X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=mdrun.c;h=26fbc871708c262a19eead0b398d8773a2941902;hp=d0636939c17b68ac6d9f0206b95b076d023aa158;hb=HEAD;hpb=dfb47bde6bf974d1b231048ec8bcda712404ccc1

diff --git a/mdrun.c b/mdrun.c
index d063693..26fbc87 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -11,17 +11,13 @@
 #include "potentials/harmonic_oscillator.h"
 #include "potentials/lennard_jones.h"
 #include "potentials/albe.h"
+#include "potentials/albe_orig.h"
 #ifdef TERSOFF_ORIG
 #include "potentials/tersoff_orig.h"
 #else
 #include "potentials/tersoff.h"
 #endif
 
-/* pse */
-#define PSE_MASS
-#include "pse.h"
-#undef PSE_MASS
-
 #define ME	"[mdrun]"
 
 /*
@@ -98,6 +94,12 @@ 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_MODIFY_ATOMS:
+			psize=sizeof(t_modify_atoms_params);
+			break;
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
@@ -128,6 +130,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_THERMAL_INIT:
 			psize=0;
 			break;
+		case STAGE_CRT:
+			psize=sizeof(t_crt_params);
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -161,11 +166,12 @@ 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;
 
 	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;
@@ -175,6 +181,8 @@ 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;
+	t_crt_params crtp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -199,6 +207,7 @@ 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));
@@ -207,6 +216,8 @@ 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));
+		memset(&crtp,0,sizeof(t_crt_params));
 
 		// get command + args
 		wcnt=0;
@@ -224,6 +235,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		if(!strncmp(word[0],"potential",9)) {
 			if(!strncmp(word[1],"albe",4))
 				mdrun->potential=MOLDYN_POTENTIAL_AM;
+			if(!strncmp(word[1],"albe_o",6))
+				mdrun->potential=MOLDYN_POTENTIAL_AO;
 			if(!strncmp(word[1],"tersoff",7))
 				mdrun->potential=MOLDYN_POTENTIAL_TM;
 			if(!strncmp(word[1],"ho",2))
@@ -293,6 +306,7 @@ 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) {
@@ -302,10 +316,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					fp.lz=atoi(word[++i]);
 					fp.lc=atof(word[++i]);
 					mdrun->lc=fp.lc;
+					continue;
 				}
 				if(!strncmp(word[i],"eb",2)) {
 					fp.fill_element=atoi(word[++i]);
 					fp.fill_brand=atoi(word[++i]);
+					continue;
 				}
 				if(word[i][0]=='p') {
 					i+=1;
@@ -341,6 +357,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						fp.p_params.d.y=atof(word[++i]);
 						fp.p_params.d.z=atof(word[++i]);
 					}
+					continue;
 				}
 				if(word[i][0]=='d') {
 					switch(word[++i][0]) {
@@ -381,8 +398,17 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						default:
 							break;
 					}
+					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);
@@ -404,24 +430,30 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					case 'e':
 						cap.type|=CHAATTR_ELEMENT;
 						break;
+					case 'n':
+						cap.type|=CHAATTR_NUMBER;
 					default:
 						break;
 				}
 			}
 			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) {
 				cap.element=atoi(word[i]);
 				i+=1;
 			}
+			if(cap.type&CHAATTR_NUMBER) {
+				cap.element=atoi(word[i]);
+				i+=1;
+			}
 			for(o=0;o<strlen(word[i]);o++) {
 				switch(word[i][o]) {
 					case 'b':
@@ -457,7 +489,9 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			csp.type=0;
 			for(i=1;i<wcnt;i++) {
 				if(!strncmp(word[i],"pctrl",5)) {
-					csp.ptau=0.01/(atof(word[++i])*GPA);
+					csp.ptau=atof(word[++i]);
+					if(csp.ptau>0)
+						csp.ptau=0.01/(csp.ptau*GPA);
 					csp.type|=CHSATTR_PCTRL;
 				}
 				if(!strncmp(word[i],"tctrl",5)) {
@@ -508,6 +542,29 @@ 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],"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]);
@@ -548,20 +605,39 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						iap.y0=atof(word[9]);
 						iap.z0=atof(word[10]);
 						break;
+					case 'P':
+						iap.type=INS_RELPOS;
+						iap.x0=atof(word[8]);
+						iap.y0=atof(word[9]);
+						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;
@@ -645,6 +721,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				stsp.tau=atof(word[2]);
 				add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 			}
+			else if(!strncmp(word[1],"crt",3)) {
+				crtp.type=atoi(word[2]);
+				crtp.steps=atoi(word[3]);
+				strncpy(crtp.file,word[4],127);
+				add_stage(mdrun,STAGE_CRT,&crtp);
+			}
 			else {
 				printf("%s unknown stage type: %s\n",
 				       ME,word[1]);
@@ -718,6 +800,80 @@ 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;
+	u8 outer;
+
+	outer=0;	
+	stage=mdrun->stage.current->data;
+	delp=stage->params;
+
+	if(delp->r<0)
+		outer=1;
+
+	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)) {
+			if(!outer) {
+				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);
+			}
+		}
+		else {
+			if(outer) {
+				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 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) {
 
