source: src/menu.cpp@ b28524

/** \file menu.cpp
 * The class in this file is responsible for displaying the menu and enabling choices.
 *
 * This class is currently being refactored. Functions were copied from builder.cpp and are
 * to be imported into the menu class.
 *
 */

#include "menu.hpp"
#include "analysis_correlation.hpp"
#include "atom.hpp"
#include "bond.hpp"
#include "bondgraph.hpp"
#include "boundary.hpp"
#include "config.hpp"
#include "element.hpp"
#include "ellipsoid.hpp"
#include "helpers.hpp"
#include "leastsquaremin.hpp"
#include "linkedcell.hpp"
#include "log.hpp"
#include "memoryusageobserverunittest.hpp"
#include "molecule.hpp"
#include "periodentafel.hpp"

/* copied methods for refactoring */
/*TODO: Move these methods inside menu class
 * and restructure menu class*/

/********************************************* Subsubmenu routine ************************************/

/** Submenu for adding atoms to the molecule.
 * \param *periode periodentafel
 * \param *molecule molecules with atoms
 */
void menu::AddAtoms(periodentafel *periode, molecule *mol)
{
  atom *first, *second, *third, *fourth;
  Vector **atoms;
  Vector x,y,z,n;  // coordinates for absolute point in cell volume
  double a,b,c;
  char choice;  // menu choice char
  bool valid;

  Log() << Verbose(0) << "===========ADD ATOM============================" << endl;
  Log() << Verbose(0) << " a - state absolute coordinates of atom" << endl;
  Log() << Verbose(0) << " b - state relative coordinates of atom wrt to reference point" << endl;
  Log() << Verbose(0) << " c - state relative coordinates of atom wrt to already placed atom" << endl;
  Log() << Verbose(0) << " d - state two atoms, two angles and a distance" << endl;
  Log() << Verbose(0) << " e - least square distance position to a set of atoms" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "Note: Specifiy angles in degrees not multiples of Pi!" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
      eLog() << Verbose(2) << "Not a valid choice." << endl;
      break;
      case 'a': // absolute coordinates of atom
        Log() << Verbose(0) << "Enter absolute coordinates." << endl;
        first = new atom;
        first->x.AskPosition(mol->cell_size, false);
        first->type = periode->AskElement();  // give type
        mol->AddAtom(first);  // add to molecule
        break;

      case 'b': // relative coordinates of atom wrt to reference point
        first = new atom;
        valid = true;
        do {
          if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
          Log() << Verbose(0) << "Enter reference coordinates." << endl;
          x.AskPosition(mol->cell_size, true);
          Log() << Verbose(0) << "Enter relative coordinates." << endl;
          first->x.AskPosition(mol->cell_size, false);
          first->x.AddVector((const Vector *)&x);
          Log() << Verbose(0) << "\n";
        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
        first->type = periode->AskElement();  // give type
        mol->AddAtom(first);  // add to molecule
        break;

      case 'c': // relative coordinates of atom wrt to already placed atom
        first = new atom;
        valid = true;
        do {
          if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
          second = mol->AskAtom("Enter atom number: ");
          Log() << Verbose(0) << "Enter relative coordinates." << endl;
          first->x.AskPosition(mol->cell_size, false);
          for (int i=NDIM;i--;) {
            first->x.x[i] += second->x.x[i];
          }
        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
        first->type = periode->AskElement();  // give type
        mol->AddAtom(first);  // add to molecule
        break;

    case 'd': // two atoms, two angles and a distance
        first = new atom;
        valid = true;
        do {
          if (!valid) {
            eLog() << Verbose(2) << "Resulting coordinates out of cell - " << first->x << endl;
          }
          Log() << Verbose(0) << "First, we need two atoms, the first atom is the central, while the second is the outer one." << endl;
          second = mol->AskAtom("Enter central atom: ");
          third = mol->AskAtom("Enter second atom (specifying the axis for first angle): ");
          fourth = mol->AskAtom("Enter third atom (specifying a plane for second angle): ");
          a = ask_value("Enter distance between central (first) and new atom: ");
          b = ask_value("Enter angle between new, first and second atom (degrees): ");
          b *= M_PI/180.;
          bound(&b, 0., 2.*M_PI);
          c = ask_value("Enter second angle between new and normal vector of plane defined by first, second and third atom (degrees): ");
          c *= M_PI/180.;
          bound(&c, -M_PI, M_PI);
          Log() << Verbose(0) << "radius: " << a << "\t phi: " << b*180./M_PI << "\t theta: " << c*180./M_PI << endl;
/*
          second->Output(1,1,(ofstream *)&cout);
          third->Output(1,2,(ofstream *)&cout);
          fourth->Output(1,3,(ofstream *)&cout);
          n.MakeNormalvector((const vector *)&second->x, (const vector *)&third->x, (const vector *)&fourth->x);
          x.Copyvector(&second->x);
          x.SubtractVector(&third->x);
          x.Copyvector(&fourth->x);
          x.SubtractVector(&third->x);

          if (!z.SolveSystem(&x,&y,&n, b, c, a)) {
            Log() << Verbose(0) << "Failure solving self-dependent linear system!" << endl;
            continue;
          }
          Log() << Verbose(0) << "resulting relative coordinates: ";
          z.Output();
          Log() << Verbose(0) << endl;
          */
          // calc axis vector
          x.CopyVector(&second->x);
          x.SubtractVector(&third->x);
          x.Normalize();
          Log() << Verbose(0) << "x: ",
          x.Output();
          Log() << Verbose(0) << endl;
          z.MakeNormalVector(&second->x,&third->x,&fourth->x);
          Log() << Verbose(0) << "z: ",
          z.Output();
          Log() << Verbose(0) << endl;
          y.MakeNormalVector(&x,&z);
          Log() << Verbose(0) << "y: ",
          y.Output();
          Log() << Verbose(0) << endl;

