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#ifndef _INTEGRATOR_H_ |
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#define _INTEGRATOR_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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/** |
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* @file Integrator.hpp |
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* @author tlin |
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* @date 11/08/2004 |
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* @time 13:25am |
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* @version 1.0 |
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*/ |
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|
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#include <string> |
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#include <vector> |
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#include "primitives/Atom.hpp" |
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#include "primitives/StuntDouble.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "primitives/SRI.hpp" |
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#include "primitives/AbstractClasses.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 "io/ZConsWriter.hpp" |
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#include "restraints/Restraints.hpp" |
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#ifndef INTEGRATORS_INTEGRATOR_HPP |
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#define INTEGRATORS_INTEGRATOR_HPP |
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|
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using namespace std; |
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const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K |
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const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm |
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const int maxIteration = 300; |
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const double tol = 1.0e-6; |
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#include "brains/ForceManager.hpp" |
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#include "io/DumpWriter.hpp" |
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#include "io/StatWriter.hpp" |
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#include "integrators/Velocitizer.hpp" |
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|
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class VelVerletConsFramework; |
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template<typename T = BaseIntegrator> class Integrator : public T { |
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namespace oopse { |
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|
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public: |
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Integrator( SimInfo *theInfo, ForceFields* the_ff ); |
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virtual ~Integrator(); |
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void integrate( void ); |
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virtual double getConservedQuantity(void); |
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virtual string getAdditionalParameters(void); |
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protected: |
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/** |
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* @class Integrator Integrator.hpp "integrators/Integrator.hpp" |
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* @brief Base class of Integrator |
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* @todo document |
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*/ |
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class Integrator { |
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public: |
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|
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virtual void integrateStep( int calcPot, int calcStress ); |
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virtual void preMove( void ); |
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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virtual void constrainA( void ); |
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virtual void constrainB( void ); |
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virtual int readyCheck( void ) { return 1; } |
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virtual ~Integrator(); |
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|
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virtual void resetIntegrator( void ) { } |
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//avoid public virtual function |
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void integrate() { |
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doIntegrate(); |
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} |
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virtual void calcForce( int calcPot, int calcStress ); |
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virtual void thermalize(); |
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void update() { |
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doUpdate(); |
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} |
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virtual bool stopIntegrator() {return false;} |
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void setForceManager(ForceManager* forceMan) { |
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if (forceMan_ != forceMan && forceMan_ != NULL) { |
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delete forceMan_; |
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} |
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forceMan_ = forceMan; |
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} |
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virtual void rotationPropagation( StuntDouble* sd, double ji[3] ); |
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void setVelocitizer(Velocitizer* velocitizer) { |
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if (velocitizer_ != velocitizer && velocitizer_ != NULL) { |
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delete velocitizer_; |
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} |
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velocitizer_ = velocitizer; |
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} |
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|
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protected: |
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void checkConstraints( void ); |
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void rotate( int axes1, int axes2, double angle, double j[3], |
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double A[3][3] ); |
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Integrator(SimInfo* info); |
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ForceFields* myFF; |
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virtual void doIntegrate() = 0; |
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SimInfo *info; // all the info we'll ever need |
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vector<StuntDouble*> integrableObjects; |
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int nAtoms; /* the number of atoms */ |
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int oldAtoms; |
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Atom **atoms; /* array of atom pointers */ |
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Molecule* molecules; |
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int nMols; |
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virtual void doUpdate() {} |
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|
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void saveConservedQuantity() { |
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currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity(); |
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} |
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|
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SimInfo* info_; |
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ForceManager* forceMan_; |
