#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
#include <math.h>
+#include <fpu_control.h>
+
+#ifdef PARALLEL
+#include <omp.h>
+#endif
+
+#if defined PTHREADS || defined VISUAL_THREAD
+#include <pthread.h>
+#endif
+
#include "moldyn.h"
+#include "report/report.h"
+
+/* potential includes */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+#include "potentials/albe_orig.h"
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+/* pse */
+#define PSE_MASS
+#define PSE_NAME
+#define PSE_COL
+#include "pse.h"
+#undef PSE_MASS
+#undef PSE_NAME
+#undef PSE_COL
+
+#ifdef PTHREADS
+/* global mutexes */
+pthread_mutex_t *amutex;
+pthread_mutex_t emutex;
+#endif
+
+/* fully constrained relaxation technique - global pointers */
+u8 crtt;
+u8 *constraints;
+double *trafo_angle;
+
+/*
+ * the moldyn functions
+ */
int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
printf("[moldyn] init\n");
+ /* only needed if compiled without -msse2 (float-store prob!) */
+ //fpu_set_rtd();
+
memset(moldyn,0,sizeof(t_moldyn));
+ moldyn->argc=argc;
+ moldyn->args=argv;
+
rand_init(&(moldyn->random),NULL,1);
moldyn->random.status|=RAND_STAT_VERBOSE;
+#ifdef PTHREADS
+ pthread_mutex_init(&emutex,NULL);
+#endif
+
return 0;
}
int moldyn_shutdown(t_moldyn *moldyn) {
+#ifdef PTHREADS
+ int i;
+#endif
+
printf("[moldyn] shutdown\n");
+#ifdef PTHREADS
+ for(i=0;i<moldyn->count;i++)
+ pthread_mutex_destroy(&(amutex[i]));
+ free(amutex);
+ pthread_mutex_destroy(&emutex);
+#endif
+
moldyn_log_shutdown(moldyn);
link_cell_shutdown(moldyn);
rand_close(&(moldyn->random));
int set_cutoff(t_moldyn *moldyn,double cutoff) {
moldyn->cutoff=cutoff;
+ moldyn->cutoff_square=cutoff*cutoff;
printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
moldyn->t_ref=t_ref;
- printf("[moldyn] temperature: %f\n",moldyn->t_ref);
+ printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
return 0;
}
moldyn->p_ref=p_ref;
- printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+ printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
+
+ 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 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] t scaling:\n");
+
+ printf(" t: %s",ttype?"yes":"no ");
+ if(ttype)
+ printf(" | type: %02x | factor: %f",ttype,ttc);
+ printf("\n");
return 0;
}
return 0;
}
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
-
- moldyn->func1b=func;
- moldyn->pot1b_params=params;
-
- return 0;
-}
-
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_potential(t_moldyn *moldyn,u8 type) {
- moldyn->func2b=func;
- moldyn->pot2b_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;
+ moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_AO:
+ moldyn->func_j1=albe_orig_mult_3bp_j1;
+ moldyn->func_j1_k0=albe_orig_mult_3bp_k1;
+ moldyn->func_j1c=albe_orig_mult_3bp_j2;
+ moldyn->func_j1_k1=albe_orig_mult_3bp_k2;
+ moldyn->check_2b_bond=albe_orig_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_AM:
+ moldyn->func_i0=albe_mult_i0;
+ moldyn->func_j0=albe_mult_i0_j0;
+ moldyn->func_j0_k0=albe_mult_i0_j0_k0;
+ moldyn->func_j0e=albe_mult_i0_j1;
+ moldyn->func_j1=albe_mult_i0_j2;
+ moldyn->func_j1_k0=albe_mult_i0_j2_k0;
+ moldyn->func_j1c=albe_mult_i0_j3;
+ moldyn->check_2b_bond=albe_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_HO:
+ moldyn->func_j0=harmonic_oscillator;
+ moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_LJ:
+ moldyn->func_j0=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_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+int set_avg_skip(t_moldyn *moldyn,int skip) {
- moldyn->func2b_post=func;
- moldyn->pot2b_params=params;
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
- moldyn->func3b=func;
- moldyn->pot3b_params=params;
+ strncpy(moldyn->vlsdir,dir,127);
return 0;
}
-int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
- strncpy(moldyn->vlsdir,dir,127);
+ strncpy(moldyn->rauthor,author,63);
+ strncpy(moldyn->rtitle,title,63);
return 0;
}
dprintf(moldyn->efd,"# total momentum log file\n");
printf("total momentum (%d)\n",timer);
break;
+ case LOG_PRESSURE:
+ moldyn->pwrite=timer;
+ snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
+ moldyn->pfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->pfd<0) {
+ perror("[moldyn] pressure log file\n");
+ return moldyn->pfd;
+ }
+ dprintf(moldyn->pfd,"# pressure log file\n");
+ printf("pressure (%d)\n",timer);
+ break;
+ case LOG_TEMPERATURE:
+ moldyn->twrite=timer;
+ snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
+ moldyn->tfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tfd<0) {
+ perror("[moldyn] temperature log file\n");
+ return moldyn->tfd;
+ }
+ 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;
}
printf("visual file (%d)\n",timer);
break;
+ case CREATE_REPORT:
+ snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+ moldyn->rfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->rfd<0) {
+ perror("[moldyn] report fd open");
+ return moldyn->rfd;
+ }
+ printf("report -> ");
+ if(moldyn->efd) {
+ snprintf(filename,127,"%s/e_plot.scr",
+ moldyn->vlsdir);
+ moldyn->epfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->epfd<0) {
+ perror("[moldyn] energy plot fd open");
+ return moldyn->epfd;
+ }
+ dprintf(moldyn->epfd,e_plot_script);
+ close(moldyn->epfd);
+ printf("energy ");
+ }
+ if(moldyn->pfd) {
+ snprintf(filename,127,"%s/pressure_plot.scr",
+ moldyn->vlsdir);
+ moldyn->ppfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->ppfd<0) {
+ perror("[moldyn] p plot fd open");
+ return moldyn->ppfd;
+ }
+ dprintf(moldyn->ppfd,pressure_plot_script);
+ close(moldyn->ppfd);
+ printf("pressure ");
+ }
+ if(moldyn->tfd) {
+ snprintf(filename,127,"%s/temperature_plot.scr",
+ moldyn->vlsdir);
+ moldyn->tpfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tpfd<0) {
+ perror("[moldyn] t plot fd open");
+ return moldyn->tpfd;
+ }
+ dprintf(moldyn->tpfd,temperature_plot_script);
+ close(moldyn->tpfd);
+ printf("temperature ");
+ }
+ dprintf(moldyn->rfd,report_start,
+ moldyn->rauthor,moldyn->rtitle);
+ printf("\n");
+ break;
default:
printf("unknown log type: %02x\n",type);
return -1;
int moldyn_log_shutdown(t_moldyn *moldyn) {
+ char sc[256];
+
printf("[moldyn] log shutdown\n");
- if(moldyn->efd) close(moldyn->efd);
+ if(moldyn->efd) {
+ close(moldyn->efd);
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_energy);
+ snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ }
if(moldyn->mfd) close(moldyn->mfd);
- if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
+ if(moldyn->pfd) {
+ close(moldyn->pfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_pressure);
+ snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->tfd) {
+ close(moldyn->tfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_temperature);
+ snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_end);
+ close(moldyn->rfd);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ }
return 0;
}
* creating lattice functions
*/
-int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
- u8 attr,u8 brand,int a,int b,int c) {
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params,
+ t_offset_params *o_params) {
int new,count;
int ret;
- t_3dvec origin;
+ t_3dvec orig;
void *ptr;
t_atom *atom;
+ char name[16];
+#ifdef PTHREADS
+ pthread_mutex_t *mutex;
+#endif
new=a*b*c;
count=moldyn->count;
/* how many atoms do we expect */
+ if(type==NONE) {
+ new*=1;
+ printf("[moldyn] WARNING: create 'none' lattice called");
+ }
+ if(type==CUBIC) new*=1;
if(type==FCC) new*=4;
if(type==DIAMOND) new*=8;
+ /* defects */
+ if(d_params->type) {
+ switch(d_params->stype) {
+ case DEFECT_STYPE_DB_X:
+ case DEFECT_STYPE_DB_Y:
+ case DEFECT_STYPE_DB_Z:
+ case DEFECT_STYPE_DB_R:
+ new*=2;
+ break;
+ default:
+ printf("[moldyn] WARNING: cl unknown defect\n");
+ break;
+ }
+ }
+
/* allocate space for atoms */
ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
if(!ptr) {
}
moldyn->atom=ptr;
atom=&(moldyn->atom[count]);
-
- v3_zero(&origin);
+
+#ifdef PTHREADS
+ ptr=realloc(amutex,(count+new)*sizeof(pthread_mutex_t));
+ if(!ptr) {
+ perror("[moldyn] mutex realloc (add atom)");
+ return -1;
+ }
+ amutex=ptr;
+ mutex=&(amutex[count]);
+#endif
+
+ /* no atoms on the boundaries (only reason: it looks better!) */
+ if(!origin) {
+ orig.x=0.5*lc;
+ orig.y=0.5*lc;
+ orig.z=0.5*lc;
+ }
+ else {
+ orig.x=origin->x;
+ orig.y=origin->y;
+ orig.z=origin->z;
+ }
switch(type) {
+ case CUBIC:
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
+ set_nn_dist(moldyn,lc);
+ ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
+ strcpy(name,"cubic");
+ break;
case FCC:
- ret=fcc_init(a,b,c,lc,atom,&origin);
+ if(!origin)
+ v3_scale(&orig,&orig,0.5);
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
+ set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
+ ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
+ strcpy(name,"fcc");
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,atom,&origin);
+ if(!origin)
+ v3_scale(&orig,&orig,0.25);
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
+ set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
+ ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
+ strcpy(name,"diamond");
break;
default:
printf("unknown lattice type (%02x)\n",type);
/* debug */
if(ret!=new) {
- printf("[moldyn] creating lattice failed\n");
+ printf("[moldyn] creating %s lattice (lc=%f) incomplete\n",
+ name,lc);
+ printf(" (ignore for partial lattice creation)\n");
printf(" amount of atoms\n");
printf(" - expected: %d\n",new);
printf(" - created: %d\n",ret);
- return -1;
- }
-
- moldyn->count+=new;
- printf("[moldyn] created lattice with %d atoms\n",new);
-
- for(ret=0;ret<new;ret++) {
- atom[ret].element=element;
- atom[ret].mass=mass;
- atom[ret].attr=attr;
- atom[ret].brand=brand;
- atom[ret].tag=count+ret;
- check_per_bound(moldyn,&(atom[ret].r));
}
- return ret;
-}
-
-/* fcc lattice init */
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
- int count;
- int i,j;
- t_3dvec o,r,n;
- t_3dvec basis[3];
- double help[3];
- double x,y,z;
-
- x=a*lc;
- y=b*lc;
- z=c*lc;
-
- if(origin) v3_copy(&o,origin);
- else v3_zero(&o);
-
- /* construct the basis */
- for(i=0;i<3;i++) {
- for(j=0;j<3;j++) {
- if(i!=j) help[j]=0.5*lc;
- else help[j]=.0;
+ moldyn->count+=ret;
+ if(ret==new)
+ printf("[moldyn] created %s lattice with %d atoms\n",name,ret);
+
+ for(new=0;new<ret;new++) {
+ atom[new].element=element;
+ atom[new].mass=pse_mass[element];
+ atom[new].attr=attr;
+ atom[new].brand=brand;
+ atom[new].tag=count+new;
+ check_per_bound(moldyn,&(atom[new].r));
+ atom[new].r_0=atom[new].r;
+#ifdef PTHREADS
+ pthread_mutex_init(&(mutex[new]),NULL);
+#endif
+ if(d_params->type) {
+ new+=1;
+ atom[new].element=d_params->element;
+ atom[new].mass=pse_mass[d_params->element];
+ atom[new].attr=d_params->attr;
+ atom[new].brand=d_params->brand;
+ atom[new].tag=count+new;
+ check_per_bound(moldyn,&(atom[new].r));
+ atom[new].r_0=atom[new].r;
+#ifdef PTHREADS
+ pthread_mutex_init(&(mutex[new]),NULL);
+#endif
}
- v3_set(&basis[i],help);
}
- v3_zero(&r);
- count=0;
-
- /* fill up the room */
- r.x=o.x;
- while(r.x<x) {
- r.y=o.y;
- while(r.y<y) {
- r.z=o.z;
- while(r.z<z) {
- v3_copy(&(atom[count].r),&r);
- atom[count].element=1;
- count+=1;
- for(i=0;i<3;i++) {
- v3_add(&n,&r,&basis[i]);
- if((n.x<x+o.x)&&
- (n.y<y+o.y)&&
- (n.z<z+o.z)) {
- v3_copy(&(atom[count].r),&n);
- count+=1;
- }
- }
- r.z+=lc;
- }
- r.y+=lc;
- }
- r.x+=lc;
+ /* fix allocation */
+ ptr=realloc(moldyn->atom,moldyn->count*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (create lattice - alloc fix)");
+ return -1;
}
+ moldyn->atom=ptr;
- /* coordinate transformation */
- help[0]=x/2.0;
- help[1]=y/2.0;
- help[2]=z/2.0;
- v3_set(&n,help);
- for(i=0;i<count;i++)
- v3_sub(&(atom[i].r),&(atom[i].r),&n);
-
- return count;
-}
-
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
- int count;
- t_3dvec o;
-
- count=fcc_init(a,b,c,lc,atom,origin);
-
- o.x=0.25*lc;
- o.y=0.25*lc;
- o.z=0.25*lc;
+// WHAT ABOUT AMUTEX !!!!
