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(); |
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; |
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); |
117 |
|
}; |
118 |
|
|
119 |
|
|
119 |
– |
class NPTi : public Integrator{ |
120 |
|
|
121 |
+ |
template<typename T> class NPTi : public T{ |
122 |
+ |
|
123 |
|
public: |
124 |
|
|
125 |
|
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
126 |
|
virtual ~NPTi() {}; |
127 |
|
|
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;} |
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 |