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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 541 by mmeineke, Fri May 30 20:19:44 2003 UTC vs.
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC

# Line 2 | Line 2
2   #define _INTEGRATOR_H_
3  
4   #include "Atom.hpp"
5 + #include "Molecule.hpp"
6   #include "SRI.hpp"
7   #include "AbstractClasses.hpp"
8   #include "SimInfo.hpp"
# Line 9 | Line 10 | class Integrator : public BaseIntegrator {
10   #include "Thermo.hpp"
11   #include "ReadWrite.hpp"
12  
13 + const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
14 + const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
15 + const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
16 + const int maxIteration = 300;
17 + const double tol = 1.0e-6;
18 +
19   class Integrator : public BaseIntegrator {
20  
21   public:
22 <  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
23 <  virtual ~Symplectic();
22 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
23 >  virtual ~Integrator();
24    void integrate( void );
25  
26  
27   protected:
21 –
28    
29    virtual void integrateStep( int calcPot, int calcStress );
30 +  virtual void preMove( void );
31    virtual void moveA( void );
32    virtual void moveB( void );
33    virtual void constrainA( void );
34    virtual void constrainB( void );
35 +  virtual int  readyCheck( void ) { return 1; }
36    
29 –  
37    void checkConstraints( void );
38    void rotate( int axes1, int axes2, double angle, double j[3],
39                 double A[3][3] );
# Line 36 | Line 43 | class Integrator : public BaseIntegrator { (protected)
43  
44    SimInfo *info; // all the info we'll ever need
45    int nAtoms;  /* the number of atoms */
46 +  int oldAtoms;
47    Atom **atoms; /* array of atom pointers */
48    Molecule* molecules;
49    int nMols;
50  
51 <  int isConstrained; /*boolean to know whether the systems contains
52 <                       constraints. */
53 <  int nConstrained; /*counter for number of constraints */
54 <  int *constrainedI; /* the i of a constraint pair */
55 <  int *constrainedJ; /* the j of a constraint pair */
56 <  double *constrainedDsqr; /* the square of the constraint distance */
51 >  int isConstrained; // boolean to know whether the systems contains
52 >                     // constraints.
53 >  int nConstrained;  // counter for number of constraints
54 >  int *constrainedA; // the i of a constraint pair
55 >  int *constrainedB; // the j of a constraint pair
56 >  double *constrainedDsqr; // the square of the constraint distance
57 >  
58 >  int* moving; // tells whether we are moving atom i
59 >  int* moved;  // tells whether we have moved atom i
60 >  double* oldPos; // pre constrained positions
61 >
62    short isFirst; /*boolean for the first time integrate is called */
63    
64    double dt;
65    double dt2;
53 –  const double eConvert;
66  
55 –  
56 –  double* pos;
57 –  double* vel;
58 –  double* frc;
59 –  double* trq;
60 –  double* Amat;
61 –  
62 –
63 –
67    Thermo *tStats;
68    StatWriter*  statOut;
69    DumpWriter*  dumpOut;
70    
71   };
72  
73 + class NVE : public Integrator{
74  
75 + public:
76 +  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
77 +    Integrator( theInfo, the_ff ){}
78 +  virtual ~NVE(){}
79 +
80 +  
81 +
82 + };
83 +
84   class NVT : public Integrator{
85  
86 <  NVT ( void );
74 <  virtual ~NVT();
86 > public:
87  
88 +  NVT ( SimInfo *theInfo, ForceFields* the_ff);
89 +  virtual ~NVT() {}
90 +
91 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
92 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
93 +
94   protected:
77 –  virtual moveA( void );
78 –  virtual moveB( void );
95  
96 < };
96 >  virtual void moveA( void );
97 >  virtual void moveB( void );
98  
99 +  virtual int readyCheck();
100 +
101 +  // chi is a propagated degree of freedom.
