| 63 |
|
#include "utils/PropertyMap.hpp" |
| 64 |
|
#include "utils/LocalIndexManager.hpp" |
| 65 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 66 |
– |
|
| 67 |
– |
//another nonsense macro declaration |
| 68 |
– |
#define __OPENMD_C |
| 69 |
– |
#include "brains/fSimulation.h" |
| 66 |
|
|
| 67 |
|
using namespace std; |
| 68 |
|
namespace OpenMD{ |
| 69 |
< |
//forward decalration |
| 69 |
> |
//forward declaration |
| 70 |
|
class SnapshotManager; |
| 71 |
|
class Molecule; |
| 72 |
|
class SelectionManager; |
| 337 |
|
int getGlobalMolMembership(int id){ |
| 338 |
|
return globalMolMembership_[id]; |
| 339 |
|
} |
| 340 |
+ |
|
| 341 |
+ |
/** |
| 342 |
+ |
* returns a vector which maps the local atom index on this |
| 343 |
+ |
* processor to the global atom index. With only one processor, |
| 344 |
+ |
* these should be identical. |
| 345 |
+ |
*/ |
| 346 |
+ |
vector<int> getGlobalAtomIndices(); |
| 347 |
+ |
|
| 348 |
+ |
/** |
| 349 |
+ |
* returns a vector which maps the local cutoff group index on |
| 350 |
+ |
* this processor to the global cutoff group index. With only one |
| 351 |
+ |
* processor, these should be identical. |
| 352 |
+ |
*/ |
| 353 |
+ |
vector<int> getGlobalGroupIndices(); |
| 354 |
|
|
| 355 |
|
string getFinalConfigFileName() { |
| 356 |
|
return finalConfigFileName_; |
| 542 |
|
bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; } |
| 543 |
|
bool usesDirectionalAtoms() { return usesDirectionalAtoms_; } |
| 544 |
|
bool usesMetallicAtoms() { return usesMetallicAtoms_; } |
| 545 |
+ |
bool usesAtomicVirial() { return usesAtomicVirial_; } |
| 546 |
+ |
bool requiresPrepair() { return requiresPrepair_; } |
| 547 |
+ |
bool requiresSkipCorrection() { return requiresSkipCorrection_;} |
| 548 |
+ |
bool requiresSelfCorrection() { return requiresSelfCorrection_;} |
| 549 |
|
|
| 550 |
|
private: |
| 551 |
|
/// Data structures holding primary simulation objects |
| 552 |
|
map<int, Molecule*> molecules_; /**< map holding pointers to LOCAL molecules */ |
| 539 |
– |
simtype fInfo_; /**< A dual struct shared by C++ |
| 540 |
– |
and Fortran to pass |
| 541 |
– |
information about what types |
| 542 |
– |
of calculation are |
| 543 |
– |
required */ |
| 553 |
|
|
| 554 |
|
/// Stamps are templates for objects that are then used to create |
| 555 |
|
/// groups of objects. For example, a molecule stamp contains |
| 566 |
|
* the simulation. It should be nGlobalAtoms_ in size. |
| 567 |
|
*/ |
| 568 |
|
vector<int> globalGroupMembership_; |
| 569 |
+ |
public: |
| 570 |
+ |
vector<int> getGlobalGroupMembership() { return globalGroupMembership_; } |
| 571 |
+ |
private: |
| 572 |
|
|
| 573 |
|
/** |
| 574 |
|
* A vector that maps between the global index of an atom and the |
| 583 |
|
* index of the AtomType. |
| 584 |
|
*/ |
| 585 |
|
vector<int> identArray_; |
| 586 |
+ |
public: |
| 587 |
|
vector<int> getIdentArray() { return identArray_; } |
| 588 |
< |
|
| 588 |
> |
private: |
| 589 |
|
|
| 590 |
|
/// lists to handle atoms needing special treatment in the non-bonded interactions |
| 591 |
|
PairList excludedInteractions_; /**< atoms excluded from interacting with each other */ |
