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();
      
    // 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();         
    }


    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.rcut = mixer.phi->getLimits().second;
      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.rcut = mixer.phi->getLimits().second;
    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) {
      *(idat.rho2) += data1.rho->getValueAt( *(idat.rij));
    }
      
    if ( *(idat.rij) < data2.rcut) {
      *(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 ( *(idat.rij) < rcj) {
      data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb );
      CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi;
      phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb);
    }
    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:
      if ( *(idat.rij) <  MixingMap[eamtid1][eamtid2].rcut) {
        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:	2033
Committed:	Sat Nov 1 14:12:16 2014 UTC (10 years, 8 months ago) by gezelter
File size:	13876 byte(s)
Log Message:	Fixed a selection issue in ParticleTimeCorrFunc, other whitespace stuff
#	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	jmichalk	2031
111	gezelter	1478	phivals.push_back(phi);
112			}
113			CubicSpline* cs = new CubicSpline();
114			cs->addPoints(rvals, phivals);
115			return cs;
116			}
117
118	gezelter	1586	void EAM::setCutoffRadius( RealType rCut ) {
119			eamRcut_ = rCut;
120			haveCutoffRadius_ = true;
121			}
122
123	gezelter	1478	void EAM::initialize() {
124			// set up the mixing method:
125	gezelter	1479	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
126	gezelter	1481	string EAMMixMeth = fopts.getEAMMixingMethod();
127	gezelter	1480	toUpper(EAMMixMeth);
128
129	gezelter	1478	if (EAMMixMeth == "JOHNSON")
130			mixMeth_ = eamJohnson;
131			else if (EAMMixMeth == "DAW")
132			mixMeth_ = eamDaw;
133			else
134			mixMeth_ = eamUnknown;
135
136			// find all of the EAM atom Types:
137	gezelter	1895	EAMtypes.clear();
138			EAMtids.clear();
139			EAMdata.clear();
140			MixingMap.clear();
141			nEAM_ = 0;
142
143			EAMtids.resize( forceField_->getNAtomType(), -1);
144	gezelter	1478
145	gezelter	1895	set<AtomType*>::iterator at;
146			for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
147			if ((*at)->isEAM()) nEAM_++;
148	gezelter	1478	}
149	gezelter	1895	EAMdata.resize(nEAM_);
150			MixingMap.resize(nEAM_);
151
152			for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
153			if ((at)->isEAM()) addType(at);
154			}
155	gezelter	1478
156			// find all of the explicit EAM interactions (setfl):
157			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
158			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
159			NonBondedInteractionType* nbt;
160
161			for (nbt = nbiTypes->beginType(j); nbt != NULL;
162			nbt = nbiTypes->nextType(j)) {
163
164			if (nbt->isEAM()) {
165
166	gezelter	1481	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
167	gezelter	1478
168			GenericData* data = nbt->getPropertyByName("EAM");
169			if (data == NULL) {
170			sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
171			"\tEAM parameters for %s - %s interaction.\n",
172			atypes.first->getName().c_str(),
173			atypes.second->getName().c_str());
174			painCave.severity = OPENMD_ERROR;
175			painCave.isFatal = 1;
176			simError();
177			}
178
179			EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
180			if (eamData == NULL) {
181			sprintf( painCave.errMsg,
182			"EAM::rebuildMixingMap could not convert GenericData to\n"
183			"\tEAMMixingData for %s - %s interaction.\n",
184			atypes.first->getName().c_str(),
185			atypes.second->getName().c_str());
186			painCave.severity = OPENMD_ERROR;
187			painCave.isFatal = 1;
188			simError();
189			}
190
191	gezelter	1479	EAMMixingParam eamParam = eamData->getData();
192	gezelter	1478
193	gezelter	1479	vector<RealType> phiAB = eamParam.phi;
194	gezelter	1478	RealType dr = eamParam.dr;
195			int nr = eamParam.nr;
196
197			addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
