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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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) {}
  
  EAMParam EAM::getEAMParam(AtomType* atomType) {
    
    // Do sanity checking on the AtomType we were passed before
    // building any data structures:
    if (!atomType->isEAM()) {
      sprintf( painCave.errMsg,
               "EAM::getEAMParam was passed an atomType (%s) that does not\n"
               "\tappear to be an embedded atom method (EAM) atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    GenericData* data = atomType->getPropertyByName("EAM");
    if (data == NULL) {
      sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n"
               "\tparameters for atomType %s.\n", 
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError(); 
    }
    
    EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
    if (eamData == NULL) {
      sprintf( painCave.errMsg,
               "EAM::getEAMParam could not convert GenericData to EAMParam for\n"
               "\tatom type %s\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    
    return eamData->getData();
  }

  CubicSpline* EAM::getZ(AtomType* atomType) {    
    EAMParam eamParam = getEAMParam(atomType);
    int nr = eamParam.nr;
    RealType dr = eamParam.dr;
    vector<RealType> rvals;
    
    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr);
      
    CubicSpline* cs = new CubicSpline();
    cs->addPoints(rvals, eamParam.Z);
    return cs;
  }

  RealType EAM::getRcut(AtomType* atomType) {    
    EAMParam eamParam = getEAMParam(atomType);
    return eamParam.rcut;
  }

  CubicSpline* EAM::getRho(AtomType* atomType) {    
    EAMParam eamParam = getEAMParam(atomType);
    int nr = eamParam.nr;
    RealType dr = eamParam.dr;
    vector<RealType> rvals;
    
    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr);
      
    CubicSpline* cs = new CubicSpline();
    cs->addPoints(rvals, eamParam.rho);
    return cs;
  }

  CubicSpline* EAM::getF(AtomType* atomType) {    
    EAMParam eamParam = getEAMParam(atomType);
    int nrho = eamParam.nrho;
    RealType drho = eamParam.drho;
    vector<RealType> rhovals;
    vector<RealType> scaledF;
    
    for (int i = 0; i < nrho; i++) {
      rhovals.push_back(RealType(i) * drho);
      scaledF.push_back( eamParam.F[i] * 23.06054 );
    }
      
    CubicSpline* cs = new CubicSpline();
    cs->addPoints(rhovals, scaledF);
    return cs;
  }
  
  CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {    
    EAMParam eamParam1 = getEAMParam(atomType1);
    EAMParam eamParam2 = getEAMParam(atomType2);
    CubicSpline* z1 = getZ(atomType1);
    CubicSpline* z2 = getZ(atomType2);

    // 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, eamParam1.rcut);
    rmax = max(rmax, eamParam1.nr * eamParam1.dr);

    rmax = max(rmax, eamParam2.rcut);
    rmax = max(rmax, eamParam2.nr * eamParam2.dr);

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

    RealType dr = min(eamParam1.dr, eamParam2.dr); 

    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 <= eamParam1.rcut ? z1->getValueAt(r) : 0.0;
      zj = r <= eamParam2.rcut ? 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){

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

    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();    

