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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 <math.h> |
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|
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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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> |
#include "brains/SimInfo.hpp" |
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> |
#include "brains/Thermo.hpp" |
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> |
#include "integrators/NPT.hpp" |
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> |
#include "math/SquareMatrix3.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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– |
|
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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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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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< |
template<typename T> NPT<T>::NPT ( 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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< |
DoubleData * chiValue; |
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< |
DoubleData * integralOfChidtValue; |
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> |
namespace oopse { |
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|
|
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< |
chiValue = NULL; |
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< |
integralOfChidtValue = NULL; |
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> |
NPT::NPT(SimInfo* info) : |
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> |
VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) { |
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|
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< |
chi = 0.0; |
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< |
integralOfChidt = 0.0; |
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< |
have_tau_thermostat = 0; |
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< |
have_tau_barostat = 0; |
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< |
have_target_temp = 0; |
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< |
have_target_pressure = 0; |
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< |
have_chi_tolerance = 0; |
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< |
have_eta_tolerance = 0; |
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< |
have_pos_iter_tolerance = 0; |
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> |
Globals* simParams = info_->getSimParams(); |
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> |
|
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> |
if (!simParams->getUseIntialExtendedSystemState()) { |
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> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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> |
currSnapshot->setChi(0.0); |
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> |
currSnapshot->setIntegralOfChiDt(0.0); |
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> |
currSnapshot->setEta(Mat3x3d(0.0)); |
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> |
} |
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> |
|
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> |
if (!simParams->haveTargetTemp()) { |
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> |
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n"); |
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> |
painCave.isFatal = 1; |
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> |
painCave.severity = OOPSE_ERROR; |
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simError(); |
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> |
} else { |
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> |
targetTemp = simParams->getTargetTemp(); |
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} |
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|
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< |
// retrieve chi and integralOfChidt from simInfo |
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data = info->getProperty(CHIVALUE_ID); |
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< |
if(data){ |
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chiValue = dynamic_cast<DoubleData*>(data); |
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} |
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> |
// We must set tauThermostat |
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if (!simParams->haveTauThermostat()) { |
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sprintf(painCave.errMsg, "If you use the constant temperature\n" |
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"\tintegrator, you must set tauThermostat.\n"); |
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|
