#include <time.h>
#include <math.h>
+#include <fpu_control.h>
+
+#ifdef PARALLEL
+#include <omp.h>
+#endif
+
+#ifdef PTHREADS
+#include <pthread.h>
+#endif
+
#include "moldyn.h"
#include "report/report.h"
-/*
- * global variables, pse and atom colors (only needed here)
- */
-
-static char *pse_name[]={
- "*",
- "H",
- "He",
- "Li",
- "Be",
- "B",
- "C",
- "N",
- "O",
- "F",
- "Ne",
- "Na",
- "Mg",
- "Al",
- "Si",
- "P",
- "S",
- "Cl",
- "Ar",
-};
-
-static char *pse_col[]={
- "*",
- "White",
- "He",
- "Li",
- "Be",
- "B",
- "Gray",
- "N",
- "Blue",
- "F",
- "Ne",
- "Na",
- "Mg",
- "Al",
- "Yellow",
- "P",
- "S",
- "Cl",
- "Ar",
-};
+/* potential includes */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+/* pse */
+#define PSE_NAME
+#define PSE_COL
+#include "pse.h"
+#undef PSE_NAME
+#undef PSE_COL
/*
* the moldyn functions
printf("[moldyn] init\n");
+ /* only needed if compiled without -msse2 (float-store prob!) */
+ //fpu_set_rtd();
+
memset(moldyn,0,sizeof(t_moldyn));
moldyn->argc=argc;
int set_cutoff(t_moldyn *moldyn,double cutoff) {
moldyn->cutoff=cutoff;
+ moldyn->cutoff_square=cutoff*cutoff;
printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
return 0;
}
-int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
-
- moldyn->bondlen[0]=b0*b0;
- moldyn->bondlen[1]=b1*b1;
- if(bm<0)
- moldyn->bondlen[2]=b0*b1;
- else
- moldyn->bondlen[2]=bm*bm;
-
- return 0;
-}
-
int set_temperature(t_moldyn *moldyn,double t_ref) {
moldyn->t_ref=t_ref;
return 0;
}
+int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
+
+ moldyn->pt_scale&=(~(P_SCALE_MASK));
+ moldyn->pt_scale|=ptype;
+ moldyn->p_tc=ptc;
+
+ printf("[moldyn] p scaling:\n");
+
+ printf(" p: %s",ptype?"yes":"no ");
+ if(ptype)
+ printf(" | type: %02x | factor: %f",ptype,ptc);
+ printf("\n");
+
+ return 0;
+}
+
+int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
+
+ moldyn->pt_scale&=(~(T_SCALE_MASK));
+ moldyn->pt_scale|=ttype;
+ moldyn->t_tc=ttc;
+
+ printf("[moldyn] t scaling:\n");
+
+ printf(" t: %s",ttype?"yes":"no ");
+ if(ttype)
+ printf(" | type: %02x | factor: %f",ttype,ttc);
+ printf("\n");
+
+ return 0;
+}
+
int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
moldyn->pt_scale=(ptype|ttype);
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;
}
return 0;
}
-int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
-
- moldyn->func1b=func;
-
- return 0;
-}
-
-int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
-
- moldyn->func2b=func;
-
- return 0;
-}
-
-int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
-
- moldyn->func3b_j1=func;
-
- return 0;
-}
-
-int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
-
- moldyn->func3b_j2=func;
-
- return 0;
-}
-
-int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
-
- moldyn->func3b_j3=func;
-
- return 0;
-}
-
-int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
-
- moldyn->func3b_k1=func;
-
- return 0;
-}
-
-int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
-
- moldyn->func3b_k2=func;
-
- return 0;
-}
-
-int set_potential_params(t_moldyn *moldyn,void *params) {
+int set_potential(t_moldyn *moldyn,u8 type) {
- moldyn->pot_params=params;
+ switch(type) {
+ case MOLDYN_POTENTIAL_TM:
+ moldyn->func1b=tersoff_mult_1bp;
+ moldyn->func3b_j1=tersoff_mult_3bp_j1;
+ moldyn->func3b_k1=tersoff_mult_3bp_k1;
+ moldyn->func3b_j2=tersoff_mult_3bp_j2;
+ moldyn->func3b_k2=tersoff_mult_3bp_k2;
+ moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_AM:
+ moldyn->func3b_j1=albe_mult_3bp_j1;
+ moldyn->func3b_k1=albe_mult_3bp_k1;
+ moldyn->func3b_j2=albe_mult_3bp_j2;
+ moldyn->func3b_k2=albe_mult_3bp_k2;
+ moldyn->check_2b_bond=albe_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_HO:
+ moldyn->func2b=harmonic_oscillator;
+ moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_LJ:
+ moldyn->func2b=lennard_jones;
