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#include <math.h> |
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< |
#include "MatVec3.h" |
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< |
#include "Atom.hpp" |
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< |
#include "SRI.hpp" |
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< |
#include "AbstractClasses.hpp" |
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< |
#include "SimInfo.hpp" |
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< |
#include "ForceFields.hpp" |
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< |
#include "Thermo.hpp" |
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< |
#include "ReadWrite.hpp" |
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< |
#include "Integrator.hpp" |
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< |
#include "simError.h" |
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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/NPTxyz.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 "mpiSimulation.hpp" |
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#endif |
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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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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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< |
template<typename T> NPTxyz<T>::NPTxyz ( 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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> |
namespace oopse { |
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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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> |
RealType NPTxyz::calcConservedQuantity(){ |
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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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} |
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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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if( theInfo->useInitXSstate ){ |
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RealType conservedQuantity; |
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RealType totalEnergy; |
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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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RealType trEta; |
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|
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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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} |
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} |
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> |
totalEnergy = thermo.getTotalE(); |
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|
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< |
template<typename T> NPTxyz<T>::~NPTxyz() { |
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> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
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|
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// empty for now |
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} |
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> |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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|
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< |
template<typename T> void NPTxyz<T>::resetIntegrator() { |
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> |
SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
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> |
trEta = tmp.trace(); |
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|
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< |
int i, j; |
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> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
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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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> |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
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|
| 96 |
< |
T::resetIntegrator(); |
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< |
} |
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> |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 97 |
> |
barostat_kinetic + barostat_potential; |
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|
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– |
template<typename T> void NPTxyz<T>::evolveEtaA() { |
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|
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< |
int i, j; |
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> |
return conservedQuantity; |
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|
| 85 |
– |
for(i = 0; i < 3; i ++){ |
| 86 |
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for(j = 0; j < 3; j++){ |
| 87 |
– |
if( i == j) |
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eta[i][j] += dt2 * instaVol * |
| 89 |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 90 |
– |
else |
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– |
eta[i][j] = 0.0; |
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– |
} |
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|
} |
