X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=af0132dff157564f46f593c3280700b045a1810c;hb=a9fbc66448c52bc4138176739b33d17ba86b7eae;hp=fe54330f002f414d345295ff73dd4d1e6b6b557d;hpb=1097ea2efb575855edd332c28a9cd8f807cd0716;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index fe54330..af0132d 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -23,206 +23,174 @@
 #include "visual/visual.h"
 #include "list/list.h"
 
-int moldyn_usage(char **argv) {
-
-	printf("\n%s usage:\n\n",argv[0]);
-	printf("--- general options ---\n");
-	printf("-E <steps> <file> (log total energy)\n");
-	printf("-M <steps> <file> (log total momentum)\n");
-	printf("-D <steps> <file> (dump total information)\n");
-	printf("-S <steps> <filebase> (single save file)\n");
-	printf("-V <steps> <filebase> (rasmol file)\n");
-	printf("--- physics options ---\n");
-	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
-	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
-	printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
-	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
-	printf(" -- integration algo --\n");
-	printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
-	printf("     0: velocity verlet\n");
-	printf(" -- potential --\n");
-	printf("  -P <number> <param1 param2 ...>\n");
-	printf("     0: harmonic oscillator\n");
-	printf("        param1: spring constant\n");
-	printf("        param2: equilibrium distance\n");
-	printf("     1: lennard jones\n");
-	printf("        param1: epsilon\n");
-	printf("        param2: sigma\n");
-	printf("\n");
+
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+	//int ret;
+
+	//ret=moldyn_parse_argv(moldyn,argc,argv);
+	//if(ret<0) return ret;
+
+	memset(moldyn,0,sizeof(t_moldyn));
+
+	rand_init(&(moldyn->random),NULL,1);
+	moldyn->random.status|=RAND_STAT_VERBOSE;
 
 	return 0;
 }
 
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
 
-	int i;
+	printf("[moldyn] shutdown\n");
+	moldyn_log_shutdown(moldyn);
+	link_cell_shutdown(moldyn);
+	rand_close(&(moldyn->random));
+	free(moldyn->atom);
 
-	memset(moldyn,0,sizeof(t_moldyn));
+	return 0;
+}
 
-	/* default values */
-	moldyn->t=MOLDYN_TEMP;
-	moldyn->tau=MOLDYN_TAU;
-	moldyn->time_steps=MOLDYN_RUNS;
-	moldyn->integrate=velocity_verlet;
-
-	/* parse argv */
-	for(i=1;i<argc;i++) {
-		if(argv[i][0]=='-') {
-			switch(argv[i][1]){
-				case 'E':
-					moldyn->ewrite=atoi(argv[++i]);
-					strncpy(moldyn->efb,argv[++i],64);
-					break;
-				case 'M':
-					moldyn->mwrite=atoi(argv[++i]);
-					strncpy(moldyn->mfb,argv[++i],64);
-					break;
-				case 'S':
-					moldyn->swrite=atoi(argv[++i]);
-					strncpy(moldyn->sfb,argv[++i],64);
-					break;
-				case 'V':
-					moldyn->vwrite=atoi(argv[++i]);
-					strncpy(moldyn->vfb,argv[++i],64);
-					break;
-				case 'T':
-					moldyn->t=atof(argv[++i]);
-					break;
-				case 't':
-					moldyn->tau=atof(argv[++i]);
-					break;
-				case 'C':
-					moldyn->cutoff=atof(argv[++i]);
-					break;
-				case 'R':
-					moldyn->time_steps=atoi(argv[++i]);
-					break;
-				case 'I':
-	/* integration algorithm */
-	switch(atoi(argv[++i])) {
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
+
+	switch(algo) {
 		case MOLDYN_INTEGRATE_VERLET:
 			moldyn->integrate=velocity_verlet;
 			break;
 		default:
-			printf("unknown integration algo %s\n",argv[i]);
-			moldyn_usage(argv);
+			printf("unknown integration algorithm: %02x\n",algo);
 			return -1;
 	}
 
