Changeset 85bc8e


Ignore:
Timestamp:
Dec 16, 2009, 12:30:16 PM (15 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
992a54
Parents:
c5f836
git-author:
Tillmann Crueger <crueger@…> (12/02/09 16:26:24)
git-committer:
Frederik Heber <heber@…> (12/16/09 12:30:16)
Message:

Started refactoring of the menu. - Created new menu class - moved all menu functions inside menu class Signed-off-by: Tillmann Crueger <crueger@…>

Files:
2 added
3 edited

Legend:

Unmodified
Added
Removed

  • doc/Doxyfile

    rc5f836 r85bc8e  
    125125# configuration options related to source browsing
    126126#---------------------------------------------------------------------------
    127 SOURCE_BROWSER         = NO
     127SOURCE_BROWSER         = YES
    128128INLINE_SOURCES         = NO
    129129STRIP_CODE_COMMENTS    = YES

  • src/Makefile.am

    rc5f836 r85bc8e  
    55ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
    66
    7 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
    8 HEADER = ${ANALYSISHEADER} ${ATOMHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
     7SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp menu.cpp
     8HEADER = ${ANALYSISHEADER} ${ATOMHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp menu.hpp
    99
    1010BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

  • src/builder.cpp

    rc5f836 r85bc8e  
    6565#include "molecule.hpp"
    6666#include "periodentafel.hpp"
    67 
    68 /********************************************* Subsubmenu routine ************************************/
    69 
    70 /** Submenu for adding atoms to the molecule.
    71  * \param *periode periodentafel
    72  * \param *molecule molecules with atoms
    73  */
    74 static void AddAtoms(periodentafel *periode, molecule *mol)
    75 {
    76   atom *first, *second, *third, *fourth;
    77   Vector **atoms;
    78   Vector x,y,z,n;  // coordinates for absolute point in cell volume
    79   double a,b,c;
    80   char choice;  // menu choice char
    81   bool valid;
    82 
    83   Log() << Verbose(0) << "===========ADD ATOM============================" << endl;
    84   Log() << Verbose(0) << " a - state absolute coordinates of atom" << endl;
    85   Log() << Verbose(0) << " b - state relative coordinates of atom wrt to reference point" << endl;
    86   Log() << Verbose(0) << " c - state relative coordinates of atom wrt to already placed atom" << endl;
    87   Log() << Verbose(0) << " d - state two atoms, two angles and a distance" << endl;
    88   Log() << Verbose(0) << " e - least square distance position to a set of atoms" << endl;
    89   Log() << Verbose(0) << "all else - go back" << endl;
    90   Log() << Verbose(0) << "===============================================" << endl;
    91   Log() << Verbose(0) << "Note: Specifiy angles in degrees not multiples of Pi!" << endl;
    92   Log() << Verbose(0) << "INPUT: ";
    93   cin >> choice;
    94 
    95   switch (choice) {
    96     default:
    97       eLog() << Verbose(2) << "Not a valid choice." << endl;
    98       break;
    99       case 'a': // absolute coordinates of atom
    100         Log() << Verbose(0) << "Enter absolute coordinates." << endl;
    101         first = new atom;
    102         first->x.AskPosition(mol->cell_size, false);
    103         first->type = periode->AskElement();  // give type
    104         mol->AddAtom(first);  // add to molecule
    105         break;
    106 
    107       case 'b': // relative coordinates of atom wrt to reference point
    108         first = new atom;
    109         valid = true;
    110         do {
    111           if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
    112           Log() << Verbose(0) << "Enter reference coordinates." << endl;
    113           x.AskPosition(mol->cell_size, true);
    114           Log() << Verbose(0) << "Enter relative coordinates." << endl;
    115           first->x.AskPosition(mol->cell_size, false);
    116           first->x.AddVector((const Vector *)&x);
    117           Log() << Verbose(0) << "\n";
    118         } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
    119         first->type = periode->AskElement();  // give type
    120         mol->AddAtom(first);  // add to molecule
    121         break;
    122 
    123       case 'c': // relative coordinates of atom wrt to already placed atom
    124         first = new atom;
    125         valid = true;
    126         do {
    127           if (!valid) eLog() << Verbose(2) << "Resulting position out of cell." << endl;
    128           second = mol->AskAtom("Enter atom number: ");
    129           Log() << Verbose(0) << "Enter relative coordinates." << endl;
    130           first->x.AskPosition(mol->cell_size, false);
    131           for (int i=NDIM;i--;) {
    132             first->x.x[i] += second->x.x[i];
    133           }
    134         } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
    135         first->type = periode->AskElement();  // give type
    136         mol->AddAtom(first);  // add to molecule
    137         break;
    138 
    139     case 'd': // two atoms, two angles and a distance
    140         first = new atom;
    141         valid = true;
    142         do {
    143           if (!valid) {
    144             eLog() << Verbose(2) << "Resulting coordinates out of cell - " << first->x << endl;
    145           }
    146           Log() << Verbose(0) << "First, we need two atoms, the first atom is the central, while the second is the outer one." << endl;
    147           second = mol->AskAtom("Enter central atom: ");
    148           third = mol->AskAtom("Enter second atom (specifying the axis for first angle): ");
    149           fourth = mol->AskAtom("Enter third atom (specifying a plane for second angle): ");
    150           a = ask_value("Enter distance between central (first) and new atom: ");
    151           b = ask_value("Enter angle between new, first and second atom (degrees): ");
    152           b *= M_PI/180.;
    153           bound(&b, 0., 2.*M_PI);
    154           c = ask_value("Enter second angle between new and normal vector of plane defined by first, second and third atom (degrees): ");
    155           c *= M_PI/180.;
    156           bound(&c, -M_PI, M_PI);
    157           Log() << Verbose(0) << "radius: " << a << "\t phi: " << b*180./M_PI << "\t theta: " << c*180./M_PI << endl;
    158 /*
    159           second->Output(1,1,(ofstream *)&cout);
    160           third->Output(1,2,(ofstream *)&cout);
    161           fourth->Output(1,3,(ofstream *)&cout);
    162           n.MakeNormalvector((const vector *)&second->x, (const vector *)&third->x, (const vector *)&fourth->x);
    163           x.Copyvector(&second->x);
    164           x.SubtractVector(&third->x);
    165           x.Copyvector(&fourth->x);
    166           x.SubtractVector(&third->x);
    167 
    168           if (!z.SolveSystem(&x,&y,&n, b, c, a)) {
    169             Log() << Verbose(0) << "Failure solving self-dependent linear system!" << endl;
    170             continue;
    171           }
    172           Log() << Verbose(0) << "resulting relative coordinates: ";
    173           z.Output();
    174           Log() << Verbose(0) << endl;
    175           */
    176           // calc axis vector
    177           x.CopyVector(&second->x);
    178           x.SubtractVector(&third->x);
    179           x.Normalize();
    180           Log() << Verbose(0) << "x: ",
    181           x.Output();
    182           Log() << Verbose(0) << endl;
    183           z.MakeNormalVector(&second->x,&third->x,&fourth->x);
    184           Log() << Verbose(0) << "z: ",
    185           z.Output();
    186           Log() << Verbose(0) << endl;
    187           y.MakeNormalVector(&x,&z);
    188           Log() << Verbose(0) << "y: ",
    189           y.Output();
    190           Log() << Verbose(0) << endl;
    191 
    192           // rotate vector around first angle
    193           first->x.CopyVector(&x);
    194           first->x.RotateVector(&z,b - M_PI);
    195           Log() << Verbose(0) << "Rotated vector: ",
    196           first->x.Output();
    197           Log() << Verbose(0) << endl;
    198           // remove the projection onto the rotation plane of the second angle
    199           n.CopyVector(&y);
