]> hackdaworld.org Git - physik/posic.git/commitdiff
sualization mods + adabtions
authorhackbard <hackbard@sage.physik.uni-augsburg.de>
Thu, 2 Aug 2007 17:07:29 +0000 (19:07 +0200)
committerhackbard <hackbard@sage.physik.uni-augsburg.de>
Thu, 2 Aug 2007 17:07:29 +0000 (19:07 +0200)
run
sic.c
visual/visual.c
visualize

diff --git a/run b/run
index 6e120d781b42e1e3d721d3b0c2a3b64df4729853..c7d454ca1629a0d29a187c159bd479bf530bd0e3 100755 (executable)
--- a/run
+++ b/run
@@ -4,7 +4,7 @@
 if [ "$?" == "0" ]; then
        #./perms
        if [ "$1" ] ; then
-               ./visualize $1
+               ./visualize -d $1
                #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
                ./ppm2avi $1
        fi
diff --git a/sic.c b/sic.c
index 1f9bbbe7b0932a7a20ee7881ef2ef005d8114395..bf33e1634f95ac9a62c6a2256f0a69568de70188 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -25,7 +25,9 @@
 #define NR_ATOMS       1
 #define R_C            1.0
 #define T_C            10.0
-#define LCNT           3
+#define LCNT           5
+#define PRERUN         200
+#define POSTRUN                500
 
 typedef struct s_hp {
        int a_count;    /* atom count */
@@ -58,7 +60,7 @@ int hook(void *moldyn,void *hook_params) {
        /* last schedule add if there is enough carbon inside */
        if(hp->a_count==(INJECT*NR_ATOMS)) {
                hp->quit=1;
-               moldyn_add_schedule(md,5000,1.0);
+               moldyn_add_schedule(md,POSTRUN,1.0);
                return 0;
        }
 
@@ -74,12 +76,17 @@ int hook(void *moldyn,void *hook_params) {
        for(j=0;j<NR_ATOMS;j++) {
                run=1;
                while(run) {
+                       /*
                        r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
                        r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
                        r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
-                       //r.x=(1.0*atoi(hp->argv[3])-4.5)/9.0*ALBE_LC_SI;
-                       //r.y=(1.0*atoi(hp->argv[4])-4.5)/9.0*ALBE_LC_SI;
-                       //r.z=(1.0*atoi(hp->argv[5])-4.5)/9.0*ALBE_LC_SI;
+                       r.x=(1.0*atoi(hp->argv[3])-4.5)/9.0*ALBE_LC_SI;
+                       r.y=(1.0*atoi(hp->argv[4])-4.5)/9.0*ALBE_LC_SI;
+                       r.z=(1.0*atoi(hp->argv[5])-4.5)/9.0*ALBE_LC_SI;
+                       */
+                       r.x=(rand_get_double(&(md->random))-0.5)*LC_SI;
+                       r.y=(rand_get_double(&(md->random))-0.5)*LC_SI;
+                       r.z=(rand_get_double(&(md->random))-0.5)*LC_SI;
                        /* assume valid coordinates */
                        run=0;
                        for(i=0;i<md->count;i++) {
@@ -124,9 +131,6 @@ int main(int argc,char **argv) {
        t_tersoff_mult_params tp;
        t_albe_mult_params ap;
 
-       /* atom injection counter */
-       int inject;
-
        /* testing location & velocity vector */
        t_3dvec r,v;
        memset(&r,0,sizeof(t_3dvec));
@@ -330,7 +334,7 @@ int main(int argc,char **argv) {
        set_pressure(&md,BAR);
 
        /* set amount of steps to skip before average calc */
-       set_avg_skip(&md,1000);
+       set_avg_skip(&md,PRERUN);
 
        /* set p/t scaling */
        //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
@@ -343,17 +347,7 @@ int main(int argc,char **argv) {
        thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
-       moldyn_add_schedule(&md,1000,1.0);
-       //moldyn_add_schedule(&md,1000,1.0);
-       //moldyn_add_schedule(&md,1000,1.0);
-       //moldyn_add_schedule(&md,1000,1.0);
-       //moldyn_add_schedule(&md,1000,1.0);
-       //moldyn_add_schedule(&md,1000,1.0);
-       /* adding atoms */
-       //for(inject=0;inject<INJECT;inject++) {
-       //      /* injecting atoms */
-       //      moldyn_add_schedule(&md,10,1.0);
-       //}
+       moldyn_add_schedule(&md,PRERUN,1.0);
 
