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();
    sHash_.resize(nTypes);
    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();                 
      }
    }

    if (atype1->isLennardJones()) {
      sHash_[atid1] |= LJ_INTERACTION;
    }
    if (atype1->isElectrostatic()) {
      sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
    }
    if (atype1->isSticky()) {
      sHash_[atid1] |= STICKY_INTERACTION;
    }
    if (atype1->isStickyPower()) {
      sHash_[atid1] |= STICKY_INTERACTION;
    }
    if (atype1->isEAM()) {
      sHash_[atid1] |= EAM_INTERACTION;
    }
    if (atype1->isSC()) {
      sHash_[atid1] |= SC_INTERACTION;
    }
    if (atype1->isGayBerne()) {
      sHash_[atid1] |= GB_INTERACTION;
    }
   
    // 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_INTERACTION;
        }
        if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
          interactions_[atid1][atid2].insert(electrostatic_);
          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
        }
        if (atype1->isSticky() && atype2->isSticky() ) {
          interactions_[atid1][atid2].insert(sticky_);
          iHash_[atid1][atid2] |= STICKY_INTERACTION;
        }
        if (atype1->isStickyPower() && atype2->isStickyPower() ) {
          interactions_[atid1][atid2].insert(sticky_);
          iHash_[atid1][atid2] |= STICKY_INTERACTION;
        }
        if (atype1->isEAM() && atype2->isEAM() ) {
          interactions_[atid1][atid2].insert(eam_);
          iHash_[atid1][atid2] |= EAM_INTERACTION;
        }
        if (atype1->isSC() && atype2->isSC() ) {
          interactions_[atid1][atid2].insert(sc_);
          iHash_[atid1][atid2] |= SC_INTERACTION;
        }
        if (atype1->isGayBerne() && atype2->isGayBerne() ) {
          interactions_[atid1][atid2].insert(gb_);
          iHash_[atid1][atid2] |= GB_INTERACTION;
        }
        if ((atype1->isGayBerne() && atype2->isLennardJones())
            || (atype1->isLennardJones() && atype2->isGayBerne())) {
          interactions_[atid1][atid2].insert(gb_);
          iHash_[atid1][atid2] |= GB_INTERACTION;
        } 
        
        // 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_INTERACTION;
            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_INTERACTION;
            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_INTERACTION;
            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_INTERACTION;
            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_INTERACTION;
            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_INTERACTION;
            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_INTERACTION) != 0) eam_->calcDensity(idat);
    if ((iHash & SC_INTERACTION) != 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& sHash = sHash_[sdat.atid];

    if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
    if ((sHash & SC_INTERACTION) != 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_INTERACTION) != 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_INTERACTION) != 0)             lj_->calcForce(idat);
    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
    if ((iHash & MAW_INTERACTION) != 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& sHash = sHash_[sdat.atid];

    if ((sHash & ELECTROSTATIC_INTERACTION) != 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:	1929
Committed:	Mon Aug 19 13:12:00 2013 UTC (11 years, 8 months ago) by gezelter
File size:	20022 byte(s)
Log Message:	Backing out fluc-rho and putting back the Electrostatic fluctuating charge with coulomb integrals for atoms within a region.
