source: src/builder.cpp@ 02da9e

/** \file builder.cpp
 *
 * By stating absolute positions or binding angles and distances atomic positions of a molecule can be constructed.
 * The output is the complete configuration file for PCP for direct use.
 * Features:
 * -# Atomic data is retrieved from a file, if not found requested and stored there for later re-use
 * -# step-by-step construction of the molecule beginning either at a centre of with a certain atom
 *
 */

/*! \mainpage Molecuilder - a molecular set builder
 *
 * This introductory shall briefly make aquainted with the program, helping in installing and a first run.
 *
 * \section about About the Program
 *
 *      Molecuilder is a short program, written in C++, that enables the construction of a coordinate set for the
 *      atoms making up an molecule by the successive statement of binding angles and distances and referencing to
 *      already constructed atoms.
 *
 *      A configuration file may be written that is compatible to the format used by PCP - a parallel Car-Parrinello
 *      molecular dynamics implementation.
 *
 * \section install Installation
 *
 *      Installation should without problems succeed as follows:
 *      -# ./configure (or: mkdir build;mkdir run;cd build; ../configure --bindir=../run)
 *      -# make
 *      -# make install
 *
 *      Further useful commands are
 *      -# make clean uninstall: deletes .o-files and removes executable from the given binary directory\n
 *      -# make doxygen-doc: Creates these html pages out of the documented source
 *
 * \section run Running
 *
 *      The program can be executed by running: ./molecuilder
 *
 *      Note, that it uses a database, called "elements.db", in the executable's directory. If the file is not found,
 *      it is created and any given data on elements of the periodic table will be stored therein and re-used on
 *      later re-execution.
 *
 * \section ref References
 *
 *      For the special configuration file format, see the documentation of pcp.
 *
 */


using namespace std;

#include "boundary.hpp"
#include "ellipsoid.hpp"
#include "helpers.hpp"
#include "molecules.hpp"

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

/** Submenu for adding atoms to the molecule.
 * \param *periode periodentafel
 * \param *molecule molecules with atoms
 */
static void 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;

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

        switch (choice) {
    default:
      cout << Verbose(0) << "Not a valid choice." << endl;
      break;
                        case 'a': // absolute coordinates of atom
        cout << 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) cout << Verbose(0) << "Resulting position out of cell." << endl;
          cout << Verbose(0) << "Enter reference coordinates." << endl;
          x.AskPosition(mol->cell_size, true);
          cout << Verbose(0) << "Enter relative coordinates." << endl;
          first->x.AskPosition(mol->cell_size, false);
          first->x.AddVector((const Vector *)&x);
          cout << 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) cout << Verbose(0) << "Resulting position out of cell." << endl;
          second = mol->AskAtom("Enter atom number: ");
          cout << 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) {
            cout << Verbose(0) << "Resulting coordinates out of cell - ";
            first->x.Output((ofstream *)&cout);
            cout << Verbose(0) << endl;
          }
          cout << 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);
          cout << 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)) {
            cout << Verbose(0) << "Failure solving self-dependent linear system!" << endl;
            continue;
          }
          cout << Verbose(0) << "resulting relative coordinates: ";
          z.Output((ofstream *)&cout);
          cout << Verbose(0) << endl;
          */
          // calc axis vector
          x.CopyVector(&second->x);
          x.SubtractVector(&third->x);
          x.Normalize();
          cout << "x: ",
          x.Output((ofstream *)&cout);
          cout << endl;
          z.MakeNormalVector(&second->x,&third->x,&fourth->x);
          cout << "z: ",
          z.Output((ofstream *)&cout);
          cout << endl;
          y.MakeNormalVector(&x,&z);
          cout << "y: ",
          y.Output((ofstream *)&cout);
          cout << endl;

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

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

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

          cout << Verbose(0) << "resulting coordinates: ";
          first->x.Output((ofstream *)&cout);
          cout << 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;
        cout << Verbose(0) << "Now we need at least three molecules.\n";
        do {
          cout << 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(atoms, i);

          first->x.Output((ofstream *)&cout);
          first->type = periode->AskElement();  // give type
          mol->AddAtom(first);  // add to molecule
        } else {
          delete first;
          cout << 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
 */
static void CenterAtoms(molecule *mol)
{
        Vector x, y, helper;
        char choice;    // menu choice char

