| 1 |
#include <stdlib.h> |
| 2 |
#include <math.h> |
| 3 |
|
| 4 |
#include "Atom.hpp" |
| 5 |
#include "SRI.hpp" |
| 6 |
#include "AbstractClasses.hpp" |
| 7 |
#include "SimInfo.hpp" |
| 8 |
#include "ForceFields.hpp" |
| 9 |
#include "Thermo.hpp" |
| 10 |
#include "ReadWrite.hpp" |
| 11 |
#include "Integrator.hpp" |
| 12 |
#include "simError.h" |
| 13 |
|
| 14 |
#ifdef IS_MPI |
| 15 |
#include "mpiSimulation.hpp" |
| 16 |
#endif |
| 17 |
|
| 18 |
|
| 19 |
// Basic isotropic thermostating and barostating via the Melchionna |
| 20 |
// modification of the Hoover algorithm: |
| 21 |
// |
| 22 |
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 23 |
// Molec. Phys., 78, 533. |
| 24 |
// |
| 25 |
// and |
| 26 |
// |
| 27 |
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 28 |
|
| 29 |
NPT::NPT ( SimInfo *theInfo, ForceFields* the_ff): |
| 30 |
Integrator( theInfo, the_ff ) |
| 31 |
{ |
| 32 |
GenericData* data; |
| 33 |
|
| 34 |
chi = 0.0; |
| 35 |
integralOfChidt = 0.0; |
| 36 |
have_tau_thermostat = 0; |
| 37 |
have_tau_barostat = 0; |
| 38 |
have_target_temp = 0; |
| 39 |
have_target_pressure = 0; |
| 40 |
have_chi_tolerance = 0; |
| 41 |
have_eta_tolerance = 0; |
| 42 |
have_pos_iter_tolerance = 0; |
| 43 |
|
| 44 |
// retrieve chi and integralOfChidt from simInfo |
| 45 |
data = info->getProperty(CHIVALUE_ID); |
| 46 |
if(data != NULL ){ |
| 47 |
chi = data->getDval(); |
| 48 |
} |
| 49 |
|
| 50 |
data = info->getProperty(INTEGRALOFCHIDT_ID); |
| 51 |
if(data != NULL ){ |
| 52 |
integralOfChidt = data->getDval(); |
| 53 |
} |
| 54 |
|
| 55 |
oldPos = new double[3*nAtoms]; |
| 56 |
oldVel = new double[3*nAtoms]; |
| 57 |
oldJi = new double[3*nAtoms]; |
| 58 |
#ifdef IS_MPI |
| 59 |
Nparticles = mpiSim->getTotAtoms(); |
| 60 |
#else |
| 61 |
Nparticles = theInfo->n_atoms; |
| 62 |
#endif |
| 63 |
|
| 64 |
} |
| 65 |
|
| 66 |
NPT::~NPT() { |
| 67 |
delete[] oldPos; |
| 68 |
delete[] oldVel; |
| 69 |
delete[] oldJi; |
| 70 |
} |
| 71 |
|
| 72 |
void NPT::moveA() { |
| 73 |
|
| 74 |
//new version of NPT |
| 75 |
int i, j, k; |
| 76 |
DirectionalAtom* dAtom; |
| 77 |
double Tb[3], ji[3]; |
| 78 |
double mass; |
| 79 |
double vel[3], pos[3], frc[3]; |
| 80 |
double sc[3]; |
| 81 |
double COM[3]; |
| 82 |
|
| 83 |
instaTemp = tStats->getTemperature(); |
| 84 |
tStats->getPressureTensor( press ); |
| 85 |
instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 86 |
instaVol = tStats->getVolume(); |
| 87 |
|
| 88 |
tStats->getCOM(COM); |
| 89 |
|
| 90 |
//evolve velocity half step |
| 91 |
for( i=0; i<nAtoms; i++ ){ |
| 92 |
|
| 93 |
atoms[i]->getVel( vel ); |
| 94 |
atoms[i]->getFrc( frc ); |
| 95 |
|
| 96 |
mass = atoms[i]->getMass(); |
| 97 |
|
| 98 |
getVelScaleA( sc, vel ); |
| 99 |
|
| 100 |
for (j=0; j < 3; j++) { |
| 101 |
|
| 102 |
// velocity half step (use chi from previous step here): |
| 103 |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
| 104 |
|
| 105 |
} |
| 106 |
|
| 107 |
atoms[i]->setVel( vel ); |
| 108 |
|
| 109 |
if( atoms[i]->isDirectional() ){ |
| 110 |
|
| 111 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 112 |
|
| 113 |
// get and convert the torque to body frame |
| 114 |
|
| 115 |
dAtom->getTrq( Tb ); |
| 116 |
dAtom->lab2Body( Tb ); |
| 117 |
|
| 118 |
// get the angular momentum, and propagate a half step |
| 119 |
|
| 120 |
dAtom->getJ( ji ); |
| 121 |
|
| 122 |