          // rotate vector around first angle
          first->x.CopyVector(&x);
          first->x.RotateVector(&z,b - M_PI);
          Log() << Verbose(0) << "Rotated vector: ",
          first->x.Output();
          Log() << Verbose(0) << endl;
          // remove the projection onto the rotation plane of the second angle
          n.CopyVector(&y);
          n.Scale(first->x.ScalarProduct(&y));
          Log() << Verbose(0) << "N1: ",
          n.Output();
          Log() << Verbose(0) << endl;
          first->x.SubtractVector(&n);
          Log() << Verbose(0) << "Subtracted vector: ",
          first->x.Output();
          Log() << Verbose(0) << endl;
          n.CopyVector(&z);
          n.Scale(first->x.ScalarProduct(&z));
          Log() << Verbose(0) << "N2: ",
          n.Output();
          Log() << Verbose(0) << endl;
          first->x.SubtractVector(&n);
          Log() << Verbose(0) << "2nd subtracted vector: ",
          first->x.Output();
          Log() << Verbose(0) << endl;

          // rotate another vector around second angle
          n.CopyVector(&y);
          n.RotateVector(&x,c - M_PI);
          Log() << Verbose(0) << "2nd Rotated vector: ",
          n.Output();
          Log() << Verbose(0) << endl;

          // add the two linear independent vectors
          first->x.AddVector(&n);
          first->x.Normalize();
          first->x.Scale(a);
          first->x.AddVector(&second->x);

          Log() << Verbose(0) << "resulting coordinates: ";
          first->x.Output();
          Log() << Verbose(0) << endl;
        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
        first->type = periode->AskElement();  // give type
        mol->AddAtom(first);  // add to molecule
        break;

      case 'e': // least square distance position to a set of atoms
        first = new atom;
        atoms = new (Vector*[128]);
        valid = true;
        for(int i=128;i--;)
          atoms[i] = NULL;
        int i=0, j=0;
        Log() << Verbose(0) << "Now we need at least three molecules.\n";
        do {
          Log() << Verbose(0) << "Enter " << i+1 << "th atom: ";
          cin >> j;
          if (j != -1) {
            second = mol->FindAtom(j);
            atoms[i++] = &(second->x);
          }
        } while ((j != -1) && (i<128));
        if (i >= 2) {
          first->x.LSQdistance((const Vector **)atoms, i);

          first->x.Output();
          first->type = periode->AskElement();  // give type
          mol->AddAtom(first);  // add to molecule
        } else {
          delete first;
          Log() << Verbose(0) << "Please enter at least two vectors!\n";
        }
        break;
  };
};

/** Submenu for centering the atoms in the molecule.
 * \param *mol molecule with all the atoms
 */
void menu::CenterAtoms(molecule *mol)
{
  Vector x, y, helper;
  char choice;  // menu choice char

  Log() << Verbose(0) << "===========CENTER ATOMS=========================" << endl;
  Log() << Verbose(0) << " a - on origin" << endl;
  Log() << Verbose(0) << " b - on center of gravity" << endl;
  Log() << Verbose(0) << " c - within box with additional boundary" << endl;
  Log() << Verbose(0) << " d - within given simulation box" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
      Log() << Verbose(0) << "Not a valid choice." << endl;
      break;
    case 'a':
      Log() << Verbose(0) << "Centering atoms in config file on origin." << endl;
      mol->CenterOrigin();
      break;
    case 'b':
      Log() << Verbose(0) << "Centering atoms in config file on center of gravity." << endl;
      mol->CenterPeriodic();
      break;
    case 'c':
      Log() << Verbose(0) << "Centering atoms in config file within given additional boundary." << endl;
      for (int i=0;i<NDIM;i++) {
        Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
        cin >> y.x[i];
      }
      mol->CenterEdge(&x);  // make every coordinate positive
      mol->Center.AddVector(&y); // translate by boundary
      helper.CopyVector(&y);
      helper.Scale(2.);
      helper.AddVector(&x);
      mol->SetBoxDimension(&helper);  // update Box of atoms by boundary
      break;
    case 'd':
      Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
      for (int i=0;i<NDIM;i++) {
        Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
        cin >> x.x[i];
      }
      // update Box of atoms by boundary
      mol->SetBoxDimension(&x);
      // center
      mol->CenterInBox();
      break;
  }
};

/** Submenu for aligning the atoms in the molecule.
 * \param *periode periodentafel
 * \param *mol molecule with all the atoms
 */
void menu::AlignAtoms(periodentafel *periode, molecule *mol)
{
  atom *first, *second, *third;
  Vector x,n;
  char choice;  // menu choice char

