ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 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 Verlet : public Integrator {
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 <  Verlet( SimInfo &info, ForceFields* the_ff );
28 <  ~Verlet();
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28 >  virtual ~Integrator();
29    void integrate( void );
30  
31 < private:
31 >
32 > protected:
33    
34 <  void move_a( double dt );
35 <  void move_b( double dt );
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 >  void checkConstraints( void );
43 >  void rotate( int axes1, int axes2, double angle, double j[3],
44 >               double A[3][3] );
45  
46 +
47    ForceFields* myFF;
48  
49 <  SimInfo *entry_plug; // all the info we'll ever need
50 <  int c_natoms;  /* the number of atoms */
51 <  Atom **c_atoms; /* array of atom pointers */
49 >  SimInfo *info; // all the info we'll ever need
50 >  int nAtoms;  /* the number of atoms */
51 >  int oldAtoms;
52 >  Atom **atoms; /* array of atom pointers */
53    Molecule* molecules;
54    int nMols;
55  
56 <  int c_is_constrained; /*boolean to know whether the systems contains
57 <                          constraints. */
58 <  int c_n_constrained; /*counter for number of constraints */
59 <  int *c_constrained_i; /* the i of a constraint pair */
60 <  int *c_constrained_j; /* the j of a constraint pair */
61 <  double *c_constrained_dsqr; /* the square of the constraint distance */
62 <  double *c_mass; /* the array of masses */
63 <  short is_first; /*boolean for the first time integrate is called */
64 <  double c_box_x;
65 <  double c_box_y;
40 <  double c_box_z;
41 < };
56 >  int isConstrained; // boolean to know whether the systems contains
57 >                     // constraints.
58 >  int nConstrained;  // counter for number of constraints
59 >  int *constrainedA; // the i of a constraint pair
60 >  int *constrainedB; // the j of a constraint pair
61 >  double *constrainedDsqr; // the square of the constraint distance
62 >  
63 >  int* moving; // tells whether we are moving atom i
64 >  int* moved;  // tells whether we have moved atom i
65 >  double* oldPos; // pre constrained positions
66  
67 < class Symplectic : public Integrator {
67 >  short isFirst; /*boolean for the first time integrate is called */
68    
69 +  double dt;
70 +  double dt2;
71 +
72 +  Thermo *tStats;
73 +  StatWriter*  statOut;
74 +  DumpWriter*  dumpOut;
75 +  
76 + };
77 +
78 + typedef Integrator<BaseIntegrator> RealIntegrator;
79 +
80 + template<typename T> class NVE : public T {
81 +
82   public:
83 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
84 <  ~Symplectic();
83 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
84 >    T( theInfo, the_ff ){}
85 >  virtual ~NVE(){}  
86 > };
87 >
88 >
89 > template<typename T> class NVT : public T {
90 >
91 > public:
92 >
93 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
94 >  virtual ~NVT() {}
95 >
96 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
97 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
98 >
99 > protected:
100 >
101 >  virtual void moveA( void );
102 >  virtual void moveB( void );
103 >
104 >  virtual int readyCheck();
105 >
106 >  // chi is a propagated degree of freedom.
107 >
108 >  double chi;
109 >
110 >  // targetTemp must be set.  tauThermostat must also be set;
111 >
112 >  double targetTemp;
113 >  double tauThermostat;
114    
115 <  void integrate( void );
115 >  short int have_tau_thermostat, have_target_temp;
116  
117 < private:
117 > };
118  
53 –  void rotate( int axes1, int axes2, double angle, double j[3],
54 –               double A[3][3] );
119  
56 –  SimInfo* entry_plug;
57 –  ForceFields* myFF;
120  
121 <  Molecule* molecules;
60 <  int nMols;
121 > template<typename T> class NPTi : public T{
122  
123 <  int is_constrained; /*boolean to know whether the systems contains
63 <                          constraints. */
64 <  int n_constrained; /*counter for number of constraints */
65 <  int *constrained_i; /* the i of a constraint pair */
66 <  int *constrained_j; /* the j of a constraint pair */
67 <  double *constrained_dsqr; /* the square of the constraint distance */
68 <  double *mass; /* the array of masses */
123 > public:
124  
125 <  short int isFirst;
125 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
126 >  virtual ~NPTi() {};
127  
128 <  SRI **srInteractions; /* array of SRI pointers */
129 <  int nSRI; /* the number of short range interactions */
128 >  virtual void integrateStep( int calcPot, int calcStress ){
129 >    calcStress = 1;
130 >    T::integrateStep( calcPot, calcStress );
131 >  }
132 >
133 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
134 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
135 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
136 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
137 >
138 > protected:
139 >
140 >  virtual void  moveA( void );
141 >  virtual void moveB( void );
142 >
143 >  virtual int readyCheck();
144 >
145 >  // chi and eta are the propagated degrees of freedom
146 >
147 >  double chi;
148 >  double eta;
149 >  double NkBT;
150 >
151 >  // targetTemp, targetPressure, and tauBarostat must be set.  
