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() {

    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::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:	1755
Committed:	Thu Jun 14 01:58:35 2012 UTC (12 years, 10 months ago) by gezelter
File size:	15275 byte(s)
Log Message:	general bugfixes
#	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	gezelter	1755
64			if (initialized_) return;
65
66	gezelter	1535	ForceField* forceField_ = info_->getForceField();
67
68	gezelter	1502	lj_->setForceField(forceField_);
69			gb_->setForceField(forceField_);
70			sticky_->setForceField(forceField_);
71			eam_->setForceField(forceField_);
72			sc_->setForceField(forceField_);
73			morse_->setForceField(forceField_);
74	gezelter	1584	electrostatic_->setSimInfo(info_);
75	gezelter	1502	electrostatic_->setForceField(forceField_);
76	gezelter	1532	maw_->setForceField(forceField_);
77	jmichalk	1656	repulsivePower_->setForceField(forceField_);
78	gezelter	1502
79			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
80			ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
81			AtomType* atype1;
82			AtomType* atype2;
83			pair<AtomType, AtomType> key;
84			pair<set<NonBondedInteraction*>::iterator, bool> ret;
85
86			for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
87			atype1 = atomTypes->nextType(i1)) {
88
89			// add it to the map:
90
91			pair<map<int,AtomType*>::iterator,bool> ret;
92	gezelter	1710	ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
93	gezelter	1502	if (ret.second == false) {
94			sprintf( painCave.errMsg,
95			"InteractionManager already had a previous entry with ident %d\n",
96	gezelter	1710	atype1->getIdent());
97	gezelter	1502	painCave.severity = OPENMD_INFO;
98			painCave.isFatal = 0;
99			simError();
100			}
101			}
102
103			// Now, iterate over all known types and add to the interaction map:
104
105			map<int, AtomType*>::iterator it1, it2;
106			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
107			atype1 = (*it1).second;
108
109			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
110			atype2 = (*it2).second;
111
112			bool vdwExplicit = false;
113			bool metExplicit = false;
114			bool hbExplicit = false;
115
116			key = make_pair(atype1, atype2);
117
118			if (atype1->isLennardJones() && atype2->isLennardJones()) {
119			interactions_[key].insert(lj_);
120			}
121			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
122			interactions_[key].insert(electrostatic_);
123			}
124			if (atype1->isSticky() && atype2->isSticky() ) {
125			interactions_[key].insert(sticky_);
126			}
127			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
128			interactions_[key].insert(sticky_);
129			}
130			if (atype1->isEAM() && atype2->isEAM() ) {
131			interactions_[key].insert(eam_);
132			}
133			if (atype1->isSC() && atype2->isSC() ) {
134			interactions_[key].insert(sc_);
135			}
136			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
137			interactions_[key].insert(gb_);
138			}
139			if ((atype1->isGayBerne() && atype2->isLennardJones())
140			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
141			interactions_[key].insert(gb_);
142			}
143
144			// look for an explicitly-set non-bonded interaction type using the
145			// two atom types.
146			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
147	gezelter	1535
148			if (nbiType != NULL) {
149	gezelter	1502
150	gezelter	1535	if (nbiType->isLennardJones()) {
151			// We found an explicit Lennard-Jones interaction.
152			// override all other vdw entries for this pair of atom types:
153			set<NonBondedInteraction*>::iterator it;
154			for (it = interactions_[key].begin();
155			it != interactions_[key].end(); ++it) {
156			InteractionFamily ifam = (*it)->getFamily();
157			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
158			}
159			interactions_[key].insert(lj_);
160			vdwExplicit = true;
161	gezelter	1502	}
162	gezelter	1535
163			if (nbiType->isMorse()) {
164			if (vdwExplicit) {
165			sprintf( painCave.errMsg,
166			"InteractionManager::initialize found more than one "
167			"explicit \n"
168			"\tvan der Waals interaction for atom types %s - %s\n",
169			atype1->getName().c_str(), atype2->getName().c_str());
170			painCave.severity = OPENMD_ERROR;
171			painCave.isFatal = 1;
172			simError();
173			}
174			// We found an explicit Morse interaction.
