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::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:	1608
Committed:	Tue Aug 9 01:58:56 2011 UTC (13 years, 8 months ago) by mciznick
File size:	16302 byte(s)
Log Message:	First OpenMP version.
#	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, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "nonbonded/InteractionManager.hpp"
43
44	namespace OpenMD {
45
46	InteractionManager::InteractionManager() {
47
48	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	}
59
60	void InteractionManager::initialize() {
61
62	ForceField* forceField_ = info_->getForceField();
63
64	lj_->setForceField(forceField_);
65	gb_->setForceField(forceField_);
66	sticky_->setForceField(forceField_);
67	eam_->setForceField(forceField_);
68	sc_->setForceField(forceField_);
69	morse_->setForceField(forceField_);
70	electrostatic_->setSimInfo(info_);
71	electrostatic_->setForceField(forceField_);
72	maw_->setForceField(forceField_);
73
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
144	if (nbiType != NULL) {
145
146	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	}
158
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	}
181
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	}
194
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	}
217
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	}
241	}
242	}
243
244
245	// Make sure every pair of atom types in this simulation has a
246	// non-bonded interaction. If not, just inform the user.
247
248	set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
249	set<AtomType*>::iterator it, jt;
250
251	for (it = simTypes.begin(); it != simTypes.end(); ++it) {
252	atype1 = (*it);
253	for (jt = it; jt != simTypes.end(); ++jt) {
254	atype2 = (*jt);
255	key = make_pair(atype1, atype2);
256
257	if (interactions_[key].size() == 0) {
258	sprintf( painCave.errMsg,
259	"InteractionManager could not find a matching non-bonded\n"
260	"\tinteraction for atom types %s - %s\n"
261	"\tProceeding without this interaction.\n",
262	atype1->getName().c_str(), atype2->getName().c_str());
263	painCave.severity = OPENMD_INFO;
264	painCave.isFatal = 0;
265	simError();
266	}
267	}
268	}
269
270	initialized_ = true;
271	}
272
273	void InteractionManager::setCutoffRadius(RealType rcut) {
274
275	electrostatic_->setCutoffRadius(rcut);
276	eam_->setCutoffRadius(rcut);
277	}
278
279	void InteractionManager::setSwitchingRadius(RealType rswitch) {
280	electrostatic_->setSwitchingRadius(rswitch);
281	}
282
283	void InteractionManager::doPrePair(InteractionData idat){
284	printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
285	/* if (!initialized_) initialize();
286
287	// excluded interaction, so just return
288	if (idat.excluded) return;
289
290	set<NonBondedInteraction*>::iterator it;
291
292	for (it = interactions_[ idat.atypes ].begin();
293	it != interactions_[ idat.atypes ].end(); ++it){
294	if ((*it)->getFamily() == METALLIC_FAMILY) {
295	dynamic_cast<MetallicInteraction>(it)->calcDensity(idat);
296	}
297	}*/
298
299	return;
300	}
301
302	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	void InteractionManager::doPreForce(SelfData sdat){
326
327	if (!initialized_) initialize();
328
329	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
330	set<NonBondedInteraction*>::iterator it;
331
332	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
333	if ((*it)->getFamily() == METALLIC_FAMILY) {
334	dynamic_cast<MetallicInteraction>(it)->calcFunctional(sdat);
335	}
336	}
337
338	return;
339	}
340
341	void InteractionManager::doPair(InteractionData idat){
342	printf("%s\tERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n", __FUNCTION__);
343	/*if (!initialized_) initialize();
344
345	set<NonBondedInteraction*>::iterator it;
346
347	for (it = interactions_[ idat.atypes ].begin();
348	it != interactions_[ idat.atypes ].end(); ++it) {
349
350	// electrostatics still has to worry about indirect
351	// contributions from excluded pairs of atoms:
352
353	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
354	(*it)->calcForce(idat);
355	}
356	}*/
357
358	return;
359	}
360
361	void InteractionManager::wrapData(InteractionDataPrv &src, InteractionData &dst) {
362	dst.A1 = src.A1;
363	dst.A2 = src.A2;
364	dst.atypes = src.atypes;
365	dst.d = &src.d;
366	dst.dfrho1 = src.dfrho1;
367	dst.dfrho2 = src.dfrho2;
368	dst.eFrame1 = src.eFrame1;
369	dst.eFrame2 = src.eFrame2;
370	dst.electroMult = &src.electroMult;
371	dst.excluded = src.excluded;
372	dst.f1 = &src.f1;
373	dst.frho1 = src.frho1;
374	dst.frho2 = src.frho2;
375	dst.particlePot1 = src.particlePot1;
376	dst.particlePot2 = src.particlePot2;
377	dst.pot = &src.pot;
378	dst.r2 = &src.r2;
379	dst.rcut = &src.rcut;
380	dst.rho1 = src.rho1;
381	dst.rho2 = src.rho2;
382	dst.rij = &src.rij;
383	dst.shiftedForce = src.shiftedForce;
384	dst.shiftedPot = src.shiftedPot;
385	dst.skippedCharge1 = src.skippedCharge1;
386	dst.skippedCharge2 = src.skippedCharge2;
387	dst.sw = &src.sw;
388	dst.t1 = src.t1;
389	dst.t2 = src.t2;
390	dst.topoDist = src.topoDist;
391	dst.vdwMult = &src.vdwMult;
392	dst.vpair = &src.vpair;
393	}
394
395	void InteractionManager::doPairOMP(InteractionDataPrv &idatThread){
396	set<NonBondedInteraction*>::iterator it;
397	InteractionData idat;
398
399	wrapData(idatThread, idat);
400
401	for (it = interactions_[ idat.atypes ].begin();
402	it != interactions_[ idat.atypes ].end(); ++it) {
403
404	// electrostatics still has to worry about indirect
405	// contributions from excluded pairs of atoms:
406
407	if (!idat.excluded \|\| (*it)->getFamily() == ELECTROSTATIC_FAMILY) {
408	(*it)->calcForce(idat);
409	}
410	}
411
412	return;
413	}
414
415	void InteractionManager::doSelfCorrection(SelfData sdat){
416
417	if (!initialized_) initialize();
418
419	pair<AtomType, AtomType> key = make_pair(sdat.atype, sdat.atype);
420	set<NonBondedInteraction*>::iterator it;
421
422	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){
423	if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
424	dynamic_cast<ElectrostaticInteraction>(it)->calcSelfCorrection(sdat);
425	}
426	}
427
428	return;
429	}
430
431	RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
432	if (!initialized_) initialize();
433
434	AtomType* atype = typeMap_[*atid];
435
436	pair<AtomType, AtomType> key = make_pair(atype, atype);
437	set<NonBondedInteraction*>::iterator it;
438	RealType cutoff = 0.0;
439
440	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
441	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
442	return cutoff;
443	}
444
445	RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) {
446	if (!initialized_) initialize();
447
448	pair<AtomType, AtomType> key = make_pair(atype, atype);
449	set<NonBondedInteraction*>::iterator it;
450	RealType cutoff = 0.0;
451
452	for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it)
453	cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key));
454	return cutoff;
455	}
456	} //end namespace OpenMD