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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include "nonbonded/InteractionManager.hpp"

namespace OpenMD {

  InteractionManager::InteractionManager() {

    initialized_ = false;
        
    lj_ = new LJ();
    gb_ = new GB();
    sticky_ = new Sticky();
    morse_ = new Morse();
    eam_ = new EAM();
    sc_ = new SC();
    electrostatic_ = new Electrostatic();
    maw_ = new MAW();
  }

  void InteractionManager::initialize() {
    
    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_);

    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:
      AtomTypeProperties atp = atype1->getATP();    
      
      pair<map<int,AtomType*>::iterator,bool> ret;    
      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
      if (ret.second == false) {
        sprintf( painCave.errMsg,
                 "InteractionManager already had a previous entry with ident %d\n",
                 atp.ident);
        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->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){
//      printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
    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::initializeOMP() {
        if (!initialized_) initialize();
  }

  void InteractionManager::doPrePairOMP(InteractionDataPrv idatThread){
        InteractionData idat;
    // excluded interaction, so just return
    if (idat.excluded) return;

    wrapData(idatThread, 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);
    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::initNonbondedForces() {
        pair<AtomType*, AtomType*> key;
                set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
                set<AtomType*>::iterator it, jt;
                set<NonBondedInteraction*>::iterator kt;
    AtomType* atype1;
    AtomType* atype2;

                for (it = simTypes.begin(); it != simTypes.end(); ++it) {
                        atype1 = (*it);
                        for (jt = it; jt != simTypes.end(); ++jt) {
                                atype2 = (*jt);
                                key = make_pair(atype1, atype2);

                                for (kt = interactions_[ key ].begin();
                                                kt != interactions_[ key ].end(); ++kt) {

                                                (*kt)->initForce();
                                }
                        }
                }

/*      lj_->initForce();
        electrostatic_->initForce();
        sticky_->initForce();
        eam_->initForce();
        sc_->initForce();
        gb_->initForce();*/

                return;
  }

  void InteractionManager::doPair(InteractionData idat){
//      printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
    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::wrapData(InteractionDataPrv &src, InteractionData &dst) {
        dst.A1 = src.A1;
        dst.A2 = src.A2;
        dst.atypes = src.atypes;
        dst.d = &src.d;
        dst.dfrho1 = src.dfrho1;
        dst.dfrho2 = src.dfrho2;
        dst.eFrame1 = src.eFrame1;
        dst.eFrame2 = src.eFrame2;
        dst.electroMult = &src.electroMult;
        dst.excluded = src.excluded;
        dst.f1 = &src.f1;
        dst.frho1 = src.frho1;
        dst.frho2 = src.frho2;
        dst.particlePot1 = src.particlePot1;
        dst.particlePot2 = src.particlePot2;
        dst.pot = &src.pot;
        dst.r2 = &src.r2;
        dst.rcut = &src.rcut;
        dst.rho1 = src.rho1;
        dst.rho2 = src.rho2;
        dst.rij = &src.rij;
        dst.shiftedForce = src.shiftedForce;
        dst.shiftedPot = src.shiftedPot;
        dst.skippedCharge1 = src.skippedCharge1;
        dst.skippedCharge2 = src.skippedCharge2;
        dst.sw = &src.sw;
        dst.t1 = src.t1;
        dst.t2 = src.t2;
        dst.topoDist = src.topoDist;
        dst.vdwMult = &src.vdwMult;
        dst.vpair = &src.vpair;
  }

  void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
    set<NonBondedInteraction*>::iterator it;
    InteractionData idat;

    wrapData(idatThread, idat);

