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nur foo ...
author
hackbard
<hackbard>
Thu, 25 Jan 2007 17:52:03 +0000
(17:52 +0000)
committer
hackbard
<hackbard>
Thu, 25 Jan 2007 17:52:03 +0000
(17:52 +0000)
moldyn.c
patch
|
blob
|
history
moldyn.h
patch
|
blob
|
history
sic.c
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diff --git
a/moldyn.c
b/moldyn.c
index
f564075
..
881f0b6
100644
(file)
--- a/
moldyn.c
+++ b/
moldyn.c
@@
-344,7
+344,10
@@
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
switch(type) {
case CUBIC:
switch(type) {
case CUBIC:
- ret=cubic_init(a,b,c,lc,atom,NULL);
+ origin.x=0.5*lc;
+ origin.y=0.5*lc;
+ origin.z=0.5*lc;
+ ret=cubic_init(a,b,c,lc,atom,&origin);
break;
case FCC:
ret=fcc_init(a,b,c,lc,atom,NULL);
break;
case FCC:
ret=fcc_init(a,b,c,lc,atom,NULL);
@@
-399,8
+402,8
@@
int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
for(i=0;i<a;i++) {
r.y=o.y;
for(j=0;j<b;j++) {
for(i=0;i<a;i++) {
r.y=o.y;
for(j=0;j<b;j++) {
+ r.z=o.z;
for(k=0;k<c;k++) {
for(k=0;k<c;k++) {
- r.z=o.z;
v3_copy(&(atom[count].r),&r);
count+=1;
r.z+=lc;
v3_copy(&(atom[count].r),&r);
count+=1;
r.z+=lc;
@@
-1149,8
+1152,10
@@
int moldyn_integrate(t_moldyn *moldyn) {
/* energy scaling factor */
energy_scale=moldyn->count*EV;
/* energy scaling factor */
energy_scale=moldyn->count*EV;
+printf("debug: %f\n",moldyn->atom[0].f.x);
/* calculate initial forces */
potential_force_calc(moldyn);
/* calculate initial forces */
potential_force_calc(moldyn);
+printf("debug: %f\n",moldyn->atom[0].f.x);
/* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
/* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
@@
-1232,8
+1237,8
@@
int moldyn_integrate(t_moldyn *moldyn) {
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d, debug: %f
| %f
",
- sched->count,i,moldyn->p/ATM
,moldyn->p/ATM
);
+ printf("\rsched: %d, steps: %d, debug: %f",
+ sched->count,i,moldyn->p/ATM);
fflush(stdout);
}
}
fflush(stdout);
}
}
diff --git
a/moldyn.h
b/moldyn.h
index
69cee96
..
0dbc1f9
100644
(file)
--- a/
moldyn.h
+++ b/
moldyn.h
@@
-146,7
+146,7
@@
typedef struct s_moldyn {
t_random random; /* random interface */
t_random random; /* random interface */
-
int debug;
/* debugging stuff, ignore */
+
double debug;
/* debugging stuff, ignore */
} t_moldyn;
#define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
} t_moldyn;
#define MOLDYN_STAT_PBX 0x01 /* periodic boudaries in x */
@@
-235,7
+235,7
@@
typedef struct s_tersoff_exchange {
t_3dvec dzeta_ji;
} t_tersoff_exchange;
t_3dvec dzeta_ji;
} t_tersoff_exchange;
-/* tersoff mult
i
(2!) potential parameters */
+/* tersoff mult (2!) potential parameters */
typedef struct s_tersoff_mult_params {
double S[2]; /* tersoff cutoff radii */
double S2[2]; /* tersoff cutoff radii squared */
typedef struct s_tersoff_mult_params {
double S[2]; /* tersoff cutoff radii */
double S2[2]; /* tersoff cutoff radii squared */
@@
-290,7
+290,7
@@
typedef struct s_tersoff_mult_params {
#define KILOGRAM (1.0/AMU) /* amu */
#define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
#define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
#define KILOGRAM (1.0/AMU) /* amu */
#define NEWTON (METER*KILOGRAM/(SECOND*SECOND)) /* A amu / fs^2 */
#define PASCAL (NEWTON/(METER*METER)) /* N / A^2 */
-#define ATM (
1.0133e5*PASCAL)
/* N / A^2 */
+#define ATM (
(1.0133e5*PASCAL))
/* N / A^2 */
#define MOLDYN_TEMP 273.0
#define MOLDYN_TAU 1.0
#define MOLDYN_TEMP 273.0
#define MOLDYN_TAU 1.0
@@
-330,7
+330,8
@@
typedef struct s_tersoff_mult_params {
#define LC_SI (0.543105e-9*METER) /* A */
#define M_SI 28.08553 /* amu */
#define LC_SI (0.543105e-9*METER) /* A */
#define M_SI 28.08553 /* amu */
-#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
+//#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* A */
+#define LJ_SIGMA_SI (LC_SI/1.122462) /* A */
#define LJ_EPSILON_SI (2.1678*EV) /* NA */
#define TM_R_SI (2.7e-10*METER) /* A */
#define LJ_EPSILON_SI (2.1678*EV) /* NA */
#define TM_R_SI (2.7e-10*METER) /* A */
diff --git
a/sic.c
b/sic.c
index
999d860
..