152 >  // One of qmass or tauThermostat must be set;
153 >
154 >  double targetTemp;
155 >  double targetPressure;
156 >  double tauThermostat;
157 >  double tauBarostat;
158 >
159 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
160 >  short int have_target_pressure;
161 >
162 > };
163 >
164 > template<typename T> class NPTim : public T{
165 >
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 >
191 >  // chi and eta are the propagated degrees of freedom
192 >
193 >  double chi;
194 >  double eta;
195 >  double NkBT;
196 >
197 >  // targetTemp, targetPressure, and tauBarostat must be set.  
198 >  // One of qmass or tauThermostat must be set;
199 >
200 >  double targetTemp;
201 >  double targetPressure;
202 >  double tauThermostat;
203 >  double tauBarostat;
204 >
205 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
206 >  short int have_target_pressure;
207 >
208 > };
209 >
210 > template<typename T> class NPTf : public T{
211 >
212 > public:
213 >
214 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
215 >  virtual ~NPTf() {};
216 >
217 >  virtual void integrateStep( int calcPot, int calcStress ){
218 >    calcStress = 1;
219 >    T::integrateStep( calcPot, calcStress );
220 >  }
221 >
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;}
226 >
227 > protected:
228 >
229 >  virtual void  moveA( void );
230 >  virtual void moveB( void );
231 >
232 >  virtual int readyCheck();
233 >
234 >  // chi and eta are the propagated degrees of freedom
235 >
236 >  double chi;
237 >  double eta[3][3];
238 >  double NkBT;
239 >
240 >  // targetTemp, targetPressure, and tauBarostat must be set.  
241 >  // One of qmass or tauThermostat must be set;
242 >
243 >  double targetTemp;
244 >  double targetPressure;
245 >  double tauThermostat;
246 >  double tauBarostat;
247 >
248 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
249 >  short int have_target_pressure;
250 >
251 > };
252 >
253 > template<typename T> class NPTfm : public T{
254 >
255 > public:
256 >
257 >  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
258 >  virtual ~NPTfm() {};
259 >
260 >  virtual void integrateStep( int calcPot, int calcStress ){
261 >    calcStress = 1;
262 >    T::integrateStep( calcPot, calcStress );
263 >  }
264 >
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 >
270 > protected:
271 >
272 >  virtual void  moveA( void );
273 >  virtual void moveB( void );
274 >
275 >  virtual int readyCheck();
276 >
277 >  Molecule* myMolecules;
278 >  Atom** myAtoms;
279 >
280 >  // chi and eta are the propagated degrees of freedom
281 >
282 >  double chi;
283 >  double eta[3][3];
284 >  double NkBT;
285 >
286 >  // targetTemp, targetPressure, and tauBarostat must be set.  
287 >  // One of qmass or tauThermostat must be set;
288 >
289 >  double targetTemp;
290 >  double targetPressure;
291 >  double tauThermostat;
292 >  double tauBarostat;
293 >
294 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
295 >  short int have_target_pressure;
296 >
297 > };
298 >
299 > template<typename T> class ZConstraint : public T {
300 >
301 > public:
302 >
303 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
304 >  ~ZConstraint();
305 >
306 >  virtual void integrateStep( int calcPot, int calcStress );
307    
308 +  
309 +  void setZConsTime(double time)                  {this->zconsTime = time;}
310 +  void getZConsTime()                             {return zconsTime;}
311 +  
312 +  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
313 +  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
314 +  
315 +  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
316 +  string getZConsOutput()                         {return zconsOutput;}
317 +
318 + #ifdef IS_MPI
319 +  virtual void update(); //which is called to indicate the molecules' migration
320 + #endif
321 +
322 + protected:
323 +
324 +  double zconsTime;
325 +  
326 +  void resetZ(void);
327 +  
328 +  vector<Molecule*> zconsMols;
329 +  vector<double> massOfZConsMols;
330 +  
331 +  vector<Molecule*> unconsMols;
332 +  vector<double> massOfUnconsMols;
333 +  double totalMassOfUncons;
334 +
335 +  vector<double> allRefZ;    
336 +  vector<double> refZ;
337 +  
338 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
339 +  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
340 +    
341 +  double* fz;
342 +  
343 + private:
344 +
345 +  int isZConstraintMol(Molecule* mol);
346 +  string zconsOutput;
347 +  ZConsWriter* fzOut;
348   };
349  
350   #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines