src/nonbonded/EAM.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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include <stdio.h>
#include <string.h>

#include <cmath>
#include "nonbonded/EAM.hpp"
#include "utils/simError.h"
#include "types/NonBondedInteractionType.hpp"


namespace OpenMD {

  EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL), 
               mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
  
  CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {   
    EAMAdapter ea1 = EAMAdapter(atomType1);
    EAMAdapter ea2 = EAMAdapter(atomType2);
    CubicSpline* z1 = ea1.getZ();
    CubicSpline* z2 = ea2.getZ();

    // make the r grid:


    // we need phi out to the largest value we'll encounter in the radial space;
    
    RealType rmax = 0.0;
    rmax = max(rmax, ea1.getRcut());
    rmax = max(rmax, ea1.getNr() * ea1.getDr());

    rmax = max(rmax, ea2.getRcut());
    rmax = max(rmax, ea2.getNr() * ea2.getDr());

    // use the smallest dr (finest grid) to build our grid:

    RealType dr = min(ea1.getDr(), ea2.getDr()); 

    int nr = int(rmax/dr + 0.5);

    vector<RealType> rvals;
    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));

    // construct the pair potential:

    vector<RealType> phivals;
    RealType phi;
    RealType r;
    RealType zi, zj;

    phivals.push_back(0.0);

    for (int i = 1; i < rvals.size(); i++ ) {
      r = rvals[i];

      // only use z(r) if we're inside this atom's cutoff radius,
      // otherwise, we'll use zero for the charge.  This effectively
      // means that our phi grid goes out beyond the cutoff of the
      // pair potential

      zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0;
      zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0;

      phi = 331.999296 * (zi * zj) / r;

      phivals.push_back(phi);
    }
      
    CubicSpline* cs = new CubicSpline();
    cs->addPoints(rvals, phivals);
    return cs;
  }

  void EAM::setCutoffRadius( RealType rCut ) {
    eamRcut_ = rCut;
    haveCutoffRadius_ = true;
  }

  void EAM::initialize() { 

    // set up the mixing method:
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    string EAMMixMeth = fopts.getEAMMixingMethod();
    toUpper(EAMMixMeth);
   
    if (EAMMixMeth == "JOHNSON") 
      mixMeth_ = eamJohnson;    
    else if (EAMMixMeth == "DAW")
      mixMeth_ = eamDaw;
    else
      mixMeth_ = eamUnknown;
      
    // find all of the EAM atom Types:
    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypes->beginType(i); at != NULL; 
         at = atomTypes->nextType(i)) {
      
      if (at->isEAM())
        addType(at);
    }
    
    // find all of the explicit EAM interactions (setfl):
    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    NonBondedInteractionType* nbt;

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isEAM()) {
        
        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("EAM");
        if (data == NULL) {
          sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
                   "\tEAM parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
        
        EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
        if (eamData == NULL) {
          sprintf( painCave.errMsg,
                   "EAM::rebuildMixingMap could not convert GenericData to\n"
                   "\tEAMMixingData for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        EAMMixingParam eamParam = eamData->getData();

        vector<RealType> phiAB = eamParam.phi;
        RealType dr = eamParam.dr;
        int nr = eamParam.nr;

        addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
      }
    }  
    initialized_ = true;
  }
      

  void EAM::addType(AtomType* atomType){

    EAMAdapter ea = EAMAdapter(atomType);
    EAMAtomData eamAtomData;

    eamAtomData.rho = ea.getRho();
    eamAtomData.F = ea.getF();
    eamAtomData.Z = ea.getZ();
    eamAtomData.rcut = ea.getRcut();

    // add it to the map:

    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = EAMlist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "EAM already had a previous entry with ident %d\n",
               atomType->getIdent());
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }

    EAMMap[atomType] = eamAtomData;
    
    // Now, iterate over all known types and add to the mixing map:
    
    map<AtomType*, EAMAtomData>::iterator it;
    for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
      
      AtomType* atype2 = (*it).first;

      EAMInteractionData mixer;
      mixer.phi = getPhi(atomType, atype2);
      mixer.explicitlySet = false;

      pair<AtomType*, AtomType*> key1, key2;
      key1 = make_pair(atomType, atype2);
      key2 = make_pair(atype2, atomType);
      
      MixingMap[key1] = mixer;
      if (key2 != key1) {
        MixingMap[key2] = mixer;
      }
    }      
    return;
  }
  
  void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2, 
                                   RealType dr, int nr,
                                   vector<RealType> phiVals) {
    
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);

