From bdb198c5a5fe38361d10f98e7db366b0915e56fb Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Wed, 5 Apr 2006 23:16:30 +0000
Subject: [PATCH] even more testing ...

---
 moldyn.c | 14 +++++++-------
 posic.c  |  4 ++--
 posic.h  |  6 +++---
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index db575e9..7f9745a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -33,7 +33,7 @@ int moldyn_usage(char **argv) {
 	printf("-V <steps> <filebase> (rasmol file)\n");
 	printf("--- physics options ---\n");
 	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
-	printf("-t <timestep tau> [s] (%f)\n",MOLDYN_TAU);
+	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
 	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
 	printf("\n");
 
@@ -520,7 +520,7 @@ int force_harmonic_oscillator(t_moldyn *moldyn) {
 			d=v3_norm(&distance);
 			if(d<=moldyn->cutoff) {
 				v3_scale(&force,&distance,
-				         (-sc*(1.0-(equi_dist/d))));
+				         -sc*(1.0-(equi_dist/d)));
 				v3_add(&(atom[i].f),&(atom[i].f),&force);
 				v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
@@ -554,7 +554,7 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 	u=0.0;
 	for(i=0;i<count;i++) {
 		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 			d=1.0/v3_absolute_square(&distance); 	/* 1/r^2 */
 			help=d*d; 				/* 1/r^4 */
 			help*=d; 				/* 1/r^6 */
@@ -580,14 +580,14 @@ int force_lennard_jones(t_moldyn *moldyn) {
 	count=moldyn->count;
 	params=moldyn->pot_params;
 	eps=params->epsilon4;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+	sig6=6*params->sigma6;
+	sig12=12*params->sigma12;
 
 	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
 
 	for(i=0;i<count;i++) {
 		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 			v3_per_bound(&distance,&(moldyn->dim));
 			d=v3_absolute_square(&distance);
 			if(d<=moldyn->cutoff_square) {
@@ -600,7 +600,7 @@ int force_lennard_jones(t_moldyn *moldyn) {
 				h2*=sig6;
 				/* actually there would be a '-',	*
 				 * but f=-d/dr potential		*/
-				d=-12.0*h1+6.0*h2;
+				d=h1+h2;
 				d*=eps;
 				v3_scale(&force,&distance,d);
 				v3_add(&(atom[i].f),&(atom[i].f),&force);
diff --git a/posic.c b/posic.c
index 992f9d1..8bbfe0e 100644
--- a/posic.c
+++ b/posic.c
@@ -60,7 +60,7 @@ int main(int argc,char **argv) {
 	/* testing purpose
 	count=2;
 	si=malloc(2*sizeof(t_atom));
-	si[0].r.x=0.23*sqrt(3.0)*LC_SI/2.0;
+	si[0].r.x=0.13*sqrt(3.0)*LC_SI/2.0;
 	si[0].r.y=0;
 	si[0].r.z=0;
 	si[0].element=SI;
@@ -111,7 +111,7 @@ int main(int argc,char **argv) {
 	lj.epsilon4=4.0*LJ_EPSILON_SI;
 
 	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-	ho.spring_constant=4.0*LJ_EPSILON_SI;
+	ho.spring_constant=1.0;
 
 	u=get_e_pot(&md);
 
diff --git a/posic.h b/posic.h
index d31331f..44caf18 100644
--- a/posic.h
+++ b/posic.h
@@ -23,9 +23,9 @@
 
 #define TEMPERATURE 273.0 
 
-#define LEN_X 3
-#define LEN_Y 3
-#define LEN_Z 3
+#define LEN_X 10
+#define LEN_Y 10
+#define LEN_Z 10
 
 #define R_CUTOFF (0.25*LEN_Z)
 
-- 
2.20.1