    200           n.Scale(first->x.ScalarProduct(&y));
    201           Log() << Verbose(0) << "N1: ",
    202           n.Output();
    203           Log() << Verbose(0) << endl;
    204           first->x.SubtractVector(&n);
    205           Log() << Verbose(0) << "Subtracted vector: ",
    206           first->x.Output();
    207           Log() << Verbose(0) << endl;
    208           n.CopyVector(&z);
    209           n.Scale(first->x.ScalarProduct(&z));
    210           Log() << Verbose(0) << "N2: ",
    211           n.Output();
    212           Log() << Verbose(0) << endl;
    213           first->x.SubtractVector(&n);
    214           Log() << Verbose(0) << "2nd subtracted vector: ",
    215           first->x.Output();
    216           Log() << Verbose(0) << endl;
    217 
    218           // rotate another vector around second angle
    219           n.CopyVector(&y);
    220           n.RotateVector(&x,c - M_PI);
    221           Log() << Verbose(0) << "2nd Rotated vector: ",
    222           n.Output();
    223           Log() << Verbose(0) << endl;
    224 
    225           // add the two linear independent vectors
    226           first->x.AddVector(&n);
    227           first->x.Normalize();
    228           first->x.Scale(a);
    229           first->x.AddVector(&second->x);
    230 
    231           Log() << Verbose(0) << "resulting coordinates: ";
    232           first->x.Output();
    233           Log() << Verbose(0) << endl;
    234         } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
    235         first->type = periode->AskElement();  // give type
    236         mol->AddAtom(first);  // add to molecule
    237         break;
    238 
    239       case 'e': // least square distance position to a set of atoms
    240         first = new atom;
    241         atoms = new (Vector*[128]);
    242         valid = true;
    243         for(int i=128;i--;)
    244           atoms[i] = NULL;
    245         int i=0, j=0;
    246         Log() << Verbose(0) << "Now we need at least three molecules.\n";
    247         do {
    248           Log() << Verbose(0) << "Enter " << i+1 << "th atom: ";
    249           cin >> j;
    250           if (j != -1) {
    251             second = mol->FindAtom(j);
    252             atoms[i++] = &(second->x);
    253           }
    254         } while ((j != -1) && (i<128));
    255         if (i >= 2) {
    256           first->x.LSQdistance((const Vector **)atoms, i);
    257 
    258           first->x.Output();
    259           first->type = periode->AskElement();  // give type
    260           mol->AddAtom(first);  // add to molecule
    261         } else {
    262           delete first;
    263           Log() << Verbose(0) << "Please enter at least two vectors!\n";
    264         }
    265         break;
    266   };
    267 };
    268 
    269 /** Submenu for centering the atoms in the molecule.
    270  * \param *mol molecule with all the atoms
    271  */
    272 static void CenterAtoms(molecule *mol)
    273 {
    274   Vector x, y, helper;
    275   char choice;  // menu choice char
    276 
    277   Log() << Verbose(0) << "===========CENTER ATOMS=========================" << endl;
    278   Log() << Verbose(0) << " a - on origin" << endl;
    279   Log() << Verbose(0) << " b - on center of gravity" << endl;
    280   Log() << Verbose(0) << " c - within box with additional boundary" << endl;
    281   Log() << Verbose(0) << " d - within given simulation box" << endl;
    282   Log() << Verbose(0) << "all else - go back" << endl;
    283   Log() << Verbose(0) << "===============================================" << endl;
    284   Log() << Verbose(0) << "INPUT: ";
    285   cin >> choice;
    286 
    287   switch (choice) {
    288     default:
    289       Log() << Verbose(0) << "Not a valid choice." << endl;
    290       break;
    291     case 'a':
    292       Log() << Verbose(0) << "Centering atoms in config file on origin." << endl;
    293       mol->CenterOrigin();
    294       break;
    295     case 'b':
    296       Log() << Verbose(0) << "Centering atoms in config file on center of gravity." << endl;
    297       mol->CenterPeriodic();
    298       break;
    299     case 'c':
    300       Log() << Verbose(0) << "Centering atoms in config file within given additional boundary." << endl;
    301       for (int i=0;i<NDIM;i++) {
    302         Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
    303         cin >> y.x[i];
    304       }
    305       mol->CenterEdge(&x);  // make every coordinate positive
    306       mol->Center.AddVector(&y); // translate by boundary
    307       helper.CopyVector(&y);
    308       helper.Scale(2.);
    309       helper.AddVector(&x);
    310       mol->SetBoxDimension(&helper);  // update Box of atoms by boundary
    311       break;
    312     case 'd':
    313       Log() << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
    314       for (int i=0;i<NDIM;i++) {
    315         Log() << Verbose(0) << "Enter axis " << i << " boundary: ";
    316         cin >> x.x[i];
    317       }
    318       // update Box of atoms by boundary
    319       mol->SetBoxDimension(&x);
    320       // center
    321       mol->CenterInBox();
    322       break;
    323   }
    324 };
    325 
    326 /** Submenu for aligning the atoms in the molecule.
    327  * \param *periode periodentafel
    328  * \param *mol molecule with all the atoms
    329  */
    330 static void AlignAtoms(periodentafel *periode, molecule *mol)
    331 {
    332   atom *first, *second, *third;
    333   Vector x,n;
    334   char choice;  // menu choice char
    335 
    336   Log() << Verbose(0) << "===========ALIGN ATOMS=========================" << endl;
    337   Log() << Verbose(0) << " a - state three atoms defining align plane" << endl;
    338   Log() << Verbose(0) << " b - state alignment vector" << endl;
    339   Log() << Verbose(0) << " c - state two atoms in alignment direction" << endl;
    340   Log() << Verbose(0) << " d - align automatically by least square fit" << endl;
    341   Log() << Verbose(0) << "all else - go back" << endl;
    342   Log() << Verbose(0) << "===============================================" << endl;
    343   Log() << Verbose(0) << "INPUT: ";
    344   cin >> choice;
    345 
    346   switch (choice) {
    347     default:
    348     case 'a': // three atoms defining mirror plane
    349       first = mol->AskAtom("Enter first atom: ");
    350       second = mol->AskAtom("Enter second atom: ");
    351       third = mol->AskAtom("Enter third atom: ");
    352 
    353       n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
    354       break;
    355     case 'b': // normal vector of mirror plane
    356       Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
    357       n.AskPosition(mol->cell_size,0);
    358       n.Normalize();
    359       break;
    360     case 'c': // three atoms defining mirror plane
    361       first = mol->AskAtom("Enter first atom: ");
    362       second = mol->AskAtom("Enter second atom: ");
    363 
    364       n.CopyVector((const Vector *)&first->x);
    365       n.SubtractVector((const Vector *)&second->x);
    366       n.Normalize();
    367       break;
    368     case 'd':
    369       char shorthand[4];
    370       Vector a;
    371       struct lsq_params param;
    372       do {
    373         fprintf(stdout, "Enter the element of atoms to be chosen: ");
    374         fscanf(stdin, "%3s", shorthand);
    375       } while ((param.type = periode->FindElement(shorthand)) == NULL);
    376       Log() << Verbose(0) << "Element is " << param.type->name << endl;
    377       mol->GetAlignvector(&param);
    378       for (int i=NDIM;i--;) {
    379         x.x[i] = gsl_vector_get(param.x,i);
    380         n.x[i] = gsl_vector_get(param.x,i+NDIM);
    381       }
    382       gsl_vector_free(param.x);
    383       Log() << Verbose(0) << "Offset vector: ";
    384       x.Output();
    385       Log() << Verbose(0) << endl;
    386       n.Normalize();
    387       break;
    388   };
    389   Log() << Verbose(0) << "Alignment vector: ";
    390   n.Output();
    391   Log() << Verbose(0) << endl;
    392   mol->Align(&n);
    393 };
    394 
    395 /** Submenu for mirroring the atoms in the molecule.
