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  • src/builder.cpp

    ra67d19 r481601  
    5252#include <cstring>
    5353
    54 #include "analysis_bonds.hpp"
    5554#include "analysis_correlation.hpp"
    5655#include "atom.hpp"
    … …  
    6968#include "periodentafel.hpp"
    7069#include "version.h"
    71 #include "World.hpp"
    7270
    7371/********************************************* Subsubmenu routine ************************************/
    … …  
    8684  bool valid;
    8785
    88   cout << Verbose(0) << "===========ADD ATOM============================" << endl;
    89   cout << Verbose(0) << " a - state absolute coordinates of atom" << endl;
    90   cout << Verbose(0) << " b - state relative coordinates of atom wrt to reference point" << endl;
    91   cout << Verbose(0) << " c - state relative coordinates of atom wrt to already placed atom" << endl;
    92   cout << Verbose(0) << " d - state two atoms, two angles and a distance" << endl;
    93   cout << Verbose(0) << " e - least square distance position to a set of atoms" << endl;
    94   cout << Verbose(0) << "all else - go back" << endl;
    95   cout << Verbose(0) << "===============================================" << endl;
    96   cout << Verbose(0) << "Note: Specifiy angles in degrees not multiples of Pi!" << endl;
    97   cout << Verbose(0) << "INPUT: ";
     86  Log() << Verbose(0) << "===========ADD ATOM============================" << endl;
     87  Log() << Verbose(0) << " a - state absolute coordinates of atom" << endl;
     88  Log() << Verbose(0) << " b - state relative coordinates of atom wrt to reference point" << endl;
     89  Log() << Verbose(0) << " c - state relative coordinates of atom wrt to already placed atom" << endl;
     90  Log() << Verbose(0) << " d - state two atoms, two angles and a distance" << endl;
     91  Log() << Verbose(0) << " e - least square distance position to a set of atoms" << endl;
     92  Log() << Verbose(0) << "all else - go back" << endl;
     93  Log() << Verbose(0) << "===============================================" << endl;
     94  Log() << Verbose(0) << "Note: Specifiy angles in degrees not multiples of Pi!" << endl;
     95  Log() << Verbose(0) << "INPUT: ";
    9896  cin >> choice;
    9997
    10098  switch (choice) {
    10199    default:
    102       DoeLog(2) && (eLog()<< Verbose(2) << "Not a valid choice." << endl);
     100      eLog() << Verbose(2) << "Not a valid choice." << endl;
    103101      break;
    104102      case 'a': // absolute coordinates of atom
    105         cout << Verbose(0) << "Enter absolute coordinates." << endl;
     103        Log() << Verbose(0) << "Enter absolute coordinates." << endl;
    106104        first = new atom;
    107         first->x.AskPosition(World::get()->cell_size, false);
     105        first->x.AskPosition(mol->cell_size, false);
    108106        first->type = periode->AskElement();  // give type
    109107        mol->AddAtom(first);  // add to molecule
    … …  
    114112        valid = true;
    115113        do {
    116           if (!valid) DoeLog(2) && (eLog()<< Verbose(2) << "Resulting position out of cell." << endl);
    117           cout << Verbose(0) << "Enter reference coordinates." << endl;
    118           x.AskPosition(World::get()->cell_size, true);
    119           cout << Verbose(0) << "Enter relative coordinates." << endl;
    120           first->x.AskPosition(World::get()->cell_size, false);
     114          if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
     115          Log() << Verbose(0) << "Enter reference coordinates." << endl;
     116          x.AskPosition(mol->cell_size, true);
     117          Log() << Verbose(0) << "Enter relative coordinates." << endl;
     118          first->x.AskPosition(mol->cell_size, false);
    121119          first->x.AddVector((const Vector *)&x);
    122           cout << Verbose(0) << "\n";
     120          Log() << Verbose(0) << "\n";
    123121        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
    124122        first->type = periode->AskElement();  // give type
    … …  
    130128        valid = true;
    131129        do {
    132           if (!valid) DoeLog(2) && (eLog()<< Verbose(2) << "Resulting position out of cell." << endl);
     130          if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
    133131          second = mol->AskAtom("Enter atom number: ");
    134           DoLog(0) && (Log() << Verbose(0) << "Enter relative coordinates." << endl);
    135           first->x.AskPosition(World::get()->cell_size, false);
     132          Log() << Verbose(0) << "Enter relative coordinates." << endl;
     133          first->x.AskPosition(mol->cell_size, false);
    136134          for (int i=NDIM;i--;) {
    137135            first->x.x[i] += second->x.x[i];
    … …  
    147145        do {
    148146          if (!valid) {
    149             DoeLog(2) && (eLog()<< Verbose(2) << "Resulting coordinates out of cell - " << first->x << endl);
     147            eLog() << Verbose(2) << "Resulting coordinates out of cell - " << first->x << endl;
    150148          }
    151           cout << Verbose(0) << "First, we need two atoms, the first atom is the central, while the second is the outer one." << endl;
     149          Log() << Verbose(0) << "First, we need two atoms, the first atom is the central, while the second is the outer one." << endl;
    152150          second = mol->AskAtom("Enter central atom: ");
    153151          third = mol->AskAtom("Enter second atom (specifying the axis for first angle): ");
    … …  
    160158          c *= M_PI/180.;
    161159          bound(&c, -M_PI, M_PI);
    162           cout << Verbose(0) << "radius: " << a << "\t phi: " << b*180./M_PI << "\t theta: " << c*180./M_PI << endl;
     160          Log() << Verbose(0) << "radius: " << a << "\t phi: " << b*180./M_PI << "\t theta: " << c*180./M_PI << endl;
    163161/*
    164162          second->Output(1,1,(ofstream *)&cout);
    … …  
    172170
    173171          if (!z.SolveSystem(&x,&y,&n, b, c, a)) {
    174          coutg() << Verbose(0) << "Failure solving self-dependent linear system!" << endl;
     172            Log() << Verbose(0) << "Failure solving self-dependent linear system!" << endl;
    175173            continue;
    176174          }
    177           DoLog(0) && (Log() << Verbose(0) << "resulting relative coordinates: ");
     175          Log() << Verbose(0) << "resulting relative coordinates: ";
    178176          z.Output();
    179           DoLog(0) && (Log() << Verbose(0) << endl);
     177          Log() << Verbose(0) << endl;
    180178          */
    181179          // calc axis vector
    … …  
    185183          Log() << Verbose(0) << "x: ",
    186184          x.Output();
    187           DoLog(0) && (Log() << Verbose(0) << endl);
     185          Log() << Verbose(0) << endl;
    188186          z.MakeNormalVector(&second->x,&third->x,&fourth->x);
    189187          Log() << Verbose(0) << "z: ",
    190188          z.Output();
    191           DoLog(0) && (Log() << Verbose(0) << endl);
     189          Log() << Verbose(0) << endl;
    192190          y.MakeNormalVector(&x,&z);
    193191          Log() << Verbose(0) << "y: ",
    194192          y.Output();
    195           DoLog(0) && (Log() << Verbose(0) << endl);
     193          Log() << Verbose(0) << endl;
    196194
    197195          // rotate vector around first angle
    … …  
    200198          Log() << Verbose(0) << "Rotated vector: ",
    201199          first->x.Output();
    202           DoLog(0) && (Log() << Verbose(0) << endl);
     200          Log() << Verbose(0) << endl;
    203201          // remove the projection onto the rotation plane of the second angle
    204202          n.CopyVector(&y);
    … …  
    206204          Log() << Verbose(0) << "N1: ",
    207205          n.Output();
    208           DoLog(0) && (Log() << Verbose(0) << endl);
     206          Log() << Verbose(0) << endl;
    209207          first->x.SubtractVector(&n);
    210208          Log() << Verbose(0) << "Subtracted vector: ",
    211209          first->x.Output();
    212           DoLog(0) && (Log() << Verbose(0) << endl);
     210          Log() << Verbose(0) << endl;
    213211          n.CopyVector(&z);
    214212          n.Scale(first->x.ScalarProduct(&z));
    215213          Log() << Verbose(0) << "N2: ",
    216214          n.Output();
    217           DoLog(0) && (Log() << Verbose(0) << endl);
     215          Log() << Verbose(0) << endl;
    218216          first->x.SubtractVector(&n);
    219217          Log() << Verbose(0) << "2nd subtracted vector: ",
    220218          first->x.Output();
    221           DoLog(0) && (Log() << Verbose(0) << endl);
     219          Log() << Verbose(0) << endl;
    222220
    223221          // rotate another vector around second angle
    … …  
    226224          Log() << Verbose(0) << "2nd Rotated vector: ",
    227225          n.Output();
    228           DoLog(0) && (Log() << Verbose(0) << endl);
     226          Log() << Verbose(0) << endl;
    229227
    230228          // add the two linear independent vectors
    … …  
    234232          first->x.AddVector(&second->x);
    235233
    236           DoLog(0) && (Log() << Verbose(0) << "resulting coordinates: ");
     234          Log() << Verbose(0) << "resulting coordinates: ";
    237235          first->x.Output();
    238           DoLog(0) && (Log() << Verbose(0) << endl);
     236          Log() << Verbose(0) << endl;
    239237        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
    240238        first->type = periode->AskElement();  // give type
    … …  
    249247          atoms[i] = NULL;
    250248        int i=0, j=0;
    251         cout << Verbose(0) << "Now we need at least three molecules.\n";
     249        Log() << Verbose(0) << "Now we need at least three molecules.\n";
    252250        do {
    253           cout << Verbose(0) << "Enter " << i+1 << "th atom: ";
     251          Log() << Verbose(0) << "Enter " << i+1 << "th atom: ";
    254252          cin >> j;
    255253          if (j != -1) {
    … …  
    266264        } else {
    267265          delete first;
    268           cout << Verbose(0) << "Please enter at least two vectors!\n";
     266          Log() << Verbose(0) << "Please enter at least two vectors!\n";
    269267        }
    270268        break;
    … …  
    280278  char choice;  // menu choice char
    281279
    282   cout << Verbose(0) << "===========CENTER ATOMS=========================" << endl;
    283   cout << Verbose(0) << " a - on origin" << endl;
    284   cout << Verbose(0) << " b - on center of gravity" << endl;
    285   cout << Verbose(0) << " c - within box with additional boundary" << endl;
    286   cout << Verbose(0) << " d - within given simulation box" << endl;
    287   cout << Verbose(0) << "all else - go back" << endl;
    288   cout << Verbose(0) << "===============================================" << endl;
    289   cout << Verbose(0) << "INPUT: ";
     280  Log() << Verbose(0) << "===========CENTER ATOMS=========================" << endl;
     281  Log() << Verbose(0) << " a - on origin" << endl;
     282  Log() << Verbose(0) << " b - on center of gravity" << endl;
     283  Log() << Verbose(0) << " c - within box with additional boundary" << endl;
     284  Log() << Verbose(0) << " d - within given simulation box" << endl;
     285  Log() << Verbose(0) << "all else - go back" << endl;
     286  Log() << Verbose(0) << "===============================================" << endl;
     287  Log() << Verbose(0) << "INPUT: ";
    290288  cin >> choice;
    291289
    292290  switch (choice) {
    293291    default:
    294       cout << Verbose(0) << "Not a valid choice." << endl;
     292      Log() << Verbose(0) << "Not a valid choice." << endl;
    295293      break;
    296294    case 'a':
    297       cout << Verbose(0) << "Centering atoms in config file on origin." << endl;
     295      Log() << Verbose(0) << "Centering atoms in config file on origin." << endl;
    298296      mol->CenterOrigin();
    299297      break;
    300298    case 'b':
    301       cout << Verbose(0) << "Centering atoms in config file on center of gravity." << endl;
     299      Log() << Verbose(0) << "Centering atoms in config file on center of gravity." << endl;
    302300      mol->CenterPeriodic();
    303301      break;
    304302    case 'c':
    305       cout << Verbose(0) << "Centering atoms in config file within given additional boundary." << endl;
     303      Log() << Verbose(0) << "Centering atoms in config file within given additional boundary." << endl;
    306304      for (int i=0;i<NDIM;i++) {
    307         cout << Verbose(0) << "Enter axis " << i << " boundary: ";
     305        Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
    308306        cin >> y.x[i];
    309307      }
    … …  
    316314      break;
    317315    case 'd':
    318       cout << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
     316      Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
    319317      for (int i=0;i<NDIM;i++) {
    320         cout << Verbose(0) << "Enter axis " << i << " boundary: ";
     318        Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
    321319        cin >> x.x[i];
    322320      }
    … …  
    339337  char choice;  // menu choice char
    340338
    341   cout << Verbose(0) << "===========ALIGN ATOMS=========================" << endl;
    342   cout << Verbose(0) << " a - state three atoms defining align plane" << endl;
    343   cout << Verbose(0) << " b - state alignment vector" << endl;
    344   cout << Verbose(0) << " c - state two atoms in alignment direction" << endl;
    345   cout << Verbose(0) << " d - align automatically by least square fit" << endl;
    346   cout << Verbose(0) << "all else - go back" << endl;
    347   cout << Verbose(0) << "===============================================" << endl;
    348   cout << Verbose(0) << "INPUT: ";
     339  Log() << Verbose(0) << "===========ALIGN ATOMS=========================" << endl;
     340  Log() << Verbose(0) << " a - state three atoms defining align plane" << endl;
     341  Log() << Verbose(0) << " b - state alignment vector" << endl;
     342  Log() << Verbose(0) << " c - state two atoms in alignment direction" << endl;
     343  Log() << Verbose(0) << " d - align automatically by least square fit" << endl;
     344  Log() << Verbose(0) << "all else - go back" << endl;
     345  Log() << Verbose(0) << "===============================================" << endl;
     346  Log() << Verbose(0) << "INPUT: ";
    349347  cin >> choice;
    350348
    … …  
    359357      break;
    360358    case 'b': // normal vector of mirror plane
    361       cout << Verbose(0) << "Enter normal vector of mirror plane." << endl;
    362       n.AskPosition(World::get()->cell_size,0);
     359      Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
     360      n.AskPosition(mol->cell_size,0);
    363361      n.Normalize();
    364362      break;
    … …  
    379377        fscanf(stdin, "%3s", shorthand);
    380378      } while ((param.type = periode->FindElement(shorthand)) == NULL);
    381       cout << Verbose(0) << "Element is " << param.type->name << endl;
     379      Log() << Verbose(0) << "Element is " << param.type->name << endl;
    382380      mol->GetAlignvector(&param);
    383381      for (int i=NDIM;i--;) {
    … …  
    386384      }
    387385      gsl_vector_free(param.x);
    388       cout << Verbose(0) << "Offset vector: ";
     386      Log() << Verbose(0) << "Offset vector: ";
    389387      x.Output();
    390       DoLog(0) && (Log() << Verbose(0) << endl);
     388      Log() << Verbose(0) << endl;
    391389      n.Normalize();
    392390      break;
    393391  };
    394   DoLog(0) && (Log() << Verbose(0) << "Alignment vector: ");
     392  Log() << Verbose(0) << "Alignment vector: ";
    395393  n.Output();
    396   DoLog(0) && (Log() << Verbose(0) << endl);
     394  Log() << Verbose(0) << endl;
    397395  mol->Align(&n);
    398396};
    … …  
    407405  char choice;  // menu choice char
    408406
    409   DoLog(0) && (Log() << Verbose(0) << "===========MIRROR ATOMS=========================" << endl);
    410   DoLog(0) && (Log() << Verbose(0) << " a - state three atoms defining mirror plane" << endl);
    411   DoLog(0) && (Log() << Verbose(0) << " b - state normal vector of mirror plane" << endl);