-				case 'P':
-	/* potential + params */
-	switch(atoi(argv[++i])) {
-		case MOLDYN_POTENTIAL_HO:
-			hop.spring_constant=atof(argv[++i]);
-			hop.equilibrium_distance=atof(argv[++i]);
-			moldyn->pot_params=malloc(sizeof(t_ho_params));
-			memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
-			moldyn->potential_force_function=harmonic_oscillator;
-			break;
-		case MOLDYN_POTENTIAL_LJ:
-			e=atof(argv[++i]);
-			s=atof(argv[++i]);
-			ljp.epsilon4=4*e;
-			ljp.sigma6=s*s*s*s*s*s;
-			ljp.sigma12=ljp.sigma6*ljp.sigma6;
-			moldyn->pot_params=malloc(sizeof(t_lj_params));
-			memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
-			moldyn->potential_force_function=lennard_jones;
-			break;
-		default:
-			printf("unknown potential %s\n",argv[i]);
-			moldyn_usage(argv);
-			return -1;
-	}
+	return 0;
+}
 
-				default:
-					printf("unknown option %s\n",argv[i]);
-					moldyn_usage(argv);
-					return -1;
-			}
-		} else {
-			moldyn_usage(argv);
-			return -1;
-		}
-	}
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+	moldyn->cutoff=cutoff;
 
 	return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn) {
+int set_temperature(t_moldyn *moldyn,double t_ref) {
 
-	moldyn->lvstat=0;
-	t_visual *vis;
+	moldyn->t_ref=t_ref;
 
-	vis=&(moldyn->vis);
+	return 0;
+}
 
-	if(moldyn->ewrite) {
-		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
-		if(moldyn->efd<0) {
-			perror("[moldyn] efd open");
-			return moldyn->efd;
-		}
-		dprintf(moldyn->efd,"# moldyn total energy logfile\n");
-		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
-	}
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 
-	if(moldyn->mwrite) {
-		moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
-		if(moldyn->mfd<0) {
-			perror("[moldyn] mfd open");
-			return moldyn->mfd;
-		}
-		dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
-		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
-	}
+	moldyn->pt_scale=(ptype|ttype);
+	moldyn->t_tc=ttc;
+	moldyn->p_tc=ptc;
+
+	return 0;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 
-	if(moldyn->swrite)
-		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+	moldyn->dim.x=x;
+	moldyn->dim.y=y;
+	moldyn->dim.z=z;
 
-	if((moldyn->vwrite)&&(vis)) {
-		moldyn->visual=vis;
-		visual_init(vis,moldyn->vfb);
-		moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+	if(visualize) {
+		moldyn->vis.dim.x=x;
+		moldyn->vis.dim.y=y;
+		moldyn->vis.dim.z=z;
 	}
 
-	moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+	return 0;
+}
+
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
 
 	return 0;
 }
 
-int moldyn_log_shutdown(t_moldyn *moldyn) {
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
-	if(moldyn->efd) close(moldyn->efd);
-	if(moldyn->mfd) close(moldyn->efd);
-	if(moldyn->dfd) close(moldyn->efd);
-	if(moldyn->visual) visual_tini(moldyn->visual);
+	if(x)
+		moldyn->status|=MOLDYN_STAT_PBX;
+
+	if(y)
+		moldyn->status|=MOLDYN_STAT_PBY;
+
+	if(z)
+		moldyn->status|=MOLDYN_STAT_PBZ;
 
 	return 0;
 }
 
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 
-	int ret;
+	moldyn->func1b=func;
+	moldyn->pot1b_params=params;
 
-	ret=moldyn_parse_argv(moldyn,argc,argv);
-	if(ret<0) return ret;
+	return 0;
+}
 
-	ret=moldyn_log_init(moldyn);
-	if(ret<0) return ret;
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 
-	rand_init(&(moldyn->random),NULL,1);
-	moldyn->random.status|=RAND_STAT_VERBOSE;
+	moldyn->func2b=func;
+	moldyn->pot2b_params=params;
 
-	moldyn->status=0;
+	return 0;
+}
+
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+	moldyn->func3b=func;
+	moldyn->pot3b_params=params;
 
