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, 24107 (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();
  }

  void InteractionManager::initialize() {
    
    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;
    pair<set<NonBondedInteraction*>::iterator, bool> ret;
    
    for (atype1 = atomTypes->beginType(i1); atype1 != NULL; 
         atype1 = atomTypes->nextType(i1)) {
      
      // add it to the map:
      AtomTypeProperties atp = atype1->getATP();    
      
      pair<map<int,AtomType*>::iterator,bool> ret;    
      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
      if (ret.second == false) {
        sprintf( painCave.errMsg,
                 "InteractionManager already had a previous entry with ident %d\n",
                 atp.ident);
        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;
        
        bool vdwExplicit = false;
        bool metExplicit = false;
        bool hbExplicit = false;
                       
        key = make_pair(atype1, atype2);
        
        if (atype1->isLennardJones() && atype2->isLennardJones()) {
          interactions_[key].insert(lj_);
        }
        if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
          interactions_[key].insert(electrostatic_);
        }
        if (atype1->isSticky() && atype2->isSticky() ) {
          interactions_[key].insert(sticky_);
        }
        if (atype1->isStickyPower() && atype2->isStickyPower() ) {
          interactions_[key].insert(sticky_);
        }
        if (atype1->isEAM() && atype2->isEAM() ) {
          interactions_[key].insert(eam_);
        }
        if (atype1->isSC() && atype2->isSC() ) {
          interactions_[key].insert(sc_);
        }
        if (atype1->isGayBerne() && atype2->isGayBerne() ) {
          interactions_[key].insert(gb_);
        }
        if ((atype1->isGayBerne() && atype2->isLennardJones())
            || (atype1->isLennardJones() && atype2->isGayBerne())) {
          interactions_[key].insert(gb_);
        } 
        
        // 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) {

          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);
            }
            interactions_[key].insert(lj_);
            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);
            }
            interactions_[key].insert(morse_);
            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);
            }
            interactions_[key].insert(repulsivePower_);
            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);
            }
            interactions_[key].insert(eam_);
            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);
            }
            interactions_[key].insert(sc_);
            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);
            }
            interactions_[key].insert(maw_);
            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::setSwitchingRadius(RealType rswitch) {
    electrostatic_->setSwitchingRadius(rswitch);
  }
  
  void InteractionManager::doPrePair(InteractionData idat){
    
    if (!initialized_) initialize();
         
    // excluded interaction, so just return
    if (idat.excluded) return;

    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);
    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();

    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();
    
