/* calculate the energy for the surface scan - same as function energy() but without observables */
double surface_energy(system_t *system, int energy_type) {
double rd_energy, coulombic_energy, polar_energy, vdw_energy;
/* zero the initial values */
rd_energy = 0;
coulombic_energy = 0;
polar_energy = 0;
vdw_energy = 0;
/* get the pairwise terms necessary for the energy calculation */
pairs(system);
// energy_type = ENERGY_TOTAL
// all other params are 0
switch(energy_type) {
case ENERGY_TOTAL:
if(!(system->sg || system->rd_only)) coulombic_energy = coulombic_nopbc(system->molecules);
if(system->polarization) polar_energy = polar(system);
if(system->polarvdw) vdw_energy = vdw(system);
if(system->sg)
rd_energy = sg_nopbc(system->molecules);
else if(system->cdvdw_exp_repulsion)
rd_energy = exp_repulsion(system);
else if(system->dreiding)
rd_energy = dreiding_nopbc(system->molecules);
else if(system->lj_buffered_14_7)
rd_energy = lj_buffered_14_7_nopbc(system);
else if(system->disp_expansion)
rd_energy = disp_expansion_nopbc(system);
else
rd_energy = lj_nopbc(system);
break;
case ENERGY_ES:
if(!(system->sg || system->rd_only)) coulombic_energy = coulombic_nopbc(system->molecules);
break;
case ENERGY_RD:
if(system->sg) {
rd_energy = sg_nopbc(system->molecules);
} else if(system->dreiding) {
rd_energy = dreiding_nopbc(system->molecules);
} else if(system->lj_buffered_14_7) {
rd_energy = lj_buffered_14_7_nopbc(system);
} else if(system->disp_expansion) {
rd_energy = disp_expansion_nopbc(system);
} else {
rd_energy = lj_nopbc(system);
}
break;
case ENERGY_POLAR:
if(system->polarization) polar_energy = polar(system);
break;
case ENERGY_VDW:
if(system->polarvdw) vdw_energy = vdw(system);
break;
}
/* return the total potential energy */
return rd_energy + coulombic_energy + polar_energy + vdw_energy;
}
/* routines, widom insertion, etc. */
double energy_no_observables(system_t *system) {
double potential_energy, rd_energy, coulombic_energy, polar_energy, vdw_energy, three_body_energy;
/* zero the initial values */
potential_energy = 0;
rd_energy = 0;
coulombic_energy = 0;
polar_energy = 0;
vdw_energy = 0;
three_body_energy = 0;
/* get the pairwise terms necessary for the energy calculation */
pairs(system);
flag_all_pairs(system);
/* get the electrostatic potential */
if(!(system->sg || system->rd_only)) {
if(system->spectre) {
coulombic_energy = coulombic_nopbc(system->molecules);
} else if(system->gwp) {
coulombic_energy = coulombic_nopbc_gwp(system);
} else {
coulombic_energy = coulombic(system);
}
/* get the polarization potential */
if(system->polarization) {
#ifdef CUDA
if(system->cuda)
polar_energy = (double)polar_cuda(system);
else
polar_energy = polar(system);
#else
polar_energy = polar(system);
#endif /* CUDA */
}
/* get the repulsion/dispersion potential */
if(system->sg)
rd_energy = sg(system);
else if(system->dreiding)
rd_energy = dreiding(system);
else if(system->lj_buffered_14_7)
rd_energy = lj_buffered_14_7(system);
else if(system->disp_expansion)
rd_energy = disp_expansion(system);
else if(system->rd_anharmonic)
rd_energy = anharmonic(system);
else if(system->cdvdw_exp_repulsion)
rd_energy = exp_repulsion(system);
else if(!system->gwp)
rd_energy = lj(system);
if(system->polarvdw) {
#ifdef CUDA
if (system->cuda) {
error("error: cuda polarvdw not yet implemented!\n");
die(-1);
}
else
vdw_energy = vdw(system);
#else
vdw_energy = vdw(system);
#endif
}
}
if (system->axilrod_teller)
three_body_energy = axilrod_teller(system);
/* sum the total potential energy */
potential_energy = rd_energy + coulombic_energy + polar_energy + vdw_energy + three_body_energy;
return(potential_energy);
}
/* returns the total potential energy for the system and updates our observables */
double energy(system_t *system) {
// molecule_t *molecule_ptr; (unused variable)