    396  * \param *mol molecule with all the atoms
    397  */
    398 static void MirrorAtoms(molecule *mol)
    399 {
    400   atom *first, *second, *third;
    401   Vector n;
    402   char choice;  // menu choice char
    403 
    404   Log() << Verbose(0) << "===========MIRROR ATOMS=========================" << endl;
    405   Log() << Verbose(0) << " a - state three atoms defining mirror plane" << endl;
    406   Log() << Verbose(0) << " b - state normal vector of mirror plane" << endl;
    407   Log() << Verbose(0) << " c - state two atoms in normal direction" << endl;
    408   Log() << Verbose(0) << "all else - go back" << endl;
    409   Log() << Verbose(0) << "===============================================" << endl;
    410   Log() << Verbose(0) << "INPUT: ";
    411   cin >> choice;
    412 
    413   switch (choice) {
    414     default:
    415     case 'a': // three atoms defining mirror plane
    416       first = mol->AskAtom("Enter first atom: ");
    417       second = mol->AskAtom("Enter second atom: ");
    418       third = mol->AskAtom("Enter third atom: ");
    419 
    420       n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
    421       break;
    422     case 'b': // normal vector of mirror plane
    423       Log() << Verbose(0) << "Enter normal vector of mirror plane." << endl;
    424       n.AskPosition(mol->cell_size,0);
    425       n.Normalize();
    426       break;
    427     case 'c': // three atoms defining mirror plane
    428       first = mol->AskAtom("Enter first atom: ");
    429       second = mol->AskAtom("Enter second atom: ");
    430 
    431       n.CopyVector((const Vector *)&first->x);
    432       n.SubtractVector((const Vector *)&second->x);
    433       n.Normalize();
    434       break;
    435   };
    436   Log() << Verbose(0) << "Normal vector: ";
    437   n.Output();
    438   Log() << Verbose(0) << endl;
    439   mol->Mirror((const Vector *)&n);
    440 };
    441 
    442 /** Submenu for removing the atoms from the molecule.
    443  * \param *mol molecule with all the atoms
    444  */
    445 static void RemoveAtoms(molecule *mol)
    446 {
    447   atom *first, *second;
    448   int axis;
    449   double tmp1, tmp2;
    450   char choice;  // menu choice char
    451 
    452   Log() << Verbose(0) << "===========REMOVE ATOMS=========================" << endl;
    453   Log() << Verbose(0) << " a - state atom for removal by number" << endl;
    454   Log() << Verbose(0) << " b - keep only in radius around atom" << endl;
    455   Log() << Verbose(0) << " c - remove this with one axis greater value" << endl;
    456   Log() << Verbose(0) << "all else - go back" << endl;
    457   Log() << Verbose(0) << "===============================================" << endl;
    458   Log() << Verbose(0) << "INPUT: ";
    459   cin >> choice;
    460 
    461   switch (choice) {
    462     default:
    463     case 'a':
    464       if (mol->RemoveAtom(mol->AskAtom("Enter number of atom within molecule: ")))
    465         Log() << Verbose(1) << "Atom removed." << endl;
    466       else
    467         Log() << Verbose(1) << "Atom not found." << endl;
    468       break;
    469     case 'b':
    470       second = mol->AskAtom("Enter number of atom as reference point: ");
    471       Log() << Verbose(0) << "Enter radius: ";
    472       cin >> tmp1;
    473       first = mol->start;
    474       second = first->next;
    475       while(second != mol->end) {
    476         first = second;
    477         second = first->next;
    478         if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
    479           mol->RemoveAtom(first);
    480       }
    481       break;
    482     case 'c':
    483       Log() << Verbose(0) << "Which axis is it: ";
    484       cin >> axis;
    485       Log() << Verbose(0) << "Lower boundary: ";
    486       cin >> tmp1;
    487       Log() << Verbose(0) << "Upper boundary: ";
    488       cin >> tmp2;
    489       first = mol->start;
    490       second = first->next;
    491       while(second != mol->end) {
    492         first = second;
    493         second = first->next;
    494         if ((first->x.x[axis] < tmp1) || (first->x.x[axis] > tmp2)) {// out of boundary ...
    495           //Log() << Verbose(0) << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
    496           mol->RemoveAtom(first);
    497         }
    498       }
    499       break;
    500   };
    501   //mol->Output();
    502   choice = 'r';
    503 };
    504 
    505 /** Submenu for measuring out the atoms in the molecule.
    506  * \param *periode periodentafel
    507  * \param *mol molecule with all the atoms
    508  */
    509 static void MeasureAtoms(periodentafel *periode, molecule *mol, config *configuration)
    510 {
    511   atom *first, *second, *third;
    512   Vector x,y;
    513   double min[256], tmp1, tmp2, tmp3;
    514   int Z;
    515   char choice;  // menu choice char
    516 
    517   Log() << Verbose(0) << "===========MEASURE ATOMS=========================" << endl;
    518   Log() << Verbose(0) << " a - calculate bond length between one atom and all others" << endl;
    519   Log() << Verbose(0) << " b - calculate bond length between two atoms" << endl;
    520   Log() << Verbose(0) << " c - calculate bond angle" << endl;
    521   Log() << Verbose(0) << " d - calculate principal axis of the system" << endl;
    522   Log() << Verbose(0) << " e - calculate volume of the convex envelope" << endl;
    523   Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
    524   Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
    525   Log() << Verbose(0) << "all else - go back" << endl;
    526   Log() << Verbose(0) << "===============================================" << endl;
    527   Log() << Verbose(0) << "INPUT: ";
    528   cin >> choice;
    529 
    530   switch(choice) {
    531     default:
    532       Log() << Verbose(1) << "Not a valid choice." << endl;
    533       break;
    534     case 'a':
    535       first = mol->AskAtom("Enter first atom: ");
    536       for (int i=MAX_ELEMENTS;i--;)
    537         min[i] = 0.;
    538 
    539       second = mol->start;
    540       while ((second->next != mol->end)) {
    541         second = second->next; // advance
    542         Z = second->type->Z;
    543         tmp1 = 0.;
    544         if (first != second) {
    545           x.CopyVector((const Vector *)&first->x);
    546           x.SubtractVector((const Vector *)&second->x);
    547           tmp1 = x.Norm();
    548         }
    549         if ((tmp1 != 0.) && ((min[Z] == 0.) || (tmp1 < min[Z]))) min[Z] = tmp1;
    550         //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << second->nr << ": " << tmp1 << " a.u." << endl;
    551       }
    552       for (int i=MAX_ELEMENTS;i--;)
    553         if (min[i] != 0.) Log() << Verbose(0) << "Minimum Bond length between " << first->type->name << " Atom " << first->nr << " and next Ion of type " << (periode->FindElement(i))->name << ": " << min[i] << " a.u." << endl;
    554       break;
    555 
    556     case 'b':
    557       first = mol->AskAtom("Enter first atom: ");
    558       second = mol->AskAtom("Enter second atom: ");
    559       for (int i=NDIM;i--;)
    560         min[i] = 0.;
    561       x.CopyVector((const Vector *)&first->x);
    562       x.SubtractVector((const Vector *)&second->x);
    563       tmp1 = x.Norm();
    564       Log() << Verbose(1) << "Distance vector is ";
    565       x.Output();
    566       Log() << Verbose(0) << "." << endl << "Norm of distance is " << tmp1 << "." << endl;
    567       break;
    568 
    569     case 'c':
    570       Log() << Verbose(0) << "Evaluating bond angle between three - first, central, last - atoms." << endl;
    571       first = mol->AskAtom("Enter first atom: ");
    572       second = mol->AskAtom("Enter central atom: ");
    573       third  = mol->AskAtom("Enter last atom: ");
    574       tmp1 = tmp2 = tmp3 = 0.;
    575       x.CopyVector((const Vector *)&first->x);
    576       x.SubtractVector((const Vector *)&second->x);
    577       y.CopyVector((const Vector *)&third->x);
    578       y.SubtractVector((const Vector *)&second->x);
    579       Log() << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
    580       Log() << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;
    581       break;
    582     case 'd':
    583       Log() << Verbose(0) << "Evaluating prinicipal axis." << endl;
    584       Log() << Verbose(0) << "Shall we rotate? [0/1]: ";
    585       cin >> Z;
    586       if ((Z >=0) && (Z <=1))
    587         mol->PrincipalAxisSystem((bool)Z);
    588       else
    589         mol->PrincipalAxisSystem(false);
    590       break;
    591     case 'e':
    592       {
    593         Log() << Verbose(0) << "Evaluating volume of the convex envelope.";
    594         class Tesselation *TesselStruct = NULL;
    595         const LinkedCell *LCList = NULL;
    596         LCList = new LinkedCell(mol, 10.);
    597         FindConvexBorder(mol, TesselStruct, LCList, NULL);
    598         double clustervolume = VolumeOfConvexEnvelope(TesselStruct, configuration);
    599         Log() << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;\
    600         delete(LCList);
    601         delete(TesselStruct);
    602       }
    603       break;
    604     case 'f':
    605       mol->OutputTemperatureFromTrajectories((ofstream *)&cout, mol->MDSteps-1, mol->MDSteps);
    606       break;
    607     case 'g':
    608       {
    609         char filename[255];
    610         Log() << Verbose(0) << "Please enter filename: " << endl;
    611         cin >> filename;
    612         Log() << Verbose(1) << "Storing temperatures in " << filename << "." << endl;
    613         ofstream *output = new ofstream(filename, ios::trunc);
    614         if (!mol->OutputTemperatureFromTrajectories(output, 0, mol->MDSteps))
    615           Log() << Verbose(2) << "File could not be written." << endl;
    616         else
    617           Log() << Verbose(2) << "File stored." << endl;
    618         output->close();
    619         delete(output);
    620       }
    621       break;
    622   }
    623 };
    624 
    625 /** Submenu for measuring out the atoms in the molecule.
