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, 234107 (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();

    // Thise prefactors convert the charge-charge interactions into
    // kcal / mol all were computed assuming distances are measured in
    // angstroms Charge-Charge, assuming charges are measured in
    // electrons.  Matches value in Electrostatics.cpp
    pre11_ = 332.0637778;

    // 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 (unsigned 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 = pre11_ * (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:
    EAMtypes.clear();
    EAMtids.clear();
    EAMdata.clear();
    MixingMap.clear();
    nEAM_ = 0;
    
    EAMtids.resize( forceField_->getNAtomType(), -1);

    set<AtomType*>::iterator at;
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isEAM()) nEAM_++;
    }
    EAMdata.resize(nEAM_);
    MixingMap.resize(nEAM_);

    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      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();
    eamAtomData.isFluctuating = atomType->isFluctuatingCharge();
      
    // add it to the map:
    int atid = atomType->getIdent();
    int eamtid = EAMtypes.size();

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

    if (eamAtomData.isFluctuating) {
      // compute charge to rho scaling:
      RealType z0 = eamAtomData.Z->getValueAt(0.0);
      RealType dr = ea.getDr();
      RealType rmax = max(eamAtomData.rcut, ea.getNr() * dr);
      int nr = int(rmax/dr + 0.5);
      RealType r;
      RealType sum(0.0);

      for (int i = 0; i < nr; i++) {
        r = RealType(i*dr);
        sum += r * r * eamAtomData.rho->getValueAt(r) * dr;       
      } 
      sum *= 4.0 * M_PI;
      eamAtomData.qToRhoScaling = sum / z0;
    }


    EAMtids[atid] = eamtid;
    EAMdata[eamtid] = eamAtomData;
    MixingMap[eamtid].resize(nEAM_);
    
    // Now, iterate over all known types and add to the mixing map:
    
    std::set<int>::iterator it;
    for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) {
      
      int eamtid2 = EAMtids[ (*it) ];
      AtomType* atype2 = forceField_->getAtomType( (*it) );

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

      MixingMap[eamtid2].resize( nEAM_ );
      
      MixingMap[eamtid][eamtid2] = mixer;
      if (eamtid2 != eamtid) {
        MixingMap[eamtid2][eamtid] = 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;

    int eamtid1 = EAMtids[ atype1->getIdent() ];
    int eamtid2 = EAMtids[ atype2->getIdent() ];
    
    MixingMap[eamtid1][eamtid2] = mixer;
    if (eamtid2 != eamtid1) {
      MixingMap[eamtid2][eamtid1] = mixer;
    }    
    return;
  }

  void EAM::calcDensity(InteractionData &idat) {
    
    if (!initialized_) initialize();
    
    EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]];
    EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]];

    if (haveCutoffRadius_) 
      if ( *(idat.rij) > eamRcut_) return;
    
    if ( *(idat.rij) < data1.rcut) {
      if (data1.isFluctuating) {
        *(idat.rho2) += (1.0 -  *(idat.flucQ1) * data1.qToRhoScaling ) * 
          data1.rho->getValueAt( *(idat.rij) );
      } else {
        *(idat.rho2) += data1.rho->getValueAt( *(idat.rij));
      }
    }
      
    if ( *(idat.rij) < data2.rcut) {
      if (data2.isFluctuating) {
        *(idat.rho1) += (1.0 -  *(idat.flucQ2) * data2.qToRhoScaling ) *
          data2.rho->getValueAt( *(idat.rij) );
      } else {
        *(idat.rho1) += data2.rho->getValueAt( *(idat.rij));
      }
    }
    
    return;  
  }
  
  void EAM::calcFunctional(SelfData &sdat) {
    
    if (!initialized_) initialize();

    EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ];
            
    data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho), *(sdat.dfrhodrho) );

    (*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho);
    if (sdat.doParticlePot) {
      *(sdat.particlePot) += *(sdat.frho);
    }

    return;
  }

 
  void EAM::calcForce(InteractionData &idat) {

    if (!initialized_) initialize();

    if (haveCutoffRadius_) 
      if ( *(idat.rij) > eamRcut_) return;
   

    int eamtid1 = EAMtids[idat.atid1];
    int eamtid2 = EAMtids[idat.atid2];
    
    EAMAtomData &data1 = EAMdata[eamtid1];
    EAMAtomData &data2 = EAMdata[eamtid2];
    
