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 {

  bool EAM::initialized_ = false;
  RealType EAM::eamRcut_ = 0.0;
  EAMMixingMethod EAM::mixMeth_ = eamJohnson;
  ForceField* EAM::forceField_ = NULL;
  std::map<int, AtomType*> EAM::EAMlist;
  std::map<AtomType*, EAMAtomData> EAM::EAMMap;
  std::map<std::pair<AtomType*, AtomType*>, EAMInteractionData> EAM::MixingMap;

  
  EAM* EAM::_instance = NULL;

  EAM* EAM::Instance() {
    if (!_instance) {
      _instance = new EAM();
    }
    return _instance;
  }
  
  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(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(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(i * drho);
      scaledF.push_back( eamParam.F[i] * 23.06054 );
    }
      
    CubicSpline* cs = new CubicSpline();
    cs->addPoints(rhovals, eamParam.F);
    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:

    // set rcut to be the smaller of the two atomic rcuts

    RealType rcut = eamParam1.rcut < eamParam2.rcut ? 
      eamParam1.rcut : eamParam2.rcut; 

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

    RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr;
    int nr = int(rcut/dr);
    vector<RealType> rvals;
    for (int i = 0; i < nr; i++) rvals.push_back(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];
      zi = z1->getValueAt(r); 
      zj = z2->getValueAt(r);

      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();
    std::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()) {
        
        std::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();    

    std::pair<std::map<int,AtomType*>::iterator,bool> ret;    
    ret = EAMlist.insert( std::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:
    
    std::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;

      std::pair<AtomType*, AtomType*> key1, key2;
      key1 = std::make_pair(atomType, atype2);
      key2 = std::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;

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

  void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij, 
                        RealType &rho_i_at_j, RealType &rho_j_at_i) {
    
    if (!initialized_) initialize();
    
    EAMAtomData data1 = EAMMap[at1];
    EAMAtomData data2 = EAMMap[at2];

    if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
    if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
    return;
  }

  void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho,
                           RealType &dfrhodrho) {

    if (!initialized_) initialize();

    EAMAtomData data1 = EAMMap[at1];
        
    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);

    frho = result.first;
    dfrhodrho = result.second;
    return;
  }

 
  void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d, 
                      RealType rij, RealType r2, RealType sw, 
                      RealType &vpair, RealType &pot, Vector3d &f1,
                      RealType rho_i, RealType rho_j, 
                      RealType dfrhodrho_i, RealType dfrhodrho_j, 
                      RealType &fshift_i, RealType &fshift_j) {

    if (!initialized_) initialize();
    
    pair<RealType, RealType> res;
    
    if (rij < eamRcut_) {

      EAMAtomData data1 = EAMMap[at1];
      EAMAtomData data2 = EAMMap[at2];

      // get type-specific cutoff radii

      RealType rci = data1.rcut;
      RealType rcj = data2.rcut;
      
      RealType rha, drha, rhb, drhb;
      RealType pha, dpha, phb, dphb;
      RealType phab, dvpdr;
      RealType drhoidr, drhojdr, dudr;
      
      if (rij < rci) {
        res = data1.rho->getValueAndDerivativeAt(rij);
        rha = res.first;
        drha = res.second;

        res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
        pha = res.first;
        dpha = res.second;
      }

      if (rij < rcj) {
        res = data2.rho->getValueAndDerivativeAt(rij);
        rhb = res.first;
        drhb = res.second;

        res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
        phb = res.first;
        dphb = res.second;
      }

      phab = 0.0;
      dvpdr = 0.0;

      switch(mixMeth_) {
      case eamJohnson:
       
        if (rij < rci) {
          phab = phab + 0.5 * (rhb / rha) * pha;
          dvpdr = dvpdr + 0.5*((rhb/rha)*dpha + 
                               pha*((drhb/rha) - (rhb*drha/rha/rha)));
        }

        if (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[make_pair(at1,at2)].phi->getValueAndDerivativeAt(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*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr; 

      f1 = d * dudr / rij;
        
      // particle_pot 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.
      //
      // Most of the particle_pot heavy lifting comes from the
      // pair interaction, and will be handled by vpair.
     
