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;
  map<int, AtomType*> EAM::EAMlist;
  map<AtomType*, EAMAtomData> EAM::EAMMap;
  map<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:


    // we need phi out to the largest value we'll encounter in the radial space;
    
    RealType rmax = 0.0;
    rmax = max(rmax, eamParam1.rcut);
    rmax = max(rmax, eamParam1.nr * eamParam1.dr);

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

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

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

    int nr = int(rmax/dr + 0.5);

    vector<RealType> rvals;
    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));

    // construct the pair potential:

    vector<RealType> phivals;
    RealType phi;
    RealType r;
    RealType zi, zj;

    phivals.push_back(0.0);

    for (int i = 1; i < rvals.size(); i++ ) {
      r = rvals[i];

      // only use z(r) if we're inside this atoms cutoff radius, otherwise, we'll use zero for the charge.
      // This effectively means that our phi grid goes out beyond the cutoff of the pair potential

      zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0;
      zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0;

      phi = 331.999296 * (zi * zj) / r;

      phivals.push_back(phi);
    }
      
    CubicSpline* cs = new CubicSpline();
    cs->addPoints(rvals, phivals);
    return cs;
  }

  void EAM::initialize() { 

    // set up the mixing method:
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    string EAMMixMeth = fopts.getEAMMixingMethod();
    toUpper(EAMMixMeth);
   
    if (EAMMixMeth == "JOHNSON") 
      mixMeth_ = eamJohnson;    
    else if (EAMMixMeth == "DAW")
      mixMeth_ = eamDaw;
    else
      mixMeth_ = eamUnknown;
      
    // find all of the EAM atom Types:
    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypes->beginType(i); at != NULL; 
         at = atomTypes->nextType(i)) {
      
      if (at->isEAM())
        addType(at);
    }
    
    // find all of the explicit EAM interactions (setfl):
    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    NonBondedInteractionType* nbt;

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isEAM()) {
        
        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("EAM");
        if (data == NULL) {
          sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
                   "\tEAM parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
        
        EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
        if (eamData == NULL) {
          sprintf( painCave.errMsg,
                   "EAM::rebuildMixingMap could not convert GenericData to\n"
                   "\tEAMMixingData for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        EAMMixingParam eamParam = eamData->getData();

        vector<RealType> phiAB = eamParam.phi;
        RealType dr = eamParam.dr;
        int nr = eamParam.nr;

        addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
      }
    }  
    initialized_ = true;
  }
      

  void EAM::addType(AtomType* atomType){

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

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

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

    EAMMap[atomType] = eamAtomData;
    
    // Now, iterate over all known types and add to the mixing map:
    
    map<AtomType*, EAMAtomData>::iterator it;
    for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
      
      AtomType* atype2 = (*it).first;

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

      pair<AtomType*, AtomType*> key1, key2;
      key1 = make_pair(atomType, atype2);
      key2 = make_pair(atype2, atomType);
      
      MixingMap[key1] = mixer;
      if (key2 != key1) {
        MixingMap[key2] = mixer;
      }
    }      
    return;
  }
  
  void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2, 
                                   RealType dr, int nr,
                                   vector<RealType> phiVals) {
    
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);

    EAMInteractionData mixer;
    CubicSpline* cs = new CubicSpline();
    vector<RealType> rVals;

    for (int i = 0; i < nr; i++) rVals.push_back(i * dr);

    cs->addPoints(rVals, phiVals);
    mixer.phi = cs;
    mixer.explicitlySet = true;