    // 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) {
      data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha);
      CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi;
      phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha);
      if (data1.isFluctuating) {
        *(idat.dVdFQ1) -= *(idat.dfrho2) * rha * data1.qToRhoScaling;
      }
    }
    
    if ( *(idat.rij) < rcj) {
      data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb );
      CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi;
      phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb);
      if (data2.isFluctuating) {
        *(idat.dVdFQ2) -= *(idat.dfrho1) * rhb * data2.qToRhoScaling;
      }
    }

    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:
      MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), phab, dvpdr);
      
      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);

        
    if (idat.doParticlePot) {
      // 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;

    int atid1 = atypes.first->getIdent();
    int atid2 = atypes.second->getIdent();
    int eamtid1 = EAMtids[atid1];
    int eamtid2 = EAMtids[atid2];
    
    if (eamtid1 != -1) {
      EAMAtomData data1 = EAMdata[eamtid1];
      cut = data1.rcut;
    }

    if (eamtid2 != -1) {
      EAMAtomData data2 = EAMdata[eamtid2];
      if (data2.rcut > cut)
        cut = data2.rcut;
    }
    
    return cut;
  }
}

Revision:	1927
Committed:	Wed Aug 14 20:19:19 2013 UTC (11 years, 11 months ago) by gezelter
File size:	14816 byte(s)
Log Message:	FlucRho/EAM initial commit
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	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	gezelter	1927	// Thise prefactors convert the charge-charge interactions into
64			// kcal / mol all were computed assuming distances are measured in
65			// angstroms Charge-Charge, assuming charges are measured in
66			// electrons. Matches value in Electrostatics.cpp
67			pre11_ = 332.0637778;
68
69	gezelter	1478	// make the r grid:
70
71	gezelter	1481	// we need phi out to the largest value we'll encounter in the radial space;
72
73			RealType rmax = 0.0;
74	gezelter	1710	rmax = max(rmax, ea1.getRcut());
75			rmax = max(rmax, ea1.getNr() * ea1.getDr());
76	gezelter	1478
77	gezelter	1710	rmax = max(rmax, ea2.getRcut());
78			rmax = max(rmax, ea2.getNr() * ea2.getDr());
79	gezelter	1481
80	gezelter	1478	// use the smallest dr (finest grid) to build our grid:
81
82	gezelter	1710	RealType dr = min(ea1.getDr(), ea2.getDr());
83	gezelter	1481
84			int nr = int(rmax/dr + 0.5);
85
86	gezelter	1478	vector<RealType> rvals;
87	gezelter	1481	for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
88	gezelter	1478
89			// construct the pair potential:
90
91			vector<RealType> phivals;
92			RealType phi;
93			RealType r;
94			RealType zi, zj;
95
96			phivals.push_back(0.0);
97
98	gezelter	1767	for (unsigned int i = 1; i < rvals.size(); i++ ) {
99	gezelter	1478	r = rvals[i];
100
101	gezelter	1502	// only use z(r) if we're inside this atom's cutoff radius,
102			// otherwise, we'll use zero for the charge. This effectively
103			// means that our phi grid goes out beyond the cutoff of the
104			// pair potential
105	gezelter	1481
106	gezelter	1710	zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0;
107			zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0;
108	gezelter	1481
109	gezelter	1927	phi = pre11_ * (zi * zj) / r;
110	gezelter	1481
111	gezelter	1478	phivals.push_back(phi);
112			}
113
114			CubicSpline* cs = new CubicSpline();
115			cs->addPoints(rvals, phivals);
116			return cs;
117			}
118
119	gezelter	1586	void EAM::setCutoffRadius( RealType rCut ) {
120			eamRcut_ = rCut;
121			haveCutoffRadius_ = true;
122			}
123
124	gezelter	1478	void EAM::initialize() {
