#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"
+/* 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)
+ */
+
+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;
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;
+ 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;
}
-int set_potential_params(t_moldyn *moldyn,void *params) {
+int set_avg_skip(t_moldyn *moldyn,int skip) {
- moldyn->pot_params=params;
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
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;
- ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ moldyn->awrite=timer;
+ ret=visual_init(moldyn,moldyn->vlsdir);
if(ret<0) {
printf("[moldyn] visual init failure\n");
return ret;
if(moldyn->rfd) {
dprintf(moldyn->rfd,report_end);
close(moldyn->rfd);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ 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 */
+ total_mass_calc(moldyn);
+
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)++; // asshole style!
+
+ ptr=realloc(atom,(count+1)*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (add atom)");
+ return -1;
+ }
+ 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;
+ 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;
-
- return 0;
-}
-
int destroy_atoms(t_moldyn *moldyn) {
if(moldyn->atom) free(moldyn->atom);
return 0;
}
+double total_mass_calc(t_moldyn *moldyn) {
+
+ int i;
+
+ moldyn->mass=0.0;
+
+ for(i=0;i<moldyn->count;i++)
+ moldyn->mass+=moldyn->atom[i].mass;
+
+ return moldyn->mass;
+}
+
double temperature_calc(t_moldyn *moldyn) {
/* assume up to date kinetic energy, which is 3/2 N k_B T */
moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
- moldyn->t_sum+=moldyn->t;
- moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
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) */
+ 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);
+ 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;
+ }
+
+ /* 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);
- }
-
- /* virial sum and mean virial */
- moldyn->virial_sum+=v;
- moldyn->mean_v=moldyn->virial_sum/moldyn->total_steps;
+ /* assume up to date virial & up to date kinetic energy */
- /* 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);
- moldyn->p_sum+=moldyn->p;
- moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
- /* 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);
- moldyn->gp_sum+=moldyn->gp;
- moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
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;
+
+ 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_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_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;
+ moldyn->tp_sum+=moldyn->tp;
+ moldyn->tp_avg=moldyn->tp_sum/denom;
+
+ return 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,ighc;
+
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ /* (temperature average)^2 */
+ temp2=moldyn->t_avg*moldyn->t_avg;
+ printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
+ moldyn->t_avg);
+
+ /* ideal gas contribution */
+ ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+ printf(" ideal gas contribution: %f\n",
+ ighc/moldyn->mass*KILOGRAM/JOULE);
+
+ /* specific heat for nvt ensemble */
+ 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_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_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;
+}
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);
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;
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;
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);
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;
char dir[128];
double ds;
double energy_scale;
+ struct timeval t1,t2;
//double tp;
sched=&(moldyn->schedule);
m=moldyn->mwrite;
s=moldyn->swrite;
v=moldyn->vwrite;
+ a=moldyn->awrite;
p=moldyn->pwrite;
t=moldyn->twrite;
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 */
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;
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);
- //tp=thermodynamic_pressure_calc(moldyn);
-//printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
+ //thermodynamic_pressure_calc(moldyn);
+
+ /* calculate fluctuations + averages */
+ 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);
+ "%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->tp/BAR,moldyn->tp_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(v) {
+ if(!(moldyn->total_steps%v)) {
+ dprintf(moldyn->vfd,
+ "%f %f\n",moldyn->time,moldyn->volume);
}
}
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));
close(fd);
}
}
- if(v) {
- if(!(i%v)) {
- visual_atoms(&(moldyn->vis),moldyn->time,
- moldyn->atom,moldyn->count);
+ if(a) {
+ if(!(moldyn->total_steps%a)) {
+ 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);
+ //if(!(moldyn->total_steps%10)) {
+ /* get current time */
+ gettimeofday(&t2,NULL);
+
+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;
+ //}
/* increase absolute time */
moldyn->time+=moldyn->tau;
}
/* check for hooks */
- if(sched->hook)
+ if(sched->hook) {
+ printf("\n ## schedule hook %d start ##\n",
+ sched->count);
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;
}
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);
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;
/* 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++) {
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[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->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;
+ /* 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;
return 0;
}
+
+/*
+ * restore function
+ */
+
