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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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< |
zeta = 0; |
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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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– |
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void ExtendedSystem::NoseHooverNVT( double dt ){ |
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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 kB, keconverter, NkBT, zetaScale, ke_temp; |
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> |
double NkBT, zetaScale, ke_temp; |
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double vx, vy, vz, jx, jy, jz; |
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< |
|
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< |
kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
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< |
keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2 / K |
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< |
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< |
ke_temp = getKinetic() * keconverter; |
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NkBT = (double)getNDF() * kB * targetTemp; |
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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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< |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin & |
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> |
ke_temp = ke * e_convert; |
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> |
NkBT = (double)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 - NkBT)/qmass); |
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> |
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zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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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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vz = atoms[i]->get_vz(); |
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atoms[i]->set_vx(vx - zetaScale * vx); |
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atoms[i]->set_vy(vy - zetaScale * vy); |
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atoms[i]->set_vz(vz - zetaScale * 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( 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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jy = dAtom->getJy(); |
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jz = dAtom->getJz(); |
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dAtom->setJx( jx - zetaScale * jx); |
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dAtom->setJy( jy - zetaScale * jy); |
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dAtom->setJz( jz - zetaScale * jz); |
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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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void ExtendedSystem::NoseHooverAndersonNPT(double pressure, double ke, |
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double dt, double temp ) { |
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> |
void ExtendedSystem::NoseHooverAndersonNPT( double dt, |
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double ke, |
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double p_int ) { |
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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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int i, j, degrees_freedom; |
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double pressure, dt, temp, pressure_units, epsilonScale; |
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double ke, kB, vxi, vyi, vzi, pressure_ext; |
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double boxx_old, boxy_old, boxz_old; |
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double keconverter, NkBT, zetaScale, ke_temp; |
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double jxi, jyi, jzi, scale; |
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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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kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
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pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
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degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
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keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K |
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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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pressure_ext = pressure * pressure_units; |
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volume = boxx*boxy*boxz; |
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ke_temp = ke * keconverter; |
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NkBT = degrees_freedom*kB*temp; |
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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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// propogate the strain rate |
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epsilon_dot += dt * ( (p_mol - pressure_ext)*volume |
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/ (tau_relax*tau_relax * kB * targetTemp) ); |
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> |
epsilonDot += dt * ((p_mol - p_ext) * volume / |
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(tauRelax*tauRelax * kB * targetTemp) ); |
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// determine the change in cell volume |
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scale = pow( (1.0 + dt * 3.0 * epsilon_dot), (1.0 / 3.0)); |
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scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0)); |
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< |
volume = volume * pow(scale, 3.0); |
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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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affine_transform( scale ); |
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> |
this->AffineTransform( oldBox, newBox ); |
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// save old lengths and update box size |
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boxx_old = boxx; |
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boxy_old = boxy; |
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boxz_old = boxz; |
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boxx = boxx_old*scale; |
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boxy = boxy_old*scale; |
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boxz = boxz_old*scale; |
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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 - NkBT) / qmass ); |
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> |
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zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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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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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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> |
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( 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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} |
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} |
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< |
void ExtendedSystem::AffineTransform( double scale ){ |
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> |
void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){ |
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int i; |
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< |
double boxx_old, boxy_old, boxz_old, percentScale; |
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< |
double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi; |
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< |
double[3] r; |
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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 rxi, ryi, rzi; |
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// first determine the scaling factor from the box size change |
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< |
percentScale = (boxx - boxx_old)/boxx_old; |
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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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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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> |
// find the minimum image coordinates of the molecular centers of mass: |
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< |
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< |
boxx_num = boxx_old*copysign(1.0,r[0])*(double)(int)(fabs(r[0]/boxx_old)+0.5); |
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> |
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
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> |
(double)(int)(fabs(r[0]/oldBox[0]) + 0.5); |
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< |
boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0); |
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< |
boxy_num = boxy_old*dsign(1.0d0,ry(i))*int(abs(ry(i)/boxy_old)+0.5d0); |
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< |
boxz_num = boxz_old*dsign(1.0d0,rz(i))*int(abs(rz(i)/boxz_old)+0.5d0); |
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> |
boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * |
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> |
(double)(int)(fabs(r[1]/oldBox[1]) + 0.5); |
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< |
rxi = rx(i) - boxx_num; |
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< |
ryi = ry(i) - boxy_num; |
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< |
rzi = rz(i) - boxz_num; |
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> |
boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * |
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> |
(double)(int)(fabs(r[2]/oldBox[2]) + 0.5); |
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+ |
rxi = r[0] - boxNum[0]; |
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+ |
ryi = r[1] - boxNum[1]; |
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+ |
rzi = r[2] - boxNum[2]; |
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+ |
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// update the minimum image coordinates using the scaling factor |
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< |
rxi = rxi + rxi*percentScale; |
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< |
ryi = ryi + ryi*percentScale; |
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< |
rzi = rzi + rzi*percentScale; |
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> |
rxi += rxi*percentScale[0]; |
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> |
ryi += ryi*percentScale[1]; |
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> |
rzi += rzi*percentScale[2]; |
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< |
rx(i) = rxi + boxx_num; |
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< |
ry(i) = ryi + boxy_num; |
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< |
rz(i) = rzi + boxz_num; |
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> |
r[0] = rxi + boxNum[0]; |
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> |
r[1] = ryi + boxNum[1]; |
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> |
r[2] = rzi + boxNum[2]; |
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> |
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> |
molecules[i].moveCOM(r); |
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} |
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} |
