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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 &info ) { |
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> |
ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) { |
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|
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// get what information we need from the SimInfo object |
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|
| 13 |
< |
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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> |
zeta = 0.0; |
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> |
epsilonDot = 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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} |
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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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|
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void ExtendedSystem::nose_hoover_nvt( double ke, double dt, double temp ){ |
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|
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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|
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< |
int i, j, degrees_freedom; |
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< |
double ke, dt, temp, kB; |
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< |
double keconverter, NkBT, zetaScale, ke_temp; |
| 31 |
< |
double vxi, vyi, vzi, jxi, jyi, jzi; |
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< |
|
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< |
degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
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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 = ke * keconverter; |
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< |
NkBT = degrees_freedom*kB*temp; |
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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; |
| 31 |
> |
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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< |
// 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 = zeta + dt*((ke_temp*2 - NkBT)/qmass); |
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< |
zetaScale = zeta * dt; |
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> |
if (this->NVTready()) { |
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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 < nmol; i++ ) { |
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< |
vxi = vx(i)*zetaScale; |
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< |
vyi = vy(i)*zetaScale; |
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< |
vzi = vz(i)*zetaScale; |
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< |
jxi = jx(i)*zetaScale; |
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< |
jyi = jy(i)*zetaScale; |
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< |
jzi = jz(i)*zetaScale; |
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< |
|
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< |
vx(i) = vx(i) - vxi; |
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< |
vy(i) = vy(i) - vyi; |
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< |
vz(i) = vz(i) - vzi; |
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< |
jx(i) = jx(i) - jxi; |
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< |
jy(i) = jy(i) - jyi; |
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jz(i) = jz(i) - jzi; |
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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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> |
|
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> |
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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|
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> |
zetaScale = zeta * dt; |
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> |
|
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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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> |
|
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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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> |
|
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> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
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> |
|
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> |
if( atoms[i]->isDirectional() ){ |
