security ci

diff --git a/moldyn.c b/moldyn.c
index 2f274c2..a978541 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -252,11 +252,12 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
        moldyn->atom=ptr;
 
        atom=moldyn->atom;
-       atom->r=*r;
-       atom->v=*v;
-       atom->element=element;
-       atom->bnum=bnum;
-       atom->attr=attr;
+       atom[count-1].r=*r;
+       atom[count-1].v=*v;
+       atom[count-1].element=element;
+       atom[count-1].mass=mass;
+       atom[count-1].bnum=bnum;
+       atom[count-1].attr=attr;
 
        return 0;
 }
@@ -327,6 +328,12 @@ int scale_velocity(t_moldyn *moldyn) {
        /*
         * - velocity scaling (E = 3/2 N k T), E: kinetic energy
         */
+
+       if(moldyn->t==0.0) {
+               printf("[moldyn] no velocity scaling for T = 0 K\n");
+               return -1;
+       }
+
        e=0.0;
        for(i=0;i<moldyn->count;i++)
                e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
@@ -587,11 +594,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
        unsigned int e,m,s,v;
        t_3dvec p;
        t_moldyn_schedule *schedule;
+       t_atom *atom;
 
        int fd;
        char fb[128];
 
        schedule=&(moldyn->schedule);
+       atom=moldyn->atom;
 
        /* initialize linked cell method */
        link_cell_init(moldyn);
@@ -609,6 +618,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* calculate initial forces */
        potential_force_calc(moldyn);
 
+       /* accuracy check */
+       ds=0.5*moldyn->tau_square*v3_norm(&(atom[0].f))/atom[0].mass;
+       if(ds>moldyn->lc.
+
        /* zero absolute time */
        moldyn->time=0.0;
 
@@ -700,7 +713,7 @@ int velocity_verlet(t_moldyn *moldyn) {
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
                v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
-               v3_per_bound(&(atom[i].r),&(moldyn->dim));
+               check_per_bound(moldyn,&(atom[i].r));
 
                /* velocities */
                v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -749,7 +762,6 @@ int potential_force_calc(t_moldyn *moldyn) {
        /* reset energy */
        moldyn->energy=0.0;
 
-printf("DEBUG: count = %d\n",count);
        for(i=0;i<count;i++) {
        
                /* reset force */
@@ -762,7 +774,6 @@ printf("DEBUG: count = %d\n",count);
                /* 2 body pair potential/force */
                if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
        
-printf("DEBUG: processing atom %d\n",i);
                        link_cell_neighbour_index(moldyn,
                                (atom[i].r.x+moldyn->dim.x/2)/lc->x,
                                (atom[i].r.y+moldyn->dim.y/2)/lc->y,
@@ -772,7 +783,6 @@ printf("DEBUG: processing atom %d\n",i);
                        countn=lc->countn;
                        dnlc=lc->dnlc;
 
-printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
                        for(j=0;j<countn;j++) {
 
                                this=&(neighbour[j]);
@@ -791,7 +801,6 @@ printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 
                                        if((btom->attr&ATOM_ATTR_2BP)&
                                           (atom[i].attr&ATOM_ATTR_2BP))
-printf("DEBUG: calling func2b\n");
                                                moldyn->func2b(moldyn,
                                                               &(atom[i]),
                                                               btom,
@@ -898,7 +907,6 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        v3_sub(&distance,&(ai->r),&(aj->r));
        
-       v3_per_bound(&distance,&(moldyn->dim));
        if(bc) check_per_bound(moldyn,&distance);
        d=v3_norm(&distance);
        if(d<=moldyn->cutoff) {
@@ -942,7 +950,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                d=+h1-h2;
                d*=eps;
                v3_scale(&force,&distance,d);
-               v3_add(&(ai->f),&(aj->f),&force);
+               v3_add(&(ai->f),&(ai->f),&force);
        }
 
        return 0;

diff --git a/sic.c b/sic.c
index 3924375..9cb2c55 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -83,6 +83,10 @@ int main(int argc,char **argv) {
        add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
        r.x=-r.x;
        add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
+       printf("[sic] check: there are %d atoms\n",md.count);
+       printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
+       printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
+       printf("[sic] check: atoms mass: %.35f %.35f\n",md.atom[0].mass,md.atom[1].mass);
 
        /* set temperature */
        printf("[sic] setting temperature\n");
@@ -91,6 +95,9 @@ int main(int argc,char **argv) {
        /* initial thermal fluctuations of particles */
        printf("[sic] thermal init\n");
        thermal_init(&md);
+       printf("[sic] check: there are %d atoms\n",md.count);
+       printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
+       printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
@@ -98,8 +105,8 @@ int main(int argc,char **argv) {
 
        /* 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",100);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
+       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
 
        /*
         * let's do the actual md algorithm now

diff --git a/visual/visual.c b/visual/visual.c
index 03c20a1..d675c5d 100644 (file)
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -94,7 +94,7 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
        dprintf(v->fd,"rotate y 10\n");
        dprintf(v->fd,"set ambient 20\n");
        dprintf(v->fd,"set specular on\n");
-       dprintf(v->fd,"label\n");
+       //dprintf(v->fd,"label\n");
        sprintf(file,"%s-%.15f.ppm",v->fb,time);
        dprintf(v->fd,"write ppm %s\n",file);
        dprintf(v->fd,"zap\n");