X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.c;h=7698c24767b90de44a165602077a46714d86d476;hp=bc4fdffdee29be7341c67692f1a3282bc049927b;hb=a16579f010cb5d53b7bf44e854089019ab9b1df0;hpb=1965279af348fbb9b69459d01516bbcd52b6f240

diff --git a/moldyn.c b/moldyn.c
index bc4fdff..7698c24 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -736,6 +736,9 @@ int del_atom(t_moldyn *moldyn,int tag) {
 
 	t_atom *new,*old;
 	int cnt;
+#if defined LOWMEM_LISTS || defined PTHREADS
+	void *ptr;
+#endif
 
 	old=moldyn->atom;
 
@@ -758,6 +761,28 @@ int del_atom(t_moldyn *moldyn,int tag) {
 
 	free(old);
 
+#ifdef LOWMEM_LISTS
+	ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
+	if(!ptr) {
+		perror("[moldyn] list realloc (del atom)");
+		return -1;
+	}
+	moldyn->lc.subcell->list=ptr;
+	// update lists
+	link_cell_update(moldyn);
+#endif
+
+#ifdef PTHREADS
+	ptr=realloc(amutex,moldyn->count*sizeof(pthread_mutex_t));
+	if(!ptr) {
+		perror("[moldyn] mutex realloc (add atom)");
+		return -1;
+	}
+	amutex=ptr;
+	pthread_mutex_destroy(&(amutex[moldyn->count+1]));
+#endif
+
+
 	return 0;
 }
 
@@ -2065,10 +2090,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(e) {
 			if(!(moldyn->total_steps%e))
 				dprintf(moldyn->efd,
-				        "%f %f %f %f\n",
+				        "%f %f %f %f %f %f\n",
 				        moldyn->time,moldyn->ekin/energy_scale,
 				        moldyn->energy/energy_scale,
-				        get_total_energy(moldyn)/energy_scale);
+				        get_total_energy(moldyn)/energy_scale,
+				        moldyn->ekin/EV,moldyn->energy/EV);
 		}
 		if(m) {
 			if(!(moldyn->total_steps%m)) {
@@ -3203,9 +3229,8 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
 	ba=data;
 
 	/* increase total bond counter
-	 * ... double counting!
 	 */
-	ba->tcnt+=2;
+	ba->tcnt+=1;
 
 	if(itom->brand==0)
 		ba->acnt[jtom->tag]+=1;
@@ -3222,10 +3247,11 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
 
 int bond_analyze(t_moldyn *moldyn,double *quality) {
 
-	// by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
-
-	int qcnt;
-	int ccnt,cset;
+	int qcnt4;
+	int qcnt3;
+	int ccnt4;
+	int ccnt3;
+	int bcnt;
 	t_ba ba;
 	int i;
 	t_atom *atom;
@@ -3245,9 +3271,9 @@ int bond_analyze(t_moldyn *moldyn,double *quality) {
 	memset(ba.bcnt,0,moldyn->count*sizeof(int));
 
 	ba.tcnt=0;
-	qcnt=0;
-	ccnt=0;
-	cset=0;
+	qcnt4=0; qcnt3=0;
+	ccnt4=0; ccnt3=0;
+	bcnt=0;
 
 	atom=moldyn->atom;
 
@@ -3256,27 +3282,30 @@ int bond_analyze(t_moldyn *moldyn,double *quality) {
 	for(i=0;i<moldyn->count;i++) {
 		if(atom[i].brand==0) {
 			if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
-				qcnt+=4;
+				qcnt4+=4;
+			if((ba.acnt[i]==0)&(ba.bcnt[i]==3))
+				qcnt3+=3;
 		}
 		else {
 			if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
-				qcnt+=4;
-				ccnt+=1;
+				qcnt4+=4;
+				ccnt4+=1;
 			}
-			cset+=1;
+			if((ba.acnt[i]==3)&(ba.bcnt[i]==0)) {
+				qcnt3+=4;
+				ccnt3+=1;
+			}
+			bcnt+=1;
 		}
 	}
 
-	printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset);
-	printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt);
-
 	if(quality) {
-		quality[0]=1.0*ccnt/cset;
-		quality[1]=1.0*qcnt/ba.tcnt;
+		quality[0]=1.0*ccnt4/bcnt;
+		quality[1]=1.0*ccnt3/bcnt;
 	}
 	else {
-		printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt);
-		printf("[moldyn] bond analyze:   tot_q=%f\n",1.0*qcnt/ba.tcnt);
+		printf("[moldyn] bond analyze: %f %f\n",
+		       1.0*ccnt4/bcnt,1.0*ccnt3/bcnt);
 	}
 
 	return 0;