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

  void EAM::calcDensity(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:	1481
Committed:	Mon Jul 26 21:55:18 2010 UTC (15 years, 3 months ago) by gezelter
File size:	19085 byte(s)
Log Message:	fixed phi mixing
#	Content
1	/*
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	#include "types/NonBondedInteractionType.hpp"
49
50
51	namespace OpenMD {
52
53	bool EAM::initialized_ = false;
54	RealType EAM::eamRcut_ = 0.0;
55	EAMMixingMethod EAM::mixMeth_ = eamJohnson;
56	ForceField* EAM::forceField_ = NULL;
57	map<int, AtomType*> EAM::EAMlist;
58	map<AtomType*, EAMAtomData> EAM::EAMMap;
59	map<pair<AtomType, AtomType>, EAMInteractionData> EAM::MixingMap;
60
61
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	RealType EAM::getRcut(AtomType* atomType) {
122	EAMParam eamParam = getEAMParam(atomType);
123	return eamParam.rcut;
124	}
125
126	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
165	// we need phi out to the largest value we'll encounter in the radial space;
166
167	RealType rmax = 0.0;
168	rmax = max(rmax, eamParam1.rcut);
169	rmax = max(rmax, eamParam1.nr * eamParam1.dr);
170
171	rmax = max(rmax, eamParam2.rcut);
172	rmax = max(rmax, eamParam2.nr * eamParam2.dr);
173
174	// use the smallest dr (finest grid) to build our grid:
175
176	RealType dr = min(eamParam1.dr, eamParam2.dr);
177
178	int nr = int(rmax/dr + 0.5);
179
180	vector<RealType> rvals;
181	for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
182
183	// construct the pair potential:
184
185	vector<RealType> phivals;
186	RealType phi;
187	RealType r;
188	RealType zi, zj;
189
190	phivals.push_back(0.0);
191
192	for (int i = 1; i < rvals.size(); i++ ) {
193	r = rvals[i];
194
195	// only use z(r) if we're inside this atoms cutoff radius, otherwise, we'll use zero for the charge.
196	// This effectively means that our phi grid goes out beyond the cutoff of the pair potential
197
198	zi = r <= eamParam1.rcut ? z1->getValueAt(r) : 0.0;
199	zj = r <= eamParam2.rcut ? z2->getValueAt(r) : 0.0;
200
201	phi = 331.999296 * (zi * zj) / r;
202
203	phivals.push_back(phi);
204	}
205
206	CubicSpline* cs = new CubicSpline();
207	cs->addPoints(rvals, phivals);
208	return cs;
209	}
210
211	void EAM::initialize() {
212
213	// set up the mixing method:
214	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
215	string EAMMixMeth = fopts.getEAMMixingMethod();
216	toUpper(EAMMixMeth);
217
218	if (EAMMixMeth == "JOHNSON")
219	mixMeth_ = eamJohnson;
220	else if (EAMMixMeth == "DAW")
221	mixMeth_ = eamDaw;
222	else
223	mixMeth_ = eamUnknown;
224
225	// find all of the EAM atom Types:
226	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
227	ForceField::AtomTypeContainer::MapTypeIterator i;
228	AtomType* at;
229
230	for (at = atomTypes->beginType(i); at != NULL;
231	at = atomTypes->nextType(i)) {
232
233	if (at->isEAM())
234	addType(at);
235	}
236
237	// find all of the explicit EAM interactions (setfl):
238	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
239	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
240	NonBondedInteractionType* nbt;
241
242	for (nbt = nbiTypes->beginType(j); nbt != NULL;
243	nbt = nbiTypes->nextType(j)) {
244
245	if (nbt->isEAM()) {
246
247	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
248
249	GenericData* data = nbt->getPropertyByName("EAM");
250	if (data == NULL) {
251	sprintf( painCave.errMsg, "EAM::rebuildMixingMap could not find\n"
252	"\tEAM parameters 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	EAMMixingData* eamData = dynamic_cast<EAMMixingData*>(data);
261	if (eamData == NULL) {
262	sprintf( painCave.errMsg,
263	"EAM::rebuildMixingMap could not convert GenericData to\n"
264	"\tEAMMixingData for %s - %s interaction.\n",
265	atypes.first->getName().c_str(),
266	atypes.second->getName().c_str());
267	painCave.severity = OPENMD_ERROR;
268	painCave.isFatal = 1;
269	simError();
270	}
271
272	EAMMixingParam eamParam = eamData->getData();
273
274	vector<RealType> phiAB = eamParam.phi;
275	RealType dr = eamParam.dr;
276	int nr = eamParam.nr;
277
278	addExplicitInteraction(atypes.first, atypes.second, dr, nr, phiAB);
279	}
280	}
281	initialized_ = true;
282	}
283
284
285
286	void EAM::addType(AtomType* atomType){