    412   DoLog(0) && (Log() << Verbose(0) << " c - state two atoms in normal direction" << endl);
    413   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    414   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
    415   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     407  Log() << Verbose(0) << "===========MIRROR ATOMS=========================" << endl;
     408  Log() << Verbose(0) << " a - state three atoms defining mirror plane" << endl;
     409  Log() << Verbose(0) << " b - state normal vector of mirror plane" << endl;
     410  Log() << Verbose(0) << " c - state two atoms in normal direction" << endl;
     411  Log() << Verbose(0) << "all else - go back" << endl;
     412  Log() << Verbose(0) << "===============================================" << endl;
     413  Log() << Verbose(0) << "INPUT: ";
    416414  cin >> choice;
    417415
    … …  
    426424      break;
    427425    case 'b': // normal vector of mirror plane
    428       DoLog(0) && (Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl);
    429       n.AskPosition(World::get()->cell_size,0);
     426      Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
     427      n.AskPosition(mol->cell_size,0);
    430428      n.Normalize();
    431429      break;
    … …  
    439437      break;
    440438  };
    441   DoLog(0) && (Log() << Verbose(0) << "Normal vector: ");
     439  Log() << Verbose(0) << "Normal vector: ";
    442440  n.Output();
    443   DoLog(0) && (Log() << Verbose(0) << endl);
     441  Log() << Verbose(0) << endl;
    444442  mol->Mirror((const Vector *)&n);
    445443};
    … …  
    455453  char choice;  // menu choice char
    456454
    457   DoLog(0) && (Log() << Verbose(0) << "===========REMOVE ATOMS=========================" << endl);
    458   DoLog(0) && (Log() << Verbose(0) << " a - state atom for removal by number" << endl);
    459   DoLog(0) && (Log() << Verbose(0) << " b - keep only in radius around atom" << endl);
    460   DoLog(0) && (Log() << Verbose(0) << " c - remove this with one axis greater value" << endl);
    461   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    462   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
    463   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     455  Log() << Verbose(0) << "===========REMOVE ATOMS=========================" << endl;
     456  Log() << Verbose(0) << " a - state atom for removal by number" << endl;
     457  Log() << Verbose(0) << " b - keep only in radius around atom" << endl;
     458  Log() << Verbose(0) << " c - remove this with one axis greater value" << endl;
     459  Log() << Verbose(0) << "all else - go back" << endl;
     460  Log() << Verbose(0) << "===============================================" << endl;
     461  Log() << Verbose(0) << "INPUT: ";
    464462  cin >> choice;
    465463
    … …  
    468466    case 'a':
    469467      if (mol->RemoveAtom(mol->AskAtom("Enter number of atom within molecule: ")))
    470         DoLog(1) && (Log() << Verbose(1) << "Atom removed." << endl);
     468        Log() << Verbose(1) << "Atom removed." << endl;
    471469      else
    472         DoLog(1) && (Log() << Verbose(1) << "Atom not found." << endl);
     470        Log() << Verbose(1) << "Atom not found." << endl;
    473471      break;
    474472    case 'b':
    475473      second = mol->AskAtom("Enter number of atom as reference point: ");
    476       DoLog(0) && (Log() << Verbose(0) << "Enter radius: ");
     474      Log() << Verbose(0) << "Enter radius: ";
    477475      cin >> tmp1;
    478476      first = mol->start;
    … …  
    486484      break;
    487485    case 'c':
    488       DoLog(0) && (Log() << Verbose(0) << "Which axis is it: ");
     486      Log() << Verbose(0) << "Which axis is it: ";
    489487      cin >> axis;
    490       DoLog(0) && (Log() << Verbose(0) << "Lower boundary: ");
     488      Log() << Verbose(0) << "Lower boundary: ";
    491489      cin >> tmp1;
    492       DoLog(0) && (Log() << Verbose(0) << "Upper boundary: ");
     490      Log() << Verbose(0) << "Upper boundary: ";
    493491      cin >> tmp2;
    494492      first = mol->start;
    … …  
    520518  char choice;  // menu choice char
    521519
    522   DoLog(0) && (Log() << Verbose(0) << "===========MEASURE ATOMS=========================" << endl);
    523   DoLog(0) && (Log() << Verbose(0) << " a - calculate bond length between one atom and all others" << endl);
    524   DoLog(0) && (Log() << Verbose(0) << " b - calculate bond length between two atoms" << endl);
    525   DoLog(0) && (Log() << Verbose(0) << " c - calculate bond angle" << endl);
    526   DoLog(0) && (Log() << Verbose(0) << " d - calculate principal axis of the system" << endl);
    527   DoLog(0) && (Log() << Verbose(0) << " e - calculate volume of the convex envelope" << endl);
    528   DoLog(0) && (Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl);
    529   DoLog(0) && (Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl);
    530   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    531   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
    532   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     520  Log() << Verbose(0) << "===========MEASURE ATOMS=========================" << endl;
     521  Log() << Verbose(0) << " a - calculate bond length between one atom and all others" << endl;
     522  Log() << Verbose(0) << " b - calculate bond length between two atoms" << endl;
     523  Log() << Verbose(0) << " c - calculate bond angle" << endl;
     524  Log() << Verbose(0) << " d - calculate principal axis of the system" << endl;
     525  Log() << Verbose(0) << " e - calculate volume of the convex envelope" << endl;
     526  Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
     527  Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
     528  Log() << Verbose(0) << "all else - go back" << endl;
     529  Log() << Verbose(0) << "===============================================" << endl;
     530  Log() << Verbose(0) << "INPUT: ";
    533531  cin >> choice;
    534532
    535533  switch(choice) {
    536534    default:
    537       DoLog(1) && (Log() << Verbose(1) << "Not a valid choice." << endl);
     535      Log() << Verbose(1) << "Not a valid choice." << endl;
    538536      break;
    539537    case 'a':
    … …  
    567565      x.SubtractVector((const Vector *)&second->x);
    568566      tmp1 = x.Norm();
    569       DoLog(1) && (Log() << Verbose(1) << "Distance vector is ");
     567      Log() << Verbose(1) << "Distance vector is ";
    570568      x.Output();
    571       DoLog(0) && (Log() << Verbose(0) << "." << endl << "Norm of distance is " << tmp1 << "." << endl);
     569      Log() << Verbose(0) << "." << endl << "Norm of distance is " << tmp1 << "." << endl;
    572570      break;
    573571
    574572    case 'c':
    575       DoLog(0) && (Log() << Verbose(0) << "Evaluating bond angle between three - first, central, last - atoms." << endl);
     573      Log() << Verbose(0) << "Evaluating bond angle between three - first, central, last - atoms." << endl;
    576574      first = mol->AskAtom("Enter first atom: ");
    577575      second = mol->AskAtom("Enter central atom: ");
    … …  
    582580      y.CopyVector((const Vector *)&third->x);
    583581      y.SubtractVector((const Vector *)&second->x);
    584       DoLog(0) && (Log() << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ");
    585       DoLog(0) && (Log() << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl);
     582      Log() << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
     583      Log() << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;
    586584      break;
    587585    case 'd':
    588       DoLog(0) && (Log() << Verbose(0) << "Evaluating prinicipal axis." << endl);
    589       DoLog(0) && (Log() << Verbose(0) << "Shall we rotate? [0/1]: ");
     586      Log() << Verbose(0) << "Evaluating prinicipal axis." << endl;
     587      Log() << Verbose(0) << "Shall we rotate? [0/1]: ";
    590588      cin >> Z;
    591589      if ((Z >=0) && (Z <=1))
    … …  
    596594    case 'e':
    597595      {
    598         DoLog(0) && (Log() << Verbose(0) << "Evaluating volume of the convex envelope.");
     596        Log() << Verbose(0) << "Evaluating volume of the convex envelope.";
    599597        class Tesselation *TesselStruct = NULL;
    600598        const LinkedCell *LCList = NULL;
    … …  
    602600        FindConvexBorder(mol, TesselStruct, LCList, NULL);
    603601        double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
    604         DoLog(0) && (Log() << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl);\
     602        Log() << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;\
    605603        delete(LCList);
    606604        delete(TesselStruct);
    … …  
    613611      {
    614612        char filename[255];
    615         DoLog(0) && (Log() << Verbose(0) << "Please enter filename: " << endl);
     613        Log() << Verbose(0) << "Please enter filename: " << endl;
    616614        cin >> filename;
    617         DoLog(1) && (Log() << Verbose(1) << "Storing temperatures in " << filename << "." << endl);
     615        Log() << Verbose(1) << "Storing temperatures in " << filename << "." << endl;
    618616        ofstream *output = new ofstream(filename, ios::trunc);
    619617        if (!mol->OutputTemperatureFromTrajectories(output, 0, mol->MDSteps))
    620           DoLog(2) && (Log() << Verbose(2) << "File could not be written." << endl);
     618          Log() << Verbose(2) << "File could not be written." << endl;
    621619        else
    622           DoLog(2) && (Log() << Verbose(2) << "File stored." << endl);
     620          Log() << Verbose(2) << "File stored." << endl;
    623621        output->close();
    624622        delete(output);
    … …  
    637635  clock_t start, end;
    638636
    639   DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
    640   DoLog(0) && (Log() << Verbose(0) << "What's the desired bond order: ");
     637  Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
     638  Log() << Verbose(0) << "What's the desired bond order: ";
    641639  cin >> Order1;
    642640  if (mol->first->next != mol->last) {  // there are bonds
    … …  
    644642    mol->FragmentMolecule(Order1, configuration);
    645643    end = clock();
    646     DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     644    Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    647645  } else
    648     DoLog(0) && (Log() << Verbose(0) << "Connection matrix has not yet been generated!" << endl);
     646    Log() << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
    649647};
    650648
    … …  
    657655static void ManipulateAtoms(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
    658656{
    659   atom *first, *second, *third;
     657  atom *first, *second;
    660658  molecule *mol = NULL;
    661659  Vector x,y,z,n; // coordinates for absolute point in cell volume
    … …  
    665663  bool valid;
    666664
    667   DoLog(0) && (Log() << Verbose(0) << "=========MANIPULATE ATOMS======================" << endl);
    668   DoLog(0) && (Log() << Verbose(0) << "a - add an atom" << endl);
    669   DoLog(0) && (Log() << Verbose(0) << "r - remove an atom" << endl);
    670   DoLog(0) && (Log() << Verbose(0) << "b - scale a bond between atoms" << endl);
    671   DoLog(0) && (Log() << Verbose(0) << "t - turn an atom round another bond" << endl);
    672   DoLog(0) && (Log() << Verbose(0) << "u - change an atoms element" << endl);
    673   DoLog(0) && (Log() << Verbose(0) << "l - measure lengths, angles, ... for an atom" << endl);
    674   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    675   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
     665  Log() << Verbose(0) << "=========MANIPULATE ATOMS======================" << endl;
     666  Log() << Verbose(0) << "a - add an atom" << endl;
     667  Log() << Verbose(0) << "r - remove an atom" << endl;
     668  Log() << Verbose(0) << "b - scale a bond between atoms" << endl;
     669  Log() << Verbose(0) << "u - change an atoms element" << endl;
     670  Log() << Verbose(0) << "l - measure lengths, angles, ... for an atom" << endl;
     671  Log() << Verbose(0) << "all else - go back" << endl;
     672  Log() << Verbose(0) << "===============================================" << endl;
    676673  if (molecules->NumberOfActiveMolecules() > 1)
    677     DoeLog(2) && (eLog()<< Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl);
    678   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     674    eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
     675  Log() << Verbose(0) << "INPUT: ";
    679676  cin >> choice;
    680677
    681678  switch (choice) {
    682679    default:
    683       DoLog(0) && (Log() << Verbose(0) << "Not a valid choice." << endl);
     680      Log() << Verbose(0) << "Not a valid choice." << endl;
    684681      break;
    685682
    … …  
    688685        if ((*ListRunner)->ActiveFlag) {
    689686        mol = *ListRunner;
    690         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     687        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    691688        AddAtoms(periode, mol);
    692689      }
    … …  
    697694        if ((*ListRunner)->ActiveFlag) {
    698695        mol = *ListRunner;
    699         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
    700         DoLog(0) && (Log() << Verbose(0) << "Scaling bond length between two atoms." << endl);
     696        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     697        Log() << Verbose(0) << "Scaling bond length between two atoms." << endl;
    701698        first = mol->AskAtom("Enter first (fixed) atom: ");
    702699        second = mol->AskAtom("Enter second (shifting) atom: ");
    … …  
    705702          minBond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
    706703        minBond = sqrt(minBond);
    707         DoLog(0) && (Log() << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl);
    708         DoLog(0) && (Log() << Verbose(0) << "Enter new bond length [a.u.]: ");
     704        Log() << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl;
     705        Log() << Verbose(0) << "Enter new bond length [a.u.]: ";
    709706        cin >> bond;
    710707        for (int i=NDIM;i--;) {
    … …  
    720717        if ((*ListRunner)->ActiveFlag) {
    721718        mol = *ListRunner;
    722         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
    723        DoLog(0) && (Log() << Verbose(0) << "Angstroem -> Bohrradius: 1.8897261\t\tBohrradius -> Angstroem: 0.52917721" << endl);
    724        DoLog(0) && (Log() << Verbose(0) << "Enter three factors: ");
     719        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     720       Log() << Verbose(0) << "Angstroem -> Bohrradius: 1.8897261\t\tBohrradius -> Angstroem: 0.52917721" << endl;
     721       Log() << Verbose(0) << "Enter three factors: ";
    725722       factor = new double[NDIM];
    726723       cin >> factor[0];
    … …  
    737734        if ((*ListRunner)->ActiveFlag) {
    738735        mol = *ListRunner;
    739         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     736        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    740737        MeasureAtoms(periode, mol, configuration);
    741738      }
    … …  
    746743        if ((*ListRunner)->ActiveFlag) {
    747744        mol = *ListRunner;
    748         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     745        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    749746        RemoveAtoms(mol);
    750747      }
    751       break;
    752 
    753     case 't': // turn/rotate atom
    754       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    755         if ((*ListRunner)->ActiveFlag) {
    756           mol = *ListRunner;
    757           DoLog(0) && (Log() << Verbose(0) << "Turning atom around another bond - first is atom to turn, second (central) and third specify bond" << endl);
    758           first = mol->AskAtom("Enter turning atom: ");
    759           second = mol->AskAtom("Enter central atom: ");
    760           third  = mol->AskAtom("Enter bond atom: ");
    761           cout << Verbose(0) << "Enter new angle in degrees: ";
    762           double tmp = 0.;
    763           cin >> tmp;
    764           // calculate old angle
