#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
#include <math.h>
#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",
+};
+
+/*
+ * the moldyn functions
+ */
+
int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
printf("[moldyn] init\n");
memset(moldyn,0,sizeof(t_moldyn));
+ moldyn->argc=argc;
+ moldyn->args=argv;
+
rand_init(&(moldyn->random),NULL,1);
moldyn->random.status|=RAND_STAT_VERBOSE;
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_mean_skip(t_moldyn *moldyn,int skip) {
+int set_avg_skip(t_moldyn *moldyn,int skip) {
printf("[moldyn] skip %d steps before starting average calc\n",skip);
- moldyn->mean_skip=skip;
+ moldyn->avg_skip=skip;
return 0;
}
break;
case VISUAL_STEP:
moldyn->vwrite=timer;
- ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ ret=visual_init(moldyn,moldyn->vlsdir);
if(ret<0) {
printf("[moldyn] visual init failure\n");
return ret;
moldyn->vlsdir);
system(sc);
}
- if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
return 0;
}
atom[ret].brand=brand;
atom[ret].tag=count+ret;
check_per_bound(moldyn,&(atom[ret].r));
+ atom[ret].r_0=atom[ret].r;
}
/* update total system mass */
return ret;
}
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+ t_3dvec *r,t_3dvec *v) {
+
+ t_atom *atom;
+ void *ptr;
+ int count;
+
+ atom=moldyn->atom;
+ count=(moldyn->count)++;
+
+ ptr=realloc(atom,(count+1)*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (add atom)");
+ return -1;
+ }
+ moldyn->atom=ptr;
+
+ atom=moldyn->atom;
+ atom[count].r=*r;
+ atom[count].v=*v;
+ atom[count].element=element;
+ atom[count].mass=mass;
+ atom[count].brand=brand;
+ atom[count].tag=count;
+ atom[count].attr=attr;
+ check_per_bound(moldyn,&(atom[count].r));
+ atom[count].r_0=atom[count].r;
+
+ /* update total system mass */
+ total_mass_calc(moldyn);
+
+ return 0;
+}
+
+int del_atom(t_moldyn *moldyn,int tag) {
+
+ t_atom *new,*old;
+ int cnt;
+
+ old=moldyn->atom;
+
+ new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
+ if(!new) {
+ perror("[moldyn]malloc (del atom)");
+ return -1;
+ }
+
+ for(cnt=0;cnt<tag;cnt++)
+ new[cnt]=old[cnt];
+
+ for(cnt=tag+1;cnt<moldyn->count;cnt++) {
+ new[cnt-1]=old[cnt];
+ new[cnt-1].tag=cnt-1;
+ }
+
+ moldyn->count-=1;
+ moldyn->atom=new;
+
+ free(old);
+
+ return 0;
+}
+
/* cubic init */
int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
return count;
}
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
- t_3dvec *r,t_3dvec *v) {
-
- t_atom *atom;
- void *ptr;
- int count;
-
- atom=moldyn->atom;
- count=(moldyn->count)++;
-
- ptr=realloc(atom,(count+1)*sizeof(t_atom));
- if(!ptr) {
- perror("[moldyn] realloc (add atom)");
- return -1;
- }
- moldyn->atom=ptr;
-
- atom=moldyn->atom;
- atom[count].r=*r;
- atom[count].v=*v;
- atom[count].element=element;
- atom[count].mass=mass;
- atom[count].brand=brand;
- atom[count].tag=count;
- atom[count].attr=attr;
-
- /* update total system mass */
- total_mass_calc(moldyn);
-
- return 0;
-}
-
int destroy_atoms(t_moldyn *moldyn) {
if(moldyn->atom) free(moldyn->atom);
moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
- if(moldyn->total_steps<moldyn->mean_skip)
- return 0;
-
- moldyn->t_sum+=moldyn->t;
- moldyn->mean_t=moldyn->t_sum/(moldyn->total_steps+1-moldyn->mean_skip);
-
return moldyn->t;
}
return p;
}
-double pressure_calc(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
int i;
double v;
t_virial *virial;
+ /* virial (sum over atom virials) */
+ v=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ v+=(virial->xx+virial->yy+virial->zz);
+ }
+ moldyn->virial=v;
+
+ /* global virial (absolute coordinates) */
+ virial=&(moldyn->gvir);
+ moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+ return moldyn->virial;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
/*
* PV = NkT + <W>
- * W = 1/3 sum_i f_i r_i
+ * with W = 1/3 sum_i f_i r_i (- skipped!)
