fixed several stupid mistakes

diff --git a/moldyn.c b/moldyn.c
index 707fe03..e02557c 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -456,8 +456,8 @@ int link_cell_init(t_moldyn *moldyn) {
        printf("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]),lc->listfd);
+               //list_init(&(lc->subcell[i]),1);
+               list_init(&(lc->subcell[i]),lc->listfd);
 
        link_cell_update(moldyn);
        
@@ -512,7 +512,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 
 
        cell[0]=lc->subcell[i+j*nx+k*a];
-       printf("%d\n",i+j*nx+k*a);
        for(ci=-1;ci<=1;ci++) {
                bx=0;
                x=i+ci;
@@ -535,16 +534,11 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
                                        bz=1;
                                }
                                if(!(ci|cj|ck)) continue;
-                               printf(" %d %d %d \n",x,y,z);
                                if(bx|by|bz) {
                                        cell[--count2]=lc->subcell[x+y*nx+z*a];
-                                       printf("%d\n",x+y*nx+z*a);
-                                       printf("--- %d\n",count2);
                                }
                                else {
                                        cell[count1++]=lc->subcell[x+y*nx+z*a];
-                                       printf("%d\n",x+y*nx+z*a);
-                                       printf("--- %d\n",count1);
                                }
                        }
                }
@@ -585,6 +579,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
        int fd;
        char fb[128];
 
+       /* initialize linked cell method */
+       link_cell_init(moldyn);
+
        /* logging & visualization */
        e=moldyn->ewrite;
        m=moldyn->mwrite;
@@ -606,9 +603,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
        for(i=0;i<moldyn->time_steps;i++) {
 
-               /* neighbour list update */
-               link_cell_update(moldyn);
-
                /* integration step */
                moldyn->integrate(moldyn);
 
@@ -686,6 +680,9 @@ int velocity_verlet(t_moldyn *moldyn) {
                v3_add(&(atom[i].v),&(atom[i].v),&delta);
        }
 
+       /* neighbour list update */
+       link_cell_update(moldyn);
+
        /* forces depending on chosen potential */
        moldyn->potential_force_function(moldyn);
 
@@ -727,30 +724,43 @@ int harmonic_oscillator(t_moldyn *moldyn) {
        equi_dist=params->equilibrium_distance;
        count=moldyn->count;
 
+       /* reset energy counter */
        u=0.0;
+
        for(i=0;i<count;i++) {
+               /* reset force */
+               v3_zero(&(atom[i].f));
+
                /* determine cell + neighbours */
                ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
                nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
                nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-               printf("%d %d %d\n",ni,nj,nk);
                c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
 
-               /* processing cell of atom i */
+               /*
+                * processing cell of atom i
+                * => no need to check for empty list (1 element at minimum)
+                */
                this=&(neighbour[0]);
-               list_reset(this); /* list has 1 element at minimum */
+               list_reset(this);
                do {
                        btom=this->current->data;
                        if(btom==&(atom[i]))
                                continue;
                        v3_sub(&distance,&(atom[i].r),&(btom->r));
                        d=v3_norm(&distance);
-                       u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-                       v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
-                       v3_add(&(atom[i].f),&(atom[i].f),&force);
+                       if(d<=moldyn->cutoff) {
+                               u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+                               v3_scale(&force,&distance,
+                                        -sc*(1.0-(equi_dist/d)));
+                               v3_add(&(atom[i].f),&(atom[i].f),&force);
+                       }
                } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
-               /* neighbours not doing boundary condition overflow */
+               /*
+                * direct neighbour cells
+                * => no boundary condition check necessary
+                */
                for(j=1;j<c;j++) {
                        this=&(neighbour[j]);
                        list_reset(this); /* there might not be a single atom */
@@ -772,7 +782,10 @@ int harmonic_oscillator(t_moldyn *moldyn) {
                        }
                }
 
-               /* neighbours due to boundary conditions */
+               /*
+                * indirect neighbour cells
+                * => check boundary conditions
+                */
                for(j=c;j<27;j++) {
                        this=&(neighbour[j]);
                        list_reset(this); /* check boundary conditions */
@@ -796,7 +809,7 @@ int harmonic_oscillator(t_moldyn *moldyn) {
                }
        }
 
