X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.c;h=1d6e0b7dec9e3032df43f33baa692ba078bb5f7a;hp=881f0b698565fe7495ee151ecca63239d32e74cf;hb=HEAD;hpb=c0ddf2bdd8067456f39f6b63fe2261624ebde6b7 diff --git a/moldyn.c b/moldyn.c index 881f0b6..1d6e0b7 100644 --- a/moldyn.c +++ b/moldyn.c @@ -13,27 +13,95 @@ #include #include #include +#include +#include #include +#include + +#ifdef PARALLEL +#include +#endif + +#if defined PTHREADS || defined VISUAL_THREAD +#include +#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;icount;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)); @@ -63,6 +131,7 @@ int set_int_alg(t_moldyn *moldyn,u8 algo) { int set_cutoff(t_moldyn *moldyn,double cutoff) { moldyn->cutoff=cutoff; + moldyn->cutoff_square=cutoff*cutoff; printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff); @@ -73,7 +142,7 @@ int set_temperature(t_moldyn *moldyn,double t_ref) { moldyn->t_ref=t_ref; - printf("[moldyn] temperature: %f\n",moldyn->t_ref); + printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref); return 0; } @@ -82,7 +151,39 @@ int set_pressure(t_moldyn *moldyn,double p_ref) { 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; } @@ -122,15 +223,12 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) { moldyn->vis.dim.z=z; } - moldyn->dv=0.000001*moldyn->volume; - printf("[moldyn] dimensions in A and A^3 respectively:\n"); printf(" x: %f\n",moldyn->dim.x); printf(" y: %f\n",moldyn->dim.y); printf(" z: %f\n",moldyn->dim.z); printf(" volume: %f\n",moldyn->volume); printf(" visualize simulation box: %s\n",visualize?"yes":"no"); - printf(" delta volume (pressure calc): %f\n",moldyn->dv); return 0; } @@ -162,34 +260,55 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) { return 0; } -int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) { +int set_potential(t_moldyn *moldyn,u8 type) { - moldyn->func1b=func; - moldyn->pot1b_params=params; - - return 0; -} - -int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) { - - moldyn->func2b=func; - moldyn->pot2b_params=params; - - return 0; -} - -int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) { - - moldyn->func2b_post=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_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) { +int set_avg_skip(t_moldyn *moldyn,int skip) { - moldyn->func3b=func; - moldyn->pot3b_params=params; + printf("[moldyn] skip %d steps before starting average calc\n",skip); + moldyn->avg_skip=skip; return 0; } @@ -243,13 +362,52 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { 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; @@ -265,18 +423,52 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { perror("[moldyn] report fd open"); return moldyn->rfd; } - snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir); - moldyn->pfd=open(filename, - O_WRONLY|O_CREAT|O_EXCL, - S_IRUSR|S_IWUSR); - if(moldyn->pfd<0) { - perror("[moldyn] plot fd open"); - return moldyn->pfd; + 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); - dprintf(moldyn->pfd,plot_script); - close(moldyn->pfd); + printf("\n"); break; default: printf("unknown log type: %02x\n",type); @@ -291,21 +483,45 @@ 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->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 && gnuplot plot.scr",moldyn->vlsdir); + snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1", + moldyn->vlsdir); system(sc); - snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir); + snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1", + moldyn->vlsdir); system(sc); - snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir); - system(sc); - snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir); + snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1", + moldyn->vlsdir); system(sc); } - if(&(moldyn->vis)) visual_tini(&(moldyn->vis)); return 0; } @@ -314,23 +530,48 @@ int moldyn_log_shutdown(t_moldyn *moldyn) { * 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) { @@ -339,21 +580,54 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, } 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: - origin.x=0.5*lc; - origin.y=0.5*lc; - origin.z=0.5*lc; - ret=cubic_init(a,b,c,lc,atom,&origin); + 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,NULL); + 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); @@ -362,35 +636,229 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, /* 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); + } + + moldyn->count+=ret; + if(ret==new) + printf("[moldyn] created %s lattice with %d atoms\n",name,ret); + + for(new=0;newtype) { + 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 + } + } + + /* 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; - moldyn->count+=new; - printf("[moldyn] created lattice with %d atoms\n",new); +// WHAT ABOUT AMUTEX !!!! - for(ret=0;retlc.subcell->list,moldyn->count*sizeof(int)); + if(!ptr) { + perror("[moldyn] list realloc (create lattice)"); + return -1; } + moldyn->lc.subcell->list=ptr; +#endif + + /* update total system mass */ + total_mass_calc(moldyn); return ret; } +int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr, + t_3dvec *r,t_3dvec *v) { + + t_atom *atom; + void *ptr; + int count; + + atom=moldyn->atom; + count=(moldyn->count)++; // asshole style! + + ptr=realloc(atom,(count+1)*sizeof(t_atom)); + if(!ptr) { + perror("[moldyn] realloc (add atom)"); + return -1; + } + moldyn->atom=ptr; + +#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=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 del_atom(t_moldyn *moldyn,int tag) { + + t_atom *new,*old; + int cnt; +#if defined LOWMEM_LISTS || defined PTHREADS + void *ptr; +#endif + + old=moldyn->atom; + + new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom)); + if(!new) { + perror("[moldyn]malloc (del atom)"); + return -1; + } + + for(cnt=0;cntcount;cnt++) { + new[cnt-1]=old[cnt]; + new[cnt-1].tag=cnt-1; + } + + moldyn->count-=1; + moldyn->atom=new; + + free(old); + +#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 + +#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 + + + return 0; +} + +#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;\ + } + /* cubic init */ -int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { +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) { 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; + + p.x=0; p.y=0; p.z=0; count=0; if(origin) @@ -398,14 +866,54 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { else v3_zero(&o); + /* 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; + } + r.x=o.x; for(i=0;itype) { + 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)d.x)&& + (fabs(dist.y)d.y)&& + (fabs(dist.z)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; @@ -423,77 +931,147 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { } /* fcc lattice init */ -int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { +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; + int i,j,k,l; t_3dvec o,r,n; t_3dvec basis[3]; - double help[3]; - double x,y,z; + t_3dvec dist; + t_3dvec p; + t_3dvec d_d,d_o,dr; - x=a*lc; - y=b*lc; - z=c*lc; + p.x=0; p.y=0; p.z=0; - if(origin) v3_copy(&o,origin); - else v3_zero(&o); + count=0; + 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; - } - v3_set(&basis[i],help); + 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; } - v3_zero(&r); - count=0; - /* fill up the room */ r.x=o.x; - while(r.xtype) { + 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)d.x)&& + (fabs(dist.y)d.y)&& + (fabs(dist.z)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)d.x)&& + (fabs(dist.y)d.y)&& + (fabs(dist.z)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.z+=lc; } r.y+=lc; } r.x+=lc; } - + /* coordinate transformation */ - help[0]=x/2.0; - help[1]=y/2.0; - help[2]=z/2.0; - v3_set(&n,help); - for(i=0;iatom; - count=(moldyn->count)++; + if(moldyn->atom) free(moldyn->atom); - ptr=realloc(atom,(count+1)*sizeof(t_atom)); - if(!ptr) { - perror("[moldyn] realloc (add atom)"); - return -1; - } - moldyn->atom=ptr; - - atom=moldyn->atom; - atom[count].r=*r; - atom[count].v=*v; - atom[count].element=element; - atom[count].mass=mass; - atom[count].brand=brand; - atom[count].tag=count; - atom[count].attr=attr; - - return 0; -} - -int destroy_atoms(t_moldyn *moldyn) { - - if(moldyn->atom) free(moldyn->atom); - - return 0; -} + return 0; +} int thermal_init(t_moldyn *moldyn,u8 equi_init) { @@ -592,11 +1141,25 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) { return 0; } +double total_mass_calc(t_moldyn *moldyn) { + + int i; + + moldyn->mass=0.0; + + for(i=0;icount;i++) + moldyn->mass+=moldyn->atom[i].mass; + + return moldyn->mass; +} + double temperature_calc(t_moldyn *moldyn) { /* assume up to date kinetic energy, which is 3/2 N k_B T */ - moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count); + if(moldyn->count) + moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count); + else moldyn->t=0.0; return moldyn->t; } @@ -650,7 +1213,7 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) { 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 */ @@ -671,117 +1234,242 @@ double ideal_gas_law_pressure(t_moldyn *moldyn) { return p; } -double pressure_calc(t_moldyn *moldyn) { +double virial_sum(t_moldyn *moldyn) { int i; - double