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();
    ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
    AtomType* atype1;
    AtomType* atype2;
    pair<AtomType*, AtomType*> key;
    
    for (atype1 = atomTypes->beginType(i1); atype1 != NULL; 
         atype1 = atomTypes->nextType(i1)) {
      
      // add it to the map:
      
      pair<map<int,AtomType*>::iterator,bool> ret;    
      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), 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;

      for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
        atype2 = (*it2).second;
                               
        key = make_pair(atype1, atype2);

        iHash_[key] = 0;
        
        if (atype1->isLennardJones() && atype2->isLennardJones()) {
          interactions_[key].insert(lj_);
          iHash_[key] |= LJ_PAIR;
        }
        if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
          interactions_[key].insert(electrostatic_);
          iHash_[key] |= ELECTROSTATIC_PAIR;
        }
        if (atype1->isSticky() && atype2->isSticky() ) {
          interactions_[key].insert(sticky_);
          iHash_[key] |= STICKY_PAIR;
        }
        if (atype1->isStickyPower() && atype2->isStickyPower() ) {
          interactions_[key].insert(sticky_);
          iHash_[key] |= STICKY_PAIR;
        }
        if (atype1->isEAM() && atype2->isEAM() ) {
          interactions_[key].insert(eam_);
          iHash_[key] |= EAM_PAIR;
        }
        if (atype1->isSC() && atype2->isSC() ) {
          interactions_[key].insert(sc_);
          iHash_[key] |= SC_PAIR;
        }
        if (atype1->isGayBerne() && atype2->isGayBerne() ) {
          interactions_[key].insert(gb_);
          iHash_[key] |= GB_PAIR;
        }
        if ((atype1->isGayBerne() && atype2->isLennardJones())
            || (atype1->isLennardJones() && atype2->isGayBerne())) {
          interactions_[key].insert(gb_);
          iHash_[key] |= 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_[key].begin(); 
                 it != interactions_[key].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[key].erase(*it);
                // work on iHash here;
              }
            }
            interactions_[key].insert(lj_);
            iHash_[key] |= 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_[key].begin(); 
                 it != interactions_[key].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[key].erase(*it);
                // work on iHash here;
              }
            }
            interactions_[key].insert(morse_);
            iHash_[key] |= 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_[key].begin(); 
                 it != interactions_[key].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[key].erase(*it);
                // work on iHash here;
              }
            }
            interactions_[key].insert(repulsivePower_);
            iHash_[key] |= 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_[key].begin(); 
                 it != interactions_[key].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == METALLIC_FAMILY) {
                interactions_[key].erase(*it);
                // work on iHash here;
              }
            }
            interactions_[key].insert(eam_);
            iHash_[key] |= 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_[key].begin(); 
                 it != interactions_[key].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == METALLIC_FAMILY) {
                interactions_[key].erase(*it);
                // work on iHash here;
              }
            }
            interactions_[key].insert(sc_);
            iHash_[key] |= 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_[key].begin(); 
                 it != interactions_[key].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[key].erase(*it);
                // work on iHash here;
              }
            }
            interactions_[key].insert(maw_);
            iHash_[key] |= 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);
      for (jt = it; jt != simTypes.end(); ++jt) {
        atype2 = (*jt);
        key = make_pair(atype1, atype2);
        
        if (interactions_[key].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.atypes];

    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();
    
    // pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);

    int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];

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

    // set<NonBondedInteraction*>::iterator it;
    
    // for (it = interactions_[key].begin(); it != interactions_[key].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.atypes];

    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_[ make_pair(sdat.atype, sdat.atype) ];

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


    // pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype);
    // set<NonBondedInteraction*>::iterator it;

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

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

    AtomType* atype = typeMap_[*atid];

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

  RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
    if (!initialized_) initialize();
    
    pair<AtomType*, AtomType*> key = make_pair(atype, atype);
    set<NonBondedInteraction*>::iterator it;
    RealType cutoff = 0.0;
    
