X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=29d3160acdc9375864ff56788a293704e8c3ccee;hb=959801961cfdd51e080e6500f51647b3397d336c;hp=6f7a2f02a0704491b5d8bf50762031e0149711ba;hpb=d7f67c88195ab155f2737e57cc5e81973d3feb0c;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index 6f7a2f0..29d3160 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -62,12 +62,12 @@ int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
 	return 0;
 }
 
-del_stages(t_mdrun *mdrun) {
+int del_stages(t_mdrun *mdrun) {
 
 	t_list *sl;
 	t_stage *stage;
 
-	sl=mdrun->stage;
+	sl=&(mdrun->stage);
 
 	list_reset_f(sl);
 
@@ -83,13 +83,16 @@ del_stages(t_mdrun *mdrun) {
 	return 0;
 }
 
-add_stage(t_mdrun *mdrun,u8 type,void *params) {
+int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 
 	int psize;
 
 	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;
@@ -106,7 +109,8 @@ add_stage(t_mdrun *mdrun,u8 type,void *params) {
 			psize=sizeof(t_chsattr_params);
 			break;
 		default:
-
+			printf("%s unknown stage type: %02x\n",ME,type);
+			return -1;
 	}
 
 	stage=malloc(sizeof(t_stage));
@@ -126,7 +130,7 @@ add_stage(t_mdrun *mdrun,u8 type,void *params) {
 
 	memcpy(stage->params,params,psize);
 
-	list_add_immediate_f(mdrun->stage,stage);
+	list_add_immediate_f(&(mdrun->stage),stage);
 
 	return 0;
 }
@@ -137,10 +141,11 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	char error[128];
 	char line[128];
 	char *wptr;
-	char word[16][32];
+	char word[16][64];
 	int wcnt;
-	int i;
+	int i,o;
 
+	t_displace_atom_params dap;
 	t_insert_atoms_params iap;
 	t_continue_params cp;
 	t_anneal_params ap;
@@ -168,6 +173,13 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		if((line[0]=='#')|(ret==1))
 			continue;
 
+		// reset
+		memset(&iap,0,sizeof(t_insert_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));
+
 		// get command + args
 		wcnt=0;
 		while(1) {
@@ -177,7 +189,7 @@ 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;
 		}
 
