into the tersoff potential

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 9d782d6..ed831ae 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -93,6 +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)
@@ -185,17 +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;
        }
@@ -204,10 +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);
@@ -223,15 +228,18 @@ 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;
                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;
 }
 
@@ -313,15 +321,15 @@ 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;
@@ -330,17 +338,14 @@ int scale_velocity(t_moldyn *moldyn) {
         * - velocity scaling (E = 3/2 N k T), E: kinetic energy
         */
 
-       if(moldyn->t==0.0) {
-               printf("[moldyn] no velocity scaling for T = 0 K\n");
-               return -1;
-       }
-
        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;
 }
@@ -526,7 +531,7 @@ 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;
@@ -596,9 +601,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
        t_3dvec p;
        t_moldyn_schedule *schedule;
        t_atom *atom;
-
        int fd;
        char fb[128];
+       double ds;
 
        schedule=&(moldyn->schedule);
        atom=moldyn->atom;
@@ -615,10 +620,20 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* sqaure of some variables */
        moldyn->tau_square=moldyn->tau*moldyn->tau;
        moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
-
        /* 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;
 
@@ -760,7 +775,7 @@ int potential_force_calc(t_moldyn *moldyn) {
        moldyn->energy=0.0;
 
        for(i=0;i<count;i++) {
-       
+
                /* reset force */
                v3_zero(&(atom[i].f));
 
@@ -809,11 +824,13 @@ int potential_force_calc(t_moldyn *moldyn) {
                                           !(btom->attr&ATOM_ATTR_3BP))
                                                continue;
 
+printf("DEBUG: problem exists here ...\n");
                                        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);
+printf("DEBUG: as you won't see that!\n");
 
                                        for(k=0;k<lc->countn;k++) {
 
@@ -957,6 +974,20 @@ 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) {