GofRAngle2.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "applications/staticProps/GofRAngle2.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 {
 
  GofRAngle2::GofRAngle2(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) {
    setAnalysisType("Radial Distribution Function");
    setOutputName(getPrefix(filename) + ".grto");
 
    deltaR_        = len_ / (double)nBins_;
    deltaCosAngle_ = 2.0 / nAngleBins_;
 
    std::stringstream params;
    params << " nBins = " << nBins_ << ", maxLen = " << len_
           << ", deltaR = " << deltaR_ << ", nAngleBins = " << nAngleBins_
           << ", deltaCosAngle = " << deltaCosAngle_;
    const std::string paramString = params.str();
    setParameterString(paramString);
 
    histogram_.resize(nBins_);
    avgGofr_.resize(nBins_);
    for (unsigned int i = 0; i < nBins_; ++i) {
      histogram_[i].resize(nAngleBins_);
      avgGofr_[i].resize(nAngleBins_);
      for (unsigned int j = 0; j < nAngleBins_; ++j) {
        histogram_[i][j].resize(nAngleBins_);
        avgGofr_[i][j].resize(nAngleBins_);
      }
    }
  }
 
  GofRAngle2::GofRAngle2(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), seleMan3_(info),
      evaluator3_(info), selectionScript3_(sele3) {
    setOutputName(getPrefix(filename) + ".grto");
 
    deltaR_        = len_ / (double)nBins_;
    deltaCosAngle_ = 2.0 / nAngleBins_;
 
    std::stringstream params;
    params << " nBins = " << nBins_ << ", maxLen = " << len_
           << ", deltaR = " << deltaR_ << ", nAngleBins = " << nAngleBins_
           << ", deltaCosAngle = " << deltaCosAngle_;
    const std::string paramString = params.str();
    setParameterString(paramString);
 
    histogram_.resize(nBins_);
    avgGofr_.resize(nBins_);
    for (unsigned int i = 0; i < nBins_; ++i) {
      histogram_[i].resize(nAngleBins_);
      avgGofr_[i].resize(nAngleBins_);
      for (unsigned int j = 0; j < nAngleBins_; ++j) {
        histogram_[i][j].resize(nAngleBins_);
        avgGofr_[i][j].resize(nAngleBins_);
      }
    }
 
    evaluator3_.loadScriptString(sele3);
    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }
  }
 
  void GofRAngle2::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 GofRAngle2::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 GofRAngle2::preProcess() {
    for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
      for (unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
        std::fill(avgGofr_[i][j].begin(), avgGofr_[i][j].end(), 0.0);
      }
    }
  }
 
  void GofRAngle2::initializeHistogram() {
    for (unsigned int i = 0; i < histogram_.size(); ++i) {
      for (unsigned int j = 0; j < histogram_.size(); ++j) {
        std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
      }
    }
  }
 
  void GofRAngle2::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_ * (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) {
        for (unsigned int k = 0; k < histogram_[i][j].size(); ++k) {
          avgGofr_[i][j][k] += RealType(histogram_[i][j][k]) / nIdeal;
        }
      }
    }
  }
 
  void GofRAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    if (sd1 == sd2) { return; }
 
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12  = pos1 - pos2;
    if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(r12);
 
    RealType distance = r12.length();
    int whichRBin     = int(distance / deltaR_);
 
    if (distance <= len_) {
      if (!sd1->isDirectional()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "GofAngle2: attempted to use a non-directional object: %s\n",
                 sd1->getType().c_str());
        painCave.isFatal = 1;
        simError();
      }
 
      if (!sd2->isDirectional()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "GofAngle2: attempted to use a non-directional object: %s\n",
                 sd2->getType().c_str());
        painCave.isFatal = 1;
        simError();
      }
 
      Vector3d dipole1, dipole2;
 
      if (sd1->isAtom()) {
        AtomType* atype1     = static_cast<Atom*>(sd1)->getAtomType();
        MultipoleAdapter ma1 = MultipoleAdapter(atype1);
        if (ma1.isDipole())
          dipole1 = sd1->getDipole();
        else
          dipole1 = sd1->getA().transpose() * V3Z;
 
      } else {
        dipole1 = sd1->getA().transpose() * V3Z;
      }
 
      if (sd2->isAtom()) {
        AtomType* atype2     = static_cast<Atom*>(sd2)->getAtomType();
        MultipoleAdapter ma2 = MultipoleAdapter(atype2);
        if (ma2.isDipole())
          dipole2 = sd2->getDipole();
        else
          dipole2 = sd2->getA().transpose() * V3Z;
      } else {
        dipole2 = sd2->getA().transpose() * V3Z;
      }
 
      r12.normalize();
      dipole1.normalize();
      dipole2.normalize();
 
      RealType cosAngle1 = dot(r12, dipole1);
      RealType cosAngle2 = dot(dipole1, dipole2);
 
      RealType halfBin = (nAngleBins_ - 1) * 0.5;
      int angleBin1    = int(halfBin * (cosAngle1 + 1.0));
      int angleBin2    = int(halfBin * (cosAngle2 + 1.0));
 
      ++histogram_[whichRBin][angleBin1][angleBin2];
    }
  }
 
  void GofRAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2,
                                    StuntDouble* sd3) {
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    if (sd1 == sd2) { return; }
 
    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_) {
      r12.normalize();
      r13.normalize();
 
      if (!sd2->isDirectional()) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "GofAngle2: attempted to use a non-directional object: %s\n",
                 sd2->getType().c_str());
        painCave.isFatal = 1;
        simError();
      }
 
      Vector3d dipole2;
 
      if (sd2->isAtom()) {
        AtomType* atype2     = static_cast<Atom*>(sd2)->getAtomType();
        MultipoleAdapter ma2 = MultipoleAdapter(atype2);
 
        if (ma2.isDipole())
          dipole2 = sd2->getDipole();
        else
          dipole2 = sd2->getA().transpose() * V3Z;
 
      } else {
        // Rigid Body:
        dipole2 = sd2->getA().transpose() * V3Z;
      }
 
      dipole2.normalize();
 
      RealType cosAngle1 = dot(r12, r13);
      RealType cosAngle2 = dot(r13, dipole2);
 
      RealType halfBin = (nAngleBins_ - 1) * 0.5;
      int angleBin1    = int(halfBin * (cosAngle1 + 1.0));
      int angleBin2    = int(halfBin * (cosAngle2 + 1.0));
 
      ++histogram_[whichRBin][angleBin1][angleBin2];
    }
  }
 
  void GofRAngle2::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 cosAngle1 = -1.0 + (j + 0.5)*deltaCosAngle_;
          for (unsigned int k = 0; k < avgGofr_[i][j].size(); ++k) {
            // RealType cosAngle2 = -1.0 + (k + 0.5)*deltaCosAngle_;
 
            ofs << avgGofr_[i][j][k] / nProcessed_ << "\t";
          }
          ofs << "\n";
        }
        ofs << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "GofRAngle2: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    ofs.close();
  }
 
}  // namespace OpenMD