| 64 |
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#include "utils/LocalIndexManager.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
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|
| 67 |
– |
//another nonsense macro declaration |
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– |
#define __OPENMD_C |
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– |
#include "brains/fSimulation.h" |
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– |
|
| 67 |
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using namespace std; |
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namespace OpenMD{ |
| 69 |
< |
//forward decalration |
| 69 |
> |
//forward declaration |
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class SnapshotManager; |
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class Molecule; |
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class SelectionManager; |
| 298 |
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|
| 299 |
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void update(); |
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/** |
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< |
* Setup Fortran Simulation |
| 301 |
> |
* Do final bookkeeping before Force managers need their data. |
| 302 |
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*/ |
| 303 |
< |
void setupFortran(); |
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> |
void prepareTopology(); |
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| 305 |
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| 306 |
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/** Returns the local index manager */ |
| 351 |
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* processor, these should be identical. |
| 352 |
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*/ |
| 353 |
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vector<int> getGlobalGroupIndices(); |
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+ |
|
| 355 |
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|
| 356 |
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string getFinalConfigFileName() { |
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return finalConfigFileName_; |
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} |
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|
| 413 |
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|
| 414 |
< |
bool isFortranInitialized() { |
| 415 |
< |
return fortranInitialized_; |
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> |
bool isTopologyDone() { |
| 415 |
> |
return topologyDone_; |
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} |
| 417 |
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|
| 418 |
|
bool getCalcBoxDipole() { |
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private: |
| 552 |
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/// Data structures holding primary simulation objects |
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map<int, Molecule*> molecules_; /**< map holding pointers to LOCAL molecules */ |
| 557 |
– |
simtype fInfo_; /**< A dual struct shared by C++ |
| 558 |
– |
and Fortran to pass |
| 559 |
– |
information about what types |
| 560 |
– |
of calculation are |
| 561 |
– |
required */ |
| 554 |
|
|
| 555 |
|
/// Stamps are templates for objects that are then used to create |
| 556 |
|
/// groups of objects. For example, a molecule stamp contains |
| 587 |
|
public: |
| 588 |
|
vector<int> getIdentArray() { return identArray_; } |
| 589 |
|
private: |
| 590 |
+ |
|
| 591 |
+ |
/** |
| 592 |
+ |
* A vector which contains the fractional contribution of an |
| 593 |
+ |
* atom's mass to the total mass of the cutoffGroup that atom |
| 594 |
+ |
* belongs to. In the case of single atom cutoff groups, the mass |
| 595 |
+ |
* factor for that atom is 1. For massless atoms, the factor is |
| 596 |
+ |
* also 1. |
| 597 |
+ |
*/ |
| 598 |
+ |
vector<RealType> massFactors_; |
| 599 |
+ |
public: |
| 600 |
+ |
vector<RealType> getMassFactors() { return massFactors_; } |
| 601 |
+ |
private: |
| 602 |
+ |
|
| 603 |
|
|
| 604 |
|
/// lists to handle atoms needing special treatment in the non-bonded interactions |
| 605 |
|
PairList excludedInteractions_; /**< atoms excluded from interacting with each other */ |
| 630 |
|
string restFileName_; |
| 631 |
|
|
| 632 |
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|
| 633 |
< |
bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
| 633 |
> |
bool topologyDone_; /** flag to indicate whether the topology has |
| 634 |
> |
been scanned and all the relevant |
| 635 |
> |
bookkeeping has been done*/ |
| 636 |
|
|
| 637 |
|
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
| 638 |
|
the simulation box dipole moment */ |
