pot hopefully ok, doing timestep tests for 450C now ...

diff --git a/moldyn.c b/moldyn.c
index f8bfd3f..5aa6d87 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -767,23 +767,23 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
        t_moldyn_schedule *schedule;
 
        schedule=&(moldyn->schedule);
-       count=++(schedule->content_count);
+       count=++(schedule->total_sched);
 
-       ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+       ptr=realloc(schedule->runs,count*sizeof(int));
        if(!ptr) {
                perror("[moldyn] realloc (runs)");
                return -1;
        }
-       moldyn->schedule.runs=ptr;
-       moldyn->schedule.runs[count-1]=runs;
+       schedule->runs=ptr;
+       schedule->runs[count-1]=runs;
 
        ptr=realloc(schedule->tau,count*sizeof(double));
        if(!ptr) {
                perror("[moldyn] realloc (tau)");
                return -1;
        }
-       moldyn->schedule.tau=ptr;
-       moldyn->schedule.tau[count-1]=tau;
+       schedule->tau=ptr;
+       schedule->tau[count-1]=tau;
 
        return 0;
 }
@@ -806,16 +806,16 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 
 int moldyn_integrate(t_moldyn *moldyn) {
 
-       int i,sched;
+       int i;
        unsigned int e,m,s,v;
        t_3dvec p;
-       t_moldyn_schedule *schedule;
+       t_moldyn_schedule *sched;
        t_atom *atom;
        int fd;
        char dir[128];
        double ds;
 
-       schedule=&(moldyn->schedule);
+       sched=&(moldyn->schedule);
        atom=moldyn->atom;
 
        /* initialize linked cell method */
@@ -852,12 +852,12 @@ int moldyn_integrate(t_moldyn *moldyn) {
        moldyn->debug=0;
 
        /* executing the schedule */
-       for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+       for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
 
                /* setting amount of runs and finite time step size */
-               moldyn->tau=schedule->tau[sched];
+               moldyn->tau=sched->tau[sched->count];
                moldyn->tau_square=moldyn->tau*moldyn->tau;
-               moldyn->time_steps=schedule->runs[sched];
+               moldyn->time_steps=sched->runs[sched->count];
 
        /* integration according to schedule */
 
@@ -907,7 +907,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
                                visual_atoms(&(moldyn->vis),moldyn->time,
                                             moldyn->atom,moldyn->count);
                                printf("\rsched: %d, steps: %d, debug: %d",
-                                      sched,i,moldyn->debug);
+                                      sched->count,i,moldyn->debug);
                                fflush(stdout);
                        }
                }
@@ -918,8 +918,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
        }
 
                /* check for hooks */
-               if(schedule->hook)
-                       schedule->hook(moldyn,schedule->hook_params);
+               if(sched->hook)
+                       sched->hook(moldyn,sched->hook_params);
 
                /* get a new info line */
                printf("\n");
@@ -1108,6 +1108,9 @@ int potential_force_calc(t_moldyn *moldyn) {
                }
 
        }
+#ifdef DEBUG
+printf("\n\n");
+#endif
 
        return 0;
 }
@@ -1397,6 +1400,14 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        /* add forces of 2bp (ij, ji) contribution
         * dVij = dVji and we sum up both: no 1/2) */
        v3_add(&(ai->f),&(ai->f),&force);
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+       printf("dVij, dVji (2bp) contrib:\n");
+       printf("%f | %f\n",force.x,ai->f.x);
+       printf("%f | %f\n",force.y,ai->f.y);
+       printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
 
        /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
        moldyn->energy+=(0.5*f_r*f_c);
@@ -1488,6 +1499,14 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        /* add force */
        v3_add(&(ai->f),&(ai->f),&force);
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+       printf("dVij (3bp) contrib:\n");
+       printf("%f | %f\n",force.x,ai->f.x);
+       printf("%f | %f\n",force.y,ai->f.y);
+       printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
 
