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);
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;
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);
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;
}
int i;
unsigned int e,m,s,d,v;
- unsigned char lvstat;
t_3dvec p;
int fd;
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;
}
params=moldyn->pot_params;
atom=moldyn->atom;
count=moldyn->count;
- eps=params->epsilon;
+ eps=params->epsilon4;
sig6=params->sigma6;
sig12=params->sigma12;
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);
}
}
atom=moldyn->atom;
count=moldyn->count;
params=moldyn->pot_params;
- eps=params->epsilon;
+ eps=params->epsilon4;
sig6=params->sigma6;
sig12=params->sigma12;
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=-12.0*h1+6.0*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);
}
}
}