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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] ); |
48 |
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47 |
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double A[3][3] ); |
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49 |
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ForceFields* myFF; |
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SimInfo *info; // all the info we'll ever need |
56 |
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int nMols; |
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int isConstrained; // boolean to know whether the systems contains |
59 |
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// constraints. |
59 |
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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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}; |
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template<typename T> class ZConstraint : public T { |
302 |
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public: |
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public: |
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class ForceSubstractionPolicy{ |
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public: |
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ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
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virtual void update() = 0; |
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virtual void update() = 0; |
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virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
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virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
311 |
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virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
312 |
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virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
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|
314 |
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protected: |
315 |
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ZConstraint<T>* zconsIntegrator;; |
311 |
> |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
312 |
> |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
313 |
> |
|
314 |
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protected: |
315 |
> |
ZConstraint<T>* zconsIntegrator;; |
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}; |
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class PolicyByNumber : ForceSubstractionPolicy{ |
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public: |
320 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {} |
321 |
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virtual void update(); |
320 |
> |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {} |
321 |
> |
virtual void update(); |
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virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
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virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
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virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
325 |
< |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
326 |
< |
|
324 |
> |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
325 |
> |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
326 |
> |
|
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private: |
328 |
< |
int totNumOfMovingAtoms; |
328 |
> |
int totNumOfMovingAtoms; |
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}; |
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class PolicyByMass :ForceSubstractionPolicy{ |
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public: |
333 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {} |
334 |
< |
|
335 |
< |
virtual void update(); |
333 |
> |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {} |
334 |
> |
|
335 |
> |
virtual void update(); |
336 |
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virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
337 |
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virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
338 |
< |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
339 |
< |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
338 |
> |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
339 |
> |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
340 |
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|
341 |
< |
private: |
342 |
< |
double totMassOfMovingAtoms; |
341 |
> |
private: |
342 |
> |
double totMassOfMovingAtoms; |
343 |
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}; |
344 |
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345 |
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public: |
350 |
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void setZConsTime(double time) {this->zconsTime = time;} |
351 |
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void getZConsTime() {return zconsTime;} |
352 |
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|
353 |
< |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
354 |
< |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
353 |
> |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
354 |
> |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
355 |
|
|
356 |
< |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
356 |
> |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
357 |
|
string getZConsOutput() {return zconsOutput;} |
358 |
|
|
359 |
|
virtual void integrate(); |
360 |
|
|
361 |
|
|
362 |
|
#ifdef IS_MPI |
363 |
< |
virtual void update(); //which is called to indicate the molecules' migration |
363 |
> |
virtual void update(); //which is called to indicate the molecules' migration |
364 |
|
#endif |
365 |
|
|
366 |
|
protected: |
367 |
|
|
368 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
369 |
< |
|
370 |
< |
|
368 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
369 |
|
|
370 |
|
virtual void calcForce( int calcPot, int calcStress ); |
371 |
|
virtual void thermalize(void); |
383 |
|
int isZConstraintMol(Molecule* mol); |
384 |
|
|
385 |
|
|
386 |
< |
double zconsTime; |
387 |
< |
double zconsTol; |
388 |
< |
double zForceConst; |
386 |
> |
double zconsTime; //sample time |
387 |
> |
double zconsTol; //tolerance of z-contratint |
388 |
> |
double zForceConst; //base force constant term |
389 |
> |
//which is estimate by OOPSE |
390 |
|
|
391 |
< |
vector<Molecule*> zconsMols; |
392 |
< |
vector<double> massOfZConsMols; |
393 |
< |
vector<double> kz; |
394 |
< |
vector<ZConsState> states; |
395 |
< |
vector<double> zPos; |
391 |
> |
vector<Molecule*> zconsMols; //z-constraint molecules array |
392 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
393 |
> |
vector<double> kz; //force constant array |
394 |
> |
vector<ZConsState> states; //state of z-constraint molecules |
395 |
> |
vector<double> zPos; // |
396 |
|
|
397 |
|
|
398 |
< |
vector<Molecule*> unconsMols; |
399 |
< |
vector<double> massOfUnconsMols; |
400 |
< |
double totalMassOfUncons; |
398 |
> |
vector<Molecule*> unconsMols; //unconstraint molecules array |
399 |
> |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
400 |
> |
double totalMassOfUncons; //total mas of unconstraint molecules |
401 |
|
|
402 |
< |
vector<ZConsParaItem>* parameters; |
402 |
> |
vector<ZConsParaItem>* parameters; // |
403 |
|
|
404 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
405 |
|
|
407 |
|
double* fz; |
408 |
|
double* curZPos; |
409 |
|
|
410 |
< |
int totNumOfUnconsAtoms; |
410 |
> |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
411 |
|
|
412 |
|
int whichDirection; //constraint direction |
413 |
|
|
414 |
|
private: |
415 |
|
|
416 |
< |
string zconsOutput; |
417 |
< |
ZConsWriter* fzOut; |
416 |
> |
string zconsOutput; //filename of zconstraint output |
417 |
> |
ZConsWriter* fzOut; //z-constraint writer |
418 |
|
|
419 |
< |
double curZconsTime; |
419 |
> |
double curZconsTime; |
420 |
|
|
421 |
|
double calcMovingMolsCOMVel(); |
422 |
|
double calcSysCOMVel(); |
423 |
|
double calcTotalForce(); |
424 |
< |
|
425 |
< |
ForceSubstractionPolicy* forcePolicy; |
424 |
> |
|
425 |
> |
ForceSubstractionPolicy* forcePolicy; //force substration policy |
426 |
|
friend class ForceSubstractionPolicy; |
427 |
|
|
428 |
|
}; |