      fshift_i = data1.F->getValueAt( rho_i - rhb );
      fshift_j = data1.F->getValueAt( rho_j - rha );

      pot += phab;

      vpair += phab;
    }

    return;
    
  }


  void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *rij,
                                 RealType* rho_i_at_j, RealType* rho_j_at_i){

    if (!initialized_) initialize();
    
    AtomType* atype1 = EAMlist[*atid1];
    AtomType* atype2 = EAMlist[*atid2];
    
    calcDensity(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i);

    return;    
  }

  void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho,
                                   RealType *dfrhodrho) {

    if (!initialized_) initialize();

    AtomType* atype1 = EAMlist[*atid1];   

    calcFunctional(atype1, *rho, *frho, *dfrhodrho);
    
    return;    
  }
  RealType EAM::getEAMcut(int *atid1) {

    if (!initialized_) initialize();
    
    AtomType* atype1 = EAMlist[*atid1];   
       
    return getRcut(atype1);
  }

  void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij, 
                        RealType *r2, RealType *sw, RealType *vpair, 
                        RealType *pot, RealType *f1, RealType *rho1,
                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
                        RealType *fshift1, RealType *fshift2) {

    if (!initialized_) initialize();
    
    AtomType* atype1 = EAMlist[*atid1];
    AtomType* atype2 = EAMlist[*atid2];
    
    Vector3d disp(d[0], d[1], d[2]);
    Vector3d frc(f1[0], f1[1], f1[2]);
    
    calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair,  *pot, frc,
              *rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2);
      
    f1[0] = frc.x();
    f1[1] = frc.y();
    f1[2] = frc.z();

    return;    
  }
  
  void EAM::setCutoffEAM(RealType *thisRcut) {
    eamRcut_ = *thisRcut;
  }
}

extern "C" {
  
#define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO)
#define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO)
#define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR)
#define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM)
#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT)

  
  void fortranCalcDensity(int *atid1, int *atid2, RealType *rij, 
                          RealType *rho_i_at_j, RealType *rho_j_at_i) {
    
    return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij, 
                                                         rho_i_at_j,  
                                                         rho_j_at_i);
  }
  void fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho,
                             RealType *dfrhodrho) {  
    
    return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho,
                                                           dfrhodrho);
    
  }
  void fortranSetCutoffEAM(RealType *rcut) {
    return OpenMD::EAM::Instance()->setCutoffEAM(rcut);
  }
  void fortranCalcForce(int *atid1, int *atid2, RealType *d, RealType *rij, 
                        RealType *r2, RealType *sw, RealType *vpair, 
                        RealType *pot, RealType *f1, RealType *rho1,
                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
                        RealType *fshift1, RealType *fshift2){
    
    return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij, 
                                                r2, sw, vpair, 
                                                pot, f1, rho1,
                                                rho2, dfrho1, dfrho2,
                                                fshift1,  fshift2);
  }
  RealType fortranGetEAMcut(int* atid) {
    return OpenMD::EAM::Instance()->getEAMcut(atid);
  }

