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
#	Content
1	/*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "nonbonded/InteractionManager.hpp"
44
45	namespace OpenMD {
46
47	InteractionManager::InteractionManager() {
48
49	initialized_ = false;
50
51	lj_ = new LJ();
52	gb_ = new GB();
53	sticky_ = new Sticky();
54	morse_ = new Morse();
55	repulsivePower_ = new RepulsivePower();
56	eam_ = new EAM();
57	sc_ = new SC();
58	electrostatic_ = new Electrostatic();
59	maw_ = new MAW();
60	}
61
62	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	void InteractionManager::initialize() {
75
76	if (initialized_) return;
77
78	ForceField* forceField_ = info_->getForceField();
79
80	lj_->setForceField(forceField_);
81	gb_->setForceField(forceField_);
82	sticky_->setForceField(forceField_);
83	eam_->setForceField(forceField_);
84	sc_->setForceField(forceField_);
85	morse_->setForceField(forceField_);
86	electrostatic_->setSimInfo(info_);
87	electrostatic_->setForceField(forceField_);
88	maw_->setForceField(forceField_);
89	repulsivePower_->setForceField(forceField_);
90
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	ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
105	if (ret.second == false) {
106	sprintf( painCave.errMsg,
107	"InteractionManager already had a previous entry with ident %d\n",
108	atype1->getIdent());
109	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	// bool hbExplicit = false;
127
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
160	if (nbiType != NULL) {
161
162	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	}
174
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	}
197
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
221
222	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	}
234
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	}
257
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	}
281	}
282	}
283
284
285	// Make sure every pair of atom types in this simulation has a
286	// non-bonded interaction. If not, just inform the user.
287
288	set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
289	set<AtomType*>::iterator it, jt;
290
291	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
292	atype1 = (*it);
293	for (jt = it; jt != simTypes.end(); ++jt) {
294	atype2 = (*jt);
295	key = make_pair(atype1, atype2);
296
297	if (interactions_[key].size() == 0) {
298	sprintf( painCave.errMsg,
299	"InteractionManager could not find a matching non-bonded\n"
300	"\tinteraction for atom types %s - %s\n"
301	"\tProceeding without this interaction.\n",
302	atype1->getName().c_str(), atype2->getName().c_str());
303	painCave.severity = OPENMD_INFO;
304	painCave.isFatal = 0;
305	simError();
306	}
307	}
308	}
309
310	initialized_ = true;
311	}
312
313	void InteractionManager::setCutoffRadius(RealType rcut) {
314
315	electrostatic_->setCutoffRadius(rcut);
316	eam_->setCutoffRadius(rcut);
317	}
318
319	void InteractionManager::doPrePair(InteractionData idat){
320
321	if (!initialized_) initialize();
322
323	// excluded interaction, so just return
324	if (idat.excluded) return;
325
326	set<NonBondedInteraction*>::iterator it;
327
328	for (it = interactions_[ idat.atypes ].begin();
329	it != interactions_[ idat.atypes ].end(); ++it){
330	if ((*it)->getFamily() == METALLIC_FAMILY) {
331	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
332	}
333	}
334
335	return;
336	}
337
338	void InteractionManager::doPreForce(SelfData sdat){
339
340	if (!initialized_) initialize();
341
342	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
343	set<NonBondedInteraction*>::iterator it;
344
345	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
346	if ((*it)->getFamily() == METALLIC_FAMILY) {
347	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
348	}
349	}
350
351	return;
352	}
353
354	void InteractionManager::doPair(InteractionData idat){
355
356	if (!initialized_) initialize();
357
358	set<NonBondedInteraction*>::iterator it;
359
360	for (it = interactions_[ idat.atypes ].begin();
361	it != interactions_[ idat.atypes ].end(); ++it) {
362
363	// electrostatics still has to worry about indirect
364	// contributions from excluded pairs of atoms:
365
366	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
367	(*it)->calcForce(idat);
368	}
369	}
370
371	return;
372	}
373
374	void InteractionManager::doSelfCorrection(SelfData sdat){
375
376	if (!initialized_) initialize();
377
378	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
379	set<NonBondedInteraction*>::iterator it;
380
381	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
382	if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
383	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
384	}
385	}
386
387	return;
388	}
389
390	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
391	if (!initialized_) initialize();
392
393	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	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
401	return cutoff;
402	}
403
404	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	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
413	return cutoff;
414	}
415	} //end namespace OpenMD