#	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	gezelter	1927	sHash_.resize(nTypes);
94	gezelter	1895	iHash_.resize(nTypes);
95			interactions_.resize(nTypes);
96	gezelter	1502	ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
97			AtomType* atype1;
98			AtomType* atype2;
99	gezelter	1895	int atid1, atid2;
100
101			// We only need to worry about the types that are actually in the simulation:
102
103			set<AtomType*> atypes = info_->getSimulatedAtomTypes();
104
105			lj_->setSimulatedAtomTypes(atypes);
106			gb_->setSimulatedAtomTypes(atypes);
107			sticky_->setSimulatedAtomTypes(atypes);
108			eam_->setSimulatedAtomTypes(atypes);
109			sc_->setSimulatedAtomTypes(atypes);
110			morse_->setSimulatedAtomTypes(atypes);
111			electrostatic_->setSimInfo(info_);
112			electrostatic_->setSimulatedAtomTypes(atypes);
113			maw_->setSimulatedAtomTypes(atypes);
114			repulsivePower_->setSimulatedAtomTypes(atypes);
115
116			set<AtomType*>::iterator at;
117
118			for (at = atypes.begin(); at != atypes.end(); ++at) {
119	gezelter	1502
120	gezelter	1895	//for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
121			// atype1 = atomTypes->nextType(i1)) {
122	gezelter	1502
123	gezelter	1895	atype1 = *at;
124			atid1 = atype1->getIdent();
125			iHash_[atid1].resize(nTypes);
126			interactions_[atid1].resize(nTypes);
127
128			// add it to the map:
129	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
130	gezelter	1895	ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
131	gezelter	1502	if (ret.second == false) {
132			sprintf( painCave.errMsg,
133			"InteractionManager already had a previous entry with ident %d\n",
134	gezelter	1710	atype1->getIdent());
135	gezelter	1502	painCave.severity = OPENMD_INFO;
136			painCave.isFatal = 0;
137			simError();
138			}
139			}
140	gezelter	1927
141			if (atype1->isLennardJones()) {
142			sHash_[atid1] \|= LJ_INTERACTION;
143			}
144			if (atype1->isElectrostatic()) {
145			sHash_[atid1] \|= ELECTROSTATIC_INTERACTION;
146			}
147			if (atype1->isSticky()) {
148			sHash_[atid1] \|= STICKY_INTERACTION;
149			}
150			if (atype1->isStickyPower()) {
151			sHash_[atid1] \|= STICKY_INTERACTION;
152			}
153			if (atype1->isEAM()) {
154			sHash_[atid1] \|= EAM_INTERACTION;
155			}
156			if (atype1->isSC()) {
157			sHash_[atid1] \|= SC_INTERACTION;
158			}
159			if (atype1->isGayBerne()) {
160			sHash_[atid1] \|= GB_INTERACTION;
161			}
162
163	gezelter	1502	// Now, iterate over all known types and add to the interaction map:
164
165			map<int, AtomType*>::iterator it1, it2;
166			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
167			atype1 = (*it1).second;
168	gezelter	1895	atid1 = atype1->getIdent();
169	gezelter	1502
170			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
171			atype2 = (*it2).second;
172	gezelter	1895	atid2 = atype2->getIdent();
173	gezelter	1879
174	gezelter	1895	iHash_[atid1][atid2] = 0;
175	gezelter	1502
176			if (atype1->isLennardJones() && atype2->isLennardJones()) {
177	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
178	gezelter	1927	iHash_[atid1][atid2] \|= LJ_INTERACTION;
179	gezelter	1502	}
180			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
181	gezelter	1929	interactions_[atid1][atid2].insert(electrostatic_);
182			iHash_[atid1][atid2] \|= ELECTROSTATIC_INTERACTION;
183	gezelter	1502	}
184			if (atype1->isSticky() && atype2->isSticky() ) {
185	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
186	gezelter	1927	iHash_[atid1][atid2] \|= STICKY_INTERACTION;
187	gezelter	1502	}
188			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
189	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
190	gezelter	1927	iHash_[atid1][atid2] \|= STICKY_INTERACTION;
191	gezelter	1502	}
192			if (atype1->isEAM() && atype2->isEAM() ) {
193	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
194	gezelter	1927	iHash_[atid1][atid2] \|= EAM_INTERACTION;
195	gezelter	1502	}
196			if (atype1->isSC() && atype2->isSC() ) {
197	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
198	gezelter	1927	iHash_[atid1][atid2] \|= SC_INTERACTION;
199	gezelter	1502	}
200			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
201	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
202	gezelter	1927	iHash_[atid1][atid2] \|= GB_INTERACTION;
203	gezelter	1502	}
204			if ((atype1->isGayBerne() && atype2->isLennardJones())
205			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
206	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
207	gezelter	1927	iHash_[atid1][atid2] \|= GB_INTERACTION;
208	gezelter	1502	}
209
210			// look for an explicitly-set non-bonded interaction type using the
211			// two atom types.
212			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
213	gezelter	1535
214			if (nbiType != NULL) {
215	gezelter	1502
216	gezelter	1879	bool vdwExplicit = false;
217			bool metExplicit = false;
218			// bool hbExplicit = false;
219
220	gezelter	1535	if (nbiType->isLennardJones()) {
221			// We found an explicit Lennard-Jones interaction.
