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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 "brains/ForceField.hpp" |
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#include "utils/PropertyMap.hpp" |
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#include "utils/LocalIndexManager.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
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/** |
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* Constructor of SimInfo |
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* |
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* @param molStampPairs MoleculeStamp Array. The first element of |
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* the pair is molecule stamp, the second element is the total |
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* number of molecules with the same molecule stamp in the system |
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* @param ff pointer to a concrete ForceField instance |
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* |
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* @param ff pointer of a concrete ForceField instance |
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* |
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* @param simParams |
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* @param simParams pointer to the simulation parameters in a Globals object |
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*/ |
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SimInfo(ForceField* ff, Globals* simParams); |
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virtual ~SimInfo(); |
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* @return return true if adding successfully, return false if the |
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* molecule is already in SimInfo |
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* |
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* @param mol molecule to be added |
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* @param mol Molecule to be added |
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*/ |
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bool addMolecule(Molecule* mol); |
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|
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return ndf_ - getFdf(); |
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} |
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|
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/** Returns the number of degrees of freedom (LOCAL) */ |
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int getNdfLocal() { |
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return ndfLocal_; |
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} |
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|
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/** Returns the number of raw degrees of freedom */ |
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int getNdfRaw() { |
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return ndfRaw_; |
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SnapshotManager* getSnapshotManager() { |
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return sman_; |
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} |
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|
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> |
/** Returns the storage layout (computed by SimCreator) */ |
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> |
int getStorageLayout() { |
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return storageLayout_; |
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} |
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> |
/** Sets the storage layout (computed by SimCreator) */ |
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> |
void setStorageLayout(int sl) { |
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storageLayout_ = sl; |
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} |
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|
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/** Sets the snapshot manager. */ |
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void setSnapshotManager(SnapshotManager* sman); |
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|
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return simParams_; |
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} |
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|
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/** Returns the velocity of center of mass of the whole system.*/ |
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Vector3d getComVel(); |
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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 |
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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 |
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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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/** Returns volume of system as estimated by an ellipsoid defined |
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by the radii of gyration*/ |
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void getGyrationalVolume(RealType &vol); |
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/** Overloaded version of gyrational volume that also returns |
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det(I) so dV/dr can be calculated*/ |
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void getGyrationalVolume(RealType &vol, RealType &detI); |
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|
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void update(); |
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/** |
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* Do final bookkeeping before Force managers need their data. |
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|
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/** |
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* Sets GlobalGroupMembership |
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* @see #SimCreator::setGlobalIndex |
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*/ |
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void setGlobalGroupMembership(const vector<int>& globalGroupMembership) { |
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assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalGroupMembership_ = globalGroupMembership; |
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> |
void setGlobalGroupMembership(const vector<int>& ggm) { |
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> |
assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalGroupMembership_ = ggm; |
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} |
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|
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/** |
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* Sets GlobalMolMembership |
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* @see #SimCreator::setGlobalIndex |
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*/ |
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void setGlobalMolMembership(const vector<int>& globalMolMembership) { |
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assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalMolMembership_ = globalMolMembership; |
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> |
void setGlobalMolMembership(const vector<int>& gmm) { |
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> |
assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ + |
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> |
nGlobalRigidBodies_))); |
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globalMolMembership_ = gmm; |
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} |
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|
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|
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|
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/// Degress of freedom |
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int ndf_; /**< number of degress of freedom (excludes constraints) (LOCAL) */ |
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int ndfLocal_; /**< number of degrees of freedom (LOCAL, excludes constraints) */ |
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int fdf_local; /**< number of frozen degrees of freedom (LOCAL) */ |
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int fdf_; /**< number of frozen degrees of freedom (GLOBAL) */ |
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int ndfRaw_; /**< number of degress of freedom (includes constraints), (LOCAL) */ |
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|
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PropertyMap properties_; /**< Generic Properties can be added */ |
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SnapshotManager* sman_; /**< SnapshotManager (handles particle positions, etc.) */ |
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+ |
int storageLayout_; /**< Bits to tell how much data to store on each object */ |
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|
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/** |
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* The reason to have a local index manager is that when molecule |
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string dumpFileName_; |
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string statFileName_; |
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string restFileName_; |
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|
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|
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bool topologyDone_; /** flag to indicate whether the topology has |
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been scanned and all the relevant |
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|
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/** |
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* Set MolToProcMap array |
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* @see #SimCreator::divideMolecules |
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*/ |
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void setMolToProcMap(const vector<int>& molToProcMap) { |
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molToProcMap_ = molToProcMap; |
