source: molecuilder/src/builder.cpp@ cffff8

/** \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 "helpers.hpp"
#include "molecules.hpp"

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

/** Submenu for adding atoms to the molecule.
 * \param *periode periodentafel
 * \param *mol the molecule to add to
 */
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) {
      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=0;i<3;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=0;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 the molecule with all the atoms
 */
void CenterAtoms(molecule *mol)
{
  vector x;
  char choice;  // menu choice char
  double min[3];
  int j;
  
  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) << "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<3;i++) {
        cout << Verbose(0) << "Enter axis " << i << " boundary: ";
        cin >> min[i];
      }
      mol->CenterEdge((ofstream *)&cout, &x);  // make every coordinate positive
      mol->SetBoxDimension(&x);  // update Box of atoms by boundary
      // translate each coordinate by boundary
      j=-1;
      for (int i=0;i<NDIM;i++) {
        j += i+1;
        x.x[i] = min[i];
        mol->cell_size[j] += x.x[i]*2.;
      }
      mol->Translate(&x);
      break;
  }
};

/** Submenu for aligning the atoms in the molecule.
 * \param *periode periodentafel
 * \param *mol the molecule with all the atoms
 */
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=0;i<3;i++) {
        x.x[i] = gsl_vector_get(param.x,i);
        n.x[i] = gsl_vector_get(param.x,i+3);
      } 
      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 the molecule with all the atoms
 */
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 the molecule with all the atoms
 */
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.Distance((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 the molecule with all the atoms
 */
void MeasureAtoms(periodentafel *periode, molecule *mol)
{
  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) << "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=0;i<256;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=0;i<256;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=0;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;
  }
};

/** Submenu for measuring out the atoms in the molecule.
 * \param *mol the molecule with all the atoms
 * \param *configuration configuration structure for the to be written config files of all fragments
 */
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;
};

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

/** Is called always as option 'T' in the menu.
 */
void testroutine(molecule *mol)
{
  // the current test routine checks the functionality of the KeySet&Graph concept:
  // We want to have a multiindex (the KeySet) describing a unique subgraph
  atom *Walker = mol->start;
  int i, comp, counter=0;
  
  // 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++;
  }
};

/** 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 *mol pointer to molecule structure with all the atoms and coordinates
 */
void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, molecule *mol)
{
  char filename[MAXSTRINGSIZE];
  ofstream output;

  cout << Verbose(0) << "Storing configuration ... " << endl;
  // get correct valence orbitals
  mol->CalculateOrbitals(*configuration);
  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
  if (ConfigFileName != NULL) {
    output.open(ConfigFileName, ios::trunc);
  } else if (strlen(configuration->configname) != 0) {
    output.open(configuration->configname, ios::trunc);
    } else {
      output.open(DEFAULTCONFIG, ios::trunc);
    }
  if (configuration->Save(&output, periode, mol))
    cout << Verbose(0) << "Saving of config file successful." << endl;
  else
    cout << Verbose(0) << "Saving of config file failed." << endl;
  output.close();
  output.clear();
  // 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);
  } 
  if (mol->OutputXYZ(&output))
    cout << Verbose(0) << "Saving of XYZ file successful." << endl;
  else
    cout << Verbose(0) << "Saving of XYZ file failed." << endl;
  output.close();
  output.clear();
  
  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    cerr << "WARNING: config is found under different path then stated in config file::defaultpath!" << endl;
  }
};

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

int main(int argc, char **argv)
{
  periodentafel *periode = new periodentafel; // and a period table of all elements
  molecule *mol = new molecule(periode);    // first we need an empty molecule
  config configuration;
  double tmp1;
  double bond, min_bond;
  atom *first, *second;
  element *finder;
  char choice;  // menu choice char
  vector x,y,z,n;  // coordinates for absolute point in cell volume
        double *factor; // unit factor if desired
  bool valid; // flag if input was valid or not
  ifstream test;
  ofstream output;
  string line;
  char filename[MAXSTRINGSIZE];
  char *ConfigFileName = NULL;
  char *ElementsFileName = NULL;
  int flag = 0;
  int Z;
  int j, axis, count, faktor;
  int MinimumRingSize = -1;
  enum ConfigStatus config_present = absent;
  MoleculeLeafClass *Subgraphs = NULL;
  clock_t start,end;
  element **Elements;
  vector **Vectors;
  int argptr;

