X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=b73cd3432b65971aabc055e7f126fc5efdb3deb4;hb=37d949bdf2aaff618e70e6fd973ef350f4dacf12;hp=a1bfcaea95c82580dc636f5655649a61d0e8cf8f;hpb=155e1cfea83209d09c2a06ae4fb7f5e1652fc00a;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index a1bfcae..b73cd34 100644 --- a/moldyn.c +++ b/moldyn.c @@ -17,6 +17,12 @@ #include #include +#include + +#ifdef PARALLEL +#include +#endif + #include "moldyn.h" #include "report/report.h" @@ -30,54 +36,12 @@ #include "potentials/tersoff.h" #endif - -/* - * global variables, pse and atom colors (only needed here) - */ - -static char *pse_name[]={ - "*", - "H", - "He", - "Li", - "Be", - "B", - "C", - "N", - "O", - "F", - "Ne", - "Na", - "Mg", - "Al", - "Si", - "P", - "S", - "Cl", - "Ar", -}; - -static char *pse_col[]={ - "*", - "White", - "He", - "Li", - "Be", - "B", - "Gray", - "N", - "Blue", - "F", - "Ne", - "Na", - "Mg", - "Al", - "Yellow", - "P", - "S", - "Cl", - "Ar", -}; +/* pse */ +#define PSE_NAME +#define PSE_COL +#include "pse.h" +#undef PSE_NAME +#undef PSE_COL /* * the moldyn functions @@ -87,6 +51,9 @@ 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; @@ -131,24 +98,13 @@ 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); return 0; } -int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) { - - moldyn->bondlen[0]=b0*b0; - moldyn->bondlen[1]=b1*b1; - if(bm<0) - moldyn->bondlen[2]=b0*b1; - else - moldyn->bondlen[2]=bm*bm; - - return 0; -} - int set_temperature(t_moldyn *moldyn,double t_ref) { moldyn->t_ref=t_ref; @@ -167,6 +123,38 @@ int set_pressure(t_moldyn *moldyn,double p_ref) { return 0; } +int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) { + + moldyn->pt_scale&=(~(P_SCALE_MASK)); + moldyn->pt_scale|=ptype; + moldyn->p_tc=ptc; + + printf("[moldyn] p 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; +} + int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) { moldyn->pt_scale=(ptype|ttype); @@ -248,7 +236,7 @@ int set_potential(t_moldyn *moldyn,u8 type) { moldyn->func3b_k1=tersoff_mult_3bp_k1; moldyn->func3b_j2=tersoff_mult_3bp_j2; moldyn->func3b_k2=tersoff_mult_3bp_k2; - // missing: check 2b bond func + moldyn->check_2b_bond=tersoff_mult_check_2b_bond; break; case MOLDYN_POTENTIAL_AM: moldyn->func3b_j1=albe_mult_3bp_j1; @@ -507,11 +495,16 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, t_3dvec orig; void *ptr; t_atom *atom; + char name[16]; 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; @@ -541,18 +534,21 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, case CUBIC: set_nn_dist(moldyn,lc); ret=cubic_init(a,b,c,lc,atom,&orig); + strcpy(name,"cubic"); break; case FCC: if(!origin) v3_scale(&orig,&orig,0.5); set_nn_dist(moldyn,0.5*sqrt(2.0)*lc); ret=fcc_init(a,b,c,lc,atom,&orig); + strcpy(name,"fcc"); break; case DIAMOND: if(!origin) v3_scale(&orig,&orig,0.25); set_nn_dist(moldyn,0.25*sqrt(3.0)*lc); ret=diamond_init(a,b,c,lc,atom,&orig); + strcpy(name,"diamond"); break; default: printf("unknown lattice type (%02x)\n",type); @@ -569,7 +565,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, } moldyn->count+=new; - printf("[moldyn] created lattice with %d atoms\n",new); + printf("[moldyn] created %s lattice with %d atoms\n",name,new); for(ret=0;retpt_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 */ @@ -1202,7 +1198,7 @@ int scale_volume(t_moldyn *moldyn) { /* scaling factor */ if(moldyn->pt_scale&P_SCALE_BERENDSEN) { - scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc; + scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc*moldyn->tau; scale=pow(scale,ONE_THIRD); } else { @@ -1322,7 +1318,8 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) { } if(lc->cells<27) - printf("[moldyn] FATAL: less then 27 subcells!