    EAMInteractionData mixer;
    CubicSpline* cs = new CubicSpline();
    vector<RealType> rVals;

    for (int i = 0; i < nr; i++) rVals.push_back(i * dr);

    cs->addPoints(rVals, phiVals);
    mixer.phi = cs;
    mixer.explicitlySet = true;

    pair<AtomType*, AtomType*> key1, key2;
    key1 = make_pair(atype1, atype2);
    key2 = make_pair(atype2, atype1);
    
    MixingMap[key1] = mixer;
    if (key2 != key1) {
      MixingMap[key2] = mixer;
    }    
    return;
  }

  void EAM::calcDensity(InteractionData &idat) {
    
    if (!initialized_) initialize();
    
    EAMAtomData data1 = EAMMap[idat.atypes.first];
    EAMAtomData data2 = EAMMap[idat.atypes.second];
    
    if (haveCutoffRadius_) 
      if ( *(idat.rij) > eamRcut_) return;
    
    if ( *(idat.rij) < data1.rcut) 
      *(idat.rho1) += data1.rho->getValueAt( *(idat.rij));
    
      
    if ( *(idat.rij) < data2.rcut) 
      *(idat.rho2) += data2.rho->getValueAt( *(idat.rij));
    
    return;  
  }
  
  void EAM::calcFunctional(SelfData &sdat) {
    
    if (!initialized_) initialize();

    EAMAtomData data1 = EAMMap[ sdat.atype ];
        
    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );

    *(sdat.frho) = result.first;
    *(sdat.dfrhodrho) = result.second;

    (*(sdat.pot))[METALLIC_FAMILY] += result.first;
    *(sdat.particlePot) += result.first;

    return;
  }

 
  void EAM::calcForce(InteractionData &idat) {

    if (!initialized_) initialize();

    if (haveCutoffRadius_) 
      if ( *(idat.rij) > eamRcut_) return;
   
    pair<RealType, RealType> res;
    
    EAMAtomData data1 = EAMMap[idat.atypes.first];
    EAMAtomData data2 = EAMMap[idat.atypes.second];
    
    // get type-specific cutoff radii
    
    RealType rci = data1.rcut;
    RealType rcj = data2.rcut;
    
    RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
    RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
    RealType phab(0.0), dvpdr(0.0);
    RealType drhoidr, drhojdr, dudr;
    
    if ( *(idat.rij) < rci) {
      res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
      rha = res.first;
      drha = res.second;
      
      res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
      pha = res.first;
      dpha = res.second;
    }
    
    if ( *(idat.rij) < rcj) {
      res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
      rhb = res.first;
      drhb = res.second;
      
      res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
      phb = res.first;
      dphb = res.second;
    }

    switch(mixMeth_) {
    case eamJohnson:
      
      if ( *(idat.rij) < rci) {
        phab = phab + 0.5 * (rhb / rha) * pha;
        dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + 
                             pha*((drhb/rha) - (rhb*drha/rha/rha)));
      }
      
      
      if ( *(idat.rij) < rcj) {
        phab = phab + 0.5 * (rha / rhb) * phb;
        dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb + 
                               phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
      }
      
      break;
      
    case eamDaw:
      res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
      phab = res.first;
      dvpdr = res.second;
      
      break;
    case eamUnknown:
    default:
      
      sprintf(painCave.errMsg,
              "EAM::calcForce hit a mixing method it doesn't know about!\n"
              );
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();        
      
    }
    
    drhoidr = drha;
    drhojdr = drhb;
    
    dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr; 
    
    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
        
    // particlePot is the difference between the full potential and
    // the full potential without the presence of a particular
    // particle (atom1).
    //
    // This reduces the density at other particle locations, so we
    // need to recompute the density at atom2 assuming atom1 didn't
    // contribute.  This then requires recomputing the density
    // functional for atom2 as well.
    
    *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha ) 
      - *(idat.frho2);
    
    *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb) 
      - *(idat.frho1);
    
    (*(idat.pot))[METALLIC_FAMILY] += phab;
    
    *(idat.vpair) += phab;
  
    return;
    