    626  * \param *mol molecule with all the atoms
    627  * \param *configuration configuration structure for the to be written config files of all fragments
    628  */
    629 static void FragmentAtoms(molecule *mol, config *configuration)
    630 {
    631   int Order1;
    632   clock_t start, end;
    633 
    634   Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
    635   Log() << Verbose(0) << "What's the desired bond order: ";
    636   cin >> Order1;
    637   if (mol->first->next != mol->last) {  // there are bonds
    638     start = clock();
    639     mol->FragmentMolecule(Order1, configuration);
    640     end = clock();
    641     Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    642   } else
    643     Log() << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
    644 };
    645 
    646 /********************************************** Submenu routine **************************************/
    647 
    648 /** Submenu for manipulating atoms.
    649  * \param *periode periodentafel
    650  * \param *molecules list of molecules whose atoms are to be manipulated
    651  */
    652 static void ManipulateAtoms(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
    653 {
    654   atom *first, *second;
    655   molecule *mol = NULL;
    656   Vector x,y,z,n; // coordinates for absolute point in cell volume
    657   double *factor; // unit factor if desired
    658   double bond, minBond;
    659   char choice;  // menu choice char
    660   bool valid;
    661 
    662   Log() << Verbose(0) << "=========MANIPULATE ATOMS======================" << endl;
    663   Log() << Verbose(0) << "a - add an atom" << endl;
    664   Log() << Verbose(0) << "r - remove an atom" << endl;
    665   Log() << Verbose(0) << "b - scale a bond between atoms" << endl;
    666   Log() << Verbose(0) << "u - change an atoms element" << endl;
    667   Log() << Verbose(0) << "l - measure lengths, angles, ... for an atom" << endl;
    668   Log() << Verbose(0) << "all else - go back" << endl;
    669   Log() << Verbose(0) << "===============================================" << endl;
    670   if (molecules->NumberOfActiveMolecules() > 1)
    671     eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
    672   Log() << Verbose(0) << "INPUT: ";
    673   cin >> choice;
    674 
    675   switch (choice) {
    676     default:
    677       Log() << Verbose(0) << "Not a valid choice." << endl;
    678       break;
    679 
    680     case 'a': // add atom
    681       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    682         if ((*ListRunner)->ActiveFlag) {
    683         mol = *ListRunner;
    684         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    685         AddAtoms(periode, mol);
    686       }
    687       break;
    688 
    689     case 'b': // scale a bond
    690       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    691         if ((*ListRunner)->ActiveFlag) {
    692         mol = *ListRunner;
    693         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    694         Log() << Verbose(0) << "Scaling bond length between two atoms." << endl;
    695         first = mol->AskAtom("Enter first (fixed) atom: ");
    696         second = mol->AskAtom("Enter second (shifting) atom: ");
    697         minBond = 0.;
    698         for (int i=NDIM;i--;)
    699           minBond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
    700         minBond = sqrt(minBond);
    701         Log() << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl;
    702         Log() << Verbose(0) << "Enter new bond length [a.u.]: ";
    703         cin >> bond;
    704         for (int i=NDIM;i--;) {
    705           second->x.x[i] -= (second->x.x[i]-first->x.x[i])/minBond*(minBond-bond);
    706         }
    707         //Log() << Verbose(0) << "New coordinates of Atom " << second->nr << " are: ";
    708         //second->Output(second->type->No, 1);
    709       }
    710       break;
    711 
    712     case 'c': // unit scaling of the metric
    713       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    714         if ((*ListRunner)->ActiveFlag) {
    715         mol = *ListRunner;
    716         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    717        Log() << Verbose(0) << "Angstroem -> Bohrradius: 1.8897261\t\tBohrradius -> Angstroem: 0.52917721" << endl;
    718        Log() << Verbose(0) << "Enter three factors: ";
    719        factor = new double[NDIM];
    720        cin >> factor[0];
    721        cin >> factor[1];
    722        cin >> factor[2];
    723        valid = true;
    724        mol->Scale((const double ** const)&factor);
    725        delete[](factor);
    726       }
    727      break;
    728 
    729     case 'l': // measure distances or angles
    730       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    731         if ((*ListRunner)->ActiveFlag) {
    732         mol = *ListRunner;
    733         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    734         MeasureAtoms(periode, mol, configuration);
    735       }
    736       break;
    737 
    738     case 'r': // remove atom
    739       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    740         if ((*ListRunner)->ActiveFlag) {
    741         mol = *ListRunner;
    742         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    743         RemoveAtoms(mol);
    744       }
    745       break;
    746 
    747     case 'u': // change an atom's element
    748       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    749         if ((*ListRunner)->ActiveFlag) {
    750         int Z;
    751         mol = *ListRunner;
    752         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    753         first = NULL;
    754         do {
    755           Log() << Verbose(0) << "Change the element of which atom: ";
    756           cin >> Z;
    757         } while ((first = mol->FindAtom(Z)) == NULL);
    758         Log() << Verbose(0) << "New element by atomic number Z: ";
    759         cin >> Z;
    760         first->type = periode->FindElement(Z);
    761         Log() << Verbose(0) << "Atom " << first->nr << "'s element is " << first->type->name << "." << endl;
    762       }
    763       break;
    764   }
    765 };
    766 
    767 /** Submenu for manipulating molecules.