- if(origin) v3_add(&o,&o,origin);
+#ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (create lattice)");
+ return -1;
+ }
+ moldyn->lc.subcell->list=ptr;
+#endif
- count+=fcc_init(a,b,c,lc,&atom[count],&o);
+ /* update total system mass */
+ total_mass_calc(moldyn);
- return count;
+ return ret;
}
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr,
t_3dvec *r,t_3dvec *v) {
t_atom *atom;
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;
+#ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,(count+1)*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (add atom)");
+ return -1;
+ }
+ moldyn->lc.subcell->list=ptr;
+#endif
+
+#ifdef PTHREADS
+ ptr=realloc(amutex,(count+1)*sizeof(pthread_mutex_t));
+ if(!ptr) {
+ perror("[moldyn] mutex realloc (add atom)");
+ return -1;
+ }
+ amutex=ptr;
+ pthread_mutex_init(&(amutex[count]),NULL);
+#endif
+
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].mass=pse_mass[element];
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 destroy_atoms(t_moldyn *moldyn) {
-
- if(moldyn->atom) free(moldyn->atom);
+int del_atom(t_moldyn *moldyn,int tag) {
- return 0;
-}
+ t_atom *new,*old;
+ int cnt;
+#if defined LOWMEM_LISTS || defined PTHREADS
+ void *ptr;
+#endif
-int thermal_init(t_moldyn *moldyn,u8 equi_init) {
+ old=moldyn->atom;
- /*
- * - gaussian distribution of velocities
- * - zero total momentum
- * - velocity scaling (E = 3/2 N k T), E: kinetic energy
- */
+ new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
+ if(!new) {
+ perror("[moldyn]malloc (del atom)");
+ return -1;
+ }
- int i;
- double v,sigma;
- t_3dvec p_total,delta;
- t_atom *atom;
- t_random *random;
+ 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;
+ }
- atom=moldyn->atom;
- random=&(moldyn->random);
+ moldyn->count-=1;
+ moldyn->atom=new;
- printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+ free(old);
- /* gaussian distribution of velocities */
- v3_zero(&p_total);
- for(i=0;i<moldyn->count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
- /* x direction */
- v=sigma*rand_get_gauss(random);
- atom[i].v.x=v;
- p_total.x+=atom[i].mass*v;
- /* y direction */
- v=sigma*rand_get_gauss(random);
- atom[i].v.y=v;
- p_total.y+=atom[i].mass*v;
- /* z direction */
- v=sigma*rand_get_gauss(random);
- atom[i].v.z=v;
- p_total.z+=atom[i].mass*v;
+#ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (del atom)");
+ return -1;
}
+ moldyn->lc.subcell->list=ptr;
+ // update lists
+ link_cell_update(moldyn);
+#endif
- /* zero total momentum */
- v3_scale(&p_total,&p_total,1.0/moldyn->count);
- for(i=0;i<moldyn->count;i++) {
- v3_scale(&delta,&p_total,1.0/atom[i].mass);
- v3_sub(&(atom[i].v),&(atom[i].v),&delta);
+#ifdef PTHREADS
+ ptr=realloc(amutex,moldyn->count*sizeof(pthread_mutex_t));
+ if(!ptr) {
+ perror("[moldyn] mutex realloc (add atom)");
+ return -1;
}
+ amutex=ptr;
+ pthread_mutex_destroy(&(amutex[moldyn->count+1]));
+#endif
- /* velocity scaling */
- scale_velocity(moldyn,equi_init);
return 0;
}
-double temperature_calc(t_moldyn *moldyn) {
-
- double double_ekin;
- int i;
- t_atom *atom;
-
- atom=moldyn->atom;
-
- for(i=0;i<moldyn->count;i++)
- double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+#define set_atom_positions(pos) \
+ if(d_params->type) {\
+ d_o.x=0; d_o.y=0; d_o.z=0;\
+ d_d.x=0; d_d.y=0; d_d.z=0;\
+ switch(d_params->stype) {\
+ case DEFECT_STYPE_DB_X:\
+ d_o.x=d_params->od;\
+ d_d.x=d_params->dd;\
+ break;\
+ case DEFECT_STYPE_DB_Y:\
+ d_o.y=d_params->od;\
+ d_d.y=d_params->dd;\
+ break;\
+ case DEFECT_STYPE_DB_Z:\
+ d_o.z=d_params->od;\
+ d_d.z=d_params->dd;\
+ break;\
+ case DEFECT_STYPE_DB_R:\
+ break;\
+ default:\
+ printf("[moldyn] WARNING: unknown defect\n");\
+ break;\
+ }\
+ v3_add(&dr,&pos,&d_o);\
+ v3_copy(&(atom[count].r),&dr);\
+ count+=1;\
+ v3_add(&dr,&pos,&d_d);\
+ v3_copy(&(atom[count].r),&dr);\
+ count+=1;\
+ }\
+ else {\
+ v3_copy(&(atom[count].r),&pos);\
+ count+=1;\
+ }
- /* kinetic energy = 3/2 N k_B T */
- moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params) {
- return moldyn->t;
-}
+ int count;
+ t_3dvec r;
+ int i,j,k;
+ t_3dvec o;
+ t_3dvec dist;
+ t_3dvec p;
+ t_3dvec d_o;
+ t_3dvec d_d;
+ t_3dvec dr;
-double get_temperature(t_moldyn *moldyn) {
+ p.x=0; p.y=0; p.z=0;
- return moldyn->t;
-}
+ count=0;
+ if(origin)
+ v3_copy(&o,origin);
+ else
+ v3_zero(&o);
-int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
+ /* shift partition values */
+ if(p_params->type) {
+ p.x=p_params->p.x+(a*lc)/2.0;
+ p.y=p_params->p.y+(b*lc)/2.0;
+ p.z=p_params->p.z+(c*lc)/2.0;
+ }
- int i;
- double e,scale;
- t_atom *atom;
+ r.x=o.x;
+ for(i=0;i<a;i++) {
+ r.y=o.y;
+ for(j=0;j<b;j++) {
+ r.z=o.z;
+ for(k=0;k<c;k++) {
+ switch(p_params->type) {
+ case PART_INSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)<
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)>=
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_INSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)<p_params->d.x)&&
+ (fabs(dist.y)<p_params->d.y)&&
+ (fabs(dist.z)<p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)>=p_params->d.x)||
+ (fabs(dist.y)>=p_params->d.y)||
+ (fabs(dist.z)>=p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ default:
+ set_atom_positions(r);
+ break;
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ for(i=0;i<count;i++) {
+ atom[i].r.x-=(a*lc)/2.0;
+ atom[i].r.y-=(b*lc)/2.0;
+ atom[i].r.z-=(c*lc)/2.0;
+ }
+
+ return count;
+}
+
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params) {
+
+ int count;
+ int i,j,k,l;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+ t_3dvec dist;
+ t_3dvec p;
+ t_3dvec d_d,d_o,dr;
+
+ p.x=0; p.y=0; p.z=0;
+
+ count=0;
+ if(origin)
+ v3_copy(&o,origin);
+ else
+ v3_zero(&o);
+
+ /* construct the basis */
+ memset(basis,0,3*sizeof(t_3dvec));
+ basis[0].x=0.5*lc;
+ basis[0].y=0.5*lc;
+ basis[1].x=0.5*lc;
+ basis[1].z=0.5*lc;
+ basis[2].y=0.5*lc;
+ basis[2].z=0.5*lc;
+
+ /* shift partition values */
+ if(p_params->type) {
+ p.x=p_params->p.x+(a*lc)/2.0;
+ p.y=p_params->p.y+(b*lc)/2.0;
+ p.z=p_params->p.z+(c*lc)/2.0;
+ }
+
+ /* fill up the room */
+ r.x=o.x;
+ for(i=0;i<a;i++) {
+ r.y=o.y;
+ for(j=0;j<b;j++) {
+ r.z=o.z;
+ for(k=0;k<c;k++) {
+ /* first atom */
+ switch(p_params->type) {
+ case PART_INSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)<
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)>=
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_INSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)<p_params->d.x)&&
+ (fabs(dist.y)<p_params->d.y)&&
+ (fabs(dist.z)<p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)>=p_params->d.x)||
+ (fabs(dist.y)>=p_params->d.y)||
+ (fabs(dist.z)>=p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ default:
+ set_atom_positions(r);
+ break;
+ }
+ /* the three face centered atoms */
+ for(l=0;l<3;l++) {
+ v3_add(&n,&r,&basis[l]);
+ switch(p_params->type) {
+ case PART_INSIDE_R:
+ v3_sub(&dist,&n,&p);
+ if(v3_absolute_square(&dist)<
+ (p_params->r*p_params->r)) {
+ set_atom_positions(n);
+ }
+ break;
+ case PART_OUTSIDE_R:
+ v3_sub(&dist,&n,&p);
+ if(v3_absolute_square(&dist)>=
+ (p_params->r*p_params->r)) {
+ set_atom_positions(n);
+ }
+ break;
+ case PART_INSIDE_D:
+ v3_sub(&dist,&n,&p);
+ if((fabs(dist.x)<p_params->d.x)&&
+ (fabs(dist.y)<p_params->d.y)&&
+ (fabs(dist.z)<p_params->d.z)) {
+ set_atom_positions(n);
+ }
+ break;
+ case PART_OUTSIDE_D:
+ v3_sub(&dist,&n,&p);
+ if((fabs(dist.x)>=p_params->d.x)||
+ (fabs(dist.y)>=p_params->d.y)||
+ (fabs(dist.z)>=p_params->d.z)) {
+ set_atom_positions(n);
+ }
+ break;
+ default:
+ set_atom_positions(n);
+ break;
+ }
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ for(i=0;i<count;i++) {
+ atom[i].r.x-=(a*lc)/2.0;
+ atom[i].r.y-=(b*lc)/2.0;
+ atom[i].r.z-=(c*lc)/2.0;
+ }
+
+ return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params) {
+
+ int count;
+ t_3dvec o;
+
+ count=fcc_init(a,b,c,lc,atom,origin,p_params,d_params);
+
+ o.x=0.25*lc;
+ o.y=0.25*lc;
+ o.z=0.25*lc;
+
+ if(origin) v3_add(&o,&o,origin);
+
+ count+=fcc_init(a,b,c,lc,&atom[count],&o,p_params,d_params);
+
+ return count;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
+
