fixed (dank rolf)

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 4b58089..707fe03 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -35,6 +35,7 @@ int moldyn_usage(char **argv) {
        printf("--- physics options ---\n");
        printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
        printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
+       printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
        printf("-R <runs> (%d)\n",MOLDYN_RUNS);
        printf(" -- integration algo --\n");
        printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
@@ -98,6 +99,9 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
                                case 't':
                                        moldyn->tau=atof(argv[++i]);
                                        break;
+                               case 'C':
+                                       moldyn->cutoff=atof(argv[++i]);
+                                       break;
                                case 'R':
                                        moldyn->time_steps=atoi(argv[++i]);
                                        break;
@@ -153,12 +157,12 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
        return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn,void *v) {
+int moldyn_log_init(t_moldyn *moldyn) {
 
        moldyn->lvstat=0;
        t_visual *vis;
 
-       vis=v;
+       vis=&(moldyn->vis);
 
        if(moldyn->ewrite) {
                moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
@@ -204,7 +208,7 @@ int moldyn_log_init(t_moldyn *moldyn,void *v) {
        return 0;
 }
 
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
 
        if(moldyn->efd) close(moldyn->efd);
        if(moldyn->mfd) close(moldyn->efd);
@@ -214,6 +218,33 @@ int moldyn_shutdown(t_moldyn *moldyn) {
        return 0;
 }
 
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+       int ret;
+
+       ret=moldyn_parse_argv(moldyn,argc,argv);
+       if(ret<0) return ret;
+
+       ret=moldyn_log_init(moldyn);
+       if(ret<0) return ret;
+
+       rand_init(&(moldyn->random),NULL,1);
+       moldyn->random.status|=RAND_STAT_VERBOSE;
+
+       moldyn->status=0;
+
+       return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+       moldyn_log_shutdown(moldyn);
+       rand_close(&(moldyn->random));
+       free(moldyn->atom);
+
+       return 0;
+}
+
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom) {
 
@@ -270,7 +301,7 @@ int destroy_lattice(t_atom *atom) {
        return 0;
 }
 
-int thermal_init(t_moldyn *moldyn,t_random *random) {
+int thermal_init(t_moldyn *moldyn) {
 
        /*
         * - gaussian distribution of velocities
@@ -282,8 +313,10 @@ int thermal_init(t_moldyn *moldyn,t_random *random) {
        double v,sigma;
        t_3dvec p_total,delta;
        t_atom *atom;
+       t_random *random;
 
        atom=moldyn->atom;
+       random=&(moldyn->random);
 
        /* gaussian distribution of velocities */
        v3_zero(&p_total);
@@ -402,9 +435,13 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 int link_cell_init(t_moldyn *moldyn) {
 
        t_linkcell *lc;
+       int i;
 
        lc=&(moldyn->lc);
 
+       /* list log fd */
+       lc->listfd=open("/dev/null",O_WRONLY);
+
        /* partitioning the md cell */
        lc->nx=moldyn->dim.x/moldyn->cutoff;
        lc->x=moldyn->dim.x/lc->nx;
@@ -413,7 +450,14 @@ int link_cell_init(t_moldyn *moldyn) {
        lc->nz=moldyn->dim.z/moldyn->cutoff;
        lc->z=moldyn->dim.z/lc->nz;
 
-       lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+       lc->cells=lc->nx*lc->ny*lc->nz;
+       lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+       printf("initializing linked cells (%d)\n",lc->cells);
+
+       for(i=0;i<lc->cells;i++)
+               list_init(&(lc->subcell[i]),1);
+               //list_init(&(lc->subcell[i]),lc->listfd);
 
        link_cell_update(moldyn);
        
@@ -434,13 +478,13 @@ int link_cell_update(t_moldyn *moldyn) {
        ny=lc->ny;
        nz=lc->nz;
 
-       for(i=0;i<nx*ny*nz;i++)
+       for(i=0;i<lc->cells;i++)
                list_destroy(&(moldyn->lc.subcell[i]));
        
        for(count=0;count<moldyn->count;count++) {
-               i=atom[count].r.x/lc->x;
-               j=atom[count].r.y/lc->y;
-               k=atom[count].r.z/lc->z;
+               i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
+               j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
+               k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
                list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
                                       &(atom[count]));
        }
@@ -461,12 +505,14 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
        lc=&(moldyn->lc);
        nx=lc->nx;
        ny=lc->ny;
-       nx=lc->nz;
+       nz=lc->nz;
        count1=1;
        count2=27;
        a=nx*ny;
 