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

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

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

        cout << Verbose(0) << "===========ALIGN ATOMS=========================" << endl;
        cout << Verbose(0) << " a - state three atoms defining align plane" << endl;
        cout << Verbose(0) << " b - state alignment vector" << endl;
        cout << Verbose(0) << " c - state two atoms in alignment direction" << endl;
        cout << Verbose(0) << " d - align automatically by least square fit" << endl;
        cout << Verbose(0) << "all else - go back" << endl;
        cout << Verbose(0) << "===============================================" << endl;
        cout << 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
                        cout << 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);
                        cout << 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);
                        cout << Verbose(0) << "Offset vector: ";
                        x.Output((ofstream *)&cout);
                        cout << Verbose(0) << endl;
                        n.Normalize();
                        break;
        };
        cout << Verbose(0) << "Alignment vector: ";
        n.Output((ofstream *)&cout);
        cout << Verbose(0) << endl;
        mol->Align(&n);
};

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

        cout << Verbose(0) << "===========MIRROR ATOMS=========================" << endl;
        cout << Verbose(0) << " a - state three atoms defining mirror plane" << endl;
        cout << Verbose(0) << " b - state normal vector of mirror plane" << endl;
        cout << Verbose(0) << " c - state two atoms in normal direction" << endl;
        cout << Verbose(0) << "all else - go back" << endl;
        cout << Verbose(0) << "===============================================" << endl;
        cout << 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
                        cout << 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;
        };
        cout << Verbose(0) << "Normal vector: ";
        n.Output((ofstream *)&cout);
        cout << Verbose(0) << endl;
        mol->Mirror((const Vector *)&n);
};

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

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

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

/** Submenu for measuring out the atoms in the molecule.
 * \param *periode periodentafel
 * \param *mol molecule with all the atoms
 */
static void 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

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

        switch(choice) {
                default:
                        cout << 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;
                                //cout << 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.) cout << 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();
                        cout << Verbose(1) << "Distance vector is ";
                        x.Output((ofstream *)&cout);
                        cout << "." << endl << "Norm of distance is " << tmp1 << "." << endl;
                        break;

                case 'c':
                        cout << 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);
                        cout << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
                        cout << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;
                        break;
                case 'd':
                        cout << Verbose(0) << "Evaluating prinicipal axis." << endl;
                        cout << Verbose(0) << "Shall we rotate? [0/1]: ";
                        cin >> Z;
                        if ((Z >=0) && (Z <=1))
                                mol->PrincipalAxisSystem((ofstream *)&cout, (bool)Z);
                        else
                                mol->PrincipalAxisSystem((ofstream *)&cout, false);
                        break;
                case 'e':
                        cout << Verbose(0) << "Evaluating volume of the convex envelope.";
                        VolumeOfConvexEnvelope((ofstream *)&cout, NULL, configuration, NULL, mol);
                        break;
                case 'f':
                        mol->OutputTemperatureFromTrajectories((ofstream *)&cout, mol->MDSteps-1, mol->MDSteps, (ofstream *)&cout);
                        break;
                case 'g':
                        {
                                char filename[255];
                                cout << "Please enter filename: " << endl;
                                cin >> filename;
                                cout << Verbose(1) << "Storing temperatures in " << filename << "." << endl;
                                ofstream *output = new ofstream(filename, ios::trunc);
                                if (!mol->OutputTemperatureFromTrajectories((ofstream *)&cout, 0, mol->MDSteps, output))
                                        cout << Verbose(2) << "File could not be written." << endl;
                                else
                                        cout << 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
 */
static void FragmentAtoms(molecule *mol, config *configuration)
{
        int Order1;
        clock_t start, end;

        cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
        cout << Verbose(0) << "What's the desired bond order: ";
        cin >> Order1;
        if (mol->first->next != mol->last) {    // there are bonds
                start = clock();
                mol->FragmentMolecule((ofstream *)&cout, Order1, configuration);
                end = clock();
                cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
        } else
                cout << 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
 */
static void ManipulateAtoms(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
{
  atom *first, *second, *third, *fourth;
  Vector **atoms;
  molecule *mol = NULL;
  Vector x,y,z,n; // coordinates for absolute point in cell volume
  double *factor; // unit factor if desired
  double a,b,c;
  double bond, min_bond;
  char choice;  // menu choice char
  bool valid;

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

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

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

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

    case 'l': // measure distances or angles
      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
        mol = *ListRunner;
        cout << 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++) {
        mol = *ListRunner;
        cout << 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++) {
        int Z;
        mol = *ListRunner;
        cout << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        first = NULL;
        do {
          cout << Verbose(0) << "Change the element of which atom: ";
          cin >> Z;
        } while ((first = mol->FindAtom(Z)) == NULL);
        cout << Verbose(0) << "New element by atomic number Z: ";
        cin >> Z;
        first->type = periode->FindElement(Z);
        cout << 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
 */
static void ManipulateMolecules(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
{
  atom *first, *second, *third, *fourth;
  Vector **atoms;
  Vector x,y,z,n; // coordinates for absolute point in cell volume
  double a,b,c;
  int j, axis, count, faktor;
  char choice;  // menu choice char
  bool valid;
  molecule *mol = NULL;
  element **Elements;
  Vector **vectors;
  MoleculeLeafClass *Subgraphs = NULL;

