well, no more segfaults -> now its getting hard to debug ...

diff --git a/moldyn.c b/moldyn.c
index 509a45d..505f496 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -156,7 +156,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
                        strncpy(moldyn->sfb,fb,63);
                        break;
                case VISUAL_STEP:
-                       moldyn->mwrite=timer;
+                       moldyn->vwrite=timer;
                        strncpy(moldyn->vfb,fb,63);
                        visual_init(&(moldyn->vis),fb);
                        break;
@@ -234,7 +234,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 }
 
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v) {
+             t_3dvec *r,t_3dvec *v) {
 
        t_atom *atom;
        void *ptr;
@@ -248,10 +248,11 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
                perror("[moldyn] realloc (add atom)");
                return -1;
        }
-       
-       atom=ptr;
-       atom->r=r;
-       atom->v=v;
+       moldyn->atom=ptr;
+
+       atom=moldyn->atom;
+       atom->r=*r;
+       atom->v=*v;
        atom->element=element;
        atom->bnum=bnum;
        atom->attr=attr;
@@ -404,6 +405,9 @@ int link_cell_init(t_moldyn *moldyn) {
 
        t_linkcell *lc;
        int i;
+       int fd;
+
+       fd=open("/dev/null",O_WRONLY);
 
        lc=&(moldyn->lc);
 
@@ -418,10 +422,11 @@ int link_cell_init(t_moldyn *moldyn) {
        lc->cells=lc->nx*lc->ny*lc->nz;
        lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-       printf("initializing linked cells (%d)\n",lc->cells);
+       printf("[moldyn] 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]),1);
+               list_init(&(lc->subcell[i]),fd);
 
        link_cell_update(moldyn);
        
@@ -541,6 +546,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
                perror("[moldyn] realloc (runs)");
                return -1;
        }
+       moldyn->schedule.runs=ptr;
        moldyn->schedule.runs[count-1]=runs;
 
        ptr=realloc(schedule->tau,count*sizeof(double));
@@ -548,6 +554,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
                perror("[moldyn] realloc (tau)");
                return -1;
        }
+       moldyn->schedule.tau=ptr;
        moldyn->schedule.tau[count-1]=tau;
 
        return 0;
@@ -650,12 +657,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
                }
                if(v) {
                        if(!(i%v)) {
-                               visual_atoms(moldyn->visual,i*moldyn->tau,
+                               visual_atoms(&(moldyn->vis),moldyn->time,
                                             moldyn->atom,moldyn->count);
-                               printf("\rsteps: %d",i);
+                               printf("\rsched: %d, steps: %d",sched,i);
                                fflush(stdout);
                        }
                }
+
        }
 
                /* check for hooks */
@@ -695,15 +703,11 @@ int velocity_verlet(t_moldyn *moldyn) {
        }
 
        /* neighbour list update */
-printf("list update ...\n");
        link_cell_update(moldyn);
-printf("done\n");
 
        /* forces depending on chosen potential */
-printf("calc potential/force ...\n");
        potential_force_calc(moldyn);
        //moldyn->potential_force_function(moldyn);
-printf("done\n");
 
        for(i=0;i<count;i++) {
                /* again velocities */

diff --git a/moldyn.h b/moldyn.h
index ae133f7..58302fb 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -296,7 +296,7 @@ int moldyn_log_shutdown(t_moldyn *moldyn);
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                    u8 attr,u8 bnum,int a,int b,int c);
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v);
+             t_3dvec *r,t_3dvec *v);
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn);

diff --git a/sic.c b/sic.c
index 47ba596..9c98857 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -31,23 +31,26 @@ int main(int argc,char **argv) {
        t_3dvec r,v;
 
        /* initialize moldyn */
+       printf("[sic] moldyn init\n");
        moldyn_init(&md,argc,argv);
 
        /* choose integration algorithm */
+       printf("[sic] setting integration algorithm\n");
        set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 
        /* choose potential */
-       //set_potential(&md,MOLDYN_1BP,tersoff_mult_1bp,&tp);
-       //set_potential(&md,MOLDYN_2BP,tersoff_mult_2bp,&tp);
-       //set_potential(&md,MOLDYN_3BP,tersoff_mult_3bp,&tp);
-       set_potential(&md,MOLDYN_2BP,lennard_jones,&lj);
+       printf("[sic] selecting potential\n");
+       //set_potential1b(&md,tersoff_mult_1bp,&tp);
+       //set_potential2b(&md,tersoff_mult_2bp,&tp);
+       //set_potential3b(&md,tersoff_mult_3bp,&tp);
+       set_potential2b(&md,lennard_jones,&lj);
 
        /*
         * potential parameters
         */
 
        /* lennard jones */
-       lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA;
+       lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
        lj.sigma6*=lj.sigma6;
        lj.sigma12=lj.sigma6*lj.sigma6;
        lj.epsilon4=4.0*LJ_EPSILON_SI;
@@ -57,15 +60,19 @@ int main(int argc,char **argv) {
        ho.spring_constant=1;
 
        /* cutoff radius */
+       printf("[sic] setting cutoff radius\n");
        set_cutoff(&md,LC_SI);
 
        /* set (initial) dimensions of simulation volume */
+       printf("[sic] setting dimensions\n");
        set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
 
        /* set periodic boundary conditions in all directions */
+       printf("[sic] setting periodic boundary conditions\n");
        set_pbc(&md,TRUE,TRUE,TRUE);
 
        /* create the lattice / place atoms */
+       printf("[sic] creating atoms\n");
        memset(&v,0,sizeof(t_3dvec));
        r.y=0;
        r.z=0;
@@ -75,13 +82,21 @@ int main(int argc,char **argv) {
        add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
 
        /* set temperature */
+       printf("[sic] setting temperature\n");
        set_temperature(&md,0.0);
        
        /* initial thermal fluctuations of particles */
+       printf("[sic] thermal init\n");
        thermal_init(&md);
 
        /* create the simulation schedule */
-       moldyn_add_schedule(&md,10000,1.0e-15);
+       printf("[sic] adding schedule\n");
+       moldyn_add_schedule(&md,1000,1.0e-15);
+
+       /* activate logging */
+       printf("[sic] activate logging\n");
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
+       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",50);
 
        /*
         * let's do the actual md algorithm now
@@ -89,12 +104,12 @@ int main(int argc,char **argv) {
         * integration of newtons equations
         */
 
+       printf("[sic] integration start, go get a coffee ...\n");
        moldyn_integrate(&md);
 
        /* close */
 
-       link_cell_shutdown(&md);
-
+       printf("[sic] shutdown\n");
        moldyn_shutdown(&md);
        
        return 0;