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) {
          
      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:	1935
Committed:	Tue Sep 24 13:52:54 2013 UTC (11 years, 7 months ago) by gezelter
File size:	19963 byte(s)
Log Message:	Fixed a bug in building the self Hash
#	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	1935
120	gezelter	1895	atype1 = *at;
121			atid1 = atype1->getIdent();
122			iHash_[atid1].resize(nTypes);
123			interactions_[atid1].resize(nTypes);
124
125			// add it to the map:
126	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
127	gezelter	1895	ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
128	gezelter	1502	if (ret.second == false) {
129			sprintf( painCave.errMsg,
130			"InteractionManager already had a previous entry with ident %d\n",
131	gezelter	1710	atype1->getIdent());
132	gezelter	1502	painCave.severity = OPENMD_INFO;
133			painCave.isFatal = 0;
134			simError();
135			}
136	gezelter	1935
137			if (atype1->isLennardJones()) {
138			sHash_[atid1] \|= LJ_INTERACTION;
139			}
140			if (atype1->isElectrostatic()) {
141			sHash_[atid1] \|= ELECTROSTATIC_INTERACTION;
142			}
143			if (atype1->isSticky()) {
144			sHash_[atid1] \|= STICKY_INTERACTION;
145			}
146			if (atype1->isStickyPower()) {
147			sHash_[atid1] \|= STICKY_INTERACTION;
148			}
149			if (atype1->isEAM()) {
150			sHash_[atid1] \|= EAM_INTERACTION;
151			}
152			if (atype1->isSC()) {
153			sHash_[atid1] \|= SC_INTERACTION;
154			}
155			if (atype1->isGayBerne()) {
156			sHash_[atid1] \|= GB_INTERACTION;
157			}
158	gezelter	1502	}
159			// Now, iterate over all known types and add to the interaction map:
160
161			map<int, AtomType*>::iterator it1, it2;
162			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
163			atype1 = (*it1).second;
164	gezelter	1895	atid1 = atype1->getIdent();
165	gezelter	1502
166			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
167			atype2 = (*it2).second;
168	gezelter	1895	atid2 = atype2->getIdent();
169	gezelter	1879
170	gezelter	1895	iHash_[atid1][atid2] = 0;
171	gezelter	1502
172			if (atype1->isLennardJones() && atype2->isLennardJones()) {
173	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
174	gezelter	1927	iHash_[atid1][atid2] \|= LJ_INTERACTION;
175	gezelter	1502	}
176			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
177	gezelter	1929	interactions_[atid1][atid2].insert(electrostatic_);
178			iHash_[atid1][atid2] \|= ELECTROSTATIC_INTERACTION;
179	gezelter	1502	}
180			if (atype1->isSticky() && atype2->isSticky() ) {
181	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
182	gezelter	1927	iHash_[atid1][atid2] \|= STICKY_INTERACTION;
183	gezelter	1502	}
184			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
185	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
186	gezelter	1927	iHash_[atid1][atid2] \|= STICKY_INTERACTION;
187	gezelter	1502	}
188			if (atype1->isEAM() && atype2->isEAM() ) {
189	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
190	gezelter	1927	iHash_[atid1][atid2] \|= EAM_INTERACTION;
191	gezelter	1502	}
192			if (atype1->isSC() && atype2->isSC() ) {
193	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
194	gezelter	1927	iHash_[atid1][atid2] \|= SC_INTERACTION;
195	gezelter	1502	}
196			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
197	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
198	gezelter	1927	iHash_[atid1][atid2] \|= GB_INTERACTION;
199	gezelter	1502	}
200			if ((atype1->isGayBerne() && atype2->isLennardJones())
201			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
202	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
203	gezelter	1927	iHash_[atid1][atid2] \|= GB_INTERACTION;
204	gezelter	1502	}
205
206			// look for an explicitly-set non-bonded interaction type using the
207			// two atom types.
208			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
209	gezelter	1535
210			if (nbiType != NULL) {
211	gezelter	1502
212	gezelter	1879	bool vdwExplicit = false;
213			bool metExplicit = false;
214			// bool hbExplicit = false;
215
216	gezelter	1535	if (nbiType->isLennardJones()) {
217			// We found an explicit Lennard-Jones interaction.
