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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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const int maxIteration = 300; |
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const double tol = 1.0e-6; |
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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 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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virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
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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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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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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 |
70 |
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|
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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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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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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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NPT ( SimInfo *theInfo, ForceFields* the_ff); |
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virtual ~NPT(); |
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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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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 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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virtual void getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]) = 0; |
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virtual void calcVelScale( void ) = 0; |
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virtual bool chiConverged( void ); |
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virtual bool etaConverged( void ) = 0; |
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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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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 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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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: |
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virtual void evolveEtaA(void); |
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virtual void evolveEtaB(void); |
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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], |
259 |
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virtual void getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]); |
261 |
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262 |
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virtual void calcVelScale( void ); |
263 |
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264 |
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double eta, oldEta, prevEta; |
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double vScale; |
266 |
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}; |
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template<typename T> class NPTzm : public T{ |
268 |
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template<typename T> class NPTf : public T{ |
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public: |
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272 |
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NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
273 |
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virtual ~NPTzm() {}; |
272 |
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NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
273 |
> |
virtual ~NPTf(); |
274 |
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|
275 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
276 |
< |
calcStress = 1; |
277 |
< |
T::integrateStep( calcPot, calcStress ); |
266 |
< |
} |
267 |
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|
268 |
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
269 |
< |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
270 |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
271 |
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void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
275 |
> |
virtual double getConservedQuantity(void); |
276 |
> |
virtual string getAdditionalParameters(void); |
277 |
> |
virtual void resetIntegrator(void); |
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protected: |
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281 |
< |
virtual void moveA( void ); |
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virtual void moveB( void ); |
281 |
> |
virtual void evolveEtaA(void); |
282 |
> |
virtual void evolveEtaB(void); |
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virtual int readyCheck(); |
284 |
> |
virtual bool etaConverged( void ); |
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virtual void resetIntegrator( void ); |
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> |
virtual void scaleSimBox( void ); |
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Molecule* myMolecules; |
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Atom** myAtoms; |
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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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// chi and eta are the propagated degrees of freedom |
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> |
virtual void calcVelScale( void ); |
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< |
double chi; |
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double eta; |
297 |
< |
double etaZ; |
298 |
< |
double NkBT; |
291 |
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|
292 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
293 |
< |
// One of qmass or tauThermostat must be set; |
294 |
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|
295 |
< |
double targetTemp; |
296 |
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double targetPressure; |
297 |
< |
double tauThermostat; |
298 |
< |
double tauBarostat; |
299 |
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|
300 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
301 |
< |
short int have_target_pressure; |
302 |
< |
|
295 |
> |
double eta[3][3]; |
296 |
> |
double oldEta[3][3]; |
297 |
> |
double prevEta[3][3]; |
298 |
> |
double vScale[3][3]; |
299 |
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}; |
300 |
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301 |
< |
template<typename T> class NPTf : public T{ |
301 |
> |
template<typename T> class NPTxyz : public T{ |
302 |
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303 |
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public: |
304 |
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|
305 |
< |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
306 |
< |
virtual ~NPTf(); |
305 |
> |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
306 |
> |
virtual ~NPTxyz(); |
307 |
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|
308 |
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virtual double getConservedQuantity(void); |
309 |
+ |
virtual string getAdditionalParameters(void); |
310 |
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virtual void resetIntegrator(void); |
311 |
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|
312 |
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protected: |
320 |
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|
321 |
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virtual void getVelScaleA( double sc[3], double vel[3] ); |
322 |
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virtual void getVelScaleB( double sc[3], int index ); |
323 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
323 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
324 |
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int index, double sc[3]); |
325 |
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|
326 |
+ |
virtual void calcVelScale( void ); |
327 |
+ |
|
328 |
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double eta[3][3]; |