        /* schedule hook function */
        memset(&hookparam,0,sizeof(t_hp));
index 3a8f7f8e2fcaeaab51f7dc03deeb2c1da88119f0..73b49410cb99574720cf618fc5f04df9a17a372a 100644 (file)
@@ -18,7 +18,7 @@
 #include "../math/math.h"
 
 /* the pse, only needed here */
-static char *pse[]={
+static char *pse_name[]={
        "*",
        "H",
        "He",
@@ -40,30 +40,56 @@ static char *pse[]={
        "Ar",
 };
 
+static char *pse_col[]={
+       "*",
+       "White",
+       "He",
+       "Li",
+       "Be",
+       "B",
+       "Gray",
+       "N",
+       "Blue",
+       "F",
+       "Ne",
+       "Na",
+       "Mg",
+       "Al",
+       "Yellow",
+       "P",
+       "S",
+       "Cl",
+       "Ar",
+};
+
 int visual_init(t_visual *v,char *filebase) {
 
        char file[128+8];
 
        strncpy(v->fb,filebase,128);
        memset(file,0,128+8);
-       sprintf(file,"%s/visualize.scr",v->fb);
+       //sprintf(file,"%s/visualize.scr",v->fb); // obsolete!
 
+       /* obsolete!
        v->fd=open(file,O_WRONLY|O_CREAT|O_EXCL,S_IRUSR|S_IWUSR);
        if(v->fd<0) {
                perror("open visual fd");
                return -1;
        }
        dprintf(v->fd,"set write on\n");
+       */
 
        return 0;
 }
 
 int visual_tini(t_visual *v) {
 
+       /* obsolete!
        if(v->fd) {
                dprintf(v->fd,"quit\n");
                close(v->fd);
        }
+       */
 
        return 0;
 }
@@ -73,13 +99,15 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
        int i,fd;
        char file[128+64];
        t_3dvec dim;
+       double help;
 
        dim.x=v->dim.x;
        dim.y=v->dim.y;
        dim.z=v->dim.z;
 
-       //sprintf(file,"%s/visualize_%07.f.xyz",v->fb,time);
-       sprintf(file,"%s/povray_%07.f.in",v->fb,time);
+       help=(dim.x+dim.y);
+
+       sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,time);
        fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
        if(fd<0) {
                perror("open visual save file fd");
@@ -87,6 +115,7 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
        }
 
        /* script file update */
+       /* obsolete!
        dprintf(v->fd,"load xyz %s\n",file);
        dprintf(v->fd,"spacefill 200\n");
        dprintf(v->fd,"rotate x 100\n");
@@ -98,17 +127,19 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
        sprintf(file,"%s/visualize_%07.f.ppm",v->fb,time);
        dprintf(v->fd,"write ppm %s\n",file);
        dprintf(v->fd,"zap\n");
+       */
 
        /* write the actual data file */
        //dprintf(fd,"%d\n",(dim.x==0)?n:n+8);
-       dprintf(fd,"# [C] %d\n",n);
-       dprintf(fd,"# [T] %07.f\n",time);
-       dprintf(fd,"# [L] <%f,%f,%f>\n",-1.0*dim.x/4.0,
-                                       1.5*dim.y,1.5*dim.z);
+       dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+               n,time,help/40.0,help/40.0,-0.8*help);
        for(i=0;i<n;i++)
-               dprintf(fd,"0.5 %f %f %f\n",atom[i].r.x,
-                                           atom[i].r.y,
-                                           atom[i].r.z);
+               dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
+                                                atom[i].r.x,
+                                                atom[i].r.y,
+                                                atom[i].r.z,
+                                                pse_col[atom[i].element],
+                                                atom[i].ekin);
        if(dim.x) {
                dprintf(fd,"# [D] %f %f %f %f %f %f\n",
                        -dim.x/2,-dim.y/2,-dim.z/2,
index b85b83939134cfd6a54ecf9e08f85feabe29539b..f24e7b76490b011ef4766078ab190eaf586f316c 100755 (executable)
--- a/visualize
+++ b/visualize
@@ -1,15 +1,60 @@
 #!/bin/sh
 