}
Revision:	1480
Committed:	Mon Jul 26 19:50:53 2010 UTC (14 years, 9 months ago) by gezelter
File size:	18792 byte(s)
Log Message:	no longer segfaults
#	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			bool EAM::initialized_ = false;
54	gezelter	1479	RealType EAM::eamRcut_ = 0.0;
55			EAMMixingMethod EAM::mixMeth_ = eamJohnson;
56	gezelter	1478	ForceField* EAM::forceField_ = NULL;
57			std::map<int, AtomType*> EAM::EAMlist;
58			std::map<AtomType*, EAMAtomData> EAM::EAMMap;
59			std::map<std::pair<AtomType, AtomType>, EAMInteractionData> EAM::MixingMap;
60	gezelter	1479
61	gezelter	1478
62			EAM* EAM::_instance = NULL;
63
64			EAM* EAM::Instance() {
65			if (!_instance) {
66			_instance = new EAM();
67			}
68			return _instance;
69			}
70
71			EAMParam EAM::getEAMParam(AtomType* atomType) {
72
73			// Do sanity checking on the AtomType we were passed before
74			// building any data structures:
75			if (!atomType->isEAM()) {
76			sprintf( painCave.errMsg,
77			"EAM::getEAMParam was passed an atomType (%s) that does not\n"
78			"\tappear to be an embedded atom method (EAM) atom.\n",
79			atomType->getName().c_str());
80			painCave.severity = OPENMD_ERROR;
81			painCave.isFatal = 1;
82			simError();
83			}
84
85			GenericData* data = atomType->getPropertyByName("EAM");
86			if (data == NULL) {
87			sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n"
88			"\tparameters for atomType %s.\n",
89			atomType->getName().c_str());
90			painCave.severity = OPENMD_ERROR;
91			painCave.isFatal = 1;
92			simError();
93			}
94
95			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
96			if (eamData == NULL) {
97			sprintf( painCave.errMsg,
98			"EAM::getEAMParam could not convert GenericData to EAMParam for\n"
99			"\tatom type %s\n", atomType->getName().c_str());
100			painCave.severity = OPENMD_ERROR;
101			painCave.isFatal = 1;
102			simError();
103			}
104
105			return eamData->getData();
106			}
107
108			CubicSpline* EAM::getZ(AtomType* atomType) {
109			EAMParam eamParam = getEAMParam(atomType);
110			int nr = eamParam.nr;
111			RealType dr = eamParam.dr;
112			vector<RealType> rvals;
113
114			for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
115
116			CubicSpline* cs = new CubicSpline();
117			cs->addPoints(rvals, eamParam.Z);
118			return cs;
119			}
120
121	gezelter	1479	RealType EAM::getRcut(AtomType* atomType) {
122			EAMParam eamParam = getEAMParam(atomType);
123			return eamParam.rcut;
124			}
125
126	gezelter	1478	CubicSpline* EAM::getRho(AtomType* atomType) {
127			EAMParam eamParam = getEAMParam(atomType);
128			int nr = eamParam.nr;
129			RealType dr = eamParam.dr;
130			vector<RealType> rvals;
131
132			for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
133
134			CubicSpline* cs = new CubicSpline();
135			cs->addPoints(rvals, eamParam.rho);
136			return cs;
137			}
138
139			CubicSpline* EAM::getF(AtomType* atomType) {
140			EAMParam eamParam = getEAMParam(atomType);
141			int nrho = eamParam.nrho;
142			RealType drho = eamParam.drho;
143			vector<RealType> rhovals;
144			vector<RealType> scaledF;
145
146			for (int i = 0; i < nrho; i++) {
147			rhovals.push_back(i * drho);
148			scaledF.push_back( eamParam.F[i] * 23.06054 );
149			}
150
151			CubicSpline* cs = new CubicSpline();
152			cs->addPoints(rhovals, eamParam.F);
153			return cs;
154			}
155
156			CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {
157			EAMParam eamParam1 = getEAMParam(atomType1);
158			EAMParam eamParam2 = getEAMParam(atomType2);
159			CubicSpline* z1 = getZ(atomType1);
160			CubicSpline* z2 = getZ(atomType2);
161
162			// make the r grid:
163
164			// set rcut to be the smaller of the two atomic rcuts
165
166			RealType rcut = eamParam1.rcut < eamParam2.rcut ?
167			eamParam1.rcut : eamParam2.rcut;
168
169			// use the smallest dr (finest grid) to build our grid:
170
171			RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr;
172			int nr = int(rcut/dr);
173			vector<RealType> rvals;
174			for (int i = 0; i < nr; i++) rvals.push_back(i*dr);
175
176			// construct the pair potential:
177
