| 1 |
< |
#include <cmath> |
| 1 |
> |
#include <math.h> |
| 2 |
> |
|
| 3 |
|
#include "Atom.hpp" |
| 4 |
|
#include "SRI.hpp" |
| 5 |
|
#include "AbstractClasses.hpp" |
| 8 |
|
#include "Thermo.hpp" |
| 9 |
|
#include "ReadWrite.hpp" |
| 10 |
|
#include "Integrator.hpp" |
| 11 |
< |
#include "simError.h" |
| 11 |
> |
#include "simError.h" |
| 12 |
|
|
| 13 |
|
#ifdef IS_MPI |
| 14 |
|
#include "mpiSimulation.hpp" |
| 18 |
|
// modification of the Hoover algorithm: |
| 19 |
|
// |
| 20 |
|
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
| 21 |
< |
// Molec. Phys., 78, 533. |
| 21 |
> |
// Molec. Phys., 78, 533. |
| 22 |
|
// |
| 23 |
|
// and |
| 24 |
< |
// |
| 24 |
> |
// |
| 25 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 26 |
|
|
| 27 |
|
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 28 |
|
T( theInfo, the_ff ) |
| 29 |
|
{ |
| 30 |
< |
int i, j; |
| 31 |
< |
chi = 0.0; |
| 32 |
< |
integralOfChidt = 0.0; |
| 30 |
> |
GenericData* data; |
| 31 |
> |
DoubleArrayData * etaValue; |
| 32 |
> |
vector<double> etaArray; |
| 33 |
> |
int i,j; |
| 34 |
|
|
| 35 |
< |
for(i = 0; i < 3; i++) |
| 36 |
< |
for (j = 0; j < 3; j++) |
| 35 |
> |
for(i = 0; i < 3; i++){ |
| 36 |
> |
for (j = 0; j < 3; j++){ |
| 37 |
> |
|
| 38 |
|
eta[i][j] = 0.0; |
| 39 |
+ |
oldEta[i][j] = 0.0; |
| 40 |
+ |
} |
| 41 |
+ |
} |
| 42 |
|
|
| 37 |
– |
have_tau_thermostat = 0; |
| 38 |
– |
have_tau_barostat = 0; |
| 39 |
– |
have_target_temp = 0; |
| 40 |
– |
have_target_pressure = 0; |
| 43 |
|
|
| 44 |
< |
have_chi_tolerance = 0; |
| 45 |
< |
have_eta_tolerance = 0; |
| 46 |
< |
have_pos_iter_tolerance = 0; |
| 44 |
> |
if( theInfo->useInitXSstate ){ |
| 45 |
> |
// retrieve eta array from simInfo if it exists |
| 46 |
> |
data = info->getProperty(ETAVALUE_ID); |
| 47 |
> |
if(data){ |
| 48 |
> |
etaValue = dynamic_cast<DoubleArrayData*>(data); |
| 49 |
> |
|
| 50 |
> |
if(etaValue){ |
| 51 |
> |
etaArray = etaValue->getData(); |
| 52 |
> |
|
| 53 |
> |
for(i = 0; i < 3; i++){ |
| 54 |
> |
for (j = 0; j < 3; j++){ |
| 55 |
> |
eta[i][j] = etaArray[3*i+j]; |
| 56 |
> |
oldEta[i][j] = eta[i][j]; |
| 57 |
> |
} |
| 58 |
> |
} |
| 59 |
> |
} |
| 60 |
> |
} |
| 61 |
> |
} |
| 62 |
|
|
| 46 |
– |
oldPos = new double[3*nAtoms]; |
| 47 |
– |
oldVel = new double[3*nAtoms]; |
| 48 |
– |
oldJi = new double[3*nAtoms]; |
| 49 |
– |
#ifdef IS_MPI |
| 50 |
– |
Nparticles = mpiSim->getTotAtoms(); |
| 51 |
– |
#else |
| 52 |
– |
Nparticles = theInfo->n_atoms; |
| 53 |
– |
#endif |
| 54 |
– |
|
| 63 |
|
} |
| 64 |
|
|
| 65 |
|
template<typename T> NPTf<T>::~NPTf() { |
| 66 |
< |
delete[] oldPos; |
| 67 |
< |
delete[] oldVel; |
| 60 |
< |
delete[] oldJi; |
| 66 |
> |
|
| 67 |
> |
// empty for now |
| 68 |
|
} |
| 69 |
|
|
| 70 |
< |
template<typename T> void NPTf<T>::moveA() { |
| 70 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 71 |
|
|
| 72 |
< |
// new version of NPTf |
| 66 |
< |
int i, j, k; |
| 67 |
< |
DirectionalAtom* dAtom; |
| 68 |
< |
double Tb[3], ji[3]; |
| 72 |
> |
int i, j; |
