vel scaling fixed/changed

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 509a45d..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);
 
@@ -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)
@@ -156,7 +164,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int 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;
@@ -170,9 +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;
 }
@@ -183,17 +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;
        }
@@ -202,10 +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);
@@ -221,12 +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;
        }
 
@@ -234,7 +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;
@@ -248,13 +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;
 }
@@ -309,15 +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;
@@ -325,12 +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;
 }
@@ -381,15 +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;     
 }
@@ -404,6 +421,9 @@ int link_cell_init(t_moldyn *moldyn) {
 
        t_linkcell *lc;
        int i;
+       int fd;
+
+       fd=open("/dev/null",O_WRONLY);
 
        lc=&(moldyn->lc);
 
@@ -418,10 +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]),1);
+               list_init(&(lc->subcell[i]),fd);
 
        link_cell_update(moldyn);
        
@@ -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;
@@ -575,11 +598,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
        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);
@@ -597,6 +622,17 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* calculate initial forces */
        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;
 
@@ -650,12 +686,13 @@ 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 */
@@ -687,7 +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);
@@ -695,15 +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 */
@@ -751,7 +784,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
                /* 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,
@@ -885,7 +918,6 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        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) {
@@ -929,7 +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;