178			vector<RealType> phivals;
179			RealType phi;
180			RealType r;
181			RealType zi, zj;
182
183			phivals.push_back(0.0);
184
185			for (int i = 1; i < rvals.size(); i++ ) {
186			r = rvals[i];
187			zi = z1->getValueAt(r);
188			zj = z2->getValueAt(r);
189
190			phi = 331.999296 * (zi * zj) / r;
191			phivals.push_back(phi);
192			}
193
194			CubicSpline* cs = new CubicSpline();
195			cs->addPoints(rvals, phivals);
196			return cs;
197			}
198
199			void EAM::initialize() {
200
201			// set up the mixing method:
202	gezelter	1479	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
203	gezelter	1480	std::string EAMMixMeth = fopts.getEAMMixingMethod();
204			toUpper(EAMMixMeth);
205
206	gezelter	1478	if (EAMMixMeth == "JOHNSON")
207			mixMeth_ = eamJohnson;
208			else if (EAMMixMeth == "DAW")
209			mixMeth_ = eamDaw;
210			else
211			mixMeth_ = eamUnknown;
212
213			// find all of the EAM atom Types:
214			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
215			ForceField::AtomTypeContainer::MapTypeIterator i;
216			AtomType* at;
217
218			for (at = atomTypes->beginType(i); at != NULL;
219			at = atomTypes->nextType(i)) {
220
221			if (at->isEAM())
222			addType(at);
223			}
224
225			// find all of the explicit EAM interactions (setfl):
226			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
227			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
228			NonBondedInteractionType* nbt;
229
230			for (nbt = nbiTypes->beginType(j); nbt != NULL;
231			nbt = nbiTypes->nextType(j)) {
232
233			if (nbt->isEAM()) {
234
235			std::pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
236
237			GenericData* data = nbt->getPropertyByName("EAM");
238			if (data == NULL) {
239			sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
240			"\tEAM parameters for %s - %s interaction.\n",
241			atypes.first->getName().c_str(),
242			atypes.second->getName().c_str());
243			painCave.severity = OPENMD_ERROR;
244			painCave.isFatal = 1;
245			simError();
246			}
247
248			EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
249			if (eamData == NULL) {
250			sprintf( painCave.errMsg,
251			"EAM::rebuildMixingMap could not convert GenericData to\n"
252			"\tEAMMixingData for %s - %s interaction.\n",
253			atypes.first->getName().c_str(),
254			atypes.second->getName().c_str());
255			painCave.severity = OPENMD_ERROR;
256			painCave.isFatal = 1;
257			simError();
258			}
259
260	gezelter	1479	EAMMixingParam eamParam = eamData->getData();
261	gezelter	1478
262	gezelter	1479	vector<RealType> phiAB = eamParam.phi;
263	gezelter	1478	RealType dr = eamParam.dr;
264			int nr = eamParam.nr;
265
266			addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
267			}
268			}
269			initialized_ = true;
270			}
271
272
273
274			void EAM::addType(AtomType* atomType){
275
276			EAMAtomData eamAtomData;
277	gezelter	1479
278	gezelter	1478	eamAtomData.rho = getRho(atomType);
279			eamAtomData.F = getF(atomType);
280			eamAtomData.Z = getZ(atomType);
281			eamAtomData.rcut = getRcut(atomType);
282
283			// add it to the map:
284			AtomTypeProperties atp = atomType->getATP();
285
286			std::pair<std::map<int,AtomType*>::iterator,bool> ret;
287			ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
288			if (ret.second == false) {
289			sprintf( painCave.errMsg,
290			"EAM already had a previous entry with ident %d\n",
291			atp.ident);
292			painCave.severity = OPENMD_INFO;
293			painCave.isFatal = 0;
294			simError();
295			}
296
297			EAMMap[atomType] = eamAtomData;
298
299			// Now, iterate over all known types and add to the mixing map:
300
301	gezelter	1479	std::map<AtomType*, EAMAtomData>::iterator it;
302	gezelter	1478	for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
303
304	gezelter	1479	AtomType* atype2 = (*it).first;
305	gezelter	1478
306			EAMInteractionData mixer;
307			mixer.phi = getPhi(atomType, atype2);
308			mixer.explicitlySet = false;
309
310			std::pair<AtomType, AtomType> key1, key2;
311			key1 = std::make_pair(atomType, atype2);
312			key2 = std::make_pair(atype2, atomType);
313
