src/nonbonded/InteractionManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "nonbonded/InteractionManager.hpp"

namespace OpenMD {

  InteractionManager::InteractionManager() {

    initialized_ = false;
        
    lj_ = new LJ();
    gb_ = new GB();
    sticky_ = new Sticky();
    morse_ = new Morse();
    repulsivePower_ = new RepulsivePower();
    eam_ = new EAM();
    sc_ = new SC();
    electrostatic_ = new Electrostatic();
    maw_ = new MAW();
  }

  InteractionManager::~InteractionManager() {
    delete lj_;
    delete gb_;
    delete sticky_;
    delete morse_;
    delete repulsivePower_;
    delete eam_;
    delete sc_;
    delete electrostatic_;
    delete maw_;
  }

  void InteractionManager::initialize() {

    if (initialized_) return; 

    ForceField* forceField_ = info_->getForceField();
    
    lj_->setForceField(forceField_);
    gb_->setForceField(forceField_);
    sticky_->setForceField(forceField_);
    eam_->setForceField(forceField_);
    sc_->setForceField(forceField_);
    morse_->setForceField(forceField_);
    electrostatic_->setSimInfo(info_);
    electrostatic_->setForceField(forceField_);
    maw_->setForceField(forceField_);
    repulsivePower_->setForceField(forceField_);

    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    int nTypes = atomTypes->size();
    iHash_.resize(nTypes);
    interactions_.resize(nTypes);
    ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
    AtomType* atype1;
    AtomType* atype2;
    int atid1, atid2;

    // We only need to worry about the types that are actually in the simulation:

    set<AtomType*> atypes = info_->getSimulatedAtomTypes();

    lj_->setSimulatedAtomTypes(atypes);
    gb_->setSimulatedAtomTypes(atypes);
    sticky_->setSimulatedAtomTypes(atypes);
    eam_->setSimulatedAtomTypes(atypes);
    sc_->setSimulatedAtomTypes(atypes);
    morse_->setSimulatedAtomTypes(atypes);
    electrostatic_->setSimInfo(info_);
    electrostatic_->setSimulatedAtomTypes(atypes);
    maw_->setSimulatedAtomTypes(atypes);
    repulsivePower_->setSimulatedAtomTypes(atypes);

    set<AtomType*>::iterator at;

    for (at = atypes.begin(); at != atypes.end(); ++at) {
    
      //for (atype1 = atomTypes->beginType(i1); atype1 != NULL; 
      //   atype1 = atomTypes->nextType(i1)) {
      
      atype1 = *at;
      atid1 = atype1->getIdent();
      iHash_[atid1].resize(nTypes);
      interactions_[atid1].resize(nTypes);

      // add it to the map:      
      pair<map<int,AtomType*>::iterator,bool> ret;    
      ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
      if (ret.second == false) {
        sprintf( painCave.errMsg,
                 "InteractionManager already had a previous entry with ident %d\n",
                 atype1->getIdent());
        painCave.severity = OPENMD_INFO;
        painCave.isFatal = 0;
        simError();                 
      }
    }
    
    // Now, iterate over all known types and add to the interaction map:
    
    map<int, AtomType*>::iterator it1, it2;
    for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
      atype1 = (*it1).second;
      atid1 = atype1->getIdent();

      for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
        atype2 = (*it2).second;
        atid2 = atype2->getIdent();
                               
        iHash_[atid1][atid2] = 0;
        
