| 25 |
|
// |
| 26 |
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
| 27 |
|
|
| 28 |
< |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
| 29 |
< |
T( theInfo, the_ff ) |
| 30 |
< |
{ |
| 28 |
> |
NPTf::NPTf (SimInfo* info): NPT(info){ |
| 29 |
|
GenericData* data; |
| 30 |
|
DoubleVectorGenericData * etaValue; |
| 31 |
|
int i,j; |
| 33 |
|
for(i = 0; i < 3; i++){ |
| 34 |
|
for (j = 0; j < 3; j++){ |
| 35 |
|
|
| 36 |
< |
eta[i][j] = 0.0; |
| 37 |
< |
oldEta[i][j] = 0.0; |
| 36 |
> |
eta(i, j) = 0.0; |
| 37 |
> |
oldEta(i, j) = 0.0; |
| 38 |
|
} |
| 39 |
|
} |
| 40 |
|
|
| 49 |
|
|
| 50 |
|
for(i = 0; i < 3; i++){ |
| 51 |
|
for (j = 0; j < 3; j++){ |
| 52 |
< |
eta[i][j] = (*etaValue)[3*i+j]; |
| 53 |
< |
oldEta[i][j] = eta[i][j]; |
| 52 |
> |
eta(i, j) = (*etaValue)[3*i+j]; |
| 53 |
> |
oldEta(i, j) = eta(i, j); |
| 54 |
|
} |
| 55 |
|
} |
| 56 |
|
} |
| 59 |
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|
| 60 |
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} |
| 61 |
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|
| 62 |
< |
template<typename T> NPTf<T>::~NPTf() { |
| 62 |
> |
NPTf::~NPTf() { |
| 63 |
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|
| 64 |
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// empty for now |
| 65 |
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} |
| 66 |
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|
| 67 |
< |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 67 |
> |
void NPTf::evolveEtaA() { |
| 68 |
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|
| 69 |
|
int i, j; |
| 70 |
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|
| 71 |
< |
for(i = 0; i < 3; i++) |
| 72 |
< |
for (j = 0; j < 3; j++) |
| 73 |
< |
eta[i][j] = 0.0; |
| 74 |
< |
|
| 75 |
< |
T::resetIntegrator(); |
| 76 |
< |
} |
| 77 |
< |
|
| 78 |
< |
template<typename T> void NPTf<T>::evolveEtaA() { |
| 81 |
< |
|
| 82 |
< |
int i, j; |
| 83 |
< |
|
| 84 |
< |
for(i = 0; i < 3; i ++){ |
| 85 |
< |
for(j = 0; j < 3; j++){ |
| 86 |
< |
if( i == j) |
| 87 |
< |
eta[i][j] += dt2 * instaVol * |
| 88 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 89 |
< |
else |
| 90 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 71 |
> |
for(i = 0; i < 3; i ++){ |
| 72 |
> |
for(j = 0; j < 3; j++){ |
| 73 |
> |
if( i == j) { |
| 74 |
> |
eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/p_convert) / (NkBT*tb2); |
| 75 |
> |
} else { |
| 76 |
> |
eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); |
| 77 |
> |
} |
| 78 |
> |
} |
| 79 |
|
} |
| 92 |
– |
} |
| 80 |
|
|
| 81 |
< |
for(i = 0; i < 3; i++) |
| 82 |
< |
for (j = 0; j < 3; j++) |
| 83 |
< |
oldEta[i][j] = eta[i][j]; |
| 81 |
> |
for(i = 0; i < 3; i++) { |
| 82 |
> |
for (j = 0; j < 3; j++) { |
| 83 |
> |
oldEta(i, j) = eta(i, j); |
| 84 |
> |
} |
| 85 |
> |
} |
| 86 |
> |
|
| 87 |
|
} |
| 88 |
|
|
| 89 |
< |
template<typename T> void NPTf<T>::evolveEtaB() { |
| 89 |
> |
void NPTf::evolveEtaB() { |
| 90 |
|
|
| 91 |
< |
int i,j; |
| 91 |
> |
int i; |
| 92 |
> |
int j; |
| 93 |
|
|
| 94 |
< |
for(i = 0; i < 3; i++) |
| 95 |
< |
for (j = 0; j < 3; j++) |
| 96 |
< |
prevEta[i][j] = eta[i][j]; |