    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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	15286 byte(s)
Log Message:	updated copyright notices
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (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			void InteractionManager::initialize() {
63
64	gezelter	1535	ForceField* forceField_ = info_->getForceField();
65
66	gezelter	1502	lj_->setForceField(forceField_);
67			gb_->setForceField(forceField_);
68			sticky_->setForceField(forceField_);
69			eam_->setForceField(forceField_);
70			sc_->setForceField(forceField_);
71			morse_->setForceField(forceField_);
72	gezelter	1584	electrostatic_->setSimInfo(info_);
73	gezelter	1502	electrostatic_->setForceField(forceField_);
74	gezelter	1532	maw_->setForceField(forceField_);
75	jmichalk	1656	repulsivePower_->setForceField(forceField_);
76	gezelter	1502
77			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
78			ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
79			AtomType* atype1;
80			AtomType* atype2;
81			pair<AtomType, AtomType> key;
82			pair<set<NonBondedInteraction*>::iterator, bool> ret;
83
84			for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
85			atype1 = atomTypes->nextType(i1)) {
86
87			// add it to the map:
88			AtomTypeProperties atp = atype1->getATP();
89
90			pair<map<int,AtomType*>::iterator,bool> ret;
91			ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
92			if (ret.second == false) {
93			sprintf( painCave.errMsg,
94			"InteractionManager already had a previous entry with ident %d\n",
95			atp.ident);
96			painCave.severity = OPENMD_INFO;
97			painCave.isFatal = 0;
98			simError();
99			}
100			}
101
102			// Now, iterate over all known types and add to the interaction map:
103
104			map<int, AtomType*>::iterator it1, it2;
105			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
106			atype1 = (*it1).second;
107
108			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
109			atype2 = (*it2).second;
110
111			bool vdwExplicit = false;
112			bool metExplicit = false;
113			bool hbExplicit = false;
114
115			key = make_pair(atype1, atype2);
116
117			if (atype1->isLennardJones() && atype2->isLennardJones()) {
118			interactions_[key].insert(lj_);
119			}
120			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
121			interactions_[key].insert(electrostatic_);
122			}
123			if (atype1->isSticky() && atype2->isSticky() ) {
124			interactions_[key].insert(sticky_);
125			}
126			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
127			interactions_[key].insert(sticky_);
128			}
129			if (atype1->isEAM() && atype2->isEAM() ) {
130			interactions_[key].insert(eam_);
131			}
132			if (atype1->isSC() && atype2->isSC() ) {
133			interactions_[key].insert(sc_);
134			}
135			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
136			interactions_[key].insert(gb_);
137			}
138			if ((atype1->isGayBerne() && atype2->isLennardJones())
139			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
140			interactions_[key].insert(gb_);
141			}
142
143			// look for an explicitly-set non-bonded interaction type using the
144			// two atom types.
145			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
146	gezelter	1535
147			if (nbiType != NULL) {
148	gezelter	1502
149	gezelter	1535	if (nbiType->isLennardJones()) {
150			// We found an explicit Lennard-Jones interaction.
151			// override all other vdw entries for this pair of atom types:
152			set<NonBondedInteraction*>::iterator it;
153			for (it = interactions_[key].begin();
154			it != interactions_[key].end(); ++it) {
155			InteractionFamily ifam = (*it)->getFamily();
156			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
157			}
158			interactions_[key].insert(lj_);
159			vdwExplicit = true;
160	gezelter	1502	}
161	gezelter	1535
162			if (nbiType->isMorse()) {
163			if (vdwExplicit) {
164			sprintf( painCave.errMsg,
165			"InteractionManager::initialize found more than one "
166			"explicit \n"
167			"\tvan der Waals interaction for atom types %s - %s\n",
168			atype1->getName().c_str(), atype2->getName().c_str());
169			painCave.severity = OPENMD_ERROR;
170			painCave.isFatal = 1;
171			simError();
172			}
173			// We found an explicit Morse interaction.
174			// override all other vdw entries for this pair of atom types:
175			set<NonBondedInteraction*>::iterator it;
176			for (it = interactions_[key].begin();
177			it != interactions_[key].end(); ++it) {
178			InteractionFamily ifam = (*it)->getFamily();
179			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
180			}
181			interactions_[key].insert(morse_);
182			vdwExplicit = true;
183	gezelter	1502	}
184	jmichalk	1656
185			if (nbiType->isRepulsivePower()) {
186			if (vdwExplicit) {
187			sprintf( painCave.errMsg,
188			"InteractionManager::initialize found more than one "
189			"explicit \n"
190			"\tvan der Waals interaction for atom types %s - %s\n",
191			atype1->getName().c_str(), atype2->getName().c_str());
192			painCave.severity = OPENMD_ERROR;
193			painCave.isFatal = 1;
194			simError();
195			}
196			// We found an explicit RepulsivePower interaction.
197			// override all other vdw entries for this pair of atom types:
198			set<NonBondedInteraction*>::iterator it;
199			for (it = interactions_[key].begin();
200			it != interactions_[key].end(); ++it) {
201			InteractionFamily ifam = (*it)->getFamily();
202			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
203			}
204			interactions_[key].insert(repulsivePower_);
205			vdwExplicit = true;
206			}
207	gezelter	1535
208	jmichalk	1656
209	gezelter	1535	if (nbiType->isEAM()) {
210			// We found an explicit EAM interaction.
211			// override all other metallic entries for this pair of atom types:
212			set<NonBondedInteraction*>::iterator it;
213			for (it = interactions_[key].begin();
214			it != interactions_[key].end(); ++it) {
215			InteractionFamily ifam = (*it)->getFamily();
216			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
217			}
218			interactions_[key].insert(eam_);
219			metExplicit = true;
220	gezelter	1502	}
221	gezelter	1535
222			if (nbiType->isSC()) {
223			if (metExplicit) {
224			sprintf( painCave.errMsg,
225			"InteractionManager::initialize found more than one "
226			"explicit\n"