        if (atype1->isLennardJones() && atype2->isLennardJones()) {
          interactions_[atid1][atid2].insert(lj_);
          iHash_[atid1][atid2] |= LJ_PAIR;
        }
        if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
          interactions_[atid1][atid2].insert(electrostatic_);
          iHash_[atid1][atid2] |= ELECTROSTATIC_PAIR;
        }
        if (atype1->isSticky() && atype2->isSticky() ) {
          interactions_[atid1][atid2].insert(sticky_);
          iHash_[atid1][atid2] |= STICKY_PAIR;
        }
        if (atype1->isStickyPower() && atype2->isStickyPower() ) {
          interactions_[atid1][atid2].insert(sticky_);
          iHash_[atid1][atid2] |= STICKY_PAIR;
        }
        if (atype1->isEAM() && atype2->isEAM() ) {
          interactions_[atid1][atid2].insert(eam_);
          iHash_[atid1][atid2] |= EAM_PAIR;
        }
        if (atype1->isSC() && atype2->isSC() ) {
          interactions_[atid1][atid2].insert(sc_);
          iHash_[atid1][atid2] |= SC_PAIR;
        }
        if (atype1->isGayBerne() && atype2->isGayBerne() ) {
          interactions_[atid1][atid2].insert(gb_);
          iHash_[atid1][atid2] |= GB_PAIR;
        }
        if ((atype1->isGayBerne() && atype2->isLennardJones())
            || (atype1->isLennardJones() && atype2->isGayBerne())) {
          interactions_[atid1][atid2].insert(gb_);
          iHash_[atid1][atid2] |= GB_PAIR;
        } 
        
        // look for an explicitly-set non-bonded interaction type using the 
        // two atom types.
        NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
        
        if (nbiType != NULL) {

          bool vdwExplicit = false;
          bool metExplicit = false;
          // bool hbExplicit = false;

          if (nbiType->isLennardJones()) {
            // We found an explicit Lennard-Jones interaction.  
            // override all other vdw entries for this pair of atom types:
            set<NonBondedInteraction*>::iterator it;
            for (it = interactions_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(lj_);
            iHash_[atid1][atid2] |= LJ_PAIR;
            vdwExplicit = true;
          }
          
          if (nbiType->isMorse()) {
            if (vdwExplicit) {
              sprintf( painCave.errMsg,
                       "InteractionManager::initialize found more than one "
                       "explicit \n"
                       "\tvan der Waals interaction for atom types %s - %s\n",
                       atype1->getName().c_str(), atype2->getName().c_str());
              painCave.severity = OPENMD_ERROR;
              painCave.isFatal = 1;
              simError();
            }
            // We found an explicit Morse interaction.  
            // override all other vdw entries for this pair of atom types:
            set<NonBondedInteraction*>::iterator it;
            for (it = interactions_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(morse_);
            iHash_[atid1][atid2] |= MORSE_PAIR;
            vdwExplicit = true;
          }

          if (nbiType->isRepulsivePower()) {
            if (vdwExplicit) {
              sprintf( painCave.errMsg,
                       "InteractionManager::initialize found more than one "
                       "explicit \n"
                       "\tvan der Waals interaction for atom types %s - %s\n",
                       atype1->getName().c_str(), atype2->getName().c_str());
              painCave.severity = OPENMD_ERROR;
              painCave.isFatal = 1;
              simError();
            }
            // We found an explicit RepulsivePower interaction.  
            // override all other vdw entries for this pair of atom types:
            set<NonBondedInteraction*>::iterator it;
            for (it = interactions_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(repulsivePower_);
            iHash_[atid1][atid2] |= REPULSIVEPOWER_PAIR;
            vdwExplicit = true;
          }
          
          
          if (nbiType->isEAM()) {
            // We found an explicit EAM interaction.  
            // override all other metallic entries for this pair of atom types:
            set<NonBondedInteraction*>::iterator it;
            for (it = interactions_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == METALLIC_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(eam_);
            iHash_[atid1][atid2] |= EAM_PAIR;
            metExplicit = true;
          }
          
          if (nbiType->isSC()) {
            if (metExplicit) {
              sprintf( painCave.errMsg,
                       "InteractionManager::initialize found more than one "
                       "explicit\n"
                       "\tmetallic interaction for atom types %s - %s\n",
                       atype1->getName().c_str(), atype2->getName().c_str());
              painCave.severity = OPENMD_ERROR;
              painCave.isFatal = 1;
              simError();
            }
            // We found an explicit Sutton-Chen interaction.  
            // override all other metallic entries for this pair of atom types:
            set<NonBondedInteraction*>::iterator it;
            for (it = interactions_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == METALLIC_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(sc_);
            iHash_[atid1][atid2] |= SC_PAIR;
            metExplicit = true;
          }
          
