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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 "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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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 int maxIteration = 300; |
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const double tol = 1.0e-6; |
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class RattleFramework; |
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template<typename T = BaseIntegrator> class Integrator : public T { |
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public: |
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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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virtual void integrateStep( int calcPot, int calcStress ); |
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virtual void preMove( void ); |
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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 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 void resetIntegrator( void ) { } |
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virtual void calcForce( int calcPot, int calcStress ); |
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virtual void calcForce( int calcPot, int calcStress ); |
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virtual void thermalize(); |
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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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virtual bool stopIntegrator() {return false;} |
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virtual void rotationPropagation( StuntDouble* sd, double ji[3] ); |
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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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ForceFields* myFF; |
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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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int isConstrained; // boolean to know whether the systems contains |
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// 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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RattleFramework* rattle; |
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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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short isFirst; /*boolean for the first time integrate is called */ |
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double dt; |
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double dt2; |
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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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typedef Integrator<BaseIntegrator> RealIntegrator; |
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// ansi instantiation |
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//template class Integrator<BaseIntegrator>; |
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template<typename T> class NVE : public T { |
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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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virtual ~NVE(){} |
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}; |
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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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protected: |
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double targetTemp; |
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double tauThermostat; |
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short int have_tau_thermostat, have_target_temp; |
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double *oldVel; |
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template<typename T> class NPTi : public T{ |
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template<typename T> class NPT : public T{ |
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public: |
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NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTi(); |
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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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/* accIntegralOfChidt(); */ |
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} |
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virtual double getConservedQuantity(void); |
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virtual double getConservedQuantity(void) = 0; |
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virtual string getAdditionalParameters(void) = 0; |
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double myTauThermo( void ) { return tauThermostat; } |
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double myTauBaro( void ) { return tauBarostat; } |
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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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virtual void resetIntegrator( void ); |
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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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193 |
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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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// chi and eta are the propagated degrees of freedom |
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double oldChi; |
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double prevChi; |
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double chi; |
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double eta; |
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double NkBT; |
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double fkBT; |
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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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double integralOfChidt; |
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// targetTemp, targetPressure, and tauBarostat must be set. |