  Log() << Verbose(0) << "===========ALIGN ATOMS=========================" << endl;
  Log() << Verbose(0) << " a - state three atoms defining align plane" << endl;
  Log() << Verbose(0) << " b - state alignment vector" << endl;
  Log() << Verbose(0) << " c - state two atoms in alignment direction" << endl;
  Log() << Verbose(0) << " d - align automatically by least square fit" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
    case 'a': // three atoms defining mirror plane
      first = mol->AskAtom("Enter first atom: ");
      second = mol->AskAtom("Enter second atom: ");
      third = mol->AskAtom("Enter third atom: ");

      n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
      break;
    case 'b': // normal vector of mirror plane
      Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
      n.AskPosition(mol->cell_size,0);
      n.Normalize();
      break;
    case 'c': // three atoms defining mirror plane
      first = mol->AskAtom("Enter first atom: ");
      second = mol->AskAtom("Enter second atom: ");

      n.CopyVector((const Vector *)&first->x);
      n.SubtractVector((const Vector *)&second->x);
      n.Normalize();
      break;
    case 'd':
      char shorthand[4];
      Vector a;
      struct lsq_params param;
      do {
        fprintf(stdout, "Enter the element of atoms to be chosen: ");
        fscanf(stdin, "%3s", shorthand);
      } while ((param.type = periode->FindElement(shorthand)) == NULL);
      Log() << Verbose(0) << "Element is " << param.type->name << endl;
      mol->GetAlignvector(&param);
      for (int i=NDIM;i--;) {
        x.x[i] = gsl_vector_get(param.x,i);
        n.x[i] = gsl_vector_get(param.x,i+NDIM);
      }
      gsl_vector_free(param.x);
      Log() << Verbose(0) << "Offset vector: ";
      x.Output();
      Log() << Verbose(0) << endl;
      n.Normalize();
      break;
  };
  Log() << Verbose(0) << "Alignment vector: ";
  n.Output();
  Log() << Verbose(0) << endl;
  mol->Align(&n);
};

/** Submenu for mirroring the atoms in the molecule.
 * \param *mol molecule with all the atoms
 */
void menu::MirrorAtoms(molecule *mol)
{
  atom *first, *second, *third;
  Vector n;
  char choice;  // menu choice char

  Log() << Verbose(0) << "===========MIRROR ATOMS=========================" << endl;
  Log() << Verbose(0) << " a - state three atoms defining mirror plane" << endl;
  Log() << Verbose(0) << " b - state normal vector of mirror plane" << endl;
  Log() << Verbose(0) << " c - state two atoms in normal direction" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
    case 'a': // three atoms defining mirror plane
      first = mol->AskAtom("Enter first atom: ");
      second = mol->AskAtom("Enter second atom: ");
      third = mol->AskAtom("Enter third atom: ");

      n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
      break;
    case 'b': // normal vector of mirror plane
      Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
      n.AskPosition(mol->cell_size,0);
      n.Normalize();
      break;
    case 'c': // three atoms defining mirror plane
      first = mol->AskAtom("Enter first atom: ");
      second = mol->AskAtom("Enter second atom: ");

      n.CopyVector((const Vector *)&first->x);
      n.SubtractVector((const Vector *)&second->x);
      n.Normalize();
      break;
  };
  Log() << Verbose(0) << "Normal vector: ";
  n.Output();
  Log() << Verbose(0) << endl;
  mol->Mirror((const Vector *)&n);
};

/** Submenu for removing the atoms from the molecule.
 * \param *mol molecule with all the atoms
 */
void menu::RemoveAtoms(molecule *mol)
{
  atom *first, *second;
  int axis;
  double tmp1, tmp2;
  char choice;  // menu choice char

  Log() << Verbose(0) << "===========REMOVE ATOMS=========================" << endl;
  Log() << Verbose(0) << " a - state atom for removal by number" << endl;
  Log() << Verbose(0) << " b - keep only in radius around atom" << endl;
  Log() << Verbose(0) << " c - remove this with one axis greater value" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
    case 'a':
      if (mol->RemoveAtom(mol->AskAtom("Enter number of atom within molecule: ")))
        Log() << Verbose(1) << "Atom removed." << endl;
      else
        Log() << Verbose(1) << "Atom not found." << endl;
      break;
    case 'b':
      second = mol->AskAtom("Enter number of atom as reference point: ");
      Log() << Verbose(0) << "Enter radius: ";
      cin >> tmp1;
      first = mol->start;
      second = first->next;
      while(second != mol->end) {
        first = second;
        second = first->next;
        if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
          mol->RemoveAtom(first);
      }
      break;
    case 'c':
      Log() << Verbose(0) << "Which axis is it: ";
      cin >> axis;
      Log() << Verbose(0) << "Lower boundary: ";
      cin >> tmp1;
      Log() << Verbose(0) << "Upper boundary: ";
      cin >> tmp2;
      first = mol->start;
      second = first->next;
      while(second != mol->end) {
        first = second;
        second = first->next;
        if ((first->x.x[axis] < tmp1) || (first->x.x[axis] > tmp2)) {// out of boundary ...
          //Log() << Verbose(0) << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
          mol->RemoveAtom(first);
        }
      }
      break;
  };
  //mol->Output();
  choice = 'r';
};

/** Submenu for measuring out the atoms in the molecule.
 * \param *periode periodentafel
 * \param *mol molecule with all the atoms
 */
void menu::MeasureAtoms(periodentafel *periode, molecule *mol, config *configuration)
{
  atom *first, *second, *third;
  Vector x,y;
  double min[256], tmp1, tmp2, tmp3;
  int Z;
  char choice;  // menu choice char