218			// override all other vdw entries for this pair of atom types:
219			set<NonBondedInteraction*>::iterator it;
220	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
221			it != interactions_[atid1][atid2].end(); ++it) {
222	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
223	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
224	gezelter	1895	interactions_[atid1][atid2].erase(*it);
225			iHash_[atid1][atid2] ^= (*it)->getHash();
226	gezelter	1879	}
227	gezelter	1535	}
228	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
229	gezelter	1927	iHash_[atid1][atid2] \|= LJ_INTERACTION;
230	gezelter	1535	vdwExplicit = true;
231	gezelter	1502	}
232	gezelter	1535
233			if (nbiType->isMorse()) {
234			if (vdwExplicit) {
235			sprintf( painCave.errMsg,
236			"InteractionManager::initialize found more than one "
237			"explicit \n"
238			"\tvan der Waals interaction for atom types %s - %s\n",
239			atype1->getName().c_str(), atype2->getName().c_str());
240			painCave.severity = OPENMD_ERROR;
241			painCave.isFatal = 1;
242			simError();
243			}
244			// We found an explicit Morse interaction.
245			// override all other vdw entries for this pair of atom types:
246			set<NonBondedInteraction*>::iterator it;
247	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
248			it != interactions_[atid1][atid2].end(); ++it) {
249	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
250	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
251	gezelter	1895	interactions_[atid1][atid2].erase(*it);
252			iHash_[atid1][atid2] ^= (*it)->getHash();
253	gezelter	1879	}
254	gezelter	1535	}
255	gezelter	1895	interactions_[atid1][atid2].insert(morse_);
256	gezelter	1927	iHash_[atid1][atid2] \|= MORSE_INTERACTION;
257	gezelter	1535	vdwExplicit = true;
258	gezelter	1502	}
259	jmichalk	1656
260			if (nbiType->isRepulsivePower()) {
261			if (vdwExplicit) {
262			sprintf( painCave.errMsg,
263			"InteractionManager::initialize found more than one "
264			"explicit \n"
265			"\tvan der Waals interaction for atom types %s - %s\n",
266			atype1->getName().c_str(), atype2->getName().c_str());
267			painCave.severity = OPENMD_ERROR;
268			painCave.isFatal = 1;
269			simError();
270			}
271			// We found an explicit RepulsivePower interaction.
272			// override all other vdw entries for this pair of atom types:
273			set<NonBondedInteraction*>::iterator it;
274	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
275			it != interactions_[atid1][atid2].end(); ++it) {
276	jmichalk	1656	InteractionFamily ifam = (*it)->getFamily();
277	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
278	gezelter	1895	interactions_[atid1][atid2].erase(*it);
279			iHash_[atid1][atid2] ^= (*it)->getHash();
280	gezelter	1879	}
281	jmichalk	1656	}
282	gezelter	1895	interactions_[atid1][atid2].insert(repulsivePower_);
283	gezelter	1927	iHash_[atid1][atid2] \|= REPULSIVEPOWER_INTERACTION;
284	jmichalk	1656	vdwExplicit = true;
285			}
286	gezelter	1535
287	jmichalk	1656
288	gezelter	1535	if (nbiType->isEAM()) {
289			// We found an explicit EAM interaction.
290			// override all other metallic entries for this pair of atom types:
291			set<NonBondedInteraction*>::iterator it;
292	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
293			it != interactions_[atid1][atid2].end(); ++it) {
294	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
295	gezelter	1879	if (ifam == METALLIC_FAMILY) {
296	gezelter	1895	interactions_[atid1][atid2].erase(*it);
297			iHash_[atid1][atid2] ^= (*it)->getHash();
298	gezelter	1879	}
299	gezelter	1535	}
300	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
301	gezelter	1927	iHash_[atid1][atid2] \|= EAM_INTERACTION;
302	gezelter	1535	metExplicit = true;
303	gezelter	1502	}
304	gezelter	1535
305			if (nbiType->isSC()) {
306			if (metExplicit) {
307			sprintf( painCave.errMsg,
308			"InteractionManager::initialize found more than one "
309			"explicit\n"
310			"\tmetallic interaction for atom types %s - %s\n",
311			atype1->getName().c_str(), atype2->getName().c_str());
312			painCave.severity = OPENMD_ERROR;
313			painCave.isFatal = 1;
314			simError();
315			}
316			// We found an explicit Sutton-Chen interaction.
