X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=34807e76bd76f646f5d587705d09ce0e05840614;hb=1965279af348fbb9b69459d01516bbcd52b6f240;hp=b2e67f371810946b5c4b67b82e6a03caab311dfe;hpb=d1ceb8d3fc8e7a2e067f7576b3e787928d556277;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index b2e67f3..34807e7 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -17,6 +17,11 @@
 #include "potentials/tersoff.h"
 #endif
 
+/* pse */
+#define PSE_MASS
+#include "pse.h"
+#undef PSE_MASS
+
 #define ME	"[mdrun]"
 
 /*
@@ -90,9 +95,15 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 	t_stage *stage;
 
 	switch(type) {
+		case STAGE_DISPLACE_ATOM:
+			psize=sizeof(t_displace_atom_params);
+			break;
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
+		case STAGE_INSERT_MIXED_ATOMS:
+			psize=sizeof(t_insert_mixed_atoms_params);
+			break;
 		case STAGE_CONTINUE:
 			psize=sizeof(t_continue_params);
 			break;
@@ -105,6 +116,18 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_CHSATTR:
 			psize=sizeof(t_chsattr_params);
 			break;
+		case STAGE_SET_TEMP:
+			psize=sizeof(t_set_temp_params);
+			break;
+		case STAGE_SET_TIMESTEP:
+			psize=sizeof(t_set_timestep_params);
+			break;
+		case STAGE_FILL:
+			psize=sizeof(t_fill_params);
+			break;
+		case STAGE_THERMAL_INIT:
+			psize=0;
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -138,15 +161,20 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	char error[128];
 	char line[128];
 	char *wptr;
-	char word[16][32];
+	char word[32][64];
 	int wcnt;
 	int i,o;
 
+	t_displace_atom_params dap;
 	t_insert_atoms_params iap;
+	t_insert_mixed_atoms_params imp;
 	t_continue_params cp;
 	t_anneal_params ap;
 	t_chaattr_params cap;
 	t_chsattr_params csp;
+	t_set_temp_params stp;
+	t_set_timestep_params stsp;
+	t_fill_params fp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -171,10 +199,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 
 		// reset
 		memset(&iap,0,sizeof(t_insert_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));
 		memset(&cap,0,sizeof(t_chaattr_params));
 		memset(&csp,0,sizeof(t_chsattr_params));
+		memset(&stp,0,sizeof(t_set_temp_params));
+		memset(&stsp,0,sizeof(t_set_timestep_params));
+		memset(&fp,0,sizeof(t_fill_params));
 
 		// get command + args
 		wcnt=0;
@@ -185,7 +217,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				wptr=strtok(line," \t");
 			if(wptr==NULL)
 				break;
-			strncpy(word[wcnt],wptr,32);
+			strncpy(word[wcnt],wptr,64);
 			wcnt+=1;
 		}
 