| 73 |
|
|
| 74 |
< |
double mass; |
| 75 |
< |
double vel[3], pos[3], frc[3]; |
| 74 |
> |
for(i = 0; i < 3; i++) |
| 75 |
> |
for (j = 0; j < 3; j++) |
| 76 |
> |
eta[i][j] = 0.0; |
| 77 |
|
|
| 78 |
< |
double rj[3]; |
| 79 |
< |
double instaTemp, instaPress, instaVol; |
| 75 |
< |
double tt2, tb2; |
| 76 |
< |
double sc[3]; |
| 77 |
< |
double eta2ij; |
| 78 |
< |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
| 79 |
< |
double bigScale, smallScale, offDiagMax; |
| 80 |
< |
double COM[3]; |
| 78 |
> |
T::resetIntegrator(); |
| 79 |
> |
} |
| 80 |
|
|
| 81 |
< |
tt2 = tauThermostat * tauThermostat; |
| 83 |
< |
tb2 = tauBarostat * tauBarostat; |
| 81 |
> |
template<typename T> void NPTf<T>::evolveEtaA() { |
| 82 |
|
|
| 83 |
< |
instaTemp = tStats->getTemperature(); |
| 86 |
< |
tStats->getPressureTensor(press); |
| 87 |
< |
instaVol = tStats->getVolume(); |
| 88 |
< |
|
| 89 |
< |
tStats->getCOM(COM); |
| 83 |
> |
int i, j; |
| 84 |
|
|
| 85 |
< |
//calculate scale factor of veloity |
| 86 |
< |
for (i = 0; i < 3; i++ ) { |
| 87 |
< |
for (j = 0; j < 3; j++ ) { |
| 88 |
< |
vScale[i][j] = eta[i][j]; |
| 89 |
< |
|
| 90 |
< |
if (i == j) { |
| 91 |
< |
vScale[i][j] += chi; |
| 98 |
< |
} |
| 85 |
> |
for(i = 0; i < 3; i ++){ |
| 86 |
> |
for(j = 0; j < 3; j++){ |
| 87 |
> |
if( i == j) |
| 88 |
> |
eta[i][j] += dt2 * instaVol * |
| 89 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 90 |
> |
else |
| 91 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 92 |
|
} |
| 93 |
|
} |
| 101 |
– |
|
| 102 |
– |
//evolve velocity half step |
| 103 |
– |
for( i=0; i<nAtoms; i++ ){ |
| 94 |
|
|
| 95 |
< |
atoms[i]->getVel( vel ); |
| 96 |
< |
atoms[i]->getFrc( frc ); |
| 95 |
> |
for(i = 0; i < 3; i++) |
| 96 |
> |
for (j = 0; j < 3; j++) |
| 97 |
> |
oldEta[i][j] = eta[i][j]; |
| 98 |
> |
} |
| 99 |
|
|
| 100 |
< |
mass = atoms[i]->getMass(); |
| 109 |
< |
|
| 110 |
< |
info->matVecMul3( vScale, vel, sc ); |
| 100 |
> |
template<typename T> void NPTf<T>::evolveEtaB() { |
| 101 |
|
|
| 102 |
< |
for (j=0; j < 3; j++) { |
| 113 |
< |
// velocity half step |
| 114 |
< |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 115 |
< |
} |
| 102 |
> |
int i,j; |
| 103 |
|
|
| 104 |
< |
atoms[i]->setVel( vel ); |
| 105 |
< |
|
| 106 |
< |
if( atoms[i]->isDirectional() ){ |
| 104 |
> |
for(i = 0; i < 3; i++) |
| 105 |
> |
for (j = 0; j < 3; j++) |
| 106 |
> |
prevEta[i][j] = eta[i][j]; |
| 107 |
|
|
| 108 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 108 |
> |
for(i = 0; i < 3; i ++){ |
| 109 |
> |
for(j = 0; j < 3; j++){ |
| 110 |
> |
if( i == j) { |
| 111 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 112 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 113 |
> |
} else { |
| 114 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 115 |
> |
} |
| 116 |
> |
} |
| 117 |
> |
} |
| 118 |
> |
} |
| 119 |
|
|
| 120 |
< |
// get and convert the torque to body frame |
| 121 |
< |
|
| 125 |
< |
dAtom->getTrq( Tb ); |
| 126 |
< |
dAtom->lab2Body( Tb ); |
| 127 |
