#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
+typedef struct s_hp {
+ int prerun_count; /* prerun count */
+ int insert_count; /* insert count */
+ int postrun_count; /* post run count */
+ unsigned char state; /* current state */
+ int argc; /* arg count */
+ char **argv; /* args */
+} t_hp;
-int hook(void *moldyn,void *hook_params) {
+#define STATE_PRERUN 0x00
+#define STATE_INSERT 0x01
+#define STATE_POSTRUN 0x02
- t_moldyn *md;
+/* include the config file */
+#include "config.h"
+
+int insert_atoms(t_moldyn *moldyn) {
+
+ int i,j;
+ u8 run;
t_3dvec r,v,dist;
double d;
- unsigned char run;
- int i,j;
+
t_atom *atom;
- md=moldyn;
+ atom=moldyn->atom;
- printf("\nschedule hook: ");
+ v.x=0; v.y=0; v.z=0;
- if(!(md->schedule.count%2)) {
- /* add carbon at random place, and enable t scaling */
- for(j=0;j<NR_ATOMS;j++) {
+ for(j=0;j<INS_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]);
+ // tetrahedral
+ /*
+ r.x=0.0;
+ r.y=0.0;
+ r.z=0.0;
+ */
+ // hexagonal
+ /*
+ r.x=-1.0/8.0*ALBE_LC_SI;
+ r.y=-1.0/8.0*ALBE_LC_SI;
+ r.z=1.0/8.0*ALBE_LC_SI;
+ */
+ // 110 dumbbell
+ /*
+ r.x=(-0.5+0.25+0.125)*ALBE_LC_SI;
+ r.y=(-0.5+0.25+0.125)*ALBE_LC_SI;
+ r.z=(-0.5+0.25)*ALBE_LC_SI;
+ md->atom[4372].r.x=(-0.5+0.125+0.125)*ALBE_LC_SI;
+ md->atom[4372].r.y=(-0.5+0.125+0.125)*ALBE_LC_SI;
+ */
+ // random
+ //
+ r.x=(rand_get_double(&(moldyn->random))-0.5)*INS_LENX;
+ r.y=(rand_get_double(&(moldyn->random))-0.5)*INS_LENY;
+ r.z=(rand_get_double(&(moldyn->random))-0.5)*INS_LENZ;
+ //
+ // offset
+ r.x+=INS_OFFSET;
+ r.y+=INS_OFFSET;
+ r.z+=INS_OFFSET;
+ /* assume valid coordinates */
+ run=0;
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
v3_sub(&dist,&(atom->r),&r);
+ check_per_bound(moldyn,&dist);
d=v3_absolute_square(&dist);
- if(d>TM_R_C)
- run=0;
+ /* reject coordinates */
+ if(d<INS_R_C) {
+ //printf("atom %d - %f\n",i,d);
+ run=1;
+ break;
+ }
}
}
- 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,
+ add_atom(moldyn,INS_TYPE,INS_MASS,INS_BRAND,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|\
+ //ATOM_ATTR_HB|ATOM_ATTR_VB,
+ 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) {
+int sic_hook(void *moldyn,void *hook_params) {
- /* check argv */
- if(argc!=3) {
- printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
- return -1;
+ t_hp *hp;
+ t_moldyn *md;
+ int steps;
+ double tau;
+
+ hp=hook_params;
+ md=moldyn;
+
+ /* switch on t scaling */
+ if(md->schedule.count==0)
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+ /* my lousy state machine ! */
+
+ /* switch to insert state immediately */
+ if(hp->state==STATE_PRERUN)
+ hp->state=STATE_INSERT;
+
+ /* act according to state */
+ switch(hp->state) {
+ case STATE_INSERT:
+ /* check temperature */
+ if(md->t_avg-md->t_ref>INS_DELTA_TC) {
+ steps=INS_RELAX;
+ tau=INS_TAU;
+ break;
+ }
+ /* insert atoms */
+ hp->insert_count+=1;
+ printf(" ### insert atoms (%d/%d) ###\n",
+ hp->insert_count*INS_ATOMS,INS_RUNS*INS_ATOMS);
+ insert_atoms(md);
+ /* change state after last insertion */
+ if(hp->insert_count==INS_RUNS)
+ hp->state=STATE_POSTRUN;
+ break;
+ case STATE_POSTRUN:
+ /* settings */
+ if(md->t-md->t_ref>POST_DELTA_TC) {
+ steps=POST_RELAX;
+ tau=POST_TAU;
+ }
+ /* decrease temperature */
+ hp->postrun_count+=1;
+ printf(" ### postrun (%d/%d) ###\n",
+ hp->postrun_count,POST_RUNS);
+ set_temperature(md,md->t_ref-POST_DT);
+ if(hp->postrun_count==POST_RUNS)
+ return 0;
+ break;
+ default:
+ printf("[hook] FATAL (default case!?!)\n");
+ break;
}
+ /* add schedule */
+ moldyn_add_schedule(md,steps,tau);
+
+ return 0;
+}
+
+int main(int argc,char **argv) {
+
/* main moldyn structure */
t_moldyn md;
+ /* hook parameter structure */
+ t_hp hookparam;
+
/* 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));
set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
/* choose potential */
- set_potential1b(&md,tersoff_mult_1bp);
-#ifdef TERSOFF_ORIG
- set_potential3b_j1(&md,tersoff_mult_2bp);
- set_potential3b_k1(&md,tersoff_mult_3bp);
- set_potential3b_j2(&md,tersoff_mult_post_2bp);
-#elif ALBE
- set_potential1b(&md,albe_mult_1bp);
+#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
- //set_potential2b(&md,lennard_jones);
- //set_potential2b(&md,harmonic_oscillator);
#ifdef ALBE