    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:	1614
Committed:	Tue Aug 23 20:55:51 2011 UTC (14 years, 2 months ago) by mciznick
File size:	17048 byte(s)
Log Message:	Updated scalability of OpenMP threads.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include "nonbonded/InteractionManager.hpp"
43
44			namespace OpenMD {
45	gezelter	1535
46	gezelter	1576	InteractionManager::InteractionManager() {
47	gezelter	1535
48	gezelter	1576	initialized_ = false;
49
50			lj_ = new LJ();
51			gb_ = new GB();
52			sticky_ = new Sticky();
53			morse_ = new Morse();
54			eam_ = new EAM();
55			sc_ = new SC();
56			electrostatic_ = new Electrostatic();
57			maw_ = new MAW();
58	gezelter	1502	}
59
60			void InteractionManager::initialize() {
61
62	gezelter	1535	ForceField* forceField_ = info_->getForceField();
63
64	gezelter	1502	lj_->setForceField(forceField_);
65			gb_->setForceField(forceField_);
66			sticky_->setForceField(forceField_);
67			eam_->setForceField(forceField_);
68			sc_->setForceField(forceField_);
69			morse_->setForceField(forceField_);
70	gezelter	1584	electrostatic_->setSimInfo(info_);
71	gezelter	1502	electrostatic_->setForceField(forceField_);
72	gezelter	1532	maw_->setForceField(forceField_);
73	gezelter	1502
74			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
75			ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
76			AtomType* atype1;
77			AtomType* atype2;
78			pair<AtomType, AtomType> key;
79			pair<set<NonBondedInteraction*>::iterator, bool> ret;
80
81			for (atype1 = atomTypes->beginType(i1); atype1 != NULL;
82			atype1 = atomTypes->nextType(i1)) {
83
84			// add it to the map:
85			AtomTypeProperties atp = atype1->getATP();
86
87			pair<map<int,AtomType*>::iterator,bool> ret;
88			ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
89			if (ret.second == false) {
90			sprintf( painCave.errMsg,
91			"InteractionManager already had a previous entry with ident %d\n",
92			atp.ident);
93			painCave.severity = OPENMD_INFO;
94			painCave.isFatal = 0;
95			simError();
96			}
97			}
98
99			// Now, iterate over all known types and add to the interaction map:
100
101			map<int, AtomType*>::iterator it1, it2;
102			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
103			atype1 = (*it1).second;
104
105			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
106			atype2 = (*it2).second;
107
108			bool vdwExplicit = false;
109			bool metExplicit = false;
110			bool hbExplicit = false;
111
112			key = make_pair(atype1, atype2);
113
114			if (atype1->isLennardJones() && atype2->isLennardJones()) {
115			interactions_[key].insert(lj_);
116			}
117			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
118			interactions_[key].insert(electrostatic_);
119			}
120			if (atype1->isSticky() && atype2->isSticky() ) {
121			interactions_[key].insert(sticky_);
122			}
123			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
124			interactions_[key].insert(sticky_);
125			}
126			if (atype1->isEAM() && atype2->isEAM() ) {
127			interactions_[key].insert(eam_);
128			}
129			if (atype1->isSC() && atype2->isSC() ) {
130			interactions_[key].insert(sc_);
131			}
132			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
133			interactions_[key].insert(gb_);
134			}
135			if ((atype1->isGayBerne() && atype2->isLennardJones())
136			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
137			interactions_[key].insert(gb_);
138			}
139
140			// look for an explicitly-set non-bonded interaction type using the
141			// two atom types.
142			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
143	gezelter	1535
144			if (nbiType != NULL) {
145	gezelter	1502
146	gezelter	1535	if (nbiType->isLennardJones()) {
147			// We found an explicit Lennard-Jones interaction.
148			// override all other vdw entries for this pair of atom types:
149			set<NonBondedInteraction*>::iterator it;
150			for (it = interactions_[key].begin();
151			it != interactions_[key].end(); ++it) {
152			InteractionFamily ifam = (*it)->getFamily();
153			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
154			}
155			interactions_[key].insert(lj_);
156			vdwExplicit = true;
157	gezelter	1502	}
158	gezelter	1535
159			if (nbiType->isMorse()) {
160			if (vdwExplicit) {
161			sprintf( painCave.errMsg,
162			"InteractionManager::initialize found more than one "
163			"explicit \n"
164			"\tvan der Waals interaction for atom types %s - %s\n",
165			atype1->getName().c_str(), atype2->getName().c_str());
166			painCave.severity = OPENMD_ERROR;
167			painCave.isFatal = 1;
168			simError();
169			}
170			// We found an explicit Morse interaction.
171			// override all other vdw entries for this pair of atom types:
172			set<NonBondedInteraction*>::iterator it;
173			for (it = interactions_[key].begin();
174			it != interactions_[key].end(); ++it) {
175			InteractionFamily ifam = (*it)->getFamily();
176			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
177			}
178			interactions_[key].insert(morse_);
179			vdwExplicit = true;
180	gezelter	1502	}
181	gezelter	1535
182			if (nbiType->isEAM()) {
183			// We found an explicit EAM interaction.
