11 |
|
|
12 |
|
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 |
+ |
const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm |
15 |
|
const int maxIteration = 300; |
16 |
|
const double tol = 1.0e-6; |
17 |
|
|
35 |
|
|
36 |
|
void checkConstraints( void ); |
37 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
38 |
< |
double A[9] ); |
38 |
> |
double A[3][3] ); |
39 |
|
|
40 |
|
|
41 |
|
ForceFields* myFF; |
63 |
|
double dt; |
64 |
|
double dt2; |
65 |
|
|
65 |
– |
double* pos; |
66 |
– |
double* vel; |
67 |
– |
double* frc; |
68 |
– |
double* trq; |
69 |
– |
double* Amat; |
70 |
– |
|
66 |
|
Thermo *tStats; |
67 |
|
StatWriter* statOut; |
68 |
|
DumpWriter* dumpOut; |
87 |
|
NVT ( SimInfo *theInfo, ForceFields* the_ff); |
88 |
|
virtual ~NVT() {} |
89 |
|
|
95 |
– |
void setQmass(double q) {qmass = q; have_qmass = 1;} |
90 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
91 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
92 |
|
|
97 |
|
|
98 |
|
virtual int readyCheck(); |
99 |
|
|
100 |
< |
// zeta is a propagated degree of freedom. |
100 |
> |
// chi is a propagated degree of freedom. |
101 |
|
|
102 |
< |
double zeta; |
102 |
> |
double chi; |
103 |
|
|
104 |
< |
// targetTemp must be set. One of qmass or tauThermostat must be set; |
104 |
> |
// targetTemp must be set. tauThermostat must also be set; |
105 |
|
|
112 |
– |
double qmass; |
106 |
|
double targetTemp; |
107 |
|
double tauThermostat; |
108 |
+ |
|
109 |
+ |
short int have_tau_thermostat, have_target_temp; |
110 |
|
|
111 |
+ |
}; |
112 |
+ |
|
113 |
+ |
|
114 |
+ |
class NPTi : public Integrator{ |
115 |
+ |
|
116 |
+ |
public: |
117 |
+ |
|
118 |
+ |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
119 |
+ |
virtual ~NPTi() {}; |
120 |
+ |
|
121 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
122 |
+ |
calcStress = 1; |
123 |
+ |
Integrator::integrateStep( calcPot, calcStress ); |
124 |
+ |
} |
125 |
+ |
|
126 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
127 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
128 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
129 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
130 |
+ |
|
131 |
+ |
protected: |
132 |
+ |
|
133 |
+ |
virtual void moveA( void ); |
134 |
+ |
virtual void moveB( void ); |
135 |
+ |
|
136 |
+ |
virtual int readyCheck(); |
137 |
+ |
|
138 |
+ |
// chi and eta are the propagated degrees of freedom |
139 |
+ |
|
140 |
+ |
double chi; |
141 |
+ |
double eta; |
142 |
|
double NkBT; |
117 |
– |
|
118 |
– |
short int have_tau_thermostat, have_target_temp, have_qmass; |
143 |
|
|
144 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
145 |
+ |
// One of qmass or tauThermostat must be set; |
146 |
+ |
|
147 |
+ |
double targetTemp; |
148 |
+ |
double targetPressure; |
149 |
+ |
double tauThermostat; |
150 |
+ |
double tauBarostat; |
151 |
+ |
|
152 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
153 |
+ |
short int have_target_pressure; |
154 |
+ |
|
155 |
|
}; |
156 |
|
|
157 |
+ |
class NPTim : public Integrator{ |
158 |
|
|
159 |
< |
class NPT : public Integrator{ |
159 |
> |
public: |
160 |
|
|
161 |
+ |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
162 |
+ |
virtual ~NPTim() {}; |
163 |
+ |
|
164 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
165 |
+ |
calcStress = 1; |
166 |
+ |
Integrator::integrateStep( calcPot, calcStress ); |
167 |
+ |
} |
168 |
+ |
|
169 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
170 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
171 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
172 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
173 |
+ |
|