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

  switch (choice) {
    default:
      cout << 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++) {
        mol = *ListRunner;
        cout << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        cout << Verbose(0) << "State the axis [(+-)123]: ";
        cin >> axis;
        cout << Verbose(0) << "State the factor: ";
        cin >> faktor;

        mol->CountAtoms((ofstream *)&cout); // 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)
            cout << Verbose(0) << "ERROR: 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((ofstream *)&cout, mol->BondDistance, configuration->GetIsAngstroem());
          // 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++) {
        mol = *ListRunner;
        cout << 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++) {
        mol = *ListRunner;
        cout << 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++) {
        mol = *ListRunner;
        cout << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        MirrorAtoms(mol);
      }
      break;

    case 'o': // create the connection matrix
      {
        double bonddistance;
        clock_t start,end;
        cout << Verbose(0) << "What's the maximum bond distance: ";
        cin >> bonddistance;
        start = clock();
        mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem());
        mol->CreateListOfBondsPerAtom((ofstream *)&cout);
        end = clock();
        cout << 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++) {
        mol = *ListRunner;
        cout << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
        cout << Verbose(0) << "Enter translation vector." << endl;
        x.AskPosition(mol->cell_size,0);
        mol->Translate((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
 */
static void EditMolecules(periodentafel *periode, MoleculeListClass *molecules)
{
  char choice;  // menu choice char
  bool valid;
  Vector Center;
  int nr, count;
  molecule *mol = NULL;
  char *molname = NULL;
  int length;
  char filename[MAXSTRINGSIZE];

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

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

    case 'l': // laod from XYZ file
      cout << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
      mol = new molecule(periode);
      do {
        cout << Verbose(0) << "Enter file name: ";
        cin >> filename;
      } while (!mol->AddXYZFile(filename));
      mol->SetNameFromFilename(filename);
      // center at set box dimensions
      mol->CenterEdge((ofstream *)&cout, &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':
      do {
        cout << Verbose(0) << "Enter index of molecule: ";
        cin >> nr;
        mol = molecules->ReturnIndex(nr);
      } while (mol != NULL);
      cout << Verbose(0) << "Enter name: ";
      cin >> filename;
      strcpy(mol->name, filename);
      break;

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

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

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


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

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

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

    case 'e':
      break;

    case 'm':
      break;

    case 's':
      break;

    case 't':
      break;
  }
};


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

/** Is called always as option 'T' in the menu.
 * \param *molecules list of molecules
 */
static void 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 {
    cerr << "I don't have anything to test on ... ";
    return;
  }
  atom *Walker = mol->start;

        // generate some KeySets
        cout << "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++;
        }
        cout << "Testing insertion of already present item in KeySets." << endl;
        KeySetTestPair test;
        test = TestSets[mol->AtomCount-1].insert(Walker->nr);
        if (test.second) {
                cout << Verbose(1) << "Insertion worked?!" << endl;
        } else {
                cout << 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
        cout << "Generating Subgraph class." << endl;
        Graph Subgraphs;

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

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

/** 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
 */
static void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, MoleculeListClass *molecules)
{
        char filename[MAXSTRINGSIZE];
        ofstream output;
        molecule *mol = new molecule(periode);

        // 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;
        molecules->SimpleMultiAdd(mol, src, N);

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

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

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

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

/** Parses the command line options.
 * \param argc argument count
 * \param **argv arguments array
 * \param *molecules list of molecules structure
 * \param *periode elements structure
 * \param configuration config file structure
 * \param *ConfigFileName pointer to config file name in **argv
 * \param *PathToDatabases pointer to db's path in **argv
 * \return exit code (0 - successful, all else - something's wrong)
 */
static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode, config& configuration, char *&ConfigFileName, char *&PathToDatabases)
{
        Vector x,y,z,n; // coordinates for absolute point in cell volume
        double *factor; // unit factor if desired
        ifstream test;
        ofstream output;
        string line;
        atom *first;
        bool SaveFlag = false;
        int ExitFlag = 0;
        int j;
        double volume = 0.;
        enum ConfigStatus config_present = absent;
        clock_t start,end;
        int argptr;
        PathToDatabases = LocalPath;

        // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
        molecule *mol = new molecule(periode);
        molecules->insert(mol);

        if (argc > 1) { // config file specified as option
                // 1. : Parse options that just set variables or print help
                argptr = 1;
                do {
                        if (argv[argptr][0] == '-') {
                                cout << Verbose(0) << "Recognized command line argument: " << argv[argptr][1] << ".\n";
                                argptr++;
                                switch(argv[argptr-1][1]) {
                                        case 'h':
                                        case 'H':
                                        case '?':
                                                cout << "MoleCuilder suite" << endl << "==================" << endl << endl;
                                                cout << "Usage: " << argv[0] << "[config file] [-{acefpsthH?vfrp}] [further arguments]" << endl;
                                                cout << "or simply " << argv[0] << " without arguments for interactive session." << endl;
                                                cout << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl;
                                                cout << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl;
                                                cout << "\t-b x1 x2 x3\tCenter atoms in domain with given edge lengths of (x1,x2,x3)." << endl;
                                                cout << "\t-B <basis>\tSetting basis to store to MPQC config files." << endl;
                                                cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
                                                cout << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
                                                cout << "\t-O\tCenter atoms in origin." << endl;
                                                cout << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
                                                cout << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl;
                                                cout << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
                                                cout << "\t-f/F <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
                                                cout << "\t-h/-H/-?\tGive this help screen." << endl;
                                                cout << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
                                                cout << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl;
                                                cout << "\t-N\tGet non-convex-envelope." << endl;
                                                cout << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl;
                                                cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
                                                cout << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl;
                                                cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
                                                cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
                                                cout << "\t-T <file> Store temperatures from the config file in <file>." << endl;
                                                cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
                                                cout << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl;
                                                cout << "\t-v/-V\t\tGives version information." << endl;
                                                cout << "Note: config files must not begin with '-' !" << endl;
                                                delete(mol);
                                                delete(periode);
                                                return (1);
                                                break;
                                        case 'v':
                                        case 'V':
                                                cout << argv[0] << " " << VERSIONSTRING << endl;
                                                cout << "Build your own molecule position set." << endl;
                                                delete(mol);
                                                delete(periode);
                                                return (1);
                                                break;
                                        case 'e':
                                                if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                                                        cerr << "Not enough or invalid arguments for specifying element db: -e <db file>" << endl;
                                                } else {
                                                        cout << "Using " << argv[argptr] << " as elements database." << endl;
                                                        PathToDatabases = argv[argptr];
                                                        argptr+=1;
                                                }
                                                break;
                                        case 'n':
                                                cout << "I won't parse trajectories." << endl;
                                                configuration.FastParsing = true;
                                                break;
                                        default:         // no match? Step on
                                                argptr++;
                                                break;
                                }
                        } else
                                argptr++;
                } while (argptr < argc);