317			// override all other metallic entries for this pair of atom types:
318			set<NonBondedInteraction*>::iterator it;
319	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
320			it != interactions_[atid1][atid2].end(); ++it) {
321	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
322	gezelter	1879	if (ifam == METALLIC_FAMILY) {
323	gezelter	1895	interactions_[atid1][atid2].erase(*it);
324			iHash_[atid1][atid2] ^= (*it)->getHash();
325	gezelter	1879	}
326	gezelter	1535	}
327	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
328	gezelter	1927	iHash_[atid1][atid2] \|= SC_INTERACTION;
329	gezelter	1535	metExplicit = true;
330	gezelter	1502	}
331	gezelter	1535
332			if (nbiType->isMAW()) {
333			if (vdwExplicit) {
334			sprintf( painCave.errMsg,
335			"InteractionManager::initialize found more than one "
336			"explicit\n"
337			"\tvan der Waals interaction for atom types %s - %s\n",
338			atype1->getName().c_str(), atype2->getName().c_str());
339			painCave.severity = OPENMD_ERROR;
340			painCave.isFatal = 1;
341			simError();
342			}
343			// We found an explicit MAW interaction.
344			// override all other vdw entries for this pair of atom types:
345			set<NonBondedInteraction*>::iterator it;
346	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
347			it != interactions_[atid1][atid2].end(); ++it) {
348	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
349	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
350	gezelter	1895	interactions_[atid1][atid2].erase(*it);
351			iHash_[atid1][atid2] ^= (*it)->getHash();
352	gezelter	1879	}
353	gezelter	1535	}
354	gezelter	1895	interactions_[atid1][atid2].insert(maw_);
355	gezelter	1927	iHash_[atid1][atid2] \|= MAW_INTERACTION;
356	gezelter	1535	vdwExplicit = true;
357			}
358	gezelter	1502	}
359			}
360			}
361
362	gezelter	1535
363	gezelter	1583	// Make sure every pair of atom types in this simulation has a
364			// non-bonded interaction. If not, just inform the user.
365	gezelter	1535
366			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
367			set<AtomType*>::iterator it, jt;
368	gezelter	1583
369	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
370			atype1 = (*it);
371	gezelter	1895	atid1 = atype1->getIdent();
372	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
373	gezelter	1535	atype2 = (*jt);
374	gezelter	1895	atid1 = atype1->getIdent();
375	gezelter	1502
376	gezelter	1895	if (interactions_[atid1][atid2].size() == 0) {
377	gezelter	1502	sprintf( painCave.errMsg,
378	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
379			"\tinteraction for atom types %s - %s\n"
380			"\tProceeding without this interaction.\n",
381	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
382			painCave.severity = OPENMD_INFO;
383	gezelter	1583	painCave.isFatal = 0;
384	gezelter	1502	simError();
385			}
386			}
387			}
388	gezelter	1535
389			initialized_ = true;
390			}
391	gezelter	1584
392			void InteractionManager::setCutoffRadius(RealType rcut) {
393	gezelter	1587
394	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
395	gezelter	1586	eam_->setCutoffRadius(rcut);
396	gezelter	1584	}
397
398	gezelter	1895	void InteractionManager::doPrePair(InteractionData &idat){
399	gezelter	1502
400			if (!initialized_) initialize();
401	gezelter	1545
402	gezelter	1587	// excluded interaction, so just return
403			if (idat.excluded) return;
404
405	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
406	gezelter	1504
407	gezelter	1927	if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
408			if ((iHash & SC_INTERACTION) != 0) sc_->calcDensity(idat);
409	gezelter	1879
410			// set<NonBondedInteraction*>::iterator it;
411
412			// for (it = interactions_[ idat.atypes ].begin();
413			// it != interactions_[ idat.atypes ].end(); ++it){
414			// if ((*it)->getFamily() == METALLIC_FAMILY) {
415			// dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
416			// }
417			// }
418	gezelter	1502
419			return;
420			}
421	gezelter	1504
422	gezelter	1895	void InteractionManager::doPreForce(SelfData &sdat){
423	gezelter	1502
