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();
    int nTypes = atomTypes->size();
    sHash_.resize(nTypes);
    iHash_.resize(nTypes);
    interactions_.resize(nTypes);
    ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
    AtomType* atype1;
    AtomType* atype2;
    int atid1, atid2;

    // We only need to worry about the types that are actually in the
    // simulation:
    
    set<AtomType*> atypes = info_->getSimulatedAtomTypes();

    lj_->setSimulatedAtomTypes(atypes);
    gb_->setSimulatedAtomTypes(atypes);
    sticky_->setSimulatedAtomTypes(atypes);
    eam_->setSimulatedAtomTypes(atypes);
    sc_->setSimulatedAtomTypes(atypes);
    morse_->setSimulatedAtomTypes(atypes);
    electrostatic_->setSimInfo(info_);
    electrostatic_->setSimulatedAtomTypes(atypes);
    maw_->setSimulatedAtomTypes(atypes);
    repulsivePower_->setSimulatedAtomTypes(atypes);

    set<AtomType*>::iterator at;

    for (at = atypes.begin(); at != atypes.end(); ++at) {
          
      atype1 = *at;
      atid1 = atype1->getIdent();
      iHash_[atid1].resize(nTypes);
      interactions_[atid1].resize(nTypes);

      // add it to the map:      
      pair<map<int,AtomType*>::iterator,bool> ret;    
      ret = typeMap_.insert( pair<int, AtomType*>(atid1, 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();                 
      }
          
      if (atype1->isLennardJones()) {
        sHash_[atid1] |= LJ_INTERACTION;
      }
      if (atype1->isElectrostatic()) {
        sHash_[atid1] |= ELECTROSTATIC_INTERACTION;
      }
      if (atype1->isSticky()) {
        sHash_[atid1] |= STICKY_INTERACTION;
      }
      if (atype1->isStickyPower()) {
        sHash_[atid1] |= STICKY_INTERACTION;
      }
      if (atype1->isEAM()) {      
        sHash_[atid1] |= EAM_INTERACTION;
      }
      if (atype1->isSC()) {
        sHash_[atid1] |= SC_INTERACTION;
      }
      if (atype1->isGayBerne()) {
        sHash_[atid1] |= GB_INTERACTION;
      }
    }
    // 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;
      atid1 = atype1->getIdent();

      for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {        
        atype2 = (*it2).second;
        atid2 = atype2->getIdent();
                               
        iHash_[atid1][atid2] = 0;
        
        if (atype1->isLennardJones() && atype2->isLennardJones()) {
          interactions_[atid1][atid2].insert(lj_);
          iHash_[atid1][atid2] |= LJ_INTERACTION;
        }
        if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
          interactions_[atid1][atid2].insert(electrostatic_);
          iHash_[atid1][atid2] |= ELECTROSTATIC_INTERACTION;
        }
        if (atype1->isSticky() && atype2->isSticky() ) {
          interactions_[atid1][atid2].insert(sticky_);
          iHash_[atid1][atid2] |= STICKY_INTERACTION;
        }
        if (atype1->isStickyPower() && atype2->isStickyPower() ) {
          interactions_[atid1][atid2].insert(sticky_);
          iHash_[atid1][atid2] |= STICKY_INTERACTION;
        }
        if (atype1->isEAM() && atype2->isEAM() ) {
          interactions_[atid1][atid2].insert(eam_);
          iHash_[atid1][atid2] |= EAM_INTERACTION;
        }
        if (atype1->isSC() && atype2->isSC() ) {
          interactions_[atid1][atid2].insert(sc_);
          iHash_[atid1][atid2] |= SC_INTERACTION;
        }
        if (atype1->isGayBerne() && atype2->isGayBerne() ) {
          interactions_[atid1][atid2].insert(gb_);
          iHash_[atid1][atid2] |= GB_INTERACTION;
        }
        if ((atype1->isGayBerne() && atype2->isLennardJones())
            || (atype1->isLennardJones() && atype2->isGayBerne())) {
          interactions_[atid1][atid2].insert(gb_);
          iHash_[atid1][atid2] |= GB_INTERACTION;
        } 
        