< |
|
| 128 |
< |
// get the angular momentum, and propagate a half step |
| 120 |
> |
template<typename T> void NPTf<T>::calcVelScale(void){ |
| 121 |
> |
int i,j; |
| 122 |
|
|
| 123 |
< |
dAtom->getJ( ji ); |
| 123 |
> |
for (i = 0; i < 3; i++ ) { |
| 124 |
> |
for (j = 0; j < 3; j++ ) { |
| 125 |
> |
vScale[i][j] = eta[i][j]; |
| 126 |
|
|
| 127 |
< |
for (j=0; j < 3; j++) |
| 128 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 129 |
< |
|
| 130 |
< |
this->rotationPropagation( dAtom, ji ); |
| 136 |
< |
|
| 137 |
< |
dAtom->setJ( ji ); |
| 138 |
< |
} |
| 127 |
> |
if (i == j) { |
| 128 |
> |
vScale[i][j] += chi; |
| 129 |
> |
} |
| 130 |
> |
} |
| 131 |
|
} |
| 132 |
+ |
} |
| 133 |
|
|
| 134 |
< |
// advance chi half step |
| 135 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 134 |
> |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
| 135 |
> |
|
| 136 |
> |
info->matVecMul3( vScale, vel, sc ); |
| 137 |
> |
} |
| 138 |
|
|
| 139 |
< |
// calculate the integral of chidt |
| 140 |
< |
integralOfChidt += dt2*chi; |
| 139 |
> |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
| 140 |
> |
int j; |
| 141 |
> |
double myVel[3]; |
| 142 |
> |
double vScale[3][3]; |
| 143 |
|
|
| 144 |
< |
// advance eta half step |
| 144 |
> |
for (j = 0; j < 3; j++) |
| 145 |
> |
myVel[j] = oldVel[3*index + j]; |
| 146 |
|
|
| 147 |
< |
for(i = 0; i < 3; i ++) |
| 148 |
< |
for(j = 0; j < 3; j++){ |
| 151 |
< |
if( i == j) |
| 152 |
< |
eta[i][j] += dt2 * instaVol * |
| 153 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 154 |
< |
else |
| 155 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 156 |
< |
} |
| 157 |
< |
|
| 158 |
< |
//save the old positions |
| 159 |
< |
for(i = 0; i < nAtoms; i++){ |
| 160 |
< |
atoms[i]->getPos(pos); |
| 161 |
< |
for(j = 0; j < 3; j++) |
| 162 |
< |
oldPos[i*3 + j] = pos[j]; |
| 163 |
< |
} |
| 164 |
< |
|
| 165 |
< |
//the first estimation of r(t+dt) is equal to r(t) |
| 166 |
< |
|
| 167 |
< |
for(k = 0; k < 4; k ++){ |
| 147 |
> |
info->matVecMul3( vScale, myVel, sc ); |
| 148 |
> |
} |
| 149 |
|
|
| 150 |
< |
for(i =0 ; i < nAtoms; i++){ |
| 150 |
> |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
| 151 |
> |
int index, double sc[3]){ |
| 152 |
> |
int j; |
| 153 |
> |
double rj[3]; |
| 154 |
|
|
| 155 |
< |
atoms[i]->getVel(vel); |
| 156 |
< |
atoms[i]->getPos(pos); |
| 155 |
> |
for(j=0; j<3; j++) |
| 156 |
> |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 157 |
|
|
| 158 |
< |
for(j = 0; j < 3; j++) |
| 159 |
< |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
| 176 |
< |
|
| 177 |
< |
info->matVecMul3( eta, rj, sc ); |
| 178 |
< |
|
| 179 |
< |
for(j = 0; j < 3; j++) |
| 180 |
< |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
| 158 |
> |
info->matVecMul3( eta, rj, sc ); |
| 159 |
> |
} |
| 160 |
|
|
| 161 |
< |
atoms[i]->setPos( pos ); |
| 161 |
> |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
| 162 |
|
|
| 163 |
< |
} |
| 163 |
> |
int i,j,k; |
| 164 |
> |
double scaleMat[3][3]; |