| 103 |
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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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> |
void NPTxyz::scaleSimBox(){ |
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|
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< |
template<typename T> void NPTxyz<T>::evolveEtaB() { |
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> |
int i,j,k; |
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> |
Mat3x3d scaleMat; |
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> |
RealType eta2ij, scaleFactor; |
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> |
RealType bigScale, smallScale, offDiagMax; |
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> |
Mat3x3d hm; |
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> |
Mat3x3d hmnew; |
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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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prevEta[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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< |
if( i == j) { |
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< |
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 { |
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< |
eta[i][j] = 0.0; |
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< |
} |
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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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< |
template<typename T> void NPTxyz<T>::calcVelScale(void) { |
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< |
int i,j; |
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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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< |
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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> |
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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< |
if (i == j) { |
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< |
vScale[i][j] += chi; |
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> |
for(i=0; i<3; i++){ |
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> |
for(j=0; j<3; j++){ |
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> |
scaleMat(i, j) = 0.0; |
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> |
if(i==j) { |
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> |
scaleMat(i, j) = 1.0; |
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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> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) { |
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< |
matVecMul3( vScale, vel, sc ); |
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< |
} |
| 134 |
> |
for(i=0;i<3;i++){ |
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|
|
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< |
template<typename T> void NPTxyz<T>::getVelScaleB(double sc[3], int index ){ |
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< |
int j; |
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< |
double myVel[3]; |
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> |
// calculate the scaleFactors |
| 137 |
|
|
| 138 |
< |
for (j = 0; j < 3; j++) |
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< |
myVel[j] = oldVel[3*index + j]; |
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> |
scaleFactor = exp(dt*eta(i, i)); |
| 139 |
|
|
| 140 |
< |
matVecMul3( vScale, myVel, sc ); |
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< |
} |
| 140 |
> |
scaleMat(i, i) = scaleFactor; |
| 141 |
|
|
| 142 |
< |
template<typename T> void NPTxyz<T>::getPosScale(double pos[3], double COM[3], |
| 143 |
< |
int index, double sc[3]){ |
| 144 |
< |
int j; |
| 145 |
< |
double rj[3]; |
| 142 |
> |
if (scaleMat(i, i) > bigScale) { |
| 143 |
> |
bigScale = scaleMat(i, i); |
| 144 |
> |
} |
| 145 |
> |
|
| 146 |
> |
if (scaleMat(i, i) < smallScale) { |
| 147 |
> |
smallScale = scaleMat(i, i); |
| 148 |
> |
} |
| 149 |
> |
} |
| 150 |
|
|
| 151 |
< |
for(j=0; j<3; j++) |
| 152 |
< |
rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
| 151 |
> |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 152 |
> |
sprintf( painCave.errMsg, |
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> |
"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
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> |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 155 |
> |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 156 |
> |
" [%lf\t%lf\t%lf]\n" |
| 157 |
> |
" [%lf\t%lf\t%lf]\n", |
| 158 |
> |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
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> |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 160 |
> |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2)); |
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> |
painCave.isFatal = 1; |
| 162 |
> |
simError(); |
| 163 |
> |
} else { |
| 164 |
|
|
| 165 |
< |
matVecMul3( eta, rj, sc ); |
| 166 |
< |
} |
| 167 |
< |
|
| 159 |
< |
template<typename T> void NPTxyz<T>::scaleSimBox( void ){ |
| 160 |
< |
|
| 161 |
< |
int i,j,k; |
| 162 |
< |
double scaleMat[3][3]; |
| 163 |
< |
double eta2ij, scaleFactor; |
| 164 |
< |
double bigScale, smallScale, offDiagMax; |
| 165 |
< |
double hm[3][3], hmnew[3][3]; |