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bool needPotential; |
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bool needStress; |
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|
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Velocitizer* velocitizer_; |
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bool needVelocityScaling; |
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double targetScalingTemp; |
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|
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DumpWriter*dumpWriter; |
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StatWriter* statWriter; |
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Thermo thermo; |
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|
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double runTime; |
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double sampleTime; |
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double statusTime; |
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double thermalTime; |
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double dt; |
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int isConstrained; // boolean to know whether the systems contains constraints. |
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int nConstrained; // counter for number of constraints |
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int *constrainedA; // the i of a constraint pair |
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int *constrainedB; // the j of a constraint pair |
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double *constrainedDsqr; // the square of the constraint distance |
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int* moving; // tells whether we are moving atom i |
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int* moved; // tells whether we have moved atom i |
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double* oldPos; // pre constrained positions |
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|
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short isFirst; /*boolean for the first time integrate is called */ |
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|
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double dt; |
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double dt2; |
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|
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Thermo *tStats; |
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StatWriter* statOut; |
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DumpWriter* dumpOut; |
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RestraintWriter* restOut; |
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RestraintReader* initRestraints; |
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|
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}; |
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|
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typedef Integrator<BaseIntegrator> RealIntegrator; |
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|
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// ansi instantiation |
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// template class Integrator<BaseIntegrator>; |
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|
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template<typename T> class NVE : public T { |
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|
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public: |
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NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
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T( theInfo, the_ff ){} |
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virtual ~NVE(){} |
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}; |
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|
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template<typename T> class NVT : public T { |
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public: |
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|
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NVT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NVT(); |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
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void setChiTolerance(double tol) {chiTolerance = tol;} |
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virtual double getConservedQuantity(void); |
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virtual string getAdditionalParameters(void); |
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|
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protected: |
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|
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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|
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virtual int readyCheck(); |
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|
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virtual void resetIntegrator( void ); |
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|
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// chi is a propagated degree of freedom. |
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|
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double chi; |
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|
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//integral of chi(t)dt |
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double integralOfChidt; |
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|
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// targetTemp must be set. tauThermostat must also be set; |
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|
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double targetTemp; |
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double tauThermostat; |
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|
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short int have_tau_thermostat, have_target_temp; |
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double *oldVel; |
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double *oldJi; |
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|
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double chiTolerance; |
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short int have_chi_tolerance; |
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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> class NPT : public T{ |
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|
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public: |
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|
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NPT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPT(); |
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|
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virtual void integrateStep( int calcPot, int calcStress ){ |
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calcStress = 1; |
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T::integrateStep( calcPot, calcStress ); |
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} |
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|
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virtual double getConservedQuantity(void) = 0; |
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virtual string getAdditionalParameters(void) = 0; |
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|
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double myTauThermo( void ) { return tauThermostat; } |
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double myTauBaro( void ) { return tauBarostat; } |
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|
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
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void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
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void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;} |
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void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;} |
