| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 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). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
/** |
| 54 |
|
#include <utility> |
| 55 |
|
#include <vector> |
| 56 |
|
|
| 57 |
< |
#include "brains/Exclude.hpp" |
| 57 |
> |
#include "brains/PairList.hpp" |
| 58 |
|
#include "io/Globals.hpp" |
| 59 |
|
#include "math/Vector3.hpp" |
| 60 |
|
#include "math/SquareMatrix3.hpp" |
| 64 |
|
#include "utils/LocalIndexManager.hpp" |
| 65 |
|
|
| 66 |
|
//another nonsense macro declaration |
| 67 |
< |
#define __C |
| 67 |
> |
#define __OPENMD_C |
| 68 |
|
#include "brains/fSimulation.h" |
| 69 |
|
|
| 70 |
< |
namespace oopse{ |
| 70 |
> |
namespace OpenMD{ |
| 71 |
|
|
| 72 |
|
//forward decalration |
| 73 |
|
class SnapshotManager; |
| 74 |
|
class Molecule; |
| 75 |
|
class SelectionManager; |
| 76 |
+ |
class StuntDouble; |
| 77 |
|
/** |
| 78 |
|
* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
| 79 |
< |
* @brief As one of the heavy weight class of OOPSE, SimInfo |
| 80 |
< |
* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
| 81 |
< |
* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
| 82 |
< |
* cutoff groups, constrains). |
| 83 |
< |
* Another major change is the index. No matter single version or parallel version, atoms and |
| 84 |
< |
* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
| 85 |
< |
* cutoff group. |
| 85 |
< |
*/ |
| 79 |
> |
* @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules. |
| 80 |
> |
* The Molecule class maintains all of the concrete objects |
| 81 |
> |
* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups, |
| 82 |
> |
* constraints). In both the single and parallel versions, atoms and |
| 83 |
> |
* rigid bodies have both global and local indices. The local index is |
| 84 |
> |
* not relevant to molecules or cutoff groups. |
| 85 |
> |
*/ |
| 86 |
|
class SimInfo { |
| 87 |
|
public: |
| 88 |
|
typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
| 95 |
|
* @param simParams |
| 96 |
|
* @note |
| 97 |
|
*/ |
| 98 |
< |
SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
| 98 |
> |
SimInfo(ForceField* ff, Globals* simParams); |
| 99 |
|
virtual ~SimInfo(); |
| 100 |
|
|
| 101 |
|
/** |
| 171 |
|
return nTorsions_; |
| 172 |
|
} |
| 173 |
|
|
| 174 |
+ |
/** Returns the number of local torsions */ |
| 175 |
+ |
unsigned int getNInversions() { |
| 176 |
+ |
return nInversions_; |
| 177 |
+ |
} |
| 178 |
|
/** Returns the number of local rigid bodies */ |
| 179 |
|
unsigned int getNRigidBodies() { |
| 180 |
|
return nRigidBodies_; |
| 211 |
|
|
| 212 |
|
/** Returns the number of degrees of freedom */ |
| 213 |
|
int getNdf() { |
| 214 |
< |
return ndf_; |
| 214 |
> |
return ndf_ - getFdf(); |
| 215 |
|
} |
| 216 |
|
|
| 217 |
|
/** Returns the number of raw degrees of freedom */ |
| 224 |
|
return ndfTrans_; |
| 225 |
|
} |
| 226 |
|
|
| 227 |
+ |
/** sets the current number of frozen degrees of freedom */ |
| 228 |
+ |
void setFdf(int fdf) { |
| 229 |
+ |
fdf_local = fdf; |
| 230 |
+ |
} |
| 231 |
+ |
|
| 232 |
+ |
int getFdf(); |
| 233 |
+ |
|
| 234 |
|
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
| 235 |
|
|
| 236 |
|
/** Returns the total number of z-constraint molecules in the system */ |
| 276 |
|
/** Returns system angular momentum */ |
| 277 |
|
Vector3d getAngularMomentum(); |
| 278 |
|
|
| 279 |
+ |
/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/ |
| 280 |
+ |
void getGyrationalVolume(RealType &vol); |
| 281 |
+ |
