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#include "Thermo.hpp" |
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#include "ExtendedSystem.hpp" |
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ExtendedSystem::ExtendedSystem( SimInfo &info ) { |
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ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) { |
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// get what information we need from the SimInfo object |
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entry_plug = &info; |
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nAtoms = entry_plug->n_atoms; |
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atoms = entry_plug->atoms; |
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nMols = entry_plug->n_mol; |
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molecules = entry_plug->molecules; |
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nOriented = entry_plug->n_oriented; |
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ndf = entry_plug->ndf; |
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entry_plug = the_entry_plug; |
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zeta = 0.0; |
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epsilonDot = 0.0; |
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} |
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void ExtendedSystem::NoseHooverNVT( double dt, double ke ){ |
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const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
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// amu*Ang^2*fs^-2/K |
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DirectionalAtom* dAtom; |
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atoms = entry_plug->atoms; |
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– |
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ke_temp = ke * e_convert; |
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< |
NkBT = (double)ndf * kB * targetTemp; |
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> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
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// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
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// qmass is set in the parameter file |
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zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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zetaScale = zeta * dt; |
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std::cerr << "zetaScale = " << zetaScale << "\n"; |
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// perform thermostat scaling on linear velocities and angular momentum |
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for(i = 0; i < nAtoms; i++){ |
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> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
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vx = atoms[i]->get_vx(); |
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vy = atoms[i]->get_vy(); |
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vz = atoms[i]->get_vz(); |
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> |
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atoms[i]->set_vx(vx * (1.0 - zetaScale)); |
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atoms[i]->set_vy(vy * (1.0 - zetaScale)); |
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atoms[i]->set_vz(vz * (1.0 - zetaScale)); |
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} |
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if( nOriented ){ |
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> |
if( entry_plug->n_oriented ){ |
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< |
for( i=0; i < nAtoms; i++ ){ |
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> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
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if( atoms[i]->isDirectional() ){ |
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const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
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// amu*Ang^2*fs^-2/K |
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+ |
int i; |
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double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp; |
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double volume, p_mol; |
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double vx, vy, vz, jx, jy, jz; |
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DirectionalAtom* dAtom; |
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int i; |
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> |
atoms = entry_plug->atoms; |
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p_ext = targetPressure * p_units; |
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p_mol = p_int * p_units; |
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entry_plug->getBox(oldBox); |
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volume = oldBox[0]*oldBox[1]*oldBox[2]; |
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ke_temp = ke * e_convert; |
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< |
NkBT = (double)ndf * kB * targetTemp; |
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> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
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// propogate the strain rate |
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zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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zetaScale = zeta * dt; |
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std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n"; |
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// apply barostating and thermostating to velocities and angular momenta |
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< |
for(i = 0; i < nAtoms; i++){ |
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> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
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vx = atoms[i]->get_vx(); |
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vy = atoms[i]->get_vy(); |
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atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale)); |
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atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale)); |
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} |
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< |
if( nOriented ){ |
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> |
if( entry_plug->n_oriented ){ |
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< |
for( i=0; i < nAtoms; i++ ){ |
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> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
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if( atoms[i]->isDirectional() ){ |
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double r[3]; |
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double boxNum[3]; |
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double percentScale[3]; |
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+ |
double delta[3]; |
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double rxi, ryi, rzi; |
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+ |
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+ |
molecules = entry_plug->molecules; |
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// first determine the scaling factor from the box size change |
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percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0]; |
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percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
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percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
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| 179 |
< |
for (i=0; i < nMols; i++) { |
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> |
for (i=0; i < entry_plug->n_mol; i++) { |
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molecules[i].getCOM(r); |
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< |
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> |
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// find the minimum image coordinates of the molecular centers of mass: |
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boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
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ryi += ryi*percentScale[1]; |
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rzi += rzi*percentScale[2]; |
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| 203 |
< |
r[0] = rxi + boxNum[0]; |
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< |
r[1] = ryi + boxNum[1]; |
| 205 |
< |
r[2] = rzi + boxNum[2]; |
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> |
delta[0] = r[0] - (rxi + boxNum[0]); |
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> |
delta[1] = r[1] - (ryi + boxNum[1]); |
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> |
delta[2] = r[2] - (rzi + boxNum[2]); |
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| 207 |
< |
molecules[i].moveCOM(r); |
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> |
molecules[i].moveCOM(delta); |
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} |
| 209 |
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} |