314			MixingMap[key1] = mixer;
315			if (key2 != key1) {
316			MixingMap[key2] = mixer;
317			}
318			}
319			return;
320			}
321
322			void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
323			RealType dr, int nr,
324			vector<RealType> phiVals) {
325
326			// in case these weren't already in the map
327			addType(atype1);
328			addType(atype2);
329
330			EAMInteractionData mixer;
331			CubicSpline* cs = new CubicSpline();
332	gezelter	1479	vector<RealType> rVals;
333	gezelter	1478
334	gezelter	1479	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
335	gezelter	1478
336			cs->addPoints(rVals, phiVals);
337			mixer.phi = cs;
338			mixer.explicitlySet = true;
339
340			std::pair<AtomType, AtomType> key1, key2;
341			key1 = std::make_pair(atype1, atype2);
342			key2 = std::make_pair(atype2, atype1);
343
344			MixingMap[key1] = mixer;
345			if (key2 != key1) {
346			MixingMap[key2] = mixer;
347			}
348			return;
349			}
350
351	gezelter	1479	void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij,
352			RealType &rho_i_at_j, RealType &rho_j_at_i) {
353
354	gezelter	1478	if (!initialized_) initialize();
355	gezelter	1479
356	gezelter	1478	EAMAtomData data1 = EAMMap[at1];
357			EAMAtomData data2 = EAMMap[at2];
358
359			if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
360			if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
361			return;
362			}
363
364	gezelter	1479	void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho,
365			RealType &dfrhodrho) {
366	gezelter	1478
367			if (!initialized_) initialize();
368
369			EAMAtomData data1 = EAMMap[at1];
370
371			pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);
372
373			frho = result.first;
374			dfrhodrho = result.second;
375			return;
376			}
377
378
379			void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d,
380			RealType rij, RealType r2, RealType sw,
381			RealType &vpair, RealType &pot, Vector3d &f1,
382	gezelter	1479	RealType rho_i, RealType rho_j,
383			RealType dfrhodrho_i, RealType dfrhodrho_j,
384			RealType &fshift_i, RealType &fshift_j) {
385	gezelter	1478
386			if (!initialized_) initialize();
387
388			pair<RealType, RealType> res;
389
390			if (rij < eamRcut_) {
391
392			EAMAtomData data1 = EAMMap[at1];
393			EAMAtomData data2 = EAMMap[at2];
394
395			// get type-specific cutoff radii
396
397			RealType rci = data1.rcut;
398			RealType rcj = data2.rcut;
399
400			RealType rha, drha, rhb, drhb;
401			RealType pha, dpha, phb, dphb;
402			RealType phab, dvpdr;
403			RealType drhoidr, drhojdr, dudr;
404
405			if (rij < rci) {
406			res = data1.rho->getValueAndDerivativeAt(rij);
407			rha = res.first;
408			drha = res.second;
409
410			res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
411			pha = res.first;
412			dpha = res.second;
413			}
414
415			if (rij < rcj) {
416			res = data2.rho->getValueAndDerivativeAt(rij);
417			rhb = res.first;
418			drhb = res.second;
419
420			res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
421			phb = res.first;
422			dphb = res.second;
423			}
424
425			phab = 0.0;
426			dvpdr = 0.0;
427
428			switch(mixMeth_) {
429			case eamJohnson:
430
431			if (rij < rci) {
432			phab = phab + 0.5 * (rhb / rha) * pha;
433			dvpdr = dvpdr + 0.5((rhb/rha)dpha +
434			pha((drhb/rha) - (rhbdrha/rha/rha)));
435			}
436
437			if (rij < rcj) {
438			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
447			res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij);
448			phab = res.first;
449			dvpdr = res.second;
450
451			break;
452			case eamUnknown:
453			default:
454
455			sprintf(painCave.errMsg,
456			"EAM::calcForce hit a mixing method it doesn't know about!\n"
457			);
458			painCave.severity = OPENMD_ERROR;
459			painCave.isFatal = 1;
460			simError();
461
462			}
463
464			drhoidr = drha;
465			drhojdr = drhb;
466
467			dudr = drhojdrdfrhodrho_i + drhoidrdfrhodrho_j + dvpdr;
468
469			f1 = d * dudr / rij;
470
471			// particle_pot is the difference between the full potential
472			// and the full potential without the presence of a particular
473			// particle (atom1).