    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "EAM already had a previous entry with ident %d\n",
               atp.ident);
      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:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 7 months ago) by gezelter
File size:	15826 byte(s)
Log Message:	Merging changes from old branch into development branch
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <stdio.h>
43			#include <string.h>
44
45			#include <cmath>
46			#include "nonbonded/EAM.hpp"
47			#include "utils/simError.h"
48	gezelter	1479	#include "types/NonBondedInteractionType.hpp"
49	gezelter	1478
50
51			namespace OpenMD {
52
53	gezelter	1502	EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL),
54	gezelter	1586	mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
55	gezelter	1478
56			EAMParam EAM::getEAMParam(AtomType* atomType) {
57
58			// Do sanity checking on the AtomType we were passed before
59			// building any data structures:
60			if (!atomType->isEAM()) {
61			sprintf( painCave.errMsg,
62			"EAM::getEAMParam was passed an atomType (%s) that does not\n"
63			"\tappear to be an embedded atom method (EAM) atom.\n",
64			atomType->getName().c_str());
65			painCave.severity = OPENMD_ERROR;
66			painCave.isFatal = 1;
67			simError();
68			}
69
70			GenericData* data = atomType->getPropertyByName("EAM");
71			if (data == NULL) {
72			sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n"
73			"\tparameters for atomType %s.\n",
74			atomType->getName().c_str());
75			painCave.severity = OPENMD_ERROR;
76			painCave.isFatal = 1;
77			simError();
78			}
79
80			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
81			if (eamData == NULL) {
82			sprintf( painCave.errMsg,
83			"EAM::getEAMParam could not convert GenericData to EAMParam for\n"
84			"\tatom type %s\n", atomType->getName().c_str());
85			painCave.severity = OPENMD_ERROR;
86			painCave.isFatal = 1;
87			simError();
88			}
89
90			return eamData->getData();
91			}
92
93			CubicSpline* EAM::getZ(AtomType* atomType) {
94			EAMParam eamParam = getEAMParam(atomType);
95			int nr = eamParam.nr;
96			RealType dr = eamParam.dr;
97			vector<RealType> rvals;
98
99	gezelter	1482	for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr);
100	gezelter	1478
101			CubicSpline* cs = new CubicSpline();
102			cs->addPoints(rvals, eamParam.Z);
103			return cs;
104			}
105
106	gezelter	1479	RealType EAM::getRcut(AtomType* atomType) {
107			EAMParam eamParam = getEAMParam(atomType);
108			return eamParam.rcut;
109			}
110
111	gezelter	1478	CubicSpline* EAM::getRho(AtomType* atomType) {
112			EAMParam eamParam = getEAMParam(atomType);
113			int nr = eamParam.nr;
114			RealType dr = eamParam.dr;
115			vector<RealType> rvals;
116
117	gezelter	1482	for (int i = 0; i < nr; i++) rvals.push_back(RealType(i) * dr);
118	gezelter	1478
119			CubicSpline* cs = new CubicSpline();
120			cs->addPoints(rvals, eamParam.rho);
121			return cs;
122			}
123
124			CubicSpline* EAM::getF(AtomType* atomType) {
125			EAMParam eamParam = getEAMParam(atomType);
126			int nrho = eamParam.nrho;
127			RealType drho = eamParam.drho;
128			vector<RealType> rhovals;
129			vector<RealType> scaledF;
130
131			for (int i = 0; i < nrho; i++) {
132	gezelter	1482	rhovals.push_back(RealType(i) * drho);
133	gezelter	1478	scaledF.push_back( eamParam.F[i] * 23.06054 );
134			}
135
136			CubicSpline* cs = new CubicSpline();
137	gezelter	1482	cs->addPoints(rhovals, scaledF);
138	gezelter	1478	return cs;
139			}
140
141			CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {
142			EAMParam eamParam1 = getEAMParam(atomType1);
143			EAMParam eamParam2 = getEAMParam(atomType2);
144			CubicSpline* z1 = getZ(atomType1);
145			CubicSpline* z2 = getZ(atomType2);
146
147			// make the r grid:
148
149
