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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 1108 by tim, Wed Apr 14 15:37:41 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;
# Line 82 | Line 92 | template<typename T> class NVE : public T { (public)
92   public:
93    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
94      T( theInfo, the_ff ){}
95 <  virtual ~NVE(){}  
95 >  virtual ~NVE(){}
96   };
97  
98  
# Line 91 | Line 101 | template<typename T> class NVT : public T { (public)
101   public:
102  
103    NVT ( SimInfo *theInfo, ForceFields* the_ff);
104 <  virtual ~NVT() {}
104 >  virtual ~NVT();
105  
106    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
107    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108 +  void setChiTolerance(double tol) {chiTolerance = tol;}
109 +  virtual double  getConservedQuantity(void);
110 +  virtual string getAdditionalParameters(void);
111  
112   protected:
113  
# Line 103 | Line 116 | template<typename T> class NVT : public T { (public)
116  
117    virtual int readyCheck();
118  
119 +  virtual void resetIntegrator( void );
120 +
121    // chi is a propagated degree of freedom.
122  
123    double chi;
124  
125 +  //integral of chi(t)dt
126 +  double integralOfChidt;
127 +
128    // targetTemp must be set.  tauThermostat must also be set;
129  
130    double targetTemp;
131    double tauThermostat;
132 <  
132 >
133    short int have_tau_thermostat, have_target_temp;
134  
135 +  double *oldVel;
136 +  double *oldJi;
137 +
138 +  double chiTolerance;
139 +  short int have_chi_tolerance;
140 +
141   };
142  
143  
144  
145 < template<typename T> class NPTi : public T{
145 > template<typename T> class NPT : public T{
146  
147   public:
148  
149 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
150 <  virtual ~NPTi() {};
149 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
150 >  virtual ~NPT();
151  
152    virtual void integrateStep( int calcPot, int calcStress ){
153      calcStress = 1;
154      T::integrateStep( calcPot, calcStress );
155    }
156  
157 +  virtual double getConservedQuantity(void) = 0;
158 +  virtual string getAdditionalParameters(void) = 0;
159 +  
160 +  double myTauThermo( void ) { return tauThermostat; }
161 +  double myTauBaro( void ) { return tauBarostat; }
162 +
163    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
165    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
166    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
167 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
168 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
169 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
170  
171   protected:
172  
# Line 142 | Line 175 | template<typename T> class NPTi : public T{ (protected
175  
176    virtual int readyCheck();
177  
178 <  // chi and eta are the propagated degrees of freedom
178 >  virtual void resetIntegrator( void );
179  
180 <  double chi;
181 <  double eta;
182 <  double NkBT;
180 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
182 >  virtual void getPosScale(double pos[3], double COM[3],
183 >                           int index, double sc[3]) = 0;
184  
185 <  // targetTemp, targetPressure, and tauBarostat must be set.  
152 <  // One of qmass or tauThermostat must be set;
185 >  virtual void calcVelScale( void ) = 0;
186  
187 <  double targetTemp;
188 <  double targetPressure;
156 <  double tauThermostat;
157 <  double tauBarostat;
187 >  virtual bool chiConverged( void );
188 >  virtual bool etaConverged( void ) = 0;
189  
190 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
191 <  short int have_target_pressure;
190 >  virtual void evolveChiA( void );
191 >  virtual void evolveEtaA( void ) = 0;
192 >  virtual void evolveChiB( void );
193 >  virtual void evolveEtaB( void ) = 0;
194  
195 < };
195 >  virtual void scaleSimBox( void ) = 0;
196  
197 < template<typename T> class NPTim : public T{
197 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
198  
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
199    // chi and eta are the propagated degrees of freedom
200  
201 +  double oldChi;
202 +  double prevChi;
203    double chi;
194  double eta;
204    double NkBT;
205 +  double fkBT;
206  
207 <  // targetTemp, targetPressure, and tauBarostat must be set.  
207 >  double tt2, tb2;
208 >  double instaTemp, instaPress, instaVol;
209 >  double press[3][3];
210 >
211 >  int Nparticles;
212 >
213 >  double integralOfChidt;
214 >
215 >  // targetTemp, targetPressure, and tauBarostat must be set.