+ if(moldyn->atom) free(moldyn->atom);
+
+ return 0;
+}
+
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
+
+ /*
+ * - gaussian distribution of velocities
+ * - zero total momentum
+ * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+ */
+
+ int i;
+ double v,sigma;
+ t_3dvec p_total,delta;
+ t_atom *atom;
+ t_random *random;
+
+ atom=moldyn->atom;
+ random=&(moldyn->random);
+
+ printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+
+ /* gaussian distribution of velocities */
+ v3_zero(&p_total);
+ for(i=0;i<moldyn->count;i++) {
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
+ /* x direction */
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.x=v;
+ p_total.x+=atom[i].mass*v;
+ /* y direction */
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.y=v;
+ p_total.y+=atom[i].mass*v;
+ /* z direction */
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.z=v;
+ p_total.z+=atom[i].mass*v;
+ }
+
+ /* zero total momentum */
+ v3_scale(&p_total,&p_total,1.0/moldyn->count);
+ for(i=0;i<moldyn->count;i++) {
+ v3_scale(&delta,&p_total,1.0/atom[i].mass);
+ v3_sub(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ /* velocity scaling */
+ scale_velocity(moldyn,equi_init);
+
+ 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 */
+
+ if(moldyn->count)
+ moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+ else moldyn->t=0.0;
+
+ return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+ return moldyn->t;
+}
+
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
+
+ int i;
+ double e,scale;
+ t_atom *atom;
int count;
atom=moldyn->atom;
scale*=2.0;
else
if(moldyn->pt_scale&T_SCALE_BERENDSEN)
- scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=1.0+(scale-1.0)*moldyn->tau/moldyn->t_tc;
scale=sqrt(scale);
/* velocity scaling */
return 0;
}
-double pressure_calc(t_moldyn *moldyn) {
-
- int i;
- t_atom *atom;
- double p1,p2,p=0;
-
- for(i=0;i<moldyn->count;i++) {
-
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
- }
+ double p;
- p1=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt1);
- p1/=moldyn->volume;
+ p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
- p2=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt2);
- p2/=moldyn->volume;
+ return p;
+}
- printf("compare pressures: %f %f\n",p1/ATM,p2/ATM);
+double virial_sum(t_moldyn *moldyn) {
- return moldyn->p;
-}
+ int i;
+ t_virial *virial;
-double get_pressure(t_moldyn *moldyn) {
+ /* 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;
+ }
- return moldyn->p;
+ /* global virial (absolute coordinates) */
+ //virial=&(moldyn->gvir);
+ //moldyn->gv=virial->xx+virial->yy+virial->zz;
+ return moldyn->virial;
}
-int scale_volume(t_moldyn *moldyn) {
+double pressure_calc(t_moldyn *moldyn) {
- t_atom *atom;
- t_3dvec *dim,*vdim;
- double scale,v;
- t_virial virial;
- t_linkcell *lc;
- int i;
+ /*
+ * PV = NkT + <W>
+ * with W = 1/3 sum_i f_i r_i (- skipped!)
+ * virial = sum_i f_i r_i
+ *
+ * => P = (2 Ekin + virial) / (3V)
+ */
- atom=moldyn->atom;
- dim=&(moldyn->dim);
- vdim=&(moldyn->vis.dim);
- lc=&(moldyn->lc);
+ /* assume up to date virial & up to date kinetic energy */
- memset(&virial,0,sizeof(t_virial));
+ /* pressure (atom virials) */
+ moldyn->p=2.0*moldyn->ekin+moldyn->virial;
+ moldyn->p/=(3.0*moldyn->volume);
- for(i=0;i<moldyn->count;i++) {
- virial.xx+=atom[i].virial.xx;
- virial.yy+=atom[i].virial.yy;
- virial.zz+=atom[i].virial.zz;
- virial.xy+=atom[i].virial.xy;
- virial.xz+=atom[i].virial.xz;
- virial.yz+=atom[i].virial.yz;
- }
-
- /* just a guess so far ... */
- v=virial.xx+virial.yy+virial.zz;
-
-printf("%f\n",v);
- /* get pressure from virial */
- moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
- moldyn->p/=moldyn->volume;
-printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
-
- /* scale factor */
- if(moldyn->pt_scale&P_SCALE_BERENDSEN)
- scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
- else
- /* should actually never be used */
- scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
-
-printf("scale = %f\n",scale);
- /* actual scaling */
- dim->x*=scale;
- dim->y*=scale;
- dim->z*=scale;
- if(vdim->x) vdim->x=dim->x;
- if(vdim->y) vdim->y=dim->y;
- if(vdim->z) vdim->z=dim->z;
- moldyn->volume*=(scale*scale*scale);
-
- /* check whether we need a new linkcell init */
- if((dim->x/moldyn->cutoff!=lc->nx)||
- (dim->y/moldyn->cutoff!=lc->ny)||
- (dim->z/moldyn->cutoff!=lc->nx)) {
- link_cell_shutdown(moldyn);
- link_cell_init(moldyn);
- }
+ //moldyn->px=2.0*moldyn->ekinx+moldyn->vir.xx;
+ //moldyn->px/=moldyn->volume;
+ //moldyn->py=2.0*moldyn->ekiny+moldyn->vir.yy;
+ //moldyn->py/=moldyn->volume;
+ //moldyn->pz=2.0*moldyn->ekinz+moldyn->vir.zz;
+ //moldyn->pz/=moldyn->volume;
- return 0;
+ /* pressure (absolute coordinates) */
+ //moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+ //moldyn->gp/=(3.0*moldyn->volume);
+ return moldyn->p;
}
-double get_e_kin(t_moldyn *moldyn) {
-
- int i;
- t_atom *atom;
+int average_reset(t_moldyn *moldyn) {
- atom=moldyn->atom;
- moldyn->ekin=0.0;
+ printf("[moldyn] average reset\n");
- for(i=0;i<moldyn->count;i++)
- moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ /* update skip value */
+ moldyn->avg_skip=moldyn->total_steps;
- return moldyn->ekin;
-}
+ /* kinetic energy */
+ moldyn->k_sum=0.0;
+ moldyn->k2_sum=0.0;
+
+ /* potential energy */
+ moldyn->v_sum=0.0;
+ moldyn->v2_sum=0.0;
-double update_e_kin(t_moldyn *moldyn) {
+ /* temperature */
+ moldyn->t_sum=0.0;
- return(get_e_kin(moldyn));
-}
+ /* virial */
+ moldyn->virial_sum=0.0;
+ //moldyn->gv_sum=0.0;
-double get_total_energy(t_moldyn *moldyn) {
+ /* pressure */
+ moldyn->p_sum=0.0;
+ //moldyn->gp_sum=0.0;
+ moldyn->tp_sum=0.0;
- return(moldyn->ekin+moldyn->energy);
+ return 0;
}
-t_3dvec get_total_p(t_moldyn *moldyn) {
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
- t_3dvec p,p_total;
- int i;
- t_atom *atom;
+ int denom;
- atom=moldyn->atom;
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
- v3_zero(&p_total);
- for(i=0;i<moldyn->count;i++) {
- v3_scale(&p,&(atom[i].v),atom[i].mass);
- v3_add(&p_total,&p_total,&p);
- }
+ denom=moldyn->total_steps+1-moldyn->avg_skip;
- return p_total;
-}
+ /* assume up to date energies, temperature, pressure etc */
-double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+ /* 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);
- double tau;
+ /* 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);
- /* nn_dist is the nearest neighbour distance */
+ /* temperature */
+ moldyn->t_sum+=moldyn->t;
+ moldyn->t_avg=moldyn->t_sum/denom;
- tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+ /* 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 tau;
+ return 0;
}
-/*
- * numerical tricks
- */
-
-/* linked list / cell method */
-
-int link_cell_init(t_moldyn *moldyn) {
+int get_heat_capacity(t_moldyn *moldyn) {
- t_linkcell *lc;
- int i;
+ double temp2,ighc;
- lc=&(moldyn->lc);
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
- /* 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;
+ /* (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);
- lc->cells=lc->nx*lc->ny*lc->nz;
- lc->subcell=malloc(lc->cells*sizeof(t_list));
+ /* ideal gas contribution */
+ ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+ printf(" ideal gas contribution: %f\n",
+ ighc/moldyn->mass*KILOGRAM/JOULE);
- if(lc->cells<27)
- printf("[moldyn] FATAL: less then 27 subcells!\n");
+ /* specific heat for nvt ensemble */
+ moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt/=moldyn->mass;
- printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ /* 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;
- for(i=0;i<lc->cells;i++)
- list_init_f(&(lc->subcell[i]));
+ 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)));
- link_cell_update(moldyn);
-
return 0;
}
-int link_cell_update(t_moldyn *moldyn) {
-
- int count,i,j,k;
- int nx,ny;
- t_atom *atom;
- t_linkcell *lc;
- double x,y,z;
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
- atom=moldyn->atom;
- lc=&(moldyn->lc);
+ t_3dvec dim;
+ //t_3dvec *tp;
+ double h,dv;
+ double y0,y1;
+ double su,sd;
+ t_atom *store;
- nx=lc->nx;
- ny=lc->ny;
+ /*
+ * dU = - p dV
+ *
