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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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|
| 19 |
< |
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| 20 |
< |
#define BASE_SEED 123456789 |
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| 22 |
< |
Thermo::Thermo( SimInfo* the_entry_plug ) { |
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entry_plug = the_entry_plug; |
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int baseSeed = BASE_SEED; |
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> |
Thermo::Thermo( SimInfo* the_info ) { |
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info = the_info; |
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> |
int baseSeed = the_info->getSeed(); |
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|
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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Atom** atoms; |
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< |
n_atoms = entry_plug->n_atoms; |
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atoms = entry_plug->atoms; |
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> |
n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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|
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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int el, nSRI; |
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Molecule* molecules; |
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| 88 |
< |
molecules = entry_plug->molecules; |
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< |
nSRI = entry_plug->n_SRI; |
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> |
molecules = info->molecules; |
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> |
nSRI = info->n_SRI; |
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potential_local = 0.0; |
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potential = 0.0; |
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< |
potential_local += entry_plug->lrPot; |
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> |
potential_local += info->lrPot; |
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|
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< |
for( el=0; el<entry_plug->n_mol; el++ ){ |
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> |
for( el=0; el<info->n_mol; el++ ){ |
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potential_local += molecules[el].getPotential(); |
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} |
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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|
| 129 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
| 129 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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return temperature; |
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} |
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double Thermo::getVolume() { |
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return entry_plug->boxVol; |
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> |
return info->boxVol; |
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} |
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double Thermo::getPressure() { |
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return pressure; |
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} |
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| 169 |
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double Thermo::getPressureX() { |
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// Relies on the calculation of the full molecular pressure tensor |
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|
| 173 |
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const double p_convert = 1.63882576e8; |
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double press[3][3]; |
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double pressureX; |
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|
| 177 |
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this->getPressureTensor(press); |
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|
| 179 |
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pressureX = p_convert * press[0][0]; |
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|
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return pressureX; |
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} |
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|
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double Thermo::getPressureY() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
| 188 |
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const double p_convert = 1.63882576e8; |
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double press[3][3]; |
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double pressureY; |
| 191 |
+ |
|
| 192 |
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this->getPressureTensor(press); |
| 193 |
+ |
|
| 194 |
+ |
pressureY = p_convert * press[1][1]; |
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+ |
|
| 196 |
+ |
return pressureY; |
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} |
| 198 |
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|
| 199 |
+ |
double Thermo::getPressureZ() { |
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+ |
|
| 201 |
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// Relies on the calculation of the full molecular pressure tensor |
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|
| 203 |
+ |
const double p_convert = 1.63882576e8; |
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+ |
double press[3][3]; |
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double pressureZ; |
| 206 |
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|
| 207 |
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this->getPressureTensor(press); |
| 208 |
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|
| 209 |
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pressureZ = p_convert * press[2][2]; |
| 210 |
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|
| 211 |
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return pressureZ; |
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} |
| 213 |
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|
| 214 |
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|
| 215 |
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void Thermo::getPressureTensor(double press[3][3]){ |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
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// routine derived via viral theorem description in: |
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double molmass, volume; |
| 223 |
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double vcom[3]; |
| 224 |
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double p_local[9], p_global[9]; |
| 225 |
< |
int i, j, k, l, nMols; |
| 225 |
> |
int i, j, k, nMols; |
| 226 |
|
Molecule* molecules; |
| 227 |
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|
| 228 |
< |
nMols = entry_plug->n_mol; |
| 229 |
< |
molecules = entry_plug->molecules; |
| 230 |
< |
//tau = entry_plug->tau; |
| 228 |
> |
nMols = info->n_mol; |
| 229 |
> |
molecules = info->molecules; |
| 230 |
> |
//tau = info->tau; |
| 231 |
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|
| 232 |
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// use velocities of molecular centers of mass and molecular masses: |
| 233 |
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for (i=0; i < 9; i++) { |
| 264 |
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for(i = 0; i < 3; i++) { |
| 265 |
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for (j = 0; j < 3; j++) { |
| 266 |
|
k = 3*i + j; |
| 267 |
< |
press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume; |
| 267 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
| 268 |
> |
|
| 269 |
|
} |
| 270 |
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} |
| 271 |
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} |
| 287 |
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int n_oriented; |
| 288 |
|
int n_constraints; |
| 289 |
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|
| 290 |
< |
atoms = entry_plug->atoms; |
| 291 |
< |
n_atoms = entry_plug->n_atoms; |
| 292 |
< |
temperature = entry_plug->target_temp; |
| 293 |
< |
n_oriented = entry_plug->n_oriented; |
| 294 |
< |
n_constraints = entry_plug->n_constraints; |
| 290 |
> |
atoms = info->atoms; |
| 291 |
> |
n_atoms = info->n_atoms; |
| 292 |
> |
temperature = info->target_temp; |
| 293 |
> |
n_oriented = info->n_oriented; |
| 294 |
> |
n_constraints = info->n_constraints; |
| 295 |
|
|
| 296 |
< |
kebar = kb * temperature * (double)entry_plug->ndf / |
| 297 |
< |
( 2.0 * (double)entry_plug->ndfRaw ); |
| 296 |
> |
kebar = kb * temperature * (double)info->ndf / |
| 297 |
> |
( 2.0 * (double)info->ndfRaw ); |
| 298 |
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|
| 299 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 300 |
|
|
| 365 |
|
// We are very careless here with the distinction between n_atoms and n_local |
| 366 |
|
// We should really fix this before someone pokes an eye out. |
| 367 |
|
|
| 368 |
< |
n_atoms = entry_plug->n_atoms; |
| 369 |
< |
atoms = entry_plug->atoms; |
| 368 |
> |
n_atoms = info->n_atoms; |
| 369 |
> |
atoms = info->atoms; |
| 370 |
|
|
| 371 |
|
mtot_local = 0.0; |
| 372 |
|
vdrift_local[0] = 0.0; |