for (j=0; j < 3; j++) |
| 123 |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 124 |
|
| 125 |
this->rotationPropagation( dAtom, ji ); |
| 126 |
|
| 127 |
dAtom->setJ( ji ); |
| 128 |
} |
| 129 |
} |
| 130 |
|
| 131 |
// evolve chi and eta half step |
| 132 |
|
| 133 |
evolveChiA(); |
| 134 |
evolveEtaA(); |
| 135 |
|
| 136 |
//calculate the integral of chidt |
| 137 |
integralOfChidt += dt2*chi; |
| 138 |
|
| 139 |
//save the old positions |
| 140 |
for(i = 0; i < nAtoms; i++){ |
| 141 |
atoms[i]->getPos(pos); |
| 142 |
for(j = 0; j < 3; j++) |
| 143 |
oldPos[i*3 + j] = pos[j]; |
| 144 |
} |
| 145 |
|
| 146 |
//the first estimation of r(t+dt) is equal to r(t) |
| 147 |
|
| 148 |
for(k = 0; k < 5; k ++){ |
| 149 |
|
| 150 |
for(i =0 ; i < nAtoms; i++){ |
| 151 |
|
| 152 |
atoms[i]->getVel(vel); |
| 153 |
atoms[i]->getPos(pos); |
| 154 |
|
| 155 |
this->getPosScale( pos, COM, i, sc ); |
| 156 |
|
| 157 |
for(j = 0; j < 3; j++) |
| 158 |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
| 159 |
|
| 160 |
atoms[i]->setPos( pos ); |
| 161 |
} |
| 162 |
|
| 163 |
if (nConstrained){ |
| 164 |
constrainA(); |
| 165 |
} |
| 166 |
} |
| 167 |
|
| 168 |
|
| 169 |
// Scale the box after all the positions have been moved: |
| 170 |
|
| 171 |
this->scaleSimBox(); |
| 172 |
} |
| 173 |
|
| 174 |
void NPT::moveB( void ){ |
| 175 |
|
| 176 |
//new version of NPT |
| 177 |
int i, j, k; |
| 178 |
DirectionalAtom* dAtom; |
| 179 |
double Tb[3], ji[3], sc[3]; |
| 180 |
double vel[3], frc[3]; |
| 181 |
double mass; |
| 182 |
|
| 183 |
// Set things up for the iteration: |
| 184 |
|
| 185 |
for( i=0; i<nAtoms; i++ ){ |
| 186 |
|
| 187 |
atoms[i]->getVel( vel ); |
| 188 |
|
| 189 |
for (j=0; j < 3; j++) |
| 190 |
oldVel[3*i + j] = vel[j]; |
| 191 |
|
| 192 |
if( atoms[i]->isDirectional() ){ |
| 193 |
|
| 194 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 195 |
|
| 196 |
dAtom->getJ( ji ); |
| 197 |
|
| 198 |
for (j=0; j < 3; j++) |
| 199 |
oldJi[3*i + j] = ji[j]; |
| 200 |
|
| 201 |
} |
| 202 |
} |
| 203 |
|
| 204 |
// do the iteration: |
| 205 |
|
| 206 |
instaVol = tStats->getVolume(); |
| 207 |
|
| 208 |
for (k=0; k < 4; k++) { |
| 209 |
|
| 210 |
instaTemp = tStats->getTemperature(); |
| 211 |
instaPress = tStats->getPressure(); |
| 212 |
|
| 213 |
// evolve chi another half step using the temperature at t + dt/2 |
| 214 |
|
| 215 |
this->evolveChiB(); |
| 216 |
this->evolveEtaB(); |
| 217 |
|
| 218 |
for( i=0; i<nAtoms; i++ ){ |
| 219 |
|
| 220 |
atoms[i]->getFrc( frc ); |
| 221 |
atoms[i]->getVel(vel); |
| 222 |
|
| 223 |
mass = atoms[i]->getMass(); |
| 224 |
|
| 225 |
getVelScaleB( sc, i ); |
| 226 |
|
| 227 |
// velocity half step |
| 228 |
for (j=0; j < 3; j++) |
| 229 |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
| 230 |
|
| 231 |
atoms[i]->setVel( vel ); |
| 232 |
|
| 233 |
if( atoms[i]->isDirectional() ){ |
| 234 |
|
| 235 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 236 |
|
| 237 |
// get and convert the torque to body frame |
| 238 |
|
| 239 |
dAtom->getTrq( Tb ); |
| 240 |
dAtom->lab2Body( Tb ); |
| 241 |
|
| 242 |
for (j=0; j < 3; j++) |
| 243 |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 244 |
|
| 245 |
dAtom->setJ( ji ); |
| 246 |
} |
| 247 |
} |
| 248 |
|
| 249 |
if (nConstrained){ |
| 250 |
constrainB(); |
| 251 |
} |
| 252 |
|
| 253 |
if ( this->chiConverged() && this->etaConverged() ) break; |