198			}
199			}
200			initialized_ = true;
201			}
202
203
204
205			void EAM::addType(AtomType* atomType){
206
207	gezelter	1710	EAMAdapter ea = EAMAdapter(atomType);
208	gezelter	1478	EAMAtomData eamAtomData;
209
210	gezelter	1710	eamAtomData.rho = ea.getRho();
211			eamAtomData.F = ea.getF();
212			eamAtomData.Z = ea.getZ();
213			eamAtomData.rcut = ea.getRcut();
214	gezelter	1927
215	gezelter	1478	// add it to the map:
216	gezelter	1895	int atid = atomType->getIdent();
217			int eamtid = EAMtypes.size();
218	gezelter	1478
219	gezelter	1895	pair<set<int>::iterator,bool> ret;
220			ret = EAMtypes.insert( atid );
221	gezelter	1478	if (ret.second == false) {
222			sprintf( painCave.errMsg,
223			"EAM already had a previous entry with ident %d\n",
224	gezelter	1895	atid);
225	gezelter	1478	painCave.severity = OPENMD_INFO;
226			painCave.isFatal = 0;
227			simError();
228			}
229
230	gezelter	1927
231	gezelter	1895	EAMtids[atid] = eamtid;
232			EAMdata[eamtid] = eamAtomData;
233			MixingMap[eamtid].resize(nEAM_);
234	gezelter	1478
235			// Now, iterate over all known types and add to the mixing map:
236
237	gezelter	1895	std::set<int>::iterator it;
238			for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) {
239	gezelter	1478
240	gezelter	1895	int eamtid2 = EAMtids[ (*it) ];
241			AtomType* atype2 = forceField_->getAtomType( (*it) );
242	gezelter	1478
243			EAMInteractionData mixer;
244			mixer.phi = getPhi(atomType, atype2);
245	gezelter	1928	mixer.rcut = mixer.phi->getLimits().second;
246	gezelter	1478	mixer.explicitlySet = false;
247
248	gezelter	1895	MixingMap[eamtid2].resize( nEAM_ );
249	gezelter	1478
250	gezelter	1895	MixingMap[eamtid][eamtid2] = mixer;
251			if (eamtid2 != eamtid) {
252			MixingMap[eamtid2][eamtid] = mixer;
253	gezelter	1478	}
254			}
255			return;
256			}
257
258			void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
259			RealType dr, int nr,
260			vector<RealType> phiVals) {
261
262			// in case these weren't already in the map
263			addType(atype1);
264			addType(atype2);
265
266			EAMInteractionData mixer;
267			CubicSpline* cs = new CubicSpline();
268	gezelter	1479	vector<RealType> rVals;
269	gezelter	1478
270	gezelter	1479	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
271	gezelter	1478
272			cs->addPoints(rVals, phiVals);
273			mixer.phi = cs;
274	gezelter	1928	mixer.rcut = mixer.phi->getLimits().second;
275	gezelter	1478	mixer.explicitlySet = true;
276
277	gezelter	1895	int eamtid1 = EAMtids[ atype1->getIdent() ];
278			int eamtid2 = EAMtids[ atype2->getIdent() ];
279	gezelter	1478
280	gezelter	1895	MixingMap[eamtid1][eamtid2] = mixer;
281			if (eamtid2 != eamtid1) {
282			MixingMap[eamtid2][eamtid1] = mixer;
283	gezelter	1478	}
284			return;
285			}
286
287	gezelter	1545	void EAM::calcDensity(InteractionData &idat) {
288	gezelter	1479
289	gezelter	1478	if (!initialized_) initialize();
290	gezelter	1479
291	gezelter	1895	EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]];
292			EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]];
293
294	gezelter	1586	if (haveCutoffRadius_)
295			if ( *(idat.rij) > eamRcut_) return;
296
297	gezelter	1927	if ( *(idat.rij) < data1.rcut) {
298	gezelter	1929	(idat.rho2) += data1.rho->getValueAt( (idat.rij));
299	gezelter	1927	}
300	gezelter	1586
301	gezelter	1927	if ( *(idat.rij) < data2.rcut) {
302	gezelter	1929	(idat.rho1) += data2.rho->getValueAt( (idat.rij));
303	gezelter	1927	}
304	gezelter	1629
305			return;
306	gezelter	1478	}
307	gezelter	1586
308	gezelter	1545	void EAM::calcFunctional(SelfData &sdat) {
309	gezelter	1586
310	gezelter	1478	if (!initialized_) initialize();
311	gezelter	1895	EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ];
312	gezelter	1927
313	gezelter	2033	data1.F->getValueAndDerivativeAt( (sdat.rho), (sdat.frho),
314			*(sdat.dfrhodrho) );
315	gezelter	1478
316	gezelter	1895	((sdat.pot))[METALLIC_FAMILY] += (sdat.frho);
317	gezelter	1711	if (sdat.doParticlePot) {
318	gezelter	1895	(sdat.particlePot) += (sdat.frho);
319	gezelter	1711	}