  Log() << Verbose(0) << "===========MEASURE ATOMS=========================" << endl;
  Log() << Verbose(0) << " a - calculate bond length between one atom and all others" << endl;
  Log() << Verbose(0) << " b - calculate bond length between two atoms" << endl;
  Log() << Verbose(0) << " c - calculate bond angle" << endl;
  Log() << Verbose(0) << " d - calculate principal axis of the system" << endl;
  Log() << Verbose(0) << " e - calculate volume of the convex envelope" << endl;
  Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
  Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch(choice) {
    default:
      Log() << Verbose(1) << "Not a valid choice." << endl;
      break;
    case 'a':
      first = mol->AskAtom("Enter first atom: ");
      for (int i=MAX_ELEMENTS;i--;)
        min[i] = 0.;

      second = mol->start;
      while ((second->next != mol->end)) {
        second = second->next; // advance
        Z = second->type->Z;
        tmp1 = 0.;
        if (first != second) {
          x.CopyVector((const Vector *)&first->x);
          x.SubtractVector((const Vector *)&second->x);
          tmp1 = x.Norm();
        }
        if ((tmp1 != 0.) && ((min[Z] == 0.) || (tmp1 < min[Z]))) min[Z] = tmp1;
        //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << second->nr << ": " << tmp1 << " a.u." << endl;
      }
      for (int i=MAX_ELEMENTS;i--;)
        if (min[i] != 0.) Log() << Verbose(0) << "Minimum Bond length between " << first->type->name << " Atom " << first->nr << " and next Ion of type " << (periode->FindElement(i))->name << ": " << min[i] << " a.u." << endl;
      break;

    case 'b':
      first = mol->AskAtom("Enter first atom: ");
      second = mol->AskAtom("Enter second atom: ");
      for (int i=NDIM;i--;)
        min[i] = 0.;
      x.CopyVector((const Vector *)&first->x);
      x.SubtractVector((const Vector *)&second->x);
      tmp1 = x.Norm();
      Log() << Verbose(1) << "Distance vector is ";
      x.Output();
      Log() << Verbose(0) << "." << endl << "Norm of distance is " << tmp1 << "." << endl;
      break;

    case 'c':
      Log() << Verbose(0) << "Evaluating bond angle between three - first, central, last - atoms." << endl;
      first = mol->AskAtom("Enter first atom: ");
      second = mol->AskAtom("Enter central atom: ");
      third  = mol->AskAtom("Enter last atom: ");
      tmp1 = tmp2 = tmp3 = 0.;
      x.CopyVector((const Vector *)&first->x);
      x.SubtractVector((const Vector *)&second->x);
      y.CopyVector((const Vector *)&third->x);
      y.SubtractVector((const Vector *)&second->x);
      Log() << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
      Log() << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;
      break;
    case 'd':
      Log() << Verbose(0) << "Evaluating prinicipal axis." << endl;
      Log() << Verbose(0) << "Shall we rotate? [0/1]: ";
      cin >> Z;
      if ((Z >=0) && (Z <=1))
        mol->PrincipalAxisSystem((bool)Z);
      else
        mol->PrincipalAxisSystem(false);
      break;
    case 'e':
      {
        Log() << Verbose(0) << "Evaluating volume of the convex envelope.";
        class Tesselation *TesselStruct = NULL;
        const LinkedCell *LCList = NULL;
        LCList = new LinkedCell(mol, 10.);
        FindConvexBorder(mol, TesselStruct, LCList, NULL);
        double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
        Log() << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;\
        delete(LCList);
        delete(TesselStruct);
      }
      break;
    case 'f':
      mol->OutputTemperatureFromTrajectories((ofstream *)&cout, mol->MDSteps-1, mol->MDSteps);
      break;
    case 'g':
      {
        char filename[255];
        Log() << Verbose(0) << "Please enter filename: " << endl;
        cin >> filename;
        Log() << Verbose(1) << "Storing temperatures in " << filename << "." << endl;
        ofstream *output = new ofstream(filename, ios::trunc);
        if (!mol->OutputTemperatureFromTrajectories(output, 0, mol->MDSteps))
          Log() << Verbose(2) << "File could not be written." << endl;
        else
          Log() << Verbose(2) << "File stored." << endl;
        output->close();
        delete(output);
      }
      break;
  }
};

/** Submenu for measuring out the atoms in the molecule.
 * \param *mol molecule with all the atoms
 * \param *configuration configuration structure for the to be written config files of all fragments
 */
void menu::FragmentAtoms(molecule *mol, config *configuration)
{
  int Order1;
  clock_t start, end;

  Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
  Log() << Verbose(0) << "What's the desired bond order: ";
  cin >> Order1;
  if (mol->first->next != mol->last) {  // there are bonds
    start = clock();
    mol->FragmentMolecule(Order1, configuration);
    end = clock();
    Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
  } else
    Log() << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
};

/********************************************** Submenu routine **************************************/

/** Submenu for manipulating atoms.
 * \param *periode periodentafel
 * \param *molecules list of molecules whose atoms are to be manipulated
 */
void menu::ManipulateAtoms(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
{
  atom *first, *second;
  molecule *mol = NULL;
  Vector x,y,z,n; // coordinates for absolute point in cell volume
  double *factor; // unit factor if desired
  double bond, minBond;
  char choice;  // menu choice char
  bool valid;

  Log() << Verbose(0) << "=========MANIPULATE ATOMS======================" << endl;
  Log() << Verbose(0) << "a - add an atom" << endl;
  Log() << Verbose(0) << "r - remove an atom" << endl;
  Log() << Verbose(0) << "b - scale a bond between atoms" << endl;
  Log() << Verbose(0) << "u - change an atoms element" << endl;
  Log() << Verbose(0) << "l - measure lengths, angles, ... for an atom" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  if (molecules->NumberOfActiveMolecules() > 1)
    eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
      Log() << Verbose(0) << "Not a valid choice." << endl;
      break;

    case 'a': // add atom
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        AddAtoms(periode, mol);
      }
      break;