| 166 |
< |
|
| 167 |
< |
|
| 168 |
< |
|
| 169 |
< |
// Scale the box after all the positions have been moved: |
| 170 |
< |
|
| 171 |
< |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 172 |
< |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 173 |
< |
|
| 174 |
< |
bigScale = 1.0; |
| 175 |
< |
smallScale = 1.0; |
| 176 |
< |
offDiagMax = 0.0; |
| 177 |
< |
|
| 178 |
< |
for(i=0; i<3; i++){ |
| 179 |
< |
for(j=0; j<3; j++){ |
| 180 |
< |
scaleMat[i][j] = 0.0; |
| 181 |
< |
if(i==j) scaleMat[i][j] = 1.0; |
| 165 |
> |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 166 |
> |
hmat = hmat *scaleMat; |
| 167 |
> |
currentSnapshot_->setHmat(hmat); |
| 168 |
|
} |
| 169 |
|
} |
| 170 |
|
|
| 171 |
< |
for(i=0;i<3;i++){ |
| 172 |
< |
|
| 187 |
< |
// calculate the scaleFactors |
| 188 |
< |
|
| 189 |
< |
scaleFactor = exp(dt*eta[i][i]); |
| 190 |
< |
|
| 191 |
< |
scaleMat[i][i] = scaleFactor; |
| 192 |
< |
|
| 193 |
< |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 194 |
< |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 171 |
> |
void NPTxyz::loadEta() { |
| 172 |
> |
eta= currentSnapshot_->getEta(); |
| 173 |
|
} |
| 174 |
|
|
| 197 |
– |
// for(i=0; i<3; i++){ |
| 198 |
– |
// for(j=0; j<3; j++){ |
| 199 |
– |
|
| 200 |
– |
// // Calculate the matrix Product of the eta array (we only need |
| 201 |
– |
// // the ij element right now): |
| 202 |
– |
|
| 203 |
– |
// eta2ij = 0.0; |
| 204 |
– |
// for(k=0; k<3; k++){ |
| 205 |
– |
// eta2ij += eta[i][k] * eta[k][j]; |
| 206 |
– |
// } |
| 207 |
– |
|
| 208 |
– |
// scaleMat[i][j] = 0.0; |
| 209 |
– |
// // identity matrix (see above): |
| 210 |
– |
// if (i == j) scaleMat[i][j] = 1.0; |
| 211 |
– |
// // Taylor expansion for the exponential truncated at second order: |
| 212 |
– |
// scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 213 |
– |
|
| 214 |
– |
// if (i != j) |
| 215 |
– |
// if (fabs(scaleMat[i][j]) > offDiagMax) |
| 216 |
– |
// offDiagMax = fabs(scaleMat[i][j]); |
| 217 |
– |
// } |
| 218 |
– |
|
| 219 |
– |
// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 220 |
– |
// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 221 |
– |
// } |
| 222 |
– |
|
| 223 |
– |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 224 |
– |
sprintf( painCave.errMsg, |
| 225 |
– |
"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
| 226 |
– |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 227 |
– |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 228 |
– |
" [%lf\t%lf\t%lf]\n" |
| 229 |
– |
" [%lf\t%lf\t%lf]\n", |
| 230 |
– |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 231 |
– |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 232 |
– |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 233 |
– |
painCave.isFatal = 1; |
| 234 |
– |
simError(); |
| 235 |
– |
} else { |
| 236 |
– |
info->getBoxM(hm); |
| 237 |
– |
matMul3(hm, scaleMat, hmnew); |
| 238 |
– |
info->setBoxM(hmnew); |
| 239 |
– |
} |
| 175 |
|
} |
| 241 |
– |
|
| 242 |
– |
template<typename T> bool NPTxyz<T>::etaConverged() { |
| 243 |
– |
int i; |
| 244 |
– |
double diffEta, sumEta; |
| 245 |
– |
|
| 246 |
– |
sumEta = 0; |
| 247 |
– |
for(i = 0; i < 3; i++) |
| 248 |
– |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 249 |
– |
|
| 250 |
– |
diffEta = sqrt( sumEta / 3.0 ); |
| 251 |
– |
|
| 252 |
– |
return ( diffEta <= etaTolerance ); |
| 253 |
– |
} |
| 254 |
– |
|
| 255 |
– |
template<typename T> double NPTxyz<T>::getConservedQuantity(void){ |
| 256 |
– |
|
| 257 |
– |
double conservedQuantity; |
| 258 |
– |
double totalEnergy; |
| 259 |
– |
double thermostat_kinetic; |
| 260 |
– |
double thermostat_potential; |
| 261 |
– |
double barostat_kinetic; |
| 262 |
– |
double barostat_potential; |
| 263 |
– |
double trEta; |
| 264 |
– |
double a[3][3], b[3][3]; |
| 265 |
– |
|
| 266 |
– |
totalEnergy = tStats->getTotalE(); |
| 267 |
– |
|
| 268 |
– |
thermostat_kinetic = fkBT * tt2 * chi * chi / |
| 269 |
– |
(2.0 * eConvert); |
| 270 |
– |
|
| 271 |
– |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 272 |
– |
|
| 273 |
– |
transposeMat3(eta, a); |
| 274 |
– |
matMul3(a, eta, b); |
| 275 |
– |
trEta = matTrace3(b); |
| 276 |
– |
|
| 277 |
– |
barostat_kinetic = NkBT * tb2 * trEta / |
| 278 |
– |
(2.0 * eConvert); |
| 279 |
– |
|
| 280 |
– |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 281 |
– |
eConvert; |
| 282 |
– |
|
| 283 |
– |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 284 |
– |
barostat_kinetic + barostat_potential; |
| 285 |
– |
|
| 286 |
– |
// cout.width(8); |
| 287 |
– |
// cout.precision(8); |
| 288 |
– |
|
| 289 |
– |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 290 |
– |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 291 |
– |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 292 |
– |
|
| 293 |
– |
return conservedQuantity; |
| 294 |
– |
|
| 295 |
– |
} |
| 296 |
– |
|
| 297 |
– |
template<typename T> string NPTxyz<T>::getAdditionalParameters(void){ |
| 298 |
– |
string parameters; |
| 299 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 300 |
– |
char buffer[BUFFERSIZE]; |
| 301 |
– |
|
| 302 |
– |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 303 |
– |
parameters += buffer; |
| 304 |
– |
|
| 305 |
– |
for(int i = 0; i < 3; i++){ |
| 306 |
– |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 307 |
– |
parameters += buffer; |
| 308 |
– |
} |
| 309 |
– |
|
| 310 |
– |
return parameters; |
| 311 |
– |
|
| 312 |
– |
} |
