X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=433be6824c9663f9bfa745ca0b82d08b566abd2b;hb=refs%2Fheads%2Forigin;hp=c21f59f516df771c5153db16232bd844db6064a8;hpb=115ab83cedba54af2d165b8900781b98c5326b55;p=physik%2Fposic.git diff --git a/moldyn.c b/moldyn.c index c21f59f..433be68 100644 --- a/moldyn.c +++ b/moldyn.c @@ -16,9 +16,12 @@ #include #include "moldyn.h" +#include "report/report.h" int moldyn_init(t_moldyn *moldyn,int argc,char **argv) { + printf("[moldyn] init\n"); + memset(moldyn,0,sizeof(t_moldyn)); rand_init(&(moldyn->random),NULL,1); @@ -30,6 +33,7 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) { int moldyn_shutdown(t_moldyn *moldyn) { printf("[moldyn] shutdown\n"); + moldyn_log_shutdown(moldyn); link_cell_shutdown(moldyn); rand_close(&(moldyn->random)); @@ -40,12 +44,16 @@ int moldyn_shutdown(t_moldyn *moldyn) { int set_int_alg(t_moldyn *moldyn,u8 algo) { + printf("[moldyn] integration algorithm: "); + switch(algo) { case MOLDYN_INTEGRATE_VERLET: moldyn->integrate=velocity_verlet; + printf("velocity verlet\n"); break; default: printf("unknown integration algorithm: %02x\n",algo); + printf("unknown\n"); return -1; } @@ -56,6 +64,8 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) { moldyn->cutoff=cutoff; + printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff); + return 0; } @@ -63,6 +73,8 @@ int set_temperature(t_moldyn *moldyn,double t_ref) { moldyn->t_ref=t_ref; + printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref); + return 0; } @@ -70,6 +82,8 @@ int set_pressure(t_moldyn *moldyn,double p_ref) { moldyn->p_ref=p_ref; + printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR); + return 0; } @@ -79,6 +93,18 @@ int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) { moldyn->t_tc=ttc; 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"); + + printf(" t: %s",ttype?"yes":"no "); + if(ttype) + printf(" | type: %02x | factor: %f",ttype,ttc); + printf("\n"); + return 0; } @@ -96,12 +122,15 @@ 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?"on":"off"); + printf(" visualize simulation box: %s\n",visualize?"yes":"no"); + printf(" delta volume (pressure calc): %f\n",moldyn->dv); return 0; } @@ -115,6 +144,8 @@ int set_nn_dist(t_moldyn *moldyn,double dist) { int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) { + printf("[moldyn] periodic boundary conditions:\n"); + if(x) moldyn->status|=MOLDYN_STAT_PBX; @@ -124,37 +155,73 @@ int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) { if(z) moldyn->status|=MOLDYN_STAT_PBZ; + printf(" x: %s\n",x?"yes":"no"); + printf(" y: %s\n",y?"yes":"no"); + printf(" z: %s\n",z?"yes":"no"); + return 0; } -int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) { +int set_potential1b(t_moldyn *moldyn,pf_func1b func) { moldyn->func1b=func; - moldyn->pot1b_params=params; return 0; } -int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) { +int set_potential2b(t_moldyn *moldyn,pf_func2b func) { moldyn->func2b=func; - moldyn->pot2b_params=params; return 0; } -int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) { +int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) { + + moldyn->func3b_j1=func; + + return 0; +} + +int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) { + + moldyn->func3b_j2=func; + + return 0; +} + +int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) { + + moldyn->func3b_j3=func; + + return 0; +} + +int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) { + + moldyn->func3b_k1=func; + + return 0; +} + +int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) { - moldyn->func2b_post=func; - moldyn->pot2b_params=params; + moldyn->func3b_k2=func; return 0; } -int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) { +int set_potential_params(t_moldyn *moldyn,void *params) { - moldyn->func3b=func; - moldyn->pot3b_params=params; + moldyn->pot_params=params; + + return 0; +} + +int set_avg_skip(t_moldyn *moldyn,int skip) { + + printf("[moldyn] skip %d steps before starting average calc\n",skip); + moldyn->avg_skip=skip; return 0; } @@ -165,12 +232,22 @@ int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) { return 0; } + +int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) { + + strncpy(moldyn->rauthor,author,63); + strncpy(moldyn->rtitle,title,63); + + return 0; +} int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { char filename[128]; int ret; + printf("[moldyn] set log: "); + switch(type) { case LOG_TOTAL_ENERGY: moldyn->ewrite=timer; @@ -183,6 +260,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { return moldyn->efd; } dprintf(moldyn->efd,"# total energy log file\n"); + printf("total energy (%d)\n",timer); break; case LOG_TOTAL_MOMENTUM: moldyn->mwrite=timer; @@ -195,9 +273,37 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { return moldyn->mfd; } 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 SAVE_STEP: moldyn->swrite=timer; + printf("save file (%d)\n",timer); break; case VISUAL_STEP: moldyn->vwrite=timer; @@ -206,9 +312,66 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { printf("[moldyn] visual init failure\n"); return ret; } + printf("visual file (%d)\n",timer); + break; + case CREATE_REPORT: + snprintf(filename,127,"%s/report.tex",moldyn->vlsdir); + moldyn->rfd=open(filename, + O_WRONLY|O_CREAT|O_EXCL, + S_IRUSR|S_IWUSR); + if(moldyn->rfd<0) { + perror("[moldyn] report fd open"); + return moldyn->rfd; + } + 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); + printf("\n"); break; default: - printf("[moldyn] unknown log mechanism: %02x\n",type); + printf("unknown log type: %02x\n",type); return -1; } @@ -217,9 +380,48 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) { 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 && pdflatex report >/dev/null 2>&1", + moldyn->vlsdir); + system(sc); + snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1", + moldyn->vlsdir); + system(sc); + snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1", + moldyn->vlsdir); + system(sc); + } if(&(moldyn->vis)) visual_tini(&(moldyn->vis)); return 0; @@ -230,11 +432,11 @@ int moldyn_log_shutdown(t_moldyn *moldyn) { */ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, - u8 attr,u8 brand,int a,int b,int c) { + u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) { int new,count; int ret; - t_3dvec origin; + t_3dvec orig; void *ptr; t_atom *atom; @@ -242,6 +444,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, count=moldyn->count; /* how many atoms do we expect */ + if(type==CUBIC) new*=1; if(type==FCC) new*=4; if(type==DIAMOND) new*=8; @@ -253,15 +456,35 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, } moldyn->atom=ptr; atom=&(moldyn->atom[count]); - - v3_zero(&origin); + + /* 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: + set_nn_dist(moldyn,lc); + ret=cubic_init(a,b,c,lc,atom,&orig); + break; case FCC: - ret=fcc_init(a,b,c,lc,atom,&origin); + 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); break; case DIAMOND: - ret=diamond_init(a,b,c,lc,atom,&origin); + 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); break; default: printf("unknown lattice type (%02x)\n",type); @@ -289,72 +512,103 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass, check_per_bound(moldyn,&(atom[ret].r)); } + /* update total system mass */ + total_mass_calc(moldyn); + return ret; } +/* cubic init */ +int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) { + + int count; + t_3dvec r; + int i,j,k; + t_3dvec o; + + count=0; + if(origin) + v3_copy(&o,origin); + else + v3_zero(&o); + + r.x=o.x; + for(i=0;iatom; random=&(moldyn->random); + printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no"); + /* gaussian distribution of velocities */ v3_zero(&p_total); for(i=0;icount;i++) { @@ -460,6 +719,32 @@ 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); + + return moldyn->t; +} + +double get_temperature(t_moldyn *moldyn) { + + return moldyn->t; +} + int scale_velocity(t_moldyn *moldyn,u8 equi_init) { int i; @@ -478,10 +763,11 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) { count=0; for(i=0;icount;i++) { if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) { - e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v)); + e+=atom[i].mass*v3_absolute_square(&(atom[i].v)); count+=1; } } + e*=0.5; if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN); else return 0; /* no atoms involved in scaling! */ @@ -515,70 +801,295 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) { return 0; } +double ideal_gas_law_pressure(t_moldyn *moldyn) { + + double p; + + p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume; + + return p; +} + +double virial_sum(t_moldyn *moldyn) { + + int i; + double v; + t_virial *virial; + + /* virial (sum over atom virials) */ + v=0.0; + for(i=0;icount;i++) { + virial=&(moldyn->atom[i].virial); + v+=(virial->xx+virial->yy+virial->zz); + } + moldyn->virial=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); + + /* pressure (absolute coordinates) */ + moldyn->gp=2.0*moldyn->ekin+moldyn->gv; + moldyn->gp/=(3.0*moldyn->volume); + + return moldyn->p; +} + +int average_and_fluctuation_calc(t_moldyn *moldyn) { + + if(moldyn->total_stepsavg_skip) + return 0; + + int 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; + + 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_up,u_down,dv; + double scale,p; + t_atom *store; + + /* + * dU = - p dV + * + * => p = - dU/dV + * + */ + + scale=0.00001; + dv=8*scale*scale*scale*moldyn->volume; + + 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 */ + memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom)); + dim=moldyn->dim; + + /* scale up dimension and atom positions */ + scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE); + scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE); + link_cell_shutdown(moldyn); + link_cell_init(moldyn,QUIET); + potential_force_calc(moldyn); + u_up=moldyn->energy; + + /* restore atomic configuration + dim */ + memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom)); + moldyn->dim=dim; + + /* scale down dimension and atom positions */ + scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE); + scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE); + link_cell_shutdown(moldyn); + link_cell_init(moldyn,QUIET); + potential_force_calc(moldyn); + u_down=moldyn->energy; + + /* calculate pressure */ + p=-(u_up-u_down)/dv; +printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR); + + /* restore atomic configuration + dim */ + memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom)); + moldyn->dim=dim; + + /* restore energy */ + potential_force_calc(moldyn); + + link_cell_shutdown(moldyn); + link_cell_init(moldyn,QUIET); + + return p; +} + +double get_pressure(t_moldyn *moldyn) { + + return moldyn->p; + +} + +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; + + return 0; +} + +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; + if(y) r->y*=scale; + if(z) r->z*=scale; + } + + 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; - 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; + scale=pow(scale,ONE_THIRD); + } + else { + scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD); + } +moldyn->debug=scale; + + /* scale the atoms and dimensions */ + scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE); + scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE); - 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; + /* visualize dimensions */ + if(vdim->x!=0) { + vdim->x=dim->x; + vdim->y=dim->y; + vdim->z=dim->z; } - /* 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)) { + /* 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; } return 0; } -double get_e_kin(t_moldyn *moldyn) { +double e_kin_calc(t_moldyn *moldyn) { int i; t_atom *atom; @@ -592,16 +1103,6 @@ double get_e_kin(t_moldyn *moldyn) { return moldyn->ekin; } -double get_e_pot(t_moldyn *moldyn) { - - return moldyn->energy; -} - -double update_e_kin(t_moldyn *moldyn) { - - return(get_e_kin(moldyn)); -} - double get_total_energy(t_moldyn *moldyn) { return(moldyn->ekin+moldyn->energy); @@ -641,7 +1142,7 @@ 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; int i; @@ -659,7 +1160,15 @@ int link_cell_init(t_moldyn *moldyn) { lc->cells=lc->nx*lc->ny*lc->nz; lc->subcell=malloc(lc->cells*sizeof(t_list)); - printf("[moldyn] initializing linked cells (%d)\n",lc->cells); + if(lc->cells<27) + printf("[moldyn] FATAL: less then 27 subcells!\n"); + + if(vol) { + printf("[moldyn] initializing linked cells (%d)\n",lc->cells); + 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); + } for(i=0;icells;i++) list_init_f(&(lc->subcell[i])); @@ -694,7 +1203,7 @@ int link_cell_update(t_moldyn *moldyn) { 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]), + list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]), &(atom[count])); } @@ -797,10 +1306,14 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) { schedule->tau=ptr; schedule->tau[count-1]=tau; + printf("[moldyn] schedule added:\n"); + printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau); + + return 0; } -int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) { +int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) { moldyn->schedule.hook=hook; moldyn->schedule.hook_params=hook_params; @@ -819,32 +1332,42 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,void *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; + t_3dvec momentum; t_moldyn_schedule *sched; t_atom *atom; int fd; char dir[128]; double ds; + double energy_scale; + //double tp; 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; + 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; + /* calculate initial forces */ potential_force_calc(moldyn); +#ifdef DEBUG +return 0; +#endif /* some stupid checks before we actually start calculating bullshit */ if(moldyn->cutoff>0.5*moldyn->dim.x) @@ -859,12 +1382,17 @@ int moldyn_integrate(t_moldyn *moldyn) { /* zero absolute time */ moldyn->time=0.0; + moldyn->total_steps=0; /* debugging, ignore */ moldyn->debug=0; + /* 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]; @@ -878,6 +1406,13 @@ int moldyn_integrate(t_moldyn *moldyn) { /* integration step */ moldyn->integrate(moldyn); + /* calculate kinetic energy, temperature and pressure */ + e_kin_calc(moldyn); + temperature_calc(moldyn); + virial_sum(moldyn); + pressure_calc(moldyn); + average_and_fluctuation_calc(moldyn); + /* p/t scaling */ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT)) scale_velocity(moldyn,FALSE); @@ -889,15 +1424,32 @@ int moldyn_integrate(t_moldyn *moldyn) { if(!(i%e)) dprintf(moldyn->efd, "%f %f %f %f\n", - moldyn->time,update_e_kin(moldyn), - moldyn->energy, - get_total_energy(moldyn)); + moldyn->time,moldyn->ekin/energy_scale, + moldyn->energy/energy_scale, + get_total_energy(moldyn)/energy_scale); } if(m) { if(!(i%m)) { - p=get_total_p(moldyn); + 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(!(i%p)) { + dprintf(moldyn->pfd, + "%f %f %f %f %f\n",moldyn->time, + moldyn->p/BAR,moldyn->p_avg/BAR, + moldyn->gp/BAR,moldyn->gp_avg/BAR); + } + } + if(t) { + if(!(i%t)) { + dprintf(moldyn->tfd, + "%f %f %f\n", + moldyn->time,moldyn->t,moldyn->t_avg); } } if(s) { @@ -918,23 +1470,35 @@ int moldyn_integrate(t_moldyn *moldyn) { if(!(i%v)) { visual_atoms(&(moldyn->vis),moldyn->time, moldyn->atom,moldyn->count); - printf("\rsched: %d, steps: %d, debug: %d", - sched->count,i,moldyn->debug); - fflush(stdout); } } + /* display progress */ + if(!(i%10)) { + printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f", + sched->count,i, + moldyn->t,moldyn->t_avg, + moldyn->p_avg/BAR,moldyn->p/BAR, + moldyn->volume); + fflush(stdout); + } + /* 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/%d start ##\n", + sched->count+1,sched->total_sched-1); 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; } @@ -946,7 +1510,7 @@ int moldyn_integrate(t_moldyn *moldyn) { int velocity_verlet(t_moldyn *moldyn) { int i,count; - double tau,tau_square; + double tau,tau_square,h; t_3dvec delta; t_atom *atom; @@ -957,14 +1521,15 @@ int velocity_verlet(t_moldyn *moldyn) { for(i=0;ienergy=0.0; - - /* get energy and force of every atom */ + + /* reset global virial */ + memset(&(moldyn->gvir),0,sizeof(t_virial)); + + /* reset force, site energy and virial of every atom */ for(i=0;ixx=0.0; virial->yy=0.0; virial->zz=0.0; virial->xy=0.0; virial->xz=0.0; virial->yz=0.0; - + /* reset site energy */ itom[i].e=0.0; + } + + /* get energy, force and virial of every atom */ + + /* first (and only) loop over atoms i */ + for(i=0;ifunc1b(moldyn,&(itom[i])); + if(moldyn->func1b) + moldyn->func1b(moldyn,&(itom[i])); if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP))) continue; @@ -1046,6 +1622,45 @@ int potential_force_calc(t_moldyn *moldyn) { dnlc=lc->dnlc; + /* first loop over atoms j */ + if(moldyn->func2b) { + for(j=0;j<27;j++) { + + this=&(neighbour_i[j]); + list_reset_f(this); + + if(this->start==NULL) + continue; + + bc_ij=(jcurrent->data; + + 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); + } + } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); + + } + } + + /* 3 body potential/force */ + + if(!(itom[i].attr&ATOM_ATTR_3BP)) + continue; + + /* copy the neighbour lists */ + memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list)); + + /* second loop over atoms j */ for(j=0;j<27;j++) { this=&(neighbour_i[j]); @@ -1062,25 +1677,25 @@ int potential_force_calc(t_moldyn *moldyn) { 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->func3b_j1) + moldyn->func3b_j1(moldyn, + &(itom[i]), + jtom, + bc_ij); - /* copy the neighbour lists */ - memcpy(neighbour_i2,neighbour_i, - 27*sizeof(t_list)); + /* in first j loop, 3bp run can be skipped */ + if(!