1 |
mmeineke |
377 |
#ifndef _INTEGRATOR_H_ |
2 |
|
|
#define _INTEGRATOR_H_ |
3 |
|
|
|
4 |
|
|
#include "Atom.hpp" |
5 |
|
|
#include "SRI.hpp" |
6 |
|
|
#include "AbstractClasses.hpp" |
7 |
|
|
#include "SimInfo.hpp" |
8 |
|
|
#include "ForceFields.hpp" |
9 |
mmeineke |
540 |
#include "Thermo.hpp" |
10 |
|
|
#include "ReadWrite.hpp" |
11 |
mmeineke |
377 |
|
12 |
mmeineke |
561 |
const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K |
13 |
|
|
const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
14 |
mmeineke |
586 |
const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm |
15 |
mmeineke |
561 |
const int maxIteration = 300; |
16 |
|
|
const double tol = 1.0e-6; |
17 |
|
|
|
18 |
mmeineke |
540 |
class Integrator : public BaseIntegrator { |
19 |
mmeineke |
377 |
|
20 |
|
|
public: |
21 |
mmeineke |
561 |
Integrator( SimInfo *theInfo, ForceFields* the_ff ); |
22 |
mmeineke |
548 |
virtual ~Integrator(); |
23 |
mmeineke |
377 |
void integrate( void ); |
24 |
|
|
|
25 |
|
|
|
26 |
mmeineke |
540 |
protected: |
27 |
mmeineke |
377 |
|
28 |
mmeineke |
540 |
virtual void integrateStep( int calcPot, int calcStress ); |
29 |
mmeineke |
548 |
virtual void preMove( void ); |
30 |
mmeineke |
540 |
virtual void moveA( void ); |
31 |
|
|
virtual void moveB( void ); |
32 |
|
|
virtual void constrainA( void ); |
33 |
|
|
virtual void constrainB( void ); |
34 |
mmeineke |
559 |
virtual int readyCheck( void ) { return 1; } |
35 |
mmeineke |
377 |
|
36 |
mmeineke |
540 |
void checkConstraints( void ); |
37 |
mmeineke |
377 |
void rotate( int axes1, int axes2, double angle, double j[3], |
38 |
mmeineke |
597 |
double A[9] ); |
39 |
mmeineke |
377 |
|
40 |
mmeineke |
540 |
|
41 |
mmeineke |
377 |
ForceFields* myFF; |
42 |
|
|
|
43 |
mmeineke |
540 |
SimInfo *info; // all the info we'll ever need |
44 |
|
|
int nAtoms; /* the number of atoms */ |
45 |
mmeineke |
548 |
int oldAtoms; |
46 |
mmeineke |
540 |
Atom **atoms; /* array of atom pointers */ |
47 |
mmeineke |
423 |
Molecule* molecules; |
48 |
|
|
int nMols; |
49 |
|
|
|
50 |
mmeineke |
548 |
int isConstrained; // boolean to know whether the systems contains |
51 |
|
|
// constraints. |
52 |
|
|
int nConstrained; // counter for number of constraints |
53 |
|
|
int *constrainedA; // the i of a constraint pair |
54 |
|
|
int *constrainedB; // the j of a constraint pair |
55 |
|
|
double *constrainedDsqr; // the square of the constraint distance |
56 |
|
|
|
57 |
|
|
int* moving; // tells whether we are moving atom i |
58 |
|
|
int* moved; // tells whether we have moved atom i |
59 |
mmeineke |
561 |
double* oldPos; // pre constrained positions |
60 |
mmeineke |
548 |
|
61 |
mmeineke |
540 |
short isFirst; /*boolean for the first time integrate is called */ |
62 |
|
|
|
63 |
|
|
double dt; |
64 |
mmeineke |
541 |
double dt2; |
65 |
gezelter |
560 |
|
66 |
mmeineke |
541 |
double* pos; |
67 |
|
|
double* vel; |
68 |
|
|
double* frc; |
69 |
|
|
double* trq; |
70 |
|
|
double* Amat; |
71 |
mmeineke |
377 |
|
72 |
mmeineke |
540 |
Thermo *tStats; |
73 |
|
|
StatWriter* statOut; |
74 |
|
|
DumpWriter* dumpOut; |
75 |
mmeineke |
377 |
|
76 |
|
|
}; |
77 |
|
|
|
78 |
mmeineke |
555 |
class NVE : public Integrator{ |
79 |
mmeineke |
540 |
|
80 |
mmeineke |
561 |
public: |
81 |
|
|
NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
82 |
mmeineke |
555 |
Integrator( theInfo, the_ff ){} |
83 |
|
|
virtual ~NVE(){} |
84 |
|
|
|
85 |
|
|
|
86 |
|
|
|
87 |
|
|
}; |
88 |
|
|
|
89 |
mmeineke |
540 |