    765           x.CopyVector((const Vector *)&first->x);
    766           x.SubtractVector((const Vector *)&second->x);
    767           y.CopyVector((const Vector *)&third->x);
    768           y.SubtractVector((const Vector *)&second->x);
    769           double alpha = (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.);
    770           cout << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
    771           cout << Verbose(0) << alpha << " degrees" << endl;
    772           // rotate
    773           z.MakeNormalVector(&x,&y);
    774           x.RotateVector(&z,(alpha-tmp)*M_PI/180.);
    775           x.AddVector(&second->x);
    776           first->x.CopyVector(&x);
    777           // check new angle
    778           x.CopyVector((const Vector *)&first->x);
    779           x.SubtractVector((const Vector *)&second->x);
    780           alpha = (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.);
    781           cout << Verbose(0) << "new Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
    782           cout << Verbose(0) << alpha << " degrees" << endl;
    783         }
    784748      break;
    785749
    … …  
    789753        int Z;
    790754        mol = *ListRunner;
    791         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     755        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    792756        first = NULL;
    793757        do {
    794           DoLog(0) && (Log() << Verbose(0) << "Change the element of which atom: ");
     758          Log() << Verbose(0) << "Change the element of which atom: ";
    795759          cin >> Z;
    796760        } while ((first = mol->FindAtom(Z)) == NULL);
    797         DoLog(0) && (Log() << Verbose(0) << "New element by atomic number Z: ");
     761        Log() << Verbose(0) << "New element by atomic number Z: ";
    798762        cin >> Z;
    799763        first->type = periode->FindElement(Z);
    800         DoLog(0) && (Log() << Verbose(0) << "Atom " << first->nr << "'s element is " << first->type->name << "." << endl);
     764        Log() << Verbose(0) << "Atom " << first->nr << "'s element is " << first->type->name << "." << endl;
    801765      }
    802766      break;
    … …  
    819783  MoleculeLeafClass *Subgraphs = NULL;
    820784
    821   DoLog(0) && (Log() << Verbose(0) << "=========MANIPULATE GLOBALLY===================" << endl);
    822   DoLog(0) && (Log() << Verbose(0) << "c - scale by unit transformation" << endl);
    823   DoLog(0) && (Log() << Verbose(0) << "d - duplicate molecule/periodic cell" << endl);
    824   DoLog(0) && (Log() << Verbose(0) << "f - fragment molecule many-body bond order style" << endl);
    825   DoLog(0) && (Log() << Verbose(0) << "g - center atoms in box" << endl);
    826   DoLog(0) && (Log() << Verbose(0) << "i - realign molecule" << endl);
    827   DoLog(0) && (Log() << Verbose(0) << "m - mirror all molecules" << endl);
    828   DoLog(0) && (Log() << Verbose(0) << "o - create connection matrix" << endl);
    829   DoLog(0) && (Log() << Verbose(0) << "t - translate molecule by vector" << endl);
    830   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    831   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
     785  Log() << Verbose(0) << "=========MANIPULATE GLOBALLY===================" << endl;
     786  Log() << Verbose(0) << "c - scale by unit transformation" << endl;
     787  Log() << Verbose(0) << "d - duplicate molecule/periodic cell" << endl;
     788  Log() << Verbose(0) << "f - fragment molecule many-body bond order style" << endl;
     789  Log() << Verbose(0) << "g - center atoms in box" << endl;
     790  Log() << Verbose(0) << "i - realign molecule" << endl;
     791  Log() << Verbose(0) << "m - mirror all molecules" << endl;
     792  Log() << Verbose(0) << "o - create connection matrix" << endl;
     793  Log() << Verbose(0) << "t - translate molecule by vector" << endl;
     794  Log() << Verbose(0) << "all else - go back" << endl;
     795  Log() << Verbose(0) << "===============================================" << endl;
    832796  if (molecules->NumberOfActiveMolecules() > 1)
    833     DoeLog(2) && (eLog()<< Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl);
    834   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     797    eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
     798  Log() << Verbose(0) << "INPUT: ";
    835799  cin >> choice;
    836800
    837801  switch (choice) {
    838802    default:
    839       DoLog(0) && (Log() << Verbose(0) << "Not a valid choice." << endl);
     803      Log() << Verbose(0) << "Not a valid choice." << endl;
    840804      break;
    841805
    … …  
    844808        if ((*ListRunner)->ActiveFlag) {
    845809        mol = *ListRunner;
    846         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
    847         DoLog(0) && (Log() << Verbose(0) << "State the axis [(+-)123]: ");
     810        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     811        Log() << Verbose(0) << "State the axis [(+-)123]: ";
    848812        cin >> axis;
    849         DoLog(0) && (Log() << Verbose(0) << "State the factor: ");
     813        Log() << Verbose(0) << "State the factor: ";
    850814        cin >> faktor;
    851815
    … …  
    864828          }
    865829          if (count != j)
    866             DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
     830            eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
    867831          x.Zero();
    868832          y.Zero();
    869           y.x[abs(axis)-1] = World::get()->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
     833          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
    870834          for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
    871835            x.AddVector(&y); // per factor one cell width further
    … …  
    890854            mol->Translate(&x);
    891855          }
    892           World::get()->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
     856          mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
    893857        }
    894858      }
    … …  
    903867        if ((*ListRunner)->ActiveFlag) {
    904868        mol = *ListRunner;
    905         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     869        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    906870        CenterAtoms(mol);
    907871      }
    … …  
    912876        if ((*ListRunner)->ActiveFlag) {
    913877        mol = *ListRunner;
    914         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     878        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    915879        AlignAtoms(periode, mol);
    916880      }
    … …  
    921885        if ((*ListRunner)->ActiveFlag) {
    922886        mol = *ListRunner;
    923         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
     887        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    924888        MirrorAtoms(mol);
    925889      }
    … …  
    932896          double bonddistance;
    933897          clock_t start,end;
    934           DoLog(0) && (Log() << Verbose(0) << "What's the maximum bond distance: ");
     898          Log() << Verbose(0) << "What's the maximum bond distance: ";
    935899          cin >> bonddistance;
    936900          start = clock();
    937901          mol->CreateAdjacencyList(bonddistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
    938902          end = clock();
    939           DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     903          Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    940904        }
    941905      break;
    … …  
    945909        if ((*ListRunner)->ActiveFlag) {
    946910        mol = *ListRunner;
    947         DoLog(0) && (Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl);
    948         DoLog(0) && (Log() << Verbose(0) << "Enter translation vector." << endl);
    949         x.AskPosition(World::get()->cell_size,0);
     911        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
     912        Log() << Verbose(0) << "Enter translation vector." << endl;
     913        x.AskPosition(mol->cell_size,0);
    950914        mol->Center.AddVector((const Vector *)&x);
    951915     }
    … …  
    974938  molecule *mol = NULL;
    975939
    976   DoLog(0) && (Log() << Verbose(0) << "==========EDIT MOLECULES=====================" << endl);
    977   DoLog(0) && (Log() << Verbose(0) << "c - create new molecule" << endl);
    978   DoLog(0) && (Log() << Verbose(0) << "l - load molecule from xyz file" << endl);
    979   DoLog(0) && (Log() << Verbose(0) << "n - change molecule's name" << endl);
    980   DoLog(0) && (Log() << Verbose(0) << "N - give molecules filename" << endl);
    981   DoLog(0) && (Log() << Verbose(0) << "p - parse atoms in xyz file into molecule" << endl);
    982   DoLog(0) && (Log() << Verbose(0) << "r - remove a molecule" << endl);
    983   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    984   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
    985   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     940  Log() << Verbose(0) << "==========EDIT MOLECULES=====================" << endl;
     941  Log() << Verbose(0) << "c - create new molecule" << endl;
     942  Log() << Verbose(0) << "l - load molecule from xyz file" << endl;
     943  Log() << Verbose(0) << "n - change molecule's name" << endl;
     944  Log() << Verbose(0) << "N - give molecules filename" << endl;
     945  Log() << Verbose(0) << "p - parse atoms in xyz file into molecule" << endl;
     946  Log() << Verbose(0) << "r - remove a molecule" << endl;
     947  Log() << Verbose(0) << "all else - go back" << endl;
     948  Log() << Verbose(0) << "===============================================" << endl;
     949  Log() << Verbose(0) << "INPUT: ";
    986950  cin >> choice;
    987951
    988952  switch (choice) {
    989953    default:
    990       DoLog(0) && (Log() << Verbose(0) << "Not a valid choice." << endl);
     954      Log() << Verbose(0) << "Not a valid choice." << endl;
    991955      break;
    992956    case 'c':
    … …  
    998962      {
    999963        char filename[MAXSTRINGSIZE];
    1000         DoLog(0) && (Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl);
     964        Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    1001965        mol = new molecule(periode);
    1002966        do {
    1003           DoLog(0) && (Log() << Verbose(0) << "Enter file name: ");
     967          Log() << Verbose(0) << "Enter file name: ";
    1004968          cin >> filename;
    1005969        } while (!mol->AddXYZFile(filename));
    … …  
    1007971        // center at set box dimensions
    1008972        mol->CenterEdge(&center);
    1009         double * const cell_size = World::get()->cell_size;
    1010         cell_size[0] = center.x[0];
    1011         cell_size[1] = 0;
    1012         cell_size[2] = center.x[1];
    1013         cell_size[3] = 0;
    1014         cell_size[4] = 0;
    1015         cell_size[5] = center.x[2];
     973        mol->cell_size[0] = center.x[0];
     974        mol->cell_size[1] = 0;
     975        mol->cell_size[2] = center.x[1];
     976        mol->cell_size[3] = 0;
     977        mol->cell_size[4] = 0;
     978        mol->cell_size[5] = center.x[2];
    1016979        molecules->insert(mol);
    1017980      }
    … …  
    1022985        char filename[MAXSTRINGSIZE];
    1023986        do {
    1024           DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule: ");
     987          Log() << Verbose(0) << "Enter index of molecule: ";
    1025988          cin >> nr;
    1026989          mol = molecules->ReturnIndex(nr);
    1027990        } while (mol == NULL);
    1028         DoLog(0) && (Log() << Verbose(0) << "Enter name: ");
     991        Log() << Verbose(0) << "Enter name: ";
    1029992        cin >> filename;
    1030993        strcpy(mol->name, filename);
    … …  
    1036999        char filename[MAXSTRINGSIZE];
    10371000        do {
    1038           DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule: ");
     1001          Log() << Verbose(0) << "Enter index of molecule: ";
    10391002          cin >> nr;
    10401003          mol = molecules->ReturnIndex(nr);
    10411004        } while (mol == NULL);
    1042         DoLog(0) && (Log() << Verbose(0) << "Enter name: ");
     1005        Log() << Verbose(0) << "Enter name: ";
    10431006        cin >> filename;
    10441007        mol->SetNameFromFilename(filename);
    … …  
    10511014        mol = NULL;
    10521015        do {
    1053           DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule: ");
     1016          Log() << Verbose(0) << "Enter index of molecule: ";
    10541017          cin >> nr;
    10551018          mol = molecules->ReturnIndex(nr);
    10561019        } while (mol == NULL);
    1057         DoLog(0) && (Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl);
     1020        Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    10581021        do {
    1059           DoLog(0) && (Log() << Verbose(0) << "Enter file name: ");
     1022          Log() << Verbose(0) << "Enter file name: ";
    10601023          cin >> filename;
    10611024        } while (!mol->AddXYZFile(filename));
    … …  
    10651028
    10661029    case 'r':
    1067       DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule: ");
     1030      Log() << Verbose(0) << "Enter index of molecule: ";
    10681031      cin >> nr;
    10691032      count = 1;
    … …  
    10881051  char choice;  // menu choice char
    10891052
    1090   DoLog(0) && (Log() << Verbose(0) << "===========MERGE MOLECULES=====================" << endl);
    1091   DoLog(0) && (Log() << Verbose(0) << "a - simple add of one molecule to another" << endl);
    1092   DoLog(0) && (Log() << Verbose(0) << "b - count the number of bonds of two elements" << endl);
    1093   DoLog(0) && (Log() << Verbose(0) << "B - count the number of bonds of three elements " << endl);
    1094   DoLog(0) && (Log() << Verbose(0) << "e - embedding merge of two molecules" << endl);
    1095   DoLog(0) && (Log() << Verbose(0) << "h - count the number of hydrogen bonds" << endl);
    1096   DoLog(0) && (Log() << Verbose(0) << "b - count the number of hydrogen bonds" << endl);
    1097   DoLog(0) && (Log() << Verbose(0) << "m - multi-merge of all molecules" << endl);
    1098   DoLog(0) && (Log() << Verbose(0) << "s - scatter merge of two molecules" << endl);
    1099   DoLog(0) && (Log() << Verbose(0) << "t - simple merge of two molecules" << endl);
    1100   DoLog(0) && (Log() << Verbose(0) << "all else - go back" << endl);
    1101   DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
    1102   DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     1053  Log() << Verbose(0) << "===========MERGE MOLECULES=====================" << endl;
     1054  Log() << Verbose(0) << "a - simple add of one molecule to another" << endl;
     1055  Log() << Verbose(0) << "e - embedding merge of two molecules" << endl;
     1056  Log() << Verbose(0) << "m - multi-merge of all molecules" << endl;
     1057  Log() << Verbose(0) << "s - scatter merge of two molecules" << endl;
     1058  Log() << Verbose(0) << "t - simple merge of two molecules" << endl;
     1059  Log() << Verbose(0) << "all else - go back" << endl;
     1060  Log() << Verbose(0) << "===============================================" << endl;
     1061  Log() << Verbose(0) << "INPUT: ";
    11031062  cin >> choice;
    11041063
    11051064  switch (choice) {
    11061065    default:
    1107       DoLog(0) && (Log() << Verbose(0) << "Not a valid choice." << endl);
     1066      Log() << Verbose(0) << "Not a valid choice." << endl;
    11081067      break;
    11091068
    … …  
    11141073        {
    11151074          do {
    1116             DoLog(0) && (Log() << Verbose(0) << "Enter index of destination molecule: ");
     1075            Log() << Verbose(0) << "Enter index of destination molecule: ";
    11171076            cin >> dest;
    11181077            destmol = molecules->ReturnIndex(dest);
    11191078          } while ((destmol == NULL) && (dest != -1));
    11201079          do {
    1121             DoLog(0) && (Log() << Verbose(0) << "Enter index of source molecule to add from: ");
     1080            Log() << Verbose(0) << "Enter index of source molecule to add from: ";
    11221081            cin >> src;
    11231082            srcmol = molecules->ReturnIndex(src);