174 |
+ |
protected: |
175 |
+ |
|
176 |
+ |
virtual void moveA( void ); |
177 |
+ |
virtual void moveB( void ); |
178 |
+ |
|
179 |
+ |
virtual int readyCheck(); |
180 |
+ |
|
181 |
+ |
// chi and eta are the propagated degrees of freedom |
182 |
+ |
|
183 |
+ |
double chi; |
184 |
+ |
double eta; |
185 |
+ |
double NkBT; |
186 |
+ |
|
187 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
188 |
+ |
// One of qmass or tauThermostat must be set; |
189 |
+ |
|
190 |
+ |
double targetTemp; |
191 |
+ |
double targetPressure; |
192 |
+ |
double tauThermostat; |
193 |
+ |
double tauBarostat; |
194 |
+ |
|
195 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
196 |
+ |
short int have_target_pressure; |
197 |
+ |
|
198 |
+ |
}; |
199 |
+ |
|
200 |
+ |
class NPTf : public Integrator{ |
201 |
+ |
|
202 |
|
public: |
203 |
|
|
204 |
< |
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
205 |
< |
virtual ~NPT() {}; |
204 |
> |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
205 |
> |
virtual ~NPTf() {}; |
206 |
|
|
207 |
< |
void setQmass(double q) {qmass = q; have_qmass = 1;} |
207 |
> |
virtual void integrateStep( int calcPot, int calcStress ){ |
208 |
> |
calcStress = 1; |
209 |
> |
Integrator::integrateStep( calcPot, calcStress ); |
210 |
> |
} |
211 |
> |
|
212 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
213 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
214 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
221 |
|
|
222 |
|
virtual int readyCheck(); |
223 |
|
|
224 |
< |
// zeta and epsilonDot are the propagated degrees of freedom. |
224 |
> |
// chi and eta are the propagated degrees of freedom |
225 |
|
|
226 |
< |
double zeta; |
227 |
< |
double epsilonDot; |
226 |
> |
double chi; |
227 |
> |
double eta[3][3]; |
228 |
> |
double NkBT; |
229 |
|
|
230 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
231 |
|
// One of qmass or tauThermostat must be set; |
232 |
|
|
151 |
– |
double qmass; |
233 |
|
double targetTemp; |
234 |
|
double targetPressure; |
235 |
|
double tauThermostat; |
236 |
|
double tauBarostat; |
237 |
|
|
238 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
239 |
< |
short int have_target_pressure, have_qmass; |
239 |
> |
short int have_target_pressure; |
240 |
|
|
241 |
|
}; |
242 |
|
|
243 |
+ |
class NPTfm : public Integrator{ |
244 |
+ |
|
245 |
+ |
public: |
246 |
+ |
|
247 |
+ |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
248 |
+ |
virtual ~NPTfm() {}; |
249 |
+ |
|
250 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
251 |
+ |
calcStress = 1; |
252 |
+ |
Integrator::integrateStep( calcPot, calcStress ); |
253 |
+ |
} |
254 |
+ |
|
255 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
256 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
257 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
258 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
259 |
+ |
|
260 |
+ |
protected: |
261 |
+ |
|
262 |
+ |
virtual void moveA( void ); |
263 |
+ |
virtual void moveB( void ); |
264 |
+ |
|
265 |
+ |
virtual int readyCheck(); |
266 |
+ |
|
267 |
+ |
// chi and eta are the propagated degrees of freedom |
268 |
+ |
|
269 |
+ |
double chi; |
270 |
+ |
double eta[3][3]; |
271 |
+ |
double NkBT; |
272 |
+ |
|
273 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
274 |
+ |
// One of qmass or tauThermostat must be set; |
275 |
+ |
|
276 |
+ |
double targetTemp; |
277 |
+ |
double targetPressure; |
278 |
+ |
double tauThermostat; |
279 |
+ |
double tauBarostat; |
280 |
+ |
|
281 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
282 |
+ |
short int have_target_pressure; |
283 |
+ |
|
284 |
+ |
}; |
285 |
+ |
|
286 |
|
#endif |