    for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));   
    return cutoff;    
  }
} //end namespace OpenMD
Revision:	1877
Committed:	Thu Jun 6 15:43:35 2013 UTC (11 years, 10 months ago) by gezelter
File size:	17739 byte(s)
Log Message:	New electrostatic method, starting to do some performance tuning.
#	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	1850	* [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	1868	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			ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
93			AtomType* atype1;
94			AtomType* atype2;
95			pair<AtomType, AtomType> key;
96
97			for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
98			atype1 = atomTypes->nextType(i1)) {
99
100			// add it to the map:
101
102			pair<map<int,AtomType*>::iterator,bool> ret;
103	gezelter	1710	ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
104	gezelter	1502	if (ret.second == false) {
105			sprintf( painCave.errMsg,
106			"InteractionManager already had a previous entry with ident %d\n",
107	gezelter	1710	atype1->getIdent());
108	gezelter	1502	painCave.severity = OPENMD_INFO;
109			painCave.isFatal = 0;
110			simError();
111			}
112			}
113
114			// Now, iterate over all known types and add to the interaction map:
115
116			map<int, AtomType*>::iterator it1, it2;
117			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
118			atype1 = (*it1).second;
119
120			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
121			atype2 = (*it2).second;
122	gezelter	1874
123	gezelter	1502	key = make_pair(atype1, atype2);
124	gezelter	1877
125			iHash_[key] = 0;
126	gezelter	1502
127			if (atype1->isLennardJones() && atype2->isLennardJones()) {
128			interactions_[key].insert(lj_);
129	gezelter	1877	iHash_[key] \|= LJ_PAIR;
130	gezelter	1502	}
131			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
132			interactions_[key].insert(electrostatic_);
133	gezelter	1877	iHash_[key] \|= ELECTROSTATIC_PAIR;
134	gezelter	1502	}
135			if (atype1->isSticky() && atype2->isSticky() ) {
136			interactions_[key].insert(sticky_);
137	gezelter	1877	iHash_[key] \|= STICKY_PAIR;
138	gezelter	1502	}
139			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
140			interactions_[key].insert(sticky_);
141	gezelter	1877	iHash_[key] \|= STICKY_PAIR;
142	gezelter	1502	}
143			if (atype1->isEAM() && atype2->isEAM() ) {
144			interactions_[key].insert(eam_);
145	gezelter	1877	iHash_[key] \|= EAM_PAIR;
146	gezelter	1502	}
147			if (atype1->isSC() && atype2->isSC() ) {
148			interactions_[key].insert(sc_);
149	gezelter	1877	iHash_[key] \|= SC_PAIR;
150	gezelter	1502	}
151			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
152			interactions_[key].insert(gb_);
153	gezelter	1877	iHash_[key] \|= GB_PAIR;
154	gezelter	1502	}
155			if ((atype1->isGayBerne() && atype2->isLennardJones())
156			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
157			interactions_[key].insert(gb_);
158	gezelter	1877	iHash_[key] \|= GB_PAIR;
159	gezelter	1502	}
160
161			// look for an explicitly-set non-bonded interaction type using the
162			// two atom types.
163			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
164	gezelter	1535
165			if (nbiType != NULL) {
166	gezelter	1502
167	gezelter	1874	bool vdwExplicit = false;
168			bool metExplicit = false;
169			// bool hbExplicit = false;
170
171	gezelter	1535	if (nbiType->isLennardJones()) {
172			// We found an explicit Lennard-Jones interaction.
173			// override all other vdw entries for this pair of atom types:
174			set<NonBondedInteraction*>::iterator it;
175			for (it = interactions_[key].begin();
176			it != interactions_[key].end(); ++it) {
177			InteractionFamily ifam = (*it)->getFamily();
178	gezelter	1877	if (ifam == VANDERWAALS_FAMILY) {
179			interactions_[key].erase(*it);
180			// work on iHash here;
181			}
182	gezelter	1535	}
183			interactions_[key].insert(lj_);
184	gezelter	1877	iHash_[key] \|= LJ_PAIR;
185	gezelter	1535	vdwExplicit = true;
186	gezelter	1502	}
187	gezelter	1535
188			if (nbiType->isMorse()) {
189			if (vdwExplicit) {
190			sprintf( painCave.errMsg,
191			"InteractionManager::initialize found more than one "
192			"explicit \n"
193			"\tvan der Waals interaction for atom types %s - %s\n",
194			atype1->getName().c_str(), atype2->getName().c_str());
195			painCave.severity = OPENMD_ERROR;
196			painCave.isFatal = 1;
197			simError();
198			}
199			// We found an explicit Morse interaction.
200			// override all other vdw entries for this pair of atom types:
201			set<NonBondedInteraction*>::iterator it;
202			for (it = interactions_[key].begin();
203			it != interactions_[key].end(); ++it) {
204			InteractionFamily ifam = (*it)->getFamily();
205	gezelter	1877	if (ifam == VANDERWAALS_FAMILY) {
206			interactions_[key].erase(*it);
207			// work on iHash here;
208			}