150	gezelter	1481	// we need phi out to the largest value we'll encounter in the radial space;
151
152			RealType rmax = 0.0;
153			rmax = max(rmax, eamParam1.rcut);
154			rmax = max(rmax, eamParam1.nr * eamParam1.dr);
155	gezelter	1478
156	gezelter	1481	rmax = max(rmax, eamParam2.rcut);
157			rmax = max(rmax, eamParam2.nr * eamParam2.dr);
158
159	gezelter	1478	// use the smallest dr (finest grid) to build our grid:
160
161	gezelter	1481	RealType dr = min(eamParam1.dr, eamParam2.dr);
162
163			int nr = int(rmax/dr + 0.5);
164
165	gezelter	1478	vector<RealType> rvals;
166	gezelter	1481	for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
167	gezelter	1478
168			// construct the pair potential:
169
170			vector<RealType> phivals;
171			RealType phi;
172			RealType r;
173			RealType zi, zj;
174
175			phivals.push_back(0.0);
176
177			for (int i = 1; i < rvals.size(); i++ ) {
178			r = rvals[i];
179
180	gezelter	1502	// only use z(r) if we're inside this atom's cutoff radius,
181			// otherwise, we'll use zero for the charge. This effectively
182			// means that our phi grid goes out beyond the cutoff of the
183			// pair potential
184	gezelter	1481
185			zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0;
186			zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0;
187
188	gezelter	1478	phi = 331.999296 * (zi * zj) / r;
189	gezelter	1481
190	gezelter	1478	phivals.push_back(phi);
191			}
192
193			CubicSpline* cs = new CubicSpline();
194			cs->addPoints(rvals, phivals);
195			return cs;
196			}
197
198	gezelter	1586	void EAM::setCutoffRadius( RealType rCut ) {
199			eamRcut_ = rCut;
200			haveCutoffRadius_ = true;
201			}
202
203	gezelter	1478	void EAM::initialize() {
204
205			// set up the mixing method:
206	gezelter	1479	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
207	gezelter	1481	string EAMMixMeth = fopts.getEAMMixingMethod();
208	gezelter	1480	toUpper(EAMMixMeth);
209
210	gezelter	1478	if (EAMMixMeth == "JOHNSON")
211			mixMeth_ = eamJohnson;
212			else if (EAMMixMeth == "DAW")
213			mixMeth_ = eamDaw;
214			else
215			mixMeth_ = eamUnknown;
216
217			// find all of the EAM atom Types:
218			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
219			ForceField::AtomTypeContainer::MapTypeIterator i;
220			AtomType* at;
221
222			for (at = atomTypes->beginType(i); at != NULL;
223			at = atomTypes->nextType(i)) {
224
225			if (at->isEAM())
226			addType(at);
227			}
228
229			// find all of the explicit EAM interactions (setfl):
230			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
231			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
232			NonBondedInteractionType* nbt;
233
234			for (nbt = nbiTypes->beginType(j); nbt != NULL;
235			nbt = nbiTypes->nextType(j)) {
236
237			if (nbt->isEAM()) {
238
239	gezelter	1481	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
240	gezelter	1478
241			GenericData* data = nbt->getPropertyByName("EAM");
242			if (data == NULL) {
243			sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
244			"\tEAM parameters for %s - %s interaction.\n",
245			atypes.first->getName().c_str(),
246			atypes.second->getName().c_str());
247			painCave.severity = OPENMD_ERROR;
248			painCave.isFatal = 1;
249			simError();
250			}
251
252			EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
253			if (eamData == NULL) {
254			sprintf( painCave.errMsg,
255			"EAM::rebuildMixingMap could not convert GenericData to\n"
256			"\tEAMMixingData for %s - %s interaction.\n",
257			atypes.first->getName().c_str(),
258			atypes.second->getName().c_str());
259			painCave.severity = OPENMD_ERROR;
260			painCave.isFatal = 1;
261			simError();
262			}
263
264	gezelter	1479	EAMMixingParam eamParam = eamData->getData();
265	gezelter	1478
266	gezelter	1479	vector<RealType> phiAB = eamParam.phi;
