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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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#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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static IntegratorBuilder<NPTxyz>* NPTxyzCreator = new IntegratorBuilder<NPTxyz>("NPTxyz"); |
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|
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double NPTxyz::calcConservedQuantity(){ |
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|
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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 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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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) { |
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scaleMat(i, j) = 1.0; |
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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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|
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// calculate the scaleFactors |
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scaleFactor = exp(dt*eta(i, i)); |
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scaleMat(i, i) = scaleFactor; |
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if (scaleMat(i, i) > bigScale) { |
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bigScale = scaleMat(i, i); |
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} |
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if (scaleMat(i, i) < smallScale) { |
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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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void NPTxyz::loadEta() { |
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eta= currentSnapshot_->getEta(); |
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} |
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|
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} |