v; t_virial *virial; - /* - * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i ) - * - * virial = f_i r_i - */ - - v=0.0; + /* 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;icount;i++) { virial=&(moldyn->atom[i].virial); - v+=(virial->xx+virial->yy+virial->zz); + moldyn->virial+=(virial->xx+virial->yy+virial->zz); + moldyn->vir.xx+=virial->xx; + moldyn->vir.yy+=virial->yy; + moldyn->vir.zz+=virial->zz; + moldyn->vir.xy+=virial->xy; + moldyn->vir.xz+=virial->xz; + moldyn->vir.yz+=virial->yz; } - /* assume up to date kinetic energy */ - moldyn->p=2.0*moldyn->ekin+v; + /* global virial (absolute coordinates) */ + //virial=&(moldyn->gvir); + //moldyn->gv=virial->xx+virial->yy+virial->zz; + + return moldyn->virial; +} + +double pressure_calc(t_moldyn *moldyn) { + + /* + * PV = NkT + + * with W = 1/3 sum_i f_i r_i (- skipped!) + * virial = sum_i f_i r_i + * + * => P = (2 Ekin + virial) / (3V) + */ + + /* assume up to date virial & up to date kinetic energy */ + + /* pressure (atom virials) */ + moldyn->p=2.0*moldyn->ekin+moldyn->virial; moldyn->p/=(3.0*moldyn->volume); + //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; + + /* pressure (absolute coordinates) */ + //moldyn->gp=2.0*moldyn->ekin+moldyn->gv; + //moldyn->gp/=(3.0*moldyn->volume); + return moldyn->p; -} +} + +int average_reset(t_moldyn *moldyn) { + + printf("[moldyn] average reset\n"); + + /* update skip value */ + moldyn->avg_skip=moldyn->total_steps; + + /* kinetic energy */ + moldyn->k_sum=0.0; + moldyn->k2_sum=0.0; + + /* potential energy */ + moldyn->v_sum=0.0; + moldyn->v2_sum=0.0; + + /* temperature */ + moldyn->t_sum=0.0; + + /* virial */ + moldyn->virial_sum=0.0; + //moldyn->gv_sum=0.0; + + /* pressure */ + moldyn->p_sum=0.0; + //moldyn->gp_sum=0.0; + moldyn->tp_sum=0.0; + + return 0; +} + +int average_and_fluctuation_calc(t_moldyn *moldyn) { + + int denom; + + if(moldyn->total_stepsavg_skip) + return 0; + + denom=moldyn->total_steps+1-moldyn->avg_skip; + + /* assume up to date energies, temperature, pressure etc */ + + /* kinetic energy */ + moldyn->k_sum+=moldyn->ekin; + moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin); + moldyn->k_avg=moldyn->k_sum/denom; + moldyn->k2_avg=moldyn->k2_sum/denom; + moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg); + + /* potential energy */ + moldyn->v_sum+=moldyn->energy; + moldyn->v2_sum+=(moldyn->energy*moldyn->energy); + moldyn->v_avg=moldyn->v_sum/denom; + moldyn->v2_avg=moldyn->v2_sum/denom; + moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg); + + /* temperature */ + moldyn->t_sum+=moldyn->t; + moldyn->t_avg=moldyn->t_sum/denom; + + /* virial */ + moldyn->virial_sum+=moldyn->virial; + moldyn->virial_avg=moldyn->virial_sum/denom; + //moldyn->gv_sum+=moldyn->gv; + //moldyn->gv_avg=moldyn->gv_sum/denom; + + /* pressure */ + moldyn->p_sum+=moldyn->p; + moldyn->p_avg=moldyn->p_sum/denom; + //moldyn->gp_sum+=moldyn->gp; + //moldyn->gp_avg=moldyn->gp_sum/denom; + moldyn->tp_sum+=moldyn->tp; + moldyn->tp_avg=moldyn->tp_sum/denom; + + return 0; +} + +int get_heat_capacity(t_moldyn *moldyn) { + + double temp2,ighc; + + /* averages needed for heat capacity calc */ + if(moldyn->total_stepsavg_skip) + return 0; + + /* (temperature average)^2 */ + temp2=moldyn->t_avg*moldyn->t_avg; + printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n", + moldyn->t_avg); + + /* ideal gas contribution */ + ighc=3.0*moldyn->count*K_BOLTZMANN/2.0; + printf(" ideal gas contribution: %f\n", + ighc/moldyn->mass*KILOGRAM/JOULE); + + /* specific heat for nvt ensemble */ + moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc; + moldyn->c_v_nvt/=moldyn->mass; + + /* specific heat for nve ensemble */ + moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2))); + moldyn->c_v_nve/=moldyn->mass; + + printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE); + printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE); +printf(" --> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM))); + + return 0; +} double thermodynamic_pressure_calc(t_moldyn *moldyn) { - t_3dvec dim,*tp; - double u,p; - double scale; + t_3dvec dim; + //t_3dvec *tp; + double h,dv; + double y0,y1; + double su,sd; t_atom *store; - tp=&(moldyn->tp); + /* + * 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; } - - /* save unscaled potential energy + atom/dim configuration */ - u=moldyn->energy; memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom)); dim=moldyn->dim; - /* derivative with respect to x direction */ - scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z); - scale_dim(moldyn,scale,TRUE,0,0); - scale_atoms(moldyn,scale,TRUE,0,0); - link_cell_shutdown(moldyn); - link_cell_init(moldyn); - potential_force_calc(moldyn); - tp->x=(moldyn->energy-u)/moldyn->dv; - p=tp->x*tp->x; - - /* restore