| 4 |
|
#include "SimInfo.hpp" |
| 5 |
|
#include "Thermo.hpp" |
| 6 |
|
#include "ExtendedSystem.hpp" |
| 7 |
+ |
#include "simError.h" |
| 8 |
|
|
| 9 |
< |
ExtendedSystem::ExtendedSystem( SimInfo &info ) { |
| 9 |
> |
ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) { |
| 10 |
|
|
| 11 |
|
// get what information we need from the SimInfo object |
| 12 |
|
|
| 13 |
< |
entry_plug = &info; |
| 14 |
< |
nAtoms = info.n_atoms; |
| 15 |
< |
atoms = info.atoms; |
| 16 |
< |
nMols = info.n_mol; |
| 17 |
< |
molecules = info.molecules; |
| 18 |
< |
zeta = 0; |
| 13 |
> |
entry_plug = the_entry_plug; |
| 14 |
> |
zeta = 0.0; |
| 15 |
> |
epsilonDot = 0.0; |
| 16 |
> |
epsilonDotX = 0.0; |
| 17 |
> |
epsilonDotY = 0.0; |
| 18 |
> |
epsilonDotZ = 0.0; |
| 19 |
> |
have_tau_thermostat = 0; |
| 20 |
> |
have_tau_barostat = 0; |
| 21 |
> |
have_target_temp = 0; |
| 22 |
> |
have_target_pressure = 0; |
| 23 |
> |
have_qmass = 0; |
| 24 |
|
|
| 25 |
|
} |
| 26 |
|
|
| 27 |
< |
ExtendedSystem::~ExtendedSystem() { |
| 22 |
< |
} |
| 27 |
> |
void ExtendedSystem::NoseHooverNVT( double dt, double ke ){ |
| 28 |
|
|
| 24 |
– |
|
| 25 |
– |
void ExtendedSystem::NoseHooverNVT( double dt ){ |
| 26 |
– |
|
| 29 |
|
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
| 30 |
|
|
| 31 |
|
int i; |
| 32 |
< |
double kB, keconverter, NkBT, zetaScale, ke_temp; |
| 32 |
> |
double NkBT, zetaScale, ke_temp; |
| 33 |
|
double vx, vy, vz, jx, jy, jz; |
| 34 |
< |
|
| 35 |
< |
kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 36 |
< |
keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2 / K |
| 37 |
< |
|
| 36 |
< |
ke_temp = getKinetic() * keconverter; |
| 37 |
< |
NkBT = (double)getNDF() * kB * targetTemp; |
| 34 |
> |
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 35 |
> |
const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
| 36 |
> |
// amu*Ang^2*fs^-2/K |
| 37 |
> |
DirectionalAtom* dAtom; |
| 38 |
|
|
| 39 |
< |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin & |
| 40 |
< |
// qmass is set in the parameter file |
| 41 |
< |
zeta += dt*((ke_temp*2 - NkBT)/qmass); |
| 42 |
< |
zetaScale = zeta * dt; |
| 39 |
> |
if (this->NVTready()) { |
| 40 |
|
|
| 41 |
< |
// perform thermostat scaling on linear velocities and angular momentum |
| 45 |
< |
|
| 46 |
< |
for(i = 0; i < n_atoms; i++){ |
| 41 |
> |
atoms = entry_plug->atoms; |
| 42 |
|
|
| 43 |
< |
vx = atoms[i]->get_vx(); |
| 44 |
< |
vy = atoms[i]->get_vy(); |
| 50 |
< |
vz = atoms[i]->get_vz(); |
| 43 |
> |
ke_temp = ke * e_convert; |
| 44 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 45 |
|
|
| 46 |
< |
atoms[i]->set_vx(vx - zetaScale * vx); |
| 47 |
< |
atoms[i]->set_vy(vy - zetaScale * vy); |
| 54 |
< |
atoms[i]->set_vz(vz - zetaScale * vz); |
| 55 |
< |
} |
| 56 |
< |
if( n_oriented ){ |
| 46 |
> |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
| 47 |
> |
// qmass is set in the parameter file |
| 48 |
|
|
| 49 |
< |
for( i=0; i < n_atoms; i++ ){ |
| 49 |
> |
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
| 50 |
> |
|
| 51 |
> |
zetaScale = zeta * dt; |
| 52 |
> |
|
| 53 |
> |
//std::cerr << "zetaScale = " << zetaScale << "\n"; |