+ * => p = - dU/dV
+ *
+ */
+
+ /* store atomic configuration + dimension */
+ store=malloc(moldyn->count*sizeof(t_atom));
+ if(store==NULL) {
+ printf("[moldyn] allocating store mem failed\n");
+ return -1;
+ }
+ 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,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);
+ 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,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);
+ y0=moldyn->energy;
+
+ /* calculate pressure */
+ moldyn->tp=-(y1-y0)/(2.0*dv);
+
+ /* restore atomic configuration */
+ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+ moldyn->dim=dim;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ //potential_force_calc(moldyn);
+
+ /* free store buffer */
+ if(store)
+ free(store);
+
+ return moldyn->tp;
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+ return moldyn->p;
+
+}
+
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
+
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ if(dir==SCALE_UP)
+ scale=1.0+scale;
+
+ if(dir==SCALE_DOWN)
+ scale=1.0-scale;
+
+ if(x) dim->x*=scale;
+ if(y) dim->y*=scale;
+ if(z) dim->z*=scale;
+
+ return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
+
+ int i;
+ t_3dvec *r;
+
+ if(dir==SCALE_UP)
+ scale=1.0+scale;
+
+ if(dir==SCALE_DOWN)
+ scale=1.0-scale;
+
+ for(i=0;i<moldyn->count;i++) {
+ r=&(moldyn->atom[i].r);
+ if(x) r->x*=scale;
+ if(y) r->y*=scale;
+ if(z) r->z*=scale;
+ }
+
+ return 0;
+}
+
+int scale_atoms_ind(t_moldyn *moldyn,double x,double y,double z) {
+
+ int i;
+ t_3dvec *r;
+
+ for(i=0;i<moldyn->count;i++) {
+ r=&(moldyn->atom[i].r);
+ r->x*=x;
+ r->y*=y;
+ r->z*=z;
+ }
+
+ return 0;
+}
+
+int scale_dim_ind(t_moldyn *moldyn,double x,double y,double z) {
+
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ dim->x*=x;
+ dim->y*=y;
+ dim->z*=z;
+
+ return 0;
+}
+
+int scale_volume(t_moldyn *moldyn) {
+
+ t_3dvec *dim,*vdim;
+ double scale;
+ t_linkcell *lc;
+ //double sx,sy,sz;
+
+ vdim=&(moldyn->vis.dim);
+ dim=&(moldyn->dim);
+ lc=&(moldyn->lc);
+
+ /* scaling factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+ scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc*moldyn->tau;
+ scale=pow(scale,ONE_THIRD);
+ }
+ else {
+ scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+ }
+
+
+ /*
+ sx=1.0-(moldyn->p_ref-moldyn->px)*moldyn->p_tc*moldyn->tau;
+ sy=1.0-(moldyn->p_ref-moldyn->py)*moldyn->p_tc*moldyn->tau;
+ sz=1.0-(moldyn->p_ref-moldyn->pz)*moldyn->p_tc*moldyn->tau;
+ sx=pow(sx,ONE_THIRD);
+ sy=pow(sy,ONE_THIRD);
+ sz=pow(sz,ONE_THIRD);
+ */
+
+ /* scale the atoms and dimensions */
+ scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+ //scale_atoms_ind(moldyn,sx,sy,sz);
+ //scale_dim_ind(moldyn,sx,sy,sz);
+
+ /* visualize dimensions */
+ if(vdim->x!=0) {
+ vdim->x=dim->x;
+ vdim->y=dim->y;
+ vdim->z=dim->z;
+ }
+
+ /* recalculate scaled volume */
+ moldyn->volume=dim->x*dim->y*dim->z;
+
+ /* adjust/reinit linkcell */
+ if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+ ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+ ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ } else {
+ lc->x*=scale;
+ lc->y*=scale;
+ lc->z*=scale;
+ //lc->x*=sx;
+ //lc->y*=sx;
+ //lc->z*=sy;
+ }
+
+ return 0;
+
+}
+
+double e_kin_calc(t_moldyn *moldyn) {
+
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ moldyn->ekin=0.0;
+ //moldyn->ekinx=0.0;
+ //moldyn->ekiny=0.0;
+ //moldyn->ekinz=0.0;
+
+ 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;
+ //moldyn->ekinx+=0.5*atom[i].mass*atom[i].v.x*atom[i].v.x;
+ //moldyn->ekiny+=0.5*atom[i].mass*atom[i].v.y*atom[i].v.y;
+ //moldyn->ekinz+=0.5*atom[i].mass*atom[i].v.z*atom[i].v.z;
+ }
+
+ return moldyn->ekin;
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+ return(moldyn->ekin+moldyn->energy);
+}
+
+t_3dvec get_total_p(t_moldyn *moldyn) {
+
+ t_3dvec p,p_total;
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ v3_zero(&p_total);
+ for(i=0;i<moldyn->count;i++) {
+ v3_scale(&p,&(atom[i].v),atom[i].mass);
+ v3_add(&p_total,&p_total,&p);
+ }
+
+ return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
- x=moldyn->dim.x/2;
- y=moldyn->dim.y/2;
- z=moldyn->dim.z/2;
+ double tau;
+
+ /* nn_dist is the nearest neighbour distance */
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+
+ return tau;
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
+
+ t_linkcell *lc;
+#ifndef LOWMEM_LISTS
+ int i;
+#endif
+
+ lc=&(moldyn->lc);
+
+ /* 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;
+ lc->cells=lc->nx*lc->ny*lc->nz;
+
+#ifdef STATIC_LISTS
+ lc->subcell=malloc(lc->cells*sizeof(int*));
+#elif LOWMEM_LISTS
+ lc->subcell=malloc(sizeof(t_lowmem_list));
+#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! (%d)\n",
+ lc->cells);
+
+ if(vol) {
+#ifdef STATIC_LISTS
+ printf("[moldyn] initializing 'static' linked cells (%d)\n",
+ lc->cells);
+#elif LOWMEM_LISTS
+ printf("[moldyn] initializing 'lowmem' 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);
+ */
+ }
+#elif LOWMEM_LISTS
+ lc->subcell->head=malloc(lc->cells*sizeof(int));
+ if(lc->subcell->head==NULL) {
+ perror("[moldyn] head init (malloc)");
+ return -1;
+ }
+ lc->subcell->list=malloc(moldyn->count*sizeof(int));
+ if(lc->subcell->list==NULL) {
+ perror("[moldyn] list init (malloc)");
+ return -1;
+ }
+#else
+ for(i=0;i<lc->cells;i++)
+ list_init_f(&(lc->subcell[i]));
+#endif
+
+ /* update the list */
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,nxy;
+ t_atom *atom;
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int p;
+#elif LOWMEM_LISTS
+ int p;
+#endif
+
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ nxy=nx*lc->ny;
for(i=0;i<lc->cells;i++)
+#ifdef STATIC_LISTS
+ memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#elif LOWMEM_LISTS
+ lc->subcell->head[i]=-1;
+#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);
- list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+
+#ifdef STATIC_LISTS
+ p=0;
+ while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
+ p++;
+
+ if(p>=MAX_ATOMS_PER_LIST) {
+ printf("[moldyn] FATAL: amount of atoms too high!\n");
+ return -1;
+ }
+
+ lc->subcell[i+j*nx+k*nxy][p]=count;
+#elif LOWMEM_LISTS
+ p=i+j*nx+k*nxy;
+ lc->subcell->list[count]=lc->subcell->head[p];
+ lc->subcell->head[p]=count;
+#else
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nxy]),
&(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
+#elif LOWMEM_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);
+
+#ifndef LOWMEM_LISTS
cell[0]=lc->subcell[i+j*nx+k*a];
+#else
+ cell[0]=lc->subcell->head[i+j*nx+k*a];
+#endif
for(ci=-1;ci<=1;ci++) {
bx=0;
x=i+ci;
}
if(!(ci|cj|ck)) continue;
if(bx|by|bz) {
+#ifndef LOWMEM_LISTS
cell[--count2]=lc->subcell[x+y*nx+z*a];
+#else
+ cell[--count2]=lc->subcell->head[x+y*nx+z*a];
+#endif
+
}
else {
+#ifndef LOWMEM_LISTS
cell[count1++]=lc->subcell[x+y*nx+z*a];
+#else
+ cell[count1++]=lc->subcell->head[x+y*nx+z*a];
+#endif
}
}
}
int link_cell_shutdown(t_moldyn *moldyn) {
+#ifndef LOWMEM_LISTS
int i;
+#endif
t_linkcell *lc;
lc=&(moldyn->lc);
- for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_destroy_f(&(moldyn->lc.subcell[i]));
+#if LOWMEM_LISTS
+ free(lc->subcell->head);
+ free(lc->subcell->list);
+
+#else
+
+ 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
+ }
+#endif
free(lc->subcell);
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- unsigned int e,m,s,v;
- t_3dvec p;
+ unsigned int e,m,s,v,p,t,a;
+ 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;
+
+#ifdef VISUAL_THREAD
+ u8 first,change;
+ pthread_t io_thread;
+ int ret;
+ t_moldyn md_copy;
+ t_atom *atom_copy;
+
+ first=1;
+ change=0;
+#endif
sched=&(moldyn->schedule);
atom=moldyn->atom;
/* initialize linked cell method */
- link_cell_init(moldyn);
+ 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);
/* calculate initial forces */
potential_force_calc(moldyn);
+#ifdef DEBUG
+//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");
- 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: cutoff > 0.5 x dim.z\n");
+ if(moldyn->count) {
+ 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");
+ }
/* zero absolute time */
- moldyn->time=0.0;
+ // should have right values!
