int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
strncpy(moldyn->vlsdir,dir,127);
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
strncpy(moldyn->vlsdir,dir,127);
/* assume up to date kinetic energy, which is 3/2 N k_B T */
moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
/* assume up to date kinetic energy, which is 3/2 N k_B T */
moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
/* assume up to date kinetic energy */
moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
moldyn->p/=(3.0*moldyn->volume);
/* assume up to date kinetic energy */
moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
moldyn->p/=(3.0*moldyn->volume);
- moldyn->p_sum+=moldyn->p;
- moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
+ if(moldyn->total_steps>=moldyn->mean_skip) {
+ moldyn->p_sum+=moldyn->p;
+ moldyn->mean_p=moldyn->p_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
+ }
/* pressure from 'absolute coordinates' virial */
virial=&(moldyn->virial);
v=virial->xx+virial->yy+virial->zz;
moldyn->gp=2.0*moldyn->ekin+v;
moldyn->gp/=(3.0*moldyn->volume);
/* pressure from 'absolute coordinates' virial */
virial=&(moldyn->virial);
v=virial->xx+virial->yy+virial->zz;
moldyn->gp=2.0*moldyn->ekin+v;
moldyn->gp/=(3.0*moldyn->volume);
- moldyn->gp_sum+=moldyn->gp;
- moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
+ if(moldyn->total_steps>=moldyn->mean_skip) {
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->mean_gp=moldyn->gp_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
+ }
/* assume up to date energies */
/* kinetic energy */
moldyn->k_sum+=moldyn->ekin;
moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
/* assume up to date energies */
/* kinetic energy */
moldyn->k_sum+=moldyn->ekin;
moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
- moldyn->k_mean=moldyn->k_sum/moldyn->total_steps;
- moldyn->k2_mean=moldyn->k2_sum/moldyn->total_steps;
+ moldyn->k_mean=moldyn->k_sum/(moldyn->total_steps+1-moldyn->mean_skip);
+ moldyn->k2_mean=moldyn->k2_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
moldyn->dk2_mean=moldyn->k2_mean-(moldyn->k_mean*moldyn->k_mean);
/* potential energy */
moldyn->v_sum+=moldyn->energy;
moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
moldyn->dk2_mean=moldyn->k2_mean-(moldyn->k_mean*moldyn->k_mean);
/* potential energy */
moldyn->v_sum+=moldyn->energy;
moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
- moldyn->v_mean=moldyn->v_sum/moldyn->total_steps;
- moldyn->v2_mean=moldyn->v2_sum/moldyn->total_steps;
+ moldyn->v_mean=moldyn->v_sum/(moldyn->total_steps+1-moldyn->mean_skip);
+ moldyn->v2_mean=moldyn->v2_sum/
+ (moldyn->total_steps+1-moldyn->mean_skip);
/* (temperature average)^2 */
temp2=moldyn->mean_t*moldyn->mean_t;
printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
/* (temperature average)^2 */
temp2=moldyn->mean_t*moldyn->mean_t;
printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);