| 94 |
> |
for(i = 0; i < 3; i++) { |
| 95 |
> |
for (j = 0; j < 3; j++) { |
| 96 |
> |
prevEta(i, j) = eta(i, j); |
| 97 |
> |
} |
| 98 |
> |
} |
| 99 |
|
|
| 100 |
< |
for(i = 0; i < 3; i ++){ |
| 101 |
< |
for(j = 0; j < 3; j++){ |
| 102 |
< |
if( i == j) { |
| 103 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 104 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 105 |
< |
} else { |
| 106 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 107 |
< |
} |
| 100 |
> |
for(i = 0; i < 3; i ++){ |
| 101 |
> |
for(j = 0; j < 3; j++){ |
| 102 |
> |
if( i == j) { |
| 103 |
> |
eta(i, j) = oldEta(i, j) + dt2 * instaVol * |
| 104 |
> |
(press(i, j) - targetPressure/p_convert) / (NkBT*tb2); |
| 105 |
> |
} else { |
| 106 |
> |
eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); |
| 107 |
> |
} |
| 108 |
> |
} |
| 109 |
|
} |
| 110 |
< |
} |
| 110 |
> |
|
| 111 |
> |
|
| 112 |
|
} |
| 113 |
|
|
| 114 |
< |
template<typename T> void NPTf<T>::calcVelScale(void){ |
| 120 |
< |
int i,j; |
| 114 |
> |
void NPTf::calcVelScale(){ |
| 115 |
|
|
| 116 |
< |
for (i = 0; i < 3; i++ ) { |
| 117 |
< |
for (j = 0; j < 3; j++ ) { |
| 118 |
< |
vScale[i][j] = eta[i][j]; |
| 116 |
> |
for (int i = 0; i < 3; i++ ) { |
| 117 |
> |
for (int j = 0; j < 3; j++ ) { |
| 118 |
> |
vScale(i, j) = eta(i, j); |
| 119 |
|
|
| 120 |
|
if (i == j) { |
| 121 |
< |
vScale[i][j] += chi; |
| 121 |
> |
vScale(i, j) += chi; |
| 122 |
|
} |
| 123 |
|
} |
| 124 |
|
} |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
| 128 |
< |
|
| 135 |
< |
matVecMul3( vScale, vel, sc ); |
| 127 |
> |
void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel);{ |
| 128 |
> |
sc = vScale * vel; |
| 129 |
|
} |
| 130 |
|
|
| 131 |
< |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
| 132 |
< |
int j; |
| 140 |
< |
double myVel[3]; |
| 141 |
< |
|
| 142 |
< |
for (j = 0; j < 3; j++) |
| 143 |
< |
myVel[j] = oldVel[3*index + j]; |
| 144 |
< |
|
| 145 |
< |
matVecMul3( vScale, myVel, sc ); |
| 131 |
> |
void NPTf::getVelScaleB(Vector3d& sc, int index ) { |
| 132 |
> |
sc = vScale * oldVel[index]; |
| 133 |
|
} |
| 134 |
|
|
| 135 |
< |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
| 136 |
< |
int index, double sc[3]){ |
| 150 |
< |
int j; |
| 151 |
< |
double rj[3]; |
| 135 |
> |
void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, |
| 136 |
> |
int index, Vector3d& sc) { |
| 137 |
|
|
| 138 |
< |
for(j=0; j<3; j++) |
| 139 |
< |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 140 |
< |
|
| 156 |
< |
matVecMul3( eta, rj, sc ); |
| 138 |
> |
/**@todo */ |
| 139 |
> |
Vector3d rj = (oldPos[index] + pos[j])/2.0 -COM; |
| 140 |
> |
sc = eta * rj; |
| 141 |
|
} |
| 142 |
|
|
| 143 |
< |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
| 143 |
> |
void NPTf::scaleSimBox(){ |
| 144 |
|
|
| 145 |
< |
int i,j,k; |
| 146 |
< |
double scaleMat[3][3]; |
| 145 |
> |
int i; |
| 146 |
> |
int j; |
| 147 |
> |
int k; |
| 148 |
> |
Mat3x3d scaleMat; |
| 149 |
|
double eta2ij; |
| 150 |
|
double bigScale, smallScale, offDiagMax; |
| 151 |
< |
double hm[3][3], hmnew[3][3]; |
| 151 |
> |
Mat3x3d hm; |
| 152 |
> |
Mat3x3d hmnew; |
| 153 |
|
|
| 154 |
|
|
| 155 |