/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/ |
| 282 |
+ |
void getGyrationalVolume(RealType &vol, RealType &detI); |
| 283 |
|
/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 284 |
|
void update(); |
| 285 |
|
|
| 314 |
|
return i != molecules_.end() ? i->second : NULL; |
| 315 |
|
} |
| 316 |
|
|
| 317 |
< |
/** Calculate the maximum cutoff radius based on the atom types */ |
| 318 |
< |
double calcMaxCutoffRadius(); |
| 317 |
> |
int getGlobalMolMembership(int id){ |
| 318 |
> |
return globalMolMembership_[id]; |
| 319 |
> |
} |
| 320 |
|
|
| 321 |
< |
double getRcut() { |
| 321 |
> |
RealType getRcut() { |
| 322 |
|
return rcut_; |
| 323 |
|
} |
| 324 |
|
|
| 325 |
< |
double getRsw() { |
| 325 |
> |
RealType getRsw() { |
| 326 |
|
return rsw_; |
| 327 |
|
} |
| 328 |
+ |
|
| 329 |
+ |
RealType getList() { |
| 330 |
+ |
return rlist_; |
| 331 |
+ |
} |
| 332 |
|
|
| 333 |
|
std::string getFinalConfigFileName() { |
| 334 |
|
return finalConfigFileName_; |
| 335 |
|
} |
| 336 |
< |
|
| 336 |
> |
|
| 337 |
|
void setFinalConfigFileName(const std::string& fileName) { |
| 338 |
|
finalConfigFileName_ = fileName; |
| 339 |
|
} |
| 340 |
|
|
| 341 |
+ |
std::string getRawMetaData() { |
| 342 |
+ |
return rawMetaData_; |
| 343 |
+ |
} |
| 344 |
+ |
void setRawMetaData(const std::string& rawMetaData) { |
| 345 |
+ |
rawMetaData_ = rawMetaData; |
| 346 |
+ |
} |
| 347 |
+ |
|
| 348 |
|
std::string getDumpFileName() { |
| 349 |
|
return dumpFileName_; |
| 350 |
|
} |
| 374 |
|
* @see #SimCreator::setGlobalIndex |
| 375 |
|
*/ |
| 376 |
|
void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
| 377 |
< |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
| 377 |
> |
assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 378 |
|
globalGroupMembership_ = globalGroupMembership; |
| 379 |
|
} |
| 380 |
|
|
| 383 |
|
* @see #SimCreator::setGlobalIndex |
| 384 |
|
*/ |
| 385 |
|
void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
| 386 |
< |
assert(globalMolMembership.size() == nGlobalAtoms_); |
| 386 |
> |
assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
| 387 |
|
globalMolMembership_ = globalMolMembership; |
| 388 |
|
} |
| 389 |
|
|
| 392 |
|
return fortranInitialized_; |
| 393 |
|
} |
| 394 |
|
|
| 395 |
+ |
bool getCalcBoxDipole() { |
| 396 |
+ |
return calcBoxDipole_; |
| 397 |
+ |
} |
| 398 |
+ |
|
| 399 |
+ |
bool getUseAtomicVirial() { |
| 400 |
+ |
return useAtomicVirial_; |
| 401 |
+ |
} |
| 402 |
+ |
|
| 403 |
|
//below functions are just forward functions |
| 404 |
|
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 405 |
|
//the other hand, has-a relation need composing. |
| 441 |
|
GenericData* getPropertyByName(const std::string& propName); |
| 442 |
|
|
| 443 |
|
/** |
| 444 |
< |
* add all exclude pairs of a molecule into exclude list. |
| 444 |
> |
* add all special interaction pairs (including excluded |
| 445 |
> |
* interactions) in a molecule into the appropriate lists. |
| 446 |
|
*/ |
| 447 |
< |
void addExcludePairs(Molecule* mol); |
| 447 |
> |
void addInteractionPairs(Molecule* mol); |
| 448 |
|
|
| 449 |
|
/** |
| 450 |
< |
* remove all exclude pairs which belong to a molecule from exclude list |
| 450 |
> |
* remove all special interaction pairs which belong to a molecule |
| 451 |
> |
* from the appropriate lists. |
| 452 |
|
*/ |
| 453 |
+ |
void removeInteractionPairs(Molecule* mol); |
| 454 |
|
|
| 417 |
– |
void removeExcludePairs(Molecule* mol); |
| 455 |
|
|
| 419 |
– |
|
| 456 |
|
/** Returns the unique atom types of local processor in an array */ |
| 457 |