        // 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_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(lj_);
            iHash_[atid1][atid2] |= LJ_INTERACTION;
            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_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(morse_);
            iHash_[atid1][atid2] |= MORSE_INTERACTION;
            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_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(repulsivePower_);
            iHash_[atid1][atid2] |= REPULSIVEPOWER_INTERACTION;
            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_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == METALLIC_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(eam_);
            iHash_[atid1][atid2] |= EAM_INTERACTION;
            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_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == METALLIC_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(sc_);
            iHash_[atid1][atid2] |= SC_INTERACTION;
            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_[atid1][atid2].begin(); 
                 it != interactions_[atid1][atid2].end(); ++it) {
              InteractionFamily ifam = (*it)->getFamily();
              if (ifam == VANDERWAALS_FAMILY) {
                interactions_[atid1][atid2].erase(*it);
                iHash_[atid1][atid2] ^= (*it)->getHash();
              }
            }
            interactions_[atid1][atid2].insert(maw_);
            iHash_[atid1][atid2] |= MAW_INTERACTION;
            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);
      atid1 = atype1->getIdent();
      for (jt = it; jt != simTypes.end(); ++jt) {
        atype2 = (*jt);
        atid2 = atype2->getIdent();
        
        if (interactions_[atid1][atid2].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.atid1][idat.atid2];

    if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
    if ((iHash & SC_INTERACTION) != 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();
    
    int& sHash = sHash_[sdat.atid];

    if ((sHash & EAM_INTERACTION) != 0)  eam_->calcFunctional(sdat);
    if ((sHash & SC_INTERACTION) != 0)  sc_->calcFunctional(sdat);

    // set<NonBondedInteraction*>::iterator it;
    
    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].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.atid1][idat.atid2];

    if ((iHash & ELECTROSTATIC_INTERACTION) != 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_INTERACTION) != 0)             lj_->calcForce(idat);
    if ((iHash & GB_INTERACTION) != 0)             gb_->calcForce(idat);
    if ((iHash & STICKY_INTERACTION) != 0)         sticky_->calcForce(idat);
    if ((iHash & MORSE_INTERACTION) != 0)          morse_->calcForce(idat);
    if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
    if ((iHash & EAM_INTERACTION) != 0)            eam_->calcForce(idat);
    if ((iHash & SC_INTERACTION) != 0)             sc_->calcForce(idat);
    if ((iHash & MAW_INTERACTION) != 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& sHash = sHash_[sdat.atid];

    if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);

    // set<NonBondedInteraction*>::iterator it;

    // for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
    //   if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
    //     dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat);
    //   }
    // }
      
    return;    
  }

  void InteractionManager::doReciprocalSpaceSum(RealType &pot){
    if (!initialized_) initialize();
    electrostatic_->ReciprocalSpaceSum(pot);
  }

  RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
    if (!initialized_) initialize();

    AtomType* atype = typeMap_[*atid];

    set<NonBondedInteraction*>::iterator it;
    RealType cutoff = 0.0;
    
    for (it = interactions_[*atid][*atid].begin(); 
         it != interactions_[*atid][*atid].end();
         ++it)
      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
                                                                     atype)));
    return cutoff;    
  }

  RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
    if (!initialized_) initialize();
    
    int atid = atype->getIdent();

    set<NonBondedInteraction*>::iterator it;
    RealType cutoff = 0.0;
    
