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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1161 by tim, Tue May 11 21:44:05 2004 UTC

# Line 4 | Line 4
4   #include <string>
5   #include <vector>
6   #include "Atom.hpp"
7 + #include "StuntDouble.hpp"
8   #include "Molecule.hpp"
9   #include "SRI.hpp"
10   #include "AbstractClasses.hpp"
# Line 20 | Line 21 | const double tol = 1.0e-6;
21   const int maxIteration = 300;
22   const double tol = 1.0e-6;
23  
23
24   template<typename T = BaseIntegrator> class Integrator : public T {
25  
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30 +  virtual double  getConservedQuantity(void);
31 +  virtual string getAdditionalParameters(void);
32  
31
33   protected:
34 <  
34 >
35    virtual void integrateStep( int calcPot, int calcStress );
36    virtual void preMove( void );
37    virtual void moveA( void );
# Line 38 | Line 39 | template<typename T = BaseIntegrator> class Integrator
39    virtual void constrainA( void );
40    virtual void constrainB( void );
41    virtual int  readyCheck( void ) { return 1; }
41  
42  void checkConstraints( void );
43  void rotate( int axes1, int axes2, double angle, double j[3],
44               double A[3][3] );
42  
43 +  virtual void resetIntegrator( void ) { }
44  
45 +  virtual void calcForce( int calcPot, int calcStress );
46 +  virtual void thermalize();
47 +
48 +  virtual bool stopIntegrator() {return false;}
49 +
50 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51 +
52 +  void checkConstraints( void );
53 +  void rotate( int axes1, int axes2, double angle, double j[3],
54 +         double A[3][3] );
55 +
56    ForceFields* myFF;
57  
58    SimInfo *info; // all the info we'll ever need
59 +  vector<StuntDouble*> integrableObjects;
60    int nAtoms;  /* the number of atoms */
61    int oldAtoms;
62    Atom **atoms; /* array of atom pointers */
# Line 54 | Line 64 | template<typename T = BaseIntegrator> class Integrator
64    int nMols;
65  
66    int isConstrained; // boolean to know whether the systems contains
67 <                     // constraints.
68 <  int nConstrained;  // counter for number of constraints
69 <  int *constrainedA; // the i of a constraint pair
70 <  int *constrainedB; // the j of a constraint pair
71 <  double *constrainedDsqr; // the square of the constraint distance
72 <  
67 >         // constraints.
68 >  int nConstrained;  // counter for number of constraints
69 >  int *constrainedA; // the i of a constraint pair
70 >  int *constrainedB; // the j of a constraint pair
71 >  double *constrainedDsqr; // the square of the constraint distance
72 >
73    int* moving; // tells whether we are moving atom i
74    int* moved;  // tells whether we have moved atom i
75 <  double* oldPos; // pre constrained positions
75 >  double* oldPos; // pre constrained positions
76  
77    short isFirst; /*boolean for the first time integrate is called */
78 <  
78 >
79    double dt;
80    double dt2;
81  
82    Thermo *tStats;
83    StatWriter*  statOut;
84    DumpWriter*  dumpOut;
85 <  
85 >
86   };
87  
88   typedef Integrator<BaseIntegrator> RealIntegrator;
89  
90 + // ansi instantiation
91 + template class Integrator<BaseIntegrator>;
92 +
93   template<typename T> class NVE : public T {
94  
95   public:
96    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
97      T( theInfo, the_ff ){}
98 <  virtual ~NVE(){}  
98 >  virtual ~NVE(){}
99   };
100  
101  
# Line 91 | Line 104 | template<typename T> class NVT : public T { (public)
104   public:
105  
106    NVT ( SimInfo *theInfo, ForceFields* the_ff);
107 <  virtual ~NVT() {}
107 >  virtual ~NVT();
108  
109    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
110    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
111 +  void setChiTolerance(double tol) {chiTolerance = tol;}
112 +  virtual double  getConservedQuantity(void);
113 +  virtual string getAdditionalParameters(void);
114  
115   protected:
116  
# Line 103 | Line 119 | template<typename T> class NVT : public T { (public)
119  
120    virtual int readyCheck();
121  
122 +  virtual void resetIntegrator( void );
123 +
124    // chi is a propagated degree of freedom.
