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#include <math.h> |
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#include "Atom.hpp" |
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#include "Molecule.hpp" |
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#include "SimInfo.hpp" |
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#include "Thermo.hpp" |
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#include "ExtendedSystem.hpp" |
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#include "simError.h" |
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|
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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 = the_entry_plug; |
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zeta = 0.0; |
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epsilonDot = 0.0; |
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epsilonDotX = 0.0; |
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epsilonDotY = 0.0; |
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epsilonDotZ = 0.0; |
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have_tau_thermostat = 0; |
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have_tau_barostat = 0; |
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have_target_temp = 0; |
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have_target_pressure = 0; |
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have_qmass = 0; |
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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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int i; |
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double NkBT, zetaScale, ke_temp; |
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double vx, vy, vz, jx, jy, jz; |
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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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|
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if (this->NVTready()) { |
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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)entry_plug->ndf * kB * targetTemp; |
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|
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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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|
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// perform thermostat scaling on linear velocities and angular momentum |
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for(i = 0; i < entry_plug->n_atoms; i++){ |
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|
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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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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( entry_plug->n_oriented ){ |
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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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dAtom = (DirectionalAtom *)atoms[i]; |
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jx = dAtom->getJx(); |
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jy = dAtom->getJy(); |
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jz = dAtom->getJz(); |
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dAtom->setJx(jx * (1.0 - zetaScale)); |
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dAtom->setJy(jy * (1.0 - zetaScale)); |
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dAtom->setJz(jz * (1.0 - zetaScale)); |
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} |
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} |
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} |
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} |
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} |
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void ExtendedSystem::NoseHooverAndersonNPT( double dt, |
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double ke, |
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double p_tensor[9] ) { |
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|
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// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500 |
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double oldBox[3]; |
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double newBox[3]; |
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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 p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
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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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|
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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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if (this->NPTready()) { |
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atoms = entry_plug->atoms; |
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p_ext = targetPressure * p_units; |
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p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0; |
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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)entry_plug->ndf * kB * targetTemp; |
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// propagate the strain rate |
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epsilonDot += dt * ((p_mol - p_ext) * volume / |
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(tauBarostat*tauBarostat * kB * targetTemp) ); |
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// determine the change in cell volume |
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scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0)); |
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//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; |
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|
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newBox[0] = oldBox[0] * scale; |
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newBox[1] = oldBox[1] * scale; |
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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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epsilonScale = epsilonDot * dt; |
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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 << " epsilonScale = " << epsilonScale << "\n"; |
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|
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// apply barostating and thermostating to velocities and angular momenta |
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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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atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale)); |
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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( entry_plug->n_oriented ){ |
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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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dAtom = (DirectionalAtom *)atoms[i]; |
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jx = dAtom->getJx(); |
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jy = dAtom->getJy(); |
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jz = dAtom->getJz(); |
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dAtom->setJx( jx * (1.0 - zetaScale)); |
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dAtom->setJy( jy * (1.0 - zetaScale)); |
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dAtom->setJz( jz * (1.0 - zetaScale)); |
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} |
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} |
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} |
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} |
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} |
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void ExtendedSystem::ConstantStress( double dt, |
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double ke, |
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double p_tensor[9] ) { |
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double oldBox[3]; |
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double newBox[3]; |
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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 p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
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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 pX_ext, pY_ext, pZ_ext; |
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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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if (this->NPTready()) { |
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atoms = entry_plug->atoms; |
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p_ext = targetPressure * p_units; |
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pX_ext = p_ext / 3.0; |
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pY_ext = p_ext / 3.0; |
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pZ_ext = p_ext / 3.0; |
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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)entry_plug->ndf * kB * targetTemp; |
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// propagate the strain rate |
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epsilonDotX += dt * ((p_tensor[0] - pX_ext) * volume / |
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(tauBarostat*tauBarostat * kB * targetTemp) ); |
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epsilonDotY += dt * ((p_tensor[4] - pY_ext) * volume / |
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(tauBarostat*tauBarostat * kB * targetTemp) ); |
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epsilonDotZ += dt * ((p_tensor[8] - pZ_ext) * volume / |