-       moldyn->energy=u;
+       moldyn->energy=0.5*u;
 
        return 0;
 }
@@ -824,18 +837,18 @@ int lennard_jones(t_moldyn *moldyn) {
        sig6=params->sigma6;
        sig12=params->sigma12;
 
+       /* reset energy counter */
        u=0.0;
+
        for(i=0;i<count;i++) {
+               /* reset force */
+               v3_zero(&(atom[i].f));
+
                /* determine cell + neighbours */
                ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
                nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
                nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-                       printf("hier atom = %08x\n",&(atom[i]));
                c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-                       printf("da atom = %08x\n",&(atom[i]));
-                       printf("da atom = %08x\n",&(moldyn->atom[i]));
-
-               printf("c = %d (%d %d %d)\n",c,ni,nj,nk);
 
                /* processing cell of atom i */
                this=&(neighbour[0]);
@@ -844,23 +857,23 @@ int lennard_jones(t_moldyn *moldyn) {
                        btom=this->current->data;
                        if(btom==&(atom[i]))
                                continue;
-               puts("foo");
                        v3_sub(&distance,&(atom[i].r),&(btom->r));
-               puts("foo");
-                       d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
-                       h1=d*d;         /* 1/r^4 */
-                       h2*=d;          /* 1/r^6 */
-                       h1=h2*h2;       /* 1/r^12 */
-                       u+=eps*(sig12*h1-sig6*h2);
-                       h2*=d;          /* 1/r^8 */
-                       h1*=d;          /* 1/r^14 */
-                       h2*=6*sig6;
-                       h1*=12*sig12;
-                       d=-h1+h2;
-                       d*=eps;
-                       v3_scale(&force,&distance,d);
-                       v3_add(&(atom[i].f),&(atom[i].f),&force);
-                       printf("test!!\n");
+                       d=v3_absolute_square(&distance);        /* 1/r^2 */
+                       if(d<=moldyn->cutoff_square) {
+                               d=1.0/d;        /* 1/r^2 */
+                               h1=d*d;         /* 1/r^4 */
+                               h2*=d;          /* 1/r^6 */
+                               h1=h2*h2;       /* 1/r^12 */
+                               u+=eps*(sig12*h1-sig6*h2);
+                               h2*=d;          /* 1/r^8 */
+                               h1*=d;          /* 1/r^14 */
+                               h2*=6*sig6;
+                               h1*=12*sig12;
+                               d=-h1+h2;
+                               d*=eps;
+                               v3_scale(&force,&distance,d);
+                               v3_add(&(atom[i].f),&(atom[i].f),&force);
+                       }
                } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
                /* neighbours not doing boundary condition overflow */
@@ -870,7 +883,6 @@ int lennard_jones(t_moldyn *moldyn) {
                        if(this->start!=NULL) {
 
                        do {
-                               printf("in bound: %d\n",j);
                                btom=this->current->data;
                                v3_sub(&distance,&(atom[i].r),&(btom->r));
                                d=v3_absolute_square(&distance); /* r^2 */
@@ -902,7 +914,6 @@ int lennard_jones(t_moldyn *moldyn) {
                        if(this->start!=NULL) {
 
                        do {
-                               printf("out bound: %d\n",j);
                                btom=this->current->data;
                                v3_sub(&distance,&(atom[i].r),&(btom->r));
                                v3_per_bound(&distance,&(moldyn->dim));
@@ -929,7 +940,7 @@ int lennard_jones(t_moldyn *moldyn) {
                }
        }
 