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void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;} |
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|
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protected: |
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|
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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|
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virtual int readyCheck(); |
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|
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virtual void resetIntegrator( void ); |
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|
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virtual void getVelScaleA( double sc[3], double vel[3] ) = 0; |
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virtual void getVelScaleB( double sc[3], int index ) = 0; |
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virtual void getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]) = 0; |
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|
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virtual void calcVelScale( void ) = 0; |
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|
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virtual bool chiConverged( void ); |
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virtual bool etaConverged( void ) = 0; |
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|
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virtual void evolveChiA( void ); |
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virtual void evolveEtaA( void ) = 0; |
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virtual void evolveChiB( void ); |
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virtual void evolveEtaB( void ) = 0; |
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|
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virtual void scaleSimBox( void ) = 0; |
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|
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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
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|
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// chi and eta are the propagated degrees of freedom |
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|
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double oldChi; |
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double prevChi; |
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double chi; |
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double NkBT; |
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double fkBT; |
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Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change |
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|
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double tt2, tb2; |
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double instaTemp, instaPress, instaVol; |
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double press[3][3]; |
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|
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int Nparticles; |
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|
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double integralOfChidt; |
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|
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// targetTemp, targetPressure, and tauBarostat must be set. |
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// One of qmass or tauThermostat must be set; |
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|
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double targetTemp; |
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double targetPressure; |
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double tauThermostat; |
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double tauBarostat; |
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|
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short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
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short int have_target_pressure; |
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|
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double *oldPos; |
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double *oldVel; |
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double *oldJi; |
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|
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double chiTolerance; |
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short int have_chi_tolerance; |
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double posIterTolerance; |
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short int have_pos_iter_tolerance; |
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double etaTolerance; |
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short int have_eta_tolerance; |
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|
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}; |
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|
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template<typename T> class NPTi : public T{ |
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|
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public: |
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NPTi( SimInfo *theInfo, ForceFields* the_ff); |
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~NPTi(); |
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|
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< |
virtual double getConservedQuantity(void); |
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virtual void resetIntegrator(void); |
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virtual string getAdditionalParameters(void); |
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protected: |
| 257 |
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|
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|
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< |
|
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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|
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virtual bool etaConverged( void ); |
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|
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virtual void scaleSimBox( void ); |
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< |
|
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< |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
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< |
virtual void getVelScaleB( double sc[3], int index ); |
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virtual void getPosScale(double pos[3], double COM[3], |
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< |
int index, double sc[3]); |
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< |
|
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< |
virtual void calcVelScale( void ); |
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< |
|
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< |
double eta, oldEta, prevEta; |
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double vScale; |
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}; |
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|
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< |
template<typename T> class NPTf : public T{ |
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|
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public: |
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< |
|
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< |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTf(); |
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< |
|
| 285 |
< |
virtual double getConservedQuantity(void); |
| 286 |
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virtual string getAdditionalParameters(void); |
| 287 |
< |
virtual void resetIntegrator(void); |
| 288 |
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|
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protected: |
| 290 |
< |
|
| 291 |
< |
virtual void evolveEtaA(void); |
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< |
virtual void evolveEtaB(void); |