                // 2. Parse the element database
                if (periode->LoadPeriodentafel(PathToDatabases)) {
                        cout << Verbose(0) << "Element list loaded successfully." << endl;
                        //periode->Output((ofstream *)&cout);
                } else {
                        cout << Verbose(0) << "Element list loading failed." << endl;
                        return 1;
                }
                // 3. Find config file name and parse if possible
                if (argv[1][0] != '-') {
                        cout << Verbose(0) << "Config file given." << endl;
                        test.open(argv[1], ios::in);
                        if (test == NULL) {
                                //return (1);
                                output.open(argv[1], ios::out);
                                if (output == NULL) {
                                        cout << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl;
                                        config_present = absent;
                                } else {
                                        cout << "Empty configuration file." << endl;
                                        ConfigFileName = argv[1];
                                        config_present = empty;
                                        output.close();
                                }
                        } else {
                                test.close();
                                ConfigFileName = argv[1];
                                cout << Verbose(1) << "Specified config file found, parsing ... ";
                                switch (configuration.TestSyntax(ConfigFileName, periode, mol)) {
                                        case 1:
                                                cout << "new syntax." << endl;
                                                configuration.Load(ConfigFileName, periode, mol);
                                                config_present = present;
                                                break;
                                        case 0:
                                                cout << "old syntax." << endl;
                                                configuration.LoadOld(ConfigFileName, periode, mol);
                                                config_present = present;
                                                break;
                                        default:
                                                cout << "Unknown syntax or empty, yet present file." << endl;
                                                config_present = empty;
                         }
                        }
                } else
                        config_present = absent;
                // 4. parse again through options, now for those depending on elements db and config presence
                argptr = 1;
                do {
                        cout << "Current Command line argument: " << argv[argptr] << "." << endl;
                        if (argv[argptr][0] == '-') {
                                argptr++;
                                if ((config_present == present) || (config_present == empty)) {
                                        switch(argv[argptr-1][1]) {
                                                case 'p':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough arguments for parsing: -p <xyz file>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                cout << Verbose(1) << "Parsing xyz file for new atoms." << endl;
                                                                if (!mol->AddXYZFile(argv[argptr]))
                                                                        cout << Verbose(2) << "File not found." << endl;
                                                                else {
                                                                        cout << Verbose(2) << "File found and parsed." << endl;
                                                                        config_present = present;
                                                                }
                                                        }
                                                        break;
                                                case 'a':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1]))) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments for adding atom: -a <element> <x> <y> <z>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                cout << Verbose(1) << "Adding new atom with element " << argv[argptr] << " at (" << argv[argptr+1] << "," << argv[argptr+2] << "," << argv[argptr+3] << "), ";
                                                                first = new atom;
                                                                first->type = periode->FindElement(atoi(argv[argptr]));
                                                                if (first->type != NULL)
                                                                        cout << Verbose(2) << "found element " << first->type->name << endl;
                                                                for (int i=NDIM;i--;)
                                                                        first->x.x[i] = atof(argv[argptr+1+i]);
                                                                if (first->type != NULL) {
                                                                        mol->AddAtom(first);    // add to molecule
                                                                        if ((config_present == empty) && (mol->AtomCount != 0))
                                                                                config_present = present;
                                                                } else
                                                                        cerr << Verbose(1) << "Could not find the specified element." << endl;
                                                                argptr+=4;
                                                        }
                                                        break;
                                                default:         // no match? Don't step on (this is done in next switch's default)
                                                        break;
                                        }
                                }
                                if (config_present == present) {
                                        switch(argv[argptr-1][1]) {
                                                case 'B':
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for setting MPQC basis: -B <basis name>" << endl;
                                                        } else {
                                                                configuration.basis = argv[argptr];
                                                                cout << Verbose(1) << "Setting MPQC basis to " << configuration.basis << "." << endl;
                                                                argptr+=1;
                                                        }
                                                        break;
                                                case 'D':
                                                        ExitFlag = 1;
                                                        {
                                                                cout << Verbose(1) << "Depth-First-Search Analysis." << endl;
                                                                MoleculeLeafClass *Subgraphs = NULL;                    // list of subgraphs from DFS analysis
                                                                int *MinimumRingSize = new int[mol->AtomCount];
                                                                atom ***ListOfLocalAtoms = NULL;
                                                                int FragmentCounter = 0;
                                                                class StackClass<bond *> *BackEdgeStack = NULL;
                                                                class StackClass<bond *> *LocalBackEdgeStack = NULL;
                                                                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem());
                                                                mol->CreateListOfBondsPerAtom((ofstream *)&cout);
                                                                Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
                                                                if (Subgraphs != NULL) {
                                                                        Subgraphs->next->FillBondStructureFromReference((ofstream *)&cout, mol, (FragmentCounter = 0), ListOfLocalAtoms, false);        // we want to keep the created ListOfLocalAtoms
                                                                        while (Subgraphs->next != NULL) {
                                                                                Subgraphs = Subgraphs->next;
                                                                                LocalBackEdgeStack = new StackClass<bond *> (Subgraphs->Leaf->BondCount);
                                                                                Subgraphs->Leaf->PickLocalBackEdges((ofstream *)&cout, ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
                                                                                Subgraphs->Leaf->CyclicStructureAnalysis((ofstream *)&cout, BackEdgeStack, MinimumRingSize);
                                                                                delete(LocalBackEdgeStack);
                                                                                delete(Subgraphs->previous);
                                                                        }
                                                                        delete(Subgraphs);
                                                                        for (int i=0;i<FragmentCounter;i++)
                                                                                Free((void **)&ListOfLocalAtoms[FragmentCounter], "ParseCommandLineOptions: **ListOfLocalAtoms[]");
                                                                        Free((void **)&ListOfLocalAtoms, "ParseCommandLineOptions: ***ListOfLocalAtoms");
                                                                }
                                                                delete(BackEdgeStack);
                                                                delete[](MinimumRingSize);
                                                        }
                                                        //argptr+=1;
                                                        break;
                                                case 'E':
                                                        ExitFlag = 1;
                                                        if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr+1][0] == '-')) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for changing element: -E <atom nr.> <element>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                cout << Verbose(1) << "Changing atom " << argv[argptr] << " to element " << argv[argptr+1] << "." << endl;
                                                                first = mol->FindAtom(atoi(argv[argptr]));