    for (it = interactions_[atid][atid].begin(); 
         it != interactions_[atid][atid].end(); ++it)
      cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
                                                                     atype)));
    return cutoff;    
  }
} //end namespace OpenMD
Revision:	2033
Committed:	Sat Nov 1 14:12:16 2014 UTC (10 years, 6 months ago) by gezelter
File size:	20107 byte(s)
Log Message:	Fixed a selection issue in ParticleTimeCorrFunc, other whitespace stuff
#	User	Rev	Content
1	gezelter	1502	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1502	*/
42
43			#include "nonbonded/InteractionManager.hpp"
44
45			namespace OpenMD {
46	gezelter	1535
47	gezelter	1576	InteractionManager::InteractionManager() {
48	gezelter	1535
49	gezelter	1576	initialized_ = false;
50
51			lj_ = new LJ();
52			gb_ = new GB();
53			sticky_ = new Sticky();
54			morse_ = new Morse();
55	jmichalk	1656	repulsivePower_ = new RepulsivePower();
56	gezelter	1576	eam_ = new EAM();
57			sc_ = new SC();
58			electrostatic_ = new Electrostatic();
59			maw_ = new MAW();
60	gezelter	1502	}
61
62	gezelter	1879	InteractionManager::~InteractionManager() {
63			delete lj_;
64			delete gb_;
65			delete sticky_;
66			delete morse_;
67			delete repulsivePower_;
68			delete eam_;
69			delete sc_;
70			delete electrostatic_;
71			delete maw_;
72			}
73
74	gezelter	1502	void InteractionManager::initialize() {
75	gezelter	1755
76			if (initialized_) return;
77
78	gezelter	1535	ForceField* forceField_ = info_->getForceField();
79
80	gezelter	1502	lj_->setForceField(forceField_);
81			gb_->setForceField(forceField_);
82			sticky_->setForceField(forceField_);
83			eam_->setForceField(forceField_);
84			sc_->setForceField(forceField_);
85			morse_->setForceField(forceField_);
86	gezelter	1584	electrostatic_->setSimInfo(info_);
87	gezelter	1502	electrostatic_->setForceField(forceField_);
88	gezelter	1532	maw_->setForceField(forceField_);
89	jmichalk	1656	repulsivePower_->setForceField(forceField_);
90	gezelter	1502
91			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
92	gezelter	1895	int nTypes = atomTypes->size();
93	gezelter	1927	sHash_.resize(nTypes);
94	gezelter	1895	iHash_.resize(nTypes);
95			interactions_.resize(nTypes);
96	gezelter	1502	ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
97			AtomType* atype1;
98			AtomType* atype2;
99	gezelter	1895	int atid1, atid2;
100
101	gezelter	2033	// We only need to worry about the types that are actually in the
102			// simulation:
103
104	gezelter	1895	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
105
106			lj_->setSimulatedAtomTypes(atypes);
107			gb_->setSimulatedAtomTypes(atypes);
108			sticky_->setSimulatedAtomTypes(atypes);
109			eam_->setSimulatedAtomTypes(atypes);
110			sc_->setSimulatedAtomTypes(atypes);
111			morse_->setSimulatedAtomTypes(atypes);
112			electrostatic_->setSimInfo(info_);
113			electrostatic_->setSimulatedAtomTypes(atypes);
114			maw_->setSimulatedAtomTypes(atypes);
115			repulsivePower_->setSimulatedAtomTypes(atypes);
116
117			set<AtomType*>::iterator at;
118
119			for (at = atypes.begin(); at != atypes.end(); ++at) {
120	gezelter	1935
121	gezelter	1895	atype1 = *at;
122			atid1 = atype1->getIdent();
123			iHash_[atid1].resize(nTypes);
124			interactions_[atid1].resize(nTypes);
125
126			// add it to the map:
127	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
128	gezelter	1895	ret = typeMap_.insert( pair<int, AtomType*>(atid1, atype1) );
129	gezelter	1502	if (ret.second == false) {
130			sprintf( painCave.errMsg,
131			"InteractionManager already had a previous entry with ident %d\n",
132	gezelter	1710	atype1->getIdent());
133	gezelter	1502	painCave.severity = OPENMD_INFO;
134			painCave.isFatal = 0;
135			simError();
136			}
137	gezelter	1935
138			if (atype1->isLennardJones()) {
139			sHash_[atid1] \|= LJ_INTERACTION;
140			}
141			if (atype1->isElectrostatic()) {