184			// override all other metallic entries for this pair of atom types:
185			set<NonBondedInteraction*>::iterator it;
186			for (it = interactions_[key].begin();
187			it != interactions_[key].end(); ++it) {
188			InteractionFamily ifam = (*it)->getFamily();
189			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
190			}
191			interactions_[key].insert(eam_);
192			metExplicit = true;
193	gezelter	1502	}
194	gezelter	1535
195			if (nbiType->isSC()) {
196			if (metExplicit) {
197			sprintf( painCave.errMsg,
198			"InteractionManager::initialize found more than one "
199			"explicit\n"
200			"\tmetallic interaction for atom types %s - %s\n",
201			atype1->getName().c_str(), atype2->getName().c_str());
202			painCave.severity = OPENMD_ERROR;
203			painCave.isFatal = 1;
204			simError();
205			}
206			// We found an explicit Sutton-Chen interaction.
207			// override all other metallic entries for this pair of atom types:
208			set<NonBondedInteraction*>::iterator it;
209			for (it = interactions_[key].begin();
210			it != interactions_[key].end(); ++it) {
211			InteractionFamily ifam = (*it)->getFamily();
212			if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it);
213			}
214			interactions_[key].insert(sc_);
215			metExplicit = true;
216	gezelter	1502	}
217	gezelter	1535
218			if (nbiType->isMAW()) {
219			if (vdwExplicit) {
220			sprintf( painCave.errMsg,
221			"InteractionManager::initialize found more than one "
222			"explicit\n"
223			"\tvan der Waals interaction for atom types %s - %s\n",
224			atype1->getName().c_str(), atype2->getName().c_str());
225			painCave.severity = OPENMD_ERROR;
226			painCave.isFatal = 1;
227			simError();
228			}
229			// We found an explicit MAW interaction.
230			// override all other vdw entries for this pair of atom types:
231			set<NonBondedInteraction*>::iterator it;
232			for (it = interactions_[key].begin();
233			it != interactions_[key].end(); ++it) {
234			InteractionFamily ifam = (*it)->getFamily();
235			if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it);
236			}
237			interactions_[key].insert(maw_);
238			vdwExplicit = true;
239			}
240	gezelter	1502	}
241			}
242			}
243
244	gezelter	1535
245	gezelter	1583	// Make sure every pair of atom types in this simulation has a
246			// non-bonded interaction. If not, just inform the user.
247	gezelter	1535
248			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
249			set<AtomType*>::iterator it, jt;
250	gezelter	1583
251	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
252			atype1 = (*it);
253	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
254	gezelter	1535	atype2 = (*jt);
255	gezelter	1502	key = make_pair(atype1, atype2);
256
257			if (interactions_[key].size() == 0) {
258			sprintf( painCave.errMsg,
259	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
260			"\tinteraction for atom types %s - %s\n"
261			"\tProceeding without this interaction.\n",
262	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
263			painCave.severity = OPENMD_INFO;
264	gezelter	1583	painCave.isFatal = 0;
265	gezelter	1502	simError();
266			}
267			}
268			}
269	gezelter	1535
270			initialized_ = true;
271			}
272	gezelter	1584
273			void InteractionManager::setCutoffRadius(RealType rcut) {
274	gezelter	1587
275	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
276	gezelter	1586	eam_->setCutoffRadius(rcut);
277	gezelter	1584	}
278
279			void InteractionManager::setSwitchingRadius(RealType rswitch) {
280			electrostatic_->setSwitchingRadius(rswitch);
281			}
282	gezelter	1502
283	gezelter	1545	void InteractionManager::doPrePair(InteractionData idat){
284	mciznick	1614	// printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
285			if (!initialized_) initialize();
286	gezelter	1545
287	gezelter	1587	// excluded interaction, so just return
288			if (idat.excluded) return;
289
290	gezelter	1504	set<NonBondedInteraction*>::iterator it;
291
292	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
293			it != interactions_[ idat.atypes ].end(); ++it){
294	gezelter	1504	if ((*it)->getFamily() == METALLIC_FAMILY) {
295	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
296	gezelter	1504	}
297	mciznick	1614	}
298	gezelter	1502
299			return;
300			}
301	gezelter	1504
302	mciznick	1608	void InteractionManager::initializeOMP() {
303			if (!initialized_) initialize();
304			}
305
306			void InteractionManager::doPrePairOMP(InteractionDataPrv idatThread){
307			InteractionData idat;
308			// excluded interaction, so just return
309			if (idat.excluded) return;
310
311			wrapData(idatThread, idat);
312
313			set<NonBondedInteraction*>::iterator it;
314
315			for (it = interactions_[ idat.atypes ].begin();
316			it != interactions_[ idat.atypes ].end(); ++it){
317			if ((*it)->getFamily() == METALLIC_FAMILY) {
318			dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
319			}
320			}
321
322			return;
323			}
324
325	gezelter	1545	void InteractionManager::doPreForce(SelfData sdat){
326	gezelter	1502
327	gezelter	1504	if (!initialized_) initialize();
328	gezelter	1545
329			pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