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> |
|
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> |
dAtom = (DirectionalAtom *)atoms[i]; |
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> |
|
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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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|
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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::nose_hoover_anderson_npt(double pressure, double ke, double dt, |
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< |
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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|
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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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|
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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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|
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< |
kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 100 |
< |
pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
| 101 |
< |
degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
| 102 |
< |
keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K |
| 99 |
> |
int i; |
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> |
double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp; |
| 101 |
> |
double volume, p_mol; |
| 102 |
> |
double vx, vy, vz, jx, jy, jz; |
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> |
DirectionalAtom* dAtom; |
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|
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< |
pressure_ext = pressure * pressure_units; |
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< |
volume = boxx*boxy*boxz; |
| 107 |
< |
ke_temp = ke * keconverter; |
| 108 |
< |
NkBT = degrees_freedom*kB*temp; |
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> |
if (this->NPTready()) { |
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> |
atoms = entry_plug->atoms; |
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> |
|
| 108 |
> |
p_ext = targetPressure * p_units; |
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> |
p_mol = p_int * p_units; |
| 110 |
> |
|
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> |
entry_plug->getBox(oldBox); |
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> |
volume = oldBox[0]*oldBox[1]*oldBox[2]; |
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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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> |
// propogate the strain rate |
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> |
|
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> |
epsilonDot += dt * ((p_mol - p_ext) * volume / |
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> |
(tauBarostat*tauBarostat * kB * targetTemp) ); |
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> |
|
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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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> |
|
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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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> |
|
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> |
entry_plug->setBox(newBox); |
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> |
|
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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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> |
|
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> |
epsilonScale = epsilonDot * dt; |
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> |
|
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> |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
| 138 |
> |
// qmass is set in the parameter file |
| 139 |
> |
|
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> |
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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> |
zetaScale = zeta * dt; |
| 142 |
> |
|
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> |
std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n"; |
| 144 |
> |
|
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> |
// apply barostating and thermostating to velocities and angular momenta |
| 146 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
| 147 |
> |
|
