int count;
atom=moldyn->atom;
- count=(moldyn->count)++;
+ count=(moldyn->count)++; // asshole style!
ptr=realloc(atom,(count+1)*sizeof(t_atom));
if(!ptr) {
moldyn->atom=ptr;
atom=moldyn->atom;
+
+ /* initialize new atom */
+ memset(&(atom[count]),0,sizeof(t_atom));
atom[count].r=*r;
atom[count].v=*v;
atom[count].element=element;
return moldyn->p;
}
+int average_reset(t_moldyn *moldyn) {
+
+ printf("[moldyn] average reset\n");
+
+ /* update skip value */
+ moldyn->avg_skip=moldyn->total_steps;
+
+ /* kinetic energy */
+ moldyn->k_sum=0.0;
+ moldyn->k2_sum=0.0;
+
+ /* potential energy */
+ moldyn->v_sum=0.0;
+ moldyn->v2_sum=0.0;
+
+ /* temperature */
+ moldyn->t_sum=0.0;
+
+ /* virial */
+ moldyn->virial_sum=0.0;
+ moldyn->gv_sum=0.0;
+
+ /* pressure */
+ moldyn->p_sum=0.0;
+ moldyn->gp_sum=0.0;
+
+ return 0;
+}
+
int average_and_fluctuation_calc(t_moldyn *moldyn) {
int denom;
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);
-
+
#ifdef STATIC_LISTS
p=0;
while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
count2=27;
a=nx*ny;
+ if(i>=nx||j>=ny||k>=nz)
+ printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
+ i,nx,j,ny,k,nz);
+
cell[0]=lc->subcell[i+j*nx+k*a];
for(ci=-1;ci<=1;ci++) {
bx=0;
/* some stupid 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");
+ 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");
+ 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");
+ 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");
+ printf("[moldyn] WARNING: forces too high / tau too small!\n");
/* zero absolute time */
moldyn->time=0.0;
tau_square=moldyn->tau_square;
for(i=0;i<count;i++) {
+ /* check whether fixed atom */
+ if(atom[i].attr&ATOM_ATTR_FP)
+ continue;
/* new positions */
h=0.5/atom[i].mass;
v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+ /* criticial check */
+ moldyn_bc_check(moldyn);
+
/* neighbour list update */
link_cell_update(moldyn);
potential_force_calc(moldyn);
for(i=0;i<count;i++) {
+ /* check whether fixed atom */
+ if(atom[i].attr&ATOM_ATTR_FP)
+ continue;
/* again velocities [actually v(t+tau)] */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
//printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
if(moldyn->time>DSTART&&moldyn->time<DEND) {
printf("force:\n");
- printf(" x: %0.40f\n",moldyn->atom[5832].f.x);
- printf(" y: %0.40f\n",moldyn->atom[5832].f.y);
- printf(" z: %0.40f\n",moldyn->atom[5832].f.z);
+ printf(" x: %0.40f\n",moldyn->atom[DATOM].f.x);
+ printf(" y: %0.40f\n",moldyn->atom[DATOM].f.y);
+ printf(" z: %0.40f\n",moldyn->atom[DATOM].f.z);
}
#endif
- /* calculate global virial */
+ /* some postprocessing */
for(i=0;i<count;i++) {
- moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
- moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
- moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
- moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
- moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
- moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+ /* calculate global virial */
+ moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
+ moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
+ moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
+ moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
+ moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
+ moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
+
+ /* check forces regarding the given timestep */
+ if(v3_norm(&(itom[i].f))>\
+ 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+ printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
+ i);
}
return 0;
int fd;
int cnt,size;
+ int fsize;
+ int corr;
fd=open(file,O_RDONLY);
if(fd<0) {
return fd;
}
+ fsize=lseek(fd,0,SEEK_END);
+ lseek(fd,0,SEEK_SET);
+
size=sizeof(t_moldyn);
while(size) {
size=moldyn->count*sizeof(t_atom);
+ /* correcting possible atom data offset */
+ corr=0;
+ if(fsize!=sizeof(t_moldyn)+size) {
+ corr=fsize-sizeof(t_moldyn)-size;
+ printf("[moldyn] WARNING: lsf (illegal file size)\n");
+ printf(" moifying offset:\n");
+ printf(" - current pos: %d\n",sizeof(t_moldyn));
+ printf(" - atom size: %d\n",size);
+ printf(" - file size: %d\n",fsize);
+ printf(" => correction: %d\n",corr);
+ lseek(fd,corr,SEEK_CUR);
+ }
+
moldyn->atom=(t_atom *)malloc(size);
if(moldyn->atom==NULL) {
perror("[moldyn] load save file malloc (atoms)");
return 0;
}
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ double d2;
+ int a_cnt;
+ int b_cnt;
+
+ atom=moldyn->atom;
+ dc[0]=0;
+ dc[1]=0;
+ dc[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+ v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
+ check_per_bound(moldyn,&dist);
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ dc[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ }
+
+ dc[2]+=d2;
+ }
+
+ return 0;
+}
+
int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
int slots;
unsigned char bc;
t_3dvec dist;
double d;
- //double norm;
+ double norm;
int o,s;
unsigned char ibrand;
lc=&(moldyn->lc);
- slots=moldyn->cutoff/dr;
+ slots=2.0*moldyn->cutoff/dr;
o=2*slots;
+ if(slots*dr<=moldyn->cutoff)
+ printf("[moldyn] WARNING: pcc (low #slots)\n");
+
printf("[moldyn] pair correlation calc info:\n");
printf(" time: %f\n",moldyn->time);
printf(" count: %d\n",moldyn->count);
d=v3_absolute_square(&dist);
/* ignore if greater or equal cutoff */
- if(d>=moldyn->cutoff_square)
+ if(d>=4.0*moldyn->cutoff_square)
continue;
/* fill the slots */
/* should never happen but it does 8) -
* related to -ffloat-store problem! */
- if(s>=slots) s=slots-1;
+ if(s>=slots) {
+ printf("[moldyn] WARNING: pcc (%d/%d)",
+ s,slots);
+ printf("\n");
+ s=slots-1;
+ }
if(ibrand!=jtom->brand) {
/* mixed */
}
}
- /* normalization
+ /* normalization */
for(i=1;i<slots;i++) {
- // normalization: 4 pi r r dr
+ // normalization: 4 pi r^2 dr
// here: not double counting pairs -> 2 pi r r dr
- norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
+ // ... and actually it's a constant times r^2
+ norm=i*i*dr*dr;
stat[i]/=norm;
stat[slots+i]/=norm;
stat[o+i]/=norm;
}
- */
+ /* */
if(ptr==NULL) {
/* todo: store/print pair correlation function */
projects / physik / posic.git / blobdiff