        /* add energy of 3bp sum */
        moldyn->energy+=(0.5*f_c*b*f_a);
@@ -1516,6 +1535,14 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        /* add force */
        v3_add(&(ai->f),&(ai->f),&force);
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+       printf("dVji (3bp) contrib:\n");
+       printf("%f | %f\n",force.x,ai->f.x);
+       printf("%f | %f\n",force.y,ai->f.y);
+       printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
 
        return 0;
 }
@@ -1777,6 +1804,14 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
                v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
                v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
                                                  /* scaled with 0.5 ^ */
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+       printf("dVjk (3bp) contrib:\n");
+       printf("%f | %f\n",temp2.x,ai->f.x);
+       printf("%f | %f\n",temp2.y,ai->f.y);
+       printf("%f | %f\n",temp2.z,ai->f.z);
+}
+#endif
 
        }
 

diff --git a/moldyn.h b/moldyn.h
index 9493f5f..38e4999 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -57,7 +57,8 @@ typedef struct s_linkcell {
 
 /* moldyn schedule structure */
 typedef struct s_moldyn_schedule {
-       int content_count;
+       int count;
+       int total_sched;
        int *runs;
        double *tau;
        int (*hook)(void *moldyn,void *hook);

diff --git a/run b/run
index 3a15543..5a3a768 100755 (executable)
--- a/run
+++ b/run
@@ -1,6 +1,6 @@
 mkdir -p saves video
 ./clean $1
-./sic $1
+./sic $@
 if [ "$?" == "0" ]; then
        #./perms
        if [ "$1" ] ; then

diff --git a/sic.c b/sic.c
index f4cdd7d..35931e0 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -14,9 +14,8 @@
 int main(int argc,char **argv) {
 
        /* check argv */
-       if(argc!=2) {
-               printf("[sic] error: arg1 (vis/log/save location) ");
-               printf("must be given!\n");
+       if(argc!=3) {
+               printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
                return -1;
        }
 
@@ -32,7 +31,7 @@ int main(int argc,char **argv) {
        double tau;
 
        /* testing location & velocity vector */
-       //t_3dvec r,v;
+       t_3dvec r,v;
 
        /* values */
        tau=1.0e-15;    /* delta t = 1 fs */
@@ -119,29 +118,30 @@ int main(int argc,char **argv) {
        moldyn_bc_check(&md);
 
        /* testing configuration */
-       //r.x=2.45/2;   v.x=0;
+       //r.x=2.95/2;   v.x=0;
        //r.y=0;                v.y=0;
        //r.z=0;                v.z=0;
        //add_atom(&md,SI,M_SI,0,
-       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
        //           &r,&v);
-       //r.x=-2.45/2;  v.x=0;
+       //r.x=-2.95/2;  v.x=0;
        //r.y=0;                v.y=0;
        //r.z=0;                v.z=0;
        //add_atom(&md,SI,M_SI,0,
-       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
        //           &r,&v);
 
        /* setting a nearest neighbour distance for the moldyn checks */
        set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
 
        /* set temperature */
-       printf("[sic] setting temperature\n");
+       printf("[sic] setting temperature -> %f\n",273+atof(argv[2]));
        //set_temperature(&md,273.0+1410.0);
-       set_temperature(&md,273.0+450.0);
+       //set_temperature(&md,273.0+450.0);
        //set_temperature(&md,273.0);
        //set_temperature(&md,1.0);
        //set_temperature(&md,0.0);
+       set_temperature(&md,atof(argv[2])+273.0);
 
        /* set pressure */
        printf("[sic] setting pressure\n");
@@ -159,13 +159,17 @@ int main(int argc,char **argv) {
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,20001,1.0);
+       moldyn_add_schedule(&md,20000,.1);
+       moldyn_add_schedule(&md,10000,.2);
+       moldyn_add_schedule(&md,6667,.3);
+       moldyn_add_schedule(&md,5000,.4);
+       moldyn_add_schedule(&md,4001,.5);
 
        /* activate logging */
        printf("[sic] activate logging\n");
        moldyn_set_log_dir(&md,argv[1]);
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,200);
-       moldyn_set_log(&md,VISUAL_STEP,200);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,100);
+       moldyn_set_log(&md,VISUAL_STEP,100);
 
        /*
         * let's do the actual md algorithm now