125  
126    double chi;
127  
128 +  //integral of chi(t)dt
129 +  double integralOfChidt;
130 +
131    // targetTemp must be set.  tauThermostat must also be set;
132  
133    double targetTemp;
134    double tauThermostat;
135 <  
135 >
136    short int have_tau_thermostat, have_target_temp;
137  
138 +  double *oldVel;
139 +  double *oldJi;
140 +
141 +  double chiTolerance;
142 +  short int have_chi_tolerance;
143 +
144   };
145  
146  
147  
148 < template<typename T> class NPTi : public T{
148 > template<typename T> class NPT : public T{
149  
150   public:
151  
152 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
153 <  virtual ~NPTi() {};
152 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
153 >  virtual ~NPT();
154  
155    virtual void integrateStep( int calcPot, int calcStress ){
156      calcStress = 1;
157      T::integrateStep( calcPot, calcStress );
158    }
159  
160 +  virtual double getConservedQuantity(void) = 0;
161 +  virtual string getAdditionalParameters(void) = 0;
162 +  
163 +  double myTauThermo( void ) { return tauThermostat; }
164 +  double myTauBaro( void ) { return tauBarostat; }
165 +
166    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
167    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
168    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
169    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
170 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
171 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
172 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
173  
174   protected:
175  
# Line 142 | Line 178 | template<typename T> class NPTi : public T{ (protected
178  
179    virtual int readyCheck();
180  
181 <  // chi and eta are the propagated degrees of freedom
181 >  virtual void resetIntegrator( void );
182  
183 <  double chi;
184 <  double eta;
185 <  double NkBT;
183 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
184 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
185 >  virtual void getPosScale(double pos[3], double COM[3],
186 >                           int index, double sc[3]) = 0;
187  
188 <  // targetTemp, targetPressure, and tauBarostat must be set.  
152 <  // One of qmass or tauThermostat must be set;
188 >  virtual void calcVelScale( void ) = 0;
189  
190 <  double targetTemp;
191 <  double targetPressure;
156 <  double tauThermostat;
157 <  double tauBarostat;
190 >  virtual bool chiConverged( void );
191 >  virtual bool etaConverged( void ) = 0;
192  
193 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
194 <  short int have_target_pressure;
193 >  virtual void evolveChiA( void );
194 >  virtual void evolveEtaA( void ) = 0;
195 >  virtual void evolveChiB( void );
196 >  virtual void evolveEtaB( void ) = 0;
197  
198 < };
198 >  virtual void scaleSimBox( void ) = 0;
199  
200 < template<typename T> class NPTim : public T{
200 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
201  
166 public:
167
168  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
169  virtual ~NPTim() {};
170
171  virtual void integrateStep( int calcPot, int calcStress ){
172    calcStress = 1;
173    T::integrateStep( calcPot, calcStress );
174  }
175
176  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
177  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
178  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
179  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
180
181 protected:
182
183  virtual void moveA( void );
184  virtual void moveB( void );
185
186  virtual int readyCheck();
187
188  Molecule* myMolecules;
189  Atom** myAtoms;
190
202    // chi and eta are the propagated degrees of freedom
203  
204 +  double oldChi;
205 +  double prevChi;
206    double chi;
194  double eta;
207    double NkBT;
208 +  double fkBT;
209  
210 <  // targetTemp, targetPressure, and tauBarostat must be set.  
210 >  double tt2, tb2;
211 >  double instaTemp, instaPress, instaVol;
212 >  double press[3][3];
213 >
214 >  int Nparticles;
215 >
216 >  double integralOfChidt;
217 >
218 >  // targetTemp, targetPressure, and tauBarostat must be set.