double potential_energy, rd_energy, coulombic_energy, polar_energy, vdw_energy, three_body_energy;
double kinetic_energy;
// struct timeval old_time, new_time; (unused variable)
// char linebuf[MAXLINE]; (unused variable)
#ifdef POLARTIMING
static double timing = 0;
static int count = 0;
#endif
/* zero the initial values */
kinetic_energy = 0;
potential_energy = 0;
rd_energy = 0;
coulombic_energy = 0;
polar_energy = 0;
vdw_energy = 0;
three_body_energy = 0;
system->natoms = countNatoms(system);
/* get the pairwise terms necessary for the energy calculation */
pairs(system);
/* only on the first simulation step, make sure that all recalculate flags are set */
/* if we made a volume change (or just reverted from one) set recalculate flags OR if replaying a trajectory */
// we set last_volume at the end of this function
if ( system->last_volume != system->pbc->volume
|| system->ensemble==ENSEMBLE_REPLAY
|| system->observables->energy == 0.0 )
flag_all_pairs(system);
/* get the electrostatic potential */
if(!(system->sg || system->rd_only)) {
if(system->spectre)
coulombic_energy = coulombic_nopbc(system->molecules);
else if(system->gwp) {
coulombic_energy = coulombic_nopbc_gwp(system);
kinetic_energy = coulombic_kinetic_gwp(system);
system->observables->kinetic_energy = kinetic_energy;
} else
coulombic_energy = coulombic(system);
system->observables->coulombic_energy = coulombic_energy;
/* get the polarization potential */
if(system->polarization) {
#ifdef POLARTIMING
/* get timing of polarization energy function for cuda comparison */
gettimeofday(&old_time, NULL);
#endif
#ifdef CUDA
if(system->cuda)
polar_energy = (double)polar_cuda(system);
else
polar_energy = polar(system);
#else
polar_energy = polar(system);
#endif /* CUDA */
#ifdef POLARTIMING
gettimeofday(&new_time, NULL);
timing = timing * (double)count/((double)count+1.0)
+ (double)((new_time.tv_sec-old_time.tv_sec)*1e6+(new_time.tv_usec-old_time.tv_usec)) * 1.0/((double)count +1.0);
count++;
if ( system->corrtime ) {
if ( count % system->corrtime == 0 ) sprintf(linebuf, "OUTPUT: Polarization energy function took %lf us\n", timing);
output(linebuf);
}
else {
sprintf(linebuf, "OUTPUT: Polarization energy function took %lf us\n", timing);
output(linebuf);
}
#endif
system->observables->polarization_energy = polar_energy;
}
if (system->polarvdw) {
#ifdef CUDA
if (system->cuda) {
error("error: cuda polarvdw not yet implemented!\n");
die(-1);
}
else
vdw_energy = vdw(system);
#else
vdw_energy = vdw(system);
#endif
system->observables->vdw_energy = vdw_energy;
}
}
/* get the repulsion/dispersion potential */
if(system->rd_anharmonic)
rd_energy = anharmonic(system);
else if(system->sg)
rd_energy = sg(system);
else if(system->dreiding)
rd_energy = dreiding(system);
else if(system->lj_buffered_14_7)
rd_energy = lj_buffered_14_7(system);
else if(system->disp_expansion)
rd_energy = disp_expansion(system);
else if(system->cdvdw_exp_repulsion)
rd_energy = exp_repulsion(system);
else if(!system->gwp)
rd_energy = lj(system);
system->observables->rd_energy = rd_energy;
if (system->axilrod_teller)
{
three_body_energy = axilrod_teller(system);
system->observables->three_body_energy = three_body_energy;
}
/* sum the total potential energy */
potential_energy = rd_energy + coulombic_energy + polar_energy + vdw_energy + three_body_energy;
/* not truly potential, but stick it there for convenience of MC */
/**
* POSSIBLE BUG: kinetic_energy was uninitialized, and previously only given a value inside the conditional:
*
* if(!(system->sg || system->rd_only)) {}
*
* If this conditional fails, but (system->gwp) is true (idk if this is possible), an un-initialized value would have been
* added to potential_energy. Now, 0 is being added, but am not sure if this is the desired behavior. -bt
