From 45f9190fc7489f3f9ff8f0d917945b1d5bc9d584 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Fri, 26 Sep 2008 11:11:52 +0200
Subject: [PATCH] io thread needed for visual atom call! changed.

---
 moldyn.c | 83 ++++++++++++++++++++++++--------------------------------
 moldyn.h |  4 +++
 2 files changed, 40 insertions(+), 47 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index 4788a81..e936b11 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1608,33 +1608,6 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
  *
  */
 
-/* helper / special functions */
-
-#ifdef PTHREADS
-void *write_save_file(void *ptr) {
-
-	int fd;
-	char dir[128];
-	t_moldyn *moldyn;
-
-	moldyn=ptr;
-
-	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);
-	if(fd<0) perror("[moldyn] save fd open");
-	else {
-		write(fd,moldyn,sizeof(t_moldyn));
-		write(fd,moldyn->atom,moldyn->count*sizeof(t_atom));
-	}
-
-	close(fd);
-
-	pthread_exit(NULL);
-
-	return 0;
-}
-#endif
-
 /* start the integration */
 
 int moldyn_integrate(t_moldyn *moldyn) {
@@ -1644,10 +1617,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	t_3dvec momentum;
 	t_moldyn_schedule *sched;
 	t_atom *atom;
-#ifndef PTHREADS
 	int fd;
 	char dir[128];
-#endif
 	double ds;
 	double energy_scale;
 	struct timeval t1,t2;
@@ -1806,6 +1777,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(s) {
 			if(!(moldyn->total_steps%s)) {
+				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);
+				if(fd<0) perror("[moldyn] save fd open");
+				else {
+					write(fd,moldyn,sizeof(t_moldyn));
+					write(fd,moldyn->atom,
+					      moldyn->count*sizeof(t_atom));
+				}
+				close(fd);
+			}	
+		}
+		if(a) {
+			if(!(moldyn->total_steps%a)) {
 #ifdef PTHREADS
 	/* check whether thread has not terminated yet */
 	if(!first) {
@@ -1828,29 +1814,14 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	md_copy.atom=atom_copy;
 	memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
 	change=0;
-	ret=pthread_create(&io_thread,NULL,write_save_file,&md_copy);
+	ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
 	if(ret) {
-		perror("[moldyn] create save file thread\n");
+		perror("[moldyn] create visual atoms thread\n");
 		return -1;
 	}
 #else
-				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);
-				if(fd<0) perror("[moldyn] save fd open");
-				else {
-					write(fd,moldyn,sizeof(t_moldyn));
-					write(fd,moldyn->atom,
-					      moldyn->count*sizeof(t_atom));
-				}
-				close(fd);
-#endif
-			}	
-		}
-		if(a) {
-			if(!(moldyn->total_steps%a)) {
 				visual_atoms(moldyn);
+#endif
 			}
 		}
 
@@ -3002,7 +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];
@@ -3011,6 +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;
@@ -3024,7 +3004,9 @@ int visual_atoms(t_moldyn *moldyn) {
 	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 */
@@ -3090,8 +3072,15 @@ int visual_atoms(t_moldyn *moldyn) {
 
 	close(vb.fd);
 
+#ifdef PTHREADS
+	pthread_exit(NULL);
+
+}
+#else
+
 	return 0;
 }
+#endif
 
 /*
  * fpu cntrol functions
diff --git a/moldyn.h b/moldyn.h
index 87c8948..31794c8 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -481,7 +481,11 @@ int bond_analyze(t_moldyn *moldyn,double *quality);
 int visual_init(t_moldyn *moldyn,char *filebase);
 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
                          void *data,u8 bc);
+#ifdef PTHREADS
+void *visual_atoms(void *ptr);
+#else
 int visual_atoms(t_moldyn *moldyn);
+#endif
 
 int fpu_set_rtd(void);
 
-- 
2.20.1