X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=bd70d007ab1f430e031de6b879aface7dd5713f3;hb=a16579f010cb5d53b7bf44e854089019ab9b1df0;hp=d0636939c17b68ac6d9f0206b95b076d023aa158;hpb=dfb47bde6bf974d1b231048ec8bcda712404ccc1;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index d063693..bd70d00 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -98,6 +98,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_DISPLACE_ATOM:
 			psize=sizeof(t_displace_atom_params);
 			break;
+		case STAGE_DEL_ATOMS:
+			psize=sizeof(t_del_atoms_params);
+			break;
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
@@ -161,7 +164,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	char error[128];
 	char line[128];
 	char *wptr;
-	char word[16][64];
+	char word[32][64];
 	int wcnt;
 	int i,o;
 
@@ -175,6 +178,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	t_set_temp_params stp;
 	t_set_timestep_params stsp;
 	t_fill_params fp;
+	t_del_atoms_params delp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -207,6 +211,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		memset(&stp,0,sizeof(t_set_temp_params));
 		memset(&stsp,0,sizeof(t_set_timestep_params));
 		memset(&fp,0,sizeof(t_fill_params));
+		memset(&delp,0,sizeof(t_del_atoms_params));
 
 		// get command + args
 		wcnt=0;
@@ -293,6 +298,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			fp.lattice=mdrun->lattice;
 			fp.p_params.type=0;
 			fp.d_params.type=0;
+			fp.d_params.stype=0;
 			// parse fill command
 			i=1;
 			while(i<wcnt) {
@@ -508,6 +514,13 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				dap.dz=atof(word[5]);
 				add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 			}
+			else if(!strncmp(word[1],"del_atoms",9)) {
+				delp.o.x=atof(word[2]);
+				delp.o.y=atof(word[3]);
+				delp.o.z=atof(word[4]);
+				delp.r=atof(word[5]);
+				add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
+			}
 			else if(!strncmp(word[1],"ins_atoms",9)) {
 				iap.ins_steps=atoi(word[2]);
 				iap.ins_atoms=atoi(word[3]);
@@ -549,19 +562,32 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						iap.z0=atof(word[10]);
 						break;
 					case 'r':
-						if(word[8][0]=='t') {
+						switch(word[8][0]) {
+
+						case 't':
 							iap.type=INS_TOTAL;
 							iap.cr=atof(word[9]);
-						}
-						else {
-							iap.type=INS_REGION;
-							iap.x0=atof(word[8]);
-							iap.y0=atof(word[9]);
-							iap.z0=atof(word[10]);
-							iap.x1=atof(word[11]);
-							iap.y1=atof(word[12]);
-							iap.z1=atof(word[13]);
-							iap.cr=atof(word[14]);
+							break;
+						case 'r':
+							iap.type=INS_RECT;
+							iap.x0=atof(word[9]);
+							iap.y0=atof(word[10]);
+							iap.z0=atof(word[11]);
+							iap.x1=atof(word[12]);
+							iap.y1=atof(word[13]);
+							iap.z1=atof(word[14]);
+							iap.cr=atof(word[15]);
+							break;
+						case 's':
+							iap.type=INS_SPHERE;
+							iap.x0=atof(word[9]);
+							iap.y0=atof(word[10]);
+							iap.z0=atof(word[11]);
+							iap.x1=atof(word[12]);
+							iap.cr=atof(word[13]);
+							break;
+						default:
+							break;
 						}
 					default:
 						break;
@@ -718,6 +744,31 @@ int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
+int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_stage *stage;
+	t_del_atoms_params *delp;
+	int i;
+	t_3dvec dist;
+	
+	stage=mdrun->stage.current->data;
+	delp=stage->params;
+
+	for(i=0;i<moldyn->count;i++) {
+		v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
+//printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
+		if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
+			del_atom(moldyn,moldyn->atom[i].tag);
+			printf("%s atom deleted: %d %d %d\n",ME,
+                               moldyn->atom[i].tag,moldyn->atom[i].element,
+			       moldyn->atom[i].brand);
+		}
+	}
+
+	return 0;
+
+}
+
 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_insert_atoms_params *iap;
@@ -764,7 +815,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 			z0=-z/2.0;
 			cr_check=TRUE;
 			break;
-		case INS_REGION:
+		case INS_RECT:
 			x=iap->x1-iap->x0;
 			x0=iap->x0;
 			y=iap->y1-iap->y0;
@@ -773,6 +824,15 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 			z0=iap->z0;
 			cr_check=TRUE;
 			break;
+		case INS_SPHERE:
+			x=2.0*iap->x1;
+			x0=iap->x0-iap->x1;
+			y=x;
+			y0=iap->y0-iap->x1;
+			z=x;
+			z0=iap->z0-iap->x1;
+			cr_check=TRUE;
+			break;
 		case INS_POS:
 			x0=iap->x0;
 			y0=iap->y0;
@@ -824,6 +884,14 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 						dmin=d;
 				}
 			}
+			if(iap->type==INS_SPHERE) {
+				if((r.x-iap->x0)*(r.x-iap->x0)+
+				   (r.y-iap->y0)*(r.y-iap->y0)+
+				   (r.z-iap->z0)*(r.z-iap->z0)>
+				   (iap->x1*iap->x1)) {
+					run=1;
+				}
+			}
 		}
 		add_atom(moldyn,iap->element,
 		         iap->brand,iap->attr,&r,&v);
@@ -1077,6 +1145,11 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				displace_atom(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
+			case STAGE_DEL_ATOMS:
+				stage_print(" -> del atoms\n\n");
+				del_atoms(moldyn,mdrun);
+				change_stage=TRUE;
+				break;
 			case STAGE_INSERT_ATOMS:
 				stage_print("  -> insert atoms\n\n");
 				iap=stage->params;