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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 "Atom.hpp" |
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#include "StuntDouble.hpp" |
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#include "Molecule.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 "ZConsWriter.hpp" |
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#include "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 "restraints/ThermoIntegrationForceManager.hpp" |
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#include "io/DumpWriter.hpp" |
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#include "io/StatWriter.hpp" |
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#include "io/RestWriter.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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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Globals* simParams; |
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ForceManager* forceMan_; |
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bool needPotential; |
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bool needStress; |
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bool needReset; |
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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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RestWriter* restWriter; |
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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 resetTime; |
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double dt; |
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|
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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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|
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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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|
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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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|
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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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|
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template<typename T> class NVT : public T { |
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|
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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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|
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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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private: |
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|
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virtual double calcConservedQuantity() = 0; |
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|
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virtual DumpWriter* createDumpWriter() = 0; |
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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); |
249 |
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~NPTi(); |
250 |
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|
251 |
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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: |
255 |
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|
256 |
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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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|
265 |
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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]); |
269 |
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|
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virtual void calcVelScale( void ); |
271 |
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|
272 |
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double eta, oldEta, prevEta; |
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double vScale; |
274 |
< |
}; |
275 |
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|
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template<typename T> class NPTf : public T{ |
277 |
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|
278 |
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public: |
279 |
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|
280 |
< |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
281 |
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virtual ~NPTf(); |
282 |
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|
283 |
< |
virtual double getConservedQuantity(void); |
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< |
virtual string getAdditionalParameters(void); |
285 |
< |
virtual void resetIntegrator(void); |
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|
287 |
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protected: |
288 |
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|
289 |
< |
virtual void evolveEtaA(void); |
290 |
< |
virtual void evolveEtaB(void); |
291 |
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|
292 |
< |
virtual bool etaConverged( void ); |
293 |
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|
294 |
< |
virtual void scaleSimBox( void ); |
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|
296 |
< |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
297 |
< |
virtual void getVelScaleB( double sc[3], int index ); |
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< |
virtual void getPosScale(double pos[3], double COM[3], |
299 |
< |
int index, double sc[3]); |
300 |
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|
301 |
< |
virtual void calcVelScale( void ); |
302 |
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|
303 |
< |
double eta[3][3]; |
304 |
< |
double oldEta[3][3]; |
305 |
< |
double prevEta[3][3]; |
306 |
< |
double vScale[3][3]; |
307 |
< |
}; |
308 |
< |
|
309 |
< |
template<typename T> class NPTxyz : public T{ |
310 |
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|
311 |
< |
public: |
312 |
< |
|
313 |
< |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
314 |
< |
virtual ~NPTxyz(); |
315 |
< |
|
316 |
< |
virtual double getConservedQuantity(void); |
317 |
< |
virtual string getAdditionalParameters(void); |
318 |
< |
virtual void resetIntegrator(void); |
319 |
< |
|
320 |
< |
protected: |
321 |
< |
|
322 |
< |
virtual void evolveEtaA(void); |
323 |
< |
