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more tersoff changes, still a mess!
author
hackbard
<hackbard>
Thu, 7 Dec 2006 02:20:27 +0000
(
02:20
+0000)
committer
hackbard
<hackbard>
Thu, 7 Dec 2006 02:20:27 +0000
(
02:20
+0000)
moldyn.c
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moldyn.h
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sic.c
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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 */
for(i=0;i<moldyn->time_steps;i++) {
/* integration step */
+printf("MOVE\n");
moldyn->integrate(moldyn);
/* p/t scaling */
moldyn->integrate(moldyn);
/* p/t scaling */
@@
-920,15
+921,14
@@
int potential_force_calc(t_moldyn *moldyn) {
/* 2bp post function */
if(moldyn->func2b_post) {
/* 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);
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;
}
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;
/* 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) {
/* 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->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;
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 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);
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;
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);
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));
/* 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_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;
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 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 h_cos,d2_h_cos2;
- double frac
,bracket,bracket_n_1,bracket_n
;
+ double frac;
double g;
int num;
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_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
dist_ij=exchange->dist_ij;
f_a=params->exchange.f_a;
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 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);
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];
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;
}
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);
/* 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;
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) {
/* 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");
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;
cos_theta=-1.0;
- else
+ }
+ else {
cos_theta=1.0;
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);
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;
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;
}
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;
t_3dvec dist_ij;
double d_ij;
- double d_ij2;
double chi;
double chi;
@@
-200,8
+199,7
@@
typedef struct s_tersoff_exchange {
u8 run2bp_post;
t_3dvec db_ij;
u8 run2bp_post;
t_3dvec db_ij;
- double sum1_3bp;
- double sum2_3bp;
+ double zeta;
} t_tersoff_exchange;
/* tersoff multi (2!) potential parameters */
} 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 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 */
#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 */
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 */
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");
/* 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");
/* create the simulation schedule */
printf("[sic] adding schedule\n");
- moldyn_add_schedule(&md,100
00
,1.0e-15);
+ moldyn_add_schedule(&md,100,1.0e-15);
/* activate logging */
printf("[sic] activate logging\n");
/* activate logging */
printf("[sic] activate logging\n");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1
00
);
- moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1
00
);
+ 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
/*
* let's do the actual md algorithm now