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);
        
        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) {

          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);
            }
            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::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:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	15332 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	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
125			if (atype1->isLennardJones() && atype2->isLennardJones()) {
126			interactions_[key].insert(lj_);
127			}
128			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
129			interactions_[key].insert(electrostatic_);
130			}
131			if (atype1->isSticky() && atype2->isSticky() ) {
132			interactions_[key].insert(sticky_);
133			}
134			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
135			interactions_[key].insert(sticky_);
136			}
137			if (atype1->isEAM() && atype2->isEAM() ) {
138			interactions_[key].insert(eam_);
139			}
140			if (atype1->isSC() && atype2->isSC() ) {
141			interactions_[key].insert(sc_);
142			}
143			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
144			interactions_[key].insert(gb_);
145			}
146			if ((atype1->isGayBerne() && atype2->isLennardJones())
147			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
148			interactions_[key].insert(gb_);
149			}
150
151			// look for an explicitly-set non-bonded interaction type using the
152			// two atom types.
153			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
154	gezelter	1535
155			if (nbiType != NULL) {
156	gezelter	1502
157	gezelter	1874	bool vdwExplicit = false;
158			bool metExplicit = false;
159			// bool hbExplicit = false;
160
161	gezelter	1535	if (nbiType->isLennardJones()) {
162			// We found an explicit Lennard-Jones interaction.
163			// override all other vdw entries for this pair of atom types:
164			set<NonBondedInteraction*>::iterator it;
165			for (it = interactions_[key].begin();
166			it != interactions_[key].end(); ++it) {
167			InteractionFamily ifam = (*it)->getFamily();
168			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
169			}
170			interactions_[key].insert(lj_);
171			vdwExplicit = true;
172	gezelter	1502	}
173	gezelter	1535
174			if (nbiType->isMorse()) {
175			if (vdwExplicit) {
176			sprintf( painCave.errMsg,
177			"InteractionManager::initialize found more than one "
178			"explicit \n"
179			"\tvan der Waals interaction for atom types %s - %s\n",
180			atype1->getName().c_str(), atype2->getName().c_str());
181			painCave.severity = OPENMD_ERROR;
182			painCave.isFatal = 1;
183			simError();
184			}
185			// We found an explicit Morse interaction.
186			// override all other vdw entries for this pair of atom types:
187			set<NonBondedInteraction*>::iterator it;
188			for (it = interactions_[key].begin();
189			it != interactions_[key].end(); ++it) {
190			InteractionFamily ifam = (*it)->getFamily();
191			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
192			}
193			interactions_[key].insert(morse_);
194			vdwExplicit = true;
195	gezelter	1502	}
196	jmichalk	1656
197			if (nbiType->isRepulsivePower()) {
198			if (vdwExplicit) {
199			sprintf( painCave.errMsg,
200			"InteractionManager::initialize found more than one "
201			"explicit \n"
202			"\tvan der Waals interaction for atom types %s - %s\n",
203			atype1->getName().c_str(), atype2->getName().c_str());
204			painCave.severity = OPENMD_ERROR;
205			painCave.isFatal = 1;
206			simError();
207			}
208			// We found an explicit RepulsivePower interaction.
209			// override all other vdw entries for this pair of atom types:
210			set<NonBondedInteraction*>::iterator it;
211			for (it = interactions_[key].begin();
212			it != interactions_[key].end(); ++it) {
213			InteractionFamily ifam = (*it)->getFamily();
214			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
215			}
216			interactions_[key].insert(repulsivePower_);
217			vdwExplicit = true;
218			}
219	gezelter	1535
220	jmichalk	1656
221	gezelter	1535	if (nbiType->isEAM()) {
222			// We found an explicit EAM interaction.
223			// override all other metallic entries for this pair of atom types:
224			set<NonBondedInteraction*>::iterator it;
225			for (it = interactions_[key].begin();
226			it != interactions_[key].end(); ++it) {
227			InteractionFamily ifam = (*it)->getFamily();
228			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
229			}
230			interactions_[key].insert(eam_);
231			metExplicit = true;
232	gezelter	1502	}
233	gezelter	1535
234			if (nbiType->isSC()) {
235			if (metExplicit) {
236			sprintf( painCave.errMsg,
237			"InteractionManager::initialize found more than one "
238			"explicit\n"
239			"\tmetallic interaction for atom types %s - %s\n",
240			atype1->getName().c_str(), atype2->getName().c_str());
241			painCave.severity = OPENMD_ERROR;
242			painCave.isFatal = 1;
243			simError();
244			}
245			// We found an explicit Sutton-Chen interaction.
246			// override all other metallic entries for this pair of atom types:
247			set<NonBondedInteraction*>::iterator it;
248			for (it = interactions_[key].begin();
249			it != interactions_[key].end(); ++it) {
250			InteractionFamily ifam = (*it)->getFamily();
251			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
252			}
253			interactions_[key].insert(sc_);
254			metExplicit = true;
255	gezelter	1502	}
256	gezelter	1535
257			if (nbiType->isMAW()) {
258			if (vdwExplicit) {
259			sprintf( painCave.errMsg,
260			"InteractionManager::initialize found more than one "
261			"explicit\n"
262			"\tvan der Waals interaction for atom types %s - %s\n",
263			atype1->getName().c_str(), atype2->getName().c_str());
264			painCave.severity = OPENMD_ERROR;
265			painCave.isFatal = 1;
266			simError();
267			}
268			// We found an explicit MAW interaction.