219    // One of qmass or tauThermostat must be set;
220  
221    double targetTemp;
# Line 205 | Line 226 | template<typename T> class NPTim : public T{ (protecte
226    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
227    short int have_target_pressure;
228  
229 +  double *oldPos;
230 +  double *oldVel;
231 +  double *oldJi;
232 +
233 +  double chiTolerance;
234 +  short int have_chi_tolerance;
235 +  double posIterTolerance;
236 +  short int have_pos_iter_tolerance;
237 +  double etaTolerance;
238 +  short int have_eta_tolerance;
239 +
240   };
241  
242 < template<typename T> class NPTf : public T{
242 > template<typename T> class NPTi : public T{
243  
244   public:
245 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
246 +  ~NPTi();
247  
248 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
249 <  virtual ~NPTf() {};
248 >  virtual double getConservedQuantity(void);
249 >  virtual void resetIntegrator(void);
250 >  virtual string getAdditionalParameters(void);
251 > protected:
252  
217  virtual void integrateStep( int calcPot, int calcStress ){
218    calcStress = 1;
219    T::integrateStep( calcPot, calcStress );
220  }
253  
222  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
223  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
224  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
225  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
254  
255 < protected:
255 >  virtual void evolveEtaA(void);
256 >  virtual void evolveEtaB(void);
257  
258 <  virtual void  moveA( void );
230 <  virtual void moveB( void );
258 >  virtual bool etaConverged( void );
259  
260 <  virtual int readyCheck();
260 >  virtual void scaleSimBox( void );
261  
262 <  // chi and eta are the propagated degrees of freedom
262 >  virtual void getVelScaleA( double sc[3], double vel[3] );
263 >  virtual void getVelScaleB( double sc[3], int index );
264 >  virtual void getPosScale(double pos[3], double COM[3],
265 >                           int index, double sc[3]);
266  
267 <  double chi;
237 <  double eta[3][3];
238 <  double NkBT;
267 >  virtual void calcVelScale( void );
268  
269 <  // targetTemp, targetPressure, and tauBarostat must be set.  
270 <  // One of qmass or tauThermostat must be set;
269 >  double eta, oldEta, prevEta;
270 >  double vScale;
271 > };
272  
273 <  double targetTemp;
244 <  double targetPressure;
245 <  double tauThermostat;
246 <  double tauBarostat;
273 > template<typename T> class NPTf : public T{
274  
275 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
249 <  short int have_target_pressure;
275 > public:
276  
277 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
278 +  virtual ~NPTf();
279 +
280 +  virtual double getConservedQuantity(void);
281 +  virtual string getAdditionalParameters(void);
282 +  virtual void resetIntegrator(void);
283 +
284 + protected:
285 +
286 +  virtual void evolveEtaA(void);
287 +  virtual void evolveEtaB(void);
288 +
289 +  virtual bool etaConverged( void );
290 +
291 +  virtual void scaleSimBox( void );
292 +
293 +  virtual void getVelScaleA( double sc[3], double vel[3] );
294 +  virtual void getVelScaleB( double sc[3], int index );
295 +  virtual void getPosScale(double pos[3], double COM[3],
296 +                           int index, double sc[3]);
297 +
298 +  virtual void calcVelScale( void );
299 +
300 +  double eta[3][3];
301 +  double oldEta[3][3];
302 +  double prevEta[3][3];
303 +  double vScale[3][3];
304   };
305  
306 < template<typename T> class NPTfm : public T{
306 > template<typename T> class NPTxyz : public T{
307  
308   public:
309  
310 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
311 <  virtual ~NPTfm() {};
310 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
311 >  virtual ~NPTxyz();
312  
313 <  virtual void integrateStep( int calcPot, int calcStress ){
314 <    calcStress = 1;
315 <    T::integrateStep( calcPot, calcStress );
263 <  }
313 >  virtual double getConservedQuantity(void);
314 >  virtual string getAdditionalParameters(void);
315 >  virtual void resetIntegrator(void);
316  
265  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
266  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
267  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
