even more testing ...

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 0fd1aca..7f9745a 100644 (file)
--- 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);
                        }
                }
        }