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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/NPTxyz.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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// Basic non-isotropic thermostating and barostating via the Melchionna |
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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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> |
namespace OpenMD { |
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|
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|
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RealType NPTxyz::calcConservedQuantity(){ |
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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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RealType conservedQuantity; |
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RealType totalEnergy; |
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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 * thermostat.first |
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> |
/ (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 |
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/ PhysicalConstants::energyConvert; |
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|
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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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void NPTxyz::scaleSimBox(){ |
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|
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int i,j,k; |
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> |
int i, j; |
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Mat3x3d scaleMat; |
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RealType eta2ij, scaleFactor; |
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RealType bigScale, smallScale, offDiagMax; |
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> |
RealType scaleFactor; |
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> |
RealType bigScale, smallScale; |
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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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|
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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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simError(); |
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} else { |
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|
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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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|
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void NPTxyz::loadEta() { |
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< |
eta= currentSnapshot_->getEta(); |
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> |
eta= snap->getBarostat(); |
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} |
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|
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} |
