| 1 |
#include <math.h> |
| 2 |
#include "Atom.hpp" |
| 3 |
#include "Molecule.hpp" |
| 4 |
#include "SimInfo.hpp" |
| 5 |
#include "Thermo.hpp" |
| 6 |
#include "ExtendedSystem.hpp" |
| 7 |
#include "simError.h" |
| 8 |
|
| 9 |
ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) { |
| 10 |
|
| 11 |
// get what information we need from the SimInfo object |
| 12 |
|
| 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 |
void ExtendedSystem::NoseHooverNVT( double dt, double ke ){ |
| 28 |
|
| 29 |
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
| 30 |
|
| 31 |
int i; |
| 32 |
double NkBT, zetaScale, ke_temp; |
| 33 |
double vx, vy, vz, jx, jy, jz; |
| 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 |
if (this->NVTready()) { |
| 40 |
|
| 41 |
atoms = entry_plug->atoms; |
| 42 |
|
| 43 |
ke_temp = ke * e_convert; |
| 44 |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 45 |
|
| 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 |
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 |
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 |
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 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 |
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 |
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 |
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 |
|
| 181 |
|
| 182 |
void ExtendedSystem::ConstantStress( double dt, |
| 183 |
double ke, |
| 184 |
double p_tensor[9] ) { |
| 185 |
|
| 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 |
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 |
if (this->NPTready()) { |
| 201 |
atoms = entry_plug->atoms; |
| 202 |
|
| 203 |
p_ext = targetPressure * p_units; |
| 204 |
|
| 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 |
ke_temp = ke * e_convert; |
| 213 |
NkBT = (double)entry_plug->ndf * kB * targetTemp; |
| 214 |
|
| 215 |
// propagate the strain rate |
| 216 |
|
| 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 |
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 |
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 oldBox[3], double newBox[3] ){ |
| 282 |
|
| 283 |
int i; |
| 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[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 |
// find the minimum image coordinates of the molecular centers of mass: |
| 302 |
|
| 303 |
boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * |
| 304 |
(double)(int)(fabs(r[0]/oldBox[0]) + 0.5); |
| 305 |
|
| 306 |
boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * |
| 307 |
(double)(int)(fabs(r[1]/oldBox[1]) + 0.5); |
| 308 |
|
| 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*percentScale[0]; |
| 318 |
ryi += ryi*percentScale[1]; |
| 319 |
rzi += rzi*percentScale[2]; |
| 320 |
|
| 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 |
|