    768  * \param *periode periodentafel
    769  * \param *molecules list of molecule to manipulate
    770  */
    771 static void ManipulateMolecules(periodentafel *periode, MoleculeListClass *molecules, config *configuration)
    772 {
    773   atom *first = NULL;
    774   Vector x,y,z,n; // coordinates for absolute point in cell volume
    775   int j, axis, count, faktor;
    776   char choice;  // menu choice char
    777   molecule *mol = NULL;
    778   element **Elements;
    779   Vector **vectors;
    780   MoleculeLeafClass *Subgraphs = NULL;
    781 
    782   Log() << Verbose(0) << "=========MANIPULATE GLOBALLY===================" << endl;
    783   Log() << Verbose(0) << "c - scale by unit transformation" << endl;
    784   Log() << Verbose(0) << "d - duplicate molecule/periodic cell" << endl;
    785   Log() << Verbose(0) << "f - fragment molecule many-body bond order style" << endl;
    786   Log() << Verbose(0) << "g - center atoms in box" << endl;
    787   Log() << Verbose(0) << "i - realign molecule" << endl;
    788   Log() << Verbose(0) << "m - mirror all molecules" << endl;
    789   Log() << Verbose(0) << "o - create connection matrix" << endl;
    790   Log() << Verbose(0) << "t - translate molecule by vector" << endl;
    791   Log() << Verbose(0) << "all else - go back" << endl;
    792   Log() << Verbose(0) << "===============================================" << endl;
    793   if (molecules->NumberOfActiveMolecules() > 1)
    794     eLog() << Verbose(2) << "There is more than one molecule active! Atoms will be added to each." << endl;
    795   Log() << Verbose(0) << "INPUT: ";
    796   cin >> choice;
    797 
    798   switch (choice) {
    799     default:
    800       Log() << Verbose(0) << "Not a valid choice." << endl;
    801       break;
    802 
    803     case 'd': // duplicate the periodic cell along a given axis, given times
    804       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    805         if ((*ListRunner)->ActiveFlag) {
    806         mol = *ListRunner;
    807         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    808         Log() << Verbose(0) << "State the axis [(+-)123]: ";
    809         cin >> axis;
    810         Log() << Verbose(0) << "State the factor: ";
    811         cin >> faktor;
    812 
    813         mol->CountAtoms(); // recount atoms
    814         if (mol->AtomCount != 0) {  // if there is more than none
    815           count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
    816           Elements = new element *[count];
    817           vectors = new Vector *[count];
    818           j = 0;
    819           first = mol->start;
    820           while (first->next != mol->end) { // make a list of all atoms with coordinates and element
    821             first = first->next;
    822             Elements[j] = first->type;
    823             vectors[j] = &first->x;
    824             j++;
    825           }
    826           if (count != j)
    827             eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
    828           x.Zero();
    829           y.Zero();
    830           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
    831           for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
    832             x.AddVector(&y); // per factor one cell width further
    833             for (int k=count;k--;) { // go through every atom of the original cell
    834               first = new atom(); // create a new body
    835               first->x.CopyVector(vectors[k]);  // use coordinate of original atom
    836               first->x.AddVector(&x);     // translate the coordinates
    837               first->type = Elements[k];  // insert original element
    838               mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
    839             }
    840           }
    841           if (mol->first->next != mol->last) // if connect matrix is present already, redo it
    842             mol->CreateAdjacencyList(mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
    843           // free memory
    844           delete[](Elements);
    845           delete[](vectors);
    846           // correct cell size
    847           if (axis < 0) { // if sign was negative, we have to translate everything
    848             x.Zero();
    849             x.AddVector(&y);
    850             x.Scale(-(faktor-1));
    851             mol->Translate(&x);
    852           }
    853           mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
    854         }
    855       }
    856       break;
    857 
    858     case 'f':
    859       FragmentAtoms(mol, configuration);
    860       break;
    861 
    862     case 'g': // center the atoms
    863       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    864         if ((*ListRunner)->ActiveFlag) {
    865         mol = *ListRunner;
    866         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    867         CenterAtoms(mol);
    868       }
    869       break;
    870 
    871     case 'i': // align all atoms
    872       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    873         if ((*ListRunner)->ActiveFlag) {
    874         mol = *ListRunner;
    875         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    876         AlignAtoms(periode, mol);
    877       }
    878       break;
    879 
    880     case 'm': // mirror atoms along a given axis
    881       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    882         if ((*ListRunner)->ActiveFlag) {
    883         mol = *ListRunner;
    884         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    885         MirrorAtoms(mol);
    886       }
    887       break;
    888 
    889     case 'o': // create the connection matrix
    890       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    891         if ((*ListRunner)->ActiveFlag) {
    892           mol = *ListRunner;
    893           double bonddistance;
    894           clock_t start,end;
    895           Log() << Verbose(0) << "What's the maximum bond distance: ";
    896           cin >> bonddistance;
    897           start = clock();
    898           mol->CreateAdjacencyList(bonddistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
    899           end = clock();
    900           Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
    901         }
    902       break;
    903 
    904     case 't': // translate all atoms
    905       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    906         if ((*ListRunner)->ActiveFlag) {
    907         mol = *ListRunner;
    908         Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
    909         Log() << Verbose(0) << "Enter translation vector." << endl;
    910         x.AskPosition(mol->cell_size,0);
    911         mol->Center.AddVector((const Vector *)&x);
    912      }
    913      break;
    914   }
    915   // Free all
    916   if (Subgraphs != NULL) {  // free disconnected subgraph list of DFS analysis was performed
    917     while (Subgraphs->next != NULL) {
    918       Subgraphs = Subgraphs->next;
    919       delete(Subgraphs->previous);
    920     }
    921     delete(Subgraphs);
    922   }
    923 };
    924 
    925 
    926 /** Submenu for creating new molecules.
    927  * \param *periode periodentafel
    928  * \param *molecules list of molecules to add to
    929  */
    930 static void EditMolecules(periodentafel *periode, MoleculeListClass *molecules)
    931 {
    932   char choice;  // menu choice char
    933   Vector center;
    934   int nr, count;
    935   molecule *mol = NULL;
    936 
    937   Log() << Verbose(0) << "==========EDIT MOLECULES=====================" << endl;
    938   Log() << Verbose(0) << "c - create new molecule" << endl;
    939   Log() << Verbose(0) << "l - load molecule from xyz file" << endl;
    940   Log() << Verbose(0) << "n - change molecule's name" << endl;
    941   Log() << Verbose(0) << "N - give molecules filename" << endl;
    942   Log() << Verbose(0) << "p - parse atoms in xyz file into molecule" << endl;
    943   Log() << Verbose(0) << "r - remove a molecule" << endl;
    944   Log() << Verbose(0) << "all else - go back" << endl;
    945   Log() << Verbose(0) << "===============================================" << endl;
    946   Log() << Verbose(0) << "INPUT: ";
    947   cin >> choice;
    948 
    949   switch (choice) {
    950     default:
    951       Log() << Verbose(0) << "Not a valid choice." << endl;
    952       break;
    953     case 'c':
    954       mol = new molecule(periode);
    955       molecules->insert(mol);
    956       break;
    957 
    958     case 'l': // load from XYZ file
    959       {
    960         char filename[MAXSTRINGSIZE];
    961         Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    962         mol = new molecule(periode);
    963         do {
    964           Log() << Verbose(0) << "Enter file name: ";
    965           cin >> filename;
    966         } while (!mol->AddXYZFile(filename));
    967         mol->SetNameFromFilename(filename);
    968         // center at set box dimensions
    969         mol->CenterEdge(&center);
    970         mol->cell_size[0] = center.x[0];
    971         mol->cell_size[1] = 0;
    972         mol->cell_size[2] = center.x[1];
    973         mol->cell_size[3] = 0;
    974         mol->cell_size[4] = 0;
    975         mol->cell_size[5] = center.x[2];
    976         molecules->insert(mol);
    977       }
    978       break;
    979 
    980     case 'n':
    981       {
    982         char filename[MAXSTRINGSIZE];
    983         do {
    984           Log() << Verbose(0) << "Enter index of molecule: ";
    985           cin >> nr;
    986           mol = molecules->ReturnIndex(nr);
    987         } while (mol == NULL);
    988         Log() << Verbose(0) << "Enter name: ";
    989         cin >> filename;
    990         strcpy(mol->name, filename);
    991       }
    992       break;
    993 
    994     case 'N':
    995       {
    996         char filename[MAXSTRINGSIZE];
    997         do {
    998           Log() << Verbose(0) << "Enter index of molecule: ";
    999           cin >> nr;
    1000           mol = molecules->ReturnIndex(nr);
    1001         } while (mol == NULL);
    1002         Log() << Verbose(0) << "Enter name: ";
    1003         cin >> filename;
    1004         mol->SetNameFromFilename(filename);
    1005       }
    1006       break;
    1007 
    1008     case 'p': // parse XYZ file
    1009       {
    1010         char filename[MAXSTRINGSIZE];
    1011         mol = NULL;
    1012         do {
    1013           Log() << Verbose(0) << "Enter index of molecule: ";
    1014           cin >> nr;
    1015           mol = molecules->ReturnIndex(nr);
    1016         } while (mol == NULL);
    1017         Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
    1018         do {
    1019           Log() << Verbose(0) << "Enter file name: ";
    1020           cin >> filename;
    1021         } while (!mol->AddXYZFile(filename));
    1022         mol->SetNameFromFilename(filename);
    1023       }
    1024       break;
    1025 
    1026     case 'r':
    1027       Log() << Verbose(0) << "Enter index of molecule: ";
    1028       cin >> nr;
    1029       count = 1;
    1030       for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    1031         if (nr == (*ListRunner)->IndexNr) {
    1032           mol = *ListRunner;
    1033           molecules->ListOfMolecules.erase(ListRunner);
    1034           delete(mol);
    1035           break;
    1036         }
    1037       break;
    1038   }
    1039 };
    1040 
    1041 
    1042 /** Submenu for merging molecules.