| 165 |
> |
double eta2ij; |
| 166 |
> |
double bigScale, smallScale, offDiagMax; |
| 167 |
> |
double hm[3][3], hmnew[3][3]; |
| 168 |
|
|
| 186 |
– |
if (nConstrained) { |
| 187 |
– |
constrainA(); |
| 188 |
– |
} |
| 189 |
– |
} |
| 169 |
|
|
| 170 |
< |
|
| 170 |
> |
|
| 171 |
|
// Scale the box after all the positions have been moved: |
| 172 |
< |
|
| 172 |
> |
|
| 173 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 174 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 175 |
< |
|
| 175 |
> |
|
| 176 |
|
bigScale = 1.0; |
| 177 |
|
smallScale = 1.0; |
| 178 |
|
offDiagMax = 0.0; |
| 179 |
< |
|
| 179 |
> |
|
| 180 |
|
for(i=0; i<3; i++){ |
| 181 |
|
for(j=0; j<3; j++){ |
| 182 |
< |
|
| 182 |
> |
|
| 183 |
|
// Calculate the matrix Product of the eta array (we only need |
| 184 |
|
// the ij element right now): |
| 185 |
< |
|
| 185 |
> |
|
| 186 |
|
eta2ij = 0.0; |
| 187 |
|
for(k=0; k<3; k++){ |
| 188 |
|
eta2ij += eta[i][k] * eta[k][j]; |
| 189 |
|
} |
| 190 |
< |
|
| 190 |
> |
|
| 191 |
|
scaleMat[i][j] = 0.0; |
| 192 |
|
// identity matrix (see above): |
| 193 |
|
if (i == j) scaleMat[i][j] = 1.0; |
| 195 |
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 196 |
|
|
| 197 |
|
if (i != j) |
| 198 |
< |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 198 |
> |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 199 |
|
offDiagMax = fabs(scaleMat[i][j]); |
| 200 |
|
} |
| 201 |
|
|
| 202 |
|
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 203 |
|
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 204 |
|
} |
| 205 |
< |
|
| 206 |
< |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 205 |
> |
|
| 206 |
> |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
| 207 |
|
sprintf( painCave.errMsg, |
| 208 |
< |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 208 |
> |
"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
| 209 |
|
" Check your tauBarostat, as it is probably too small!\n\n" |
| 210 |
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 211 |
|
" [%lf\t%lf\t%lf]\n" |
| 215 |
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 216 |
|
painCave.isFatal = 1; |
| 217 |
|
simError(); |
| 218 |
< |
} else if (offDiagMax > 0.1) { |
| 218 |
> |
} else if (offDiagMax > 0.01) { |
| 219 |
|
sprintf( painCave.errMsg, |
| 220 |
< |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 220 |
> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
| 221 |
|
" Check your tauBarostat, as it is probably too small!\n\n" |
| 222 |
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 223 |
|
" [%lf\t%lf\t%lf]\n" |
| 232 |
|
info->matMul3(hm, scaleMat, hmnew); |
| 233 |
|
info->setBoxM(hmnew); |
| 234 |
|
} |
| 256 |
– |
|
| 235 |
|
} |
| 236 |
|
|
| 237 |
< |
template<typename T> void NPTf<T>::moveB( void ){ |
| 237 |
> |
template<typename T> bool NPTf<T>::etaConverged() { |
| 238 |
> |
int i; |
| 239 |
> |
double diffEta, sumEta; |
| 240 |
|
|
| 241 |
< |
//new version of NPTf |
| 262 |
< |
int i, j, k; |
| 263 |
< |
DirectionalAtom* dAtom; |
