SC.cpp

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 *
 * 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] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "nonbonded/SC.hpp"
 
#include <cmath>
#include <cstdio>
#include <cstring>
 
#include "types/NonBondedInteractionType.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  SC::SC() : name_("SC"), initialized_(false), forceField_(NULL), np_(3000) {}
 
  SC::~SC() {
    initialized_ = false;
 
    MixingMap.clear();
    SCtypes.clear();
    SCdata.clear();
    SCtids.clear();
  }
 
  RealType SC::getM(AtomType* atomType1, AtomType* atomType2) {
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType m1            = sca1.getM();
    RealType m2            = sca2.getM();
    return 0.5 * (m1 + m2);
  }
 
  RealType SC::getN(AtomType* atomType1, AtomType* atomType2) {
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType n1            = sca1.getN();
    RealType n2            = sca2.getN();
    return 0.5 * (n1 + n2);
  }
 
  RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) {
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType alpha1        = sca1.getAlpha();
    RealType alpha2        = sca2.getAlpha();
 
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    std::string DistanceMix  = fopts.getDistanceMixingRule();
    toUpper(DistanceMix);
 
    if (DistanceMix == "GEOMETRIC")
      return sqrt(alpha1 * alpha2);
    else
      return 0.5 * (alpha1 + alpha2);
  }
 
  RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType epsilon1      = sca1.getEpsilon();
    RealType epsilon2      = sca2.getEpsilon();
    return sqrt(epsilon1 * epsilon2);
  }
 
  void SC::initialize() {
    // find all of the SC atom Types:
    SCtypes.clear();
    SCtids.clear();
    SCdata.clear();
    MixingMap.clear();
    nSC_ = 0;
 
    SCtids.resize(forceField_->getNAtomType(), -1);
 
    AtomTypeSet::iterator at;
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isSC()) nSC_++;
    }
    SCdata.resize(nSC_);
    MixingMap.resize(nSC_);
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isSC()) addType((*at));
    }
    initialized_ = true;
  }
 
  void SC::addType(AtomType* atomType) {
    SuttonChenAdapter sca = SuttonChenAdapter(atomType);
    SCAtomData scAtomData;
 
    scAtomData.c       = sca.getC();
    scAtomData.m       = sca.getM();
    scAtomData.n       = sca.getN();
    scAtomData.alpha   = sca.getAlpha();
    scAtomData.epsilon = sca.getEpsilon();
    scAtomData.rCut    = 2.0 * scAtomData.alpha;
 
    // add it to the map:
    int atid  = atomType->getIdent();
    int sctid = SCtypes.size();
 
    pair<set<int>::iterator, bool> ret;
    ret = SCtypes.insert(atid);
    if (ret.second == false) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SC already had a previous entry with ident %d\n", atid);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal  = 0;
      simError();
    }
 
    SCtids[atid]  = sctid;
    SCdata[sctid] = scAtomData;
    MixingMap[sctid].resize(nSC_);
 
    // Now, iterate over all known types and add to the mixing map:
 
    std::set<int>::iterator it;
    for (it = SCtypes.begin(); it != SCtypes.end(); ++it) {
      int sctid2       = SCtids[(*it)];
      AtomType* atype2 = forceField_->getAtomType((*it));
 
      SCInteractionData mixer;
 
      mixer.alpha   = getAlpha(atomType, atype2);
      mixer.rCut    = 2.0 * mixer.alpha;
      mixer.epsilon = getEpsilon(atomType, atype2);
      mixer.m       = getM(atomType, atype2);
      mixer.n       = getN(atomType, atype2);
 
      RealType dr = mixer.rCut / (np_ - 1);
      vector<RealType> rvals;
      vector<RealType> vvals;
      vector<RealType> phivals;
 
      rvals.push_back(0.0);
      vvals.push_back(0.0);
      phivals.push_back(0.0);
 
      for (int k = 1; k < np_; k++) {
        RealType r = dr * k;
        rvals.push_back(r);
        vvals.push_back(mixer.epsilon * pow(mixer.alpha / r, mixer.n));
        phivals.push_back(pow(mixer.alpha / r, mixer.m));
      }
 
      mixer.vCut = mixer.epsilon * pow(mixer.alpha / mixer.rCut, mixer.n);
 
      CubicSpline* V = new CubicSpline();
      V->addPoints(rvals, vvals);
 
      CubicSpline* phi = new CubicSpline();
      phi->addPoints(rvals, phivals);
 
      mixer.V   = V;
      mixer.phi = phi;
 
      mixer.explicitlySet = false;
 
      MixingMap[sctid2].resize(nSC_);
 
      MixingMap[sctid][sctid2] = mixer;
      if (sctid2 != sctid) { MixingMap[sctid2][sctid] = mixer; }
    }
    return;
  }
 
  void SC::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
                                  RealType epsilon, RealType m, RealType n,
                                  RealType alpha) {
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);
 
