#include <math.h>
#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
-
#include "posic.h"
+/* potential */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/tersoff.h"
+//#include "potentials/tersoff_orig.h"
+
+#define INJECT 1
+#define NR_ATOMS 4
+
+int hook(void *moldyn,void *hook_params) {
+
+ t_moldyn *md;
+ t_3dvec r,v,dist;
+ double d;
+ unsigned char run;
+ int i,j;
+ t_atom *atom;
+
+ md=moldyn;
+
+ printf("\nschedule hook: ");
+
+ if(!(md->schedule.count%2)) {
+ /* add carbon at random place, and enable t scaling */
+ for(j=0;j<NR_ATOMS;j++) {
+ run=1;
+ while(run) {
+ r.x=rand_get_double(&(md->random))*md->dim.x;
+ r.y=rand_get_double(&(md->random))*md->dim.y;
+ r.z=rand_get_double(&(md->random))*md->dim.z;
+ for(i=0;i<md->count;i++) {
+ atom=&(md->atom[i]);
+ v3_sub(&dist,&(atom->r),&r);
+ d=v3_absolute_square(&dist);
+ if(d>TM_R_C)
+ run=0;
+ }
+ }
+ v.x=0; v.y=0; v.z=0;
+ add_atom(md,C,M_C,1,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ &r,&v);
+ }
+ printf("adding atoms & enable t scaling\n");
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+ }
+ else {
+ /* disable t scaling */
+ printf("disabling t scaling\n");
+ set_pt_scale(md,0,0,0,0);
+ }
+
+ return 0;
+}
+
int main(int argc,char **argv) {
+
+ /* check argv */
+ if(argc!=3) {
+ printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+ return -1;
+ }
+
/* main moldyn structure */
t_moldyn md;
t_ho_params ho;
t_tersoff_mult_params tp;
- /* misc parameters */
- double tau;
+ /* atom injection counter */
+ int inject;
/* testing location & velocity vector */
t_3dvec r,v;
-
- /* values */
- tau=1.0e-15; /* delta t = 1 fs */
+ memset(&r,0,sizeof(t_3dvec));
+ memset(&v,0,sizeof(t_3dvec));
/* initialize moldyn */
- printf("[sic] moldyn init\n");
moldyn_init(&md,argc,argv);
/* choose integration algorithm */
- printf("[sic] setting integration algorithm\n");
set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
/* choose potential */
- printf("[sic] selecting potential\n");
- set_potential1b(&md,tersoff_mult_1bp,&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_potential1b(&md,tersoff_mult_1bp);
+ set_potential2b(&md,tersoff_mult_2bp);
+ //set_potential3b_j1(&md,tersoff_mult_2bp);
+ //set_potential3b_k1(&md,tersoff_mult_3bp);
+ //set_potential3b_j3(&md,tersoff_mult_post_2bp);
+ set_potential3b_j1(&md,tersoff_mult_3bp_j1);
+ set_potential3b_k1(&md,tersoff_mult_3bp_k1);
+ set_potential3b_j2(&md,tersoff_mult_3bp_j2);
+ set_potential3b_k2(&md,tersoff_mult_3bp_k2);
+ //set_potential2b(&md,lennard_jones);
+ //set_potential2b(&md,harmonic_oscillator);
+ set_potential_params(&md,&tp);
+ //set_potential_params(&md,&lj);
+ //set_potential_params(&md,&ho);
+
+ /* cutoff radius */
+ set_cutoff(&md,TM_S_SI);
+ //set_cutoff(&md,LC_SI*sqrt(3.0));
+ //set_cutoff(&md,2.0*LC_SI);
/*
* potential parameters
lj.sigma6*=lj.sigma6;
lj.sigma12=lj.sigma6*lj.sigma6;
lj.epsilon4=4.0*LJ_EPSILON_SI;
+ lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
/* harmonic oscillator */
ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
- ho.spring_constant=1;
+ //ho.equilibrium_distance=LC_SI;
+ ho.spring_constant=LJ_EPSILON_SI;
/*
* tersoff mult potential parameters for SiC
tersoff_mult_complete_params(&tp);
- /* cutoff radius */
- printf("[sic] setting cutoff radius\n");
- set_cutoff(&md,TM_S_SI);
- //set_cutoff(&md,2*LC_SI);
-
/* set (initial) dimensions of simulation volume */
- printf("[sic] setting dimensions\n");
- set_dim(&md,5*LC_SI,5*LC_SI,5*LC_SI,TRUE);
+ set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
/* set periodic boundary conditions in all directions */
- printf("[sic] setting periodic boundary conditions\n");
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
- printf("[sic] creating atoms\n");
+ //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,
- 0,5,5,5);
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ 0,6,6,6);
+ moldyn_bc_check(&md);
/* testing configuration */
- //r.x=2.45/2; v.x=0;
+ //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
+ //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
//r.y=0; v.y=0;
//r.z=0; v.z=0;
//add_atom(&md,SI,M_SI,0,
// ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
// &r,&v);
- //r.x=-2.45/2; v.x=0;
+ //r.x=-r.x; v.x=-v.x;
//r.y=0; v.y=0;
//r.z=0; v.z=0;
//add_atom(&md,SI,M_SI,0,
// ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
+ //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
+ //r.y=0; v.y=0;
+ //r.x=0; v.x=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.z=-r.z; v.z=-v.z;
+ //r.y=0; v.y=0;
+ //r.x=0; v.x=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
// &r,&v);
- /* setting a nearest neighbour distance for the moldyn checks */
- 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 & pressure */
+ set_temperature(&md,atof(argv[2])+273.0);
+ set_pressure(&md,BAR);
/* set p/t scaling */
- printf("[sic] set p/t scaling\n");
- set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
+ //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
+ // T_SCALE_BERENDSEN,100.0);
+ //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
+ //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
/* initial thermal fluctuations of particles (in equilibrium) */
- printf("[sic] thermal init\n");
thermal_init(&md,TRUE);
/* create the simulation schedule */
- printf("[sic] adding schedule\n");
- moldyn_add_schedule(&md,1000,1.0);
+ /* initial configuration */
+ moldyn_add_schedule(&md,10000,1.0);
+ /* adding atoms */
+ //for(inject=0;inject<INJECT;inject++) {
+ // /* injecting atom and run with enabled t scaling */
+ // moldyn_add_schedule(&md,900,1.0);
+ // /* continue running with disabled t scaling */
+ // moldyn_add_schedule(&md,1100,1.0);
+ //}
+
+ /* schedule hook function */
+ moldyn_set_schedule_hook(&md,&hook,NULL);
/* activate logging */
- printf("[sic] activate logging\n");
- moldyn_set_log_dir(&md,"saves/test");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,10);
- moldyn_set_log(&md,VISUAL_STEP,10);
+ 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,LOG_TEMPERATURE,1);
+ moldyn_set_log(&md,LOG_PRESSURE,1);
+ moldyn_set_log(&md,VISUAL_STEP,100);
+ moldyn_set_log(&md,SAVE_STEP,100);
+ moldyn_set_log(&md,CREATE_REPORT,0);
/*
* let's do the actual md algorithm now
*
* integration of newtons equations
*/
-
- printf("[sic] integration start, go get a coffee ...\n");
moldyn_integrate(&md);
/* close */
-
- printf("[sic] shutdown\n");
moldyn_shutdown(&md);
return 0;
projects / physik / posic.git / blobdiff