NanoLength.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/staticProps/NanoLength.hpp"
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
 
using namespace OpenMD;
 
bool pairComparator(const evIndex& l, const evIndex& r) {
  return l.first < r.first;
}
 
NanoLength::NanoLength(SimInfo* info, const std::string& filename,
                       const std::string& sele) :
    StaticAnalyser(info, filename, 1),
    selectionScript_(sele), seleMan_(info), evaluator_(info) {
  setOutputName(getPrefix(filename) + ".length");
 
  osq.open(getOutputFileName().c_str());
 
  evaluator_.loadScriptString(sele);
  if (!evaluator_.isDynamic()) {
    seleMan_.setSelectionSet(evaluator_.evaluate());
  }
  frameCounter_ = 0;
}
 
void NanoLength::process() {
  StuntDouble* sd;
  Vector3d vec;
  int i;
 
  DumpReader reader(info_, dumpFilename_);
  int nFrames   = reader.getNFrames();
  frameCounter_ = 0;
 
  theAtoms_.reserve(info_->getNGlobalAtoms());
 
  for (int istep = 0; istep < nFrames; istep += step_) {
    reader.readFrame(istep);
    frameCounter_++;
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    RealType time    = currentSnapshot_->getTime();
 
    // Clear pos vector between each frame.
    theAtoms_.clear();
 
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
 
    // outer loop is over the selected StuntDoubles:
 
    for (sd = seleMan_.beginSelected(i); sd != NULL;
         sd = seleMan_.nextSelected(i)) {
      theAtoms_.push_back(sd);
    }
 
    RealType rodLength = getLength(theAtoms_);
 
    osq.precision(7);
    if (osq.is_open()) { osq << time << "\t" << rodLength << std::endl; }
  }
  osq.close();
}
 
RealType NanoLength::getLength(std::vector<StuntDouble*> atoms) {
  Vector3d COM(0.0);
  RealType mass = 0.0;
  RealType mtmp;
  for (std::vector<StuntDouble*>::iterator i = atoms.begin(); i != atoms.end();
       ++i) {
    mtmp = (*i)->getMass();
    mass += mtmp;
    COM += (*i)->getPos() * mtmp;
  }
  COM /= mass;
 
  // Moment of Inertia calculation
  Mat3x3d Itmp(0.0);
  for (std::vector<StuntDouble*>::iterator i = atoms.begin(); i != atoms.end();
       ++i) {
    Mat3x3d IAtom(0.0);
    mtmp           = (*i)->getMass();
    Vector3d delta = (*i)->getPos() - COM;
    IAtom -= outProduct(delta, delta) * mtmp;
    RealType r2 = delta.lengthSquare();
    IAtom(0, 0) += mtmp * r2;
    IAtom(1, 1) += mtmp * r2;
    IAtom(2, 2) += mtmp * r2;
    Itmp += IAtom;
  }
 
  // diagonalize
  Vector3d evals;
  Mat3x3d evects;
  Mat3x3d::diagonalize(Itmp, evals, evects);
 
  // we need to re-order the axes so that the smallest moment of
  // inertia (which corresponds to the long axis of the rod) is
  // along the z-axis. We'll just reverse the order of the three
  // axes.  Python has an argsort function, but we had to invent our
  // own:
 
  std::vector<evIndex> evals_prime;
  for (int i = 0; i < 3; i++)
    evals_prime.push_back(std::make_pair(evals[i], i));
  std::sort(evals_prime.begin(), evals_prime.end(), pairComparator);
 
  RotMat3x3d A;
  Mat3x3d I;
 
  for (int i = 0; i < 3; i++) {
    int index = evals_prime[2 - i].second;
    A.setColumn(i, evects.getColumn(index));
    I(i, i) = evals[index];
  }
 
  // now project the delta from the center of mass onto the long
  // axis of the object
 
  Vector3d longAxis   = A.getColumn(2);
  RealType axisLength = longAxis.length();
  RealType projmin    = 0.0;
  RealType projmax    = 0.0;
 
  for (std::vector<StuntDouble*>::iterator i = atoms.begin(); i != atoms.end();
       ++i) {
    Vector3d delta      = (*i)->getPos() - COM;
    RealType projection = dot(delta, longAxis) / axisLength;
    if (projection > projmax) projmax = projection;
    if (projection < projmin) projmin = projection;
  }
 
  return projmax - projmin;
}