|
|
| 170 |
|
|
| 171 |
|
eta2ij = 0.0; |
| 172 |
|
for(k=0; k<3; k++){ |
| 173 |
< |
eta2ij += eta[i][k] * eta[k][j]; |
| 173 |
> |
eta2ij += eta(i, k) * eta(k, j); |
| 174 |
|
} |
| 175 |
|
|
| 176 |
< |
scaleMat[i][j] = 0.0; |
| 176 |
> |
scaleMat(i, j) = 0.0; |
| 177 |
|
// identity matrix (see above): |
| 178 |
< |
if (i == j) scaleMat[i][j] = 1.0; |
| 178 |
> |
if (i == j) scaleMat(i, j) = 1.0; |
| 179 |
|
// Taylor expansion for the exponential truncated at second order: |
| 180 |
< |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 180 |
> |
scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
| 181 |
|
|
| 182 |
|
|
| 183 |
|
if (i != j) |
| 184 |
< |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 185 |
< |
offDiagMax = fabs(scaleMat[i][j]); |
| 184 |
> |
if (fabs(scaleMat(i, j)) > offDiagMax) |
| 185 |
> |
offDiagMax = fabs(scaleMat(i, j)); |
| 186 |
|
} |
| 187 |
|
|
| 188 |
< |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 189 |
< |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 188 |
> |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
| 189 |
> |
if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
| 190 |
|
} |
| 191 |
|
|
| 192 |
|
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
| 199 |
|
" eta = [%lf\t%lf\t%lf]\n" |
| 200 |
|
" [%lf\t%lf\t%lf]\n" |
| 201 |
|
" [%lf\t%lf\t%lf]\n", |
| 202 |
< |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 203 |
< |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 204 |
< |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
| 205 |
< |
eta[0][0],eta[0][1],eta[0][2], |
| 206 |
< |
eta[1][0],eta[1][1],eta[1][2], |
| 207 |
< |
eta[2][0],eta[2][1],eta[2][2]); |
| 202 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 203 |
> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 204 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
| 205 |
> |
eta(0, 0),eta(0, 1),eta(0, 2), |
| 206 |
> |
eta(1, 0),eta(1, 1),eta(1, 2), |
| 207 |
> |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 208 |
|
painCave.isFatal = 1; |
| 209 |
|
simError(); |
| 210 |
|
} else if (offDiagMax > 0.01) { |
| 217 |
|
" eta = [%lf\t%lf\t%lf]\n" |
| 218 |
|
" [%lf\t%lf\t%lf]\n" |
| 219 |
|
" [%lf\t%lf\t%lf]\n", |
| 220 |
< |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 221 |
< |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 222 |
< |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
| 223 |
< |
eta[0][0],eta[0][1],eta[0][2], |
| 224 |
< |
eta[1][0],eta[1][1],eta[1][2], |
| 225 |
< |
eta[2][0],eta[2][1],eta[2][2]); |
| 220 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 221 |
> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 222 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
| 223 |
> |
eta(0, 0),eta(0, 1),eta(0, 2), |
| 224 |
> |
eta(1, 0),eta(1, 1),eta(1, 2), |
| 225 |
> |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 226 |
|
painCave.isFatal = 1; |
| 227 |
|
simError(); |
| 228 |
|
} else { |
| 232 |
|
} |
| 233 |
|
} |
| 234 |
|
|
| 235 |
< |
template<typename T> bool NPTf<T>::etaConverged() { |
| 236 |
< |
int i; |
| 237 |
< |
double diffEta, sumEta; |
| 235 |
> |
bool NPTf::etaConverged() { |
| 236 |
