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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 "brains/SimInfo.hpp" |
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#include "integrators/IntegratorCreator.hpp" |
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#include "integrators/NPTf.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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// 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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// 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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void NPTf::evolveEtaA() { |
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void NPTf::evolveEtaA() { |
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|
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int i, j; |
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int i, j; |
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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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if( i == j) { |
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eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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} |
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} |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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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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for (j = 0; j < 3; j++) { |
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for (j = 0; j < 3; j++) { |
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oldEta(i, j) = eta(i, j); |
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} |
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} |
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} |
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|
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} |
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} |
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|
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void NPTf::evolveEtaB() { |
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void NPTf::evolveEtaB() { |
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|
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int i; |
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int j; |
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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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prevEta(i, j) = eta(i, j); |
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} |
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for (j = 0; j < 3; j++) { |
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prevEta(i, j) = eta(i, j); |
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} |
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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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if( i == j) { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * |
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(press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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} |
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} |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * |
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(press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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} |
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} |
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} |
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} |
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} |
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void NPTf::calcVelScale(){ |
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void NPTf::calcVelScale(){ |
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for (int i = 0; i < 3; i++ ) { |
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for (int j = 0; j < 3; j++ ) { |
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vScale(i, j) = eta(i, j); |
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for (int i = 0; i < 3; i++ ) { |
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for (int j = 0; j < 3; j++ ) { |
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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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if (i == j) { |
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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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} |
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} |
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void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ |
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void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ |
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sc = vScale * vel; |
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} |
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} |
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void NPTf::getVelScaleB(Vector3d& sc, int index ) { |
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sc = vScale * oldVel[index]; |
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} |
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void NPTf::getVelScaleB(Vector3d& sc, int index ) { |
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sc = vScale * oldVel[index]; |
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} |
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void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { |
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void NPTf::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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void NPTf::scaleSimBox(){ |
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void NPTf::scaleSimBox(){ |
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int i; |
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int j; |