(moldyn->run3bp)) + continue; + + /* first loop over atoms k */ + if(moldyn->func3b_k1) { - /* get neighbours of i */ for(k=0;k<27;k++) { that=&(neighbour_i2[k]); @@ -1104,831 +1719,150 @@ int potential_force_calc(t_moldyn *moldyn) { if(ktom==&(itom[i])) continue; - moldyn->func3b(moldyn, - &(itom[i]), - jtom, - ktom, - bc_ik|bc_ij); + moldyn->func3b_k1(moldyn, + &(itom[i]), + jtom, + ktom, + bc_ik|bc_ij); } while(list_next_f(that)!=\ L_NO_NEXT_ELEMENT); } - /* 2bp post function */ - if(moldyn->func2b_post) { - moldyn->func2b_post(moldyn, - &(itom[i]), - jtom,bc_ij); } - - } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); - - } - - } -#ifdef DEBUG -printf("\n\n"); -#endif -#ifdef VDEBUG -printf("\n\n"); -#endif - - return 0; -} - -/* - * periodic boundayr checking - */ - -inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) { - - double x,y,z; - t_3dvec *dim; - - dim=&(moldyn->dim); - - x=dim->x/2; - y=dim->y/2; - z=dim->z/2; - - if(moldyn->status&MOLDYN_STAT_PBX) { - if(a->x>=x) a->x-=dim->x; - else if(-a->x>x) a->x+=dim->x; - } - if(moldyn->status&MOLDYN_STAT_PBY) { - if(a->y>=y) a->y-=dim->y; - else if(-a->y>y) a->y+=dim->y; - } - if(moldyn->status&MOLDYN_STAT_PBZ) { - if(a->z>=z) a->z-=dim->z; - else if(-a->z>z) a->z+=dim->z; - } - - return 0; -} - - -/* - * 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; - double sc,equi_dist; - - params=moldyn->pot2b_params; - sc=params->spring_constant; - equi_dist=params->equilibrium_distance; - - v3_sub(&distance,&(aj->r),&(ai->r)); - - if(bc) check_per_bound(moldyn,&distance); - d=v3_norm(&distance); - if(d<=moldyn->cutoff) { - /* energy is 1/2 (d-d0)^2, but we will add this twice ... */ - moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist)); - /* f = -grad E; grad r_ij = -1 1/r_ij distance */ - v3_scale(&force,&distance,sc*(1.0-(equi_dist/d))); - v3_add(&(ai->f),&(ai->f),&force); - } - - return 0; -} - -/* 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; - - v3_sub(&distance,&(aj->r),&(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 */ - /* energy is eps*..., but we will add this twice ... */ - moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2); - 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,-1.0*d); /* f = - grad E */ - v3_add(&(ai->f),&(ai->f),&force); - } - - return 0; -} - -/* - * tersoff potential & force for 2 sorts of atoms - */ - -/* 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); - - return 0; -} -/* tersoff 1 body part */ -int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) { + if(moldyn->func3b_j2) + moldyn->func3b_j2(moldyn, + &(itom[i]), + jtom, + bc_ij); - int brand; - t_tersoff_mult_params *params; - t_tersoff_exchange *exchange; - - brand=ai->brand; - params=moldyn->pot1b_params; - exchange=&(params->exchange); + /* second loop over atoms k */ + if(moldyn->func3b_k2) { - /* - * simple: point constant parameters only depending on atom i to - * their right values - */ + for(k=0;k<27;k++) { - 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]); + that=&(neighbour_i2[k]); + list_reset_f(that); + + if(that->start==NULL) + continue; - 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; + bc_ik=(kpot2b_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 - * - */ + do { - /* 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; - } + ktom=that->current->data; - /* 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(!(ktom->attr&ATOM_ATTR_3BP)) + continue; - /* if d_ij2 > S2 => no force & potential energy contribution */ - if(d_ij2>S2) - return 0; + if(ktom==jtom) + continue; - /* 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; - } + if(ktom==&(itom[i])) + continue; - /* 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; - - /* 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; - - /* f_c, df_c calc (again, same for ij and ji) */ - if(d_ij r > R */ - exchange->d_ij_between_rs=1; - } + moldyn->func3b_k2(moldyn, + &(itom[i]), + jtom, + ktom, + bc_ik|bc_ij); - /* 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(list_next_f(that)!=\ + L_NO_NEXT_ELEMENT); - /* 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; + } + + } + /* 2bp post function */ + if(moldyn->func3b_j3) { + moldyn->func3b_j3(moldyn, + &(itom[i]), + jtom,bc_ij); + } + + } while(list_next_f(this)!