X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=062224b99f65ff80a9b5f97c338ed184e9524538;hb=f0e4c6422ec1aff0cf86597fef919335bba75c1b;hp=f402e40e1566eb198166aaa12effc443a9370310;hpb=0dcc7bab1d1dbd22996c9de848ed54d5d9be656b;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index f402e40..062224b 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -96,6 +96,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_DEL_ATOMS:
 			psize=sizeof(t_del_atoms_params);
 			break;
+		case STAGE_MODIFY_ATOMS:
+			psize=sizeof(t_modify_atoms_params);
+			break;
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
@@ -164,6 +167,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	int i,o;
 
 	t_displace_atom_params dap;
+	t_modify_atoms_params map;
 	t_insert_atoms_params iap;
 	t_insert_mixed_atoms_params imp;
 	t_continue_params cp;
@@ -198,6 +202,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 
 		// reset
 		memset(&iap,0,sizeof(t_insert_atoms_params));
+		memset(&map,0,sizeof(t_modify_atoms_params));
 		memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 		memset(&cp,0,sizeof(t_continue_params));
 		memset(&ap,0,sizeof(t_anneal_params));
@@ -388,6 +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);
@@ -415,12 +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) {
@@ -522,6 +535,22 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				delp.r=atof(word[5]);
 				add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
 			}
+			else if(!strncmp(word[1],"mod_atoms",8)) {
+				i=2;
+				while(i<wcnt) {
+					if(!strncmp(word[i],"t",1)) {
+						map.tag=atoi(word[++i]);
+						i+=1;
+					}
+					if(!strncmp(word[i],"ekin",5)) {
+						map.ekin.x=atof(word[++i])*EV;
+						map.ekin.y=atof(word[++i])*EV;
+						map.ekin.z=atof(word[++i])*EV;
+						i+=1;
+					}
+				}
+				add_stage(mdrun,STAGE_MODIFY_ATOMS,&map);
+			}
 			else if(!strncmp(word[1],"ins_atoms",9)) {
 				iap.ins_steps=atoi(word[2]);
 				iap.ins_atoms=atoi(word[3]);
@@ -767,7 +796,39 @@ int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	}
 
 	return 0;
+}
+
+int modify_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 
+	t_modify_atoms_params *map;
+	t_stage *stage;
+	t_atom *atom;
+	t_3dvec v;
+	int i;
+
+	atom=moldyn->atom;
+	stage=mdrun->stage.current->data;
+	map=stage->params;
+	v.x=0.0; v.y=0.0; v.z=0.0;
+
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].tag==map->tag) {
+			v.x=sqrt(2.0*fabs(map->ekin.x)/atom[i].mass);
+			if(map->ekin.x<0.0)
+				v.x=-v.x;
+			v.y=sqrt(2.0*fabs(map->ekin.y)/atom[i].mass);
+			if(map->ekin.y<0.0)
+				v.y=-v.y;
+			v.z=sqrt(2.0*fabs(map->ekin.z)/atom[i].mass);
+			if(map->ekin.z<0.0)
+				v.z=-v.z;
+			v3_copy(&(atom[i].v),&v);
+			printf("%s atom modified: v = (%f %f %f)\n",
+                               ME,v.x,v.y,v.z);
+		}
+	}	
+
+	return 0;
 }
 
 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
@@ -899,7 +960,23 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 		printf("%s atom inserted (%d/%d): %f %f %f\n",
 		       ME,(iap->cnt_steps+1)*iap->ins_atoms,
 		       iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
-		printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
+		printf("  attributes: ");
+		if(iap->attr&ATOM_ATTR_VB)
+			printf("b ");
+		if(iap->attr&ATOM_ATTR_HB)
+			printf("h ");
+		if(iap->attr&ATOM_ATTR_VA)
+			printf("v ");
+		if(iap->attr&ATOM_ATTR_FP)
+			printf("f ");
+		if(iap->attr&ATOM_ATTR_1BP)
+			printf("1 ");
+		if(iap->attr&ATOM_ATTR_2BP)
+			printf("2 ");
+		if(iap->attr&ATOM_ATTR_3BP)
+			printf("3 ");
+		printf("\n");
+		printf("  d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 		cnt+=1;
 	}
 
@@ -1026,22 +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;
 }
 
@@ -1151,6 +1233,11 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				del_atoms(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
+			case STAGE_MODIFY_ATOMS:
+				stage_print(" -> modify atoms\n\n");
+				modify_atoms(moldyn,mdrun);
+				change_stage=TRUE;
+				break;
 			case STAGE_INSERT_ATOMS:
 				stage_print("  -> insert atoms\n\n");
 				iap=stage->params;
@@ -1238,7 +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;
@@ -1249,7 +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:
@@ -1262,7 +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);