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#include <math.h> |
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< |
|
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< |
#include "math/MatVec3.h" |
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< |
#include "primitives/Atom.hpp" |
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< |
#include "primitives/SRI.hpp" |
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< |
#include "primitives/AbstractClasses.hpp" |
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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 "UseTheForce/ForceFields.hpp" |
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#include "brains/Thermo.hpp" |
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< |
#include "io/ReadWrite.hpp" |
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< |
#include "integrators/Integrator.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/simError.h" |
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|
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< |
#ifdef IS_MPI |
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#include "brains/mpiSimulation.hpp" |
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< |
#endif |
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> |
namespace oopse { |
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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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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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< |
template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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DoubleArrayData * etaValue; |
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vector<double> etaArray; |
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int i,j; |
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> |
void NPTf::evolveEtaA() { |
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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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> |
int i, j; |
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|
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< |
eta[i][j] = 0.0; |
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< |
oldEta[i][j] = 0.0; |
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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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} |
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} |
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|
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|
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if( theInfo->useInitXSstate ){ |
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// retrieve eta array from simInfo if it exists |
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data = info->getProperty(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleArrayData*>(data); |
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|
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if(etaValue){ |
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etaArray = etaValue->getData(); |
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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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eta[i][j] = etaArray[3*i+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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for(i = 0; i < 3; i++) { |
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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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< |
template<typename T> NPTf<T>::~NPTf() { |
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> |
void NPTf::evolveEtaB() { |
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|
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// empty for now |
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} |
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int i; |
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> |
int j; |
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|
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< |
template<typename T> void NPTf<T>::resetIntegrator() { |
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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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} |
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|
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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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< |
eta[i][j] = 0.0; |
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|
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T::resetIntegrator(); |
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} |
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< |
|
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< |
template<typename T> void NPTf<T>::evolveEtaA() { |
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< |
|
