From: hackbard <hackbard>
Date: Thu, 14 Dec 2006 13:52:42 +0000 (+0000)
Subject: safety ci
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=785f05e0c0ddb57428dc71b0a3f7798673799871;p=physik%2Fposic.git

safety ci
---

diff --git a/Makefile b/Makefile
index 0250883..42ff2bd 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,9 @@
 CC=gcc-3.4
 #CC=gcc
-CFLAGS=-Wall# -O3 #-DSIMPLE_TESTING
+CFLAGS=-Wall
+CFLAGS+=-O3
+CFLAGS+=-g
+CFLAGS+=-ffloat-store
 LDFLAGS=-lm
 
 OBJS=visual/visual.o random/random.o
diff --git a/moldyn.c b/moldyn.c
index 7a77898..c25fed3 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -19,11 +19,6 @@
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
-	//int ret;
-
-	//ret=moldyn_parse_argv(moldyn,argc,argv);
-	//if(ret<0) return ret;
-
 	memset(moldyn,0,sizeof(t_moldyn));
 
 	rand_init(&(moldyn->random),NULL,1);
@@ -101,7 +96,7 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
-	printf("[moldyn] dimensions in A and A^2 respectively:\n");
+	printf("[moldyn] dimensions in A and A^3 respectively:\n");
 	printf("  x: %f\n",moldyn->dim.x);
 	printf("  y: %f\n",moldyn->dim.y);
 	printf("  z: %f\n",moldyn->dim.z);
@@ -230,6 +225,10 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * creating lattice functions
+ */
+
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                    u8 attr,u8 bnum,int a,int b,int c) {
 
@@ -288,6 +287,90 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	return ret;
 }
 
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j;
+	t_3dvec o,r,n;
+	t_3dvec basis[3];
+	double help[3];
+	double x,y,z;
+
+	x=a*lc;
+	y=b*lc;
+	z=c*lc;
+
+	if(origin) v3_copy(&o,origin);
+	else v3_zero(&o);
+
+	/* construct the basis */
+	for(i=0;i<3;i++) {
+		for(j=0;j<3;j++) {
+			if(i!=j) help[j]=0.5*lc;
+			else help[j]=.0;
+		}
+		v3_set(&basis[i],help);
+	}
+
+	v3_zero(&r);
+	count=0;
+	
+	/* fill up the room */
+	r.x=o.x;
+	while(r.x<x) {
+		r.y=o.y;
+		while(r.y<y) {
+			r.z=o.z;
+			while(r.z<z) {
+				v3_copy(&(atom[count].r),&r);
+				atom[count].element=1;
+				count+=1;
+				for(i=0;i<3;i++) {
+					v3_add(&n,&r,&basis[i]);
+					if((n.x<x+o.x)&&
+					   (n.y<y+o.y)&&
+					   (n.z<z+o.z)) {
+						v3_copy(&(atom[count].r),&n);
+						count+=1;
+					}
+				}
+				r.z+=lc;	
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	/* coordinate transformation */
+	help[0]=x/2.0;
+	help[1]=y/2.0;
+	help[2]=z/2.0;
+	v3_set(&n,help);
+	for(i=0;i<count;i++)
+		v3_sub(&(atom[i].r),&(atom[i].r),&n);
+		
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}
+
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
              t_3dvec *r,t_3dvec *v) {
 
@@ -571,24 +654,28 @@ int link_cell_init(t_moldyn *moldyn) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny,nz;
+	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+	double x,y,z;
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
 	ny=lc->ny;
-	nz=lc->nz;
+
+	x=moldyn->dim.x/2;
+	y=moldyn->dim.y/2;
+	z=moldyn->dim.z/2;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy_f(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(lc->subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
-		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
-		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
-		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
+		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
 		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 		                     &(atom[count]));
 	}
@@ -777,11 +864,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
-{
-printf("going to do p scale ...\n");
 			scale_volume(moldyn);
-printf("done\n");
-}
 
 		/* check for log & visualization */
 		if(e) {
@@ -860,16 +943,13 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-//if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 		check_per_bound(moldyn,&(atom[i].r));
-//if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
-//moldyn_bc_check(moldyn);
 	/* neighbour list update */
 	link_cell_update(moldyn);
 
@@ -1027,7 +1107,7 @@ int potential_force_calc(t_moldyn *moldyn) {
  * periodic boundayr checking
  */
 