330	gezelter	1504	set<NonBondedInteraction*>::iterator it;
331	gezelter	1502
332	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
333			if ((*it)->getFamily() == METALLIC_FAMILY) {
334	gezelter	1545	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
335	gezelter	1504	}
336			}
337
338	gezelter	1502	return;
339			}
340
341	mciznick	1614	void InteractionManager::initNonbondedForces() {
342			pair<AtomType, AtomType> key;
343			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
344			set<AtomType*>::iterator it, jt;
345			set<NonBondedInteraction*>::iterator kt;
346			AtomType* atype1;
347			AtomType* atype2;
348
349			for (it = simTypes.begin(); it != simTypes.end(); ++it) {
350			atype1 = (*it);
351			for (jt = it; jt != simTypes.end(); ++jt) {
352			atype2 = (*jt);
353			key = make_pair(atype1, atype2);
354
355			for (kt = interactions_[ key ].begin();
356			kt != interactions_[ key ].end(); ++kt) {
357
358			(*kt)->initForce();
359			}
360			}
361			}
362
363			/* lj_->initForce();
364			electrostatic_->initForce();
365			sticky_->initForce();
366			eam_->initForce();
367			sc_->initForce();
368			gb_->initForce();*/
369
370			return;
371			}
372
373	gezelter	1545	void InteractionManager::doPair(InteractionData idat){
374	mciznick	1614	// printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
375			if (!initialized_) initialize();
376	gezelter	1587
377	gezelter	1502	set<NonBondedInteraction*>::iterator it;
378
379	gezelter	1571	for (it = interactions_[ idat.atypes ].begin();
380	gezelter	1587	it != interactions_[ idat.atypes ].end(); ++it) {
381	gezelter	1502
382	gezelter	1587	// electrostatics still has to worry about indirect
383			// contributions from excluded pairs of atoms:
384	gezelter	1502
385	gezelter	1587	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
386			(*it)->calcForce(idat);
387	gezelter	1504	}
388	mciznick	1614	}
389	gezelter	1502
390	gezelter	1504	return;
391	gezelter	1502	}
392
393	mciznick	1608	void InteractionManager::wrapData(InteractionDataPrv &src, InteractionData &dst) {
394			dst.A1 = src.A1;
395			dst.A2 = src.A2;
396			dst.atypes = src.atypes;
397			dst.d = &src.d;
398			dst.dfrho1 = src.dfrho1;
399			dst.dfrho2 = src.dfrho2;
400			dst.eFrame1 = src.eFrame1;
401			dst.eFrame2 = src.eFrame2;
402			dst.electroMult = &src.electroMult;
403			dst.excluded = src.excluded;
404			dst.f1 = &src.f1;
405			dst.frho1 = src.frho1;
406			dst.frho2 = src.frho2;
407			dst.particlePot1 = src.particlePot1;
408			dst.particlePot2 = src.particlePot2;
409			dst.pot = &src.pot;
410			dst.r2 = &src.r2;
411			dst.rcut = &src.rcut;
412			dst.rho1 = src.rho1;
413			dst.rho2 = src.rho2;
414			dst.rij = &src.rij;
415			dst.shiftedForce = src.shiftedForce;
416			dst.shiftedPot = src.shiftedPot;
417			dst.skippedCharge1 = src.skippedCharge1;
418			dst.skippedCharge2 = src.skippedCharge2;
419			dst.sw = &src.sw;
420			dst.t1 = src.t1;
421			dst.t2 = src.t2;
422			dst.topoDist = src.topoDist;
423			dst.vdwMult = &src.vdwMult;
424			dst.vpair = &src.vpair;
425			}
426
427			void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
428			set<NonBondedInteraction*>::iterator it;
429			InteractionData idat;
430
431			wrapData(idatThread, idat);
432
433			for (it = interactions_[ idat.atypes ].begin();
434			it != interactions_[ idat.atypes ].end(); ++it) {
435
436			// electrostatics still has to worry about indirect
437			// contributions from excluded pairs of atoms:
438
439			if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
440			(*it)->calcForce(idat);
441			}
442			}
443
444			return;
445			}
446
447	gezelter	1545	void InteractionManager::doSelfCorrection(SelfData sdat){
448	gezelter	1502
449			if (!initialized_) initialize();
450	gezelter	1504
451	gezelter	1545	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
452	gezelter	1504	set<NonBondedInteraction*>::iterator it;
453	gezelter	1502
454	gezelter	1504	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
455			if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
456	gezelter	1545	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
457	gezelter	1504	}
458			}
459	gezelter	1536
460	gezelter	1504	return;
461	gezelter	1502	}
462
463	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
464			if (!initialized_) initialize();
465
466			AtomType* atype = typeMap_[*atid];
467
468			pair<AtomType, AtomType> key = make_pair(atype, atype);
469			set<NonBondedInteraction*>::iterator it;
470			RealType cutoff = 0.0;
471
472			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
473	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
474	gezelter	1505	return cutoff;
475			}
476
477	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
478			if (!initialized_) initialize();
479
480			pair<AtomType, AtomType> key = make_pair(atype, atype);
481			set<NonBondedInteraction*>::iterator it;
482			RealType cutoff = 0.0;
483
484			for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
485	gezelter	1545	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
486	gezelter	1528	return cutoff;
487			}
488	gezelter	1502	} //end namespace OpenMD