X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.c;h=1d6e0b7dec9e3032df43f33baa692ba078bb5f7a;hp=12cb49b4f7f1cb4fb8d8da5a80727f085dbdad4f;hb=HEAD;hpb=0d2f9a11030dff3583104dac5d4dcb9f040a1327 diff --git a/moldyn.c b/moldyn.c index 12cb49b..1d6e0b7 100644 --- a/moldyn.c +++ b/moldyn.c @@ -34,6 +34,7 @@ #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 @@ -55,6 +56,11 @@ 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 */ @@ -265,19 +271,29 @@ int set_potential(t_moldyn *moldyn,u8 type) { 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->func3b_j1=albe_mult_3bp_j1; - moldyn->func3b_k1=albe_mult_3bp_k1; - moldyn->func3b_j2=albe_mult_3bp_j2; - moldyn->func3b_k2=albe_mult_3bp_k2; + 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->func2b=harmonic_oscillator; + moldyn->func_j0=harmonic_oscillator; moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond; break; case MOLDYN_POTENTIAL_LJ: - moldyn->func2b=lennard_jones; + moldyn->func_j0=lennard_jones; moldyn->check_2b_bond=lennard_jones_check_2b_bond; break; default: @@ -516,7 +532,8 @@ 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 +605,8 @@ 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 +614,8 @@ 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 +623,8 @@ 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"); @@ -802,8 +825,6 @@ int del_atom(t_moldyn *moldyn,int tag) { case DEFECT_STYPE_DB_Z:\ d_o.z=d_params->od;\ d_d.z=d_params->dd;\ -d_d.x=0.9;\ -d_d.y=0.9;\ break;\ case DEFECT_STYPE_DB_R:\ break;\ @@ -2228,6 +2249,59 @@ 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; +} + +/* basis trafo */ + +#define FORWARD 0 +#define BACKWARD 1 + +int basis_trafo(t_3dvec *r,u8 dir,double z,double x) { + + t_3dvec tmp; + + if(dir==FORWARD) { + if(z!=0.0) { + v3_copy(&tmp,r); + r->x=cos(z)*tmp.x-sin(z)*tmp.y; + r->y=sin(z)*tmp.x+cos(z)*tmp.y; + } + if(x!=0.0) { + v3_copy(&tmp,r); + r->y=cos(x)*tmp.y-sin(x)*tmp.z; + r->z=sin(x)*tmp.y+cos(x)*tmp.z; + } + } + else { + if(x!=0.0) { + v3_copy(&tmp,r); + r->y=cos(-x)*tmp.y-sin(-x)*tmp.z; + r->z=sin(-x)*tmp.y+cos(-x)*tmp.z; + } + if(z!=0.0) { + v3_copy(&tmp,r); + r->x=cos(-z)*tmp.x-sin(-z)*tmp.y; + r->y=sin(-z)*tmp.x+cos(-z)*tmp.y; + } + } + return 0; } @@ -2246,13 +2320,44 @@ int velocity_verlet(t_moldyn *moldyn) { tau_square=moldyn->tau_square; for(i=0;ifunc1b) - moldyn->func1b(moldyn,&(itom[i])); + if(moldyn->func_i0) + moldyn->func_i0(moldyn,&(itom[i])); if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP))) continue; @@ -2382,8 +2514,14 @@ 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->func2b) { + if(moldyn->func_j0) { for(j=0;j<27;j++) { bc_ij=(jrun3bp=1; + if((jtom->attr&ATOM_ATTR_2BP)& (itom[i].attr&ATOM_ATTR_2BP)) { - moldyn->func2b(moldyn, - &(itom[i]), - jtom, - bc_ij); + 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 } @@ -2433,7 +2628,7 @@ int potential_force_calc(t_moldyn *moldyn) { } } - /* 3 body potential/force */ + /* continued 3 body potential/force */ if(!(itom[i].attr&ATOM_ATTR_3BP)) continue; @@ -2486,18 +2681,18 @@ int potential_force_calc(t_moldyn *moldyn) { /* reset 3bp run */ moldyn->run3bp=1; - if(moldyn->func3b_j1) - moldyn->func3b_j1(moldyn, - &(itom[i]), - jtom, - bc_ij); + if(moldyn->func_j1) + moldyn->func_j1(moldyn, + &(itom[i]), + jtom, + bc_ij); - /* in first j loop, 3bp run can be skipped */ + /* in j loop, 3bp run can be skipped */ if(!(moldyn->run3bp)) continue; - /* first loop over atoms k */ - if(moldyn->func3b_k1) { + /* first loop over atoms k in second j loop */ + if(moldyn->func_j1_k0) { for(k=0;k<27;k++) { @@ -2530,8 +2725,8 @@ int potential_force_calc(t_moldyn *moldyn) { if(!(ktom->attr&ATOM_ATTR_3BP)) continue; - if(ktom==jtom) - continue; + //if(ktom==jtom) + // continue; if(ktom==&(itom[i])) continue; @@ -2555,14 +2750,15 @@ int potential_force_calc(t_moldyn *moldyn) { } - if(moldyn->func3b_j2) - moldyn->func3b_j2(moldyn, - &(itom[i]), - jtom, - bc_ij); + /* 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->func3b_k2) { + if(moldyn->func_j1_k1) { for(k=0;k<27;k++) { @@ -2595,17 +2791,17 @@ int potential_force_calc(t_moldyn *moldyn) { if(!(ktom->attr&ATOM_ATTR_3BP)) continue; - if(ktom==jtom) - continue; + //if(ktom==jtom) + // continue; if(ktom==&(itom[i])) continue; - moldyn->func3b_k2(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 } @@ -2620,11 +2816,11 @@ int potential_force_calc(t_moldyn *moldyn) { } - /* 2bp post function */ - if(moldyn->func3b_j3) { - moldyn->func3b_j3(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 } @@ -2635,7 +2831,7 @@ int potential_force_calc(t_moldyn *moldyn) { #endif } - + #ifdef DEBUG //printf("\n\n"); #endif @@ -2862,7 +3058,7 @@ 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); @@ -3148,6 +3344,57 @@ 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;