@@ -191,8 +203,12 @@ 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))
+			mdrun->nnd=atof(word[1]);
 		else if(!strncmp(word[0],"intalgo",7)) {
 			if(!strncmp(word[1],"verlet",5))
 				mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
@@ -234,51 +250,53 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		}
 		else if(!strncmp(word[0],"element1",8)) {
 			mdrun->element1=atoi(word[1]);
-			switch(mdrun->element1) {
-				case SI:
-					mdrun->m1=M_SI;
-					break;
-				case C:
-					mdrun->m1=M_C;
-					break;
-				default:
-					printf("%s unknown element1: %s|%d\n",
-					       ME,word[1],mdrun->element1);
-					return -1;
-			}
+			mdrun->m1=pse_mass[mdrun->element1];
 		}
 		else if(!strncmp(word[0],"element2",8)) {
 			mdrun->element2=atoi(word[1]);
-			switch(mdrun->element2) {
-				case SI:
-					mdrun->m2=M_SI;
-					break;
-				case C:
-					mdrun->m2=M_C;
-					break;
-				default:
-					printf("%s unknown element2: %s|%d\n",
-					       ME,word[1],mdrun->element2);
-					return -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]);
 		}
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
 			// containing one schedule of 0 loops ...
-			if(!strncmp(word[1],"all",3)) {
-				cap.type=
-
-
-				HIER WEITER
+			for(i=0;i<strlen(word[1]);i++) {
+				switch(word[1][i]) {
+					case 't':
+						cap.type|=CHAATTR_TOTALV;
+						break;
+					case 'r':
+						cap.type|=CHAATTR_REGION;
+						break;
+					case 'e':
+						cap.type|=CHAATTR_ELEMENT;
+						break;
+					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]);
+				i+=6;
 			}
-			for(i=0;i<strlen(wptr)) {
-				switch(word[2][i]) {
+			if(cap.type&CHAATTR_ELEMENT) {
+				cap.element=atoi(word[i]);
+				i+=1;
+			}
+			for(o=0;o<strlen(word[i]);o++) {
+				switch(word[i][o]) {
 					case 'b':
 						cap.attr|=ATOM_ATTR_VB;
 						break;
@@ -306,9 +324,37 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			}
 			add_stage(mdrun,STAGE_CHAATTR,&cap);
 		}
-		else if(!strncmp(word[0],"ectrl",5)) {
-			mdrun->p_tau=atof(word[1]);
-			mdrun->t_tau=atof(word[2]);
+		else if(!strncmp(word[0],"sattr",5)) {
+			// for satrib line we need a special stage
+			// containing one schedule of 0 loops ...
+			csp.type=0;
+			for(i=1;i<wcnt;i++) {
+				if(!strncmp(word[i],"pctrl",5)) {
+					csp.ptau=0.01/(atof(word[++i])*GPA);
+					csp.type|=CHSATTR_PCTRL;
+				}
+				if(!strncmp(word[i],"tctrl",5)) {
+					csp.ttau=atof(word[++i]);
+					csp.type|=CHSATTR_TCTRL;
+				}
+				if(!strncmp(word[i],"prelax",6)) {
+					csp.dp=atof(word[++i])*BAR;
+					csp.type|=CHSATTR_PRELAX;
+				}
+				if(!strncmp(word[i],"trelax",6)) {
+					csp.dt=atof(word[++i]);
+					csp.type|=CHSATTR_TRELAX;
+				}
+				if(!strncmp(word[i],"rsteps",6)) {
+					csp.rsteps=atoi(word[++i]);
+					csp.type|=CHSATTR_RSTEPS;
+				}
+				if(!strncmp(word[i],"avgrst",6)) {
+					csp.avgrst=atoi(word[++i]);
+					csp.type|=CHSATTR_AVGRST;
+				}
+			}
+			add_stage(mdrun,STAGE_CHSATTR,&csp);
 		}
 		else if(!strncmp(word[0],"prerun",6))
 			mdrun->prerun=atoi(word[1]);
@@ -328,10 +374,92 @@ 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
-			printf("%s stage: %s\n",ME,word[1]);
+			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]);
+				iap.brand=atoi(word[5]);
+				for(i=0;i<strlen(word[6]);i++) {
+					switch(word[6][i]) {
+						case 'b':
+							iap.attr|=ATOM_ATTR_VB;
+							break;
+						case 'h':
+							iap.attr|=ATOM_ATTR_HB;
+							break;
+						case 'v':
+							iap.attr|=ATOM_ATTR_VA;
+							break;
+						case 'f':
+							iap.attr|=ATOM_ATTR_FP;
+							break;
+						case '1':
+							iap.attr|=ATOM_ATTR_1BP;
+							break;
+						case '2':
+							iap.attr|=ATOM_ATTR_2BP;
+							break;
+						case '3':
+							iap.attr|=ATOM_ATTR_3BP;
+							break;
+						default:
+							break;
+					}
+				}
+				switch(word[7][0]) {
+					// insertion types
+					case 'p':
+						iap.type=INS_POS;
+						iap.x0=atof(word[8]);
+						iap.y0=atof(word[9]);
+						iap.z0=atof(word[10]);
+						break;
+					case 'r':
+						if(word[8][0]=='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]);
+						}
+					default:
+						break;
+				}
+				add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
+			}
+			else if(!strncmp(word[1],"continue",8)) {
+				cp.runs=atoi(word[2]);
+				add_stage(mdrun,STAGE_CONTINUE,&cp);
+			}
+			else if(!strncmp(word[1],"anneal",6)) {
+				ap.count=0;
+				ap.runs=atoi(word[2]);
+				ap.dt=atof(word[3]);
+				add_stage(mdrun,STAGE_ANNEAL,&ap);
+			}
+			else {
+				printf("%s unknown stage type: %s\n",
+				       ME,word[1]);
+				return -1;
+			}
 		}
 		else {
-			printf("%s unknown command %s, skipped!\n",ME,word[0]);
+			printf("%s unknown keyword '%s', skipped!\n",
+			       ME,word[0]);
 			continue;
 		}
 	}
@@ -346,8 +474,9 @@ int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	double delta;
 
