shapedLattice.cpp

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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 "lattice/shapedLattice.hpp"
 
#include <cstdlib>
 
#include "brains/Register.hpp"
#include "lattice/LatticeFactory.hpp"
#include "math/Vector3.hpp"
 
using namespace std;
namespace OpenMD {
  shapedLattice::shapedLattice(RealType latticeConstant, string latticeType) :
      latticeConstant_(latticeConstant), latticeType_(latticeType) {
    registerLattice();
    simpleLattice_ = LatticeFactory::getInstance().createLattice(latticeType);
    if (simpleLattice_ == NULL) {
      std::cerr << "shapedLattice:: Error creating lattice" << std::endl;
      exit(1);
    }
 
    // Set the lattice constant
    std::vector<RealType> lc;
    lc.push_back(latticeConstant_);
    simpleLattice_->setLatticeConstant(lc);
    sitesComputed_ = false;
  }
 
  void shapedLattice::setGridDimension(Vector3d dimension) {
    dimension_ = dimension;
    // Find     number of unit cells in each direction
    beginNx_       = -(int)ceil(0.5 * dimension_[0] / latticeConstant_);
    beginNy_       = -(int)ceil(0.5 * dimension_[1] / latticeConstant_);
    beginNz_       = -(int)ceil(0.5 * dimension_[2] / latticeConstant_);
    endNx_         = (int)ceil(0.5 * dimension_[0] / latticeConstant_);
    endNy_         = (int)ceil(0.5 * dimension_[1] / latticeConstant_);
    endNz_         = (int)ceil(0.5 * dimension_[2] / latticeConstant_);
    sitesComputed_ = false;
  }
 
  void shapedLattice::setOrigin(Vector3d origin) {
    origin_ = origin;
    simpleLattice_->setOrigin(origin_);
    sitesComputed_ = false;
  }
 
  void shapedLattice::findSites() {
    sites_.clear();
    orientations_.clear();
 
    std::vector<Vector3d> latticePos;
    std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt();
    int numMolPerCell               = simpleLattice_->getNumSitesPerCell();
 
    for (int i = beginNx_; i <= endNx_; i++) {
      for (int j = beginNy_; j <= endNy_; j++) {
        for (int k = beginNz_; k <= endNz_; k++) {
          // get the position of the cell sites
          simpleLattice_->getLatticePointsPos(latticePos, i, j, k);
          for (int l = 0; l < numMolPerCell; l++) {
            if (isInterior(latticePos[l])) {
              Vector3d myPoint = latticePos[l];
              Vector3d myOrt   = pointsOrt[l];
              sites_.push_back(myPoint);
              orientations_.push_back(myOrt);
            }
          }
        }
      }
    }
    sitesComputed_ = true;
  }
 
  std::vector<Vector3d> shapedLattice::getSites() {
    if (!sitesComputed_) { findSites(); }
    return sites_;
  }
 
  std::vector<Vector3d> shapedLattice::getOrientations() {
    if (!sitesComputed_) { findSites(); }
    return orientations_;
  }
}  // namespace OpenMD