set_potential_params(&md,&ap);
#else
set_potential_params(&md,&tp);
#endif
- //set_potential_params(&md,&lj);
- //set_potential_params(&md,&ho);
- /* cutoff radius */
+ /* cutoff radius & bondlen */
+#ifdef ALBE
set_cutoff(&md,ALBE_S_SI);
- //set_cutoff(&md,TM_S_SI);
- //set_cutoff(&md,LC_SI*sqrt(3.0));
- //set_cutoff(&md,2.0*LC_SI);
+ set_bondlen(&md,ALBE_S_SI,ALBE_S_C,ALBE_S_SIC);
+ //set_cutoff(&md,ALBE_S_C);
+#else
+ set_cutoff(&md,TM_S_SI);
+ set_bondlen(&md,TM_S_SI,TM_S_C,-1.0);
+ //set_cutoff(&md,TM_S_C);
+#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
*/
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_C,6*LC_C,6*LC_C,TRUE);
- //set_dim(&md,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,6*TM_LC_3C_SIC,TRUE);
+#ifdef ALBE
+ set_dim(&md,LCNTX*ALBE_LC_SI,LCNTY*ALBE_LC_SI,LCNTZ*ALBE_LC_SI,TRUE);
+ //set_dim(&md,LCNTX*ALBE_LC_C,LCNTY*ALBE_LC_C,LCNTZ*ALBE_LC_C,TRUE);
+ //set_dim(&md,LCNTX*ALBE_LC_SIC,LCNTY*ALBE_LC_SIC,LCNTZ*ALBE_LC_SIC,TRUE);
+#else
+ set_dim(&md,LCNTX*LC_SI,LCNTY*LC_SI,LCNTZ*LC_SI,TRUE);
+ //set_dim(&md,LCNTX*LC_C,LCNTY*LC_C,LCNTZ*LC_C,TRUE);
+ //set_dim(&md,LCNTX*TM_LC_SIC,LCNTY*TM_LC_SIC,LCNTZ*TM_LC_SIC,TRUE);
+#endif
/* 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,
+ //
+#ifdef ALBE
+ create_lattice(&md,DIAMOND,ALBE_LC_SI,SI,M_SI,
+ //create_lattice(&md,DIAMOND,ALBE_LC_C,C,M_C,
+#else
create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
- //create_lattice(&md,DIAMOND,LC_C,C,M_C,
+#endif
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*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
- //create_lattice(&md,FCC,TM_LC_3C_SIC,SI,M_SI,
- // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
- // 0,6,6,6,&r);
- //r.x+=0.25*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
- //create_lattice(&md,FCC,TM_LC_3C_SIC,C,M_C,
- // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
- // 1,6,6,6,&r);
+ 0,LCNTX,LCNTY,LCNTZ,NULL);
+ // 1,LCNTX,LCNTY,LCNTZ,NULL);
+
+ /* create zinkblende structure */
+ /*
+#ifdef ALBE
+ r.x=0.5*0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,ALBE_LC_SIC,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,LCNTX,LCNTY,LCNTZ,&r);
+ r.x+=0.25*ALBE_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,ALBE_LC_SIC,C,M_C,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 1,LCNTX,LCNTY,LCNTZ,&r);
+#else
+ r.x=0.5*0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,TM_LC_SIC,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,LCNTX,LCNTY,LCNTZ,&r);
+ r.x+=0.25*TM_LC_SIC; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,TM_LC_SIC,C,M_C,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 1,LCNTX,LCNTY,LCNTZ,&r);
+#endif
+ */
+ /* check for right atom placing */
moldyn_bc_check(&md);
/* testing configuration */
set_temperature(&md,atof(argv[2])+273.0);
set_pressure(&md,BAR);
+ /* set amount of steps to skip before average calc */
+ set_avg_skip(&md,AVG_SKIP);
+
/* set p/t scaling */
+ //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);
thermal_init(&md,TRUE);
/* create the simulation schedule */
- /* initial configuration */
- moldyn_add_schedule(&md,100,1.0);
- /* 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);
- //}
+ moldyn_add_schedule(&md,PRERUN,PRE_TAU);
/* schedule hook function */
- moldyn_set_schedule_hook(&md,&hook,NULL);
+ memset(&hookparam,0,sizeof(t_hp));
+ hookparam.argc=argc;
+ hookparam.argv=argv;
+ moldyn_set_schedule_hook(&md,&sic_hook,&hookparam);
+ //moldyn_set_schedule_hook(&md,&hook_del_atom,&hookparam);
+ //moldyn_add_schedule(&md,POSTRUN,1.0);
/* 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,LOG_TEMPERATURE,1);
- moldyn_set_log(&md,LOG_PRESSURE,1);
- moldyn_set_log(&md,VISUAL_STEP,1);
- moldyn_set_log(&md,SAVE_STEP,1);
+ moldyn_set_report(&md,"Frank Zirkelbach",R_TITLE);
+ moldyn_set_log(&md,LOG_TOTAL_ENERGY,LOG_E);
+ moldyn_set_log(&md,LOG_TEMPERATURE,LOG_T);
+ moldyn_set_log(&md,LOG_PRESSURE,LOG_P);
+ moldyn_set_log(&md,VISUAL_STEP,LOG_V);
+ moldyn_set_log(&md,SAVE_STEP,LOG_S);
moldyn_set_log(&md,CREATE_REPORT,0);
/*
* integration of newtons equations
*/
moldyn_integrate(&md);
-#ifdef DEBUG
+#ifdef dEBUG
return 0;
#endif
+ /*
+ * post processing the data
+ */
+
/* close */
moldyn_shutdown(&md);
projects / physik / posic.git / blobdiff