atomic configuration + dim */ - memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom)); - moldyn->dim=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; - /* derivative with respect to y direction */ - scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z); - scale_dim(moldyn,scale,0,TRUE,0); - scale_atoms(moldyn,scale,0,TRUE,0); + /* 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); + link_cell_init(moldyn,QUIET); potential_force_calc(moldyn); - tp->y=(moldyn->energy-u)/moldyn->dv; - p+=tp->y*tp->y; + y1=moldyn->energy; /* restore atomic configuration + dim */ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom)); moldyn->dim=dim; - /* derivative with respect to z direction */ - scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y); - scale_dim(moldyn,scale,0,0,TRUE); - scale_atoms(moldyn,scale,0,0,TRUE); + /* 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); + link_cell_init(moldyn,QUIET); potential_force_calc(moldyn); - tp->z=(moldyn->energy-u)/moldyn->dv; - p+=tp->z*tp->z; + y0=moldyn->energy; + + /* calculate pressure */ + moldyn->tp=-(y1-y0)/(2.0*dv); - /* restore atomic configuration + dim */ + /* restore atomic configuration */ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom)); moldyn->dim=dim; - - printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z); - - scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD); - -printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x); - scale_dim(moldyn,scale,1,1,1); - scale_atoms(moldyn,scale,1,1,1); link_cell_shutdown(moldyn); - link_cell_init(moldyn); - potential_force_calc(moldyn); -printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x); + link_cell_init(moldyn,QUIET); + //potential_force_calc(moldyn); - printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM); + /* free store buffer */ + if(store) + free(store); - /* restore atomic configuration + dim */ - memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom)); - moldyn->dim=dim; - - /* restore energy */ - moldyn->energy=u; - - link_cell_shutdown(moldyn); - link_cell_init(moldyn); - - return sqrt(p); + return moldyn->tp; } double get_pressure(t_moldyn *moldyn) { @@ -790,12 +1478,18 @@ double get_pressure(t_moldyn *moldyn) { } -int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) { +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; @@ -803,11 +1497,17 @@ int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) { return 0; } -int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) { +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;icount;i++) { r=&(moldyn->atom[i].r); if(x) r->x*=scale; @@ -818,88 +1518,121 @@ int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) { return 0; } +int scale_atoms_ind(t_moldyn *moldyn,double x,double y,double z) { + + int i; + t_3dvec *r; + + for(i=0;icount;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_atom *atom; t_3dvec *dim,*vdim; - double scale,v; - t_virial virial; + double scale; t_linkcell *lc; - int i; + //double sx,sy,sz; - atom=moldyn->atom; - dim=&(moldyn->dim); vdim=&(moldyn->vis.dim); + dim=&(moldyn->dim); lc=&(moldyn->lc); - memset(&virial,0,sizeof(t_virial)); + /* 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); + } + - for(i=0;icount;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)) { + /* + 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); + 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 get_e_kin(t_moldyn *moldyn) { +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;icount;i++) - moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v)); + for(i=0;icount;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 update_e_kin(t_moldyn *moldyn) { - - return(get_e_kin(moldyn)); -} - double get_total_energy(t_moldyn *moldyn) { return(moldyn->ekin+moldyn->energy); @@ -939,10 +1672,12 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) { /* linked list / cell method */ -int link_cell_init(t_moldyn *moldyn) { +int link_cell_init(t_moldyn *moldyn,u8 vol) { t_linkcell *lc; +#ifndef LOWMEM_LISTS int i; +#endif lc=&(moldyn->lc); @@ -953,56 +1688,147 @@ int link_cell_init(t_moldyn *moldyn) { 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->cells<27) - printf("[moldyn] FATAL: less then 27 subcells!