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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 = info.n_atoms; |
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atoms = info.atoms; |
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nMols = info.n_mol; |
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molecules = info.molecules; |
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entry_plug = the_entry_plug; |
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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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zeta = 0.0; |
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epsilonDot = 0.0; |
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} |
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ExtendedSystem::~ExtendedSystem() { |
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} |
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void ExtendedSystem::NoseHooverNVT( double dt, double ke ){ |
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
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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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ke_temp = ke * e_convert; |
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NkBT = (double)getNDF() * kB * targetTemp; |
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NkBT = (double)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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zetaScale = zeta * dt; |
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// perform thermostat scaling on linear velocities and angular momentum |
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for(i = 0; i < n_atoms; i++){ |
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for(i = 0; i < nAtoms; 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)); |
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atoms[i]->set_vz(vz * (1.0 - zetaScale)); |
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} |
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if( n_oriented ){ |
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if( nOriented ){ |
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for( i=0; i < n_atoms; i++ ){ |
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for( i=0; i < nAtoms; 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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< |
double p_ext; |
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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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p_ext = targetPressure * p_units; |
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p_mol = p_int * p_units; |
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getBox(oldBox); |
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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)getNDF() * kB * targetTemp; |
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NkBT = (double)ndf * kB * targetTemp; |
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// propogate the strain rate |
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newBox[2] = oldBox[2] * scale; |
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volume = newBox[0]*newBox[1]*newBox[2]; |
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entry_plug->setBox(newBox); |
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// perform affine transform to update positions with volume fluctuations |
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this->AffineTransform( oldBox, newBox ); |
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zetaScale = zeta * dt; |
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// apply barostating and thermostating to velocities and angular momenta |
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for(i = 0; i < n_atoms; i++){ |
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for(i = 0; i < nAtoms; 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( n_oriented ){ |
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if( nOriented ){ |
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< |
for( i=0; i < n_atoms; i++ ){ |
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for( i=0; i < nAtoms; i++ ){ |
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if( atoms[i]->isDirectional() ){ |
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for (i=0; i < nMols; i++) { |
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< |
molecules[i]->getCOM(r); |
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molecules[i].getCOM(r); |
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// find the minimum image coordinates of the molecular centers of mass: |
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r[1] = ryi + boxNum[1]; |
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r[2] = rzi + boxNum[2]; |
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< |
molecules[i]->moveCOM(r); |
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> |
molecules[i].moveCOM(r); |
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} |
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} |