**/
if(system->gwp) potential_energy += kinetic_energy;
system->observables->energy = potential_energy;
countN(system);
system->observables->spin_ratio /= system->observables->N;
/* for NVE */
if(system->ensemble == ENSEMBLE_NVE) {
system->observables->kinetic_energy = system->total_energy - potential_energy;
system->observables->temperature = (2.0/3.0)*system->observables->kinetic_energy/system->observables->N;
}
/* need this for the isosteric heat */
system->observables->NU = system->observables->N*system->observables->energy;
/* set last known volume*/
system->last_volume = system->pbc->volume;
if(system->cavity_autoreject_absolute)
potential_energy += cavity_absolute_check( system );
return(potential_energy);
}
float vdw_conf_hv(int i_res, int i_conf, int j_res, int j_conf, PROT prot)
{
float e = 0.0;
int iatom, jatom;
ATOM *connect123[MAX_CONNECTED2], *connect14[MAX_CONNECTED3];
ATOM *iatom_p, *jatom_p;
int connect123_res[MAX_CONNECTED2], connect14_res[MAX_CONNECTED3];
int iconnect, jconnect, kconnect, n_connect123, n_connect14, cal_vdw;
if (!prot.res[i_res].conf[i_conf].n_atom) return e;
if (!prot.res[j_res].conf[j_conf].n_atom) return e;
if (!prot.res[i_res].cal_vdw) {
if ( !param_get("CAL_VDW",prot.res[i_res].resName, "", &cal_vdw) ) {
prot.res[i_res].cal_vdw = cal_vdw;
}
else prot.res[i_res].cal_vdw = 1;
}
if (!prot.res[j_res].cal_vdw) {
if ( !param_get("CAL_VDW",prot.res[j_res].resName, "", &cal_vdw) ) {
prot.res[j_res].cal_vdw = cal_vdw;
}
else prot.res[j_res].cal_vdw = 1;
}
if (!prot.res[i_res].cal_vdw || !prot.res[j_res].cal_vdw) return e;
for (iatom=0; iatom<prot.res[i_res].conf[i_conf].n_atom; iatom++) {
iatom_p = &prot.res[i_res].conf[i_conf].atom[iatom];
if (!iatom_p->on) continue;
if (iatom_p->name[1] == 'H') continue;
n_connect123 = 0;
n_connect14 = 0;
memset(connect123, 0,MAX_CONNECTED2*sizeof(ATOM *));
memset(connect123_res,0,MAX_CONNECTED2*sizeof(int));
memset(connect14, 0,MAX_CONNECTED3*sizeof(ATOM *));
memset(connect14_res,0,MAX_CONNECTED3*sizeof(int));
for (iconnect = 0; iconnect < MAX_CONNECTED; iconnect++) {
if (!iatom_p->on) break;
if (!iatom_p->connect12[iconnect]) break;
n_connect123++;
connect123[n_connect123-1] = iatom_p->connect12[iconnect];
connect123_res[n_connect123-1] = iatom_p->connect12_res[iconnect];
for (jconnect = 0; jconnect < MAX_CONNECTED; jconnect++) {
if (!iatom_p->connect12[iconnect]->on) break;
if (!iatom_p->connect12[iconnect]->connect12[jconnect]) break;
n_connect123++;
connect123[n_connect123-1] = iatom_p->connect12[iconnect]->connect12[jconnect];
connect123_res[n_connect123-1] = iatom_p->connect12[iconnect]->connect12_res[jconnect];
for (kconnect = 0; kconnect < MAX_CONNECTED; kconnect++) {
if (!iatom_p->connect12[iconnect]->connect12[jconnect]->on) break;
if (!iatom_p->connect12[iconnect]->connect12[jconnect]->connect12[kconnect]) break;
n_connect14++;
connect14[n_connect14-1] = iatom_p->connect12[iconnect]->connect12[jconnect]->connect12[kconnect];
connect14_res[n_connect14-1] = iatom_p->connect12[iconnect]->connect12[jconnect]->connect12_res[kconnect];
}
}
}
for (jatom=0; jatom<prot.res[j_res].conf[j_conf].n_atom; jatom++) {
jatom_p = &prot.res[j_res].conf[j_conf].atom[jatom];
if (!jatom_p->on) continue;
if (jatom_p->name[1] == 'H') continue;
if (iatom_p == jatom_p) continue;
for (iconnect = 0; iconnect < n_connect123; iconnect++) {
if (j_res == connect123_res[iconnect] && !strcmp(jatom_p->name,connect123[iconnect]->name)) break;
}
if (iconnect < n_connect123) continue;
for (iconnect = 0; iconnect < n_connect14; iconnect++) {
if (j_res == connect14_res[iconnect] && !strcmp(jatom_p->name,connect14[iconnect]->name)) break;
}
if (iconnect < n_connect14) {
e += vdw(*iatom_p, *jatom_p) * env.factor_14lj;
continue;
}
e += vdw(*iatom_p, *jatom_p);
}
}
if (i_res == j_res && i_conf == j_conf) return 0.5*e;
else return e;
}