+ //moldyn->time=0.0;
+ //moldyn->total_steps=0;
/* debugging, ignore */
moldyn->debug=0;
+ /* zero & init moldyn copy */
+#ifdef VISUAL_THREAD
+ memset(&md_copy,0,sizeof(t_moldyn));
+ atom_copy=malloc(moldyn->count*sizeof(t_atom));
+ if(atom_copy==NULL) {
+ perror("[moldyn] malloc atom copy (init)");
+ return -1;
+ }
+#endif
+
+#ifdef PTHREADS
+ printf("##################\n");
+ printf("# USING PTHREADS #\n");
+ printf("##################\n");
+#endif
/* tell the world */
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++) {
/* integration step */
moldyn->integrate(moldyn);
+ /* calculate kinetic energy, temperature and pressure */
+ e_kin_calc(moldyn);
+ temperature_calc(moldyn);
+ virial_sum(moldyn);
+ pressure_calc(moldyn);
+#ifdef PDEBUG
+ thermodynamic_pressure_calc(moldyn);
+ printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
+ moldyn->tp/BAR);
+#endif
+
+ /* calculate fluctuations + averages */
+ average_and_fluctuation_calc(moldyn);
+
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
scale_volume(moldyn);
/* check for log & visualization */
-//double ax;
-//double ao;
-//double av;
if(e) {
- if(!(i%e))
-//ao=sqrt(0.1/M_SI);
-//ax=((0.28-0.25)*sqrt(3)*LC_SI/2)*cos(ao*i);
-//av=ao*(0.28-0.25)*sqrt(3)*LC_SI/2*sin(ao*i);
- update_e_kin(moldyn);
+ if(!(moldyn->total_steps%e))
dprintf(moldyn->efd,
- "%f %f %f %f\n",
- moldyn->time,moldyn->ekin,
- moldyn->energy,
- get_total_energy(moldyn));
-//moldyn->atom[0].r.x,ax,av*av*M_SI,0.1*ax*ax,av*av*M_SI+0.1*ax*ax);
+ "%f %f %f %f %f %f\n",
+ moldyn->time,moldyn->ekin/energy_scale,
+ moldyn->energy/energy_scale,
+ get_total_energy(moldyn)/energy_scale,
+ moldyn->ekin/EV,moldyn->energy/EV);
}
if(m) {
- if(!(i%m)) {
- p=get_total_p(moldyn);
+ if(!(moldyn->total_steps%m)) {
+ momentum=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%f %f\n",moldyn->time,v3_norm(&p));
+ "%f %f %f %f %f\n",moldyn->time,
+ momentum.x,momentum.y,momentum.z,
+ v3_norm(&momentum));
+ }
+ }
+ if(p) {
+ if(!(moldyn->total_steps%p)) {
+ dprintf(moldyn->pfd,
+ "%f %f %f %f %f %f %f\n",moldyn->time,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->tp/BAR,moldyn->tp_avg/BAR);
+ }
+ }
+ if(t) {
+ if(!(moldyn->total_steps%t)) {
+ dprintf(moldyn->tfd,
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->t_avg);
+ }
+ }
+ if(v) {
+ if(!(moldyn->total_steps%v)) {
+ dprintf(moldyn->vfd,
+ "%f %f %f %f %f\n",moldyn->time,
+ moldyn->volume,
+ moldyn->dim.x,
+ moldyn->dim.y,
+ moldyn->dim.z);
}
}
if(s) {
- if(!(i%s)) {
- snprintf(dir,128,"%s/s-%07.f.save",
+ if(!(moldyn->total_steps%s)) {
+ snprintf(dir,128,"%s/s-%08.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);
- printf("\rsched: %d, steps: %d, debug: %d",
- sched->count,i,moldyn->debug);
- fflush(stdout);
+ if(a) {
+ if(!(moldyn->total_steps%a)) {
+#ifdef VISUAL_THREAD
+ /* check whether thread has not terminated yet */
+ if(!first) {
+ ret=pthread_join(io_thread,NULL);
+ }
+ first=0;
+ /* prepare and start thread */
+ if(moldyn->count!=md_copy.count) {
+ free(atom_copy);
+ change=1;
+ }
+ memcpy(&md_copy,moldyn,sizeof(t_moldyn));
+ if(change) {
+ atom_copy=malloc(moldyn->count*sizeof(t_atom));
+ if(atom_copy==NULL) {
+ perror("[moldyn] malloc atom copy (change)");
+ return -1;
+ }
+ }
+ md_copy.atom=atom_copy;
+ memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
+ change=0;
+ ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
+ if(ret) {
+ perror("[moldyn] create visual atoms thread\n");
+ return -1;
+ }
+#else
+ visual_atoms(moldyn);
+#endif
}
}
- /* increase absolute time */
- moldyn->time+=moldyn->tau;
+ /* display progress */
+#ifndef PDEBUG
+ if(!(i%10)) {
+#endif
+ /* get current time */
+ gettimeofday(&t2,NULL);
+
+printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
+ sched->count,i,moldyn->total_steps,
+ moldyn->t,moldyn->t_avg,
+#ifndef PDEBUG
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+#else
+ moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
+#endif
+ moldyn->volume,
+ (int)(t2.tv_sec-t1.tv_sec));
+
+ fflush(stdout);
+
+ /* copy over time */
+ t1=t2;
+#ifndef PDEBUG
+ }
+#endif
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+ moldyn->total_steps+=1;
}
/* 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;
+
+ }
+
+ /* writing a final save file! */
+ if(s) {
+ snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
+ 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));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ }
+ /* writing a final visual file! */
+ if(a)
+ visual_atoms(moldyn);
+
+ return 0;
+}
+
+/* basis trafo */
+
+#define FORWARD 0
+#define BACKWARD 1
+int basis_trafo(t_3dvec *r,u8 dir,double z,double x) {
+
+ t_3dvec tmp;
+
+ if(dir==FORWARD) {
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(z)*tmp.x-sin(z)*tmp.y;
+ r->y=sin(z)*tmp.x+cos(z)*tmp.y;
+ }
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(x)*tmp.y-sin(x)*tmp.z;
+ r->z=sin(x)*tmp.y+cos(x)*tmp.z;
+ }
+ }
+ else {
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(-x)*tmp.y-sin(-x)*tmp.z;
+ r->z=sin(-x)*tmp.y+cos(-x)*tmp.z;
+ }
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(-z)*tmp.x-sin(-z)*tmp.y;
+ r->y=sin(-z)*tmp.x+cos(-z)*tmp.y;
+ }
}
return 0;
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;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ }
+
+#ifndef QUENCH
v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
+#endif
v3_scale(&delta,&(atom[i].f),h*tau_square);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ //check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
check_per_bound(moldyn,&(atom[i].r));
/* velocities [actually v(t+tau/2)] */
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+ /* criticial check */
+ moldyn_bc_check(moldyn);
+
/* neighbour list update */
link_cell_update(moldyn);
/* forces depending on chosen potential */
- potential_force_calc(moldyn);
+#ifndef ALBE_FAST
+ // if albe, use albe force calc routine
+ //if(moldyn->func3b_j1==albe_mult_3bp_j1)
+ // albe_potential_force_calc(moldyn);
+ //else
+ potential_force_calc(moldyn);
+#else
+ albe_potential_force_calc(moldyn);
+#endif
for(i=0;i<count;i++) {
+ /* check whether fixed atom */
+ if(atom[i].attr&ATOM_ATTR_FP)
+ continue;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ }
+
/* 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;
+#elif LOWMEM_LISTS
+ int neighbour_i[27];
+ int p,q;
+#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;
- moldyn->vt2=0.0;
-
- /* get energy and force of every atom */
+ /* reset global virial */
+ memset(&(moldyn->gvir),0,sizeof(t_virial));
+
+ /* reset force, site energy and virial of every atom */
+#ifdef PARALLEL
+ i=omp_get_thread_num();
+ #pragma omp parallel for private(virial)
+#endif
for(i=0;i<count;i++) {
/* reset force */
v3_zero(&(itom[i].f));
- /* reset viral of atom i */
- virial=&(itom[i].virial);
+ /* reset virial */
+ virial=(&(itom[i].virial));
virial->xx=0.0;
virial->yy=0.0;
virial->zz=0.0;
virial->xy=0.0;
virial->xz=0.0;
virial->yz=0.0;
- moldyn->vt1=0.0;
-
+
/* reset site energy */
itom[i].e=0.0;
+ }
+
+ /* get energy, force and virial of every atom */
+
+ /* first (and only) loop over atoms i */
+ for(i=0;i<count;i++) {
+
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
- moldyn->func1b(moldyn,&(itom[i]));
+ if(moldyn->func_i0)
+ moldyn->func_i0(moldyn,&(itom[i]));
if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
continue;
dnlc=lc->dnlc;
+#ifndef STATIC_LISTS
+ /* check for later 3 body interaction */
+ if(itom[i].attr&ATOM_ATTR_3BP)
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
+
+ /* first loop over atoms j */
+ if(moldyn->func_j0) {
+ for(j=0;j<27;j++) {
+
+ bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour_i[j][p]!=-1) {
+
+ jtom=&(atom[neighbour_i[j][p]]);
+ p++;
+#elif LOWMEM_LISTS
+ p=neighbour_i[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
+#else
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+ jtom=this->current->data;
+#endif
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ /* reset 3bp run */
+ moldyn->run3bp=1;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func_j0(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+
+ /* 3 body potential/force */
+
+ /* in j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(moldyn->func_j0_k0==NULL)
+ continue;
+
+ /* first loop over atoms k in first j loop */
+ 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;
+
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ //if(ktom==jtom)
+ // continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func_j0_k0(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
+ }
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+
+ }
+ }
+
+ /* continued 3 body potential/force */
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* copy the neighbour lists */
+#ifdef STATIC_LISTS
+ /* no copy needed for static lists */
+#elif LOWMEM_LISTS
+ /* no copy needed for lowmem 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]!=-1) {
+
+ jtom=&(atom[neighbour_i[j][p]]);
+ p++;
+#elif LOWMEM_LISTS
+ p=neighbour_i[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[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;
- if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
- }
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- /* 3 body potential/force */
+ /* reset 3bp run */
+ moldyn->run3bp=1;
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
- continue;
+ if(moldyn->func_j1)
+ moldyn->func_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ /* in j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ /* first loop over atoms k in second j loop */
+ if(moldyn->func_j1_k0) {
- /* get neighbours of i */
for(k=0;k<27;k++) {
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
+
+ while(neighbour_i[k][q]!=-1) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#elif LOWMEM_LISTS
+ q=neighbour_i[k];
+
+ while(q!=-1) {
+
+ ktom=&(itom[q]);
+ q=lc->subcell->list[q];
+#else
that=&(neighbour_i2[k]);
list_reset_f(that);
if(that->start==NULL)
continue;
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ //if(ktom==jtom)
+ // continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func3b_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+#endif
+
+ }
+
+ }
+
+ /* continued j loop after first k loop */
+ if(moldyn->func_j1c)
+ moldyn->func_j1c(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+ /* second loop over atoms k */
+ if(moldyn->func_j1_k1) {
+
+ for(k=0;k<27;k++) {
+
bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
- do {
+ while(neighbour_i[k][q]!=-1) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#elif LOWMEM_LISTS
+ q=neighbour_i[k];
+
+ while(q!=-1) {
+
+ ktom=&(itom[q]);
+ q=lc->subcell->list[q];
+#else
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
+ do {
ktom=that->current->data;
+#endif
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func3b(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func_j1_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
+#endif
+ }
+
}
- /* 2bp post function */
- if(moldyn->func2b_post) {
- moldyn->func2b_post(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ /* finish of j loop after second k loop */
+ if(moldyn->func_j1e) {
+ moldyn->func_j1e(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
}
-
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
}
- }
-#ifdef DEBUG