    case 'b': // scale a bond
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        Log() << Verbose(0) << "Scaling bond length between two atoms." << endl;
        first = mol->AskAtom("Enter first (fixed) atom: ");
        second = mol->AskAtom("Enter second (shifting) atom: ");
        minBond = 0.;
        for (int i=NDIM;i--;)
          minBond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
        minBond = sqrt(minBond);
        Log() << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl;
        Log() << Verbose(0) << "Enter new bond length [a.u.]: ";
        cin >> bond;
        for (int i=NDIM;i--;) {
          second->x.x[i] -= (second->x.x[i]-first->x.x[i])/minBond*(minBond-bond);
        }
        //Log() << Verbose(0) << "New coordinates of Atom " << second->nr << " are: ";
        //second->Output(second->type->No, 1);
      }
      break;

    case 'c': // unit scaling of the metric
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
       Log() << Verbose(0) << "Angstroem -> Bohrradius: 1.8897261\t\tBohrradius -> Angstroem: 0.52917721" << endl;
       Log() << Verbose(0) << "Enter three factors: ";
       factor = new double[NDIM];
       cin >> factor[0];
       cin >> factor[1];
       cin >> factor[2];
       valid = true;
       mol->Scale((const double ** const)&factor);
       delete[](factor);
      }
     break;

    case 'l': // measure distances or angles
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        MeasureAtoms(periode, mol, configuration);
      }
      break;

    case 'r': // remove atom
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        RemoveAtoms(mol);
      }
      break;

    case 'u': // change an atom's element
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        int Z;
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        first = NULL;
        do {
          Log() << Verbose(0) << "Change the element of which atom: ";
          cin >> Z;
        } while ((first = mol->FindAtom(Z)) == NULL);
        Log() << Verbose(0) << "New element by atomic number Z: ";
        cin >> Z;
        first->type = periode->FindElement(Z);
        Log() << Verbose(0) << "Atom " << first->nr << "'s element is " << first->type->name << "." << endl;
      }
      break;
  }
};

/** Submenu for manipulating molecules.
 * \param *periode periodentafel
 * \param *molecules list of molecule to manipulate
 */
void menu::ManipulateMolecules(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
{
  atom *first = NULL;
  Vector x,y,z,n; // coordinates for absolute point in cell volume
  int j, axis, count, faktor;
  char choice;  // menu choice char
  molecule *mol = NULL;
  element **Elements;
  Vector **vectors;
  MoleculeLeafClass *Subgraphs = NULL;

  Log() << Verbose(0) << "=========MANIPULATE GLOBALLY===================" << endl;
  Log() << Verbose(0) << "c - scale by unit transformation" << endl;
  Log() << Verbose(0) << "d - duplicate molecule/periodic cell" << endl;
  Log() << Verbose(0) << "f - fragment molecule many-body bond order style" << endl;
  Log() << Verbose(0) << "g - center atoms in box" << endl;
  Log() << Verbose(0) << "i - realign molecule" << endl;
  Log() << Verbose(0) << "m - mirror all molecules" << endl;
  Log() << Verbose(0) << "o - create connection matrix" << endl;
  Log() << Verbose(0) << "t - translate molecule by vector" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  if (molecules->NumberOfActiveMolecules() > 1)
    eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
      Log() << Verbose(0) << "Not a valid choice." << endl;
      break;

    case 'd': // duplicate the periodic cell along a given axis, given times
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        Log() << Verbose(0) << "State the axis [(+-)123]: ";
        cin >> axis;
        Log() << Verbose(0) << "State the factor: ";
        cin >> faktor;

        mol->CountAtoms(); // recount atoms
        if (mol->AtomCount != 0) {  // if there is more than none
          count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
          Elements = new element *[count];
          vectors = new Vector *[count];
          j = 0;
          first = mol->start;
          while (first->next != mol->end) { // make a list of all atoms with coordinates and element
            first = first->next;
            Elements[j] = first->type;
            vectors[j] = &first->x;
            j++;
          }
          if (count != j)
            eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
          x.Zero();
          y.Zero();
          y.x[abs(axis)-1] = mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
          for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
            x.AddVector(&y); // per factor one cell width further
            for (int k=count;k--;) { // go through every atom of the original cell
              first = new atom(); // create a new body
              first->x.CopyVector(vectors[k]);  // use coordinate of original atom
              first->x.AddVector(&x);     // translate the coordinates
              first->type = Elements[k];  // insert original element
              mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
            }
          }
          if (mol->first->next != mol->last) // if connect matrix is present already, redo it
            mol->CreateAdjacencyList(mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
          // free memory
          delete[](Elements);
          delete[](vectors);
          // correct cell size
          if (axis < 0) { // if sign was negative, we have to translate everything
            x.Zero();
            x.AddVector(&y);
            x.Scale(-(faktor-1));
            mol->Translate(&x);
          }
          mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
        }
      }
      break;

    case 'f':
      FragmentAtoms(mol, configuration);
      break;

    case 'g': // center the atoms
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        CenterAtoms(mol);
      }
      break;

    case 'i': // align all atoms
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        AlignAtoms(periode, mol);
      }
      break;

    case 'm': // mirror atoms along a given axis
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        MirrorAtoms(mol);
      }
      break;

    case 'o': // create the connection matrix
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
          mol = *ListRunner;
          double bonddistance;
          clock_t start,end;
          Log() << Verbose(0) << "What's the maximum bond distance: ";
          cin >> bonddistance;
          start = clock();
          mol->CreateAdjacencyList(bonddistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
          end = clock();
          Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
        }
      break;

    case 't': // translate all atoms
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if ((*ListRunner)->ActiveFlag) {
        mol = *ListRunner;
        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        Log() << Verbose(0) << "Enter translation vector." << endl;
        x.AskPosition(mol->cell_size,0);
        mol->Center.AddVector((const Vector *)&x);
     }
     break;
  }
  // Free all
  if (Subgraphs != NULL) {  // free disconnected subgraph list of DFS analysis was performed
    while (Subgraphs->next != NULL) {
      Subgraphs = Subgraphs->next;
      delete(Subgraphs->previous);
    }
    delete(Subgraphs);
  }
};


