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);

        iHash_[key] = 0;
        
        if (atype1->isLennardJones() && atype2->isLennardJones()) {
          interactions_[key].insert(lj_);
          iHash_[key] |= LJ_PAIR;
        }
        if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
          interactions_[key].insert(electrostatic_);
          iHash_[key] |= ELECTROSTATIC_PAIR;
        }
        if (atype1->isSticky() && atype2->isSticky() ) {
          interactions_[key].insert(sticky_);
          iHash_[key] |= STICKY_PAIR;
        }
        if (atype1->isStickyPower() && atype2->isStickyPower() ) {
          interactions_[key].insert(sticky_);
          iHash_[key] |= STICKY_PAIR;
        }
        if (atype1->isEAM() && atype2->isEAM() ) {
          interactions_[key].insert(eam_);
          iHash_[key] |= EAM_PAIR;
        }
        if (atype1->isSC() && atype2->isSC() ) {
          interactions_[key].insert(sc_);
          iHash_[key] |= SC_PAIR;
        }
        if (atype1->isGayBerne() && atype2->isGayBerne() ) {
          interactions_[key].insert(gb_);
          iHash_[key] |= GB_PAIR;
        }
        if ((atype1->isGayBerne() && atype2->isLennardJones())
            || (atype1->isLennardJones() && atype2->isGayBerne())) {
          interactions_[key].insert(gb_);
          iHash_[key] |= GB_PAIR;
        } 
        
        // 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);
                // work on iHash here;
              }
            }
            interactions_[key].insert(lj_);
            iHash_[key] |= LJ_PAIR;
            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);
                // work on iHash here;
              }
            }
            interactions_[key].insert(morse_);
            iHash_[key] |= MORSE_PAIR;
            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);
                // work on iHash here;
              }
            }
            interactions_[key].insert(repulsivePower_);
            iHash_[key] |= REPULSIVEPOWER_PAIR;
            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);
                // work on iHash here;
              }
            }
            interactions_[key].insert(eam_);
            iHash_[key] |= EAM_PAIR;
            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);
                // work on iHash here;
              }
            }
            interactions_[key].insert(sc_);
            iHash_[key] |= SC_PAIR;
            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);
                // work on iHash here;
              }
            }
            interactions_[key].insert(maw_);
            iHash_[key] |= MAW_PAIR;
            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;

    int& iHash = iHash_[idat.atypes];

    if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
    if ((iHash & SC_PAIR) != 0)  sc_->calcDensity(idat);

    // 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);

    int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];

    if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
    if ((iHash & SC_PAIR) != 0)  sc_->calcFunctional(sdat);

    // 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();

    int& iHash = iHash_[idat.atypes];

    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
       
    // electrostatics still has to worry about indirect
    // contributions from excluded pairs of atoms, but nothing else does:

    if (idat.excluded) return; 

    if ((iHash & LJ_PAIR) != 0)             lj_->calcForce(idat);
    if ((iHash & GB_PAIR) != 0)             gb_->calcForce(idat);
    if ((iHash & STICKY_PAIR) != 0)         sticky_->calcForce(idat);
    if ((iHash & MORSE_PAIR) != 0)          morse_->calcForce(idat);
    if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
    if ((iHash & EAM_PAIR) != 0)            eam_->calcForce(idat);
    if ((iHash & SC_PAIR) != 0)             sc_->calcForce(idat);
    if ((iHash & MAW_PAIR) != 0)            maw_->calcForce(idat);

    // 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();
    
    int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];

    if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);


