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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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< |
template<typename T> NPTxyz<T>::NPTxyz ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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> |
NPTxyz::NPTxyz ( SimInfo *theInfo, ForceFields* the_ff): |
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> |
NPT( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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DoubleArrayData * etaValue; |
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vector<double> etaArray; |
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> |
double *etaArray; |
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int i,j; |
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for(i = 0; i < 3; i++){ |
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// retrieve eta array from simInfo if it exists |
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data = info->getProperty(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleArrayData*>(data); |
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< |
|
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if(etaValue){ |
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etaArray = etaValue->getData(); |
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< |
|
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> |
if(data != NULL){ |
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> |
|
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> |
int test = data->getDarray(etaArray); |
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> |
|
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> |
if( test == 9 ){ |
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> |
|
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for(i = 0; i < 3; i++){ |
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< |
for (j = 0; j < 3; j++){ |
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< |
eta[i][j] = etaArray[3*i+j]; |
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< |
oldEta[i][j] = eta[i][j]; |
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} |
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} |
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> |
for (j = 0; j < 3; j++){ |
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> |
eta[i][j] = etaArray[3*i+j]; |
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> |
oldEta[i][j] = eta[i][j]; |
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> |
} |
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> |
} |
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> |
delete[] etaArray; |
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} |
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+ |
else |
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+ |
std::cerr << "NPTxyz error: etaArray is not length 9 (actual = " << test |
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+ |
<< ").\n" |
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<< " Simulation wil proceed with eta = 0;\n"; |
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} |
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– |
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} |
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< |
template<typename T> NPTxyz<T>::~NPTxyz() { |
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> |
NPTxyz::~NPTxyz() { |
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// empty for now |
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} |
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< |
template<typename T> void NPTxyz<T>::resetIntegrator() { |
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> |
void NPTxyz::resetIntegrator() { |
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int i, j; |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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< |
T::resetIntegrator(); |
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> |
NPT::resetIntegrator(); |
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} |
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< |
template<typename T> void NPTxyz<T>::evolveEtaA() { |
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> |
void NPTxyz::evolveEtaA() { |
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int i, j; |
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oldEta[i][j] = eta[i][j]; |
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} |
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< |
template<typename T> void NPTxyz<T>::evolveEtaB() { |
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> |
void NPTxyz::evolveEtaB() { |
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int i,j; |
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} |
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} |
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< |
template<typename T> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) { |
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> |
void NPTxyz::getVelScaleA(double sc[3], double vel[3]) { |
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int i,j; |
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double vScale[3][3]; |
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info->matVecMul3( vScale, vel, sc ); |
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} |
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< |
template<typename T> void NPTxyz<T>::getVelScaleB(double sc[3], int index ){ |
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> |
void NPTxyz::getVelScaleB(double sc[3], int index ){ |
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int i,j; |
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double myVel[3]; |
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double vScale[3][3]; |
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info->matVecMul3( vScale, myVel, sc ); |
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} |
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|
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< |
template<typename T> void NPTxyz<T>::getPosScale(double pos[3], double COM[3], |
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> |
void NPTxyz::getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]){ |
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int j; |
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double rj[3]; |
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info->matVecMul3( eta, rj, sc ); |
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} |
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|
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< |
template<typename T> void NPTxyz<T>::scaleSimBox( void ){ |
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> |
void NPTxyz::scaleSimBox( void ){ |
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|
| 170 |
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int i,j,k; |
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double scaleMat[3][3]; |
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} |
| 249 |
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} |
| 250 |
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|
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< |
template<typename T> bool NPTxyz<T>::etaConverged() { |
| 251 |
> |
bool NPTxyz::etaConverged() { |
| 252 |
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int i; |
| 253 |
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double diffEta, sumEta; |
| 254 |
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|
| 261 |
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return ( diffEta <= etaTolerance ); |
| 262 |
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} |
| 263 |
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|
| 264 |
< |
template<typename T> double NPTxyz<T>::getConservedQuantity(void){ |
| 264 |
> |
double NPTxyz::getConservedQuantity(void){ |
| 265 |
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|
| 266 |
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double conservedQuantity; |
| 267 |
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double totalEnergy; |
| 303 |
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|
| 304 |
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} |
| 305 |
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|
| 306 |
< |
template<typename T> string NPTxyz<T>::getAdditionalParameters(void){ |
| 304 |
< |
string parameters; |
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< |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 306 |
< |
char buffer[BUFFERSIZE]; |
| 306 |
> |
char* NPTxyz::getAdditionalParameters(void){ |
| 307 |
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|
| 308 |
< |
sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt); |
| 309 |
< |
parameters += buffer; |
| 308 |
> |
sprintf(addParamBuffer, |
| 309 |
> |
"\t%G\t%G;" |
| 310 |
> |
"\t%G\t%G\t%G;" |
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> |
"\t%G\t%G\t%G;" |
| 312 |
> |
"\t%G\t%G\t%G;", |
| 313 |
> |
chi, integralOfChidt, |
| 314 |
> |
eta[0][0], eta[0][1], eta[0][2], |
| 315 |
> |
eta[1][0], eta[1][1], eta[1][2], |
| 316 |
> |
eta[2][0], eta[2][1], eta[2][2] |
| 317 |
> |
); |
| 318 |
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|
| 319 |
< |
for(int i = 0; i < 3; i++){ |
| 312 |
< |
sprintf(buffer,"\t%lf\t%lf\t%lf;", eta[3*i], eta[3*i+1], eta[3*i+2]); |
| 313 |
< |
parameters += buffer; |
| 314 |
< |
} |
| 315 |
< |
|
| 316 |
< |
return parameters; |
| 317 |
< |
|
| 319 |
> |
return addParamBuffer; |
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} |
