fixed missing init for new atoms (especially force!) + increased insert

relaxation time + added some more critical debugging checks

diff --git a/config.h b/config.h
index f0919b7..f43f006 100644 (file)
--- a/config.h
+++ b/config.h
@@ -41,7 +41,7 @@
 
 #define INS_R_C                1.5
 #define INS_DELTA_TC   1.0
-#define INS_RELAX      50
+#define INS_RELAX      100
 #define INS_TAU                1.0
 
 // postrun

diff --git a/moldyn.c b/moldyn.c
index ec96712..94beb04 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -595,7 +595,7 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
        int count;
        
        atom=moldyn->atom;
-       count=(moldyn->count)++;
+       count=(moldyn->count)++;        // asshole style!
 
        ptr=realloc(atom,(count+1)*sizeof(t_atom));
        if(!ptr) {
@@ -605,6 +605,9 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
        moldyn->atom=ptr;
 
        atom=moldyn->atom;
+
+       /* initialize new atom */
+       memset(&(atom[count]),0,sizeof(t_atom));
        atom[count].r=*r;
        atom[count].v=*v;
        atom[count].element=element;
@@ -956,6 +959,8 @@ double pressure_calc(t_moldyn *moldyn) {
 
 int average_reset(t_moldyn *moldyn) {
 
+       printf("[moldyn] average reset\n");
+
        /* update skip value */
        moldyn->avg_skip=moldyn->total_steps;
 
@@ -1369,7 +1374,7 @@ int link_cell_update(t_moldyn *moldyn) {
                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);
-
+       
 #ifdef STATIC_LISTS
                p=0;
                while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
@@ -1419,6 +1424,10 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
        count2=27;
        a=nx*ny;
 
+       if(i>=nx||j>=ny||k>=nz)
+               printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
+                      i,nx,j,ny,k,nz);
+
        cell[0]=lc->subcell[i+j*nx+k*a];
        for(ci=-1;ci<=1;ci++) {
                bx=0;
@@ -1569,14 +1578,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
        /* some stupid checks before we actually start calculating bullshit */
        if(moldyn->cutoff>0.5*moldyn->dim.x)
-               printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+               printf("[moldyn] WARNING: cutoff > 0.5 x dim.x\n");
        if(moldyn->cutoff>0.5*moldyn->dim.y)
-               printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+               printf("[moldyn] WARNING: cutoff > 0.5 x dim.y\n");
        if(moldyn->cutoff>0.5*moldyn->dim.z)
-               printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+               printf("[moldyn] WARNING: cutoff > 0.5 x dim.z\n");
        ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
        if(ds>0.05*moldyn->nnd)
-               printf("[moldyn] warning: forces too high / tau too small!\n");
+               printf("[moldyn] WARNING: forces too high / tau too small!\n");
 
        /* zero absolute time */
        moldyn->time=0.0;
@@ -2085,14 +2094,21 @@ int potential_force_calc(t_moldyn *moldyn) {
        }
 #endif
 
-       /* calculate global virial */
+       /* some postprocessing */
        for(i=0;i<count;i++) {
-               moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
-               moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
-               moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
-               moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
-               moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
-               moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+               /* calculate global virial */
+               moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
+               moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
+               moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
+               moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
+               moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
+               moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
+
+               /* check forces regarding the given timestep */
+               if(v3_norm(&(itom[i].f))>\
+                  0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+                       printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
+                              i);
        }
 
        return 0;
@@ -2308,6 +2324,9 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
        slots=moldyn->cutoff/dr;
        o=2*slots;
 
+       if(slots*dr<=moldyn->cutoff)
+               printf("[moldyn] WARNING: pcc (low #slots)\n");
+
        printf("[moldyn] pair correlation calc info:\n");
        printf("  time: %f\n",moldyn->time);
        printf("  count: %d\n",moldyn->count);
@@ -2389,8 +2408,9 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
                                /* should never happen but it does 8) -
                                 * related to -ffloat-store problem! */
                                if(s>=slots) {
-                                       printf("[moldyn] WARNING pcc (%d/%d)\n",
+                                       printf("[moldyn] WARNING: pcc (%d/%d)",
                                               s,slots);
+                                       printf("\n");
                                        s=slots-1;
                                }
 

diff --git a/sic.c b/sic.c
index a7613e2..fb20a56 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -122,6 +122,9 @@ int sic_hook(void *moldyn,void *hook_params) {
        hp=hook_params;
        md=moldyn;
 
+       tau=1.0;
+       steps=0;
+
        /* switch on t scaling */
        if(md->schedule.count==0)
                set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
@@ -438,6 +441,9 @@ int main(int argc,char **argv) {
        moldyn_set_log(&md,SAVE_STEP,LOG_S);
        moldyn_set_log(&md,CREATE_REPORT,0);
 
+       /* next neighbour distance for critical checking */
+       set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
+
        /*
         * let's do the actual md algorithm now
         *