\n"); + printf("[moldyn] FATAL: less then 27 subcells! (%d)\n", + lc->cells); if(vol) { #ifdef STATIC_LISTS @@ -1581,7 +1578,6 @@ int moldyn_integrate(t_moldyn *moldyn) { /* sqaure of some variables */ moldyn->tau_square=moldyn->tau*moldyn->tau; - moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff; /* get current time */ gettimeofday(&t1,NULL); @@ -1599,13 +1595,16 @@ int moldyn_integrate(t_moldyn *moldyn) { 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) + 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; - moldyn->total_steps=0; + // should have right values! + //moldyn->time=0.0; + //moldyn->total_steps=0; /* debugging, ignore */ moldyn->debug=0; @@ -1637,7 +1636,11 @@ int moldyn_integrate(t_moldyn *moldyn) { temperature_calc(moldyn); virial_sum(moldyn); pressure_calc(moldyn); - //thermodynamic_pressure_calc(moldyn); + /* + thermodynamic_pressure_calc(moldyn); + printf("\n\nDEBUG: numeric pressure calc: %f\n\n", + moldyn->tp/BAR); + */ /* calculate fluctuations + averages */ average_and_fluctuation_calc(moldyn); @@ -1718,6 +1721,7 @@ printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)", sched->count,i,moldyn->total_steps, moldyn->t,moldyn->t_avg, moldyn->p/BAR,moldyn->p_avg/BAR, + //moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR, moldyn->volume, (int)(t2.tv_sec-t1.tv_sec)); @@ -1787,7 +1791,11 @@ int velocity_verlet(t_moldyn *moldyn) { link_cell_update(moldyn); /* forces depending on chosen potential */ +#ifndef ALBE_FAST potential_force_calc(moldyn); +#else + albe_potential_force_calc(moldyn); +#endif for(i=0;igvir),0,sizeof(t_virial)); /* reset force, site energy and virial of every atom */ +#ifdef PARALLEL + #pragma omp parallel for private(virial) +#endif for(i=0;iattr&ATOM_ATTR_2BP)& - (itom[i].attr&ATOM_ATTR_2BP)) { - moldyn->func2b(moldyn, - &(itom[i]), - jtom, - bc_ij); - } - } #else this=&(neighbour_i[j]); list_reset_f(this); @@ -1917,6 +1916,7 @@ int potential_force_calc(t_moldyn *moldyn) { do { jtom=this->current->data; +#endif if(jtom==&(itom[i])) continue; @@ -1928,6 +1928,9 @@ int potential_force_calc(t_moldyn *moldyn) { jtom, bc_ij); } +#ifdef STATIC_LISTS + } +#else } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); #endif @@ -2127,6 +2130,9 @@ int potential_force_calc(t_moldyn *moldyn) { #endif /* some postprocessing */ +#ifdef PARALLEL + #pragma omp parallel for +#endif for(i=0;igvir.xx+=itom[i].r.x*itom[i].f.x; @@ -2138,7 +2144,7 @@ int potential_force_calc(t_moldyn *moldyn) { /* check forces regarding the given timestep */ if(v3_norm(&(itom[i].f))>\ - 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square) + 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square) printf("[moldyn] WARNING: pfc (high force: atom %d)\n", i); } @@ -2341,16 +2347,13 @@ int process_2b_bonds(t_moldyn *moldyn,void *data, int p; #else t_list neighbour[27]; + t_list *this; #endif u8 bc; t_atom *itom,*jtom; int i,j; - t_list *this; lc=&(moldyn->lc); - - link_cell_init(moldyn,VERBOSE); - itom=moldyn->atom; for(i=0;icount;i++) { @@ -2414,7 +2417,8 @@ int get_line(int fd,char *line,int max) { ret=read(fd,line+count,1); if(ret<=0) return ret; if(line[count]=='\n') { - line[count]='\0'; + memset(line+count,0,max-count-1); + //line[count]='\0'; return count+1; } count+=1; @@ -2609,8 +2613,6 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE) return 0; - d=sqrt(d); - /* now count this bonding ... */ ba=data; @@ -2705,39 +2707,48 @@ int visual_init(t_moldyn *moldyn,char *filebase) { return 0; } +int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, + void *data,u8 bc) { + + t_vb *vb; + + vb=data; + + if(itom->tag>=jtom->tag) + return 0; + + if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE) + return 0; + + if((itom->attr&ATOM_ATTR_VB)|(jtom->attr&ATOM_ATTR_VB)) + dprintf(vb->fd,"# [B] %f %f %f %f %f %f\n", + itom->r.x,itom->r.y,itom->r.z, + jtom->r.x,jtom->r.y,jtom->r.z); + + return 0; +} + int visual_atoms(t_moldyn *moldyn) { - int i,j,fd; + int i; char file[128+64]; t_3dvec dim; double help; t_visual *v; t_atom *atom; - t_atom *btom; - t_linkcell *lc; -#ifdef STATIC_LISTS - int *neighbour[27]; - int p; -#else - t_list neighbour[27]; -#endif - u8 bc; - t_3dvec dist; - double d2; - u8 brand; + t_vb vb; v=&(moldyn->vis); dim.x=v->dim.x; dim.y=v->dim.y; dim.z=v->dim.z; atom=moldyn->atom; - lc=&(moldyn->lc); help=(dim.x+dim.y); sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time); - fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR); - if(fd<0) { + vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR); + if(vb.fd<0) { perror("open visual save file fd"); return -1; } @@ -2745,118 +2756,84 @@ int visual_atoms(t_moldyn *moldyn) { /* write the actual data file */ // povray header - dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n", + dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n", moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help); // atomic configuration - for(i=0;icount;i++) { + for(i=0;icount;i++) // atom type, positions, color and kinetic energy - dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element], - atom[i].r.x, - atom[i].r.y, - atom[i].r.z, - pse_col[atom[i].element], - atom[i].ekin); - - /* - * bond detection should usually be done by potential - * functions. brrrrr! EVIL! - * - * todo: potentials need to export a 'find_bonds' function! - */ - - // bonds between atoms - if(!(atom[i].attr&ATOM_ATTR_VB)) - continue; - link_cell_neighbour_index(moldyn, - (atom[i].r.x+moldyn->dim.x/2)/lc->x, - (atom[i].r.y+moldyn->dim.y/2)/lc->y, - (atom[i].r.z+moldyn->dim.z/2)/lc->z, - neighbour); - for(j=0;j<27;j++) { - bc=jdnlc?0:1; -#ifdef STATIC_LISTS - p=0; - while(neighbour[j][p]!=0) { - btom=&(atom[neighbour[j][p]]); - p++; -#else - list_reset_f(&neighbour[j]); - if(neighbour[j].start==NULL) - continue; - do { - btom=neighbour[j].current->data; -#endif - if(btom==&atom[i]) // skip identical atoms - continue; - //if(btom<&atom[i]) // skip half of them - // continue; - v3_sub(&dist,&(atom[i].r),&(btom->r)); - if(bc) check_per_bound(moldyn,&dist); - d2=v3_absolute_square(&dist); - brand=atom[i].brand; - if(brand==btom->brand) { - if(d2>moldyn->bondlen[brand]) - continue; - } - else { - if(d2>moldyn->bondlen[2]) - continue; - } - dprintf(fd,"# [B] %f %f %f %f %f %f\n", - atom[i].r.x,atom[i].r.y,atom[i].r.z, - btom->r.x,btom->r.y,btom->r.z); -#ifdef STATIC_LISTS - } -#else - } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT); -#endif - } - } - + dprintf(vb.fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element], + atom[i].r.x, + atom[i].r.y, + atom[i].r.z, + pse_col[atom[i].element], + atom[i].ekin); + + // bonds between atoms + process_2b_bonds(moldyn,&vb,visual_bonds_process); + // boundaries if(dim.x) { - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,-dim.y/2,-dim.z/2, dim.x/2,-dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,-dim.y/2,-dim.z/2, -dim.x/2,dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", dim.x/2,dim.y/2,-dim.z/2, dim.x/2,-dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,dim.y/2,-dim.z/2, dim.x/2,dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,-dim.y/2,dim.z/2, dim.x/2,-dim.y/2,dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,-dim.y/2,dim.z/2, -dim.x/2,dim.y/2,dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", dim.x/2,dim.y/2,dim.z/2, dim.x/2,-dim.y/2,dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,dim.y/2,dim.z/2, dim.x/2,dim.y/2,dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,-dim.y/2,dim.z/2, -dim.x/2,-dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", -dim.x/2,dim.y/2,dim.z/2, -dim.x/2,dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", dim.x/2,-dim.y/2,dim.z/2, dim.x/2,-dim.y/2,-dim.z/2); - dprintf(fd,"# [D] %f %f %f %f %f %f\n", + dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n", dim.x/2,dim.y/2,dim.z/2, dim.x/2,dim.y/2,-dim.z/2); } - close(fd); + close(vb.fd); + + return 0; +} + +/* + * 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; }