227			"\tmetallic interaction for atom types %s - %s\n",
228			atype1->getName().c_str(), atype2->getName().c_str());
229			painCave.severity = OPENMD_ERROR;
230			painCave.isFatal = 1;
231			simError();
232			}
233			// We found an explicit Sutton-Chen interaction.
234			// override all other metallic entries for this pair of atom types:
235			set<NonBondedInteraction*>::iterator it;
236			for (it = interactions_[key].begin();
237			it != interactions_[key].end(); ++it) {
238			InteractionFamily ifam = (*it)->getFamily();
239			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
240			}
241			interactions_[key].insert(sc_);
242			metExplicit = true;
243	gezelter	1502	}
244	gezelter	1535
245			if (nbiType->isMAW()) {
246			if (vdwExplicit) {
247			sprintf( painCave.errMsg,
248			"InteractionManager::initialize found more than one "
249			"explicit\n"
250			"\tvan der Waals interaction for atom types %s - %s\n",
251			atype1->getName().c_str(), atype2->getName().c_str());
252			painCave.severity = OPENMD_ERROR;
253			painCave.isFatal = 1;
254			simError();
255			}
256			// We found an explicit MAW interaction.
257			// override all other vdw entries for this pair of atom types:
258			set<NonBondedInteraction*>::iterator it;
259			for (it = interactions_[key].begin();
260			it != interactions_[key].end(); ++it) {
261			InteractionFamily ifam = (*it)->getFamily();
262			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
263			}
264			interactions_[key].insert(maw_);
265			vdwExplicit = true;
266			}
267	gezelter	1502	}
268			}
269			}
270
271	gezelter	1535
272	gezelter	1583	// Make sure every pair of atom types in this simulation has a
273			// non-bonded interaction. If not, just inform the user.
274	gezelter	1535
275			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
276			set<AtomType*>::iterator it, jt;
277	gezelter	1583
278	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
279			atype1 = (*it);
280	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
281	gezelter	1535	atype2 = (*jt);
282	gezelter	1502	key = make_pair(atype1, atype2);
283
284			if (interactions_[key].size() == 0) {
285			sprintf( painCave.errMsg,
286	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
287			"\tinteraction for atom types %s - %s\n"
288			"\tProceeding without this interaction.\n",
289	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
290			painCave.severity = OPENMD_INFO;
291	gezelter	1583	painCave.isFatal = 0;
292	gezelter	1502	simError();
293			}
294			}
295			}
296	gezelter	1535
297			initialized_ = true;
298			}
299	gezelter	1584
300			void InteractionManager::setCutoffRadius(RealType rcut) {
301	gezelter	1587
302	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
303	gezelter	1586	eam_->setCutoffRadius(rcut);
304	gezelter	1584	}
305
306			void InteractionManager::setSwitchingRadius(RealType rswitch) {
307			electrostatic_->setSwitchingRadius(rswitch);
308			}
309	gezelter	1502
310	gezelter	1545	void InteractionManager::doPrePair(InteractionData idat){
311	gezelter	1502
312			if (!initialized_) initialize();
313	gezelter	1545
314	gezelter	1587	// excluded interaction, so just return
315			if (idat.excluded) return;
316
317	gezelter	1504	set<NonBondedInteraction*>::iterator it;
318
319	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
320			it != interactions_[ idat.atypes ].end(); ++it){
321	gezelter	1504	if ((*it)->getFamily() == METALLIC_FAMILY) {
322	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
323	gezelter	1504	}
324			}
325	gezelter	1502
326			return;
327			}
328	gezelter	1504
329	gezelter	1545	void InteractionManager::doPreForce(SelfData sdat){
330	gezelter	1502
331	gezelter	1504	if (!initialized_) initialize();
332	gezelter	1545
333			pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
334	gezelter	1504	set<NonBondedInteraction*>::iterator it;
335	gezelter	1502
336	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
337			if ((*it)->getFamily() == METALLIC_FAMILY) {
338	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
339	gezelter	1504	}
340			}
341
342	gezelter	1502	return;
343			}
344
345	gezelter	1545	void InteractionManager::doPair(InteractionData idat){
346	gezelter	1504
347	gezelter	1502	if (!initialized_) initialize();
348	gezelter	1587
349	gezelter	1502	set<NonBondedInteraction*>::iterator it;
350
351	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
352	gezelter	1587	it != interactions_[ idat.atypes ].end(); ++it) {
353	gezelter	1502
354	gezelter	1587	// electrostatics still has to worry about indirect
355			// contributions from excluded pairs of atoms:
356	gezelter	1502
357	gezelter	1587	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
358			(*it)->calcForce(idat);
359	gezelter	1504	}
360			}
361	gezelter	1502
362	gezelter	1504	return;
363	gezelter	1502	}
364
365	gezelter	1545	void InteractionManager::doSelfCorrection(SelfData sdat){
366	gezelter	1502
367			if (!initialized_) initialize();
368	gezelter	1504
369	gezelter	1545	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
370	gezelter	1504	set<NonBondedInteraction*>::iterator it;
371	gezelter	1502
372	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
373			if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
374	gezelter	1545	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
375	gezelter	1504	}
376			}
377	gezelter	1536
378	gezelter	1504	return;
379	gezelter	1502	}
380
381	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
382			if (!initialized_) initialize();
383
384			AtomType* atype = typeMap_[*atid];
385
386			pair<AtomType, AtomType> key = make_pair(atype, atype);
387			set<NonBondedInteraction*>::iterator it;
388			RealType cutoff = 0.0;
389
390			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
391	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
392	gezelter	1505	return cutoff;
393			}
394
395	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
396			if (!initialized_) initialize();
397
398			pair<AtomType, AtomType> key = make_pair(atype, atype);
399			set<NonBondedInteraction*>::iterator it;
400			RealType cutoff = 0.0;
401
402			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
403	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
404	gezelter	1528	return cutoff;
405			}
406	gezelter	1502	} //end namespace OpenMD