142			sHash_[atid1] \|= ELECTROSTATIC_INTERACTION;
143			}
144			if (atype1->isSticky()) {
145			sHash_[atid1] \|= STICKY_INTERACTION;
146			}
147			if (atype1->isStickyPower()) {
148			sHash_[atid1] \|= STICKY_INTERACTION;
149			}
150			if (atype1->isEAM()) {
151			sHash_[atid1] \|= EAM_INTERACTION;
152			}
153			if (atype1->isSC()) {
154			sHash_[atid1] \|= SC_INTERACTION;
155			}
156			if (atype1->isGayBerne()) {
157			sHash_[atid1] \|= GB_INTERACTION;
158			}
159	gezelter	1502	}
160			// Now, iterate over all known types and add to the interaction map:
161
162			map<int, AtomType*>::iterator it1, it2;
163			for (it1 = typeMap_.begin(); it1 != typeMap_.end(); ++it1) {
164			atype1 = (*it1).second;
165	gezelter	1895	atid1 = atype1->getIdent();
166	gezelter	1502
167			for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) {
168			atype2 = (*it2).second;
169	gezelter	1895	atid2 = atype2->getIdent();
170	gezelter	1879
171	gezelter	1895	iHash_[atid1][atid2] = 0;
172	gezelter	1502
173			if (atype1->isLennardJones() && atype2->isLennardJones()) {
174	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
175	gezelter	1927	iHash_[atid1][atid2] \|= LJ_INTERACTION;
176	gezelter	1502	}
177			if (atype1->isElectrostatic() && atype2->isElectrostatic() ) {
178	gezelter	1929	interactions_[atid1][atid2].insert(electrostatic_);
179			iHash_[atid1][atid2] \|= ELECTROSTATIC_INTERACTION;
180	gezelter	1502	}
181			if (atype1->isSticky() && atype2->isSticky() ) {
182	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
183	gezelter	1927	iHash_[atid1][atid2] \|= STICKY_INTERACTION;
184	gezelter	1502	}
185			if (atype1->isStickyPower() && atype2->isStickyPower() ) {
186	gezelter	1895	interactions_[atid1][atid2].insert(sticky_);
187	gezelter	1927	iHash_[atid1][atid2] \|= STICKY_INTERACTION;
188	gezelter	1502	}
189			if (atype1->isEAM() && atype2->isEAM() ) {
190	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
191	gezelter	1927	iHash_[atid1][atid2] \|= EAM_INTERACTION;
192	gezelter	1502	}
193			if (atype1->isSC() && atype2->isSC() ) {
194	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
195	gezelter	1927	iHash_[atid1][atid2] \|= SC_INTERACTION;
196	gezelter	1502	}
197			if (atype1->isGayBerne() && atype2->isGayBerne() ) {
198	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
199	gezelter	1927	iHash_[atid1][atid2] \|= GB_INTERACTION;
200	gezelter	1502	}
201			if ((atype1->isGayBerne() && atype2->isLennardJones())
202			\|\| (atype1->isLennardJones() && atype2->isGayBerne())) {
203	gezelter	1895	interactions_[atid1][atid2].insert(gb_);
204	gezelter	1927	iHash_[atid1][atid2] \|= GB_INTERACTION;
205	gezelter	1502	}
206
207			// look for an explicitly-set non-bonded interaction type using the
208			// two atom types.
209			NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName());
210	gezelter	1535
211			if (nbiType != NULL) {
212	gezelter	1502
213	gezelter	1879	bool vdwExplicit = false;
214			bool metExplicit = false;
215			// bool hbExplicit = false;
216
217	gezelter	1535	if (nbiType->isLennardJones()) {
218			// We found an explicit Lennard-Jones interaction.
219			// override all other vdw entries for this pair of atom types:
220			set<NonBondedInteraction*>::iterator it;
221	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
222			it != interactions_[atid1][atid2].end(); ++it) {
223	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
224	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
225	gezelter	1895	interactions_[atid1][atid2].erase(*it);
226			iHash_[atid1][atid2] ^= (*it)->getHash();
227	gezelter	1879	}
228	gezelter	1535	}
229	gezelter	1895	interactions_[atid1][atid2].insert(lj_);
230	gezelter	1927	iHash_[atid1][atid2] \|= LJ_INTERACTION;
231	gezelter	1535	vdwExplicit = true;
232	gezelter	1502	}
233	gezelter	1535
234			if (nbiType->isMorse()) {
235			if (vdwExplicit) {
236			sprintf( painCave.errMsg,
237			"InteractionManager::initialize found more than one "
