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Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1848 by gezelter, Mon Feb 4 21:13:46 2013 UTC

# Line 36 | Line 36
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   /**
# 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  
66 – //another nonsense macro declaration
67 – #define __OPENMD_C
68 – #include "brains/fSimulation.h"
69 –
68   using namespace std;
69   namespace OpenMD{
70 <
73 <  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 284 | Line 291 | namespace OpenMD{
291        return simParams_;
292      }
293  
287 –    /** Returns the velocity of center of mass of the whole system.*/
288 –    Vector3d getComVel();
289 –
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          
# Line 489 | Line 475 | namespace OpenMD{
475          
476    private:
477  
478 <    /** fill up the simtype struct*/
479 <    void setupSimType();
478 >    /** fill up the simtype struct and other simulation-related variables */
479 >    void setupSimVariables();
480  
495 –    /**
496 –     * Setup Fortran Simulation
497 –     * @see #setupFortranParallel
498 –     */
499 –    void setupFortranSim();
481  
501 –    /** Figure out the cutoff radius */
502 –    void setupCutoffRadius();
503 –    /** Figure out the cutoff method */
504 –    void setupCutoffMethod();
505 –    /** Figure out the switching radius */
506 –    void setupSwitchingRadius();
507 –    /** Figure out the neighbor list skin thickness */
508 –    void setupSkinThickness();
509 –    /** Figure out which polynomial type to use for the switching function */
510 –    void setupSwitchingFunction();
511 –
482      /** Determine if we need to accumulate the simulation box dipole */
483      void setupAccumulateBoxDipole();
484  
# Line 537 | Line 507 | namespace OpenMD{
507      int nIntegrableObjects_;  /**< number of integrable objects in local processor */
508      int nCutoffGroups_;       /**< number of cutoff groups in local processor */
509      int nConstraints_;        /**< number of constraints in local processors */
510 +    int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
511          
512      /// Counts of global objects
513      int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
# Line 544 | Line 515 | namespace OpenMD{
515      int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
516      int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
517      int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
518 +    int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
519 +    
520        
521      /// Degress of freedom
522      int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
523 +    int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
524      int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
525      int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
526      int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
# Line 558 | Line 532 | namespace OpenMD{
532      bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
533      bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
534      bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
535 +    bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
536      bool usesAtomicVirial_;       /**< are we computing atomic virials? */
537      bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
538      bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
539      bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
540  
541 +  public:
542 +    bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
543 +    bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
544 +    bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
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 */
553 <    simtype fInfo_;                   /**< A dual struct shared by C++
569 <                                         and Fortran to pass
570 <                                         information about what types
571 <                                         of calculation are
572 <                                         required */
573 <    
553 >
554      /// Stamps are templates for objects that are then used to create
555      /// groups of objects.  For example, a molecule stamp contains
556      /// information on how to build that molecule (i.e. the topology,
# Line 586 | Line 566 | namespace OpenMD{
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
# Line 593 | Line 576 | namespace OpenMD{
576       * by SimCreator once and only once, since it is never changed
577       * during the simulation. It shoudl be nGlobalAtoms_ in size.
578       */
579 <    vector<int> globalMolMembership_;        
579 >    vector<int> globalMolMembership_;
580 >
581 >    /**
582 >     * A vector that maps between the local 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 >  private:
589 >    
590 >    /**
591 >     * A vector which contains the fractional contribution of an
592 >     * atom's mass to the total mass of the cutoffGroup that atom
593 >     * belongs to.  In the case of single atom cutoff groups, the mass
594 >     * factor for that atom is 1.  For massless atoms, the factor is
595 >     * also 1.
596 >     */
597 >    vector<RealType> massFactors_;
598 >  public:
599 >    vector<RealType> getMassFactors() { return massFactors_; }
600 >
601 >    PairList* getExcludedInteractions() { return &excludedInteractions_; }
602 >    PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
603 >    PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
604 >    PairList* getOneFourInteractions() { return &oneFourInteractions_; }
605 >
606 >  private:
607                
608      /// lists to handle atoms needing special treatment in the non-bonded interactions
609      PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
# Line 603 | Line 613 | namespace OpenMD{
613  
614      PropertyMap properties_;       /**< Generic Properties can be added */
615      SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
616 +    int storageLayout_;            /**< Bits to tell how much data to store on each object */
617  
618      /**
619       * The reason to have a local index manager is that when molecule
# Line 622 | Line 633 | namespace OpenMD{
633      string dumpFileName_;
634      string statFileName_;
635      string restFileName_;
625 –        
626 –    RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
627 –    RealType switchingRadius_;      /**< inner radius of switching function */
628 –    RealType listRadius_;           /**< Verlet neighbor list radius */
629 –    RealType skinThickness_;        /**< Verlet neighbor list skin thickness */    
630 –    CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
636  
637 <    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
637 >    bool topologyDone_;  /** flag to indicate whether the topology has
638 >                             been scanned and all the relevant
639 >                             bookkeeping has been done*/
640      
641      bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
642                              the simulation box dipole moment */
# Line 663 | Line 670 | namespace OpenMD{
670      
671      /**
672       * Set MolToProcMap array
666 –     * @see #SimCreator::divideMolecules
673       */
674      void setMolToProcMap(const vector<int>& molToProcMap) {
675        molToProcMap_ = molToProcMap;
676      }
677          
678    private:
673 –
674 –    void setupFortranParallel();
679          
680      /**
681       * The size of molToProcMap_ is equal to total number of molecules

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