269			// override all other vdw entries for this pair of atom types:
270			set<NonBondedInteraction*>::iterator it;
271			for (it = interactions_[key].begin();
272			it != interactions_[key].end(); ++it) {
273			InteractionFamily ifam = (*it)->getFamily();
274			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
275			}
276			interactions_[key].insert(maw_);
277			vdwExplicit = true;
278			}
279	gezelter	1502	}
280			}
281			}
282
283	gezelter	1535
284	gezelter	1583	// Make sure every pair of atom types in this simulation has a
285			// non-bonded interaction. If not, just inform the user.
286	gezelter	1535
287			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
288			set<AtomType*>::iterator it, jt;
289	gezelter	1583
290	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
291			atype1 = (*it);
292	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
293	gezelter	1535	atype2 = (*jt);
294	gezelter	1502	key = make_pair(atype1, atype2);
295
296			if (interactions_[key].size() == 0) {
297			sprintf( painCave.errMsg,
298	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
299			"\tinteraction for atom types %s - %s\n"
300			"\tProceeding without this interaction.\n",
301	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
302			painCave.severity = OPENMD_INFO;
303	gezelter	1583	painCave.isFatal = 0;
304	gezelter	1502	simError();
305			}
306			}
307			}
308	gezelter	1535
309			initialized_ = true;
310			}
311	gezelter	1584
312			void InteractionManager::setCutoffRadius(RealType rcut) {
313	gezelter	1587
314	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
315	gezelter	1586	eam_->setCutoffRadius(rcut);
316	gezelter	1584	}
317
318	gezelter	1545	void InteractionManager::doPrePair(InteractionData idat){
319	gezelter	1502
320			if (!initialized_) initialize();
321	gezelter	1545
322	gezelter	1587	// excluded interaction, so just return
323			if (idat.excluded) return;
324
325	gezelter	1504	set<NonBondedInteraction*>::iterator it;
326
327	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
328			it != interactions_[ idat.atypes ].end(); ++it){
329	gezelter	1504	if ((*it)->getFamily() == METALLIC_FAMILY) {
330	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
331	gezelter	1504	}
332			}
333	gezelter	1502
334			return;
335			}
336	gezelter	1504
337	gezelter	1545	void InteractionManager::doPreForce(SelfData sdat){
338	gezelter	1502
339	gezelter	1504	if (!initialized_) initialize();
340	gezelter	1545
341			pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
342	gezelter	1504	set<NonBondedInteraction*>::iterator it;
343	gezelter	1502
344	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
345			if ((*it)->getFamily() == METALLIC_FAMILY) {
346	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
347	gezelter	1504	}
348			}
349
350	gezelter	1502	return;
351			}
352
353	gezelter	1545	void InteractionManager::doPair(InteractionData idat){
354	gezelter	1504
355	gezelter	1502	if (!initialized_) initialize();
356	gezelter	1587
357	gezelter	1502	set<NonBondedInteraction*>::iterator it;
358
359	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
360	gezelter	1587	it != interactions_[ idat.atypes ].end(); ++it) {
361	gezelter	1502
362	gezelter	1587	// electrostatics still has to worry about indirect
363			// contributions from excluded pairs of atoms:
364	gezelter	1502
365	gezelter	1587	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
366			(*it)->calcForce(idat);
367	gezelter	1504	}
368			}
369	gezelter	1502
370	gezelter	1504	return;
371	gezelter	1502	}
372
373	gezelter	1545	void InteractionManager::doSelfCorrection(SelfData sdat){
374	gezelter	1502
375			if (!initialized_) initialize();
376	gezelter	1504
377	gezelter	1545	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
378	gezelter	1504	set<NonBondedInteraction*>::iterator it;
379	gezelter	1502
380	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
381			if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
382	gezelter	1545	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
383	gezelter	1504	}
384			}
385	gezelter	1536
386	gezelter	1504	return;
387	gezelter	1502	}
388
389	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
390			if (!initialized_) initialize();
391	gezelter	1755
392	gezelter	1505	AtomType* atype = typeMap_[*atid];
393
394			pair<AtomType, AtomType> key = make_pair(atype, atype);
395			set<NonBondedInteraction*>::iterator it;
396			RealType cutoff = 0.0;
397
398			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
399	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
400	gezelter	1505	return cutoff;
401			}
402
403	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
404			if (!initialized_) initialize();
405
406			pair<AtomType, AtomType> key = make_pair(atype, atype);
407			set<NonBondedInteraction*>::iterator it;
408			RealType cutoff = 0.0;
409
410			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
411	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
412	gezelter	1528	return cutoff;
413			}
414	gezelter	1502	} //end namespace OpenMD