    … …  
    11291088      break;
    11301089
    1131     case 'b':
    1132       {
    1133         const int nr = 2;
    1134         char *names[nr] = {"first", "second"};
    1135         int Z[nr];
    1136         element *elements[nr];
    1137         for (int i=0;i<nr;i++) {
    1138           Z[i] = 0;
    1139           do {
    1140             cout << "Enter " << names[i] << " element: ";
    1141             cin >> Z[i];
    1142           } while ((Z[i] <= 0) && (Z[i] > MAX_ELEMENTS));
    1143           elements[i] = periode->FindElement(Z[i]);
    1144         }
    1145         const int count = CountBondsOfTwo(molecules, elements[0], elements[1]);
    1146         cout << endl << "There are " << count << " ";
    1147         for (int i=0;i<nr;i++) {
    1148           if (i==0)
    1149             cout << elements[i]->symbol;
    1150           else
    1151             cout << "-" << elements[i]->symbol;
    1152         }
    1153         cout << " bonds." << endl;
    1154       }
    1155     break;
    1156 
    1157     case 'B':
    1158       {
    1159         const int nr = 3;
    1160         char *names[nr] = {"first", "second", "third"};
    1161         int Z[nr];
    1162         element *elements[nr];
    1163         for (int i=0;i<nr;i++) {
    1164           Z[i] = 0;
    1165           do {
    1166             cout << "Enter " << names[i] << " element: ";
    1167             cin >> Z[i];
    1168           } while ((Z[i] <= 0) && (Z[i] > MAX_ELEMENTS));
    1169           elements[i] = periode->FindElement(Z[i]);
    1170         }
    1171         const int count = CountBondsOfThree(molecules, elements[0], elements[1], elements[2]);
    1172         cout << endl << "There are " << count << " ";
    1173         for (int i=0;i<nr;i++) {
    1174           if (i==0)
    1175             cout << elements[i]->symbol;
    1176           else
    1177             cout << "-" << elements[i]->symbol;
    1178         }
    1179         cout << " bonds." << endl;
    1180       }
    1181     break;
    1182 
    11831090    case 'e':
    11841091      {
    … …  
    11861093        molecule *srcmol = NULL, *destmol = NULL;
    11871094        do {
    1188           DoLog(0) && (Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ");
     1095          Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ";
    11891096          cin >> src;
    11901097          srcmol = molecules->ReturnIndex(src);
    11911098        } while ((srcmol == NULL) && (src != -1));
    11921099        do {
    1193           DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ");
     1100          Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ";
    11941101          cin >> dest;
    11951102          destmol = molecules->ReturnIndex(dest);
    … …  
    12001107      break;
    12011108
    1202     case 'h':
    1203       {
    1204         int Z;
    1205         cout << "Please enter interface element: ";
    1206         cin >> Z;
    1207         element * const InterfaceElement = periode->FindElement(Z);
    1208         cout << endl << "There are " << CountHydrogenBridgeBonds(molecules, InterfaceElement) << " hydrogen bridges with connections to " << (InterfaceElement != 0 ? InterfaceElement->name : "None") << "." << endl;
    1209       }
    1210       break;
    1211 
    12121109    case 'm':
    12131110      {
    … …  
    12151112        molecule *mol = NULL;
    12161113        do {
    1217           DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule to merge into: ");
     1114          Log() << Verbose(0) << "Enter index of molecule to merge into: ";
    12181115          cin >> nr;
    12191116          mol = molecules->ReturnIndex(nr);
    … …  
    12321129
    12331130    case 's':
    1234       DoLog(0) && (Log() << Verbose(0) << "Not implemented yet." << endl);
     1131      Log() << Verbose(0) << "Not implemented yet." << endl;
    12351132      break;
    12361133
    … …  
    12411138        {
    12421139          do {
    1243             DoLog(0) && (Log() << Verbose(0) << "Enter index of destination molecule: ");
     1140            Log() << Verbose(0) << "Enter index of destination molecule: ";
    12441141            cin >> dest;
    12451142            destmol = molecules->ReturnIndex(dest);
    12461143          } while ((destmol == NULL) && (dest != -1));
    12471144          do {
    1248             DoLog(0) && (Log() << Verbose(0) << "Enter index of source molecule to merge into: ");
     1145            Log() << Verbose(0) << "Enter index of source molecule to merge into: ";
    12491146            cin >> src;
    12501147            srcmol = molecules->ReturnIndex(src);
    … …  
    12751172    mol = (molecules->ListOfMolecules.front())->CopyMolecule();
    12761173  else {
    1277     DoeLog(0) && (eLog()<< Verbose(0) << "I don't have anything to test on ... ");
     1174    eLog() << Verbose(0) << "I don't have anything to test on ... ";
    12781175    performCriticalExit();
    12791176    return;
    … …  
    12821179
    12831180  // generate some KeySets
    1284   DoLog(0) && (Log() << Verbose(0) << "Generating KeySets." << endl);
     1181  Log() << Verbose(0) << "Generating KeySets." << endl;
    12851182  KeySet TestSets[mol->AtomCount+1];
    12861183  i=1;
    … …  
    12921189    i++;
    12931190  }
    1294   DoLog(0) && (Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl);
     1191  Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl;
    12951192  KeySetTestPair test;
    12961193  test = TestSets[mol->AtomCount-1].insert(Walker->nr);
    12971194  if (test.second) {
    1298     DoLog(1) && (Log() << Verbose(1) << "Insertion worked?!" << endl);
     1195    Log() << Verbose(1) << "Insertion worked?!" << endl;
    12991196  } else {
    1300     DoLog(1) && (Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl);
     1197    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
    13011198  }
    13021199  TestSets[mol->AtomCount].insert(mol->end->previous->nr);
    … …  
    13041201
    13051202  // constructing Graph structure
    1306   DoLog(0) && (Log() << Verbose(0) << "Generating Subgraph class." << endl);
     1203  Log() << Verbose(0) << "Generating Subgraph class." << endl;
    13071204  Graph Subgraphs;
    13081205
    13091206  // insert KeySets into Subgraphs
    1310   DoLog(0) && (Log() << Verbose(0) << "Inserting KeySets into Subgraph class." << endl);
     1207  Log() << Verbose(0) << "Inserting KeySets into Subgraph class." << endl;
    13111208  for (int j=0;j<mol->AtomCount;j++) {
    13121209    Subgraphs.insert(GraphPair (TestSets[j],pair<int, double>(counter++, 1.)));
    13131210  }
    1314   DoLog(0) && (Log() << Verbose(0) << "Testing insertion of already present item in Subgraph." << endl);
     1211  Log() << Verbose(0) << "Testing insertion of already present item in Subgraph." << endl;
    13151212  GraphTestPair test2;
    13161213  test2 = Subgraphs.insert(GraphPair (TestSets[mol->AtomCount],pair<int, double>(counter++, 1.)));
    13171214  if (test2.second) {
    1318     DoLog(1) && (Log() << Verbose(1) << "Insertion worked?!" << endl);
     1215    Log() << Verbose(1) << "Insertion worked?!" << endl;
    13191216  } else {
    1320     DoLog(1) && (Log() << Verbose(1) << "Insertion rejected: Present object is " << (*(test2.first)).second.first << "." << endl);
     1217    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*(test2.first)).second.first << "." << endl;
    13211218  }
    13221219
    13231220  // show graphs
    1324   DoLog(0) && (Log() << Verbose(0) << "Showing Subgraph's contents, checking that it's sorted." << endl);
     1221  Log() << Verbose(0) << "Showing Subgraph's contents, checking that it's sorted." << endl;
    13251222  Graph::iterator A = Subgraphs.begin();
    13261223  while (A !=  Subgraphs.end()) {
    1327     DoLog(0) && (Log() << Verbose(0) << (*A).second.first << ": ");
     1224    Log() << Verbose(0) << (*A).second.first << ": ";
    13281225    KeySet::iterator key = (*A).first.begin();
    13291226    comp = -1;
    13301227    while (key != (*A).first.end()) {
    13311228      if ((*key) > comp)
    1332         DoLog(0) && (Log() << Verbose(0) << (*key) << " ");
     1229        Log() << Verbose(0) << (*key) << " ";
    13331230      else
    1334         DoLog(0) && (Log() << Verbose(0) << (*key) << "! ");
     1231        Log() << Verbose(0) << (*key) << "! ";
    13351232      comp = (*key);
    13361233      key++;
    13371234    }
    1338     DoLog(0) && (Log() << Verbose(0) << endl);
     1235    Log() << Verbose(0) << endl;
    13391236    A++;
    13401237  }
    … …  
    13561253
    13571254  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1358     DoeLog(2) && (eLog()<< Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl);
     1255    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    13591256  }
    13601257
    … …  
    13651262  if (output == NULL)
    13661263    strcpy(filename,"main_pcp_linux");
    1367   DoLog(0) && (Log() << Verbose(0) << "Saving as pdb input ");
     1264  Log() << Verbose(0) << "Saving as pdb input ";
    13681265  if (configuration->SavePDB(filename, molecules))
    1369     DoLog(0) && (Log() << Verbose(0) << "done." << endl);
     1266    Log() << Verbose(0) << "done." << endl;
    13701267  else
    1371     DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
     1268    Log() << Verbose(0) << "failed." << endl;
    13721269
    13731270  // then save as tremolo data file
    … …  
    13761273  if (output == NULL)
    13771274    strcpy(filename,"main_pcp_linux");
    1378   DoLog(0) && (Log() << Verbose(0) << "Saving as tremolo data input ");
     1275  Log() << Verbose(0) << "Saving as tremolo data input ";
    13791276  if (configuration->SaveTREMOLO(filename, molecules))
    1380     DoLog(0) && (Log() << Verbose(0) << "done." << endl);
     1277    Log() << Verbose(0) << "done." << endl;
    13811278  else
    1382     DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
     1279    Log() << Verbose(0) << "failed." << endl;
    13831280
    13841281  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
    … …  
    14001297  }
    14011298
    1402   DoLog(0) && (Log() << Verbose(0) << "Storing configuration ... " << endl);
     1299  Log() << Verbose(0) << "Storing configuration ... " << endl;
    14031300  // get correct valence orbitals
    14041301  mol->CalculateOrbitals(*configuration);
    … …  
    14161313  output.close();
    14171314  output.clear();
    1418   DoLog(0) && (Log() << Verbose(0) << "Saving of config file ");
     1315  Log() << Verbose(0) << "Saving of config file ";
    14191316  if (configuration->Save(filename, periode, mol))
    1420     DoLog(0) && (Log() << Verbose(0) << "successful." << endl);
     1317    Log() << Verbose(0) << "successful." << endl;
    14211318  else
    1422     DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
     1319    Log() << Verbose(0) << "failed." << endl;
    14231320
    14241321  // and save to xyz file
    … …  
    14331330    output.open(filename, ios::trunc);
    14341331  }
    1435   DoLog(0) && (Log() << Verbose(0) << "Saving of XYZ file ");
     1332  Log() << Verbose(0) << "Saving of XYZ file ";
    14361333  if (mol->MDSteps <= 1) {
    14371334    if (mol->OutputXYZ(&output))
    1438       DoLog(0) && (Log() << Verbose(0) << "successful." << endl);
     1335      Log() << Verbose(0) << "successful." << endl;
    14391336    else
    1440       DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
     1337      Log() << Verbose(0) << "failed." << endl;
    14411338  } else {
    14421339    if (mol->OutputTrajectoriesXYZ(&output))
    1443       DoLog(0) && (Log() << Verbose(0) << "successful." << endl);
     1340      Log() << Verbose(0) << "successful." << endl;
    14441341    else
    1445       DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
     1342      Log() << Verbose(0) << "failed." << endl;
    14461343  }
    14471344  output.close();
    … …  
    14531350  if (output == NULL)
    14541351    strcpy(filename,"main_pcp_linux");
    1455   DoLog(0) && (Log() << Verbose(0) << "Saving as mpqc input ");
     1352  Log() << Verbose(0) << "Saving as mpqc input ";
    14561353  if (configuration->SaveMPQC(filename, mol))
    1457     DoLog(0) && (Log() << Verbose(0) << "done." << endl);
     1354    Log() << Verbose(0) << "done." << endl;
    14581355  else
    1459     DoLog(0) && (Log() << Verbose(0) << "failed." << endl);
     1356    Log() << Verbose(0) << "failed." << endl;
    14601357
    14611358  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1462     DoeLog(2) && (eLog()<< Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl);
     1359    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    14631360  }
    14641361
    … …  
    14901387  enum ConfigStatus configPresent = absent;
    14911388  clock_t start,end;
    1492   double MaxDistance = -1;
    14931389  int argptr;
    14941390  molecule *mol = NULL;
    … …  
    15021398    do {
    15031399      if (argv[argptr][0] == '-') {
    1504         DoLog(0) && (Log() << Verbose(0) << "Recognized command line argument: " << argv[argptr][1] << ".\n");
     1400        Log() << Verbose(0) << "Recognized command line argument: " << argv[argptr][1] << ".\n";
    15051401        argptr++;
    15061402        switch(argv[argptr-1][1]) {
    … …  
    15081404          case 'H':
    15091405          case '?':
    1510             DoLog(0) && (Log() << Verbose(0) << "MoleCuilder suite" << endl << "==================" << endl << endl);
    1511             DoLog(0) && (Log() << Verbose(0) << "Usage: " << argv[0] << "[config file] [-{acefpsthH?vfrp}] [further arguments]" << endl);
    1512             DoLog(0) && (Log() << Verbose(0) << "or simply " << argv[0] << " without arguments for interactive session." << endl);
    1513             DoLog(0) && (Log() << Verbose(0) << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl);
    1514             DoLog(0) && (Log() << Verbose(0) << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl);
    1515             DoLog(0) && (Log() << Verbose(0) << "\t-b xx xy xz yy yz zz\tCenter atoms in domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl);
    1516             DoLog(0) && (Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl);
    1517             DoLog(0) && (Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl);
    1518             DoLog(0) && (Log() << Verbose(0) << "\t-C <type> [params] <output> <bin output> <BinWidth> <BinStart> <BinEnd>\tPair Correlation analysis." << endl);
    1519             DoLog(0) && (Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl);
    1520             DoLog(0) && (Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl);
    1521             DoLog(0) && (Log() << Verbose(0) << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl);
    1522             DoLog(0) && (Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl);
    1523             DoLog(0) && (Log() << Verbose(0) << "\t-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);
    1524             DoLog(0) && (Log() << Verbose(0) << "\t-F <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
    1525             DoLog(0) && (Log() << Verbose(0) << "\t-FF <MaxDistance> <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
    1526             DoLog(0) && (Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl);
    1527             DoLog(0) && (Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl);
    1528             DoLog(0) && (Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl);
    1529             DoLog(0) && (Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl);
    1530             DoLog(0) && (Log() << Verbose(0) << "\t-J\t<path> Store adjacency per atom to file." << endl);
    1531             DoLog(0) && (Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl);
    1532             DoLog(0) && (Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl);
    1533             DoLog(0) && (Log() << Verbose(0) << "\t-M <basis>\tSetting basis to store to MPQC config files." << endl);
    1534             DoLog(0) && (Log() << Verbose(0) << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl);
    1535             DoLog(0) && (Log() << Verbose(0) << "\t-N <radius> <file>\tGet non-convex-envelope." << endl);
    1536             DoLog(0) && (Log() << Verbose(0) << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl);
