| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 60 |
|
#include "math/Vector3.hpp" |
| 61 |
|
#include "math/SquareMatrix3.hpp" |
| 62 |
|
#include "types/MoleculeStamp.hpp" |
| 63 |
< |
#include "UseTheForce/ForceField.hpp" |
| 63 |
> |
#include "brains/ForceField.hpp" |
| 64 |
|
#include "utils/PropertyMap.hpp" |
| 65 |
|
#include "utils/LocalIndexManager.hpp" |
| 66 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 67 |
|
|
| 67 |
– |
//another nonsense macro declaration |
| 68 |
– |
#define __OPENMD_C |
| 69 |
– |
#include "brains/fSimulation.h" |
| 70 |
– |
|
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD{ |
| 70 |
< |
enum CutoffMethod { |
| 74 |
< |
HARD, |
| 75 |
< |
SWITCHING_FUNCTION, |
| 76 |
< |
SHIFTED_POTENTIAL, |
| 77 |
< |
SHIFTED_FORCE |
| 78 |
< |
}; |
| 79 |
< |
|
| 80 |
< |
//forward decalration |
| 70 |
> |
//forward declaration |
| 71 |
|
class SnapshotManager; |
| 72 |
|
class Molecule; |
| 73 |
|
class SelectionManager; |
| 167 |
|
return nAtoms_; |
| 168 |
|
} |
| 169 |
|
|
| 170 |
+ |
/** Returns the number of effective cutoff groups on local processor */ |
| 171 |
+ |
unsigned int getNLocalCutoffGroups(); |
| 172 |
+ |
|
| 173 |
|
/** Returns the number of local bonds */ |
| 174 |
|
unsigned int getNBonds(){ |
| 175 |
|
return nBonds_; |
| 223 |
|
*/ |
| 224 |
|
Molecule* nextMolecule(MoleculeIterator& i); |
| 225 |
|
|
| 226 |
+ |
/** Returns the total number of fluctuating charges that are present */ |
| 227 |
+ |
int getNFluctuatingCharges() { |
| 228 |
+ |
return nGlobalFluctuatingCharges_; |
| 229 |
+ |
} |
| 230 |
+ |
|
| 231 |
|
/** Returns the number of degrees of freedom */ |
| 232 |
|
int getNdf() { |
| 233 |
|
return ndf_ - getFdf(); |
| 304 |
|
/** Overloaded version of gyrational volume that also returns |
| 305 |
|
det(I) so dV/dr can be calculated*/ |
| 306 |
|
void getGyrationalVolume(RealType &vol, RealType &detI); |
| 307 |
< |
/** main driver function to interact with fortran during the |
| 310 |
< |
initialization and molecule migration */ |
| 307 |
> |
|
| 308 |
|
void update(); |
| 309 |
+ |
/** |
| 310 |
+ |
* Do final bookkeeping before Force managers need their data. |
| 311 |
+ |
*/ |
| 312 |
+ |
void prepareTopology(); |
| 313 |
|
|
| 314 |
+ |
|
| 315 |
|
/** Returns the local index manager */ |
| 316 |
|
LocalIndexManager* getLocalIndexManager() { |
| 317 |
|
return &localIndexMan_; |
| 345 |
|
|
| 346 |
|
int getGlobalMolMembership(int id){ |
| 347 |
|
return globalMolMembership_[id]; |
| 346 |
– |
} |
| 347 |
– |
|
| 348 |
– |
RealType getCutoffRadius() { |
| 349 |
– |
return cutoffRadius_; |
| 348 |
|
} |
| 349 |
|
|
| 350 |
< |
RealType getSwitchingRadius() { |
| 351 |
< |
return switchingRadius_; |
| 352 |
< |
} |
| 350 |
> |
/** |
| 351 |
> |
* returns a vector which maps the local atom index on this |
| 352 |
> |
* processor to the global atom index. With only one processor, |
| 353 |
> |
* these should be identical. |
| 354 |
> |
*/ |
| 355 |
> |
vector<int> getGlobalAtomIndices(); |
| 356 |
|
|
| 357 |
< |
RealType getListRadius() { |
| 358 |
< |
return listRadius_; |
| 359 |
< |
} |
| 357 |
> |
/** |
| 358 |
> |
* returns a vector which maps the local cutoff group index on |
| 359 |
> |
* this processor to the global cutoff group index. With only one |
| 360 |
> |
* processor, these should be identical. |
| 361 |
> |
*/ |
| 362 |
> |
vector<int> getGlobalGroupIndices(); |
| 363 |
> |
|
| 364 |
|
|
| 365 |
|
string getFinalConfigFileName() { |
| 366 |
|
return finalConfigFileName_; |
| 420 |
|
} |
| 421 |
|
|
| 422 |
|
|
| 423 |
< |
bool isFortranInitialized() { |
| 424 |
< |
return fortranInitialized_; |
| 423 |
> |