287
288	EAMAtomData eamAtomData;
289
290	eamAtomData.rho = getRho(atomType);
291	eamAtomData.F = getF(atomType);
292	eamAtomData.Z = getZ(atomType);
293	eamAtomData.rcut = getRcut(atomType);
294
295	// add it to the map:
296	AtomTypeProperties atp = atomType->getATP();
297
298	pair<map<int,AtomType*>::iterator,bool> ret;
299	ret = EAMlist.insert( pair<int, AtomType*>(atp.ident, atomType) );
300	if (ret.second == false) {
301	sprintf( painCave.errMsg,
302	"EAM already had a previous entry with ident %d\n",
303	atp.ident);
304	painCave.severity = OPENMD_INFO;
305	painCave.isFatal = 0;
306	simError();
307	}
308
309	EAMMap[atomType] = eamAtomData;
310
311	// Now, iterate over all known types and add to the mixing map:
312
313	map<AtomType*, EAMAtomData>::iterator it;
314	for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
315
316	AtomType* atype2 = (*it).first;
317
318	EAMInteractionData mixer;
319	mixer.phi = getPhi(atomType, atype2);
320	mixer.explicitlySet = false;
321
322	pair<AtomType, AtomType> key1, key2;
323	key1 = make_pair(atomType, atype2);
324	key2 = make_pair(atype2, atomType);
325
326	MixingMap[key1] = mixer;
327	if (key2 != key1) {
328	MixingMap[key2] = mixer;
329	}
330	}
331	return;
332	}
333
334	void EAM::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
335	RealType dr, int nr,
336	vector<RealType> phiVals) {
337
338	// in case these weren't already in the map
339	addType(atype1);
340	addType(atype2);
341
342	EAMInteractionData mixer;
343	CubicSpline* cs = new CubicSpline();
344	vector<RealType> rVals;
345
346	for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
347
348	cs->addPoints(rVals, phiVals);
349	mixer.phi = cs;
350	mixer.explicitlySet = true;
351
352	pair<AtomType, AtomType> key1, key2;
353	key1 = make_pair(atype1, atype2);
354	key2 = make_pair(atype2, atype1);
355
356	MixingMap[key1] = mixer;
357	if (key2 != key1) {
358	MixingMap[key2] = mixer;
359	}
360	return;
361	}
362
363	void EAM::calcDensity(AtomType* at1, AtomType* at2, const RealType rij,
364	RealType &rho_i_at_j, RealType &rho_j_at_i) {
365
366	if (!initialized_) initialize();
367
368	EAMAtomData data1 = EAMMap[at1];
369	EAMAtomData data2 = EAMMap[at2];
370
371	if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
372	if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
373	return;
374	}
375
376	void EAM::calcFunctional(AtomType* at1, RealType rho, RealType &frho,
377	RealType &dfrhodrho) {
378
379	if (!initialized_) initialize();
380
381	EAMAtomData data1 = EAMMap[at1];
382
383	pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);
384
385	frho = result.first;
386	dfrhodrho = result.second;
387	return;
388	}
389
390
391	void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d,
392	RealType rij, RealType r2, RealType sw,
393	RealType &vpair, RealType &pot, Vector3d &f1,
394	RealType rho_i, RealType rho_j,
395	RealType dfrhodrho_i, RealType dfrhodrho_j,
396	RealType &fshift_i, RealType &fshift_j) {
397
398	if (!initialized_) initialize();
399
400	pair<RealType, RealType> res;
401
402	if (rij < eamRcut_) {
403
404	EAMAtomData data1 = EAMMap[at1];
405	EAMAtomData data2 = EAMMap[at2];
406
407	// get type-specific cutoff radii
408
409	RealType rci = data1.rcut;
410	RealType rcj = data2.rcut;
411
412	RealType rha, drha, rhb, drhb;
413	RealType pha, dpha, phb, dphb;
414	RealType phab, dvpdr;
415	RealType drhoidr, drhojdr, dudr;
416
417	if (rij < rci) {
418	res = data1.rho->getValueAndDerivativeAt(rij);
419	rha = res.first;
420	drha = res.second;
421
422	res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
423	pha = res.first;
424	dpha = res.second;
425	}
426
427	if (rij < rcj) {
428	res = data2.rho->getValueAndDerivativeAt(rij);
429	rhb = res.first;
430	drhb = res.second;
431
432	res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
433	phb = res.first;
434	dphb = res.second;
435	}
436
437	phab = 0.0;
438	dvpdr = 0.0;
439
440	switch(mixMeth_) {
441	case eamJohnson:
442
443	if (rij < rci) {
444	phab = phab + 0.5 * (rhb / rha) * pha;
445	dvpdr = dvpdr + 0.5((rhb/rha)dpha +
446	pha((drhb/rha) - (rhbdrha/rha/rha)));
447	}
448
449	if (rij < rcj) {
450	phab = phab + 0.5 * (rha / rhb) * phb;
451	dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
452	phb((drha/rhb) - (rhadrhb/rhb/rhb)));