 	return 0;
 }
 
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 
-	moldyn_log_shutdown(moldyn);
-	rand_close(&(moldyn->random));
-	free(moldyn->atom);
+	switch(type) {
+		case LOG_TOTAL_ENERGY:
+			moldyn->ewrite=timer;
+			moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			if(moldyn->efd<0) {
+				perror("[moldyn] efd open");
+				return moldyn->efd;
+			}
+			dprintf(moldyn->efd,"# total energy log file\n");
+			break;
+		case LOG_TOTAL_MOMENTUM:
+			moldyn->mwrite=timer;
+			moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+			if(moldyn->mfd<0) {
+				perror("[moldyn] mfd open");
+				return moldyn->mfd;
+			}
+			dprintf(moldyn->efd,"# total momentum log file\n");
+			break;
+		case SAVE_STEP:
+			moldyn->swrite=timer;
+			strncpy(moldyn->sfb,fb,63);
+			break;
+		case VISUAL_STEP:
+			moldyn->vwrite=timer;
+			strncpy(moldyn->vfb,fb,63);
+			visual_init(&(moldyn->vis),fb);
+			break;
+		default:
+			printf("unknown log mechanism: %02x\n",type);
+			return -1;
+	}
+
+	return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+	printf("[moldyn] log shutdown\n");
+	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->mfd) close(moldyn->mfd);
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
@@ -233,16 +201,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	int count;
 	int ret;
 	t_3dvec origin;
-	t_atom *atom;
 
 	count=a*b*c;
-	atom=moldyn->atom;
 
 	if(type==FCC) count*=4;
+
 	if(type==DIAMOND) count*=8;
 
-	atom=malloc(count*sizeof(t_atom));
-	if(atom==NULL) {
+	moldyn->atom=malloc(count*sizeof(t_atom));
+	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
 		return -1;
 	}
@@ -251,10 +218,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	switch(type) {
 		case FCC:
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,atom,&origin);
+			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -269,19 +236,24 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		return -1;
 	}
 
+	moldyn->count=count;
+	printf("[moldyn] created lattice with %d atoms\n",count);
+
 	while(count) {
-		atom[count-1].element=element;
-		atom[count-1].mass=mass;
-		atom[count-1].attr=attr;
-		atom[count-1].bnum=bnum;
 		count-=1;
+		moldyn->atom[count].element=element;
+		moldyn->atom[count].mass=mass;
+		moldyn->atom[count].attr=attr;
+		moldyn->atom[count].bnum=bnum;
+		check_per_bound(moldyn,&(moldyn->atom[count].r));
 	}
 
+
 	return ret;
 }
 
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v) {
+             t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
 	void *ptr;
@@ -295,13 +267,15 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 		perror("[moldyn] realloc (add atom)");
 		return -1;
 	}
-	
-	atom=ptr;
-	atom->r=r;
-	atom->v=v;
-	atom->element=element;
-	atom->bnum=bnum;
-	atom->attr=attr;
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	atom[count-1].r=*r;
+	atom[count-1].v=*v;
+	atom[count-1].element=element;
+	atom[count-1].mass=mass;
+	atom[count-1].bnum=bnum;
+	atom[count-1].attr=attr;
 
 	return 0;
 }
@@ -313,7 +287,7 @@ int destroy_atoms(t_moldyn *moldyn) {
 	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -333,7 +307,7 @@ int thermal_init(t_moldyn *moldyn) {
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<moldyn->count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
 		atom[i].v.x=v;
@@ -356,44 +330,75 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn);
+	scale_velocity(moldyn,equi_init);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
-	double e,c;
+	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
 	/*
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
+
+	/* get kinetic energy / temperature & count involved atoms */
 	e=0.0;
+	count=0;
+	for(i=0;i<moldyn->count;i++) {
+		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	else return 0;	/* no atoms involved in scaling! */
+	
+	/* (temporary) hack for e,t = 0 */
+	if(e==0.0) {
+	moldyn->t=0.0;
+		if(moldyn->t_ref!=0.0)
+			thermal_init(moldyn,equi_init);
+		else
+			return 0; /* no scaling needed */
+	}
+
+
+	/* get scaling factor */
+	scale=moldyn->t_ref/moldyn->t;
+	if(equi_init&TRUE)
+		scale*=2.0;
+	else
+		if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+			scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
+	scale=sqrt(scale);
+
+	/* velocity scaling */
 	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
-	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
 
-double get_e_kin(t_atom *atom,int count) {
+double get_e_kin(t_moldyn *moldyn) {
 
 	int i;
-	double e;
+	t_atom *atom;
 
-	e=0.0;
+	atom=moldyn->atom;
+	moldyn->ekin=0.0;
 
