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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 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 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
22 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
23    virtual ~Integrator();
24    void integrate( void );
25  
# Line 50 | Line 57 | class Integrator : public BaseIntegrator { (protected)
57    
58    int* moving; // tells whether we are moving atom i
59    int* moved;  // tells whether we have moved atom i
60 <  double* prePos; // pre constrained positions
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;
66  
60 –  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
61 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
62 –  const int maxIteration = 300;
63 –  const double tol = 1.0e-6;
64 –  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
67    Thermo *tStats;
68    StatWriter*  statOut;
69    DumpWriter*  dumpOut;
# Line 76 | Line 72 | class NVE : public Integrator{
72  
73   class NVE : public Integrator{
74  
75 <  NVE ( void ):
75 > public:
76 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
77      Integrator( theInfo, the_ff ){}
78    virtual ~NVE(){}
79  
# Line 88 | Line 85 | class NVT : public Integrator{ (public)
85  
86   public:
87  
88 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
89 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
88 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
89 >  virtual ~NVT() {}
90  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
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:
95  
96 <  virtual moveA( void );
97 <  virtual moveB( void );
96 >  virtual void moveA( void );
97 >  virtual void moveB( void );
98  
99 <  int readyCheck();
99 >  virtual int readyCheck();
100  
101 <  Atom** atoms;
101 >  // chi is a propagated degree of freedom.
102  
103 <  // zeta is a propagated degree of freedom.
103 >  double chi;
104  
105 <  double zeta;
105 >  // targetTemp must be set.  tauThermostat must also be set;
106  
107 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
107 >  double targetTemp;
108 >  double tauThermostat;
109 >  
110 >  short int have_tau_thermostat, have_target_temp;
111  
112 <  double qmass;
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_target_temp, have_qmass;
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 < class NPT : public Integrator{
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 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
209 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
208 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
209 >  virtual ~NPTf() {};
210  
211 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
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;}
# Line 136 | Line 220 | class NPT : public Integrator{ (protected)
220  
221   protected:
222  
223 <  virtual moveA( void );
224 <  virtual moveB( void );
223 >  virtual void  moveA( void );
224 >  virtual void moveB( void );
225  
226 <  int readyCheck();
226 >  virtual int readyCheck();
227  
228 <  Atom** atoms;
228 >  // chi and eta are the propagated degrees of freedom
229  
230 <  // zeta and epsilonDot are the propagated degrees of freedom.
230 >  double chi;
231 >  double eta[3][3];
232 >  double NkBT;
233  
234 <  double zeta;
235 <  double epsilonDot;
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  
154 –  double qmass;
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, have_qmass;
289 >  short int have_target_pressure;
290  
291   };
292  

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