28 |
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virtual ~Integrator(); |
29 |
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void integrate( void ); |
30 |
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virtual double getConservedQuantity(void); |
31 |
+ |
virtual string getAdditionalParameters(void); |
32 |
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33 |
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protected: |
34 |
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41 |
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virtual int readyCheck( void ) { return 1; } |
42 |
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43 |
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virtual void resetIntegrator( void ) { } |
44 |
< |
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45 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
44 |
> |
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45 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
46 |
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virtual void thermalize(); |
47 |
< |
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47 |
> |
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48 |
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virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
49 |
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50 |
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void checkConstraints( void ); |
51 |
< |
void rotate( int axes1, int axes2, double angle, double j[3], |
51 |
> |
void rotate( int axes1, int axes2, double angle, double j[3], |
52 |
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double A[3][3] ); |
53 |
< |
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53 |
> |
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54 |
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ForceFields* myFF; |
55 |
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56 |
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SimInfo *info; // all the info we'll ever need |
62 |
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63 |
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int isConstrained; // boolean to know whether the systems contains |
64 |
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// constraints. |
65 |
< |
int nConstrained; // counter for number of constraints |
66 |
< |
int *constrainedA; // the i of a constraint pair |
67 |
< |
int *constrainedB; // the j of a constraint pair |
68 |
< |
double *constrainedDsqr; // the square of the constraint distance |
69 |
< |
|
65 |
> |
int nConstrained; // counter for number of constraints |
66 |
> |
int *constrainedA; // the i of a constraint pair |
67 |
> |
int *constrainedB; // the j of a constraint pair |
68 |
> |
double *constrainedDsqr; // the square of the constraint distance |
69 |
> |
|
70 |
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int* moving; // tells whether we are moving atom i |
71 |
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int* moved; // tells whether we have moved atom i |
72 |
< |
double* oldPos; // pre constrained positions |
72 |
> |
double* oldPos; // pre constrained positions |
73 |
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74 |
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short isFirst; /*boolean for the first time integrate is called */ |
75 |
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75 |
> |
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76 |
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double dt; |
77 |
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double dt2; |
78 |
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79 |
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Thermo *tStats; |
80 |
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StatWriter* statOut; |
81 |
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DumpWriter* dumpOut; |
82 |
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82 |
> |
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83 |
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}; |
84 |
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typedef Integrator<BaseIntegrator> RealIntegrator; |
89 |
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public: |
90 |
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NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
91 |
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T( theInfo, the_ff ){} |
92 |
< |
virtual ~NVE(){} |
92 |
> |
virtual ~NVE(){} |
93 |
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}; |
94 |
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104 |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
105 |
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void setChiTolerance(double tol) {chiTolerance = tol;} |
106 |
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virtual double getConservedQuantity(void); |
107 |
+ |
virtual string getAdditionalParameters(void); |
108 |
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109 |
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protected: |
110 |
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126 |
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127 |
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double targetTemp; |
128 |
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double tauThermostat; |
129 |
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129 |
> |
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130 |
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short int have_tau_thermostat, have_target_temp; |
131 |
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132 |
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double *oldVel; |
145 |
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146 |
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NPT ( SimInfo *theInfo, ForceFields* the_ff); |
147 |
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virtual ~NPT(); |
148 |
< |
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148 |
> |
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149 |
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virtual void integrateStep( int calcPot, int calcStress ){ |
150 |
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calcStress = 1; |
151 |
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T::integrateStep( calcPot, calcStress ); |
152 |
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} |
153 |
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154 |
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virtual double getConservedQuantity(void) = 0; |
155 |
< |
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155 |
> |
virtual string getAdditionalParameters(void) = 0; |
156 |
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
157 |
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void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
158 |
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void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
172 |
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173 |
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virtual void getVelScaleA( double sc[3], double vel[3] ) = 0; |
174 |
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virtual void getVelScaleB( double sc[3], int index ) = 0; |
175 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
175 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
176 |
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int index, double sc[3]) = 0; |
177 |
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178 |
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virtual bool chiConverged( void ); |
179 |
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virtual bool etaConverged( void ) = 0; |
180 |
< |
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180 |
> |
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181 |
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virtual void evolveChiA( void ); |
182 |
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virtual void evolveEtaA( void ) = 0; |
183 |
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virtual void evolveChiB( void ); |
203 |