-	for(i=0;i<count;i++) {
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	}
+	for(i=0;i<moldyn->count;i++)
+		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 
-	return e;
+	return moldyn->ekin;
 }
 
 double get_e_pot(t_moldyn *moldyn) {
@@ -401,23 +406,26 @@ double get_e_pot(t_moldyn *moldyn) {
 	return moldyn->energy;
 }
 
-double get_total_energy(t_moldyn *moldyn) {
+double update_e_kin(t_moldyn *moldyn) {
 
-	double e;
+	return(get_e_kin(moldyn));
+}
 
-	e=get_e_kin(moldyn->atom,moldyn->count);
-	e+=get_e_pot(moldyn);
+double get_total_energy(t_moldyn *moldyn) {
 
-	return e;
+	return(moldyn->ekin+moldyn->energy);
 }
 
-t_3dvec get_total_p(t_atom *atom, int count) {
+t_3dvec get_total_p(t_moldyn *moldyn) {
 
 	t_3dvec p,p_total;
 	int i;
+	t_atom *atom;
+
+	atom=moldyn->atom;
 
 	v3_zero(&p_total);
-	for(i=0;i<count;i++) {
+	for(i=0;i<moldyn->count;i++) {
 		v3_scale(&p,&(atom[i].v),atom[i].mass);
 		v3_add(&p_total,&p_total,&p);
 	}
@@ -425,15 +433,19 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 	return p_total;
 }
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 	double tau;
 
-	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
-	tau*=1.0E-9;
-	if(tau<moldyn->tau)
-		printf("[moldyn] warning: time step  (%f > %.15f)\n",
-		       moldyn->tau,tau);
+	/* nn_dist is the nearest neighbour distance */
+
+	if(moldyn->t==5.0) {
+		printf("[moldyn] i do not estimate timesteps below %f K!\n",
+		       MOLDYN_CRITICAL_EST_TEMP);
+		return 23.42;
+	}
+
+	tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 
 	return tau;	
 }
@@ -448,11 +460,11 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
+	int fd;
 
-	lc=&(moldyn->lc);
+	fd=open("/dev/null",O_WRONLY);
 
-	/* list log fd */
-	lc->listfd=open("/dev/null",O_WRONLY);
+	lc=&(moldyn->lc);
 
 	/* partitioning the md cell */
 	lc->nx=moldyn->dim.x/moldyn->cutoff;
@@ -465,11 +477,11 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("initializing linked cells (%d)\n",lc->cells);
+	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
 		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]));
+		list_init(&(lc->subcell[i]),fd);
 
  	link_cell_update(moldyn);
 	
@@ -493,7 +505,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	for(i=0;i<lc->cells;i++)
 		list_destroy(&(moldyn->lc.subcell[i]));
 	
-	for(count=0;count<moedyn->count;count++) {
+	for(count=0;count<moldyn->count;count++) {
 		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
@@ -522,7 +534,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	count2=27;
 	a=nx*ny;
 
-
 	cell[0]=lc->subcell[i+j*nx+k*a];
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
@@ -556,7 +567,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
-	lc->dnlc=count2;
+	lc->dnlc=count1;
 	lc->countn=27;
 
 	return count2;
@@ -572,18 +583,16 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 		list_shutdown(&(moldyn->lc.subcell[i]));
 
-	if(lc->listfd) close(lc->listfd);
-
 	return 0;
 }
 
-int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau ) {
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 
 	int count;
 	void *ptr;
 	t_moldyn_schedule *schedule;
 
-	schedule=moldyn->schedule;
+	schedule=&(moldyn->schedule);
 	count=++(schedule->content_count);
 
 	ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
@@ -591,6 +600,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau ) {
 		perror("[moldyn] realloc (runs)");
 		return -1;
 	}
+	moldyn->schedule.runs=ptr;
 	moldyn->schedule.runs[count-1]=runs;
 
 	ptr=realloc(schedule->tau,count*sizeof(double));
@@ -598,6 +608,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau ) {
 		perror("[moldyn] realloc (tau)");
 		return -1;
 	}
+	moldyn->schedule.tau=ptr;
 	moldyn->schedule.tau[count-1]=tau;
 
 	return 0;
@@ -622,11 +633,16 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i,sched;
-	unsigned int e,m,s,d,v;
+	unsigned int e,m,s,v;
 	t_3dvec p;
-
+	t_moldyn_schedule *schedule;
+	t_atom *atom;
 	int fd;
 	char fb[128];
+	double ds;
+
+	schedule=&(moldyn->schedule);
+	atom=moldyn->atom;
 
