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#include "brains/SimInfo.hpp" |
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#include "brains/Thermo.hpp" |
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#include "integrators/IntegratorCreator.hpp" |
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#include "integrators/NPTxyz.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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namespace oopse { |
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/* |
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NPTxyz::NPTxyz (SimInfo* info): NPT(info) { |
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GenericData* data; |
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DoubleVectorGenericData * etaValue; |
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int i,j; |
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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) = 0.0; |
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oldEta(i, j) = 0.0; |
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} |
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} |
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if( theInfo->useInitXSstate ){ |
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// retrieve eta array from simInfo if it exists |
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data = info->getPropertyByName(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleVectorGenericData*>(data); |
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if(etaValue){ |
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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) = (*etaValue)[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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} |
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} |
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} |
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} |
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void NPTxyz::evolveEtaA() { |
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int i, j; |
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta(i, j) += dt2 * instaVol *(press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) = 0.0; |
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} |
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} |
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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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oldEta(i, j) = eta(i, j); |
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} |
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} |
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static IntegratorBuilder<NPTxyz>* NPTxyzCreator = new IntegratorBuilder<NPTxyz>("NPTxyz"); |
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} |
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void NPTxyz::evolveEtaB() { |
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int i,j; |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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prevEta(i, j) = eta(i, j); |
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * |
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(press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) = 0.0; |
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} |
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} |
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} |
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} |
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void NPTxyz::calcVelScale(void) { |
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int i,j; |
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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale(i, j) = eta(i, j); |
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if (i == j) { |
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vScale(i, j) += chi; |
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} |
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} |
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} |
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} |
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void NPTxyz::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
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sc = vScale * vel; |
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} |
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void NPTxyz::getVelScaleB(Vector3d& sc, int index ) { |
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sc = vScale * oldVel[index]; |
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} |
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void NPTxyz::getPosScale(const Vector3d& pos, const Vector3d& COM, |
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int index, Vector3d& sc) { |
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Vector3d rj = (oldPos[index] + pos[j])/2.0 -COM; |
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sc = eta * rj; |
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} |
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bool NPTxyz::etaConverged() { |
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int i; |
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double diffEta, sumEta; |
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sumEta = 0; |
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for(i = 0; i < 3; i++) |
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sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
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diffEta = sqrt( sumEta / 3.0 ); |
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return ( diffEta <= etaTolerance ); |
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} |
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*/ |
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double NPTxyz::calcConservedQuantity(){ |
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double conservedQuantity; |
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} |
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} |
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void NPTxyz::loadEta() { |
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eta= currentSnapshot_->getEta(); |
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} |
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} |
