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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 576 by gezelter, Tue Jul 8 21:10:16 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC

# Line 1 | Line 1
1   #ifndef _INTEGRATOR_H_
2   #define _INTEGRATOR_H_
3  
4 + #include <string>
5 + #include <vector>
6   #include "Atom.hpp"
7 + #include "Molecule.hpp"
8   #include "SRI.hpp"
9   #include "AbstractClasses.hpp"
10   #include "SimInfo.hpp"
11   #include "ForceFields.hpp"
12   #include "Thermo.hpp"
13   #include "ReadWrite.hpp"
14 + #include "ZConsWriter.hpp"
15  
16 + using namespace std;
17   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
18   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19 + const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
20   const int maxIteration = 300;
21   const double tol = 1.0e-6;
22  
17 – class Integrator : public BaseIntegrator {
23  
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
# Line 31 | Line 38 | class Integrator : public BaseIntegrator { (protected)
38    virtual void constrainA( void );
39    virtual void constrainB( void );
40    virtual int  readyCheck( void ) { return 1; }
41 +
42 +  virtual void calcForce( int calcPot, int calcStress );  
43 +  virtual void thermalize();
44    
45    void checkConstraints( void );
46    void rotate( int axes1, int axes2, double angle, double j[3],
47 <               double A[9] );
48 <
39 <
47 >               double A[3][3] );
48 >              
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
# Line 62 | Line 71 | class Integrator : public BaseIntegrator { (protected)
71    double dt;
72    double dt2;
73  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
74    Thermo *tStats;
75    StatWriter*  statOut;
76    DumpWriter*  dumpOut;
77    
78   };
79  
80 < class NVE : public Integrator{
80 > typedef Integrator<BaseIntegrator> RealIntegrator;
81  
82 + template<typename T> class NVE : public T {
83 +
84   public:
85    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
86 <    Integrator( theInfo, the_ff ){}
87 <  virtual ~NVE(){}
83 <
84 <  
85 <
86 >    T( theInfo, the_ff ){}
87 >  virtual ~NVE(){}  
88   };
89  
88 – class NVT : public Integrator{
90  
91 + template<typename T> class NVT : public T {
92 +
93   public:
94  
95    NVT ( SimInfo *theInfo, ForceFields* the_ff);
# Line 116 | Line 119 | class NPTi : public Integrator{
119   };
120  
121  
119 – class NPTi : public Integrator{
122  
123 + template<typename T> class NPTi : public T{
124 +
125   public:
126  
127    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
128    virtual ~NPTi() {};
129  
130 +  virtual void integrateStep( int calcPot, int calcStress ){
131 +    calcStress = 1;
132 +    T::integrateStep( calcPot, calcStress );
133 +  }
134 +
135    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
136    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
137    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 154 | Line 163 | class NPTf : public Integrator{
163  
164   };
165  
166 < class NPTf : public Integrator{
166 > template<typename T> class NPTim : public T{
167  
168   public:
169  
170 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
171 +  virtual ~NPTim() {};
172 +
173 +  virtual void integrateStep( int calcPot, int calcStress ){
174 +    calcStress = 1;
175 +    T::integrateStep( calcPot, calcStress );
176 +  }
177 +
178 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
179 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
180 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
181 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
182 +
183 + protected:
184 +
185 +  virtual void moveA( void );
186 +  virtual void moveB( void );
187 +
188 +  virtual int readyCheck();
189 +
190 +  Molecule* myMolecules;
191 +  Atom** myAtoms;
192 +
193 +  // chi and eta are the propagated degrees of freedom
194 +
195 +  double chi;
196 +  double eta;
197 +  double NkBT;
198 +
199 +  // targetTemp, targetPressure, and tauBarostat must be set.  
200 +  // One of qmass or tauThermostat must be set;
201 +
202 +  double targetTemp;
203 +  double targetPressure;
204 +  double tauThermostat;
205 +  double tauBarostat;
206 +
207 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
208 +  short int have_target_pressure;
209 +
210 + };
211 +
212 + template<typename T> class NPTf : public T{
213 +
214 + public:
215 +
216    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
217    virtual ~NPTf() {};
218  
219 +  virtual void integrateStep( int calcPot, int calcStress ){
220 +    calcStress = 1;
221 +    T::integrateStep( calcPot, calcStress );
222 +  }
223 +
224    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 176 | Line 236 | class NPTf : public Integrator{ (protected)
236    // chi and eta are the propagated degrees of freedom
237  
238    double chi;
239 <  double eta[9];
239 >  double eta[3][3];
240 >  double NkBT;
241 >
242 >  // targetTemp, targetPressure, and tauBarostat must be set.  
