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Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

# Line 35 | Line 35
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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   /**
# Line 59 | Line 60
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;
# Line 101 | Line 91 | namespace OpenMD{
91      /**
92       * Constructor of SimInfo
93       *
94 <     * @param molStampPairs MoleculeStamp Array. The first element of
105 <     * the pair is molecule stamp, the second element is the total
106 <     * number of molecules with the same molecule stamp in the system
94 >     * @param ff pointer to a concrete ForceField instance
95       *
96 <     * @param ff pointer of a concrete ForceField instance
109 <     *
110 <     * @param simParams
96 >     * @param simParams pointer to the simulation parameters in a Globals object
97       */
98      SimInfo(ForceField* ff, Globals* simParams);
99      virtual ~SimInfo();
# Line 118 | Line 104 | namespace OpenMD{
104       * @return return true if adding successfully, return false if the
105       * molecule is already in SimInfo
106       *
107 <     * @param mol molecule to be added
107 >     * @param mol Molecule to be added
108       */
109      bool addMolecule(Molecule* mol);
110  
# Line 177 | Line 163 | namespace OpenMD{
163        return nAtoms_;
164      }
165  
166 +    /** Returns the number of effective cutoff groups on local processor */
167 +    unsigned int getNLocalCutoffGroups();
168 +
169      /** Returns the number of local bonds */        
170      unsigned int getNBonds(){
171        return nBonds_;
# Line 230 | Line 219 | namespace OpenMD{
219       */
220      Molecule* nextMolecule(MoleculeIterator& i);
221  
222 +    /** Returns the total number of fluctuating charges that are present */
223 +    int getNFluctuatingCharges() {
224 +      return nGlobalFluctuatingCharges_;
225 +    }
226 +
227      /** Returns the number of degrees of freedom */
228      int getNdf() {
229        return ndf_ - getFdf();
230      }
231  
232 +    /** Returns the number of degrees of freedom (LOCAL) */
233 +    int getNdfLocal() {
234 +      return ndfLocal_;
235 +    }
236 +
237      /** Returns the number of raw degrees of freedom */
238      int getNdfRaw() {
239        return ndfRaw_;
# Line 271 | Line 270 | namespace OpenMD{
270      SnapshotManager* getSnapshotManager() {
271        return sman_;
272      }
273 <
273 >    /** Returns the storage layout (computed by SimCreator) */
274 >    int getStorageLayout() {
275 >      return storageLayout_;
276 >    }
277 >    /** Sets the storage layout (computed by SimCreator) */
278 >    void setStorageLayout(int sl) {
279 >      storageLayout_ = sl;
280 >    }
281 >    
282      /** Sets the snapshot manager. */
283      void setSnapshotManager(SnapshotManager* sman);
284          
# Line 283 | Line 290 | namespace OpenMD{
290      Globals* getSimParams() {
291        return simParams_;
292      }
286 –
287 –    /** Returns the velocity of center of mass of the whole system.*/
288 –    Vector3d getComVel();
293  
290 –    /** Returns the center of the mass of the whole system.*/
291 –    Vector3d getCom();
292 –    /** Returns the center of the mass and Center of Mass velocity of
293 –        the whole system.*/
294 –    void getComAll(Vector3d& com,Vector3d& comVel);
295 –
296 –    /** Returns intertia tensor for the entire system and system
297 –        Angular Momentum.*/
298 –    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
299 –    
300 –    /** Returns system angular momentum */
301 –    Vector3d getAngularMomentum();
302 –
303 –    /** Returns volume of system as estimated by an ellipsoid defined
304 –        by the radii of gyration*/
305 –    void getGyrationalVolume(RealType &vol);
306 –    /** Overloaded version of gyrational volume that also returns
307 –        det(I) so dV/dr can be calculated*/
308 –    void getGyrationalVolume(RealType &vol, RealType &detI);
309 –    /** main driver function to interact with fortran during the
310 –        initialization and molecule migration */
294      void update();
295 +    /**
296 +     * Do final bookkeeping before Force managers need their data.
297 +     */
298 +    void prepareTopology();
299  
300 +
301      /** Returns the local index manager */
302      LocalIndexManager* getLocalIndexManager() {
303        return &localIndexMan_;
# Line 345 | Line 333 | namespace OpenMD{
333        return globalMolMembership_[id];
334      }
335  
336 <    RealType getCutoffRadius() {
337 <      return cutoffRadius_;
338 <    }
336 >    /**
337 >     * returns a vector which maps the local atom index on this
338 >     * processor to the global atom index.  With only one processor,
339 >     * these should be identical.
340 >     */
341 >    vector<int> getGlobalAtomIndices();
342  
343 <    RealType getSwitchingRadius() {
344 <      return switchingRadius_;
345 <    }
343 >    /**
344 >     * returns a vector which maps the local cutoff group index on
345 >     * this processor to the global cutoff group index.  With only one
346 >     * processor, these should be identical.
