vel scaling fixed/changed
[physik/posic.git] / moldyn.c
index c0b99eb..d52fcd3 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -41,8 +41,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 int moldyn_shutdown(t_moldyn *moldyn) {
 
-       link_cell_shutdown(moldyn);
+       printf("[moldyn] shutdown\n");
        moldyn_log_shutdown(moldyn);
+       link_cell_shutdown(moldyn);
        rand_close(&(moldyn->random));
        free(moldyn->atom);
 
@@ -51,12 +52,12 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 
 int set_int_alg(t_moldyn *moldyn,u8 algo) {
 
-       switch(alg) {
-               case 'MOLDYN_INTEGRATE_VERLET':
+       switch(algo) {
+               case MOLDYN_INTEGRATE_VERLET:
                        moldyn->integrate=velocity_verlet;
                        break;
                default:
-                       printf("unknown integration algorithm: %02x\",alg);
+                       printf("unknown integration algorithm: %02x\n",algo);
                        return -1;
        }
 
@@ -92,6 +93,13 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
        return 0;
 }
 
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+       moldyn->nnd=dist;
+
+       return 0;
+}
+
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
        if(x)
@@ -106,25 +114,26 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
        return 0;
 }
 
-int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 
-       switch(type) {
-               case MOLDYN_1BP:
-                       moldyn->pf_func1b=func;
-                       moldyn->pot1b_params=params;
-                       break;
-               case MOLDYN_2BP:
-                       moldyn->pf_func2b=func;
-                       moldyn->pot2b_params=params;
-                       break;
-               case MOLDYN_3BP:
-                       moldyn->pf_func3b=func;
-                       moldyn->pot3b_params=params;
-                       break;
-               default:
-                       printf("unknown potential type: %02x\n",type);
-                       return -1;
-       }
+       moldyn->func1b=func;
+       moldyn->pot1b_params=params;
+
+       return 0;
+}
+
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+
+       moldyn->func2b=func;
+       moldyn->pot2b_params=params;
+
+       return 0;
+}
+
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+       moldyn->func3b=func;
+       moldyn->pot3b_params=params;
 
        return 0;
 }
@@ -139,7 +148,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
                                perror("[moldyn] efd open");
                                return moldyn->efd;
                        }
-                       dprintf("# moldyn total energy log file\n");
+                       dprintf(moldyn->efd,"# total energy log file\n");
                        break;
                case LOG_TOTAL_MOMENTUM:
                        moldyn->mwrite=timer;
@@ -148,14 +157,14 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
                                perror("[moldyn] mfd open");
                                return moldyn->mfd;
                        }
-                       dprintf("# moldyn total momentum log file\n");
+                       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->mwrite=timer;
+                       moldyn->vwrite=timer;
                        strncpy(moldyn->vfb,fb,63);
                        visual_init(&(moldyn->vis),fb);
                        break;
@@ -169,9 +178,10 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 
 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->visual) visual_tini(moldyn->visual);
+       if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
        return 0;
 }
@@ -182,17 +192,15 @@ 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;
        }
@@ -201,10 +209,10 @@ 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);
@@ -220,12 +228,13 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        }
 
        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;
+               moldyn->atom[count-1].element=element;
+               moldyn->atom[count-1].mass=mass;
+               moldyn->atom[count-1].attr=attr;
+               moldyn->atom[count-1].bnum=bnum;
                count-=1;
        }
 
@@ -233,7 +242,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 }
 
 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;
@@ -247,13 +256,15 @@ 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;
 }
@@ -308,15 +319,15 @@ int thermal_init(t_moldyn *moldyn) {
        }
 
        /* velocity scaling */
-       scale_velocity(moldyn);
+       scale_velocity(moldyn,VSCALE_INIT_EQUI);
 
        return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 type) {
 
        int i;
-       double e,c;
+       double e,scale;
        t_atom *atom;
 
        atom=moldyn->atom;
@@ -324,12 +335,15 @@ int scale_velocity(t_moldyn *moldyn) {
        /*
         * - velocity scaling (E = 3/2 N k T), E: kinetic energy
         */
+
        e=0.0;
        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));
+       scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+       if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
+       scale=sqrt(scale);
        for(i=0;i<moldyn->count;i++)
-               v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+               v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
        return 0;
 }
@@ -353,9 +367,14 @@ double get_e_pot(t_moldyn *moldyn) {
        return moldyn->energy;
 }
 
