#include "moldyn.h"
#include "report/report.h"
+/* 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
+
+
/*
* global variables, pse and atom colors (only needed here)
*/
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_potential(t_moldyn *moldyn,u8 type) {
-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) {
-
- 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;
+ // missing: check 2b bond func
+ 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;
+ 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");
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));
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);
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
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 moldyn_free_save_file(t_moldyn *moldyn) {
+
+ free(moldyn->atom);
+
+ return 0;
+}
+
int moldyn_load(t_moldyn *moldyn) {
// later ...
return 0;
}
+/*
+ * 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)) {
+
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+#endif
+ u8 bc;
+ t_atom *itom,*jtom;
+ int i,j;
+ t_list *this;
+
+ lc=&(moldyn->lc);
+
+ 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);
+
+ 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
+
+ /* process bond */
+ process(moldyn,&(itom[i]),jtom,data,bc);
+
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
+
+ return 0;
+
+}
+
/*
* post processing functions
*/
return 0;
}
-int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+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) {
- 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;
+ int s;
+ t_pcc *pcc;
- lc=&(moldyn->lc);
+ /* 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;
+}
- slots=moldyn->cutoff/dr;
- o=2*slots;
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+ t_pcc pcc;
+ double norm;
+ int i;
- if(slots*dr<=moldyn->cutoff)
+ 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(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
if(ptr!=NULL) {
- stat=(double *)ptr;
+ pcc.stat=(double *)ptr;
}
else {
- stat=(double *)malloc(3*slots*sizeof(double));
- if(stat==NULL) {
+ pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+ if(pcc.stat==NULL) {
perror("[moldyn] pair correlation malloc");
return -1;
}
}
- memset(stat,0,3*slots*sizeof(double));
+ memset(pcc.stat,0,3*pcc.o1*sizeof(double));
- link_cell_init(moldyn,VERBOSE);
+ /* process */
+ process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
- 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);
+ /* normalization */
+ for(i=1;i<pcc.o1;i++) {
+ // normalization: 4 pi r^2 dr
+ // here: not double counting pairs -> 2 pi r r dr
+ // ... 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;
+ }
+ /* */
- /* brand of atom i */
- ibrand=itom[i].brand;
-
- for(j=0;j<27;j++) {
+ if(ptr==NULL) {
+ /* todo: store/print pair correlation function */
+ free(pcc.stat);
+ }
- bc=(j<lc->dnlc)?0:1;
+ return 0;
+}
-#ifdef STATIC_LISTS
- p=0;
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
- while(neighbour[j][p]!=0) {
+ t_ba *ba;
+ t_3dvec dist;
+ double d;
- jtom=&(moldyn->atom[neighbour[j][p]]);
- p++;
-#else
- this=&(neighbour[j]);
- list_reset_f(this);
+ if(itom->tag>=jtom->tag)
+ return 0;
- if(this->start==NULL)
- continue;
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
- do {
+ /* ignore if greater or equal cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
- jtom=this->current->data;
-#endif
- /* only count pairs once,
- * skip same atoms */
- if(itom[i].tag>=jtom->tag)
- continue;
+ /* check for potential bond */
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
- /*
- * pair correlation calc
- */
+ d=sqrt(d);
- /* distance */
- v3_sub(&dist,&(jtom->r),&(itom[i].r));
- if(bc) check_per_bound(moldyn,&dist);
- d=v3_absolute_square(&dist);
+ /* now count this bonding ... */
+ ba=data;
- /* ignore if greater or equal cutoff */
- if(d>=moldyn->cutoff_square)
- continue;
+ /* increase total bond counter
+ * ... double counting!
+ */
+ ba->tcnt+=2;
- /* 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(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;
- 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
- }
- }
+ return 0;
+}
- /* 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;
+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));
- if(ptr==NULL) {
- /* todo: store/print pair correlation function */
- free(stat);
+ 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));
- free(moldyn->atom);
+ ba.tcnt=0;
+ qcnt=0;
+ ccnt=0;
+ cset=0;
- link_cell_shutdown(moldyn);
+ atom=moldyn->atom;
- return 0;
-}
+ 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;
+ }
+ }
-int analyze_bonds(t_moldyn *moldyn) {
+ 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;
}
projects / physik / posic.git / blobdiff