474			//
475			// This reduces the density at other particle locations, so
476			// we need to recompute the density at atom2 assuming atom1
477			// didn't contribute. This then requires recomputing the
478			// density functional for atom2 as well.
479			//
480			// Most of the particle_pot heavy lifting comes from the
481			// pair interaction, and will be handled by vpair.
482
483			fshift_i = data1.F->getValueAt( rho_i - rhb );
484			fshift_j = data1.F->getValueAt( rho_j - rha );
485
486			pot += phab;
487
488			vpair += phab;
489			}
490
491			return;
492
493			}
494
495
496	gezelter	1479	void EAM::calc_eam_prepair_rho(int atid1, int atid2, RealType *rij,
497	gezelter	1478	RealType* rho_i_at_j, RealType* rho_j_at_i){
498	gezelter	1479
499	gezelter	1478	if (!initialized_) initialize();
500	gezelter	1479
501	gezelter	1478	AtomType* atype1 = EAMlist[*atid1];
502			AtomType* atype2 = EAMlist[*atid2];
503
504	gezelter	1479	calcDensity(atype1, atype2, rij, rho_i_at_j, *rho_j_at_i);
505	gezelter	1478
506			return;
507			}
508
509			void EAM::calc_eam_preforce_Frho(int atid1, RealType rho, RealType *frho,
510			RealType *dfrhodrho) {
511
512			if (!initialized_) initialize();
513
514			AtomType* atype1 = EAMlist[*atid1];
515
516			calcFunctional(atype1, rho, frho, *dfrhodrho);
517
518			return;
519			}
520	gezelter	1479	RealType EAM::getEAMcut(int *atid1) {
521	gezelter	1478
522	gezelter	1479	if (!initialized_) initialize();
523
524			AtomType* atype1 = EAMlist[*atid1];
525
526			return getRcut(atype1);
527			}
528
529	gezelter	1478	void EAM::do_eam_pair(int atid1, int atid2, RealType d, RealType rij,
530			RealType r2, RealType sw, RealType *vpair,
531			RealType pot, RealType f1, RealType *rho1,
532			RealType rho2, RealType dfrho1, RealType *dfrho2,
533			RealType fshift1, RealType fshift2) {
534
535			if (!initialized_) initialize();
536
537	gezelter	1479	AtomType* atype1 = EAMlist[*atid1];
538			AtomType* atype2 = EAMlist[*atid2];
539	gezelter	1478
540			Vector3d disp(d[0], d[1], d[2]);
541			Vector3d frc(f1[0], f1[1], f1[2]);
542
543			calcForce(atype1, atype2, disp, rij, r2, sw, vpair, *pot, frc,
544			rho1, rho2, dfrho1, dfrho2, fshift1, fshift2);
545
546			f1[0] = frc.x();
547			f1[1] = frc.y();
548			f1[2] = frc.z();
549
550			return;
551			}
552
553			void EAM::setCutoffEAM(RealType *thisRcut) {
554	gezelter	1479	eamRcut_ = *thisRcut;
555	gezelter	1478	}
556			}
557
558			extern "C" {
559
560			#define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO)
561			#define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO)
562			#define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR)
563			#define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM)
564	gezelter	1479	#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT)
565
566	gezelter	1478
567	gezelter	1479	void fortranCalcDensity(int atid1, int atid2, RealType *rij,
568			RealType rho_i_at_j, RealType rho_j_at_i) {
569
570			return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij,
571			rho_i_at_j,
572			rho_j_at_i);
573	gezelter	1478	}
574	gezelter	1479	void fortranCalcFunctional(int atid1, RealType rho, RealType *frho,
575			RealType *dfrhodrho) {
576
577			return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho,
578			dfrhodrho);
579
580	gezelter	1478	}
581	gezelter	1479	void fortranSetCutoffEAM(RealType *rcut) {
582	gezelter	1478	return OpenMD::EAM::Instance()->setCutoffEAM(rcut);
583			}
584	gezelter	1479	void fortranCalcForce(int atid1, int atid2, RealType d, RealType rij,
585	gezelter	1478	RealType r2, RealType sw, RealType *vpair,
586			RealType pot, RealType f1, RealType *rho1,
587			RealType rho2, RealType dfrho1, RealType *dfrho2,
588			RealType fshift1, RealType fshift2){
589
590	gezelter	1479	return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij,
591			r2, sw, vpair,
592			pot, f1, rho1,
593			rho2, dfrho1, dfrho2,
594			fshift1, fshift2);
595	gezelter	1478	}
596	gezelter	1479	RealType fortranGetEAMcut(int* atid) {
597			return OpenMD::EAM::Instance()->getEAMcut(atid);
598			}
599
600	gezelter	1478	}