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) {}
  
  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::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 ( *(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();

    pair<RealType, RealType> res;
    
    if ( *(idat.rij) < eamRcut_) {

      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:	1575
Committed:	Fri Jun 3 21:39:49 2011 UTC (14 years, 5 months ago) by gezelter
Original Path:	*branches/development/src/nonbonded/EAM.cpp*
File size:	15630 byte(s)
Log Message:	more parallel fixes
#	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			mixMeth_(eamJohnson), eamRcut_(0.0) {}
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			void EAM::initialize() {
199
200			// set up the mixing method:
201	gezelter	1479	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
202	gezelter	1481	string EAMMixMeth = fopts.getEAMMixingMethod();
203	gezelter	1480	toUpper(EAMMixMeth);
204
205	gezelter	1478	if (EAMMixMeth == "JOHNSON")
206			mixMeth_ = eamJohnson;
207			else if (EAMMixMeth == "DAW")
208			mixMeth_ = eamDaw;
209			else
210			mixMeth_ = eamUnknown;
211
212			// find all of the EAM atom Types:
213			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
214			ForceField::AtomTypeContainer::MapTypeIterator i;
215			AtomType* at;
216
217			for (at = atomTypes->beginType(i); at != NULL;
218			at = atomTypes->nextType(i)) {
219
220			if (at->isEAM())
221			addType(at);
222			}
223
224			// find all of the explicit EAM interactions (setfl):
225			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
226			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
227			NonBondedInteractionType* nbt;
228
229			for (nbt = nbiTypes->beginType(j); nbt != NULL;
230			nbt = nbiTypes->nextType(j)) {
231
232			if (nbt->isEAM()) {
233
234	gezelter	1481	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
235	gezelter	1478
236			GenericData* data = nbt->getPropertyByName("EAM");
237			if (data == NULL) {
238			sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
239			"\tEAM parameters for %s - %s interaction.\n",
240			atypes.first->getName().c_str(),
241			atypes.second->getName().c_str());
242			painCave.severity = OPENMD_ERROR;
243			painCave.isFatal = 1;
244			simError();
245			}
246
247			EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
248			if (eamData == NULL) {
249			sprintf( painCave.errMsg,
250			"EAM::rebuildMixingMap could not convert GenericData to\n"
251			"\tEAMMixingData for %s - %s interaction.\n",
252			atypes.first->getName().c_str(),
253			atypes.second->getName().c_str());
254			painCave.severity = OPENMD_ERROR;
255			painCave.isFatal = 1;
256			simError();
257			}
258
259	gezelter	1479	EAMMixingParam eamParam = eamData->getData();
260	gezelter	1478
261	gezelter	1479	vector<RealType> phiAB = eamParam.phi;
262	gezelter	1478	RealType dr = eamParam.dr;
263			int nr = eamParam.nr;
264
265			addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
266			}
267			}
268			initialized_ = true;
269			}
270
271
272
273			void EAM::addType(AtomType* atomType){
274
275			EAMAtomData eamAtomData;
276	gezelter	1479
277	gezelter	1478	eamAtomData.rho = getRho(atomType);
278			eamAtomData.F = getF(atomType);
279			eamAtomData.Z = getZ(atomType);
280			eamAtomData.rcut = getRcut(atomType);
281
282			// add it to the map:
283			AtomTypeProperties atp = atomType->getATP();
284
285	gezelter	1481	pair<map<int,AtomType*>::iterator,bool> ret;
286			ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) );