/** Submenu for creating new molecules.
 * \param *periode periodentafel
 * \param *molecules list of molecules to add to
 */
void menu::EditMolecules(periodentafel *periode, MoleculeListClass *molecules)
{
  char choice;  // menu choice char
  Vector center;
  int nr, count;
  molecule *mol = NULL;

  Log() << Verbose(0) << "==========EDIT MOLECULES=====================" << endl;
  Log() << Verbose(0) << "c - create new molecule" << endl;
  Log() << Verbose(0) << "l - load molecule from xyz file" << endl;
  Log() << Verbose(0) << "n - change molecule's name" << endl;
  Log() << Verbose(0) << "N - give molecules filename" << endl;
  Log() << Verbose(0) << "p - parse atoms in xyz file into molecule" << endl;
  Log() << Verbose(0) << "r - remove a molecule" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
      Log() << Verbose(0) << "Not a valid choice." << endl;
      break;
    case 'c':
      mol = new molecule(periode);
      molecules->insert(mol);
      break;

    case 'l': // load from XYZ file
      {
        char filename[MAXSTRINGSIZE];
        Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
        mol = new molecule(periode);
        do {
          Log() << Verbose(0) << "Enter file name: ";
          cin >> filename;
        } while (!mol->AddXYZFile(filename));
        mol->SetNameFromFilename(filename);
        // center at set box dimensions
        mol->CenterEdge(&center);
        mol->cell_size[0] = center.x[0];
        mol->cell_size[1] = 0;
        mol->cell_size[2] = center.x[1];
        mol->cell_size[3] = 0;
        mol->cell_size[4] = 0;
        mol->cell_size[5] = center.x[2];
        molecules->insert(mol);
      }
      break;

    case 'n':
      {
        char filename[MAXSTRINGSIZE];
        do {
          Log() << Verbose(0) << "Enter index of molecule: ";
          cin >> nr;
          mol = molecules->ReturnIndex(nr);
        } while (mol == NULL);
        Log() << Verbose(0) << "Enter name: ";
        cin >> filename;
        strcpy(mol->name, filename);
      }
      break;

    case 'N':
      {
        char filename[MAXSTRINGSIZE];
        do {
          Log() << Verbose(0) << "Enter index of molecule: ";
          cin >> nr;
          mol = molecules->ReturnIndex(nr);
        } while (mol == NULL);
        Log() << Verbose(0) << "Enter name: ";
        cin >> filename;
        mol->SetNameFromFilename(filename);
      }
      break;

    case 'p': // parse XYZ file
      {
        char filename[MAXSTRINGSIZE];
        mol = NULL;
        do {
          Log() << Verbose(0) << "Enter index of molecule: ";
          cin >> nr;
          mol = molecules->ReturnIndex(nr);
        } while (mol == NULL);
        Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
        do {
          Log() << Verbose(0) << "Enter file name: ";
          cin >> filename;
        } while (!mol->AddXYZFile(filename));
        mol->SetNameFromFilename(filename);
      }
      break;

    case 'r':
      Log() << Verbose(0) << "Enter index of molecule: ";
      cin >> nr;
      count = 1;
      for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
        if (nr == (*ListRunner)->IndexNr) {
          mol = *ListRunner;
          molecules->ListOfMolecules.erase(ListRunner);
          delete(mol);
          break;
        }
      break;
  }
};


/** Submenu for merging molecules.
 * \param *periode periodentafel
 * \param *molecules list of molecules to add to
 */
void menu::MergeMolecules(periodentafel *periode, MoleculeListClass *molecules)
{
  char choice;  // menu choice char

  Log() << Verbose(0) << "===========MERGE MOLECULES=====================" << endl;
  Log() << Verbose(0) << "a - simple add of one molecule to another" << endl;
  Log() << Verbose(0) << "e - embedding merge of two molecules" << endl;
  Log() << Verbose(0) << "m - multi-merge of all molecules" << endl;
  Log() << Verbose(0) << "s - scatter merge of two molecules" << endl;
  Log() << Verbose(0) << "t - simple merge of two molecules" << endl;
  Log() << Verbose(0) << "all else - go back" << endl;
  Log() << Verbose(0) << "===============================================" << endl;
  Log() << Verbose(0) << "INPUT: ";
  cin >> choice;

  switch (choice) {
    default:
      Log() << Verbose(0) << "Not a valid choice." << endl;
      break;

    case 'a':
      {
        int src, dest;
        molecule *srcmol = NULL, *destmol = NULL;
        {
          do {
            Log() << Verbose(0) << "Enter index of destination molecule: ";
            cin >> dest;
            destmol = molecules->ReturnIndex(dest);
          } while ((destmol == NULL) && (dest != -1));
          do {
            Log() << Verbose(0) << "Enter index of source molecule to add from: ";
            cin >> src;
            srcmol = molecules->ReturnIndex(src);
          } while ((srcmol == NULL) && (src != -1));
          if ((src != -1) && (dest != -1))
            molecules->SimpleAdd(srcmol, destmol);
        }
      }
      break;