222			// override all other vdw entries for this pair of atom types:
223			set<NonBondedInteraction*>::iterator it;
224	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
225			it != interactions_[atid1][atid2].end(); ++it) {
226	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
227	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
228	gezelter	1895	interactions_[atid1][atid2].erase(*it);
229			iHash_[atid1][atid2] ^= (*it)->getHash();
230	gezelter	1879	}
231	gezelter	1535	}
232	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
233	gezelter	1927	iHash_[atid1][atid2] \|= LJ_INTERACTION;
234	gezelter	1535	vdwExplicit = true;
235	gezelter	1502	}
236	gezelter	1535
237			if (nbiType->isMorse()) {
238			if (vdwExplicit) {
239			sprintf( painCave.errMsg,
240			"InteractionManager::initialize found more than one "
241			"explicit \n"
242			"\tvan der Waals interaction for atom types %s - %s\n",
243			atype1->getName().c_str(), atype2->getName().c_str());
244			painCave.severity = OPENMD_ERROR;
245			painCave.isFatal = 1;
246			simError();
247			}
248			// We found an explicit Morse interaction.
249			// override all other vdw entries for this pair of atom types:
250			set<NonBondedInteraction*>::iterator it;
251	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
252			it != interactions_[atid1][atid2].end(); ++it) {
253	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
254	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
255	gezelter	1895	interactions_[atid1][atid2].erase(*it);
256			iHash_[atid1][atid2] ^= (*it)->getHash();
257	gezelter	1879	}
258	gezelter	1535	}
259	gezelter	1895	interactions_[atid1][atid2].insert(morse_);
260	gezelter	1927	iHash_[atid1][atid2] \|= MORSE_INTERACTION;
261	gezelter	1535	vdwExplicit = true;
262	gezelter	1502	}
263	jmichalk	1656
264			if (nbiType->isRepulsivePower()) {
265			if (vdwExplicit) {
266			sprintf( painCave.errMsg,
267			"InteractionManager::initialize found more than one "
268			"explicit \n"
269			"\tvan der Waals interaction for atom types %s - %s\n",
270			atype1->getName().c_str(), atype2->getName().c_str());
271			painCave.severity = OPENMD_ERROR;
272			painCave.isFatal = 1;
273			simError();
274			}
275			// We found an explicit RepulsivePower interaction.
276			// override all other vdw entries for this pair of atom types:
277			set<NonBondedInteraction*>::iterator it;
278	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
279			it != interactions_[atid1][atid2].end(); ++it) {
280	jmichalk	1656	InteractionFamily ifam = (*it)->getFamily();
281	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
282	gezelter	1895	interactions_[atid1][atid2].erase(*it);
283			iHash_[atid1][atid2] ^= (*it)->getHash();
284	gezelter	1879	}
285	jmichalk	1656	}
286	gezelter	1895	interactions_[atid1][atid2].insert(repulsivePower_);
287	gezelter	1927	iHash_[atid1][atid2] \|= REPULSIVEPOWER_INTERACTION;
288	jmichalk	1656	vdwExplicit = true;
289			}
290	gezelter	1535
291	jmichalk	1656
292	gezelter	1535	if (nbiType->isEAM()) {
293			// We found an explicit EAM interaction.
294			// override all other metallic entries for this pair of atom types:
295			set<NonBondedInteraction*>::iterator it;
296	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
297			it != interactions_[atid1][atid2].end(); ++it) {
298	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
299	gezelter	1879	if (ifam == METALLIC_FAMILY) {
300	gezelter	1895	interactions_[atid1][atid2].erase(*it);
301			iHash_[atid1][atid2] ^= (*it)->getHash();
302	gezelter	1879	}
303	gezelter	1535	}
304	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
305	gezelter	1927	iHash_[atid1][atid2] \|= EAM_INTERACTION;
306	gezelter	1535	metExplicit = true;
307	gezelter	1502	}
308	gezelter	1535
309			if (nbiType->isSC()) {
310			if (metExplicit) {
311			sprintf( painCave.errMsg,
312			"InteractionManager::initialize found more than one "
313			"explicit\n"
314			"\tmetallic interaction for atom types %s - %s\n",
315			atype1->getName().c_str(), atype2->getName().c_str());
316			painCave.severity = OPENMD_ERROR;
317			painCave.isFatal = 1;
318			simError();
319			}
320			// We found an explicit Sutton-Chen interaction.