-printf("\n\n");
-#endif
-#ifdef VDEBUG
-printf("\n\n");
-#endif
+#ifdef DEBUG
+ //printf("\n\n");
+#endif
+#ifdef VDEBUG
+ printf("\n\n");
+#endif
+
+ }
+
+#ifdef DEBUG
+ //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
+
+ /* some postprocessing */
+#ifdef PARALLEL
+ #pragma omp parallel for
+#endif
+ for(i=0;i<count;i++) {
+ /* 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;
+}
+
+/*
+ * virial calculation
+ */
+
+//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+ a->virial.xx+=f->x*d->x;
+ a->virial.yy+=f->y*d->y;
+ a->virial.zz+=f->z*d->z;
+ a->virial.xy+=f->x*d->y;
+ a->virial.xz+=f->x*d->z;
+ a->virial.yz+=f->y*d->z;
+
+ return 0;
+}
+
+/*
+ * periodic boundary checking
+ */
+
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+
+ double x,y,z;
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
+
+ if(moldyn->status&MOLDYN_STAT_PBX) {
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
+ }
+
+ return 0;
+}
+
+int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a) {
+
+ double x,y,z;
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
+
+ if(moldyn->status&MOLDYN_STAT_PBX) {
+ if(a->r.x>=x) {
+ a->pbc[0]+=1;
+ a->r.x-=dim->x;
+ }
+ else if(-a->r.x>x) {
+ a->pbc[0]-=1;
+ a->r.x+=dim->x;
+ }
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->r.y>=y) {
+ a->pbc[1]+=1;
+ a->r.y-=dim->y;
+ }
+ else if(-a->r.y>y) {
+ a->pbc[1]-=1;
+ a->r.y+=dim->y;
+ }
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->r.z>=z) {
+ a->pbc[2]+=1;
+ a->r.z-=dim->z;
+ }
+ else if(-a->r.z>z) {
+ a->pbc[2]-=1;
+ a->r.z+=dim->z;
+ }
+ }
+
+ return 0;
+}
+
+/*
+ * debugging / critical check functions
+ */
+
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+ t_atom *atom;
+ t_3dvec *dim;
+ int i;
+ double x;
+ u8 byte;
+ int j,k;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+ x=dim->x/2;
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
+ printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+ i,atom[i].r.x,dim->x/2);
+ printf("diagnostic:\n");
+ printf("-----------\natom.r.x:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ printf("---------------\nx=dim.x/2:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&x)+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ if(atom[i].r.x==x) printf("the same!\n");
+ else printf("different!\n");
+ }
+ if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+ printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+ i,atom[i].r.y,dim->y/2);
+ if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+ printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+ i,atom[i].r.z,dim->z/2);
+ }
+
+ 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(" modifying 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;
+ }
+
+#ifdef PTHREADS
+ amutex=malloc(moldyn->count*sizeof(pthread_mutex_t));
+ if(amutex==NULL) {
+ perror("[moldyn] load save file (mutexes)");
+ return -1;
+ }
+ for(cnt=0;cnt<moldyn->count;cnt++)
+ pthread_mutex_init(&(amutex[cnt]),NULL);
+#endif
+
+ // 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;
+#elif LOWMEM_LISTS
+ int neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+ t_list *this;
+#endif
+ u8 bc;
+ t_atom *itom,*jtom;
+ int i,j;
+
+ 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]!=-1) {
+
+ jtom=&(moldyn->atom[neighbour[j][p]]);
+ p++;
+#elif LOWMEM_LISTS
+ p=neighbour[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[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
+ }
+#elif LOWMEM_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
+
+ return 0;
+
+}
+
+/*
+ * function to find neighboured atoms
+ */
+
+int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+ int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+ void *data,u8 bc)) {
+
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#elif LOWMEM_LISTS
+ int neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+ t_list *this;
+#endif
+ u8 bc;
+ t_atom *natom;
+ int j;
+
+ lc=&(moldyn->lc);
+
+ /* neighbour indexing */
+ link_cell_neighbour_index(moldyn,
+ (atom->r.x+moldyn->dim.x/2)/lc->x,
+ (atom->r.y+moldyn->dim.y/2)/lc->x,
+ (atom->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;
- moldyn->vt2=0.0;
- for(i=0;i<count;i++)
- moldyn->vt2-=v3_scalar_product(&(itom[i].r),&(itom[i].f));
+ while(neighbour[j][p]!=-1) {
-//printf("compare: vt1: %f vt2: %f\n",moldyn->vt1,moldyn->vt2);
+ natom=&(moldyn->atom[neighbour[j][p]]);
+ p++;
+#elif LOWMEM_LISTS
+ p=neighbour[j];
-//pressure_calc(moldyn);
+ while(p!=-1) {
- return 0;
-}
+ natom=&(moldyn->atom[p]);
+ p=lc->subcell->list[p];
+#else
+ this=&(neighbour[j]);
+ list_reset_f(this);
-/*
- * virial calculation
- */
+ if(this->start==NULL)
+ continue;
+
+ do {
-inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+ natom=this->current->data;
+#endif
+
+ /* process bond */
+ process(moldyn,atom,natom,data,bc);
- a->virial.xx-=f->x*d->x;
- a->virial.yy-=f->y*d->y;
- a->virial.zz-=f->z*d->z;
- a->virial.xy-=f->x*d->y;
- a->virial.xz-=f->x*d->z;
- a->virial.yz-=f->y*d->z;
+#ifdef STATIC_LISTS
+ }
+#elif LOWMEM_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
return 0;
+
}
/*
- * periodic boundayr checking
+ * post processing functions
*/
-inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
-
- double x,y,z;
- t_3dvec *dim;
+int get_line(int fd,char *line,int max) {
- dim=&(moldyn->dim);
+ int count,ret;
- x=dim->x/2;
- y=dim->y/2;
- z=dim->z/2;
+ count=0;
- if(moldyn->status&MOLDYN_STAT_PBX) {
- if(a->x>=x) a->x-=dim->x;
- else if(-a->x>x) a->x+=dim->x;
- }
- if(moldyn->status&MOLDYN_STAT_PBY) {
- if(a->y>=y) a->y-=dim->y;
- else if(-a->y>y) a->y+=dim->y;
- }
- if(moldyn->status&MOLDYN_STAT_PBZ) {
- if(a->z>=z) a->z-=dim->z;
- else if(-a->z>z) a->z+=dim->z;
+ while(1) {
+ if(count==max) return count;
+ ret=read(fd,line+count,1);
+ if(ret<=0) return ret;
+ if(line[count]=='\n') {
+ memset(line+count,0,max-count-1);
+ //line[count]='\0';
+ return count+1;
+ }
+ count+=1;
}
+}
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
+
+
return 0;
}
-
-
-/*
- * example potentials
- */
-/* harmonic oscillator potential and force */
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ t_3dvec final_r;
+ double d2;
+ int a_cnt;
+ int b_cnt;
- t_ho_params *params;
- t_3dvec force,distance;
- double d,f;
- double sc,equi_dist;
+ atom=moldyn->atom;
+ dc[0]=0;
+ dc[1]=0;
+ dc[2]=0;
+ a_cnt=0;
+ b_cnt=0;
- params=moldyn->pot2b_params;
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
+ for(i=0;i<moldyn->count;i++) {
- if(ai<aj) return 0;
+ /* care for pb crossing */
+ final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+ final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+ final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+ /* calculate distance */
+ v3_sub(&dist,&final_r,&(atom[i].r_0));
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ dc[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ dc[0]+=d2;
+ }
- v3_sub(&distance,&(aj->r),&(ai->r));
-
- if(bc) check_per_bound(moldyn,&distance);
- d=v3_norm(&distance);
- if(d<=moldyn->cutoff) {
- moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
- /* f = -grad E; grad r_ij = -1 1/r_ij distance */
- f=sc*(1.0-equi_dist/d);
- v3_scale(&force,&distance,f);
- v3_add(&(ai->f),&(ai->f),&force);
- virial_calc(ai,&force,&distance);
- virial_calc(aj,&force,&distance); /* f and d signe switched */
- v3_scale(&force,&distance,-f);
- v3_add(&(aj->f),&(aj->f),&force);
+ 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;
}
-/* lennard jones potential & force for one sort of atoms */
-
-int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_lj_params *params;
- t_3dvec force,distance;
- double d,h1,h2;
- double eps,sig6,sig12;
-
- params=moldyn->pot2b_params;
- eps=params->epsilon4;
- sig6=params->sigma6;
- sig12=params->sigma12;
-
- if(ai<aj) return 0;
-
- v3_sub(&distance,&(aj->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&distance);
- d=v3_absolute_square(&distance); /* 1/r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h2=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
- h2*=d; /* 1/r^8 */
- h1*=d; /* 1/r^14 */
- h2*=6*sig6;
- h1*=12*sig12;
- d=+h1-h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(aj->f),&(aj->f),&force);
- v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
- v3_add(&(ai->f),&(ai->f),&force);
- virial_calc(ai,&force,&distance);
- virial_calc(aj,&force,&distance); /* f and d signe switched */
- moldyn->vt1-=v3_scalar_product(&force,&distance);
+int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ t_3dvec final_r;
+ double d2;
+ int a_cnt;
+ int b_cnt;
+
+ atom=moldyn->atom;
+ msd[0]=0;
+ msd[1]=0;
+ msd[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+ /* care for pb crossing */
+ if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+ printf("[moldyn] msd pb crossings for atom %d\n",i);
+ printf(" x: %d y: %d z: %d\n",
+ atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+ }
+ final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+ final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+ final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+ /* calculate distance */
+ v3_sub(&dist,&final_r,&(atom[i].r_0));
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ msd[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ msd[0]+=d2;
+ }
+
+ msd[2]+=d2;
}
+ msd[0]/=a_cnt;
+ msd[1]/=b_cnt;
+ msd[2]/=moldyn->count;
+
return 0;
}
-/*
- * tersoff potential & force for 2 sorts of atoms
- */
-
-/* create mixed terms from parameters and set them */
-int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
-
- printf("[moldyn] tersoff parameter completion\n");
- p->S2[0]=p->S[0]*p->S[0];
- p->S2[1]=p->S[1]*p->S[1];
- p->Smixed=sqrt(p->S[0]*p->S[1]);
- p->S2mixed=p->Smixed*p->Smixed;
- p->Rmixed=sqrt(p->R[0]*p->R[1]);
- p->Amixed=sqrt(p->A[0]*p->A[1]);
- p->Bmixed=sqrt(p->B[0]*p->B[1]);
- p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
- p->mu_m=0.5*(p->mu[0]+p->mu[1]);
-
- printf("[moldyn] tersoff mult parameter info:\n");
- printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
- printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
- printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
- printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
- printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
- p->lambda_m);
- printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
- printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
- printf(" n | %f | %f\n",p->n[0],p->n[1]);
- printf(" c | %f | %f\n",p->c[0],p->c[1]);
- printf(" d | %f | %f\n",p->d[0],p->d[1]);
- printf(" h | %f | %f\n",p->h[0],p->h[1]);
- printf(" chi | %f \n",p->chi);
+int bonding_analyze(t_moldyn *moldyn,double *cnt) {
return 0;
}
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+ t_atom *jtom,void *data,u8 bc) {
- int brand;
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
-
- brand=ai->brand;
- params=moldyn->pot1b_params;
- exchange=&(params->exchange);
+ t_3dvec dist;
+ double d;
+ int s;
+ t_pcc *pcc;
+
+ /* only count pairs once,
+ * skip same atoms */
+ if(itom->tag>=jtom->tag)
+ return 0;
/*
- * simple: point constant parameters only depending on atom i to
- * their right values
+ * pair correlation calc
*/
- exchange->beta_i=&(params->beta[brand]);
- exchange->n_i=&(params->n[brand]);
- exchange->c_i=&(params->c[brand]);
- exchange->d_i=&(params->d[brand]);
