more tersoff changes, still a mess!

diff --git a/moldyn.c b/moldyn.c
index 3608658..f09c93a 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -697,6 +697,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
        for(i=0;i<moldyn->time_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_ik<R) {
-               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));
-       }
-       
-       v3_sub(&dist_jk,&(aj->r),&(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<R) {
+               /* f_c_ik = 1, df_c_ik = 0 */   
+               /* => 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 (file)
--- 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 (file)
--- 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