268  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
269
317   protected:
318  
319 <  virtual void  moveA( void );
320 <  virtual void moveB( void );
319 >  virtual void evolveEtaA(void);
320 >  virtual void evolveEtaB(void);
321  
322 <  virtual int readyCheck();
322 >  virtual bool etaConverged( void );
323  
324 <  Molecule* myMolecules;
278 <  Atom** myAtoms;
324 >  virtual void scaleSimBox( void );
325  
326 <  // chi and eta are the propagated degrees of freedom
327 <
328 <  double chi;
326 >  virtual void getVelScaleA( double sc[3], double vel[3] );
327 >  virtual void getVelScaleB( double sc[3], int index );
328 >  virtual void getPosScale(double pos[3], double COM[3],
329 >                           int index, double sc[3]);
330 >
331 >  virtual void calcVelScale( void );
332 >
333    double eta[3][3];
334 <  double NkBT;
334 >  double oldEta[3][3];
335 >  double prevEta[3][3];
336 >  double vScale[3][3];
337 > };
338  
286  // targetTemp, targetPressure, and tauBarostat must be set.  
287  // One of qmass or tauThermostat must be set;
339  
340 <  double targetTemp;
290 <  double targetPressure;
291 <  double tauThermostat;
292 <  double tauBarostat;
340 > template<typename T> class ZConstraint : public T {
341  
342 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
343 <  short int have_target_pressure;
342 >  public:
343 >  class ForceSubtractionPolicy{
344 >    public:
345 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
346  
347 < };
347 >      virtual void update() = 0;
348 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
349 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
350 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
351 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
352  
353 < template<typename T> class ZConstraint : public T {
353 >   protected:
354 >     ZConstraint<T>* zconsIntegrator;
355 >  };
356  
357 +  class PolicyByNumber : public ForceSubtractionPolicy{
358 +
359 +    public:
360 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
361 +      virtual void update();
362 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
363 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
364 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
365 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
366 +
367 +    private:
368 +      int totNumOfMovingAtoms;
369 +  };
370 +
371 +  class PolicyByMass : public ForceSubtractionPolicy{
372 +
373 +    public:
374 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
375 +
376 +      virtual void update();
377 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
378 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
379 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
380 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
381 +
382 +   private:
383 +     double totMassOfMovingAtoms;
384 +  };
385 +
386   public:
387  
388    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
389    ~ZConstraint();
390  
306  virtual void integrateStep( int calcPot, int calcStress );
307  
308  
391    void setZConsTime(double time)                  {this->zconsTime = time;}
392    void getZConsTime()                             {return zconsTime;}
393 <  
394 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
395 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
396 <  
397 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
393 >
394 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
395 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
396 >
397 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
398    string getZConsOutput()                         {return zconsOutput;}
399  
400 +  virtual void integrate();
401 +
402 +
403   #ifdef IS_MPI
404 <  virtual void update(); //which is called to indicate the molecules' migration
404 >  virtual void update();                      //which is called to indicate the molecules' migration
405   #endif
406  
407 +  enum ZConsState {zcsMoving, zcsFixed};
408 +
409 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
410 +  vector<ZConsState> states;                 //state of z-constraint molecules
411 +
412 +
413 +
414 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
415 +  double totalMassOfUncons;                //total mas of unconstraint molecules
