X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=22210255abab5145bee92bd98e44f1280506aa1d;hb=57847266c05bc38218bf162efdb08e8dd40894d7;hp=5f50bd802440865c0585ff57e9f5395c35fa387c;hpb=15dd7ee084a5db24a3e1a15428cd47e8d61fda5b;p=physik%2Fposic.git

diff --git a/sic.c b/sic.c
index 5f50bd8..2221025 100644
--- a/sic.c
+++ b/sic.c
@@ -8,13 +8,71 @@
 #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/tersoff.h"
+//#include "potentials/tersoff_orig.h"
+
+#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;
+
+	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 */
+	if(argc!=3) {
+		printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+		return -1;
+	}
+
 	/* main moldyn structure */
 	t_moldyn md;
 
@@ -23,27 +81,40 @@ int main(int argc,char **argv) {
 	t_ho_params ho;
 	t_tersoff_mult_params tp;
 
-	/* misc parameters */
-	double tau;
+	/* atom injection counter */
+	int inject;
 
-	/* values */
-	tau=1.0e-15;	/* delta t = 1 fs */
+	/* testing location & velocity vector */
+	t_3dvec r,v;
+	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);
+	set_potential1b(&md,tersoff_mult_1bp);
+	//set_potential2b(&md,tersoff_mult_2bp);
+	//set_potential3b_j1(&md,tersoff_mult_2bp);
+	//set_potential3b_k1(&md,tersoff_mult_3bp);
+	//set_potential3b_j3(&md,tersoff_mult_post_2bp);
+	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);
+	//set_potential2b(&md,lennard_jones);
+	//set_potential2b(&md,harmonic_oscillator);
+	set_potential_params(&md,&tp);
+	//set_potential_params(&md,&lj);
+	//set_potential_params(&md,&ho);
+
+	/* cutoff radius */
+	set_cutoff(&md,TM_S_SI);
+	//set_cutoff(&md,LC_SI*sqrt(3.0));
+	//set_cutoff(&md,2.0*LC_SI);
 
 	/*
 	 * potential parameters
@@ -54,10 +125,12 @@ int main(int argc,char **argv) {
 	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.spring_constant=1;
+	//ho.equilibrium_distance=LC_SI;
+	ho.spring_constant=LJ_EPSILON_SI;
 
 	/*
          * tersoff mult potential parameters for SiC
@@ -90,61 +163,98 @@ 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 (initial) dimensions of simulation volume */
-	printf("[sic] setting dimensions\n");
-	set_dim(&md,3*LC_SI,3*LC_SI,3*LC_SI,TRUE);
+	set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,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,CUBIC,LC_SI,SI,M_SI,
+	//create_lattice(&md,FCC,LC_SI,SI,M_SI,
 	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
-	               //ATOM_ATTR_2BP|ATOM_ATTR_HB,
-	               0,3,3,3);
+	//               ATOM_ATTR_2BP|ATOM_ATTR_HB,
+	               0,6,6,6);
+	moldyn_bc_check(&md);
 
-	/* setting a nearest neighbour distance for the moldyn checks */
-	set_nn_dist(&md,sqrt(3.0)*LC_SI/4.0); /* diamond ! */
+	/* 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 */
-	printf("[sic] setting temperature\n");
-	set_temperature(&md,0.0);
+	/* set temperature & pressure */
+	set_temperature(&md,atof(argv[2])+273.0);
+	set_pressure(&md,BAR);
 
 	/* set p/t scaling */
-	printf("[sic] set p/t scaling\n");
-	set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100*tau);
+	//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 (in equilibrium) */
-	printf("[sic] thermal init\n");
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,100,1.0e-15);
+	/* 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);
+	//}
+
+	/* schedule hook function */
+	moldyn_set_schedule_hook(&md,&hook,NULL);
 
 	/* 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","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_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);
 
 	/* close */
-
-	printf("[sic] shutdown\n");
 	moldyn_shutdown(&md);
 	
 	return 0;