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int k; |
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Mat3x3d scaleMat; |
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double eta2ij; |
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double bigScale, smallScale, offDiagMax; |
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Mat3x3d hm; |
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Mat3x3d hmnew; |
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int i; |
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int j; |
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int k; |
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Mat3x3d scaleMat; |
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RealType eta2ij; |
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RealType bigScale, smallScale, offDiagMax; |
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Mat3x3d hm; |
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Mat3x3d hmnew; |
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// Scale the box after all the positions have been moved: |
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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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// 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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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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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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// Calculate the matrix Product of the eta array (we only need |
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// the ij element right now): |
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// Calculate the matrix Product of the eta array (we only need |
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// the ij element right now): |
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|
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eta2ij = 0.0; |
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for(k=0; k<3; k++){ |
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eta2ij += eta(i, k) * eta(k, j); |
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} |
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eta2ij = 0.0; |
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for(k=0; k<3; k++){ |
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eta2ij += eta(i, k) * eta(k, j); |
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} |
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|
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scaleMat(i, j) = 0.0; |
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// identity matrix (see above): |
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if (i == j) scaleMat(i, j) = 1.0; |
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// Taylor expansion for the exponential truncated at second order: |
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scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
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scaleMat(i, j) = 0.0; |
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// identity matrix (see above): |
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if (i == j) scaleMat(i, j) = 1.0; |
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// Taylor expansion for the exponential truncated at second order: |
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scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
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if (i != j) |
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if (fabs(scaleMat(i, j)) > offDiagMax) |
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offDiagMax = fabs(scaleMat(i, j)); |
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if (i != j) |
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if (fabs(scaleMat(i, j)) > offDiagMax) |
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offDiagMax = fabs(scaleMat(i, j)); |
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} |
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|
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if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
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if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
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} |
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|
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< |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
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if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
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< |
} |
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if ((bigScale > 1.01) || (smallScale < 0.99)) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting a Box scaling of more than 1 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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" eta = [%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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> |
eta(0, 0),eta(0, 1),eta(0, 2), |
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> |
eta(1, 0),eta(1, 1),eta(1, 2), |
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> |
eta(2, 0),eta(2, 1),eta(2, 2)); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} else if (offDiagMax > 0.01) { |
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sprintf( painCave.errMsg, |
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> |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 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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> |
" eta = [%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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> |
eta(0, 0),eta(0, 1),eta(0, 2), |
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> |
eta(1, 0),eta(1, 1),eta(1, 2), |
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> |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 221 |
> |
painCave.isFatal = 1; |