\n"); + if(lc->subcell==NULL) { + perror("[moldyn] cell init (malloc)"); + return -1; + } - printf("[moldyn] initializing linked cells (%d)\n",lc->cells); + 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;icells;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;icells;i++) list_init_f(&(lc->subcell[i])); +#endif + + /* update the list */ + link_cell_update(moldyn); - link_cell_update(moldyn); - return 0; } int link_cell_update(t_moldyn *moldyn) { int count,i,j,k; - int nx,ny; + int nx,nxy; t_atom *atom; t_linkcell *lc; - double x,y,z; +#ifdef STATIC_LISTS + int p; +#elif LOWMEM_LISTS + int p; +#endif atom=moldyn->atom; lc=&(moldyn->lc); nx=lc->nx; - ny=lc->ny; - - x=moldyn->dim.x/2; - y=moldyn->dim.y/2; - z=moldyn->dim.z/2; + nxy=nx*lc->ny; for(i=0;icells;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;countcount;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; @@ -1020,7 +1846,15 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) { 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; @@ -1044,10 +1878,19 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) { } 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 } } } @@ -1060,13 +1903,28 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) { int link_cell_shutdown(t_moldyn *moldyn) { +#ifndef LOWMEM_LISTS int i; +#endif t_linkcell *lc; lc=&(moldyn->lc); - for(i=0;inx*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;icells;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); @@ -1124,67 +1982,106 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) { 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; - /* energy scaling factor */ - energy_scale=moldyn->count*EV; + /* get current time */ + gettimeofday(&t1,NULL); -printf("debug: %f\n",moldyn->atom[0].f.x); /* calculate initial forces */ potential_force_calc(moldyn); -printf("debug: %f\n",moldyn->atom[0].f.x); +#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->counttotal_sched;sched->count++) { + sched->count=0; + while(sched->counttotal_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;itime_steps;i++) { @@ -1192,38 +2089,77 @@ printf("debug: %f\n",moldyn->atom[0].f.x); /* 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); if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT)) scale_volume(moldyn); - update_e_kin(moldyn); - temperature_calc(moldyn); - pressure_calc(moldyn); - //thermodynamic_pressure_calc(moldyn); - /* check for log & visualization */ if(e) { - if(!(i%e)) + if(!(moldyn->total_steps%e)) dprintf(moldyn->efd, - "%f %f %f %f\n", + "%f %f %f %f %f %f\n", moldyn->time,moldyn->ekin/energy_scale, moldyn->energy/energy_scale, - get_total_energy(moldyn)/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)); @@ -1233,54 +2169,198 @@ printf("debug: %f\n",moldyn->atom[0].f.x); close(fd); } } - if(v) { - if(!(i%v)) { - visual_atoms(&(moldyn->vis),moldyn->time, - moldyn->atom,moldyn->count); - printf("\rsched: %d, steps: %d, debug: %f", - sched->count,i,moldyn->p/ATM); - 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 } } + /* 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; } -/* velocity verlet */ +/* basis trafo */ -int velocity_verlet(t_moldyn *moldyn) { +#define FORWARD 0 +#define BACKWARD 1 - int i,count; - double tau,tau_square,h; - t_3dvec delta; - t_atom *atom; +int basis_trafo(t_3dvec *r,u8 dir,double z,double x) { - atom=moldyn->atom; - count=moldyn->count; - tau=moldyn->tau; - tau_square=moldyn->tau_square; + 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; +} + +/* velocity verlet */ + +int velocity_verlet(t_moldyn *moldyn) { + + int i,count; + double tau,tau_square,h; + t_3dvec delta; + t_atom *atom; + + atom=moldyn->atom; + count=moldyn->count; + tau=moldyn->tau; + tau_square=moldyn->tau_square; + + for(i=0;ifunc3b_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;icount; itom=moldyn->atom; lc=&(moldyn->lc); +#ifdef STATIC_LISTS + atom=moldyn->atom; +#endif /* reset energy */ moldyn->energy=0.0; + /* 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;ifunc1b(moldyn,&(itom[i])); + if(moldyn->func_i0) + moldyn->func_i0(moldyn,&(itom[i])); if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP))) continue; @@ -1371,94 +2514,362 @@ int potential_force_calc(t_moldyn *moldyn) { 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=(jsubcell->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=(kstart==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=(jsubcell->list[p]; +#else this=&(neighbour_i[j]); list_reset_f(this); if(this->start==NULL) continue; - bc_ij=(jcurrent->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=(ksubcell->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=(ksubcell->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"); + //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z); + if(moldyn->time>DSTART&&moldyn->timeatom[DATOM].f.x); + printf(" y: %0.40f\n",moldyn->atom[DATOM].f.y); + printf(" z: %0.40f\n",moldyn->atom[DATOM].f.z); + } #endif -#ifdef VDEBUG -printf("\n\n"); + + /* some postprocessing */ +#ifdef PARALLEL + #pragma omp parallel for #endif + for(i=0;igvir.