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204 |
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double integralOfChidt; |
205 |
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|
206 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
206 |
> |
// targetTemp, targetPressure, and tauBarostat must be set. |
207 |
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// One of qmass or tauThermostat must be set; |
208 |
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209 |
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double targetTemp; |
228 |
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}; |
229 |
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230 |
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template<typename T> class NPTi : public T{ |
231 |
< |
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231 |
> |
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232 |
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public: |
233 |
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NPTi( SimInfo *theInfo, ForceFields* the_ff); |
234 |
|
~NPTi(); |
235 |
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|
236 |
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virtual double getConservedQuantity(void); |
237 |
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virtual void resetIntegrator(void); |
238 |
< |
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238 |
> |
virtual string getAdditionalParameters(void); |
239 |
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protected: |
240 |
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239 |
– |
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241 |
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242 |
+ |
|
243 |
|
virtual void evolveEtaA(void); |
244 |
|
virtual void evolveEtaB(void); |
245 |
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249 |
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250 |
|
virtual void getVelScaleA( double sc[3], double vel[3] ); |
251 |
|
virtual void getVelScaleB( double sc[3], int index ); |
252 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
252 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
253 |
|
int index, double sc[3]); |
254 |
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|
255 |
|
double eta, oldEta, prevEta; |
263 |
|
virtual ~NPTf(); |
264 |
|
|
265 |
|
virtual double getConservedQuantity(void); |
266 |
+ |
virtual string getAdditionalParameters(void); |
267 |
|
virtual void resetIntegrator(void); |
268 |
|
|
269 |
|
protected: |
277 |
|
|
278 |
|
virtual void getVelScaleA( double sc[3], double vel[3] ); |
279 |
|
virtual void getVelScaleB( double sc[3], int index ); |
280 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
280 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
281 |
|
int index, double sc[3]); |
282 |
|
|
283 |
|
double eta[3][3]; |
293 |
|
virtual ~NPTxyz(); |
294 |
|
|
295 |
|
virtual double getConservedQuantity(void); |
296 |
+ |
virtual string getAdditionalParameters(void); |
297 |
|
virtual void resetIntegrator(void); |
298 |
|
|
299 |
|
protected: |
307 |
|
|
308 |
|
virtual void getVelScaleA( double sc[3], double vel[3] ); |
309 |
|
virtual void getVelScaleB( double sc[3], int index ); |
310 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
310 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
311 |
|
int index, double sc[3]); |
312 |
|
|
313 |
|
double eta[3][3]; |
317 |
|
|
318 |
|
|
319 |
|
template<typename T> class ZConstraint : public T { |
320 |
< |
|
321 |
< |
public: |
320 |
> |
|
321 |
> |
public: |
322 |
|
class ForceSubtractionPolicy{ |
323 |
|
public: |
324 |
|
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
325 |
|
|
326 |
< |
virtual void update() = 0; |
326 |
> |
virtual void update() = 0; |
327 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
328 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
329 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
330 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
331 |
< |
|
331 |
> |
|
332 |
|
protected: |
333 |
|
ZConstraint<T>* zconsIntegrator; |
334 |
|
}; |
336 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
337 |
|
|
338 |
|
public: |
339 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
340 |
< |
virtual void update(); |
339 |
> |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
340 |
> |
virtual void update(); |
341 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
342 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
343 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
344 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
345 |
< |
|
345 |
> |
|
346 |
|
private: |
347 |
|
int totNumOfMovingAtoms; |
348 |
|
}; |
350 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
351 |
|
|
352 |
|
public: |
353 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
354 |
< |
|
355 |
< |
virtual void update(); |
353 |
> |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
354 |
> |
|
355 |
> |
virtual void update(); |
356 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
357 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
358 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
366 |
|
|
367 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
368 |
|
~ZConstraint(); |
369 |
< |
|
369 |
> |
|
370 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
371 |
|
void getZConsTime() {return zconsTime;} |
372 |
< |
|
372 |
> |
|
373 |
|
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
374 |
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
375 |
< |
|
375 |
> |
|
376 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
377 |
|
string getZConsOutput() {return zconsOutput;} |
378 |
< |
|
378 |
> |
|
379 |
|
virtual void integrate(); |
376 |
– |
|
380 |
|
|
381 |
+ |
|
382 |
|
#ifdef IS_MPI |
383 |
|
virtual void update(); //which is called to indicate the molecules' migration |
384 |
|
#endif |
385 |
|
|
386 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
386 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
387 |
|
|
388 |
|
vector<Molecule*> zconsMols; //z-constraint molecules array |
389 |
|
vector<ZConsState> states; //state of z-constraint molecules |
390 |
|
|
387 |
– |
|
391 |
|
|
392 |
+ |
|
393 |
|
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
394 |
|
double totalMassOfUncons; //total mas of unconstraint molecules |
395 |
|
|
397 |
|
protected: |
398 |
|
|
399 |
|
|
400 |
< |
|
401 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
400 |
> |
|
401 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
402 |
|
virtual void thermalize(void); |
403 |
< |
|
403 |
> |
|
404 |
|
void zeroOutVel(); |
405 |
|
void doZconstraintForce(); |
406 |
|
void doHarmonic(); |
418 |
|
double zconsTol; //tolerance of z-contratint |
419 |
|
double zForceConst; //base force constant term |
420 |
|
//which is estimate by OOPSE |
417 |
– |
|
421 |
|
|
422 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
422 |
> |
|
423 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
424 |
|
vector<double> kz; //force constant array |
425 |
|
|
426 |
|
vector<double> zPos; // |
427 |
< |
|
428 |
< |
|
427 |
> |
|
428 |
> |
|
429 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
430 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
431 |
|
|
432 |
|
|
433 |
|
vector<ZConsParaItem>* parameters; // |
434 |
< |
|
434 |
> |
|
435 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
436 |
|
|
437 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
437 |
> |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
438 |
|
double* fz; |
439 |
|
double* curZPos; |
436 |
– |
|
440 |
|
|
441 |
|
|
442 |
< |
int whichDirection; //constraint direction |
443 |
< |
|
442 |
> |
|
443 |
> |
int whichDirection; //constraint direction |
444 |
> |
|
445 |
|
private: |
446 |
< |
|
446 |
> |
|
447 |
|
string zconsOutput; //filename of zconstraint output |
448 |
|
ZConsWriter* fzOut; //z-constraint writer |
449 |
|
|
450 |
< |
double curZconsTime; |
450 |
> |
double curZconsTime; |
451 |
|
|
452 |
|
double calcMovingMolsCOMVel(); |
453 |
|
double calcSysCOMVel(); |
454 |
|
double calcTotalForce(); |
455 |
< |
|
455 |
> |
|
456 |
|
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
457 |
|
friend class ForceSubtractionPolicy; |
458 |
|
|