  }

  RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   

    RealType cut = 0.0;

    map<AtomType*, EAMAtomData>::iterator it;

    it = EAMMap.find(atypes.first);
    if (it != EAMMap.end()) {
      EAMAtomData data1 = (*it).second;
      cut = data1.rcut;
    }

    it = EAMMap.find(atypes.second);
    if (it != EAMMap.end()) {
      EAMAtomData data2 = (*it).second;
      if (data2.rcut > cut)
        cut = data2.rcut;
    }

    return cut;
  }
}

Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	13231 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	User	Rev	Content
1	gezelter	1478	/*
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	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	1478	*/
42
43			#include <stdio.h>
44			#include <string.h>
45
46			#include <cmath>
47			#include "nonbonded/EAM.hpp"
48			#include "utils/simError.h"
49	gezelter	1479	#include "types/NonBondedInteractionType.hpp"
50	gezelter	1478
51
52			namespace OpenMD {
53
54	gezelter	1502	EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL),
55	gezelter	1586	mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
56	gezelter	1478
57	gezelter	1710	CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {
58			EAMAdapter ea1 = EAMAdapter(atomType1);
59			EAMAdapter ea2 = EAMAdapter(atomType2);
60			CubicSpline* z1 = ea1.getZ();
61			CubicSpline* z2 = ea2.getZ();
62	gezelter	1478
63			// make the r grid:
64
65
66	gezelter	1481	// we need phi out to the largest value we'll encounter in the radial space;
67
68			RealType rmax = 0.0;
69	gezelter	1710	rmax = max(rmax, ea1.getRcut());
70			rmax = max(rmax, ea1.getNr() * ea1.getDr());
71	gezelter	1478
72	gezelter	1710	rmax = max(rmax, ea2.getRcut());
73			rmax = max(rmax, ea2.getNr() * ea2.getDr());
74	gezelter	1481
75	gezelter	1478	// use the smallest dr (finest grid) to build our grid:
76
77	gezelter	1710	RealType dr = min(ea1.getDr(), ea2.getDr());
78	gezelter	1481
79			int nr = int(rmax/dr + 0.5);
80
81	gezelter	1478	vector<RealType> rvals;
82	gezelter	1481	for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
83	gezelter	1478
84			// construct the pair potential:
85
86			vector<RealType> phivals;
87			RealType phi;
88			RealType r;
89			RealType zi, zj;
90
91			phivals.push_back(0.0);
92
93			for (int i = 1; i < rvals.size(); i++ ) {
94			r = rvals[i];
95
96	gezelter	1502	// only use z(r) if we're inside this atom's cutoff radius,
97			// otherwise, we'll use zero for the charge. This effectively
98			// means that our phi grid goes out beyond the cutoff of the
99			// pair potential
100	gezelter	1481
101	gezelter	1710	zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0;
102			zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0;
103	gezelter	1481
104	gezelter	1478	phi = 331.999296 * (zi * zj) / r;
105	gezelter	1481
106	gezelter	1478	phivals.push_back(phi);
107			}
108
109			CubicSpline* cs = new CubicSpline();
110			cs->addPoints(rvals, phivals);
111			return cs;
112			}
113
114	gezelter	1586	void EAM::setCutoffRadius( RealType rCut ) {
115			eamRcut_ = rCut;
116			haveCutoffRadius_ = true;
117			}
118
119	gezelter	1478	void EAM::initialize() {
120
121			// set up the mixing method:
122	gezelter	1479	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
123	gezelter	1481	string EAMMixMeth = fopts.getEAMMixingMethod();
124	gezelter	1480	toUpper(EAMMixMeth);
125
126	gezelter	1478	if (EAMMixMeth == "JOHNSON")
127			mixMeth_ = eamJohnson;
128			else if (EAMMixMeth == "DAW")
129			mixMeth_ = eamDaw;
130			else
131			mixMeth_ = eamUnknown;
132
133			// find all of the EAM atom Types:
134			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
135			ForceField::AtomTypeContainer::MapTypeIterator i;
136			AtomType* at;
137
138			for (at = atomTypes->beginType(i); at != NULL;
139			at = atomTypes->nextType(i)) {
140
141			if (at->isEAM())
142			addType(at);
143			}
144
145			// find all of the explicit EAM interactions (setfl):
146			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
147			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
148			NonBondedInteractionType* nbt;
149
150			for (nbt = nbiTypes->beginType(j); nbt != NULL;
151			nbt = nbiTypes->nextType(j)) {
152
153			if (nbt->isEAM()) {
154
155	gezelter	1481	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