| 222 |
> |
simError(); |
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> |
} else { |
| 224 |
|
|
| 225 |
< |
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
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< |
sprintf( painCave.errMsg, |
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< |
"NPTf error: Attempting a Box scaling of more than 1 percent.\n" |
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< |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 190 |
< |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 191 |
< |
" [%lf\t%lf\t%lf]\n" |
| 192 |
< |
" [%lf\t%lf\t%lf]\n" |
| 193 |
< |
" eta = [%lf\t%lf\t%lf]\n" |
| 194 |
< |
" [%lf\t%lf\t%lf]\n" |
| 195 |
< |
" [%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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< |
eta(0, 0),eta(0, 1),eta(0, 2), |
| 200 |
< |
eta(1, 0),eta(1, 1),eta(1, 2), |
| 201 |
< |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 202 |
< |
painCave.isFatal = 1; |
| 203 |
< |
simError(); |
| 204 |
< |
} else if (offDiagMax > 0.01) { |
| 205 |
< |
sprintf( painCave.errMsg, |
| 206 |
< |
"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n" |
| 207 |
< |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 208 |
< |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 209 |
< |
" [%lf\t%lf\t%lf]\n" |
| 210 |
< |
" [%lf\t%lf\t%lf]\n" |
| 211 |
< |
" eta = [%lf\t%lf\t%lf]\n" |
| 212 |
< |
" [%lf\t%lf\t%lf]\n" |
| 213 |
< |
" [%lf\t%lf\t%lf]\n", |
| 214 |
< |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 215 |
< |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 216 |
< |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
| 217 |
< |
eta(0, 0),eta(0, 1),eta(0, 2), |
| 218 |
< |
eta(1, 0),eta(1, 1),eta(1, 2), |
| 219 |
< |
eta(2, 0),eta(2, 1),eta(2, 2)); |
| 220 |
< |
painCave.isFatal = 1; |
| 221 |
< |
simError(); |
| 222 |
< |
} else { |
| 223 |
< |
|
| 224 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 225 |
< |
hmat = hmat *scaleMat; |
| 226 |
< |
currentSnapshot_->setHmat(hmat); |
| 225 |
> |
Mat3x3d hmat = snap->getHmat(); |
| 226 |
> |
hmat = hmat *scaleMat; |
| 227 |
> |
snap->setHmat(hmat); |
| 228 |
|
|
| 229 |
+ |
} |
| 230 |
|
} |
| 229 |
– |
} |
| 231 |
|
|
| 232 |
< |
bool NPTf::etaConverged() { |
| 232 |
> |
bool NPTf::etaConverged() { |
| 233 |
|
int i; |
| 234 |
< |
double diffEta, sumEta; |
| 234 |
> |
RealType diffEta, sumEta; |
| 235 |
|
|
| 236 |
|
sumEta = 0; |
| 237 |
|
for(i = 0; i < 3; i++) { |
| 238 |
< |
sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
| 238 |
> |
sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
| 239 |
|
} |
| 240 |
|
|
| 241 |
|
diffEta = sqrt( sumEta / 3.0 ); |
| 242 |
|
|
| 243 |
|
return ( diffEta <= etaTolerance ); |
| 244 |
< |
} |
| 244 |
> |
} |
| 245 |
|
|
| 246 |
< |
double NPTf::calcConservedQuantity(){ |
| 247 |
< |
|
| 248 |
< |
chi= currentSnapshot_->getChi(); |
| 248 |
< |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 246 |
> |
RealType NPTf::calcConservedQuantity(){ |
| 247 |
> |
|
| 248 |
> |
thermostat = snap->getThermostat(); |
| 249 |
|
loadEta(); |
| 250 |
|
|
| 251 |
|
// We need NkBT a lot, so just set it here: This is the RAW number |
| 252 |
|
// of integrableObjects, so no subtraction or addition of constraints or |
| 253 |
|
// orientational degrees of freedom: |
| 254 |
< |
NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
| 254 |
> |
NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp; |
| 255 |
|
|
| 256 |
|
// fkBT is used because the thermostat operates on more degrees of freedom |
| 257 |
|
// than the barostat (when there are particles with orientational degrees |
| 258 |
|
// of freedom). |
| 259 |
< |
fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
| 259 |
> |
fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; |
| 260 |
|
|
| 261 |
< |
double conservedQuantity; |
| 262 |
< |
double totalEnergy; |
| 263 |
< |
double thermostat_kinetic; |
| 264 |
< |
double thermostat_potential; |
| 265 |
< |
double barostat_kinetic; |
| 266 |
< |
double barostat_potential; |
| 267 |
< |
double trEta; |
| 261 |
> |
RealType conservedQuantity; |
| 262 |
> |
RealType totalEnergy; |
| 263 |
> |
RealType thermostat_kinetic; |
| 264 |
> |
RealType thermostat_potential; |
| 265 |
> |
RealType barostat_kinetic; |
| 266 |
> |
RealType barostat_potential; |
| 267 |
> |
RealType trEta; |
| 268 |
|
|
| 269 |
< |
totalEnergy = thermo.getTotalE(); |
| 269 |
> |
totalEnergy = thermo.getTotalEnergy(); |
| 270 |
> |
|
| 271 |
> |
thermostat_kinetic = fkBT * tt2 * thermostat.first * |
| 272 |
> |
thermostat.first /(2.0 * PhysicalConstants::energyConvert); |
| 273 |
|
|
| 274 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 274 |
> |
thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert; |
| 275 |
|
|
| 276 |
< |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 274 |
< |
|
| 275 |
< |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
| 276 |
> |
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
| 277 |
|
trEta = tmp.trace(); |
| 278 |
|
|
| 279 |
< |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
| 279 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
| 280 |
|
|
| 281 |
< |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
| 281 |
> |
barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; |
| 282 |
|
|
| 283 |
|
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 284 |
< |
barostat_kinetic + barostat_potential; |
| 284 |
> |
barostat_kinetic + barostat_potential; |
| 285 |
|
|
| 286 |
|
return conservedQuantity; |
| 287 |
|
|
| 288 |
< |
} |
| 288 |
> |
} |
| 289 |
|
|
| 290 |
< |
void NPTf::loadEta() { |
| 291 |
< |
eta= currentSnapshot_->getEta(); |
| 290 |
> |
void NPTf::loadEta() { |
| 291 |
> |
eta= snap->getBarostat(); |
| 292 |
|
|
| 293 |
|
//if (!eta.isDiagonal()) { |
| 294 |
|
// sprintf( painCave.errMsg, |
| 296 |
|
// painCave.isFatal = 1; |
| 297 |
|
// simError(); |
| 298 |
|
//} |
| 299 |
< |
} |
| 299 |
> |
} |
| 300 |
|
|
| 301 |
< |
void NPTf::saveEta() { |
| 302 |
< |
currentSnapshot_->setEta(eta); |
| 303 |
< |
} |
| 301 |
> |
void NPTf::saveEta() { |
| 302 |
> |
snap->setBarostat(eta); |
| 303 |
> |
} |
| 304 |
|
|
| 305 |
|
} |