  // =========================== PARSE COMMAND LINE OPTIONS ====================================
  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-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
            cout << "\t-e <file>\tSets the element database to be parsed from this file (default: elements.db in same dir as " << argv[0] << ")." << endl;
            cout << "\t-e <dist> <order>\tFragments the molecule in BOSSANOVA manner and stores config files in same dir as config." << endl;
            cout << "\t-h/-H/-?\tGive this help screen." << endl;
            cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << 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-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
            cout << "\t-v/-V\t\tGives version information." << endl;
            cout << "Note: config files must not begin with '-' !" << endl;
            delete(mol);
            delete(periode);
            return (0);
            break;
          case 'v':
          case 'V':
            cout << argv[0] << " " << VERSIONSTRING << endl;
            cout << "Build your own molecule position set." << endl;
            delete(mol);
            delete(periode);
            return (0);
            break;
          case 'e':
            cout << "Using " << argv[argptr] << " as elements database." << endl;
            ElementsFileName = argv[argptr];
            argptr+=1;
            break;
          default:   // no match? Step on
            argptr++;
            break;
        }
          } else
            argptr++;
    } while (argptr < argc);
        
        // 2. Parse the element database
    if (periode->LoadPeriodentafel(ElementsFileName))
      cout << Verbose(0) << "Element list loaded successfully." << endl;
    else
      cout << Verbose(0) << "Element list loading failed." << endl;
    
        // 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 {
      if (argv[argptr][0] == '-') {
        argptr++;
        if ((config_present == present) || (config_present == empty)) {
          switch(argv[argptr-1][1]) {
            case 'p':
              flag = 1;
              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;
            default:   // no match? Don't step on (this is done in next switch's default)
              break;
          }
        }
        if (config_present != empty) { 
          if (config_present == present) {
            switch(argv[argptr-1][1]) {
              case 't':
                flag = 1;
                cout << Verbose(1) << "Translating all ions to new origin." << endl;
                for (int i=0;i<3;i++)
                  x.x[i] = atof(argv[argptr+i]);
                mol->Translate((const vector *)&x);
                argptr+=3;
                break;
              case 'a':
                flag = 1;
                cout << Verbose(1) << "Adding new atom." << endl;
                first = new atom;
                for (int i=0;i<3;i++)
                  first->x.x[i] = atof(argv[argptr+1+i]);
                finder = periode->start;
                while (finder != periode->end) {
                  finder = finder->next;
                  if (strncmp(finder->symbol,argv[argptr+1],3) == 0) {
                    first->type = finder;
                    break;
                  }
                }
                mol->AddAtom(first);  // add to molecule
                argptr+=4;
                break;
              case 's':
                flag = 1;
                j = -1;
                cout << Verbose(1) << "Scaling all ion positions by factor." << endl;
                factor = (double *) Malloc(sizeof(double)*NDIM, "main: *factor");
                factor[0] = atof(argv[argptr]);
                if (argc > argptr+1)
                  argptr++;
                factor[1] = atof(argv[argptr]);
                if (argc > argptr+1)
                  argptr++;
                factor[2] = atof(argv[argptr]);
                mol->Scale(&factor);
                for (int i=0;i<3;i++) {
                  j += i+1;
                  x.x[i] = atof(argv[3+i]);
                  mol->cell_size[j]*=factor[i];
                }
                Free((void **)&factor, "main: *factor");
                argptr+=1;
                break;
              case 'c':
                flag = 1;
                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<3;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 'r':
                flag = 1;
                cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
                break;
              case 'f':
                if (flag ==0) flag = 2;  // only set if not already by other command line switch
                cout << "Fragmenting molecule with bond distance " << argv[argptr] << " angstroem, order of " << argv[argptr+1] << "." << endl;
                if (argc >= argptr+2) {
                  cout << Verbose(0) << "Creating connection matrix..." << endl;
                  start = clock();
                  mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]));
                  cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
                  if (mol->first->next != mol->last) {
                    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+=1;
                } else {
                  cerr << "Not enough arguments for fragmentation: -f <max. bond distance> <bond order>" << endl;
                }
                break;
              default:   // no match? Step on
                argptr++;
                break;
            }
          }
        }
          } else argptr++;
        } while (argptr < argc);
    if (flag == 1) // 1 means save and exit
      SaveConfig(ConfigFileName, &configuration, periode, mol);
    if (flag > 1) { // 2 means just exit
      delete(mol);
      delete(periode);
      return (0);
    }
  } else {  // no arguments, hence scan the elements db
    if (periode->LoadPeriodentafel(ElementsFileName))
      cout << Verbose(0) << "Element list loaded successfully." << endl;
    else
      cout << Verbose(0) << "Element list loading failed." << endl;
    configuration.RetrieveConfigPathAndName("main_pcp_linux");
  }