          if (nbiType->isMAW()) {
            if (vdwExplicit) {
              sprintf( painCave.errMsg,
                       "InteractionManager::initialize found more than one "
                       "explicit\n"
                       "\tvan der Waals interaction for atom types %s - %s\n",
                       atype1->getName().c_str(), atype2->getName().c_str());
              painCave.severity = OPENMD_ERROR;
              painCave.isFatal = 1;
              simError();
            }
            // We found an explicit MAW interaction.  
            // override all other vdw entries for this pair of atom types:
            set<NonBondedInteraction*>::iterator it;
            for (it = interactions_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(maw_);
            iHash_[atid1][atid2] |= MAW_PAIR;
            vdwExplicit = true;
          }        
        }
      }
    }
    
    
    // Make sure every pair of atom types in this simulation has a
    // non-bonded interaction.  If not, just inform the user.

    set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
    set<AtomType*>::iterator it, jt;

    for (it = simTypes.begin(); it != simTypes.end(); ++it) {
      atype1 = (*it);
      atid1 = atype1->getIdent();
      for (jt = it; jt != simTypes.end(); ++jt) {
        atype2 = (*jt);
        atid1 = atype1->getIdent();
        
        if (interactions_[atid1][atid2].size() == 0) {
          sprintf( painCave.errMsg,
                   "InteractionManager could not find a matching non-bonded\n"
                   "\tinteraction for atom types %s - %s\n"
                   "\tProceeding without this interaction.\n",
                   atype1->getName().c_str(), atype2->getName().c_str());
          painCave.severity = OPENMD_INFO;
          painCave.isFatal = 0;
          simError();
        }
      }
    }

    initialized_ = true;
  }

  void InteractionManager::setCutoffRadius(RealType rcut) {
    
    electrostatic_->setCutoffRadius(rcut);
    eam_->setCutoffRadius(rcut);
  }

  void InteractionManager::doPrePair(InteractionData &idat){
    
    if (!initialized_) initialize();
         
    // excluded interaction, so just return
    if (idat.excluded) return;

    int& iHash = iHash_[idat.atid1][idat.atid2];

    if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
    if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);

    // set<NonBondedInteraction*>::iterator it;

    // for (it = interactions_[ idat.atypes ].begin(); 
    //      it != interactions_[ idat.atypes ].end(); ++it){
    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
    //     dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
    //   }
    // }
    
    return;    
  }
  
  void InteractionManager::doPreForce(SelfData &sdat){

    if (!initialized_) initialize();
    
    int& iHash = iHash_[sdat.atid][sdat.atid];

    if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
    if ((iHash & SC_PAIR) != 0)  sc_->calcFunctional(sdat);

    // set<NonBondedInteraction*>::iterator it;
    
    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
    //   if ((*it)->getFamily() == METALLIC_FAMILY) {
    //     dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat);
    //   }
    // }
    
    return;    
  }

  void InteractionManager::doPair(InteractionData &idat){
    
    if (!initialized_) initialize();

    int& iHash = iHash_[idat.atid1][idat.atid2];

    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
       
    // electrostatics still has to worry about indirect
    // contributions from excluded pairs of atoms, but nothing else does:

    if (idat.excluded) return; 

    if ((iHash & LJ_PAIR) != 0)             lj_->calcForce(idat);
    if ((iHash & GB_PAIR) != 0)             gb_->calcForce(idat);
    if ((iHash & STICKY_PAIR) != 0)         sticky_->calcForce(idat);
    if ((iHash & MORSE_PAIR) != 0)          morse_->calcForce(idat);
    if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
    if ((iHash & EAM_PAIR) != 0)            eam_->calcForce(idat);
    if ((iHash & SC_PAIR) != 0)             sc_->calcForce(idat);
    if ((iHash & MAW_PAIR) != 0)            maw_->calcForce(idat);

    // set<NonBondedInteraction*>::iterator it;