+ moldyn->check_2b_bond=lennard_jones_check_2b_bond;
+ break;
+ default:
+ printf("[moldyn] set potential: unknown type %02x\n",
+ type);
+ return -1;
+ }
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");
t_3dvec orig;
void *ptr;
t_atom *atom;
+ char name[16];
new=a*b*c;
count=moldyn->count;
/* how many atoms do we expect */
+ if(type==NONE) {
+ new*=1;
+ printf("[moldyn] WARNING: create 'none' lattice called");
+ }
if(type==CUBIC) new*=1;
if(type==FCC) new*=4;
if(type==DIAMOND) new*=8;
case CUBIC:
set_nn_dist(moldyn,lc);
ret=cubic_init(a,b,c,lc,atom,&orig);
+ strcpy(name,"cubic");
break;
case FCC:
if(!origin)
v3_scale(&orig,&orig,0.5);
set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
ret=fcc_init(a,b,c,lc,atom,&orig);
+ strcpy(name,"fcc");
break;
case DIAMOND:
if(!origin)
v3_scale(&orig,&orig,0.25);
set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
ret=diamond_init(a,b,c,lc,atom,&orig);
+ strcpy(name,"diamond");
break;
default:
printf("unknown lattice type (%02x)\n",type);
}
moldyn->count+=new;
- printf("[moldyn] created lattice with %d atoms\n",new);
+ printf("[moldyn] created %s lattice with %d atoms\n",name,new);
for(ret=0;ret<new;ret++) {
atom[ret].element=element;
}
moldyn->atom=ptr;
+#ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,(count+1)*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (add atom)");
+ return -1;
+ }
+ moldyn->lc.subcell->list=ptr;
+#endif
+
atom=moldyn->atom;
/* initialize new atom */
scale*=2.0;
else
if(moldyn->pt_scale&T_SCALE_BERENDSEN)
- scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=1.0+(scale-1.0)*moldyn->tau/moldyn->t_tc;
scale=sqrt(scale);
/* velocity scaling */
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*moldyn->tau;
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 link_cell_init(t_moldyn *moldyn,u8 vol) {
t_linkcell *lc;
+#ifndef LOWMEM_LISTS
int i;
+#endif
lc=&(moldyn->lc);
#ifdef STATIC_LISTS
lc->subcell=malloc(lc->cells*sizeof(int*));
+#elif LOWMEM_LISTS
+ lc->subcell=malloc(sizeof(t_lowmem_list));
#else
lc->subcell=malloc(lc->cells*sizeof(t_list));
#endif
}
if(lc->cells<27)
- printf("[moldyn] FATAL: less then 27 subcells!\n");
+ printf("[moldyn] FATAL: less then 27 subcells! (%d)\n",
+ lc->cells);
if(vol) {
#ifdef STATIC_LISTS
printf("[moldyn] initializing 'static' linked cells (%d)\n",
lc->cells);
+#elif LOWMEM_LISTS
+ printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
+ lc->cells);
#else
printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
lc->cells);
i,lc->subcell[0],lc->subcell);
*/
}
+#elif LOWMEM_LISTS
+ lc->subcell->head=malloc(lc->cells*sizeof(int));
+ if(lc->subcell->head==NULL) {
+ perror("[moldyn] head init (malloc)");
+ return -1;
+ }
+ lc->subcell->list=malloc(moldyn->count*sizeof(int));
+ if(lc->subcell->list==NULL) {
+ perror("[moldyn] list init (malloc)");
+ return -1;
+ }
#else
for(i=0;i<lc->cells;i++)
list_init_f(&(lc->subcell[i]));
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny;
+ int nx,nxy;
t_atom *atom;
t_linkcell *lc;
#ifdef STATIC_LISTS
int p;
+#elif LOWMEM_LISTS
+ int p;
#endif
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
- ny=lc->ny;
+ nxy=nx*lc->ny;
for(i=0;i<lc->cells;i++)
#ifdef STATIC_LISTS
- memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+ memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#elif LOWMEM_LISTS
+ lc->subcell->head[i]=-1;
#else
list_destroy_f(&(lc->subcell[i]));
#endif
#ifdef STATIC_LISTS
p=0;
- while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+ while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
p++;
if(p>=MAX_ATOMS_PER_LIST) {
return -1;
}
- lc->subcell[i+j*nx+k*nx*ny][p]=count;
+ lc->subcell[i+j*nx+k*nxy][p]=count;
+#elif LOWMEM_LISTS
+ p=i+j*nx+k*nxy;
+ lc->subcell->list[count]=lc->subcell->head[p];
+ lc->subcell->head[p]=count;
#else
- list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nxy]),
