AtomVisitor.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 "visitors/AtomVisitor.hpp"
 
#include <cstring>
#include <memory>
 
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
#include "types/GayBerneAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
 
namespace OpenMD {
 
  BaseAtomVisitor::BaseAtomVisitor(SimInfo* info) : BaseVisitor() {
    storageLayout_ = info->getAtomStorageLayout();
  }
 
  void BaseAtomVisitor::visit(RigidBody*) {
    // vector<Atom*> myAtoms;
    // vector<Atom*>::iterator atomIter;
 
    // myAtoms = rb->getAtoms();
 
    // for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
    //  (*atomIter)->accept(this);
  }
 
  void BaseAtomVisitor::setVisited(Atom* atom) {
    std::shared_ptr<GenericData> data;
    data = atom->getPropertyByName("VISITED");
 
    // if visited property is not existed, add it as new property
    if (data == nullptr) {
      data = std::make_shared<GenericData>();
      data->setID("VISITED");
      atom->addProperty(data);
    }
  }
 
  bool BaseAtomVisitor::isVisited(Atom* atom) {
    std::shared_ptr<GenericData> data;
    data = atom->getPropertyByName("VISITED");
    return data == nullptr ? false : true;
  }
 
  //------------------------------------------------------------------------//
 
  void DefaultAtomVisitor::visit(Atom* atom) {
    std::shared_ptr<AtomData> atomData;
    std::shared_ptr<AtomInfo> atomInfo;
    AtomType* atype = atom->getAtomType();
 
    if (isVisited(atom)) return;
 
    atomInfo               = std::make_shared<AtomInfo>();
    atomInfo->atomTypeName = atom->getType();
    atomInfo->globalID     = atom->getGlobalIndex();
    atomInfo->pos          = atom->getPos();
    atomInfo->vel          = atom->getVel();
    atomInfo->frc          = atom->getFrc();
    atomInfo->vec          = V3Zero;
    atomInfo->hasVelocity  = true;
    atomInfo->hasForce     = true;
    atomInfo->hasGlobalID  = true;
 
    FixedChargeAdapter fca = FixedChargeAdapter(atype);
    if (fca.isFixedCharge()) {
      atomInfo->hasCharge = true;
      atomInfo->charge    = fca.getCharge();
    }
 
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
    if (fqa.isFluctuatingCharge()) {
      atomInfo->hasCharge = true;
      atomInfo->charge += atom->getFlucQPos();
    }
 
    if ((storageLayout_ & DataStorage::dslElectricField) &&
        (atype->isElectrostatic())) {
      atomInfo->hasElectricField = true;
      atomInfo->eField           = atom->getElectricField();
    }
 
    atomData = std::make_shared<AtomData>();
    atomData->setID("ATOMDATA");
    atomData->addAtomInfo(atomInfo);
 
    atom->addProperty(atomData);
 
    setVisited(atom);
  }
 
  void DefaultAtomVisitor::visit(DirectionalAtom* datom) {
    std::shared_ptr<AtomData> atomData;
    std::shared_ptr<AtomInfo> atomInfo;
    AtomType* atype = datom->getAtomType();
 
    if (isVisited(datom)) return;
 
    atomInfo               = std::make_shared<AtomInfo>();
    atomInfo->atomTypeName = datom->getType();
    atomInfo->globalID     = datom->getGlobalIndex();
    atomInfo->pos          = datom->getPos();
    atomInfo->vel          = datom->getVel();
    atomInfo->frc          = datom->getFrc();
    atomInfo->hasVelocity  = true;
    atomInfo->hasForce     = true;
    atomInfo->hasGlobalID  = true;
 
    FixedChargeAdapter fca = FixedChargeAdapter(atype);
    if (fca.isFixedCharge()) {
      atomInfo->hasCharge = true;
      atomInfo->charge    = fca.getCharge();
    }
 
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
    if (fqa.isFluctuatingCharge()) {
      atomInfo->hasCharge = true;
      atomInfo->charge += datom->getFlucQPos();
    }
 
    if ((storageLayout_ & DataStorage::dslElectricField) &&
        (atype->isElectrostatic())) {
      atomInfo->hasElectricField = true;
      atomInfo->eField           = datom->getElectricField();
    }
 
    GayBerneAdapter gba = GayBerneAdapter(atype);
    MultipoleAdapter ma = MultipoleAdapter(atype);
 
    if (gba.isGayBerne()) {
      atomInfo->hasVector = true;
      atomInfo->vec       = datom->getA().transpose() * V3Z;
    } else if (ma.isDipole()) {
      atomInfo->hasVector = true;
      atomInfo->vec       = datom->getDipole();
    } else if (ma.isQuadrupole()) {
      atomInfo->hasVector = true;
      atomInfo->vec       = datom->getA().transpose() * V3Z;
    }
 
    atomData = std::make_shared<AtomData>();
    atomData->setID("ATOMDATA");
    atomData->addAtomInfo(atomInfo);
 
    datom->addProperty(atomData);
 
    setVisited(datom);
  }
 
  const std::string DefaultAtomVisitor::toString() {
    char buffer[65535];
    std::string result;
 
    snprintf(
        buffer, 65535,
        "--------------------------------------------------------------\n");
    result += buffer;
 
    snprintf(buffer, 65535, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;
 
    snprintf(buffer, 65535,
             "Visitor Description: copy atom infomation into atom data\n");
    result += buffer;
 
    snprintf(
        buffer, 65535,
        "--------------------------------------------------------------\n");
    result += buffer;
 
    return result;
  }
}  // namespace OpenMD