                                                                first->type = periode->FindElement(atoi(argv[argptr+1]));
                                                                argptr+=2;
                                                        }
                                                        break;
                                                case 'A':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                                                                ExitFlag =255;
                                                                cerr << "Missing source file for bonds in molecule: -A <bond sourcefile>" << endl;
                                                        } else {
                                                                cout << "Parsing bonds from " << argv[argptr] << "." << endl;
                                                                ifstream *input = new ifstream(argv[argptr]);
                                                                mol->CreateAdjacencyList2((ofstream *)&cout, input);
                                                                input->close();
                                                                argptr+=1;
                                                        }
                                                        break;
                                                case 'N':
                                                        ExitFlag = 1;
                                                        if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-')){
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for non-convex envelope: -o <radius> <tecplot output file>" << endl;
                                                        } else {
                                                                class Tesselation T;
                                                                int N = 15;
                                                                int number = 100;
                                                                string filename(argv[argptr+1]);
                                                                filename.append(".csv");
                                                                cout << Verbose(0) << "Evaluating non-convex envelope.";
                                                                cout << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl;
                                                                LinkedCell LCList(mol, atof(argv[argptr]));             // \NOTE not twice the radius??
                                                                Find_non_convex_border((ofstream *)&cout, mol, &T, &LCList, argv[argptr+1], atof(argv[argptr]));
                                                                //FindDistributionOfEllipsoids((ofstream *)&cout, &T, &LCList, N, number, filename.c_str());
                                                                argptr+=2;
                                                        }
                                                        break;
                                                case 'T':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for storing tempature: -T <temperature file>" << endl;
                                                        } else {
                                                                cout << Verbose(1) << "Storing temperatures in " << argv[argptr] << "." << endl;
                                                                ofstream *output = new ofstream(argv[argptr], ios::trunc);
                                                                if (!mol->OutputTemperatureFromTrajectories((ofstream *)&cout, 0, mol->MDSteps, output))
                                                                        cout << Verbose(2) << "File could not be written." << endl;
                                                                else
                                                                        cout << Verbose(2) << "File stored." << endl;
                                                                output->close();
                                                                delete(output);
                                                                argptr+=1;
                                                        }
                                                        break;
                                                case 'P':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for parsing and integrating forces: -P <forces file>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                cout << Verbose(1) << "Parsing forces file and Verlet integrating." << endl;
                                                                if (!mol->VerletForceIntegration(argv[argptr], configuration.Deltat, configuration.GetIsAngstroem()))
                                                                        cout << Verbose(2) << "File not found." << endl;
                                                                else
                                                                        cout << Verbose(2) << "File found and parsed." << endl;
                                                                argptr+=1;
                                                        }
                                                        break;
                                                case 't':
                                                        ExitFlag = 1;
                                                        if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for translation: -t <x> <y> <z>" << endl;
                                                        } else {
                                                                ExitFlag = 1;
                                                                SaveFlag = true;
                                                                cout << Verbose(1) << "Translating all ions to new origin." << endl;
                                                                for (int i=NDIM;i--;)
                                                                        x.x[i] = atof(argv[argptr+i]);
                                                                mol->Translate((const Vector *)&x);
                                                                argptr+=3;
                                                        }
                                                        break;
                                                case 's':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) ) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for scaling: -s <factor/[factor_x]> [factor_y] [factor_z]" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                j = -1;
                                                                cout << Verbose(1) << "Scaling all ion positions by factor." << endl;
                                                                factor = new double[NDIM];
                                                                factor[0] = atof(argv[argptr]);
                                                                if ((argptr < argc) && (IsValidNumber(argv[argptr])))
                                                                        argptr++;
                                                                factor[1] = atof(argv[argptr]);
                                                                if ((argptr < argc) && (IsValidNumber(argv[argptr])))
                                                                        argptr++;
                                                                factor[2] = atof(argv[argptr]);
                                                                mol->Scale(&factor);
                                                                for (int i=0;i<NDIM;i++) {
                                                                        j += i+1;
                                                                        x.x[i] = atof(argv[NDIM+i]);
                                                                        mol->cell_size[j]*=factor[i];
                                                                }
                                                                delete[](factor);
                                                                argptr+=1;
                                                        }
                                                        break;
                                                case 'b':
                                                        ExitFlag = 1;
                                                        if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for centering in box: -b <length_x> <length_y> <length_z>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                j = -1;
                                                                cout << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
                                                                j=-1;
                                                                for (int i=0;i<NDIM;i++) {
                                                                        j += i+1;
                                                                        x.x[i] = atof(argv[argptr++]);
                                                                        mol->cell_size[j] += x.x[i]*2.;
                                                                }
                                                                // center
                                                                mol->CenterInBox((ofstream *)&cout, &x);
                                                                // update Box of atoms by boundary
                                                                mol->SetBoxDimension(&x);
                                                        }
                                                        break;
                                                case 'c':
                                                        ExitFlag = 1;
                                                        if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for centering with boundary: -c <boundary_x> <boundary_y> <boundary_z>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                j = -1;
                                                                cout << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl;
                                                                // make every coordinate positive
                                                                mol->CenterEdge((ofstream *)&cout, &x);
                                                                // update Box of atoms by boundary
                                                                mol->SetBoxDimension(&x);
                                                                // translate each coordinate by boundary
                                                                j=-1;
                                                                for (int i=0;i<NDIM;i++) {
                                                                        j += i+1;
                                                                        x.x[i] = atof(argv[argptr++]);
                                                                        mol->cell_size[j] += x.x[i]*2.;
                                                                }
                                                                mol->Translate((const Vector *)&x);
