FluxOut.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/sequentialProps/FluxOut.hpp"
 
#include <algorithm>
#include <functional>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  FluxOut::FluxOut(SimInfo* info, const std::string& filename,
                   const std::string& sele1, int axis) :
    SequentialAnalyzer(info, filename, sele1, sele1), axis_(axis) {
    setOutputName(getPrefix(filename) + ".fluxOut");
  }
  
  void FluxOut::doFrame(int frame) {
    StuntDouble* sd;
    int i;
    
    if (evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    
    unsigned int count1 = seleMan1_.getSelectionCount();
    counts_.push_back(count1);
 
    RealType area;
    switch (axis_) {
    case 0:
      area = 2.0 * currentSnapshot_->getYZarea();
      break;
    case 1:
      area = 2.0 * currentSnapshot_->getXZarea();
      break;
    case 2:
    default:
      area = 2.0 * currentSnapshot_->getXYarea();
    }
 
    int n = times_.size();
    if (n > 1) {
      RealType deltaT = times_[n] - times_[n-1];
      RealType deltaC = counts_[n] - counts_[n-1];      
      values_.push_back(deltaC / (area * deltaT));
    }
  }
  
  void FluxOut::writeSequence() {
    std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
    
    if (ofs.is_open()) {
      Revision r;
      
      ofs << "# " << getSequenceType() << "\n";
      ofs << "# OpenMD " << r.getFullRevision() << "\n";
      ofs << "# " << r.getBuildDate() << "\n";
      ofs << "# selection script1: \"" << selectionScript1_;
      ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
      if (!paramString_.empty())
        ofs << "# parameters: " << paramString_ << "\n";
      
      ofs << "#time\tvalue\n";
      
      for (unsigned int i = 1; i < times_.size(); ++i) {
        ofs << times_[i] << "\t" << values_[i] << "\n";
      }
      
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "FluxOut::writeSequence Error: failed to open %s\n",
               outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    
    ofs.close();
  }
}  // namespace OpenMD