| 264 |
< |
double Tb[3], ji[3]; |
| 265 |
< |
double vel[3], myVel[3], frc[3]; |
| 266 |
< |
double mass; |
| 267 |
< |
|
| 268 |
< |
double instaTemp, instaPress, instaVol; |
| 269 |
< |
double tt2, tb2; |
| 270 |
< |
double sc[3]; |
| 271 |
< |
double press[3][3], vScale[3][3]; |
| 272 |
< |
double oldChi, prevChi; |
| 273 |
< |
double oldEta[3][3], prevEta[3][3], diffEta; |
| 274 |
< |
|
| 275 |
< |
tt2 = tauThermostat * tauThermostat; |
| 276 |
< |
tb2 = tauBarostat * tauBarostat; |
| 277 |
< |
|
| 278 |
< |
// Set things up for the iteration: |
| 279 |
< |
|
| 280 |
< |
oldChi = chi; |
| 281 |
< |
|
| 241 |
> |
sumEta = 0; |
| 242 |
|
for(i = 0; i < 3; i++) |
| 243 |
< |
for(j = 0; j < 3; j++) |
| 284 |
< |
oldEta[i][j] = eta[i][j]; |
| 243 |
> |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 244 |
|
|
| 245 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 245 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
| 246 |
|
|
| 247 |
< |
atoms[i]->getVel( vel ); |
| 289 |
< |
|
| 290 |
< |
for (j=0; j < 3; j++) |
| 291 |
< |
oldVel[3*i + j] = vel[j]; |
| 292 |
< |
|
| 293 |
< |
if( atoms[i]->isDirectional() ){ |
| 294 |
< |
|
| 295 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 296 |
< |
|
| 297 |
< |
dAtom->getJ( ji ); |
| 298 |
< |
|
| 299 |
< |
for (j=0; j < 3; j++) |
| 300 |
< |
oldJi[3*i + j] = ji[j]; |
| 301 |
< |
|
| 302 |
< |
} |
| 303 |
< |
} |
| 304 |
< |
|
| 305 |
< |
// do the iteration: |
| 306 |
< |
|
| 307 |
< |
instaVol = tStats->getVolume(); |
| 308 |
< |
|
| 309 |
< |
for (k=0; k < 4; k++) { |
| 310 |
< |
|
| 311 |
< |
instaTemp = tStats->getTemperature(); |
| 312 |
< |
tStats->getPressureTensor(press); |
| 313 |
< |
|
| 314 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
| 315 |
< |
|
| 316 |
< |
prevChi = chi; |
| 317 |
< |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 318 |
< |
|
| 319 |
< |
for(i = 0; i < 3; i++) |
| 320 |
< |
for(j = 0; j < 3; j++) |
| 321 |
< |
prevEta[i][j] = eta[i][j]; |
| 322 |
< |
|
| 323 |
< |
//advance eta half step and calculate scale factor for velocity |
| 324 |
< |
|
| 325 |
< |
for(i = 0; i < 3; i ++) |
| 326 |
< |
for(j = 0; j < 3; j++){ |
| 327 |
< |
if( i == j) { |
| 328 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 329 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 330 |
< |
vScale[i][j] = eta[i][j] + chi; |
| 331 |
< |
} else { |
| 332 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 333 |
< |
vScale[i][j] = eta[i][j]; |
| 334 |
< |
} |
| 335 |
< |
} |
| 336 |
< |
|
| 337 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 338 |
< |
|
| 339 |
< |
atoms[i]->getFrc( frc ); |
| 340 |
< |
atoms[i]->getVel(vel); |
| 341 |
< |
|
| 342 |
< |
mass = atoms[i]->getMass(); |
| 343 |
< |
|
| 344 |
< |
for (j = 0; j < 3; j++) |
| 345 |
< |
myVel[j] = oldVel[3*i + j]; |
| 346 |
< |
|
| 347 |
< |
info->matVecMul3( vScale, myVel, sc ); |
| 348 |
< |
|
| 349 |
< |
// velocity half step |
| 350 |
< |
for (j=0; j < 3; j++) { |
| 351 |
< |
// velocity half step (use chi from previous step here): |
