From 7c856cfd07e2e9d57ff0af3172b7f271fc5b22e0 Mon Sep 17 00:00:00 2001 From: hackbard Date: Thu, 10 Jul 2008 22:11:59 +0200 Subject: [PATCH] secured original albe implementation --- potentials/albe_orig.c | 548 +++++++++++++++++++++++++++++++++++++++++ potentials/albe_orig.h | 131 ++++++++++ 2 files changed, 679 insertions(+) create mode 100644 potentials/albe_orig.c create mode 100644 potentials/albe_orig.h diff --git a/potentials/albe_orig.c b/potentials/albe_orig.c new file mode 100644 index 0000000..c01ab15 --- /dev/null +++ b/potentials/albe_orig.c @@ -0,0 +1,548 @@ +/* + * albe.c - albe potential + * + * author: Frank Zirkelbach + * + */ + +#define _GNU_SOURCE +#include +#include +#include +#include +#include +#include +#include +#include + +#include "../moldyn.h" +#include "../math/math.h" +#include "albe.h" + +/* create mixed terms from parameters and set them */ +int albe_mult_set_params(t_moldyn *moldyn,int element1,int element2) { + + t_albe_mult_params *p; + + // set cutoff before parameters (actually only necessary for some pots) + if(moldyn->cutoff==0.0) { + printf("[albe] WARNING: no cutoff!\n"); + return -1; + } + + /* alloc mem for potential parameters */ + moldyn->pot_params=malloc(sizeof(t_albe_mult_params)); + if(moldyn->pot_params==NULL) { + perror("[albe] pot params alloc"); + return -1; + } + + /* these are now albe parameters */ + p=moldyn->pot_params; + + // only 1 combination by now :p + switch(element1) { + case SI: + /* type: silicon */ + p->S[0]=ALBE_S_SI; + p->R[0]=ALBE_R_SI; + p->A[0]=ALBE_A_SI; + p->B[0]=ALBE_B_SI; + p->r0[0]=ALBE_R0_SI; + p->lambda[0]=ALBE_LAMBDA_SI; + p->mu[0]=ALBE_MU_SI; + p->gamma[0]=ALBE_GAMMA_SI; + p->c[0]=ALBE_C_SI; + p->d[0]=ALBE_D_SI; + p->h[0]=ALBE_H_SI; + switch(element2) { + case C: + /* type: carbon */ + p->S[1]=ALBE_S_C; + p->R[1]=ALBE_R_C; + p->A[1]=ALBE_A_C; + p->B[1]=ALBE_B_C; + p->r0[1]=ALBE_R0_C; + p->lambda[1]=ALBE_LAMBDA_C; + p->mu[1]=ALBE_MU_C; + p->gamma[1]=ALBE_GAMMA_C; + p->c[1]=ALBE_C_C; + p->d[1]=ALBE_D_C; + p->h[1]=ALBE_H_C; + /* mixed type: silicon carbide */ + p->Smixed=ALBE_S_SIC; + p->Rmixed=ALBE_R_SIC; + p->Amixed=ALBE_A_SIC; + p->Bmixed=ALBE_B_SIC; + p->r0_mixed=ALBE_R0_SIC; + p->lambda_m=ALBE_LAMBDA_SIC; + p->mu_m=ALBE_MU_SIC; + p->gamma_m=ALBE_GAMMA_SIC; + p->c_mixed=ALBE_C_SIC; + p->d_mixed=ALBE_D_SIC; + p->h_mixed=ALBE_H_SIC; + break; + default: + printf("[albe] WARNING: element2\n"); + return -1; + } + break; + default: + printf("[albe] WARNING: element1\n"); + return -1; + } + + printf("[albe] parameter completion\n"); + p->S2[0]=p->S[0]*p->S[0]; + p->S2[1]=p->S[1]*p->S[1]; + p->S2mixed=p->Smixed*p->Smixed; + + printf("[albe] 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(" gamma | %f | %f\n",p->gamma[0],p->gamma[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]); + + return 0; +} + +/* albe 3 body potential function (first ij loop) */ +int albe_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { + + t_albe_mult_params *params; + t_albe_exchange *exchange; + unsigned char brand; + double S2; + t_3dvec dist_ij; + double d_ij2,d_ij; + + params=moldyn->pot_params; + exchange=&(params->exchange); + + /* reset zeta sum */ + exchange->zeta_ij=0.0; + + /* + * set ij depending