#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;
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);
int average_and_fluctuation_calc(t_moldyn *moldyn) {
+ int denom;
+
if(moldyn->total_steps<moldyn->avg_skip)
return 0;
- int denom=moldyn->total_steps+1-moldyn->avg_skip;
+ denom=moldyn->total_steps+1-moldyn->avg_skip;
/* assume up to date energies, temperature, pressure etc */
double thermodynamic_pressure_calc(t_moldyn *moldyn) {
- t_3dvec dim,*tp;
+ t_3dvec dim;
+ //t_3dvec *tp;
double u_up,u_down,dv;
double scale,p;
t_atom *store;
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;
}
lc->y=moldyn->dim.y/lc->ny;
lc->nz=moldyn->dim.z/moldyn->cutoff;
lc->z=moldyn->dim.z/lc->nz;
-
lc->cells=lc->nx*lc->ny*lc->nz;
+
+#ifdef STATIC_LISTS
+ lc->subcell=malloc(lc->cells*sizeof(int*));
+#else
lc->subcell=malloc(lc->cells*sizeof(t_list));
+#endif
+
+ if(lc->subcell==NULL) {
+ perror("[moldyn] cell init (malloc)");
+ return -1;
+ }
if(lc->cells<27)
printf("[moldyn] FATAL: less then 27 subcells!\n");
if(vol) {
- printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+#ifdef STATIC_LISTS
+ printf("[moldyn] initializing 'static' linked cells (%d)\n",
+ lc->cells);
+#else
+ printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
+ lc->cells);
+#endif
printf(" x: %d x %f A\n",lc->nx,lc->x);
printf(" y: %d x %f A\n",lc->ny,lc->y);
printf(" z: %d x %f A\n",lc->nz,lc->z);
}
+#ifdef STATIC_LISTS
+ /* list init */
+ for(i=0;i<lc->cells;i++) {
+ lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
+ if(lc->subcell[i]==NULL) {
+ perror("[moldyn] list init (malloc)");
+ return -1;
+ }
+ /*
+ if(i==0)
+ printf(" ---> %d malloc %p (%p)\n",
+ i,lc->subcell[0],lc->subcell);
+ */
+ }
+#else
for(i=0;i<lc->cells;i++)
list_init_f(&(lc->subcell[i]));
+#endif
+
+ /* update the list */
+ link_cell_update(moldyn);
- link_cell_update(moldyn);
-
return 0;
}
int nx,ny;
t_atom *atom;
t_linkcell *lc;
- double x,y,z;
+#ifdef STATIC_LISTS
+ int p;
+#endif
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- x=moldyn->dim.x/2;
- y=moldyn->dim.y/2;
- z=moldyn->dim.z/2;
-
for(i=0;i<lc->cells;i++)
+#ifdef STATIC_LISTS
+ memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#else
list_destroy_f(&(lc->subcell[i]));
-
+#endif
+
for(count=0;count<moldyn->count;count++) {
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)
+ p++;
+
+ if(p>=MAX_ATOMS_PER_LIST) {
+ printf("[moldyn] FATAL: amount of atoms too high!\n");
+ return -1;
+ }
+
+ lc->subcell[i+j*nx+k*nx*ny][p]=count;
+#else
list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
&(atom[count]));
+ /*
+ if(j==0&&k==0)
+ printf(" ---> %d %d malloc %p (%p)\n",
+ i,count,lc->subcell[i].current,lc->subcell);
+ */
+#endif
}
return 0;
}
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
+#ifdef STATIC_LISTS
+ int **cell
+#else
+ t_list *cell
+#endif
+ ) {
t_linkcell *lc;
int a;
lc=&(moldyn->lc);
- for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_destroy_f(&(moldyn->lc.subcell[i]));
+ for(i=0;i<lc->cells;i++) {
+#ifdef STATIC_LISTS
+ free(lc->subcell[i]);
+#else
+ //printf(" ---> %d free %p\n",i,lc->subcell[i].start);
+ list_destroy_f(&(lc->subcell[i]));
+#endif
+ }
free(lc->subcell);
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 */
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++) {
/* 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->p_avg/BAR,
}
}
if(t) {
- if(!(i%t)) {
+ if(!(moldyn->total_steps%t)) {
dprintf(moldyn->tfd,
"%f %f %f\n",
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:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
- sched->count,i,
- moldyn->t,moldyn->t_avg,
- moldyn->p_avg/BAR,moldyn->p/BAR,
- moldyn->volume);
- fflush(stdout);
- }
+ //if(!(moldyn->total_steps%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)",
+ sched->count,i,moldyn->total_steps,
+ 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->hook) {
- printf("\n ## schedule hook %d/%d start ##\n",
- sched->count+1,sched->total_sched-1);
+ printf("\n ## schedule hook %d start ##\n",
+ sched->count);
sched->hook(moldyn,sched->hook_params);
printf(" ## schedule hook end ##\n");
}
t_atom *itom,*jtom,*ktom;
t_virial *virial;