&(atom[count]));
/*
if(j==0&&k==0)
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
#ifdef STATIC_LISTS
int **cell
+#elif LOWMEM_LISTS
+ int *cell
#else
t_list *cell
#endif
printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
i,nx,j,ny,k,nz);
+#ifndef LOWMEM_LISTS
cell[0]=lc->subcell[i+j*nx+k*a];
+#else
+ cell[0]=lc->subcell->head[i+j*nx+k*a];
+#endif
for(ci=-1;ci<=1;ci++) {
bx=0;
x=i+ci;
}
if(!(ci|cj|ck)) continue;
if(bx|by|bz) {
+#ifndef LOWMEM_LISTS
cell[--count2]=lc->subcell[x+y*nx+z*a];
+#else
+ cell[--count2]=lc->subcell->head[x+y*nx+z*a];
+#endif
+
}
else {
+#ifndef LOWMEM_LISTS
cell[count1++]=lc->subcell[x+y*nx+z*a];
+#else
+ cell[count1++]=lc->subcell->head[x+y*nx+z*a];
+#endif
}
}
}
int link_cell_shutdown(t_moldyn *moldyn) {
+#ifndef LOWMEM_LISTS
int i;
+#endif
t_linkcell *lc;
lc=&(moldyn->lc);
+#if LOWMEM_LISTS
+ free(lc->subcell->head);
+ free(lc->subcell->list);
+
+#else
+
for(i=0;i<lc->cells;i++) {
#ifdef STATIC_LISTS
free(lc->subcell[i]);
list_destroy_f(&(lc->subcell[i]));
#endif
}
+#endif
free(lc->subcell);
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;
struct timeval t1,t2;
//double tp;
+#ifdef PTHREADS
+ u8 first,change;
+ pthread_t io_thread;
+ int ret;
+ t_moldyn md_copy;
+ t_atom *atom_copy;
+
+ first=1;
+ change=0;
+#endif
+
sched=&(moldyn->schedule);
atom=moldyn->atom;
m=moldyn->mwrite;
s=moldyn->swrite;
v=moldyn->vwrite;
+ a=moldyn->awrite;
p=moldyn->pwrite;
t=moldyn->twrite;
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
- moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
/* get current time */
gettimeofday(&t1,NULL);
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)
+ if(moldyn->count) {
+ 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;
- moldyn->total_steps=0;
+ // should have right values!
+ //moldyn->time=0.0;
+ //moldyn->total_steps=0;
/* debugging, ignore */
moldyn->debug=0;
+ /* zero & init moldyn copy */
+#ifdef PTHREADS
+ memset(&md_copy,0,sizeof(t_moldyn));
+ atom_copy=malloc(moldyn->count*sizeof(t_atom));
+ if(atom_copy==NULL) {
+ perror("[moldyn] malloc atom copy (init)");
+ return -1;
+ }
+#endif
+
/* tell the world */
printf("[moldyn] integration start, go get a coffee ...\n");
temperature_calc(moldyn);
virial_sum(moldyn);
pressure_calc(moldyn);
+ /*
+ thermodynamic_pressure_calc(moldyn);
+ printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
+ moldyn->tp/BAR);
+ */
+
+ /* 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",
+ snprintf(dir,128,"%s/s-%08.f.save",
moldyn->vlsdir,moldyn->time);
fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
S_IRUSR|S_IWUSR);
close(fd);
}
}
- if(v) {
- if(!(moldyn->total_steps%v)) {
+ if(a) {
+ if(!(moldyn->total_steps%a)) {
+#ifdef PTHREADS
+ /* check whether thread has not terminated yet */
+ if(!first) {
+ ret=pthread_join(io_thread,NULL);
+ }
+ first=0;
+ /* prepare and start thread */
+ if(moldyn->count!=md_copy.count) {
+ free(atom_copy);
+ change=1;
+ }
+ memcpy(&md_copy,moldyn,sizeof(t_moldyn));
+ if(change) {
+ atom_copy=malloc(moldyn->count*sizeof(t_atom));
+ if(atom_copy==NULL) {
+ perror("[moldyn] malloc atom copy (change)");
+ return -1;
+ }
+ }
+ md_copy.atom=atom_copy;
+ memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
+ change=0;
+ ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
+ if(ret) {
+ perror("[moldyn] create visual atoms thread\n");
+ return -1;
+ }
+#else
visual_atoms(moldyn);
+#endif
}
}
/* display progress */
- //if(!(moldyn->total_steps%10)) {
+ if(!(i%10)) {
/* 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->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
moldyn->volume,
(int)(t2.tv_sec-t1.tv_sec));
/* copy over time */
t1=t2;
- //}
+ }
/* increase absolute time */
moldyn->time+=moldyn->tau;
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);
link_cell_update(moldyn);
