X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=d50c35ea353021153c172a08fa8bfbb2db9cecfc;hb=58fd691b276fbe87593036714f26dbfe7486cbeb;hp=c4355b3305a8995a79aa1cc3f90244510cb0364f;hpb=150c5f804a5088a01ef2bb1e934b5e65d10ac23e;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index c4355b3..d50c35e 100644
--- a/sic.c
+++ b/sic.c
@@ -8,9 +8,74 @@
 #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
+
+int hook(void *moldyn,void *hook_params) {
+
+	t_moldyn *md;
+	t_3dvec r,v,dist;
+	double d;
+	unsigned char run;
+	int i,j;
+	t_atom *atom;
+
+	md=moldyn;
+
+// vortrag
+set_temperature(moldyn,(4-md->schedule.count)*1000.0);
+set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+return 0;
+
+	printf("\nschedule hook: ");
+
+	if(!(md->schedule.count%2)) {
+		/* add carbon at random place, and enable t scaling */
+		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;
+			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;
+			}
+		}
+		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);
+	}
+
+	return 0;
+}
+
 int main(int argc,char **argv) {
 
 	/* check argv */
@@ -23,49 +88,54 @@ int main(int argc,char **argv) {
 	t_moldyn md;
 
 	/* potential parameters */
-	t_lj_params lj;
-	t_ho_params ho;
 	t_tersoff_mult_params tp;
+	t_albe_mult_params ap;
 
-	/* misc parameters */
-	double tau;
+	/* atom injection counter */
+	int inject;
 
 	/* testing location & velocity vector */
 	t_3dvec r,v;
-
-	/* values */
-	tau=1.0e-15;	/* delta t = 1 fs */
+	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_potential2b_post(&md,tersoff_mult_post_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 */
+#ifdef ALBE
+	set_cutoff(&md,ALBE_S_SI);
+#else
+	set_cutoff(&md,TM_S_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;
-
-	/* harmonic oscillator */
-	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-	ho.spring_constant=1;
-
 	/*
          * tersoff mult potential parameters for SiC
 	 */
@@ -97,90 +167,174 @@ int main(int argc,char **argv) {
 
 	tersoff_mult_complete_params(&tp);
 
-	/* cutoff radius */
-	printf("[sic] setting cutoff radius\n");
-	set_cutoff(&md,TM_S_SI);
-	//set_cutoff(&md,2*LC_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,5*LC_SI,5*LC_SI,5*LC_SI,TRUE);
+	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);
 
 	/* 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");
 	//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-	//               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
-	//               0,5,5,5);
-	//moldyn_bc_check(&md);
+	//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,
+	//               ATOM_ATTR_2BP|ATOM_ATTR_HB,
+	               0,6,6,6,NULL);
+	//               1,6,6,6,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,
+	               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,
+	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	               1,6,6,6,&r);
+	*/
+
+	moldyn_bc_check(&md);
 
 	/* testing configuration */
-	r.x=2.8/2;	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,
-	           &r,&v);
-	r.x=-2.8/2;	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,
-	           &r,&v);
-
-	/* setting a nearest neighbour distance for the moldyn checks */
-	set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
-
-	/* set temperature */
-	printf("[sic] setting temperature -> %f\n",273+atof(argv[2]));
-	//set_temperature(&md,273.0+1410.0);
-	//set_temperature(&md,273.0+450.0);
-	//set_temperature(&md,273.0);
-	//set_temperature(&md,1.0);
-	//set_temperature(&md,0.0);
+	//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 */
-	printf("[sic] setting pressure\n");
-	set_pressure(&md,ATM);
+	set_pressure(&md,BAR);
 
 	/* set p/t scaling */
-	printf("[sic] set p/t scaling\n");
-	//set_pt_scale(&md,P_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_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);
+	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,10000,.1);
+	/* initial configuration */
+	moldyn_add_schedule(&md,10000,1.0);
+	//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,900,1.0);
+	//	/* continue running with disabled t scaling */
+	//	moldyn_add_schedule(&md,1100,1.0);
+	//}
+
+
+	/* schedule hook function */
+	moldyn_set_schedule_hook(&md,&hook,NULL);
 
 	/* activate logging */
-	printf("[sic] activate logging\n");
 	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,VISUAL_STEP,20);
+	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);
 
 	/*
 	 * 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
+	 */
+
+	/* response functions expressed by energy fluctuations */
+	calc_fluctuations(1000.0,9999.0,&md);
+	get_heat_capacity(&md);
 
-	printf("[sic] shutdown\n");
+	/* close */
 	moldyn_shutdown(&md);
 	
 	return 0;