#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/albe.h"
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+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;
+
+#define STATE_PRERUN 0x00
+#define STATE_INSERT 0x01
+#define STATE_POSTRUN 0x02
+
+/* 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,dmin;
+
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ v.x=0; v.y=0; v.z=0;
+
+ for(j=0;j<INS_ATOMS;j++) {
+ run=1;
+ while(run) {
+ // 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;
+ dmin=10000000000.0; // for sure too high!
+ 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);
+ /* reject coordinates */
+ if(d<INS_R_C) {
+ //printf("atom %d - %f\n",i,d);
+ run=1;
+ break;
+ }
+ if(d<dmin)
+ dmin=d;
+ }
+ }
+ 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(" %02d: atom %d | %f %f %f | %f\n",
+ j,moldyn->count-1,r.x,r.y,r.z,dmin);
+ }
+
+ return 0;
+}
+
+int sic_hook(void *moldyn,void *hook_params) {
+
+ t_hp *hp;
+ t_moldyn *md;
+ int steps;
+ double tau;
+ double dt;
+
+ 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:
+ /* assigne values */
+ steps=INS_RELAX;
+ tau=INS_TAU;
+ /* check temperature */
+ dt=md->t_avg-md->t_ref;
+ if(dt<0)
+ dt=-dt;
+ if(dt>INS_DELTA_TC)
+ 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:
+ /* assigne values */
+ steps=POST_RELAX;
+ tau=POST_TAU;
+ /* check temperature */
+ dt=md->t_avg-md->t_ref;
+ if(dt<0)
+ dt=-dt;
+ if(dt>INS_DELTA_TC)
+ break;
+ /* 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;
+ }
+
+ /* reset the average counters */
+ average_reset(md);
+
+ /* 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;
- /* misc parameters */
- double tau;
-
- /* values */
- tau=1.0e-15; /* delta t = 1 fs */
+ /* testing location & velocity vector */
+ t_3dvec r,v;
+ 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_potential3b(&md,tersoff_mult_3bp,&tp);
- //set_potential2b(&md,lennard_jones,&lj);
+#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 & bondlen */
+#ifdef ALBE
+ set_cutoff(&md,ALBE_S_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;
-
- /* harmonic oscillator */
- ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
- ho.spring_constant=1;
-
/*
* tersoff mult potential parameters for SiC
*/
tp.n[1]=TM_N_C;
tp.c[1]=TM_C_C;
tp.d[1]=TM_D_C;
+ tp.h[1]=TM_H_C;
tp.chi=TM_CHI_SIC;
tersoff_mult_complete_params(&tp);
- /* cutoff radius */
- printf("[sic] setting cutoff radius\n");
- set_cutoff(&md,TM_S_SI);
+ /*
+ * 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 */
- printf("[sic] setting dimensions\n");
- set_dim(&md,4*LC_SI,4*LC_SI,4*LC_SI,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 */
- printf("[sic] setting periodic boundary conditions\n");
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
- printf("[sic] creating atoms\n");
+ //
+#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,
+#endif
ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
- //ATOM_ATTR_2BP|ATOM_ATTR_HB,
- 0,4,4,4);
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ 0,LCNTX,LCNTY,LCNTZ,NULL);
+ // 1,LCNTX,LCNTY,LCNTZ,NULL);
- /* setting a nearest neighbour distance for the moldyn checks */
- set_nn_dist(&md,sqrt(3.0)*LC_SI/4.0); /* diamond ! */
+ /* 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 */
+ //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=-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);
+
+ /* set temperature & pressure */
+ set_temperature(&md,atof(argv[2])+273.0);
+ set_pressure(&md,BAR);
- /* set temperature */
- printf("[sic] setting temperature\n");
- set_temperature(&md,0.0);
+ /* set amount of steps to skip before average calc */
+ set_avg_skip(&md,AVG_SKIP);
/* set p/t scaling */
- printf("[sic] set p/t scaling\n");
- set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100*tau);
+ //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,100,1.0e-15);
+ moldyn_add_schedule(&md,PRERUN,PRE_TAU);
+
+ /* schedule hook function */
+ 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 */
- printf("[sic] activate logging\n");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
- moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
+ moldyn_set_log_dir(&md,argv[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);
/*
* let's do the actual md algorithm now
*
* integration of newtons equations
*/
-
- printf("[sic] integration start, go get a coffee ...\n");
moldyn_integrate(&md);
+#ifdef dEBUG
+return 0;
+#endif
- /* close */
+ /*
+ * post processing the data
+ */
- printf("[sic] shutdown\n");
+ /* close */
moldyn_shutdown(&md);
return 0;