102 +
103 +  double chi;
104 +
105 +  // targetTemp must be set.  tauThermostat must also be set;
106 +
107 +  double targetTemp;
108 +  double tauThermostat;
109    
110 +  short int have_tau_thermostat, have_target_temp;
111  
112 + };
113  
114 +
115 + class NPTi : public Integrator{
116 +
117 + public:
118 +
119 +  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
120 +  virtual ~NPTi() {};
121 +
122 +  virtual void integrateStep( int calcPot, int calcStress ){
123 +    calcStress = 1;
124 +    Integrator::integrateStep( calcPot, calcStress );
125 +  }
126 +
127 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
128 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
129 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
130 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
131 +
132 + protected:
133 +
134 +  virtual void  moveA( void );
135 +  virtual void moveB( void );
136 +
137 +  virtual int readyCheck();
138 +
139 +  // chi and eta are the propagated degrees of freedom
140 +
141 +  double chi;
142 +  double eta;
143 +  double NkBT;
144 +
145 +  // targetTemp, targetPressure, and tauBarostat must be set.  
146 +  // One of qmass or tauThermostat must be set;
147 +
148 +  double targetTemp;
149 +  double targetPressure;
150 +  double tauThermostat;
151 +  double tauBarostat;
152 +
153 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
154 +  short int have_target_pressure;
155 +
156 + };
157 +
158 + class NPTim : public Integrator{
159 +
160 + public:
161 +
162 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
163 +  virtual ~NPTim() {};
164 +
165 +  virtual void integrateStep( int calcPot, int calcStress ){
166 +    calcStress = 1;
167 +    Integrator::integrateStep( calcPot, calcStress );
168 +  }
169 +
170 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
172 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
173 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
174 +
175 + protected:
176 +
177 +  virtual void moveA( void );
178 +  virtual void moveB( void );
179 +
180 +  virtual int readyCheck();
181 +
182 +  Molecule* myMolecules;
183 +  Atom** myAtoms;
184 +
185 +  // chi and eta are the propagated degrees of freedom
186 +
187 +  double chi;
188 +  double eta;
189 +  double NkBT;
190 +
191 +  // targetTemp, targetPressure, and tauBarostat must be set.  
192 +  // One of qmass or tauThermostat must be set;
193 +
194 +  double targetTemp;
195 +  double targetPressure;
196 +  double tauThermostat;
197 +  double tauBarostat;
198 +
199 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
200 +  short int have_target_pressure;
201 +
202 + };
203 +
204 + class NPTf : public Integrator{
205 +
206 + public:
207 +
208 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
209 +  virtual ~NPTf() {};
210 +
211 +  virtual void integrateStep( int calcPot, int calcStress ){
212 +    calcStress = 1;
213 +    Integrator::integrateStep( calcPot, calcStress );
214 +  }
215 +
216 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
217 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
218 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
219 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
220 +
221 + protected:
222 +
223 +  virtual void  moveA( void );
224 +  virtual void moveB( void );
225 +
226 +  virtual int readyCheck();
227 +
228 +  // chi and eta are the propagated degrees of freedom
229 +
230 +  double chi;
231 +  double eta[3][3];
232 +  double NkBT;
233 +
234 +  // targetTemp, targetPressure, and tauBarostat must be set.  
235 +  // One of qmass or tauThermostat must be set;
236 +
237 +  double targetTemp;
238 +  double targetPressure;
239 +  double tauThermostat;
240 +  double tauBarostat;
241 +
242 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
243 +  short int have_target_pressure;
244 +
245 + };
246 +
247 + class NPTfm : public Integrator{
248 +
249 + public:
250 +
251 +  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
252 +  virtual ~NPTfm() {};
253 +
254 +  virtual void integrateStep( int calcPot, int calcStress ){
255 +    calcStress = 1;
256 +    Integrator::integrateStep( calcPot, calcStress );
257 +  }
258 +
259 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
260 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
261 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
262 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
263 +
264 + protected:
265 +
266 +  virtual void  moveA( void );
267 +  virtual void moveB( void );
268 +
269 +  virtual int readyCheck();
270 +
271 +  Molecule* myMolecules;
272 +  Atom** myAtoms;
273 +
274 +  // chi and eta are the propagated degrees of freedom
275 +
276 +  double chi;
277 +  double eta[3][3];
278 +  double NkBT;
279 +
280 +  // targetTemp, targetPressure, and tauBarostat must be set.  
281 +  // One of qmass or tauThermostat must be set;
282 +
283 +  double targetTemp;
284 +  double targetPressure;
285 +  double tauThermostat;
286 +  double tauBarostat;
287 +
288 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
289 +  short int have_target_pressure;
290 +
291 + };
292 +
293   #endif

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