    // for (it = interactions_[ idat.atypes ].begin(); 
    //      it != interactions_[ idat.atypes ].end(); ++it) {

    //   // electrostatics still has to worry about indirect
    //   // contributions from excluded pairs of atoms:

    //   if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
    //     (*it)->calcForce(idat);
    //   }
    // }
    
    return;    
  }

  void InteractionManager::doSelfCorrection(SelfData &sdat){

    if (!initialized_) initialize();
    
    int& iHash = iHash_[sdat.atid][sdat.atid];

    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);

    // set<NonBondedInteraction*>::iterator it;

    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
    //   }
    // }
      
    return;    
  }

  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
    if (!initialized_) initialize();
    electrostatic_->ReciprocalSpaceSum(pot);
  }

  RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
    if (!initialized_) initialize();

    AtomType* atype = typeMap_[*atid];

    set<NonBondedInteraction*>::iterator it;
    RealType cutoff = 0.0;
    
    for (it = interactions_[*atid][*atid].begin(); 
         it != interactions_[*atid][*atid].end();
         ++it)
      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));   
    return cutoff;    
  }

  RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
    if (!initialized_) initialize();
    
    int atid = atype->getIdent();

    set<NonBondedInteraction*>::iterator it;
    RealType cutoff = 0.0;
    