| 352 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 353 |
< |
} |
| 354 |
< |
|
| 355 |
< |
atoms[i]->setVel( vel ); |
| 356 |
< |
|
| 357 |
< |
if( atoms[i]->isDirectional() ){ |
| 358 |
< |
|
| 359 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 360 |
< |
|
| 361 |
< |
// get and convert the torque to body frame |
| 362 |
< |
|
| 363 |
< |
dAtom->getTrq( Tb ); |
| 364 |
< |
dAtom->lab2Body( Tb ); |
| 365 |
< |
|
| 366 |
< |
for (j=0; j < 3; j++) |
| 367 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 368 |
< |
|
| 369 |
< |
dAtom->setJ( ji ); |
| 370 |
< |
} |
| 371 |
< |
} |
| 372 |
< |
|
| 373 |
< |
if (nConstrained) { |
| 374 |
< |
constrainB(); |
| 375 |
< |
} |
| 376 |
< |
|
| 377 |
< |
diffEta = 0; |
| 378 |
< |
for(i = 0; i < 3; i++) |
| 379 |
< |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 380 |
< |
|
| 381 |
< |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
| 382 |
< |
break; |
| 383 |
< |
} |
| 384 |
< |
|
| 385 |
< |
//calculate integral of chidt |
| 386 |
< |
integralOfChidt += dt2*chi; |
| 387 |
< |
|
| 247 |
> |
return ( diffEta <= etaTolerance ); |
| 248 |
|
} |
| 249 |
|
|
| 390 |
– |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 391 |
– |
int i,j; |
| 392 |
– |
|
| 393 |
– |
chi = 0.0; |
| 394 |
– |
|
| 395 |
– |
for(i = 0; i < 3; i++) |
| 396 |
– |
for (j = 0; j < 3; j++) |
| 397 |
– |
eta[i][j] = 0.0; |
| 398 |
– |
|
| 399 |
– |
} |
| 400 |
– |
|
| 401 |
– |
template<typename T> int NPTf<T>::readyCheck() { |
| 402 |
– |
|
| 403 |
– |
//check parent's readyCheck() first |
| 404 |
– |
if (T::readyCheck() == -1) |
| 405 |
– |
return -1; |
| 406 |
– |
|
| 407 |
– |
// First check to see if we have a target temperature. |
| 408 |
– |
// Not having one is fatal. |
| 409 |
– |
|
| 410 |
– |
if (!have_target_temp) { |
| 411 |
– |
sprintf( painCave.errMsg, |
| 412 |
– |
"NPTf error: You can't use the NPTf integrator\n" |
| 413 |
– |
" without a targetTemp!\n" |
| 414 |
– |
); |
| 415 |
– |
painCave.isFatal = 1; |
| 416 |
– |
simError(); |
| 417 |
– |
return -1; |
| 418 |
– |
} |
| 419 |
– |
|
| 420 |
– |
if (!have_target_pressure) { |
| 421 |
– |
sprintf( painCave.errMsg, |
| 422 |
– |
"NPTf error: You can't use the NPTf integrator\n" |
| 423 |
– |
" without a targetPressure!\n" |
| 424 |
– |
); |
| 425 |
– |
painCave.isFatal = 1; |
| 426 |
– |
simError(); |
| 427 |
– |
return -1; |
| 428 |
– |
} |
| 429 |
– |
|
| 430 |
– |
// We must set tauThermostat. |
| 431 |
– |
|
| 432 |
– |
if (!have_tau_thermostat) { |
| 433 |
– |
sprintf( painCave.errMsg, |
| 434 |
– |
"NPTf error: If you use the NPTf\n" |
| 435 |
– |
" integrator, you must set tauThermostat.\n"); |
| 436 |
– |
painCave.isFatal = 1; |
| 437 |
– |
simError(); |
| 438 |
– |
return -1; |
| 439 |
– |
} |
| 440 |
– |
|
| 441 |
– |
// We must set tauBarostat. |
| 442 |
– |
|
| 443 |
– |
if (!have_tau_barostat) { |
| 444 |
– |
sprintf( painCave.errMsg, |
| 445 |
– |
"NPTf error: If you use the NPTf\n" |
| 446 |
– |
" integrator, you must set tauBarostat.\n"); |
