X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=e936b11d0ce5a977330d9989bc7c156cfc25e014;hb=45f9190fc7489f3f9ff8f0d917945b1d5bc9d584;hp=6da2b959c32fb3afbdd10b90a8903bc94925b5ab;hpb=99a9305339d568641a7ec55783faa161b3c33311;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 6da2b95..e936b11 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -23,6 +23,10 @@
 #include <omp.h>
 #endif
 
+#ifdef PTHREADS
+#include <pthread.h>
+#endif
+
 #include "moldyn.h"
 #include "report/report.h"
 
@@ -1620,6 +1624,17 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	struct timeval t1,t2;
 	//double tp;
 
+#ifdef PTHREADS
+	u8 first,change;
+	pthread_t io_thread;
+	int ret;
+	t_moldyn md_copy;
+	t_atom *atom_copy;
+
+	first=1;
+	change=0;
+#endif
+
 	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
 
@@ -1668,6 +1683,16 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* debugging, ignore */
 	moldyn->debug=0;
 
+	/* zero & init moldyn copy */
+#ifdef PTHREADS
+	memset(&md_copy,0,sizeof(t_moldyn));
+	atom_copy=malloc(moldyn->count*sizeof(t_atom));
+	if(atom_copy==NULL) {
+		perror("[moldyn] malloc atom copy (init)");
+		return -1;
+	}
+#endif
+
 	/* tell the world */
 	printf("[moldyn] integration start, go get a coffee ...\n");
 
@@ -1752,7 +1777,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(s) {
 			if(!(moldyn->total_steps%s)) {
-				snprintf(dir,128,"%s/s-%07.f.save",
+				snprintf(dir,128,"%s/s-%08.f.save",
 				         moldyn->vlsdir,moldyn->time);
 				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
 				        S_IRUSR|S_IWUSR);
@@ -1767,12 +1792,41 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(a) {
 			if(!(moldyn->total_steps%a)) {
+#ifdef PTHREADS
+	/* check whether thread has not terminated yet */
+	if(!first) {
+		ret=pthread_join(io_thread,NULL);
+	}
+	first=0;
+	/* prepare and start thread */
+	if(moldyn->count!=md_copy.count) {
+		free(atom_copy);
+		change=1;
+	}
+	memcpy(&md_copy,moldyn,sizeof(t_moldyn));
+	if(change) {
+		atom_copy=malloc(moldyn->count*sizeof(t_atom));
+		if(atom_copy==NULL) {
+			perror("[moldyn] malloc atom copy (change)");
+			return -1;
+		}
+	}
+	md_copy.atom=atom_copy;
+	memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
+	change=0;
+	ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
+	if(ret) {
+		perror("[moldyn] create visual atoms thread\n");
+		return -1;
+	}
+#else
 				visual_atoms(moldyn);
+#endif
 			}
 		}
 
 		/* display progress */
-		//if(!(moldyn->total_steps%10)) {
+		if(!(i%10)) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
@@ -1788,7 +1842,7 @@ printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
 
 			/* copy over time */
 			t1=t2;
-		//}
+		}
 
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
@@ -2515,6 +2569,84 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 }
 
+/*
+ * function to find neighboured atoms
+ */
+
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+                       int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+		                      void *data,u8 bc)) {
+
+	t_linkcell *lc;
+#ifdef STATIC_LISTS
+	int *neighbour[27];
+	int p;
+#elif LOWMEM_LISTS
+	int neighbour[27];
+	int p;
+#else
+	t_list neighbour[27];
+	t_list *this;
+#endif
+	u8 bc;
+	t_atom *natom;
+	int j;
+
+	lc=&(moldyn->lc);
+	
+	/* neighbour indexing */
+	link_cell_neighbour_index(moldyn,
+	                          (atom->r.x+moldyn->dim.x/2)/lc->x,
+	                          (atom->r.y+moldyn->dim.y/2)/lc->x,
+	                          (atom->r.z+moldyn->dim.z/2)/lc->x,
+	                          neighbour);
+
+	for(j=0;j<27;j++) {
+
+		bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+		p=0;
+
+		while(neighbour[j][p]!=-1) {
+
+			natom=&(moldyn->atom[neighbour[j][p]]);
+			p++;
+#elif LOWMEM_LISTS
+		p=neighbour[j];
+
+		while(p!=-1) {
+
+			natom=&(moldyn->atom[p]);
+			p=lc->subcell->list[p];
+#else
+		this=&(neighbour[j]);
+		list_reset_f(this);
+
+		if(this->start==NULL)
+			continue;
+
+		do {
+
+			natom=this->current->data;
+#endif
+
+			/* process bond */
+			process(moldyn,atom,natom,data,bc);
+
+#ifdef STATIC_LISTS
+		}
+#elif LOWMEM_LISTS
+		}
+#else
+		} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+	}
+
+	return 0;
+
+}
+
 /*
  * post processing functions
  */
@@ -2841,7 +2973,11 @@ int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
 	return 0;
 }
 
+#ifdef PTHREADS
+void *visual_atoms(void *ptr) {
+#else
 int visual_atoms(t_moldyn *moldyn) {
+#endif
 
 	int i;
  	char file[128+64];
@@ -2850,6 +2986,11 @@ int visual_atoms(t_moldyn *moldyn) {
 	t_visual *v;
 	t_atom *atom;
 	t_vb vb;
+#ifdef PTHREADS
+	t_moldyn *moldyn;
+
+	moldyn=ptr;
+#endif
 
 	v=&(moldyn->vis);
 	dim.x=v->dim.x;
@@ -2859,17 +3000,19 @@ int visual_atoms(t_moldyn *moldyn) {
 
 	help=(dim.x+dim.y);
 
-	sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
+	sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
 	vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
 	if(vb.fd<0) {
 		perror("open visual save file fd");
+#ifndef PTHREADS
 		return -1;
+#endif
 	}
 
 	/* write the actual data file */
 
 	// povray header
-	dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n",
+	dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
 	        moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
 
 	// atomic configuration
@@ -2929,8 +3072,15 @@ int visual_atoms(t_moldyn *moldyn) {
 
 	close(vb.fd);
 
+#ifdef PTHREADS
+	pthread_exit(NULL);
+
+}
+#else
+
 	return 0;
 }
+#endif
 
 /*
  * fpu cntrol functions