-	if(!(mdrun->sattr&SATTR_PRELAX))
+	if(!(mdrun->sattr&SATTR_PRELAX)) {
 		return TRUE;
+	}
 
 	delta=moldyn->p_avg-moldyn->p_ref;
 
@@ -378,33 +507,67 @@ 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) {
 
-	insert_atoms_params *iap;
+	t_insert_atoms_params *iap;
 	t_stage *stage;
 	t_atom *atom;
 	t_3dvec r,v,dist;
-	double d,dmin;
+	double d,dmin,o;
 	int cnt,i;
 	double x,y,z;
 	double x0,y0,z0;
 	u8 cr_check,run;
 	
-	stage=mdrun->stage->current->data;
+	stage=mdrun->stage.current->data;
 	iap=stage->params;
 
 	cr_check=FALSE;
 
 	v.x=0.0; v.y=0.0; v.z=0.0;
+	x=0; y=0; z=0;
+	o=0; dmin=0;
+
+	switch(mdrun->lattice) {
+		case CUBIC:
+			o=0.5*mdrun->lc;
+			break;
+		case FCC:
+			o=0.25*mdrun->lc;
+			break;
+		case DIAMOND:
+		case ZINCBLENDE:
+			o=0.125*mdrun->lc;
+			break;
+		default:
+			break;
+	}
 
 	switch(iap->type) {
 		case INS_TOTAL:
 			x=moldyn->dim.x;
-			x0=0.0;
+			x0=-x/2.0;
 			y=moldyn->dim.y;
-			y0=0.0;
+			y0=-y/2.0;
 			z=moldyn->dim.z;
-			z0=0.0;
+			z0=-z/2.0;
 			cr_check=TRUE;
 			break;
 		case INS_REGION:
@@ -416,8 +579,15 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 			z0=iap->z0;
 			cr_check=TRUE;
 			break;
+		case INS_POS:
+			x0=iap->x0;
+			y0=iap->y0;
+			z0=iap->z0;
+			cr_check=FALSE;
+			break;
 		default:
-			printf("%s unknown insertion mode\n");
+			printf("%s unknown insertion mode: %02x\n",
+			       ME,iap->type);
 			return -1;
 	}
 
@@ -425,9 +595,25 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	while(cnt<iap->ins_atoms) {
 		run=1;
 		while(run) {
-			r.x=(rand_get_double(&(moldyn->random))-0.5)*x+x0;
-			r.y=(rand_get_double(&(moldyn->random))-0.5)*y+y0;
-			r.z=(rand_get_double(&(moldyn->random))-0.5)*z+z0;
+			if(iap->type!=INS_POS) {
+				r.x=rand_get_double(&(moldyn->random))*x;
+				r.y=rand_get_double(&(moldyn->random))*y;
+				r.z=rand_get_double(&(moldyn->random))*z;
+			}
+			else {
+				r.x=0.0;
+				r.y=0.0;
+				r.z=0.0;
+			}
+			r.x+=x0;
+			r.y+=y0;
+			r.z+=z0;
+			// offset
+			if(iap->type!=INS_TOTAL) {
+				r.x+=o;
+				r.y+=o;
+				r.z+=o;
+			}
 			run=0;
 			if(cr_check==TRUE) {
 				dmin=1000;	// for sure too high!
@@ -447,22 +633,24 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 		}
 		add_atom(moldyn,iap->element,pse_mass[iap->element],
 		         iap->brand,iap->attr,&r,&v);
-		printf("%s atom inserted: %f %f %f | d squared = %f\n",
-		       ME,r.x,r.y,r.z,dmin);
+		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);
 		cnt+=1;
 	}
 
 	return 0;
 }
 
-int chaatrib(t_moldyn *moldyn,t_mdrun *mdrun) {
+int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_stage *stage;
 	t_chaattr_params *cap;
 	t_atom *atom;
-	u8 assigne;
+	int i;
 