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

  // =========================== 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) << "============Element list=======================" << endl;
    mol->Checkout((ofstream *)&cout);
    cout << Verbose(0) << "============Atom list==========================" << endl;
    mol->Output((ofstream *)&cout);
    cout << Verbose(0) << "============Menu===============================" << 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) << "-----------------------------------------------" << endl;
    cout << Verbose(0) << "p - Parse xyz file" << endl;
    cout << Verbose(0) << "e - edit the current configuration" << endl;
    cout << Verbose(0) << "o - create connection matrix" << endl;
    cout << Verbose(0) << "f - fragment molecule many-body bond order style" << endl;
    cout << Verbose(0) << "-----------------------------------------------" << endl;
    cout << Verbose(0) << "d - duplicate molecule/periodic cell" << endl;
    cout << Verbose(0) << "i - realign molecule" << endl; 
    cout << Verbose(0) << "m - mirror all molecules" << endl; 
    cout << Verbose(0) << "t - translate molecule by vector" << endl;
    cout << Verbose(0) << "c - scale by unit transformation" << endl;
    cout << Verbose(0) << "g - center atoms in box" << 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) {
      default:
      case 'q': // quit 
        break;
        
      case 'a': // add atom
        AddAtoms(periode, mol);
        choice = 'a'; 
        break;
      
      case 'd': // duplicate the periodic cell along a given axis, given times
        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 = (element **) Malloc(sizeof(element *)*count, "main: duplicateCell - **Elements");
          Vectors = (vector **) Malloc(sizeof(vector *)*count, "main: duplicateCell - **Vectors");
          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=0;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);
          // free memory
          Free((void **)&Elements, "main: duplicateCell - **Elements");
          Free((void **)&Vectors, "main: duplicateCell - **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 'g': // center the atoms
        CenterAtoms(mol);
        break;
        
      case 'b': // scale a bond
        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=0;i<3;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=0;i<3;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 'i': // align all atoms 
        AlignAtoms(periode, mol);
        break;

      case 'm': // mirror atoms along a given axis
        MirrorAtoms(mol);
        break;
       
      case 't': // translate all atoms
             cout << Verbose(0) << "Enter translation vector." << endl;       
             x.AskPosition(mol->cell_size,0);
       mol->Translate((const vector *)&x);
             break;
  
      case 'e': // edit each field of the configuration
       configuration.Edit(mol);
       break;
        
      case 'c': // unit scaling of the metric 
         cout << Verbose(0) << "Enter three factors: ";
       factor = (double *) Malloc(sizeof(double)*NDIM, "main: *factor");
       cin >> factor[0];
       cin >> factor[1];
       cin >> factor[2];
       valid = true;
       mol->Scale(&factor);
             Free((void **)&factor, "main: *factor");
       break;
                         
      case 'r': // remove atom
        RemoveAtoms(mol);        
        break;
        
      case 'l': // measure distances or angles
        MeasureAtoms(periode, mol);
        break;

      case 'p': // parse and XYZ file
        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));
        break;

      case 'o': // create the connection matrix
        cout << Verbose(0) << "What's the maximum bond distance: ";
        cin >> tmp1;
        start = clock();
        mol->CreateAdjacencyList((ofstream *)&cout, tmp1);
        //mol->CreateListOfBondsPerAtom((ofstream *)&cout);
        Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, false, MinimumRingSize);
        while (Subgraphs->next != NULL) {
          Subgraphs = Subgraphs->next;
          delete(Subgraphs->previous);
        }
        delete(Subgraphs);    // we don't need the list here, so free everything
        Subgraphs = NULL;
        end = clock();
        cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
        break;
        
      case 'f':
        FragmentAtoms(mol, &configuration);
        break;
        
      case 'u': // change an atom's element
        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;
        
      case 'T':
        testroutine(mol);
        break;
      
      case 's': // save to config file
        SaveConfig(ConfigFileName, &configuration, periode, mol);
        break;
    };
  } while (choice != 'q');
  
  // save element data base
  if (periode->StorePeriodentafel()) //ElementsFileName
    cout << Verbose(0) << "Saving of elements.db successful." << endl;
  else
    cout << Verbose(0) << "Saving of elements.db failed." << endl;

  // 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);
  }
  delete(mol);
  delete(periode);
  return (0);
}

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