    for (it = interactions_[atid][atid].begin(); 
         it != interactions_[atid][atid].end(); ++it)
      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));   
    return cutoff;    
  }
} //end namespace OpenMD
Revision:	1925
Committed:	Wed Aug 7 15:24:16 2013 UTC (11 years, 8 months ago) by gezelter
File size:	19263 byte(s)
Log Message:	More ewald fixes, reporting reciprocal potential in stats.
#	User	Rev	Content
1	gezelter	1502	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
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.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1502	*/
42
43			#include "nonbonded/InteractionManager.hpp"
44
45			namespace OpenMD {
46	gezelter	1535
47	gezelter	1576	InteractionManager::InteractionManager() {
48	gezelter	1535
49	gezelter	1576	initialized_ = false;
50
51			lj_ = new LJ();
52			gb_ = new GB();
53			sticky_ = new Sticky();
54			morse_ = new Morse();
55	jmichalk	1656	repulsivePower_ = new RepulsivePower();
56	gezelter	1576	eam_ = new EAM();
57			sc_ = new SC();
58			electrostatic_ = new Electrostatic();
59			maw_ = new MAW();
60	gezelter	1502	}
61
62	gezelter	1879	InteractionManager::~InteractionManager() {
63			delete lj_;
64			delete gb_;
65			delete sticky_;
66			delete morse_;
67			delete repulsivePower_;
68			delete eam_;
69			delete sc_;
70			delete electrostatic_;
71			delete maw_;
72			}
73
74	gezelter	1502	void InteractionManager::initialize() {
75	gezelter	1755
76			if (initialized_) return;
77
78	gezelter	1535	ForceField* forceField_ = info_->getForceField();
79
80	gezelter	1502	lj_->setForceField(forceField_);
81			gb_->setForceField(forceField_);
82			sticky_->setForceField(forceField_);
83			eam_->setForceField(forceField_);
84			sc_->setForceField(forceField_);
85			morse_->setForceField(forceField_);
86	gezelter	1584	electrostatic_->setSimInfo(info_);
87	gezelter	1502	electrostatic_->setForceField(forceField_);
88	gezelter	1532	maw_->setForceField(forceField_);
89	jmichalk	1656	repulsivePower_->setForceField(forceField_);
90	gezelter	1502
91			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
92	gezelter	1895	int nTypes = atomTypes->size();
93			iHash_.resize(nTypes);
94			interactions_.resize(nTypes);
95	gezelter	1502	ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
96			AtomType* atype1;
97			AtomType* atype2;
98	gezelter	1895	int atid1, atid2;
99
100			// We only need to worry about the types that are actually in the simulation:
101
102			set<AtomType*> atypes = info_->getSimulatedAtomTypes();
103
104			lj_->setSimulatedAtomTypes(atypes);
105			gb_->setSimulatedAtomTypes(atypes);
106			sticky_->setSimulatedAtomTypes(atypes);
107			eam_->setSimulatedAtomTypes(atypes);
108			sc_->setSimulatedAtomTypes(atypes);
109			morse_->setSimulatedAtomTypes(atypes);
110			electrostatic_->setSimInfo(info_);
111			electrostatic_->setSimulatedAtomTypes(atypes);
112			maw_->setSimulatedAtomTypes(atypes);
113			repulsivePower_->setSimulatedAtomTypes(atypes);
114
115			set<AtomType*>::iterator at;
116
117			for (at = atypes.begin(); at != atypes.end(); ++at) {
118	gezelter	1502
119	gezelter	1895	//for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
120			// atype1 = atomTypes->nextType(i1)) {
121	gezelter	1502
122	gezelter	1895	atype1 = *at;
123			atid1 = atype1->getIdent();
124			iHash_[atid1].resize(nTypes);
125			interactions_[atid1].resize(nTypes);
126
127			// add it to the map:
128	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
129	gezelter	1895	ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
130	gezelter	1502	if (ret.second == false) {
131			sprintf( painCave.errMsg,
132			"InteractionManager already had a previous entry with ident %d\n",
133	gezelter	1710	atype1->getIdent());
134	gezelter	1502	painCave.severity = OPENMD_INFO;
135			painCave.isFatal = 0;
136			simError();
137			}
138			}
139
140			// Now, iterate over all known types and add to the interaction map:
141
142			map<int, AtomType*>::iterator it1, it2;
143			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
144			atype1 = (*it1).second;
145	gezelter	1895	atid1 = atype1->getIdent();
146	gezelter	1502
147			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
148			atype2 = (*it2).second;
149	gezelter	1895	atid2 = atype2->getIdent();
150	gezelter	1879
151	gezelter	1895	iHash_[atid1][atid2] = 0;
152	gezelter	1502
153			if (atype1->isLennardJones() && atype2->isLennardJones()) {
154	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
155			iHash_[atid1][atid2] \|= LJ_PAIR;
156	gezelter	1502	}
157			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