216    // One of qmass or tauThermostat must be set;
217  
218    double targetTemp;
# Line 205 | Line 223 | template<typename T> class NPTim : public T{ (protecte
223    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
224    short int have_target_pressure;
225  
226 +  double *oldPos;
227 +  double *oldVel;
228 +  double *oldJi;
229 +
230 +  double chiTolerance;
231 +  short int have_chi_tolerance;
232 +  double posIterTolerance;
233 +  short int have_pos_iter_tolerance;
234 +  double etaTolerance;
235 +  short int have_eta_tolerance;
236 +
237   };
238  
239 < template<typename T> class NPTf : public T{
239 > template<typename T> class NPTi : public T{
240  
241   public:
242 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
243 +  ~NPTi();
244  
245 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
246 <  virtual ~NPTf() {};
245 >  virtual double getConservedQuantity(void);
246 >  virtual void resetIntegrator(void);
247 >  virtual string getAdditionalParameters(void);
248 > protected:
249  
217  virtual void integrateStep( int calcPot, int calcStress ){
218    calcStress = 1;
219    T::integrateStep( calcPot, calcStress );
220  }
250  
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;}
251  
252 < protected:
252 >  virtual void evolveEtaA(void);
253 >  virtual void evolveEtaB(void);
254  
255 <  virtual void  moveA( void );
230 <  virtual void moveB( void );
255 >  virtual bool etaConverged( void );
256  
257 <  virtual int readyCheck();
257 >  virtual void scaleSimBox( void );
258  
259 <  // chi and eta are the propagated degrees of freedom
259 >  virtual void getVelScaleA( double sc[3], double vel[3] );
260 >  virtual void getVelScaleB( double sc[3], int index );
261 >  virtual void getPosScale(double pos[3], double COM[3],
262 >                           int index, double sc[3]);
263  
264 <  double chi;
237 <  double eta[3][3];
238 <  double NkBT;
264 >  virtual void calcVelScale( void );
265  
266 <  // targetTemp, targetPressure, and tauBarostat must be set.  
267 <  // One of qmass or tauThermostat must be set;
266 >  double eta, oldEta, prevEta;
267 >  double vScale;
268 > };
269  
270 <  double targetTemp;
244 <  double targetPressure;
245 <  double tauThermostat;
246 <  double tauBarostat;
270 > template<typename T> class NPTf : public T{
271  
272 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
249 <  short int have_target_pressure;
272 > public:
273  
274 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
275 +  virtual ~NPTf();
276 +
277 +  virtual double getConservedQuantity(void);
278 +  virtual string getAdditionalParameters(void);
279 +  virtual void resetIntegrator(void);
280 +
281 + protected:
282 +
283 +  virtual void evolveEtaA(void);
284 +  virtual void evolveEtaB(void);
285 +
286 +  virtual bool etaConverged( void );
287 +
288 +  virtual void scaleSimBox( void );
289 +
290 +  virtual void getVelScaleA( double sc[3], double vel[3] );
291 +  virtual void getVelScaleB( double sc[3], int index );
292 +  virtual void getPosScale(double pos[3], double COM[3],
293 +                           int index, double sc[3]);
294 +
295 +  virtual void calcVelScale( void );
296 +
297 +  double eta[3][3];
298 +  double oldEta[3][3];
299 +  double prevEta[3][3];
300 +  double vScale[3][3];
301   };
302  
303 < template<typename T> class NPTfm : public T{
303 > template<typename T> class NPTxyz : public T{
304  
305   public:
306  
307 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
308 <  virtual ~NPTfm() {};
307 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
308 >  virtual ~NPTxyz();
309  
310 <  virtual void integrateStep( int calcPot, int calcStress ){
311 <    calcStress = 1;
312 <    T::integrateStep( calcPot, calcStress );
263 <  }
310 >  virtual double getConservedQuantity(void);
311 >  virtual string getAdditionalParameters(void);
312 >  virtual void resetIntegrator(void);
313  
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
314   protected:
315  
316 <  virtual void  moveA( void );
317 <  virtual void moveB( void );
316 >  virtual void evolveEtaA(void);
317 >  virtual void evolveEtaB(void);
318  
319 <  virtual int readyCheck();
319 >  virtual bool etaConverged( void );
320  
321 <  Molecule* myMolecules;
278 <  Atom** myAtoms;
321 >  virtual void scaleSimBox( void );
322  
323 <  // chi and eta are the propagated degrees of freedom
324 <
325 <  double chi;
323 >  virtual void getVelScaleA( double sc[3], double vel[3] );
324 >  virtual void getVelScaleB( double sc[3], int index );
325 >  virtual void getPosScale(double pos[3], double COM[3],
326 >                           int index, double sc[3]);
327 >
328 >  virtual void calcVelScale( void );
329 >
330    double eta[3][3];
331 <  double NkBT;
331 >  double oldEta[3][3];
332 >  double prevEta[3][3];
333 >  double vScale[3][3];
334 > };
335  
286  // targetTemp, targetPressure, and tauBarostat must be set.  