=L_NO_NEXT_ELEMENT); + + } + #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); -} + //printf("\n\n"); #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); -} + printf("\n\n"); #endif - /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */ - moldyn->energy+=(0.5*f_r*f_c); - - /* save for use in 3bp */ - exchange->f_c=f_c; - exchange->df_c=df_c; - - /* enable the run of 3bp function and 2bp post processing */ - exchange->run3bp=1; - exchange->run2bp_post=1; - - /* reset 3bp sums */ - exchange->zeta_ij=0.0; - exchange->zeta_ji=0.0; - v3_zero(&(exchange->dzeta_ij)); - v3_zero(&(exchange->dzeta_ji)); - - return 0; -} - -/* tersoff 2 body post part */ - -int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { - - /* - * 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 - * - */ - - t_tersoff_mult_params *params; - t_tersoff_exchange *exchange; - - 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; - - params=moldyn->pot2b_params; - exchange=&(params->exchange); - - /* we do not run if f_c_ij was detected to be 0! */ - if(!(exchange->run2bp_post)) - return 0; - - 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 ... */ - db=0.0; - b=chi; - v3_scale(&force,dist_ij,df_a*b*f_c); } - 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; #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); -} + printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->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); -} -#endif - - /* add energy of 3bp sum */ - moldyn->energy+=(0.5*f_c*b*f_a); - /* dVji */ - zeta=exchange->zeta_ji; - if(zeta==0.0) { - moldyn->debug++; - b=chi; - v3_scale(&force,dist_ij,df_a*b*f_c); - } - 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); + /* calculate global virial */ + for(i=0;igvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x; + moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y; + moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z; + moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x; + moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x; + moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y; } - 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??) */ - 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); -} -#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); -} -#endif 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; - - /* - * 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 - * - */ - - /* - * get exchange data - */ +/* + * virial calculation + */ - /* dist_ij, d_ij - this is < S_ij ! */ - dist_ij=exchange->dist_ij; - d_ij=exchange->d_ij; - d_ij2=exchange->d_ij2; +//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) { - /* f_c_ij, df_c_ij (same for ji) */ - f_c=exchange->f_c; - df_c=exchange->df_c; + a->virial.xx+=f->x*d->x; + a->virial.yy+=f->y*d->y; + a->virial.zz+=f->z*d->z; + a->virial.xy+=f->x*d->y; + a->virial.xz+=f->x*d->z; + a->virial.yz+=f->y*d->z; - /* - * calculate unknown values now ... - */ + return 0; +} - /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */ +/* + * periodic boundary checking + */ - /* 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); +//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; - /* ik constants */ - brand=ai->brand; - if(brand==ak->brand) { - R=params->R[brand]; - S=params->S[brand]; - S2=params->S2[brand]; - } - else { - R=params->Rmixed; - S=params->Smixed; - S2=params->S2mixed; - } + dim=&(moldyn->dim); - /* 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); - } - } + x=dim->x/2; + y=dim->y/2; + z=dim->z/2; - /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */ - - /* 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); - - /* 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(moldyn->status&MOLDYN_STAT_PBX) { + if(a->x>=x) a->x-=dim->x; + else if(-a->x>x) a->x+=dim->x; } - else { - R=params->Rmixed; - S=params->Smixed; - S2=params->S2mixed; - B=params->Bmixed; - mu=params->mu_m; - chi=params->chi; + if(moldyn->status&MOLDYN_STAT_PBY) { + if(a->y>=y) a->y-=dim->y; + else if(-a->y>y) a->y+=dim->y; } - - /* 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); - } - 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; - - /* dzeta_ji */ - v3_scale(&temp1,&temp1,f_c_jk); - v3_add(dzeta,dzeta,&temp1); - } - - /* 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; - -#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); -} -#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); -} -#endif - + if(moldyn->status&MOLDYN_STAT_PBZ) { + if(a->z>=z) a->z-=dim->z; + else if(-a->z>z) a->z+=dim->z; } return 0; } - - + /* * debugging / critical check functions */ @@ -1980,3 +1914,26 @@ int moldyn_bc_check(t_moldyn *moldyn) { return 0; } + +/* + * 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') { + line[count]='\0'; + return count+1; + } + count+=1; + } +} +