    SCInteractionData mixer;
 
    mixer.epsilon = epsilon;
    mixer.m       = m;
    mixer.n       = n;
    mixer.alpha   = alpha;
    mixer.rCut    = 2.0 * mixer.alpha;
 
    RealType dr = mixer.rCut / (np_ - 1);
    vector<RealType> rvals;
    vector<RealType> vvals;
    vector<RealType> phivals;
 
    rvals.push_back(0.0);
    vvals.push_back(0.0);
    phivals.push_back(0.0);
 
    for (int k = 1; k < np_; k++) {
      RealType r = dr * k;
      rvals.push_back(r);
      vvals.push_back(mixer.epsilon * pow(mixer.alpha / r, mixer.n));
      phivals.push_back(pow(mixer.alpha / r, mixer.m));
    }
 
    mixer.vCut = mixer.epsilon * pow(mixer.alpha / mixer.rCut, mixer.n);
 
    CubicSpline* V = new CubicSpline();
    V->addPoints(rvals, vvals);
 
    CubicSpline* phi = new CubicSpline();
    phi->addPoints(rvals, phivals);
 
    mixer.V   = V;
    mixer.phi = phi;
 
    mixer.explicitlySet = true;
 
    int sctid1 = SCtids[atype1->getIdent()];
    int sctid2 = SCtids[atype2->getIdent()];
 
    MixingMap[sctid1][sctid2] = mixer;
    if (sctid2 != sctid1) { MixingMap[sctid2][sctid1] = mixer; }
    return;
  }
 
  void SC::calcDensity(InteractionData& idat) {
    if (!initialized_) initialize();
    int sctid1 = SCtids[idat.atid1];
    int sctid2 = SCtids[idat.atid2];
 
    SCInteractionData& mixer = MixingMap[sctid1][sctid2];
 
    RealType rcij = mixer.rCut;
 
    if (idat.rij < rcij) {
      RealType rho = mixer.phi->getValueAt(idat.rij);
      idat.rho1 += rho;
      idat.rho2 += rho;
    }
 
    return;
  }
 
  void SC::calcFunctional(SelfData& sdat) {
    if (!initialized_) initialize();
 
    SCAtomData& data1 = SCdata[SCtids[sdat.atid]];
 
    RealType u     = -data1.c * data1.epsilon * sqrt(sdat.rho);
    sdat.frho      = u;
    sdat.dfrhodrho = 0.5 * sdat.frho / sdat.rho;
 
    sdat.selfPot[METALLIC_EMBEDDING_FAMILY] += u;
 
    if (sdat.isSelected) sdat.selePot[METALLIC_EMBEDDING_FAMILY] += u;
 
    if (sdat.doParticlePot) { sdat.particlePot += u; }
 
    return;
  }
 
  void SC::calcForce(InteractionData& idat) {
    if (!initialized_) initialize();
 
    int& sctid1 = SCtids[idat.atid1];
    int& sctid2 = SCtids[idat.atid2];
 
    SCAtomData& data1 = SCdata[sctid1];
    SCAtomData& data2 = SCdata[sctid2];
 
    SCInteractionData& mixer = MixingMap[sctid1][sctid2];
 
    RealType rcij = mixer.rCut;
 
    if (idat.rij < rcij) {
      RealType vcij = mixer.vCut;
      RealType rhtmp, drhodr, vptmp, dvpdr;
 
      mixer.phi->getValueAndDerivativeAt(idat.rij, rhtmp, drhodr);
      mixer.V->getValueAndDerivativeAt(idat.rij, vptmp, dvpdr);
 
      RealType pot_temp = vptmp - vcij;
      idat.vpair += pot_temp;
 
      RealType dudr = drhodr * (idat.dfrho1 + 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.c * data2.epsilon * sqrt(idat.rho2 - rhtmp) + idat.frho2;
 
        idat.particlePot2 -=
            data1.c * data1.epsilon * sqrt(idat.rho1 - rhtmp) + idat.frho1;
      }
 
      idat.pot[METALLIC_PAIR_FAMILY] += pot_temp;
 
      if (idat.isSelected) idat.selePot[METALLIC_PAIR_FAMILY] += pot_temp;
    }
 
    return;
  }
 
  RealType SC::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();
 
    int atid1   = atypes.first->getIdent();
    int atid2   = atypes.second->getIdent();
    int& sctid1 = SCtids[atid1];
    int& sctid2 = SCtids[atid2];
 
    if (sctid1 == -1 || sctid2 == -1) {
      return 0.0;
    } else {
      return MixingMap[sctid1][sctid2].rCut;
    }
  }
}  // namespace OpenMD