 	t_insert_atoms_params *iap;
@@ -764,7 +920,7 @@ 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;
@@ -773,7 +929,17 @@ 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:
+		case INS_RELPOS:
 			x0=iap->x0;
 			y0=iap->y0;
 			z0=iap->z0;
@@ -789,7 +955,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	while(cnt<iap->ins_atoms) {
 		run=1;
 		while(run) {
-			if(iap->type!=INS_POS) {
+			if((iap->type!=INS_POS)&&(iap->type!=INS_RELPOS)) {
 				r.x=rand_get_double(&(moldyn->random))*x;
 				r.y=rand_get_double(&(moldyn->random))*y;
 				r.z=rand_get_double(&(moldyn->random))*z;
@@ -799,9 +965,16 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 				r.y=0.0;
 				r.z=0.0;
 			}
-			r.x+=x0;
-			r.y+=y0;
-			r.z+=z0;
+			if(iap->type==INS_RELPOS) {
+				r.x+=x0*mdrun->lc;
+				r.y+=y0*mdrun->lc;
+				r.z+=z0*mdrun->lc;
+			}
+			else {
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+			}
 			// offset
 			if(iap->type!=INS_TOTAL) {
 				r.x+=o;
@@ -824,13 +997,37 @@ 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);
 		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;
 	}
 
@@ -956,23 +1153,32 @@ int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 			if(cap->element!=atom->element)
 				continue;
 		}
+		if(cap->type&CHAATTR_NUMBER) {
+			if(cap->element!=atom->tag)
+				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;
 }
 