/* forces depending on chosen potential */
+#ifndef ALBE_FAST
potential_force_calc(moldyn);
+#else
+ albe_potential_force_calc(moldyn);
+#endif
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);
int *neighbour_i[27];
int p,q;
t_atom *atom;
+#elif LOWMEM_LISTS
+ int neighbour_i[27];
+ int p,q;
#else
t_list neighbour_i[27];
t_list neighbour_i2[27];
#endif
u8 bc_ij,bc_ik;
int dnlc;
+#ifdef PTHREADS
+ int ret;
+ pthread_t kthread[27];
+ t_kdata kdata[27];
+#endif
count=moldyn->count;
itom=moldyn->atom;
atom=moldyn->atom;
#endif
+#ifdef PTHREADS
+ memset(kdata,0,27*sizeof(t_kdata));
+#endif
+
/* reset energy */
moldyn->energy=0.0;
memset(&(moldyn->gvir),0,sizeof(t_virial));
/* reset force, site energy and virial of every atom */
+#ifdef PARALLEL
+ i=omp_get_thread_num();
+ #pragma omp parallel for private(virial)
+#endif
for(i=0;i<count;i++) {
/* reset force */
#ifdef STATIC_LISTS
p=0;
- while(neighbour_i[j][p]!=0) {
+ while(neighbour_i[j][p]!=-1) {
jtom=&(atom[neighbour_i[j][p]]);
p++;
+#elif LOWMEM_LISTS
+ p=neighbour_i[j];
- if(jtom==&(itom[i]))
- continue;
+ while(p!=-1) {
- if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
- }
- }
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
#else
this=&(neighbour_i[j]);
list_reset_f(this);
do {
jtom=this->current->data;
+#endif
if(jtom==&(itom[i]))
continue;
jtom,
bc_ij);
}
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
#endif
/* copy the neighbour lists */
#ifdef STATIC_LISTS
/* no copy needed for static lists */
+#elif LOWMEM_LISTS
+ /* no copy needed for lowmem lists */
#else
memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
#endif
#ifdef STATIC_LISTS
p=0;
- while(neighbour_i[j][p]!=0) {
+ while(neighbour_i[j][p]!=-1) {
jtom=&(atom[neighbour_i[j][p]]);
p++;
+#elif LOWMEM_LISTS
+ p=neighbour_i[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
#else
this=&(neighbour_i[j]);
list_reset_f(this);
continue;
/* first loop over atoms k */
+#ifndef PTHREADS
if(moldyn->func3b_k1) {
+#endif
for(k=0;k<27;k++) {
#ifdef STATIC_LISTS
q=0;
- while(neighbour_i[j][q]!=0) {
+ while(neighbour_i[k][q]!=-1) {
ktom=&(atom[neighbour_i[k][q]]);
q++;
+#elif LOWMEM_LISTS
+ q=neighbour_i[k];
+
+ while(q!=-1) {
+
+ ktom=&(itom[q]);
+ q=lc->subcell->list[q];
#else
that=&(neighbour_i2[k]);
list_reset_f(that);
if(ktom==&(itom[i]))
continue;
+#ifdef PTHREADS
+ kdata[k].moldyn=moldyn;
+ kdata[k].ai=&(itom[i]);
+ kdata[k].aj=jtom;
+ kdata[k].ak=ktom;
+ kdata[k].bc=bc_ik;
+ ret=pthread_create(&(kthread[k]),NULL,moldyn->func3b_k1,&(kdata[k]));
+ if(ret) {
+ perror("[moldyn] create k1 thread");
+ return ret;
+ }
+#else
moldyn->func3b_k1(moldyn,
&(itom[i]),
jtom,
ktom,
bc_ik|bc_ij);
+#endif
+
#ifdef STATIC_LISTS
}
+#elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
+#ifndef PTHREADS
}
+#endif
if(moldyn->func3b_j2)
moldyn->func3b_j2(moldyn,
#ifdef STATIC_LISTS
q=0;
- while(neighbour_i[j][q]!=0) {
+ while(neighbour_i[k][q]!=-1) {
ktom=&(atom[neighbour_i[k][q]]);
q++;
+#elif LOWMEM_LISTS
+ q=neighbour_i[k];
+
+ while(q!=-1) {
+
+ ktom=&(itom[q]);
+ q=lc->subcell->list[q];
#else
that=&(neighbour_i2[k]);
list_reset_f(that);
#ifdef STATIC_LISTS
}
+#elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
#ifdef STATIC_LISTS
}
+#elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
#endif
//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
/* some postprocessing */
+#ifdef PARALLEL
+ #pragma omp parallel for
+#endif
for(i=0;i<count;i++) {
/* calculate global virial */
moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
/* check forces regarding the given timestep */
if(v3_norm(&(itom[i].f))>\
- 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+ 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
i);
}
return 0;
}
-int moldyn_load(t_moldyn *moldyn) {
+int moldyn_free_save_file(t_moldyn *moldyn) {
- // later ...
