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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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> |
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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; |
| 96 |
> |
p_mol = p_int; |
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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; |
| 102 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
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// propogate the strain rate |
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epsilonDot += dt * ((p_mol - p_ext) * volume / |
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(tauRelax*tauRelax * kB * targetTemp) ); |
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|
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+ |
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| 110 |
+ |
std::cerr << "dt = " << dt << " tauRelax = " << tauRelax << " kB = " << kB << "targetTemp = " << targetTemp << "\n"; |
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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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| 115 |
+ |
std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; |
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+ |
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| 117 |
+ |
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| 118 |
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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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zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
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zetaScale = zeta * dt; |
| 135 |
+ |
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| 136 |
+ |
std::cerr << "zetaScale = " << zetaScale << "epsilonScale = " << epsilonScale << "\n"; |
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|
| 138 |
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// apply barostating and thermostating to velocities and angular momenta |
| 139 |
< |
for(i = 0; i < nAtoms; i++){ |
| 139 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
| 140 |
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|
| 141 |
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vx = atoms[i]->get_vx(); |
| 142 |
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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)); |
| 148 |
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} |
| 149 |
< |
if( nOriented ){ |
| 149 |
> |
if( entry_plug->n_oriented ){ |
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|
| 151 |
< |
for( i=0; i < nAtoms; i++ ){ |
| 151 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
| 152 |
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|
| 153 |
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if( atoms[i]->isDirectional() ){ |
| 154 |
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double boxNum[3]; |
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double percentScale[3]; |
| 175 |
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double rxi, ryi, rzi; |
| 176 |
+ |
|
| 177 |
+ |
molecules = entry_plug->molecules; |
| 178 |
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| 179 |
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// first determine the scaling factor from the box size change |
| 180 |
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percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0]; |
| 181 |
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percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
| 182 |
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percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
| 183 |
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|
| 184 |
< |
for (i=0; i < nMols; i++) { |
| 184 |
> |
std::cerr << "ps = " << percentScale[0] <<" " << percentScale[1] << " " << percentScale[2] << "\n"; |
| 185 |
> |
|
| 186 |
> |
|
| 187 |
> |
for (i=0; i < entry_plug->n_mol; i++) { |
| 188 |
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|
| 189 |
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molecules[i].getCOM(r); |
| 190 |
< |
|
| 190 |
> |
|
| 191 |
|
// find the minimum image coordinates of the molecular centers of mass: |
| 192 |
|
|
| 193 |
|
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
| 199 |
|
boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * |
| 200 |
|
(double)(int)(fabs(r[2]/oldBox[2]) + 0.5); |
| 201 |
|
|
| 202 |
+ |
|
| 203 |
+ |
std::cerr << "boxNum = " << boxNum[0] << " " << boxNum[1] << " " << boxNum[2] << "\n"; |
| 204 |
+ |
|
| 205 |
|
rxi = r[0] - boxNum[0]; |
| 206 |
|
ryi = r[1] - boxNum[1]; |
| 207 |
|
rzi = r[2] - boxNum[2]; |
