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#include "utils/LocalIndexManager.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
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//another nonsense macro declaration |
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#define __OPENMD_C |
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#include "brains/fSimulation.h" |
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using namespace std; |
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namespace OpenMD{ |
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< |
//forward decalration |
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> |
//forward declaration |
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class SnapshotManager; |
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class Molecule; |
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class SelectionManager; |
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return nAtoms_; |
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} |
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|
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+ |
/** Returns the number of effective cutoff groups on local processor */ |
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unsigned int getNLocalCutoffGroups(); |
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|
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/** Returns the number of local bonds */ |
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unsigned int getNBonds(){ |
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return nBonds_; |
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|
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void update(); |
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/** |
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< |
* Setup Fortran Simulation |
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> |
* Do final bookkeeping before Force managers need their data. |
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*/ |
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< |
void setupFortran(); |
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> |
void prepareTopology(); |
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/** Returns the local index manager */ |
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int getGlobalMolMembership(int id){ |
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return globalMolMembership_[id]; |
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} |
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+ |
|
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/** |
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* returns a vector which maps the local atom index on this |
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* processor to the global atom index. With only one processor, |
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* these should be identical. |
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*/ |
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vector<int> getGlobalAtomIndices(); |
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|
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/** |
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* returns a vector which maps the local cutoff group index on |
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* this processor to the global cutoff group index. With only one |
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* processor, these should be identical. |
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+ |
*/ |
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vector<int> getGlobalGroupIndices(); |
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+ |
|
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string getFinalConfigFileName() { |
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return finalConfigFileName_; |
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} |
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|
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< |
bool isFortranInitialized() { |
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< |
return fortranInitialized_; |
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> |
bool isTopologyDone() { |
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> |
return topologyDone_; |
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} |
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|
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bool getCalcBoxDipole() { |
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bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; } |
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bool usesDirectionalAtoms() { return usesDirectionalAtoms_; } |
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bool usesMetallicAtoms() { return usesMetallicAtoms_; } |
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+ |
bool usesAtomicVirial() { return usesAtomicVirial_; } |
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bool requiresPrepair() { return requiresPrepair_; } |
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bool requiresSkipCorrection() { return requiresSkipCorrection_;} |
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bool requiresSelfCorrection() { return requiresSelfCorrection_;} |
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private: |
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/// Data structures holding primary simulation objects |
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map<int, Molecule*> molecules_; /**< map holding pointers to LOCAL molecules */ |
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simtype fInfo_; /**< A dual struct shared by C++ |
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and Fortran to pass |
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information about what types |
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of calculation are |
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required */ |
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|
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/// Stamps are templates for objects that are then used to create |
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/// groups of objects. For example, a molecule stamp contains |
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* the simulation. It should be nGlobalAtoms_ in size. |
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*/ |
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vector<int> globalGroupMembership_; |
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+ |
public: |
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+ |
vector<int> getGlobalGroupMembership() { return globalGroupMembership_; } |
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+ |
private: |
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|
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/** |
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* A vector that maps between the global index of an atom and the |
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* by SimCreator once and only once, since it is never changed |
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* during the simulation. It shoudl be nGlobalAtoms_ in size. |
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*/ |
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< |
vector<int> globalMolMembership_; |
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> |
vector<int> globalMolMembership_; |
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> |
|
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> |
/** |
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> |
* A vector that maps between the local index of an atom and the |
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> |
* index of the AtomType. |
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> |
*/ |
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> |
vector<int> identArray_; |
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> |
public: |
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> |
vector<int> getIdentArray() { return identArray_; } |
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> |
private: |
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> |
|
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> |
/** |
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> |
* A vector which contains the fractional contribution of an |
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> |
* atom's mass to the total mass of the cutoffGroup that atom |
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> |
* belongs to. In the case of single atom cutoff groups, the mass |
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> |
* factor for that atom is 1. For massless atoms, the factor is |
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> |
* also 1. |
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> |
*/ |
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> |
vector<RealType> massFactors_; |
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> |
public: |
| 603 |
> |
vector<RealType> getMassFactors() { return massFactors_; } |
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> |
|
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> |
PairList getExcludedInteractions() { return excludedInteractions_; } |
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> |
PairList getOneTwoInteractions() { return oneTwoInteractions_; } |
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> |
PairList getOneThreeInteractions() { return oneThreeInteractions_; } |
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> |
PairList getOneFourInteractions() { return oneFourInteractions_; } |
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> |
|
| 610 |
> |
private: |
| 611 |
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|
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|
/// lists to handle atoms needing special treatment in the non-bonded interactions |
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|
PairList excludedInteractions_; /**< atoms excluded from interacting with each other */ |
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|
string restFileName_; |
| 639 |
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|
| 640 |
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|
| 641 |
< |
bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
| 641 |
> |
bool topologyDone_; /** flag to indicate whether the topology has |
| 642 |
> |
been scanned and all the relevant |
| 643 |
> |
bookkeeping has been done*/ |
| 644 |
|
|
| 645 |
|
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
| 646 |
|
the simulation box dipole moment */ |