+ free(moldyn->atom);
return 0;
}
-/*
- * post processing functions
- */
-
-int get_line(int fd,char *line,int max) {
-
- int count,ret;
-
- count=0;
-
- while(1) {
- if(count==max) return count;
- ret=read(fd,line+count,1);
- if(ret<=0) return ret;
- if(line[count]=='\n') {
- line[count]='\0';
- return count+1;
- }
- count+=1;
- }
-}
+int moldyn_load(t_moldyn *moldyn) {
-int pair_correlation_init(t_moldyn *moldyn,double dr) {
+ // later ...
-
return 0;
}
-int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+/*
+ * function to find/callback all combinations of 2 body bonds
+ */
+
+int process_2b_bonds(t_moldyn *moldyn,void *data,
+ int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc)) {
- int slots;
- double *stat;
- int i,j;
t_linkcell *lc;
#ifdef STATIC_LISTS
int *neighbour[27];
int p;
+#elif LOWMEM_LISTS
+ int neighbour[27];
+ int p;
#else
t_list neighbour[27];
+ t_list *this;
#endif
+ u8 bc;
t_atom *itom,*jtom;
- t_list *this;
- unsigned char bc;
- t_3dvec dist;
- double d;
- //double norm;
- int o,s;
- unsigned char ibrand;
+ int i,j;
lc=&(moldyn->lc);
-
- slots=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);
- printf(" cutoff: %f\n",moldyn->cutoff);
- printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
-
- if(ptr!=NULL) {
- stat=(double *)ptr;
- }
- else {
- stat=(double *)malloc(3*slots*sizeof(double));
- if(stat==NULL) {
- perror("[moldyn] pair correlation malloc");
- return -1;
- }
- }
-
- memset(stat,0,3*slots*sizeof(double));
-
- link_cell_init(moldyn,VERBOSE);
-
itom=moldyn->atom;
for(i=0;i<moldyn->count;i++) {
(itom[i].r.z+moldyn->dim.z/2)/lc->x,
neighbour);
- /* brand of atom i */
- ibrand=itom[i].brand;
-
for(j=0;j<27;j++) {
bc=(j<lc->dnlc)?0:1;
#ifdef STATIC_LISTS
p=0;
- while(neighbour[j][p]!=0) {
+ while(neighbour[j][p]!=-1) {
jtom=&(moldyn->atom[neighbour[j][p]]);
p++;
+#elif LOWMEM_LISTS
+ p=neighbour[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
#else
this=&(neighbour[j]);
list_reset_f(this);
jtom=this->current->data;
#endif
- /* only count pairs once,
- * skip same atoms */
- if(itom[i].tag>=jtom->tag)
- continue;
- /*
- * pair correlation calc
- */
+ /* process bond */
+ process(moldyn,&(itom[i]),jtom,data,bc);
- /* distance */
- v3_sub(&dist,&(jtom->r),&(itom[i].r));
- if(bc) check_per_bound(moldyn,&dist);
- d=v3_absolute_square(&dist);
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
- /* ignore if greater or equal cutoff */
- if(d>=moldyn->cutoff_square)
- continue;
+ return 0;
- /* fill the slots */
- d=sqrt(d);
- s=(int)(d/dr);
-
- /* should never happen but it does 8) -
- * related to -ffloat-store problem! */
- if(s>=slots) {
- printf("[moldyn] WARNING: pcc (%d/%d)",
- s,slots);
- printf("\n");
- s=slots-1;
- }
+}
- if(ibrand!=jtom->brand) {
- /* mixed */
- stat[s]+=1;
- }
- else {
- /* type a - type a bonds */
- if(ibrand==0)
- stat[s+slots]+=1;
- else
- /* type b - type b bonds */
- stat[s+o]+=1;
- }
+/*
+ * function to find neighboured atoms
+ */
+
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+ int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+ void *data,u8 bc)) {
+
+ t_linkcell *lc;
#ifdef STATIC_LISTS
- }
+ int *neighbour[27];
+ int p;
+#elif LOWMEM_LISTS
+ int neighbour[27];
+ int p;
#else
- } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+ t_list neighbour[27];
+ t_list *this;
#endif
+ u8 bc;
+ t_atom *natom;
+ int j;
+
+ lc=&(moldyn->lc);
+
+ /* neighbour indexing */
+ link_cell_neighbour_index(moldyn,
+ (atom->r.x+moldyn->dim.x/2)/lc->x,
+ (atom->r.y+moldyn->dim.y/2)/lc->x,
+ (atom->r.z+moldyn->dim.z/2)/lc->x,
+ neighbour);
+
+ for(j=0;j<27;j++) {
+
+ bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour[j][p]!=-1) {
+
+ natom=&(moldyn->atom[neighbour[j][p]]);
+ p++;
+#elif LOWMEM_LISTS
+ p=neighbour[j];
+
+ while(p!=-1) {
+
+ natom=&(moldyn->atom[p]);
+ p=lc->subcell->list[p];
+#else
+ this=&(neighbour[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+
+ natom=this->current->data;
+#endif
+
+ /* process bond */
+ process(moldyn,atom,natom,data,bc);
+
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+
+ return 0;
+
+}
+
+/*
+ * post processing functions
+ */
+
+int get_line(int fd,char *line,int max) {
+
+ int count,ret;
+
+ count=0;
+
+ while(1) {
+ if(count==max) return count;
+ ret=read(fd,line+count,1);
+ if(ret<=0) return ret;
+ if(line[count]=='\n') {
+ memset(line+count,0,max-count-1);
+ //line[count]='\0';
+ return count+1;
+ }
+ count+=1;
+ }
+}
+
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
+
+
+ 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 bonding_analyze(t_moldyn *moldyn,double *cnt) {
+
+ return 0;
+}
+
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+ t_atom *jtom,void *data,u8 bc) {
+
+ t_3dvec dist;
+ double d;
+ int s;
+ t_pcc *pcc;
+
+ /* only count pairs once,
+ * skip same atoms */
+ if(itom->tag>=jtom->tag)
+ return 0;
+
+ /*
+ * pair correlation calc
+ */
+
+ /* get pcc data */
+ pcc=data;
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+
+ /* ignore if greater cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
+
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/pcc->dr);
+
+ /* should never happen but it does 8) -
+ * related to -ffloat-store problem! */
+ if(s>=pcc->o1) {
+ printf("[moldyn] WARNING: pcc (%d/%d)",
+ s,pcc->o1);
+ printf("\n");
+ s=pcc->o1-1;
+ }
+
+ if(itom->brand!=jtom->brand) {
+ /* mixed */
+ pcc->stat[s]+=1;
+ }
+ else {
+ /* type a - type a bonds */
+ if(itom->brand==0)
+ pcc->stat[s+pcc->o1]+=1;
+ else
+ /* type b - type b bonds */
+ pcc->stat[s+pcc->o2]+=1;
+ }
+
+ return 0;
+}
+
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+ t_pcc pcc;
+ double norm;
+ int i;
+
+ pcc.dr=dr;
+ pcc.o1=moldyn->cutoff/dr;
+ pcc.o2=2*pcc.o1;
+
+ if(pcc.o1*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);
+ printf(" cutoff: %f\n",moldyn->cutoff);
+ printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
+
+ if(ptr!=NULL) {
+ pcc.stat=(double *)ptr;
+ }
+ else {
+ pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+ if(pcc.stat==NULL) {
+ perror("[moldyn] pair correlation malloc");
+ return -1;
}
}
- /* normalization
- for(i=1;i<slots;i++) {
- // normalization: 4 pi r r dr
+ memset(pcc.stat,0,3*pcc.o1*sizeof(double));
+
+ /* process */
+ process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
+
+ /* normalization */
+ for(i=1;i<pcc.o1;i++) {
+ // 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;
- stat[i]/=norm;
- stat[slots+i]/=norm;
- stat[o+i]/=norm;
+ // ... and actually it's a constant times r^2
+ norm=i*i*dr*dr;
+ pcc.stat[i]/=norm;
+ pcc.stat[pcc.o1+i]/=norm;
+ pcc.stat[pcc.o2+i]/=norm;
}
- */
+ /* */
if(ptr==NULL) {
/* todo: store/print pair correlation function */
- free(stat);
+ free(pcc.stat);
}
- free(moldyn->atom);
+ return 0;
+}
- link_cell_shutdown(moldyn);
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
+
+ t_ba *ba;
+ t_3dvec dist;
+ double d;
+
+ if(itom->tag>=jtom->tag)
+ return 0;
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+
+ /* ignore if greater or equal cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
+
+ /* check for potential bond */
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
+
+ /* now count this bonding ... */
+ ba=data;
+
+ /* increase total bond counter
+ * ... double counting!