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data = info->getProperty(INTEGRALOFCHIDT_ID); |
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if(data){ |
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integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
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} |
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> |
painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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> |
tauThermostat = simParams->getTauThermostat(); |
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} |
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|
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// chi and integralOfChidt should appear by pair |
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if(chiValue && integralOfChidtValue){ |
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chi = chiValue->getData(); |
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integralOfChidt = integralOfChidtValue->getData(); |
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} |
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> |
if (!simParams->haveTargetPressure()) { |
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sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n" |
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" without a targetPressure!\n"); |
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|
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oldPos = new double[3*integrableObjects.size()]; |
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oldVel = new double[3*integrableObjects.size()]; |
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oldJi = new double[3*integrableObjects.size()]; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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targetPressure = simParams->getTargetPressure(); |
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} |
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> |
|
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> |
if (!simParams->haveTauBarostat()) { |
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> |
sprintf(painCave.errMsg, |
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"If you use the NPT integrator, you must set tauBarostat.\n"); |
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> |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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} else { |
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> |
tauBarostat = simParams->getTauBarostat(); |
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> |
} |
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> |
|
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> |
tt2 = tauThermostat * tauThermostat; |
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> |
tb2 = tauBarostat * tauBarostat; |
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|
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< |
} |
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> |
update(); |
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> |
} |
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|
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< |
template<typename T> NPT<T>::~NPT() { |
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< |
delete[] oldPos; |
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delete[] oldVel; |
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delete[] oldJi; |
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} |
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> |
NPT::~NPT() { |
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} |
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|
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< |
template<typename T> void NPT<T>::moveA() { |
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> |
void NPT::doUpdate() { |
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|
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//new version of NPT |
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int i, j, k; |
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double Tb[3], ji[3]; |
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double mass; |
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double vel[3], pos[3], frc[3]; |
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double sc[3]; |
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double COM[3]; |
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> |
oldPos.resize(info_->getNIntegrableObjects()); |
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> |
oldVel.resize(info_->getNIntegrableObjects()); |
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> |
oldJi.resize(info_->getNIntegrableObjects()); |
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|