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; } @@ -1467,7 +2878,8 @@ printf("\n\n"); * virial calculation */ -inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) { +//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; @@ -1480,10 +2892,11 @@ inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) { } /* - * periodic boundayr checking + * periodic boundary checking */ -inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { +//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; @@ -1510,826 +2923,869 @@ inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { return 0; } +int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a) { + + double x,y,z; + t_3dvec *dim; -/* - * example potentials - */ - -/* harmonic oscillator potential and force */ - -int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { - - t_ho_params *params; - t_3dvec force,distance; - double d,f; - double sc,equi_dist; - - params=moldyn->pot2b_params; - sc=params->spring_constant; - equi_dist=params->equilibrium_distance; + dim=&(moldyn->dim); - if(aix/2; + y=dim->y/2; + z=dim->z/2; - 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); + 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; -/* 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(air),&(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,&force,-1.0); /* 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 */ + for(i=0;icount;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<=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; } /* - * tersoff potential & force for 2 sorts of atoms + * restore function */ -/* 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 moldyn_read_save_file(t_moldyn *moldyn,char *file) { - return 0; -} + 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; + } -/* tersoff 1 body part */ -int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { + fsize=lseek(fd,0,SEEK_END); + lseek(fd,0,SEEK_SET); - int brand; - t_tersoff_mult_params *params; - t_tersoff_exchange *exchange; - - brand=ai->brand; - params=moldyn->pot1b_params; - exchange=&(params->exchange); + size=sizeof(t_moldyn); - /* - * simple: point constant parameters only depending on atom i to - * their right values - */ + while(size) { + cnt=read(fd,moldyn,size); + if(cnt<0) { + perror("[moldyn] load save file read (moldyn)"); + return cnt; + } + size-=cnt; + } - 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]); + 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); + } - 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; + 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;cntcount;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; -/* 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 - * - */ + for(i=0;icount;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); - /* 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; - } - 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; + for(j=0;j<27;j++) { - /* 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; - } - 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; - } + bc=(jdnlc)?0:1; - /* 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; +#ifdef STATIC_LISTS + p=0; - /* 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; + while(neighbour[j][p]!=-1) { - /* f_c, df_c calc (again, same for ij and ji) */ - if(d_ij r > R */ - exchange->d_ij_between_rs=1; - } + jtom=&(moldyn->atom[neighbour[j][p]]); + p++; +#elif LOWMEM_LISTS + p=neighbour[j]; - /* add forces of 2bp (ij, ji) contribution - * dVij = dVji and we sum up both: no 1/2) */ - v3_add(&(ai->f),&(ai->f),&force); + while(p!=-1) { - /* 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; + jtom=&(itom[p]); + p=lc->subcell->list[p]; +#else + this=&(neighbour[j]); + list_reset_f(this); -#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); -} + if(this->start==NULL) + continue; + + do { + + jtom=this->current->data; #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); + + /* 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; - /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */ - moldyn->energy+=(0.5*f_r*f_c); + 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); - /* save for use in 3bp */ - exchange->f_c=f_c; - exchange->df_c=df_c; + for(j=0;j<27;j++) { - /* enable the run of 3bp function and 2bp post processing */ - exchange->run3bp=1; - exchange->run2bp_post=1; + bc=(jdnlc)?0:1; - /* reset 3bp sums */ - exchange->zeta_ij=0.0; - exchange->zeta_ji=0.0; - v3_zero(&(exchange->dzeta_ij)); - v3_zero(&(exchange->dzeta_ji)); +#ifdef STATIC_LISTS + p=0; - return 0; -} + while(neighbour[j][p]!