209	gezelter	1535	}
210			interactions_[key].insert(morse_);
211	gezelter	1877	iHash_[key] \|= MORSE_PAIR;
212	gezelter	1535	vdwExplicit = true;
213	gezelter	1502	}
214	jmichalk	1656
215			if (nbiType->isRepulsivePower()) {
216			if (vdwExplicit) {
217			sprintf( painCave.errMsg,
218			"InteractionManager::initialize found more than one "
219			"explicit \n"
220			"\tvan der Waals interaction for atom types %s - %s\n",
221			atype1->getName().c_str(), atype2->getName().c_str());
222			painCave.severity = OPENMD_ERROR;
223			painCave.isFatal = 1;
224			simError();
225			}
226			// We found an explicit RepulsivePower interaction.
227			// override all other vdw entries for this pair of atom types:
228			set<NonBondedInteraction*>::iterator it;
229			for (it = interactions_[key].begin();
230			it != interactions_[key].end(); ++it) {
231			InteractionFamily ifam = (*it)->getFamily();
232	gezelter	1877	if (ifam == VANDERWAALS_FAMILY) {
233			interactions_[key].erase(*it);
234			// work on iHash here;
235			}
236	jmichalk	1656	}
237			interactions_[key].insert(repulsivePower_);
238	gezelter	1877	iHash_[key] \|= REPULSIVEPOWER_PAIR;
239	jmichalk	1656	vdwExplicit = true;
240			}
241	gezelter	1535
242	jmichalk	1656
243	gezelter	1535	if (nbiType->isEAM()) {
244			// We found an explicit EAM interaction.
245			// override all other metallic entries for this pair of atom types:
246			set<NonBondedInteraction*>::iterator it;
247			for (it = interactions_[key].begin();
248			it != interactions_[key].end(); ++it) {
249			InteractionFamily ifam = (*it)->getFamily();
250	gezelter	1877	if (ifam == METALLIC_FAMILY) {
251			interactions_[key].erase(*it);
252			// work on iHash here;
253			}
254	gezelter	1535	}
255			interactions_[key].insert(eam_);
256	gezelter	1877	iHash_[key] \|= EAM_PAIR;
257	gezelter	1535	metExplicit = true;
258	gezelter	1502	}
259	gezelter	1535
260			if (nbiType->isSC()) {
261			if (metExplicit) {
262			sprintf( painCave.errMsg,
263			"InteractionManager::initialize found more than one "
264			"explicit\n"
265			"\tmetallic 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 Sutton-Chen interaction.
272			// override all other metallic entries for this pair of atom types:
273			set<NonBondedInteraction*>::iterator it;
274			for (it = interactions_[key].begin();
275			it != interactions_[key].end(); ++it) {
276			InteractionFamily ifam = (*it)->getFamily();
277	gezelter	1877	if (ifam == METALLIC_FAMILY) {
278			interactions_[key].erase(*it);
279			// work on iHash here;
280			}
281	gezelter	1535	}
282			interactions_[key].insert(sc_);
283	gezelter	1877	iHash_[key] \|= SC_PAIR;
284	gezelter	1535	metExplicit = true;
285	gezelter	1502	}
286	gezelter	1535
287			if (nbiType->isMAW()) {
288			if (vdwExplicit) {
289			sprintf( painCave.errMsg,
290			"InteractionManager::initialize found more than one "
291			"explicit\n"
292			"\tvan der Waals interaction for atom types %s - %s\n",
293			atype1->getName().c_str(), atype2->getName().c_str());
294			painCave.severity = OPENMD_ERROR;
295			painCave.isFatal = 1;
296			simError();
297			}
298			// We found an explicit MAW interaction.
299			// override all other vdw entries for this pair of atom types:
300			set<NonBondedInteraction*>::iterator it;
301			for (it = interactions_[key].begin();
302			it != interactions_[key].end(); ++it) {
303			InteractionFamily ifam = (*it)->getFamily();
304	gezelter	1877	if (ifam == VANDERWAALS_FAMILY) {
305			interactions_[key].erase(*it);
306			// work on iHash here;
307			}
308	gezelter	1535	}
309			interactions_[key].insert(maw_);
310	gezelter	1877	iHash_[key] \|= MAW_PAIR;
311	gezelter	1535	vdwExplicit = true;
312			}
313	gezelter	1502	}
314			}
315			}
316
317	gezelter	1535
318	gezelter	1583	// Make sure every pair of atom types in this simulation has a
319			// non-bonded interaction. If not, just inform the user.
320	gezelter	1535
321			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
322			set<AtomType*>::iterator it, jt;
323	gezelter	1583
324	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
325			atype1 = (*it);
326	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
327	gezelter	1535	atype2 = (*jt);
328	gezelter	1502	key = make_pair(atype1, atype2);
329
330			if (interactions_[key].size() == 0) {
331			sprintf( painCave.errMsg,
332	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
333			"\tinteraction for atom types %s - %s\n"
334			"\tProceeding without this interaction.\n",
335	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
336			painCave.severity = OPENMD_INFO;
337	gezelter	1583	painCave.isFatal = 0;
338	gezelter	1502	simError();
339			}
340			}
341			}
342	gezelter	1535
343			initialized_ = true;
344			}
345	gezelter	1584
346			void InteractionManager::setCutoffRadius(RealType rcut) {
347	gezelter	1587
348	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