238			"explicit \n"
239			"\tvan der Waals interaction for atom types %s - %s\n",
240			atype1->getName().c_str(), atype2->getName().c_str());
241			painCave.severity = OPENMD_ERROR;
242			painCave.isFatal = 1;
243			simError();
244			}
245			// We found an explicit Morse interaction.
246			// override all other vdw entries for this pair of atom types:
247			set<NonBondedInteraction*>::iterator it;
248	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
249			it != interactions_[atid1][atid2].end(); ++it) {
250	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
251	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
252	gezelter	1895	interactions_[atid1][atid2].erase(*it);
253			iHash_[atid1][atid2] ^= (*it)->getHash();
254	gezelter	1879	}
255	gezelter	1535	}
256	gezelter	1895	interactions_[atid1][atid2].insert(morse_);
257	gezelter	1927	iHash_[atid1][atid2] \|= MORSE_INTERACTION;
258	gezelter	1535	vdwExplicit = true;
259	gezelter	1502	}
260	jmichalk	1656
261			if (nbiType->isRepulsivePower()) {
262			if (vdwExplicit) {
263			sprintf( painCave.errMsg,
264			"InteractionManager::initialize found more than one "
265			"explicit \n"
266			"\tvan der Waals interaction for atom types %s - %s\n",
267			atype1->getName().c_str(), atype2->getName().c_str());
268			painCave.severity = OPENMD_ERROR;
269			painCave.isFatal = 1;
270			simError();
271			}
272			// We found an explicit RepulsivePower interaction.
273			// override all other vdw entries for this pair of atom types:
274			set<NonBondedInteraction*>::iterator it;
275	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
276			it != interactions_[atid1][atid2].end(); ++it) {
277	jmichalk	1656	InteractionFamily ifam = (*it)->getFamily();
278	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
279	gezelter	1895	interactions_[atid1][atid2].erase(*it);
280			iHash_[atid1][atid2] ^= (*it)->getHash();
281	gezelter	1879	}
282	jmichalk	1656	}
283	gezelter	1895	interactions_[atid1][atid2].insert(repulsivePower_);
284	gezelter	1927	iHash_[atid1][atid2] \|= REPULSIVEPOWER_INTERACTION;
285	jmichalk	1656	vdwExplicit = true;
286			}
287	gezelter	1535
288	jmichalk	1656
289	gezelter	1535	if (nbiType->isEAM()) {
290			// We found an explicit EAM interaction.
291			// override all other metallic entries for this pair of atom types:
292			set<NonBondedInteraction*>::iterator it;
293	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
294			it != interactions_[atid1][atid2].end(); ++it) {
295	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
296	gezelter	1879	if (ifam == METALLIC_FAMILY) {
297	gezelter	1895	interactions_[atid1][atid2].erase(*it);
298			iHash_[atid1][atid2] ^= (*it)->getHash();
299	gezelter	1879	}
300	gezelter	1535	}
301	gezelter	1895	interactions_[atid1][atid2].insert(eam_);
302	gezelter	1927	iHash_[atid1][atid2] \|= EAM_INTERACTION;
303	gezelter	1535	metExplicit = true;
304	gezelter	1502	}
305	gezelter	1535
306			if (nbiType->isSC()) {
307			if (metExplicit) {
308			sprintf( painCave.errMsg,
309			"InteractionManager::initialize found more than one "
310			"explicit\n"
311			"\tmetallic interaction for atom types %s - %s\n",
312			atype1->getName().c_str(), atype2->getName().c_str());
313			painCave.severity = OPENMD_ERROR;
314			painCave.isFatal = 1;
315			simError();
316			}
317			// We found an explicit Sutton-Chen interaction.
318			// override all other metallic entries for this pair of atom types:
319			set<NonBondedInteraction*>::iterator it;
320	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
321			it != interactions_[atid1][atid2].end(); ++it) {
322	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
323	gezelter	1879	if (ifam == METALLIC_FAMILY) {
324	gezelter	1895	interactions_[atid1][atid2].erase(*it);
325			iHash_[atid1][atid2] ^= (*it)->getHash();
326	gezelter	1879	}
327	gezelter	1535	}
328	gezelter	1895	interactions_[atid1][atid2].insert(sc_);
329	gezelter	1927	iHash_[atid1][atid2] \|= SC_INTERACTION;