    1043  * \param *periode periodentafel
    1044  * \param *molecules list of molecules to add to
    1045  */
    1046 static void MergeMolecules(periodentafel *periode, MoleculeListClass *molecules)
    1047 {
    1048   char choice;  // menu choice char
    1049 
    1050   Log() << Verbose(0) << "===========MERGE MOLECULES=====================" << endl;
    1051   Log() << Verbose(0) << "a - simple add of one molecule to another" << endl;
    1052   Log() << Verbose(0) << "e - embedding merge of two molecules" << endl;
    1053   Log() << Verbose(0) << "m - multi-merge of all molecules" << endl;
    1054   Log() << Verbose(0) << "s - scatter merge of two molecules" << endl;
    1055   Log() << Verbose(0) << "t - simple merge of two molecules" << endl;
    1056   Log() << Verbose(0) << "all else - go back" << endl;
    1057   Log() << Verbose(0) << "===============================================" << endl;
    1058   Log() << Verbose(0) << "INPUT: ";
    1059   cin >> choice;
    1060 
    1061   switch (choice) {
    1062     default:
    1063       Log() << Verbose(0) << "Not a valid choice." << endl;
    1064       break;
    1065 
    1066     case 'a':
    1067       {
    1068         int src, dest;
    1069         molecule *srcmol = NULL, *destmol = NULL;
    1070         {
    1071           do {
    1072             Log() << Verbose(0) << "Enter index of destination molecule: ";
    1073             cin >> dest;
    1074             destmol = molecules->ReturnIndex(dest);
    1075           } while ((destmol == NULL) && (dest != -1));
    1076           do {
    1077             Log() << Verbose(0) << "Enter index of source molecule to add from: ";
    1078             cin >> src;
    1079             srcmol = molecules->ReturnIndex(src);
    1080           } while ((srcmol == NULL) && (src != -1));
    1081           if ((src != -1) && (dest != -1))
    1082             molecules->SimpleAdd(srcmol, destmol);
    1083         }
    1084       }
    1085       break;
    1086 
    1087     case 'e':
    1088       {
    1089         int src, dest;
    1090         molecule *srcmol = NULL, *destmol = NULL;
    1091         do {
    1092           Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ";
    1093           cin >> src;
    1094           srcmol = molecules->ReturnIndex(src);
    1095         } while ((srcmol == NULL) && (src != -1));
    1096         do {
    1097           Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ";
    1098           cin >> dest;
    1099           destmol = molecules->ReturnIndex(dest);
    1100         } while ((destmol == NULL) && (dest != -1));
    1101         if ((src != -1) && (dest != -1))
    1102           molecules->EmbedMerge(destmol, srcmol);
    1103       }
    1104       break;
    1105 
    1106     case 'm':
    1107       {
    1108         int nr;
    1109         molecule *mol = NULL;
    1110         do {
    1111           Log() << Verbose(0) << "Enter index of molecule to merge into: ";
    1112           cin >> nr;
    1113           mol = molecules->ReturnIndex(nr);
    1114         } while ((mol == NULL) && (nr != -1));
    1115         if (nr != -1) {
    1116           int N = molecules->ListOfMolecules.size()-1;
    1117           int *src = new int(N);
    1118           for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    1119             if ((*ListRunner)->IndexNr != nr)
    1120               src[N++] = (*ListRunner)->IndexNr;       
    1121           molecules->SimpleMultiMerge(mol, src, N);
    1122           delete[](src);
    1123         }
    1124       }
    1125       break;
    1126 
    1127     case 's':
    1128       Log() << Verbose(0) << "Not implemented yet." << endl;
    1129       break;
    1130 
    1131     case 't':
    1132       {
    1133         int src, dest;
    1134         molecule *srcmol = NULL, *destmol = NULL;
    1135         {
    1136           do {
    1137             Log() << Verbose(0) << "Enter index of destination molecule: ";
    1138             cin >> dest;
    1139             destmol = molecules->ReturnIndex(dest);
    1140           } while ((destmol == NULL) && (dest != -1));
    1141           do {
    1142             Log() << Verbose(0) << "Enter index of source molecule to merge into: ";
    1143             cin >> src;
    1144             srcmol = molecules->ReturnIndex(src);
    1145           } while ((srcmol == NULL) && (src != -1));
    1146           if ((src != -1) && (dest != -1))
    1147             molecules->SimpleMerge(srcmol, destmol);
    1148         }
    1149       }
    1150       break;
    1151   }
    1152 };
    1153 
    1154 
    1155 /********************************************** Test routine **************************************/
    1156 
    1157 /** Is called always as option 'T' in the menu.
