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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "brains/SimInfo.hpp" |
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#include "integrators/IntegratorCreator.hpp" |
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#include "integrators/NPAT.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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void NPAT::evolveEtaA() { |
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|
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< |
eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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> |
eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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oldEta = eta; |
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} |
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|
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|
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prevEta = eta; |
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eta(2,2) = oldEta(2, 2) + dt2 * instaVol * |
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(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} |
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|
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void NPAT::calcVelScale(){ |
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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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> |
vScale(i, j) += thermostat.first; |
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} |
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} |
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} |
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void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { |
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|
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/**@todo */ |
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Vector3d rj = (oldPos[index] + pos)/2.0 -COM; |
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> |
Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM; |
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sc = eta * rj; |
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} |
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|
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} |
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|
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scaleMat(2, 2) = exp(dt*eta(2, 2)); |
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< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
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> |
Mat3x3d hmat = snap->getHmat(); |
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hmat = hmat *scaleMat; |
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< |
currentSnapshot_->setHmat(hmat); |
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> |
snap->setHmat(hmat); |
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} |
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|
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bool NPAT::etaConverged() { |
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int i; |
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< |
double diffEta, sumEta; |
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> |
RealType 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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return ( diffEta <= etaTolerance ); |
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} |
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|
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< |
double NPAT::calcConservedQuantity(){ |
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> |
RealType NPAT::calcConservedQuantity(){ |
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|
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< |
chi= currentSnapshot_->getChi(); |
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< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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> |
thermostat = snap->getThermostat(); |
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loadEta(); |
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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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> |
NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::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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> |
fkBT = info_->getNdf()*PhysicalConstants::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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> |
RealType conservedQuantity; |
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> |
RealType totalEnergy; |
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> |
RealType thermostat_kinetic; |
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> |
RealType thermostat_potential; |
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> |
RealType barostat_kinetic; |
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> |
RealType barostat_potential; |
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> |
RealType trEta; |
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|
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< |
totalEnergy = thermo.getTotalE(); |
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> |
totalEnergy = thermo.getTotalEnergy(); |
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|
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< |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
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> |
thermostat_kinetic = fkBT * tt2 * thermostat.first * |
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> |
thermostat.first /(2.0 * PhysicalConstants::energyConvert); |
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|
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< |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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> |
thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
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|
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< |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
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> |
SquareMatrix<RealType, 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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> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
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|
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< |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
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> |
barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::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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void NPAT::loadEta() { |
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< |
eta= currentSnapshot_->getEta(); |
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> |
eta= snap->getBarostat(); |
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|
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|
//if (!eta.isDiagonal()) { |
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// sprintf( painCave.errMsg, |
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} |
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|
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void NPAT::saveEta() { |
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< |
currentSnapshot_->setEta(eta); |
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> |
snap->setBarostat(eta); |
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} |
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|
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} |
