added offset feature

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 12cb49b..15dcede 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -78,6 +78,10 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
        pthread_mutex_init(&emutex,NULL);
 #endif
 
+#ifdef CONSTRAINT_110_5832
+       printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
+       printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
+#endif
        return 0;
 }
 
@@ -516,7 +520,8 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                    u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
-                   t_part_params *p_params,t_defect_params *d_params) {
+                   t_part_params *p_params,t_defect_params *d_params,
+                   t_offset_params *o_params) {
 
        int new,count;
        int ret;
@@ -588,6 +593,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
 
        switch(type) {
                case CUBIC:
+                       if(o_params->use)
+                               v3_add(&orig,&orig,&(o_params->o));
                        set_nn_dist(moldyn,lc);
                        ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
                        strcpy(name,"cubic");
@@ -595,6 +602,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                case FCC:
                        if(!origin)
                                v3_scale(&orig,&orig,0.5);
+                       if(o_params->use)
+                               v3_add(&orig,&orig,&(o_params->o));
                        set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
                        ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
                        strcpy(name,"fcc");
@@ -602,6 +611,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                case DIAMOND:
                        if(!origin)
                                v3_scale(&orig,&orig,0.25);
+                       if(o_params->use)
+                               v3_add(&orig,&orig,&(o_params->o));
                        set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
                        ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
                        strcpy(name,"diamond");
@@ -802,8 +813,6 @@ int del_atom(t_moldyn *moldyn,int tag) {
                        case DEFECT_STYPE_DB_Z:\
                                d_o.z=d_params->od;\
                                d_d.z=d_params->dd;\
-d_d.x=0.9;\
-d_d.y=0.9;\
                                break;\
                        case DEFECT_STYPE_DB_R:\
                                break;\
@@ -2228,6 +2237,22 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
 
        }
 
+       /* writing a final save file! */
+       if(s) {
+               snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
+               fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+               if(fd<0) perror("[moldyn] save fd open");
+               else {
+                       write(fd,moldyn,sizeof(t_moldyn));
+                       write(fd,moldyn->atom,
+                             moldyn->count*sizeof(t_atom));
+               }
+               close(fd);
+       }
+       /* writing a final visual file! */
+       if(a)
+               visual_atoms(moldyn);
+
        return 0;
 }
 
@@ -2245,6 +2270,12 @@ int velocity_verlet(t_moldyn *moldyn) {
        tau=moldyn->tau;
        tau_square=moldyn->tau_square;
 
+#ifdef CONSTRAINT_110_5832
+       if(count==5833) {
+               atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
+               atom[5832].f.y=-atom[5832].f.x;
+       }
+#endif
        for(i=0;i<count;i++) {
                /* check whether fixed atom */
                if(atom[i].attr&ATOM_ATTR_FP)
@@ -2252,8 +2283,20 @@ int velocity_verlet(t_moldyn *moldyn) {
                /* new positions */
                h=0.5/atom[i].mass;
                v3_scale(&delta,&(atom[i].v),tau);
+#ifdef CONSTRAINT_110_5832
+               if(i==5832) {
+                       delta.y=-delta.x;
+               }
+#endif
+#ifndef QUENCH
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
+#endif
                v3_scale(&delta,&(atom[i].f),h*tau_square);
+#ifdef CONSTRAINT_110_5832
+               if(i==5832) {
+                       delta.y=-delta.x;
+               }
+#endif
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
                //check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
                check_per_bound(moldyn,&(atom[i].r));
@@ -2280,6 +2323,12 @@ int velocity_verlet(t_moldyn *moldyn) {
        albe_potential_force_calc(moldyn);
 #endif
 
+#ifdef CONSTRAINT_110_5832
+       if(count==5833) {
+               atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
+               atom[5832].f.y=-atom[5832].f.x;
+       }
+#endif
        for(i=0;i<count;i++) {
                /* check whether fixed atom */
                if(atom[i].attr&ATOM_ATTR_FP)
@@ -2862,7 +2911,7 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
        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("  modifying offset:\n");
                printf("  - current pos: %d\n",sizeof(t_moldyn));
                printf("  - atom size: %d\n",size);
                printf("  - file size: %d\n",fsize);