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;
    pair<set<NonBondedInteraction*>::iterator, bool> ret;
    
    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;
        
        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::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:	1868
Committed:	Tue Apr 30 15:56:54 2013 UTC (12 years ago) by gezelter
File size:	15384 byte(s)
Log Message:	CLearing out some memory leaks
#	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			pair<set<NonBondedInteraction*>::iterator, bool> ret;
97
98			for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
99			atype1 = atomTypes->nextType(i1)) {
100
101			// add it to the map:
102
103			pair<map<int,AtomType*>::iterator,bool> ret;
104	gezelter	1710	ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
105	gezelter	1502	if (ret.second == false) {
106			sprintf( painCave.errMsg,
107			"InteractionManager already had a previous entry with ident %d\n",
108	gezelter	1710	atype1->getIdent());
109	gezelter	1502	painCave.severity = OPENMD_INFO;
110			painCave.isFatal = 0;
111			simError();
112			}
113			}
114
115			// Now, iterate over all known types and add to the interaction map:
116
117			map<int, AtomType*>::iterator it1, it2;
118			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
119			atype1 = (*it1).second;
120
121			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
122			atype2 = (*it2).second;
123
124			bool vdwExplicit = false;
125			bool metExplicit = false;
126	gezelter	1825	// bool hbExplicit = false;
127	gezelter	1502
128			key = make_pair(atype1, atype2);
129
130			if (atype1->isLennardJones() && atype2->isLennardJones()) {
131			interactions_[key].insert(lj_);
132			}
133			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
134			interactions_[key].insert(electrostatic_);
135			}
136			if (atype1->isSticky() && atype2->isSticky() ) {
137			interactions_[key].insert(sticky_);
138			}
139			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
140			interactions_[key].insert(sticky_);
141			}
142			if (atype1->isEAM() && atype2->isEAM() ) {
143			interactions_[key].insert(eam_);
144			}
145			if (atype1->isSC() && atype2->isSC() ) {
146			interactions_[key].insert(sc_);
147			}
148			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
149			interactions_[key].insert(gb_);
150			}
151			if ((atype1->isGayBerne() && atype2->isLennardJones())
152			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
153			interactions_[key].insert(gb_);
154			}
155
156			// look for an explicitly-set non-bonded interaction type using the
157			// two atom types.
158			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
159	gezelter	1535
160			if (nbiType != NULL) {
161	gezelter	1502
162	gezelter	1535	if (nbiType->isLennardJones()) {
163			// We found an explicit Lennard-Jones interaction.
164			// override all other vdw entries for this pair of atom types:
165			set<NonBondedInteraction*>::iterator it;
166			for (it = interactions_[key].begin();
167			it != interactions_[key].end(); ++it) {
168			InteractionFamily ifam = (*it)->getFamily();
169			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
170			}
171			interactions_[key].insert(lj_);
172			vdwExplicit = true;
173	gezelter	1502	}
174	gezelter	1535
175			if (nbiType->isMorse()) {
176			if (vdwExplicit) {
177			sprintf( painCave.errMsg,
178			"InteractionManager::initialize found more than one "
179			"explicit \n"
180			"\tvan der Waals interaction for atom types %s - %s\n",
181			atype1->getName().c_str(), atype2->getName().c_str());
182			painCave.severity = OPENMD_ERROR;
183			painCave.isFatal = 1;
184			simError();
185			}
186			// We found an explicit Morse interaction.
187			// override all other vdw entries for this pair of atom types:
188			set<NonBondedInteraction*>::iterator it;
189			for (it = interactions_[key].begin();
190			it != interactions_[key].end(); ++it) {
191			InteractionFamily ifam = (*it)->getFamily();
192			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
193			}
194			interactions_[key].insert(morse_);
195			vdwExplicit = true;
196	gezelter	1502	}
197	jmichalk	1656
198			if (nbiType->isRepulsivePower()) {
199			if (vdwExplicit) {
200			sprintf( painCave.errMsg,
201			"InteractionManager::initialize found more than one "
202			"explicit \n"
203			"\tvan der Waals interaction for atom types %s - %s\n",
204			atype1->getName().c_str(), atype2->getName().c_str());
205			painCave.severity = OPENMD_ERROR;
206			painCave.isFatal = 1;
207			simError();
208			}
209			// We found an explicit RepulsivePower interaction.
210			// override all other vdw entries for this pair of atom types:
211			set<NonBondedInteraction*>::iterator it;
212			for (it = interactions_[key].begin();
213			it != interactions_[key].end(); ++it) {
214			InteractionFamily ifam = (*it)->getFamily();
215			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
216			}
217			interactions_[key].insert(repulsivePower_);
218			vdwExplicit = true;
219			}
220	gezelter	1535
221	jmichalk	1656
222	gezelter	1535	if (nbiType->isEAM()) {
223			// We found an explicit EAM interaction.
224			// override all other metallic entries for this pair of atom types:
225			set<NonBondedInteraction*>::iterator it;
226			for (it = interactions_[key].begin();
227			it != interactions_[key].end(); ++it) {
228			InteractionFamily ifam = (*it)->getFamily();
229			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
230			}
231			interactions_[key].insert(eam_);
232			metExplicit = true;
233	gezelter	1502	}
234	gezelter	1535
235			if (nbiType->isSC()) {
236			if (metExplicit) {
237			sprintf( painCave.errMsg,
238			"InteractionManager::initialize found more than one "
239			"explicit\n"
240			"\tmetallic interaction for atom types %s - %s\n",
241			atype1->getName().c_str(), atype2->getName().c_str());
242			painCave.severity = OPENMD_ERROR;
243			painCave.isFatal = 1;
244			simError();
245			}
246			// We found an explicit Sutton-Chen interaction.