321			// override all other metallic entries for this pair of atom types:
322			set<NonBondedInteraction*>::iterator it;
323	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
324			it != interactions_[atid1][atid2].end(); ++it) {
325	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
326	gezelter	1879	if (ifam == METALLIC_FAMILY) {
327	gezelter	1895	interactions_[atid1][atid2].erase(*it);
328			iHash_[atid1][atid2] ^= (*it)->getHash();
329	gezelter	1879	}
330	gezelter	1535	}
331	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
332	gezelter	1927	iHash_[atid1][atid2] \|= SC_INTERACTION;
333	gezelter	1535	metExplicit = true;
334	gezelter	1502	}
335	gezelter	1535
336			if (nbiType->isMAW()) {
337			if (vdwExplicit) {
338			sprintf( painCave.errMsg,
339			"InteractionManager::initialize found more than one "
340			"explicit\n"
341			"\tvan der Waals interaction for atom types %s - %s\n",
342			atype1->getName().c_str(), atype2->getName().c_str());
343			painCave.severity = OPENMD_ERROR;
344			painCave.isFatal = 1;
345			simError();
346			}
347			// We found an explicit MAW interaction.
348			// override all other vdw entries for this pair of atom types:
349			set<NonBondedInteraction*>::iterator it;
350	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
351			it != interactions_[atid1][atid2].end(); ++it) {
352	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
353	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
354	gezelter	1895	interactions_[atid1][atid2].erase(*it);
355			iHash_[atid1][atid2] ^= (*it)->getHash();
356	gezelter	1879	}
357	gezelter	1535	}
358	gezelter	1895	interactions_[atid1][atid2].insert(maw_);
359	gezelter	1927	iHash_[atid1][atid2] \|= MAW_INTERACTION;
360	gezelter	1535	vdwExplicit = true;
361			}
362	gezelter	1502	}
363			}
364			}
365
366	gezelter	1535
367	gezelter	1583	// Make sure every pair of atom types in this simulation has a
368			// non-bonded interaction. If not, just inform the user.
369	gezelter	1535
370			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
371			set<AtomType*>::iterator it, jt;
372	gezelter	1583
373	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
374			atype1 = (*it);
375	gezelter	1895	atid1 = atype1->getIdent();
376	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
377	gezelter	1535	atype2 = (*jt);
378	gezelter	1895	atid1 = atype1->getIdent();
379	gezelter	1502
380	gezelter	1895	if (interactions_[atid1][atid2].size() == 0) {
381	gezelter	1502	sprintf( painCave.errMsg,
382	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
383			"\tinteraction for atom types %s - %s\n"
384			"\tProceeding without this interaction.\n",
385	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
386			painCave.severity = OPENMD_INFO;
387	gezelter	1583	painCave.isFatal = 0;
388	gezelter	1502	simError();
389			}
390			}
391			}
392	gezelter	1535
393			initialized_ = true;
394			}
395	gezelter	1584
396			void InteractionManager::setCutoffRadius(RealType rcut) {
397	gezelter	1587
398	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
399	gezelter	1586	eam_->setCutoffRadius(rcut);
400	gezelter	1584	}
401
402	gezelter	1895	void InteractionManager::doPrePair(InteractionData &idat){
403	gezelter	1502
404			if (!initialized_) initialize();
405	gezelter	1545
406	gezelter	1587	// excluded interaction, so just return
407			if (idat.excluded) return;
408
409	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
410	gezelter	1504
411	gezelter	1927	if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
412			if ((iHash & SC_INTERACTION) != 0) sc_->calcDensity(idat);
413	gezelter	1879
414			// set<NonBondedInteraction*>::iterator it;
415
416			// for (it = interactions_[ idat.atypes ].begin();
417			// it != interactions_[ idat.atypes ].end(); ++it){
418			// if ((*it)->getFamily() == METALLIC_FAMILY) {
419			// dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
420			// }
421			// }
422	gezelter	1502
423			return;
424			}
425	gezelter	1504
426	gezelter	1895	void InteractionManager::doPreForce(SelfData &sdat){
427	gezelter	1502
