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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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* non-exclusive, royalty free, license to use, modify and |
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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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* 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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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|
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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/NPAT.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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namespace oopse { |
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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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oldEta = eta; |
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} |
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|
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void NPAT::evolveEtaB() { |
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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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} |
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|
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void NPAT::calcVelScale(){ |
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|
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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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} |
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} |
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} |
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} |
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|
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void NPAT::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 NPAT::getVelScaleB(Vector3d& sc, int index ) { |
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sc = vScale * oldVel[index]; |
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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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sc = eta * rj; |
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} |
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|
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void NPAT::scaleSimBox(){ |
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|
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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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|
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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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|
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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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|
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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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|
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|
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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 ((bigScale > 1.01) || (smallScale < 0.99)) { |
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sprintf( painCave.errMsg, |
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"NPAT 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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"NPAT 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)); |
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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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|
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bool NPAT::etaConverged() { |
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int i; |
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double 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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sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
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} |
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|
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diffEta = sqrt( sumEta / 3.0 ); |
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|
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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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|
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chi= currentSnapshot_->getChi(); |
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integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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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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|
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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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return conservedQuantity; |
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|
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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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|
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//if (!eta.isDiagonal()) { |
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// sprintf( painCave.errMsg, |
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// "NPAT 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 NPAT::saveEta() { |
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currentSnapshot_->setEta(eta); |
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} |
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|
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} |
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|