156	gezelter	1478
157			GenericData* data = nbt->getPropertyByName("EAM");
158			if (data == NULL) {
159			sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
160			"\tEAM parameters for %s - %s interaction.\n",
161			atypes.first->getName().c_str(),
162			atypes.second->getName().c_str());
163			painCave.severity = OPENMD_ERROR;
164			painCave.isFatal = 1;
165			simError();
166			}
167
168			EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
169			if (eamData == NULL) {
170			sprintf( painCave.errMsg,
171			"EAM::rebuildMixingMap could not convert GenericData to\n"
172			"\tEAMMixingData for %s - %s interaction.\n",
173			atypes.first->getName().c_str(),
174			atypes.second->getName().c_str());
175			painCave.severity = OPENMD_ERROR;
176			painCave.isFatal = 1;
177			simError();
178			}
179
180	gezelter	1479	EAMMixingParam eamParam = eamData->getData();
181	gezelter	1478
182	gezelter	1479	vector<RealType> phiAB = eamParam.phi;
183	gezelter	1478	RealType dr = eamParam.dr;
184			int nr = eamParam.nr;
185
186			addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
187			}
188			}
189			initialized_ = true;
190			}
191
192
193
194			void EAM::addType(AtomType* atomType){
195
196	gezelter	1710	EAMAdapter ea = EAMAdapter(atomType);
197	gezelter	1478	EAMAtomData eamAtomData;
198
199	gezelter	1710	eamAtomData.rho = ea.getRho();
200			eamAtomData.F = ea.getF();
201			eamAtomData.Z = ea.getZ();
202			eamAtomData.rcut = ea.getRcut();
203
204	gezelter	1478	// add it to the map:
205
206	gezelter	1481	pair<map<int,AtomType*>::iterator,bool> ret;
207	gezelter	1710	ret = EAMlist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) );
208	gezelter	1478	if (ret.second == false) {
209			sprintf( painCave.errMsg,
210			"EAM already had a previous entry with ident %d\n",
211	gezelter	1710	atomType->getIdent());
212	gezelter	1478	painCave.severity = OPENMD_INFO;
213			painCave.isFatal = 0;
214			simError();
215			}
216
217			EAMMap[atomType] = eamAtomData;
218
219			// Now, iterate over all known types and add to the mixing map:
220
221	gezelter	1481	map<AtomType*, EAMAtomData>::iterator it;
222	gezelter	1478	for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
223
224	gezelter	1479	AtomType* atype2 = (*it).first;
225	gezelter	1478
226			EAMInteractionData mixer;
227			mixer.phi = getPhi(atomType, atype2);
228			mixer.explicitlySet = false;
229
230	gezelter	1481	pair<AtomType, AtomType> key1, key2;
231			key1 = make_pair(atomType, atype2);
232			key2 = make_pair(atype2, atomType);
233	gezelter	1478
234			MixingMap[key1] = mixer;
235			if (key2 != key1) {
236			MixingMap[key2] = mixer;
237			}
238			}
239			return;
240			}
241
242			void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
243			RealType dr, int nr,
244			vector<RealType> phiVals) {
245
246			// in case these weren't already in the map
247			addType(atype1);
248			addType(atype2);
249
250			EAMInteractionData mixer;
251			CubicSpline* cs = new CubicSpline();
252	gezelter	1479	vector<RealType> rVals;
253	gezelter	1478
254	gezelter	1479	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
255	gezelter	1478
256			cs->addPoints(rVals, phiVals);
257			mixer.phi = cs;
258			mixer.explicitlySet = true;
259
260	gezelter	1481	pair<AtomType, AtomType> key1, key2;
261			key1 = make_pair(atype1, atype2);
262			key2 = make_pair(atype2, atype1);
263	gezelter	1478
264			MixingMap[key1] = mixer;
265			if (key2 != key1) {
266			MixingMap[key2] = mixer;
267			}
268			return;
269			}
270
271	gezelter	1545	void EAM::calcDensity(InteractionData &idat) {
272	gezelter	1479
273	gezelter	1478	if (!initialized_) initialize();
274	gezelter	1479
275	gezelter	1571	EAMAtomData data1 = EAMMap[idat.atypes.first];
276			EAMAtomData data2 = EAMMap[idat.atypes.second];
277	gezelter	1586
278			if (haveCutoffRadius_)
279			if ( *(idat.rij) > eamRcut_) return;
280
281	gezelter	1629	if ( *(idat.rij) < data1.rcut)
282	gezelter	1575	(idat.rho1) += data1.rho->getValueAt( (idat.rij));
283	gezelter	1629
284	gezelter	1586
285	gezelter	1629	if ( *(idat.rij) < data2.rcut)
286			(idat.rho2) += data2.rho->getValueAt( (idat.rij));
287
288			return;
289	gezelter	1478	}
290	gezelter	1586
291	gezelter	1545	void EAM::calcFunctional(SelfData &sdat) {
292	gezelter	1586
293	gezelter	1478	if (!initialized_) initialize();