175			// override all other vdw entries for this pair of atom types:
176			set<NonBondedInteraction*>::iterator it;
177			for (it = interactions_[key].begin();
178			it != interactions_[key].end(); ++it) {
179			InteractionFamily ifam = (*it)->getFamily();
180			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
181			}
182			interactions_[key].insert(morse_);
183			vdwExplicit = true;
184	gezelter	1502	}
185	jmichalk	1656
186			if (nbiType->isRepulsivePower()) {
187			if (vdwExplicit) {
188			sprintf( painCave.errMsg,
189			"InteractionManager::initialize found more than one "
190			"explicit \n"
191			"\tvan der Waals interaction for atom types %s - %s\n",
192			atype1->getName().c_str(), atype2->getName().c_str());
193			painCave.severity = OPENMD_ERROR;
194			painCave.isFatal = 1;
195			simError();
196			}
197			// We found an explicit RepulsivePower interaction.
198			// override all other vdw entries for this pair of atom types:
199			set<NonBondedInteraction*>::iterator it;
200			for (it = interactions_[key].begin();
201			it != interactions_[key].end(); ++it) {
202			InteractionFamily ifam = (*it)->getFamily();
203			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
204			}
205			interactions_[key].insert(repulsivePower_);
206			vdwExplicit = true;
207			}
208	gezelter	1535
209	jmichalk	1656
210	gezelter	1535	if (nbiType->isEAM()) {
211			// We found an explicit EAM interaction.
212			// override all other metallic entries for this pair of atom types:
213			set<NonBondedInteraction*>::iterator it;
214			for (it = interactions_[key].begin();
215			it != interactions_[key].end(); ++it) {
216			InteractionFamily ifam = (*it)->getFamily();
217			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
218			}
219			interactions_[key].insert(eam_);
220			metExplicit = true;
221	gezelter	1502	}
222	gezelter	1535
223			if (nbiType->isSC()) {
224			if (metExplicit) {
225			sprintf( painCave.errMsg,
226			"InteractionManager::initialize found more than one "
227			"explicit\n"
228			"\tmetallic interaction for atom types %s - %s\n",
229			atype1->getName().c_str(), atype2->getName().c_str());
230			painCave.severity = OPENMD_ERROR;
231			painCave.isFatal = 1;
232			simError();
233			}
234			// We found an explicit Sutton-Chen interaction.
235			// override all other metallic entries for this pair of atom types:
236			set<NonBondedInteraction*>::iterator it;
237			for (it = interactions_[key].begin();
238			it != interactions_[key].end(); ++it) {
239			InteractionFamily ifam = (*it)->getFamily();
240			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
241			}
242			interactions_[key].insert(sc_);
243			metExplicit = true;
244	gezelter	1502	}
245	gezelter	1535
246			if (nbiType->isMAW()) {
247			if (vdwExplicit) {
248			sprintf( painCave.errMsg,
249			"InteractionManager::initialize found more than one "
250			"explicit\n"
251			"\tvan der Waals interaction for atom types %s - %s\n",
252			atype1->getName().c_str(), atype2->getName().c_str());
253			painCave.severity = OPENMD_ERROR;
254			painCave.isFatal = 1;
255			simError();
256			}
257			// We found an explicit MAW interaction.
258			// override all other vdw entries for this pair of atom types:
259			set<NonBondedInteraction*>::iterator it;
260			for (it = interactions_[key].begin();
261			it != interactions_[key].end(); ++it) {
262			InteractionFamily ifam = (*it)->getFamily();
263			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
264			}
265			interactions_[key].insert(maw_);
266			vdwExplicit = true;
267			}
268	gezelter	1502	}
269			}
270			}
271
272	gezelter	1535
273	gezelter	1583	// Make sure every pair of atom types in this simulation has a
274			// non-bonded interaction. If not, just inform the user.