330	gezelter	1535	metExplicit = true;
331	gezelter	1502	}
332	gezelter	1535
333			if (nbiType->isMAW()) {
334			if (vdwExplicit) {
335			sprintf( painCave.errMsg,
336			"InteractionManager::initialize found more than one "
337			"explicit\n"
338			"\tvan der Waals interaction for atom types %s - %s\n",
339			atype1->getName().c_str(), atype2->getName().c_str());
340			painCave.severity = OPENMD_ERROR;
341			painCave.isFatal = 1;
342			simError();
343			}
344			// We found an explicit MAW interaction.
345			// override all other vdw entries for this pair of atom types:
346			set<NonBondedInteraction*>::iterator it;
347	gezelter	1895	for (it = interactions_[atid1][atid2].begin();
348			it != interactions_[atid1][atid2].end(); ++it) {
349	gezelter	1535	InteractionFamily ifam = (*it)->getFamily();
350	gezelter	1879	if (ifam == VANDERWAALS_FAMILY) {
351	gezelter	1895	interactions_[atid1][atid2].erase(*it);
352			iHash_[atid1][atid2] ^= (*it)->getHash();
353	gezelter	1879	}
354	gezelter	1535	}
355	gezelter	1895	interactions_[atid1][atid2].insert(maw_);
356	gezelter	1927	iHash_[atid1][atid2] \|= MAW_INTERACTION;
357	gezelter	1535	vdwExplicit = true;
358			}
359	gezelter	1502	}
360			}
361			}
362
363	gezelter	1535
364	gezelter	1583	// Make sure every pair of atom types in this simulation has a
365			// non-bonded interaction. If not, just inform the user.
366	gezelter	1535
367			set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
368			set<AtomType*>::iterator it, jt;
369	gezelter	1583
370	gezelter	1535	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
371			atype1 = (*it);
372	gezelter	1895	atid1 = atype1->getIdent();
373	gezelter	1583	for (jt = it; jt != simTypes.end(); ++jt) {
374	gezelter	1535	atype2 = (*jt);
375	gezelter	2005	atid2 = atype2->getIdent();
376	gezelter	1502
377	gezelter	1895	if (interactions_[atid1][atid2].size() == 0) {
378	gezelter	1502	sprintf( painCave.errMsg,
379	gezelter	1583	"InteractionManager could not find a matching non-bonded\n"
380			"\tinteraction for atom types %s - %s\n"
381			"\tProceeding without this interaction.\n",
382	gezelter	1502	atype1->getName().c_str(), atype2->getName().c_str());
383			painCave.severity = OPENMD_INFO;
384	gezelter	1583	painCave.isFatal = 0;
385	gezelter	1502	simError();
386			}
387			}
388			}
389	gezelter	1535
390			initialized_ = true;
391			}
392	gezelter	1584
393			void InteractionManager::setCutoffRadius(RealType rcut) {
394	gezelter	1587
395	gezelter	1584	electrostatic_->setCutoffRadius(rcut);
396	gezelter	1586	eam_->setCutoffRadius(rcut);
397	gezelter	1584	}
398
399	gezelter	1895	void InteractionManager::doPrePair(InteractionData &idat){
400	gezelter	1502
401			if (!initialized_) initialize();
402	gezelter	1545
403	gezelter	1587	// excluded interaction, so just return
404			if (idat.excluded) return;
405
406	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
407	gezelter	1504
408	gezelter	1927	if ((iHash & EAM_INTERACTION) != 0) eam_->calcDensity(idat);
409			if ((iHash & SC_INTERACTION) != 0) sc_->calcDensity(idat);
410	gezelter	1879
411			// set<NonBondedInteraction*>::iterator it;
412
413			// for (it = interactions_[ idat.atypes ].begin();
414			// it != interactions_[ idat.atypes ].end(); ++it){
415			// if ((*it)->getFamily() == METALLIC_FAMILY) {
416			// dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
417			// }
418			// }
419	gezelter	1502
420			return;
421			}
422	gezelter	1504
423	gezelter	1895	void InteractionManager::doPreForce(SelfData &sdat){
424	gezelter	1502
425	gezelter	1504	if (!initialized_) initialize();
426	gezelter	1545
427	gezelter	1927	int& sHash = sHash_[sdat.atid];
428	gezelter	1879
429	jmichalk	2031	if ((sHash & EAM_INTERACTION) != 0) eam_->calcFunctional(sdat);
430	gezelter	1927	if ((sHash & SC_INTERACTION) != 0) sc_->calcFunctional(sdat);
431	gezelter	1879
432			// set<NonBondedInteraction*>::iterator it;
433	gezelter	1502