|
std::set<AtomType*> getUniqueAtomTypes(); |
| 458 |
|
|
| 459 |
|
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
| 460 |
|
|
| 461 |
< |
void getCutoff(double& rcut, double& rsw); |
| 461 |
> |
void getCutoff(RealType& rcut, RealType& rsw); |
| 462 |
|
|
| 463 |
|
private: |
| 464 |
|
|
| 475 |
|
void setupCutoff(); |
| 476 |
|
|
| 477 |
|
/** Figure out which coulombic correction method to use and pass to fortran */ |
| 478 |
< |
void setupCoulombicCorrection( int isError ); |
| 478 |
> |
void setupElectrostaticSummationMethod( int isError ); |
| 479 |
|
|
| 480 |
+ |
/** Figure out which polynomial type to use for the switching function */ |
| 481 |
+ |
void setupSwitchingFunction(); |
| 482 |
+ |
|
| 483 |
+ |
/** Determine if we need to accumulate the simulation box dipole */ |
| 484 |
+ |
void setupAccumulateBoxDipole(); |
| 485 |
+ |
|
| 486 |
|
/** Calculates the number of degress of freedom in the whole system */ |
| 487 |
|
void calcNdf(); |
| 488 |
|
void calcNdfRaw(); |
| 489 |
|
void calcNdfTrans(); |
| 490 |
|
|
| 491 |
+ |
ForceField* forceField_; |
| 492 |
+ |
Globals* simParams_; |
| 493 |
+ |
|
| 494 |
+ |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 495 |
+ |
|
| 496 |
|
/** |
| 497 |
|
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
| 498 |
|
* system. |
| 499 |
|
*/ |
| 500 |
|
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 454 |
– |
|
| 455 |
– |
MakeStamps* stamps_; |
| 456 |
– |
ForceField* forceField_; |
| 457 |
– |
Globals* simParams_; |
| 458 |
– |
|
| 459 |
– |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 501 |
|
|
| 502 |
|
//degress of freedom |
| 503 |
|
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 504 |
+ |
int fdf_local; /**< number of frozen degrees of freedom */ |
| 505 |
+ |
int fdf_; /**< number of frozen degrees of freedom */ |
| 506 |
|
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 507 |
|
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 508 |
|
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 521 |
|
std::vector<int> globalGroupMembership_; |
| 522 |
|
|
| 523 |
|
/** |
| 524 |
< |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 524 |
> |
* the size of globalMolMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 525 |
|
* corresponding content is the global index of molecule this atom belong to. |
| 526 |
|
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 527 |
|
*/ |
| 532 |
|
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 533 |
|
|
| 534 |
|
//number of local objects |
| 535 |
< |
int nAtoms_; /**< number of atoms in local processor */ |
| 536 |
< |
int nBonds_; /**< number of bonds in local processor */ |
| 537 |
< |
int nBends_; /**< number of bends in local processor */ |
| 538 |
< |
int nTorsions_; /**< number of torsions in local processor */ |
| 539 |
< |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 540 |
< |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 541 |
< |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 542 |
< |
int nConstraints_; /**< number of constraints in local processors */ |
| 535 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
| 536 |
> |
int nBonds_; /**< number of bonds in local processor */ |
| 537 |
> |
int nBends_; /**< number of bends in local processor */ |
| 538 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
| 539 |
> |
int nInversions_; /**< number of inversions in local processor */ |
| 540 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 541 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 542 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 543 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
