X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=7f9745ad29ef2f8e7dd52a52301a4f0a05ad0283;hb=bdb198c5a5fe38361d10f98e7db366b0915e56fb;hp=0fd1aca88d3b7243ee58cbe2d219cf0e4e2190f9;hpb=512390ceb93a2dd630943165b35bba683e0ffcfc;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 0fd1aca..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);
 			}
@@ -547,19 +547,19 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 	params=moldyn->pot_params;
 	atom=moldyn->atom;
 	count=moldyn->count;
-	eps=params->epsilon;
+	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
 	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 */
 			d=help*help; 				/* 1/r^12 */
-			u+=eps*(sig12*d-sig6*help);
+			u+=eps*(sig6*help-sig12*d);
 		}
 	}
 	
@@ -579,15 +579,15 @@ int force_lennard_jones(t_moldyn *moldyn) {
 	atom=moldyn->atom;	
 	count=moldyn->count;
 	params=moldyn->pot_params;
-	eps=params->epsilon;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+	eps=params->epsilon4;
+	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) {
@@ -598,11 +598,13 @@ int force_lennard_jones(t_moldyn *moldyn) {
 				h1*=h2;				/* 1/r^14 */
 				h1*=sig12;
 				h2*=sig6;
-				d=12.0*h1-6.0*h2;
+				/* actually there would be a '-',	*
+				 * but f=-d/dr potential		*/
+				d=h1+h2;
 				d*=eps;
 				v3_scale(&force,&distance,d);
-				v3_add(&(atom[j].f),&(atom[j].f),&force);
-				v3_sub(&(atom[i].f),&(atom[i].f),&force);
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+				v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
 		}
 	}