#include <math.h>
#include "moldyn.h"
-
#include "posic.h"
+/* potential */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+#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;
- /* switch to direct scaling in first hook */
- if(md->schedule.count==0)
+// vortrag
+set_temperature(moldyn,(4-md->schedule.count)*1000.0);
+set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+return 0;
+
+ 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);
- /* switch off temp scaling in second hook */
- if(md->schedule.count==1)
+ }
+ else {
+ /* disable t scaling */
+ printf("disabling t scaling\n");
set_pt_scale(md,0,0,0,0);
-
- //set_temperature(md,md->t_ref-100.0);
+ }
return 0;
}
t_moldyn md;
/* potential parameters */
- t_lj_params lj;
- t_ho_params ho;
t_tersoff_mult_params tp;
+ t_albe_mult_params ap;
+
+ /* atom injection counter */
+ int inject;
/* testing location & velocity vector */
t_3dvec r,v;
+ memset(&r,0,sizeof(t_3dvec));
+ memset(&v,0,sizeof(t_3dvec));
/* initialize moldyn */
moldyn_init(&md,argc,argv);
set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
/* choose potential */
- //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_potential2b(&md,harmonic_oscillator,&ho);
+#ifdef ALBE
+ set_potential3b_j1(&md,albe_mult_3bp_j1);
+ set_potential3b_k1(&md,albe_mult_3bp_k1);
+ set_potential3b_j2(&md,albe_mult_3bp_j2);
+ set_potential3b_k2(&md,albe_mult_3bp_k2);
+#else
+ set_potential1b(&md,tersoff_mult_1bp);
+ 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);
+#endif
+
+#ifdef ALBE
+ set_potential_params(&md,&ap);
+#else
+ set_potential_params(&md,&tp);
+#endif
/* cutoff radius */
- //set_cutoff(&md,TM_S_SI);
- //set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
- set_cutoff(&md,2.0*LC_SI);
+#ifdef ALBE
+ set_cutoff(&md,ALBE_S_SI);
+#else
+ set_cutoff(&md,TM_S_SI);
+#endif
/*
* potential parameters
*/
- /* lennard jones */
- lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
- 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.equilibrium_distance=LC_SI;
- ho.spring_constant=LJ_EPSILON_SI;
-
/*
* tersoff mult potential parameters for SiC
*/
tersoff_mult_complete_params(&tp);
+ /*
+ * albe mult potential parameters for SiC
+ */
+ ap.S[0]=ALBE_S_SI;
+ ap.R[0]=ALBE_R_SI;
+ ap.A[0]=ALBE_A_SI;
+ ap.B[0]=ALBE_B_SI;
+ ap.r0[0]=ALBE_R0_SI;
+ ap.lambda[0]=ALBE_LAMBDA_SI;
+ ap.mu[0]=ALBE_MU_SI;
+ ap.gamma[0]=ALBE_GAMMA_SI;
+ ap.c[0]=ALBE_C_SI;
+ ap.d[0]=ALBE_D_SI;
+ ap.h[0]=ALBE_H_SI;
+
+ ap.S[1]=ALBE_S_C;
+ ap.R[1]=ALBE_R_C;
+ ap.A[1]=ALBE_A_C;
+ ap.B[1]=ALBE_B_C;
+ ap.r0[1]=ALBE_R0_C;
+ ap.lambda[1]=ALBE_LAMBDA_C;
+ ap.mu[1]=ALBE_MU_C;
+ ap.gamma[1]=ALBE_GAMMA_C;
+ ap.c[1]=ALBE_C_C;
+ ap.d[1]=ALBE_D_C;
+ ap.h[1]=ALBE_H_C;
+
+ ap.Smixed=ALBE_S_SIC;
+ ap.Rmixed=ALBE_R_SIC;
+ ap.Amixed=ALBE_A_SIC;
+ ap.Bmixed=ALBE_B_SIC;
+ ap.r0_mixed=ALBE_R0_SIC;
+ ap.lambda_m=ALBE_LAMBDA_SIC;
+ ap.mu_m=ALBE_MU_SIC;
+ ap.gamma_m=ALBE_GAMMA_SIC;
+ ap.c_mixed=ALBE_C_SIC;
+ ap.d_mixed=ALBE_D_SIC;
+ ap.h_mixed=ALBE_H_SIC;
+
+ albe_mult_complete_params(&ap);
+
/* set (initial) dimensions of simulation volume */
- set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
+ set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
+ //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
+ //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
+ //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
+ //set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,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,
- 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,
- 0,6,6,6);
+ //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
+ create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ 0,6,6,6,NULL);
+ // 1,6,6,6,NULL);
+
+ /* create centered zinc blende lattice */
+ /*
+ r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,6,6,6,&r);
+ r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 1,6,6,6,&r);
+ */
+
moldyn_bc_check(&md);
/* testing configuration */
- //r.x=0.28*sqrt(3)*LC_SI/2; v.x=0;
- //r.x=1.75*LC_SI; v.x=-0.01;
+ //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.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);
/* set temperature & pressure */
set_temperature(&md,atof(argv[2])+273.0);
- set_pressure(&md,ATM);
+ set_pressure(&md,BAR);
/* set p/t scaling */
//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
thermal_init(&md,TRUE);
/* create the simulation schedule */
- moldyn_add_schedule(&md,101,1.0);
- //moldyn_add_schedule(&md,501,1.0);
- //moldyn_add_schedule(&md,501,1.0);
+ /* initial configuration */
+ moldyn_add_schedule(&md,10000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ /* 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);
+ moldyn_set_schedule_hook(&md,&hook,NULL);
/* activate logging */
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,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);
/*
* integration of newtons equations
*/
moldyn_integrate(&md);
+#ifdef DEBUG
+return 0;
+#endif
+
+ /*
+ * post processing the data
+ */
+
+ /* response functions expressed by energy fluctuations */
+ calc_fluctuations(1000.0,9999.0,&md);
+ get_heat_capacity(&md);
/* close */
moldyn_shutdown(&md);
projects / physik / posic.git / blobdiff