-if [ ! -d $1 ] ; then
-       echo "no such directory -> $1"
-       exit
+#
+# visualization script
+# author: frank.zirkelbach@physik.uni-augsburg.de
+#
+
+directory="doesnt_exist____for_sure"
+width="1024"
+height="768"
+radius="1.0"
+x0=""; y0=""; z0="";
+x1=""; y1=""; z1="";
+cx=""; cy=""; cz="";
+lx="0"; ly="-100"; lz="100";
+
+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)             lx=$2; ly=$3; lz=$4;    shift 4;;
+               -o)             ortographic=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 "visualization volume:"
+                               echo "  -nll <x> <y> <z> (near lower left)"
+                               echo "  -fur <x> <y> <z> (far upper right)"
+                               echo "  -o (ortographic)"
+                               echo "povray:"
+                               echo "  -c <x> <y> <z> (camera position)"
+                               echo "  -l <x> <y> <z> (light source)"
+                               exit 1;;
+       esac
+done
+               
+if [ ! -d $directory ] ; then
+       echo "no valid directory"
+       exit 1
 fi
 
-POVRAY="povray -W1024 -H768 -d" 
+POVRAY="povray -W${width} -H${height} -d" 
 
-echo "processing $1 ..."
+for file in $directory/atomic_conf_*.xyz; do
 
-for file in $1/povray_*.in ; do
        cat > temp.pov <<-EOF
 #include "colors.inc"
 #include "textures.inc"
@@ -21,49 +66,75 @@ for file in $1/povray_*.in ; do
 EOF
 
        # meta info
-       count=`grep '# \[C\]' $file | awk '{ print $3 }'`
-       time=`grep '# \[T\]' $file | awk '{ print $3 }'`
-       camloc=`grep '# \[L\]' $file | awk '{ print $3 }'`
+       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
-       cat $file | grep -v '#' | while read radius x y z ; do #temp dis; do
-               cat >> temp.pov <<-EOF
+       if [ -n "$x0" ]; then
+               export x0 y0 z0 x1 y1 z1 radius
+               cat $file | grep -v '#' | awk '\
+               BEGIN {
+                       x0=ENVIRON["x0"]; y0==ENVIRON["y0"]; z0==ENVIRON["z0"];
+                       x1=ENVIRON["x1"]; y0==ENVIRON["y1"]; z0==ENVIRON["z1"];
+                       radius=ENVIRON["radius"];
+               }
+               {
+                       if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
+                          ($2<=x1)&&($3<=y1)&&($4<=z1)) {
+                               print "sphere { <"$2","$4","$3">, "radius" ";
+                               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>, $radius
-       texture {
-               pigment { color Yellow }
-               finish {
-                       phong 1
-                       metallic
-                }
-       }
+<$x, $z, $y>, $radius
+texture {
+pigment { color $color }
+finish {
+phong 1
+metallic
+}
+}
 }
 EOF
-       done
+               done
+       fi
 
        # boundaries
+       if [ -z "$x0" ]; then
        cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
                cat >> temp.pov <<-EOF
 cylinder {
-       <$x1, $z1, $y1>, <$x2, $z2, $y2>, 0.05
-       pigment { color White }
+<$x1, $z1, $y1>, <$x2, $z2, $y2>, 0.05
+pigment { color White }
 }
 EOF
        done
+       fi
 
        # add camera and light source
        cat >> temp.pov <<-EOF
 camera {
-//     orthographic
-       location $camloc
-       look_at <0,0,0>
+EOF
+       if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
+orthographic
+EOF
+       fi
+       cat >> temp.pov <<-EOF
+location $camloc
+look_at <0,0,0>
 }
-light_source { <0,10000,0> color White shadowless }
+light_source { <0,100,-100> color White shadowless }
 EOF
 
        # mv png
        $POVRAY temp.pov > /dev/null 2>&1
-       mv temp.png `echo $file | sed 's/\.in/\.png/'`
+       mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 
 done