287	gezelter	1478	if (ret.second == false) {
288			sprintf( painCave.errMsg,
289			"EAM already had a previous entry with ident %d\n",
290			atp.ident);
291			painCave.severity = OPENMD_INFO;
292			painCave.isFatal = 0;
293			simError();
294			}
295
296			EAMMap[atomType] = eamAtomData;
297
298			// Now, iterate over all known types and add to the mixing map:
299
300	gezelter	1481	map<AtomType*, EAMAtomData>::iterator it;
301	gezelter	1478	for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
302
303	gezelter	1479	AtomType* atype2 = (*it).first;
304	gezelter	1478
305			EAMInteractionData mixer;
306			mixer.phi = getPhi(atomType, atype2);
307			mixer.explicitlySet = false;
308
309	gezelter	1481	pair<AtomType, AtomType> key1, key2;
310			key1 = make_pair(atomType, atype2);
311			key2 = make_pair(atype2, atomType);
312	gezelter	1478
313			MixingMap[key1] = mixer;
314			if (key2 != key1) {
315			MixingMap[key2] = mixer;
316			}
317			}
318			return;
319			}
320
321			void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
322			RealType dr, int nr,
323			vector<RealType> phiVals) {
324
325			// in case these weren't already in the map
326			addType(atype1);
327			addType(atype2);
328
329			EAMInteractionData mixer;
330			CubicSpline* cs = new CubicSpline();
331	gezelter	1479	vector<RealType> rVals;
332	gezelter	1478
333	gezelter	1479	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
334	gezelter	1478
335			cs->addPoints(rVals, phiVals);
336			mixer.phi = cs;
337			mixer.explicitlySet = true;
338
339	gezelter	1481	pair<AtomType, AtomType> key1, key2;
340			key1 = make_pair(atype1, atype2);
341			key2 = make_pair(atype2, atype1);
342	gezelter	1478
343			MixingMap[key1] = mixer;
344			if (key2 != key1) {
345			MixingMap[key2] = mixer;
346			}
347			return;
348			}
349
350	gezelter	1545	void EAM::calcDensity(InteractionData &idat) {
351	gezelter	1479
352	gezelter	1478	if (!initialized_) initialize();
353	gezelter	1479
354	gezelter	1571	EAMAtomData data1 = EAMMap[idat.atypes.first];
355			EAMAtomData data2 = EAMMap[idat.atypes.second];
356	gezelter	1478
357	gezelter	1554	if ( *(idat.rij) < data1.rcut)
358	gezelter	1575	(idat.rho1) += data1.rho->getValueAt( (idat.rij));
359	gezelter	1502
360	gezelter	1575
361	gezelter	1554	if ( *(idat.rij) < data2.rcut)
362	gezelter	1575	(idat.rho2) += data2.rho->getValueAt( (idat.rij));
363	gezelter	1502
364	gezelter	1478	return;
365			}
366
367	gezelter	1545	void EAM::calcFunctional(SelfData &sdat) {
368	gezelter	1478
369			if (!initialized_) initialize();
370
371	gezelter	1554	EAMAtomData data1 = EAMMap[ sdat.atype ];
372	gezelter	1478
373	gezelter	1554	pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );
374	gezelter	1478
375	gezelter	1554	*(sdat.frho) = result.first;
376			*(sdat.dfrhodrho) = result.second;
377	gezelter	1575
378			sdat.pot[METALLIC_FAMILY] += result.first;
379			*(sdat.particlePot) += result.first;
380
381	gezelter	1478	return;
382			}
383
384
385	gezelter	1536	void EAM::calcForce(InteractionData &idat) {
386	gezelter	1478
387			if (!initialized_) initialize();
388	gezelter	1481
389	gezelter	1478	pair<RealType, RealType> res;
390
391	gezelter	1554	if ( *(idat.rij) < eamRcut_) {
392	gezelter	1478
393	gezelter	1571	EAMAtomData data1 = EAMMap[idat.atypes.first];
394			EAMAtomData data2 = EAMMap[idat.atypes.second];
395	gezelter	1478
396			// get type-specific cutoff radii
397
398			RealType rci = data1.rcut;
399			RealType rcj = data2.rcut;
400