 	/* initialize linked cell method */
 	link_cell_init(moldyn);
@@ -635,27 +651,33 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	e=moldyn->ewrite;
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
-	d=moldyn->dwrite;
 	v=moldyn->vwrite;
 
-	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
-		printf("[moldyn] warning, lv system not initialized\n");
-		return -1;
-	}
-
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
-
 	/* calculate initial forces */
-	moldyn->potential_force_function(moldyn);
+	potential_force_calc(moldyn);
 
+	/* do some checks before we actually start calculating bullshit */
+	if(moldyn->cutoff>0.5*moldyn->dim.x)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.y)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.z)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+	if(ds>0.05*moldyn->nnd)
+		printf("[moldyn] warning: forces too high / tau too small!\n");
+
+	/* zero absolute time */
+	moldyn->time=0.0;
 	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 
-		/* setting amont of runs and finite time step size */
+		/* setting amount of runs and finite time step size */
 		moldyn->tau=schedule->tau[sched];
 		moldyn->tau_square=moldyn->tau*moldyn->tau;
-		moldyn->timesteps=schedule->runs[sched];
+		moldyn->time_steps=schedule->runs[sched];
 
 	/* integration according to schedule */
 
@@ -664,18 +686,27 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* integration step */
 		moldyn->integrate(moldyn);
 
+		/* p/t scaling */
+		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+			scale_velocity(moldyn,FALSE);
+
+		/* increase absolute time */
+		moldyn->time+=moldyn->tau;
+
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
 				dprintf(moldyn->efd,
-				        "%.15f %.45f\n",i*moldyn->tau,
+				        "%.15f %.45f %.45f %.45f\n",
+				        moldyn->time,update_e_kin(moldyn),
+				        moldyn->energy,
 				        get_total_energy(moldyn));
 		}
 		if(m) {
 			if(!(i%m)) {
-				p=get_total_p(moldyn->atom,moldyn->count);
+				p=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
-				        "%.15f %.45f\n",i*moldyn->tau,
+				        "%.15f %.45f\n",moldyn->time,
 				        v3_norm(&p));
 			}
 		}
@@ -695,18 +726,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(v) {
 			if(!(i%v)) {
-				visual_atoms(moldyn->visual,i*moldyn->tau,
+				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsteps: %d",i);
+				printf("\rsched: %d, steps: %d",sched,i);
 				fflush(stdout);
 			}
 		}
+
 	}
 
 		/* check for hooks */
 		if(schedule->hook)
 			schedule->hook(moldyn,schedule->hook_params);
 
+	}
+
 	return 0;
 }
 
@@ -730,7 +764,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+		check_per_bound(moldyn,&(atom[i].r));
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -738,15 +772,11 @@ int velocity_verlet(t_moldyn *moldyn) {
 	}
 
 	/* neighbour list update */
-printf("list update ...\n");
 	link_cell_update(moldyn);
-printf("done\n");
 
 	/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
 	potential_force_calc(moldyn);
 	//moldyn->potential_force_function(moldyn);
-printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -768,105 +798,156 @@ printf("done\n");
 
 int potential_force_calc(t_moldyn *moldyn) {
 
-	int i,count;
-	t_atom *atom;
+	int i,j,k,count;
+	t_atom *itom,*jtom,*ktom;
 	t_linkcell *lc;
-	t_list neighbour[27];
-	t_list *this;
-	double u;
-	u8 bc,bc3;
+	t_list neighbour_i[27];
+	t_list neighbour_i2[27];
+	//t_list neighbour_j[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ijk;
 	int countn,dnlc;
 
 	count=moldyn->count;
-	atom=moldyn->atom;
+	itom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	/* reset energy */
 	moldyn->energy=0.0;
 
 	for(i=0;i<count;i++) {
-	
+
 		/* reset force */
-		v3_zero(&(atom[i].f));
+		v3_zero(&(itom[i].f));
 
 		/* single particle potential/force */
-		if(atom[i].attr&ATOM_ATTR_1BP)
-			moldyn->pf_func1b(moldyn,&(atom[i]));
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
 