t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour_i[27];
+ int p,q;
+ t_atom *atom;
+#else
t_list neighbour_i[27];
t_list neighbour_i2[27];
t_list *this,*that;
+#endif
u8 bc_ij,bc_ik;
int dnlc;
count=moldyn->count;
itom=moldyn->atom;
lc=&(moldyn->lc);
+#ifdef STATIC_LISTS
+ atom=moldyn->atom;
+#endif
/* reset energy */
moldyn->energy=0.0;
if(moldyn->func2b) {
for(j=0;j<27;j++) {
+ bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour_i[j][p]!=0) {
+
+ jtom=&(atom[neighbour_i[j][p]]);
+ p++;
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+ }
+#else
this=&(neighbour_i[j]);
list_reset_f(this);
if(this->start==NULL)
continue;
- bc_ij=(j<dnlc)?0:1;
-
do {
jtom=this->current->data;
bc_ij);
}
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
}
}
continue;
/* copy the neighbour lists */
+#ifdef STATIC_LISTS
+ /* no copy needed for static lists */
+#else
memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
/* second loop over atoms j */
for(j=0;j<27;j++) {
+ bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour_i[j][p]!=0) {
+
+ jtom=&(atom[neighbour_i[j][p]]);
+ p++;
+#else
this=&(neighbour_i[j]);
list_reset_f(this);
if(this->start==NULL)
continue;
- bc_ij=(j<dnlc)?0:1;
-
do {
+
jtom=this->current->data;
+#endif
if(jtom==&(itom[i]))
continue;
for(k=0;k<27;k++) {
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
+
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
that=&(neighbour_i2[k]);
list_reset_f(that);
if(that->start==NULL)
continue;
- bc_ik=(k<dnlc)?0:1;
-
do {
-
ktom=that->current->data;
+#endif
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
jtom,
ktom,
bc_ik|bc_ij);
-
+#ifdef STATIC_LISTS
+ }
+#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
+#endif
}
for(k=0;k<27;k++) {
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
+
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
that=&(neighbour_i2[k]);
list_reset_f(that);
if(that->start==NULL)
continue;
- bc_ik=(k<dnlc)?0:1;
-
do {
-
ktom=that->current->data;
+#endif
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
ktom,
bc_ik|bc_ij);
+#ifdef STATIC_LISTS
+ }
+#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
+#endif
}
&(itom[i]),
jtom,bc_ij);
}
-
+#ifdef STATIC_LISTS
+ }
+#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
}
}
#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 */
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);
+
+ while(size) {
+ cnt=read(fd,moldyn,size);
+ if(cnt<0) {
+ perror("[moldyn] load save file read (moldyn)");
+ return cnt;
+ }
+ size-=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;
+ }
+
+ while(size) {
+ cnt=read(fd,moldyn->atom,size);
+ if(cnt<0) {
+ perror("[moldyn] load save file read (atoms)");
+ return cnt;
+ }
+ size-=cnt;
+ }
+
+ // hooks etc ...
+
+ 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;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+#endif
+ t_atom *itom,*jtom;
+ t_list *this;
+ unsigned char bc;
+ t_3dvec dist;
+ double d;
+ //double norm;
+ int o,s;
+ unsigned char ibrand;
+
+ lc=&(moldyn->lc);
+
+ slots=moldyn->cutoff/dr;
+ o=2*slots;
+
+ 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++) {
+ /* 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++) {
+
+ bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour[j][p]!=0) {
+
+ jtom=&(moldyn->atom[neighbour[j][p]]);
+ p++;
+#else
+ this=&(neighbour[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+
+ jtom=this->current->data;
+#endif
+ /* only count pairs once,
+ * skip same atoms */
+ 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 or equal cutoff */
+ if(d>=moldyn->cutoff_square)
+ continue;
+
+ /* 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) 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;
+ }
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
+
+ /* 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;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+#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) {
+ 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++) {
+ 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
+ }
+ }
+
+ // 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;
+}
+
projects / physik / posic.git / blobdiff