GofRAngle.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/staticProps/GofRAngle.hpp"
 
#include <algorithm>
#include <fstream>
#include <sstream>
 
#include "primitives/Atom.hpp"
#include "types/MultipoleAdapter.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  GofRAngle::GofRAngle(SimInfo* info, const std::string& filename,
                       const std::string& sele1, const std::string& sele2,
                       RealType len, int nrbins, int nangleBins) :
      RadialDistrFunc(info, filename, sele1, sele2, nrbins),
      nAngleBins_(nangleBins), len_(len), doSele3_(false), seleMan3_(info),
      evaluator3_(info) {
    deltaR_        = len_ / (double)nBins_;
    deltaCosAngle_ = 2.0 / (double)nAngleBins_;
    histogram_.resize(nBins_);
    avgGofr_.resize(nBins_);
    for (unsigned int i = 0; i < nBins_; ++i) {
      histogram_[i].resize(nAngleBins_);
      avgGofr_[i].resize(nAngleBins_);
    }
 
    setAnalysisType("Radial Distribution Function");
 
    std::stringstream params;
    params << " nBins = " << nBins_ << ", maxLen = " << len_
           << ", deltaR = " << deltaR_ << ", nAngleBins = " << nAngleBins_
           << ", deltaCosAngle = " << deltaCosAngle_;
    const std::string paramString = params.str();
    setParameterString(paramString);
  }
 
  GofRAngle::GofRAngle(SimInfo* info, const std::string& filename,
                       const std::string& sele1, const std::string& sele2,
                       const std::string& sele3, RealType len, int nrbins,
                       int nangleBins) :
      RadialDistrFunc(info, filename, sele1, sele2, nrbins),
      nAngleBins_(nangleBins), len_(len), doSele3_(true),
      selectionScript3_(sele3), seleMan3_(info), evaluator3_(info) {
    deltaR_        = len_ / (double)nBins_;
    deltaCosAngle_ = 2.0 / (double)nAngleBins_;
    histogram_.resize(nBins_);
    avgGofr_.resize(nBins_);
    for (unsigned int i = 0; i < nBins_; ++i) {
      histogram_[i].resize(nAngleBins_);
      avgGofr_[i].resize(nAngleBins_);
    }
 
    evaluator3_.loadScriptString(sele3);
    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }
  }
 
  void GofRAngle::processNonOverlapping(SelectionManager& sman1,
                                        SelectionManager& sman2) {
    StuntDouble* sd1;
    StuntDouble* sd2;
    StuntDouble* sd3;
    int i;
    int j;
    int k;
 
    // This is the same as a non-overlapping pairwise loop structure:
    // for (int i = 0;  i < ni ; ++i ) {
    //   for (int j = 0; j < nj; ++j) {}
    // }
 
    if (doSele3_) {
      if (evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
      }
      if (sman1.getSelectionCount() != seleMan3_.getSelectionCount()) {
        RadialDistrFunc::processNonOverlapping(sman1, sman2);
      }
 
      for (sd1 = sman1.beginSelected(i), sd3 = seleMan3_.beginSelected(k);
           sd1 != NULL && sd3 != NULL;
           sd1 = sman1.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) {
        for (sd2 = sman2.beginSelected(j); sd2 != NULL;
             sd2 = sman2.nextSelected(j)) {
          collectHistogram(sd1, sd2, sd3);
        }
      }
    } else {
      RadialDistrFunc::processNonOverlapping(sman1, sman2);
    }
  }
 
  void GofRAngle::processOverlapping(SelectionManager& sman) {
    StuntDouble* sd1;
    StuntDouble* sd2;
    StuntDouble* sd3;
    int i;
    int j;
    int k;
 
    // This is the same as a pairwise loop structure:
    // for (int i = 0;  i < n-1 ; ++i ) {
    //   for (int j = i + 1; j < n; ++j) {}
    // }
 
    if (doSele3_) {
      if (evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
      }
      if (sman.getSelectionCount() != seleMan3_.getSelectionCount()) {
        RadialDistrFunc::processOverlapping(sman);
      }
      for (sd1 = sman.beginSelected(i), sd3 = seleMan3_.beginSelected(k);
           sd1 != NULL && sd3 != NULL;
           sd1 = sman.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) {
        for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL;
             sd2 = sman.nextSelected(j)) {
          collectHistogram(sd1, sd2, sd3);
        }
      }
    } else {
      RadialDistrFunc::processOverlapping(sman);
    }
  }
 
  void GofRAngle::preProcess() {
    for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
      std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
    }
  }
 
  void GofRAngle::initializeHistogram() {
    npairs_ = 0;
    for (unsigned int i = 0; i < histogram_.size(); ++i) {
      std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
    }
  }
 
  void GofRAngle::processHistogram() {
    int nPairs = getNPairs();
    RealType volume =
        info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity  = nPairs / volume;
    RealType pairConstant = (4.0 * Constants::PI * pairDensity) / 3.0;
 
    for (unsigned int i = 0; i < histogram_.size(); ++i) {
      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice =
          (rUpper * rUpper * rUpper) - (rLower * rLower * rLower);
      RealType nIdeal = volSlice * pairConstant;
 
      for (unsigned int j = 0; j < histogram_[i].size(); ++j) {
        avgGofr_[i][j] += histogram_[i][j] / nIdeal;
      }
    }
  }
 
  void GofRTheta::processHistogram() {
    int nPairs = getNPairs();
    RealType volume =
        info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs / volume;
    RealType pairConstant =
        (4.0 * Constants::PI * pairDensity) / (3.0 * (double)nAngleBins_);
 
    for (unsigned int i = 0; i < histogram_.size(); ++i) {
      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice =
          (rUpper * rUpper * rUpper) - (rLower * rLower * rLower);
      RealType nIdeal = volSlice * pairConstant;
 
      for (unsigned int j = 0; j < histogram_[i].size(); ++j) {
        avgGofr_[i][j] += histogram_[i][j] / nIdeal;
      }
    }
  }
 
  void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
    if (sd1 == sd2) { return; }
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12  = pos2 - pos1;
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(r12);
 