| 447 |
– |
painCave.isFatal = 1; |
| 448 |
– |
simError(); |
| 449 |
– |
return -1; |
| 450 |
– |
} |
| 451 |
– |
|
| 452 |
– |
|
| 453 |
– |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 454 |
– |
// of particles, so no subtraction or addition of constraints or |
| 455 |
– |
// orientational degrees of freedom: |
| 456 |
– |
|
| 457 |
– |
NkBT = (double)Nparticles * kB * targetTemp; |
| 458 |
– |
|
| 459 |
– |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 460 |
– |
// than the barostat (when there are particles with orientational degrees |
| 461 |
– |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
| 462 |
– |
|
| 463 |
– |
fkBT = (double)info->ndf * kB * targetTemp; |
| 464 |
– |
|
| 465 |
– |
return 1; |
| 466 |
– |
} |
| 467 |
– |
|
| 250 |
|
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 251 |
|
|
| 252 |
|
double conservedQuantity; |
| 253 |
< |
double Energy; |
| 253 |
> |
double totalEnergy; |
| 254 |
|
double thermostat_kinetic; |
| 255 |
|
double thermostat_potential; |
| 256 |
|
double barostat_kinetic; |
| 258 |
|
double trEta; |
| 259 |
|
double a[3][3], b[3][3]; |
| 260 |
|
|
| 261 |
< |
Energy = tStats->getTotalE(); |
| 261 |
> |
totalEnergy = tStats->getTotalE(); |
| 262 |
|
|
| 263 |
< |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 263 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 264 |
|
(2.0 * eConvert); |
| 265 |
|
|
| 266 |
|
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 269 |
|
info->matMul3(a, eta, b); |
| 270 |
|
trEta = info->matTrace3(b); |
| 271 |
|
|
| 272 |
< |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
| 272 |
> |
barostat_kinetic = NkBT * tb2 * trEta / |
| 273 |
|
(2.0 * eConvert); |
| 274 |
< |
|
| 275 |
< |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 274 |
> |
|
| 275 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 276 |
|
eConvert; |
| 277 |
|
|
| 278 |
< |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 278 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 279 |
|
barostat_kinetic + barostat_potential; |
| 498 |
– |
|
| 499 |
– |
cout.width(8); |
| 500 |
– |
cout.precision(8); |
| 280 |
|
|
| 281 |
< |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 503 |
< |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 504 |
< |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 281 |
> |
return conservedQuantity; |
| 282 |
|
|
| 506 |
– |
return conservedQuantity; |
| 283 |
|
} |
| 284 |
+ |
|
| 285 |
+ |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
| 286 |
+ |
string parameters; |
| 287 |
+ |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 288 |
+ |
char buffer[BUFFERSIZE]; |
| 289 |
+ |
|
| 290 |
+ |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 291 |
+ |
parameters += buffer; |
| 292 |
+ |
|
| 293 |
+ |
for(int i = 0; i < 3; i++){ |
| 294 |
+ |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 295 |
+ |
parameters += buffer; |
| 296 |
+ |
} |
| 297 |
+ |
|
| 298 |
+ |
return parameters; |
| 299 |
+ |
|
| 300 |
+ |
} |