-	stage=mdrun->stage->current->data;
+	stage=mdrun->stage.current->data;
 	cap=stage->params;
 
 	for(i=0;i<moldyn->count;i++) {
@@ -496,41 +684,54 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 	t_stage *stage;
 	t_chsattr_params *csp;
 
-	stage=mdrun->stage->current->data;
+	stage=mdrun->stage.current->data;
 	csp=stage->params;
 
-	switch(csp->type) {
-		case CHSATTR_PCTRL:
-			set_p_scale(moldyn,csp->ctrl_type,csp->tau);
-			break;
-		case CHSATTR_TCTRL:
-			set_t_scale(moldyn,csp->ctrl_type,csp->tau);
-			break;
-		case CHSATTR_PRELAX:
-			mdrun->sattr&=(^(SATTR_PRELAX));
-			if(csp->ctrl==TRUE)
-				mdrun->sattr|=SATTR_PRELAX;
-			break;
-		case CHSATTR_TRELAX:
-			mdrun->sattr&=(^(SATTR_TRELAX));
-			if(csp->ctrl==TRUE)
-				mdrun->sattr|=SATTR_TRELAX;
-			break;
-		case CHSATTR_AVGRST:
-			mdrun->sattr&=(^(SATTR_AVGRST));
-			if(csp->ctrl==TRUE)
-				mdrun->sattr|=SATTR_AVGRST;
-			break;
-		default:
-			printf("%s unknown system attribute change\n",ME);
-			return -1;
+	if(csp->type&CHSATTR_PCTRL) {
+		if(csp->ptau>0)
+			set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+		else
+			set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+	}
+	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);
+	}
+	if(csp->type&CHSATTR_PRELAX) {
+		if(csp->dp<0)
+			mdrun->sattr&=(~(SATTR_PRELAX));
+		else
+			mdrun->sattr|=SATTR_PRELAX;
+		mdrun->dp=csp->dp;
+	}
+	if(csp->type&CHSATTR_TRELAX) {
+		if(csp->dt<0)
+			mdrun->sattr&=(~(SATTR_TRELAX));
+		else
+			mdrun->sattr|=SATTR_TRELAX;
+		mdrun->dt=csp->dt;
+	}
+	if(csp->type&CHSATTR_AVGRST) {
+		if(csp->avgrst)
+			mdrun->sattr|=SATTR_AVGRST;
+		else
+			mdrun->sattr&=(~(SATTR_AVGRST));
+	}
+	if(csp->type&CHSATTR_RSTEPS) {
+		mdrun->relax_steps=csp->rsteps;
 	}
 
 	return 0;
 }
 
-int mdrun_hook(t_moldyn *moldyn,void *ptr) {
+#define stage_print(m)	if(!(stage->executed)) \
+				printf("%s",m)
 
+int mdrun_hook(void *ptr1,void *ptr2) {
+
+	t_moldyn *moldyn;
 	t_mdrun *mdrun;
 	t_stage *stage;
 	t_list *sl;
@@ -542,8 +743,10 @@ int mdrun_hook(t_moldyn *moldyn,void *ptr) {
 	t_continue_params *cp;
 	t_anneal_params *ap;
 
-	mdrun=ptr;
-	sl=mdrun->stage;
+	moldyn=ptr1;
+	mdrun=ptr2;
+
+	sl=&(mdrun->stage);
 
 	change_stage=FALSE;
 
@@ -552,18 +755,30 @@ int mdrun_hook(t_moldyn *moldyn,void *ptr) {
 		return 0;
 
 	/* get stage description */
-	stage=mdrun->sl->current->data;
+	stage=sl->current->data;
 