329 |
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double oldEta[3][3]; |
330 |
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double prevEta[3][3]; |
331 |
+ |
double vScale[3][3]; |
332 |
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}; |
333 |
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334 |
– |
template<typename T> class NPTxym : public T{ |
334 |
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|
335 |
< |
public: |
335 |
> |
template<typename T> class ZConstraint : public T { |
336 |
|
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337 |
< |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
339 |
< |
virtual ~NPTxym() {}; |
340 |
< |
|
341 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
342 |
< |
calcStress = 1; |
343 |
< |
T::integrateStep( calcPot, calcStress ); |
344 |
< |
} |
345 |
< |
|
346 |
< |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
347 |
< |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
348 |
< |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
349 |
< |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
350 |
< |
|
351 |
< |
protected: |
352 |
< |
|
353 |
< |
virtual void moveA( void ); |
354 |
< |
virtual void moveB( void ); |
355 |
< |
|
356 |
< |
virtual int readyCheck(); |
357 |
< |
|
358 |
< |
virtual void resetIntegrator( void ); |
359 |
< |
|
360 |
< |
Molecule* myMolecules; |
361 |
< |
Atom** myAtoms; |
362 |
< |
|
363 |
< |
// chi and eta are the propagated degrees of freedom |
364 |
< |
|
365 |
< |
double chi; |
366 |
< |
double eta; |
367 |
< |
double etaX; |
368 |
< |
double etaY; |
369 |
< |
double NkBT; |
370 |
< |
|
371 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
372 |
< |
// One of qmass or tauThermostat must be set; |
373 |
< |
|
374 |
< |
double targetTemp; |
375 |
< |
double targetPressure; |
376 |
< |
double tauThermostat; |
377 |
< |
double tauBarostat; |
378 |
< |
|
379 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
380 |
< |
short int have_target_pressure; |
381 |
< |
|
382 |
< |
}; |
383 |
< |
|
384 |
< |
template<typename T> class ZConstraint : public T { |
385 |
< |
|
386 |
< |
public: |
337 |
> |
public: |
338 |
|
class ForceSubtractionPolicy{ |
339 |
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public: |
340 |
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ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
341 |
|
|
342 |
< |
virtual void update() = 0; |
342 |
> |
virtual void update() = 0; |
343 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
344 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
345 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
346 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
347 |
< |
|
347 |
> |
|
348 |
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protected: |
349 |
|
ZConstraint<T>* zconsIntegrator; |
350 |
|
}; |
352 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
353 |
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|
354 |
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public: |
355 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
356 |
< |
virtual void update(); |
355 |
> |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
356 |
> |
virtual void update(); |
357 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
358 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
359 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
360 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
361 |
< |
|
361 |
> |
|
362 |
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private: |
363 |
|
int totNumOfMovingAtoms; |
364 |
|
}; |
366 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
367 |
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|
368 |
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public: |
369 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
370 |
< |
|
371 |
< |
virtual void update(); |
369 |
> |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
370 |
> |
|
371 |
> |
virtual void update(); |
372 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
373 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
374 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
382 |
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|
383 |
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ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
384 |
|
~ZConstraint(); |
385 |
< |
|
385 |
> |
|
386 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
387 |
|
void getZConsTime() {return zconsTime;} |
388 |
< |
|
388 |
> |
|
389 |
|
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
390 |
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
391 |
< |
|
391 |
> |
|
392 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
393 |
|
string getZConsOutput() {return zconsOutput;} |
394 |
< |
|
394 |
> |
|
395 |
|
virtual void integrate(); |
445 |
– |
|
396 |
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|
397 |
+ |
|
398 |
|
#ifdef IS_MPI |
399 |
|
virtual void update(); //which is called to indicate the molecules' migration |
400 |
|
#endif |
401 |
|
|
402 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
402 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
403 |
|
|
404 |
|
vector<Molecule*> zconsMols; //z-constraint molecules array |
405 |
|
vector<ZConsState> states; //state of z-constraint molecules |
406 |
|
|
456 |
– |
|
407 |
|
|
408 |
+ |
|
409 |
|
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
410 |
|
double totalMassOfUncons; //total mas of unconstraint molecules |
411 |
|
|
413 |
|
protected: |
414 |
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|
415 |
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|
416 |
< |
|
417 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
416 |
> |
|
417 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
418 |
|
virtual void thermalize(void); |
419 |
< |
|
419 |
> |
|
420 |
|
void zeroOutVel(); |
421 |
|
void doZconstraintForce(); |
422 |
< |
void doHarmonic(); |
422 |
> |
void doHarmonic(vector<double>& resPos); |
423 |
|
bool checkZConsState(); |
424 |
|
|
425 |
|
bool haveFixedZMols(); |
434 |
|
double zconsTol; //tolerance of z-contratint |
435 |
|
double zForceConst; //base force constant term |
436 |
|
//which is estimate by OOPSE |
486 |
– |
|
437 |
|
|
438 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
438 |
> |
|
439 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
440 |
|
vector<double> kz; //force constant array |
441 |
|
|
442 |
|
vector<double> zPos; // |
443 |
< |
|
444 |
< |
|
443 |
> |
|
444 |
> |
|
445 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
446 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
447 |
|
|
448 |
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|
449 |
|
vector<ZConsParaItem>* parameters; // |
450 |
< |
|
450 |
> |
|
451 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
452 |
|
|
453 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
454 |
< |
double* fz; |
455 |
< |
double* curZPos; |
505 |
< |
|
453 |
> |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
454 |
> |
vector<double> fz; |
455 |
> |
vector<double> curZPos; |
456 |
|
|
457 |
+ |
bool usingSMD; |
458 |
+ |
vector<double> cantPos; |
459 |
+ |
vector<double> cantVel; |
460 |
|
|
461 |
< |
int whichDirection; //constraint direction |
461 |
> |
double zconsFixTime; |
462 |
> |
double zconsGap; |
463 |
> |
bool hasZConsGap; |
464 |
> |
vector<double> endFixTime; |
465 |
|
|
466 |
+ |
int whichDirection; //constraint direction |
467 |
+ |
|
468 |
|
private: |
469 |
< |
|
469 |
> |
|
470 |
|
string zconsOutput; //filename of zconstraint output |
471 |
|
ZConsWriter* fzOut; //z-constraint writer |
472 |
|
|
473 |
< |
double curZconsTime; |
473 |
> |
double curZconsTime; |
474 |
|
|
475 |
|
double calcMovingMolsCOMVel(); |
476 |
|
double calcSysCOMVel(); |
477 |
|
double calcTotalForce(); |
478 |
+ |
void updateZPos(); |
479 |
+ |
void updateCantPos(); |
480 |
|
|
481 |
|
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
482 |
|
friend class ForceSubtractionPolicy; |
483 |
|
|
484 |
|
}; |
485 |
|
|
486 |
+ |
/* |
487 |
+ |
//Steered Molecular Dynamics |
488 |
+ |
template<typename T> class SMD : public T{ |
489 |
+ |
public: |
490 |
+ |
SMD( SimInfo *theInfo, ForceFields* the_ff); |
491 |
+ |
~SMD(); |
492 |
+ |
|
493 |
+ |
virtual void integrate(); |
494 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
495 |
+ |
}; |
496 |
+ |
*/ |
497 |
|
#endif |