125			// set up the mixing method:
126	gezelter	1479	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
127	gezelter	1481	string EAMMixMeth = fopts.getEAMMixingMethod();
128	gezelter	1480	toUpper(EAMMixMeth);
129
130	gezelter	1478	if (EAMMixMeth == "JOHNSON")
131			mixMeth_ = eamJohnson;
132			else if (EAMMixMeth == "DAW")
133			mixMeth_ = eamDaw;
134			else
135			mixMeth_ = eamUnknown;
136
137			// find all of the EAM atom Types:
138	gezelter	1895	EAMtypes.clear();
139			EAMtids.clear();
140			EAMdata.clear();
141			MixingMap.clear();
142			nEAM_ = 0;
143
144			EAMtids.resize( forceField_->getNAtomType(), -1);
145	gezelter	1478
146	gezelter	1895	set<AtomType*>::iterator at;
147			for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
148			if ((*at)->isEAM()) nEAM_++;
149	gezelter	1478	}
150	gezelter	1895	EAMdata.resize(nEAM_);
151			MixingMap.resize(nEAM_);
152
153			for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
154			if ((at)->isEAM()) addType(at);
155			}
156	gezelter	1478
157			// find all of the explicit EAM interactions (setfl):
158			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
159			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
160			NonBondedInteractionType* nbt;
161
162			for (nbt = nbiTypes->beginType(j); nbt != NULL;
163			nbt = nbiTypes->nextType(j)) {
164
165			if (nbt->isEAM()) {
166
167	gezelter	1481	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
168	gezelter	1478
169			GenericData* data = nbt->getPropertyByName("EAM");
170			if (data == NULL) {
171			sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
172			"\tEAM parameters 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			EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
181			if (eamData == NULL) {
182			sprintf( painCave.errMsg,
183			"EAM::rebuildMixingMap could not convert GenericData to\n"
184			"\tEAMMixingData for %s - %s interaction.\n",
185			atypes.first->getName().c_str(),
186			atypes.second->getName().c_str());
187			painCave.severity = OPENMD_ERROR;
188			painCave.isFatal = 1;
189			simError();
190			}
191
192	gezelter	1479	EAMMixingParam eamParam = eamData->getData();
193	gezelter	1478
194	gezelter	1479	vector<RealType> phiAB = eamParam.phi;
195	gezelter	1478	RealType dr = eamParam.dr;
196			int nr = eamParam.nr;
197
198			addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
199			}
200			}
201			initialized_ = true;
202			}
203
204
205
206			void EAM::addType(AtomType* atomType){
207
208	gezelter	1710	EAMAdapter ea = EAMAdapter(atomType);
209	gezelter	1478	EAMAtomData eamAtomData;
210
211	gezelter	1710	eamAtomData.rho = ea.getRho();
212			eamAtomData.F = ea.getF();
213			eamAtomData.Z = ea.getZ();
214			eamAtomData.rcut = ea.getRcut();
215	gezelter	1927	eamAtomData.isFluctuating = atomType->isFluctuatingCharge();
216
217	gezelter	1478	// add it to the map:
218	gezelter	1895	int atid = atomType->getIdent();
219			int eamtid = EAMtypes.size();
220	gezelter	1478
221	gezelter	1895	pair<set<int>::iterator,bool> ret;
222			ret = EAMtypes.insert( atid );
223	gezelter	1478	if (ret.second == false) {
224			sprintf( painCave.errMsg,
225			"EAM already had a previous entry with ident %d\n",
226	gezelter	1895	atid);
227	gezelter	1478	painCave.severity = OPENMD_INFO;
228			painCave.isFatal = 0;
229			simError();
230			}
231
232	gezelter	1927	if (eamAtomData.isFluctuating) {
233			// compute charge to rho scaling:
234			RealType z0 = eamAtomData.Z->getValueAt(0.0);
235			RealType dr = ea.getDr();
236			RealType rmax = max(eamAtomData.rcut, ea.getNr() * dr);
237			int nr = int(rmax/dr + 0.5);
238			RealType r;
239			RealType sum(0.0);
240
241			for (int i = 0; i < nr; i++) {
242			r = RealType(i*dr);
243			sum += r * r * eamAtomData.rho->getValueAt(r) * dr;
244			}
245			sum = 4.0 M_PI;