+ */
+ ba->tcnt+=2;
+
+ if(itom->brand==0)
+ ba->acnt[jtom->tag]+=1;
+ else
+ ba->bcnt[jtom->tag]+=1;
+
+ if(jtom->brand==0)
+ ba->acnt[itom->tag]+=1;
+ else
+ ba->bcnt[itom->tag]+=1;
return 0;
}
-int analyze_bonds(t_moldyn *moldyn) {
+int bond_analyze(t_moldyn *moldyn,double *quality) {
-
-
+ // by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
+
+ int qcnt;
+ int ccnt,cset;
+ t_ba ba;
+ int i;
+ t_atom *atom;
+
+ ba.acnt=malloc(moldyn->count*sizeof(int));
+ if(ba.acnt==NULL) {
+ perror("[moldyn] bond analyze malloc (a)");
+ return -1;
+ }
+ memset(ba.acnt,0,moldyn->count*sizeof(int));
+
+ ba.bcnt=malloc(moldyn->count*sizeof(int));
+ if(ba.bcnt==NULL) {
+ perror("[moldyn] bond analyze malloc (b)");
+ return -1;
+ }
+ memset(ba.bcnt,0,moldyn->count*sizeof(int));
+
+ ba.tcnt=0;
+ qcnt=0;
+ ccnt=0;
+ cset=0;
+
+ atom=moldyn->atom;
+
+ process_2b_bonds(moldyn,&ba,bond_analyze_process);
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].brand==0) {
+ if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
+ qcnt+=4;
+ }
+ else {
+ if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
+ qcnt+=4;
+ ccnt+=1;
+ }
+ cset+=1;
+ }
+ }
+
+ printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset);
+ printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt);
+
+ if(quality) {
+ quality[0]=1.0*ccnt/cset;
+ quality[1]=1.0*qcnt/ba.tcnt;
+ }
+ else {
+ printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt);
+ printf("[moldyn] bond analyze: tot_q=%f\n",1.0*qcnt/ba.tcnt);
+ }
return 0;
}
return 0;
}
+int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
+
+ t_vb *vb;
+
+ vb=data;
+
+ if(itom->tag>=jtom->tag)
+ return 0;
+
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
+
+ if((itom->attr&ATOM_ATTR_VB)|(jtom->attr&ATOM_ATTR_VB))
+ dprintf(vb->fd,"# [B] %f %f %f %f %f %f\n",
+ itom->r.x,itom->r.y,itom->r.z,
+ jtom->r.x,jtom->r.y,jtom->r.z);
+
+ return 0;
+}
+
+#ifdef PTHREADS
+void *visual_atoms(void *ptr) {
+#else
int visual_atoms(t_moldyn *moldyn) {
+#endif
- int i,j,fd;
+ int i;
char file[128+64];
t_3dvec dim;
double help;
t_visual *v;
t_atom *atom;
- t_atom *btom;
- t_linkcell *lc;
-#ifdef STATIC_LISTS
- int *neighbour[27];
- int p;
-#else
- t_list neighbour[27];
+ t_vb vb;
+#ifdef PTHREADS
+ t_moldyn *moldyn;
+
+ moldyn=ptr;
#endif
- u8 bc;
- t_3dvec dist;
- double d2;
- u8 brand;
v=&(moldyn->vis);
dim.x=v->dim.x;
dim.y=v->dim.y;
dim.z=v->dim.z;
atom=moldyn->atom;
- lc=&(moldyn->lc);
help=(dim.x+dim.y);
- sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
- fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
- if(fd<0) {
+ sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
+ vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+ if(vb.fd<0) {
perror("open visual save file fd");
+#ifndef PTHREADS
return -1;
+#endif
}
/* write the actual data file */
// povray header
- dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+ dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
// atomic configuration
- for(i=0;i<moldyn->count;i++) {
+ for(i=0;i<moldyn->count;i++)
// atom type, positions, color and kinetic energy
- dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
- atom[i].r.x,
- atom[i].r.y,
- atom[i].r.z,
- pse_col[atom[i].element],
- atom[i].ekin);
-
- /*
- * bond detection should usually be done by potential
- * functions. brrrrr! EVIL!