    1537             DoLog(0) && (Log() << Verbose(0) << "\t-O\tCenter atoms in origin." << endl);
    1538             DoLog(0) && (Log() << Verbose(0) << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl);
    1539             DoLog(0) && (Log() << Verbose(0) << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl);
    1540             DoLog(0) && (Log() << Verbose(0) << "\t-r <id>\t\tRemove an atom with given id." << endl);
    1541             DoLog(0) && (Log() << Verbose(0) << "\t-R <id> <radius>\t\tRemove all atoms out of sphere around a given one." << endl);
    1542             DoLog(0) && (Log() << Verbose(0) << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl);
    1543             DoLog(0) && (Log() << Verbose(0) << "\t-S <file> Store temperatures from the config file in <file>." << endl);
    1544             DoLog(0) && (Log() << Verbose(0) << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl);
    1545             DoLog(0) && (Log() << Verbose(0) << "\t-T x1 x2 x3\tTranslate periodically all atoms by this vector (x1,x2,x3)." << endl);
    1546             DoLog(0) && (Log() << Verbose(0) << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl);
    1547             DoLog(0) && (Log() << Verbose(0) << "\t-v\t\tsets verbosity (more is more)." << endl);
    1548             DoLog(0) && (Log() << Verbose(0) << "\t-V\t\tGives version information." << endl);
    1549             DoLog(0) && (Log() << Verbose(0) << "\t-X\t\tset default name of a molecule." << endl);
    1550             DoLog(0) && (Log() << Verbose(0) << "Note: config files must not begin with '-' !" << endl);
     1406            Log() << Verbose(0) << "MoleCuilder suite" << endl << "==================" << endl << endl;
     1407            Log() << Verbose(0) << "Usage: " << argv[0] << "[config file] [-{acefpsthH?vfrp}] [further arguments]" << endl;
     1408            Log() << Verbose(0) << "or simply " << argv[0] << " without arguments for interactive session." << endl;
     1409            Log() << Verbose(0) << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl;
     1410            Log() << Verbose(0) << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl;
     1411            Log() << Verbose(0) << "\t-b xx xy xz yy yz zz\tCenter atoms in domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
     1412            Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
     1413            Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
     1414            Log() << Verbose(0) << "\t-C <Z> <output> <bin output>\tPair Correlation analysis." << endl;
     1415            Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
     1416            Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
     1417            Log() << Verbose(0) << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl;
     1418            Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
     1419            Log() << Verbose(0) << "\t-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;
     1420            Log() << Verbose(0) << "\t-F <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl;
     1421            Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl;
     1422            Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
     1423            Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl;
     1424            Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl;
     1425            Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
     1426            Log() << Verbose(0) << "\t-M <basis>\tSetting basis to store to MPQC config files." << endl;
     1427            Log() << Verbose(0) << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl;
     1428            Log() << Verbose(0) << "\t-N <radius> <file>\tGet non-convex-envelope." << endl;
     1429            Log() << Verbose(0) << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl;
     1430            Log() << Verbose(0) << "\t-O\tCenter atoms in origin." << endl;
     1431            Log() << Verbose(0) << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
     1432            Log() << Verbose(0) << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl;
     1433            Log() << Verbose(0) << "\t-r <id>\t\tRemove an atom with given id." << endl;
     1434            Log() << Verbose(0) << "\t-R <id> <radius>\t\tRemove all atoms out of sphere around a given one." << endl;
     1435            Log() << Verbose(0) << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
     1436            Log() << Verbose(0) << "\t-S <file> Store temperatures from the config file in <file>." << endl;
     1437            Log() << Verbose(0) << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
     1438            Log() << Verbose(0) << "\t-T x1 x2 x3\tTranslate periodically all atoms by this vector (x1,x2,x3)." << endl;
     1439            Log() << Verbose(0) << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl;
     1440            Log() << Verbose(0) << "\t-v\t\tsets verbosity (more is more)." << endl;
     1441            Log() << Verbose(0) << "\t-V\t\tGives version information." << endl;
     1442            Log() << Verbose(0) << "Note: config files must not begin with '-' !" << endl;
    15511443            return (1);
    15521444            break;
    … …  
    15561448            }
    15571449            setVerbosity(verbosity);
    1558             DoLog(0) && (Log() << Verbose(0) << "Setting verbosity to " << verbosity << "." << endl);
     1450            Log() << Verbose(0) << "Setting verbosity to " << verbosity << "." << endl;
    15591451            break;
    15601452          case 'V':
    1561             DoLog(0) && (Log() << Verbose(0) << argv[0] << " " << VERSIONSTRING << endl);
    1562             DoLog(0) && (Log() << Verbose(0) << "Build your own molecule position set." << endl);
     1453            Log() << Verbose(0) << argv[0] << " " << VERSIONSTRING << endl;
     1454            Log() << Verbose(0) << "Build your own molecule position set." << endl;
    15631455            return (1);
    1564             break;
    1565           case 'B':
    1566             if (ExitFlag == 0) ExitFlag = 1;
    1567             if ((argptr+5 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
    1568               ExitFlag = 255;
    1569               DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for bounding in box: -B <xx> <xy> <xz> <yy> <yz> <zz>" << endl);
    1570               performCriticalExit();
    1571             } else {
    1572               SaveFlag = true;
    1573               j = -1;
    1574               DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl);
    1575               double * const cell_size = World::get()->cell_size;
    1576               for (int i=0;i<6;i++) {
    1577                 cell_size[i] = atof(argv[argptr+i]);
    1578               }
    1579               argptr+=6;
    1580             }
    15811456            break;
    15821457          case 'e':
    15831458            if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    1584               DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for specifying element db: -e <db file>" << endl);
     1459              eLog() << Verbose(0) << "Not enough or invalid arguments for specifying element db: -e <db file>" << endl;
    15851460              performCriticalExit();
    15861461            } else {
    1587               DoLog(0) && (Log() << Verbose(0) << "Using " << argv[argptr] << " as elements database." << endl);
     1462              Log() << Verbose(0) << "Using " << argv[argptr] << " as elements database." << endl;
    15881463              strncpy (configuration.databasepath, argv[argptr], MAXSTRINGSIZE-1);
    15891464              argptr+=1;
    … …  
    15921467          case 'g':
    15931468            if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    1594               DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for specifying bond length table: -g <table file>" << endl);
     1469              eLog() << Verbose(0) << "Not enough or invalid arguments for specifying bond length table: -g <table file>" << endl;
    15951470              performCriticalExit();
    15961471            } else {
    15971472              BondGraphFileName = argv[argptr];
    1598               DoLog(0) && (Log() << Verbose(0) << "Using " << BondGraphFileName << " as bond length table." << endl);
     1473              Log() << Verbose(0) << "Using " << BondGraphFileName << " as bond length table." << endl;
    15991474              argptr+=1;
    16001475            }
    16011476            break;
    16021477          case 'n':
    1603             DoLog(0) && (Log() << Verbose(0) << "I won't parse trajectories." << endl);
     1478            Log() << Verbose(0) << "I won't parse trajectories." << endl;
    16041479            configuration.FastParsing = true;
    1605             break;
    1606           case 'X':
    1607             {
    1608               char **name = &(World::get()->DefaultName);
    1609               delete[](*name);
    1610               const int length = strlen(argv[argptr]);
    1611               *name = new char[length+2];
    1612               strncpy(*name, argv[argptr], length);
    1613               DoLog(0) && (Log() << Verbose(0) << "Default name of new molecules set to " << *name << "." << endl);
    1614             }
    16151480            break;
    16161481          default:   // no match? Step on
    … …  
    16241489    // 3a. Parse the element database
    16251490    if (periode->LoadPeriodentafel(configuration.databasepath)) {
    1626       DoLog(0) && (Log() << Verbose(0) << "Element list loaded successfully." << endl);
     1491      Log() << Verbose(0) << "Element list loaded successfully." << endl;
    16271492      //periode->Output();
    16281493    } else {
    1629       DoLog(0) && (Log() << Verbose(0) << "Element list loading failed." << endl);
     1494      Log() << Verbose(0) << "Element list loading failed." << endl;
    16301495      return 1;
    16311496    }
    … …  
    16331498    if (argv[1][0] != '-') {
    16341499      // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
    1635       DoLog(0) && (Log() << Verbose(0) << "Config file given." << endl);
     1500      Log() << Verbose(0) << "Config file given." << endl;
    16361501      test.open(argv[1], ios::in);
    16371502      if (test == NULL) {
    … …  
    16391504        output.open(argv[1], ios::out);
    16401505        if (output == NULL) {
    1641           DoLog(1) && (Log() << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl);
     1506          Log() << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl;
    16421507          configPresent = absent;
    16431508        } else {
    1644           DoLog(0) && (Log() << Verbose(0) << "Empty configuration file." << endl);
     1509          Log() << Verbose(0) << "Empty configuration file." << endl;
    16451510          ConfigFileName = argv[1];
    16461511          configPresent = empty;
    … …  
    16501515        test.close();
    16511516        ConfigFileName = argv[1];
    1652         DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
     1517        Log() << Verbose(1) << "Specified config file found, parsing ... ";
    16531518        switch (configuration.TestSyntax(ConfigFileName, periode)) {
    16541519          case 1:
    1655             DoLog(0) && (Log() << Verbose(0) << "new syntax." << endl);
     1520            Log() << Verbose(0) << "new syntax." << endl;
    16561521            configuration.Load(ConfigFileName, BondGraphFileName, periode, molecules);
    16571522            configPresent = present;
    16581523            break;
    16591524          case 0:
    1660             DoLog(0) && (Log() << Verbose(0) << "old syntax." << endl);
     1525            Log() << Verbose(0) << "old syntax." << endl;
    16611526            configuration.LoadOld(ConfigFileName, BondGraphFileName, periode, molecules);
    16621527            configPresent = present;
    16631528            break;
    16641529          default:
    1665             DoLog(0) && (Log() << Verbose(0) << "Unknown syntax or empty, yet present file." << endl);
     1530            Log() << Verbose(0) << "Unknown syntax or empty, yet present file." << endl;
    16661531            configPresent = empty;
    16671532       }
    … …  
    16871552       configuration.BG = new BondGraph(configuration.GetIsAngstroem());
    16881553       if ((!BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
    1689          DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
     1554         Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
    16901555       } else {
    1691          DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
     1556         eLog() << Verbose(1) << "Bond length table loading failed." << endl;
    16921557       }
    16931558     }
    … …  
    16961561    argptr = 1;
    16971562    do {
    1698       DoLog(0) && (Log() << Verbose(0) << "Current Command line argument: " << argv[argptr] << "." << endl);
     1563      Log() << Verbose(0) << "Current Command line argument: " << argv[argptr] << "." << endl;
    16991564      if (argv[argptr][0] == '-') {
    17001565        argptr++;
    … …  
    17051570              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    17061571                ExitFlag = 255;
    1707                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough arguments for parsing: -p <xyz file>" << endl);
     1572                eLog() << Verbose(0) << "Not enough arguments for parsing: -p <xyz file>" << endl;
    17081573                performCriticalExit();
    17091574              } else {
    17101575                SaveFlag = true;
    1711                 DoLog(1) && (Log() << Verbose(1) << "Parsing xyz file for new atoms." << endl);
     1576                Log() << Verbose(1) << "Parsing xyz file for new atoms." << endl;
    17121577                if (!mol->AddXYZFile(argv[argptr]))
    1713                   DoLog(2) && (Log() << Verbose(2) << "File not found." << endl);
     1578                  Log() << Verbose(2) << "File not found." << endl;
    17141579                else {
    1715                   DoLog(2) && (Log() << Verbose(2) << "File found and parsed." << endl);
     1580                  Log() << Verbose(2) << "File found and parsed." << endl;
    17161581                  configPresent = present;
    17171582                }
    … …  
    17221587              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3]))) {
    17231588                ExitFlag = 255;
    1724                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for adding atom: -a <element> <x> <y> <z>" << endl);
     1589                eLog() << Verbose(0) << "Not enough or invalid arguments for adding atom: -a <element> <x> <y> <z>" << endl;
    17251590                performCriticalExit();
    17261591              } else {
    17271592                SaveFlag = true;
    1728                 DoLog(1) && (Log() << Verbose(1) << "Adding new atom with element " << argv[argptr] << " at (" << argv[argptr+1] << "," << argv[argptr+2] << "," << argv[argptr+3] << "), ");
     1593                Log() << Verbose(1) << "Adding new atom with element " << argv[argptr] << " at (" << argv[argptr+1] << "," << argv[argptr+2] << "," << argv[argptr+3] << "), ";
    17291594                first = new atom;
    17301595                first->type = periode->FindElement(atoi(argv[argptr]));
    17311596                if (first->type != NULL)
    1732                   DoLog(2) && (Log() << Verbose(2) << "found element " << first->type->name << endl);
     1597                  Log() << Verbose(2) << "found element " << first->type->name << endl;
    17331598                for (int i=NDIM;i--;)
    17341599                  first->x.x[i] = atof(argv[argptr+1+i]);
    … …  
    17381603                    configPresent = present;
    17391604                } else
    1740                   DoeLog(1) && (eLog()<< Verbose(1) << "Could not find the specified element." << endl);
     1605                  eLog() << Verbose(1) << "Could not find the specified element." << endl;
    17411606                argptr+=4;
    17421607              }
    … …  
    17511616              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    17521617                ExitFlag = 255;
