From 0acbade9c8d1ed354c333955dc2c5575540a9236 Mon Sep 17 00:00:00 2001 From: hackbard Date: Thu, 7 Dec 2006 02:20:27 +0000 Subject: [PATCH] more tersoff changes, still a mess! --- moldyn.c | 153 ++++++++++++++++++++++++------------------------------- moldyn.h | 6 +-- sic.c | 12 ++--- 3 files changed, 74 insertions(+), 97 deletions(-) diff --git a/moldyn.c b/moldyn.c index 3608658..f09c93a 100644 --- a/moldyn.c +++ b/moldyn.c @@ -697,6 +697,7 @@ int moldyn_integrate(t_moldyn *moldyn) { for(i=0;itime_steps;i++) { /* integration step */ +printf("MOVE\n"); moldyn->integrate(moldyn); /* p/t scaling */ @@ -920,15 +921,14 @@ int potential_force_calc(t_moldyn *moldyn) { /* 2bp post function */ if(moldyn->func2b_post) { -printf("pre(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x); moldyn->func2b_post(moldyn, &(itom[i]), jtom,bc_ij); -printf("post(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x); } } } +printf("debug atom %d: %.15f %.15f %.15f\n",i,itom[i].r.x,itom[i].v.x,itom[i].f.x); } return 0; @@ -1135,7 +1135,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { /* save for use in 3bp */ exchange->d_ij=d_ij; exchange->dist_ij=dist_ij; - exchange->d_ij2=d_ij*d_ij; /* constants */ if(num==aj->bnum) { @@ -1195,8 +1194,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { exchange->run2bp_post=1; /* reset 3bp sums */ - exchange->sum1_3bp=0.0; - exchange->sum2_3bp=0.0; + exchange->zeta=0.0; v3_zero(&(exchange->db_ij)); return 0; @@ -1215,9 +1213,8 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { double db_ij_scale1,db_ij_scale2; double b_ij; double f_c,df_c,f_a,df_a; - double chi,betan; - double help; - double n; + double chi,n,n_betan; + double zeta; params=moldyn->pot2b_params; exchange=&(params->exchange); @@ -1231,17 +1228,19 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) { df_c=exchange->df_c; f_a=exchange->f_a; df_a=exchange->df_a; - betan=exchange->betan; + n_betan=exchange->n_betan; n=*(exchange->n); chi=exchange->chi; dist_ij=&(exchange->dist_ij); + zeta=exchange->zeta; - db_ij_scale1=(1+betan*exchange->sum1_3bp); - db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp); - help=pow(db_ij_scale1,-1.0/(2*n)-1); - b_ij=chi*db_ij_scale1*help; - db_ij_scale1=-chi/(2*n)*help; -printf("debug: %.20f %.20f %.20f\n",db_ij->x,exchange->sum1_3bp,exchange->sum2_3bp); + db_ij_scale2=pow(zeta,n-1.0); +printf("DEBUG: %.15f %.15f\n",zeta,db_ij_scale2); + db_ij_scale1=db_ij_scale2*zeta; + db_ij_scale2*=n_betan; + db_ij_scale1=pow((1.0+n_betan*db_ij_scale1),-1.0/(2*n)-1); + b_ij=chi*db_ij_scale1*(1.0+n_betan*db_ij_scale1); + db_ij_scale1*=(-1.0*chi/(2*n)); /* db_ij part */ v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2)); @@ -1272,19 +1271,18 @@ 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 dist_ij,dist_ik; t_3dvec temp,force; double R,S,s_r; - double d_ij,d_ij2,d_ik,d_jk; + double d_ij,d_ik; + double rijrik,dijdik; double f_c,df_c,f_a,df_a; double f_c_ik,df_c_ik,arg; double n,c,d,h; double c2,d2,c2d2; - double numer,denom; - double theta,cos_theta,sin_theta; - double d_theta,d_theta1,d_theta2; + double cos_theta,d_costheta1,d_costheta2; double h_cos,d2_h_cos2; - double frac,bracket,bracket_n_1,bracket_n; + double frac; double g; int num; @@ -1302,7 +1300,6 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { */ d_ij=exchange->d_ij; - d_ij2=exchange->d_ij2; dist_ij=exchange->dist_ij; f_a=params->exchange.f_a; @@ -1318,8 +1315,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { * * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta * - * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik, - * w_ik, + * - for db_ij: d_costheta, cos_theta, f_c_ik, df_c_ik, w_ik * */ @@ -1327,7 +1323,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { if(bc) check_per_bound(moldyn,&dist_ik); d_ik=v3_norm(&dist_ik); - /* constants for f_c_ik calc */ + /* constants */ if(num==ak->bnum) { R=params->R[num]; S=params->S[num]; @@ -1337,25 +1333,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { S=params->Smixed; } - /* calc of f_c_ik */ - if(d_ik>S) { - f_c_ik=0.0; - df_c_ik=0.0; - } - else if(d_ikr),&(ak->r)); - if(bc) check_per_bound(moldyn,&dist_jk); - d_jk=v3_norm(&dist_jk); + /* there is no contribution if f_c_ik = 0 */ + if(d_ik>S) + return 0; /* get exchange data */ n=*(exchange->n); @@ -1366,34 +1346,27 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) { d2=exchange->d2; c2d2=exchange->c2d2; - /* cosine of theta by scalaproduct, * - * derivation of theta by law of cosines! */ - numer=d_ij2+d_ik*d_ik-d_jk*d_jk; - denom=2*d_ij*d_ik; - cos_theta=numer/denom; - cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik); -printf("cos theta: %.25f\n",cos_theta); + /* cosine of theta by scalaproduct */ + rijrik=v3_scalar_product(&dist_ij,&dist_ik); + dijdik=d_ij*d_ik; + cos_theta=rijrik/dijdik; /* hack - cos theta machine accuracy problems! */ if(cos_theta>1.0||cos_theta<-1.0) { + printf("THETA CORRECTION\n"); moldyn->debug++; if(fabs(cos_theta)>1.0+ACCEPTABLE_ERROR) printf("[moldyn] WARNING: cos theta failure!