247			// override all other metallic entries for this pair of atom types:
248			set<NonBondedInteraction*>::iterator it;
249			for (it = interactions_[key].begin();
250			it != interactions_[key].end(); ++it) {
251			InteractionFamily ifam = (*it)->getFamily();
252			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
253			}
254			interactions_[key].insert(sc_);
255			metExplicit = true;
256	gezelter	1502	}
257	gezelter	1535
258			if (nbiType->isMAW()) {
259			if (vdwExplicit) {
260			sprintf( painCave.errMsg,
261			"InteractionManager::initialize found more than one "
262			"explicit\n"
263			"\tvan der Waals interaction for atom types %s - %s\n",
264			atype1->getName().c_str(), atype2->getName().c_str());
265			painCave.severity = OPENMD_ERROR;
266			painCave.isFatal = 1;
267			simError();
268			}
269			// We found an explicit MAW interaction.
270			// override all other vdw entries for this pair of atom types:
271			set<NonBondedInteraction*>::iterator it;
272			for (it = interactions_[key].begin();
273			it != interactions_[key].end(); ++it) {
274			InteractionFamily ifam = (*it)->getFamily();
275			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
276			}
277			interactions_[key].insert(maw_);
278			vdwExplicit = true;
279			}
280	gezelter	1502	}
281			}
282			}
283
284	gezelter	1535
285	gezelter	1583	// Make sure every pair of atom types in this simulation has a
286			// non-bonded interaction. If not, just inform the user.
287	gezelter	1535
288			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
289			set<AtomType*>::iterator it, jt;
290	gezelter	1583
291	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
292			atype1 = (*it);
293	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
294	gezelter	1535	atype2 = (*jt);
295	gezelter	1502	key = make_pair(atype1, atype2);
296
297			if (interactions_[key].size() == 0) {
298			sprintf( painCave.errMsg,
299	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
300			"\tinteraction for atom types %s - %s\n"
301			"\tProceeding without this interaction.\n",
302	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
303			painCave.severity = OPENMD_INFO;
304	gezelter	1583	painCave.isFatal = 0;
305	gezelter	1502	simError();
306			}
307			}
308			}
309	gezelter	1535
310			initialized_ = true;
311			}
312	gezelter	1584
313			void InteractionManager::setCutoffRadius(RealType rcut) {
314	gezelter	1587
315	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
316	gezelter	1586	eam_->setCutoffRadius(rcut);
317	gezelter	1584	}
318
319	gezelter	1545	void InteractionManager::doPrePair(InteractionData idat){
320	gezelter	1502
321			if (!initialized_) initialize();
322	gezelter	1545
323	gezelter	1587	// excluded interaction, so just return
324			if (idat.excluded) return;
325
326	gezelter	1504	set<NonBondedInteraction*>::iterator it;
327
328	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
329			it != interactions_[ idat.atypes ].end(); ++it){
330	gezelter	1504	if ((*it)->getFamily() == METALLIC_FAMILY) {
331	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
332	gezelter	1504	}
333			}
334	gezelter	1502
335			return;
336			}
337	gezelter	1504
338	gezelter	1545	void InteractionManager::doPreForce(SelfData sdat){
339	gezelter	1502
340	gezelter	1504	if (!initialized_) initialize();
341	gezelter	1545
342			pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
343	gezelter	1504	set<NonBondedInteraction*>::iterator it;
344	gezelter	1502
345	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
346			if ((*it)->getFamily() == METALLIC_FAMILY) {
347	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
348	gezelter	1504	}
349			}
350
351	gezelter	1502	return;
352			}
353
354	gezelter	1545	void InteractionManager::doPair(InteractionData idat){
355	gezelter	1504
356	gezelter	1502	if (!initialized_) initialize();
357	gezelter	1587
358	gezelter	1502	set<NonBondedInteraction*>::iterator it;
359
360	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
361	gezelter	1587	it != interactions_[ idat.atypes ].end(); ++it) {
362	gezelter	1502
363	gezelter	1587	// electrostatics still has to worry about indirect
364			// contributions from excluded pairs of atoms:
365	gezelter	1502
366	gezelter	1587	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
367			(*it)->calcForce(idat);
368	gezelter	1504	}
369			}
370	gezelter	1502
371	gezelter	1504	return;
372	gezelter	1502	}
373
374	gezelter	1545	void InteractionManager::doSelfCorrection(SelfData sdat){
375	gezelter	1502
376			if (!initialized_) initialize();
377	gezelter	1504
378	gezelter	1545	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
379	gezelter	1504	set<NonBondedInteraction*>::iterator it;
380	gezelter	1502
381	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
382			if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
383	gezelter	1545	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
384	gezelter	1504	}
385			}
386	gezelter	1536
387	gezelter	1504	return;
388	gezelter	1502	}
389
390	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
391			if (!initialized_) initialize();
392	gezelter	1755
393	gezelter	1505	AtomType* atype = typeMap_[*atid];
394
395			pair<AtomType, AtomType> key = make_pair(atype, atype);
396			set<NonBondedInteraction*>::iterator it;
397			RealType cutoff = 0.0;
398
399			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
400	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
401	gezelter	1505	return cutoff;
402			}
403
404	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
405			if (!initialized_) initialize();
406
407			pair<AtomType, AtomType> key = make_pair(atype, atype);
408			set<NonBondedInteraction*>::iterator it;
409			RealType cutoff = 0.0;
410
411			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
412	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
413	gezelter	1528	return cutoff;
414			}
415	gezelter	1502	} //end namespace OpenMD