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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 542 by mmeineke, Fri May 30 21:31:48 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 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 < class Integrator : public BaseIntegrator {
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  
23 +
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27 <  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
28 <  virtual ~Symplectic();
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28 >  virtual ~Integrator();
29    void integrate( void );
30  
31  
32   protected:
21 –
33    
34    virtual void integrateStep( int calcPot, int calcStress );
35 +  virtual void preMove( void );
36    virtual void moveA( void );
37    virtual void moveB( void );
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    
29 –  
45    void checkConstraints( void );
46    void rotate( int axes1, int axes2, double angle, double j[3],
47 <               double A[3][3] );
48 <
34 <
47 >         double A[3][3] );
48 >        
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
52    int nAtoms;  /* the number of atoms */
53 +  int oldAtoms;
54    Atom **atoms; /* array of atom pointers */
55    Molecule* molecules;
56    int nMols;
57  
58 <  int isConstrained; /*boolean to know whether the systems contains
59 <                       constraints. */
60 <  int nConstrained; /*counter for number of constraints */
61 <  int *constrainedI; /* the i of a constraint pair */
62 <  int *constrainedJ; /* the j of a constraint pair */
63 <  double *constrainedDsqr; /* the square of the constraint distance */
58 >  int isConstrained; // boolean to know whether the systems contains
59 >         // constraints.
60 >  int nConstrained;  // counter for number of constraints
61 >  int *constrainedA; // the i of a constraint pair
62 >  int *constrainedB; // the j of a constraint pair
63 >  double *constrainedDsqr; // the square of the constraint distance
64 >  
65 >  int* moving; // tells whether we are moving atom i
66 >  int* moved;  // tells whether we have moved atom i
67 >  double* oldPos; // pre constrained positions
68 >
69    short isFirst; /*boolean for the first time integrate is called */
70    
71    double dt;
72    double dt2;
53 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
73  
55 –  
56 –  double* pos;
57 –  double* vel;
58 –  double* frc;
59 –  double* trq;
60 –  double* Amat;
61 –  
62 –
63 –
74    Thermo *tStats;
75    StatWriter*  statOut;
76    DumpWriter*  dumpOut;
77    
78   };
79  
80 + typedef Integrator<BaseIntegrator> RealIntegrator;
81  
82 < class NVT : public Integrator{
82 > template<typename T> class NVE : public T {
83  
84 <  NVT ( void );
85 <  virtual ~NVT();
84 > public:
85 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
86 >    T( theInfo, the_ff ){}
87 >  virtual ~NVE(){}  
88 > };
89  
90 +
91 + template<typename T> class NVT : public T {
92 +
93 + public:
94 +
95 +  NVT ( SimInfo *theInfo, ForceFields* the_ff);
96 +  virtual ~NVT() {}
97 +
98 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
99 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
100 +
101   protected:
77 –  virtual moveA( void );
78 –  virtual moveB( void );
102  
103 +  virtual void moveA( void );
104 +  virtual void moveB( void );
105 +
106 +  virtual int readyCheck();
107 +
108 +  // chi is a propagated degree of freedom.
109 +
110 +  double chi;
111 +
112 +  // targetTemp must be set.  tauThermostat must also be set;
113 +
114 +  double targetTemp;
115 +  double tauThermostat;
116 +  
117 +  short int have_tau_thermostat, have_target_temp;
118 +
119   };
120  
121 +
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;}
138 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
139 +
140 + protected:
141 +
142 +  virtual void  moveA( void );
143 +  virtual void moveB( void );
144 +
145 +  virtual int readyCheck();
146 +
147 +  // chi and eta are the propagated degrees of freedom
148 +
149 +  double chi;
150 +  double eta;
151 +  double NkBT;
152 +
153 +  // targetTemp, targetPressure, and tauBarostat must be set.  
154 +  // One of qmass or tauThermostat must be set;
155 +
156 +  double targetTemp;
157 +  double targetPressure;
158 +  double tauThermostat;
159 +  double tauBarostat;
160 +
161 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
162 +  short int have_target_pressure;
163 +
164 + };
165 +
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;}
227 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
228 +
229 + protected:
230 +
231 +  virtual void  moveA( void );
232 +  virtual void moveB( void );
233 +
234 +  virtual int readyCheck();
235 +
236 +  // chi and eta are the propagated degrees of freedom
237 +
238 +  double chi;
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.  
289 +  // One of qmass or tauThermostat must be set;
290 +
291 +  double targetTemp;
292 +  double targetPressure;
293 +  double tauThermostat;
294 +  double tauBarostat;
295 +
296 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297 +  short int have_target_pressure;
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 +  virtual void calcForce( int calcPot, int calcStress );
371 +  virtual void thermalize(void);
372 +  
373 +  void zeroOutVel();
374 +  void doZconstraintForce();
375 +  void doHarmonic();
376 +  bool checkZConsState();
377 +
378 +  bool haveFixedZMols();
379 +  bool haveMovingZMols();
380 +
381 +  double calcZSys();
382 +
383 +  int isZConstraintMol(Molecule* mol);
384 +
385 +
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;              //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;           //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; //
403 +  
404 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
405 +
406 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
407 +  double* fz;
408 +  double* curZPos;
409 +  
410 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
411 +
412 +  int whichDirection;                           //constraint direction
413 +  
414 + private:
415 +  
416 +  string zconsOutput;                         //filename of zconstraint output
417 +  ZConsWriter* fzOut;                         //z-constraint writer
418 +
419 +  double curZconsTime;                      
420 +
421 +  double calcMovingMolsCOMVel();
422 +  double calcSysCOMVel();
423 +  double calcTotalForce();
424 +  
425 +  ForceSubstractionPolicy* forcePolicy; //force substration policy
426 +  friend class ForceSubstractionPolicy;
427 +
428 + };
429 +
430 + #endif

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