287  // One of qmass or tauThermostat must be set;
336  
337 <  double targetTemp;
290 <  double targetPressure;
291 <  double tauThermostat;
292 <  double tauBarostat;
337 > template<typename T> class ZConstraint : public T {
338  
339 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
340 <  short int have_target_pressure;
339 >  public:
340 >  class ForceSubtractionPolicy{
341 >    public:
342 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343  
344 < };
344 >      virtual void update() = 0;
345 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349  
350 < template<typename T> class ZConstraint : public T {
350 >   protected:
351 >     ZConstraint<T>* zconsIntegrator;
352 >  };
353  
354 +  class PolicyByNumber : public ForceSubtractionPolicy{
355 +
356 +    public:
357 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 +      virtual void update();
359 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363 +
364 +    private:
365 +      int totNumOfMovingAtoms;
366 +  };
367 +
368 +  class PolicyByMass : public ForceSubtractionPolicy{
369 +
370 +    public:
371 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372 +
373 +      virtual void update();
374 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
377 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
378 +
379 +   private:
380 +     double totMassOfMovingAtoms;
381 +  };
382 +
383   public:
384  
385    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
386    ~ZConstraint();
387  
306  virtual void integrateStep( int calcPot, int calcStress );
307  
308  
388    void setZConsTime(double time)                  {this->zconsTime = time;}
389    void getZConsTime()                             {return zconsTime;}
390 <  
391 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
392 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
393 <  
394 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
390 >
391 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
393 >
394 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
395    string getZConsOutput()                         {return zconsOutput;}
396  
397 +  virtual void integrate();
398 +
399 +
400   #ifdef IS_MPI
401 <  virtual void update(); //which is called to indicate the molecules' migration
401 >  virtual void update();                      //which is called to indicate the molecules' migration
402   #endif
403  
404 +  enum ZConsState {zcsMoving, zcsFixed};
405 +
406 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
407 +  vector<ZConsState> states;                 //state of z-constraint molecules
408 +
409 +
410 +
411 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
412 +  double totalMassOfUncons;                //total mas of unconstraint molecules
413 +
414 +
415   protected:
416  
417 <  double zconsTime;
417 >
418 >
419 >  virtual void calcForce( int calcPot, int calcStress );
420 >  virtual void thermalize(void);
421 >
422 >  void zeroOutVel();
423 >  void doZconstraintForce();
424 >  void doHarmonic(vector<double>& resPos);
425 >  bool checkZConsState();
426 >
427 >  bool haveFixedZMols();
428 >  bool haveMovingZMols();
429 >
430 >  double calcZSys();
431 >
432 >  int isZConstraintMol(Molecule* mol);
433 >
434 >
435 >  double zconsTime;                              //sample time
436 >  double zconsTol;                                 //tolerance of z-contratint
437 >  double zForceConst;                           //base force constant term
438 >                                                          //which is estimate by OOPSE
439 >
440 >
441 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
442 >  vector<double> kz;                              //force constant array
443 >
444 >  vector<double> zPos;                          //
445 >
446 >
447 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
448 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
449 >
450 >
451 >  vector<ZConsParaItem>* parameters; //
452 >
453 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454 >
455 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 >  vector<double> fz;
457 >  vector<double> curZPos;
458 >
459 >  bool usingSMD;
460 >  vector<double> cantPos;
461 >  vector<double> cantVel;
462 >
463 >  double zconsFixTime;  
464 >  double zconsGap;
465 >  bool hasZConsGap;
466 >  vector<double> endFixTime;
467    
468 <  void resetZ(void);
327 <  
328 <  vector<Molecule*> zconsMols;
329 <  vector<double> massOfZConsMols;
330 <  
331 <  vector<Molecule*> unconsMols;
332 <  vector<double> massOfUnconsMols;
333 <  double totalMassOfUncons;
468 >  int whichDirection;                           //constraint direction
469  
470 <  vector<double> allRefZ;    
471 <  vector<double> refZ;
470 > private:
471 >
472 >  string zconsOutput;                         //filename of zconstraint output
473 >  ZConsWriter* fzOut;                         //z-constraint writer
474 >
475 >  double curZconsTime;
476 >
477 >  double calcMovingMolsCOMVel();
478 >  double calcSysCOMVel();
479 >  double calcTotalForce();
480 >  void updateZPos();
481 >  void updateCantPos();
482    
483 <  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
484 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
483 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
484 >  friend class ForceSubtractionPolicy;
485 >
486 > };
487 >
488 > /*
489 > template<typename T> class SingleZConstrain : public T{
490 >
491 >
492 > };
493 > */
494 >
495 > template<typename T> class NonEquMD : public T {
496 >  public:
497      
498 <  double* fz;
498 >
499 >
500 > };
501 >
502 >
503 > //
504 > template<typename T> class SingleZConstraint : public T{
505 >  public:
506 >    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
507 >    ~SingleZConstraint();
508 >    
509 >    bool stopIntegrator();
510 >    
511 >  protected:
512 >    
513 > };
514 >
515 > //Steered Molecular Dynamics, curret implement only support one steered molecule
516 > template<typename T> class SMD : public T{
517 >  public:
518 >    SMD( SimInfo *theInfo, ForceFields* the_ff);
519 >    ~SMD();
520    
521 < private:
521 >    virtual void integrate();
522 >    virtual void calcForce( int calcPot, int calcStress );  
523 >    bool stopIntegrator();
524 >  private:
525 >    
526 > };
527  
528 <  int isZConstraintMol(Molecule* mol);
529 <  string zconsOutput;
530 <  ZConsWriter* fzOut;
528 > //By using state pattern, Coordinate Drive is responsible for switching back and forth between
529 > //Driven Molecular Dynamics and ZConstraint Method.
530 > template<typename T> class CoordinateDriver : public T {
531 >  public:
532 >    typedef T ParentIntegrator;
533 >
534 >    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
535 >    ~CoordinateDriver();
536 >    
537 >    virtual void integrate();
538 >
539 >  private:    
540 >    BaseIntegrator* zconsIntegrator;
541 >    BaseIntegrator* drivenIntegrator;
542 >    
543   };
544  
545   #endif

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