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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++){ |
| 88 |
< |
if( i == j) |
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< |
eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (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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> |
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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} |
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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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– |
oldEta[i][j] = eta[i][j]; |
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} |
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|
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< |
template<typename T> void NPTf<T>::evolveEtaB() { |
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> |
void NPTf::calcVelScale(){ |
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|
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< |
int 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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< |
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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< |
|
| 109 |
< |
for(i = 0; i < 3; i ++){ |
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< |
for(j = 0; j < 3; j++){ |
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< |
if( i == j) { |
| 112 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
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< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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< |
} else { |
| 115 |
< |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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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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< |
template<typename T> void NPTf<T>::calcVelScale(void){ |
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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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< |
vScale[i][j] = eta[i][j]; |
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< |
|
| 128 |
< |
if (i == j) { |
| 129 |
< |
vScale[i][j] += chi; |
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< |
} |
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< |
} |
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< |
} |
| 122 |
> |
void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ |
| 123 |
> |
sc = vScale * vel; |
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|
} |
| 125 |
|
|
| 126 |
< |
template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
| 127 |
< |
|
| 137 |
< |
matVecMul3( vScale, vel, sc ); |
| 126 |
> |
void NPTf::getVelScaleB(Vector3d& sc, int index ) { |
| 127 |
> |
sc = vScale * oldVel[index]; |
| 128 |
|
} |
| 129 |
|
|
| 130 |
< |
template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){ |
| 141 |
< |
int j; |
| 142 |
< |
double myVel[3]; |
| 130 |
> |
void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { |
| 131 |
|
|
| 132 |
< |
for (j = 0; j < 3; j++) |
| 133 |
< |
myVel[j] = oldVel[3*index + j]; |
| 134 |
< |
|
| 147 |
< |
matVecMul3( vScale, myVel, sc ); |
| 132 |
> |
/**@todo */ |
| 133 |
> |
Vector3d rj = (oldPos[index] + pos)/2.0 -COM; |
| 134 |
> |
sc = eta * rj; |
| 135 |
|
} |
| 136 |
|
|
| 137 |
< |
template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3], |
| 151 |
< |
int index, double sc[3]){ |
| 152 |
< |
int j; |
| 153 |
< |
double rj[3]; |
| 137 |
> |
void NPTf::scaleSimBox(){ |
| 138 |
|
|
| 139 |
< |
for(j=0; j<3; j++) |
| 140 |
< |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 141 |
< |
|
| 142 |
< |
matVecMul3( eta, rj, sc ); |
| 159 |
< |
} |
| 160 |
< |
|
| 161 |
< |
template<typename T> void NPTf<T>::scaleSimBox( void ){ |
| 162 |
< |
|
| 163 |
< |
int i,j,k; |
| 164 |
< |
double scaleMat[3][3]; |
| 139 |
> |
int i; |
| 140 |
> |
int j; |
| 141 |
> |
int k; |
| 142 |
> |
Mat3x3d scaleMat; |
| 143 |
|
double eta2ij; |
| 144 |
|
double bigScale, smallScale, offDiagMax; |
| 145 |
< |
double hm[3][3], hmnew[3][3]; |
| 145 |
> |
Mat3x3d hm; |
| 146 |
> |
Mat3x3d hmnew; |
| 147 |
|
|
| 148 |
|
|
| 149 |
|
|
| 164 |
|
|
| 165 |
|
eta2ij = 0.0; |
| 166 |
|
for(k=0; k<3; k++){ |
| 167 |
< |
eta2ij += eta[i][k] * eta[k][j]; |
| 167 |
> |
eta2ij += eta(i, k) * eta(k, j); |
| 168 |
|
} |
| 169 |
|
|
| 170 |
< |
scaleMat[i][j] = 0.0; |
| 170 |
> |
scaleMat(i, j) = 0.0; |
| 171 |
|
// identity matrix (see above): |
| 172 |
< |
if (i == j) scaleMat[i][j] = 1.0; |
| 172 |
> |
if (i == j) scaleMat(i, j) = 1.0; |
| 173 |
|
// Taylor expansion for the exponential truncated at second order: |
| 174 |
< |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 174 |
> |
scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
| 175 |
|
|
| 176 |
|
|
| 177 |
|
if (i != j) |
| 178 |
< |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 179 |
< |
offDiagMax = fabs(scaleMat[i][j]); |
| 178 |
> |
if (fabs(scaleMat(i, j)) > offDiagMax) |
| 179 |
> |
offDiagMax = fabs(scaleMat(i, j)); |
| 180 |
|
} |
| 181 |
|
|
| 182 |