401	gezelter	1575	RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
402			RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
403			RealType phab(0.0), dvpdr(0.0);
404	gezelter	1478	RealType drhoidr, drhojdr, dudr;
405
406	gezelter	1554	if ( *(idat.rij) < rci) {
407			res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
408	gezelter	1478	rha = res.first;
409			drha = res.second;
410
411	gezelter	1571	res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
412	gezelter	1478	pha = res.first;
413			dpha = res.second;
414			}
415
416	gezelter	1554	if ( *(idat.rij) < rcj) {
417			res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
418	gezelter	1478	rhb = res.first;
419			drhb = res.second;
420
421	gezelter	1571	res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
422	gezelter	1478	phb = res.first;
423			dphb = res.second;
424			}
425
426			switch(mixMeth_) {
427			case eamJohnson:
428
429	gezelter	1554	if ( *(idat.rij) < rci) {
430	gezelter	1478	phab = phab + 0.5 * (rhb / rha) * pha;
431			dvpdr = dvpdr + 0.5((rhb/rha)dpha +
432			pha((drhb/rha) - (rhbdrha/rha/rha)));
433			}
434	gezelter	1575
435
436	gezelter	1478
437	gezelter	1554	if ( *(idat.rij) < rcj) {
438	gezelter	1478	phab = phab + 0.5 * (rha / rhb) * phb;
439			dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
440			phb((drha/rhb) - (rhadrhb/rhb/rhb)));
441			}
442
443			break;
444
445			case eamDaw:
446	gezelter	1571	res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
447	gezelter	1478	phab = res.first;
448			dvpdr = res.second;
449
450			break;
451			case eamUnknown:
452			default:
453
454			sprintf(painCave.errMsg,
455			"EAM::calcForce hit a mixing method it doesn't know about!\n"
456			);
457			painCave.severity = OPENMD_ERROR;
458			painCave.isFatal = 1;
459			simError();
460
461			}
462
463			drhoidr = drha;
464			drhojdr = drhb;
465
466	gezelter	1554	dudr = drhojdr* (idat.dfrho1) + drhoidr *(idat.dfrho2) + dvpdr;
467	gezelter	1478
468	gezelter	1554	(idat.f1) = (idat.d) * dudr / *(idat.rij);
469	gezelter	1478
470	gezelter	1575	// particlePot is the difference between the full potential and
471			// the full potential without the presence of a particular
472	gezelter	1478	// particle (atom1).
473			//
474	gezelter	1575	// This reduces the density at other particle locations, so we
475			// need to recompute the density at atom2 assuming atom1 didn't
476			// contribute. This then requires recomputing the density
477			// functional for atom2 as well.
478	gezelter	1478
479	gezelter	1575	(idat.particlePot1) += data2.F->getValueAt( (idat.rho2) - rha )
480			- *(idat.frho2);
481
482			(idat.particlePot2) += data1.F->getValueAt( (idat.rho1) - rhb)
483			- *(idat.frho1);
484
485	gezelter	1554	idat.pot[METALLIC_FAMILY] += phab;
486	gezelter	1478
487	gezelter	1554	*(idat.vpair) += phab;
488	gezelter	1478	}
489
490			return;
491
492			}
493	gezelter	1505
494	gezelter	1545	RealType EAM::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
495	gezelter	1505	if (!initialized_) initialize();
496
497			RealType cut = 0.0;
498
499			map<AtomType*, EAMAtomData>::iterator it;
500
501	gezelter	1545	it = EAMMap.find(atypes.first);
502	gezelter	1505	if (it != EAMMap.end()) {
503			EAMAtomData data1 = (*it).second;
504			cut = data1.rcut;
505			}
506
507	gezelter	1545	it = EAMMap.find(atypes.second);
508	gezelter	1505	if (it != EAMMap.end()) {
509			EAMAtomData data2 = (*it).second;
510			if (data2.rcut > cut)
511			cut = data2.rcut;
512			}
513
514			return cut;
515			}
516	gezelter	1478	}
517