X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=749600f58b6fe1371b5cc1ac1aa6049e23e7b364;hb=a35a47e5a070e5615313e2b612996cd572bccae9;hp=cea2644a6db4031931c437ddef4395e499058f0c;hpb=92ef07d77a4c879527180224acea73a3f6564497;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index cea2644..749600f 100644
--- a/sic.c
+++ b/sic.c
@@ -21,8 +21,34 @@
 #include "potentials/tersoff.h"
 #endif
 
-#define INJECT		1
-#define NR_ATOMS	4
+#define INJECT		800
+#define NR_ATOMS	10
+#define R_C		1.5
+#define T_C		10.0
+#define INJ_LENX	(10*ALBE_LC_SIC)
+#define INJ_LENY	(10*ALBE_LC_SIC)
+#define INJ_LENZ	(10*ALBE_LC_SIC)
+#define INJ_OFFSET	(ALBE_LC_SI/8.0)
+
+#define LCNTX		50
+#define LCNTY		50
+#define LCNTZ		50
+#define PRERUN		1000
+#define POSTRUN		10000
+
+#define R_TITLE		"Insertion of 8000 carbon atoms in silicon"
+#define LOG_E		10
+#define LOG_T		10
+#define LOG_P		10
+#define LOG_S		100
+#define LOG_V		100
+
+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) {
 
@@ -32,40 +58,67 @@ int hook(void *moldyn,void *hook_params) {
 	unsigned char run;
 	int i,j;
 	t_atom *atom;
+	t_hp *hp;
 
 	md=moldyn;
+	hp=hook_params;
 
-	printf("\nschedule hook: ");
+	/* quit */
+	if(hp->quit)
+		return 0;
 
-	if(!(md->schedule.count%2)) {
-		/* add carbon at random place, and enable t scaling */
-		for(j=0;j<NR_ATOMS;j++) {
+	/* switch on t scaling */
+	if(md->schedule.count==0)
+		set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+	/* last schedule add if there is enough carbon inside */
+	if(hp->a_count==(INJECT*NR_ATOMS)) {
+		hp->quit=1;
+		moldyn_add_schedule(md,POSTRUN,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;
+	}
+
+	/* 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)*INJ_LENX;
+			r.x+=INJ_OFFSET;
+			r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
+			r.y+=INJ_OFFSET;
+			r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
+			r.z+=INJ_OFFSET;
+			/* 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,
+		//add_atom(md,C,M_C,1,
+		add_atom(md,SI,M_SI,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;
 }
@@ -73,21 +126,21 @@ 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_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));
@@ -122,8 +175,10 @@ int main(int argc,char **argv) {
 	/* cutoff radius */
 #ifdef ALBE
 	set_cutoff(&md,ALBE_S_SI);
+	//set_cutoff(&md,ALBE_S_C);
 #else
 	set_cutoff(&md,TM_S_SI);
+	//set_cutoff(&md,TM_S_C);
 #endif
 
 	/*
@@ -203,36 +258,55 @@ int main(int argc,char **argv) {
 	albe_mult_complete_params(&ap);
 
 	/* set (initial) dimensions of simulation volume */
-	//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);
+#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,LCNT*LC_SI,LCNT*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 */
+#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_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,
+#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);
+	               0,LCNTX,LCNTY,LCNTZ,NULL);
+	//               1,LCNTX,LCNTY,LCNTZ,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,
+	/* 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,
-	               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,
+	               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,
-	               1,6,6,6,&r);
-	/**/
+	               1,LCNTX,LCNTY,LCNTZ,&r);
+#endif
+	*/
 
+	/* check for right atom placing */
 	moldyn_bc_check(&md);
 
 	/* testing configuration */
@@ -271,7 +345,11 @@ int main(int argc,char **argv) {
 	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,(8.0/10.0*PRERUN));
+
 	/* 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);
@@ -281,27 +359,22 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	/* 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);
-	//}
+	moldyn_add_schedule(&md,PRERUN,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,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_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);
 
 	/*
@@ -310,10 +383,14 @@ int main(int argc,char **argv) {
 	 * integration of newtons equations
 	 */
 	moldyn_integrate(&md);
-#ifdef DEBUG
+#ifdef dEBUG
 return 0;
 #endif
 
+	/*
+	 * post processing the data
+	 */
+
 	/* close */
 	moldyn_shutdown(&md);