bool isTopologyDone() { |
| 424 |
> |
return topologyDone_; |
| 425 |
|
} |
| 426 |
|
|
| 427 |
|
bool getCalcBoxDipole() { |
| 481 |
|
*/ |
| 482 |
|
void removeInteractionPairs(Molecule* mol); |
| 483 |
|
|
| 479 |
– |
|
| 480 |
– |
/** Returns the unique atom types of local processor in an array */ |
| 481 |
– |
set<AtomType*> getUniqueAtomTypes(); |
| 482 |
– |
|
| 484 |
|
/** Returns the set of atom types present in this simulation */ |
| 485 |
|
set<AtomType*> getSimulatedAtomTypes(); |
| 486 |
|
|
| 493 |
|
/** fill up the simtype struct and other simulation-related variables */ |
| 494 |
|
void setupSimVariables(); |
| 495 |
|
|
| 495 |
– |
/** |
| 496 |
– |
* Setup Fortran Simulation |
| 497 |
– |
* @see #setupFortranParallel |
| 498 |
– |
*/ |
| 499 |
– |
void setupFortranSim(); |
| 500 |
– |
|
| 501 |
– |
/** Figure out the cutoff radius and cutoff method */ |
| 502 |
– |
void setupCutoffs(); |
| 503 |
– |
/** Figure out the switching radius and polynomial type for the switching function */ |
| 504 |
– |
void setupSwitching(); |
| 505 |
– |
/** Figure out the simulation variables associated with electrostatics */ |
| 506 |
– |
void setupElectrostatics(); |
| 507 |
– |
/** Figure out the neighbor list skin thickness */ |
| 508 |
– |
void setupNeighborlists(); |
| 496 |
|
|
| 497 |
|
/** Determine if we need to accumulate the simulation box dipole */ |
| 498 |
|
void setupAccumulateBoxDipole(); |
| 522 |
|
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 523 |
|
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 524 |
|
int nConstraints_; /**< number of constraints in local processors */ |
| 525 |
+ |
int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */ |
| 526 |
|
|
| 527 |
|
/// Counts of global objects |
| 528 |
|
int nGlobalMols_; /**< number of molecules in the system (GLOBAL) */ |
| 530 |
|
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system (GLOBAL) */ |
| 531 |
|
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
| 532 |
|
int nGlobalRigidBodies_; /**< number of rigid bodies in this system (GLOBAL) */ |
| 533 |
+ |
int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */ |
| 534 |
+ |
|
| 535 |
|
|
| 536 |
|
/// Degress of freedom |
| 537 |
|
int ndf_; /**< number of degress of freedom (excludes constraints) (LOCAL) */ |
| 546 |
|
bool usesDirectionalAtoms_; /**< are there atoms with position AND orientation? */ |
| 547 |
|
bool usesMetallicAtoms_; /**< are there transition metal atoms? */ |
| 548 |
|
bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */ |
| 549 |
+ |
bool usesFluctuatingCharges_; /**< are there fluctuating charges? */ |
| 550 |
|
bool usesAtomicVirial_; /**< are we computing atomic virials? */ |
| 551 |
|
bool requiresPrepair_; /**< does this simulation require a pre-pair loop? */ |
| 552 |
|
bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */ |
| 553 |
|
bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */ |
| 554 |
|
|
| 555 |
+ |
public: |
| 556 |
+ |
bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; } |
| 557 |
+ |
bool usesDirectionalAtoms() { return usesDirectionalAtoms_; } |
| 558 |
+ |
bool usesFluctuatingCharges() { return usesFluctuatingCharges_; } |
| 559 |
+ |
bool usesAtomicVirial() { return usesAtomicVirial_; } |
| 560 |
+ |
bool requiresPrepair() { return requiresPrepair_; } |
| 561 |
+ |
bool requiresSkipCorrection() { return requiresSkipCorrection_;} |
| 562 |
+ |
bool requiresSelfCorrection() { return requiresSelfCorrection_;} |
| 563 |
+ |
|
| 564 |
+ |
private: |
| 565 |
|
/// Data structures holding primary simulation objects |
| 566 |
|
map<int, Molecule*> molecules_; /**< map holding pointers to LOCAL molecules */ |