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(tauBarostat*tauBarostat * kB * targetTemp) ); |
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// determine the change in cell volume |
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//scale = pow( (1.0 + dt * 3.0 * (epsilonDot), (1.0 / 3.0)); |
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//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; |
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newBox[0] = oldBox[0] * scale; |
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newBox[1] = oldBox[1] * scale; |
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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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epsilonScale = epsilonDot * dt; |
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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 |
243 |
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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 < 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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256 |
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atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale)); |
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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( entry_plug->n_oriented ){ |
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for( i=0; i < entry_plug->n_atoms; i++ ){ |
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264 |
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if( atoms[i]->isDirectional() ){ |
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266 |
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dAtom = (DirectionalAtom *)atoms[i]; |
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jx = dAtom->getJx(); |
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jy = dAtom->getJy(); |
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jz = dAtom->getJz(); |
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dAtom->setJx( jx * (1.0 - zetaScale)); |
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dAtom->setJy( jy * (1.0 - zetaScale)); |
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dAtom->setJz( jz * (1.0 - zetaScale)); |
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} |
276 |
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} |
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gezelter |
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} |
278 |
gezelter |
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} |
279 |
gezelter |
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} |
280 |
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281 |
gezelter |
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void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){ |
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gezelter |
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|
283 |
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int i; |
284 |
gezelter |
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double r[3]; |
285 |
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double boxNum[3]; |
286 |
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double percentScale[3]; |
287 |
gezelter |
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double delta[3]; |
288 |
gezelter |
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double rxi, ryi, rzi; |
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gezelter |
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|
290 |
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molecules = entry_plug->molecules; |
291 |
gezelter |
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|
292 |
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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]; |
294 |
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percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
295 |
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percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
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gezelter |
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|
297 |
gezelter |
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for (i=0; i < entry_plug->n_mol; i++) { |
298 |
gezelter |
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|
299 |
gezelter |
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molecules[i].getCOM(r); |
300 |
gezelter |
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|
301 |
gezelter |
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// find the minimum image coordinates of the molecular centers of mass: |
302 |
gezelter |
453 |
|
303 |
gezelter |
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boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
304 |
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(double)(int)(fabs(r[0]/oldBox[0]) + 0.5); |
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gezelter |
453 |
|
306 |
gezelter |
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boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * |
307 |
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(double)(int)(fabs(r[1]/oldBox[1]) + 0.5); |
308 |
gezelter |
453 |
|
309 |
gezelter |
457 |
boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * |
310 |
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(double)(int)(fabs(r[2]/oldBox[2]) + 0.5); |
311 |
gezelter |
453 |
|
312 |
gezelter |
457 |
rxi = r[0] - boxNum[0]; |
313 |
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ryi = r[1] - boxNum[1]; |
314 |
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rzi = r[2] - boxNum[2]; |
315 |
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|
316 |
gezelter |
453 |
// update the minimum image coordinates using the scaling factor |
317 |
gezelter |
457 |
rxi += rxi*percentScale[0]; |
318 |
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ryi += ryi*percentScale[1]; |
319 |
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rzi += rzi*percentScale[2]; |
320 |
gezelter |
453 |
|
321 |
gezelter |
476 |
delta[0] = r[0] - (rxi + boxNum[0]); |
322 |
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delta[1] = r[1] - (ryi + boxNum[1]); |
323 |
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delta[2] = r[2] - (rzi + boxNum[2]); |
324 |
gezelter |
457 |
|
325 |
gezelter |
476 |
molecules[i].moveCOM(delta); |
326 |
gezelter |
453 |
} |
327 |
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} |
328 |
gezelter |
481 |
|
329 |
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short int ExtendedSystem::NVTready() { |
330 |
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const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
331 |
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double NkBT; |
332 |
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333 |
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if (!have_target_temp) { |
334 |
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sprintf( painCave.errMsg, |
335 |
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"ExtendedSystem error: You can't use NVT without a targetTemp!\n" |
336 |
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); |
337 |
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painCave.isFatal = 1; |
338 |
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simError(); |
339 |
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return -1; |
340 |
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} |
341 |
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342 |
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if (!have_qmass) { |
343 |
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if (have_tau_thermostat) { |
344 |
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345 |
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NkBT = (double)entry_plug->ndf * kB * targetTemp; |
346 |
|
|
std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n"; |
347 |
|
|
this->setQmass(tauThermostat * NkBT); |
348 |
|
|
|
349 |
|
|
} else { |
350 |
|
|
sprintf( painCave.errMsg, |
351 |
|
|
"ExtendedSystem error: If you use the constant temperature\n" |
352 |
|
|
" ensemble, you must set either tauThermostat or qMass.\n"); |
353 |
|
|
painCave.isFatal = 1; |
354 |
|
|
simError(); |
355 |
|
|
} |
356 |
|
|
} |
357 |
|
|
|
358 |
gezelter |
483 |
return 1; |
359 |
gezelter |
481 |
} |
360 |
|
|
|
361 |
|
|
short int ExtendedSystem::NPTready() { |
362 |
|
|
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
363 |
|
|
double NkBT; |
364 |
|
|
|
365 |
|
|
if (!have_target_temp) { |
366 |
|
|
sprintf( painCave.errMsg, |
367 |
|
|
"ExtendedSystem error: You can't use NPT without a targetTemp!\n" |
368 |
|
|
); |
369 |
|
|
painCave.isFatal = 1; |
370 |
|
|
simError(); |
371 |
|
|
return -1; |
372 |
|
|
} |
373 |
|
|
|
374 |
|
|
if (!have_target_pressure) { |
375 |
|
|
sprintf( painCave.errMsg, |
376 |
|
|
"ExtendedSystem error: You can't use NPT without a targetPressure!\n" |
377 |
|
|
); |
378 |
|
|
painCave.isFatal = 1; |
379 |
|
|
simError(); |
380 |
|
|
return -1; |
381 |
|
|
} |
382 |
|
|
|
383 |
|
|
if (!have_tau_barostat) { |
384 |
|
|
sprintf( painCave.errMsg, |
385 |
|
|
"ExtendedSystem error: If you use the NPT\n" |
386 |
|
|
" ensemble, you must set tauBarostat.\n"); |
387 |
|
|
painCave.isFatal = 1; |
388 |
|
|
simError(); |
389 |
|
|
} |
390 |
|
|
|
391 |
|
|
if (!have_qmass) { |
392 |
|
|
if (have_tau_thermostat) { |
393 |
|
|
|
394 |
|
|
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
395 |
|
|
std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n"; |
396 |
|
|
this->setQmass(tauThermostat * NkBT); |
397 |
|
|
|
398 |
|
|
} else { |
399 |
|
|
sprintf( painCave.errMsg, |
400 |
|
|
"ExtendedSystem error: If you use the NPT\n" |
401 |
|
|
" ensemble, you must set either tauThermostat or qMass.\n"); |
402 |
|
|
painCave.isFatal = 1; |
403 |
|
|
simError(); |
404 |
|
|
} |
405 |
|
|
} |
406 |
gezelter |
483 |
return 1; |
407 |
gezelter |
481 |
} |
408 |
|
|
|