| 54 |
> |
|
| 55 |
> |
// perform thermostat scaling on linear velocities and angular momentum |
| 56 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
| 57 |
|
|
| 58 |
< |
if( atoms[i]->isDirectional() ){ |
| 59 |
< |
|
| 60 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 58 |
> |
vx = atoms[i]->get_vx(); |
| 59 |
> |
vy = atoms[i]->get_vy(); |
| 60 |
> |
vz = atoms[i]->get_vz(); |
| 61 |
> |
|
| 62 |
> |
atoms[i]->set_vx(vx * (1.0 - zetaScale)); |
| 63 |
> |
atoms[i]->set_vy(vy * (1.0 - zetaScale)); |
| 64 |
> |
atoms[i]->set_vz(vz * (1.0 - zetaScale)); |
| 65 |
> |
} |
| 66 |
> |
if( entry_plug->n_oriented ){ |
| 67 |
> |
|
| 68 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
| 69 |
|
|
| 70 |
< |
jx = dAtom->getJx(); |
| 71 |
< |
jy = dAtom->getJy(); |
| 72 |
< |
jz = dAtom->getJz(); |
| 73 |
< |
|
| 74 |
< |
dAtom->setJx( jx - zetaScale * jx); |
| 75 |
< |
dAtom->setJy( jy - zetaScale * jy); |
| 76 |
< |
dAtom->setJz( jz - zetaScale * jz); |
| 77 |
< |
} |
| 78 |
< |
} |
| 70 |
> |
if( atoms[i]->isDirectional() ){ |
| 71 |
> |
|
| 72 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
| 73 |
> |
|
| 74 |
> |
jx = dAtom->getJx(); |
| 75 |
> |
jy = dAtom->getJy(); |
| 76 |
> |
jz = dAtom->getJz(); |
| 77 |
> |
|
| 78 |
> |
dAtom->setJx(jx * (1.0 - zetaScale)); |
| 79 |
> |
dAtom->setJy(jy * (1.0 - zetaScale)); |
| 80 |
> |
dAtom->setJz(jz * (1.0 - zetaScale)); |
| 81 |
> |
} |
| 82 |
> |
} |
| 83 |
> |
} |
| 84 |
|
} |
| 85 |
|
} |
| 86 |
|
|
| 87 |
|
|
| 88 |
< |
void ExtendedSystem::NoseHooverAndersonNPT(double pressure, double ke, |
| 89 |
< |
double dt, double temp ) { |
| 88 |
> |
void ExtendedSystem::NoseHooverAndersonNPT( double dt, |
| 89 |
> |
double ke, |
| 90 |
> |
double p_tensor[9] ) { |
| 91 |
|
|
| 92 |
|
// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
| 93 |
|
// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500 |
| 94 |
|
|
| 95 |
< |
int i, j, degrees_freedom; |
| 96 |
< |
double pressure, dt, temp, pressure_units, epsilonScale; |
| 97 |
< |
double ke, kB, vxi, vyi, vzi, pressure_ext; |
| 98 |
< |
double boxx_old, boxy_old, boxz_old; |
| 99 |
< |
double keconverter, NkBT, zetaScale, ke_temp; |
| 100 |
< |
double jxi, jyi, jzi, scale; |
| 95 |
> |
double oldBox[3]; |
| 96 |
> |
double newBox[3]; |
| 97 |
> |
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 98 |
> |
const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
| 99 |
> |
const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
| 100 |
> |
// amu*Ang^2*fs^-2/K |
| 101 |
|
|
| 102 |
< |
kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 103 |
< |
pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
| 104 |
< |
degrees_freedom = 6*nmol; // number of degrees of freedom for the system |
| 105 |
< |
keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K |
| 102 |
> |
int i; |
| 103 |
> |
double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp; |
| 104 |
> |
double volume, p_mol; |
| 105 |
> |
double vx, vy, vz, jx, jy, jz; |
| 106 |
> |
DirectionalAtom* dAtom; |
| 107 |
|
|
| 108 |
< |
pressure_ext = pressure * pressure_units; |
| 109 |
< |
volume = boxx*boxy*boxz; |
| 110 |
< |