    1753                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for setting MPQC basis: -B <basis name>" << endl);
     1618                eLog() << Verbose(0) << "Not enough or invalid arguments given for setting MPQC basis: -B <basis name>" << endl;
    17541619                performCriticalExit();
    17551620              } else {
    17561621                configuration.basis = argv[argptr];
    1757                 DoLog(1) && (Log() << Verbose(1) << "Setting MPQC basis to " << configuration.basis << "." << endl);
     1622                Log() << Verbose(1) << "Setting MPQC basis to " << configuration.basis << "." << endl;
    17581623                argptr+=1;
    17591624              }
    … …  
    17621627              if (ExitFlag == 0) ExitFlag = 1;
    17631628              {
    1764                 DoLog(1) && (Log() << Verbose(1) << "Depth-First-Search Analysis." << endl);
     1629                Log() << Verbose(1) << "Depth-First-Search Analysis." << endl;
    17651630                MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
    17661631                int *MinimumRingSize = new int[mol->AtomCount];
    … …  
    17931658              break;
    17941659            case 'I':
    1795               DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
     1660              Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl;
    17961661              // @TODO rather do the dissection afterwards
    17971662              molecules->DissectMoleculeIntoConnectedSubgraphs(periode, &configuration);
    … …  
    18041669                  }
    18051670              }
    1806               if ((mol == NULL) && (!molecules->ListOfMolecules.empty())) {
     1671              if (mol == NULL) {
    18071672                mol = *(molecules->ListOfMolecules.begin());
    1808                 if (mol != NULL)
    1809                   mol->ActiveFlag = true;
     1673                mol->ActiveFlag = true;
    18101674              }
    18111675              break;
    18121676            case 'C':
    1813               {
    1814                 int ranges[3] = {1, 1, 1};
    1815                 bool periodic = (argv[argptr-1][2] =='p');
    1816                 if (ExitFlag == 0) ExitFlag = 1;
    1817                 if ((argptr >= argc)) {
    1818                   ExitFlag = 255;
    1819                   DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C[p] <type: E/P/S> [more params] <output> <bin output> <BinStart> <BinEnd>" << endl);
    1820                   performCriticalExit();
    1821                 } else {
    1822                   switch(argv[argptr][0]) {
    1823                     case 'E':
    1824                       {
    1825                         if ((argptr+6 >= argc) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+5])) || (!IsValidNumber(argv[argptr+6])) || (!IsValidNumber(argv[argptr+2])) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-') || (argv[argptr+3][0] == '-') || (argv[argptr+4][0] == '-')) {
    1826                           ExitFlag = 255;
    1827                           DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C E <Z1> <Z2> <output> <bin output>" << endl);
    1828                           performCriticalExit();
    1829                         } else {
    1830                           ofstream output(argv[argptr+3]);
    1831                           ofstream binoutput(argv[argptr+4]);
    1832                           const double BinStart = atof(argv[argptr+5]);
    1833                           const double BinEnd = atof(argv[argptr+6]);
    1834 
    1835                           element *elemental = periode->FindElement((const int) atoi(argv[argptr+1]));
    1836                           element *elemental2 = periode->FindElement((const int) atoi(argv[argptr+2]));
    1837                           PairCorrelationMap *correlationmap = NULL;
    1838                           if (periodic)
    1839                             correlationmap = PeriodicPairCorrelation(molecules, elemental, elemental2, ranges);
    1840                           else
    1841                             correlationmap = PairCorrelation(molecules, elemental, elemental2);
    1842                           //OutputCorrelationToSurface(&output, correlationmap);
    1843                           BinPairMap *binmap = BinData( correlationmap, 0.5, BinStart, BinEnd );
    1844                           OutputCorrelation ( &binoutput, binmap );
    1845                           output.close();
    1846                           binoutput.close();
    1847                           delete(binmap);
    1848                           delete(correlationmap);
    1849                           argptr+=7;
    1850                         }
    1851                       }
    1852                       break;
    1853 
    1854                     case 'P':
    1855                       {
    1856                         if ((argptr+8 >= argc) || (!IsValidNumber(argv[argptr+1])) ||  (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+7])) || (!IsValidNumber(argv[argptr+8])) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-') || (argv[argptr+3][0] == '-') || (argv[argptr+4][0] == '-') || (argv[argptr+5][0] == '-') || (argv[argptr+6][0] == '-')) {
    1857                           ExitFlag = 255;
    1858                           DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C P <Z1> <x> <y> <z> <output> <bin output>" << endl);
    1859                           performCriticalExit();
    1860                         } else {
    1861                           ofstream output(argv[argptr+5]);
    1862                           ofstream binoutput(argv[argptr+6]);
    1863                           const double BinStart = atof(argv[argptr+7]);
    1864                           const double BinEnd = atof(argv[argptr+8]);
    1865 
    1866                           element *elemental = periode->FindElement((const int) atoi(argv[argptr+1]));
    1867                           Vector *Point = new Vector((const double) atof(argv[argptr+1]),(const double) atof(argv[argptr+2]),(const double) atof(argv[argptr+3]));
    1868                           CorrelationToPointMap *correlationmap = NULL;
    1869                           if (periodic)
    1870                             correlationmap  = PeriodicCorrelationToPoint(molecules, elemental, Point, ranges);
    1871                           else
    1872                             correlationmap = CorrelationToPoint(molecules, elemental, Point);
    1873                           //OutputCorrelationToSurface(&output, correlationmap);
    1874                           BinPairMap *binmap = BinData( correlationmap, 0.5, BinStart, BinEnd );
    1875                           OutputCorrelation ( &binoutput, binmap );
    1876                           output.close();
    1877                           binoutput.close();
    1878                           delete(Point);
    1879                           delete(binmap);
    1880                           delete(correlationmap);
    1881                           argptr+=9;
    1882                         }
    1883                       }
    1884                       break;
    1885 
    1886                     case 'S':
    1887                       {
    1888                         if ((argptr+6 >= argc) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) || (!IsValidNumber(argv[argptr+6])) || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-') || (argv[argptr+3][0] == '-')) {
    1889                           ExitFlag = 255;
    1890                           DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C S <Z> <output> <bin output> <BinWidth> <BinStart> <BinEnd>" << endl);
    1891                           performCriticalExit();
    1892                         } else {
    1893                           ofstream output(argv[argptr+2]);
    1894                           ofstream binoutput(argv[argptr+3]);
    1895                           const double radius = 4.;
    1896                           const double BinWidth = atof(argv[argptr+4]);
    1897                           const double BinStart = atof(argv[argptr+5]);
    1898                           const double BinEnd = atof(argv[argptr+6]);
    1899                           double LCWidth = 20.;
    1900                           if (BinEnd > 0) {
    1901                             if (BinEnd > 2.*radius)
    1902                                 LCWidth = BinEnd;
    1903                             else
    1904                               LCWidth = 2.*radius;
    1905                           }
    1906 
    1907                           // get the boundary
    1908                           class molecule *Boundary = NULL;
    1909                           class Tesselation *TesselStruct = NULL;
    1910                           const LinkedCell *LCList = NULL;
    1911                           // find biggest molecule
    1912                           int counter  = 0;
    1913                           for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
    1914                             if ((Boundary == NULL) || (Boundary->AtomCount < (*BigFinder)->AtomCount)) {
    1915                               Boundary = *BigFinder;
    1916                             }
    1917                             counter++;
    1918                           }
    1919                           bool *Actives = Malloc<bool>(counter, "ParseCommandLineOptions() - case C -- *Actives");
    1920                           counter = 0;
    1921                           for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
    1922                             Actives[counter++] = (*BigFinder)->ActiveFlag;
    1923                             (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
    1924                           }
    1925                           LCList = new LinkedCell(Boundary, LCWidth);
    1926                           element *elemental = periode->FindElement((const int) atoi(argv[argptr+1]));
    1927                           FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
    1928                           CorrelationToSurfaceMap *surfacemap = NULL;
    1929                           if (periodic)
    1930                             surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges);
    1931                           else
    1932                             surfacemap = CorrelationToSurface( molecules, elemental, TesselStruct, LCList);
    1933                           OutputCorrelationToSurface(&output, surfacemap);
    1934                           // check whether radius was appropriate
    1935                           {
    1936                             double start; double end;
    1937                             GetMinMax( surfacemap, start, end);
    1938                             if (LCWidth < end)
    1939                               DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
    1940                           }
    1941                           BinPairMap *binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
    1942                           OutputCorrelation ( &binoutput, binmap );
    1943                           output.close();
    1944                           binoutput.close();
    1945                           for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
    1946                             (*BigFinder)->ActiveFlag = Actives[counter++];
    1947                           Free(&Actives);
    1948                           delete(LCList);
    1949                           delete(TesselStruct);
    1950                           delete(binmap);
    1951                           delete(surfacemap);
    1952                           argptr+=7;
    1953                         }
    1954                       }
    1955                       break;
    1956 
    1957                     default:
    1958                       ExitFlag = 255;
    1959                       DoeLog(0) && (eLog()<< Verbose(0) << "Invalid type given for pair correlation analysis: -C <type: E/P/S> [more params] <output> <bin output>" << endl);
    1960                       performCriticalExit();
    1961                       break;
     1677              if (ExitFlag == 0) ExitFlag = 1;
     1678              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr][0] == '-') || (argv[argptr+1][0] == '-') || (argv[argptr+2][0] == '-')) {
     1679                ExitFlag = 255;
     1680                eLog() << Verbose(0) << "Not enough or invalid arguments given for pair correlation analysis: -C <Z> <output> <bin output>" << endl;
     1681                performCriticalExit();
     1682              } else {
     1683                ofstream output(argv[argptr+1]);
     1684                ofstream binoutput(argv[argptr+2]);
     1685                const double radius = 5.;
     1686
     1687                // get the boundary
     1688                class molecule *Boundary = NULL;
     1689                class Tesselation *TesselStruct = NULL;
     1690                const LinkedCell *LCList = NULL;
     1691                // find biggest molecule
     1692                int counter  = 0;
     1693                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
     1694                  if ((Boundary == NULL) || (Boundary->AtomCount < (*BigFinder)->AtomCount)) {
     1695                    Boundary = *BigFinder;
    19621696                  }
     1697                  counter++;
    19631698                }
    1964                 break;
    1965               }
     1699                bool *Actives = Malloc<bool>(counter, "ParseCommandLineOptions() - case C -- *Actives");
     1700                counter = 0;
     1701                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
     1702                  Actives[counter++] = (*BigFinder)->ActiveFlag;
     1703                  (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
     1704                }
     1705                LCList = new LinkedCell(Boundary, 2.*radius);
     1706                element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
     1707                FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
     1708                int ranges[NDIM] = {1,1,1};
     1709                CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
     1710                OutputCorrelationToSurface(&output, surfacemap);
     1711                BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 0. );
     1712                OutputCorrelation ( &binoutput, binmap );
     1713                output.close();
     1714                binoutput.close();
     1715                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
     1716                  (*BigFinder)->ActiveFlag = Actives[counter++];
     1717                Free(&Actives);
     1718                delete(LCList);
     1719                delete(TesselStruct);
     1720                argptr+=3;
     1721              }
     1722              break;
    19661723            case 'E':
    19671724              if (ExitFlag == 0) ExitFlag = 1;
    19681725              if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr+1][0] == '-')) {
    19691726                ExitFlag = 255;
    1970                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for changing element: -E <atom nr.> <element>" << endl);
     1727                eLog() << Verbose(0) << "Not enough or invalid arguments given for changing element: -E <atom nr.> <element>" << endl;
    19711728                performCriticalExit();
    19721729              } else {
    19731730                SaveFlag = true;
    1974                 DoLog(1) && (Log() << Verbose(1) << "Changing atom " << argv[argptr] << " to element " << argv[argptr+1] << "." << endl);
     1731                Log() << Verbose(1) << "Changing atom " << argv[argptr] << " to element " << argv[argptr+1] << "." << endl;
    19751732                first = mol->FindAtom(atoi(argv[argptr]));
    19761733                first->type = periode->FindElement(atoi(argv[argptr+1]));
    … …  
    19801737            case 'F':
    19811738              if (ExitFlag == 0) ExitFlag = 1;
    1982               MaxDistance = -1;
    1983               if (argv[argptr-1][2] == 'F') { // option is -FF?
