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 561 by mmeineke, Fri Jun 20 20:29:36 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 + 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 34 | Line 41 | class Integrator : public BaseIntegrator { (protected)
41    
42    void checkConstraints( void );
43    void rotate( int axes1, int axes2, double angle, double j[3],
44 <               double A[9] );
44 >               double A[3][3] );
45  
46  
47    ForceFields* myFF;
# Line 62 | Line 69 | class Integrator : public BaseIntegrator { (protected)
69    double dt;
70    double dt2;
71  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
72    Thermo *tStats;
73    StatWriter*  statOut;
74    DumpWriter*  dumpOut;
75    
76   };
77  
78 < class NVE : public Integrator{
78 > typedef Integrator<BaseIntegrator> RealIntegrator;
79  
80 + template<typename T> class NVE : public T {
81 +
82   public:
83    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
84 <    Integrator( theInfo, the_ff ){}
85 <  virtual ~NVE(){}
83 <
84 <  
85 <
84 >    T( theInfo, the_ff ){}
85 >  virtual ~NVE(){}  
86   };
87  
88 – class NVT : public Integrator{
88  
89 + template<typename T> class NVT : public T {
90 +
91   public:
92  
93    NVT ( SimInfo *theInfo, ForceFields* the_ff);
94    virtual ~NVT() {}
95  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
96    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
97    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
98  
# Line 103 | Line 103 | class NVT : public Integrator{ (protected)
103  
104    virtual int readyCheck();
105  
106 <  // zeta is a propagated degree of freedom.
106 >  // chi is a propagated degree of freedom.
107  
108 <  double zeta;
108 >  double chi;
109  
110 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
110 >  // targetTemp must be set.  tauThermostat must also be set;
111  
112 –  double qmass;
112    double targetTemp;
113    double tauThermostat;
115 –
116 –  double NkBT;
114    
115 <  short int have_tau_thermostat, have_target_temp, have_qmass;
115 >  short int have_tau_thermostat, have_target_temp;
116  
117   };
118  
119  
123 – class NPT : public Integrator{
120  
121 + template<typename T> class NPTi : public T{
122 +
123   public:
124  
125 <  NPT ( SimInfo *theInfo, ForceFields* the_ff);
126 <  virtual ~NPT();
125 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
126 >  virtual ~NPTi() {};
127  
128 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
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;}
# Line 140 | Line 142 | class NPT : public Integrator{ (protected)
142  
143    virtual int readyCheck();
144  
145 <  Atom** atoms;
145 >  // chi and eta are the propagated degrees of freedom
146  
147 <  // zeta and epsilonDot are the propagated degrees of freedom.
147 >  double chi;
148 >  double eta;
149 >  double NkBT;
150  
151 <  double zeta;
152 <  double epsilonDot;
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  
153 –  double qmass;
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, have_qmass;
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