values + */ + + brand=ai->brand; + if(brand==aj->brand) { + S2=params->S2[brand]; + } + else { + S2=params->S2mixed; + } + + /* dist_ij, d_ij2 */ + v3_sub(&dist_ij,&(aj->r),&(ai->r)); + if(bc) check_per_bound(moldyn,&dist_ij); + d_ij2=v3_absolute_square(&dist_ij); + + /* if d_ij2 > S2 => no force & potential energy contribution */ + if(d_ij2>S2) { + moldyn->run3bp=0; + return 0; + } + + /* d_ij */ + d_ij=sqrt(d_ij2); + + /* store values */ + exchange->dist_ij=dist_ij; + exchange->d_ij2=d_ij2; + exchange->d_ij=d_ij; + + /* reset k counter for first k loop */ + exchange->kcount=0; + + return 0; +} + +/* albe 3 body potential function (first k loop) */ +int albe_mult_3bp_k1(t_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { + + t_albe_mult_params *params; + t_albe_exchange *exchange; + unsigned char brand; + double R,S,S2; + t_3dvec dist_ij,dist_ik; + double d_ik2,d_ik,d_ij; + double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg; + double f_c_ik,df_c_ik; + int kcount; + + params=moldyn->pot_params; + exchange=&(params->exchange); + kcount=exchange->kcount; + + if(kcount>ALBE_MAXN) { + printf("FATAL: neighbours = %d\n",kcount); + printf(" -> %d %d %d\n",ai->tag,aj->tag,ak->tag); + } + + /* ik constants */ + brand=ai->brand; + if(brand==ak->brand) { + R=params->R[brand]; + S=params->S[brand]; + S2=params->S2[brand]; + /* albe needs i,k depending c,d,h and gamma values */ + exchange->gamma_i=&(params->gamma[brand]); + exchange->c_i=&(params->c[brand]); + exchange->d_i=&(params->d[brand]); + exchange->h_i=&(params->h[brand]); + } + else { + R=params->Rmixed; + S=params->Smixed; + S2=params->S2mixed; + /* albe needs i,k depending c,d,h and gamma values */ + exchange->gamma_i=&(params->gamma_m); + exchange->c_i=&(params->c_mixed); + exchange->d_i=&(params->d_mixed); + exchange->h_i=&(params->h_mixed); + } + exchange->ci2=*(exchange->c_i)**(exchange->c_i); + exchange->di2=*(exchange->d_i)**(exchange->d_i); + exchange->ci2di2=exchange->ci2/exchange->di2; + + /* dist_ik, d_ik2 */ + v3_sub(&dist_ik,&(ak->r),&(ai->r)); + if(bc) check_per_bound(moldyn,&dist_ik); + d_ik2=v3_absolute_square(&dist_ik); + + /* store data for second k loop */ + exchange->dist_ik[kcount]=dist_ik; + exchange->d_ik2[kcount]=d_ik2; + + /* return if not within cutoff */ + if(d_ik2>S2) { + exchange->kcount++; + return 0; + } + + /* d_ik */ + d_ik=sqrt(d_ik2); + + /* dist_ij, d_ij */ + dist_ij=exchange->dist_ij; + d_ij=exchange->d_ij; + + /* cos theta */ + cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik); + + /* g_ijk */ + h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism + d2_h_cos2=exchange->di2+(h_cos*h_cos); + frac=exchange->ci2/d2_h_cos2; + g=*(exchange->gamma_i)*(1.0+exchange->ci2di2-frac); + dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f.. + + /* zeta sum += f_c_ik * g_ijk */ + if(d_ik<=R) { + exchange->zeta_ij+=g; + f_c_ik=1.0; + df_c_ik=0.0; + } + else { + 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)); + exchange->zeta_ij+=f_c_ik*g; + } + + /* store even more data for second k loop */ + exchange->g[kcount]=g; + exchange->dg[kcount]=dg; + exchange->d_ik[kcount]=d_ik; + exchange->cos_theta[kcount]=cos_theta; + exchange->f_c_ik[kcount]=f_c_ik; + exchange->df_c_ik[kcount]=df_c_ik; + + /* increase k counter */ + exchange->kcount++; + + return 0; +} + +int albe_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { + + t_albe_mult_params *params; + t_albe_exchange *exchange; + t_3dvec force; + double f_a,df_a,b,db,f_c,df_c; + double f_r,df_r; + double scale; + double mu,B; + double lambda,A; + double d_ij,r0; + unsigned char brand; + double S,R,s_r,arg; + double energy; + + params=moldyn->pot_params; + exchange=&(params->exchange); + + brand=aj->brand; + if(brand==ai->brand) { + S=params->S[brand]; + R=params->R[brand]; + B=params->B[brand]; + A=params->A[brand]; + r0=params->r0[brand]; + mu=params->mu[brand]; + lambda=params->lambda[brand]; + } + else { + S=params->Smixed; + R=params->Rmixed; + B=params->Bmixed; + A=params->Amixed; + r0=params->r0_mixed; + mu=params->mu_m; + lambda=params->lambda_m; + } + + d_ij=exchange->d_ij; + + /* f_c, df_c */ + if(d_ijzeta_ij==0.0) { + b=1.0; + db=0.0; + } + else { + b=1.0/sqrt(1.0+exchange->zeta_ij); + db=-0.5*b/(1.0+exchange->zeta_ij); + } + + /* force contribution for atom i */ + scale=-0.5*(f_c*(df_r-b*df_a)+df_c*(f_r-b*f_a)); // - in albe formalism + v3_scale(&force,&(exchange->dist_ij),scale); + v3_add(&(ai->f),&(ai->f),&force); + + /* force contribution for atom j */ + v3_scale(&force,&force,-1.0); // dri rij = - drj rij + v3_add(&(aj->f),&(aj->f),&force); + + /* virial */ + virial_calc(aj,&force,&(exchange->dist_ij)); + +#ifdef DEBUG +if(moldyn->time>DSTART&&moldyn->timeatom[DATOM]))|(aj==&(moldyn->atom[DATOM]))) { + printf("force 3bp (j2): [%d %d sum]\n",ai->tag,aj->tag); + printf(" adding %f %f %f\n",force.x,force.y,force.z); + if(ai==&(moldyn->atom[0])) + printf(" total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z); + if(aj==&(moldyn->atom[0])) + printf(" total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z); + printf(" energy: %f = %f %f %f %f\n",0.5*f_c*(b*f_a+f_r), + f_c,b,f_a,f_r); + printf(" %f %f %f\n",exchange->zeta_ij,.0,.0); + } +} +#endif + + /* dzeta prefactor = - f_c f_a db, (* -0.5 due to force calc) */ + exchange->pre_dzeta=0.5*f_a*f_c*db; + + /* energy contribution */ + energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism + moldyn->energy+=energy; + ai->e+=energy; + + /* reset k counter for second k loop */ + exchange->kcount=0; + + return 0; +} + +/* albe 3 body potential function (second k loop) */ +int albe_mult_3bp_k2(t_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { + + t_albe_mult_params *params; + t_albe_exchange *exchange; + int kcount; + t_3dvec dist_ik,dist_ij; + double d_ik2,d_ik,d_ij2,d_ij; + unsigned char brand; + double S2; + double g,dg,cos_theta; + double pre_dzeta; + double f_c_ik,df_c_ik; + double dijdik_inv,fcdg,dfcg; + t_3dvec dcosdrj,dcosdrk; + t_3dvec force,tmp; + + params=moldyn->pot_params; + exchange=&(params->exchange); + kcount=exchange->kcount; + + if(kcount>ALBE_MAXN) + printf("FATAL: neighbours!\n"); + + /* d_ik2 */ + d_ik2=exchange->d_ik2[kcount]; + + brand=ak->brand; + if(brand==ai->brand) + S2=params->S2[brand]; + else + S2=params->S2mixed; + + /* return if d_ik > S */ + if(d_ik2>S2) { + exchange->kcount++; + return 0; + } + + /* prefactor dzeta */ + pre_dzeta=exchange->pre_dzeta; + + /* dist_ik, d_ik */ + dist_ik=exchange->dist_ik[kcount]; + d_ik=exchange->d_ik[kcount]; + + /* f_c_ik, df_c_ik */ + f_c_ik=exchange->f_c_ik[kcount]; + df_c_ik=exchange->df_c_ik[kcount]; + + /* dist_ij, d_ij2, d_ij */ + dist_ij=exchange->dist_ij; + d_ij2=exchange->d_ij2; + d_ij=exchange->d_ij; + + /* g, dg, cos_theta */ + g=exchange->g[kcount]; + dg=exchange->dg[kcount]; + cos_theta=exchange->cos_theta[kcount]; + + /* cos_theta derivatives wrt j,k */ + dijdik_inv=1.0/(d_ij*d_ik); + v3_scale(&dcosdrj,&dist_ik,dijdik_inv); // j + v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2); + v3_add(&dcosdrj,&dcosdrj,&tmp); + v3_scale(&dcosdrk,&dist_ij,dijdik_inv); // k + v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2); + v3_add(&dcosdrk,&dcosdrk,&tmp); + + /* f_c_ik * dg, df_c_ik * g */ + fcdg=f_c_ik*dg; + dfcg=df_c_ik*g; + + /* derivative wrt j */ + v3_scale(&force,&dcosdrj,fcdg*pre_dzeta); + + /* force contribution */ + v3_add(&(aj->f),&(aj->f),&force); + +#ifdef DEBUG +if(moldyn->time>DSTART&&moldyn->timeatom[DATOM])) { + printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag); + printf(" adding %f %f %f\n",force.x,force.y,force.z); + printf(" total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z); + printf(" angle: %f\n",acos(cos_theta)*360.0/(2*M_PI)); + printf(" d ij ik = %f %f\n",d_ij,d_ik); + } +} +#endif + + /* force contribution to atom i */ + v3_scale(&force,&force,-1.0); + v3_add(&(ai->f),&(ai->f),&force); + + /* virial */ + virial_calc(ai,&force,&dist_ij); + + /* derivative wrt k */ + v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik + v3_scale(&tmp,&dcosdrk,fcdg); + v3_add(&force,&force,&tmp); + v3_scale(&force,&force,pre_dzeta); + + /* force contribution */ + v3_add(&(ak->f),&(ak->f),&force); + +#ifdef DEBUG +if(moldyn->time>DSTART&&moldyn->timeatom[DATOM])) { + printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag); + printf(" adding %f %f %f\n",force.x,force.y,force.z); + printf(" total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z); + printf(" angle: %f\n",acos(cos_theta)*360.0/(2*M_PI)); + printf(" d ij ik = %f %f\n",d_ij,d_ik); + } +} +#endif + + /* force contribution to atom i */ + v3_scale(&force,&force,-1.0); + v3_add(&(ai->f),&(ai->f),&force); + + /* virial */ + virial_calc(ai,&force,&dist_ik); + + /* increase k counter */ + exchange->kcount++; + + return 0; + +} + +int albe_mult_check_2b_bond(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,u8 bc) { + + t_albe_mult_params *params; + t_3dvec dist; + double d; + u8 brand; + + v3_sub(&dist,&(jtom->r),&(itom->r)); + if(bc) check_per_bound(moldyn,&dist); + d=v3_absolute_square(&dist); + + params=moldyn->pot_params; + brand=itom->brand; + + if(brand==jtom->brand) { + if(d<=params->S2[brand]) + return TRUE; + } + else { + if(d<=params->S2mixed) + return TRUE; + } + + return FALSE; +} diff --git a/potentials/albe_orig.h b/potentials/albe_orig.h new file mode 100644 index 0000000..15386e7 --- /dev/null +++ b/potentials/albe_orig.h @@ -0,0 +1,131 @@ +/* + * albe.h - albe potential header file + * + * author: Frank Zirkelbach + * + */ + +#ifndef ALBE_H +#define ALBE_H + +#define ALBE_MAXN 16*27 + +/* albe exchange type */ +typedef struct s_albe_exchange { + + t_3dvec dist_ij; + double