X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=bd70d007ab1f430e031de6b879aface7dd5713f3;hb=a16579f010cb5d53b7bf44e854089019ab9b1df0;hp=6effe1aff6c56f33b635da11e332e27a4252b65e;hpb=d843bfcc38ac4ad1ceffbb82a1aba8096f791b41;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index 6effe1a..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;
@@ -277,66 +282,115 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				mdrun->lattice=DIAMOND;
 			if(!strncmp(word[1],"none",4))
 				mdrun->lattice=NONE;
+			if(wcnt==3)
+				mdrun->lc=atof(word[2]);
 		}
 		else if(!strncmp(word[0],"element1",8)) {
 			mdrun->element1=atoi(word[1]);
-			mdrun->m1=pse_mass[mdrun->element1];
 		}
 		else if(!strncmp(word[0],"element2",8)) {
 			mdrun->element2=atoi(word[1]);
-			mdrun->m2=pse_mass[mdrun->element2];
 		}
 		else if(!strncmp(word[0],"fill",6)) {
-			fp.lx=atoi(word[2]);
-			fp.ly=atoi(word[3]);
-			fp.lz=atoi(word[4]);
-			fp.lc=atof(word[5]);
-			mdrun->lc=fp.lc;
-			if(!strncmp(word[1],"lc",2)) {
-				if(wcnt==8) {
-					fp.fill_element=atoi(word[6]);
-					fp.fill_brand=atoi(word[7]);
+			// default values
+			fp.fill_element=mdrun->element1;
+			fp.fill_brand=0;
+			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) {
+				if(!strncmp(word[i],"lc",2)) {
+					fp.lx=atoi(word[++i]);
+					fp.ly=atoi(word[++i]);
+					fp.lz=atoi(word[++i]);
+					fp.lc=atof(word[++i]);
+					mdrun->lc=fp.lc;
 				}
-				else {
-					fp.fill_element=mdrun->element1;
-					fp.fill_brand=0;
+				if(!strncmp(word[i],"eb",2)) {
+					fp.fill_element=atoi(word[++i]);
+					fp.fill_brand=atoi(word[++i]);
 				}
-			}
-			else {
-				switch(word[6][0]) {
+				if(word[i][0]=='p') {
+					i+=1;
+					switch(word[i][0]) {
 					case 'i':
-						if(word[6][1]=='r')
-							fp.p_type=PART_INSIDE_R;
+						if(word[i][1]=='r')
+						fp.p_params.type=PART_INSIDE_R;
 						else
-							fp.p_type=PART_INSIDE_D;
+						fp.p_params.type=PART_INSIDE_D;
 						break;
 					case 'o':
-						if(word[6][1]=='r')
-						fp.p_type=PART_OUTSIDE_R;
+						if(word[i][1]=='r')
+						fp.p_params.type=PART_OUTSIDE_R;
 						else
-						fp.p_type=PART_OUTSIDE_D;
+						fp.p_params.type=PART_OUTSIDE_D;
 						break;
 					default:
 						break;
+					}
+					if((fp.p_params.type==PART_INSIDE_R)||
+                         		  (fp.p_params.type==PART_OUTSIDE_R)) {
+						fp.p_params.r=atof(word[++i]);	
+						fp.p_params.p.x=atof(word[++i]);
+						fp.p_params.p.y=atof(word[++i]);
+						fp.p_params.p.z=atof(word[++i]);
+					}
+					if((fp.p_params.type==PART_INSIDE_D)||
+					   (fp.p_params.type==PART_OUTSIDE_D)) {
+						fp.p_params.p.x=atof(word[++i]);
+						fp.p_params.p.y=atof(word[++i]);
+						fp.p_params.p.z=atof(word[++i]);
+						fp.p_params.d.x=atof(word[++i]);
+						fp.p_params.d.y=atof(word[++i]);
+						fp.p_params.d.z=atof(word[++i]);
+					}
 				}
+				if(word[i][0]=='d') {
+					switch(word[++i][0]) {
+						case '0':
+
+				fp.d_params.type=DEFECT_TYPE_0D;
+				if(!strncmp(word[i+1],"dbx",3)) {
+					fp.d_params.stype=DEFECT_STYPE_DB_X;
+				}
+				if(!strncmp(word[i+1],"dby",3)) {
+					fp.d_params.stype=DEFECT_STYPE_DB_Y;
+				}
+				if(!strncmp(word[i+1],"dbz",3)) {
+					fp.d_params.stype=DEFECT_STYPE_DB_Z;
+				}
+				if(!strncmp(word[i+1],"dbr",3)) {
+					fp.d_params.stype=DEFECT_STYPE_DB_R;
+				}
+				i+=1;
+				fp.d_params.od=atof(word[++i]);
+				fp.d_params.dd=atof(word[++i]);
+				fp.d_params.element=atoi(word[++i]);
+				fp.d_params.brand=atoi(word[++i]);
+				// parsed in future
+		fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
+		fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+				break;
+
+						case '1':
+				fp.d_params.type=DEFECT_TYPE_1D;
+				break;
+						case '2':
+				fp.d_params.type=DEFECT_TYPE_2D;
+				break;
+						case '3':
+				fp.d_params.type=DEFECT_TYPE_3D;
+				break;
+						default:
+							break;
+					}
+
+				}
+				i+=1;
 			}
-			if((fp.p_type==PART_INSIDE_R)||