158	gezelter	1895	interactions_[atid1][atid2].insert(electrostatic_);
159			iHash_[atid1][atid2] \|= ELECTROSTATIC_PAIR;
160	gezelter	1502	}
161			if (atype1->isSticky() && atype2->isSticky() ) {
162	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
163			iHash_[atid1][atid2] \|= STICKY_PAIR;
164	gezelter	1502	}
165			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
166	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
167			iHash_[atid1][atid2] \|= STICKY_PAIR;
168	gezelter	1502	}
169			if (atype1->isEAM() && atype2->isEAM() ) {
170	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
171			iHash_[atid1][atid2] \|= EAM_PAIR;
172	gezelter	1502	}
173			if (atype1->isSC() && atype2->isSC() ) {
174	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
175			iHash_[atid1][atid2] \|= SC_PAIR;
176	gezelter	1502	}
177			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
178	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
179			iHash_[atid1][atid2] \|= GB_PAIR;
180	gezelter	1502	}
181			if ((atype1->isGayBerne() && atype2->isLennardJones())
182			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
183	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
184			iHash_[atid1][atid2] \|= GB_PAIR;
185	gezelter	1502	}
186
187			// look for an explicitly-set non-bonded interaction type using the
188			// two atom types.
189			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
190	gezelter	1535
191			if (nbiType != NULL) {
192	gezelter	1502
193	gezelter	1879	bool vdwExplicit = false;
194			bool metExplicit = false;
195			// bool hbExplicit = false;
196
197	gezelter	1535	if (nbiType->isLennardJones()) {
198			// We found an explicit Lennard-Jones interaction.
199			// override all other vdw entries for this pair of atom types:
200			set<NonBondedInteraction*>::iterator it;
201	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
202			it != interactions_[atid1][atid2].end(); ++it) {
203	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
204	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
205	gezelter	1895	interactions_[atid1][atid2].erase(*it);
206			iHash_[atid1][atid2] ^= (*it)->getHash();
207	gezelter	1879	}
208	gezelter	1535	}
209	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
210			iHash_[atid1][atid2] \|= LJ_PAIR;
211	gezelter	1535	vdwExplicit = true;
212	gezelter	1502	}
213	gezelter	1535
214			if (nbiType->isMorse()) {
215			if (vdwExplicit) {
216			sprintf( painCave.errMsg,
217			"InteractionManager::initialize found more than one "
218			"explicit \n"
219			"\tvan der Waals interaction for atom types %s - %s\n",
220			atype1->getName().c_str(), atype2->getName().c_str());
221			painCave.severity = OPENMD_ERROR;
222			painCave.isFatal = 1;
223			simError();
224			}
225			// We found an explicit Morse interaction.
226			// override all other vdw entries for this pair of atom types:
227			set<NonBondedInteraction*>::iterator it;
228	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
229			it != interactions_[atid1][atid2].end(); ++it) {
230	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
231	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
232	gezelter	1895	interactions_[atid1][atid2].erase(*it);
233			iHash_[atid1][atid2] ^= (*it)->getHash();
234	gezelter	1879	}
235	gezelter	1535	}
236	gezelter	1895	interactions_[atid1][atid2].insert(morse_);
237			iHash_[atid1][atid2] \|= MORSE_PAIR;
238	gezelter	1535	vdwExplicit = true;
239	gezelter	1502	}
240	jmichalk	1656
241			if (nbiType->isRepulsivePower()) {
242			if (vdwExplicit) {
243			sprintf( painCave.errMsg,
244			"InteractionManager::initialize found more than one "
245			"explicit \n"
246			"\tvan der Waals interaction for atom types %s - %s\n",
247			atype1->getName().c_str(), atype2->getName().c_str());
248			painCave.severity = OPENMD_ERROR;
249			painCave.isFatal = 1;
250			simError();
251			}
252			// We found an explicit RepulsivePower interaction.
253			// override all other vdw entries for this pair of atom types:
254			set<NonBondedInteraction*>::iterator it;
255	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
256			it != interactions_[atid1][atid2].end(); ++it) {
257	jmichalk	1656	InteractionFamily ifam = (*it)->getFamily();
258	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
259	gezelter	1895	interactions_[atid1][atid2].erase(*it);
260			iHash_[atid1][atid2] ^= (*it)->getHash();
261	gezelter	1879	}
262	jmichalk	1656	}
263	gezelter	1895	interactions_[atid1][atid2].insert(repulsivePower_);
264			iHash_[atid1][atid2] \|= REPULSIVEPOWER_PAIR;
265	jmichalk	1656	vdwExplicit = true;
266			}