* virial = sum_i f_i r_i
*
* => P = (2 Ekin + virial) / (3V)
*/
- v=0.0;
- for(i=0;i<moldyn->count;i++) {
- virial=&(moldyn->atom[i].virial);
- v+=(virial->xx+virial->yy+virial->zz);
- }
+ /* assume up to date virial & up to date kinetic energy */
- /* virial sum and mean virial */
- moldyn->virial_sum+=v;
- if(moldyn->total_steps>=moldyn->mean_skip)
- moldyn->mean_v=moldyn->virial_sum/
- (moldyn->total_steps+1-moldyn->mean_skip);
-
- /* assume up to date kinetic energy */
- moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
+ /* pressure (atom virials) */
+ moldyn->p=2.0*moldyn->ekin+moldyn->virial;
moldyn->p/=(3.0*moldyn->volume);
- if(moldyn->total_steps>=moldyn->mean_skip) {
- moldyn->p_sum+=moldyn->p;
- moldyn->mean_p=moldyn->p_sum/
- (moldyn->total_steps+1-moldyn->mean_skip);
- }
- /* pressure from 'absolute coordinates' virial */
- virial=&(moldyn->virial);
- v=virial->xx+virial->yy+virial->zz;
- moldyn->gp=2.0*moldyn->ekin+v;
+ /* pressure (absolute coordinates) */
+ moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
moldyn->gp/=(3.0*moldyn->volume);
- if(moldyn->total_steps>=moldyn->mean_skip) {
- moldyn->gp_sum+=moldyn->gp;
- moldyn->mean_gp=moldyn->gp_sum/
- (moldyn->total_steps+1-moldyn->mean_skip);
- }
return moldyn->p;
}
-int energy_fluctuation_calc(t_moldyn *moldyn) {
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
- if(moldyn->total_steps<moldyn->mean_skip)
+ if(moldyn->total_steps<moldyn->avg_skip)
return 0;
- /* assume up to date energies */
+ int denom=moldyn->total_steps+1-moldyn->avg_skip;
+
+ /* assume up to date energies, temperature, pressure etc */
/* kinetic energy */
moldyn->k_sum+=moldyn->ekin;
moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
- moldyn->k_mean=moldyn->k_sum/(moldyn->total_steps+1-moldyn->mean_skip);
- moldyn->k2_mean=moldyn->k2_sum/
- (moldyn->total_steps+1-moldyn->mean_skip);
- moldyn->dk2_mean=moldyn->k2_mean-(moldyn->k_mean*moldyn->k_mean);
+ moldyn->k_avg=moldyn->k_sum/denom;
+ moldyn->k2_avg=moldyn->k2_sum/denom;
+ moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
/* potential energy */
moldyn->v_sum+=moldyn->energy;
moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
- moldyn->v_mean=moldyn->v_sum/(moldyn->total_steps+1-moldyn->mean_skip);
- moldyn->v2_mean=moldyn->v2_sum/
- (moldyn->total_steps+1-moldyn->mean_skip);
- moldyn->dv2_mean=moldyn->v2_mean-(moldyn->v_mean*moldyn->v_mean);
+ moldyn->v_avg=moldyn->v_sum/denom;
+ moldyn->v2_avg=moldyn->v2_sum/denom;
+ moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
+
+ /* temperature */
+ moldyn->t_sum+=moldyn->t;
+ moldyn->t_avg=moldyn->t_sum/denom;
+
+ /* virial */
+ moldyn->virial_sum+=moldyn->virial;
+ moldyn->virial_avg=moldyn->virial_sum/denom;
+ moldyn->gv_sum+=moldyn->gv;
+ moldyn->gv_avg=moldyn->gv_sum/denom;
+
+ /* pressure */
+ moldyn->p_sum+=moldyn->p;
+ moldyn->p_avg=moldyn->p_sum/denom;
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->gp_avg=moldyn->gp_sum/denom;
return 0;
}
double temp2,ighc;
/* averages needed for heat capacity calc */
- if(moldyn->total_steps<moldyn->mean_skip)
+ if(moldyn->total_steps<moldyn->avg_skip)
return 0;
/* (temperature average)^2 */
- temp2=moldyn->mean_t*moldyn->mean_t;
+ temp2=moldyn->t_avg*moldyn->t_avg;
printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
- moldyn->mean_t);
+ moldyn->t_avg);
/* ideal gas contribution */
ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
ighc/moldyn->mass*KILOGRAM/JOULE);
/* specific heat for nvt ensemble */
- moldyn->c_v_nvt=moldyn->dv2_mean/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
moldyn->c_v_nvt/=moldyn->mass;
/* specific heat for nve ensemble */
- moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_mean/(ighc*K_BOLTZMANN*temp2)));
+ moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
moldyn->c_v_nve/=moldyn->mass;
printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
-printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_mean,1.5*moldyn->count*K_B2*moldyn->mean_t*moldyn->mean_t*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
+printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
return 0;
}
atom=moldyn->atom;
moldyn->ekin=0.0;
- for(i=0;i<moldyn->count;i++)
- moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ for(i=0;i<moldyn->count;i++) {
+ atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ moldyn->ekin+=atom[i].ekin;
+ }
return moldyn->ekin;
}
char dir[128];
double ds;