 		/* 2 body pair potential/force */
-		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-		
+		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+	
 			link_cell_neighbour_index(moldyn,
-				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
-				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
-				(atom[i].r.z+moldyn->dim.z/2)/lc->z,
-				neighbour);
+				(itom[i].r.x+moldyn->dim.x/2)/lc->x,
+				(itom[i].r.y+moldyn->dim.y/2)/lc->y,
+				(itom[i].r.z+moldyn->dim.z/2)/lc->z,
+				neighbour_i);
 
 			countn=lc->countn;
 			dnlc=lc->dnlc;
 
 			for(j=0;j<countn;j++) {
 
-				this=&(neighbour[j]);
+				this=&(neighbour_i[j]);
 				list_reset(this);
 
 				if(this->start==NULL)
 					continue;
 
-				bc=(j<dnlc)?0:1;
+				bc_ij=(j<dnlc)?0:1;
 
 				do {
-					btom=this->current->data;
+					jtom=this->current->data;
 
-					if(btom==&(atom[i]))
+					if(jtom==&(itom[i]))
 						continue;
 
-					if((btom->attr&ATOM_ATTR_2BP)&
-					   (atom[i].attr&ATOM_ATTR_2BP))
-						moldyn->pf_func2b(moldyn,
-						                  &(atom[i]),
-						                  btom,
-						                  bc);
+					if((jtom->attr&ATOM_ATTR_2BP)&
+					   (itom[i].attr&ATOM_ATTR_2BP))
+						moldyn->func2b(moldyn,
+						               &(itom[i]),
+						               jtom,
+						               bc_ij);
 
 					/* 3 body potential/force */
 
-					if(!(atom[i].attr&ATOM_ATTR_3BP)||
-					   !(btom->attr&ATOM_ATTR_3BP))
+					if(!(itom[i].attr&ATOM_ATTR_3BP)||
+					   !(jtom->attr&ATOM_ATTR_3BP))
 						continue;
 
-					link_cell_neighbour_index(moldyn,
-					   (btom->r.x+moldyn->dim.x/2)/lc->x,
-					   (btom->r.y+moldyn->dim.y/2)/lc->y,
-					   (btom->r.z+moldyn->dim.z/2)/lc->z,
-					   neighbourk);
-
-					for(k=0;k<lc->countn;k++) {
-
-						thisk=&(neighbourk[k]);
-						list_reset(thisk);
+			/*
+			 * according to mr. nordlund, we dont need to take the 
+			 * sum over all atoms now, as 'this is centered' around
+			 * atom i ...
+			 * i am not quite sure though! there is a not vanishing
+			 * part even if f_c_ik is zero ...
+			 * this analytical potentials suck!
+			 * switching from mc to md to dft soon!
+			 */
+
+			//		link_cell_neighbour_index(moldyn,
+			//		   (jtom->r.x+moldyn->dim.x/2)/lc->x,
+			//		   (jtom->r.y+moldyn->dim.y/2)/lc->y,
+			//		   (jtom->r.z+moldyn->dim.z/2)/lc->z,
+			//		   neighbour_j);
+
+//					/* neighbours of j */
+//					for(k=0;k<lc->countn;k++) {
+//
+//						that=&(neighbour_j[k]);
+//						list_reset(that);
+//					
+//						if(that->start==NULL)
+//							continue;
+//
+//						bc_ijk=(k<lc->dnlc)?0:1;
+//
+//						do {
+//
+//			ktom=that->current->data;
+//
+//			if(!(ktom->attr&ATOM_ATTR_3BP))
+//				continue;
+//
+//			if(ktom==jtom)
+//				continue;
+//
+//			if(ktom==&(itom[i]))
+//				continue;
+//
+//			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+//
+/*						} while(list_next(that)!=\ */
+//						        L_NO_NEXT_ELEMENT);
+//
+//					}
+			
+					/* copy the neighbour lists */
+					memcpy(neighbour_i2,neighbour_i,
+					       27*sizeof(t_list));
+
+					/* get neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i2[k]);
+						list_reset(that);
 					
-						if(thisk->start==NULL)
+						if(that->start==NULL)
 							continue;
 
-						bck=(k<lc->dnlc)?0:1;
+						bc_ijk=(k<dnlc)?0:1;
 
 						do {
 
-			ktom=thisk->current->data;
+			ktom=that->current->data;
 
 			if(!(ktom->attr&ATOM_ATTR_3BP))
 				continue;
 
-			if(ktom==btom)
+			if(ktom==jtom)
 				continue;
 
