X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=edda007d9290ff6cfe1001d4105c3f8a9ab12863;hb=e1080fc0dd66b0cf5b7715c5e99e7a34ac04a8cf;hp=56817795283d87b38f648283cfb2d4eeac47306f;hpb=e84546faff88301a68958b58f66f546b03294503;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 5681779..edda007 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -956,10 +956,12 @@ double pressure_calc(t_moldyn *moldyn) {
 
 int average_and_fluctuation_calc(t_moldyn *moldyn) {
 
+	int denom;
+
 	if(moldyn->total_steps<moldyn->avg_skip)
 		return 0;
 
-	int denom=moldyn->total_steps+1-moldyn->avg_skip;
+	denom=moldyn->total_steps+1-moldyn->avg_skip;
 
 	/* assume up to date energies, temperature, pressure etc */
 
@@ -1031,7 +1033,8 @@ printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->coun
 
 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 
-	t_3dvec dim,*tp;
+	t_3dvec dim;
+	//t_3dvec *tp;
 	double u_up,u_down,dv;
 	double scale,p;
 	t_atom *store;
@@ -1436,7 +1439,6 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 
 	for(i=0;i<lc->cells;i++) {
 #ifdef STATIC_LISTS
-		//printf(" ---> %d free %p\n",i,lc->subcell[i]);
 		free(lc->subcell[i]);
 #else
 		//printf(" ---> %d free %p\n",i,lc->subcell[i].start);
@@ -1650,13 +1652,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
-	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
-	       sched->count,i,
-	       moldyn->t,moldyn->t_avg,
-	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
-	       moldyn->volume,
-	       (int)(t2.tv_sec-t1.tv_sec));
-	fflush(stdout);
+printf("\rsched:%d, steps:%d/%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+       sched->count,i,moldyn->total_steps,
+       moldyn->t,moldyn->t_avg,
+       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+       moldyn->volume,
+       (int)(t2.tv_sec-t1.tv_sec));
+
+			fflush(stdout);
 
 			/* copy over time */
 			t1=t2;
@@ -1670,8 +1673,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 		/* check for hooks */
 		if(sched->hook) {
-			printf("\n ## schedule hook %d/%d start ##\n",
-			       sched->count+1,sched->total_sched-1);
+			printf("\n ## schedule hook %d start ##\n",
+			       sched->count);
 			sched->hook(moldyn,sched->hook_params);
 			printf(" ## schedule hook end ##\n");
 		}
@@ -2182,10 +2185,14 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 	}
 
 	size=sizeof(t_moldyn);
-	cnt=read(fd,moldyn,size);
-	if(cnt!=size) {
-		perror("[moldyn] load save file read (moldyn)");
-		return cnt;
+
+	while(size) {
+		cnt=read(fd,moldyn,size);
+		if(cnt<0) {
+			perror("[moldyn] load save file read (moldyn)");
+			return cnt;
+		}
+		size-=cnt;
 	}
 
 	size=moldyn->count*sizeof(t_atom);
@@ -2196,10 +2203,13 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 		return -1;
 	}
 
-	cnt=read(fd,moldyn->atom,size);
-	if(cnt!=size) {
-		perror("[moldyn] load save file read (atoms)");
-		return cnt;
+	while(size) {
+		cnt=read(fd,moldyn->atom,size);
+		if(cnt<0) {
+			perror("[moldyn] load save file read (atoms)");
+			return cnt;
+		}
+		size-=cnt;
 	}
 
 	// hooks etc ...
@@ -2258,13 +2268,14 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 	t_list *this;
 	unsigned char bc;
 	t_3dvec dist;
-	double d,norm;
+	double d;
+	//double norm;
 	int o,s;
 	unsigned char ibrand;
 
 	lc=&(moldyn->lc);
 
-	slots=(int)(moldyn->cutoff/dr);
+	slots=moldyn->cutoff/dr;
 	o=2*slots;
 
 	printf("[moldyn] pair correlation calc info:\n");
@@ -2323,12 +2334,9 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 
 				jtom=this->current->data;
 #endif
-
-				if(jtom==&(itom[i]))
-					continue;
-
-				/* only count pairs once */
-				if(itom[i].tag>jtom->tag)
+				/* only count pairs once,
+				 * skip same atoms */
+				if(itom[i].tag>=jtom->tag)
 					continue;
 
 				/*
@@ -2340,14 +2348,18 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 				if(bc) check_per_bound(moldyn,&dist);
 				d=v3_absolute_square(&dist);
 
-				/* ignore if greater cutoff */
-				if(d>moldyn->cutoff_square)
+				/* ignore if greater or equal cutoff */
+				if(d>=moldyn->cutoff_square)
 					continue;
 
 				/* fill the slots */
 				d=sqrt(d);
 				s=(int)(d/dr);
 
+				/* should never happen but it does 8) -
+				 * related to -ffloat-store problem! */
+				if(s>=slots) s=slots-1;
+
 				if(ibrand!=jtom->brand) {
 					/* mixed */
 					stat[s]+=1;
@@ -2360,7 +2372,6 @@ int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
 					/* type b - type b bonds */
 						stat[s+o]+=1;
 				}
-
 #ifdef STATIC_LISTS
 			}
 #else