347 >     */
348 >    vector<int> getGlobalGroupIndices();
349  
356 –    RealType getListRadius() {
357 –      return listRadius_;
358 –    }
350          
351      string getFinalConfigFileName() {
352        return finalConfigFileName_;
# Line 398 | Line 389 | namespace OpenMD{
389  
390      /**
391       * Sets GlobalGroupMembership
401 –     * @see #SimCreator::setGlobalIndex
392       */  
393 <    void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
394 <      assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
395 <      globalGroupMembership_ = globalGroupMembership;
393 >    void setGlobalGroupMembership(const vector<int>& ggm) {
394 >      assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
395 >      globalGroupMembership_ = ggm;
396      }
397  
398      /**
399       * Sets GlobalMolMembership
410 –     * @see #SimCreator::setGlobalIndex
400       */        
401 <    void setGlobalMolMembership(const vector<int>& globalMolMembership) {
402 <      assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
403 <      globalMolMembership_ = globalMolMembership;
401 >    void setGlobalMolMembership(const vector<int>& gmm) {
402 >      assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
403 >                                                nGlobalRigidBodies_)));
404 >      globalMolMembership_ = gmm;
405      }
406  
407  
408 <    bool isFortranInitialized() {
409 <      return fortranInitialized_;
408 >    bool isTopologyDone() {
409 >      return topologyDone_;
410      }
411          
412      bool getCalcBoxDipole() {
# Line 476 | Line 466 | namespace OpenMD{
466       */
467      void removeInteractionPairs(Molecule* mol);
468  
479 –
480 –    /** Returns the unique atom types of local processor in an array */
481 –    set<AtomType*> getUniqueAtomTypes();
482 –
469      /** Returns the set of atom types present in this simulation */
470      set<AtomType*> getSimulatedAtomTypes();
471 +
472 +    /** Returns the global count of atoms of a particular type */
473 +    int getGlobalCountOfType(AtomType* atype);
474          
475      friend ostream& operator <<(ostream& o, SimInfo& info);
476  
# Line 492 | Line 481 | namespace OpenMD{
481      /** fill up the simtype struct and other simulation-related variables */
482      void setupSimVariables();
483  
495 –    /**
496 –     * Setup Fortran Simulation
497 –     * @see #setupFortranParallel
498 –     */
499 –    void setupFortranSim();
484  
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();
509 –
485      /** Determine if we need to accumulate the simulation box dipole */
486      void setupAccumulateBoxDipole();
487  
# Line 535 | Line 510 | namespace OpenMD{
510      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
511      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
512      int nConstraints_;        /**< number of constraints in local processors */
513 +    int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
514          
515      /// Counts of global objects
516      int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
# Line 542 | Line 518 | namespace OpenMD{
518      int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
519      int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
520      int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
521 +    int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
522 +    
523        
524      /// Degress of freedom
525      int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
526 +    int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
527      int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
528      int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
529      int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
# Line 556 | Line 535 | namespace OpenMD{
535      bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
536      bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
537      bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
538 +    bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
539      bool usesAtomicVirial_;       /**< are we computing atomic virials? */
540      bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
541      bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
542      bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
543  
544 +  public:
545 +    bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
546 +    bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
547 +    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
548 +    bool usesAtomicVirial() { return usesAtomicVirial_; }
549 +    bool requiresPrepair() { return requiresPrepair_; }
550 +    bool requiresSkipCorrection() { return requiresSkipCorrection_;}
551 +    bool requiresSelfCorrection() { return requiresSelfCorrection_;}
552 +
553 +  private:
554      /// Data structures holding primary simulation objects
555      map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
556 <    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 <    
556 >
557      /// Stamps are templates for objects that are then used to create
558      /// groups of objects.  For example, a molecule stamp contains
559      /// information on how to build that molecule (i.e. the topology,
# Line 584 | Line 569 | namespace OpenMD{
569       * the simulation.  It should be nGlobalAtoms_ in size.
570       */
571      vector<int> globalGroupMembership_;
572 +  public:
573 +    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
574 +  private:
575  
576      /**
577       * A vector that maps between the global index of an atom and the
# Line 591 | Line 579 | namespace OpenMD{
579       * by SimCreator once and only once, since it is never changed
580       * during the simulation. It shoudl be nGlobalAtoms_ in size.
581       */
582 <    vector<int> globalMolMembership_;        
582 >    vector<int> globalMolMembership_;
583 >
584 >    /**
585 >     * A vector that maps between the local index of an atom and the
586 >     * index of the AtomType.
587 >     */
588 >    vector<int> identArray_;
589 >  public:
590 >    vector<int> getIdentArray() { return identArray_; }
591 >  private:
592 >    
593 >    /**
594 >     * A vector which contains the fractional contribution of an
595 >     * atom's mass to the total mass of the cutoffGroup that atom
596 >     * belongs to.  In the case of single atom cutoff groups, the mass
597 >     * factor for that atom is 1.  For massless atoms, the factor is
598 >     * also 1.
599 >     */
600 >    vector<RealType> massFactors_;
601 >  public:
602 >    vector<RealType> getMassFactors() { return massFactors_; }
603 >
604 >    PairList* getExcludedInteractions() { return &excludedInteractions_; }
605 >    PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
606 >    PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
607 >    PairList* getOneFourInteractions() { return &oneFourInteractions_; }
608 >
609 >  private:
610                
611      /// lists to handle atoms needing special treatment in the non-bonded interactions
612      PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
# Line 601 | Line 616 | namespace OpenMD{
616  
617      PropertyMap properties_;       /**< Generic Properties can be added */
618      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
619 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
620  
621      /**
622       * The reason to have a local index manager is that when molecule
# Line 620 | Line 636 | namespace OpenMD{
636      string dumpFileName_;
637      string statFileName_;
638      string restFileName_;
623 –        
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 */
639  
640 <    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
640 >    bool topologyDone_;  /** flag to indicate whether the topology has
641 >                             been scanned and all the relevant
642 >                             bookkeeping has been done*/
643      
644      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
645                              the simulation box dipole moment */
# Line 662 | Line 673 | namespace OpenMD{
673      
674      /**
675       * Set MolToProcMap array
665 –     * @see #SimCreator::divideMolecules
676       */
677      void setMolToProcMap(const vector<int>& molToProcMap) {
678        molToProcMap_ = molToProcMap;
679      }
680          
681    private:
672 –
673 –    void setupFortranParallel();
682          
683      /**
684       * The size of molToProcMap_ is equal to total number of molecules

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