267	gezelter	1535
268	jmichalk	1656
269	gezelter	1535	if (nbiType->isEAM()) {
270			// We found an explicit EAM interaction.
271			// override all other metallic entries for this pair of atom types:
272			set<NonBondedInteraction*>::iterator it;
273	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
274			it != interactions_[atid1][atid2].end(); ++it) {
275	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
276	gezelter	1879	if (ifam == METALLIC_FAMILY) {
277	gezelter	1895	interactions_[atid1][atid2].erase(*it);
278			iHash_[atid1][atid2] ^= (*it)->getHash();
279	gezelter	1879	}
280	gezelter	1535	}
281	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
282			iHash_[atid1][atid2] \|= EAM_PAIR;
283	gezelter	1535	metExplicit = true;
284	gezelter	1502	}
285	gezelter	1535
286			if (nbiType->isSC()) {
287			if (metExplicit) {
288			sprintf( painCave.errMsg,
289			"InteractionManager::initialize found more than one "
290			"explicit\n"
291			"\tmetallic interaction for atom types %s - %s\n",
292			atype1->getName().c_str(), atype2->getName().c_str());
293			painCave.severity = OPENMD_ERROR;
294			painCave.isFatal = 1;
295			simError();
296			}
297			// We found an explicit Sutton-Chen interaction.
298			// override all other metallic entries for this pair of atom types:
299			set<NonBondedInteraction*>::iterator it;
300	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
301			it != interactions_[atid1][atid2].end(); ++it) {
302	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
303	gezelter	1879	if (ifam == METALLIC_FAMILY) {
304	gezelter	1895	interactions_[atid1][atid2].erase(*it);
305			iHash_[atid1][atid2] ^= (*it)->getHash();
306	gezelter	1879	}
307	gezelter	1535	}
308	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
309			iHash_[atid1][atid2] \|= SC_PAIR;
310	gezelter	1535	metExplicit = true;
311	gezelter	1502	}
312	gezelter	1535
313			if (nbiType->isMAW()) {
314			if (vdwExplicit) {
315			sprintf( painCave.errMsg,
316			"InteractionManager::initialize found more than one "
317			"explicit\n"
318			"\tvan der Waals interaction for atom types %s - %s\n",
319			atype1->getName().c_str(), atype2->getName().c_str());
320			painCave.severity = OPENMD_ERROR;
321			painCave.isFatal = 1;
322			simError();
323			}
324			// We found an explicit MAW interaction.
325			// override all other vdw entries for this pair of atom types:
326			set<NonBondedInteraction*>::iterator it;
327	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
328			it != interactions_[atid1][atid2].end(); ++it) {
329	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
330	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
331	gezelter	1895	interactions_[atid1][atid2].erase(*it);
332			iHash_[atid1][atid2] ^= (*it)->getHash();
333	gezelter	1879	}
334	gezelter	1535	}
335	gezelter	1895	interactions_[atid1][atid2].insert(maw_);
336			iHash_[atid1][atid2] \|= MAW_PAIR;
337	gezelter	1535	vdwExplicit = true;
338			}
339	gezelter	1502	}
340			}
341			}
342
343	gezelter	1535
344	gezelter	1583	// Make sure every pair of atom types in this simulation has a
345			// non-bonded interaction. If not, just inform the user.
346	gezelter	1535
347			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
348			set<AtomType*>::iterator it, jt;
349	gezelter	1583
350	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
351			atype1 = (*it);
352	gezelter	1895	atid1 = atype1->getIdent();
353	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
354	gezelter	1535	atype2 = (*jt);
355	gezelter	1895	atid1 = atype1->getIdent();
356	gezelter	1502
357	gezelter	1895	if (interactions_[atid1][atid2].size() == 0) {
358	gezelter	1502	sprintf( painCave.errMsg,
359	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
360			"\tinteraction for atom types %s - %s\n"
361			"\tProceeding without this interaction.\n",
362	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
363			painCave.severity = OPENMD_INFO;
364	gezelter	1583	painCave.isFatal = 0;
365	gezelter	1502	simError();
366			}
367			}
368			}
369	gezelter	1535
370			initialized_ = true;
371			}
372	gezelter	1584
373			void InteractionManager::setCutoffRadius(RealType rcut) {
374	gezelter	1587
375	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
376	gezelter	1586	eam_->setCutoffRadius(rcut);
377	gezelter	1584	}
378
379	gezelter	1895	void InteractionManager::doPrePair(InteractionData &idat){
380	gezelter	1502
381			if (!initialized_) initialize();
382	gezelter	1545
383	gezelter	1587	// excluded interaction, so just return
384			if (idat.excluded) return;
385
386	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