-                           (fp.p_type==PART_OUTSIDE_R)) {
-				fp.p_vals.r=atof(word[7]);	
-				fp.p_vals.p.x=atof(word[8]);	
-				fp.p_vals.p.y=atof(word[9]);	
-				fp.p_vals.p.z=atof(word[10]);
-			}
-			if((fp.p_type==PART_INSIDE_D)||
-                           (fp.p_type==PART_OUTSIDE_D)) {
-				fp.p_vals.p.x=atof(word[7]);	
-				fp.p_vals.p.y=atof(word[8]);	
-				fp.p_vals.p.z=atof(word[9]);
-				fp.p_vals.d.x=atof(word[10]);	
-				fp.p_vals.d.y=atof(word[11]);	
-				fp.p_vals.d.z=atof(word[12]);
-			}
-			fp.lattice=mdrun->lattice;
 			add_stage(mdrun,STAGE_FILL,&fp);
 		}
 		else if(!strncmp(word[0],"thermal_init",12)) {
@@ -460,6 +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]);
@@ -501,19 +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;
@@ -670,6 +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;
@@ -716,7 +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;
@@ -725,6 +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;
@@ -776,8 +884,16 @@ 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,pse_mass[iap->element],
+		add_atom(moldyn,iap->element,
 		         iap->brand,iap->attr,&r,&v);
 		printf("%s atom inserted (%d/%d): %f %f %f\n",
 		       ME,(iap->cnt_steps+1)*iap->ins_atoms,
@@ -846,7 +962,7 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 					if(dmin>cmax)
 						retry=1;
 			}
-			add_atom(moldyn,imp->element1,pse_mass[imp->element1],
+			add_atom(moldyn,imp->element1,
                                  imp->brand1,imp->attr1,&r,&v);
 			printf("%s (mixed) atom inserted (%d): %f %f %f\n",
                                ME,imp->amount1,r.x,r.y,r.z);
@@ -880,7 +996,7 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 					if(dmin>cmax)
 						retry=1;
 			}
-			add_atom(moldyn,imp->element2,pse_mass[imp->element2],
+			add_atom(moldyn,imp->element2,
                                  imp->brand2,imp->attr2,&r,&v);
 			printf("%s (mixed) atom inserted (%d): %f %f %f\n",
                                ME,imp->amount2,r.x,r.y,r.z);
@@ -1029,6 +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;
@@ -1103,39 +1224,44 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 			case STAGE_FILL:
 				stage_print("  -> fill lattice\n\n");
 				fp=stage->params;
-				if(fp->lattice!=ZINCBLENDE) {
-					create_lattice(moldyn,
-					               fp->lattice,fp->lc,
-					               mdrun->element1,
-					               mdrun->m1,
-					               DEFAULT_ATOM_ATTR,0,
-					               fp->lx,fp->ly,fp->lz,
-					               NULL,fp->p_type,
-					               &(fp->p_vals));
-				}
-				else {
+				switch(fp->lattice) {
+					case ZINCBLENDE:
+
 					o.x=0.5*0.25*fp->lc;
 					o.y=o.x;
 					o.z=o.x;
 					create_lattice(moldyn,
 					               FCC,fp->lc,
 					               mdrun->element1,
-					               mdrun->m1,
 					               DEFAULT_ATOM_ATTR,0,
 					               fp->lx,fp->ly,fp->lz,
-					               &o,fp->p_type,
-					               &(fp->p_vals));
+					               &o,
+					               &(fp->p_params),
+					               &(fp->d_params));
 					o.x+=0.25*fp->lc;
 					o.y=o.x;
 					o.z=o.x;
 					create_lattice(moldyn,
 					               FCC,fp->lc,
 					               mdrun->element2,
-					               mdrun->m2,
 					               DEFAULT_ATOM_ATTR,1,
 					               fp->lx,fp->ly,fp->lz,
-					               &o,fp->p_type,
-					               &(fp->p_vals));
+					               &o,
+					               &(fp->p_params),
+					               &(fp->d_params));
+					break;
+
+					default:
+
+					create_lattice(moldyn,
+					               fp->lattice,fp->lc,
+					               mdrun->element1,
+					               DEFAULT_ATOM_ATTR,0,
+					               fp->lx,fp->ly,fp->lz,
+					               NULL,
+					               &(fp->p_params),
+					               &(fp->d_params));
+					break;
 				}
 				moldyn_bc_check(moldyn);
 				change_stage=TRUE;