428	gezelter	1504	if (!initialized_) initialize();
429	gezelter	1545
430	gezelter	1927	int& sHash = sHash_[sdat.atid];
431	gezelter	1879
432	gezelter	1927	if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
433			if ((sHash & SC_INTERACTION) != 0) sc_->calcFunctional(sdat);
434	gezelter	1879
435			// set<NonBondedInteraction*>::iterator it;
436	gezelter	1502
437	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
438	gezelter	1879	// if ((*it)->getFamily() == METALLIC_FAMILY) {
439			// dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
440			// }
441			// }
442	gezelter	1504
443	gezelter	1502	return;
444			}
445
446	gezelter	1895	void InteractionManager::doPair(InteractionData &idat){
447	gezelter	1504
448	gezelter	1502	if (!initialized_) initialize();
449	gezelter	1587
450	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
451	gezelter	1502
452	gezelter	1927	if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
453	gezelter	1879
454			// electrostatics still has to worry about indirect
455			// contributions from excluded pairs of atoms, but nothing else does:
456	gezelter	1502
457	gezelter	1879	if (idat.excluded) return;
458	gezelter	1502
459	gezelter	1927	if ((iHash & LJ_INTERACTION) != 0) lj_->calcForce(idat);
460			if ((iHash & GB_INTERACTION) != 0) gb_->calcForce(idat);
461			if ((iHash & STICKY_INTERACTION) != 0) sticky_->calcForce(idat);
462			if ((iHash & MORSE_INTERACTION) != 0) morse_->calcForce(idat);
463			if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
464			if ((iHash & EAM_INTERACTION) != 0) eam_->calcForce(idat);
465			if ((iHash & SC_INTERACTION) != 0) sc_->calcForce(idat);
466			if ((iHash & MAW_INTERACTION) != 0) maw_->calcForce(idat);
467	gezelter	1879
468			// set<NonBondedInteraction*>::iterator it;
469
470			// for (it = interactions_[ idat.atypes ].begin();
471			// it != interactions_[ idat.atypes ].end(); ++it) {
472
473			// // electrostatics still has to worry about indirect
474			// // contributions from excluded pairs of atoms:
475
476			// if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
477			// (*it)->calcForce(idat);
478			// }
479			// }
480	gezelter	1502
481	gezelter	1504	return;
482	gezelter	1502	}
483
484	gezelter	1895	void InteractionManager::doSelfCorrection(SelfData &sdat){
485	gezelter	1502
486			if (!initialized_) initialize();
487	gezelter	1504
488	gezelter	1927	int& sHash = sHash_[sdat.atid];
489	gezelter	1502
490	gezelter	1927	if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
491	gezelter	1879
492			// set<NonBondedInteraction*>::iterator it;
493
494	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
495	gezelter	1879	// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
496			// dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
497			// }
498			// }
499	gezelter	1536
500	gezelter	1504	return;
501	gezelter	1502	}
502
503	gezelter	1925	void InteractionManager::doReciprocalSpaceSum(RealType &pot){
504	gezelter	1915	if (!initialized_) initialize();
505	gezelter	1921	electrostatic_->ReciprocalSpaceSum(pot);
506	gezelter	1915	}
507
508	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
509			if (!initialized_) initialize();
510	gezelter	1755
511	gezelter	1505	AtomType* atype = typeMap_[*atid];
512
513			set<NonBondedInteraction*>::iterator it;
514			RealType cutoff = 0.0;
515
516	gezelter	1921	for (it = interactions_[atid][atid].begin();
517			it != interactions_[atid][atid].end();
518	gezelter	1895	++it)
519			cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));
520	gezelter	1505	return cutoff;
521			}
522
523	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
524			if (!initialized_) initialize();
525
526	gezelter	1895	int atid = atype->getIdent();
527
528	gezelter	1528	set<NonBondedInteraction*>::iterator it;
529			RealType cutoff = 0.0;
530
531	gezelter	1921	for (it = interactions_[atid][atid].begin();
532			it != interactions_[atid][atid].end(); ++it)
533	gezelter	1895	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));
534	gezelter	1528	return cutoff;
535			}
536	gezelter	1502	} //end namespace OpenMD