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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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double targetTemp; |
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}; |
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template<typename T> class NPTim : public T{ |
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template<typename T> class NPTi : public T{ |
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public: |
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NPTi( SimInfo *theInfo, ForceFields* the_ff); |
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~NPTi(); |
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NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPTim() {} |
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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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accIntegralOfChidt(); |
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} |
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|
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virtual double getConservedQuantity(void); |
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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;} |
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void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
228 |
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|
252 |
> |
virtual void resetIntegrator(void); |
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> |
virtual string getAdditionalParameters(void); |
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protected: |
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231 |
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virtual void moveA( void ); |
232 |
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virtual void moveB( void ); |
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234 |
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virtual int readyCheck(); |
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258 |
< |
virtual void resetIntegrator( void ); |
258 |
> |
virtual void evolveEtaA(void); |
259 |
> |
virtual void evolveEtaB(void); |
260 |
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|
261 |
< |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
239 |
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|
240 |
< |
Molecule* myMolecules; |
241 |
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Atom** myAtoms; |
261 |
> |
virtual bool etaConverged( void ); |
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|
263 |
< |
// chi and eta are the propagated degrees of freedom |
263 |
> |
virtual void scaleSimBox( void ); |
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|
265 |
< |
double chi; |
266 |
< |
double eta; |
267 |
< |
double NkBT; |
268 |
< |
double integralOfChidt; |
265 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
266 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
267 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
268 |
> |
int index, double sc[3]); |
269 |
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|
270 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
251 |
< |
// One of qmass or tauThermostat must be set; |
270 |
> |
virtual void calcVelScale( void ); |
271 |
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|
272 |
< |
double targetTemp; |
273 |
< |
double targetPressure; |
255 |
< |
double tauThermostat; |
256 |
< |
double tauBarostat; |
257 |
< |
|
258 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
259 |
< |
short int have_target_pressure; |
260 |
< |
double chiTolerance; |
261 |
< |
short int have_chi_tolerance; |
262 |
< |
double posIterTolerance; |
263 |
< |
short int have_pos_iter_tolerance; |
264 |
< |
|
272 |
> |
double eta, oldEta, prevEta; |
273 |
> |
double vScale; |
274 |
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}; |
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276 |
< |
template<typename T> class NPTzm : public T{ |
276 |
> |
template<typename T> class NPTf : public T{ |
277 |
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278 |
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public: |
279 |
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|
280 |
< |
NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
281 |
< |
virtual ~NPTzm() {}; |
280 |
> |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
281 |
> |
virtual ~NPTf(); |
282 |
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|
283 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
284 |
< |
calcStress = 1; |
285 |
< |
T::integrateStep( calcPot, calcStress ); |
277 |
< |
} |
283 |
> |
virtual double getConservedQuantity(void); |
284 |
> |
virtual string getAdditionalParameters(void); |
285 |
> |
virtual void resetIntegrator(void); |
286 |
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|
279 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
280 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
281 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
282 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
283 |
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|
287 |
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protected: |
288 |
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|
289 |
< |
virtual void moveA( void ); |
290 |
< |
virtual void moveB( void ); |
289 |
> |
virtual void evolveEtaA(void); |
290 |
> |
virtual void evolveEtaB(void); |
291 |
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|
292 |
< |
virtual int readyCheck(); |
292 |
> |
virtual bool etaConverged( void ); |
293 |
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|
294 |
< |
virtual void resetIntegrator( void ); |
294 |
> |
virtual void scaleSimBox( void ); |
295 |
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|
296 |
< |
Molecule* myMolecules; |
297 |
< |
Atom** myAtoms; |
296 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
297 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
298 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
299 |
> |
int index, double sc[3]); |
300 |
|
|
301 |
< |
// chi and eta are the propagated degrees of freedom |
301 |
> |
virtual void calcVelScale( void ); |
302 |
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|
303 |
< |
double chi; |
304 |
< |
double eta; |
305 |
< |
double etaZ; |
306 |
< |
double NkBT; |
302 |