275	gezelter	1535
276			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
277			set<AtomType*>::iterator it, jt;
278	gezelter	1583
279	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
280			atype1 = (*it);
281	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
282	gezelter	1535	atype2 = (*jt);
283	gezelter	1502	key = make_pair(atype1, atype2);
284
285			if (interactions_[key].size() == 0) {
286			sprintf( painCave.errMsg,
287	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
288			"\tinteraction for atom types %s - %s\n"
289			"\tProceeding without this interaction.\n",
290	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
291			painCave.severity = OPENMD_INFO;
292	gezelter	1583	painCave.isFatal = 0;
293	gezelter	1502	simError();
294			}
295			}
296			}
297	gezelter	1535
298			initialized_ = true;
299			}
300	gezelter	1584
301			void InteractionManager::setCutoffRadius(RealType rcut) {
302	gezelter	1587
303	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
304	gezelter	1586	eam_->setCutoffRadius(rcut);
305	gezelter	1584	}
306
307			void InteractionManager::setSwitchingRadius(RealType rswitch) {
308			electrostatic_->setSwitchingRadius(rswitch);
309			}
310	gezelter	1502
311	gezelter	1545	void InteractionManager::doPrePair(InteractionData idat){
312	gezelter	1502
313			if (!initialized_) initialize();
314	gezelter	1545
315	gezelter	1587	// excluded interaction, so just return
316			if (idat.excluded) return;
317
318	gezelter	1504	set<NonBondedInteraction*>::iterator it;
319
320	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
321			it != interactions_[ idat.atypes ].end(); ++it){
322	gezelter	1504	if ((*it)->getFamily() == METALLIC_FAMILY) {
323	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
324	gezelter	1504	}
325			}
326	gezelter	1502
327			return;
328			}
329	gezelter	1504
330	gezelter	1545	void InteractionManager::doPreForce(SelfData sdat){
331	gezelter	1502
332	gezelter	1504	if (!initialized_) initialize();
333	gezelter	1545
334			pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
335	gezelter	1504	set<NonBondedInteraction*>::iterator it;
336	gezelter	1502
337	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
338			if ((*it)->getFamily() == METALLIC_FAMILY) {
339	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
340	gezelter	1504	}
341			}
342
343	gezelter	1502	return;
344			}
345
346	gezelter	1545	void InteractionManager::doPair(InteractionData idat){
347	gezelter	1504
348	gezelter	1502	if (!initialized_) initialize();
349	gezelter	1587
350	gezelter	1502	set<NonBondedInteraction*>::iterator it;
351
352	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
353	gezelter	1587	it != interactions_[ idat.atypes ].end(); ++it) {
354	gezelter	1502
355	gezelter	1587	// electrostatics still has to worry about indirect
356			// contributions from excluded pairs of atoms:
357	gezelter	1502
358	gezelter	1587	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
359			(*it)->calcForce(idat);
360	gezelter	1504	}
361			}
362	gezelter	1502
363	gezelter	1504	return;
364	gezelter	1502	}
365
366	gezelter	1545	void InteractionManager::doSelfCorrection(SelfData sdat){
367	gezelter	1502
368			if (!initialized_) initialize();
369	gezelter	1504
370	gezelter	1545	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
371	gezelter	1504	set<NonBondedInteraction*>::iterator it;
372	gezelter	1502
373	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
374			if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
375	gezelter	1545	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
376	gezelter	1504	}
377			}
378	gezelter	1536
379	gezelter	1504	return;
380	gezelter	1502	}
381
382	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
383			if (!initialized_) initialize();
384	gezelter	1755
385	gezelter	1505	AtomType* atype = typeMap_[*atid];
386
387			pair<AtomType, AtomType> key = make_pair(atype, atype);
388			set<NonBondedInteraction*>::iterator it;
389			RealType cutoff = 0.0;
390
391			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
392	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
393	gezelter	1505	return cutoff;
394			}
395
396	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
397			if (!initialized_) initialize();
398
399			pair<AtomType, AtomType> key = make_pair(atype, atype);
400			set<NonBondedInteraction*>::iterator it;
401			RealType cutoff = 0.0;
402
403			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
404	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
405	gezelter	1528	return cutoff;
406			}
407	gezelter	1502	} //end namespace OpenMD