246			eamAtomData.qToRhoScaling = sum / z0;
247			}
248
249
250	gezelter	1895	EAMtids[atid] = eamtid;
251			EAMdata[eamtid] = eamAtomData;
252			MixingMap[eamtid].resize(nEAM_);
253	gezelter	1478
254			// Now, iterate over all known types and add to the mixing map:
255
256	gezelter	1895	std::set<int>::iterator it;
257			for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) {
258	gezelter	1478
259	gezelter	1895	int eamtid2 = EAMtids[ (*it) ];
260			AtomType* atype2 = forceField_->getAtomType( (*it) );
261	gezelter	1478
262			EAMInteractionData mixer;
263			mixer.phi = getPhi(atomType, atype2);
264			mixer.explicitlySet = false;
265
266	gezelter	1895	MixingMap[eamtid2].resize( nEAM_ );
267	gezelter	1478
268	gezelter	1895	MixingMap[eamtid][eamtid2] = mixer;
269			if (eamtid2 != eamtid) {
270			MixingMap[eamtid2][eamtid] = mixer;
271	gezelter	1478	}
272			}
273			return;
274			}
275
276			void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
277			RealType dr, int nr,
278			vector<RealType> phiVals) {
279
280			// in case these weren't already in the map
281			addType(atype1);
282			addType(atype2);
283
284			EAMInteractionData mixer;
285			CubicSpline* cs = new CubicSpline();
286	gezelter	1479	vector<RealType> rVals;
287	gezelter	1478
288	gezelter	1479	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
289	gezelter	1478
290			cs->addPoints(rVals, phiVals);
291			mixer.phi = cs;
292			mixer.explicitlySet = true;
293
294	gezelter	1895	int eamtid1 = EAMtids[ atype1->getIdent() ];
295			int eamtid2 = EAMtids[ atype2->getIdent() ];
296	gezelter	1478
297	gezelter	1895	MixingMap[eamtid1][eamtid2] = mixer;
298			if (eamtid2 != eamtid1) {
299			MixingMap[eamtid2][eamtid1] = mixer;
300	gezelter	1478	}
301			return;
302			}
303
304	gezelter	1545	void EAM::calcDensity(InteractionData &idat) {
305	gezelter	1479
306	gezelter	1478	if (!initialized_) initialize();
307	gezelter	1479
308	gezelter	1895	EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]];
309			EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]];
310
311	gezelter	1586	if (haveCutoffRadius_)
312			if ( *(idat.rij) > eamRcut_) return;
313
314	gezelter	1927	if ( *(idat.rij) < data1.rcut) {
315			if (data1.isFluctuating) {
316			(idat.rho2) += (1.0 - (idat.flucQ1) * data1.qToRhoScaling ) *
317			data1.rho->getValueAt( *(idat.rij) );
318			} else {
319			(idat.rho2) += data1.rho->getValueAt( (idat.rij));
320			}
321			}
322	gezelter	1586
323	gezelter	1927	if ( *(idat.rij) < data2.rcut) {
324			if (data2.isFluctuating) {
325			(idat.rho1) += (1.0 - (idat.flucQ2) * data2.qToRhoScaling ) *
326			data2.rho->getValueAt( *(idat.rij) );
327			} else {
328			(idat.rho1) += data2.rho->getValueAt( (idat.rij));
329			}
330			}
331	gezelter	1629
332			return;
333	gezelter	1478	}
334	gezelter	1586
335	gezelter	1545	void EAM::calcFunctional(SelfData &sdat) {
336	gezelter	1586
337	gezelter	1478	if (!initialized_) initialize();
338
339	gezelter	1895	EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ];
340	gezelter	1927
341	gezelter	1895	data1.F->getValueAndDerivativeAt( (sdat.rho), (sdat.frho), *(sdat.dfrhodrho) );
342	gezelter	1478
343	gezelter	1895	((sdat.pot))[METALLIC_FAMILY] += (sdat.frho);
344	gezelter	1711	if (sdat.doParticlePot) {
345	gezelter	1895	(sdat.particlePot) += (sdat.frho);
346	gezelter	1711	}
347	gezelter	1575
348	gezelter	1478	return;
349			}
350
351
352	gezelter	1536	void EAM::calcForce(InteractionData &idat) {
353	gezelter	1478
354			if (!initialized_) initialize();
355	gezelter	1481
356	gezelter	1586	if (haveCutoffRadius_)
357			if ( *(idat.rij) > eamRcut_) return;
358
359	gezelter	1895
360			int eamtid1 = EAMtids[idat.atid1];
361			int eamtid2 = EAMtids[idat.atid2];
362	gezelter	1478
363	gezelter	1895	EAMAtomData &data1 = EAMdata[eamtid1];
364			EAMAtomData &data2 = EAMdata[eamtid2];