=-1) { -/* tersoff 2 body post part */ + natom=&(moldyn->atom[neighbour[j][p]]); + p++; +#elif LOWMEM_LISTS + p=neighbour[j]; -int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { + while(p!=-1) { - /* - * 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 - * - */ + natom=&(moldyn->atom[p]); + p=lc->subcell->list[p]; +#else + this=&(neighbour[j]); + list_reset_f(this); - t_tersoff_mult_params *params; - t_tersoff_exchange *exchange; + if(this->start==NULL) + continue; - 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; + do { - params=moldyn->pot2b_params; - exchange=&(params->exchange); + natom=this->current->data; +#endif - /* we do not run if f_c_ij was detected to be 0! */ - if(!(exchange->run2bp_post)) - return 0; + /* process bond */ + process(moldyn,atom,natom,data,bc); - 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); +#ifdef STATIC_LISTS + } +#elif LOWMEM_LISTS + } +#else + } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); +#endif } - 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); - /* 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; + return 0; -#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); + +/* + * post processing functions + */ + +int get_line(int fd,char *line,int max) { + + int count,ret; + + count=0; + + while(1) { + if(count==max) return count; + ret=read(fd,line+count,1); + if(ret<=0) return ret; + if(line[count]=='\n') { + 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; } -#endif - /* add energy of 3bp sum */ - moldyn->energy+=(0.5*f_c*b*f_a); +int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) { - /* dVji */ - zeta=exchange->zeta_ji; - if(zeta==0.0) { - moldyn->debug++; - b=chi; - v3_scale(&force,dist_ij,df_a*b*f_c); + int i; + t_atom *atom; + t_3dvec dist; + t_3dvec final_r; + double d2; + int a_cnt; + int b_cnt; + + atom=moldyn->atom; + dc[0]=0; + dc[1]=0; + dc[2]=0; + a_cnt=0; + b_cnt=0; + + for(i=0;icount;i++) { + + /* 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; + } + + dc[2]+=d2; } - 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; -#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); + 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; } -#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); + +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;icount;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; } -#endif + +int bonding_analyze(t_moldyn *moldyn,double *cnt) { 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)) - return 0; +int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom, + t_atom *jtom,void *data,u8 bc) { - /* - * 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 - * - */ + t_3dvec dist; + double d; + int s; + t_pcc *pcc; + + /* only count pairs once, + * skip same atoms */ + if(itom->tag>=jtom->tag) + return 0; /* - * get exchange data + * pair correlation calc */ - /* dist_ij, d_ij - this is < S_ij ! */ - dist_ij=exchange->dist_ij; - d_ij=exchange->d_ij; - d_ij2=exchange->d_ij2; + /* get pcc data */ + pcc=data; - /* f_c_ij, df_c_ij (same for ji) */ - f_c=exchange->f_c; - df_c=exchange->df_c; + /* distance */ + v3_sub(&dist,&(jtom->r),&(itom->r)); + if(bc) check_per_bound(moldyn,&dist); + d=v3_absolute_square(&dist); - /* - * calculate unknown values now ... - */ + /* ignore if greater cutoff */ + if(d>moldyn->cutoff_square) + return 0; - /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */ + /* fill the slots */ + d=sqrt(d); + s=(int)(d/pcc->dr); - /* 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); + /* 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; + } - /* ik constants */ - brand=ai->brand; - if(brand==ak->brand) { - R=params->R[brand]; - S=params->S[brand]; - S2=params->S2[brand]; + if(itom->brand!=jtom->brand) { + /* mixed */ + pcc->stat[s]+=1; } else { - R=params->Rmixed; - S=params->Smixed; - S2=params->S2mixed; - } - - /* zeta_ij/dzeta_ij contribution only for d_ik < S */ - if(d_ik2n_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 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); - } + /* 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; } - /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */ + return 0; +} + +int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) { + + t_pcc pcc; + double norm; + int i; + + pcc.dr=dr; + pcc.o1=moldyn->cutoff/dr; + pcc.o2=2*pcc.o1; + + if(pcc.o1*dr<=moldyn->cutoff) + printf("[moldyn] WARNING: pcc (low #slots)\n"); - /* 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); + 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); - /* 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; + if(ptr!