    // 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:	1877
Committed:	Thu Jun 6 15:43:35 2013 UTC (11 years, 10 months ago) by gezelter
File size:	17739 byte(s)
Log Message:	New electrostatic method, starting to do some performance tuning.
#	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
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	ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
104	if (ret.second == false) {
105	sprintf( painCave.errMsg,
106	"InteractionManager already had a previous entry with ident %d\n",
107	atype1->getIdent());
108	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
123	key = make_pair(atype1, atype2);
124
125	iHash_[key] = 0;
126
127	if (atype1->isLennardJones() && atype2->isLennardJones()) {
128	interactions_[key].insert(lj_);
129	iHash_[key] \|= LJ_PAIR;
130	}
131	if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
132	interactions_[key].insert(electrostatic_);
133	iHash_[key] \|= ELECTROSTATIC_PAIR;
134	}
135	if (atype1->isSticky() && atype2->isSticky() ) {
136	interactions_[key].insert(sticky_);
137	iHash_[key] \|= STICKY_PAIR;
138	}
139	if (atype1->isStickyPower() && atype2->isStickyPower() ) {
140	interactions_[key].insert(sticky_);
141	iHash_[key] \|= STICKY_PAIR;
142	}
143	if (atype1->isEAM() && atype2->isEAM() ) {
144	interactions_[key].insert(eam_);
145	iHash_[key] \|= EAM_PAIR;
146	}
147	if (atype1->isSC() && atype2->isSC() ) {
148	interactions_[key].insert(sc_);
149	iHash_[key] \|= SC_PAIR;
150	}
151	if (atype1->isGayBerne() && atype2->isGayBerne() ) {
152	interactions_[key].insert(gb_);
153	iHash_[key] \|= GB_PAIR;
154	}
155	if ((atype1->isGayBerne() && atype2->isLennardJones())
156	\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
157	interactions_[key].insert(gb_);
158	iHash_[key] \|= GB_PAIR;
159	}
160
161	// look for an explicitly-set non-bonded interaction type using the
162	// two atom types.
163	NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
164
165	if (nbiType != NULL) {
166
167	bool vdwExplicit = false;
168	bool metExplicit = false;
169	// bool hbExplicit = false;
170
171	if (nbiType->isLennardJones()) {
172	// We found an explicit Lennard-Jones interaction.
173	// override all other vdw entries for this pair of atom types:
174	set<NonBondedInteraction*>::iterator it;
175	for (it = interactions_[key].begin();
176	it != interactions_[key].end(); ++it) {
177	InteractionFamily ifam = (*it)->getFamily();
178	if (ifam == VANDERWAALS_FAMILY) {
179	interactions_[key].erase(*it);
180	// work on iHash here;
181	}
182	}
183	interactions_[key].insert(lj_);
184	iHash_[key] \|= LJ_PAIR;
185	vdwExplicit = true;
186	}
187
188	if (nbiType->isMorse()) {
189	if (vdwExplicit) {
190	sprintf( painCave.errMsg,
191	"InteractionManager::initialize found more than one "
192	"explicit \n"
193	"\tvan der Waals interaction for atom types %s - %s\n",
194	atype1->getName().c_str(), atype2->getName().c_str());
195	painCave.severity = OPENMD_ERROR;
196	painCave.isFatal = 1;
197	simError();
198	}
199	// We found an explicit Morse interaction.
200	// override all other vdw entries for this pair of atom types:
201	set<NonBondedInteraction*>::iterator it;
202	for (it = interactions_[key].begin();
203	it != interactions_[key].end(); ++it) {
204	InteractionFamily ifam = (*it)->getFamily();
205	if (ifam == VANDERWAALS_FAMILY) {
206	interactions_[key].erase(*it);
207	// work on iHash here;
208	}
209	}
210	interactions_[key].insert(morse_);
211	iHash_[key] \|= MORSE_PAIR;
212	vdwExplicit = true;
213	}
214
215	if (nbiType->isRepulsivePower()) {
216	if (vdwExplicit) {
217	sprintf( painCave.errMsg,
218	"InteractionManager::initialize found more than one "
219	"explicit \n"
220	"\tvan der Waals interaction for atom types %s - %s\n",
221	atype1->getName().c_str(), atype2->getName().c_str());
222	painCave.severity = OPENMD_ERROR;
223	painCave.isFatal = 1;
224	simError();
225	}