ke_temp = ke * keconverter; |
| 111 |
< |
NkBT = degrees_freedom*kB*temp; |
| 108 |
> |
if (this->NPTready()) { |
| 109 |
> |
atoms = entry_plug->atoms; |
| 110 |
> |
|
| 111 |
> |
p_ext = targetPressure * p_units; |
| 112 |
> |
p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0; |
| 113 |
> |
|
| 114 |
> |
entry_plug->getBox(oldBox); |
| 115 |
> |
volume = oldBox[0]*oldBox[1]*oldBox[2]; |
| 116 |
> |
|
| 117 |
> |
ke_temp = ke * e_convert; |
| 118 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 119 |
> |
|
| 120 |
> |
// propagate the strain rate |
| 121 |
> |
|
| 122 |
> |
epsilonDot += dt * ((p_mol - p_ext) * volume / |
| 123 |
> |
(tauBarostat*tauBarostat * kB * targetTemp) ); |
| 124 |
> |
|
| 125 |
> |
// determine the change in cell volume |
| 126 |
> |
scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0)); |
| 127 |
> |
//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; |
| 128 |
> |
|
| 129 |
> |
newBox[0] = oldBox[0] * scale; |
| 130 |
> |
newBox[1] = oldBox[1] * scale; |
| 131 |
> |
newBox[2] = oldBox[2] * scale; |
| 132 |
> |
volume = newBox[0]*newBox[1]*newBox[2]; |
| 133 |
> |
|
| 134 |
> |
entry_plug->setBox(newBox); |
| 135 |
> |
|
| 136 |
> |
// perform affine transform to update positions with volume fluctuations |
| 137 |
> |
this->AffineTransform( oldBox, newBox ); |
| 138 |
> |
|
| 139 |
> |
epsilonScale = epsilonDot * dt; |
| 140 |
> |
|
| 141 |
> |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
| 142 |
> |
// qmass is set in the parameter file |
| 143 |
> |
|
| 144 |
> |
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
| 145 |
> |
zetaScale = zeta * dt; |
| 146 |
> |
|
| 147 |
> |
//std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n"; |
| 148 |
> |
|
| 149 |
> |
// apply barostating and thermostating to velocities and angular momenta |
| 150 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
| 151 |
> |
|
| 152 |
> |
vx = atoms[i]->get_vx(); |
| 153 |
> |
vy = atoms[i]->get_vy(); |
| 154 |
> |
vz = atoms[i]->get_vz(); |
| 155 |
> |
|
| 156 |
> |
atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale)); |
| 157 |
> |
atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale)); |
| 158 |
> |
atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale)); |
| 159 |
> |
} |
| 160 |
> |
if( entry_plug->n_oriented ){ |
| 161 |
> |
|
| 162 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
| 163 |
> |
|
| 164 |
> |
if( atoms[i]->isDirectional() ){ |
| 165 |
> |
|
| 166 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
| 167 |
> |
|
| 168 |
> |
jx = dAtom->getJx(); |
| 169 |
> |
jy = dAtom->getJy(); |
| 170 |
> |
jz = dAtom->getJz(); |
| 171 |
> |
|
| 172 |
> |
dAtom->setJx( jx * (1.0 - zetaScale)); |
| 173 |
> |
dAtom->setJy( jy * (1.0 - zetaScale)); |
| 174 |
> |
dAtom->setJz( jz * (1.0 - zetaScale)); |
| 175 |
> |
} |
| 176 |
> |
} |
| 177 |
> |
} |
| 178 |
> |
} |
| 179 |
> |
} |
| 180 |
|
|
| 100 |
– |
// propogate the strain rate |
| 181 |
|
|
| 182 |
< |
epsilon_dot += dt * ( (p_mol - pressure_ext)*volume |
| 183 |
< |
/ (tau_relax*tau_relax * kB * targetTemp) ); |
| 182 |
> |
void ExtendedSystem::ConstantStress( double dt, |
| 183 |
> |
double ke, |