+
        cell[0]=lc->subcell[i+j*nx+k*a];
+       printf("%d\n",i+j*nx+k*a);
        for(ci=-1;ci<=1;ci++) {
                bx=0;
                x=i+ci;
@@ -488,12 +534,17 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
                                        z=(z+nz)%nz;
                                        bz=1;
                                }
-                               if(!(x|y|z)) continue;
+                               if(!(ci|cj|ck)) continue;
+                               printf(" %d %d %d \n",x,y,z);
                                if(bx|by|bz) {
                                        cell[--count2]=lc->subcell[x+y*nx+z*a];
+                                       printf("%d\n",x+y*nx+z*a);
+                                       printf("--- %d\n",count2);
                                }
                                else {
                                        cell[count1++]=lc->subcell[x+y*nx+z*a];
+                                       printf("%d\n",x+y*nx+z*a);
+                                       printf("--- %d\n",count1);
                                }
                        }
                }
@@ -512,6 +563,8 @@ int link_cell_shutdown(t_moldyn *moldyn) {
        for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
                list_shutdown(&(moldyn->lc.subcell[i]));
 
+       if(lc->listfd) close(lc->listfd);
+
        return 0;
 }
 
@@ -548,15 +601,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
        moldyn->tau_square=moldyn->tau*moldyn->tau;
        moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
-       /* create the neighbour list */
-       link_cell_update(moldyn);
-
        /* calculate initial forces */
        moldyn->potential_force_function(moldyn);
 
        for(i=0;i<moldyn->time_steps;i++) {
-               /* show runs */
-               printf(".");
 
                /* neighbour list update */
                link_cell_update(moldyn);
@@ -599,9 +647,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
                }
                if(v) {
-                       if(!(i%v))
+                       if(!(i%v)) {
                                visual_atoms(moldyn->visual,i*moldyn->tau,
                                             moldyn->atom,moldyn->count);
+                               printf("\rsteps: %d",i);
+                               fflush(stdout);
+                       }
                }
        }
 
@@ -679,9 +730,10 @@ int harmonic_oscillator(t_moldyn *moldyn) {
        u=0.0;
        for(i=0;i<count;i++) {
                /* determine cell + neighbours */
-               ni=atom[i].r.x/lc->x;
-               nj=atom[i].r.y/lc->y;
-               nk=atom[i].r.z/lc->z;
+               ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+               nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+               nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+               printf("%d %d %d\n",ni,nj,nk);
                c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
 
                /* processing cell of atom i */
@@ -775,10 +827,15 @@ int lennard_jones(t_moldyn *moldyn) {
        u=0.0;
        for(i=0;i<count;i++) {
                /* determine cell + neighbours */
-               ni=atom[i].r.x/lc->x;
-               nj=atom[i].r.y/lc->y;
-               nk=atom[i].r.z/lc->z;
+               ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+               nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+               nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+                       printf("hier atom = %08x\n",&(atom[i]));
                c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+                       printf("da atom = %08x\n",&(atom[i]));
+                       printf("da atom = %08x\n",&(moldyn->atom[i]));
+
+               printf("c = %d (%d %d %d)\n",c,ni,nj,nk);
 
                /* processing cell of atom i */
                this=&(neighbour[0]);
@@ -787,7 +844,9 @@ int lennard_jones(t_moldyn *moldyn) {
                        btom=this->current->data;
                        if(btom==&(atom[i]))
                                continue;
+               puts("foo");
                        v3_sub(&distance,&(atom[i].r),&(btom->r));
+               puts("foo");
                        d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
                        h1=d*d;         /* 1/r^4 */
                        h2*=d;          /* 1/r^6 */
@@ -801,6 +860,7 @@ int lennard_jones(t_moldyn *moldyn) {
                        d*=eps;
                        v3_scale(&force,&distance,d);
                        v3_add(&(atom[i].f),&(atom[i].f),&force);
+                       printf("test!!\n");
                } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
                /* neighbours not doing boundary condition overflow */
@@ -810,6 +870,7 @@ int lennard_jones(t_moldyn *moldyn) {
                        if(this->start!=NULL) {
 
                        do {
+                               printf("in bound: %d\n",j);
                                btom=this->current->data;
                                v3_sub(&distance,&(atom[i].r),&(btom->r));
                                d=v3_absolute_square(&distance); /* r^2 */
@@ -841,6 +902,7 @@ int lennard_jones(t_moldyn *moldyn) {
                        if(this->start!=NULL) {
 
                        do {
+                               printf("out bound: %d\n",j);
                                btom=this->current->data;
                                v3_sub(&distance,&(atom[i].r),&(btom->r));
                                v3_per_bound(&distance,&(moldyn->dim));