X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=062224b99f65ff80a9b5f97c338ed184e9524538;hb=f0e4c6422ec1aff0cf86597fef919335bba75c1b;hp=f0edd0bac7546bed88625c1d7a3242a0a2632650;hpb=03dbca0a50d2f2e929c1feac3b145abf5575490b;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index f0edd0b..062224b 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -393,6 +393,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					continue;
 
 				}
+				// offset
+				if(word[i][0]=='o') {
+					fp.o_params.o.x=atof(word[++i])*fp.lc;
+					fp.o_params.o.y=atof(word[++i])*fp.lc;
+					fp.o_params.o.z=atof(word[++i])*fp.lc;
+					fp.o_params.use=1;
+					continue;
+				}
 				i+=1;
 			}
 			add_stage(mdrun,STAGE_FILL,&fp);
@@ -420,12 +428,12 @@ 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 +1103,27 @@ 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;
 		}
+		if(!(cap->type&CHAATTR_TOTALV))
+			printf("  changing attributes of atom %d (0x%x)\n",
+			       i,cap->attr);
 		atom->attr=cap->attr;
 	}
 
+	printf("\n\n");
+
 	return 0;
 }
 
@@ -1312,7 +1325,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					               fp->lx,fp->ly,fp->lz,
 					               &o,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					o.x+=0.25*fp->lc;
 					o.y=o.x;
 					o.z=o.x;
@@ -1323,7 +1337,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					               fp->lx,fp->ly,fp->lz,
 					               &o,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					break;
 
 					default:
@@ -1336,7 +1351,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					               fp->lx,fp->ly,fp->lz,
 					               NULL,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					break;
 				}
 				moldyn_bc_check(moldyn);