From: hackbard <hackbard>
Date: Tue, 5 Dec 2006 15:49:56 +0000 (+0000)
Subject: some bugfixes ... com'on
X-Git-Url: https://www.hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=commitdiff_plain;h=746278fb5c566b621b70c78b38d8b6c0b4e2677f

some bugfixes ... com'on
---

diff --git a/Makefile b/Makefile
index b037404..dabf04c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,8 +1,8 @@
 CC=gcc
-CFLAGS=-Wall #-DSIMPLE_TESTING
+CFLAGS=-Wall -O3 #-DSIMPLE_TESTING
 LDFLAGS=-lm
 
-OBJS=init/init.o visual/visual.o math/math.o random/random.o list/list.o
+OBJS=init/init.o visual/visual.o random/random.o list/list.o
 OBJS+=moldyn.o
 
 all: sic
diff --git a/moldyn.c b/moldyn.c
index 716a087..2631d6a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -873,15 +873,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 					   !(jtom->attr&ATOM_ATTR_3BP))
 						continue;
 
-			/*
-			 * according to mr. nordlund, we dont need to take the 
-			 * sum over all atoms now, as 'this is centered' around
-			 * atom i ...
-			 * i am not quite sure though! there is a not vanishing
-			 * part even if f_c_ik is zero ...
-			 * this analytical potentials suck!
-			 * switching from mc to md to dft soon!
-			 */
+			/* neighbourhood of atom j is not needed! */
 
 			//		link_cell_neighbour_index(moldyn,
 			//		   (jtom->r.x+moldyn->dim.x/2)/lc->x,
@@ -1156,6 +1148,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	exchange=&(params->exchange);
 
 	exchange->run3bp=0;
+	exchange->run2bp_post=0;
 	
 	/*
 	 * we need: f_c, df_c, f_r, df_r
@@ -1200,7 +1193,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	f_r=A*exp(-lambda*d_ij);
 	df_r=-lambda*f_r/d_ij;
 
-	/* f_a, df_a calc + save for 3bp use */
+	/* f_a, df_a calc + save for later use */
 	exchange->f_a=-B*exp(-mu*d_ij);
 	exchange->df_a=-mu*exchange->f_a/d_ij;
 
@@ -1228,8 +1221,9 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	exchange->f_c=f_c;
 	exchange->df_c=df_c;
 
-	/* enable the run of 3bp function */
+	/* enable the run of 3bp function and 2bp post processing */
 	exchange->run3bp=1;
+	exchange->run2bp_post=1;
 
 	/* reset 3bp sums */
 	exchange->sum1_3bp=0.0;
@@ -1259,6 +1253,10 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	params=moldyn->pot2b_params;
 	exchange=&(params->exchange);
 
+	/* we do not run if f_c_ij was dtected to be 0! */
+	if(!(exchange->run2bp_post))
+		return 0;
+
 	db_ij=&(exchange->db_ij);
 	f_c=exchange->f_c;
 	df_c=exchange->df_c;
@@ -1266,6 +1264,7 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	df_a=exchange->df_a;
 	betan=exchange->betan;
 	n=*(exchange->n);
+	chi=exchange->chi;
 	dist_ij=&(exchange->dist_ij);
 
 	db_ij_scale1=(1+betan*exchange->sum1_3bp);
@@ -1274,19 +1273,24 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	b_ij=chi*db_ij_scale1*help;
 	db_ij_scale1=-chi/(2*n)*help;
 
+	/* db_ij part */
 	v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
 	v3_scale(db_ij,db_ij,f_a);
 
+	/* df_a part */
 	v3_scale(&temp,dist_ij,b_ij*df_a);
 
+	/* db_ij + df_a part */
 	v3_add(&force,&temp,db_ij);
 	v3_scale(&force,&force,f_c);
 
+	/* df_c part */
 	v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
 
 	/* add energy of 3bp sum */
 	moldyn->energy+=(0.5*f_c*b_ij*f_a);
-	/* add force of 3bp calculation */	
+
+	/* add force of 3bp calculation (all three parts) */
 	v3_add(&(ai->f),&temp,&force);
 
 	return 0;
@@ -1415,13 +1419,13 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		bracket=0.0;
 		bracket_n_1=0.0;
 		bracket_n=0.0;
-		printf("Foo -> 0: ");
+		//printf("Foo -> 0: ");
 	}
 	else {
 		bracket=f_c_ik*g;
 		bracket_n_1=pow(bracket,n-1.0);
 		bracket_n=bracket_n_1*bracket;
-		printf("Foo -> 1: ");
+		//printf("Foo -> 1: ");
 	}
 //printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket);
 
diff --git a/moldyn.h b/moldyn.h
index 09471a1..1145f8a 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -197,6 +197,7 @@ typedef struct s_tersoff_exchange {
 	double n_betan;
 
 	u8 run3bp;
+	u8 run2bp_post;
 
 	t_3dvec db_ij;
 	double sum1_3bp;
diff --git a/sic.c b/sic.c
index 5f50bd8..26bb8c8 100644
--- a/sic.c
+++ b/sic.c
@@ -96,7 +96,7 @@ int main(int argc,char **argv) {
 
 	/* 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,5*LC_SI,5*LC_SI,5*LC_SI,TRUE);
 
 	/* set periodic boundary conditions in all directions */
 	printf("[sic] setting periodic boundary conditions\n");
@@ -106,15 +106,17 @@ int main(int argc,char **argv) {
 	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,
+	               //ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,
 	               //ATOM_ATTR_2BP|ATOM_ATTR_HB,
-	               0,3,3,3);
+	               0,5,5,5);
 
 	/* setting a nearest neighbour distance for the moldyn checks */
 	set_nn_dist(&md,sqrt(3.0)*LC_SI/4.0); /* diamond ! */
 
 	/* set temperature */
 	printf("[sic] setting temperature\n");
-	set_temperature(&md,0.0);
+	set_temperature(&md,273.0+450.0);
+	//set_temperature(&md,0.0);
 
 	/* set p/t scaling */
 	printf("[sic] set p/t scaling\n");
@@ -126,12 +128,12 @@ int main(int argc,char **argv) {
 
 	/* create the simulation schedule */
 	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,100,1.0e-15);
+	moldyn_add_schedule(&md,10000,1.0e-15);
 
 	/* 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(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
+	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100);
 
 	/*
 	 * let's do the actual md algorithm now