\n"); - if(cos_theta<0) + if(cos_theta<0) { cos_theta=-1.0; - else + } + else { cos_theta=1.0; - printf("THETA CORRECTION\n"); + } } - sin_theta=sqrt(1.0-(cos_theta*cos_theta)); - theta=acos(cos_theta); - d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom); - d_theta1=2*denom-numer*2*d_ik/d_ij; - d_theta2=2*denom-numer*2*d_ij/d_ik; - d_theta1*=d_theta; - d_theta2*=d_theta; -printf("FOO %.15f %.15f\n",sin_theta,cos_theta); + d_costheta1=dijdik-rijrik*d_ik/d_ij; + d_costheta2=dijdik-rijrik*d_ij/d_ik; h_cos=(h-cos_theta); d2_h_cos2=d2+(h_cos*h_cos); @@ -1401,36 +1374,42 @@ printf("FOO %.15f %.15f\n",sin_theta,cos_theta); frac=c2/(d2_h_cos2); g=1.0+c2d2-frac; - if(f_c_ik==0.0) { - bracket=0.0; - bracket_n_1=0.0; - bracket_n=0.0; - } - else { - bracket=f_c_ik*g; - bracket_n_1=pow(bracket,n-1.0); - bracket_n=bracket_n_1*bracket; - } + /* d_costheta contrib to db_ij (needed in all remaining cases) */ + v3_scale(&temp,&dist_ij,d_costheta1); + v3_scale(&force,&dist_ik,d_costheta2); + v3_add(&force,&force,&temp); + v3_scale(&force,&force,-2.0*frac*h_cos/d2_h_cos2); /* f_c_ik missing */ - /* calc of db_ij and the 2 sums */ - exchange->sum1_3bp+=bracket_n; - exchange->sum2_3bp+=bracket_n_1; + if(d_ik only d_costheta contrib to db_ij */ + // => do nothing ... - /* derivation of theta */ - v3_scale(&force,&dist_ij,d_theta1); - v3_scale(&temp,&dist_ik,d_theta2); - v3_add(&force,&force,&temp); + /* zeta, f_c_ik = 1 */ + exchange->zeta+=g; + } + 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)); -printf("DA:%.20f %.20f %.20f\n",d_theta1,force.x,temp.x); - /* part 1 of db_ij */ - v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2); + /* scale d_costheta contrib with f_c_ik */ + v3_scale(&force,&force,f_c_ik); - /* part 2 of db_ij */ - v3_scale(&temp,&dist_ik,df_c_ik*g); + /* df_c_ik contrib to db_ij */ + v3_scale(&temp,&dist_ik,df_c_ik*g); - /* sum up and add to db_ij */ - v3_add(&temp,&temp,&force); - v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp); + /* sum up both parts */ + v3_add(&force,&force,&temp); + + /* zeta */ + exchange->zeta+=f_c_ik*g; + } +printf("%.30f\n",exchange->zeta); + + /* add to db_ij */ + v3_add(&(exchange->db_ij),&(exchange->db_ij),&force); return 0; } diff --git a/moldyn.h b/moldyn.h index c5fed60..32025fd 100644 --- a/moldyn.h +++ b/moldyn.h @@ -180,7 +180,6 @@ typedef struct s_tersoff_exchange { t_3dvec dist_ij; double d_ij; - double d_ij2; double chi; @@ -200,8 +199,7 @@ typedef struct s_tersoff_exchange { u8 run2bp_post; t_3dvec db_ij; - double sum1_3bp; - double sum2_3bp; + double zeta; } t_tersoff_exchange; /* tersoff multi (2!) potential parameters */ @@ -284,7 +282,7 @@ typedef struct s_tersoff_mult_params { #define LC_SI 0.543105e-9 /* m */ #define M_SI (28.085*AMU) /* kg */ #define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */ -#define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */ +#define LJ_EPSILON_SI (2.1678*EV) /* Nm */ #define TM_R_SI 2.7e-10 /* m */ #define TM_S_SI 3.0e-10 /* m */ diff --git a/sic.c b/sic.c index d6e85fb..8073559 100644 --- a/sic.c +++ b/sic.c @@ -110,12 +110,12 @@ int main(int argc,char **argv) { 0,5,5,5); /* setting a nearest neighbour distance for the moldyn checks */ - set_nn_dist(&md,sqrt(3.0)*LC_SI/4.0); /* diamond ! */ + set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */ /* set temperature */ printf("[sic] setting temperature\n"); - set_temperature(&md,273.0+450.0); - //set_temperature(&md,0.0); + //set_temperature(&md,273.0+450.0); + set_temperature(&md,0.0); /* set p/t scaling */ printf("[sic] set p/t scaling\n"); @@ -127,12 +127,12 @@ int main(int argc,char **argv) { /* create the simulation schedule */ printf("[sic] adding schedule\n"); - moldyn_add_schedule(&md,10000,1.0e-15); + moldyn_add_schedule(&md,100,1.0e-15); /* activate logging */ printf("[sic] activate logging\n"); - moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100); - moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100); + moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1); + moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1); /* * let's do the actual md algorithm now -- 2.20.1