226	// We found an explicit RepulsivePower interaction.
227	// override all other vdw entries for this pair of atom types:
228	set<NonBondedInteraction*>::iterator it;
229	for (it = interactions_[key].begin();
230	it != interactions_[key].end(); ++it) {
231	InteractionFamily ifam = (*it)->getFamily();
232	if (ifam == VANDERWAALS_FAMILY) {
233	interactions_[key].erase(*it);
234	// work on iHash here;
235	}
236	}
237	interactions_[key].insert(repulsivePower_);
238	iHash_[key] \|= REPULSIVEPOWER_PAIR;
239	vdwExplicit = true;
240	}
241
242
243	if (nbiType->isEAM()) {
244	// We found an explicit EAM interaction.
245	// override all other metallic entries for this pair of atom types:
246	set<NonBondedInteraction*>::iterator it;
247	for (it = interactions_[key].begin();
248	it != interactions_[key].end(); ++it) {
249	InteractionFamily ifam = (*it)->getFamily();
250	if (ifam == METALLIC_FAMILY) {
251	interactions_[key].erase(*it);
252	// work on iHash here;
253	}
254	}
255	interactions_[key].insert(eam_);
256	iHash_[key] \|= EAM_PAIR;
257	metExplicit = true;
258	}
259
260	if (nbiType->isSC()) {
261	if (metExplicit) {
262	sprintf( painCave.errMsg,
263	"InteractionManager::initialize found more than one "
264	"explicit\n"
265	"\tmetallic interaction for atom types %s - %s\n",
266	atype1->getName().c_str(), atype2->getName().c_str());
267	painCave.severity = OPENMD_ERROR;
268	painCave.isFatal = 1;
269	simError();
270	}
271	// We found an explicit Sutton-Chen interaction.
272	// override all other metallic entries for this pair of atom types:
273	set<NonBondedInteraction*>::iterator it;
274	for (it = interactions_[key].begin();
275	it != interactions_[key].end(); ++it) {
276	InteractionFamily ifam = (*it)->getFamily();
277	if (ifam == METALLIC_FAMILY) {
278	interactions_[key].erase(*it);
279	// work on iHash here;
280	}
281	}
282	interactions_[key].insert(sc_);
283	iHash_[key] \|= SC_PAIR;
284	metExplicit = true;
285	}
286
287	if (nbiType->isMAW()) {
288	if (vdwExplicit) {
289	sprintf( painCave.errMsg,
290	"InteractionManager::initialize found more than one "
291	"explicit\n"
292	"\tvan der Waals interaction for atom types %s - %s\n",
293	atype1->getName().c_str(), atype2->getName().c_str());
294	painCave.severity = OPENMD_ERROR;
295	painCave.isFatal = 1;
296	simError();
297	}
298	// We found an explicit MAW interaction.
299	// override all other vdw entries for this pair of atom types:
300	set<NonBondedInteraction*>::iterator it;
301	for (it = interactions_[key].begin();
302	it != interactions_[key].end(); ++it) {
303	InteractionFamily ifam = (*it)->getFamily();
304	if (ifam == VANDERWAALS_FAMILY) {
305	interactions_[key].erase(*it);
306	// work on iHash here;
307	}
308	}
309	interactions_[key].insert(maw_);
310	iHash_[key] \|= MAW_PAIR;
311	vdwExplicit = true;
312	}
313	}
314	}
315	}
316
317
318	// Make sure every pair of atom types in this simulation has a
319	// non-bonded interaction. If not, just inform the user.
320
321	set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
322	set<AtomType*>::iterator it, jt;
323
324	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
325	atype1 = (*it);
326	for (jt = it; jt != simTypes.end(); ++jt) {
327	atype2 = (*jt);
328	key = make_pair(atype1, atype2);
329
330	if (interactions_[key].size() == 0) {
331	sprintf( painCave.errMsg,
332	"InteractionManager could not find a matching non-bonded\n"
333	"\tinteraction for atom types %s - %s\n"
334	"\tProceeding without this interaction.\n",
335	atype1->getName().c_str(), atype2->getName().c_str());
336	painCave.severity = OPENMD_INFO;
337	painCave.isFatal = 0;
338	simError();
339	}
340	}
341	}
342
343	initialized_ = true;
344	}
345
346	void InteractionManager::setCutoffRadius(RealType rcut) {
347
348	electrostatic_->setCutoffRadius(rcut);
349	eam_->setCutoffRadius(rcut);
350	}
351
352	void InteractionManager::doPrePair(InteractionData idat){
353
354	if (!initialized_) initialize();
355
