From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Wed, 29 Jul 2009 16:51:34 +0000 (+0200)
Subject: fixed attrr region + ifdef'ed constraints along 110 + write final save and visual... 
X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=commitdiff_plain;h=beac6be36b6859ff09d1d5c426b762a9fb34c03d

fixed attrr region + ifdef'ed constraints along 110 + write final save and visual file!
---

diff --git a/mdrun.c b/mdrun.c
index f0edd0b..31e5f0a 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -420,12 +420,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			}
 			i=2;
 			if(cap.type&CHAATTR_REGION) {
-				cap.x0=atof(word[1]);	
-				cap.y0=atof(word[2]);	
-				cap.z0=atof(word[3]);	
-				cap.x1=atof(word[4]);	
-				cap.y1=atof(word[5]);	
-				cap.z1=atof(word[6]);
+				cap.x0=atof(word[2]);	
+				cap.y0=atof(word[3]);	
+				cap.z0=atof(word[4]);	
+				cap.x1=atof(word[5]);	
+				cap.y1=atof(word[6]);	
+				cap.z1=atof(word[7]);
 				i+=6;
 			}
 			if(cap.type&CHAATTR_ELEMENT) {
@@ -1095,22 +1095,25 @@ int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 				continue;
 		}
 		if(cap->type&CHAATTR_REGION) {
-			if(cap->x0<atom->r.x)
+			if(cap->x0>atom->r.x)
 				continue;
-			if(cap->y0<atom->r.y)
+			if(cap->y0>atom->r.y)
 				continue;
-			if(cap->z0<atom->r.z)
+			if(cap->z0>atom->r.z)
 				continue;
-			if(cap->x1>atom->r.x)
+			if(cap->x1<atom->r.x)
 				continue;
-			if(cap->y1>atom->r.y)
+			if(cap->y1<atom->r.y)
 				continue;
-			if(cap->z1>atom->r.z)
+			if(cap->z1<atom->r.z)
 				continue;
 		}
+		printf("  changing attributes of atom %d (0x%x)\n",i,cap->attr);
 		atom->attr=cap->attr;
 	}
 
+	printf("\n\n");
+
 	return 0;
 }
 
diff --git a/moldyn.c b/moldyn.c
index 12cb49b..d3d63eb 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -78,6 +78,10 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 	pthread_mutex_init(&emutex,NULL);
 #endif
 
+#ifdef CONSTRAINT_110_5832
+	printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
+	printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
+#endif
 	return 0;
 }
 
@@ -2228,6 +2232,22 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
 
 	}
 
+	/* writing a final save file! */
+	if(s) {
+		snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
+		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);
+	}
+	/* writing a final visual file! */
+	if(a)
+		visual_atoms(moldyn);
+
 	return 0;
 }
 
@@ -2245,6 +2265,12 @@ int velocity_verlet(t_moldyn *moldyn) {
 	tau=moldyn->tau;
 	tau_square=moldyn->tau_square;
 
+#ifdef CONSTRAINT_110_5832
+	if(count==5833) {
+		atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
+		atom[5832].f.y=-atom[5832].f.x;
+	}
+#endif
 	for(i=0;i<count;i++) {
 		/* check whether fixed atom */
 		if(atom[i].attr&ATOM_ATTR_FP)
@@ -2252,8 +2278,18 @@ int velocity_verlet(t_moldyn *moldyn) {
 		/* new positions */
 		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
+#ifdef CONSTRAINT_110_5832
+		if(i==5832) {
+			delta.y=-delta.x;
+		}
+#endif
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),h*tau_square);
+#ifdef CONSTRAINT_110_5832
+		if(i==5832) {
+			delta.y=-delta.x;
+		}
+#endif
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		//check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
 		check_per_bound(moldyn,&(atom[i].r));
@@ -2280,6 +2316,12 @@ int velocity_verlet(t_moldyn *moldyn) {
 	albe_potential_force_calc(moldyn);
 #endif
 
+#ifdef CONSTRAINT_110_5832
+	if(count==5833) {
+		atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
+		atom[5832].f.y=-atom[5832].f.x;
+	}
+#endif
 	for(i=0;i<count;i++) {
 		/* check whether fixed atom */
 		if(atom[i].attr&ATOM_ATTR_FP)
@@ -2862,7 +2904,7 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 	if(fsize!=sizeof(t_moldyn)+size) {
 		corr=fsize-sizeof(t_moldyn)-size;
 		printf("[moldyn] WARNING: lsf (illegal file size)\n");
-		printf("  moifying offset:\n");
+		printf("  modifying offset:\n");
 		printf("  - current pos: %d\n",sizeof(t_moldyn));
 		printf("  - atom size: %d\n",size);
 		printf("  - file size: %d\n",fsize);