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#include "brains/Exclude.hpp" |
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#include "io/Globals.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "utils/PropertyMap.hpp" |
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class SelectionManager; |
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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< |
* @brief As one of the heavy weight class of OOPSE, SimInfo |
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* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
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* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
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* cutoff groups, constrains). |
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* Another major change is the index. No matter single version or parallel version, atoms and |
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* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
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* cutoff group. |
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> |
* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules. |
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* The Molecule class maintains all of the concrete objects |
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> |
* (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains). |
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* In both the single and parallel versions, atoms and |
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> |
* rigid bodies have both global and local indices. The local index is |
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> |
* not relevant to molecules or cutoff groups. |
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*/ |
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class SimInfo { |
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public: |
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* @param simParams |
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* @note |
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*/ |
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SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
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> |
SimInfo(ForceField* ff, Globals* simParams); |
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virtual ~SimInfo(); |
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|
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/** |
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|
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/** Returns the number of degrees of freedom */ |
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int getNdf() { |
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return ndf_; |
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> |
return ndf_ - getFdf(); |
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} |
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|
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/** Returns the number of raw degrees of freedom */ |
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return ndfTrans_; |
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} |
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|
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/** sets the current number of frozen degrees of freedom */ |
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void setFdf(int fdf) { |
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fdf_local = fdf; |
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} |
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|
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int getFdf(); |
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|
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//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
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|
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/** Returns the total number of z-constraint molecules in the system */ |
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|
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/** Returns the center of the mass of the whole system.*/ |
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Vector3d getCom(); |
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/** Returns the center of the mass and Center of Mass velocity of the whole system.*/ |
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void getComAll(Vector3d& com,Vector3d& comVel); |
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|
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/** Returns intertia tensor for the entire system and system Angular Momentum.*/ |
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void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum); |
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|
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/** Returns system angular momentum */ |
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Vector3d getAngularMomentum(); |
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|
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/** main driver function to interact with fortran during the initialization and molecule migration */ |
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void update(); |
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|
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return i != molecules_.end() ? i->second : NULL; |
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} |
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|
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< |
/** Calculate the maximum cutoff radius based on the atom types */ |
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< |
double calcMaxCutoffRadius(); |
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< |
|
| 296 |
< |
double getRcut() { |
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> |
RealType getRcut() { |
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return rcut_; |
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} |
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|
| 312 |
< |
double getRsw() { |
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> |
RealType getRsw() { |
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|
return rsw_; |
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} |
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+ |
|
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+ |
RealType getList() { |
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+ |
return rlist_; |
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+ |
} |
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|
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std::string getFinalConfigFileName() { |
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return finalConfigFileName_; |
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return fortranInitialized_; |
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} |
| 374 |
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|
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+ |
bool getCalcBoxDipole() { |
| 376 |
+ |
return calcBoxDipole_; |
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+ |
} |
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+ |
|
| 379 |
|
//below functions are just forward functions |
| 380 |
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//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 381 |
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//the other hand, has-a relation need composing. |
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|
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friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
| 435 |
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|
| 436 |
< |
void getCutoff(double& rcut, double& rsw); |
| 436 |
> |
void getCutoff(RealType& rcut, RealType& rsw); |
| 437 |
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|
| 438 |
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private: |
| 439 |
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|
| 449 |
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/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
| 450 |
|
void setupCutoff(); |
| 451 |
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|
| 452 |
+ |
/** Figure out which coulombic correction method to use and pass to fortran */ |
| 453 |
+ |
void setupElectrostaticSummationMethod( int isError ); |
| 454 |
+ |
|
| 455 |
+ |
/** Figure out which polynomial type to use for the switching function */ |
| 456 |
+ |
void setupSwitchingFunction(); |
| 457 |
+ |
|
| 458 |
+ |
/** Determine if we need to accumulate the simulation box dipole */ |
| 459 |
+ |
void setupAccumulateBoxDipole(); |
| 460 |
+ |
|
| 461 |
|
/** Calculates the number of degress of freedom in the whole system */ |
| 462 |
|
void calcNdf(); |
| 463 |
|
void calcNdfRaw(); |
| 464 |
|
void calcNdfTrans(); |
| 465 |
|
|
| 466 |
+ |
ForceField* forceField_; |
| 467 |
+ |
Globals* simParams_; |
| 468 |
+ |
|
| 469 |
+ |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 470 |
+ |
|
| 471 |
|
/** |
| 472 |
|
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
| 473 |
|
* system. |
| 474 |
|
*/ |
| 475 |
|
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 442 |
– |
|
| 443 |
– |
MakeStamps* stamps_; |
| 444 |
– |
ForceField* forceField_; |
| 445 |
– |
Globals* simParams_; |
| 446 |
– |
|
| 447 |
– |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 476 |
|
|
| 477 |
|
//degress of freedom |
| 478 |
|
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 479 |
+ |
int fdf_local; /**< number of frozen degrees of freedom */ |
| 480 |
+ |
int fdf_; /**< number of frozen degrees of freedom */ |
| 481 |
|
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 482 |
|
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 483 |
|
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 535 |
|
std::string statFileName_; |
| 536 |
|
std::string restFileName_; |
| 537 |
|
|
| 538 |
< |
double rcut_; /**< cutoff radius*/ |
| 539 |
< |
double rsw_; /**< radius of switching function*/ |
| 538 |
> |
RealType rcut_; /**< cutoff radius*/ |
| 539 |
> |
RealType rsw_; /**< radius of switching function*/ |
| 540 |
> |
RealType rlist_; /**< neighbor list radius */ |
| 541 |
|
|
| 542 |
|
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 543 |
|
|
| 544 |
+ |
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate the simulation box dipole moment */ |
| 545 |
+ |
|
| 546 |
|
#ifdef IS_MPI |
| 547 |
|
//in Parallel version, we need MolToProc |
| 548 |
|
public: |
