Changeset c67e16


Ignore:
Timestamp:
Apr 28, 2008, 1:46:05 PM (17 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:
555063
Parents:
140e34
Message:

removed some output lines (commented-out) mostly in ScanForPeriodicCorrection, CenterEdge, AddHydrogenReplacement and StoreFragmentFromKeySet

Location:
src
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • src/moleculelist.cpp

    r140e34 rc67e16  
    418418          if (Walker->type->Z == runner->Z) {
    419419            if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a real father, prints its index
    420               cerr << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", its number " << Walker->GetTrueFather()->nr << " and index " << SortIndex[Walker->GetTrueFather()->nr] << "." << endl; 
     420              //cout << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", its number " << Walker->GetTrueFather()->nr << " and index " << SortIndex[Walker->GetTrueFather()->nr] << "." << endl; 
    421421              output <<  SortIndex[Walker->GetTrueFather()->nr] << "\t";
    422422            } else  // otherwise a -1 to indicate an added saturation hydrogen

  • src/molecules.cpp

    r140e34 rc67e16  
    186186  double *matrix;
    187187
    188         *out << Verbose(3) << "Begin of AddHydrogenReplacementAtom." << endl;
     188//      *out << Verbose(3) << "Begin of AddHydrogenReplacementAtom." << endl;
    189189  // create vector in direction of bond
    190190  InBondVector.CopyVector(&TopReplacement->x);
    … …  
    196196   // due to TopReplacement or Origin being on the wrong side!
    197197  if (bondlength > BondDistance) {
    198     *out << Verbose(4) << "InBondVector is: ";
    199     InBondVector.Output(out);
    200     *out << endl;
     198//    *out << Verbose(4) << "InBondVector is: ";
     199//    InBondVector.Output(out);
     200//    *out << endl;
    201201    OrthoVector1.Zero();
    202202    for (int i=0;i<NDIM;i++) {
    … …  
    211211    Free((void **)&matrix, "molecule::AddHydrogenReplacementAtom: *matrix");
    212212    bondlength = InBondVector.Norm();
    213     *out << Verbose(4) << "Corrected InBondVector is now: ";
    214     InBondVector.Output(out);
    215     *out << endl;
     213//    *out << Verbose(4) << "Corrected InBondVector is now: ";
     214//    InBondVector.Output(out);
     215//    *out << endl;
    216216  } // periodic correction finished
    217217 
    … …  
    244244      FirstOtherAtom->x.AddVector(&InBondVector);  // ... and add distance vector to replacement atom
    245245      AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
    246       *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
    247       FirstOtherAtom->x.Output(out);
    248       *out << endl;
     246//      *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
     247//      FirstOtherAtom->x.Output(out);
     248//      *out << endl;
    249249      Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
    250250      Binder->Cyclic = false;
    … …  
    271271      }
    272272      if (FirstOtherAtom != NULL) { // then we just have this double bond and the plane does not matter at all
    273         *out << Verbose(3) << "Regarding the double bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") to be constructed: Taking " << FirstOtherAtom->Name << " and " << SecondOtherAtom->Name << " along with " << TopOrigin->Name << " to determine orthogonal plane." << endl;
     273//        *out << Verbose(3) << "Regarding the double bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") to be constructed: Taking " << FirstOtherAtom->Name << " and " << SecondOtherAtom->Name << " along with " << TopOrigin->Name << " to determine orthogonal plane." << endl;
    274274       
    275275        // determine the plane of these two with the *origin
    … …  
    309309//      OrthoVector1.Output(out);
    310310//      *out << endl;
    311       *out << Verbose(3) << "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle) << endl;
     311//      *out << Verbose(3) << "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle) << endl;
    312312      FirstOtherAtom->x.Zero();
    313313      SecondOtherAtom->x.Zero();
    … …  
    326326      AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
    327327      AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
    328       *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
    329       FirstOtherAtom->x.Output(out);
    330       *out << endl;
    331       *out << Verbose(4) << "Added " << *SecondOtherAtom << " at: ";
    332       SecondOtherAtom->x.Output(out);
    333       *out << endl;
     328//      *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
     329//      FirstOtherAtom->x.Output(out);
