linked cell list updates (not well working by now!)

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 4b58089..6e76bc0 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);
        
@@ -461,7 +505,7 @@ 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;
@@ -512,6 +556,8 @@ 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;
 }
 
@@ -548,9 +594,6 @@ 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);