    RealType distance = r12.length();
    int whichRBin     = int(distance / deltaR_);
 
    if (distance <= len_) {
      RealType cosAngle = evaluateAngle(sd1, sd2);
      RealType halfBin  = (nAngleBins_ - 1) * 0.5;
      int whichThetaBin = int(halfBin * (cosAngle + 1.0));
      ++histogram_[whichRBin][whichThetaBin];
 
      ++npairs_;
    }
  }
 
  void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2,
                                   StuntDouble* sd3) {
    if (sd1 == sd2) { return; }
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d p1 = sd1->getPos();
    Vector3d p3 = sd3->getPos();
 
    Vector3d c   = 0.5 * (p1 + p3);
    Vector3d r13 = p3 - p1;
 
    Vector3d r12 = sd2->getPos() - c;
 
    if (usePeriodicBoundaryConditions_) {
      currentSnapshot_->wrapVector(r12);
      currentSnapshot_->wrapVector(r13);
    }
 
    RealType distance = r12.length();
    int whichRBin     = int(distance / deltaR_);
 
    if (distance <= len_) {
      RealType cosAngle = evaluateAngle(sd1, sd2, sd3);
      RealType halfBin  = (nAngleBins_ - 1) * 0.5;
      int whichThetaBin = int(halfBin * (cosAngle + 1.0));
      ++histogram_[whichRBin][whichThetaBin];
 
      ++npairs_;
    }
  }
 
  void GofRAngle::writeRdf() {
    std::ofstream ofs(outputFilename_.c_str());
    if (ofs.is_open()) {
      Revision r;
      ofs << "# " << getAnalysisType() << "\n";
      ofs << "# OpenMD " << r.getFullRevision() << "\n";
      ofs << "# " << r.getBuildDate() << "\n";
      ofs << "# selection script1: \"" << selectionScript1_;
      ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"";
      if (doSele3_) {
        ofs << "\tselection script3: \"" << selectionScript3_ << "\"\n";
      } else {
        ofs << "\n";
      }
 
      if (!paramString_.empty())
        ofs << "# parameters: " << paramString_ << "\n";
 
      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
        // RealType r = deltaR_ * (i + 0.5);
 
        for (unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
          // RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
          ofs << avgGofr_[i][j] / nProcessed_ << "\t";
        }
 
        ofs << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofRAngle: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    ofs.close();
  }
 
  RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12  = pos2 - pos1;
 
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(r12);
 
    r12.normalize();
 
    Vector3d vec;
 
    if (!sd1->isDirectional()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofRTheta: attempted to use a non-directional object: %s\n",
               sd1->getType().c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    if (sd1->isAtom()) {
      AtomType* atype1     = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
 
      if (ma1.isDipole())
        vec = sd1->getDipole();
      else
        vec = sd1->getA().transpose() * V3Z;
    } else {
      vec = sd1->getA().transpose() * V3Z;
    }
 
    vec.normalize();
 
    return dot(r12, vec);
  }
 
  RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
                                    StuntDouble* sd3) {
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d p1 = sd1->getPos();
    Vector3d p3 = sd3->getPos();
 
    Vector3d c   = 0.5 * (p1 + p3);
    Vector3d r13 = p3 - p1;
 
    Vector3d r12 = sd2->getPos() - c;
 
    if (usePeriodicBoundaryConditions_) {
      currentSnapshot_->wrapVector(r12);
      currentSnapshot_->wrapVector(r13);
    }
 
    r12.normalize();
    r13.normalize();
 
    return dot(r12, r13);
  }
 
  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d v1, v2;
 
    if (!sd1->isDirectional()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofROmega: attempted to use a non-directional object: %s\n",
               sd1->getType().c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    if (sd1->isAtom()) {
      AtomType* atype1     = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
      if (ma1.isDipole())
        v1 = sd1->getDipole();
      else
        v1 = sd1->getA().transpose() * V3Z;
    } else {
      v1 = sd1->getA().transpose() * V3Z;
    }
 
    if (!sd2->isDirectional()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofROmega attempted to use a non-directional object: %s\n",
               sd2->getType().c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    if (sd2->isAtom()) {
      AtomType* atype2     = static_cast<Atom*>(sd2)->getAtomType();
      MultipoleAdapter ma2 = MultipoleAdapter(atype2);
 
      if (ma2.isDipole())
        v2 = sd2->getDipole();
      else
        v2 = sd2->getA().transpose() * V3Z;
    } else {
      v2 = sd2->getA().transpose() * V3Z;
    }
 
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
  }
 
  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
                                    StuntDouble* sd3) {
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Vector3d v1;
    Vector3d v2;
 
    v1 = sd3->getPos() - sd1->getPos();
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(v1);
 
    if (!sd2->isDirectional()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofROmega: attempted to use a non-directional object: %s\n",
               sd2->getType().c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    if (sd2->isAtom()) {
      AtomType* atype2     = static_cast<Atom*>(sd2)->getAtomType();
      MultipoleAdapter ma2 = MultipoleAdapter(atype2);
 
      if (ma2.isDipole())
        v2 = sd2->getDipole();
      else
        v2 = sd2->getA().transpose() * V3Z;
    } else {
      v2 = sd2->getA().transpose() * V3Z;
    }
 
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
  }
}  // namespace OpenMD