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");
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);
/* pressure */
moldyn->p_sum=0.0;
moldyn->gp_sum=0.0;
+ moldyn->tp_sum=0.0;
return 0;
}
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);
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;
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));
projects / physik / posic.git / blobdiff