434	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
435	gezelter	1879	// if ((*it)->getFamily() == METALLIC_FAMILY) {
436			// dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
437			// }
438			// }
439	gezelter	1504
440	gezelter	1502	return;
441			}
442
443	gezelter	1895	void InteractionManager::doPair(InteractionData &idat){
444	gezelter	1504
445	gezelter	1502	if (!initialized_) initialize();
446	gezelter	1587
447	gezelter	1895	int& iHash = iHash_[idat.atid1][idat.atid2];
448	gezelter	1502
449	gezelter	1927	if ((iHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcForce(idat);
450	gezelter	1879
451			// electrostatics still has to worry about indirect
452			// contributions from excluded pairs of atoms, but nothing else does:
453	gezelter	1502
454	gezelter	1879	if (idat.excluded) return;
455	gezelter	1502
456	gezelter	1927	if ((iHash & LJ_INTERACTION) != 0) lj_->calcForce(idat);
457			if ((iHash & GB_INTERACTION) != 0) gb_->calcForce(idat);
458			if ((iHash & STICKY_INTERACTION) != 0) sticky_->calcForce(idat);
459			if ((iHash & MORSE_INTERACTION) != 0) morse_->calcForce(idat);
460			if ((iHash & REPULSIVEPOWER_INTERACTION) != 0) repulsivePower_->calcForce(idat);
461			if ((iHash & EAM_INTERACTION) != 0) eam_->calcForce(idat);
462			if ((iHash & SC_INTERACTION) != 0) sc_->calcForce(idat);
463			if ((iHash & MAW_INTERACTION) != 0) maw_->calcForce(idat);
464	gezelter	1879
465			// set<NonBondedInteraction*>::iterator it;
466
467			// for (it = interactions_[ idat.atypes ].begin();
468			// it != interactions_[ idat.atypes ].end(); ++it) {
469
470			// // electrostatics still has to worry about indirect
471			// // contributions from excluded pairs of atoms:
472
473			// if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
474			// (*it)->calcForce(idat);
475			// }
476			// }
477	gezelter	1502
478	gezelter	1504	return;
479	gezelter	1502	}
480
481	gezelter	1895	void InteractionManager::doSelfCorrection(SelfData &sdat){
482	gezelter	1502
483			if (!initialized_) initialize();
484	gezelter	1504
485	gezelter	1927	int& sHash = sHash_[sdat.atid];
486	gezelter	1502
487	gezelter	1927	if ((sHash & ELECTROSTATIC_INTERACTION) != 0) electrostatic_->calcSelfCorrection(sdat);
488	gezelter	1879
489			// set<NonBondedInteraction*>::iterator it;
490
491	gezelter	1895	// for (it = interactions_[atid1][atid2].begin(); it != interactions_[atid1][atid2].end(); ++it){
492	gezelter	1879	// if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
493			// dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
494			// }
495			// }
496	gezelter	1536
497	gezelter	1504	return;
498	gezelter	1502	}
499
500	gezelter	1925	void InteractionManager::doReciprocalSpaceSum(RealType &pot){
501	gezelter	1915	if (!initialized_) initialize();
502	gezelter	1921	electrostatic_->ReciprocalSpaceSum(pot);
503	gezelter	1915	}
504
505	gezelter	1505	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
506			if (!initialized_) initialize();
507	gezelter	1755
508	gezelter	1505	AtomType* atype = typeMap_[*atid];
509
510			set<NonBondedInteraction*>::iterator it;
511			RealType cutoff = 0.0;
512
513	gezelter	1921	for (it = interactions_[atid][atid].begin();
514			it != interactions_[atid][atid].end();
515	gezelter	1895	++it)
516	gezelter	2033	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
517			atype)));
518	gezelter	1505	return cutoff;
519			}
520
521	gezelter	1528	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
522			if (!initialized_) initialize();
523
524	gezelter	1895	int atid = atype->getIdent();
525
526	gezelter	1528	set<NonBondedInteraction*>::iterator it;
527			RealType cutoff = 0.0;
528
529	gezelter	1921	for (it = interactions_[atid][atid].begin();
530			it != interactions_[atid][atid].end(); ++it)
531	gezelter	2033	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(make_pair(atype,
532			atype)));
533	gezelter	1528	return cutoff;
534			}
535	gezelter	1502	} //end namespace OpenMD