class NVT : public Integrator{ |
90 |
|
|
|
91 |
gezelter |
560 |
public: |
92 |
|
|
|
93 |
mmeineke |
561 |
NVT ( SimInfo *theInfo, ForceFields* the_ff); |
94 |
|
|
virtual ~NVT() {} |
95 |
mmeineke |
540 |
|
96 |
gezelter |
560 |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
97 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
98 |
|
|
|
99 |
mmeineke |
540 |
protected: |
100 |
gezelter |
560 |
|
101 |
mmeineke |
561 |
virtual void moveA( void ); |
102 |
|
|
virtual void moveB( void ); |
103 |
mmeineke |
540 |
|
104 |
mmeineke |
561 |
virtual int readyCheck(); |
105 |
gezelter |
560 |
|
106 |
gezelter |
565 |
// chi is a propagated degree of freedom. |
107 |
gezelter |
560 |
|
108 |
gezelter |
565 |
double chi; |
109 |
gezelter |
560 |
|
110 |
gezelter |
565 |
// targetTemp must be set. tauThermostat must also be set; |
111 |
gezelter |
560 |
|
112 |
|
|
double targetTemp; |
113 |
|
|
double tauThermostat; |
114 |
mmeineke |
561 |
|
115 |
gezelter |
565 |
short int have_tau_thermostat, have_target_temp; |
116 |
gezelter |
560 |
|
117 |
mmeineke |
540 |
}; |
118 |
|
|
|
119 |
|
|
|
120 |
gezelter |
574 |
class NPTi : public Integrator{ |
121 |
mmeineke |
540 |
|
122 |
gezelter |
560 |
public: |
123 |
|
|
|
124 |
gezelter |
574 |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
125 |
|
|
virtual ~NPTi() {}; |
126 |
gezelter |
560 |
|
127 |
mmeineke |
594 |
virtual void integrateStep( int calcPot, int calcStress ){ |
128 |
|
|
calcStress = 1; |
129 |
|
|
Integrator::integrateStep( calcPot, calcStress ); |
130 |
|
|
} |
131 |
|
|
|
132 |
gezelter |
560 |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
133 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
134 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
135 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
136 |
|
|
|
137 |
|
|
protected: |
138 |
|
|
|
139 |
mmeineke |
561 |
virtual void moveA( void ); |
140 |
|
|
virtual void moveB( void ); |
141 |
gezelter |
560 |
|
142 |
mmeineke |
561 |
virtual int readyCheck(); |
143 |
gezelter |
560 |
|
144 |
gezelter |
565 |
// chi and eta are the propagated degrees of freedom |
145 |
gezelter |
560 |
|
146 |
gezelter |
565 |
double chi; |
147 |
|
|
double eta; |
148 |
gezelter |
574 |
double NkBT; |
149 |
gezelter |
560 |
|
150 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
151 |
|
|
// One of qmass or tauThermostat must be set; |
152 |
|
|
|
153 |
|
|
double targetTemp; |
154 |
|
|
double targetPressure; |
155 |
|
|
double tauThermostat; |
156 |
|
|
double tauBarostat; |
157 |
|
|
|
158 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
159 |
gezelter |
565 |
short int have_target_pressure; |
160 |
gezelter |
560 |
|
161 |
|
|
}; |
162 |
|
|
|
163 |
gezelter |
596 |
class NPTim : public Integrator{ |
164 |
|
|
|
165 |
|
|
public: |
166 |
|
|
|
167 |
|
|
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
168 |
|
|
virtual ~NPTim() {}; |
169 |
|
|
|
170 |
|
|
virtual void integrateStep( int calcPot, int calcStress ){ |
171 |
|
|
calcStress = 1; |
172 |
|
|
Integrator::integrateStep( calcPot, calcStress ); |
173 |
|
|
} |
174 |
|
|
|
175 |
|
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
176 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
177 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
178 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
179 |
|
|
|
180 |
|
|
protected: |
181 |
|
|
|
182 |
|
|
virtual void moveA( void ); |
183 |
|
|
virtual void moveB( void ); |
184 |
|
|
|
185 |
|
|
virtual int readyCheck(); |