-       moldyn->energy=u;
+       moldyn->energy=0.5*u;
        
        return 0;
 }

diff --git a/moldyn.h b/moldyn.h
index 0022208..3016bc4 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -131,7 +131,7 @@ typedef struct s_lj_params {
 #define SI                     0x0e
 #define LC_SI                  0.543105e-9                             /* m */
 #define M_SI                   (28.085*AMU)                            /* kg */
-#define LJ_SIGMA_SI            ((0.25*sqrt(3.0)*LC_SI)/1.122462)       /* m */
+#define LJ_SIGMA_SI            ((0.20*sqrt(3.0)*LC_SI)/1.122462)       /* m */
 #define LJ_EPSILON_SI          (2.1678*1.60e-19)                       /* Nm */
 
 /* function prototypes */

diff --git a/posic.c b/posic.c
index c185d16..fba11d2 100644 (file)
--- a/posic.c
+++ b/posic.c
@@ -48,7 +48,7 @@ int main(int argc,char **argv) {
        lj.sigma12=lj.sigma6*lj.sigma6;
        lj.epsilon4=4.0*LJ_EPSILON_SI;
        ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-       ho.spring_constant=1.0;
+       ho.spring_constant=1;
        /* assignement */
        md.potential_force_function=lennard_jones;
        //md.potential_force_function=harmonic_oscillator;
@@ -95,9 +95,9 @@ int main(int argc,char **argv) {
        md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&(md.atom));
        printf("created silicon lattice (#atoms = %d)\n",md.count);
 #else
-       md.count=2;
-       md.atom=malloc(2*sizeof(t_atom));
-       md.atom[0].r.x=0.13*sqrt(3.0)*LC_SI/2.0;
+       md.count=3;
+       md.atom=malloc(md.count*sizeof(t_atom));
+       md.atom[0].r.x=0.21*sqrt(3.0)*LC_SI/2.0;
        md.atom[0].r.y=0;
        md.atom[0].r.z=0;
        md.atom[0].element=SI;
@@ -107,6 +107,18 @@ int main(int argc,char **argv) {
        md.atom[1].r.z=0;
        md.atom[1].element=SI;
        md.atom[1].mass=M_SI;
+
+       md.atom[2].r.x=0.5*(a-1)*LC_SI;
+       md.atom[2].r.y=0.5*(b-1)*LC_SI;
+       md.atom[2].r.z=0;
+       md.atom[2].element=C;
+       md.atom[2].mass=M_C;
+
+       //md.atom[3].r.x=0.5*(a-1)*LC_SI;
+       //md.atom[3].r.y=0;
+       //md.atom[3].r.z=0;
+       //md.atom[3].element=SI;
+       //md.atom[3].mass=M_SI;
 #endif
 
        /* initial thermal fluctuations of particles */
@@ -116,6 +128,8 @@ int main(int argc,char **argv) {
        thermal_init(&md);
 #else
        for(a=0;a<md.count;a++) v3_zero(&(md.atom[0].v));
+       md.atom[2].v.x=-320;
+       md.atom[2].v.y=-320;
 #endif
 
        /* check kinetic energy */
@@ -132,9 +146,6 @@ int main(int argc,char **argv) {
        printf("estimated accurate time step: %.30f [s]\n",
               estimate_time_step(&md,3.0,md.t));
 
-       /* initialize linked list / cell method */
-       link_cell_init(&md);
-
        /*
         * let's do the actual md algorithm now
         *

diff --git a/posic.h b/posic.h
index 44caf18..0ca2ac8 100644 (file)
--- a/posic.h
+++ b/posic.h
@@ -18,7 +18,8 @@
 #define POSIC_H
 
 #define RUNS 10000000
-#define TAU 0.000000000000001
+//#define TAU 0.000000000000001
+#define TAU 0.000000000001
 #define WRITE_FILE 100000
 
 #define TEMPERATURE 273.0 

diff --git a/visual/visual.c b/visual/visual.c
index 29d9469..03c20a1 100644 (file)
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -94,6 +94,7 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
        dprintf(v->fd,"rotate y 10\n");
        dprintf(v->fd,"set ambient 20\n");
        dprintf(v->fd,"set specular on\n");
+       dprintf(v->fd,"label\n");
        sprintf(file,"%s-%.15f.ppm",v->fb,time);
        dprintf(v->fd,"write ppm %s\n",file);
        dprintf(v->fd,"zap\n");