320	gezelter	1575
321	gezelter	1478	return;
322			}
323
324
325	gezelter	1536	void EAM::calcForce(InteractionData &idat) {
326	gezelter	1478
327			if (!initialized_) initialize();
328	gezelter	1481
329	gezelter	1586	if (haveCutoffRadius_)
330			if ( *(idat.rij) > eamRcut_) return;
331
332	gezelter	1895
333			int eamtid1 = EAMtids[idat.atid1];
334			int eamtid2 = EAMtids[idat.atid2];
335			EAMAtomData &data1 = EAMdata[eamtid1];
336			EAMAtomData &data2 = EAMdata[eamtid2];
337	gezelter	1586
338			// get type-specific cutoff radii
339
340			RealType rci = data1.rcut;
341			RealType rcj = data2.rcut;
342	jmichalk	2031
343	gezelter	1586
344			RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
345			RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
346			RealType phab(0.0), dvpdr(0.0);
347			RealType drhoidr, drhojdr, dudr;
348
349			if ( *(idat.rij) < rci) {
350	gezelter	1895	data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha);
351			CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi;
352			phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha);
353	gezelter	1586	}
354
355			if ( *(idat.rij) < rcj) {
356	gezelter	1895	data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb );
357			CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi;
358			phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb);
359	gezelter	1586	}
360			switch(mixMeth_) {
361			case eamJohnson:
362	gezelter	1554	if ( *(idat.rij) < rci) {
363	gezelter	1586	phab = phab + 0.5 * (rhb / rha) * pha;
364			dvpdr = dvpdr + 0.5((rhb/rha)dpha +
365			pha((drhb/rha) - (rhbdrha/rha/rha)));
366	gezelter	1478	}
367	gezelter	2033
368	gezelter	1554	if ( *(idat.rij) < rcj) {
369	gezelter	1586	phab = phab + 0.5 * (rha / rhb) * phb;
370			dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
371			phb((drha/rhb) - (rhadrhb/rhb/rhb)));
372	gezelter	1478	}
373	gezelter	1586	break;
374			case eamDaw:
375	gezelter	1928	if ( *(idat.rij) < MixingMap[eamtid1][eamtid2].rcut) {
376			MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij),
377			phab, dvpdr);
378			}
379	gezelter	1586	break;
380			case eamUnknown:
381			default:
382
383			sprintf(painCave.errMsg,
384			"EAM::calcForce hit a mixing method it doesn't know about!\n"
385			);
386			painCave.severity = OPENMD_ERROR;
387			painCave.isFatal = 1;
388			simError();
389
390			}
391
392			drhoidr = drha;
393			drhojdr = drhb;
394
395			dudr = drhojdr* (idat.dfrho1) + drhoidr *(idat.dfrho2) + dvpdr;
396
397			(idat.f1) += (idat.d) * dudr / *(idat.rij);
398	gezelter	1927
399	gezelter	1711	if (idat.doParticlePot) {
400			// particlePot is the difference between the full potential and
401			// the full potential without the presence of a particular
402			// particle (atom1).
403			//
404			// This reduces the density at other particle locations, so we
405			// need to recompute the density at atom2 assuming atom1 didn't
406			// contribute. This then requires recomputing the density
407			// functional for atom2 as well.
408
409			(idat.particlePot1) += data2.F->getValueAt( (idat.rho2) - rha )
410			- *(idat.frho2);
411
412			(idat.particlePot2) += data1.F->getValueAt( (idat.rho1) - rhb)
413			- *(idat.frho1);
414			}
415	gezelter	1586
416	gezelter	2033	(*(idat.pot))[METALLIC_FAMILY] += phab;
417			*(idat.vpair) += phab;
418			return;
419	gezelter	1478	}
420	gezelter	1505
421	gezelter	1545	RealType EAM::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
422	gezelter	1505	if (!initialized_) initialize();
423
424			RealType cut = 0.0;
425
426	gezelter	1895	int atid1 = atypes.first->getIdent();
427			int atid2 = atypes.second->getIdent();
428			int eamtid1 = EAMtids[atid1];
429			int eamtid2 = EAMtids[atid2];
430
431			if (eamtid1 != -1) {
432			EAMAtomData data1 = EAMdata[eamtid1];
433	gezelter	1505	cut = data1.rcut;
434			}
435
436	gezelter	1895	if (eamtid2 != -1) {
437			EAMAtomData data2 = EAMdata[eamtid2];
438	gezelter	1505	if (data2.rcut > cut)
439			cut = data2.rcut;
440			}
441	gezelter	1895
442	gezelter	1505	return cut;
443			}
444	gezelter	1478	}
445