csg_dump.cc

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/*
 * Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
 
// Standard includes
#include <cstdlib>
 
// Local VOTCA includes
#include "votca/csg/csgapplication.h"
 
using namespace std;
using namespace votca::csg;
 
class CsgDumpApp : public CsgApplication {
  string ProgramName() override { return "csg_dump"; }
  void HelpText(ostream &out) override {
    out << "Print atoms that are read from topology file to help"
           " debugging atom naming.";
  }
  void Initialize() override {
    CsgApplication::Initialize();
    AddProgramOptions("Specific options")(
        "excl", "  display exclusion list instead of molecule list");
  }
 
  bool EvaluateTopology(Topology *top, Topology *top_ref) override;
 
  bool DoMapping() override { return true; }
  bool DoMappingDefault(void) override { return false; }
};
 
int main(int argc, char **argv) {
  CsgDumpApp app;
 
  return app.Exec(argc, argv);
}
 
bool CsgDumpApp::EvaluateTopology(Topology *top, Topology *) {
  if (!OptionsMap().count("excl")) {
    cout << "Boundary Condition: ";
    if (top->getBoxType() == BoundaryCondition::typeAuto) {
      cout << "auto";
    } else if (top->getBoxType() == BoundaryCondition::typeTriclinic) {
      cout << "triclinic";
    } else if (top->getBoxType() == BoundaryCondition::typeOrthorhombic) {
      cout << "orthorhombic";
    } else if (top->getBoxType() == BoundaryCondition::typeOpen) {
      cout << "open";
    }
    cout << endl;
    if (top->getBoxType() != BoundaryCondition::typeOpen) {
      cout << " Box matix:";
      Eigen::Matrix3d box = top->getBox();
      for (votca::Index i = 0; i < 3; i++) {
        for (votca::Index j = 0; j < 3; j++) {
          cout << " " << box(i, j);
        }
        cout << endl << "           ";
      }
    }
 
    cout << "\nList of residues:\n";
    for (votca::Index i = 0; i < top->ResidueCount(); i++) {
      cout << i << " name: " << top->getResidue(i).getName()
           << " id: " << top->getResidue(i).getId() << endl;
    }
 
    cout << "\nList of molecules:\n";
    for (const auto &mol : top->Molecules()) {
      cout << "molecule: " << mol.getId() + 1 << " " << mol.getName()
           << " beads: " << mol.BeadCount() << endl;
      for (votca::Index i = 0; i < mol.BeadCount(); ++i) {
        votca::Index resnr = mol.getBead(i)->getResnr();
        cout << mol.getBeadId(i) << " Name " << mol.getBeadName(i) << " Type "
             << mol.getBead(i)->getType() << " Mass "
             << mol.getBead(i)->getMass() << " Resnr " << resnr << " Resname "
             << top->getResidue(resnr).getName() << " Charge "
             << mol.getBead(i)->getQ() << endl;
      }
    }
  } else {
    cout << "\nList of exclusions:\n" << top->getExclusions();
  }
 
  return true;
}