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< |
|
| 294 |
< |
virtual bool etaConverged( void ); |
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< |
|
| 296 |
< |
virtual void scaleSimBox( void ); |
| 297 |
< |
|
| 298 |
< |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
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< |
virtual void getVelScaleB( double sc[3], int index ); |
| 300 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
| 301 |
< |
int index, double sc[3]); |
| 302 |
< |
|
| 303 |
< |
virtual void calcVelScale( void ); |
| 304 |
< |
|
| 305 |
< |
double eta[3][3]; |
| 306 |
< |
double oldEta[3][3]; |
| 307 |
< |
double prevEta[3][3]; |
| 308 |
< |
double vScale[3][3]; |
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< |
}; |
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< |
|
| 311 |
< |
template<typename T> class NPTxyz : public T{ |
| 312 |
< |
|
| 313 |
< |
public: |
| 314 |
< |
|
| 315 |
< |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
| 316 |
< |
virtual ~NPTxyz(); |
| 317 |
< |
|
| 318 |
< |
virtual double getConservedQuantity(void); |
| 319 |
< |
virtual string getAdditionalParameters(void); |
| 320 |
< |
virtual void resetIntegrator(void); |
| 321 |
< |
|
| 322 |
< |
protected: |
| 323 |
< |
|
| 324 |
< |
virtual void evolveEtaA(void); |
| 325 |
< |
virtual void evolveEtaB(void); |
| 326 |
< |
|
| 327 |
< |
virtual bool etaConverged( void ); |
| 328 |
< |
|
| 329 |
< |
virtual void scaleSimBox( void ); |
| 330 |
< |
|
| 331 |
< |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
| 332 |
< |
virtual void getVelScaleB( double sc[3], int index ); |
| 333 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
| 334 |
< |
int index, double sc[3]); |
| 335 |
< |
|
| 336 |
< |
virtual void calcVelScale( void ); |
| 337 |
< |
|
| 338 |
< |
double eta[3][3]; |
| 339 |
< |
double oldEta[3][3]; |
| 340 |
< |
double prevEta[3][3]; |
| 341 |
< |
double vScale[3][3]; |
| 342 |
< |
}; |
| 343 |
< |
|
| 344 |
< |
|
| 345 |
< |
template<typename T> class ZConstraint : public T { |
| 346 |
< |
|
| 347 |
< |
public: |
| 348 |
< |
class ForceSubtractionPolicy{ |
| 349 |
< |
public: |
| 350 |
< |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
| 351 |
< |
|
| 352 |
< |
virtual void update() = 0; |
| 353 |
< |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
| 354 |
< |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
| 355 |
< |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
| 356 |
< |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
| 357 |
< |
|
| 358 |
< |
protected: |
| 359 |
< |
ZConstraint<T>* zconsIntegrator; |
| 360 |
< |
}; |
| 361 |
< |
|
| 362 |
< |
class PolicyByNumber : public ForceSubtractionPolicy{ |
| 363 |
< |
|
| 364 |
< |
public: |
| 365 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
| 366 |
< |
virtual void update(); |
| 367 |
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virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
| 368 |
< |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
| 369 |
< |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
| 370 |
< |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
| 371 |
< |
|
| 127 |
> |
|
| 128 |
|
private: |
| 129 |
< |
int totNumOfMovingAtoms; |
| 130 |
< |
}; |
| 131 |
< |
|
| 132 |
< |
class PolicyByMass : public ForceSubtractionPolicy{ |
| 133 |
< |
|
| 134 |
< |
public: |
| 379 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
| 380 |
< |
|
| 381 |
< |
virtual void update(); |
| 382 |
< |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
| 383 |
< |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
| 384 |
< |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
| 385 |
< |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
| 386 |
< |
|
| 387 |
< |
private: |
| 388 |
< |
double totMassOfMovingAtoms; |
| 389 |
< |
}; |
| 390 |
< |
|
| 391 |
< |
public: |
| 392 |
< |
|
| 393 |
< |
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
| 394 |
< |
~ZConstraint(); |
| 395 |
< |
|
| 396 |
< |
void setZConsTime(double time) {this->zconsTime = time;} |
| 397 |
< |
void getZConsTime() {return zconsTime;} |
| 398 |
< |
|
| 399 |
< |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
| 400 |
< |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
| 401 |
< |
|
| 402 |
< |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
| 403 |
< |
string getZConsOutput() {return zconsOutput;} |
| 404 |
< |
|
| 405 |
< |
virtual void integrate(); |
| 406 |
< |
|
| 407 |
< |
|
| 408 |
< |
#ifdef IS_MPI |
| 409 |
< |
virtual void update(); //which is called to indicate the molecules' migration |
| 410 |
< |
#endif |
| 411 |
< |
|
| 412 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
| 413 |
< |
|
| 414 |
< |
vector<Molecule*> zconsMols; //z-constraint molecules array |
| 415 |
< |
vector<ZConsState> states; //state of z-constraint molecules |
| 416 |
< |
|
| 417 |
< |
|
| 418 |
< |
|
| 419 |
< |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
| 420 |
< |
double totalMassOfUncons; //total mas of unconstraint molecules |
| 421 |
< |
|
| 422 |
< |
|
| 423 |
< |
protected: |
| 424 |
< |
|
| 425 |
< |
|
| 426 |
< |
|
| 427 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
| 428 |
< |
virtual void thermalize(void); |
| 429 |
< |
|
| 430 |
< |
void zeroOutVel(); |
| 431 |
< |
void doZconstraintForce(); |
| 432 |
< |
void doHarmonic(vector<double>& resPos); |
| 433 |
< |
bool checkZConsState(); |
| 434 |
< |
|
| 435 |
< |
bool haveFixedZMols(); |
| 436 |
< |
bool haveMovingZMols(); |
| 437 |
< |
|
| 438 |
< |
double calcZSys(); |
| 439 |
< |
|
| 440 |
< |
int isZConstraintMol(Molecule* mol); |
| 441 |
< |
|
| 442 |
< |
|
| 443 |
< |
double zconsTime; //sample time |
| 444 |
< |
double zconsTol; //tolerance of z-contratint |
| 445 |
< |
double zForceConst; //base force constant term |
| 446 |
< |
//which is estimate by OOPSE |
| 447 |
< |
|
| 448 |
< |
|
| 449 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
| 450 |
< |
vector<double> kz; //force constant array |
| 451 |
< |
|
| 452 |
< |
vector<double> zPos; // |
| 453 |
< |
|
| 454 |
< |
|
| 455 |
< |
vector<Molecule*> unconsMols; //unconstraint molecules array |
| 456 |
< |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
| 457 |
< |
|
| 458 |
< |
|
| 459 |
< |
vector<ZConsParaItem>* parameters; // |
| 460 |
< |
|
| 461 |
< |
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
| 462 |
< |
|
| 463 |
< |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
| 464 |
< |
vector<double> fz; |
| 465 |
< |
vector<double> curZPos; |
| 466 |
< |
|
| 467 |
< |
bool usingSMD; |
| 468 |
< |
vector<double> prevCantPos; |
| 469 |
< |
vector<double> cantPos; |
| 470 |
< |
vector<double> cantVel; |
| 471 |
< |
|
| 472 |
< |
double zconsFixTime; |
| 473 |
< |
double zconsGap; |
| 474 |
< |
bool hasZConsGap; |
| 475 |
< |
vector<double> endFixTime; |
| 476 |
< |
|
| 477 |
< |
int whichDirection; //constraint direction |
| 478 |
< |
|
| 479 |
< |
private: |
| 480 |
< |
|
| 481 |
< |
string zconsOutput; //filename of zconstraint output |
| 482 |
< |
ZConsWriter* fzOut; //z-constraint writer |
| 483 |
< |
|
| 484 |
< |
double curZconsTime; |
| 485 |
< |
|
| 486 |
< |
double calcMovingMolsCOMVel(); |
| 487 |
< |
double calcSysCOMVel(); |
| 488 |
< |
double calcTotalForce(); |
| 489 |
< |
void updateZPos(); |
| 490 |
< |
void updateCantPos(); |
| 491 |
< |
|
| 492 |
< |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
| 493 |
< |
friend class ForceSubtractionPolicy; |
| 494 |
< |
|
| 129 |
> |
|
| 130 |
> |
virtual double calcConservedQuantity() = 0; |
| 131 |
> |
|
| 132 |
> |
virtual DumpWriter* createDumpWriter() = 0; |
| 133 |
> |
|
| 134 |
> |
virtual StatWriter* createStatWriter() = 0; |
| 135 |
|
}; |
| 136 |
|
|
| 497 |
– |
|
| 498 |
– |
//Sympletic quaternion Scheme Integrator |
| 499 |
– |
//Reference: |
| 500 |
– |
// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna |
| 501 |
– |
//Symplectic quaternion Scheme for biophysical molecular dynamics |
| 502 |
– |
//116(20), 8649, J. Chem. Phys. (2002) |
| 503 |
– |
template<typename T> class SQSIntegrator : public T{ |
| 504 |
– |
public: |
| 505 |
– |
virtual void moveA(); |
| 506 |
– |
virtual void moveB(); |
| 507 |
– |
protected: |
| 508 |
– |
void freeRotor(); |
| 509 |
– |
void rotate(int k, double dt); |
| 137 |
|
|
| 138 |
< |
}; |
| 139 |
< |
#endif |
| 138 |
> |
} |
| 139 |
> |
#endif //INTEGRATORS_INTEGRATOR_HPP |