virtual void evolveEtaB(void); |
324 |
< |
|
325 |
< |
virtual bool etaConverged( void ); |
326 |
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|
327 |
< |
virtual void scaleSimBox( void ); |
328 |
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|
329 |
< |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
330 |
< |
virtual void getVelScaleB( double sc[3], int index ); |
331 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
332 |
< |
int index, double sc[3]); |
333 |
< |
|
334 |
< |
virtual void calcVelScale( void ); |
335 |
< |
|
336 |
< |
double eta[3][3]; |
337 |
< |
double oldEta[3][3]; |
338 |
< |
double prevEta[3][3]; |
339 |
< |
double vScale[3][3]; |
340 |
< |
}; |
341 |
< |
|
342 |
< |
|
343 |
< |
template<typename T> class ZConstraint : public T { |
344 |
< |
|
345 |
< |
public: |
346 |
< |
class ForceSubtractionPolicy{ |
347 |
< |
public: |
348 |
< |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
349 |
< |
|
350 |
< |
virtual void update() = 0; |
351 |
< |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
352 |
< |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
353 |
< |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
354 |
< |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
355 |
< |
|
356 |
< |
protected: |
357 |
< |
ZConstraint<T>* zconsIntegrator; |
139 |
> |
virtual StatWriter* createStatWriter() = 0; |
140 |
|
}; |
141 |
|
|
360 |
– |
class PolicyByNumber : public ForceSubtractionPolicy{ |
361 |
– |
|
362 |
– |
public: |
363 |
– |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
364 |
– |
virtual void update(); |
365 |
– |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
366 |
– |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
367 |
– |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
368 |
– |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
369 |
– |
|
370 |
– |
private: |
371 |
– |
int totNumOfMovingAtoms; |
372 |
– |
}; |
373 |
– |
|
374 |
– |
class PolicyByMass : public ForceSubtractionPolicy{ |
375 |
– |
|
376 |
– |
public: |
377 |
– |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
378 |
– |
|
379 |
– |
virtual void update(); |
380 |
– |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
381 |
– |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
382 |
– |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
383 |
– |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
384 |
– |
|
385 |
– |
private: |
386 |
– |
double totMassOfMovingAtoms; |
387 |
– |
}; |
388 |
– |
|
389 |
– |
public: |
390 |
– |
|
391 |
– |
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
392 |
– |
~ZConstraint(); |
393 |
– |
|
394 |
– |
void setZConsTime(double time) {this->zconsTime = time;} |
395 |
– |
void getZConsTime() {return zconsTime;} |
396 |
– |
|
397 |
– |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
398 |
– |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
399 |
– |
|
400 |
– |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
401 |
– |
string getZConsOutput() {return zconsOutput;} |
402 |
– |
|
403 |
– |
virtual void integrate(); |
404 |
– |
|
405 |
– |
|
406 |
– |
#ifdef IS_MPI |
407 |
– |
virtual void update(); //which is called to indicate the molecules' migration |
408 |
– |
#endif |
409 |
– |
|
410 |
– |
enum ZConsState {zcsMoving, zcsFixed}; |
411 |
– |
|
412 |
– |
vector<Molecule*> zconsMols; //z-constraint molecules array |
413 |
– |
vector<ZConsState> states; //state of z-constraint molecules |
414 |
– |
|
415 |
– |
|
416 |
– |
|
417 |
– |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
418 |
– |
double totalMassOfUncons; //total mas of unconstraint molecules |
419 |
– |
|
420 |
– |
|
421 |
– |
protected: |
422 |
– |
|
423 |
– |
|
424 |
– |
|
425 |
– |
virtual void calcForce( int calcPot, int calcStress ); |
426 |
– |
virtual void thermalize(void); |
427 |
– |
|
428 |
– |
void zeroOutVel(); |
429 |
– |
void doZconstraintForce(); |
430 |
– |
void doHarmonic(vector<double>& resPos); |
431 |
– |
bool checkZConsState(); |
432 |
– |
|
433 |
– |
bool haveFixedZMols(); |
434 |
– |
bool haveMovingZMols(); |
435 |
– |
|
436 |
– |
double calcZSys(); |
437 |
– |
|
438 |
– |
int isZConstraintMol(Molecule* mol); |
439 |
– |
|
440 |
– |
|
441 |
– |
double zconsTime; //sample time |
442 |
– |
double zconsTol; //tolerance of z-contratint |
443 |
– |
double zForceConst; //base force constant term |
444 |
– |
//which is estimate by OOPSE |
445 |
– |
|
446 |
– |
|
447 |
– |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
448 |
– |
vector<double> kz; //force constant array |
449 |
– |
|
450 |
– |
vector<double> zPos; // |
451 |
– |
|
452 |
– |
|
453 |
– |
vector<Molecule*> unconsMols; //unconstraint molecules array |
454 |
– |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
455 |
– |
|
456 |
– |
|
457 |
– |
vector<ZConsParaItem>* parameters; // |
458 |
– |
|
459 |
– |
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
460 |
– |
|
461 |
– |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
462 |
– |
vector<double> fz; |
463 |
– |
vector<double> curZPos; |
464 |
– |
|
465 |
– |
bool usingSMD; |
466 |
– |
vector<double> prevCantPos; |
467 |
– |
vector<double> cantPos; |
468 |
– |
vector<double> cantVel; |
469 |
– |
|
470 |
– |
double zconsFixTime; |
471 |
– |
double zconsGap; |
472 |
– |
bool hasZConsGap; |
473 |
– |
vector<double> endFixTime; |
474 |
– |
|
475 |
– |
int whichDirection; //constraint direction |
476 |
– |
|
477 |
– |
private: |
478 |
– |
|
479 |
– |
string zconsOutput; //filename of zconstraint output |
480 |
– |
ZConsWriter* fzOut; //z-constraint writer |
481 |
– |
|
482 |
– |
double curZconsTime; |
483 |
– |
|
484 |
– |
double calcMovingMolsCOMVel(); |
485 |
– |
double calcSysCOMVel(); |
486 |
– |
double calcTotalForce(); |
487 |
– |
void updateZPos(); |
488 |
– |
void updateCantPos(); |
489 |
– |
|
490 |
– |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
491 |
– |
friend class ForceSubtractionPolicy; |
492 |
– |
|
493 |
– |
}; |
494 |
– |
|
495 |
– |
|
496 |
– |
//Sympletic quaternion Scheme Integrator |
497 |
– |
//Reference: |
498 |
– |
// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna |
499 |
– |
//Symplectic quaternion Scheme for biophysical molecular dynamics |
500 |
– |
//116(20), 8649, J. Chem. Phys. (2002) |
501 |
– |
template<typename T> class SQSIntegrator : public T{ |
502 |
– |
public: |
503 |
– |
virtual void moveA(); |
504 |
– |
virtual void moveB(); |
505 |
– |
protected: |
506 |
– |
void freeRotor(); |
507 |
– |
void rotate(int k, double dt); |
142 |
|
|
143 |
< |
}; |
144 |
< |
#endif |
143 |
> |
} |
144 |
> |
#endif //INTEGRATORS_INTEGRATOR_HPP |