< |
|
303 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
304 |
< |
// One of qmass or tauThermostat must be set; |
305 |
< |
|
306 |
< |
double targetTemp; |
307 |
< |
double targetPressure; |
308 |
< |
double tauThermostat; |
309 |
< |
double tauBarostat; |
310 |
< |
|
311 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
312 |
< |
short int have_target_pressure; |
313 |
< |
|
303 |
> |
double eta[3][3]; |
304 |
> |
double oldEta[3][3]; |
305 |
> |
double prevEta[3][3]; |
306 |
> |
double vScale[3][3]; |
307 |
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}; |
308 |
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|
309 |
< |
template<typename T> class NPTf : public T{ |
309 |
> |
template<typename T> class NPTxyz : public T{ |
310 |
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311 |
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public: |
312 |
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|
313 |
< |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
314 |
< |
virtual ~NPTf(); |
313 |
> |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
314 |
> |
virtual ~NPTxyz(); |
315 |
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|
323 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
324 |
– |
calcStress = 1; |
325 |
– |
T::integrateStep( calcPot, calcStress ); |
326 |
– |
} |
327 |
– |
|
316 |
|
virtual double getConservedQuantity(void); |
317 |
+ |
virtual string getAdditionalParameters(void); |
318 |
+ |
virtual void resetIntegrator(void); |
319 |
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|
330 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
331 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
332 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
333 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
334 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
335 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
336 |
– |
|
320 |
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protected: |
321 |
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|
322 |
< |
virtual void moveA( void ); |
323 |
< |
virtual void moveB( void ); |
322 |
> |
virtual void evolveEtaA(void); |
323 |
> |
virtual void evolveEtaB(void); |
324 |
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|
325 |
< |
virtual void resetIntegrator( void ); |
325 |
> |
virtual bool etaConverged( void ); |
326 |
|
|
327 |
< |
virtual int readyCheck(); |
327 |
> |
virtual void scaleSimBox( void ); |
328 |
|
|
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 |
< |
// chi and eta are the propagated degrees of freedom |
334 |
> |
virtual void calcVelScale( void ); |
335 |
|
|
349 |
– |
double chi; |
336 |
|
double eta[3][3]; |
337 |
< |
double NkBT; |
338 |
< |
double fkBT; |
339 |
< |
|
354 |
< |
int Nparticles; |
355 |
< |
|
356 |
< |
double *oldPos; |
357 |
< |
double *oldVel; |
358 |
< |
double *oldJi; |
359 |
< |
|
360 |
< |
double integralOfChidt; |
361 |
< |
|
362 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
363 |
< |
// One of qmass or tauThermostat must be set; |
364 |
< |
|
365 |
< |
double targetTemp; |
366 |
< |
double targetPressure; |
367 |
< |
double tauThermostat; |
368 |
< |
double tauBarostat; |
369 |
< |
|
370 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
371 |
< |
short int have_target_pressure; |
372 |
< |
double chiTolerance; |
373 |
< |
short int have_chi_tolerance; |
374 |
< |
double posIterTolerance; |
375 |
< |
short int have_pos_iter_tolerance; |
376 |
< |
double etaTolerance; |
377 |
< |
short int have_eta_tolerance; |
337 |
> |
double oldEta[3][3]; |
338 |
> |
double prevEta[3][3]; |
339 |
> |
double vScale[3][3]; |
340 |
|
}; |
341 |
|
|
380 |
– |
template<typename T> class NPTxym : public T{ |
342 |
|
|
382 |
– |
public: |
383 |
– |
|
384 |
– |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
385 |
– |
virtual ~NPTxym() {}; |
386 |
– |
|
387 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
388 |
– |
calcStress = 1; |
389 |
– |
T::integrateStep( calcPot, calcStress ); |
390 |
– |
} |
391 |
– |
|
392 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
393 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
394 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
395 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
396 |
– |
|
397 |
– |
protected: |
398 |
– |
|
399 |
– |
virtual void moveA( void ); |
400 |
– |
virtual void moveB( void ); |
401 |
– |
|
402 |
– |
virtual int readyCheck(); |
403 |
– |
|
404 |
– |
virtual void resetIntegrator( void ); |
405 |
– |
|
406 |
– |
Molecule* myMolecules; |
407 |
– |
Atom** myAtoms; |
408 |
– |
|
409 |
– |
// chi and eta are the propagated degrees of freedom |
410 |
– |
|
411 |
– |
double chi; |
412 |
– |
double eta; |
413 |
– |
double etaX; |
414 |
– |
double etaY; |
415 |
– |
double NkBT; |
416 |
– |
|
417 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
418 |
– |
// One of qmass or tauThermostat must be set; |
419 |
– |
|
420 |
– |
double targetTemp; |
421 |
– |
double targetPressure; |
422 |
– |
double tauThermostat; |
423 |
– |
double tauBarostat; |
424 |
– |
|
425 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
426 |
– |
short int have_target_pressure; |
427 |
– |
|
428 |
– |
}; |
429 |
– |
|
430 |
– |
|
431 |
– |
template<typename T> class NPTfm : public T{ |
432 |
– |
|
433 |
– |
public: |
434 |
– |
|
435 |
– |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
436 |
– |
virtual ~NPTfm() {}; |
437 |
– |
|
438 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
439 |
– |
calcStress = 1; |
440 |
– |
T::integrateStep( calcPot, calcStress ); |
441 |
– |
accIntegralOfChidt(); |
442 |
– |
} |
443 |
– |
|
444 |
– |
virtual double getConservedQuantity(void); |
445 |
– |
|
446 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
447 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
448 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
449 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
450 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
451 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
452 |
– |
|
453 |
– |
protected: |
454 |
– |
|
455 |
– |
virtual void moveA( void ); |
456 |
– |
virtual void moveB( void ); |
457 |
– |
|
458 |
– |
virtual void resetIntegrator( void ); |
459 |
– |
|
460 |
– |
virtual int readyCheck(); |
461 |
– |
|
462 |
– |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
463 |