| 184 |
> |
double p_tensor[9] ) { |
| 185 |
|
|
| 186 |
< |
// determine the change in cell volume |
| 187 |
< |
scale = pow( (1.0 + dt * 3.0 * epsilon_dot), (1.0 / 3.0)); |
| 186 |
> |
double oldBox[3]; |
| 187 |
> |
double newBox[3]; |
| 188 |
> |
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 189 |
> |
const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1 |
| 190 |
> |
const double e_convert = 4.184e-4; // to convert ke from kcal/mol to |
| 191 |
> |
// amu*Ang^2*fs^-2/K |
| 192 |
|
|
| 193 |
< |
volume = volume * pow(scale, 3.0); |
| 193 |
> |
int i; |
| 194 |
> |
double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp; |
| 195 |
> |
double pX_ext, pY_ext, pZ_ext; |
| 196 |
> |
double volume, p_mol; |
| 197 |
> |
double vx, vy, vz, jx, jy, jz; |
| 198 |
> |
DirectionalAtom* dAtom; |
| 199 |
|
|
| 200 |
< |
// perform affine transform to update positions with volume fluctuations |
| 201 |
< |
affine_transform( scale ); |
| 200 |
> |
if (this->NPTready()) { |
| 201 |
> |
atoms = entry_plug->atoms; |
| 202 |
> |
|
| 203 |
> |
p_ext = targetPressure * p_units; |
| 204 |
|
|
| 205 |
< |
// save old lengths and update box size |
| 206 |
< |
boxx_old = boxx; |
| 207 |
< |
boxy_old = boxy; |
| 208 |
< |
boxz_old = boxz; |
| 209 |
< |
|
| 210 |
< |
boxx = boxx_old*scale; |
| 119 |
< |
boxy = boxy_old*scale; |
| 120 |
< |
boxz = boxz_old*scale; |
| 121 |
< |
|
| 122 |
< |
epsilonScale = epsilonDot * dt; |
| 123 |
< |
|
| 124 |
< |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
| 125 |
< |
// qmass is set in the parameter file |
| 126 |
< |
zeta += dt * ( (ke_temp*2 - NkBT) / qmass ); |
| 127 |
< |
zetaScale = zeta * dt; |
| 128 |
< |
|
| 129 |
< |
// apply barostating and thermostating to velocities and angular momenta |
| 130 |
< |
for(i = 0; i < n_atoms; i++){ |
| 205 |
> |
pX_ext = p_ext / 3.0; |
| 206 |
> |
pY_ext = p_ext / 3.0; |
| 207 |
> |
pZ_ext = p_ext / 3.0; |
| 208 |
> |
|
| 209 |
> |
entry_plug->getBox(oldBox); |
| 210 |
> |
volume = oldBox[0]*oldBox[1]*oldBox[2]; |
| 211 |
|
|
| 212 |
< |
vx = atoms[i]->get_vx(); |
| 213 |
< |
vy = atoms[i]->get_vy(); |
| 134 |
< |
vz = atoms[i]->get_vz(); |
| 212 |
> |
ke_temp = ke * e_convert; |
| 213 |
> |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 214 |
|
|
| 215 |
< |
atoms[i]->set_vx(vx * (1.0 - zetaScale * epsilonScale)); |
| 137 |
< |
atoms[i]->set_vy(vy * (1.0 - zetaScale * epsilonScale)); |
| 138 |
< |
atoms[i]->set_vz(vz * (1.0 - zetaScale * epsilonScale)); |
| 139 |
< |
} |
| 140 |
< |
if( n_oriented ){ |
| 215 |
> |
// propagate the strain rate |
| 216 |
|
|
| 217 |
< |
for( i=0; i < n_atoms; i++ ){ |
| 217 |
> |
epsilonDotX += dt * ((p_tensor[0] - pX_ext) * volume / |
| 218 |
> |
(tauBarostat*tauBarostat * kB * targetTemp) ); |
| 219 |
> |
epsilonDotY += dt * ((p_tensor[4] - pY_ext) * volume / |
| 220 |
> |
(tauBarostat*tauBarostat * kB * targetTemp) ); |
| 221 |
> |
epsilonDotZ += dt * ((p_tensor[8] - pZ_ext) * volume / |
| 222 |
> |
(tauBarostat*tauBarostat * kB * targetTemp) ); |
| 223 |
> |
|
| 224 |
> |
// determine the change in cell volume |
| 225 |
> |
|
| 226 |
> |
//scale = pow( (1.0 + dt * 3.0 * (epsilonDot), (1.0 / 3.0)); |