424	gezelter	1504	if (!initialized_) initialize();
425	gezelter	1545
426	gezelter	1927	int& sHash = sHash_[sdat.atid];
427	gezelter	1879
428	gezelter	1927	if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
429			if ((sHash & SC_INTERACTION) != 0) sc_->calcFunctional(sdat);
430	gezelter	1879
431			// set<NonBondedInteraction*>::iterator it;
432	gezelter	1502
433	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
434	gezelter	1879	// if ((*it)->getFamily() == METALLIC_FAMILY) {
435			// dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
436			// }
437			// }
438	gezelter	1504
439	gezelter	1502	return;
440			}
441
442	gezelter	1895	void InteractionManager::doPair(InteractionData &idat){
443	gezelter	1504
444	gezelter	1502	if (!initialized_) initialize();
445	gezelter	1587
446	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
447	gezelter	1502
448	gezelter	1927	if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
449	gezelter	1879
450			// electrostatics still has to worry about indirect
451			// contributions from excluded pairs of atoms, but nothing else does:
452	gezelter	1502
453	gezelter	1879	if (idat.excluded) return;
454	gezelter	1502
455	gezelter	1927	if ((iHash & LJ_INTERACTION) != 0) lj_->calcForce(idat);
456			if ((iHash & GB_INTERACTION) != 0) gb_->calcForce(idat);
457			if ((iHash & STICKY_INTERACTION) != 0) sticky_->calcForce(idat);
458			if ((iHash & MORSE_INTERACTION) != 0) morse_->calcForce(idat);
459			if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
460			if ((iHash & EAM_INTERACTION) != 0) eam_->calcForce(idat);
461			if ((iHash & SC_INTERACTION) != 0) sc_->calcForce(idat);
462			if ((iHash & MAW_INTERACTION) != 0) maw_->calcForce(idat);
463	gezelter	1879
464			// set<NonBondedInteraction*>::iterator it;
465
466			// for (it = interactions_[ idat.atypes ].begin();
467			// it != interactions_[ idat.atypes ].end(); ++it) {
468
469			// // electrostatics still has to worry about indirect
470			// // contributions from excluded pairs of atoms:
471
472			// if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
473			// (*it)->calcForce(idat);
474			// }
475			// }
476	gezelter	1502
477	gezelter	1504	return;
478	gezelter	1502	}
479
480	gezelter	1895	void InteractionManager::doSelfCorrection(SelfData &sdat){
481	gezelter	1502
482			if (!initialized_) initialize();
483	gezelter	1504
484	gezelter	1927	int& sHash = sHash_[sdat.atid];
485	gezelter	1502
486	gezelter	1927	if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
487	gezelter	1879
488			// set<NonBondedInteraction*>::iterator it;
489
490	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
491	gezelter	1879	// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
492			// dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
493			// }
494			// }
495	gezelter	1536
496	gezelter	1504	return;
497	gezelter	1502	}
498
499	gezelter	1925	void InteractionManager::doReciprocalSpaceSum(RealType &pot){
500	gezelter	1915	if (!initialized_) initialize();
501	gezelter	1921	electrostatic_->ReciprocalSpaceSum(pot);
502	gezelter	1915	}
503
504	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
505			if (!initialized_) initialize();
506	gezelter	1755
507	gezelter	1505	AtomType* atype = typeMap_[*atid];
508
509			set<NonBondedInteraction*>::iterator it;
510			RealType cutoff = 0.0;
511
512	gezelter	1921	for (it = interactions_[atid][atid].begin();
513			it != interactions_[atid][atid].end();
514	gezelter	1895	++it)
515			cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));
516	gezelter	1505	return cutoff;
517			}
518
519	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
520			if (!initialized_) initialize();
521
522	gezelter	1895	int atid = atype->getIdent();
523
524	gezelter	1528	set<NonBondedInteraction*>::iterator it;
525			RealType cutoff = 0.0;
526
527	gezelter	1921	for (it = interactions_[atid][atid].begin();
528			it != interactions_[atid][atid].end(); ++it)
529	gezelter	1895	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype, atype)));
530	gezelter	1528	return cutoff;
531			}
532	gezelter	1502	} //end namespace OpenMD