#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)
*/
"Ar",
};
+/*
+static double pse_mass[]={
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ M_C,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ M_SI,
+ 0,
+ 0,
+ 0,
+ 0,
+};
+
+static double pse_lc[]={
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ LC_C,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ LC_SI,
+ 0,
+ 0,
+ 0,
+ 0,
+};
+*/
+
/*
* the moldyn functions
*/
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/t 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] p/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) {
+int set_potential(t_moldyn *moldyn,u8 type) {
- 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;
+ 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;
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;
int count;
atom=moldyn->atom;
- count=(moldyn->count)++;
+ count=(moldyn->count)++; // asshole style!
ptr=realloc(atom,(count+1)*sizeof(t_atom));
if(!ptr) {
moldyn->atom=ptr;
atom=moldyn->atom;
+
+ /* initialize new atom */
+ memset(&(atom[count]),0,sizeof(t_atom));
atom[count].r=*r;
atom[count].v=*v;
atom[count].element=element;
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);
return moldyn->p;
}
+int average_reset(t_moldyn *moldyn) {
+
+ printf("[moldyn] average reset\n");
+
+ /* update skip value */
+ moldyn->avg_skip=moldyn->total_steps;
+
+ /* kinetic energy */
+ moldyn->k_sum=0.0;
+ moldyn->k2_sum=0.0;
+
+ /* potential energy */
+ moldyn->v_sum=0.0;
+ moldyn->v2_sum=0.0;
+
+ /* temperature */
+ moldyn->t_sum=0.0;
+
+ /* virial */
+ moldyn->virial_sum=0.0;
+ moldyn->gv_sum=0.0;
+
+ /* pressure */
+ moldyn->p_sum=0.0;
+ moldyn->gp_sum=0.0;
+ moldyn->tp_sum=0.0;
+
+ return 0;
+}
+
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 */
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;
}
double thermodynamic_pressure_calc(t_moldyn *moldyn) {
- t_3dvec dim,*tp;
- double u_up,u_down,dv;
- double scale,p;
+ t_3dvec dim;
+ //t_3dvec *tp;
+ 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);
/* linked list / cell method */
-#ifdef STATIC_LISTS
-
int link_cell_init(t_moldyn *moldyn,u8 vol) {
t_linkcell *lc;
int i;
- int *foo;
lc=&(moldyn->lc);
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) {
+#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));
perror("[moldyn] list init (malloc)");
return -1;
}
-//if(i==0) printf(" --- add one here! %d %p %p ----\n",i,lc->subcell,lc->subcell[0]);
+ /*
+ 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);
int nx,ny;
t_atom *atom;
t_linkcell *lc;
+#ifdef STATIC_LISTS
int p;
+#endif
atom=moldyn->atom;
lc=&(moldyn->lc);
ny=lc->ny;
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++;
}
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,int **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;
count2=27;
a=nx*ny;
+ if(i>=nx||j>=ny||k>=nz)
+ printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
+ i,nx,j,ny,k,nz);
+
cell[0]=lc->subcell[i+j*nx+k*a];
for(ci=-1;ci<=1;ci++) {
bx=0;
int i;
t_linkcell *lc;
- int *foo;
lc=&(moldyn->lc);
- for(i=0;i<lc->cells;i++)
-{
-//printf(" --- free %p , %d\n",lc->subcell[i],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);
return 0;
}
-#else
-
-int link_cell_init(t_moldyn *moldyn,u8 vol) {
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
- t_linkcell *lc;
- int i;
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
- lc=&(moldyn->lc);
+ schedule=&(moldyn->schedule);
+ count=++(schedule->total_sched);
- /* partitioning the md cell */
- lc->nx=moldyn->dim.x/moldyn->cutoff;
- lc->x=moldyn->dim.x/lc->nx;
- lc->ny=moldyn->dim.y/moldyn->cutoff;
- lc->y=moldyn->dim.y/lc->ny;
- lc->nz=moldyn->dim.z/moldyn->cutoff;
- lc->z=moldyn->dim.z/lc->nz;
+ ptr=realloc(schedule->runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ schedule->runs=ptr;
+ schedule->runs[count-1]=runs;
- lc->cells=lc->nx*lc->ny*lc->nz;
- lc->subcell=malloc(lc->cells*sizeof(t_list));
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ schedule->tau=ptr;
+ schedule->tau[count-1]=tau;
- if(lc->cells<27)
- printf("[moldyn] FATAL: less then 27 subcells!\n");
+ printf("[moldyn] schedule added:\n");
+ printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+
- if(vol) {
- printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
- lc->cells);
- 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);