365	gezelter	1586
366			// get type-specific cutoff radii
367
368			RealType rci = data1.rcut;
369			RealType rcj = data2.rcut;
370
371			RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
372			RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
373			RealType phab(0.0), dvpdr(0.0);
374			RealType drhoidr, drhojdr, dudr;
375
376			if ( *(idat.rij) < rci) {
377	gezelter	1895	data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha);
378			CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi;
379			phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha);
380	gezelter	1927	if (data1.isFluctuating) {
381			(idat.dVdFQ1) -= (idat.dfrho2) * rha * data1.qToRhoScaling;
382			}
383	gezelter	1586	}
384
385			if ( *(idat.rij) < rcj) {
386	gezelter	1895	data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb );
387			CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi;
388			phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb);
389	gezelter	1927	if (data2.isFluctuating) {
390			(idat.dVdFQ2) -= (idat.dfrho1) * rhb * data2.qToRhoScaling;
391			}
392	gezelter	1586	}
393	gezelter	1478
394	gezelter	1586	switch(mixMeth_) {
395			case eamJohnson:
396	gezelter	1478
397	gezelter	1554	if ( *(idat.rij) < rci) {
398	gezelter	1586	phab = phab + 0.5 * (rhb / rha) * pha;
399			dvpdr = dvpdr + 0.5((rhb/rha)dpha +
400			pha((drhb/rha) - (rhbdrha/rha/rha)));
401	gezelter	1478	}
402	gezelter	1586
403
404
405	gezelter	1554	if ( *(idat.rij) < rcj) {
406	gezelter	1586	phab = phab + 0.5 * (rha / rhb) * phb;
407			dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
408			phb((drha/rhb) - (rhadrhb/rhb/rhb)));
409	gezelter	1478	}
410
411	gezelter	1586	break;
412
413			case eamDaw:
414	gezelter	1895	MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), phab, dvpdr);
415	gezelter	1586
416			break;
417			case eamUnknown:
418			default:
419
420			sprintf(painCave.errMsg,
421			"EAM::calcForce hit a mixing method it doesn't know about!\n"
422			);
423			painCave.severity = OPENMD_ERROR;
424			painCave.isFatal = 1;
425			simError();
426
427			}
428
429			drhoidr = drha;
430			drhojdr = drhb;
431
432			dudr = drhojdr* (idat.dfrho1) + drhoidr *(idat.dfrho2) + dvpdr;
433
434			(idat.f1) += (idat.d) * dudr / *(idat.rij);
435	gezelter	1927
436	gezelter	1478
437	gezelter	1711	if (idat.doParticlePot) {
438			// particlePot is the difference between the full potential and
439			// the full potential without the presence of a particular
440			// particle (atom1).
441			//
442			// This reduces the density at other particle locations, so we
443			// need to recompute the density at atom2 assuming atom1 didn't
444			// contribute. This then requires recomputing the density
445			// functional for atom2 as well.
446
447			(idat.particlePot1) += data2.F->getValueAt( (idat.rho2) - rha )
448			- *(idat.frho2);
449
450			(idat.particlePot2) += data1.F->getValueAt( (idat.rho1) - rhb)
451			- *(idat.frho1);
452			}
453	gezelter	1586
454			(*(idat.pot))[METALLIC_FAMILY] += phab;
455
456			*(idat.vpair) += phab;
457
458	gezelter	1478	return;
459
460			}
461	gezelter	1505
462	gezelter	1545	RealType EAM::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
463	gezelter	1505	if (!initialized_) initialize();
464
465			RealType cut = 0.0;
466
467	gezelter	1895	int atid1 = atypes.first->getIdent();
468			int atid2 = atypes.second->getIdent();
469			int eamtid1 = EAMtids[atid1];
470			int eamtid2 = EAMtids[atid2];
471
472			if (eamtid1 != -1) {
473			EAMAtomData data1 = EAMdata[eamtid1];
474	gezelter	1505	cut = data1.rcut;
475			}
476
477	gezelter	1895	if (eamtid2 != -1) {
478			EAMAtomData data2 = EAMdata[eamtid2];
479	gezelter	1505	if (data2.rcut > cut)
480			cut = data2.rcut;
481			}
482	gezelter	1895
483	gezelter	1505	return cut;
484			}
485	gezelter	1478	}
486