-			if(ktom==&(atom[i]))
+			if(ktom==&(itom[i]))
 				continue;
 
-			moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
+printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
 
-						} while(list_next(thisk)!=\
+						} while(list_next(that)!=\
 						        L_NO_NEXT_ELEMENT);
+
+					}
 					
 				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
 			}
@@ -883,20 +964,26 @@ int potential_force_calc(t_moldyn *moldyn) {
 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
 	double x,y,z;
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
 
 	x=0.5*dim->x;
 	y=0.5*dim->y;
 	z=0.5*dim->z;
 
-	if(moldyn->MOLDYN_ATTR_PBX)
+	if(moldyn->status&MOLDYN_STAT_PBX) {
 		if(a->x>=x) a->x-=dim->x;
 		else if(-a->x>x) a->x+=dim->x;
-	if(moldyn->MOLDYN_ATTR_PBY)
+	}
+	if(moldyn->status&MOLDYN_STAT_PBY) {
 		if(a->y>=y) a->y-=dim->y;
 		else if(-a->y>y) a->y+=dim->y;
-	if(moldyn->MOLDYN_ATTR_PBZ)
+	}
+	if(moldyn->status&MOLDYN_STAT_PBZ) {
 		if(a->z>=z) a->z-=dim->z;
 		else if(-a->z>z) a->z+=dim->z;
+	}
 
 	return 0;
 }
@@ -908,7 +995,7 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 
 /* harmonic oscillator potential and force */
 
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_ho_params *params;
 	t_3dvec force,distance;
@@ -919,9 +1006,8 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
 
-	v3_sub(&distance,&(ai->r),&(aj->r);
+	v3_sub(&distance,&(ai->r),&(aj->r));
 	
-	v3_per_bound(&distance,&(moldyn->dim));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
@@ -940,10 +1026,10 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_lj_params *params;
 	t_3dvec force,distance;
-	double d,h1,h2,u;
+	double d,h1,h2;
 	double eps,sig6,sig12;
 
-	params=moldyn->pot_params;
+	params=moldyn->pot2b_params;
 	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
@@ -965,7 +1051,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		d=+h1-h2;
 		d*=eps;
 		v3_scale(&force,&distance,d);
-		v3_add(&(ai->f),&(aj->f),&force);
+		v3_add(&(ai->f),&(ai->f),&force);
 	}
 
 	return 0;
@@ -975,6 +1061,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
  * tersoff potential & force for 2 sorts of atoms
  */
 
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+	printf("[moldyn] tersoff parameter completion\n");
+	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	p->Rmixed=sqrt(p->R[0]*p->R[1]);
+	p->Amixed=sqrt(p->A[0]*p->A[1]);
+	p->Bmixed=sqrt(p->B[0]*p->B[1]);
+	p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+	p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+	return 0;
+}
+
 /* tersoff 1 body part */
 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 
@@ -1010,12 +1110,17 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_tersoff_mult_params *params;
 	t_tersoff_exchange *exchange;
-	t_3dvec dist_ij;
+	t_3dvec dist_ij,force;
 	double d_ij;
-	double A,B,R,S,lambda;
+	double A,B,R,S,lambda,mu;
+	double f_r,df_r;
+	double f_c,df_c;
 	int num;
+	double s_r;
+	double arg;
+	double scale;
 
-	params=moldyn->pot_params;
+	params=moldyn->pot2b_params;
 	num=ai->bnum;
 	exchange=&(params->exchange);
 
@@ -1031,8 +1136,11 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	if(bc) check_per_bound(moldyn,&dist_ij);
 
-	/* save for use in 3bp */ /* REALLY ?!?!?! */
-	exchange->dist_ij=dist_ij;
+	d_ij=v3_norm(&dist_ij);
+
+	/* save for use in 3bp */
+	exchange->dist_ij=dist_ij; /* <- needed ? */
+	exchange->d_ij=d_ij;
 
 	/* constants */
 	if(num==aj->bnum) {
@@ -1042,7 +1150,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		lambda=params->lambda[num];
 		/* more constants depending of atoms i and j, needed in 3bp */
 		params->exchange.B=&(params->B[num]);
-		params->exchange.mu=params->mu[num];
+		params->exchange.mu=&(params->mu[num]);
+		mu=params->mu[num];
 		params->exchange.chi=1.0;
 	}
 	else {
@@ -1053,18 +1162,14 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		/* more constants depending of atoms i and j, needed in 3bp */
 		params->exchange.B=&(params->Bmixed);
 		params->exchange.mu=&(params->mu_m);
+		mu=params->mu_m;
 		params->exchange.chi=params->chi;
 	}
 