     330//      *out << endl;
     331//      *out << Verbose(4) << "Added " << *SecondOtherAtom << " at: ";
     332//      SecondOtherAtom->x.Output(out);
     333//      *out << endl;
    334334      Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
    335335      Binder->Cyclic = false;
    … …  
    359359      // we need to vectors orthonormal the InBondVector
    360360      AllWentWell = AllWentWell && OrthoVector1.GetOneNormalVector(&InBondVector);
    361       *out << Verbose(3) << "Orthovector1: ";
    362       OrthoVector1.Output(out);
    363       *out << endl;
     361//      *out << Verbose(3) << "Orthovector1: ";
     362//      OrthoVector1.Output(out);
     363//      *out << endl;
    364364      AllWentWell = AllWentWell && OrthoVector2.MakeNormalVector(&InBondVector, &OrthoVector1);
    365       *out << Verbose(3) << "Orthovector2: ";
    366       OrthoVector2.Output(out);
    367       *out << endl;
     365//      *out << Verbose(3) << "Orthovector2: ";
     366//      OrthoVector2.Output(out);
     367//      *out << endl;
    368368     
    369369      // create correct coordination for the three atoms
    … …  
    374374      f = b/sqrt(3.);   // length for OrthVector1
    375375      g = b/2.;         // length for OrthVector2
    376       *out << Verbose(3) << "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", " << endl;
    377       *out << Verbose(3) << "The three Bond lengths: " << sqrt(d*d+f*f) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << ", "  << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << endl;
     376//      *out << Verbose(3) << "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", " << endl;
     377//      *out << Verbose(3) << "The three Bond lengths: " << sqrt(d*d+f*f) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << ", "  << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << endl;
    378378      factors[0] = d;
    379379      factors[1] = f;
    … …  
    400400      AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
    401401      AllWentWell = AllWentWell && AddAtom(ThirdOtherAtom);
    402       *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
    403       FirstOtherAtom->x.Output(out);
    404       *out << endl;
    405       *out << Verbose(4) << "Added " << *SecondOtherAtom << " at: ";
    406       SecondOtherAtom->x.Output(out);
    407       *out << endl;
    408       *out << Verbose(4) << "Added " << *ThirdOtherAtom << " at: ";
    409       ThirdOtherAtom->x.Output(out);
    410       *out << endl;
     402//      *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
     403//      FirstOtherAtom->x.Output(out);
     404//      *out << endl;
     405//      *out << Verbose(4) << "Added " << *SecondOtherAtom << " at: ";
     406//      SecondOtherAtom->x.Output(out);
     407//      *out << endl;
     408//      *out << Verbose(4) << "Added " << *ThirdOtherAtom << " at: ";
     409//      ThirdOtherAtom->x.Output(out);
     410//      *out << endl;
    411411      Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
    412412      Binder->Cyclic = false;
    … …  
    425425  }
    426426
    427         *out << Verbose(3) << "End of AddHydrogenReplacementAtom." << endl;
     427//      *out << Verbose(3) << "End of AddHydrogenReplacementAtom." << endl;
    428428  return AllWentWell;
    429429};
    … …  
    606606  vector *min = new vector;
    607607 
    608   *out << Verbose(3) << "Begin of CenterEdge." << endl;
     608//  *out << Verbose(3) << "Begin of CenterEdge." << endl;
    609609  atom *ptr = start->next;  // start at first in list
    610610  if (ptr != end) {   //list not empty?
    … …  
    621621      }
    622622    }
    623     *out << Verbose(4) << "Maximum is ";
    624     max->Output(out);
    625     *out << ", Minimum is ";
    626     min->Output(out);
    627     *out << endl;
     623//    *out << Verbose(4) << "Maximum is ";
     624//    max->Output(out);
     625//    *out << ", Minimum is ";
     626//    min->Output(out);
     627//    *out << endl;
    628628   
    629629    for (int i=0;i<NDIM;i++) {
    … …  
    634634  }
    635635  delete(min);
    636   *out << Verbose(3) << "End of CenterEdge." << endl;
     636//  *out << Verbose(3) << "End of CenterEdge." << endl;
    637637};
    638638
    … …  
    18671867    line >> AtomNr;
    18681868    if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
    1869       CurrentSet.insert(AtomNr);
     1869      CurrentSet.insert(AtomNr);  // insert at end, hence in same order as in file!
    18701870      status++;
    18711871    } // else it's "-1" or else and thus must not be added
    … …  
    27902790  molecule *Leaf = new molecule(elemente);
    27912791 
    2792   *out << Verbose(1) << "Begin of StoreFragmentFromKeyset." << endl;