@@ -988,13 +1194,13 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 		if(csp->ptau>0)
 			set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 		else
-			set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+			set_p_scale(moldyn,P_SCALE_NONE,1.0);
 	}
 	if(csp->type&CHSATTR_TCTRL) {
 		if(csp->ttau>0)
 			set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 		else
-			set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+			set_t_scale(moldyn,T_SCALE_NONE,1.0);
 	}
 	if(csp->type&CHSATTR_PRELAX) {
 		if(csp->dp<0)
@@ -1023,6 +1229,138 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
+int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_stage *stage;
+	t_crt_params *crtp;
+
+	int fd;
+	char line[128];
+	char *wptr;
+	int acount;
+	int ret;
+	void *ptr;
+
+	t_atom *atom;
+	t_3dvec disp;
+	double frac;
+	int i;
+	
+	stage=mdrun->stage.current->data;
+	crtp=stage->params;
+
+	acount=0;
+
+	/* initial stuff */
+
+	if(crtp->count==0) {
+		printf("  crt init\n");
+		// read final positions, constraints and do the alloc
+		fd=open(crtp->file,O_RDONLY);
+		if(fd<0) {
+			perror("[mdrun] FATAL reading constraints file");
+			return fd;
+		}
+		while(1) {
+			ret=get_line(fd,line,128);
+			// check for end of file
+			if(ret<=0) {
+				printf("  read %d atom positions\n",acount);
+				if(acount!=moldyn->count)
+					printf("  atom count mismatch!!!\n");
+				printf("\n");
+				break;
+			}
+			// ignore # lines and \n
+			if((line[0]=='#')|(ret==1))
+				continue;
+			// allocate new memory
+			ptr=realloc(crtp->r_fin,(acount+1)*sizeof(t_3dvec));
+			if(ptr==NULL) {
+				perror("[mdrun] FATAL realloc crt positions");
+				return -1;
+			}
+			crtp->r_fin=ptr;
+			ptr=realloc(constraints,(acount+1)*3*sizeof(u8));
+			if(ptr==NULL) {
+				perror("[mdrun] FATAL realloc crt constraints");
+				return -1;
+			}
+			constraints=ptr;
+			// ignore type
+			wptr=strtok(line," \t");
+			// read x y z
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].x=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].y=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].z=atof(wptr);
+			// read constraints
+			wptr=strtok(NULL," \t");
+			constraints[3*acount]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[3*acount+1]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[3*acount+2]=atoi(wptr);
+			// done reading
+			acount+=1;
+		}
+		close(fd);
+		// allocate trafo angles
+		trafo_angle=malloc(acount*2*sizeof(double));
+		if(trafo_angle==NULL) {
+			perror("[mdrun] FATAL alloc trafo angles");
+			return -1;
+		}
+		// set crt mode
+		crtt=crtp->type;
+	}
+
+	/* write a save file s-crt_xofy.save */
+	snprintf(line,128,"%s/s-crt_%03dof%03d.save",
+	         moldyn->vlsdir,crtp->count,crtp->steps);
+	fd=open(line,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+	if(fd<0) perror("[mdrun] crt save fd open");
+	else {
+		write(fd,moldyn,sizeof(t_moldyn));
+		write(fd,moldyn->atom,
+		      moldyn->count*sizeof(t_atom));
+	}
+	close(fd);
+	/* visualize atoms */
+	visual_atoms(moldyn);
+
+	/* output energy */
+	printf("  crt energy: %d - %f\n\n",
+	       crtp->count,(moldyn->ekin+moldyn->energy)/EV);
+
+	/* crt routines: calculate displacement + set individual constraints */
+
+	printf("  crt step %d of %d in total\n\n",crtp->count+1,crtp->steps);
+
+	if((crtp->type==1)|(crtp->count==0))
+		printf("  crt angle update\n\n");
+		
+	for(i=0;i<moldyn->count;i++) {
+		// calc displacements
+		atom=moldyn->atom;
+		v3_sub(&disp,&(crtp->r_fin[i]),&(atom[i].r));
+		// angles
+		if((crtp->type==1)|(crtp->count==0)) {
+			trafo_angle[2*i]=atan2(disp.x,disp.y);
+			trafo_angle[2*i+1]=-atan2(disp.z,
+			                   sqrt(disp.x*disp.x+disp.y*disp.y));
+		}
+		// move atoms
+		frac=1.0/(crtp->steps-crtp->count);
+		v3_scale(&disp,&disp,frac);
+		v3_add(&(atom[i].r),&(atom[i].r),&disp);
+	}
+
+	return 0;
+}
+
 #define stage_print(m)	if(!(stage->executed)) \
 				printf("%s",m)
 
@@ -1043,6 +1381,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_set_temp_params *stp;
 	t_set_timestep_params *stsp;
 	t_fill_params *fp;
+	t_crt_params *crtp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -1077,6 +1416,16 @@ 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_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;
@@ -1164,7 +1513,8 @@ 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;
@@ -1175,19 +1525,22 @@ 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:
 
 					create_lattice(moldyn,
 					               fp->lattice,fp->lc,
-					               mdrun->element1,
-					               DEFAULT_ATOM_ATTR,0,
+					               fp->fill_element,
+					               DEFAULT_ATOM_ATTR,
+					               fp->fill_brand,
 					               fp->lx,fp->ly,fp->lz,
 					               NULL,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					break;
 				}
 				moldyn_bc_check(moldyn);
@@ -1198,6 +1551,20 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				thermal_init(moldyn,TRUE);
 				change_stage=TRUE;
 				break;
+			case STAGE_CRT:
+				stage_print("  -> constraint relaxation");
+				stage_print(" technique\n\n");
+				crtp=stage->params;
+				if(crtp->count==crtp->steps) {
+					free(constraints);
+					free(trafo_angle);
+					free(crtp->r_fin);
+					change_stage=TRUE;
+					break;
+				}
+				crt(moldyn,mdrun);
+				crtp->count+=1;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -1241,6 +1608,11 @@ int main(int argc,char **argv) {
 	memset(&mdrun,0,sizeof(t_mdrun));
 	memset(&moldyn,0,sizeof(t_moldyn));
 
+	/* init crt variables */
+	crtt=0;
+	constraints=NULL;
+	trafo_angle=NULL;
+
 	/* parse arguments */
 	if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 		return -1;
@@ -1284,6 +1656,11 @@ int main(int argc,char **argv) {
 			                     mdrun.element1,
 			                     mdrun.element2);
 			break;
+		case MOLDYN_POTENTIAL_AO:
+			albe_orig_mult_set_params(&moldyn,
+			                          mdrun.element1,
+			                          mdrun.element2);
+			break;
 		case MOLDYN_POTENTIAL_TM:
 			tersoff_mult_set_params(&moldyn,
 			                        mdrun.element1,