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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(); |
| 151 |
> |
|
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> |
atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale)); |
| 153 |
> |
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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> |
} |
| 156 |
> |
if( entry_plug->n_oriented ){ |
| 157 |
> |
|
| 158 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
| 159 |
> |
|
| 160 |
> |
if( atoms[i]->isDirectional() ){ |
| 161 |
> |
|
| 162 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
| 163 |
> |
|
| 164 |
> |
jx = dAtom->getJx(); |
| 165 |
> |
jy = dAtom->getJy(); |
| 166 |
> |
jz = dAtom->getJz(); |
| 167 |
> |
|
| 168 |
> |
dAtom->setJx( jx * (1.0 - zetaScale)); |
| 169 |
> |
dAtom->setJy( jy * (1.0 - zetaScale)); |
| 170 |
> |
dAtom->setJz( jz * (1.0 - zetaScale)); |
| 171 |
> |
} |
| 172 |
> |
} |
| 173 |
> |
} |
| 174 |
> |
} |
| 175 |
> |
} |
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|
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< |
// propogate the strain rate |
| 177 |
> |
void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){ |
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|
| 179 |
< |
epsilon_dot += dt * ( (p_mol - pressure_ext)*volume |
| 180 |
< |
/ (tau_relax*tau_relax * kB * temp) ); |
| 179 |
> |
int i; |
| 180 |
> |
double r[3]; |
| 181 |
> |
double boxNum[3]; |
| 182 |
> |
double percentScale[3]; |
| 183 |
> |
double delta[3]; |
| 184 |
> |
double rxi, ryi, rzi; |
| 185 |
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|
| 186 |
< |
// determine the change in cell volume |
| 187 |
< |
scale = pow( (1.0 + dt * 3.0 * epsilon_dot), (1.0 / 3.0)); |
| 186 |
> |
molecules = entry_plug->molecules; |
| 187 |
> |
|
| 188 |
> |
// first determine the scaling factor from the box size change |
| 189 |
> |
percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0]; |
| 190 |
> |
percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
| 191 |
> |
percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
| 192 |
> |
|
| 193 |
> |
for (i=0; i < entry_plug->n_mol; i++) { |
| 194 |
> |
|
| 195 |
> |
molecules[i].getCOM(r); |
| 196 |
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|
| 197 |
< |
volume = volume * pow(scale, 3.0); |
| 197 |
> |
// find the minimum image coordinates of the molecular centers of mass: |
| 198 |
> |
|
| 199 |
> |
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
| 200 |
> |
(double)(int)(fabs(r[0]/oldBox[0]) + 0.5); |
| 201 |
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|
| 202 |
< |
// perform affine transform to update positions with volume fluctuations |
| 203 |
< |
affine_transform( scale ); |
| 202 |
> |
boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * |
| 203 |
> |
(double)(int)(fabs(r[1]/oldBox[1]) + 0.5); |
| 204 |
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|
| 205 |
< |
// save old lengths and update box size |
| 206 |
< |
boxx_old = boxx; |
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< |
boxy_old = boxy; |
| 98 |
< |
boxz_old = boxz; |
| 205 |
> |
boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * |
| 206 |
> |
(double)(int)(fabs(r[2]/oldBox[2]) + 0.5); |
| 207 |
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|
| 208 |
< |
boxx = boxx_old*scale; |
| 209 |
< |
boxy = boxy_old*scale; |
| 210 |
< |
boxz = boxz_old*scale; |
| 208 |
> |
rxi = r[0] - boxNum[0]; |
| 209 |
> |
ryi = r[1] - boxNum[1]; |
| 210 |
> |
rzi = r[2] - boxNum[2]; |
| 211 |
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|
| 212 |
< |
epsilonScale = epsilon_dot * dt; |
| 212 |
> |
// update the minimum image coordinates using the scaling factor |
| 213 |
> |
rxi += rxi*percentScale[0]; |
| 214 |
> |
ryi += ryi*percentScale[1]; |
| 215 |
> |
rzi += rzi*percentScale[2]; |
| 216 |
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|
| 217 |
< |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
| 218 |
< |
// qmass is set in the parameter file |
| 219 |
< |
zeta += dt * ( (ke_temp*2 - NkBT) / qmass ); |
| 109 |
< |
zetaScale = zeta * dt; |
| 110 |
< |
|
| 111 |
< |
// apply barostating and thermostating to velocities and angular momenta |
| 112 |
< |
|
| 113 |
< |
for (i=0; i < nmol; i++) { |
| 217 |
> |
delta[0] = r[0] - (rxi + boxNum[0]); |
| 218 |
> |
delta[1] = r[1] - (ryi + boxNum[1]); |
| 219 |
> |
delta[2] = r[2] - (rzi + boxNum[2]); |
| 220 |
|
|
| 221 |
< |
vxi = vx(i)*epsilonScale; |
| 222 |
< |
vyi = vy(i)*epsilonScale; |
| 223 |
< |
vzi = vz(i)*epsilonScale; |
| 118 |
< |
vxi = vxi + vx(i)*zetaScale; |
| 119 |
< |
vyi = vyi + vy(i)*zetaScale; |
| 120 |