- }
+ return 0;
+}
- for(i=0;i<lc->cells;i++)
- list_init_f(&(lc->subcell[i]));
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
- link_cell_update(moldyn);
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
return 0;
}
-int link_cell_update(t_moldyn *moldyn) {
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
- int count,i,j,k;
- int nx,ny;
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+ int i;
+ unsigned int e,m,s,v,p,t,a;
+ t_3dvec momentum;
+ t_moldyn_schedule *sched;
t_atom *atom;
- t_linkcell *lc;
- double x,y,z;
+ int fd;
+ char dir[128];
+ double ds;
+ double energy_scale;
+ struct timeval t1,t2;
+ //double tp;
+ sched=&(moldyn->schedule);
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++)
- list_destroy_f(&(lc->subcell[i]));
-
- 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);
- list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
- &(atom[count]));
-//if(i==0&&j==0&&k==0) printf(" --- add one here! %d %p ----\n",count,lc->subcell[0].current);
- }
-
- return 0;
-}
-
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
-
- t_linkcell *lc;
- int a;
- int count1,count2;
- int ci,cj,ck;
- int nx,ny,nz;
- int x,y,z;
- u8 bx,by,bz;
-
- lc=&(moldyn->lc);
- nx=lc->nx;
- ny=lc->ny;
- nz=lc->nz;
- count1=1;
- count2=27;
- a=nx*ny;
-
- cell[0]=lc->subcell[i+j*nx+k*a];
- for(ci=-1;ci<=1;ci++) {
- bx=0;
- x=i+ci;
- if((x<0)||(x>=nx)) {
- x=(x+nx)%nx;
- bx=1;
- }
- for(cj=-1;cj<=1;cj++) {
- by=0;
- y=j+cj;
- if((y<0)||(y>=ny)) {
- y=(y+ny)%ny;
- by=1;
- }
- for(ck=-1;ck<=1;ck++) {
- bz=0;
- z=k+ck;
- if((z<0)||(z>=nz)) {
- z=(z+nz)%nz;
- bz=1;
- }
- if(!(ci|cj|ck)) continue;
- if(bx|by|bz) {
- cell[--count2]=lc->subcell[x+y*nx+z*a];
- }
- else {
- cell[count1++]=lc->subcell[x+y*nx+z*a];
- }
- }
- }
- }
-
- lc->dnlc=count1;
-
- return count1;
-}
-
-int link_cell_shutdown(t_moldyn *moldyn) {
-
- int i;
- t_linkcell *lc;
-
- lc=&(moldyn->lc);
-
-printf("FOO:\n");
- for(i=0;i<lc->nx*lc->ny*lc->nz;i++) {
-printf(" %d\n",i);
- list_destroy_f(&(moldyn->lc.subcell[i]));
-printf(" %d!\n",i);
-}
-
- free(lc->subcell);
-
- return 0;
-}
-
-#endif
-
-int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
-
- int count;
- void *ptr;
- t_moldyn_schedule *schedule;
-
- schedule=&(moldyn->schedule);
- count=++(schedule->total_sched);
-
- ptr=realloc(schedule->runs,count*sizeof(int));
- if(!ptr) {
- perror("[moldyn] realloc (runs)");
- return -1;
- }
- schedule->runs=ptr;
- schedule->runs[count-1]=runs;
-
- ptr=realloc(schedule->tau,count*sizeof(double));
- if(!ptr) {
- perror("[moldyn] realloc (tau)");
- return -1;
- }
- schedule->tau=ptr;
- schedule->tau[count-1]=tau;
-
- printf("[moldyn] schedule added:\n");
- printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
-
-
- return 0;
-}
-
-int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
-
- moldyn->schedule.hook=hook;
- moldyn->schedule.hook_params=hook_params;
-
- return 0;
-}
-
-/*
- *
- * 'integration of newtons equation' - algorithms
- *
- */
-
-/* start the integration */
-
-int moldyn_integrate(t_moldyn *moldyn) {
-
- int i;
- unsigned int e,m,s,v,p,t;
- t_3dvec momentum;
- t_moldyn_schedule *sched;
- t_atom *atom;
- int fd;
- char dir[128];
- double ds;
- double energy_scale;
- struct timeval t1,t2;
- //double tp;
-
- sched=&(moldyn->schedule);
- atom=moldyn->atom;
-
- /* initialize linked cell method */
- link_cell_init(moldyn,VERBOSE);
+ /* initialize linked cell method */
+ link_cell_init(moldyn,VERBOSE);
/* logging & visualization */
e=moldyn->ewrite;
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);
/* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
- printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ printf("[moldyn] WARNING: cutoff > 0.5 x dim.x\n");
if(moldyn->cutoff>0.5*moldyn->dim.y)
- printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ 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");
+ 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)
- printf("[moldyn] warning: forces too high / tau too small!\n");
+ printf("[moldyn] WARNING: forces too high / tau too small!\n");
/* zero absolute time */
moldyn->time=0.0;
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",
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, 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);
+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/BAR,moldyn->p_avg/BAR,