    1158  * \param *molecules list of molecules
    1159  */
    1160 static void testroutine(MoleculeListClass *molecules)
    1161 {
    1162   // the current test routine checks the functionality of the KeySet&Graph concept:
    1163   // We want to have a multiindex (the KeySet) describing a unique subgraph
    1164   int i, comp, counter=0;
    1165 
    1166   // create a clone
    1167   molecule *mol = NULL;
    1168   if (molecules->ListOfMolecules.size() != 0) // clone
    1169     mol = (molecules->ListOfMolecules.front())->CopyMolecule();
    1170   else {
    1171     eLog() << Verbose(0) << "I don't have anything to test on ... ";
    1172     performCriticalExit();
    1173     return;
    1174   }
    1175   atom *Walker = mol->start;
    1176 
    1177   // generate some KeySets
    1178   Log() << Verbose(0) << "Generating KeySets." << endl;
    1179   KeySet TestSets[mol->AtomCount+1];
    1180   i=1;
    1181   while (Walker->next != mol->end) {
    1182     Walker = Walker->next;
    1183     for (int j=0;j<i;j++) {
    1184       TestSets[j].insert(Walker->nr);
    1185     }
    1186     i++;
    1187   }
    1188   Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl;
    1189   KeySetTestPair test;
    1190   test = TestSets[mol->AtomCount-1].insert(Walker->nr);
    1191   if (test.second) {
    1192     Log() << Verbose(1) << "Insertion worked?!" << endl;
    1193   } else {
    1194     Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
    1195   }
    1196   TestSets[mol->AtomCount].insert(mol->end->previous->nr);
    1197   TestSets[mol->AtomCount].insert(mol->end->previous->previous->previous->nr);
    1198 
    1199   // constructing Graph structure
    1200   Log() << Verbose(0) << "Generating Subgraph class." << endl;
    1201   Graph Subgraphs;
    1202 
    1203   // insert KeySets into Subgraphs
    1204   Log() << Verbose(0) << "Inserting KeySets into Subgraph class." << endl;
    1205   for (int j=0;j<mol->AtomCount;j++) {
    1206     Subgraphs.insert(GraphPair (TestSets[j],pair<int, double>(counter++, 1.)));
    1207   }
    1208   Log() << Verbose(0) << "Testing insertion of already present item in Subgraph." << endl;
    1209   GraphTestPair test2;
    1210   test2 = Subgraphs.insert(GraphPair (TestSets[mol->AtomCount],pair<int, double>(counter++, 1.)));
    1211   if (test2.second) {
    1212     Log() << Verbose(1) << "Insertion worked?!" << endl;
    1213   } else {
    1214     Log() << Verbose(1) << "Insertion rejected: Present object is " << (*(test2.first)).second.first << "." << endl;
    1215   }
    1216 
    1217   // show graphs
    1218   Log() << Verbose(0) << "Showing Subgraph's contents, checking that it's sorted." << endl;
    1219   Graph::iterator A = Subgraphs.begin();
    1220   while (A !=  Subgraphs.end()) {
    1221     Log() << Verbose(0) << (*A).second.first << ": ";
    1222     KeySet::iterator key = (*A).first.begin();
    1223     comp = -1;
    1224     while (key != (*A).first.end()) {
    1225       if ((*key) > comp)
    1226         Log() << Verbose(0) << (*key) << " ";
    1227       else
    1228         Log() << Verbose(0) << (*key) << "! ";
    1229       comp = (*key);
    1230       key++;
    1231     }
    1232     Log() << Verbose(0) << endl;
    1233     A++;
    1234   }
    1235   delete(mol);
    1236 };
    1237 
    1238 /** Tries given filename or standard on saving the config file.
    1239  * \param *ConfigFileName name of file
    1240  * \param *configuration pointer to configuration structure with all the values
    1241  * \param *periode pointer to periodentafel structure with all the elements
    1242  * \param *molecules list of molecules structure with all the atoms and coordinates
    1243  */
    1244 static void SaveConfig(char *ConfigFileName, config *configuration, periodentafel *periode, MoleculeListClass *molecules)
    1245 {
    1246   char filename[MAXSTRINGSIZE];
    1247   ofstream output;
    1248   molecule *mol = new molecule(periode);
    1249 
    1250   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1251     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1252   }
    1253 
    1254 
    1255   // first save as PDB data
    1256   if (ConfigFileName != NULL)
    1257     strcpy(filename, ConfigFileName);
    1258   if (output == NULL)
    1259     strcpy(filename,"main_pcp_linux");
    1260   Log() << Verbose(0) << "Saving as pdb input ";
    1261   if (configuration->SavePDB(filename, molecules))
    1262     Log() << Verbose(0) << "done." << endl;
    1263   else
    1264     Log() << Verbose(0) << "failed." << endl;
    1265 
    1266   // then save as tremolo data file
    1267   if (ConfigFileName != NULL)
    1268     strcpy(filename, ConfigFileName);
    1269   if (output == NULL)
    1270     strcpy(filename,"main_pcp_linux");
    1271   Log() << Verbose(0) << "Saving as tremolo data input ";
    1272   if (configuration->SaveTREMOLO(filename, molecules))
    1273     Log() << Verbose(0) << "done." << endl;
    1274   else
    1275     Log() << Verbose(0) << "failed." << endl;
    1276 
    1277   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
    1278   int N = molecules->ListOfMolecules.size();
    1279   int *src = new int[N];
    1280   N=0;
    1281   for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    1282     src[N++] = (*ListRunner)->IndexNr;
    1283     (*ListRunner)->Translate(&(*ListRunner)->Center);
    1284   }
    1285   molecules->SimpleMultiAdd(mol, src, N);
    1286   delete[](src);
    1287 
    1288   // ... and translate back
    1289   for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
    1290     (*ListRunner)->Center.Scale(-1.);
    1291     (*ListRunner)->Translate(&(*ListRunner)->Center);
    1292     (*ListRunner)->Center.Scale(-1.);
    1293   }
    1294 
    1295   Log() << Verbose(0) << "Storing configuration ... " << endl;
    1296   // get correct valence orbitals
    1297   mol->CalculateOrbitals(*configuration);
    1298   configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
    1299   if (ConfigFileName != NULL) { // test the file name
    1300     strcpy(filename, ConfigFileName);
    1301     output.open(filename, ios::trunc);
    1302   } else if (strlen(configuration->configname) != 0) {
    1303     strcpy(filename, configuration->configname);
    1304     output.open(configuration->configname, ios::trunc);
    1305     } else {
    1306       strcpy(filename, DEFAULTCONFIG);
    1307       output.open(DEFAULTCONFIG, ios::trunc);
    1308     }
    1309   output.close();
    1310   output.clear();
    1311   Log() << Verbose(0) << "Saving of config file ";
    1312   if (configuration->Save(filename, periode, mol))
    1313     Log() << Verbose(0) << "successful." << endl;
    1314   else
    1315     Log() << Verbose(0) << "failed." << endl;
    1316 
    1317   // and save to xyz file
    1318   if (ConfigFileName != NULL) {
    1319     strcpy(filename, ConfigFileName);
    1320     strcat(filename, ".xyz");
    1321     output.open(filename, ios::trunc);
    1322   }
    1323   if (output == NULL) {
    1324     strcpy(filename,"main_pcp_linux");
    1325     strcat(filename, ".xyz");
    1326     output.open(filename, ios::trunc);
    1327   }
    1328   Log() << Verbose(0) << "Saving of XYZ file ";
    1329   if (mol->MDSteps <= 1) {
    1330     if (mol->OutputXYZ(&output))
    1331       Log() << Verbose(0) << "successful." << endl;
    1332     else
    1333       Log() << Verbose(0) << "failed." << endl;
    1334   } else {
    1335     if (mol->OutputTrajectoriesXYZ(&output))
    1336       Log() << Verbose(0) << "successful." << endl;
    1337     else
    1338       Log() << Verbose(0) << "failed." << endl;
    1339   }
    1340   output.close();
    1341   output.clear();
    1342 
    1343   // and save as MPQC configuration
    1344   if (ConfigFileName != NULL)
    1345     strcpy(filename, ConfigFileName);
    1346   if (output == NULL)
    1347     strcpy(filename,"main_pcp_linux");
    1348   Log() << Verbose(0) << "Saving as mpqc input ";
    1349   if (configuration->SaveMPQC(filename, mol))
    1350     Log() << Verbose(0) << "done." << endl;
    1351   else
    1352     Log() << Verbose(0) << "failed." << endl;
    1353 
    1354   if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
    1355     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
    1356   }
    1357 
    1358   delete(mol);
    1359 };
     67#include "menu.hpp"
    136068
    136169/** Parses the command line options.