– |
|
464 |
– |
Molecule* myMolecules; |
465 |
– |
Atom** myAtoms; |
466 |
– |
|
467 |
– |
// chi and eta are the propagated degrees of freedom |
468 |
– |
|
469 |
– |
double chi; |
470 |
– |
double eta[3][3]; |
471 |
– |
double NkBT; |
472 |
– |
double integralOfChidt; |
473 |
– |
|
474 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
475 |
– |
// One of qmass or tauThermostat must be set; |
476 |
– |
|
477 |
– |
double targetTemp; |
478 |
– |
double targetPressure; |
479 |
– |
double tauThermostat; |
480 |
– |
double tauBarostat; |
481 |
– |
|
482 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
483 |
– |
short int have_target_pressure; |
484 |
– |
double chiTolerance; |
485 |
– |
short int have_chi_tolerance; |
486 |
– |
double posIterTolerance; |
487 |
– |
short int have_pos_iter_tolerance; |
488 |
– |
|
489 |
– |
}; |
490 |
– |
|
491 |
– |
|
492 |
– |
template<typename T> class NPTpr : public T{ |
493 |
– |
|
494 |
– |
public: |
495 |
– |
|
496 |
– |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
497 |
– |
virtual ~NPTpr() {}; |
498 |
– |
|
499 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
500 |
– |
calcStress = 1; |
501 |
– |
T::integrateStep( calcPot, calcStress ); |
502 |
– |
} |
503 |
– |
|
504 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
505 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
506 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
507 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
508 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
509 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
510 |
– |
|
511 |
– |
protected: |
512 |
– |
|
513 |
– |
virtual void moveA( void ); |
514 |
– |
virtual void moveB( void ); |
515 |
– |
|
516 |
– |
virtual int readyCheck(); |
517 |
– |
|
518 |
– |
virtual void resetIntegrator( void ); |
519 |
– |
|
520 |
– |
// chi and eta are the propagated degrees of freedom |
521 |
– |
|
522 |
– |
double chi; |
523 |
– |
double eta[3][3]; |
524 |
– |
double NkBT; |
525 |
– |
|
526 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
527 |
– |
// One of qmass or tauThermostat must be set; |
528 |
– |
|
529 |
– |
double targetTemp; |
530 |
– |
double targetPressure; |
531 |
– |
double tauThermostat; |
532 |
– |
double tauBarostat; |
533 |
– |
|
534 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
535 |
– |
short int have_target_pressure; |
536 |
– |
double chiTolerance; |
537 |
– |
short int have_chi_tolerance; |
538 |
– |
double posIterTolerance; |
539 |
– |
short int have_pos_iter_tolerance; |
540 |
– |
|
541 |
– |
}; |
542 |
– |
|
543 |
– |
|
343 |
|
template<typename T> class ZConstraint : public T { |
344 |
< |
|
345 |
< |
public: |
344 |
> |
|
345 |
> |
public: |
346 |
|
class ForceSubtractionPolicy{ |
347 |
|
public: |
348 |
|
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
349 |
|
|
350 |
< |
virtual void update() = 0; |
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 |
< |
|
355 |
> |
|
356 |
|
protected: |
357 |
< |
ZConstraint<T>* zconsIntegrator;; |
357 |
> |
ZConstraint<T>* zconsIntegrator; |
358 |
|
}; |
359 |
|
|
360 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
361 |
|
|
362 |
|
public: |
363 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
364 |
< |
virtual void update(); |
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 |
< |
|
369 |
> |
|
370 |
|
private: |
371 |
|
int totNumOfMovingAtoms; |
372 |
|
}; |
374 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
375 |
|
|
376 |
|
public: |
377 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
378 |
< |
|
379 |
< |
virtual void update(); |
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); |
390 |
|
|
391 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
392 |
|
~ZConstraint(); |
393 |
< |
|
393 |
> |
|
394 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
395 |
|
void getZConsTime() {return zconsTime;} |
396 |
< |
|
396 |
> |
|
397 |
|
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
398 |
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
399 |
< |
|
399 |
> |
|
400 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
401 |
|
string getZConsOutput() {return zconsOutput;} |
402 |
< |
|
402 |
> |
|
403 |
|
virtual void integrate(); |
605 |
– |
|
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 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
424 |
< |
|
425 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
423 |
> |
|
424 |
> |
|
425 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
426 |
|
virtual void thermalize(void); |
427 |
< |
|
427 |
> |
|
428 |
|
void zeroOutVel(); |
429 |
|
void doZconstraintForce(); |
430 |
< |
void doHarmonic(); |
430 |
> |
void doHarmonic(vector<double>& resPos); |
431 |
|
bool checkZConsState(); |
432 |
|
|
433 |
|
bool haveFixedZMols(); |
442 |
|
double zconsTol; //tolerance of z-contratint |
443 |
|
double zForceConst; //base force constant term |
444 |
|
//which is estimate by OOPSE |
445 |
< |
|
446 |
< |
vector<Molecule*> zconsMols; //z-constraint molecules array |
447 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
445 |
> |
|
446 |
> |
|
447 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
448 |
|
vector<double> kz; //force constant array |
449 |
< |
vector<ZConsState> states; //state of z-constraint molecules |
449 |
> |
|
450 |
|
vector<double> zPos; // |
451 |
< |
|
452 |
< |
|
451 |
> |
|
452 |
> |
|
453 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
454 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
645 |
– |
double totalMassOfUncons; //total mas of unconstraint molecules |
455 |
|
|
456 |
+ |
|
457 |
|
vector<ZConsParaItem>* parameters; // |
458 |
< |
|
458 |
> |
|
459 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
460 |
|
|
461 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
462 |
< |
double* fz; |
463 |
< |
double* curZPos; |
654 |
< |
|
655 |
< |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
461 |
> |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
462 |
> |
vector<double> fz; |
463 |
> |
vector<double> curZPos; |
464 |
|
|
465 |
< |
int whichDirection; //constraint direction |
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 |
< |
|
478 |
> |
|
479 |
|
string zconsOutput; //filename of zconstraint output |
480 |
|
ZConsWriter* fzOut; //z-constraint writer |
481 |
|
|
482 |
< |
double curZconsTime; |
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; |