186 |
|
|
|
187 |
|
|
// chi and eta are the propagated degrees of freedom |
188 |
|
|
|
189 |
|
|
double chi; |
190 |
|
|
double eta; |
191 |
|
|
double NkBT; |
192 |
|
|
|
193 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
194 |
|
|
// One of qmass or tauThermostat must be set; |
195 |
|
|
|
196 |
|
|
double targetTemp; |
197 |
|
|
double targetPressure; |
198 |
|
|
double tauThermostat; |
199 |
|
|
double tauBarostat; |
200 |
|
|
|
201 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
202 |
|
|
short int have_target_pressure; |
203 |
|
|
|
204 |
|
|
}; |
205 |
|
|
|
206 |
gezelter |
576 |
class NPTf : public Integrator{ |
207 |
|
|
|
208 |
|
|
public: |
209 |
|
|
|
210 |
|
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
211 |
|
|
virtual ~NPTf() {}; |
212 |
|
|
|
213 |
mmeineke |
594 |
virtual void integrateStep( int calcPot, int calcStress ){ |
214 |
|
|
calcStress = 1; |
215 |
|
|
Integrator::integrateStep( calcPot, calcStress ); |
216 |
|
|
} |
217 |
|
|
|
218 |
gezelter |
576 |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
219 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
220 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
221 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
222 |
|
|
|
223 |
|
|
protected: |
224 |
|
|
|
225 |
|
|
virtual void moveA( void ); |
226 |
|
|
virtual void moveB( void ); |
227 |
|
|
|
228 |
|
|
virtual int readyCheck(); |
229 |
|
|
|
230 |
|
|
// chi and eta are the propagated degrees of freedom |
231 |
|
|
|
232 |
|
|
double chi; |
233 |
gezelter |
588 |
double eta[3][3]; |
234 |
gezelter |
576 |
double NkBT; |
235 |
|
|
|
236 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
237 |
|
|
// One of qmass or tauThermostat must be set; |
238 |
|
|
|
239 |
|
|
double targetTemp; |
240 |
|
|
double targetPressure; |
241 |
|
|
double tauThermostat; |
242 |
|
|
double tauBarostat; |
243 |
|
|
|
244 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
245 |
|
|
short int have_target_pressure; |
246 |
|
|
|
247 |
|
|
}; |
248 |
|
|
|
249 |
gezelter |
596 |
class NPTfm : public Integrator{ |
250 |
|
|
|
251 |
|
|
public: |
252 |
|
|
|
253 |
|
|
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
254 |
|
|
virtual ~NPTfm() {}; |
255 |
|
|
|
256 |
|
|
virtual void integrateStep( int calcPot, int calcStress ){ |
257 |
|
|
calcStress = 1; |
258 |
|
|
Integrator::integrateStep( calcPot, calcStress ); |
259 |
|
|
} |
260 |
|
|
|
261 |
|
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
262 |
|
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
263 |
|
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
264 |
|
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
265 |
|
|
|
266 |
|
|
protected: |
267 |
|
|
|
268 |
|
|
virtual void moveA( void ); |
269 |
|
|
virtual void moveB( void ); |
270 |
|
|
|
271 |
|
|
virtual int readyCheck(); |
272 |
|
|
|
273 |
|
|
// chi and eta are the propagated degrees of freedom |
274 |
|
|
|
275 |
|
|
double chi; |
276 |
|
|
double eta[3][3]; |
277 |
|
|
double NkBT; |
278 |
|
|
|
279 |
|
|
// targetTemp, targetPressure, and tauBarostat must be set. |
280 |
|
|
// One of qmass or tauThermostat must be set; |
281 |
|
|
|
282 |
|
|
double targetTemp; |
283 |
|
|
double targetPressure; |
284 |
|
|
double tauThermostat; |
285 |
|
|
double tauBarostat; |
286 |
|
|
|
287 |
|
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
288 |
|
|
short int have_target_pressure; |
289 |
|
|
|
290 |
|
|
}; |
291 |
|
|
|
292 |
mmeineke |
377 |
#endif |