X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=05de728c9e9cdd4be50bf73a1e1a51fd6956d195;hb=b5b47daaa3718c4dec2056fe5147668023575b8e;hp=9cb2c554f42c0d81e98e202ab12223d65c19b976;hpb=56fe12b9eabe0cfa493e2f1b1d0d7d219ae8705b;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 9cb2c55..05de728 100644
--- a/sic.c
+++ b/sic.c
@@ -8,118 +8,444 @@
 #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"
 
-#define TRUE 1
-#define FALSE 0
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+//#define INJECT		800
+#define INJECT		1
+#define NR_ATOMS	1
+#define R_C		1.5
+#define T_C		5.0
+//#define INJ_LENX	(1*ALBE_LC_SIC)
+//#define INJ_LENY	(1*ALBE_LC_SIC)
+//#define INJ_LENZ	(1*ALBE_LC_SIC)
+#define INJ_LENX	(1*ALBE_LC_SI)
+#define INJ_LENY	(1*ALBE_LC_SI)
+#define INJ_LENZ	(1*ALBE_LC_SI)
+#define INJ_TYPE_SILICON
+//#define INJ_TYPE_CARBON
+#define INJ_OFFSET	(ALBE_LC_SI/8.0)
+#define RELAX_S		20
+
+#define LCNTX		9
+#define LCNTY		9
+#define LCNTZ		9
+#define PRERUN		40
+#define POSTRUN		3000
+
+#define R_TITLE		"Silicon self-interstitial"
+#define LOG_E		10
+#define LOG_T		10
+#define LOG_P		10
+#define LOG_S		100
+#define LOG_V		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_del_atom(void *moldyn,void *hook_params) {
+
+	t_moldyn *md;
+	t_hp *hp;
+
+	md=moldyn;
+	hp=hook_params;
+
+	set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+	del_atom(md,2);
+
+	return 0;
+}
+
+int hook_add_atom(void *moldyn,void *hook_params) {
+
+	t_moldyn *md;
+	t_3dvec r,v,dist;
+	double d;
+	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);
+
+	/* 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,RELAX_S,1.0);
+		return 0;
+	}
+
+	/* inject carbon atoms */
+	printf("injecting another %d 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) {
+			// 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(&(md->random))-0.5)*INJ_LENX;
+			r.y=(rand_get_double(&(md->random))-0.5)*INJ_LENY;
+			r.z=(rand_get_double(&(md->random))-0.5)*INJ_LENZ;
+			*/
+			// offset
+			r.x+=INJ_OFFSET;
+			r.y+=INJ_OFFSET;
+			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);
+				/* reject coordinates */
+				if(d<R_C) {
+					//printf("atom %d - %f\n",i,d);
+					run=1;
+					break;
+				}
+			}
+		}
+		v.x=0; v.y=0; v.z=0;
+#ifdef INJ_TYPE_CARBON
+		add_atom(md,C,M_C,1,
+#else
+		add_atom(md,SI,M_SI,0,
+#endif
+		         ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB|ATOM_ATTR_VB,
+		         &r,&v);
+	}
+	hp->a_count+=NR_ATOMS;
+
+	/* add schedule for simulating injected atoms ;) */
+	moldyn_add_schedule(md,RELAX_S,1.0);
+
+	return 0;
+}
 
 int main(int argc,char **argv) {
 
+	/* check argv */
+	//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;
 
-	/* misc variables, mainly to initialize stuff */
+	/* testing location & velocity vector */
 	t_3dvec r,v;
-
-	/* temperature */
-	double t;
+	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;
+	/*
+         * tersoff mult potential parameters for SiC
+	 */
+	tp.S[0]=TM_S_SI;
+	tp.R[0]=TM_R_SI;
+	tp.A[0]=TM_A_SI;
+	tp.B[0]=TM_B_SI;
+	tp.lambda[0]=TM_LAMBDA_SI;
+	tp.mu[0]=TM_MU_SI;
+	tp.beta[0]=TM_BETA_SI;
+	tp.n[0]=TM_N_SI;
+	tp.c[0]=TM_C_SI;
+	tp.d[0]=TM_D_SI;
+	tp.h[0]=TM_H_SI;
+
+	tp.S[1]=TM_S_C;
+	tp.R[1]=TM_R_C;
+	tp.A[1]=TM_A_C;
+	tp.B[1]=TM_B_C;
+	tp.lambda[1]=TM_LAMBDA_C;
+	tp.mu[1]=TM_MU_C;
+	tp.beta[1]=TM_BETA_C;
+	tp.n[1]=TM_N_C;
+	tp.c[1]=TM_C_C;
+	tp.d[1]=TM_D_C;
+	tp.h[1]=TM_H_C;
 
-	/* harmonic oscillator */
-	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-	ho.spring_constant=1;
+	tp.chi=TM_CHI_SIC;
 
-	/* cutoff radius */
-	printf("[sic] setting cutoff radius\n");
-	set_cutoff(&md,LC_SI);
+	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 */
-	printf("[sic] setting dimensions\n");
-	set_dim(&md,10*LC_SI,10*LC_SI,10*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");
-	memset(&v,0,sizeof(t_3dvec));
-	r.y=0;
-	r.z=0;
-	r.x=0.23*sqrt(3.0)*LC_SI/2.0;
-	add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
-	r.x=-r.x;
-	add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
-	printf("[sic] check: there are %d atoms\n",md.count);
-	printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
-	printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
-	printf("[sic] check: atoms mass: %.35f %.35f\n",md.atom[0].mass,md.atom[1].mass);
-
-	/* set temperature */
-	printf("[sic] setting temperature\n");
-	set_temperature(&md,0.0);
+	//
+#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,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 */
+	//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 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);
+	//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 	
-	/* initial thermal fluctuations of particles */
-	printf("[sic] thermal init\n");
-	thermal_init(&md);
-	printf("[sic] check: there are %d atoms\n",md.count);
-	printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
-	printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
+	/* initial thermal fluctuations of particles (in equilibrium) */
+	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,10000,1.0e-12);
+	moldyn_add_schedule(&md,PRERUN,1.0);
+
+	/* schedule hook function */
+	memset(&hookparam,0,sizeof(t_hp));
+	hookparam.argc=argc;
+	hookparam.argv=argv;
+	moldyn_set_schedule_hook(&md,&hook_add_atom,&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;