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#include <math.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 "NPTi.hpp" |
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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/NPT.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 isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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// Basic isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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template<typename T> NPTi<T>::NPTi ( 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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NPTi::NPTi ( SimInfo *info) : NPT(info){ |
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|
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eta = 0.0; |
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oldEta = 0.0; |
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} |
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|
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if( theInfo->useInitXSstate ){ |
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// retrieve eta from simInfo if |
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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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eta = etaArray[0]; |
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oldEta = eta; |
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} |
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} |
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void NPTi::evolveEtaA() { |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(OOPSEConstant::pressureConvert*NkBT*tb2)); |
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oldEta = eta; |
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} |
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} |
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|
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template<typename T> NPTi<T>::~NPTi() { |
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//nothing for now |
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} |
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void NPTi::evolveEtaB() { |
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|
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template<typename T> void NPTi<T>::resetIntegrator() { |
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eta = 0.0; |
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T::resetIntegrator(); |
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} |
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prevEta = eta; |
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eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
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(OOPSEConstant::pressureConvert*NkBT*tb2)); |
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} |
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|
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template<typename T> void NPTi<T>::evolveEtaA() { |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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oldEta = eta; |
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} |
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void NPTi::calcVelScale() { |
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vScale = chi + eta; |
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} |
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|
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template<typename T> void NPTi<T>::evolveEtaB() { |
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void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
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sc = vel * vScale; |
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} |
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|
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prevEta = eta; |
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eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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} |
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void NPTi::getVelScaleB(Vector3d& sc, int index ){ |
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sc = oldVel[index] * vScale; |
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} |
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|
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template<typename T> void NPTi<T>::calcVelScale(void) { |
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vScale = chi + eta; |
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} |
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|
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template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) { |
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int i; |
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void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, |
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int index, Vector3d& sc){ |
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/**@todo*/ |
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sc = (oldPos[index] + pos)/2.0 -COM; |
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sc *= eta; |
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} |
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for(i=0; i<3; i++) sc[i] = vel[i] * vScale; |
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} |
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void NPTi::scaleSimBox(){ |
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|
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template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){ |
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int i; |
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double scaleFactor; |
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|
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for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale; |
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} |
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scaleFactor = exp(dt*eta); |
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTi error: Attempting a Box scaling of more than 10 percent" |
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" check your tauBarostat, as it is probably too small!\n" |
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" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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hmat *= scaleFactor; |
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currentSnapshot_->setHmat(hmat); |
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} |
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|
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template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]){ |
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int j; |
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} |
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for(j=0; j<3; j++) |
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sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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bool NPTi::etaConverged() { |
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for(j=0; j<3; j++) |
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sc[j] *= eta; |
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} |
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|
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template<typename T> void NPTi<T>::scaleSimBox( void ){ |
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|
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double scaleFactor; |
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|
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scaleFactor = exp(dt*eta); |
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|
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTi error: Attempting a Box scaling of more than 10 percent" |
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" check your tauBarostat, as it is probably too small!\n" |
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" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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info->scaleBox(scaleFactor); |
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return ( fabs(prevEta - eta) <= etaTolerance ); |
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} |
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|
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} |
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double NPTi::calcConservedQuantity(){ |
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|
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template<typename T> bool NPTi<T>::etaConverged() { |
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chi= currentSnapshot_->getChi(); |
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integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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loadEta(); |
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
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|
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return ( fabs(prevEta - eta) <= etaTolerance ); |
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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 Energy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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double barostat_kinetic; |
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double barostat_potential; |
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|
|
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template<typename T> double NPTi<T>::getConservedQuantity(void){ |
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Energy =thermo.getTotalE(); |
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|
|
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double conservedQuantity; |
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double Energy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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double barostat_kinetic; |
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double barostat_potential; |
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thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
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|
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Energy = tStats->getTotalE(); |
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thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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|
|
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thermostat_kinetic = fkBT* tt2 * chi * chi / |
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(2.0 * eConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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> |
barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert); |
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|
|
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+ |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) / |
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OOPSEConstant::energyConvert; |
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|
|
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barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta / |
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(2.0 * eConvert); |
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> |
conservedQuantity = Energy + 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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barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
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eConvert; |
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> |
void NPTi::loadEta() { |
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> |
Mat3x3d etaMat = currentSnapshot_->getEta(); |
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> |
eta = etaMat(0,0); |
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> |
//if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) { |
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// sprintf( painCave.errMsg, |
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> |
// "NPTi error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix"); |
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// painCave.isFatal = 1; |
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> |
// simError(); |
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> |
//} |
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> |
} |
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|
|
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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// cout.width(8); |
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// cout.precision(8); |
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|
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// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
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// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
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< |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
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< |
return conservedQuantity; |
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> |
void NPTi::saveEta() { |
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> |
Mat3x3d etaMat(0.0); |
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> |
etaMat(0, 0) = eta; |
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> |
etaMat(1, 1) = eta; |
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> |
etaMat(2, 2) = eta; |
| 182 |
> |
currentSnapshot_->setEta(etaMat); |
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> |
} |
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|
} |
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|
| 161 |
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template<typename T> string NPTi<T>::getAdditionalParameters(void){ |
| 162 |
– |
string parameters; |
| 163 |
– |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 164 |
– |
char buffer[BUFFERSIZE]; |
| 165 |
– |
|
| 166 |
– |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 167 |
– |
parameters += buffer; |
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– |
|
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– |
sprintf(buffer,"\t%G\t0\t0;", eta); |
| 170 |
– |
parameters += buffer; |
| 171 |
– |
|
| 172 |
– |
sprintf(buffer,"\t0\t%G\t0;", eta); |
| 173 |
– |
parameters += buffer; |
| 174 |
– |
|
| 175 |
– |
sprintf(buffer,"\t0\t0\t%G;", eta); |
| 176 |
– |
parameters += buffer; |
| 177 |
– |
|
| 178 |
– |
return parameters; |
| 179 |
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|
| 180 |
– |
} |