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< |
instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor( press ); |
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instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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instaVol = tStats->getVolume(); |
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> |
} |
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|
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tStats->getCOM(COM); |
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> |
void NPT::moveA() { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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Vector3d Tb, ji; |
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RealType mass; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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> |
Vector3d sc; |
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> |
int index; |
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|
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< |
//evolve velocity half step |
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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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> |
instaTemp =thermo.getTemperature(); |
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> |
press = thermo.getPressureTensor(); |
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> |
instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; |
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> |
instaVol =thermo.getVolume(); |
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|
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< |
calcVelScale(); |
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< |
|
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< |
for( i=0; i<integrableObjects.size(); i++ ){ |
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> |
Vector3d COM = info_->getCom(); |
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|
|
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< |
integrableObjects[i]->getVel( vel ); |
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< |
integrableObjects[i]->getFrc( frc ); |
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> |
//evolve velocity half step |
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|
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< |
mass = integrableObjects[i]->getMass(); |
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> |
calcVelScale(); |
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|
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< |
getVelScaleA( sc, vel ); |
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> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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> |
integrableObject = mol->nextIntegrableObject(j)) { |
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> |
|
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> |
vel = integrableObject->getVel(); |
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> |
frc = integrableObject->getFrc(); |
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|
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< |
for (j=0; j < 3; j++) { |
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> |
mass = integrableObject->getMass(); |
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|
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< |
// velocity half step (use chi from previous step here): |
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< |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
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> |
getVelScaleA(sc, vel); |
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|
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< |
} |
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> |
// velocity half step (use chi from previous step here): |
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> |
//vel[j] += dt2 * ((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]); |
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> |
vel += dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
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> |
integrableObject->setVel(vel); |
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|
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< |
integrableObjects[i]->setVel( vel ); |
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> |
if (integrableObject->isDirectional()) { |
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|
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< |
if( integrableObjects[i]->isDirectional() ){ |
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> |
// get and convert the torque to body frame |
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|
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< |