294
295	gezelter	1554	EAMAtomData data1 = EAMMap[ sdat.atype ];
296	gezelter	1478
297	gezelter	1554	pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );
298	gezelter	1478
299	gezelter	1554	*(sdat.frho) = result.first;
300			*(sdat.dfrhodrho) = result.second;
301	gezelter	1575
302	gezelter	1586	(*(sdat.pot))[METALLIC_FAMILY] += result.first;
303	gezelter	1575	*(sdat.particlePot) += result.first;
304
305	gezelter	1478	return;
306			}
307
308
309	gezelter	1536	void EAM::calcForce(InteractionData &idat) {
310	gezelter	1478
311			if (!initialized_) initialize();
312	gezelter	1481
313	gezelter	1586	if (haveCutoffRadius_)
314			if ( *(idat.rij) > eamRcut_) return;
315
316	gezelter	1478	pair<RealType, RealType> res;
317
318	gezelter	1586	EAMAtomData data1 = EAMMap[idat.atypes.first];
319			EAMAtomData data2 = EAMMap[idat.atypes.second];
320
321			// get type-specific cutoff radii
322
323			RealType rci = data1.rcut;
324			RealType rcj = data2.rcut;
325
326			RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
327			RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
328			RealType phab(0.0), dvpdr(0.0);
329			RealType drhoidr, drhojdr, dudr;
330
331			if ( *(idat.rij) < rci) {
332			res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
333			rha = res.first;
334			drha = res.second;
335
336			res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
337			pha = res.first;
338			dpha = res.second;
339			}
340
341			if ( *(idat.rij) < rcj) {
342			res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
343			rhb = res.first;
344			drhb = res.second;
345
346			res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
347			phb = res.first;
348			dphb = res.second;
349			}
350	gezelter	1478
351	gezelter	1586	switch(mixMeth_) {
352			case eamJohnson:
353	gezelter	1478
354	gezelter	1554	if ( *(idat.rij) < rci) {
355	gezelter	1586	phab = phab + 0.5 * (rhb / rha) * pha;
356			dvpdr = dvpdr + 0.5((rhb/rha)dpha +
357			pha((drhb/rha) - (rhbdrha/rha/rha)));
358	gezelter	1478	}
359	gezelter	1586
360
361
362	gezelter	1554	if ( *(idat.rij) < rcj) {
363	gezelter	1586	phab = phab + 0.5 * (rha / rhb) * phb;
364			dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
365			phb((drha/rhb) - (rhadrhb/rhb/rhb)));
366	gezelter	1478	}
367
368	gezelter	1586	break;
369
370			case eamDaw:
371			res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
372			phab = res.first;
373			dvpdr = res.second;
374
375			break;
376			case eamUnknown:
377			default:
378
379			sprintf(painCave.errMsg,
380			"EAM::calcForce hit a mixing method it doesn't know about!\n"
381			);
382			painCave.severity = OPENMD_ERROR;
383			painCave.isFatal = 1;
384			simError();
385
386			}
387
388			drhoidr = drha;
389			drhojdr = drhb;
390
391			dudr = drhojdr* (idat.dfrho1) + drhoidr *(idat.dfrho2) + dvpdr;
392
393			(idat.f1) += (idat.d) * dudr / *(idat.rij);
394	gezelter	1478
395	gezelter	1586	// particlePot is the difference between the full potential and
396			// the full potential without the presence of a particular
397			// particle (atom1).
398			//
399			// This reduces the density at other particle locations, so we
400			// need to recompute the density at atom2 assuming atom1 didn't
401			// contribute. This then requires recomputing the density
402			// functional for atom2 as well.
403
404			(idat.particlePot1) += data2.F->getValueAt( (idat.rho2) - rha )
405			- *(idat.frho2);
406
407			(idat.particlePot2) += data1.F->getValueAt( (idat.rho1) - rhb)
408			- *(idat.frho1);
409
410			(*(idat.pot))[METALLIC_FAMILY] += phab;
411
412			*(idat.vpair) += phab;
413
414	gezelter	1478	return;
415
416			}
417	gezelter	1505
418	gezelter	1545	RealType EAM::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
419	gezelter	1505	if (!initialized_) initialize();
420
421			RealType cut = 0.0;
422
423			map<AtomType*, EAMAtomData>::iterator it;
424
425	gezelter	1545	it = EAMMap.find(atypes.first);
426	gezelter	1505	if (it != EAMMap.end()) {
427			EAMAtomData data1 = (*it).second;
428			cut = data1.rcut;
429			}
430
431	gezelter	1545	it = EAMMap.find(atypes.second);
432	gezelter	1505	if (it != EAMMap.end()) {
433			EAMAtomData data2 = (*it).second;
434			if (data2.rcut > cut)
435			cut = data2.rcut;
436			}
437
438			return cut;
439			}
440	gezelter	1478	}
441