@@ -199,6 +231,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			if(!strncmp(word[1],"lj",2))
 				mdrun->potential=MOLDYN_POTENTIAL_LJ;
 		}
+		else if(!strncmp(word[0],"continue",8))
+			strncpy(mdrun->continue_file,word[1],128);
 		else if(!strncmp(word[0],"cutoff",6))
 			mdrun->cutoff=atof(word[1]);
 		else if(!strncmp(word[0],"nnd",3))
@@ -241,21 +275,121 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				mdrun->lattice=FCC;
 			if(!strncmp(word[1],"diamond",7))
 				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)) {
-			// only lc mode by now
-			mdrun->lx=atoi(word[2]);
-			mdrun->ly=atoi(word[3]);
-			mdrun->lz=atoi(word[4]);
-			mdrun->lc=atof(word[5]);
+			// 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;
+				}
+				if(!strncmp(word[i],"eb",2)) {
+					fp.fill_element=atoi(word[++i]);
+					fp.fill_brand=atoi(word[++i]);
+				}
+				if(word[i][0]=='p') {
+					i+=1;
+					switch(word[i][0]) {
+					case 'i':
+						if(word[i][1]=='r')
+						fp.p_params.type=PART_INSIDE_R;
+						else
+						fp.p_params.type=PART_INSIDE_D;
+						break;
+					case 'o':
+						if(word[i][1]=='r')
+						fp.p_params.type=PART_OUTSIDE_R;
+						else
+						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;
+			}
+			add_stage(mdrun,STAGE_FILL,&fp);
+		}
+		else if(!strncmp(word[0],"thermal_init",12)) {
+			add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 		}
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
@@ -368,7 +502,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			mdrun->visualize=atoi(word[1]);
 		else if(!strncmp(word[0],"stage",5)) {
 			// for every stage line, add a stage
-			if(!strncmp(word[1],"ins_atoms",9)) {
+			if(!strncmp(word[1],"displace",8)) {
+				dap.nr=atoi(word[2]);	
+				dap.dx=atof(word[3]);
+				dap.dy=atof(word[4]);
+				dap.dz=atof(word[5]);
+				add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
+			}
+			else if(!strncmp(word[1],"ins_atoms",9)) {
 				iap.ins_steps=atoi(word[2]);
 				iap.ins_atoms=atoi(word[3]);
 				iap.element=atoi(word[4]);
@@ -409,25 +550,89 @@ 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;
 				}
 				add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 			}
+
+
+			// HERE WE GO ...
+
+			else if(!strncmp(word[1],"ins_m_atoms",11)) {
+				imp.element1=atoi(word[2]);
+				imp.element2=atoi(word[3]);
+				imp.amount1=atoi(word[4]);
+				imp.amount2=atoi(word[5]);
+				imp.brand1=atoi(word[6]);
+				imp.brand2=atoi(word[7]);
+				imp.crmin=atof(word[8]);
+				imp.crmax=atof(word[9]);
+				/* do this later ...
+				for(i=0;i<strlen(word[8]);i++) {
+					switch(word[8][i]) {
+						case 'b':
+							imp.attr|=ATOM_ATTR_VB;
+							break;
+						case 'h':
+							imp.attr|=ATOM_ATTR_HB;
+							break;
+						case 'v':
+							imp.attr|=ATOM_ATTR_VA;
+							break;
+						case 'f':
+							imp.attr|=ATOM_ATTR_FP;
+							break;
+						case '1':
+							imp.attr|=ATOM_ATTR_1BP;
+							break;
+						case '2':
+							imp.attr|=ATOM_ATTR_2BP;
+							break;
+						case '3':
+							imp.attr|=ATOM_ATTR_3BP;
+							break;
+						default:
+							break;
+					}
+				}
+				*/
+				imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+				imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+				add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
+			}
+
+
+
+
+
 			else if(!strncmp(word[1],"continue",8)) {
 				cp.runs=atoi(word[2]);
 				add_stage(mdrun,STAGE_CONTINUE,&cp);
@@ -436,8 +641,24 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				ap.count=0;
 				ap.runs=atoi(word[2]);
 				ap.dt=atof(word[3]);
+				ap.interval=atoi(word[4]);
 				add_stage(mdrun,STAGE_ANNEAL,&ap);
 			}
+			else if(!strncmp(word[1],"set_temp",8)) {
+				if(word[2][0]=='c') {
+					stp.type=SET_TEMP_CURRENT;
+					stp.val=0.0;
+				}
+				else {
+					stp.type=SET_TEMP_VALUE;
+					stp.val=atof(word[2]);
+				}
+				add_stage(mdrun,STAGE_SET_TEMP,&stp);
+			}
+			else if(!strncmp(word[1],"set_timestep",12)) {
+				stsp.tau=atof(word[2]);
+				add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
+			}
 			else {
 				printf("%s unknown stage type: %s\n",
 				       ME,word[1]);
@@ -494,6 +715,23 @@ int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return TRUE;
 }
 
