From 7aface2e184e527132819f17b0fa18a6e1ba4bc3 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Tue, 28 Nov 2006 15:37:00 +0000
Subject: [PATCH] well, no more segfaults -> now its getting hard to debug ...

---
 moldyn.c | 32 ++++++++++++++++++--------------
 moldyn.h |  2 +-
 sic.c    | 31 +++++++++++++++++++++++--------
 3 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index 509a45d..505f496 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -156,7 +156,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 			strncpy(moldyn->sfb,fb,63);
 			break;
 		case VISUAL_STEP:
-			moldyn->mwrite=timer;
+			moldyn->vwrite=timer;
 			strncpy(moldyn->vfb,fb,63);
 			visual_init(&(moldyn->vis),fb);
 			break;
@@ -234,7 +234,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 }
 
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v) {
+             t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
 	void *ptr;
@@ -248,10 +248,11 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 		perror("[moldyn] realloc (add atom)");
 		return -1;
 	}
-	
-	atom=ptr;
-	atom->r=r;
-	atom->v=v;
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	atom->r=*r;
+	atom->v=*v;
 	atom->element=element;
 	atom->bnum=bnum;
 	atom->attr=attr;
@@ -404,6 +405,9 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
+	int fd;
+
+	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -418,10 +422,11 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("initializing linked cells (%d)\n",lc->cells);
+	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		list_init(&(lc->subcell[i]),1);
+		//list_init(&(lc->subcell[i]),1);
+		list_init(&(lc->subcell[i]),fd);
 
  	link_cell_update(moldyn);
 	
@@ -541,6 +546,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 		perror("[moldyn] realloc (runs)");
 		return -1;
 	}
+	moldyn->schedule.runs=ptr;
 	moldyn->schedule.runs[count-1]=runs;
 
 	ptr=realloc(schedule->tau,count*sizeof(double));
@@ -548,6 +554,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 		perror("[moldyn] realloc (tau)");
 		return -1;
 	}
+	moldyn->schedule.tau=ptr;
 	moldyn->schedule.tau[count-1]=tau;
 
 	return 0;
@@ -650,12 +657,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(v) {
 			if(!(i%v)) {
-				visual_atoms(moldyn->visual,i*moldyn->tau,
+				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsteps: %d",i);
+				printf("\rsched: %d, steps: %d",sched,i);
 				fflush(stdout);
 			}
 		}
+
 	}
 
 		/* check for hooks */
@@ -695,15 +703,11 @@ int velocity_verlet(t_moldyn *moldyn) {
 	}
 
 	/* neighbour list update */
-printf("list update ...\n");
 	link_cell_update(moldyn);
-printf("done\n");
 
 	/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
 	potential_force_calc(moldyn);
 	//moldyn->potential_force_function(moldyn);
-printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
diff --git a/moldyn.h b/moldyn.h
index ae133f7..58302fb 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -296,7 +296,7 @@ int moldyn_log_shutdown(t_moldyn *moldyn);
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                    u8 attr,u8 bnum,int a,int b,int c);
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v);
+             t_3dvec *r,t_3dvec *v);
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn);
diff --git a/sic.c b/sic.c
index 47ba596..9c98857 100644
--- a/sic.c
+++ b/sic.c
@@ -31,23 +31,26 @@ int main(int argc,char **argv) {
 	t_3dvec r,v;
 
 	/* initialize moldyn */
+	printf("[sic] moldyn init\n");
 	moldyn_init(&md,argc,argv);
 
 	/* choose integration algorithm */
+	printf("[sic] setting integration algorithm\n");
 	set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 
 	/* choose potential */
-	//set_potential(&md,MOLDYN_1BP,tersoff_mult_1bp,&tp);
-	//set_potential(&md,MOLDYN_2BP,tersoff_mult_2bp,&tp);
-	//set_potential(&md,MOLDYN_3BP,tersoff_mult_3bp,&tp);
-	set_potential(&md,MOLDYN_2BP,lennard_jones,&lj);
+	printf("[sic] selecting potential\n");
+	//set_potential1b(&md,tersoff_mult_1bp,&tp);
+	//set_potential2b(&md,tersoff_mult_2bp,&tp);
+	//set_potential3b(&md,tersoff_mult_3bp,&tp);
+	set_potential2b(&md,lennard_jones,&lj);
 
 	/*
 	 * potential parameters
 	 */
 
 	/* lennard jones */
-	lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA;
+	lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
 	lj.sigma6*=lj.sigma6;
 	lj.sigma12=lj.sigma6*lj.sigma6;
 	lj.epsilon4=4.0*LJ_EPSILON_SI;
@@ -57,15 +60,19 @@ int main(int argc,char **argv) {
 	ho.spring_constant=1;
 
 	/* cutoff radius */
+	printf("[sic] setting cutoff radius\n");
 	set_cutoff(&md,LC_SI);
 
 	/* set (initial) dimensions of simulation volume */
+	printf("[sic] setting dimensions\n");
 	set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
 
 	/* set periodic boundary conditions in all directions */
+	printf("[sic] setting periodic boundary conditions\n");
 	set_pbc(&md,TRUE,TRUE,TRUE);
 
 	/* create the lattice / place atoms */
+	printf("[sic] creating atoms\n");
 	memset(&v,0,sizeof(t_3dvec));
 	r.y=0;
 	r.z=0;
@@ -75,13 +82,21 @@ int main(int argc,char **argv) {
 	add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
 
 	/* set temperature */
+	printf("[sic] setting temperature\n");
 	set_temperature(&md,0.0);
 	
 	/* initial thermal fluctuations of particles */
+	printf("[sic] thermal init\n");
 	thermal_init(&md);
 
 	/* create the simulation schedule */
-	moldyn_add_schedule(&md,10000,1.0e-15);
+	printf("[sic] adding schedule\n");
+	moldyn_add_schedule(&md,1000,1.0e-15);
+
+	/* activate logging */
+	printf("[sic] activate logging\n");
+	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
+	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",50);
 
 	/*
 	 * let's do the actual md algorithm now
@@ -89,12 +104,12 @@ int main(int argc,char **argv) {
 	 * integration of newtons equations
 	 */
 
+	printf("[sic] integration start, go get a coffee ...\n");
 	moldyn_integrate(&md);
 
 	/* close */
 
-	link_cell_shutdown(&md);
-
+	printf("[sic] shutdown\n");
 	moldyn_shutdown(&md);
 	
 	return 0;
-- 
2.20.1