267	gezelter	1478	RealType dr = eamParam.dr;
268			int nr = eamParam.nr;
269
270			addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
271			}
272			}
273			initialized_ = true;
274			}
275
276
277
278			void EAM::addType(AtomType* atomType){
279
280			EAMAtomData eamAtomData;
281	gezelter	1479
282	gezelter	1478	eamAtomData.rho = getRho(atomType);
283			eamAtomData.F = getF(atomType);
284			eamAtomData.Z = getZ(atomType);
285			eamAtomData.rcut = getRcut(atomType);
286
287			// add it to the map:
288			AtomTypeProperties atp = atomType->getATP();
289
290	gezelter	1481	pair<map<int,AtomType*>::iterator,bool> ret;
291			ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) );
292	gezelter	1478	if (ret.second == false) {
293			sprintf( painCave.errMsg,
294			"EAM already had a previous entry with ident %d\n",
295			atp.ident);
296			painCave.severity = OPENMD_INFO;
297			painCave.isFatal = 0;
298			simError();
299			}
300
301			EAMMap[atomType] = eamAtomData;
302
303			// Now, iterate over all known types and add to the mixing map:
304
305	gezelter	1481	map<AtomType*, EAMAtomData>::iterator it;
306	gezelter	1478	for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
307
308	gezelter	1479	AtomType* atype2 = (*it).first;
309	gezelter	1478
310			EAMInteractionData mixer;
311			mixer.phi = getPhi(atomType, atype2);
312			mixer.explicitlySet = false;
313
314	gezelter	1481	pair<AtomType, AtomType> key1, key2;
315			key1 = make_pair(atomType, atype2);
316			key2 = make_pair(atype2, atomType);
317	gezelter	1478
318			MixingMap[key1] = mixer;
319			if (key2 != key1) {
320			MixingMap[key2] = mixer;
321			}
322			}
323			return;
324			}
325
326			void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
327			RealType dr, int nr,
328			vector<RealType> phiVals) {
329
330			// in case these weren't already in the map
331			addType(atype1);
332			addType(atype2);
333
334			EAMInteractionData mixer;
335			CubicSpline* cs = new CubicSpline();
336	gezelter	1479	vector<RealType> rVals;
337	gezelter	1478
338	gezelter	1479	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
339	gezelter	1478
340			cs->addPoints(rVals, phiVals);
341			mixer.phi = cs;
342			mixer.explicitlySet = true;
343
344	gezelter	1481	pair<AtomType, AtomType> key1, key2;
345			key1 = make_pair(atype1, atype2);
346			key2 = make_pair(atype2, atype1);
347	gezelter	1478
348			MixingMap[key1] = mixer;
349			if (key2 != key1) {
350			MixingMap[key2] = mixer;
351			}
352			return;
353			}
354
355	gezelter	1545	void EAM::calcDensity(InteractionData &idat) {
356	gezelter	1479
357	gezelter	1478	if (!initialized_) initialize();
358	gezelter	1479
359	gezelter	1571	EAMAtomData data1 = EAMMap[idat.atypes.first];
360			EAMAtomData data2 = EAMMap[idat.atypes.second];
361	gezelter	1586
362			if (haveCutoffRadius_)
363			if ( *(idat.rij) > eamRcut_) return;
364
365	gezelter	1629	if ( *(idat.rij) < data1.rcut)
366	gezelter	1575	(idat.rho1) += data1.rho->getValueAt( (idat.rij));
367	gezelter	1629
368	gezelter	1586
369	gezelter	1629	if ( *(idat.rij) < data2.rcut)
370			(idat.rho2) += data2.rho->getValueAt( (idat.rij));
371
372			return;
373	gezelter	1478	}
374	gezelter	1586
375	gezelter	1545	void EAM::calcFunctional(SelfData &sdat) {
376	gezelter	1586
377	gezelter	1478	if (!initialized_) initialize();
378
379	gezelter	1554	EAMAtomData data1 = EAMMap[ sdat.atype ];
380	gezelter	1478
381	gezelter	1554	pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );
382	gezelter	1478
383	gezelter	1554	*(sdat.frho) = result.first;
384			*(sdat.dfrhodrho) = result.second;
385	gezelter	1575
386	gezelter	1586	(*(sdat.pot))[METALLIC_FAMILY] += result.first;
387	gezelter	1575	*(sdat.particlePot) += result.first;
388
389	gezelter	1478	return;
390			}
391
392
393	gezelter	1536	void EAM::calcForce(InteractionData &idat) {