416 +
417 +
418   protected:
419  
420 <  double zconsTime;
420 >
421 >
422 >  virtual void calcForce( int calcPot, int calcStress );
423 >  virtual void thermalize(void);
424 >
425 >  void zeroOutVel();
426 >  void doZconstraintForce();
427 >  void doHarmonic(vector<double>& resPos);
428 >  bool checkZConsState();
429 >
430 >  bool haveFixedZMols();
431 >  bool haveMovingZMols();
432 >
433 >  double calcZSys();
434 >
435 >  int isZConstraintMol(Molecule* mol);
436 >
437 >
438 >  double zconsTime;                              //sample time
439 >  double zconsTol;                                 //tolerance of z-contratint
440 >  double zForceConst;                           //base force constant term
441 >                                                          //which is estimate by OOPSE
442 >
443 >
444 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
445 >  vector<double> kz;                              //force constant array
446 >
447 >  vector<double> zPos;                          //
448 >
449 >
450 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
451 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
452 >
453 >
454 >  vector<ZConsParaItem>* parameters; //
455 >
456 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
457 >
458 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
459 >  vector<double> fz;
460 >  vector<double> curZPos;
461 >
462 >  bool usingSMD;
463 >  vector<double> prevCantPos;
464 >  vector<double> cantPos;
465 >  vector<double> cantVel;
466 >
467 >  double zconsFixTime;  
468 >  double zconsGap;
469 >  bool hasZConsGap;
470 >  vector<double> endFixTime;
471    
472 <  void resetZ(void);
327 <  
328 <  vector<Molecule*> zconsMols;
329 <  vector<double> massOfZConsMols;
330 <  
331 <  vector<Molecule*> unconsMols;
332 <  vector<double> massOfUnconsMols;
333 <  double totalMassOfUncons;
472 >  int whichDirection;                           //constraint direction
473  
474 <  vector<double> allRefZ;    
475 <  vector<double> refZ;
474 > private:
475 >
476 >  string zconsOutput;                         //filename of zconstraint output
477 >  ZConsWriter* fzOut;                         //z-constraint writer
478 >
479 >  double curZconsTime;
480 >
481 >  double calcMovingMolsCOMVel();
482 >  double calcSysCOMVel();
483 >  double calcTotalForce();
484 >  void updateZPos();
485 >  void updateCantPos();
486    
487 <  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
488 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
487 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
488 >  friend class ForceSubtractionPolicy;
489 >
490 > };
491 >
492 > /*
493 > template<typename T> class SingleZConstrain : public T{
494 >
495 >
496 > };
497 > */
498 >
499 > template<typename T> class NonEquMD : public T {
500 >  public:
501      
502 <  double* fz;
502 >
503 >
504 > };
505 >
506 >
507 > //
508 > template<typename T> class SingleZConstraint : public T{
509 >  public:
510 >    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
511 >    ~SingleZConstraint();
512 >    
513 >    bool stopIntegrator();
514 >    
515 >  protected:
516 >    
517 > };
518 >
519 > //Steered Molecular Dynamics, curret implement only support one steered molecule
520 > template<typename T> class SMD : public T{
521 >  public:
522 >    SMD( SimInfo *theInfo, ForceFields* the_ff);
523 >    ~SMD();
524    
525 < private:
525 >    virtual void integrate();
526 >    virtual void calcForce( int calcPot, int calcStress );  
527 >    bool stopIntegrator();
528 >  private:
529 >    
530 > };
531  
532 <  int isZConstraintMol(Molecule* mol);
533 <  string zconsOutput;
534 <  ZConsWriter* fzOut;
532 > //By using state pattern, Coordinate Drive is responsible for switching back and forth between
533 > //Driven Molecular Dynamics and ZConstraint Method.
534 > template<typename T> class CoordinateDriver : public T {
535 >  public:
536 >    typedef T ParentIntegrator;
537 >
538 >    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
539 >    ~CoordinateDriver();
540 >    
541 >    virtual void integrate();
542 >
543 >  private:    
544 >    BaseIntegrator* zconsIntegrator;
545 >    BaseIntegrator* drivenIntegrator;
546 >    
547   };
548  
549   #endif

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