- exchange->h_i=&(params->h[brand]);
+ /* get pcc data */
+ pcc=data;
- exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
- exchange->ci2=params->c[brand]*params->c[brand];
- exchange->di2=params->d[brand]*params->d[brand];
- exchange->ci2di2=exchange->ci2/exchange->di2;
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
- return 0;
-}
-
-/* tersoff 2 body part */
-int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,force;
- double d_ij,d_ij2;
- double A,B,R,S,S2,lambda,mu;
- double f_r,df_r;
- double f_c,df_c;
- int brand;
- double s_r;
- double arg;
-
- params=moldyn->pot2b_params;
- brand=aj->brand;
- exchange=&(params->exchange);
-
- /* clear 3bp and 2bp post run */
- exchange->run3bp=0;
- exchange->run2bp_post=0;
-
- /* reset S > r > R mark */
- exchange->d_ij_between_rs=0;
-
- /*
- * calc of 2bp contribution of V_ij and dV_ij/ji
- *
- * for Vij and dV_ij we need:
- * - f_c_ij, df_c_ij
- * - f_r_ij, df_r_ij
- *
- * for dV_ji we need:
- * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
- * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
- *
- */
+ /* ignore if greater cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
+
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/pcc->dr);
- /* constants */
- if(brand==ai->brand) {
- S=params->S[brand];
- S2=params->S2[brand];
- R=params->R[brand];
- A=params->A[brand];
- B=params->B[brand];
- lambda=params->lambda[brand];
- mu=params->mu[brand];
- exchange->chi=1.0;
+ /* 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;
}
- else {
- S=params->Smixed;
- S2=params->S2mixed;
- R=params->Rmixed;
- A=params->Amixed;
- B=params->Bmixed;
- lambda=params->lambda_m;
- mu=params->mu_m;
- params->exchange.chi=params->chi;
- }
-
- /* dist_ij, d_ij */
- v3_sub(&dist_ij,&(aj->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ij);
- d_ij2=v3_absolute_square(&dist_ij);
-
- /* if d_ij2 > S2 => no force & potential energy contribution */
- if(d_ij2>S2)
- return 0;
- /* now we will need the distance */
- //d_ij=v3_norm(&dist_ij);
- d_ij=sqrt(d_ij2);
-
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
- exchange->d_ij2=d_ij2;
- exchange->dist_ij=dist_ij;
-
- /* more constants */
- exchange->beta_j=&(params->beta[brand]);
- exchange->n_j=&(params->n[brand]);
- exchange->c_j=&(params->c[brand]);
- exchange->d_j=&(params->d[brand]);
- exchange->h_j=&(params->h[brand]);
- if(brand==ai->brand) {
- exchange->betajnj=exchange->betaini;
- exchange->cj2=exchange->ci2;
- exchange->dj2=exchange->di2;
- exchange->cj2dj2=exchange->ci2di2;
+ if(itom->brand!=jtom->brand) {
+ /* mixed */
+ pcc->stat[s]+=1;
}
else {
- exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
- exchange->cj2=params->c[brand]*params->c[brand];
- exchange->dj2=params->d[brand]*params->d[brand];
- exchange->cj2dj2=exchange->cj2/exchange->dj2;
+ /* 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;
}
- /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
- f_r=A*exp(-lambda*d_ij);
- df_r=lambda*f_r/d_ij;
+ 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;
- /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
- exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=mu*exchange->f_a/d_ij;
+ if(pcc.o1*dr<=moldyn->cutoff)
+ printf("[moldyn] WARNING: pcc (low #slots)\n");
- /* f_c, df_c calc (again, same for ij and ji) */
- if(d_ij<R) {
- /* f_c = 1, df_c = 0 */
- f_c=1.0;
- df_c=0.0;
- /* two body contribution (ij, ji) */
- v3_scale(&force,&dist_ij,-df_r);
+ 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 {
- s_r=S-R;
- arg=M_PI*(d_ij-R)/s_r;
- f_c=0.5+0.5*cos(arg);
- df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
- /* two body contribution (ij, ji) */
- v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
- /* tell 3bp that S > r > R */
- exchange->d_ij_between_rs=1;
+ pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+ if(pcc.stat==NULL) {
+ perror("[moldyn] pair correlation malloc");
+ return -1;
+ }
}
- /* add forces of 2bp (ij, ji) contribution
- * dVij = dVji and we sum up both: no 1/2) */
- v3_add(&(ai->f),&(ai->f),&force);
+ memset(pcc.stat,0,3*pcc.o1*sizeof(double));
- /* virial */
- ai->virial.xx-=force.x*dist_ij.x;
- ai->virial.yy-=force.y*dist_ij.y;
- ai->virial.zz-=force.z*dist_ij.z;
- ai->virial.xy-=force.x*dist_ij.y;
- ai->virial.xz-=force.x*dist_ij.z;
- ai->virial.yz-=force.y*dist_ij.z;
+ /* process */
+ process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
+ /* 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;
}
-#endif
- /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
- moldyn->energy+=(0.5*f_r*f_c);
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
- /* save for use in 3bp */
- exchange->f_c=f_c;
- exchange->df_c=df_c;
+ t_ba *ba;
+ t_3dvec dist;
+ double d;
- /* enable the run of 3bp function and 2bp post processing */
- exchange->run3bp=1;
- exchange->run2bp_post=1;
+ if(itom->tag>=jtom->tag)
+ return 0;
- /* reset 3bp sums */
- exchange->zeta_ij=0.0;
- exchange->zeta_ji=0.0;
- v3_zero(&(exchange->dzeta_ij));
- v3_zero(&(exchange->dzeta_ji));
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
- return 0;
-}
+ /* ignore if greater or equal cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
-/* tersoff 2 body post part */
+ /* check for potential bond */
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
-int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ /* now count this bonding ... */
+ ba=data;
- /*
- * here we have to allow for the 3bp sums
- *
- * that is:
- * - zeta_ij, dzeta_ij
- * - zeta_ji, dzeta_ji
- *
- * to compute the 3bp contribution to:
- * - Vij, dVij
- * - dVji
- *
+ /* increase total bond counter
*/
+ ba->tcnt+=1;
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
+ 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;
- t_3dvec force,temp;
- t_3dvec *dist_ij;
- double b,db,tmp;
- double f_c,df_c,f_a,df_a;
- double chi,ni,betaini,nj,betajnj;
- double zeta;
+ return 0;
+}
- params=moldyn->pot2b_params;
- exchange=&(params->exchange);
+int bond_analyze(t_moldyn *moldyn,double *quality) {
- /* we do not run if f_c_ij was detected to be 0! */
- if(!(exchange->run2bp_post))
- return 0;
+ int qcnt4;
+ int qcnt3;
+ int ccnt4;
+ int ccnt3;
+ int bcnt;
+ t_ba ba;
+ int i;
+ t_atom *atom;
- f_c=exchange->f_c;
- df_c=exchange->df_c;
- f_a=exchange->f_a;
- df_a=exchange->df_a;
- betaini=exchange->betaini;
- betajnj=exchange->betajnj;
- ni=*(exchange->n_i);
- nj=*(exchange->n_j);
- chi=exchange->chi;
- dist_ij=&(exchange->dist_ij);
-
- /* Vij and dVij */
- zeta=exchange->zeta_ij;
- if(zeta==0.0) {
- moldyn->debug++; /* just for debugging ... */
- b=chi;
- v3_scale(&force,dist_ij,df_a*b*f_c);
+ ba.acnt=malloc(moldyn->count*sizeof(int));
+ if(ba.acnt==NULL) {
+ perror("[moldyn] bond analyze malloc (a)");
+ return -1;
}
- else {
- tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
- b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
- db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
- b=db*b; /* b_ij */
- db*=-0.5*tmp; /* db_ij */
- v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
- v3_scale(&temp,dist_ij,df_a*b);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,f_c);
- }
- v3_scale(&temp,dist_ij,df_c*b*f_a);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,-0.5);
-
- /* add force */
- v3_add(&(ai->f),&(ai->f),&force);
+ memset(ba.acnt,0,moldyn->count*sizeof(int));
- /* virial */
- ai->virial.xx-=force.x*dist_ij->x;
- ai->virial.yy-=force.y*dist_ij->y;
- ai->virial.zz-=force.z*dist_ij->z;
- ai->virial.xy-=force.x*dist_ij->y;
- ai->virial.xz-=force.x*dist_ij->z;
- ai->virial.yz-=force.y*dist_ij->z;
+ 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));
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
-}
-#endif
+ ba.tcnt=0;
+ qcnt4=0; qcnt3=0;
+ ccnt4=0; ccnt3=0;
+ bcnt=0;
+
+ atom=moldyn->atom;
+
+ process_2b_bonds(moldyn,&ba,bond_analyze_process);
- /* add energy of 3bp sum */
- moldyn->energy+=(0.5*f_c*b*f_a);
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].brand==0) {
+ if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
+ qcnt4+=4;
+ if((ba.acnt[i]==0)&(ba.bcnt[i]==3))
+ qcnt3+=3;
+ }
+ else {
+ if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
+ qcnt4+=4;
+ ccnt4+=1;
+ }
+ if((ba.acnt[i]==3)&(ba.bcnt[i]==0)) {
+ qcnt3+=4;
+ ccnt3+=1;
+ }
+ bcnt+=1;
+ }
+ }
- /* dVji */
- zeta=exchange->zeta_ji;
- if(zeta==0.0) {
- moldyn->debug++;
- b=chi;
- v3_scale(&force,dist_ij,df_a*b*f_c);
+ if(quality) {
+ quality[0]=1.0*ccnt4/bcnt;
+ quality[1]=1.0*ccnt3/bcnt;
}
else {
- tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
- b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
- db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
- b=db*b; /* b_ij */
- db*=-0.5*tmp; /* db_ij */
- v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
- v3_scale(&temp,dist_ij,df_a*b);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,f_c);
- }
- v3_scale(&temp,dist_ij,df_c*b*f_a);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,-0.5);
-
- /* add force */
- v3_add(&(ai->f),&(ai->f),&force);
-
- /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-// TEST ... with a minus instead
- ai->virial.xx-=force.x*dist_ij->x;
- ai->virial.yy-=force.y*dist_ij->y;
- ai->virial.zz-=force.z*dist_ij->z;
- ai->virial.xy-=force.x*dist_ij->y;
- ai->virial.xz-=force.x*dist_ij->z;
- ai->virial.yz-=force.y*dist_ij->z;
+ printf("[moldyn] bond analyze: %f %f\n",
+ 1.0*ccnt4/bcnt,1.0*ccnt3/bcnt);
+ }
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+ return 0;
}
-#endif
+
+/*
+ * visualization code
+ */
+
+int visual_init(t_moldyn *moldyn,char *filebase) {
+
+ strncpy(moldyn->vis.fb,filebase,128);
return 0;
}
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec temp1,temp2;
- t_3dvec *dzeta;
- double R,S,S2,s_r;
- double B,mu;
- double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
- double rr,dd;
- double f_c,df_c;
- double f_c_ik,df_c_ik,arg;
- double f_c_jk;
- double n,c,d,h;
- double c2,d2,c2d2;
- double cos_theta,d_costheta1,d_costheta2;
- double h_cos,d2_h_cos2;
- double frac,g,zeta,chi;
- double tmp;
- int brand;
-
- params=moldyn->pot3b_params;
- exchange=&(params->exchange);
-
- if(!(exchange->run3bp))
+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;
- /*
- * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
- * 2bp contribution of dV_jk
- *
- * for Vij and dV_ij we still need:
- * - b_ij, db_ij (zeta_ij)
- * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
- *
- * for dV_ji we still need:
- * - b_ji, db_ji (zeta_ji)
- * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
- *
- * for dV_jk we need:
- * - f_c_jk
- * - f_a_jk
- * - db_jk (zeta_jk)
- * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
- *
- */
+ 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);
- /*
- * get exchange data
- */
+ return 0;
+}
- /* dist_ij, d_ij - this is < S_ij ! */
- dist_ij=exchange->dist_ij;
- d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
+#ifdef VISUAL_THREAD
+void *visual_atoms(void *ptr) {
+#else
+int visual_atoms(t_moldyn *moldyn) {
+#endif
- /* f_c_ij, df_c_ij (same for ji) */
- f_c=exchange->f_c;
- df_c=exchange->df_c;
+ int i;
+ char file[128+64];
+ t_3dvec dim;
+ double help;
+ t_visual *v;
+ t_atom *atom;
+ t_vb vb;
+ t_3dvec strain;
+#ifdef VISUAL_THREAD
+ t_moldyn *moldyn;
- /*
- * calculate unknown values now ...