    … …  
    136977 * \return exit code (0 - successful, all else - something's wrong)
    137078 */
    1371 static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode, config& configuration, char *&ConfigFileName)
     79static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
     80                                   config& configuration, char *&ConfigFileName, menu *main_menu)
    137281{
    137382  Vector x,y,z,n;  // coordinates for absolute point in cell volume
    … …  
    2170879    } while (argptr < argc);
    2171880    if (SaveFlag)
    2172       SaveConfig(ConfigFileName, &configuration, periode, molecules);
     881      main_menu->SaveConfig(ConfigFileName, &configuration, periode, molecules);
    2173882  } else {  // no arguments, hence scan the elements db
    2174883    if (periode->LoadPeriodentafel(configuration.databasepath))
    … …  
    2185894int main(int argc, char **argv)
    2186895{
    2187   periodentafel *periode = new periodentafel; // and a period table of all elements
    2188   MoleculeListClass *molecules = new MoleculeListClass;  // list of all molecules
    2189   molecule *mol = NULL;
    2190   config *configuration = new config;
    2191   char choice;  // menu choice char
    2192   Vector x,y,z,n;  // coordinates for absolute point in cell volume
    2193   ifstream test;
    2194   ofstream output;
    2195   string line;
    2196   char *ConfigFileName = NULL;
    2197   int j;
    2198 
    2199   setVerbosity(0);
    2200 
    2201   // =========================== PARSE COMMAND LINE OPTIONS ====================================
    2202   j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName);
    2203   switch(j) {
    2204     case 255:  // something went wrong
    2205     case 2:  // just for -f option
    2206     case 1:  // just for -v and -h options
    2207       delete(molecules); // also free's all molecules contained
    2208       delete(periode);
    2209       delete(configuration);
    2210       Log() << Verbose(0) <<  "Maximum of allocated memory: "
    2211         << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
    2212       Log() << Verbose(0) <<  "Remaining non-freed memory: "
    2213         << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
    2214       MemoryUsageObserver::getInstance()->purgeInstance();
    2215       logger::purgeInstance();
    2216       errorLogger::purgeInstance();
    2217      return (j == 1 ? 0 : j);
    2218     default:
    2219       break;
    2220   }
    2221 
    2222   // General stuff
    2223   if (molecules->ListOfMolecules.size() == 0) {
    2224     mol = new molecule(periode);
    2225     if (mol->cell_size[0] == 0.) {
    2226       Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
    2227       for (int i=0;i<6;i++) {
    2228         Log() << Verbose(1) << "Cell size" << i << ": ";
    2229         cin >> mol->cell_size[i];
    2230       }
     896  periodentafel *periode = new periodentafel;
     897    MoleculeListClass *molecules = new MoleculeListClass;
     898    molecule *mol = NULL;
     899    config *configuration = new config;
     900    Vector x, y, z, n;
     901    ifstream test;
     902    ofstream output;
     903    string line;
     904    char *ConfigFileName = NULL;
     905    int j;
     906    menu *main_menu;
     907    main_menu = new menu;
     908    setVerbosity(0);
     909    /* main menu is needed to call actions inside the menu */
     910    /* structure of ParseCommandLineOptions will be refactored later */
     911    j = ParseCommandLineOptions(argc, argv, molecules, periode, *configuration, ConfigFileName,main_menu);
     912    switch (j){
     913        case 255:
     914        case 2:
     915        case 1:
     916            delete (molecules);
     917            delete (periode);
     918            delete (configuration);
     919            Log() << Verbose(0) << "Maximum of allocated memory: " << MemoryUsageObserver::getInstance()->getMaximumUsedMemory() << endl;
     920            Log() << Verbose(0) << "Remaining non-freed memory: " << MemoryUsageObserver::getInstance()->getUsedMemorySize() << endl;
     921            MemoryUsageObserver::getInstance()->purgeInstance();
     922            logger::purgeInstance();
     923            errorLogger::purgeInstance();
     924            return (j == 1 ? 0 : j);
     925        default:
     926            break;
    2231927    }
    2232     mol->ActiveFlag = true;
    2233     molecules->insert(mol);
    2234   }
    2235 
    2236   // =========================== START INTERACTIVE SESSION ====================================
    2237 
    2238   // now the main construction loop
    2239   Log() << Verbose(0) << endl << "Now comes the real construction..." << endl;
    2240   do {
    2241     Log() << Verbose(0) << endl << endl;
    2242     Log() << Verbose(0) << "============Molecule list=======================" << endl;
    2243     molecules->Enumerate((ofstream *)&cout);
    2244     Log() << Verbose(0) << "============Menu===============================" << endl;
    2245     Log() << Verbose(0) << "a - set molecule (in)active" << endl;
    2246     Log() << Verbose(0) << "e - edit molecules (load, parse, save)" << endl;
    2247     Log() << Verbose(0) << "g - globally manipulate atoms in molecule" << endl;
    2248     Log() << Verbose(0) << "M - Merge molecules" << endl;
    2249     Log() << Verbose(0) << "m - manipulate atoms" << endl;
    2250     Log() << Verbose(0) << "-----------------------------------------------" << endl;
    2251     Log() << Verbose(0) << "c - edit the current configuration" << endl;
    2252     Log() << Verbose(0) << "-----------------------------------------------" << endl;
    2253     Log() << Verbose(0) << "s - save current setup to config file" << endl;
    2254     Log() << Verbose(0) << "T - call the current test routine" << endl;
    2255     Log() << Verbose(0) << "q - quit" << endl;
    2256     Log() << Verbose(0) << "===============================================" << endl;
    2257     Log() << Verbose(0) << "Input: ";
    2258     cin >> choice;
    2259 
    2260     switch (choice) {
    2261       case 'a':  // (in)activate molecule
    2262         {
    2263           Log() << Verbose(0) << "Enter index of molecule: ";
    2264           cin >> j;
    2265           for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
    2266             if ((*ListRunner)->IndexNr == j)
    2267               (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
     928    if(molecules->ListOfMolecules.size() == 0){
     929        mol = new molecule(periode);
     930        if(mol->cell_size[0] == 0.){
     931            Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
     932            for(int i = 0;i < 6;i++){
     933                Log() << Verbose(1) << "Cell size" << i << ": ";
     934                cin >> mol->cell_size[i];
     935            }
    2268936        }
    2269         break;
    2270 
    2271       case 'c': // edit each field of the configuration
    2272        configuration->Edit();
    2273        break;
    2274 
    2275       case 'e': // create molecule
    2276         EditMolecules(periode, molecules);
    2277         break;
    2278 
    2279       case 'g': // manipulate molecules
    2280         ManipulateMolecules(periode, molecules, configuration);
    2281         break;
    2282 
    2283       case 'M':  // merge molecules
    2284         MergeMolecules(periode, molecules);
    2285         break;
    2286 
    2287       case 'm': // manipulate atoms
    2288         ManipulateAtoms(periode, molecules, configuration);
    2289         break;
    2290 
    2291       case 'q': // quit
    2292         break;
    2293 
    2294       case 's': // save to config file
    2295         SaveConfig(ConfigFileName, configuration, periode, molecules);
    2296         break;
    2297 
    2298       case 'T':
    2299         testroutine(molecules);
    2300         break;
    2301 
    2302       default:
    2303         break;
    2304     };
    2305   } while (choice != 'q');
    2306 
    2307   // save element data base
    2308   if (periode->StorePeriodentafel(configuration->databasepath)) //ElementsFileName
    2309     Log() << Verbose(0) << "Saving of elements.db successful." << endl;
    2310   else
    2311     Log() << Verbose(0) << "Saving of elements.db failed." << endl;
    2312 
    2313   delete(molecules); // also free's all molecules contained
    2314   delete(periode);
     937
     938        mol->ActiveFlag = true;
     939        molecules->insert(mol);
     940    }
     941
     942
     943
     944    main_menu->perform(molecules, configuration, periode, ConfigFileName);
     945
     946    if(periode->StorePeriodentafel(configuration->databasepath))
     947        Log() << Verbose(0) << "Saving of elements.db successful." << endl;
     948
     949    else
     950        Log() << Verbose(0) << "Saving of elements.db failed." << endl;
     951
     952    delete (molecules);
     953    delete(periode);
    2315954  delete(configuration);
    2316955
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