- *
- * todo: potentials need to export a 'find_bonds' function!
- */
-
- // bonds between atoms
- if(!(atom[i].attr&ATOM_ATTR_VB))
- continue;
- link_cell_neighbour_index(moldyn,
- (atom[i].r.x+moldyn->dim.x/2)/lc->x,
- (atom[i].r.y+moldyn->dim.y/2)/lc->y,
- (atom[i].r.z+moldyn->dim.z/2)/lc->z,
- neighbour);
- for(j=0;j<27;j++) {
- bc=j<lc->dnlc?0:1;
-#ifdef STATIC_LISTS
- p=0;
- while(neighbour[j][p]!=0) {
- btom=&(atom[neighbour[j][p]]);
- p++;
-#else
- list_reset_f(&neighbour[j]);
- if(neighbour[j].start==NULL)
- continue;
- do {
- btom=neighbour[j].current->data;
-#endif
- if(btom==&atom[i]) // skip identical atoms
- continue;
- //if(btom<&atom[i]) // skip half of them
- // continue;
- v3_sub(&dist,&(atom[i].r),&(btom->r));
- if(bc) check_per_bound(moldyn,&dist);
- d2=v3_absolute_square(&dist);
- brand=atom[i].brand;
- if(brand==btom->brand) {
- if(d2>moldyn->bondlen[brand])
- continue;
- }
- else {
- if(d2>moldyn->bondlen[2])
- continue;
- }
- dprintf(fd,"# [B] %f %f %f %f %f %f\n",
- atom[i].r.x,atom[i].r.y,atom[i].r.z,
- btom->r.x,btom->r.y,btom->r.z);
-#ifdef STATIC_LISTS
- }
-#else
- } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
-#endif
- }
- }
-
+ dprintf(vb.fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
+ atom[i].r.x,
+ atom[i].r.y,
+ atom[i].r.z,
+ pse_col[atom[i].element],
+ atom[i].ekin);
+
+ // bonds between atoms
+ process_2b_bonds(moldyn,&vb,visual_bonds_process);
+
// boundaries
if(dim.x) {
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,-dim.z/2,
dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,-dim.z/2,
-dim.x/2,dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,dim.y/2,-dim.z/2,
dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,dim.y/2,-dim.z/2,
dim.x/2,dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,dim.z/2,
dim.x/2,-dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,dim.z/2,
-dim.x/2,dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,dim.y/2,dim.z/2,
dim.x/2,-dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,dim.y/2,dim.z/2,
dim.x/2,dim.y/2,dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,-dim.y/2,dim.z/2,
-dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
-dim.x/2,dim.y/2,dim.z/2,
-dim.x/2,dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,-dim.y/2,dim.z/2,
dim.x/2,-dim.y/2,-dim.z/2);
- dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
dim.x/2,dim.y/2,dim.z/2,
dim.x/2,dim.y/2,-dim.z/2);
}
- close(fd);
+ close(vb.fd);
+
+#ifdef PTHREADS
+ pthread_exit(NULL);
+
+}
+#else
+
+ return 0;
+}
+#endif
+
+/*
+ * fpu cntrol functions
+ */
+
+// set rounding to double (eliminates -ffloat-store!)
+int fpu_set_rtd(void) {
+
+ fpu_control_t ctrl;
+
+ _FPU_GETCW(ctrl);
+
+ ctrl&=~_FPU_EXTENDED;
+ ctrl|=_FPU_DOUBLE;
+
+ _FPU_SETCW(ctrl);
return 0;
}
projects / physik / posic.git / blobdiff