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; |
93 |
|
NVT ( SimInfo *theInfo, ForceFields* the_ff); |
94 |
|
virtual ~NVT() {} |
95 |
|
|
95 |
– |
void setQmass(double q) {qmass = q; have_qmass = 1;} |
96 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
97 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
98 |
|
|
103 |
|
|
104 |
|
virtual int readyCheck(); |
105 |
|
|
106 |
< |
// zeta is a propagated degree of freedom. |
106 |
> |
// chi is a propagated degree of freedom. |
107 |
|
|
108 |
< |
double zeta; |
108 |
> |
double chi; |
109 |
|
|
110 |
< |
// targetTemp must be set. One of qmass or tauThermostat must be set; |
110 |
> |
// targetTemp must be set. tauThermostat must also be set; |
111 |
|
|
112 |
– |
double qmass; |
112 |
|
double targetTemp; |
113 |
|
double tauThermostat; |
114 |
+ |
|
115 |
+ |
short int have_tau_thermostat, have_target_temp; |
116 |
|
|
117 |
+ |
}; |
118 |
+ |
|
119 |
+ |
|
120 |
+ |
class NPTi : public Integrator{ |
121 |
+ |
|
122 |
+ |
public: |
123 |
+ |
|
124 |
+ |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
125 |
+ |
virtual ~NPTi() {}; |
126 |
+ |
|
127 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
128 |
+ |
calcStress = 1; |
129 |
+ |
Integrator::integrateStep( calcPot, calcStress ); |
130 |
+ |
} |
131 |
+ |
|
132 |
+ |
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 |
+ |
virtual void moveA( void ); |
140 |
+ |
virtual void moveB( void ); |
141 |
+ |
|
142 |
+ |
virtual int readyCheck(); |
143 |
+ |
|
144 |
+ |
// chi and eta are the propagated degrees of freedom |
145 |
+ |
|
146 |
+ |
double chi; |
147 |
+ |
double eta; |
148 |
|
double NkBT; |
117 |
– |
|
118 |
– |
short int have_tau_thermostat, have_target_temp, have_qmass; |
149 |
|
|
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 |
+ |
short int have_target_pressure; |
160 |
+ |
|
161 |
|
}; |
162 |
|
|
163 |
+ |
class NPTim : public Integrator{ |
164 |
|
|
165 |
< |
class NPT : public Integrator{ |
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 |
+ |
class NPTf : public Integrator{ |
207 |
+ |
|
208 |
|
public: |
209 |
|
|
210 |
< |
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
211 |
< |
virtual ~NPT(); |
210 |
> |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
211 |
> |
virtual ~NPTf() {}; |
212 |
|
|
213 |
< |
void setQmass(double q) {qmass = q; have_qmass = 1;} |
213 |
> |
virtual void integrateStep( int calcPot, int calcStress ){ |
214 |
> |
calcStress = 1; |
215 |
> |
Integrator::integrateStep( calcPot, calcStress ); |
216 |
> |
} |
217 |
> |
|
218 |
|
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;} |
227 |
|
|
228 |
|
virtual int readyCheck(); |
229 |
|
|
230 |
< |
Atom** atoms; |
230 |
> |
// chi and eta are the propagated degrees of freedom |
231 |
|
|
232 |
< |
// zeta and epsilonDot are the propagated degrees of freedom. |
232 |
> |
double chi; |
233 |
> |
double eta[3][3]; |
234 |
> |
double NkBT; |
235 |
|
|
236 |
< |
double zeta; |
237 |
< |
double epsilonDot; |
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 |
+ |
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 |
|
|
153 |
– |
double qmass; |
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, have_qmass; |
288 |
> |
short int have_target_pressure; |
289 |
|
|
290 |
|
}; |
291 |
|
|