< |
vzi = vzi + vz(i)*zetaScale; |
| 121 |
< |
jxi = jx(i)*zetaScale; |
| 122 |
< |
jyi = jy(i)*zetaScale; |
| 123 |
< |
jzi = jz(i)*zetaScale; |
| 221 |
> |
molecules[i].moveCOM(delta); |
| 222 |
> |
} |
| 223 |
> |
} |
| 224 |
|
|
| 225 |
< |
vx(i) = vx(i) - vxi; |
| 226 |
< |
vy(i) = vy(i) - vyi; |
| 227 |
< |
vz(i) = vz(i) - vzi; |
| 228 |
< |
jx(i) = jx(i) - jxi; |
| 229 |
< |
jy(i) = jy(i) - jyi; |
| 230 |
< |
jz(i) = jz(i) - jzi; |
| 225 |
> |
short int ExtendedSystem::NVTready() { |
| 226 |
> |
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 227 |
> |
double NkBT; |
| 228 |
> |
|
| 229 |
> |
if (!have_target_temp) { |
| 230 |
> |
sprintf( painCave.errMsg, |
| 231 |
> |
"ExtendedSystem error: You can't use NVT without a targetTemp!\n" |
| 232 |
> |
); |
| 233 |
> |
painCave.isFatal = 1; |
| 234 |
> |
simError(); |
| 235 |
> |
return -1; |
| 236 |
|
} |
| 237 |
< |
|
| 237 |
> |
|
| 238 |
> |
if (!have_qmass) { |
| 239 |
> |
if (have_tau_thermostat) { |
| 240 |
|
|
| 241 |
+ |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 242 |
+ |
std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n"; |
| 243 |
+ |
this->setQmass(tauThermostat * NkBT); |
| 244 |
|
|
| 245 |
+ |
} else { |
| 246 |
+ |
sprintf( painCave.errMsg, |
| 247 |
+ |
"ExtendedSystem error: If you use the constant temperature\n" |
| 248 |
+ |
" ensemble, you must set either tauThermostat or qMass.\n"); |
| 249 |
+ |
painCave.isFatal = 1; |
| 250 |
+ |
simError(); |
| 251 |
+ |
} |
| 252 |
+ |
} |
| 253 |
+ |
|
| 254 |
+ |
return 0; |
| 255 |
|
} |
| 256 |
|
|
| 257 |
< |
void ExtendedSystem::affine_transform( double scale ){ |
| 257 |
> |
short int ExtendedSystem::NPTready() { |
| 258 |
> |
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 259 |
> |
double NkBT; |
| 260 |
|
|
| 261 |
< |
int i; |
| 262 |
< |
double boxx_old, boxy_old, boxz_old, percentScale; |
| 263 |
< |
double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi; |
| 264 |
< |
double[3] r; |
| 265 |
< |
|
| 266 |
< |
// first determine the scaling factor from the box size change |
| 267 |
< |
percentScale = (boxx - boxx_old)/boxx_old; |
| 268 |
< |
|
| 261 |
> |
if (!have_target_temp) { |
| 262 |
> |
sprintf( painCave.errMsg, |
| 263 |
> |
"ExtendedSystem error: You can't use NPT without a targetTemp!\n" |
| 264 |
> |
); |
| 265 |
> |
painCave.isFatal = 1; |
| 266 |
> |
simError(); |
| 267 |
> |
return -1; |
| 268 |
> |
} |
| 269 |
|
|
| 270 |
< |
for (i=0; i < nMols; i++) { |
| 270 |
> |
if (!have_target_pressure) { |
| 271 |
> |
sprintf( painCave.errMsg, |
| 272 |
> |
"ExtendedSystem error: You can't use NPT without a targetPressure!\n" |
| 273 |
> |
); |
| 274 |
> |
painCave.isFatal = 1; |
| 275 |
> |
simError(); |
| 276 |
> |
return -1; |
| 277 |
> |
} |
| 278 |
|
|
| 279 |
< |
molecules[i]->getCOM(r); |
| 280 |
< |
|
| 281 |
< |
// find the minimum image coordinates of the molecular centers of mass: |
| 282 |
< |
|
| 283 |
< |
|
| 284 |
< |
boxx_num = boxx_old*copysign(1.0,r[0])*(double)(int)(fabs(r[0]/boxx_old)+0.5); |
| 279 |
> |
if (!have_tau_barostat) { |
| 280 |
> |
sprintf( painCave.errMsg, |
| 281 |
> |
"ExtendedSystem error: If you use the NPT\n" |
| 282 |
> |
" ensemble, you must set tauBarostat.\n"); |
| 283 |
> |
painCave.isFatal = 1; |
| 284 |
> |
simError(); |
| 285 |
> |
} |
| 286 |
|
|
| 287 |
< |
boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0); |
| 288 |
< |
boxy_num = boxy_old*dsign(1.0d0,ry(i))*int(abs(ry(i)/boxy_old)+0.5d0); |
| 159 |
< |
boxz_num = boxz_old*dsign(1.0d0,rz(i))*int(abs(rz(i)/boxz_old)+0.5d0); |
| 287 |
> |
if (!have_qmass) { |
| 288 |
> |
if (have_tau_thermostat) { |
| 289 |
|
|
| 290 |
< |
rxi = rx(i) - boxx_num; |
| 291 |
< |
ryi = ry(i) - boxy_num; |
| 292 |
< |
rzi = rz(i) - boxz_num; |
| 290 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 291 |
> |
std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n"; |
| 292 |
> |
this->setQmass(tauThermostat * NkBT); |
| 293 |
|
|
| 294 |
< |
// update the minimum image coordinates using the scaling factor |
| 295 |
< |
rxi = rxi + rxi*percentScale; |
| 296 |
< |
ryi = ryi + ryi*percentScale; |
| 297 |
< |
rzi = rzi + rzi*percentScale; |
| 298 |
< |
|
| 299 |
< |
rx(i) = rxi + boxx_num; |
| 300 |
< |
ry(i) = ryi + boxy_num; |
| 172 |
< |
rz(i) = rzi + boxz_num; |
| 294 |
> |
} else { |
| 295 |
> |
sprintf( painCave.errMsg, |
| 296 |
> |
"ExtendedSystem error: If you use the NPT\n" |
| 297 |
> |
" ensemble, you must set either tauThermostat or qMass.\n"); |
| 298 |
> |
painCave.isFatal = 1; |
| 299 |
> |
simError(); |
| 300 |
> |
} |
| 301 |
|
} |
| 302 |
+ |
return 0; |
| 303 |
|
} |
| 304 |
+ |
|