453	}
454
455	break;
456
457	case eamDaw:
458	res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij);
459	phab = res.first;
460	dvpdr = res.second;
461
462	break;
463	case eamUnknown:
464	default:
465
466	sprintf(painCave.errMsg,
467	"EAM::calcForce hit a mixing method it doesn't know about!\n"
468	);
469	painCave.severity = OPENMD_ERROR;
470	painCave.isFatal = 1;
471	simError();
472
473	}
474
475	drhoidr = drha;
476	drhojdr = drhb;
477
478	dudr = drhojdrdfrhodrho_i + drhoidrdfrhodrho_j + dvpdr;
479
480	f1 = d * dudr / rij;
481
482	// particle_pot is the difference between the full potential
483	// and the full potential without the presence of a particular
484	// particle (atom1).
485	//
486	// This reduces the density at other particle locations, so
487	// we need to recompute the density at atom2 assuming atom1
488	// didn't contribute. This then requires recomputing the
489	// density functional for atom2 as well.
490	//
491	// Most of the particle_pot heavy lifting comes from the
492	// pair interaction, and will be handled by vpair.
493
494	fshift_i = data1.F->getValueAt( rho_i - rhb );
495	fshift_j = data1.F->getValueAt( rho_j - rha );
496
497	pot += phab;
498
499	vpair += phab;
500	}
501
502	return;
503
504	}
505
506
507	void EAM::calc_eam_prepair_rho(int atid1, int atid2, RealType *rij,
508	RealType* rho_i_at_j, RealType* rho_j_at_i){
509
510	if (!initialized_) initialize();
511
512	AtomType* atype1 = EAMlist[*atid1];
513	AtomType* atype2 = EAMlist[*atid2];
514
515	calcDensity(atype1, atype2, rij, rho_i_at_j, *rho_j_at_i);
516
517	return;
518	}
519
520	void EAM::calc_eam_preforce_Frho(int atid1, RealType rho, RealType *frho,
521	RealType *dfrhodrho) {
522
523	if (!initialized_) initialize();
524
525	AtomType* atype1 = EAMlist[*atid1];
526
527	calcFunctional(atype1, rho, frho, *dfrhodrho);
528
529	return;
530	}
531	RealType EAM::getEAMcut(int *atid1) {
532
533	if (!initialized_) initialize();
534
535	AtomType* atype1 = EAMlist[*atid1];
536
537	return getRcut(atype1);
538	}
539
540	void EAM::do_eam_pair(int atid1, int atid2, RealType d, RealType rij,
541	RealType r2, RealType sw, RealType *vpair,
542	RealType pot, RealType f1, RealType *rho1,
543	RealType rho2, RealType dfrho1, RealType *dfrho2,
544	RealType fshift1, RealType fshift2) {
545
546	if (!initialized_) initialize();
547
548	AtomType* atype1 = EAMlist[*atid1];
549	AtomType* atype2 = EAMlist[*atid2];
550
551	Vector3d disp(d[0], d[1], d[2]);
552	Vector3d frc(f1[0], f1[1], f1[2]);
553
554	calcForce(atype1, atype2, disp, rij, r2, sw, vpair, *pot, frc,
555	rho1, rho2, dfrho1, dfrho2, fshift1, fshift2);
556
557	f1[0] = frc.x();
558	f1[1] = frc.y();
559	f1[2] = frc.z();
560
561	return;
562	}
563
564	void EAM::setCutoffEAM(RealType *thisRcut) {
565	eamRcut_ = *thisRcut;
566	}
567	}
568
569	extern "C" {
570
571	#define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO)
572	#define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO)
573	#define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR)
574	#define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM)
575	#define fortranGetEAMcut FC_FUNC(geteamcut, GETEAMCUT)
576
577
578	void fortranCalcDensity(int atid1, int atid2, RealType *rij,
579	RealType rho_i_at_j, RealType rho_j_at_i) {
580
581	return OpenMD::EAM::Instance()->calc_eam_prepair_rho(atid1, atid2, rij,
582	rho_i_at_j,
583	rho_j_at_i);
584	}
585	void fortranCalcFunctional(int atid1, RealType rho, RealType *frho,
586	RealType *dfrhodrho) {
587
588	return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(atid1, rho, frho,
589	dfrhodrho);
590
591	}
592	void fortranSetCutoffEAM(RealType *rcut) {
593	return OpenMD::EAM::Instance()->setCutoffEAM(rcut);
594	}
595	void fortranCalcForce(int atid1, int atid2, RealType d, RealType rij,
596	RealType r2, RealType sw, RealType *vpair,
597	RealType pot, RealType f1, RealType *rho1,
598	RealType rho2, RealType dfrho1, RealType *dfrho2,
599	RealType fshift1, RealType fshift2){
600
601	return OpenMD::EAM::Instance()->do_eam_pair(atid1, atid2, d, rij,
602	r2, sw, vpair,
603	pot, f1, rho1,
604	rho2, dfrho1, dfrho2,
605	fshift1, fshift2);
606	}
607	RealType fortranGetEAMcut(int* atid) {
608	return OpenMD::EAM::Instance()->getEAMcut(atid);
609	}
610
611	}