349	gezelter	1586	eam_->setCutoffRadius(rcut);
350	gezelter	1584	}
351
352	gezelter	1545	void InteractionManager::doPrePair(InteractionData idat){
353	gezelter	1502
354			if (!initialized_) initialize();
355	gezelter	1545
356	gezelter	1587	// excluded interaction, so just return
357			if (idat.excluded) return;
358
359	gezelter	1877	int& iHash = iHash_[idat.atypes];
360	gezelter	1504
361	gezelter	1877	if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
362			if ((iHash & SC_PAIR) != 0) sc_->calcDensity(idat);
363
364			// set<NonBondedInteraction*>::iterator it;
365
366			// for (it = interactions_[ idat.atypes ].begin();
367			// it != interactions_[ idat.atypes ].end(); ++it){
368			// if ((*it)->getFamily() == METALLIC_FAMILY) {
369			// dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
370			// }
371			// }
372	gezelter	1502
373			return;
374			}
375	gezelter	1504
376	gezelter	1545	void InteractionManager::doPreForce(SelfData sdat){
377	gezelter	1502
378	gezelter	1504	if (!initialized_) initialize();
379	gezelter	1545
380	gezelter	1877	// pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
381
382			int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];
383
384			if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
385			if ((iHash & SC_PAIR) != 0) sc_->calcFunctional(sdat);
386
387			// set<NonBondedInteraction*>::iterator it;
388	gezelter	1502
389	gezelter	1877	// for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
390			// if ((*it)->getFamily() == METALLIC_FAMILY) {
391			// dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
392			// }
393			// }
394	gezelter	1504
395	gezelter	1502	return;
396			}
397
398	gezelter	1545	void InteractionManager::doPair(InteractionData idat){
399	gezelter	1504
400	gezelter	1502	if (!initialized_) initialize();
401	gezelter	1587
402	gezelter	1877	int& iHash = iHash_[idat.atypes];
403	gezelter	1502
404	gezelter	1877	if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
405
406			// electrostatics still has to worry about indirect
407			// contributions from excluded pairs of atoms, but nothing else does:
408	gezelter	1502
409	gezelter	1877	if (idat.excluded) return;
410	gezelter	1502
411	gezelter	1877	if ((iHash & LJ_PAIR) != 0) lj_->calcForce(idat);
412			if ((iHash & GB_PAIR) != 0) gb_->calcForce(idat);
413			if ((iHash & STICKY_PAIR) != 0) sticky_->calcForce(idat);
414			if ((iHash & MORSE_PAIR) != 0) morse_->calcForce(idat);
415			if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
416			if ((iHash & EAM_PAIR) != 0) eam_->calcForce(idat);
417			if ((iHash & SC_PAIR) != 0) sc_->calcForce(idat);
418			if ((iHash & MAW_PAIR) != 0) maw_->calcForce(idat);
419
420			// set<NonBondedInteraction*>::iterator it;
421
422			// for (it = interactions_[ idat.atypes ].begin();
423			// it != interactions_[ idat.atypes ].end(); ++it) {
424
425			// // electrostatics still has to worry about indirect
426			// // contributions from excluded pairs of atoms:
427
428			// if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
429			// (*it)->calcForce(idat);
430			// }
431			// }
432	gezelter	1502
433	gezelter	1504	return;
434	gezelter	1502	}
435
436	gezelter	1545	void InteractionManager::doSelfCorrection(SelfData sdat){
437	gezelter	1502
438			if (!initialized_) initialize();
439	gezelter	1504
440	gezelter	1877	int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];
441	gezelter	1502
442	gezelter	1877	if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
443
444
445			// pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
446			// set<NonBondedInteraction*>::iterator it;
447
448			// for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
449			// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
450			// dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
451			// }
452			// }
453	gezelter	1536
454	gezelter	1504	return;
455	gezelter	1502	}
456
457	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
458			if (!initialized_) initialize();
459	gezelter	1755
460	gezelter	1505	AtomType* atype = typeMap_[*atid];
461
462			pair<AtomType, AtomType> key = make_pair(atype, atype);
463			set<NonBondedInteraction*>::iterator it;
464			RealType cutoff = 0.0;
465
466			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
467	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
468	gezelter	1505	return cutoff;
469			}
470
471	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
472			if (!initialized_) initialize();
473
474			pair<AtomType, AtomType> key = make_pair(atype, atype);
475			set<NonBondedInteraction*>::iterator it;
476			RealType cutoff = 0.0;
477
478			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
479	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
480	gezelter	1528	return cutoff;
481			}
482	gezelter	1502	} //end namespace OpenMD