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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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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, 234107 (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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#include "NPTi.hpp" |
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#include "brains/Thermo.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/PhysicalConstants.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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namespace OpenMD { |
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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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// 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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NPTi::NPTi ( SimInfo *info) : NPT(info){ |
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NPTi::NPTi ( SimInfo *info) : NPT(info){ |
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} |
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} |
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void NPTi::evolveEtaA() { |
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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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(PhysicalConstants::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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void NPTi::evolveEtaB() { |
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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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(PhysicalConstants::pressureConvert*NkBT*tb2)); |
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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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void NPTi::calcVelScale() { |
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vScale = thermostat.first + eta; |
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} |
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void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
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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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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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void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, |
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int index, Vector3d& sc){ |
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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 = (oldPos[index] + pos)/(RealType)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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void NPTi::scaleSimBox(){ |
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double scaleFactor; |
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RealType scaleFactor; |
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scaleFactor = exp(dt*eta); |
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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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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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Mat3x3d hmat = snap->getHmat(); |
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hmat *= scaleFactor; |
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snap->setHmat(hmat); |
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} |
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} |
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} |
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bool NPTi::etaConverged() { |
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bool NPTi::etaConverged() { |
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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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RealType NPTi::calcConservedQuantity(){ |
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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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// 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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// 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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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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RealType conservedQuantity; |
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RealType Energy; |
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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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Energy =thermo.getTotalE(); |
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Energy =thermo.getTotalEnergy(); |
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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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thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
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barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert); |
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barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert); |
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barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) / |
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OOPSEConstant::energyConvert; |
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barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) / |
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PhysicalConstants::energyConvert; |
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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barostat_kinetic + barostat_potential; |
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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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void NPTi::loadEta() { |
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Mat3x3d etaMat = snap->getBarostat(); |
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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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//if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) { |
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// sprintf( painCave.errMsg, |
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// "NPTi error: the diagonal elements of eta matrix are not the 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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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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snap->setBarostat(etaMat); |
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} |
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} |
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– |
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} |
