AtomicBeadModel.cpp

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 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "hydrodynamics/AtomicBeadModel.hpp"
 
#include "hydrodynamics/CompositeShape.hpp"
#include "hydrodynamics/Sphere.hpp"
 
namespace OpenMD {
 
  std::size_t AtomicBeadModel::assignElements() {
    if (shape_ != NULL) {
      if (shape_->isComposite()) {
        createBeads(dynamic_cast<CompositeShape*>(shape_));
      } else {
        if (shape_->isSpherical()) {
          createSingleBead(dynamic_cast<Sphere*>(shape_));
        } else {
          snprintf(
              painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
              "AtomicBeadModel::assignElements Error: GayBerne and other "
              "non-spherical\n"
              "\tatoms should use the RoughShell or BoundaryElement models\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal  = 1;
          simError();
        }
      }
      return elements_.size();
    }
    return 0;
  }
 
  void AtomicBeadModel::createBeads(Shape* shape) {
    if (shape != NULL) {
      if (shape->isComposite()) {
        std::vector<Shape*> shapes =
            dynamic_cast<CompositeShape*>(shape)->getShapes();
        for (std::vector<Shape*>::iterator i = shapes.begin();
             i != shapes.end(); ++i) {
          if ((*i)->isComposite()) {
            createBeads(dynamic_cast<CompositeShape*>((*i)));
          } else {
            if ((*i)->isSpherical()) {
              createSingleBead(dynamic_cast<Sphere*>((*i)));
            } else {
              snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                       "AtomicBeadModel::createBeads Error: GayBerne and other "
                       "non-spherical\n"
                       "\tatoms should use the RoughShell or BoundaryElement "
                       "models\n");
              painCave.severity = OPENMD_ERROR;
              painCave.isFatal  = 1;
              simError();
            }
          }
        }
      } else {
        if (shape->isSpherical()) {
          createSingleBead(dynamic_cast<Sphere*>(shape_));
        } else {
          snprintf(
              painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
              "AtomicBeadModel::createBeads Error: GayBerne and other "
              "non-spherical\n"
              "\tatoms should use the RoughShell or BoundaryElement models\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal  = 1;
          simError();
        }
      }
    }
  }
 
  bool AtomicBeadModel::createSingleBead(Sphere* sphere) {
    HydrodynamicsElement currBead;
    currBead.name   = sphere->getName();
    currBead.pos    = sphere->getOrigin();
    currBead.radius = sphere->getRadius();
    elements_.push_back(currBead);
    return true;
  }
}  // namespace OpenMD