even more testing ...

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index f2ac637..7f9745a 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -30,9 +30,10 @@ int moldyn_usage(char **argv) {
        printf("-M <steps> <file> (log total momentum)\n");
        printf("-D <steps> <file> (dump total information)\n");
        printf("-S <steps> <filebase> (single save file)\n");
+       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");
 
@@ -70,9 +71,13 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
                                        moldyn->swrite=atoi(argv[++i]);
                                        strncpy(moldyn->sfb,argv[++i],64);
                                        break;
-                               case 'T':
+                               case 'V':
+                                       moldyn->vwrite=atoi(argv[++i]);
+                                       strncpy(moldyn->vfb,argv[++i],64);
                                        break;
+                               case 'T':
                                        moldyn->t=atof(argv[++i]);
+                                       break;
                                case 't':
                                        moldyn->tau=atof(argv[++i]);
                                        break;
@@ -93,9 +98,12 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
        return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn) {
+int moldyn_log_init(t_moldyn *moldyn,void *v) {
 
        moldyn->lvstat=0;
+       t_visual *vis;
+
+       vis=v;
 
        if(moldyn->ewrite) {
                moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
@@ -130,8 +138,23 @@ int moldyn_log_init(t_moldyn *moldyn) {
                moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
        }
 
-       if(moldyn->dwrite)
+       if((moldyn->vwrite)&&(vis)) {
+               moldyn->visual=vis;
+               visual_init(vis,moldyn->vfb);
                moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+       }
+
+       moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+
+       return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+       if(moldyn->efd) close(moldyn->efd);
+       if(moldyn->mfd) close(moldyn->efd);
+       if(moldyn->dfd) close(moldyn->efd);
+       if(moldyn->visual) visual_tini(moldyn->visual);
 
        return 0;
 }
@@ -328,7 +351,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
        int i;
        unsigned int e,m,s,d,v;
-       unsigned char lvstat;
        t_3dvec p;
 
        int fd;
@@ -340,7 +362,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
        d=moldyn->dwrite;
        v=moldyn->vwrite;
 
-       if(!(lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+       if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
                printf("[moldyn] warning, lv system not initialized\n");
                return -1;
        }
@@ -498,7 +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);
                        }
@@ -525,19 +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);
                }
        }
        
@@ -557,15 +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) {
@@ -576,11 +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);
                        }
                }
        }