AtomStamp.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 "types/AtomStamp.hpp"
 
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <iostream>
 
namespace OpenMD {
  AtomStamp::AtomStamp(int index) :
      havePos_(false), haveOrt_(false), hasOverride_(false), index_(index) {
    DefineParameter(Type, "type");
  }
 
  bool AtomStamp::setPosition(const std::vector<RealType>& pos) {
    bool ret = false;
    if (pos.size() == 3) {
      position_[0] = pos[0];
      position_[1] = pos[1];
      position_[2] = pos[2];
      havePos_     = true;
    } else {
      std::ostringstream oss;
      oss << "position" << containerToString(pos) << " is invalid" << std::endl;
      throw OpenMDException(oss.str());
    }
    return ret;
  }
 
  bool AtomStamp::setOrientation(const std::vector<RealType>& ort) {
    bool ret = false;
    if (ort.size() == 3) {
      orientation_[0] = ort[0];
      orientation_[1] = ort[1];
      orientation_[2] = ort[2];
      haveOrt_        = true;
    } else {
      std::ostringstream oss;
      oss << "orientation" << containerToString(ort) << " is invalid"
          << std::endl;
      throw OpenMDException(oss.str());
    }
 
    return ret;
  }
 
  void AtomStamp::validate() {
    DataHolder::validate();
    CheckParameter(Type, isNotEmpty());
  }
}  // namespace OpenMD