    1984                 // fetch first argument as max distance to surface
    1985                 MaxDistance = atof(argv[argptr++]);
    1986                 DoLog(0) && (Log() << Verbose(0) << "Filling with maximum layer distance of " << MaxDistance << "." << endl);
    1987               }
    1988               if ((argptr+7 >=argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) || (!IsValidNumber(argv[argptr+6])) || (!IsValidNumber(argv[argptr+7]))) {
     1739              if (argptr+6 >=argc) {
    19891740                ExitFlag = 255;
    1990                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <xyz of filler> <dist_x> <dist_y> <dist_z> <boundary> <randatom> <randmol> <DoRotate>" << endl);
     1741                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <boundary> <randatom> <randmol> <DoRotate>" << endl;
    19911742                performCriticalExit();
    19921743              } else {
    19931744                SaveFlag = true;
    1994                 DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules." << endl);
     1745                Log() << Verbose(1) << "Filling Box with water molecules." << endl;
    19951746                // construct water molecule
    19961747                molecule *filler = new molecule(periode);
    1997                 if (!filler->AddXYZFile(argv[argptr])) {
    1998                   DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << argv[argptr] << "." << endl);
    1999                 }
    2000                 filler->SetNameFromFilename(argv[argptr]);
    2001                 configuration.BG->ConstructBondGraph(filler);
    20021748                molecule *Filling = NULL;
     1749                atom *second = NULL, *third = NULL;
     1750//                first = new atom();
     1751//                first->type = periode->FindElement(5);
     1752//                first->x.Zero();
     1753//                filler->AddAtom(first);
     1754                first = new atom();
     1755                first->type = periode->FindElement(1);
     1756                first->x.Init(0.441, -0.143, 0.);
     1757                filler->AddAtom(first);
     1758                second = new atom();
     1759                second->type = periode->FindElement(1);
     1760                second->x.Init(-0.464, 1.137, 0.0);
     1761                filler->AddAtom(second);
     1762                third = new atom();
     1763                third->type = periode->FindElement(8);
     1764                third->x.Init(-0.464, 0.177, 0.);
     1765                filler->AddAtom(third);
     1766                filler->AddBond(first, third, 1);
     1767                filler->AddBond(second, third, 1);
    20031768                // call routine
    20041769                double distance[NDIM];
    20051770                for (int i=0;i<NDIM;i++)
    2006                   distance[i] = atof(argv[argptr+i+1]);
    2007                 Filling = FillBoxWithMolecule(molecules, filler, configuration, MaxDistance, distance, atof(argv[argptr+4]), atof(argv[argptr+5]), atof(argv[argptr+6]), atoi(argv[argptr+7]));
     1771                  distance[i] = atof(argv[argptr+i]);
     1772                Filling = FillBoxWithMolecule(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atof(argv[argptr+5]), atoi(argv[argptr+6]));
    20081773                if (Filling != NULL) {
    20091774                  Filling->ActiveFlag = false;
    … …  
    20181783              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    20191784                ExitFlag =255;
    2020                 DoeLog(0) && (eLog()<< Verbose(0) << "Missing source file for bonds in molecule: -A <bond sourcefile>" << endl);
     1785                eLog() << Verbose(0) << "Missing source file for bonds in molecule: -A <bond sourcefile>" << endl;
    20211786                performCriticalExit();
    20221787              } else {
    2023                 DoLog(0) && (Log() << Verbose(0) << "Parsing bonds from " << argv[argptr] << "." << endl);
     1788                Log() << Verbose(0) << "Parsing bonds from " << argv[argptr] << "." << endl;
    20241789                ifstream *input = new ifstream(argv[argptr]);
    20251790                mol->CreateAdjacencyListFromDbondFile(input);
    … …  
    20281793              }
    20291794              break;
    2030 
    2031             case 'J':
    2032               if (ExitFlag == 0) ExitFlag = 1;
    2033               if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    2034                 ExitFlag =255;
    2035                 DoeLog(0) && (eLog()<< Verbose(0) << "Missing path of adjacency file: -j <path>" << endl);
    2036                 performCriticalExit();
    2037               } else {
    2038                 DoLog(0) && (Log() << Verbose(0) << "Storing adjacency to path " << argv[argptr] << "." << endl);
    2039                 configuration.BG->ConstructBondGraph(mol);
    2040                 mol->StoreAdjacencyToFile(NULL, argv[argptr]);
    2041                 argptr+=1;
    2042               }
    2043               break;
    2044 
    2045             case 'j':
    2046               if (ExitFlag == 0) ExitFlag = 1;
    2047               if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    2048                 ExitFlag =255;
    2049                 DoeLog(0) && (eLog()<< Verbose(0) << "Missing path of bonds file: -j <path>" << endl);
    2050                 performCriticalExit();
    2051               } else {
    2052                 DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << argv[argptr] << "." << endl);
    2053                 configuration.BG->ConstructBondGraph(mol);
    2054                 mol->StoreBondsToFile(NULL, argv[argptr]);
    2055                 argptr+=1;
    2056               }
    2057               break;
    2058 
    20591795            case 'N':
    20601796              if (ExitFlag == 0) ExitFlag = 1;
    20611797              if ((argptr+1 >= argc) || (argv[argptr+1][0] == '-')){
    20621798                ExitFlag = 255;
    2063                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for non-convex envelope: -o <radius> <tecplot output file>" << endl);
     1799                eLog() << Verbose(0) << "Not enough or invalid arguments given for non-convex envelope: -o <radius> <tecplot output file>" << endl;
    20641800                performCriticalExit();
    20651801              } else {
    … …  
    20691805                //string filename(argv[argptr+1]);
    20701806                //filename.append(".csv");
    2071                 DoLog(0) && (Log() << Verbose(0) << "Evaluating non-convex envelope of biggest molecule.");
    2072                 DoLog(1) && (Log() << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl);
     1807                Log() << Verbose(0) << "Evaluating non-convex envelope of biggest molecule.";
     1808                Log() << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl;
    20731809                // find biggest molecule
    20741810                int counter  = 0;
    … …  
    20801816                  counter++;
    20811817                }
    2082                 DoLog(1) && (Log() << Verbose(1) << "Biggest molecule has " << Boundary->AtomCount << " atoms." << endl);
     1818                Log() << Verbose(1) << "Biggest molecule has " << Boundary->AtomCount << " atoms." << endl;
    20831819                start = clock();
    20841820                LCList = new LinkedCell(Boundary, atof(argv[argptr])*2.);
    … …  
    20871823                //FindDistributionOfEllipsoids(T, &LCList, N, number, filename.c_str());
    20881824                end = clock();
    2089                 DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     1825                Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    20901826                delete(LCList);
    20911827                delete(T);
    … …  
    20971833              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    20981834                ExitFlag = 255;
    2099                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for storing tempature: -S <temperature file>" << endl);
     1835                eLog() << Verbose(0) << "Not enough or invalid arguments given for storing tempature: -S <temperature file>" << endl;
    21001836                performCriticalExit();
    21011837              } else {
    2102                 DoLog(1) && (Log() << Verbose(1) << "Storing temperatures in " << argv[argptr] << "." << endl);
     1838                Log() << Verbose(1) << "Storing temperatures in " << argv[argptr] << "." << endl;
    21031839                ofstream *output = new ofstream(argv[argptr], ios::trunc);
    21041840                if (!mol->OutputTemperatureFromTrajectories(output, 0, mol->MDSteps))
    2105                   DoLog(2) && (Log() << Verbose(2) << "File could not be written." << endl);
     1841                  Log() << Verbose(2) << "File could not be written." << endl;
    21061842                else
    2107                   DoLog(2) && (Log() << Verbose(2) << "File stored." << endl);
     1843                  Log() << Verbose(2) << "File stored." << endl;
    21081844                output->close();
    21091845                delete(output);
    … …  
    21151851              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    21161852                ExitFlag = 255;
    2117                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for storing tempature: -L <step0> <step1> <prefix> <identity mapping?>" << endl);
     1853                eLog() << Verbose(0) << "Not enough or invalid arguments given for storing tempature: -L <step0> <step1> <prefix> <identity mapping?>" << endl;
    21181854                performCriticalExit();
    21191855              } else {
    21201856                SaveFlag = true;
    2121                 DoLog(1) && (Log() << Verbose(1) << "Linear interpolation between configuration " << argv[argptr] << " and " << argv[argptr+1] << "." << endl);
     1857                Log() << Verbose(1) << "Linear interpolation between configuration " << argv[argptr] << " and " << argv[argptr+1] << "." << endl;
    21221858                if (atoi(argv[argptr+3]) == 1)
    2123                   DoLog(1) && (Log() << Verbose(1) << "Using Identity for the permutation map." << endl);
     1859                  Log() << Verbose(1) << "Using Identity for the permutation map." << endl;
    21241860                if (!mol->LinearInterpolationBetweenConfiguration(atoi(argv[argptr]), atoi(argv[argptr+1]), argv[argptr+2], configuration, atoi(argv[argptr+3])) == 1 ? true : false)
    2125                   DoLog(2) && (Log() << Verbose(2) << "Could not store " << argv[argptr+2] << " files." << endl);
     1861                  Log() << Verbose(2) << "Could not store " << argv[argptr+2] << " files." << endl;
    21261862                else
    2127                   DoLog(2) && (Log() << Verbose(2) << "Steps created and " << argv[argptr+2] << " files stored." << endl);
     1863                  Log() << Verbose(2) << "Steps created and " << argv[argptr+2] << " files stored." << endl;
    21281864                argptr+=4;
    21291865              }
    … …  
    21331869              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
    21341870                ExitFlag = 255;
    2135                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for parsing and integrating forces: -P <forces file>" << endl);
     1871                eLog() << Verbose(0) << "Not enough or invalid arguments given for parsing and integrating forces: -P <forces file>" << endl;
    21361872                performCriticalExit();
    21371873              } else {
    21381874                SaveFlag = true;
    2139                 DoLog(1) && (Log() << Verbose(1) << "Parsing forces file and Verlet integrating." << endl);
     1875                Log() << Verbose(1) << "Parsing forces file and Verlet integrating." << endl;
    21401876                if (!mol->VerletForceIntegration(argv[argptr], configuration))
    2141                   DoLog(2) && (Log() << Verbose(2) << "File not found." << endl);
     1877                  Log() << Verbose(2) << "File not found." << endl;
    21421878                else
    2143                   DoLog(2) && (Log() << Verbose(2) << "File found and parsed." << endl);
     1879                  Log() << Verbose(2) << "File found and parsed." << endl;
    21441880                argptr+=1;
    21451881              }
    … …  
    21491885              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])))  {
    21501886                ExitFlag = 255;
    2151                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for removing atoms: -R <id> <distance>" << endl);
     1887                eLog() << Verbose(0) << "Not enough or invalid arguments given for removing atoms: -R <id> <distance>" << endl;
    21521888                performCriticalExit();
    21531889              } else {
    21541890                SaveFlag = true;
    2155                 DoLog(1) && (Log() << Verbose(1) << "Removing atoms around " << argv[argptr] << " with radius " << argv[argptr+1] << "." << endl);
     1891                Log() << Verbose(1) << "Removing atoms around " << argv[argptr] << " with radius " << argv[argptr+1] << "." << endl;
    21561892                double tmp1 = atof(argv[argptr+1]);
    21571893                atom *third = mol->FindAtom(atoi(argv[argptr]));
    … …  
    21661902                  }
    21671903                } else {
    2168                   DoeLog(1) && (eLog()<< Verbose(1) << "Removal failed due to missing atoms on molecule or wrong id." << endl);
     1904                  eLog() << Verbose(1) << "Removal failed due to missing atoms on molecule or wrong id." << endl;
    21691905                }
    21701906                argptr+=2;
    … …  
    21751911              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    21761912                ExitFlag = 255;
    2177                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for translation: -t <x> <y> <z>" << endl);
     1913                eLog() << Verbose(0) << "Not enough or invalid arguments given for translation: -t <x> <y> <z>" << endl;
    21781914                performCriticalExit();
    21791915              } else {
    21801916                if (ExitFlag == 0) ExitFlag = 1;
    21811917                SaveFlag = true;
    2182                 DoLog(1) && (Log() << Verbose(1) << "Translating all ions by given vector." << endl);
     1918                Log() << Verbose(1) << "Translating all ions by given vector." << endl;
    21831919                for (int i=NDIM;i--;)
    21841920                  x.x[i] = atof(argv[argptr+i]);
    … …  
    21911927              if ((argptr+2 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    21921928                ExitFlag = 255;
    2193                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for periodic translation: -T <x> <y> <z>" << endl);
     1929                eLog() << Verbose(0) << "Not enough or invalid arguments given for periodic translation: -T <x> <y> <z>" << endl;
    21941930                performCriticalExit();
    21951931              } else {
    21961932                if (ExitFlag == 0) ExitFlag = 1;
    21971933                SaveFlag = true;
    2198                 DoLog(1) && (Log() << Verbose(1) << "Translating all ions periodically by given vector." << endl);
     1934                Log() << Verbose(1) << "Translating all ions periodically by given vector." << endl;
    21991935                for (int i=NDIM;i--;)
    22001936                  x.x[i] = atof(argv[argptr+i]);
    … …  
    22071943              if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    22081944                ExitFlag = 255;
    2209                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for scaling: -s <factor_x> [factor_y] [factor_z]" << endl);
     1945                eLog() << Verbose(0) << "Not enough or invalid arguments given for scaling: -s <factor_x> [factor_y] [factor_z]" << endl;
    22101946                performCriticalExit();
    22111947              } else {
    22121948                SaveFlag = true;
    22131949                j = -1;
    2214                 DoLog(1) && (Log() << Verbose(1) << "Scaling all ion positions by factor." << endl);
     1950                Log() << Verbose(1) << "Scaling all ion positions by factor." << endl;
    22151951                factor = new double[NDIM];
    22161952                factor[0] = atof(argv[argptr]);
    … …  
    22181954                factor[2] = atof(argv[argptr+2]);
    22191955                mol->Scale((const double ** const)&factor);
    2220                 double * const cell_size = World::get()->cell_size;
    22211956                for (int i=0;i<NDIM;i++) {
    22221957                  j += i+1;
    22231958                  x.x[i] = atof(argv[NDIM+i]);
    2224                   cell_size[j]*=factor[i];
     1959                  mol->cell_size[j]*=factor[i];
    22251960                }
    22261961                delete[](factor);
    … …  
    22321967              if ((argptr+5 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
    22331968                ExitFlag = 255;
    2234                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for centering in box: -b <xx> <xy> <xz> <yy> <yz> <zz>" << endl);
     1969                eLog() << Verbose(0) << "Not enough or invalid arguments given for centering in box: -b <xx> <xy> <xz> <yy> <yz> <zz>" << endl;
    22351970                performCriticalExit();
    22361971              } else {
    22371972                SaveFlag = true;
    22381973                j = -1;
    2239                 DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl);
    2240                 double * const cell_size = World::get()->cell_size;
     1974                Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
    22411975                for (int i=0;i<6;i++) {
    2242                   cell_size[i] = atof(argv[argptr+i]);
     1976                  mol->cell_size[i] = atof(argv[argptr+i]);
    22431977                }
    22441978                // center
    … …  
    22511985              if ((argptr+5 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
    22521986                ExitFlag = 255;
    2253                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for bounding in box: -B <xx> <xy> <xz> <yy> <yz> <zz>" << endl);
     1987                eLog() << Verbose(0) << "Not enough or invalid arguments given for bounding in box: -B <xx> <xy> <xz> <yy> <yz> <zz>" << endl;
    22541988                performCriticalExit();
    22551989              } else {