+int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_displace_atom_params *dap;
+	t_stage *stage;
+	t_atom *atom;
+
+	stage=mdrun->stage.current->data;
+	dap=stage->params;
+
+	atom=&(moldyn->atom[dap->nr]);
+	atom->r.x+=dap->dx;
+	atom->r.y+=dap->dy;
+	atom->r.z+=dap->dz;
+
+	return 0;
+}
+
 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_insert_atoms_params *iap;
@@ -540,7 +778,7 @@ 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;
@@ -549,6 +787,15 @@ 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;
@@ -600,8 +847,16 @@ 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,
@@ -613,6 +868,109 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
+int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_stage *stage;
+	t_insert_mixed_atoms_params *imp;
+	t_atom *atom;
+	double x,x0,y,y0,z,z0;
+	double dmin,d,cmin,cmax;
+	u8 retry;
+	t_3dvec r,v,dist;
+	int i;
+	
+
+	stage=mdrun->stage.current->data;
+	imp=stage->params;
+
+	x=moldyn->dim.x;
+	x0=-x/2.0;
+	y=moldyn->dim.y;
+	y0=-y/2.0;
+	z=moldyn->dim.z;
+	z0=-z/2.0;
+
+	v.x=0.0;
+	v.y=0.0;
+	v.z=0.0;
+
+	cmin=imp->crmin*imp->crmin;
+	cmax=imp->crmax*imp->crmax;
+
+	while(imp->amount1|imp->amount2) {
+		if(imp->amount1) {
+			retry=1;
+			while(retry) {
+				retry=0;
+				r.x=rand_get_double(&(moldyn->random))*x;
+				r.y=rand_get_double(&(moldyn->random))*y;
+				r.z=rand_get_double(&(moldyn->random))*z;
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+				dmin=1000.0;	// for sure too high!
+				for(i=0;i<moldyn->count;i++) {
+					atom=&(moldyn->atom[i]);
+					v3_sub(&dist,&(atom->r),&r);
+					check_per_bound(moldyn,&dist);
+					d=v3_absolute_square(&dist);
+					if(d<cmin) {
+						retry=1;
+						break;
+					}
+					if(d<dmin)
+						dmin=d;
+				}
+				if(dmin!=1000.0)
+					if(dmin>cmax)
+						retry=1;
+			}
+			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);
+			printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
+			imp->amount1-=1;
+		}
+		if(imp->amount2) {
+			retry=1;
+			while(retry) {
+				retry=0;
+				r.x=rand_get_double(&(moldyn->random))*x;
+				r.y=rand_get_double(&(moldyn->random))*y;
+				r.z=rand_get_double(&(moldyn->random))*z;
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+				dmin=1000.0;	// for sure too high!
+				for(i=0;i<moldyn->count;i++) {
+					atom=&(moldyn->atom[i]);
+					v3_sub(&dist,&(atom->r),&r);
+					check_per_bound(moldyn,&dist);
+					d=v3_absolute_square(&dist);
+					if(d<cmin) {
+						retry=1;
+						break;
+					}
+					if(d<dmin)
+						dmin=d;
+				}
+				if(dmin!=1000.0)
+					if(dmin>cmax)
+						retry=1;
+			}
+			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);
+			printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
+			imp->amount2-=1;
+		}
+	}
+
+	return 0;
+}
+
 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_stage *stage;
@@ -706,12 +1064,16 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_stage *stage;
 	t_list *sl;
 	int steps;
-	double tau;
 	u8 change_stage;
+	t_3dvec o;
 
 	t_insert_atoms_params *iap;
+	t_insert_mixed_atoms_params *imp;
 	t_continue_params *cp;
 	t_anneal_params *ap;
+	t_set_temp_params *stp;
+	t_set_timestep_params *stsp;
+	t_fill_params *fp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -727,9 +1089,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	/* get stage description */
 	stage=sl->current->data;
 
-	/* default steps and tau values */
+	/* steps in next schedule */
 	steps=mdrun->relax_steps;
-	tau=mdrun->timestep;
 
 	/* check whether relaxation steps are necessary */
 	if((check_pressure(moldyn,mdrun)==TRUE)&\
@@ -742,6 +1103,11 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 		
 		/* stage specific stuff */
 		switch(stage->type) {
+			case STAGE_DISPLACE_ATOM:
+				stage_print("  -> displace atom\n\n");
+				displace_atom(moldyn,mdrun);
+				change_stage=TRUE;
+				break;
 			case STAGE_INSERT_ATOMS:
 				stage_print("  -> insert atoms\n\n");
 				iap=stage->params;
@@ -751,7 +1117,19 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				}
 				insert_atoms(moldyn,mdrun);
 				iap->cnt_steps+=1;
-					break;
+				break;
+
+
+
+			case STAGE_INSERT_MIXED_ATOMS:
+				stage_print("  -> insert mixed atoms\n\n");
+				imp=stage->params;
+				insert_mixed_atoms(moldyn,mdrun);
+				change_stage=TRUE;
+				break;
+
+
+
 			case STAGE_CONTINUE:
 				stage_print("  -> continue\n\n");
 				if(stage->executed==TRUE) {
@@ -760,7 +1138,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				}
 				cp=stage->params;
 				steps=cp->runs;
-					break;
+				break;
 			case STAGE_ANNEAL:
 				stage_print("  -> anneal\n\n");
 				ap=stage->params;
@@ -772,17 +1150,85 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					set_temperature(moldyn,
 					                moldyn->t_ref+ap->dt);
 				ap->count+=1;
+				steps=ap->interval;
 				break;
 			case STAGE_CHAATTR:
-				stage_print("  -> chaattr\n\n");
+				stage_print("  -> change atom attributes\n\n");
 				chaatr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			case STAGE_CHSATTR:
-				stage_print("  -> chsattr\n\n");
+				stage_print("  -> change sys attributes\n\n");
 				chsattr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
+			case STAGE_SET_TEMP:
+				stage_print("  -> set temperature\n\n");
+				stp=stage->params;
+				if(stp->type&SET_TEMP_CURRENT) {
+					set_temperature(moldyn,moldyn->t_avg);
+				}
+				else {
+					set_temperature(moldyn,stp->val);
+				}
+				change_stage=TRUE;
+				break;
+			case STAGE_SET_TIMESTEP:
+				stage_print("  -> set timestep\n\n");
+				stsp=stage->params;
+				mdrun->timestep=stsp->tau;
+				change_stage=TRUE;
+				break;
+			case STAGE_FILL:
+				stage_print("  -> fill lattice\n\n");
+				fp=stage->params;
+				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,
+					               DEFAULT_ATOM_ATTR,0,
+					               fp->lx,fp->ly,fp->lz,
+					               &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,
+					               DEFAULT_ATOM_ATTR,1,
+					               fp->lx,fp->ly,fp->lz,
+					               &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;
+				break;
+			case STAGE_THERMAL_INIT:
+				stage_print("  -> thermal init\n\n");
+				thermal_init(moldyn,TRUE);
+				change_stage=TRUE;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -799,7 +1245,6 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				return 0;
 			}
 			steps=0;
-			tau=mdrun->timestep;
 		}
 
