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#include "brains/SimInfo.hpp" |
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#include "brains/Thermo.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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#include "utils/simError.h" |
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|
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// Basic non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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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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|
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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|
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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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|
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|
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if( theInfo->useInitXSstate ){ |
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|
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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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|
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if(etaValue){ |
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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) = (*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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|
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|
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|
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void NPTxyz::evolveEtaA() { |
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|
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int i, j; |
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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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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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|
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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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|
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} |
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|
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void NPTxyz::evolveEtaB() { |
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|
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int i,j; |
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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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prevEta(i, j) = eta(i, j); |
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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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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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|
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void NPTxyz::calcVelScale(void) { |
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int i,j; |
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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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vScale(i, j) = eta(i, j); |
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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bool NPTxyz::etaConverged() { |
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int i; |
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double diffEta, sumEta; |
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|
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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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|
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diffEta = sqrt( sumEta / 3.0 ); |
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|
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return ( diffEta <= etaTolerance ); |
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} |
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|
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*/ |
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|
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double NPTxyz::calcConservedQuantity(){ |
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|
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double conservedQuantity; |
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double totalEnergy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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double barostat_kinetic; |
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double barostat_potential; |
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double trEta; |
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|
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totalEnergy = thermo.getTotalE(); |
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|
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thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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|
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SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
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trEta = tmp.trace(); |
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|
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barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
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|
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barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
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|
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conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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|
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return conservedQuantity; |
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|
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} |
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|
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|
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void NPTxyz::scaleSimBox(){ |
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|
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int i,j,k; |
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Mat3x3d scaleMat; |
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double eta2ij, scaleFactor; |
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double bigScale, smallScale, offDiagMax; |
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Mat3x3d hm; |
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Mat3x3d hmnew; |
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|
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|
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|
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// Scale the box after all the positions have been moved: |
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|
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// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
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// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
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|
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bigScale = 1.0; |
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smallScale = 1.0; |
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offDiagMax = 0.0; |
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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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scaleMat(i, j) = 0.0; |
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if(i==j) scaleMat(i, j) = 1.0; |
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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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|
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// calculate the scaleFactors |
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|
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scaleFactor = exp(dt*eta(i, i)); |
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|
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scaleMat(i, i) = scaleFactor; |
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|
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if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
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if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
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} |
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|
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
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scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
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scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2)); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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|
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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hmat = hmat *scaleMat; |
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currentSnapshot_->setHmat(hmat); |
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} |
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} |
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|
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} |