387	gezelter	1504
388	gezelter	1879	if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
389			if ((iHash & SC_PAIR) != 0) sc_->calcDensity(idat);
390
391			// set<NonBondedInteraction*>::iterator it;
392
393			// for (it = interactions_[ idat.atypes ].begin();
394			// it != interactions_[ idat.atypes ].end(); ++it){
395			// if ((*it)->getFamily() == METALLIC_FAMILY) {
396			// dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
397			// }
398			// }
399	gezelter	1502
400			return;
401			}
402	gezelter	1504
403	gezelter	1895	void InteractionManager::doPreForce(SelfData &sdat){
404	gezelter	1502
405	gezelter	1504	if (!initialized_) initialize();
406	gezelter	1545
407	gezelter	1895	int& iHash = iHash_[sdat.atid][sdat.atid];
408	gezelter	1879
409			if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
410			if ((iHash & SC_PAIR) != 0) sc_->calcFunctional(sdat);
411
412			// set<NonBondedInteraction*>::iterator it;
413	gezelter	1502
414	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
415	gezelter	1879	// if ((*it)->getFamily() == METALLIC_FAMILY) {
416			// dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
417			// }
418			// }
419	gezelter	1504
420	gezelter	1502	return;
421			}
422
423	gezelter	1895	void InteractionManager::doPair(InteractionData &idat){
424	gezelter	1504
425	gezelter	1502	if (!initialized_) initialize();
426	gezelter	1587
427	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
428	gezelter	1502
429	gezelter	1879	if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
430
431			// electrostatics still has to worry about indirect
432			// contributions from excluded pairs of atoms, but nothing else does:
433	gezelter	1502
434	gezelter	1879	if (idat.excluded) return;
435	gezelter	1502
436	gezelter	1879	if ((iHash & LJ_PAIR) != 0) lj_->calcForce(idat);
437			if ((iHash & GB_PAIR) != 0) gb_->calcForce(idat);
438			if ((iHash & STICKY_PAIR) != 0) sticky_->calcForce(idat);
439			if ((iHash & MORSE_PAIR) != 0) morse_->calcForce(idat);
440			if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
441			if ((iHash & EAM_PAIR) != 0) eam_->calcForce(idat);
442			if ((iHash & SC_PAIR) != 0) sc_->calcForce(idat);
443			if ((iHash & MAW_PAIR) != 0) maw_->calcForce(idat);
444
445			// set<NonBondedInteraction*>::iterator it;
446
447			// for (it = interactions_[ idat.atypes ].begin();
448			// it != interactions_[ idat.atypes ].end(); ++it) {
449
450			// // electrostatics still has to worry about indirect
451			// // contributions from excluded pairs of atoms:
452
453			// if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
454			// (*it)->calcForce(idat);
455			// }
456			// }
457	gezelter	1502
458	gezelter	1504	return;
459	gezelter	1502	}
460
461	gezelter	1895	void InteractionManager::doSelfCorrection(SelfData &sdat){
462	gezelter	1502
463			if (!initialized_) initialize();
464	gezelter	1504
465	gezelter	1895	int& iHash = iHash_[sdat.atid][sdat.atid];
466	gezelter	1502
467	gezelter	1879	if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
468
469			// set<NonBondedInteraction*>::iterator it;
470
471	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
472	gezelter	1879	// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473			// dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
474			// }
475			// }
476	gezelter	1536
477	gezelter	1504	return;
478	gezelter	1502	}
479
480	gezelter	1925	void InteractionManager::doReciprocalSpaceSum(RealType &pot){
481	gezelter	1915	if (!initialized_) initialize();
482	gezelter	1921	electrostatic_->ReciprocalSpaceSum(pot);
483	gezelter	1915	}
484
485	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
486			if (!initialized_) initialize();
487	gezelter	1755
488	gezelter	1505	AtomType* atype = typeMap_[*atid];
489
490			set<NonBondedInteraction*>::iterator it;
491			RealType cutoff = 0.0;
492
493	gezelter	1921	for (it = interactions_[atid][atid].begin();
494			it != interactions_[atid][atid].end();
495	gezelter	1895	++it)
496			cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));
497	gezelter	1505	return cutoff;
498			}
499
500	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
501			if (!initialized_) initialize();
502
503	gezelter	1895	int atid = atype->getIdent();
504
505	gezelter	1528	set<NonBondedInteraction*>::iterator it;
506			RealType cutoff = 0.0;
507
508	gezelter	1921	for (it = interactions_[atid][atid].begin();
509			it != interactions_[atid][atid].end(); ++it)
510	gezelter	1895	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));
511	gezelter	1528	return cutoff;
512			}
513	gezelter	1502	} //end namespace OpenMD