extended debugging, implemented fixed position attribute

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 94beb04..80cf572 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -1738,6 +1738,9 @@ int velocity_verlet(t_moldyn *moldyn) {
        tau_square=moldyn->tau_square;
 
        for(i=0;i<count;i++) {
+               /* check whether fixed atom */
+               if(atom[i].attr&ATOM_ATTR_FP)
+                       continue;
                /* new positions */
                h=0.5/atom[i].mass;
                v3_scale(&delta,&(atom[i].v),tau);
@@ -1761,6 +1764,9 @@ int velocity_verlet(t_moldyn *moldyn) {
        potential_force_calc(moldyn);
 
        for(i=0;i<count;i++) {
+               /* check whether fixed atom */
+               if(atom[i].attr&ATOM_ATTR_FP)
+                       continue;
                /* again velocities [actually v(t+tau)] */
                v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
                v3_add(&(atom[i].v),&(atom[i].v),&delta);
@@ -2088,9 +2094,9 @@ int potential_force_calc(t_moldyn *moldyn) {
        //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
        if(moldyn->time>DSTART&&moldyn->time<DEND) {
                printf("force:\n");
-               printf("  x: %0.40f\n",moldyn->atom[5832].f.x);
-               printf("  y: %0.40f\n",moldyn->atom[5832].f.y);
-               printf("  z: %0.40f\n",moldyn->atom[5832].f.z);
+               printf("  x: %0.40f\n",moldyn->atom[DATOM].f.x);
+               printf("  y: %0.40f\n",moldyn->atom[DATOM].f.y);
+               printf("  z: %0.40f\n",moldyn->atom[DATOM].f.z);
        }
 #endif
 
@@ -2223,6 +2229,8 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 
        int fd;
        int cnt,size;
+       int fsize;
+       int corr;
 
        fd=open(file,O_RDONLY);
        if(fd<0) {
@@ -2230,6 +2238,9 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
                return fd;
        }
 
+       fsize=lseek(fd,0,SEEK_END);
+       lseek(fd,0,SEEK_SET);
+
        size=sizeof(t_moldyn);
 
        while(size) {
@@ -2243,6 +2254,19 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 
        size=moldyn->count*sizeof(t_atom);
 
+       /* correcting possible atom data offset */
+       corr=0;
+       if(fsize!=sizeof(t_moldyn)+size) {
+               corr=fsize-sizeof(t_moldyn)-size;
+               printf("[moldyn] WARNING: lsf (illegal file size)\n");
+               printf("  moifying offset:\n");
+               printf("  - current pos: %d\n",sizeof(t_moldyn));
+               printf("  - atom size: %d\n",size);
+               printf("  - file size: %d\n",fsize);
+               printf("  => correction: %d\n",corr);
+               lseek(fd,corr,SEEK_CUR);
+       }
+
        moldyn->atom=(t_atom *)malloc(size);
        if(moldyn->atom==NULL) {
                perror("[moldyn] load save file malloc (atoms)");