243 >  // One of qmass or tauThermostat must be set;
244 >
245 >  double targetTemp;
246 >  double targetPressure;
247 >  double tauThermostat;
248 >  double tauBarostat;
249 >
250 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251 >  short int have_target_pressure;
252 >
253 > };
254 >
255 > template<typename T> class NPTfm : public T{
256 >
257 > public:
258 >
259 >  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
260 >  virtual ~NPTfm() {};
261 >
262 >  virtual void integrateStep( int calcPot, int calcStress ){
263 >    calcStress = 1;
264 >    T::integrateStep( calcPot, calcStress );
265 >  }
266 >
267 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
268 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
269 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
270 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
271 >
272 > protected:
273 >
274 >  virtual void  moveA( void );
275 >  virtual void moveB( void );
276 >
277 >  virtual int readyCheck();
278 >
279 >  Molecule* myMolecules;
280 >  Atom** myAtoms;
281 >
282 >  // chi and eta are the propagated degrees of freedom
283 >
284 >  double chi;
285 >  double eta[3][3];
286    double NkBT;
287  
288    // targetTemp, targetPressure, and tauBarostat must be set.  
# Line 192 | Line 298 | class NPTf : public Integrator{ (protected)
298  
299   };
300  
301 + template<typename T> class ZConstraint : public T {
302 +        
303 +  public:      
304 +  class ForceSubstractionPolicy{
305 +    public:
306 +      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
307 +
308 +                virtual void update() = 0;              
309 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
310 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
311 +           virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
312 +                virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
313 +                
314 +         protected:
315 +           ZConstraint<T>* zconsIntegrator;;
316 +  };
317 +
318 +  class PolicyByNumber : ForceSubstractionPolicy{
319 +    public:
320 +                PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}              
321 +                virtual void update();          
322 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
323 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
324 +           virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
325 +                virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
326 +                
327 +    private:
328 +                int totNumOfMovingAtoms;
329 +  };
330 +
331 +  class PolicyByMass :ForceSubstractionPolicy{
332 +    public:
333 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
334 +                        
335 +                virtual void update();          
336 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
337 +      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);
340 +
341 +         private:
342 +           double totMassOfMovingAtoms;
343 +  };
344 +
345 + public:
346 +
347 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
348 +  ~ZConstraint();
349 +    
350 +  void setZConsTime(double time)                  {this->zconsTime = time;}
351 +  void getZConsTime()                             {return zconsTime;}
352 +  
353 +  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
354 +  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
355 +  
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
364   #endif
365 +
366 + protected:
367 +
368 +  enum ZConsState {zcsMoving, zcsFixed};
369 +
370 +
371 +
372 +  virtual void calcForce( int calcPot, int calcStress );
373 +  virtual void thermalize(void);
374 +  
375 +  void zeroOutVel();
376 +  void doZconstraintForce();
377 +  void doHarmonic();
378 +  bool checkZConsState();
379 +
380 +  bool haveFixedZMols();
381 +  bool haveMovingZMols();
382 +
383 +  double calcZSys();
384 +
385 +  int isZConstraintMol(Molecule* mol);
386 +
387 +
388 +  double zconsTime;
389 +  double zconsTol;
390 +  double zForceConst;
391 +  
392 +  vector<Molecule*> zconsMols;
393 +  vector<double> massOfZConsMols;
394 +  vector<double> kz;
395 +  vector<ZConsState> states;
396 +  vector<double> zPos;
397 +  
398 +  
399 +  vector<Molecule*> unconsMols;
400 +  vector<double> massOfUnconsMols;
401 +  double totalMassOfUncons;
402 +
403 +  vector<ZConsParaItem>* parameters;
404 +  
405 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
406 +
407 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
408 +  double* fz;
409 +  double* curZPos;
410 +  
411 +  int totNumOfUnconsAtoms;
412 +
413 +  int whichDirection;                           //constraint direction
414 +  
415 + private:
416 +  
417 +  string zconsOutput;
418 +  ZConsWriter* fzOut;
419 +
420 +  double curZconsTime;
421 +
422 +  double calcMovingMolsCOMVel();
423 +  double calcSysCOMVel();
424 +  double calcTotalForce();
425 +        
426 +  ForceSubstractionPolicy* forcePolicy;
427 +  friend class ForceSubstractionPolicy;
428 +
429 + };
430 +
431 + #endif

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