 	/* default steps and tau values */
 	steps=mdrun->relax_steps;
 	tau=mdrun->timestep;
 
 	/* check whether relaxation steps are necessary */
-	if(!((check_pressure==FALSE)|(check_temperature==FALSE))) {
+	if((check_pressure(moldyn,mdrun)==TRUE)&\
+	   (check_temperature(moldyn,mdrun)==TRUE)) {
+	
+		/* be verbose */
+		stage_print("\n###########################\n");
+		stage_print("# [mdrun] executing stage #\n");
+		stage_print("###########################\n\n");
 		
 		/* 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;
 				if(iap->cnt_steps==iap->ins_steps) {
 					change_stage=TRUE;
@@ -571,30 +786,36 @@ int mdrun_hook(t_moldyn *moldyn,void *ptr) {
 				}
 				insert_atoms(moldyn,mdrun);
 				iap->cnt_steps+=1;
-					break;
+				break;
 			case STAGE_CONTINUE:
+				stage_print("  -> continue\n\n");
 				if(stage->executed==TRUE) {
 					change_stage=TRUE;
 					break;
 				}
 				cp=stage->params;
 				steps=cp->runs;
-					break;
+				break;
 			case STAGE_ANNEAL:
+				stage_print("  -> anneal\n\n");
 				ap=stage->params;
 				if(ap->count==ap->runs) {
 					change_stage=TRUE;
 					break;
 				}
-				set_temperature(moldyn,moldyn->t_ref+ap->dt);
+				if(moldyn->t_ref+ap->dt>=0.0)
+					set_temperature(moldyn,
+					                moldyn->t_ref+ap->dt);
 				ap->count+=1;
 				break;
 			case STAGE_CHAATTR:
-				chaatrib(moldyn,mdrun);
+				stage_print("  -> chaattr\n\n");
+				chaatr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			case STAGE_CHSATTR:
-				chsatrib(moldyn,mdrun);
+				stage_print("  -> chsattr\n\n");
+				chsattr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			default:
@@ -637,8 +858,9 @@ int main(int argc,char **argv) {
 	t_moldyn moldyn;
 	t_3dvec o;
 
-	/* clear mdrun struct */
+	/* clear structs */
 	memset(&mdrun,0,sizeof(t_mdrun));
+	memset(&moldyn,0,sizeof(t_moldyn));
 
 	/* parse arguments */
 	if(mdrun_parse_argv(&mdrun,argc,argv)<0)
@@ -656,9 +878,24 @@ 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;
@@ -684,27 +921,35 @@ 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);
 	switch(mdrun.lattice) {
 		case FCC:
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-			               mdrun.m1,0,0,mdrun.lx,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 			               mdrun.ly,mdrun.lz,NULL);
 			break;
 		case DIAMOND:
 			create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-			               mdrun.m1,0,0,mdrun.lx,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 			               mdrun.ly,mdrun.lz,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.m1,0,0,mdrun.lx,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
-			               mdrun.m2,0,0,mdrun.lx,
+			               mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			break;
 		default:
@@ -713,10 +958,17 @@ int main(int argc,char **argv) {
 			return -1;
 	}
 	moldyn_bc_check(&moldyn);
+
+	/* temperature and pressure */
 	set_temperature(&moldyn,mdrun.temperature);
 	set_pressure(&moldyn,mdrun.pressure);
 	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)
@@ -734,12 +986,6 @@ int main(int argc,char **argv) {
 	moldyn_set_log(&moldyn,CREATE_REPORT,0);
 	set_avg_skip(&moldyn,mdrun.avgskip);
 
-	/* pt scaling */
-	if(mdrun.p_tau!=0)
-		set_p_scale(&moldyn,P_SCALE_BERENDSEN,mdrun.p_tau);
-	if(mdrun.t_tau!=0)
-		set_t_scale(&moldyn,T_SCALE_BERENDSEN,mdrun.t_tau);
-
 	/* prepare the hook function */
 	moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);