    22561990                SaveFlag = true;
    22571991                j = -1;
    2258                 DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl);
    2259                 double * const cell_size = World::get()->cell_size;
     1992                Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
    22601993                for (int i=0;i<6;i++) {
    2261                   cell_size[i] = atof(argv[argptr+i]);
     1994                  mol->cell_size[i] = atof(argv[argptr+i]);
    22621995                }
    22631996                // center
    … …  
    22702003              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    22712004                ExitFlag = 255;
    2272                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for centering with boundary: -c <boundary_x> <boundary_y> <boundary_z>" << endl);
     2005                eLog() << Verbose(0) << "Not enough or invalid arguments given for centering with boundary: -c <boundary_x> <boundary_y> <boundary_z>" << endl;
    22732006                performCriticalExit();
    22742007              } else {
    22752008                SaveFlag = true;
    22762009                j = -1;
    2277                 DoLog(1) && (Log() << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl);
     2010                Log() << Verbose(1) << "Centering atoms in config file within given additional boundary." << endl;
    22782011                // make every coordinate positive
    22792012                mol->CenterEdge(&x);
    … …  
    22812014                mol->SetBoxDimension(&x);
    22822015                // translate each coordinate by boundary
    2283                 double * const cell_size = World::get()->cell_size;
    22842016                j=-1;
    22852017                for (int i=0;i<NDIM;i++) {
    22862018                  j += i+1;
    22872019                  x.x[i] = atof(argv[argptr+i]);
    2288                   cell_size[j] += x.x[i]*2.;
     2020                  mol->cell_size[j] += x.x[i]*2.;
    22892021                }
    22902022                mol->Translate((const Vector *)&x);
    … …  
    22952027              if (ExitFlag == 0) ExitFlag = 1;
    22962028              SaveFlag = true;
    2297               DoLog(1) && (Log() << Verbose(1) << "Centering atoms on edge and setting box dimensions." << endl);
     2029              Log() << Verbose(1) << "Centering atoms on edge and setting box dimensions." << endl;
    22982030              x.Zero();
    22992031              mol->CenterEdge(&x);
    … …  
    23052037              if ((argptr >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])))  {
    23062038                ExitFlag = 255;
    2307                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for removing atoms: -r <id>" << endl);
     2039                eLog() << Verbose(0) << "Not enough or invalid arguments given for removing atoms: -r <id>" << endl;
    23082040                performCriticalExit();
    23092041              } else {
    23102042                SaveFlag = true;
    2311                 DoLog(1) && (Log() << Verbose(1) << "Removing atom " << argv[argptr] << "." << endl);
     2043                Log() << Verbose(1) << "Removing atom " << argv[argptr] << "." << endl;
    23122044                atom *first = mol->FindAtom(atoi(argv[argptr]));
    23132045                mol->RemoveAtom(first);
    … …  
    23192051              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1]))) {
    23202052                ExitFlag = 255;
    2321                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl);
     2053                eLog() << Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl;
    23222054                performCriticalExit();
    23232055              } else {
    2324                 DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << argv[argptr] << " angstroem, order of " << argv[argptr+1] << "." << endl);
    2325                 DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
     2056                Log() << Verbose(0) << "Fragmenting molecule with bond distance " << argv[argptr] << " angstroem, order of " << argv[argptr+1] << "." << endl;
     2057                Log() << Verbose(0) << "Creating connection matrix..." << endl;
    23262058                start = clock();
    23272059                mol->CreateAdjacencyList(atof(argv[argptr++]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
    2328                 DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
     2060                Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
    23292061                if (mol->first->next != mol->last) {
    23302062                  ExitFlag = mol->FragmentMolecule(atoi(argv[argptr]), &configuration);
    23312063                }
    23322064                end = clock();
    2333                 DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     2065                Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    23342066                argptr+=2;
    23352067              }
    … …  
    23392071              j = atoi(argv[argptr++]);
    23402072              if ((j<0) || (j>1)) {
    2341                 DoeLog(1) && (eLog()<< Verbose(1) << "Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl);
     2073                eLog() << Verbose(1) << "Argument of '-m' should be either 0 for no-rotate or 1 for rotate." << endl;
    23422074                j = 0;
    23432075              }
    23442076              if (j) {
    23452077                SaveFlag = true;
    2346                 DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
     2078                Log() << Verbose(0) << "Converting to prinicipal axis system." << endl;
    23472079              } else
    2348                 DoLog(0) && (Log() << Verbose(0) << "Evaluating prinicipal axis." << endl);
     2080                Log() << Verbose(0) << "Evaluating prinicipal axis." << endl;
    23492081              mol->PrincipalAxisSystem((bool)j);
    23502082              break;
    … …  
    23532085              if ((argptr+1 >= argc) || (argv[argptr][0] == '-')){
    23542086                ExitFlag = 255;
    2355                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for convex envelope: -o <convex output file> <non-convex output file>" << endl);
     2087                eLog() << Verbose(0) << "Not enough or invalid arguments given for convex envelope: -o <convex output file> <non-convex output file>" << endl;
    23562088                performCriticalExit();
    23572089              } else {
    23582090                class Tesselation *TesselStruct = NULL;
    23592091                const LinkedCell *LCList = NULL;
    2360                 DoLog(0) && (Log() << Verbose(0) << "Evaluating volume of the convex envelope.");
    2361                 DoLog(1) && (Log() << Verbose(1) << "Storing tecplot convex data in " << argv[argptr] << "." << endl);
    2362                 DoLog(1) && (Log() << Verbose(1) << "Storing tecplot non-convex data in " << argv[argptr+1] << "." << endl);
     2092                Log() << Verbose(0) << "Evaluating volume of the convex envelope.";
     2093                Log() << Verbose(1) << "Storing tecplot convex data in " << argv[argptr] << "." << endl;
     2094                Log() << Verbose(1) << "Storing tecplot non-convex data in " << argv[argptr+1] << "." << endl;
    23632095                LCList = new LinkedCell(mol, 10.);
    23642096                //FindConvexBorder(mol, LCList, argv[argptr]);
    … …  
    23672099                double volumedifference = ConvexizeNonconvexEnvelope(TesselStruct, mol, argv[argptr]);
    23682100                double clustervolume = VolumeOfConvexEnvelope(TesselStruct, &configuration);
    2369                 DoLog(0) && (Log() << Verbose(0) << "The tesselated volume area is " << clustervolume << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl);
    2370                 DoLog(0) && (Log() << Verbose(0) << "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl);
     2101                Log() << Verbose(0) << "The tesselated volume area is " << clustervolume << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
     2102                Log() << Verbose(0) << "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
    23712103                delete(TesselStruct);
    23722104                delete(LCList);
    … …  
    23782110              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) ) {
    23792111                ExitFlag = 255;
    2380                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for suspension with specified volume: -U <volume> <density>" << endl);
     2112                eLog() << Verbose(0) << "Not enough or invalid arguments given for suspension with specified volume: -U <volume> <density>" << endl;
    23812113                performCriticalExit();
    23822114              } else {
    23832115                volume = atof(argv[argptr++]);
    2384                 DoLog(0) && (Log() << Verbose(0) << "Using " << volume << " angstrom^3 as the volume instead of convex envelope one's." << endl);
     2116                Log() << Verbose(0) << "Using " << volume << " angstrom^3 as the volume instead of convex envelope one's." << endl;
    23852117              }
    23862118            case 'u':
    … …  
    23892121                if (volume != -1)
    23902122                  ExitFlag = 255;
    2391                   DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for suspension: -u <density>" << endl);
     2123                  eLog() << Verbose(0) << "Not enough or invalid arguments given for suspension: -u <density>" << endl;
    23922124                  performCriticalExit();
    23932125              } else {
    23942126                double density;
    23952127                SaveFlag = true;
    2396                 DoLog(0) && (Log() << Verbose(0) << "Evaluating necessary cell volume for a cluster suspended in water.");
     2128                Log() << Verbose(0) << "Evaluating necessary cell volume for a cluster suspended in water.";
    23972129                density = atof(argv[argptr++]);
    23982130                if (density < 1.0) {
    2399                   DoeLog(1) && (eLog()<< Verbose(1) << "Density must be greater than 1.0g/cm^3 !" << endl);
     2131                  eLog() << Verbose(1) << "Density must be greater than 1.0g/cm^3 !" << endl;
    24002132                  density = 1.3;
    24012133                }
    … …  
    24032135//                  repetition[i] = atoi(argv[argptr++]);
    24042136//                  if (repetition[i] < 1)
    2405 //                    DoeLog(1) && (eLog()<< Verbose(1) << "repetition value must be greater 1!" << endl);
     2137//                    eLog() << Verbose(1) << "repetition value must be greater 1!" << endl;
    24062138//                  repetition[i] = 1;
    24072139//                }
    … …  
    24132145              if ((argptr+2 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) ) {
    24142146                ExitFlag = 255;
    2415                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for repeating cells: -d <repeat_x> <repeat_y> <repeat_z>" << endl);
     2147                eLog() << Verbose(0) << "Not enough or invalid arguments given for repeating cells: -d <repeat_x> <repeat_y> <repeat_z>" << endl;
    24162148                performCriticalExit();
    24172149              } else {
    24182150                SaveFlag = true;
    2419                 double * const cell_size = World::get()->cell_size;
    24202151                for (int axis = 1; axis <= NDIM; axis++) {
    24212152                  int faktor = atoi(argv[argptr++]);
    … …  
    24242155                  Vector ** vectors;
    24252156                  if (faktor < 1) {
    2426                     DoeLog(1) && (eLog()<< Verbose(1) << "Repetition factor mus be greater than 1!" << endl);
     2157                    eLog() << Verbose(1) << "Repetition factor mus be greater than 1!" << endl;
    24272158                    faktor = 1;
    24282159                  }
    … …  
    24412172                    }
    24422173                    if (count != j)
    2443                       DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
     2174                      eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
    24442175                    x.Zero();
    24452176                    y.Zero();
    2446                     y.x[abs(axis)-1] = cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
     2177                    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
    24472178                    for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
    24482179                      x.AddVector(&y); // per factor one cell width further
    … …  
    24652196                      mol->Translate(&x);
    24662197                    }
    2467                     cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
     2198                    mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
    24682199                  }
    24692200                }
    … …  
    24822213  } else {  // no arguments, hence scan the elements db
    24832214    if (periode->LoadPeriodentafel(configuration.databasepath))
    2484       DoLog(0) && (Log() << Verbose(0) << "Element list loaded successfully." << endl);
     2215      Log() << Verbose(0) << "Element list loaded successfully." << endl;
    24852216    else
    2486       DoLog(0) && (Log() << Verbose(0) << "Element list loading failed." << endl);
     2217      Log() << Verbose(0) << "Element list loading failed." << endl;
    24872218    configuration.RetrieveConfigPathAndName("main_pcp_linux");
    24882219  }
    … …  
    25072238
    25082239  cout << ESPACKVersion << endl;
    2509 
    2510   DoLog(1) && (Log() << Verbose(1) << "test" << endl);
    2511   DoLog(3) && (Log() << Verbose(1) << "test");
    25122240
    25132241  setVerbosity(0);
    … …  
    25372265  if (molecules->ListOfMolecules.size() == 0) {
    25382266    mol = new molecule(periode);
    2539     double * const cell_size = World::get()->cell_size;
    2540     if (cell_size[0] == 0.) {
    2541       DoLog(0) && (Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl);
     2267    if (mol->cell_size[0] == 0.) {
     2268      Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
    25422269      for (int i=0;i<6;i++) {
    2543         DoLog(1) && (Log() << Verbose(1) << "Cell size" << i << ": ");
    2544         cin >> cell_size[i];
     2270        Log() << Verbose(1) << "Cell size" << i << ": ";
     2271        cin >> mol->cell_size[i];
    25452272      }
    25462273    }
    … …  
    25522279
    25532280  // now the main construction loop
    2554   DoLog(0) && (Log() << Verbose(0) << endl << "Now comes the real construction..." << endl);
     2281  Log() << Verbose(0) << endl << "Now comes the real construction..." << endl;
    25552282  do {
    2556     DoLog(0) && (Log() << Verbose(0) << endl << endl);
    2557     DoLog(0) && (Log() << Verbose(0) << "============Molecule list=======================" << endl);
     2283    Log() << Verbose(0) << endl << endl;
     2284    Log() << Verbose(0) << "============Molecule list=======================" << endl;
    25582285    molecules->Enumerate((ofstream *)&cout);
    2559     DoLog(0) && (Log() << Verbose(0) << "============Menu===============================" << endl);
    2560     DoLog(0) && (Log() << Verbose(0) << "a - set molecule (in)active" << endl);
    2561     DoLog(0) && (Log() << Verbose(0) << "e - edit molecules (load, parse, save)" << endl);
    2562     DoLog(0) && (Log() << Verbose(0) << "g - globally manipulate atoms in molecule" << endl);
    2563     DoLog(0) && (Log() << Verbose(0) << "M - Merge molecules" << endl);
    2564     DoLog(0) && (Log() << Verbose(0) << "m - manipulate atoms" << endl);
    2565     DoLog(0) && (Log() << Verbose(0) << "-----------------------------------------------" << endl);
    2566     DoLog(0) && (Log() << Verbose(0) << "c - edit the current configuration" << endl);
    2567     DoLog(0) && (Log() << Verbose(0) << "-----------------------------------------------" << endl);
    2568     DoLog(0) && (Log() << Verbose(0) << "s - save current setup to config file" << endl);
    2569     DoLog(0) && (Log() << Verbose(0) << "T - call the current test routine" << endl);
    2570     DoLog(0) && (Log() << Verbose(0) << "q - quit" << endl);
    2571     DoLog(0) && (Log() << Verbose(0) << "===============================================" << endl);
    2572     DoLog(0) && (Log() << Verbose(0) << "Input: ");
     2286    Log() << Verbose(0) << "============Menu===============================" << endl;
     2287    Log() << Verbose(0) << "a - set molecule (in)active" << endl;
     2288    Log() << Verbose(0) << "e - edit molecules (load, parse, save)" << endl;
     2289    Log() << Verbose(0) << "g - globally manipulate atoms in molecule" << endl;
     2290    Log() << Verbose(0) << "M - Merge molecules" << endl;
     2291    Log() << Verbose(0) << "m - manipulate atoms" << endl;
     2292    Log() << Verbose(0) << "-----------------------------------------------" << endl;
     2293    Log() << Verbose(0) << "c - edit the current configuration" << endl;
     2294    Log() << Verbose(0) << "-----------------------------------------------" << endl;
     2295    Log() << Verbose(0) << "s - save current setup to config file" << endl;
     2296    Log() << Verbose(0) << "T - call the current test routine" << endl;
     2297    Log() << Verbose(0) << "q - quit" << endl;
     2298    Log() << Verbose(0) << "===============================================" << endl;
     2299    Log() << Verbose(0) << "Input: ";
    25732300    cin >> choice;
    25742301
    … …  
    25762303      case 'a':  // (in)activate molecule
    25772304        {
    2578           DoLog(0) && (Log() << Verbose(0) << "Enter index of molecule: ");
     2305          Log() << Verbose(0) << "Enter index of molecule: ";
    25792306          cin >> j;
    25802307          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    … …  
    26222349  // save element data base
    26232350  if (periode->StorePeriodentafel(configuration->databasepath)) //ElementsFileName
    2624     DoLog(0) && (Log() << Verbose(0) << "Saving of elements.db successful." << endl);
     2351    Log() << Verbose(0) << "Saving of elements.db successful." << endl;
    26252352  else
    2626     DoLog(0) && (Log() << Verbose(0) << "Saving of elements.db failed." << endl);
     2353    Log() << Verbose(0) << "Saving of elements.db failed." << endl;
    26272354
    26282355  delete(molecules); // also free's all molecules contained
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