// get and convert the torque to body frame |
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> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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|
|
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< |
integrableObjects[i]->getTrq( Tb ); |
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< |
integrableObjects[i]->lab2Body( Tb ); |
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> |
// get the angular momentum, and propagate a half step |
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|
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< |
// get the angular momentum, and propagate a half step |
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> |
ji = integrableObject->getJ(); |
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|
|
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< |
integrableObjects[i]->getJ( ji ); |
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> |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
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> |
ji += dt2*OOPSEConstant::energyConvert * Tb - dt2*chi* ji; |
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> |
|
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> |
rotAlgo->rotate(integrableObject, ji, dt); |
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|
|
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< |
for (j=0; j < 3; j++) |
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< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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> |
integrableObject->setJ(ji); |
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> |
} |
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> |
|
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> |
} |
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> |
} |
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> |
// evolve chi and eta half step |
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|
|
| 200 |
< |
this->rotationPropagation( integrableObjects[i], ji ); |
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> |
chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2; |
| 201 |
> |
|
| 202 |
> |
evolveEtaA(); |
| 203 |
|
|
| 204 |
< |
integrableObjects[i]->setJ( ji ); |
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> |
//calculate the integral of chidt |
| 205 |
> |
integralOfChidt += dt2 * chi; |
| 206 |
> |
|
| 207 |
> |
index = 0; |
| 208 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 209 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 210 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 211 |
> |
oldPos[index++] = integrableObject->getPos(); |
| 212 |
> |
} |
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|
} |
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< |
} |
| 214 |
> |
|
| 215 |
> |
//the first estimation of r(t+dt) is equal to r(t) |
| 216 |
|
|
| 217 |
< |
// evolve chi and eta half step |
| 217 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
| 218 |
> |
index = 0; |
| 219 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 220 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 221 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 222 |
|
|
| 223 |
< |
evolveChiA(); |
| 224 |
< |
evolveEtaA(); |
| 223 |
> |
vel = integrableObject->getVel(); |
| 224 |
> |
pos = integrableObject->getPos(); |
| 225 |
|
|
| 226 |
< |
//calculate the integral of chidt |
| 142 |
< |
integralOfChidt += dt2*chi; |
| 226 |
> |
this->getPosScale(pos, COM, index, sc); |
| 227 |
|
|
| 228 |
< |
//save the old positions |
| 229 |
< |
for(i = 0; i < integrableObjects.size(); i++){ |
| 146 |
< |
integrableObjects[i]->getPos(pos); |
| 147 |
< |
for(j = 0; j < 3; j++) |
| 148 |
< |
oldPos[i*3 + j] = pos[j]; |
| 149 |
< |
} |
| 228 |
> |
pos = oldPos[index] + dt * (vel + sc); |
| 229 |
> |
integrableObject->setPos(pos); |
| 230 |
|
|
| 231 |
< |
//the first estimation of r(t+dt) is equal to r(t) |
| 231 |
> |
++index; |
| 232 |
> |
} |
| 233 |
> |
} |
| 234 |
|
|
| 235 |
< |
for(k = 0; k < 5; k ++){ |
| 235 |
> |
rattle->constraintA(); |
| 236 |
> |
} |
| 237 |
|
|
| 238 |
< |
for(i =0 ; i < integrableObjects.size(); i++){ |
| 238 |
> |
// Scale the box after all the positions have been moved: |
| 239 |
|
|
| 240 |
< |
integrableObjects[i]->getVel(vel); |
| 158 |
< |
integrableObjects[i]->getPos(pos); |
| 240 |
> |
this->scaleSimBox(); |
| 241 |
|
|
| 242 |
< |
this->getPosScale( pos, COM, i, sc ); |
| 242 |
> |
currentSnapshot_->setChi(chi); |
| 243 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 244 |
|
|
| 245 |
< |
for(j = 0; j < 3; j++) |
| 163 |
< |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
| 164 |
< |
|
| 165 |
< |
integrableObjects[i]->setPos( pos ); |
| 166 |
< |
} |
| 167 |
< |
|
| 168 |
< |
if(nConstrained) |
| 169 |
< |
constrainA(); |
| 245 |
> |
saveEta(); |
| 246 |