| 227 |
> |
//std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; |
| 228 |
> |
|
| 229 |
> |
newBox[0] = oldBox[0] * scale; |
| 230 |
> |
newBox[1] = oldBox[1] * scale; |
| 231 |
> |
newBox[2] = oldBox[2] * scale; |
| 232 |
> |
volume = newBox[0]*newBox[1]*newBox[2]; |
| 233 |
> |
|
| 234 |
> |
entry_plug->setBox(newBox); |
| 235 |
> |
|
| 236 |
> |
// perform affine transform to update positions with volume fluctuations |
| 237 |
> |
this->AffineTransform( oldBox, newBox ); |
| 238 |
> |
|
| 239 |
> |
epsilonScale = epsilonDot * dt; |
| 240 |
> |
|
| 241 |
> |
// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin |
| 242 |
> |
// qmass is set in the parameter file |
| 243 |
> |
|
| 244 |
> |
zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass ); |
| 245 |
> |
zetaScale = zeta * dt; |
| 246 |
> |
|
| 247 |
> |
//std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n"; |
| 248 |
> |
|
| 249 |
> |
// apply barostating and thermostating to velocities and angular momenta |
| 250 |
> |
for(i = 0; i < entry_plug->n_atoms; i++){ |
| 251 |
|
|
| 252 |
< |
if( atoms[i]->isDirectional() ){ |
| 253 |
< |
|
| 254 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 252 |
> |
vx = atoms[i]->get_vx(); |
| 253 |
> |
vy = atoms[i]->get_vy(); |
| 254 |
> |
vz = atoms[i]->get_vz(); |
| 255 |
> |
|
| 256 |
> |
atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale)); |
| 257 |
> |
atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale)); |
| 258 |
> |
atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale)); |
| 259 |
> |
} |
| 260 |
> |
if( entry_plug->n_oriented ){ |
| 261 |
> |
|
| 262 |
> |
for( i=0; i < entry_plug->n_atoms; i++ ){ |
| 263 |
|
|
| 264 |
< |
jx = dAtom->getJx(); |
| 265 |
< |
jy = dAtom->getJy(); |
| 266 |
< |
jz = dAtom->getJz(); |
| 267 |
< |
|
| 268 |
< |
dAtom->setJx( jx * (1.0 - zetaScale)); |
| 269 |
< |
dAtom->setJy( jy * (1.0 - zetaScale)); |
| 270 |
< |
dAtom->setJz( jz * (1.0 - zetaScale)); |
| 271 |
< |
} |
| 272 |
< |
} |
| 264 |
> |
if( atoms[i]->isDirectional() ){ |
| 265 |
> |
|
| 266 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
| 267 |
> |
|
| 268 |
> |
jx = dAtom->getJx(); |
| 269 |
> |
jy = dAtom->getJy(); |
| 270 |
> |
jz = dAtom->getJz(); |
| 271 |
> |
|
| 272 |
> |
dAtom->setJx( jx * (1.0 - zetaScale)); |
| 273 |
> |
dAtom->setJy( jy * (1.0 - zetaScale)); |
| 274 |
> |
dAtom->setJz( jz * (1.0 - zetaScale)); |
| 275 |
> |
} |
| 276 |
> |
} |
| 277 |
> |
} |
| 278 |
|
} |
| 279 |
|
} |
| 280 |
|
|
| 281 |
< |
void ExtendedSystem::AffineTransform( double scale ){ |
| 281 |
> |
void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){ |
| 282 |
|
|
| 283 |
|
int i; |
| 284 |
< |
double boxx_old, boxy_old, boxz_old, percentScale; |
| 285 |
< |
double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi; |
| 286 |
< |
double[3] r; |
| 284 |
> |
double r[3]; |
| 285 |
> |
double boxNum[3]; |
| 286 |
> |
double percentScale[3]; |
| 287 |
> |
double delta[3]; |
| 288 |
> |
double rxi, ryi, rzi; |
| 289 |
> |
|
| 290 |
> |
molecules = entry_plug->molecules; |
| 291 |
|
|
| 292 |
|
// first determine the scaling factor from the box size change |
| 293 |
< |
