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#include "NPTi.hpp" |
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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/NPT.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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namespace oopse { |
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|
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static IntegratorBuilder<NPTi>* NPTiCreator = new IntegratorBuilder<NPTi>("NPTi"); |
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|
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// Basic 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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NPTi::NPTi ( SimInfo *info) : NPT(info){ |
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|
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} |
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|
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void NPTi::evolveEtaA() { |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(OOPSEConstant::pressureConvert*NkBT*tb2)); |
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oldEta = eta; |
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} |
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|
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void NPTi::evolveEtaB() { |
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|
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prevEta = eta; |
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eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
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(OOPSEConstant::pressureConvert*NkBT*tb2)); |
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} |
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|
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void NPTi::calcVelScale() { |
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vScale = chi + eta; |
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} |
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|
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void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
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sc = vel * vScale; |
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} |
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|
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void NPTi::getVelScaleB(Vector3d& sc, int index ){ |
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sc = oldVel[index] * vScale; |
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} |
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|
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|
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void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, |
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int index, Vector3d& sc){ |
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/**@todo*/ |
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sc = oldPos[index] + pos/2.0 -COM; |
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sc *= eta; |
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} |
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|
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void NPTi::scaleSimBox(){ |
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|
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double scaleFactor; |
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|
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scaleFactor = exp(dt*eta); |
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|
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTi error: Attempting a Box scaling of more than 10 percent" |
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" check your tauBarostat, as it is probably too small!\n" |
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" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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hmat *= scaleFactor; |
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currentSnapshot_->setHmat(hmat); |
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} |
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|
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} |
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|
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bool NPTi::etaConverged() { |
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|
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return ( fabs(prevEta - eta) <= etaTolerance ); |
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} |
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|
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double NPTi::calcConservedQuantity(){ |
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|
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chi= currentSnapshot_->getChi(); |
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integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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loadEta(); |
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
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// than the barostat (when there are particles with orientational degrees |
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// of freedom). |
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fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
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|
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double conservedQuantity; |
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double Energy; |
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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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|
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Energy =thermo.getTotalE(); |
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thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
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thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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|
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barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert); |
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|
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barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) / |
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OOPSEConstant::energyConvert; |
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|
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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std::cout << "--------------------------------------------------------------" << std::endl; |
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std::cout << "time: " << currentSnapshot_->getTime() << std:: endl; |
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std::cout << "chi : " << chi << std::endl; |
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std::cout << "integralOfChidt : " << integralOfChidt << std::endl; |
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std::cout << "eta : " << eta << std::endl; |
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std::cout << "NkBT: " << NkBT << std::endl; |
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std::cout << "fkBT: " << fkBT << std::endl; |
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std::cout << "thermostat_kinetic : " << thermostat_kinetic<< std::endl; |
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std::cout << "thermostat_potential : " << thermostat_potential << std::endl; |
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std::cout << "barostat_kinetic : " << barostat_kinetic << std::endl; |
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std::cout << "barostat_potential : " << barostat_potential << std::endl; |
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std::cout << "Total Energy: " << Energy << std::endl; |
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std::cout << "Conserved Quantity: " << conservedQuantity <<std::endl; |
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std::cout << "--------------------------------------------------------------" << std::endl; |
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return conservedQuantity; |
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} |
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|
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void NPTi::loadEta() { |
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Mat3x3d etaMat = currentSnapshot_->getEta(); |
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eta = etaMat(0,0); |
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if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) { |
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sprintf( painCave.errMsg, |
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"NPTi error: the diagonal elements of are eta matrix is not same or etaMat is not a diagonal matrix"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void NPTi::saveEta() { |
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Mat3x3d etaMat(0.0); |
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etaMat(0, 0) = eta; |
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etaMat(1, 1) = eta; |
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etaMat(2, 2) = eta; |
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currentSnapshot_->setEta(etaMat); |
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} |
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|
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} |