- */
+ moldyn=ptr;
+#endif
- /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+ v=&(moldyn->vis);
+ dim.x=v->dim.x;
+ dim.y=v->dim.y;
+ dim.z=v->dim.z;
+ atom=moldyn->atom;
- /* dist_ik, d_ik */
- v3_sub(&dist_ik,&(ak->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik2=v3_absolute_square(&dist_ik);
+ help=(dim.x+dim.y);
- /* ik constants */
- brand=ai->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- }
-
- /* zeta_ij/dzeta_ij contribution only for d_ik < S */
- if(d_ik2<S2) {
-
- /* now we need d_ik */
- d_ik=sqrt(d_ik2);
-
- /* get constants_i from exchange data */
- n=*(exchange->n_i);
- c=*(exchange->c_i);
- d=*(exchange->d_i);
- h=*(exchange->h_i);
- c2=exchange->ci2;
- d2=exchange->di2;
- c2d2=exchange->ci2di2;
-
- /* cosine of theta_ijk by scalaproduct */
- rr=v3_scalar_product(&dist_ij,&dist_ik);
- dd=d_ij*d_ik;
- cos_theta=rr/dd;
-
- /* d_costheta */
- tmp=1.0/dd;
- d_costheta1=cos_theta/d_ij2-tmp;
- d_costheta2=cos_theta/d_ik2-tmp;
-
- /* some usefull values */
- h_cos=(h-cos_theta);
- d2_h_cos2=d2+(h_cos*h_cos);
- frac=c2/(d2_h_cos2);
-
- /* g(cos_theta) */
- g=1.0+c2d2-frac;
-
- /* d_costheta_ij and dg(cos_theta) - needed in any case! */
- v3_scale(&temp1,&dist_ij,d_costheta1);
- v3_scale(&temp2,&dist_ik,d_costheta2);
- v3_add(&temp1,&temp1,&temp2);
- v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
-
- /* f_c_ik & df_c_ik + {d,}zeta contribution */
- dzeta=&(exchange->dzeta_ij);
- if(d_ik<R) {
- /* {d,}f_c_ik */
- // => f_c_ik=1.0;
- // => df_c_ik=0.0; of course we do not set this!
-
- /* zeta_ij */
- exchange->zeta_ij+=g;
-
- /* dzeta_ij */
- v3_add(dzeta,dzeta,&temp1);
- }
- else {
- /* {d,}f_c_ik */
- s_r=S-R;
- arg=M_PI*(d_ik-R)/s_r;
- f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
-
- /* zeta_ij */
- exchange->zeta_ij+=f_c_ik*g;
-
- /* dzeta_ij */
- v3_scale(&temp1,&temp1,f_c_ik);
- v3_scale(&temp2,&dist_ik,g*df_c_ik);
- v3_add(&temp1,&temp1,&temp2);
- v3_add(dzeta,dzeta,&temp1);
- }
+ sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
+ vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+ if(vb.fd<0) {
+ perror("open visual save file fd");
+#ifndef VISUAL_THREAD
+ return -1;
+#endif
}
- /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+ /* write the actual data file */
- /* dist_jk, d_jk */
- v3_sub(&dist_jk,&(ak->r),&(aj->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk2=v3_absolute_square(&dist_jk);
+ // povray header
+ dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
+ moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
- /* jk constants */
- brand=aj->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- B=params->B[brand];
- mu=params->mu[brand];
- chi=1.0;
+ // atomic configuration
+ for(i=0;i<moldyn->count;i++) {
+ v3_sub(&strain,&(atom[i].r),&(atom[i].r_0));
+ check_per_bound(moldyn,&strain);
+ // atom type, positions, color and kinetic energy
+ 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);
+ sqrt(v3_absolute_square(&strain)));
+ }
+
+ // bonds between atoms
+#ifndef VISUAL_THREAD
+ process_2b_bonds(moldyn,&vb,visual_bonds_process);
+#endif
+
+ // boundaries
+ if(dim.x) {
+ 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(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(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(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(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(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(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(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(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(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(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(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);
}
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- B=params->Bmixed;
- mu=params->mu_m;
- chi=params->chi;
- }
-
- /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
- if(d_jk2<S2) {
-
- /* now we need d_ik */
- d_jk=sqrt(d_jk2);
-
- /* constants_j from exchange data */
- n=*(exchange->n_j);
- c=*(exchange->c_j);
- d=*(exchange->d_j);
- h=*(exchange->h_j);
- c2=exchange->cj2;
- d2=exchange->dj2;
- c2d2=exchange->cj2dj2;
-
- /* cosine of theta_jik by scalaproduct */
- rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
- dd=d_ij*d_jk;
- cos_theta=rr/dd;
-
- /* d_costheta */
- d_costheta1=1.0/dd;
- d_costheta2=cos_theta/d_ij2;
-
- /* some usefull values */
- h_cos=(h-cos_theta);
- d2_h_cos2=d2+(h_cos*h_cos);
- frac=c2/(d2_h_cos2);
-
- /* g(cos_theta) */
- g=1.0+c2d2-frac;
-
- /* d_costheta_jik and dg(cos_theta) - needed in any case! */
- v3_scale(&temp1,&dist_jk,d_costheta1);
- v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
- //v3_add(&temp1,&temp1,&temp2);
- v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
- v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
-
- /* store dg in temp2 and use it for dVjk later */
- v3_copy(&temp2,&temp1);
-
- /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
- dzeta=&(exchange->dzeta_ji);
- if(d_jk<R) {
- /* f_c_jk */
- f_c_jk=1.0;
-
- /* zeta_ji */
- exchange->zeta_ji+=g;
-
- /* dzeta_ji */
- v3_add(dzeta,dzeta,&temp1);
- }
- else {
- /* f_c_jk */
- s_r=S-R;
- arg=M_PI*(d_jk-R)/s_r;
- f_c_jk=0.5+0.5*cos(arg);
-
- /* zeta_ji */
- exchange->zeta_ji+=f_c_jk*g;
- /* dzeta_ji */
- v3_scale(&temp1,&temp1,f_c_jk);
- v3_add(dzeta,dzeta,&temp1);
- }
+ close(vb.fd);
- /* dV_jk stuff | add force contribution on atom i immediately */
- if(exchange->d_ij_between_rs) {
- zeta=f_c*g;
- v3_scale(&temp1,&temp2,f_c);
- v3_scale(&temp2,&dist_ij,df_c*g);
- v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
- }
- else {
- zeta=g;
- // dzeta_jk is simply dg, which is stored in temp2
- }
- /* betajnj * zeta_jk ^ nj-1 */
- tmp=exchange->betajnj*pow(zeta,(n-1.0));
- tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
- v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
- v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
- /* scaled with 0.5 ^ */
-
- /* virial */
- ai->virial.xx-=temp2.x*dist_jk.x;
- ai->virial.yy-=temp2.y*dist_jk.y;
- ai->virial.zz-=temp2.z*dist_jk.z;
- ai->virial.xy-=temp2.x*dist_jk.y;
- ai->virial.xz-=temp2.x*dist_jk.z;
- ai->virial.yz-=temp2.y*dist_jk.z;
+#ifdef VISUAL_THREAD
+ pthread_exit(NULL);
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x,ai->f.x);
- printf("%f | %f\n",temp2.y,ai->f.y);
- printf("%f | %f\n",temp2.z,ai->f.z);
}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
- printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
- printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
-}
-#endif
-
- }
+#else
return 0;
}
-
+#endif
/*
- * debugging / critical check functions
+ * fpu cntrol functions
*/
-int moldyn_bc_check(t_moldyn *moldyn) {
+// set rounding to double (eliminates -ffloat-store!)
+int fpu_set_rtd(void) {
- t_atom *atom;
- t_3dvec *dim;
- int i;
- double x;
- u8 byte;
- int j,k;
+ fpu_control_t ctrl;
- atom=moldyn->atom;
- dim=&(moldyn->dim);
- x=dim->x/2;
+ _FPU_GETCW(ctrl);
- for(i=0;i<moldyn->count;i++) {
- if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
- printf("FATAL: atom %d: x: %.20f (%.20f)\n",
- i,atom[i].r.x,dim->x/2);
- printf("diagnostic:\n");
- printf("-----------\natom.r.x:\n");
- for(j=0;j<8;j++) {
- memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
- for(k=0;k<8;k++)
- printf("%d%c",
- ((byte)&(1<<k))?1:0,
- (k==7)?'\n':'|');
- }
- printf("---------------\nx=dim.x/2:\n");
- for(j=0;j<8;j++) {
- memcpy(&byte,(u8 *)(&x)+j,1);
- for(k=0;k<8;k++)
- printf("%d%c",
- ((byte)&(1<<k))?1:0,
- (k==7)?'\n':'|');
- }
- if(atom[i].r.x==x) printf("the same!\n");
- else printf("different!\n");
- }
- if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
- printf("FATAL: atom %d: y: %.20f (%.20f)\n",
- i,atom[i].r.y,dim->y/2);
- if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
- printf("FATAL: atom %d: z: %.20f (%.20f)\n",
- i,atom[i].r.z,dim->z/2);
- }
+ ctrl&=~_FPU_EXTENDED;
+ ctrl|=_FPU_DOUBLE;
+
+ _FPU_SETCW(ctrl);
return 0;
}
+
projects / physik / posic.git / blobdiff