| 567 |
< |
simtype fInfo_; /**< A dual struct shared by C++ |
| 567 |
< |
and Fortran to pass |
| 568 |
< |
information about what types |
| 569 |
< |
of calculation are |
| 570 |
< |
required */ |
| 571 |
< |
|
| 567 |
> |
|
| 568 |
|
/// Stamps are templates for objects that are then used to create |
| 569 |
|
/// groups of objects. For example, a molecule stamp contains |
| 570 |
|
/// information on how to build that molecule (i.e. the topology, |
| 580 |
|
* the simulation. It should be nGlobalAtoms_ in size. |
| 581 |
|
*/ |
| 582 |
|
vector<int> globalGroupMembership_; |
| 583 |
+ |
public: |
| 584 |
+ |
vector<int> getGlobalGroupMembership() { return globalGroupMembership_; } |
| 585 |
+ |
private: |
| 586 |
|
|
| 587 |
|
/** |
| 588 |
|
* A vector that maps between the global index of an atom and the |
| 590 |
|
* by SimCreator once and only once, since it is never changed |
| 591 |
|
* during the simulation. It shoudl be nGlobalAtoms_ in size. |
| 592 |
|
*/ |
| 593 |
< |
vector<int> globalMolMembership_; |
| 593 |
> |
vector<int> globalMolMembership_; |
| 594 |
> |
|
| 595 |
> |
/** |
| 596 |
> |
* A vector that maps between the local index of an atom and the |
| 597 |
> |
* index of the AtomType. |
| 598 |
> |
*/ |
| 599 |
> |
vector<int> identArray_; |
| 600 |
> |
public: |
| 601 |
> |
vector<int> getIdentArray() { return identArray_; } |
| 602 |
> |
private: |
| 603 |
> |
|
| 604 |
> |
/** |
| 605 |
> |
* A vector which contains the fractional contribution of an |
| 606 |
> |
* atom's mass to the total mass of the cutoffGroup that atom |
| 607 |
> |
* belongs to. In the case of single atom cutoff groups, the mass |
| 608 |
> |
* factor for that atom is 1. For massless atoms, the factor is |
| 609 |
> |
* also 1. |
| 610 |
> |
*/ |
| 611 |
> |
vector<RealType> massFactors_; |
| 612 |
> |
public: |
| 613 |
> |
vector<RealType> getMassFactors() { return massFactors_; } |
| 614 |
> |
|
| 615 |
> |
PairList* getExcludedInteractions() { return &excludedInteractions_; } |
| 616 |
> |
PairList* getOneTwoInteractions() { return &oneTwoInteractions_; } |
| 617 |
> |
PairList* getOneThreeInteractions() { return &oneThreeInteractions_; } |
| 618 |
> |
PairList* getOneFourInteractions() { return &oneFourInteractions_; } |
| 619 |
> |
|
| 620 |
> |
private: |
| 621 |
|
|
| 622 |
|
/// lists to handle atoms needing special treatment in the non-bonded interactions |
| 623 |
|
PairList excludedInteractions_; /**< atoms excluded from interacting with each other */ |
| 647 |
|
string statFileName_; |
| 648 |
|
string restFileName_; |
| 649 |
|
|
| 624 |
– |
RealType cutoffRadius_; /**< cutoff radius for non-bonded interactions */ |
| 625 |
– |
RealType switchingRadius_; /**< inner radius of switching function */ |
| 626 |
– |
RealType listRadius_; /**< Verlet neighbor list radius */ |
| 627 |
– |
RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
| 628 |
– |
CutoffMethod cutoffMethod_; /**< Cutoff Method for most non-bonded interactions */ |
| 629 |
– |
SwitchingFunctionType sft_; /**< Type of switching function in use */ |
| 650 |
|
|
| 651 |
< |
bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
| 651 |
> |
bool topologyDone_; /** flag to indicate whether the topology has |
| 652 |
> |
been scanned and all the relevant |
| 653 |
> |
bookkeeping has been done*/ |
| 654 |
|
|
| 655 |
|
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
| 656 |
|
the simulation box dipole moment */ |
| 691 |
|
} |
| 692 |
|
|
| 693 |
|
private: |
| 672 |
– |
|
| 673 |
– |
void setupFortranParallel(); |
| 694 |
|
|
| 695 |
|
/** |
| 696 |
|
* The size of molToProcMap_ is equal to total number of molecules |