d_ij2; + double d_ij; + + t_3dvec dist_ik[ALBE_MAXN]; + double d_ik2[ALBE_MAXN]; + double d_ik[ALBE_MAXN]; + + double f_c_ik[ALBE_MAXN]; + double df_c_ik[ALBE_MAXN]; + + double g[ALBE_MAXN]; + double dg[ALBE_MAXN]; + double cos_theta[ALBE_MAXN]; + + double *gamma_i; + double *c_i; + double *d_i; + double *h_i; + + double ci2; + double di2; + double ci2di2; + + double zeta_ij; + double pre_dzeta; + + int kcount; +} t_albe_exchange; + +/* albe mult (2!) potential parameters */ +typedef struct s_albe_mult_params { + double S[2]; /* albe cutoff radii */ + double S2[2]; /* albe cutoff radii squared */ + double R[2]; /* albe cutoff radii */ + double Smixed; /* mixed S radius */ + double S2mixed; /* mixed S radius squared */ + double Rmixed; /* mixed R radius */ + double A[2]; /* factor of albe attractive part */ + double B[2]; /* factor of albe repulsive part */ + double r0[2]; /* r_0 */ + double Amixed; /* mixed A factor */ + double Bmixed; /* mixed B factor */ + double r0_mixed; /* mixed r_0 */ + double lambda[2]; /* albe lambda */ + double lambda_m; /* mixed lambda */ + double mu[2]; /* albe mu */ + double mu_m; /* mixed mu */ + + double gamma[2]; + double gamma_m; + double c[2]; + double c_mixed; + double d[2]; + double d_mixed; + double h[2]; + double h_mixed; + + t_albe_exchange exchange; /* exchange between 2bp and 3bp calc */ +} t_albe_mult_params; + +/* function prototypes */ +int albe_mult_set_params(t_moldyn *moldyn,int element1,int elemnt2); +int albe_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); +int albe_mult_3bp_k1(t_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bc); +int albe_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc); +int albe_mult_3bp_k2(t_moldyn *moldyn, + t_atom *ai,t_atom *aj,t_atom *ak,u8 bc); +int albe_mult_check_2b_bond(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,u8 bc); + +/* albe potential parameter defines */ + +// silicon +#define ALBE_R_SI (2.82-0.14) +#define ALBE_S_SI (2.82+0.14) +#define ALBE_A_SI (3.24*EV/0.842) +#define ALBE_B_SI (-1.842*3.24*EV/0.842) +#define ALBE_R0_SI 2.232 +#define ALBE_LAMBDA_SI (1.4761*sqrt(2.0*1.842)) +#define ALBE_MU_SI (1.4761*sqrt(2.0/1.842)) +#define ALBE_GAMMA_SI 0.114354 +#define ALBE_C_SI 2.00494 +#define ALBE_D_SI 0.81472 +#define ALBE_H_SI 0.259 +#define ALBE_LC_SI 5.429 + +// carbon +#define ALBE_R_C (2.00-0.15) +#define ALBE_S_C (2.00+0.15) +#define ALBE_A_C (6.00*EV/1.167) +#define ALBE_B_C (-2.167*6.00*EV/1.167) +#define ALBE_R0_C 1.4276 +#define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167)) +#define ALBE_MU_C (2.0099*sqrt(2.0/2.167)) +#define ALBE_GAMMA_C 0.11233 +#define ALBE_C_C 181.910 +#define ALBE_D_C 6.28433 +#define ALBE_H_C 0.5556 +#define ALBE_LC_C 3.566 + +// mixed: silicon carbide +#define ALBE_R_SIC (2.40-0.20) +#define ALBE_S_SIC (2.40+0.20) +#define ALBE_A_SIC (4.36*EV/0.847) +#define ALBE_B_SIC (-1.847*4.36*EV/0.847) +#define ALBE_R0_SIC 1.79 +#define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847)) +#define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847)) +#define ALBE_GAMMA_SIC 0.011877 +#define ALBE_C_SIC 273987 +#define ALBE_D_SIC 180.314 +#define ALBE_H_SIC 0.68 +#define ALBE_LC_SIC 4.359 + +#endif -- 2.20.1