+ moldyn->volume,
+ (int)(t2.tv_sec-t1.tv_sec));
+
+ fflush(stdout);
/* copy over time */
t1=t2;
/* 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");
}
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);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+ /* criticial check */
+ moldyn_bc_check(moldyn);
+
/* neighbour list update */
link_cell_update(moldyn);
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
- /* calculate global virial */
+ /* some postprocessing */
for(i=0;i<count;i++) {
- 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;
+ /* calculate global virial */
+ moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
+ moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
+ moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
+ moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
+ moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
+ moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
+
+ /* check forces regarding the given timestep */
+ if(v3_norm(&(itom[i].f))>\
+ 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+ printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
+ i);
}
return 0;
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);
- cnt=read(fd,moldyn,size);
- if(cnt!=size) {
- perror("[moldyn] load save file read (moldyn)");
- return cnt;
+
+ 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);
+ /* 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 -1;
}
- cnt=read(fd,moldyn->atom,size);
- if(cnt!=size) {
- perror("[moldyn] load save file read (atoms)");
- return cnt;
+ while(size) {
+ cnt=read(fd,moldyn->atom,size);
+ if(cnt<0) {
+ perror("[moldyn] load save file read (atoms)");
+ return cnt;
+ }
+ size-=cnt;
}
- // hooks
+ // hooks etc ...
+
+ return 0;
+}
+
+int moldyn_free_save_file(t_moldyn *moldyn) {
+
+ free(moldyn->atom);
return 0;
}
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);
+ 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
*/
ret=read(fd,line+count,1);
if(ret<=0) return ret;
if(line[count]=='\n') {
- line[count]='\0';
+ memset(line+count,0,max-count-1);
+ //line[count]='\0';
return count+1;
}
count+=1;
return 0;
}
-int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
- 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;
+ int i;
+ t_atom *atom;
t_3dvec dist;
- double d,norm;
- int o,s;
- unsigned char ibrand;
+ double d2;
+ int a_cnt;
+ int b_cnt;
- lc=&(moldyn->lc);
+ 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;
- slots=(int)(moldyn->cutoff/dr);
- o=2*slots;
+ /* 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(" 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
+ /* check for potential bond */
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
- if(jtom==&(itom[i]))
- continue;
+ d=sqrt(d);
- /* only count pairs once */
- if(itom[i].tag>jtom->tag)
- continue;
+ /* now count this bonding ... */
+ ba=data;
- /*
- * pair correlation calc
- */
+ /* increase total bond counter
+ * ... double counting!
+ */
+ ba->tcnt+=2;
- /* distance */
- v3_sub(&dist,&(jtom->r),&(itom[i].r));
- if(bc) check_per_bound(moldyn,&dist);
- d=v3_absolute_square(&dist);
+ 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;
- /* ignore if greater cutoff */
- if(d>moldyn->cutoff_square)
- continue;
+ return 0;
+}
- /* fill the slots */
- d=sqrt(d);
- s=(int)(d/dr);
+int bond_analyze(t_moldyn *moldyn,double *quality) {
- 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;
- }
+ // by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
-#ifdef STATIC_LISTS
- }
-#else
- } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
-#endif
- }
- }
+ int qcnt;
+ int ccnt,cset;
+ t_ba ba;
+ int i;
+ t_atom *atom;
- /* 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;
+ 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);
-int analyze_bonds(t_moldyn *moldyn) {
+ 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;
+}
+
int visual_atoms(t_moldyn *moldyn) {
- 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];
-#endif
- u8 bc;
- t_3dvec dist;
- double d2;
- u8 brand;
+ t_vb vb;
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) {
+ vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+ if(vb.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",
+ dprintf(vb.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++) {
+ 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);
return 0;
}