+int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
+
+ int fd;
+ int cnt,size;
+ int fsize;
+ int corr;
+
+ fd=open(file,O_RDONLY);
+ if(fd<0) {
+ perror("[moldyn] load save file open");
+ return fd;
+ }
+
+ fsize=lseek(fd,0,SEEK_END);
+ lseek(fd,0,SEEK_SET);
+
+ 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);
+
+ /* 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;
+ }
+
+ 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_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
+ */
+
+int get_line(int fd,char *line,int max) {
+
+ int count,ret;
+
+ count=0;
+
+ while(1) {
+ if(count==max) return count;
+ ret=read(fd,line+count,1);
+ if(ret<=0) return ret;
+ if(line[count]=='\n') {
+ line[count]='\0';
+ return count+1;
+ }
+ count+=1;
+ }
+}
+
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
+
+
+ return 0;
+}
+
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ double d2;
+ int a_cnt;
+ int b_cnt;
+
+ atom=moldyn->atom;
+ dc[0]=0;
+ dc[1]=0;
+ dc[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+ v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
+ check_per_bound(moldyn,&dist);
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ dc[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ dc[0]+=d2;
+ }
+
+ dc[2]+=d2;
+ }
+
+ dc[0]*=(1.0/(6.0*moldyn->time*a_cnt));
+ dc[1]*=(1.0/(6.0*moldyn->time*b_cnt));
+ dc[2]*=(1.0/(6.0*moldyn->time*moldyn->count));
+
+ return 0;
+}
+
+int bonding_analyze(t_moldyn *moldyn,double *cnt) {
+
+ return 0;
+}
+
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+ t_atom *jtom,void *data,u8 bc) {
+
+ t_3dvec dist;
+ double d;
+ int s;
+ t_pcc *pcc;
+
+ /* only count pairs once,
+ * skip same atoms */
+ if(itom->tag>=jtom->tag)
+ return 0;
+
+ /*
+ * pair correlation calc
+ */
+
+ /* get pcc data */
+ pcc=data;
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+
+ /* ignore if greater cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
+
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/pcc->dr);
+
+ /* should never happen but it does 8) -
+ * related to -ffloat-store problem! */
+ if(s>=pcc->o1) {
+ printf("[moldyn] WARNING: pcc (%d/%d)",
+ s,pcc->o1);
+ printf("\n");
+ s=pcc->o1-1;
+ }
+
+ if(itom->brand!=jtom->brand) {
+ /* mixed */
+ pcc->stat[s]+=1;
+ }
+ else {
+ /* type a - type a bonds */
+ if(itom->brand==0)
+ pcc->stat[s+pcc->o1]+=1;
+ else
+ /* type b - type b bonds */
+ pcc->stat[s+pcc->o2]+=1;
+ }
+
+ return 0;
+}
+
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+ t_pcc pcc;
+ double norm;
+ int i;
+
+ pcc.dr=dr;
+ pcc.o1=moldyn->cutoff/dr;
+ pcc.o2=2*pcc.o1;
+
+ if(pcc.o1*dr<=moldyn->cutoff)
+ printf("[moldyn] WARNING: pcc (low #slots)\n");
+
+ printf("[moldyn] pair correlation calc info:\n");
+ printf(" time: %f\n",moldyn->time);
+ printf(" count: %d\n",moldyn->count);
+ printf(" cutoff: %f\n",moldyn->cutoff);
+ printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
+
+ if(ptr!=NULL) {
+ pcc.stat=(double *)ptr;
+ }
+ else {
+ pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+ if(pcc.stat==NULL) {
+ perror("[moldyn] pair correlation malloc");
+ return -1;
+ }
+ }
+
+ memset(pcc.stat,0,3*pcc.o1*sizeof(double));
+
+ /* process */
+ process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
+
+ /* normalization */
+ for(i=1;i<pcc.o1;i++) {
+ // normalization: 4 pi r^2 dr
+ // here: not double counting pairs -> 2 pi r r dr
+ // ... and actually it's a constant times r^2
+ norm=i*i*dr*dr;
+ pcc.stat[i]/=norm;
+ pcc.stat[pcc.o1+i]/=norm;
+ pcc.stat[pcc.o2+i]/=norm;
+ }
+ /* */
+
+ if(ptr==NULL) {
+ /* todo: store/print pair correlation function */
+ free(pcc.stat);
+ }
+
+ return 0;
+}
+
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
+
+ t_ba *ba;
+ t_3dvec dist;
+ double d;
+
+ if(itom->tag>=jtom->tag)
+ return 0;
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+
+ /* ignore if greater or equal cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
+
+ /* check for potential bond */
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
+
+ d=sqrt(d);
+
+ /* now count this bonding ... */
+ ba=data;
+
+ /* increase total bond counter
+ * ... double counting!
+ */
+ ba->tcnt+=2;
+
+ if(itom->brand==0)
+ ba->acnt[jtom->tag]+=1;
+ else
+ ba->bcnt[jtom->tag]+=1;
+
+ if(jtom->brand==0)
+ ba->acnt[itom->tag]+=1;
+ else
+ ba->bcnt[itom->tag]+=1;
+
+ return 0;
+}
+
+int bond_analyze(t_moldyn *moldyn,double *quality) {
+
+ // by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
+
+ int qcnt;
+ int ccnt,cset;
+ t_ba ba;
+ int i;
+ t_atom *atom;
+
+ ba.acnt=malloc(moldyn->count*sizeof(int));
+ if(ba.acnt==NULL) {
+ perror("[moldyn] bond analyze malloc (a)");
+ return -1;
+ }
+ memset(ba.acnt,0,moldyn->count*sizeof(int));
+
+ ba.bcnt=malloc(moldyn->count*sizeof(int));
+ if(ba.bcnt==NULL) {
+ perror("[moldyn] bond analyze malloc (b)");
+ return -1;
+ }
+ memset(ba.bcnt,0,moldyn->count*sizeof(int));
+
+ ba.tcnt=0;
+ qcnt=0;
+ ccnt=0;
+ cset=0;
+
+ atom=moldyn->atom;
+
+ process_2b_bonds(moldyn,&ba,bond_analyze_process);
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].brand==0) {
+ if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
+ qcnt+=4;
+ }
+ else {
+ if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
+ qcnt+=4;
+ ccnt+=1;
+ }
+ cset+=1;
+ }
+ }
+
+ printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset);
+ printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt);
+
+ if(quality) {
+ quality[0]=1.0*ccnt/cset;
+ quality[1]=1.0*qcnt/ba.tcnt;
+ }
+ else {
+ printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt);
+ printf("[moldyn] bond analyze: tot_q=%f\n",1.0*qcnt/ba.tcnt);
+ }
+
+ return 0;
+}
+
+/*
+ * 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;
+}
+