| 254 |
} |
| 255 |
|
| 256 |
//calculate integral of chida |
| 257 |
integralOfChidt += dt2*chi; |
| 258 |
|
| 259 |
|
| 260 |
} |
| 261 |
|
| 262 |
void NPT::resetIntegrator() { |
| 263 |
chi = 0.0; |
| 264 |
Integrator::resetIntegrator(); |
| 265 |
} |
| 266 |
|
| 267 |
void NPT::evolveChiA() { |
| 268 |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 269 |
oldChi = chi; |
| 270 |
} |
| 271 |
|
| 272 |
void NPT::evolveChiB() { |
| 273 |
|
| 274 |
prevChi = chi; |
| 275 |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 276 |
} |
| 277 |
|
| 278 |
bool NPT::chiConverged() { |
| 279 |
|
| 280 |
return ( fabs( prevChi - chi ) <= chiTolerance ); |
| 281 |
} |
| 282 |
|
| 283 |
int NPT::readyCheck() { |
| 284 |
|
| 285 |
//check parent's readyCheck() first |
| 286 |
if (Integrator::readyCheck() == -1) |
| 287 |
return -1; |
| 288 |
|
| 289 |
// First check to see if we have a target temperature. |
| 290 |
// Not having one is fatal. |
| 291 |
|
| 292 |
if (!have_target_temp) { |
| 293 |
sprintf( painCave.errMsg, |
| 294 |
"NPT error: You can't use the NPT integrator\n" |
| 295 |
" without a targetTemp!\n" |
| 296 |
); |
| 297 |
painCave.isFatal = 1; |
| 298 |
simError(); |
| 299 |
return -1; |
| 300 |
} |
| 301 |
|
| 302 |
if (!have_target_pressure) { |
| 303 |
sprintf( painCave.errMsg, |
| 304 |
"NPT error: You can't use the NPT integrator\n" |
| 305 |
" without a targetPressure!\n" |
| 306 |
); |
| 307 |
painCave.isFatal = 1; |
| 308 |
simError(); |
| 309 |
return -1; |
| 310 |
} |
| 311 |
|
| 312 |
// We must set tauThermostat. |
| 313 |
|
| 314 |
if (!have_tau_thermostat) { |
| 315 |
sprintf( painCave.errMsg, |
| 316 |
"NPT error: If you use the NPT\n" |
| 317 |
" integrator, you must set tauThermostat.\n"); |
| 318 |
painCave.isFatal = 1; |
| 319 |
simError(); |
| 320 |
return -1; |
| 321 |
} |
| 322 |
|
| 323 |
// We must set tauBarostat. |
| 324 |
|
| 325 |
if (!have_tau_barostat) { |
| 326 |
sprintf( painCave.errMsg, |
| 327 |
"NPT error: If you use the NPT\n" |
| 328 |
" integrator, you must set tauBarostat.\n"); |
| 329 |
painCave.isFatal = 1; |
| 330 |
simError(); |
| 331 |
return -1; |
| 332 |
} |
| 333 |
|
| 334 |
if (!have_chi_tolerance) { |
| 335 |
sprintf( painCave.errMsg, |
| 336 |
"NPT warning: setting chi tolerance to 1e-6\n"); |
| 337 |
chiTolerance = 1e-6; |
| 338 |
have_chi_tolerance = 1; |
| 339 |
painCave.isFatal = 0; |
| 340 |
simError(); |
| 341 |
} |
| 342 |
|
| 343 |
if (!have_eta_tolerance) { |
| 344 |
sprintf( painCave.errMsg, |
| 345 |
"NPT warning: setting eta tolerance to 1e-6\n"); |
| 346 |
etaTolerance = 1e-6; |
| 347 |
have_eta_tolerance = 1; |
| 348 |
painCave.isFatal = 0; |
| 349 |
simError(); |
| 350 |
} |
| 351 |
|
| 352 |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 353 |
// of particles, so no subtraction or addition of constraints or |
| 354 |
// orientational degrees of freedom: |
| 355 |
|
| 356 |
NkBT = (double)Nparticles * kB * targetTemp; |
| 357 |
|
| 358 |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 359 |
// than the barostat (when there are particles with orientational degrees |
| 360 |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
| 361 |
|
| 362 |
fkBT = (double)info->ndf * kB * targetTemp; |
| 363 |
|
| 364 |
tt2 = tauThermostat * tauThermostat; |
| 365 |
tb2 = tauBarostat * tauBarostat; |
| 366 |
|
| 367 |
return 1; |
| 368 |
} |