double energy_scale;
+ struct timeval t1,t2;
//double tp;
sched=&(moldyn->schedule);
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
- /* energy scaling factor */
- energy_scale=moldyn->count*EV;
+ /* get current time */
+ gettimeofday(&t1,NULL);
/* calculate initial forces */
potential_force_calc(moldyn);
#ifdef DEBUG
-return 0;
+//return 0;
#endif
/* some stupid checks before we actually start calculating bullshit */
printf("[moldyn] integration start, go get a coffee ...\n");
/* executing the schedule */
- for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+ sched->count=0;
+ while(sched->count<sched->total_sched) {
/* setting amount of runs and finite time step size */
moldyn->tau=sched->tau[sched->count];
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->time_steps=sched->runs[sched->count];
+ /* energy scaling factor (might change!) */
+ energy_scale=moldyn->count*EV;
+
/* integration according to schedule */
for(i=0;i<moldyn->time_steps;i++) {
/* calculate kinetic energy, temperature and pressure */
e_kin_calc(moldyn);
temperature_calc(moldyn);
+ virial_sum(moldyn);
pressure_calc(moldyn);
- energy_fluctuation_calc(moldyn);
- //tp=thermodynamic_pressure_calc(moldyn);
-//printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
+ average_and_fluctuation_calc(moldyn);
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
/* check for log & visualization */
if(e) {
- if(!(i%e))
+ if(!(moldyn->total_steps%e))
dprintf(moldyn->efd,
"%f %f %f %f\n",
moldyn->time,moldyn->ekin/energy_scale,
get_total_energy(moldyn)/energy_scale);
}
if(m) {
- if(!(i%m)) {
+ if(!(moldyn->total_steps%m)) {
momentum=get_total_p(moldyn);
dprintf(moldyn->mfd,
"%f %f %f %f %f\n",moldyn->time,
}
}
if(p) {
- if(!(i%p)) {
+ if(!(moldyn->total_steps%p)) {
dprintf(moldyn->pfd,
"%f %f %f %f %f\n",moldyn->time,
- moldyn->p/BAR,moldyn->mean_p/BAR,
- moldyn->gp/BAR,moldyn->mean_gp/BAR);
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->gp/BAR,moldyn->gp_avg/BAR);
}
}
if(t) {
- if(!(i%t)) {
+ if(!(moldyn->total_steps%t)) {
dprintf(moldyn->tfd,
"%f %f %f\n",
- moldyn->time,moldyn->t,moldyn->mean_t);
+ moldyn->time,moldyn->t,moldyn->t_avg);
}
}
if(s) {
- if(!(i%s)) {
+ if(!(moldyn->total_steps%s)) {
snprintf(dir,128,"%s/s-%07.f.save",
moldyn->vlsdir,moldyn->time);
- fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
+ S_IRUSR|S_IWUSR);
if(fd<0) perror("[moldyn] save fd open");
else {
write(fd,moldyn,sizeof(t_moldyn));
}
}
if(v) {
- if(!(i%v)) {
- visual_atoms(&(moldyn->vis),moldyn->time,
- moldyn->atom,moldyn->count);
+ if(!(moldyn->total_steps%v)) {
+ visual_atoms(moldyn);
}
}
/* display progress */
- if(!(i%10)) {
- printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
- sched->count,i,
- moldyn->mean_t,
- moldyn->mean_p/BAR,
- moldyn->mean_gp/BAR,
- moldyn->volume);
- fflush(stdout);
-printf("\n");
-get_heat_capacity(moldyn);
- }
+ //if(!(moldyn->total_steps%10)) {
+ /* get current time */
+ gettimeofday(&t2,NULL);
+
+ printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+ sched->count,i,
+ moldyn->t,moldyn->t_avg,
+ moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+ moldyn->volume,
+ (int)(t2.tv_sec-t1.tv_sec));
+ fflush(stdout);
+
+ /* copy over time */
+ t1=t2;
+ //}
/* increase absolute time */
moldyn->time+=moldyn->tau;
}
/* check for hooks */
- if(sched->count+1<sched->total_sched)
- if(sched->hook)
- sched->hook(moldyn,sched->hook_params);
+ if(sched->hook) {
+ printf("\n ## schedule hook %d/%d start ##\n",
+ sched->count+1,sched->total_sched-1);
+ sched->hook(moldyn,sched->hook_params);
+ printf(" ## schedule hook end ##\n");
+ }
- /* get a new info line */
- printf("\n");
+ /* increase the schedule counter */
+ sched->count+=1;
}
moldyn->energy=0.0;
/* reset global virial */
- memset(&(moldyn->virial),0,sizeof(t_virial));
+ memset(&(moldyn->gvir),0,sizeof(t_virial));
/* reset force, site energy and virial of every atom */
for(i=0;i<count;i++) {
}
#ifdef DEBUG
- printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
+ //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);
+ }
#endif
/* calculate global virial */
for(i=0;i<count;i++) {
- moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
- moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
- moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
- moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
- moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
- moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+ 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;
}
return 0;
return 0;
}
+/*
+ * restore function
+ */
+
+int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
+
+ int fd;
+ int cnt,size;
+
+ fd=open(file,O_RDONLY);
+ if(fd<0) {
+ perror("[moldyn] load save file open");
+ return fd;
+ }
+
+ size=sizeof(t_moldyn);
+ cnt=read(fd,moldyn,size);
+ if(cnt!=size) {
+ perror("[moldyn] load save file read (moldyn)");
+ return cnt;
+ }
+
+ size=moldyn->count*sizeof(t_atom);
+
+ moldyn->atom=(t_atom *)malloc(size);
+ if(moldyn->atom==NULL) {
+ perror("[moldyn] load save file malloc (atoms)");
+ return -1;
+ }
+
+ cnt=read(fd,moldyn->atom,size);
+ if(cnt!=size) {
+ perror("[moldyn] load save file read (atoms)");
+ return cnt;
+ }
+
+ // hooks
+
+ return 0;
+}
+
+int moldyn_load(t_moldyn *moldyn) {
+
+ // later ...
+
+ return 0;
+}
+
/*
* post processing functions
*/
}
}
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
+
+
+ return 0;
+}
+
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+ int slots;
+ double *stat;
+ int i,j;
+ t_linkcell *lc;
+ t_list neighbour[27];
+ t_atom *itom,*jtom;
+ t_list *this;
+ unsigned char bc;
+ t_3dvec dist;
+ double d,norm;
+ int o,s;
+ unsigned char ibrand;
+
+ lc=&(moldyn->lc);
+
+ slots=(int)(moldyn->cutoff/dr);
+ o=2*slots;
+
+ 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++) {
+ /* neighbour indexing */
+ link_cell_neighbour_index(moldyn,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->x,
+ (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++) {
+ /* prepare the neighbour cell list */
+ this=&(neighbour[j]);
+ list_reset_f(this);
+
+ /* check for atoms */
+ if(this->start==NULL)
+ continue;
+
+ /* boundary check */
+ bc=(j<lc->dnlc)?0:1;
+
+ do {
+ jtom=this->current->data;
+
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ /* only count pairs once */
+ if(itom[i].tag>jtom->tag)
+ continue;
+
+ /*
+ * pair correlation calc
+ */
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom[i].r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+
+ /* ignore if greater cutoff */
+ if(d>moldyn->cutoff_square)
+ continue;
+
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/dr);
+
+ 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;
+ }
+
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+ }
+ }
+
+ /* normalization */
+ for(i=1;i<slots;i++) {
+ /*
+ * normalization: 4 pi r r 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;
+ }
+
+ if(ptr==NULL) {
+ /* todo: store/print pair correlation function */
+ free(stat);
+ }
+
+ free(moldyn->atom);
+
+ link_cell_shutdown(moldyn);
+
+ return 0;
+}
+
+int analyze_bonds(t_moldyn *moldyn) {
+
+
+
+
+ return 0;
+}
+
+/*
+ * visualization code
+ */
+
+int visual_init(t_moldyn *moldyn,char *filebase) {
+
+ strncpy(moldyn->vis.fb,filebase,128);
+
+ return 0;
+}
+
+int visual_atoms(t_moldyn *moldyn) {
+
+ int i,j,fd;
+ char file[128+64];
+ t_3dvec dim;
+ double help;
+ t_visual *v;
+ t_atom *atom;
+ t_atom *btom;
+ t_linkcell *lc;
+ t_list neighbour[27];
+ 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) {
+ perror("open visual save file fd");
+ return -1;
+ }
+
+ /* write the actual data file */
+
+ // povray header
+ dprintf(fd,"# [P] %d %07.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++) {
+ // 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++) {
+ list_reset_f(&neighbour[j]);
+ if(neighbour[j].start==NULL)
+ continue;
+ bc=j<lc->dnlc?0:1;
+ do {
+ btom=neighbour[j].current->data;
+ 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);
+ } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
+ }
+ }
+
+ // boundaries
+ if(dim.x) {
+ dprintf(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",
+ -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",
+ 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",
+ -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",
+ -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",
+ -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",
+ 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",
+ -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",
+ -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",
+ -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",
+ 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",
+ dim.x/2,dim.y/2,dim.z/2,
+ dim.x/2,dim.y/2,-dim.z/2);
+ }
+
+ close(fd);
+
+ return 0;
+}
+