OnsagerCorrFunc.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 "applications/dynamicProps/OnsagerCorrFunc.hpp"
 
#include <string>
 
#include "applications/dynamicProps/TimeCorrFunc.hpp"
#include "brains/DataStorage.hpp"
#include "brains/ForceManager.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "primitives/StuntDouble.hpp"
#include "utils/Constants.hpp"
#include "utils/Revision.hpp"
#include "utils/StringUtils.hpp"
 
namespace OpenMD {
  OnsagerCorrFunc::OnsagerCorrFunc(SimInfo* info, const std::string& filename,
                                   const std::string& sele1,
                                   const std::string& sele2) :
      SystemCCF<Vector3d>(info, filename, sele1, sele2) {
    setCorrFuncType("OnsagerCorrFunc");
    setOutputName(getPrefix(dumpFilename_) + ".onsager");
    setLabelString("L_ii\tL_ij\tL_jj");
 
    R1_.resize(nTimeBins_);
    R2_.resize(nTimeBins_);
  }
 
  void OnsagerCorrFunc::computeProperty1(int frame) {
    int i;
    StuntDouble* sd;
 
    for (sd = seleMan1_.beginSelected(i); sd != NULL;
         sd = seleMan1_.nextSelected(i)) {
      R1_[frame] += sd->getPos();
    }
  }
 
  void OnsagerCorrFunc::computeProperty2(int frame) {
    int j;
    StuntDouble* sd;
 
    for (sd = seleMan2_.beginSelected(j); sd != NULL;
         sd = seleMan2_.nextSelected(j)) {
      R2_[frame] += sd->getPos();
    }
  }
 
  Vector3d OnsagerCorrFunc::calcCorrVal(int frame1, int frame2) {
    Vector3d v1 = R1_[frame2] - R1_[frame1];
    Vector3d v2 = R2_[frame2] - R2_[frame1];
 
    Vector3d result {dot(v1, v1), dot(v1, v2), dot(v2, v2)};
 
    return result;
  }
}  // namespace OpenMD