< |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 183 |
< |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 182 |
> |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
| 183 |
> |
if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
| 184 |
|
} |
| 185 |
|
|
| 186 |
|
if ((bigScale > 1.01) || (smallScale < 0.99)) { |
| 193 |
|
" eta = [%lf\t%lf\t%lf]\n" |
| 194 |
|
" [%lf\t%lf\t%lf]\n" |
| 195 |
|
" [%lf\t%lf\t%lf]\n", |
| 196 |
< |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 197 |
< |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 198 |
< |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2], |
| 199 |
< |
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]); |
| 196 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 197 |
> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 198 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2), |
| 199 |
> |
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) { |
| 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]); |
| 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 |
< |
info->getBoxM(hm); |
| 224 |
< |
matMul3(hm, scaleMat, hmnew); |
| 225 |
< |
info->setBoxM(hmnew); |
| 223 |
> |
|
| 224 |
> |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 225 |
> |
hmat = hmat *scaleMat; |
| 226 |
> |
currentSnapshot_->setHmat(hmat); |
| 227 |
> |
|
| 228 |
|
} |
| 229 |
|
} |
| 230 |
|
|
| 231 |
< |
template<typename T> bool NPTf<T>::etaConverged() { |
| 232 |
< |
int i; |
| 233 |
< |
double diffEta, sumEta; |
| 231 |
> |
bool NPTf::etaConverged() { |
| 232 |
> |
int i; |
| 233 |
> |
double diffEta, sumEta; |
| 234 |
|
|
| 235 |
< |
sumEta = 0; |
| 236 |
< |
for(i = 0; i < 3; i++) |
| 237 |
< |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 235 |
> |
sumEta = 0; |
| 236 |
> |
for(i = 0; i < 3; i++) { |
| 237 |
> |
sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
> |
diffEta = sqrt( sumEta / 3.0 ); |
| 241 |
|
|
| 242 |
< |
diffEta = sqrt( sumEta / 3.0 ); |
| 259 |
< |
|
| 260 |
< |
return ( diffEta <= etaTolerance ); |
| 242 |
> |
return ( diffEta <= etaTolerance ); |
| 243 |
|
} |
| 244 |
|
|
| 245 |
< |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 245 |
> |
double NPTf::calcConservedQuantity(){ |
| 246 |
|
|
| 247 |
< |
double conservedQuantity; |
| 248 |
< |
double totalEnergy; |
| 249 |
< |
double thermostat_kinetic; |
| 250 |
< |
double thermostat_potential; |
| 251 |
< |
double barostat_kinetic; |
| 252 |
< |
double barostat_potential; |
| 253 |
< |
double trEta; |
| 254 |
< |
double a[3][3], b[3][3]; |
| 247 |
> |
chi= currentSnapshot_->getChi(); |
| 248 |
> |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 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; |
| 255 |
|
|
| 256 |
< |
totalEnergy = tStats->getTotalE(); |
| 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; |
| 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; |
| 268 |
|
|
| 269 |
< |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 277 |
< |
(2.0 * eConvert); |
| 269 |
> |
totalEnergy = thermo.getTotalE(); |
| 270 |
|
|
| 271 |
< |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 271 |
> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
| 272 |
|
|
| 273 |
< |
transposeMat3(eta, a); |
| 282 |
< |
matMul3(a, eta, b); |
| 283 |
< |
trEta = matTrace3(b); |
| 273 |
> |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
| 274 |
|
|
| 275 |
< |
barostat_kinetic = NkBT * tb2 * trEta / |
| 276 |
< |
(2.0 * eConvert); |
| 275 |
> |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
| 276 |
> |
trEta = tmp.trace(); |
| 277 |
> |
|
| 278 |
> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
| 279 |
|
|
| 280 |
< |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 289 |
< |
eConvert; |
| 280 |
> |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
| 281 |
|
|
| 282 |
< |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 283 |
< |
barostat_kinetic + barostat_potential; |
| 282 |
> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 283 |
> |
barostat_kinetic + barostat_potential; |
| 284 |
|
|
| 285 |
< |
return conservedQuantity; |
| 285 |
> |
return conservedQuantity; |
| 286 |
|
|
| 287 |
|
} |
| 288 |
|
|
| 289 |
< |
template<typename T> string NPTf<T>::getAdditionalParameters(void){ |
| 290 |
< |
string parameters; |
| 300 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 301 |
< |
char buffer[BUFFERSIZE]; |
| 289 |
> |
void NPTf::loadEta() { |
| 290 |
> |
eta= currentSnapshot_->getEta(); |
| 291 |
|
|
| 292 |
< |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 293 |
< |
parameters += buffer; |
| 292 |
> |
//if (!eta.isDiagonal()) { |
| 293 |
> |
// sprintf( painCave.errMsg, |
| 294 |
> |
// "NPTf error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix"); |
| 295 |
> |
// painCave.isFatal = 1; |
| 296 |
> |
// simError(); |
| 297 |
> |
//} |
| 298 |
> |
} |
| 299 |
|
|
| 300 |
< |
for(int i = 0; i < 3; i++){ |
| 301 |
< |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 302 |
< |
parameters += buffer; |
| 309 |
< |
} |
| 300 |
> |
void NPTf::saveEta() { |
| 301 |
> |
currentSnapshot_->setEta(eta); |
| 302 |
> |
} |
| 303 |
|
|
| 311 |
– |
return parameters; |
| 312 |
– |
|
| 304 |
|
} |
