X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=1f9bbbe7b0932a7a20ee7881ef2ef005d8114395;hb=c1f74e23422d004f7b9d2493cc747871c7ebfbae;hp=682d89ee6fcd46d96b1cb341b6c4b8d708a61a85;hpb=ea612b88a0588b8f46fafaebf3b37fb46c83c0cf;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 682d89e..1f9bbbe 100644
--- a/sic.c
+++ b/sic.c
@@ -13,10 +13,26 @@
 /* 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	1
+#define R_C		1.0
+#define T_C		10.0
+#define LCNT		3
 
-#define INJECT		20
-#define NR_ATOMS	20	
+typedef struct s_hp {
+	int a_count;	/* atom count */
+	u8 quit;	/* quit mark */
+	int argc;	/* arg count */
+	char **argv;	/* args */
+} t_hp;
 
 int hook(void *moldyn,void *hook_params) {
 
@@ -26,40 +42,66 @@ int hook(void *moldyn,void *hook_params) {
 	unsigned char run;
 	int i,j;
 	t_atom *atom;
+	t_hp *hp;
 
 	md=moldyn;
+	hp=hook_params;
+
+	/* quit */
+	if(hp->quit)
+		return 0;
+
+	/* switch on t scaling */
+	if(md->schedule.count==0)
+		set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
 
-	printf("\nschedule hook: ");
+	/* last schedule add if there is enough carbon inside */
+	if(hp->a_count==(INJECT*NR_ATOMS)) {
+		hp->quit=1;
+		moldyn_add_schedule(md,5000,1.0);
+		return 0;
+	}
+
+	/* more relaxing time for too high temperatures */
+	if(md->t-md->t_ref>T_C) {
+		moldyn_add_schedule(md,10,1.0);
+		return 0;
+	}
 
-	if(!(md->schedule.count%2)) {
-		/* add carbon at random place, and enable t scaling */
-		for(j=0;j<NR_ATOMS;j++) {
+	/* inject carbon atoms */
+	printf("injecting another %d carbon atoms ...(-> %d / %d)\n",
+	       NR_ATOMS,hp->a_count+NR_ATOMS,INJECT*NR_ATOMS);
+	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;
+			r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
+			r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
+			r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
+			//r.x=(1.0*atoi(hp->argv[3])-4.5)/9.0*ALBE_LC_SI;
+			//r.y=(1.0*atoi(hp->argv[4])-4.5)/9.0*ALBE_LC_SI;
+			//r.z=(1.0*atoi(hp->argv[5])-4.5)/9.0*ALBE_LC_SI;
+			/* assume valid coordinates */
+			run=0;
 			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;
+				/* reject coordinates */
+				if(d<R_C) {
+					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,
 		         &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);
 	}
+	hp->a_count+=NR_ATOMS;
+
+	/* add schedule for simulating injected atoms ;) */
+	moldyn_add_schedule(md,10,1.0);
 
 	return 0;
 }
@@ -67,18 +109,20 @@ int hook(void *moldyn,void *hook_params) {
 int main(int argc,char **argv) {
 
 	/* check argv */
-	if(argc!=3) {
-		printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
-		return -1;
-	}
+	//if(argc!=3) {
+	//	printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+	//	return -1;
+	//}
 
 	/* 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;
@@ -95,37 +139,36 @@ int main(int argc,char **argv) {
 	set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
 
 	/* choose potential */
+#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_potential2b(&md,tersoff_mult_2bp);
-	set_potential2b_post(&md,tersoff_mult_post_2bp);
-	set_potential3b(&md,tersoff_mult_3bp);
-	//set_potential2b(&md,lennard_jones);
-	//set_potential2b(&md,harmonic_oscillator);
+	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);
-	//set_potential_params(&md,&lj);
-	//set_potential_params(&md,&ho);
+#endif
 
 	/* cutoff radius */
+#ifdef ALBE
+	set_cutoff(&md,ALBE_S_SI);
+#else
 	set_cutoff(&md,TM_S_SI);
-	//set_cutoff(&md,LC_SI*sqrt(3.0));
-	//set_cutoff(&md,2.0*LC_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
 	 */
@@ -157,19 +200,97 @@ int main(int argc,char **argv) {
 
 	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);
+#ifdef ALBE
+	set_dim(&md,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,LCNT*ALBE_LC_SI,TRUE);
+	//set_dim(&md,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,LCNT*ALBE_LC_C,TRUE);
+	//set_dim(&md,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,LCNT*ALBE_LC_SIC,TRUE);
+#else
+	//set_dim(&md,LCNT*LC_SI,LCNT*LC_SI,LCNT*LC_SI,TRUE);
+	//set_dim(&md,LCNT*LC_C,LCNT*LC_C,LCNT*LC_C,TRUE);
+	set_dim(&md,LCNT*TM_LC_SIC,LCNT*TM_LC_SIC,LCNT*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,
-	create_lattice(&md,DIAMOND,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,
+#endif
 	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 	//               ATOM_ATTR_2BP|ATOM_ATTR_HB,
-	               0,6,6,6);
+	               0,LCNT,LCNT,LCNT,NULL);
+	//               1,LCNT,LCNT,LCNT,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,LCNT,LCNT,LCNT,&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,LCNT,LCNT,LCNT,&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,LCNT,LCNT,LCNT,&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,LCNT,LCNT,LCNT,&r);
+#endif
+	*/
+
+	/* check for right atom placing */
 	moldyn_bc_check(&md);
 
 	/* testing configuration */
@@ -188,9 +309,17 @@ int main(int argc,char **argv) {
 	//           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;
-	//r.y=0;	v.y=0;
-	//r.z=sin(M_PI*60.0/180.0)*(TM_S_SI+TM_R_SI)/4.0;	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,
@@ -198,9 +327,13 @@ int main(int argc,char **argv) {
 
 	/* set temperature & pressure */
 	set_temperature(&md,atof(argv[2])+273.0);
-	set_pressure(&md,ATM);
+	set_pressure(&md,BAR);
+
+	/* set amount of steps to skip before average calc */
+	set_avg_skip(&md,1000);
 
 	/* 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);
@@ -210,25 +343,30 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	/* initial configuration */
-	moldyn_add_schedule(&md,500,1.0);
+	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);
+	//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,400,1.0);
-		/* continue running with disabled t scaling */
-		moldyn_add_schedule(&md,100,1.0);
-	}
+	//for(inject=0;inject<INJECT;inject++) {
+	//	/* injecting atoms */
+	//	moldyn_add_schedule(&md,10,1.0);
+	//}
 
 	/* 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,&hook,&hookparam);
 
 	/* activate logging */
 	moldyn_set_log_dir(&md,argv[1]);
 	moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
-	moldyn_set_log(&md,LOG_TOTAL_ENERGY,10);
-	moldyn_set_log(&md,LOG_TEMPERATURE,10);
-	moldyn_set_log(&md,LOG_PRESSURE,10);
+	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);
@@ -239,6 +377,13 @@ int main(int argc,char **argv) {
 	 * integration of newtons equations
 	 */
 	moldyn_integrate(&md);
+#ifdef dEBUG
+return 0;
+#endif
+
+	/*
+	 * post processing the data
+	 */
 
 	/* close */
 	moldyn_shutdown(&md);