+double update_e_kin(t_moldyn *moldyn) {
+
+       return(get_e_kin(moldyn));
+}
+
 double get_total_energy(t_moldyn *moldyn) {
 
-       return(get_e_kin(moldyn)+get_e_pot(moldyn));
+       return(moldyn->ekin+moldyn->energy);
 }
 
 t_3dvec get_total_p(t_moldyn *moldyn) {
@@ -367,7 +386,7 @@ t_3dvec get_total_p(t_moldyn *moldyn) {
        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);
        }
@@ -375,15 +394,19 @@ t_3dvec get_total_p(t_moldyn *moldyn) {
        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;     
 }
@@ -398,11 +421,11 @@ 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;
@@ -415,11 +438,11 @@ 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);
        
@@ -443,7 +466,7 @@ 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;
@@ -522,8 +545,6 @@ 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;
 }
 
@@ -533,7 +554,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
        void *ptr;
        t_moldyn_schedule *schedule;
 
-       schedule=moldyn->schedule;
+       schedule=&(moldyn->schedule);
        count=++(schedule->content_count);
 
        ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
@@ -541,6 +562,7 @@ 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));
@@ -548,6 +570,7 @@ 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;
@@ -572,11 +595,16 @@ 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);
@@ -585,27 +613,35 @@ 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 */
 
@@ -614,18 +650,23 @@ int moldyn_integrate(t_moldyn *moldyn) {
                /* integration step */
                moldyn->integrate(moldyn);
 
+               /* 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));
                        }
                }
@@ -645,18 +686,21 @@ 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;
 }
 
@@ -680,7 +724,7 @@ 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);
@@ -688,15 +732,11 @@ 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 */
@@ -718,13 +758,12 @@ printf("done\n");
 
 int potential_force_calc(t_moldyn *moldyn) {
 
-       int i,count;
-       t_atom *atom;
+       int i,j,k,count;
+       t_atom *atom,*btom,*ktom;
        t_linkcell *lc;
        t_list neighbour[27];
-       t_list *this;
-       double u;
-       u8 bc,bc3;
+       t_list *this,*thisk,*neighbourk;
+       u8 bc,bck;
        int countn,dnlc;
 
        count=moldyn->count;
@@ -741,11 +780,11 @@ int potential_force_calc(t_moldyn *moldyn) {
 
                /* single particle potential/force */
                if(atom[i].attr&ATOM_ATTR_1BP)
-                       moldyn->pf_func1b(moldyn,&(atom[i]));
+                       moldyn->func1b(moldyn,&(atom[i]));
 
                /* 2 body pair potential/force */
                if(atom[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,
@@ -773,10 +812,10 @@ int potential_force_calc(t_moldyn *moldyn) {
 
                                        if((btom->attr&ATOM_ATTR_2BP)&
                                           (atom[i].attr&ATOM_ATTR_2BP))
-                                               moldyn->pf_func2b(moldyn,
-                                                                 &(atom[i]),
-                                                                 btom,
-                                                                 bc);
+                                               moldyn->func2b(moldyn,
+                                                              &(atom[i]),
+                                                              btom,
+                                                              bc);
 
                                        /* 3 body potential/force */
 
@@ -813,10 +852,12 @@ int potential_force_calc(t_moldyn *moldyn) {
                        if(ktom==&(atom[i]))
                                continue;
 
-                       moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
+                       moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
 
                                                } while(list_next(thisk)!=\
                                                        L_NO_NEXT_ELEMENT);
+
+                                       }
                                        
                                } while(list_next(this)!=L_NO_NEXT_ELEMENT);
                        }
@@ -833,20 +874,26 @@ 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;
 }
@@ -858,7 +905,7 @@ 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;
@@ -869,9 +916,8 @@ 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) {
@@ -890,10 +936,10 @@ 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;
@@ -915,7 +961,7 @@ 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;
@@ -960,12 +1006,17 @@ 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);
 
@@ -992,7 +1043,8 @@ 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 {
@@ -1003,6 +1055,7 @@ 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;
        }
 
@@ -1014,7 +1067,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        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 */
@@ -1029,9 +1082,9 @@ 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);
        }
@@ -1060,15 +1113,24 @@ 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;
@@ -1098,7 +1160,7 @@ 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);
 
@@ -1123,9 +1185,9 @@ 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));
@@ -1146,7 +1208,7 @@ 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;
@@ -1171,12 +1233,12 @@ 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);