356	// excluded interaction, so just return
357	if (idat.excluded) return;
358
359	int& iHash = iHash_[idat.atypes];
360
361	if ((iHash & EAM_PAIR) != 0) eam_->calcDensity(idat);
362	if ((iHash & SC_PAIR) != 0) sc_->calcDensity(idat);
363
364	// set<NonBondedInteraction*>::iterator it;
365
366	// for (it = interactions_[ idat.atypes ].begin();
367	// it != interactions_[ idat.atypes ].end(); ++it){
368	// if ((*it)->getFamily() == METALLIC_FAMILY) {
369	// dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
370	// }
371	// }
372
373	return;
374	}
375
376	void InteractionManager::doPreForce(SelfData sdat){
377
378	if (!initialized_) initialize();
379
380	// pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
381
382	int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];
383
384	if ((iHash & EAM_PAIR) != 0) eam_->calcFunctional(sdat);
385	if ((iHash & SC_PAIR) != 0) sc_->calcFunctional(sdat);
386
387	// set<NonBondedInteraction*>::iterator it;
388
389	// for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
390	// if ((*it)->getFamily() == METALLIC_FAMILY) {
391	// dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
392	// }
393	// }
394
395	return;
396	}
397
398	void InteractionManager::doPair(InteractionData idat){
399
400	if (!initialized_) initialize();
401
402	int& iHash = iHash_[idat.atypes];
403
404	if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcForce(idat);
405
406	// electrostatics still has to worry about indirect
407	// contributions from excluded pairs of atoms, but nothing else does:
408
409	if (idat.excluded) return;
410
411	if ((iHash & LJ_PAIR) != 0) lj_->calcForce(idat);
412	if ((iHash & GB_PAIR) != 0) gb_->calcForce(idat);
413	if ((iHash & STICKY_PAIR) != 0) sticky_->calcForce(idat);
414	if ((iHash & MORSE_PAIR) != 0) morse_->calcForce(idat);
415	if ((iHash & REPULSIVEPOWER_PAIR) != 0) repulsivePower_->calcForce(idat);
416	if ((iHash & EAM_PAIR) != 0) eam_->calcForce(idat);
417	if ((iHash & SC_PAIR) != 0) sc_->calcForce(idat);
418	if ((iHash & MAW_PAIR) != 0) maw_->calcForce(idat);
419
420	// set<NonBondedInteraction*>::iterator it;
421
422	// for (it = interactions_[ idat.atypes ].begin();
423	// it != interactions_[ idat.atypes ].end(); ++it) {
424
425	// // electrostatics still has to worry about indirect
426	// // contributions from excluded pairs of atoms:
427
428	// if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
429	// (*it)->calcForce(idat);
430	// }
431	// }
432
433	return;
434	}
435
436	void InteractionManager::doSelfCorrection(SelfData sdat){
437
438	if (!initialized_) initialize();
439
440	int& iHash = iHash_[ make_pair(sdat.atype, sdat.atype) ];
441
442	if ((iHash & ELECTROSTATIC_PAIR) != 0) electrostatic_->calcSelfCorrection(sdat);
443
444
445	// pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
446	// set<NonBondedInteraction*>::iterator it;
447
448	// for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
449	// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
450	// dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
451	// }
452	// }
453
454	return;
455	}
456
457	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
458	if (!initialized_) initialize();
459
460	AtomType* atype = typeMap_[*atid];
461
462	pair<AtomType, AtomType> key = make_pair(atype, atype);
463	set<NonBondedInteraction*>::iterator it;
464	RealType cutoff = 0.0;
465
466	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
467	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
468	return cutoff;
469	}
470
471	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
472	if (!initialized_) initialize();
473
474	pair<AtomType, AtomType> key = make_pair(atype, atype);
475	set<NonBondedInteraction*>::iterator it;
476	RealType cutoff = 0.0;
477
478	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
479	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
480	return cutoff;
481	}
482	} //end namespace OpenMD