X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=82ae543c073457a47372253f6c238f76d1bfe6b5;hb=0d1dfb1e5027d215fced8ca306dd658f692a2a44;hp=def5079dbbd949fa55e4f65b9aa4a77e165077db;hpb=4c2140b0f76fb191bdd9b9c2a329877eb0aae531;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index def5079..82ae543 100644 --- a/moldyn.c +++ b/moldyn.c @@ -79,6 +79,52 @@ static char *pse_col[]={ "Ar", }; +/* +static double pse_mass[]={ + 0, + 0, + 0, + 0, + 0, + 0, + M_C, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + M_SI, + 0, + 0, + 0, + 0, +}; + +static double pse_lc[]={ + 0, + 0, + 0, + 0, + 0, + 0, + LC_C, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + LC_SI, + 0, + 0, + 0, + 0, +}; +*/ + /* * the moldyn functions */ @@ -131,24 +177,13 @@ 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 +202,38 @@ 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/t scaling:\n"); + + printf(" p: %s",ptype?"yes":"no "); + if(ptype) + printf(" | type: %02x | factor: %f",ptype,ptc); + printf("\n"); + + return 0; +} + +int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) { + + moldyn->pt_scale&=(~(T_SCALE_MASK)); + moldyn->pt_scale|=ttype; + moldyn->t_tc=ttc; + + printf("[moldyn] p/t scaling:\n"); + + printf(" t: %s",ttype?"yes":"no "); + if(ttype) + printf(" | type: %02x | factor: %f",ttype,ttc); + printf("\n"); + + return 0; +} + int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) { moldyn->pt_scale=(ptype|ttype); @@ -257,6 +324,14 @@ int set_potential(t_moldyn *moldyn,u8 type) { moldyn->func3b_k2=albe_mult_3bp_k2; moldyn->check_2b_bond=albe_mult_check_2b_bond; break; + case MOLDYN_POTENTIAL_HO: + moldyn->func2b=harmonic_oscillator; + moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond; + break; + case MOLDYN_POTENTIAL_LJ: + moldyn->func2b=lennard_jones; + moldyn->check_2b_bond=lennard_jones_check_2b_bond; + break; default: printf("[moldyn] set potential: unknown type %02x\n", type); @@ -499,6 +574,7 @@ 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; @@ -533,18 +609,21 @@ 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); @@ -561,7 +640,7 @@ 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;rettau_square=moldyn->tau*moldyn->tau; - moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff; /* get current time */ gettimeofday(&t1,NULL); @@ -1629,7 +1707,11 @@ 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); @@ -2340,9 +2422,6 @@ int process_2b_bonds(t_moldyn *moldyn,void *data, t_list *this; lc=&(moldyn->lc); - - link_cell_init(moldyn,VERBOSE); - itom=moldyn->atom; for(i=0;icount;i++) { @@ -2406,7 +2485,8 @@ 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; @@ -2697,39 +2777,48 @@ 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; } @@ -2737,118 +2826,65 @@ 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; }