    case 'e':
      {
        int src, dest;
        molecule *srcmol = NULL, *destmol = NULL;
        do {
          Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ";
          cin >> src;
          srcmol = molecules->ReturnIndex(src);
        } while ((srcmol == NULL) && (src != -1));
        do {
          Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ";
          cin >> dest;
          destmol = molecules->ReturnIndex(dest);
        } while ((destmol == NULL) && (dest != -1));
        if ((src != -1) && (dest != -1))
          molecules->EmbedMerge(destmol, srcmol);
      }
      break;

    case 'm':
      {
        int nr;
        molecule *mol = NULL;
        do {
          Log() << Verbose(0) << "Enter index of molecule to merge into: ";
          cin >> nr;
          mol = molecules->ReturnIndex(nr);
        } while ((mol == NULL) && (nr != -1));
        if (nr != -1) {
          int N = molecules->ListOfMolecules.size()-1;
          int *src = new int(N);
          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
            if ((*ListRunner)->IndexNr != nr)
              src[N++] = (*ListRunner)->IndexNr;
          molecules->SimpleMultiMerge(mol, src, N);
          delete[](src);
        }
      }
      break;

    case 's':
      Log() << Verbose(0) << "Not implemented yet." << endl;
      break;

    case 't':
      {
        int src, dest;
        molecule *srcmol = NULL, *destmol = NULL;
        {
          do {
            Log() << Verbose(0) << "Enter index of destination molecule: ";
            cin >> dest;
            destmol = molecules->ReturnIndex(dest);
          } while ((destmol == NULL) && (dest != -1));
          do {
            Log() << Verbose(0) << "Enter index of source molecule to merge into: ";
            cin >> src;
            srcmol = molecules->ReturnIndex(src);
          } while ((srcmol == NULL) && (src != -1));
          if ((src != -1) && (dest != -1))
            molecules->SimpleMerge(srcmol, destmol);
        }
      }
      break;
  }
};


/********************************************** Test routine **************************************/

/** Is called always as option 'T' in the menu.
 * \param *molecules list of molecules
 */
void menu::testroutine(MoleculeListClass *molecules)
{
  // the current test routine checks the functionality of the KeySet&Graph concept:
  // We want to have a multiindex (the KeySet) describing a unique subgraph
  int i, comp, counter=0;

  // create a clone
  molecule *mol = NULL;
  if (molecules->ListOfMolecules.size() != 0) // clone
    mol = (molecules->ListOfMolecules.front())->CopyMolecule();
  else {
    eLog() << Verbose(0) << "I don't have anything to test on ... ";
    performCriticalExit();
    return;
  }
  atom *Walker = mol->start;

  // generate some KeySets
  Log() << Verbose(0) << "Generating KeySets." << endl;
  KeySet TestSets[mol->AtomCount+1];
  i=1;
  while (Walker->next != mol->end) {
    Walker = Walker->next;
    for (int j=0;j<i;j++) {
      TestSets[j].insert(Walker->nr);
    }
    i++;
  }
  Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl;
  KeySetTestPair test;
  test = TestSets[mol->AtomCount-1].insert(Walker->nr);
  if (test.second) {
    Log() << Verbose(1) << "Insertion worked?!" << endl;
  } else {
    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
  }
  TestSets[mol->AtomCount].insert(mol->end->previous->nr);
  TestSets[mol->AtomCount].insert(mol->end->previous->previous->previous->nr);

  // constructing Graph structure
  Log() << Verbose(0) << "Generating Subgraph class." << endl;
  Graph Subgraphs;

  // insert KeySets into Subgraphs
  Log() << Verbose(0) << "Inserting KeySets into Subgraph class." << endl;
  for (int j=0;j<mol->AtomCount;j++) {
    Subgraphs.insert(GraphPair (TestSets[j],pair<int, double>(counter++, 1.)));
  }
  Log() << Verbose(0) << "Testing insertion of already present item in Subgraph." << endl;
  GraphTestPair test2;
  test2 = Subgraphs.insert(GraphPair (TestSets[mol->AtomCount],pair<int, double>(counter++, 1.)));
  if (test2.second) {
    Log() << Verbose(1) << "Insertion worked?!" << endl;
  } else {
    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*(test2.first)).second.first << "." << endl;
  }

  // show graphs
  Log() << Verbose(0) << "Showing Subgraph's contents, checking that it's sorted." << endl;
  Graph::iterator A = Subgraphs.begin();
  while (A !=  Subgraphs.end()) {
    Log() << Verbose(0) << (*A).second.first << ": ";
    KeySet::iterator key = (*A).first.begin();
    comp = -1;
    while (key != (*A).first.end()) {
      if ((*key) > comp)
        Log() << Verbose(0) << (*key) << " ";
      else
        Log() << Verbose(0) << (*key) << "! ";
      comp = (*key);
      key++;
    }
    Log() << Verbose(0) << endl;
    A++;
  }
  delete(mol);
};

menu::menu()
{
  // TODO Auto-generated constructor stub
}

menu::~menu()
{
  // TODO Auto-generated destructor stub
}

void menu::perform(MoleculeListClass *molecules, config *configuration, periodentafel *periode, char *ConfigFileName)
{
    char choice;
    int j;
    Log() << Verbose(0) << endl << "Now comes the real construction..." << endl;
    do {
    Log() << Verbose(0) << endl << endl;
    Log() << Verbose(0) << "============Molecule list=======================" << endl;
    molecules->Enumerate((ofstream *)&cout);
    Log() << Verbose(0) << "============Menu===============================" << endl;
    Log() << Verbose(0) << "a - set molecule (in)active" << endl;
    Log() << Verbose(0) << "e - edit molecules (load, parse, save)" << endl;
    Log() << Verbose(0) << "g - globally manipulate atoms in molecule" << endl;
    Log() << Verbose(0) << "M - Merge molecules" << endl;
    Log() << Verbose(0) << "m - manipulate atoms" << endl;
    Log() << Verbose(0) << "-----------------------------------------------" << endl;
    Log() << Verbose(0) << "c - edit the current configuration" << endl;
    Log() << Verbose(0) << "-----------------------------------------------" << endl;
    Log() << Verbose(0) << "s - save current setup to config file" << endl;
    Log() << Verbose(0) << "T - call the current test routine" << endl;
    Log() << Verbose(0) << "q - quit" << endl;
    Log() << Verbose(0) << "===============================================" << endl;
    Log() << Verbose(0) << "Input: ";
    cin >> choice;