394	gezelter	1478
395			if (!initialized_) initialize();
396	gezelter	1481
397	gezelter	1586	if (haveCutoffRadius_)
398			if ( *(idat.rij) > eamRcut_) return;
399
400	gezelter	1478	pair<RealType, RealType> res;
401
402	gezelter	1586	EAMAtomData data1 = EAMMap[idat.atypes.first];
403			EAMAtomData data2 = EAMMap[idat.atypes.second];
404
405			// get type-specific cutoff radii
406
407			RealType rci = data1.rcut;
408			RealType rcj = data2.rcut;
409
410			RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
411			RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
412			RealType phab(0.0), dvpdr(0.0);
413			RealType drhoidr, drhojdr, dudr;
414
415			if ( *(idat.rij) < rci) {
416			res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
417			rha = res.first;
418			drha = res.second;
419
420			res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
421			pha = res.first;
422			dpha = res.second;
423			}
424
425			if ( *(idat.rij) < rcj) {
426			res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
427			rhb = res.first;
428			drhb = res.second;
429
430			res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
431			phb = res.first;
432			dphb = res.second;
433			}
434	gezelter	1478
435	gezelter	1586	switch(mixMeth_) {
436			case eamJohnson:
437	gezelter	1478
438	gezelter	1554	if ( *(idat.rij) < rci) {
439	gezelter	1586	phab = phab + 0.5 * (rhb / rha) * pha;
440			dvpdr = dvpdr + 0.5((rhb/rha)dpha +
441			pha((drhb/rha) - (rhbdrha/rha/rha)));
442	gezelter	1478	}
443	gezelter	1586
444
445
446	gezelter	1554	if ( *(idat.rij) < rcj) {
447	gezelter	1586	phab = phab + 0.5 * (rha / rhb) * phb;
448			dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
449			phb((drha/rhb) - (rhadrhb/rhb/rhb)));
450	gezelter	1478	}
451
452	gezelter	1586	break;
453
454			case eamDaw:
455			res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
456			phab = res.first;
457			dvpdr = res.second;
458
459			break;
460			case eamUnknown:
461			default:
462
463			sprintf(painCave.errMsg,
464			"EAM::calcForce hit a mixing method it doesn't know about!\n"
465			);
466			painCave.severity = OPENMD_ERROR;
467			painCave.isFatal = 1;
468			simError();
469
470			}
471
472			drhoidr = drha;
473			drhojdr = drhb;
474
475			dudr = drhojdr* (idat.dfrho1) + drhoidr *(idat.dfrho2) + dvpdr;
476
477			(idat.f1) += (idat.d) * dudr / *(idat.rij);
478	gezelter	1478
479	gezelter	1586	// particlePot is the difference between the full potential and
480			// the full potential without the presence of a particular
481			// particle (atom1).
482			//
483			// This reduces the density at other particle locations, so we
484			// need to recompute the density at atom2 assuming atom1 didn't
485			// contribute. This then requires recomputing the density
486			// functional for atom2 as well.
487
488			(idat.particlePot1) += data2.F->getValueAt( (idat.rho2) - rha )
489			- *(idat.frho2);
490
491			(idat.particlePot2) += data1.F->getValueAt( (idat.rho1) - rhb)
492			- *(idat.frho1);
493
494			(*(idat.pot))[METALLIC_FAMILY] += phab;
495
496			*(idat.vpair) += phab;
497
498	gezelter	1478	return;
499
500			}
501	gezelter	1505
502	gezelter	1545	RealType EAM::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
503	gezelter	1505	if (!initialized_) initialize();
504
505			RealType cut = 0.0;
506
507			map<AtomType*, EAMAtomData>::iterator it;
508
509	gezelter	1545	it = EAMMap.find(atypes.first);
510	gezelter	1505	if (it != EAMMap.end()) {
511			EAMAtomData data1 = (*it).second;
512			cut = data1.rcut;
513			}
514
515	gezelter	1545	it = EAMMap.find(atypes.second);
516	gezelter	1505	if (it != EAMMap.end()) {
517			EAMAtomData data2 = (*it).second;
518			if (data2.rcut > cut)
519			cut = data2.rcut;
520			}
521
522			return cut;
523			}
524	gezelter	1478	}
525