                                                        }
                                                        break;
                                                case 'O':
                                                        ExitFlag = 1;
                                                        SaveFlag = true;
                                                        cout << Verbose(1) << "Centering atoms in origin." << endl;
                                                        mol->CenterOrigin((ofstream *)&cout, &x);
                                                        mol->SetBoxDimension(&x);
                                                        break;
                                                case 'r':
                                                        ExitFlag = 1;
                                                        SaveFlag = true;
                                                        cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
                                                        break;
                                                case 'F':
                                                case 'f':
                                                        ExitFlag = 1;
                                                        if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1]))) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl;
                                                        } else {
                                                                cout << "Fragmenting molecule with bond distance " << argv[argptr] << " angstroem, order of " << argv[argptr+1] << "." << endl;
                                                                cout << Verbose(0) << "Creating connection matrix..." << endl;
                                                                start = clock();
                                                                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem());
                                                                cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
                                                                if (mol->first->next != mol->last) {
                                                                        ExitFlag = mol->FragmentMolecule((ofstream *)&cout, atoi(argv[argptr]), &configuration);
                                                                }
                                                                end = clock();
                                                                cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
                                                                argptr+=2;
                                                        }
                                                        break;
                                                case 'm':
                                                        ExitFlag = 1;
                                                        j = atoi(argv[argptr++]);
                                                        if ((j<0) || (j>1)) {
                                                                cerr << Verbose(1) << "ERROR: Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl;
                                                                j = 0;
                                                        }
                                                        if (j) {
                                                                SaveFlag = true;
                                                                cout << Verbose(0) << "Converting to prinicipal axis system." << endl;
                                                        } else
                                                                cout << Verbose(0) << "Evaluating prinicipal axis." << endl;
                                                        mol->PrincipalAxisSystem((ofstream *)&cout, (bool)j);
                                                        break;
                                                case 'o':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (argv[argptr][0] == '-')){
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for convex envelope: -o <tecplot output file>" << endl;
                                                        } else {
                                                                cout << Verbose(0) << "Evaluating volume of the convex envelope.";
                                                                cout << Verbose(1) << "Storing tecplot data in " << argv[argptr] << "." << endl;
                                                                VolumeOfConvexEnvelope((ofstream *)&cout, argv[argptr], &configuration, NULL, mol);
                                                                argptr+=1;
                                                        }
                                                        break;
                                                case 'U':
                                                        ExitFlag = 1;
                                                        if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) ) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for suspension with specified volume: -U <volume> <density>" << endl;
                                                                volume = -1; // for case 'u': don't print error again
                                                        } else {
                                                                volume = atof(argv[argptr++]);
                                                                cout << Verbose(0) << "Using " << volume << " angstrom^3 as the volume instead of convex envelope one's." << endl;
                                                        }
                                                case 'u':
                                                        ExitFlag = 1;
                                                        if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) ) {
                                                                if (volume != -1)
                                                                        ExitFlag = 255;
                                                                        cerr << "Not enough arguments given for suspension: -u <density>" << endl;
                                                        } else {
                                                                double density;
                                                                SaveFlag = true;
                                                                cout << Verbose(0) << "Evaluating necessary cell volume for a cluster suspended in water.";
                                                                density = atof(argv[argptr++]);
                                                                if (density < 1.0) {
                                                                        cerr << Verbose(0) << "Density must be greater than 1.0g/cm^3 !" << endl;
                                                                        density = 1.3;
                                                                }
//                                                              for(int i=0;i<NDIM;i++) {
//                                                                      repetition[i] = atoi(argv[argptr++]);
//                                                                      if (repetition[i] < 1)
//                                                                              cerr << Verbose(0) << "ERROR: repetition value must be greater 1!" << endl;
//                                                                      repetition[i] = 1;
//                                                              }
                                                                PrepareClustersinWater((ofstream *)&cout, &configuration, mol, volume, density);        // if volume == 0, will calculate from ConvexEnvelope
                                                        }
                                                        break;
                                                case 'd':
                                                        ExitFlag = 1;
                                                        if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
                                                                ExitFlag = 255;
                                                                cerr << "Not enough or invalid arguments given for repeating cells: -d <repeat_x> <repeat_y> <repeat_z>" << endl;
                                                        } else {
                                                                SaveFlag = true;
                                                                for (int axis = 1; axis <= NDIM; axis++) {
                                                                        int faktor = atoi(argv[argptr++]);
                                                                        int count;
                                                                        element ** Elements;
                                                                        Vector ** vectors;
                                                                        if (faktor < 1) {
                                                                                cerr << Verbose(0) << "ERROR: Repetition faktor mus be greater than 1!" << endl;
                                                                                faktor = 1;
                                                                        }
                                                                        mol->CountAtoms((ofstream *)&cout);     // 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)
                                                                                        cout << Verbose(0) << "ERROR: 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, ...)
                                                                                        }
                                                                                }
                                                                                // 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;
                                                default:         // no match? Step on
                                                        if ((argptr < argc) && (argv[argptr][0] != '-')) // if it started with a '-' we've already made a step!
                                                                argptr++;
                                                        break;
                                        }
                                }
                        } else argptr++;
                } while (argptr < argc);
                if (SaveFlag)
                        SaveConfig(ConfigFileName, &configuration, periode, molecules);
                if ((ExitFlag >= 1)) {
                        delete(mol);
                        delete(periode);
                        return (ExitFlag);
                }
        } else {        // no arguments, hence scan the elements db
                if (periode->LoadPeriodentafel(PathToDatabases))
                        cout << Verbose(0) << "Element list loaded successfully." << endl;
                else
                        cout << Verbose(0) << "Element list loading failed." << endl;
                configuration.RetrieveConfigPathAndName("main_pcp_linux");
        }
        return(0);
};