7e1249c
100644
(file)
--- a/
sic.c
+++ b/
sic.c
@@
-59,13
+59,13
@@
int main(int argc,char **argv) {
//set_potential2b(&md,tersoff_mult_2bp,&tp);
//set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
//set_potential3b(&md,tersoff_mult_3bp,&tp);
//set_potential2b(&md,tersoff_mult_2bp,&tp);
//set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
//set_potential3b(&md,tersoff_mult_3bp,&tp);
-
//
set_potential2b(&md,lennard_jones,&lj);
- set_potential2b(&md,harmonic_oscillator,&ho);
+ set_potential2b(&md,lennard_jones,&lj);
+
//
set_potential2b(&md,harmonic_oscillator,&ho);
/* cutoff radius */
//set_cutoff(&md,TM_S_SI);
//set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
/* cutoff radius */
//set_cutoff(&md,TM_S_SI);
//set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
- set_cutoff(&md,
1.1
*LC_SI);
+ set_cutoff(&md,
2.0
*LC_SI);
/*
* potential parameters
/*
* potential parameters
@@
-81,7
+81,7
@@
int main(int argc,char **argv) {
/* harmonic oscillator */
//ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
ho.equilibrium_distance=LC_SI;
/* harmonic oscillator */
//ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
ho.equilibrium_distance=LC_SI;
- ho.spring_constant=
.1
;
+ ho.spring_constant=
LJ_EPSILON_SI
;
/*
* tersoff mult potential parameters for SiC
/*
* tersoff mult potential parameters for SiC
@@
-115,18
+115,18
@@
int main(int argc,char **argv) {
tersoff_mult_complete_params(&tp);
/* set (initial) dimensions of simulation volume */
tersoff_mult_complete_params(&tp);
/* set (initial) dimensions of simulation volume */
- //set_dim(&md,8*LC_SI*0.5*sqrt(1.5),8*LC_SI*0.5*sqrt(1.5),8*LC_SI*0.5*sqrt(1.5),TRUE);
- set_dim(&md,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
+ set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
/* set periodic boundary conditions in all directions */
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
/* set periodic boundary conditions in all directions */
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
+ //create_lattice(&md,FCC,LC_SI,SI,M_SI,
//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
// ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
ATOM_ATTR_2BP|ATOM_ATTR_HB,
//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
// ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
ATOM_ATTR_2BP|ATOM_ATTR_HB,
- 0,
8,8,8
);
+ 0,
6,6,6
);
moldyn_bc_check(&md);
/* testing configuration */
moldyn_bc_check(&md);
/* testing configuration */
@@
-171,7
+171,7
@@
int main(int argc,char **argv) {
thermal_init(&md,TRUE);
/* create the simulation schedule */
thermal_init(&md,TRUE);
/* create the simulation schedule */
- moldyn_add_schedule(&md,1001,1.0);
+ moldyn_add_schedule(&md,100
00
1,1.0);
//moldyn_add_schedule(&md,501,1.0);
//moldyn_add_schedule(&md,501,1.0);
//moldyn_add_schedule(&md,501,1.0);
//moldyn_add_schedule(&md,501,1.0);
@@
-182,7
+182,7
@@
int main(int argc,char **argv) {
moldyn_set_log_dir(&md,argv[1]);
moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
moldyn_set_log_dir(&md,argv[1]);
moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
- moldyn_set_log(&md,VISUAL_STEP,10);
+ moldyn_set_log(&md,VISUAL_STEP,10
00
);
moldyn_set_log(&md,CREATE_REPORT,0);
/*
moldyn_set_log(&md,CREATE_REPORT,0);
/*