|
} |
| 247 |
|
|
| 248 |
+ |
void NPT::moveB(void) { |
| 249 |
+ |
SimInfo::MoleculeIterator i; |
| 250 |
+ |
Molecule::IntegrableObjectIterator j; |
| 251 |
+ |
Molecule* mol; |
| 252 |
+ |
StuntDouble* integrableObject; |
| 253 |
+ |
int index; |
| 254 |
+ |
Vector3d Tb; |
| 255 |
+ |
Vector3d ji; |
| 256 |
+ |
Vector3d sc; |
| 257 |
+ |
Vector3d vel; |
| 258 |
+ |
Vector3d frc; |
| 259 |
+ |
RealType mass; |
| 260 |
|
|
| 173 |
– |
// Scale the box after all the positions have been moved: |
| 261 |
|
|
| 262 |
< |
this->scaleSimBox(); |
| 263 |
< |
} |
| 262 |
> |
chi= currentSnapshot_->getChi(); |
| 263 |
> |
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 264 |
> |
RealType oldChi = chi; |
| 265 |
> |
RealType prevChi; |
| 266 |
|
|
| 267 |
< |
template<typename T> void NPT<T>::moveB( void ){ |
| 268 |
< |
|
| 269 |
< |
//new version of NPT |
| 270 |
< |
int i, j, k; |
| 271 |
< |
double Tb[3], ji[3], sc[3]; |
| 272 |
< |
double vel[3], frc[3]; |
| 273 |
< |
double mass; |
| 274 |
< |
|
| 275 |
< |
// Set things up for the iteration: |
| 276 |
< |
|
| 277 |
< |
for( i=0; i<integrableObjects.size(); i++ ){ |
| 278 |
< |
|
| 190 |
< |
integrableObjects[i]->getVel( vel ); |
| 191 |
< |
|
| 192 |
< |
for (j=0; j < 3; j++) |
| 193 |
< |
oldVel[3*i + j] = vel[j]; |
| 194 |
< |
|
| 195 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 196 |
< |
|
| 197 |
< |
integrableObjects[i]->getJ( ji ); |
| 198 |
< |
|
| 199 |
< |
for (j=0; j < 3; j++) |
| 200 |
< |
oldJi[3*i + j] = ji[j]; |
| 201 |
< |
|
| 267 |
> |
loadEta(); |
| 268 |
> |
|
| 269 |
> |
//save velocity and angular momentum |
| 270 |
> |
index = 0; |
| 271 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 272 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 273 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 274 |
> |
|
| 275 |
> |
oldVel[index] = integrableObject->getVel(); |
| 276 |
> |
oldJi[index] = integrableObject->getJ(); |
| 277 |
> |
++index; |
| 278 |
> |
} |
| 279 |
|
} |
| 203 |
– |
} |
| 280 |
|
|
| 281 |
< |
// do the iteration: |
| 281 |
> |
// do the iteration: |
| 282 |
> |
instaVol =thermo.getVolume(); |
| 283 |
|
|
| 284 |
< |
instaVol = tStats->getVolume(); |
| 284 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
| 285 |
> |
instaTemp =thermo.getTemperature(); |
| 286 |
> |
instaPress =thermo.getPressure(); |
| 287 |
|
|
| 288 |
< |
for (k=0; k < 4; k++) { |
| 288 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
| 289 |
> |
prevChi = chi; |
| 290 |
> |
chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2; |
| 291 |
|
|
| 292 |
< |
instaTemp = tStats->getTemperature(); |
| 293 |
< |
instaPress = tStats->getPressure(); |
| 292 |
> |
//evolve eta |
| 293 |
> |
this->evolveEtaB(); |
| 294 |
> |
this->calcVelScale(); |
| 295 |
|
|
| 296 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
| 296 |
> |
index = 0; |
| 297 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 298 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 299 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 300 |
|
|
| 301 |
< |
this->evolveChiB(); |
| 302 |
< |
this->evolveEtaB(); |
| 218 |
< |
this->calcVelScale(); |
| 301 |
> |
frc = integrableObject->getFrc(); |
| 302 |
> |
vel = integrableObject->getVel(); |
| 303 |
|
|
| 304 |
< |
for( i=0; i<integrableObjects.size(); i++ ){ |
| 304 |
> |
mass = integrableObject->getMass(); |
| 305 |
|
|
| 306 |
< |
integrableObjects[i]->getFrc( frc ); |
| 223 |
< |
integrableObjects[i]->getVel(vel); |
| 306 |
> |
getVelScaleB(sc, index); |
| 307 |
|
|
| 308 |
< |
mass = integrableObjects[i]->getMass(); |
| 308 |
> |
// velocity half step |
| 309 |
> |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]); |
| 310 |
> |
vel = oldVel[index] + dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
| 311 |
> |
integrableObject->setVel(vel); |
| 312 |
|
|
| 313 |
< |
getVelScaleB( sc, i ); |
| 313 |
> |
if (integrableObject->isDirectional()) { |
| 314 |
> |
// get and convert the torque to body frame |
| 315 |
> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 316 |
|
|
| 317 |
< |
// velocity half step |
| 318 |
< |
for (j=0; j < 3; j++) |
| 319 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
| 317 |
> |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi[3*i+j]*chi); |
| 318 |
> |
ji = oldJi[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi*oldJi[index]; |
| 319 |
> |
integrableObject->setJ(ji); |
| 320 |
> |
} |
| 321 |
|
|
| 322 |
< |
integrableObjects[i]->setVel( vel ); |
| 323 |
< |
|
| 235 |
< |
if( integrableObjects[i]->isDirectional() ){ |
| 236 |
< |
|
| 237 |
< |
// get and convert the torque to body frame |
| 238 |
< |
|
| 239 |
< |
integrableObjects[i]->getTrq( Tb ); |
| 240 |
< |
integrableObjects[i]->lab2Body( Tb ); |
| 241 |
< |
|
| 242 |
< |
for (j=0; j < 3; j++) |
| 243 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 244 |
< |
|
| 245 |
< |
integrableObjects[i]->setJ( ji ); |
| 322 |
> |
