/5.480" "$4/5.480" -> "nx/5.480" "ny/5.480" "nz/5.480" ...";
				print "sphere { <"nx","nz","ny">, "radius" ";
				if(extra)
		print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
				else
		print "texture { pigment { color "$5" } ";
				print "finish { phong 1 metallic } } }";
			}
			nx=$2-my1; ny=$3-my2; nz=$4-my3;
			if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
			   (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
				print "sphere { <"nx","nz","ny">, "radius" ";
				if(extra)
		print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
				else
		print "texture { pigment { color "$5" } ";
				print "finish { phong 1 metallic } } }";
			}
			nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
			if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
			   (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
				print "sphere { <"nx","nz","ny">, "radius" ";
				if(extra)
		print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
				else
		print "texture { pigment { color "$5" } ";
				print "finish { phong 1 metallic } } }";
			}

			}

		}' >> temp.pov
	else
		cat $file | grep -v '#' | while read name x y z color temp; do
			cat >> temp.pov <<-EOF
sphere {
<$x, $z, $y>, $radius
texture {
pigment { color $color }
finish {
phong 1
metallic
}
}
}
EOF
		done
	fi

	# boundaries
	if [ -z "$bx0" ]; then

	#if [ -z "$x0" ]; then

	cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
		draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05
	done

	#else

		# manually drawing the 3x4 boundaries ...
#		draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
#		draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
#		draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
#		draw_cyl $x0 $y1 $z0 $x1 $y1 $z0

#		draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
#		draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
#		draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
#		draw_cyl $x0 $y1 $z1 $x1 $y1 $z1

#		draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
#		draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
#		draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
#		draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
#	fi

	else

		# manually drawing the 3x4 boundaries specified by argv ...
		draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
		draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
		draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
		draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0

		draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
		draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
		draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
		draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1

		draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
		draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
		draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
		draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0

	fi	

	# bonds
	if [ -n "$bcr" ]; then

		if [ -z "$x0" ]; then

	cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
		draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
	done

		else

		export x0 y0 z0 x1 y1 z1 bcr
		cat $file | grep '# \[B\]' | awk '\
		BEGIN {
			x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
			x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
			bcr=ENVIRON["bcr"];
		}
		{
			if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
			   ($3<=x1)&&($4<=y1)&&($5<=z1)) {
				print "cylinder {";
				print "<"$3","$5","$4">,";
				print "<"$6","$8","$7">, "bcr;
				print "pigment { color Blue }";
				print "}";
			}
		}' >> temp.pov

		fi
	fi

	# auto bonds
	if [ "$ab" != "0" ]; then
		((cnt=1))
		while [ $cnt -le $ab ]; do
			anr=${anr[$cnt]}

		((tmp=anr+1))
		line="`sed -n ${tmp}p $file`"
		aX=`echo $line | awk '{ print $2 }'`
		aY=`echo $line | awk '{ print $3 }'`
		aZ=`echo $line | awk '{ print $4 }'`
		export aX aY aZ cutoff mirror
		cat $file | grep -v '#' | awk '\
		BEGIN {
			x=ENVIRON["aX"]; y=ENVIRON["aY"]; z=ENVIRON["aZ"];
			co=ENVIRON["cutoff"]; dist=0; bcr=ENVIRON["bcr"];
			mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
			mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
			my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
			mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
			mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
		}
		{
			dist=sqrt((x-$2)^2+(y-$3)^2+(z-$4)^2);
			if((dist<=co)&&(dist>0.01)) {
				print "cylinder {";
				print "<"x","z","y">,";
				print "<"$2","$4","$3">, "bcr;
				print "pigment { color Blue }";
				print "}";
			}

			if(mirror) {
				nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
				dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
				if((dist<=co)&&(dist>0.01)) {
					print "cylinder {";
					print "<"x","z","y">,";
					print "<"nx","nz","ny">, "bcr;
					print "pigment { color Blue }";
					print "}";
				}
				nx=$2-my1; ny=$3-my2; nz=$4-my3;
				dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
				if((dist<=co)&&(dist>0.01)) {
					print "cylinder {";
					print "<"x","z","y">,";
					print "<"nx","nz","ny">, "bcr;
					print "pigment { color Blue }";
					print "}";
				}
				nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
				dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
				if((dist<=co)&&(dist>0.01)) {
					print "cylinder {";
					print "<"x","z","y">,";
					print "<"nx","nz","ny">, "bcr;
					print "pigment { color Blue }";
					print "}";
				}
			}

		}' >> temp.pov

			((cnt+=1))
		done
	fi

	# add camera and light source
	cat >> temp.pov <<-EOF
camera {
EOF
	if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
orthographic
EOF
	fi
	cat >> temp.pov <<-EOF
location $camloc
look_at <$clx,$clz,$clz>
}
light_source { <0,100,-100> color White shadowless }
EOF

	# mv png
	$POVRAY temp.pov > /dev/null 2>&1
	time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'`
	if [ ! -z $displace ]; then
	convert $COPTS -draw "text 5,20 'd = $displace %'" temp.png temp.png
	else
	convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png
	fi
	mv temp.png `echo $file | sed 's/\.xyz/\.png/'`

done

echo "done"