| 544 |
|
|
| 545 |
|
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 546 |
< |
Exclude exclude_; |
| 546 |
> |
PairList excludedInteractions_; |
| 547 |
> |
PairList oneTwoInteractions_; |
| 548 |
> |
PairList oneThreeInteractions_; |
| 549 |
> |
PairList oneFourInteractions_; |
| 550 |
|
PropertyMap properties_; /**< Generic Property */ |
| 551 |
|
SnapshotManager* sman_; /**< SnapshotManager */ |
| 552 |
|
|
| 558 |
|
*/ |
| 559 |
|
LocalIndexManager localIndexMan_; |
| 560 |
|
|
| 561 |
+ |
// unparsed MetaData block for storing in Dump and EOR files: |
| 562 |
+ |
std::string rawMetaData_; |
| 563 |
+ |
|
| 564 |
|
//file names |
| 565 |
|
std::string finalConfigFileName_; |
| 566 |
|
std::string dumpFileName_; |
| 567 |
|
std::string statFileName_; |
| 568 |
|
std::string restFileName_; |
| 569 |
|
|
| 570 |
< |
double rcut_; /**< cutoff radius*/ |
| 571 |
< |
double rsw_; /**< radius of switching function*/ |
| 570 |
> |
RealType rcut_; /**< cutoff radius*/ |
| 571 |
> |
RealType rsw_; /**< radius of switching function*/ |
| 572 |
> |
RealType rlist_; /**< neighbor list radius */ |
| 573 |
|
|
| 574 |
< |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 574 |
> |
int ljsp_; /**< use shifted potential for LJ*/ |
| 575 |
> |
int ljsf_; /**< use shifted force for LJ*/ |
| 576 |
|
|
| 577 |
< |
#ifdef IS_MPI |
| 577 |
> |
bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
| 578 |
> |
|
| 579 |
> |
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
| 580 |
> |
the simulation box dipole moment */ |
| 581 |
> |
|
| 582 |
> |
bool useAtomicVirial_; /**< flag to indicate whether or not we use |
| 583 |
> |
Atomic Virials to calculate the pressure */ |
| 584 |
> |
|
| 585 |
> |
public: |
| 586 |
> |
/** |
| 587 |
> |
* return an integral objects by its global index. In MPI version, if the StuntDouble with specified |
| 588 |
> |
* global index does not belong to local processor, a NULL will be return. |
| 589 |
> |
*/ |
| 590 |
> |
StuntDouble* getIOIndexToIntegrableObject(int index); |
| 591 |
> |
void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v); |
| 592 |
> |
private: |
| 593 |
> |
std::vector<StuntDouble*> IOIndexToIntegrableObject; |
| 594 |
> |
//public: |
| 595 |
> |
//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v); |
| 596 |
> |
/** |
| 597 |
> |
* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified |
| 598 |
> |
* global index does not belong to local processor, a NULL will be return. |
| 599 |
> |
*/ |
| 600 |
> |
//StuntDouble* getStuntDoubleFromGlobalIndex(int index); |
| 601 |
> |
//private: |
| 602 |
> |
//std::vector<StuntDouble*> sdByGlobalIndex_; |
| 603 |
> |
|
| 604 |
|
//in Parallel version, we need MolToProc |
| 605 |
|
public: |
| 606 |
|
|
| 627 |
|
void setupFortranParallel(); |
| 628 |
|
|
| 629 |
|
/** |
| 630 |
< |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 631 |
< |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 632 |
< |
* once. |
| 630 |
> |
* The size of molToProcMap_ is equal to total number of molecules |
| 631 |
> |
* in the system. It maps a molecule to the processor on which it |
| 632 |
> |
* resides. it is filled by SimCreator once and only once. |
| 633 |
|
*/ |
| 634 |
|
std::vector<int> molToProcMap_; |
| 635 |
|
|
| 558 |
– |
#endif |
| 636 |
|
|
| 637 |
|
}; |
| 638 |
|
|
| 639 |
< |
} //namespace oopse |
| 639 |
> |
} //namespace OpenMD |
| 640 |
|
#endif //BRAINS_SIMMODEL_HPP |
| 641 |
|
|
