moldyn->vis.dim.z=z;
}
- moldyn->dv=0.000001*moldyn->volume;
-
printf("[moldyn] dimensions in A and A^3 respectively:\n");
printf(" x: %f\n",moldyn->dim.x);
printf(" y: %f\n",moldyn->dim.y);
printf(" z: %f\n",moldyn->dim.z);
printf(" volume: %f\n",moldyn->volume);
printf(" visualize simulation box: %s\n",visualize?"yes":"no");
- printf(" delta volume (pressure calc): %f\n",moldyn->dv);
return 0;
}
dprintf(moldyn->tfd,"# temperature log file\n");
printf("temperature (%d)\n",timer);
break;
+ case LOG_VOLUME:
+ moldyn->vwrite=timer;
+ snprintf(filename,127,"%s/volume",moldyn->vlsdir);
+ moldyn->vfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->vfd<0) {
+ perror("[moldyn] volume log file\n");
+ return moldyn->vfd;
+ }
+ dprintf(moldyn->vfd,"# volume log file\n");
+ printf("volume (%d)\n",timer);
+ break;
case SAVE_STEP:
moldyn->swrite=timer;
printf("save file (%d)\n",timer);
break;
case VISUAL_STEP:
- moldyn->vwrite=timer;
+ moldyn->awrite=timer;
ret=visual_init(moldyn,moldyn->vlsdir);
if(ret<0) {
printf("[moldyn] visual init failure\n");
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;
double virial_sum(t_moldyn *moldyn) {
int i;
- double v;
t_virial *virial;
/* virial (sum over atom virials) */
- v=0.0;
+ moldyn->virial=0.0;
+ moldyn->vir.xx=0.0;
+ moldyn->vir.yy=0.0;
+ moldyn->vir.zz=0.0;
+ moldyn->vir.xy=0.0;
+ moldyn->vir.xz=0.0;
+ moldyn->vir.yz=0.0;
for(i=0;i<moldyn->count;i++) {
virial=&(moldyn->atom[i].virial);
- v+=(virial->xx+virial->yy+virial->zz);
+ moldyn->virial+=(virial->xx+virial->yy+virial->zz);
+ moldyn->vir.xx+=virial->xx;
+ moldyn->vir.yy+=virial->yy;
+ moldyn->vir.zz+=virial->zz;
+ moldyn->vir.xy+=virial->xy;
+ moldyn->vir.xz+=virial->xz;
+ moldyn->vir.yz+=virial->yz;
}
- moldyn->virial=v;
/* global virial (absolute coordinates) */
virial=&(moldyn->gvir);
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;
+ moldyn->tp_sum=0.0;
+
+ return 0;
+}
+
int average_and_fluctuation_calc(t_moldyn *moldyn) {
int denom;
moldyn->p_avg=moldyn->p_sum/denom;
moldyn->gp_sum+=moldyn->gp;
moldyn->gp_avg=moldyn->gp_sum/denom;
+ moldyn->tp_sum+=moldyn->tp;
+ moldyn->tp_avg=moldyn->tp_sum/denom;
return 0;
}
t_3dvec dim;
//t_3dvec *tp;
- double u_up,u_down,dv;
- double scale,p;
+ double h,dv;
+ double y0,y1;
+ double su,sd;
t_atom *store;
/*
*
*/
- scale=0.00001;
- dv=8*scale*scale*scale*moldyn->volume;
-
+ /* store atomic configuration + dimension */
store=malloc(moldyn->count*sizeof(t_atom));
if(store==NULL) {
printf("[moldyn] allocating store mem failed\n");
return -1;
}
-
- /* save unscaled potential energy + atom/dim configuration */
memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
dim=moldyn->dim;
+ /* x1, y1 */
+ sd=0.00001;
+ h=(1.0-sd)*(1.0-sd)*(1.0-sd);
+ su=pow(2.0-h,ONE_THIRD)-1.0;
+ dv=(1.0-h)*moldyn->volume;
+
/* scale up dimension and atom positions */
- scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
- scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- u_up=moldyn->energy;
+ y1=moldyn->energy;
/* restore atomic configuration + dim */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
moldyn->dim=dim;
/* scale down dimension and atom positions */
- scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
- scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- u_down=moldyn->energy;
+ y0=moldyn->energy;
/* calculate pressure */
- p=-(u_up-u_down)/dv;
-printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
+ moldyn->tp=-(y1-y0)/(2.0*dv);
- /* restore atomic configuration + dim */
+ /* restore atomic configuration */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
moldyn->dim=dim;
-
- /* restore energy */
- potential_force_calc(moldyn);
-
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
+ //potential_force_calc(moldyn);
- return p;
+ /* free store buffer */
+ if(store)
+ free(store);
+
+ return moldyn->tp;
}
double get_pressure(t_moldyn *moldyn) {
/* scaling factor */
if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
- scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+ scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc;
scale=pow(scale,ONE_THIRD);
}
else {
scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
}
-moldyn->debug=scale;
/* scale the atoms and dimensions */
scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
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;
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- unsigned int e,m,s,v,p,t;
+ unsigned int e,m,s,v,p,t,a;
t_3dvec momentum;
t_moldyn_schedule *sched;
t_atom *atom;
m=moldyn->mwrite;
s=moldyn->swrite;
v=moldyn->vwrite;
+ a=moldyn->awrite;
p=moldyn->pwrite;
t=moldyn->twrite;
/* 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;
temperature_calc(moldyn);
virial_sum(moldyn);
pressure_calc(moldyn);
+ //thermodynamic_pressure_calc(moldyn);
+
+ /* calculate fluctuations + averages */
average_and_fluctuation_calc(moldyn);
/* p/t scaling */
if(p) {
if(!(moldyn->total_steps%p)) {
dprintf(moldyn->pfd,
- "%f %f %f %f %f\n",moldyn->time,
+ "%f %f %f %f %f %f %f\n",moldyn->time,
moldyn->p/BAR,moldyn->p_avg/BAR,
- moldyn->gp/BAR,moldyn->gp_avg/BAR);
+ moldyn->gp/BAR,moldyn->gp_avg/BAR,
+ moldyn->tp/BAR,moldyn->tp_avg/BAR);
}
}
if(t) {
moldyn->time,moldyn->t,moldyn->t_avg);
}
}
+ if(v) {
+ if(!(moldyn->total_steps%v)) {
+ dprintf(moldyn->vfd,
+ "%f %f\n",moldyn->time,moldyn->volume);
+ }
+ }
if(s) {
if(!(moldyn->total_steps%s)) {
snprintf(dir,128,"%s/s-%07.f.save",
close(fd);
}
}
- if(v) {
- if(!(moldyn->total_steps%v)) {
+ if(a) {
+ if(!(moldyn->total_steps%a)) {
visual_atoms(moldyn);
}
}
/* get current time */
gettimeofday(&t2,NULL);
-printf("\rsched:%d, steps:%d/%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
sched->count,i,moldyn->total_steps,
moldyn->t,moldyn->t_avg,
- moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
moldyn->volume,
(int)(t2.tv_sec-t1.tv_sec));
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[0]+=d2;
+ }
+
+ dc[2]+=d2;
+ }
+
+ dc[0]*=(1.0/(6.0*moldyn->time*a_cnt));
+ dc[1]*=(1.0/(6.0*moldyn->time*b_cnt));
+ dc[2]*=(1.0/(6.0*moldyn->time*moldyn->count));
+
+ 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