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
 	double x,y,z;
 	t_3dvec *dim;
@@ -1746,91 +1826,3 @@ x=dim->x/2;
 
 	return 0;
 }
-
-/*
- * lattice creation functions
- */
-
-/* fcc lattice init */
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
-	int count;
-	int i,j;
-	t_3dvec o,r,n;
-	t_3dvec basis[3];
-	double help[3];
-	double x,y,z;
-
-	x=a*lc;
-	y=b*lc;
-	z=c*lc;
-
-	if(origin) v3_copy(&o,origin);
-	else v3_zero(&o);
-
-	/* construct the basis */
-	for(i=0;i<3;i++) {
-		for(j=0;j<3;j++) {
-			if(i!=j) help[j]=0.5*lc;
-			else help[j]=.0;
-		}
-		v3_set(&basis[i],help);
-	}
-
-	v3_zero(&r);
-	count=0;
-	
-	/* fill up the room */
-	r.x=o.x;
-	while(r.x<x) {
-		r.y=o.y;
-		while(r.y<y) {
-			r.z=o.z;
-			while(r.z<z) {
-				v3_copy(&(atom[count].r),&r);
-				atom[count].element=1;
-				count+=1;
-				for(i=0;i<3;i++) {
-					v3_add(&n,&r,&basis[i]);
-					if((n.x<x+o.x)&&
-					   (n.y<y+o.y)&&
-					   (n.z<z+o.z)) {
-						v3_copy(&(atom[count].r),&n);
-						count+=1;
-					}
-				}
-				r.z+=lc;	
-			}
-			r.y+=lc;
-		}
-		r.x+=lc;
-	}
-
-	/* coordinate transformation */
-	help[0]=x/2.0;
-	help[1]=y/2.0;
-	help[2]=z/2.0;
-	v3_set(&n,help);
-	for(i=0;i<count;i++)
-		v3_sub(&(atom[i].r),&(atom[i].r),&n);
-		
-	return count;
-}
-
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
-	int count;
-	t_3dvec o;
-
-	count=fcc_init(a,b,c,lc,atom,origin);
-
-	o.x=0.25*lc;
-	o.y=0.25*lc;
-	o.z=0.25*lc;
-
-	if(origin) v3_add(&o,&o,origin);
-
-	count+=fcc_init(a,b,c,lc,&atom[count],&o);
-
-	return count;
-}
diff --git a/moldyn.h b/moldyn.h
index af54cef..c01bc9f 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -377,6 +377,8 @@ 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 fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
              t_3dvec *r,t_3dvec *v);
 int destroy_atoms(t_moldyn *moldyn);
@@ -404,6 +406,8 @@ int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
 int potential_force_calc(t_moldyn *moldyn);
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
+	__attribute__((always_inline));
 int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
@@ -415,7 +419,4 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-
 #endif
diff --git a/ppm2avi b/ppm2avi
index 4a630a7..74e65cf 100755
--- a/ppm2avi
+++ b/ppm2avi
@@ -2,4 +2,4 @@ for i in $1/*.ppm; do
 	convert $i $1/$(basename $i ppm)png
 done
 
-mencoder mf://$1/*.png -ovc copy -o video/md.avi
+mencoder mf://$1/*.png -ovc copy -o $1/md.avi
diff --git a/run b/run
index af5d425..2110d43 100755
--- a/run
+++ b/run
@@ -1,6 +1,6 @@
 mkdir -p saves video
 ./clean $1
-./sic
+./sic $1
 if [ "$?" == "0" ]; then
 	#./perms
 	if [ "$1" ] ; then
diff --git a/sic.c b/sic.c
index 45e671f..7ab3dc9 100644
--- a/sic.c
+++ b/sic.c
@@ -12,6 +12,14 @@
 #include "posic.h"
 
 int main(int argc,char **argv) {
+
+	/* check argv */
+	if(argc!=2) {
+		printf("[sic] error: arg1 (vis/log/save location) ");
+		printf("must be given!\n");
+		return -1;
+	}
+
 	/* main moldyn structure */
 	t_moldyn md;
 
@@ -24,7 +32,7 @@ int main(int argc,char **argv) {
 	double tau;
 
 	/* testing location & velocity vector */
-	t_3dvec r,v;
+	//t_3dvec r,v;
 
 	/* values */
 	tau=1.0e-15;	/* delta t = 1 fs */
@@ -129,8 +137,8 @@ int main(int argc,char **argv) {
 
 	/* set temperature */
 	printf("[sic] setting temperature\n");
-	set_temperature(&md,273.0+1410.0);
-	//set_temperature(&md,273.0+450.0);
+	//set_temperature(&md,273.0+1410.0);
+	set_temperature(&md,273.0+450.0);
 	//set_temperature(&md,273.0);
 	//set_temperature(&md,1.0);
 	//set_temperature(&md,0.0);
@@ -150,11 +158,11 @@ int main(int argc,char **argv) {
 
 	/* create the simulation schedule */
 	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,100001,1.0);
+	moldyn_add_schedule(&md,30001,1.0);
 
 	/* activate logging */
 	printf("[sic] activate logging\n");
-	moldyn_set_log_dir(&md,"saves/si_melting_point");
+	moldyn_set_log_dir(&md,argv[1]);
 	moldyn_set_log(&md,LOG_TOTAL_ENERGY,200);
 	moldyn_set_log(&md,VISUAL_STEP,200);