percentScale = (boxx - boxx_old)/boxx_old; |
| 293 |
> |
percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0]; |
| 294 |
> |
percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1]; |
| 295 |
> |
percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2]; |
| 296 |
|
|
| 297 |
+ |
for (i=0; i < entry_plug->n_mol; i++) { |
| 298 |
+ |
|
| 299 |
+ |
molecules[i].getCOM(r); |
| 300 |
|
|
| 301 |
< |
for (i=0; i < nMols; i++) { |
| 301 |
> |
// find the minimum image coordinates of the molecular centers of mass: |
| 302 |
|
|
| 303 |
< |
molecules[i]->getCOM(r); |
| 304 |
< |
|
| 175 |
< |
// find the minimum image coordinates of the molecular centers of mass: |
| 176 |
< |
|
| 177 |
< |
|
| 178 |
< |
boxx_num = boxx_old*copysign(1.0,r[0])*(double)(int)(fabs(r[0]/boxx_old)+0.5); |
| 303 |
> |
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
| 304 |
> |
(double)(int)(fabs(r[0]/oldBox[0]) + 0.5); |
| 305 |
|
|
| 306 |
< |
boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0); |
| 307 |
< |
boxy_num = boxy_old*dsign(1.0d0,ry(i))*int(abs(ry(i)/boxy_old)+0.5d0); |
| 182 |
< |
boxz_num = boxz_old*dsign(1.0d0,rz(i))*int(abs(rz(i)/boxz_old)+0.5d0); |
| 306 |
> |
boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * |
| 307 |
> |
(double)(int)(fabs(r[1]/oldBox[1]) + 0.5); |
| 308 |
|
|
| 309 |
< |
rxi = rx(i) - boxx_num; |
| 310 |
< |
ryi = ry(i) - boxy_num; |
| 186 |
< |
rzi = rz(i) - boxz_num; |
| 309 |
> |
boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * |
| 310 |
> |
(double)(int)(fabs(r[2]/oldBox[2]) + 0.5); |
| 311 |
|
|
| 312 |
+ |
rxi = r[0] - boxNum[0]; |
| 313 |
+ |
ryi = r[1] - boxNum[1]; |
| 314 |
+ |
rzi = r[2] - boxNum[2]; |
| 315 |
+ |
|
| 316 |
|
// update the minimum image coordinates using the scaling factor |
| 317 |
< |
rxi = rxi + rxi*percentScale; |
| 318 |
< |
ryi = ryi + ryi*percentScale; |
| 319 |
< |
rzi = rzi + rzi*percentScale; |
| 317 |
> |
rxi += rxi*percentScale[0]; |
| 318 |
> |
ryi += ryi*percentScale[1]; |
| 319 |
> |
rzi += rzi*percentScale[2]; |
| 320 |
|
|
| 321 |
< |
rx(i) = rxi + boxx_num; |
| 322 |
< |
ry(i) = ryi + boxy_num; |
| 323 |
< |
rz(i) = rzi + boxz_num; |
| 321 |
> |
delta[0] = r[0] - (rxi + boxNum[0]); |
| 322 |
> |
delta[1] = r[1] - (ryi + boxNum[1]); |
| 323 |
> |
delta[2] = r[2] - (rzi + boxNum[2]); |
| 324 |
> |
|
| 325 |
> |
molecules[i].moveCOM(delta); |
| 326 |
|
} |
| 327 |
|
} |
| 328 |
+ |
|
| 329 |
+ |
short int ExtendedSystem::NVTready() { |
| 330 |
+ |
const double kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K |
| 331 |
+ |
double NkBT; |
| 332 |
+ |
|
| 333 |
+ |
if (!have_target_temp) { |
| 334 |
+ |
sprintf( painCave.errMsg, |
| 335 |
+ |
"ExtendedSystem error: You can't use NVT without a targetTemp!\n" |
| 336 |
+ |
); |
| 337 |
+ |
painCave.isFatal = 1; |
| 338 |
+ |
simError(); |
| 339 |
+ |
return -1; |
| 340 |
+ |
} |
| 341 |
+ |
|
| 342 |
+ |
if (!have_qmass) { |
| 343 |
+ |
if (have_tau_thermostat) { |
| 344 |
+ |
|
| 345 |
+ |
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 |
+ |
return 1; |
| 359 |
+ |
} |
| 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 |
+ |
return 1; |
| 407 |
+ |
} |
| 408 |
+ |
|
