X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=cea4c3934c823a4b6d1003c1de3cb1d04a956512;hb=f939e7a6413390ca309302bb145434d68daeca10;hp=3c815bac57a9ce9d0325bb4e43523177e25ad79e;hpb=acdd9a6aa72f3692ccd03cc0df20e3d60555f555;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 3c815ba..cea4c39 100644
--- a/sic.c
+++ b/sic.c
@@ -8,85 +8,196 @@
 #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
+
+/* include the config file */
+#include "config.h"
+
+int insert_atoms(t_moldyn *moldyn) {
 
-	t_moldyn *md;
-	t_3dvec r,v,dist;
-	double d;
-	unsigned char run;
 	int i,j;
+	u8 run;
+	t_3dvec r,v,dist;
+	double d,dmin;
+
 	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]);
+#ifdef INS_TETRA
+			// tetrahedral
+			r.x=0.0;
+			r.y=0.0;
+			r.z=0.0;
+#endif
+#ifdef INS_HEXA
+			// 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;
+#endif
+#ifdef INS_110DB
+			// 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;
+#endif
+#ifdef INS_RAND
+			// 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;
+#endif
+			// 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);
-				if(d>TM_R_C)
-					run=0;
+				/* reject coordinates */
+				if(d<INS_R_C) {
+					//printf("atom %d - %f\n",i,d);
+					run=1;
+					break;
+				}
+				if(d<dmin)
+					dmin=d;
 			}
 		}
-		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|\
+			 INS_ATTR,
 		         &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);
+		printf(" %02d: atom %d | %f %f %f | %f\n",
+		       j,moldyn->count-1,r.x,r.y,r.z,dmin);
 	}
 
 	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;
+	double dt;
+
+	hp=hook_params;
+	md=moldyn;
+
+	tau=1.0;
+	steps=0;
+
+	/* 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>POST_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;
-
-	/* atom injection counter */
-	int inject;
+	t_albe_mult_params ap;
 
 	/* testing location & velocity vector */
 	t_3dvec r,v;
@@ -100,44 +211,40 @@ int main(int argc,char **argv) {
 	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);
+#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);
-	//set_potential_params(&md,&lj);
-	//set_potential_params(&md,&ho);
+#endif
 
-	/* cutoff radius */
+	/* 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_cutoff(&md,LC_SI*sqrt(3.0));
-	//set_cutoff(&md,2.0*LC_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
 	 */
@@ -169,31 +276,98 @@ 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);
-	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,
-	//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-	//create_lattice(&md,DIAMOND,LC_C,C,M_C,
-	//               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	//
+#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,
-	//               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*TM_LC_3C_SIC; r.y=r.x; r.z=r.x;
-	create_lattice(&md,FCC,TM_LC_3C_SIC,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,
+	               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,
-	               0,6,6,6,&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,
+	               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 */
@@ -232,7 +406,11 @@ 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,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);
@@ -242,39 +420,43 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	/* initial configuration */
-	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);
-	//}
+	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,10);
-	moldyn_set_log(&md,SAVE_STEP,10);
+	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);
 
+	/* next neighbour distance for critical checking */
+	set_nn_dist(&md,0.25*ALBE_LC_SI*sqrt(3.0));
+
 	/*
 	 * let's do the actual md algorithm now
 	 *
 	 * integration of newtons equations
 	 */
 	moldyn_integrate(&md);
-#ifdef DEBUG
+#ifdef dEBUG
 return 0;
 #endif
 
+	/*
+	 * post processing the data
+	 */
+
 	/* close */
 	moldyn_shutdown(&md);