> |
int i; |
| 237 |
> |
double diffEta, sumEta; |
| 238 |
|
|
| 239 |
< |
sumEta = 0; |
| 240 |
< |
for(i = 0; i < 3; i++) |
| 241 |
< |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 239 |
> |
sumEta = 0; |
| 240 |
> |
for(i = 0; i < 3; i++) { |
| 241 |
> |
sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
| 242 |
> |
} |
| 243 |
> |
|
| 244 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
| 245 |
|
|
| 246 |
< |
diffEta = sqrt( sumEta / 3.0 ); |
| 257 |
< |
|
| 258 |
< |
return ( diffEta <= etaTolerance ); |
| 246 |
> |
return ( diffEta <= etaTolerance ); |
| 247 |
|
} |
| 248 |
|
|
| 249 |
< |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 249 |
> |
double NPTf::calcConservedQuantity(){ |
| 250 |
|
|
| 251 |
< |
double conservedQuantity; |
| 252 |
< |
double totalEnergy; |
| 253 |
< |
double thermostat_kinetic; |
| 254 |
< |
double thermostat_potential; |
| 255 |
< |
double barostat_kinetic; |
| 256 |
< |
double barostat_potential; |
| 257 |
< |
double trEta; |
| 270 |
< |
double a[3][3], b[3][3]; |
| 251 |
> |
double conservedQuantity; |
| 252 |
> |
double totalEnergy; |
| 253 |
> |
double thermostat_kinetic; |
| 254 |
> |
double thermostat_potential; |
| 255 |
> |
double barostat_kinetic; |
| 256 |
> |
double barostat_potential; |
| 257 |
> |
double trEta; |
| 258 |
|
|
| 259 |
< |
totalEnergy = tStats->getTotalE(); |
| 259 |
> |
totalEnergy = tStats->getTotalE(); |
| 260 |
|
|
| 261 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 275 |
< |
(2.0 * eConvert); |
| 261 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * eConvert); |
| 262 |
|
|
| 263 |
< |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 263 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 264 |
|
|
| 265 |
< |
transposeMat3(eta, a); |
| 266 |
< |
matMul3(a, eta, b); |
| 267 |
< |
trEta = matTrace3(b); |
| 265 |
> |
trEta = (eta.transpose() * eta).trace(); |
| 266 |
> |
|
| 267 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * eConvert); |
| 268 |
|
|
| 269 |
< |
barostat_kinetic = NkBT * tb2 * trEta / |
| 284 |
< |
(2.0 * eConvert); |
| 269 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /eConvert; |
| 270 |
|
|
| 271 |
< |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 272 |
< |
eConvert; |
| 271 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 272 |
> |
barostat_kinetic + barostat_potential; |
| 273 |
|
|
| 274 |
< |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 290 |
< |
barostat_kinetic + barostat_potential; |
| 274 |
> |
return conservedQuantity; |
| 275 |
|
|
| 292 |
– |
return conservedQuantity; |
| 293 |
– |
|
| 276 |
|
} |
| 277 |
|
|
| 296 |
– |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
| 297 |
– |
string parameters; |
| 298 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 299 |
– |
char buffer[BUFFERSIZE]; |
| 300 |
– |
|
| 301 |
– |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 302 |
– |
parameters += buffer; |
| 303 |
– |
|
| 304 |
– |
for(int i = 0; i < 3; i++){ |
| 305 |
– |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 306 |
– |
parameters += buffer; |
| 307 |
– |
} |
| 308 |
– |
|
| 309 |
– |
return parameters; |
| 310 |
– |
|
| 311 |
– |
} |