=NULL) { + pcc.stat=(double *)ptr; } 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_jk2n_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_jkzeta_ji+=g; - - /* dzeta_ji */ - v3_add(dzeta,dzeta,&temp1); + pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double)); + if(pcc.stat==NULL) { + perror("[moldyn] pair correlation malloc"); + return -1; } - 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; + memset(pcc.stat,0,3*pcc.o1*sizeof(double)); - /* dzeta_ji */ - v3_scale(&temp1,&temp1,f_c_jk); - v3_add(dzeta,dzeta,&temp1); - } + /* process */ + process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process); - /* 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; + /* normalization */ + for(i=1;i 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; + } + /* */ -#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); + if(ptr==NULL) { + /* todo: store/print pair correlation function */ + free(pcc.stat); + } + + return 0; } -#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); + +int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, + void *data,u8 bc) { + + t_ba *ba; + t_3dvec dist; + double d; + + if(itom->tag>=jtom->tag) + return 0; + + /* distance */ + v3_sub(&dist,&(jtom->r),&(itom->r)); + if(bc) check_per_bound(moldyn,&dist); + d=v3_absolute_square(&dist); + + /* ignore if greater or equal cutoff */ + if(d>moldyn->cutoff_square) + return 0; + + /* check for potential bond */ + if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE) + return 0; + + /* now count this bonding ... */ + ba=data; + + /* increase total bond counter + */ + ba->tcnt+=1; + + if(itom->brand==0) + ba->acnt[jtom->tag]+=1; + else + ba->bcnt[jtom->tag]+=1; + + if(jtom->brand==0) + ba->acnt[itom->tag]+=1; + else + ba->bcnt[itom->tag]+=1; + + return 0; } -#endif +int bond_analyze(t_moldyn *moldyn,double *quality) { + + int qcnt4; + int qcnt3; + int ccnt4; + int ccnt3; + int bcnt; + t_ba ba; + int i; + t_atom *atom; + + ba.acnt=malloc(moldyn->count*sizeof(int)); + if(ba.acnt==NULL) { + perror("[moldyn] bond analyze malloc (a)"); + return -1; + } + memset(ba.acnt,0,moldyn->count*sizeof(int)); + + ba.bcnt=malloc(moldyn->count*sizeof(int)); + if(ba.bcnt==NULL) { + perror("[moldyn] bond analyze malloc (b)"); + return -1; + } + memset(ba.bcnt,0,moldyn->count*sizeof(int)); + + ba.tcnt=0; + qcnt4=0; qcnt3=0; + ccnt4=0; ccnt3=0; + bcnt=0; + + atom=moldyn->atom; + + process_2b_bonds(moldyn,&ba,bond_analyze_process); + + for(i=0;icount;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; + } + } + + if(quality) { + quality[0]=1.0*ccnt4/bcnt; + quality[1]=1.0*ccnt3/bcnt; + } + else { + printf("[moldyn] bond analyze: %f %f\n", + 1.0*ccnt4/bcnt,1.0*ccnt3/bcnt); } return 0; } - /* - * debugging / critical check functions + * visualization code */ -int moldyn_bc_check(t_moldyn *moldyn) { +int visual_init(t_moldyn *moldyn,char *filebase) { + + strncpy(moldyn->vis.fb,filebase,128); + + return 0; +} + +int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, + void *data,u8 bc) { + + t_vb *vb; + + vb=data; + + if(itom->tag>=jtom->tag) + return 0; + + if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE) + return 0; + + if((itom->attr&ATOM_ATTR_VB)|(jtom->attr&ATOM_ATTR_VB)) + dprintf(vb->fd,"# [B] %f %f %f %f %f %f\n", + itom->r.x,itom->r.y,itom->r.z, + jtom->r.x,jtom->r.y,jtom->r.z); + + return 0; +} + +#ifdef VISUAL_THREAD +void *visual_atoms(void *ptr) { +#else +int visual_atoms(t_moldyn *moldyn) { +#endif - t_atom *atom; - t_3dvec *dim; int i; - double x; - u8 byte; - int j,k; + 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; + moldyn=ptr; +#endif + + v=&(moldyn->vis); + dim.x=v->dim.x; + dim.y=v->dim.y; + dim.z=v->dim.z; atom=moldyn->atom; - dim=&(moldyn->dim); - x=dim->x/2; + help=(dim.x+dim.y); + + 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 + } + + /* write the actual data file */ + + // 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); + + // atomic configuration for(i=0;icount;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<=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); + 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); + } + + close(vb.fd); + +#ifdef VISUAL_THREAD + pthread_exit(NULL); + +} +#else + + return 0; +} +#endif + +/* + * fpu cntrol functions + */ + +// set rounding to double (eliminates -ffloat-store!) +int fpu_set_rtd(void) { + + fpu_control_t ctrl; + + _FPU_GETCW(ctrl); + + ctrl&=~_FPU_EXTENDED; + ctrl|=_FPU_DOUBLE; + + _FPU_SETCW(ctrl); return 0; } +