-	d_ij=v3_norm(&dist_ij);
-
-	/* save for use in 3bp */
-	exchange->d_ij=d_ij;
-
 	if(d_ij>S)
 		return 0;
 
-	f_r=A*exp(-lamda*d_ij);
+	f_r=A*exp(-lambda*d_ij);
 	df_r=-lambda*f_r/d_ij;
 
 	/* f_a, df_a calc + save for 3bp use */
@@ -1079,17 +1184,17 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	}
 	else {
 		s_r=S-R;
-		arg=PI*(d_ij-R)/s_r;
+		arg=M_PI*(d_ij-R)/s_r;
 		f_c=0.5+0.5*cos(arg);
-		df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+		df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
 		scale=df_c*f_r+df_r*f_c;
 		v3_scale(&force,&dist_ij,scale);
 	}
 
 	/* add forces */
 	v3_add(&(ai->f),&(ai->f),&force);
-	/* energy is 0.5 f_r f_c, but we will sum it up twice ... */
-	moldyn->energy+=(0.25*f_r*f_c);
+	/* energy is 0.5 f_r f_c ... */
+	moldyn->energy+=(0.5*f_r*f_c);
 
 	/* save for use in 3bp */
 	exchange->f_c=f_c;
@@ -1110,15 +1215,24 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	t_3dvec dist_ij,dist_ik,dist_jk;
 	t_3dvec temp,force;
 	double R,S,s_r;
-	double d_ij,d_ik,d_jk;
+	double d_ij,d_ij2,d_ik,d_jk;
 	double f_c,df_c,b_ij,f_a,df_a;
-	double n,c,d,h,neta,betan,betan_1;
+	double f_c_ik,df_c_ik,arg;
+	double scale;
+	double chi;
+	double n,c,d,h,beta,betan;
+	double c2,d2,c2d2;
+	double numer,denom;
 	double theta,cos_theta,sin_theta;
+	double d_theta,d_theta1,d_theta2;
+	double h_cos,h_cos2,d2_h_cos2;
+	double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
+	double bracket3,bracket3_pow_1,bracket3_pow;
 	int num;
 
-	params=moldyn->pot_params;
+	params=moldyn->pot3b_params;
 	num=ai->bnum;
-	exchange=params->exchange;
+	exchange=&(params->exchange);
 
 	if(!(exchange->run3bp))
 		return 0;
@@ -1148,7 +1262,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	 */
 
 	
-	v3_sub(&dist_ik,&(aj->i),&(ak->r));
+	v3_sub(&dist_ik,&(ai->r),&(ak->r));
 	if(bc) check_per_bound(moldyn,&dist_ik);
 	d_ik=v3_norm(&dist_ik);
 
@@ -1173,9 +1287,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	}
 	else {
 		s_r=S-R;
-		arg=PI*(d_ik-R)/s_r;
+		arg=M_PI*(d_ik-R)/s_r;
 		f_c_ik=0.5+0.5*cos(arg);
-		df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
+		df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
 	}
 	
 	v3_sub(&dist_jk,&(aj->r),&(ak->r));
@@ -1196,7 +1310,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	denom=2*d_ij*d_ik;
 	cos_theta=numer/denom;
 	sin_theta=sqrt(1.0-(cos_theta*cos_theta));
-	theta=arccos(cos_theta);
+	theta=acos(cos_theta);
 	d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
 	d_theta1=2*denom-numer*2*d_ik/d_ij;
 	d_theta2=2*denom-numer*2*d_ij/d_ik;
@@ -1221,12 +1335,12 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	b_ij=chi*bracket3_pow;
 
 	/* derivation of theta */
-	v3_scale(&force,&dist_ij,d1_theta);
+	v3_scale(&force,&dist_ij,d_theta1);
 	v3_scale(&temp,&dist_ik,d_theta2);
 	v3_add(&force,&force,&temp);
 
 	/* part 1 of derivation of b_ij */
-	v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
+	v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
 
 	/* part 2 of derivation of b_ij */
 	v3_scale(&temp,&dist_ik,df_c_ik*bracket1);