    switch (choice) {
      case 'a':  // (in)activate molecule
        {
          Log() << Verbose(0) << "Enter index of molecule: ";
          cin >> j;
          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
            if ((*ListRunner)->IndexNr == j)
              (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
        }
        break;

      case 'c': // edit each field of the configuration
       configuration->Edit();
       break;

      case 'e': // create molecule
        EditMolecules(periode, molecules);
        break;

      case 'g': // manipulate molecules
        ManipulateMolecules(periode, molecules, configuration);
        break;

      case 'M':  // merge molecules
        MergeMolecules(periode, molecules);
        break;

      case 'm': // manipulate atoms
        ManipulateAtoms(periode, molecules, configuration);
        break;

      case 'q': // quit
        break;

      case 's': // save to config file
        SaveConfig(ConfigFileName, configuration, periode, molecules);
        break;

      case 'T':
        testroutine(molecules);
        break;

      default:
        break;
    };
  } while (choice != 'q');
};

/** Tries given filename or standard on saving the config file.
 * \param *ConfigFileName name of file
 * \param *configuration pointer to configuration structure with all the values
 * \param *periode pointer to periodentafel structure with all the elements
 * \param *molecules list of molecules structure with all the atoms and coordinates
 */
void menu::SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, MoleculeListClass *molecules)
{
  char filename[MAXSTRINGSIZE];
  ofstream output;
  molecule *mol = new molecule(periode);

  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
  }


  // first save as PDB data
  if (ConfigFileName != NULL)
    strcpy(filename, ConfigFileName);
  else
    strcpy(filename,"main_pcp_linux");
  Log() << Verbose(0) << "Saving as pdb input ";
  if (configuration->SavePDB(filename, molecules))
    Log() << Verbose(0) << "done." << endl;
  else
    Log() << Verbose(0) << "failed." << endl;

  // then save as tremolo data file
  if (ConfigFileName != NULL)
    strcpy(filename, ConfigFileName);
  else
    strcpy(filename,"main_pcp_linux");
  Log() << Verbose(0) << "Saving as tremolo data input ";
  if (configuration->SaveTREMOLO(filename, molecules))
    Log() << Verbose(0) << "done." << endl;
  else
    Log() << Verbose(0) << "failed." << endl;

  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
  int N = molecules->ListOfMolecules.size();
  int *src = new int[N];
  N=0;
  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    src[N++] = (*ListRunner)->IndexNr;
    (*ListRunner)->Translate(&(*ListRunner)->Center);
  }
  molecules->SimpleMultiAdd(mol, src, N);
  delete[](src);

  // ... and translate back
  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    (*ListRunner)->Center.Scale(-1.);
    (*ListRunner)->Translate(&(*ListRunner)->Center);
    (*ListRunner)->Center.Scale(-1.);
  }

  Log() << Verbose(0) << "Storing configuration ... " << endl;
  // get correct valence orbitals
  mol->CalculateOrbitals(*configuration);
  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
  if (ConfigFileName != NULL) { // test the file name
    strcpy(filename, ConfigFileName);
    output.open(filename, ios::trunc);
  } else if (strlen(configuration->configname) != 0) {
    strcpy(filename, configuration->configname);
    output.open(configuration->configname, ios::trunc);
    } else {
      strcpy(filename, DEFAULTCONFIG);
      output.open(DEFAULTCONFIG, ios::trunc);
    }
  output.close();
  output.clear();
  Log() << Verbose(0) << "Saving of config file ";
  if (configuration->Save(filename, periode, mol))
    Log() << Verbose(0) << "successful." << endl;
  else
    Log() << Verbose(0) << "failed." << endl;

  // and save to xyz file
  if (ConfigFileName != NULL) {
    strcpy(filename, ConfigFileName);
    strcat(filename, ".xyz");
    output.open(filename, ios::trunc);
  }
  else {
    strcpy(filename,"main_pcp_linux");
    strcat(filename, ".xyz");
    output.open(filename, ios::trunc);
  }
  Log() << Verbose(0) << "Saving of XYZ file ";
  if (mol->MDSteps <= 1) {
    if (mol->OutputXYZ(&output))
      Log() << Verbose(0) << "successful." << endl;
    else
      Log() << Verbose(0) << "failed." << endl;
  } else {
    if (mol->OutputTrajectoriesXYZ(&output))
      Log() << Verbose(0) << "successful." << endl;
    else
      Log() << Verbose(0) << "failed." << endl;
  }
  output.close();
  output.clear();

  // and save as MPQC configuration
  if (ConfigFileName != NULL)
    strcpy(filename, ConfigFileName);
  else
    strcpy(filename,"main_pcp_linux");
  Log() << Verbose(0) << "Saving as mpqc input ";
  if (configuration->SaveMPQC(filename, mol))
    Log() << Verbose(0) << "done." << endl;
  else
    Log() << Verbose(0) << "failed." << endl;

  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
  }

  delete(mol);
};