/********************************************** Main routine **************************************/

int main(int argc, char **argv)
{
        periodentafel *periode = new periodentafel; // and a period table of all elements
        MoleculeListClass *molecules = new MoleculeListClass;  // list of all molecules
        molecule *mol = NULL;
        config configuration;
        double tmp1;
        atom *first, *second;
        char choice;    // menu choice char
        Vector x,y,z,n; // coordinates for absolute point in cell volume
        bool valid; // flag if input was valid or not
        ifstream test;
        ofstream output;
        string line;
        char *ConfigFileName = NULL;
        char *ElementsFileName = NULL;
        int Z;
        int j, axis, count, faktor;

        // =========================== PARSE COMMAND LINE OPTIONS ====================================
        j = ParseCommandLineOptions(argc, argv, molecules, periode, configuration, ConfigFileName, ElementsFileName);
        if (j == 1) return 0; // just for -v and -h options
        if (j) return j;        // something went wrong

        // General stuff
        if (molecules->ListOfMolecules.size() == 0) {
    mol = new molecule(periode);
    if (mol->cell_size[0] == 0.) {
      cout << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
      for (int i=0;i<6;i++) {
        cout << Verbose(1) << "Cell size" << i << ": ";
        cin >> mol->cell_size[i];
      }
    }
    molecules->insert(mol);
        }

        // =========================== START INTERACTIVE SESSION ====================================

        // now the main construction loop
        cout << Verbose(0) << endl << "Now comes the real construction..." << endl;
        do {
                cout << Verbose(0) << endl << endl;
                cout << Verbose(0) << "============Molecule list=======================" << endl;
                molecules->Enumerate((ofstream *)&cout);
                cout << Verbose(0) << "============Menu===============================" << endl;
    cout << Verbose(0) << "a - set molecule (in)active" << endl;
    cout << Verbose(0) << "e - edit new molecules" << endl;
    cout << Verbose(0) << "g - globally manipulate atoms in molecule" << endl;
    cout << Verbose(0) << "M - Merge molecules" << endl;
    cout << Verbose(0) << "m - manipulate atoms" << endl;
    cout << Verbose(0) << "-----------------------------------------------" << endl;
    cout << Verbose(0) << "c - edit the current configuration" << endl;
    cout << Verbose(0) << "-----------------------------------------------" << endl;
    cout << Verbose(0) << "s - save current setup to config file" << endl;
    cout << Verbose(0) << "T - call the current test routine" << endl;
    cout << Verbose(0) << "q - quit" << endl;
    cout << Verbose(0) << "===============================================" << endl;
    cout << Verbose(0) << "Input: ";
    cin >> choice;

                switch (choice) {
                        case 'a':  // (in)activate molecule
        {
          cout << "Enter index of molecule: ";
          cin >> j;
          count = 1;
          MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin();
          for(; ((ListRunner != molecules->ListOfMolecules.end()) && (count < j)); ListRunner++);
          if (count == 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');

        // save element data base
        if (periode->StorePeriodentafel(ElementsFileName)) //ElementsFileName
                cout << Verbose(0) << "Saving of elements.db successful." << endl;
        else
                cout << Verbose(0) << "Saving of elements.db failed." << endl;

        delete(molecules);
        delete(periode);
        return (0);
}

/********************************************** E N D **************************************************/