 	}
@@ -812,7 +1257,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	}
 
 	/* continue simulation */
-	moldyn_add_schedule(moldyn,steps,tau);
+	moldyn_add_schedule(moldyn,steps,mdrun->timestep);
 
 	return 0;
 }
@@ -821,7 +1266,7 @@ int main(int argc,char **argv) {
 
 	t_mdrun mdrun;
 	t_moldyn moldyn;
-	t_3dvec o;
+	//t_3dvec o;
 
 	/* clear structs */
 	memset(&mdrun,0,sizeof(t_mdrun));
@@ -843,9 +1288,24 @@ int main(int argc,char **argv) {
 	/* sanity check! */
 
 	/* prepare simulation */
-	moldyn_init(&moldyn,argc,argv);
+
+	if(mdrun.continue_file[0]) {
+		// read the save file
+		moldyn_read_save_file(&moldyn,mdrun.continue_file);
+		// manualaadjusting some stuff
+		moldyn.argc=argc;
+		moldyn.args=argv;
+		rand_init(&(moldyn.random),NULL,1);
+		moldyn.random.status|=RAND_STAT_VERBOSE;
+	}
+	else {
+		moldyn_init(&moldyn,argc,argv);
+	}
+	
 	if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 		return -1;
+
+	/* potential */
 	set_cutoff(&moldyn,mdrun.cutoff);
 	if(set_potential(&moldyn,mdrun.potential)<0)
 		return -1;
@@ -871,28 +1331,43 @@ int main(int argc,char **argv) {
 			       ME,mdrun.potential);
 			return -1;
 	}
+
+	/* if it is a continue run, reset schedule and skip lattice init */
+	if(mdrun.continue_file[0]) {
+		memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
+		goto addsched;
+	}
+
+	/* initial lattice and dimensions */
 	set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 	set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
+	/* replaced by fill stage !! 
 	switch(mdrun.lattice) {
 		case FCC:
-			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-			               mdrun.ly,mdrun.lz,NULL);
+			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
+			               mdrun.ly,mdrun.lz,NULL,0,NULL);
 			break;
 		case DIAMOND:
-			create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-			               mdrun.ly,mdrun.lz,NULL);
+			create_lattice(&moldyn,DIAMOND,mdrun.lc,
+                                       mdrun.fill_element,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
+			               mdrun.ly,mdrun.lz,NULL,0,NULL);
 			break;
 		case ZINCBLENDE:
 			o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-			               mdrun.ly,mdrun.lz,&o);
+			               mdrun.ly,mdrun.lz,&o,0,NULL);
 			o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 			               mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
-			               mdrun.ly,mdrun.lz,&o);
+			               mdrun.ly,mdrun.lz,&o,0,NULL);
+			break;
+		case NONE:
+			set_nn_dist(&moldyn,mdrun.nnd);
 			break;
 		default:
 			printf("%s unknown lattice type: %02x\n",
@@ -900,10 +1375,20 @@ int main(int argc,char **argv) {
 			return -1;
 	}
 	moldyn_bc_check(&moldyn);
+	replaced by fill stage !! */
+
+	/* temperature and pressure */
 	set_temperature(&moldyn,mdrun.temperature);
 	set_pressure(&moldyn,mdrun.pressure);
+	/* replaced thermal_init stage
 	thermal_init(&moldyn,TRUE);
+	*/
+
+addsched:
+	/* first schedule */
 	moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
+
+	/* log */
 	moldyn_set_log_dir(&moldyn,mdrun.sdir);
 	moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 	if(mdrun.elog)