X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.c;h=bd29afc9a3e6853bded38acae91dfafdf15a662a;hp=bc4fdffdee29be7341c67692f1a3282bc049927b;hb=8524173a28f2c22a539ef1b0910a1136d9cb254b;hpb=dfb47bde6bf974d1b231048ec8bcda712404ccc1 diff --git a/moldyn.c b/moldyn.c index bc4fdff..bd29afc 100644 --- a/moldyn.c +++ b/moldyn.c @@ -78,6 +78,14 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) { pthread_mutex_init(&emutex,NULL); #endif +#ifdef CONSTRAINT_110_5832 + printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n"); + printf("\n\n\n!! -- constraints enabled -- !!\n\n\n"); +#endif +#ifdef CONSTRAINT_11X_5832 + printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n"); + printf("\n\n\n!! -- constraints enabled -- !!\n\n\n"); +#endif return 0; } @@ -258,7 +266,7 @@ int set_potential(t_moldyn *moldyn,u8 type) { switch(type) { case MOLDYN_POTENTIAL_TM: - moldyn->func1b=tersoff_mult_1bp; + //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; @@ -516,7 +524,8 @@ int moldyn_log_shutdown(t_moldyn *moldyn) { 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_part_params *p_params,t_defect_params *d_params, + t_offset_params *o_params) { int new,count; int ret; @@ -588,6 +597,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element, switch(type) { case CUBIC: + if(o_params->use) + v3_add(&orig,&orig,&(o_params->o)); set_nn_dist(moldyn,lc); ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params); strcpy(name,"cubic"); @@ -595,6 +606,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element, case FCC: 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"); @@ -602,6 +615,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element, case DIAMOND: 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"); @@ -736,6 +751,9 @@ 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; @@ -758,6 +776,28 @@ int del_atom(t_moldyn *moldyn,int tag) { 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; } @@ -2046,11 +2086,11 @@ int moldyn_integrate(t_moldyn *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); @@ -2065,10 +2105,11 @@ int moldyn_integrate(t_moldyn *moldyn) { if(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(!(moldyn->total_steps%m)) { @@ -2156,15 +2197,20 @@ int moldyn_integrate(t_moldyn *moldyn) { } /* 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, - //moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/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)); @@ -2172,7 +2218,9 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n", /* copy over time */ t1=t2; +#ifndef PDEBUG } +#endif /* increase absolute time */ moldyn->time+=moldyn->tau; @@ -2193,6 +2241,22 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n", } + /* 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; } @@ -2204,12 +2268,44 @@ int velocity_verlet(t_moldyn *moldyn) { double tau,tau_square,h; t_3dvec delta; t_atom *atom; +#ifdef CONSTRAINT_11X_5832 + double xt,yt,zt; + double xtt,ytt,ztt; +#endif atom=moldyn->atom; count=moldyn->count; tau=moldyn->tau; tau_square=moldyn->tau_square; +#ifdef CONSTRAINT_110_5832 + if(count==5833) { + atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y); + atom[5832].f.y=-atom[5832].f.x; + } +#endif +#ifdef CONSTRAINT_11X_5832 + if(count==5833) { + // second trafo + xt=atom[5832].f.x; + yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129); + zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129); + // first trafo + xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0); + ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0); + ztt=zt; + // apply constraints + ytt=0.0; + // first trafo backwards + xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0); + yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0); + zt=ztt; + // second trafo backwards + atom[5832].f.x=xt; + atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129); + atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129); + } +#endif 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 +#ifdef CONSTRAINT_110_5832 + if(count==5833) { + atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y); + atom[5832].f.y=-atom[5832].f.x; + } +#endif +#ifdef CONSTRAINT_11X_5832 + if(count==5833) { + // second trafo + xt=atom[5832].f.x; + yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129); + zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129); + // first trafo + xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0); + ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0); + ztt=zt; + // apply constraints + ytt=0.0; + // first trafo backwards + xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0); + yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0); + zt=ztt; + // second trafo backwards + atom[5832].f.x=xt; + atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129); + atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129); + } +#endif for(i=0;idim); + + x=dim->x/2; + y=dim->y/2; + z=dim->z/2; + + if(moldyn->status&MOLDYN_STAT_PBX) { + if(a->r.x>=x) { + a->pbc[0]+=1; + a->r.x-=dim->x; + } + else if(-a->r.x>x) { + a->pbc[0]-=1; + a->r.x+=dim->x; + } + } + if(moldyn->status&MOLDYN_STAT_PBY) { + if(a->r.y>=y) { + a->pbc[1]+=1; + a->r.y-=dim->y; + } + else if(-a->r.y>y) { + a->pbc[1]-=1; + a->r.y+=dim->y; + } + } + if(moldyn->status&MOLDYN_STAT_PBZ) { + if(a->r.z>=z) { + a->pbc[2]+=1; + a->r.z-=dim->z; + } + else if(-a->r.z>z) { + a->pbc[2]-=1; + a->r.z+=dim->z; + } + } + + return 0; +} + /* * debugging / critical check functions */ @@ -2777,7 +3011,7 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) { if(fsize!=sizeof(t_moldyn)+size) { corr=fsize-sizeof(t_moldyn)-size; printf("[moldyn] WARNING: lsf (illegal file size)\n"); - printf(" moifying offset:\n"); + printf(" modifying offset:\n"); printf(" - current pos: %d\n",sizeof(t_moldyn)); printf(" - atom size: %d\n",size); printf(" - file size: %d\n",fsize); @@ -3022,6 +3256,7 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) { int i; t_atom *atom; t_3dvec dist; + t_3dvec final_r; double d2; int a_cnt; int b_cnt; @@ -3035,8 +3270,12 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) { for(i=0;icount;i++) { - v3_sub(&dist,&(atom[i].r),&(atom[i].r_0)); - check_per_bound(moldyn,&dist); + /* 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) { @@ -3058,6 +3297,57 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) { return 0; } +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; +} + int bonding_analyze(t_moldyn *moldyn,double *cnt) { return 0; @@ -3203,9 +3493,8 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, ba=data; /* increase total bond counter - * ... double counting! */ - ba->tcnt+=2; + ba->tcnt+=1; if(itom->brand==0) ba->acnt[jtom->tag]+=1; @@ -3222,10 +3511,11 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom, int bond_analyze(t_moldyn *moldyn,double *quality) { - // by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total - - int qcnt; - int ccnt,cset; + int qcnt4; + int qcnt3; + int ccnt4; + int ccnt3; + int bcnt; t_ba ba; int i; t_atom *atom; @@ -3245,9 +3535,9 @@ int bond_analyze(t_moldyn *moldyn,double *quality) { memset(ba.bcnt,0,moldyn->count*sizeof(int)); ba.tcnt=0; - qcnt=0; - ccnt=0; - cset=0; + qcnt4=0; qcnt3=0; + ccnt4=0; ccnt3=0; + bcnt=0; atom=moldyn->atom; @@ -3256,27 +3546,30 @@ int bond_analyze(t_moldyn *moldyn,double *quality) { for(i=0;icount;i++) { if(atom[i].brand==0) { if((ba.acnt[i]==0)&(ba.bcnt[i]==4)) - qcnt+=4; + qcnt4+=4; + if((ba.acnt[i]==0)&(ba.bcnt[i]==3)) + qcnt3+=3; } else { if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) { - qcnt+=4; - ccnt+=1; + qcnt4+=4; + ccnt4+=1; + } + if((ba.acnt[i]==3)&(ba.bcnt[i]==0)) { + qcnt3+=4; + ccnt3+=1; } - cset+=1; + bcnt+=1; } } - printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset); - printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt); - if(quality) { - quality[0]=1.0*ccnt/cset; - quality[1]=1.0*qcnt/ba.tcnt; + quality[0]=1.0*ccnt4/bcnt; + quality[1]=1.0*ccnt3/bcnt; } else { - printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt); - printf("[moldyn] bond analyze: tot_q=%f\n",1.0*qcnt/ba.tcnt); + printf("[moldyn] bond analyze: %f %f\n", + 1.0*ccnt4/bcnt,1.0*ccnt3/bcnt); } return 0;