LegendreCorrFuncZ.cpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * 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/LegendreCorrFuncZ.hpp"
 
#include <sstream>
 
#include "math/LegendrePolynomial.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
  LegendreCorrFuncZ::LegendreCorrFuncZ(SimInfo* info,
                                       const std::string& filename,
                                       const std::string& sele1,
                                       const std::string& sele2, int order,
                                       int nZbins, int axis) :
      ObjectACF<Vector3d>(info, filename, sele1, sele2),
      nZBins_(nZbins), axis_(axis) {
    setCorrFuncType("Legendre Correlation Function of Z");
    setOutputName(getPrefix(dumpFilename_) + ".lcorrZ");
 
    std::stringstream params;
    params << " order = " << order << ", nzbins = " << nZBins_;
    const std::string paramString = params.str();
    setParameterString(paramString);
 
    if (!uniqueSelections_) { seleMan2_ = seleMan1_; }
 
    // Compute complementary axes to the privileged axis
    xaxis_ = (axis_ + 1) % 3;
    yaxis_ = (axis_ + 2) % 3;
 
    switch (axis_) {
    case 0:
      axisLabel_ = "x";
      break;
    case 1:
      axisLabel_ = "y";
      break;
    case 2:
    default:
      axisLabel_ = "z";
      break;
    }
 
    rotMats_.resize(nTimeBins_);
    zbin_.resize(nTimeBins_);
    histogram_.resize(nTimeBins_);
    counts_.resize(nTimeBins_);
    for (unsigned int i = 0; i < nTimeBins_; i++) {
      histogram_[i].resize(nZBins_);
      std::fill(histogram_[i].begin(), histogram_[i].end(), 0.0);
      counts_[i].resize(nZBins_);
      std::fill(counts_[i].begin(), counts_[i].end(), 0);
    }
    LegendrePolynomial polynomial(order);
    legendre_ = polynomial.getLegendrePolynomial(order);
  }
 
  void LegendreCorrFuncZ::computeFrame(int frame) {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    boxZ_        = hmat(axis_, axis_);
    halfBoxZ_    = boxZ_ / 2.0;
 
    ObjectACF<Vector3d>::computeFrame(frame);
  }
 
  int LegendreCorrFuncZ::computeProperty1(int frame, StuntDouble* sd) {
    RotMat3x3d A = sd->getA();
    rotMats_[frame].push_back(A);
 
    Vector3d pos = sd->getPos();
    if (info_->getSimParams()->getUsePeriodicBoundaryConditions())
      currentSnapshot_->wrapVector(pos);
    int zBin = int(nZBins_ * (halfBoxZ_ + pos[axis_]) / boxZ_);
    zbin_[frame].push_back(zBin);
 
    return rotMats_[frame].size() - 1;
  }
 
  Vector3d LegendreCorrFuncZ::calcCorrVal(int frame1, int frame2, int id1,
                                          int id2) {
    Vector3d v1x = rotMats_[frame1][id1].getRow(xaxis_);
    Vector3d v1y = rotMats_[frame1][id1].getRow(yaxis_);
    Vector3d v1z = rotMats_[frame1][id1].getRow(axis_);
 
    Vector3d v2x = rotMats_[frame2][id2].getRow(xaxis_);
    Vector3d v2y = rotMats_[frame2][id2].getRow(yaxis_);
    Vector3d v2z = rotMats_[frame2][id2].getRow(axis_);
 
    RealType uxprod =
        legendre_.evaluate(dot(v1x, v2x) / (v1x.length() * v2x.length()));
    RealType uyprod =
        legendre_.evaluate(dot(v1y, v2y) / (v1y.length() * v2y.length()));
    RealType uzprod =
        legendre_.evaluate(dot(v1z, v2z) / (v1z.length() * v2z.length()));
 
    return Vector3d(uxprod, uyprod, uzprod);
  }
 
  void LegendreCorrFuncZ::correlateFrames(int frame1, int frame2, int timeBin) {
    std::vector<int> s1;
    std::vector<int> s2;
 
    std::vector<int>::iterator i1;
    std::vector<int>::iterator i2;
 
    Vector3d corrVal(0.0);
 
    s1 = sele1ToIndex_[frame1];
 
    if (uniqueSelections_)
      s2 = sele2ToIndex_[frame2];
    else
      s2 = sele1ToIndex_[frame2];
 
    for (i1 = s1.begin(), i2 = s2.begin(); i1 != s1.end() && i2 != s2.end();
         ++i1, ++i2) {
      // If the selections are dynamic, they might not have the
      // same objects in both frames, so we need to roll either of
      // the selections until we have the same object to
      // correlate.
 
      while (i1 != s1.end() && *i1 < *i2) {
        ++i1;
      }
 
      while (i2 != s2.end() && *i2 < *i1) {
        ++i2;
      }
 
      if (i1 == s1.end() || i2 == s2.end()) break;
 
      corrVal  = calcCorrVal(frame1, frame2, i1 - s1.begin(), i2 - s2.begin());
      int zBin = zbin_[frame1][i1 - s1.begin()];
      histogram_[timeBin][zBin] += corrVal;
      counts_[timeBin][zBin]++;
    }
  }
 
  void LegendreCorrFuncZ::postCorrelate() {
    for (unsigned int i = 0; i < nTimeBins_; ++i) {
      for (unsigned int j = 0; j < nZBins_; ++j) {
        if (counts_[i][j] > 0) { histogram_[i][j] /= counts_[i][j]; }
      }
    }
  }
 
  void LegendreCorrFuncZ::validateSelection(SelectionManager&) {
    StuntDouble* sd;
    int i;
    for (sd = seleMan1_.beginSelected(i); sd != NULL;
         sd = seleMan1_.nextSelected(i)) {
      if (!sd->isDirectional()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "LegendreCorrFuncZ::validateSelection Error: "
                 "at least one of the selected objects is not Directional\n");
        painCave.isFatal = 1;
        simError();
      }
    }
  }
 
  void LegendreCorrFuncZ::writeCorrelate() {
    std::ofstream ofs(getOutputFileName().c_str());
 
    if (ofs.is_open()) {
      Revision r;
 
      ofs << "# " << getCorrFuncType() << "\n";
      ofs << "# OpenMD " << r.getFullRevision() << "\n";
      ofs << "# " << r.getBuildDate() << "\n";
      ofs << "# selection script1: \"" << selectionScript1_;
      ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
      ofs << "# privilegedAxis computed as " << axisLabel_ << " axis \n";
      if (!paramString_.empty())
        ofs << "# parameters: " << paramString_ << "\n";
 
      ofs << "#time\tPn(costheta_z)\n";
 
      for (unsigned int i = 0; i < nTimeBins_; ++i) {
        ofs << times_[i] - times_[0];
 
        for (unsigned int j = 0; j < nZBins_; ++j) {
          ofs << "\t" << histogram_[i][j](2);
        }
        ofs << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "LegendreCorrFuncZ::writeCorrelate Error: failed to open %s\n",
               getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();
    }
    ofs.close();
  }
}  // namespace OpenMD