SequentialAnalyzer.cpp

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 *    this software without specific prior written permission.
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 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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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/SequentialAnalyzer.hpp"
 
#include <algorithm>
#include <functional>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Revision.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  SequentialAnalyzer::SequentialAnalyzer(SimInfo* info,
                                         const std::string& filename,
                                         const std::string& sele1,
                                         const std::string& sele2) :
      info_(info),
      currentSnapshot_(NULL), dumpFilename_(filename), seleMan1_(info),
      selectionScript1_(sele1), evaluator1_(info), seleMan2_(info),
      selectionScript2_(sele2), evaluator2_(info), step_(1) {
    paramString_.clear();
 
    evaluator1_.loadScriptString(selectionScript1_);
    evaluator2_.loadScriptString(selectionScript2_);
 
    // if selections are static, we only need to evaluate them once
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
  }
 
  void SequentialAnalyzer::doSequence() {
    preSequence();
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
 
    // storageLayout_ = info_->getStorageLayout();
 
    for (frame_ = 0; frame_ < nFrames; frame_ += step_) {
      reader.readFrame(frame_);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      times_.push_back(currentSnapshot_->getTime());
 
      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
      }
 
      doFrame(frame_);
    }
 
    postSequence();
    writeSequence();
  }
 
  void SequentialAnalyzer::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 = 0; i < times_.size(); ++i) {
        ofs << times_[i] << "\t" << values_[i] << "\n";
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SequentialAnalyzer::writeSequence Error: failed to open %s\n",
               outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
 
    ofs.close();
  }
 
}  // namespace OpenMD