++index; |
| 323 |
> |
} |
| 324 |
|
} |
| 325 |
+ |
|
| 326 |
+ |
rattle->constraintB(); |
| 327 |
+ |
|
| 328 |
+ |
if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged()) |
| 329 |
+ |
break; |
| 330 |
|
} |
| 331 |
|
|
| 332 |
< |
if(nConstrained) |
| 333 |
< |
constrainB(); |
| 332 |
> |
//calculate integral of chidt |
| 333 |
> |
integralOfChidt += dt2 * chi; |
| 334 |
|
|
| 335 |
< |
if ( this->chiConverged() && this->etaConverged() ) break; |
| 336 |
< |
} |
| 335 |
> |
currentSnapshot_->setChi(chi); |
| 336 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 337 |
|
|
| 338 |
< |
//calculate integral of chida |
| 256 |
< |
integralOfChidt += dt2*chi; |
| 257 |
< |
|
| 258 |
< |
|
| 259 |
< |
} |
| 260 |
< |
|
| 261 |
< |
template<typename T> void NPT<T>::resetIntegrator() { |
| 262 |
< |
chi = 0.0; |
| 263 |
< |
T::resetIntegrator(); |
| 264 |
< |
} |
| 265 |
< |
|
| 266 |
< |
template<typename T> void NPT<T>::evolveChiA() { |
| 267 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 268 |
< |
oldChi = chi; |
| 269 |
< |
} |
| 270 |
< |
|
| 271 |
< |
template<typename T> void NPT<T>::evolveChiB() { |
| 272 |
< |
|
| 273 |
< |
prevChi = chi; |
| 274 |
< |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 275 |
< |
} |
| 276 |
< |
|
| 277 |
< |
template<typename T> bool NPT<T>::chiConverged() { |
| 278 |
< |
|
| 279 |
< |
return ( fabs( prevChi - chi ) <= chiTolerance ); |
| 280 |
< |
} |
| 281 |
< |
|
| 282 |
< |
template<typename T> int NPT<T>::readyCheck() { |
| 283 |
< |
|
| 284 |
< |
//check parent's readyCheck() first |
| 285 |
< |
if (T::readyCheck() == -1) |
| 286 |
< |
return -1; |
| 287 |
< |
|
| 288 |
< |
// First check to see if we have a target temperature. |
| 289 |
< |
// Not having one is fatal. |
| 290 |
< |
|
| 291 |
< |
if (!have_target_temp) { |
| 292 |
< |
sprintf( painCave.errMsg, |
| 293 |
< |
"NPT error: You can't use the NPT integrator\n" |
| 294 |
< |
" without a targetTemp!\n" |
| 295 |
< |
); |
| 296 |
< |
painCave.isFatal = 1; |
| 297 |
< |
simError(); |
| 298 |
< |
return -1; |
| 338 |
> |
saveEta(); |
| 339 |
|
} |
| 340 |
|
|
| 341 |
< |
if (!have_target_pressure) { |
| 342 |
< |
sprintf( painCave.errMsg, |
| 343 |
< |
"NPT error: You can't use the NPT integrator\n" |
| 344 |
< |
" without a targetPressure!\n" |
| 305 |
< |
); |
| 306 |
< |
painCave.isFatal = 1; |
| 307 |
< |
simError(); |
| 308 |
< |
return -1; |
| 341 |
> |
void NPT::resetIntegrator(){ |
| 342 |
> |
currentSnapshot_->setChi(0.0); |
| 343 |
> |
currentSnapshot_->setIntegralOfChiDt(0.0); |
| 344 |
> |
resetEta(); |
| 345 |
|
} |
| 346 |
|
|
| 311 |
– |
// We must set tauThermostat. |
| 347 |
|
|
| 348 |
< |
if (!have_tau_thermostat) { |
| 349 |
< |
sprintf( painCave.errMsg, |
| 350 |
< |
"NPT error: If you use the NPT\n" |
| 351 |
< |
" integrator, you must set tauThermostat.\n"); |
| 352 |
< |
painCave.isFatal = 1; |
| 318 |
< |
simError(); |
| 319 |
< |
return -1; |
| 320 |
< |
} |
| 321 |
< |
|
| 322 |
< |
// We must set tauBarostat. |
| 323 |
< |
|
| 324 |
< |
if (!have_tau_barostat) { |
| 325 |
< |
sprintf( painCave.errMsg, |
| 326 |
< |
"If you use the NPT integrator, you must set tauBarostat.\n"); |
| 327 |
< |
painCave.severity = OOPSE_ERROR; |
| 328 |
< |
painCave.isFatal = 1; |
| 329 |
< |
simError(); |
| 330 |
< |
return -1; |
| 331 |
< |
} |
| 332 |
< |
|
| 333 |
< |
if (!have_chi_tolerance) { |
| 334 |
< |
sprintf( painCave.errMsg, |
| 335 |
< |
"Setting chi tolerance to 1e-6 in NPT integrator\n"); |
| 336 |
< |
chiTolerance = 1e-6; |
| 337 |
< |
have_chi_tolerance = 1; |
| 338 |
< |
painCave.severity = OOPSE_INFO; |
| 339 |
< |
painCave.isFatal = 0; |
| 340 |
< |
simError(); |
| 341 |
< |
} |
| 342 |
< |
|
| 343 |
< |
if (!have_eta_tolerance) { |
| 344 |
< |
sprintf( painCave.errMsg, |
| 345 |
< |
"Setting eta tolerance to 1e-6 in NPT integrator"); |
| 346 |
< |
etaTolerance = 1e-6; |
| 347 |
< |
have_eta_tolerance = 1; |
| 348 |
< |
painCave.severity = OOPSE_INFO; |
| 349 |
< |
painCave.isFatal = 0; |
| 350 |
< |
simError(); |
| 351 |
< |
} |
| 352 |
< |
|
| 353 |
< |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 354 |
< |
// of integrableObjects, so no subtraction or addition of constraints or |
| 355 |
< |
// orientational degrees of freedom: |
| 356 |
< |
|
| 357 |
< |
NkBT = (double)(info->getTotIntegrableObjects()) * kB * targetTemp; |
| 358 |
< |
|
| 359 |
< |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 360 |
< |
// than the barostat (when there are particles with orientational degrees |
| 361 |
< |
// of freedom). |
| 362 |
< |
|
| 363 |
< |
fkBT = (double)(info->getNDF()) * kB * targetTemp; |
| 364 |
< |
|
| 365 |
< |
tt2 = tauThermostat * tauThermostat; |
| 366 |
< |
tb2 = tauBarostat * tauBarostat; |
| 367 |
< |
|
| 368 |
< |
return 1; |
| 348 |
> |
void NPT::resetEta() { |
| 349 |
> |
Mat3x3d etaMat(0.0); |
| 350 |
> |
currentSnapshot_->setEta(etaMat); |
| 351 |
> |
} |
| 352 |
> |
|
| 353 |
|
} |