     2792//  *out << Verbose(1) << "Begin of StoreFragmentFromKeyset." << endl;
    27932793 
    27942794  Leaf->BondDistance = BondDistance;
    … …  
    28022802  // first create the minimal set of atoms from the KeySet
    28032803  for(KeySet::iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
    2804     FatherOfRunner =  FindAtom((*runner));
     2804    FatherOfRunner =  FindAtom((*runner));  // find the id
    28052805    SonList[FatherOfRunner->nr] = Leaf->AddCopyAtom(FatherOfRunner);
    28062806  }
    28072807 
    28082808  // create the bonds between all: Make it an induced subgraph and add hydrogen
    2809   *out << Verbose(2) << "Creating bonds from father graph (i.e. induced subgraph creation)." << endl;
     2809//  *out << Verbose(2) << "Creating bonds from father graph (i.e. induced subgraph creation)." << endl;
    28102810  Runner = Leaf->start;
    28112811  while (Runner->next != Leaf->end) {
    … …  
    28162816      for (int i=0;i<NumberOfBondsPerAtom[FatherOfRunner->nr];i++) { // go through every bond of father
    28172817        OtherFather = ListOfBondsPerAtom[FatherOfRunner->nr][i]->GetOtherAtom(FatherOfRunner);
    2818         *out << Verbose(2) << "Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->nr] << " is bound to " << *OtherFather;
     2818//        *out << Verbose(2) << "Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->nr] << " is bound to " << *OtherFather;
    28192819        if (SonList[OtherFather->nr] != NULL) {
    2820           *out << ", whose son is " << *SonList[OtherFather->nr] << "." << endl;
     2820//          *out << ", whose son is " << *SonList[OtherFather->nr] << "." << endl;
    28212821          if (OtherFather->nr > FatherOfRunner->nr) { // add bond (nr check is for adding only one of both variants: ab, ba)
    2822             *out << Verbose(3) << "Adding Bond: " << Leaf->AddBond(Runner, SonList[OtherFather->nr], ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree) << "." << endl;
     2822//            *out << Verbose(3) << "Adding Bond: " << Leaf->AddBond(Runner, SonList[OtherFather->nr], ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree) << "." << endl;
    28232823            //NumBonds[Runner->nr]++;
    28242824          } else {
    2825             *out << Verbose(3) << "Not adding bond, labels in wrong order." << endl;
     2825//            *out << Verbose(3) << "Not adding bond, labels in wrong order." << endl;
    28262826          }
    28272827        } else {
    2828           *out << ", who has no son in this fragment molecule." << endl;
     2828//          *out << ", who has no son in this fragment molecule." << endl;
    28292829#ifdef ADDHYDROGEN
    2830           *out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
     2830//          *out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
    28312831          Leaf->AddHydrogenReplacementAtom(out, ListOfBondsPerAtom[FatherOfRunner->nr][i], Runner, FatherOfRunner, OtherFather, ListOfBondsPerAtom[FatherOfRunner->nr],NumberOfBondsPerAtom[FatherOfRunner->nr], IsAngstroem);
    28322832#endif
    … …  
    28452845  //Leaflet->Leaf->ScanForPeriodicCorrection(out);
    28462846  Free((void **)&SonList, "molecule::StoreFragmentFromStack: **SonList");
    2847   *out << Verbose(1) << "End of StoreFragmentFromKeyset." << endl;
     2847//  *out << Verbose(1) << "End of StoreFragmentFromKeyset." << endl;
    28482848  return Leaf;
    28492849};
    … …  
    35083508  bool flag = true;
    35093509
    3510   *out << Verbose(1) << "Begin of ScanForPeriodicCorrection." << endl;
     3510//  *out << Verbose(1) << "Begin of ScanForPeriodicCorrection." << endl;
    35113511
    35123512  ColorList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
    … …  
    35263526          OtherBinder = Binder->next; // note down binding partner for later re-insertion
    35273527          unlink(Binder);   // unlink bond
    3528           *out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
     3528//          *out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
    35293529          flag = true;
    35303530          break;
    … …  
    35643564      link(Binder, OtherBinder);
    35653565    } else {
    3566       *out << Verbose(2) << "No corrections for this fragment." << endl;
     3566//      *out << Verbose(2) << "No corrections for this fragment." << endl;
    35673567    }
    35683568    //delete(CompStack);
    … …  
    35733573  Free((void **)&ColorList, "molecule::ScanForPeriodicCorrection: *ColorList");
    35743574  Free((void **)&matrix, "molecule::ScanForPeriodicCorrection: *matrix");
    3575   *out << Verbose(1) << "End of ScanForPeriodicCorrection." << endl;
     3575//  *out << Verbose(1) << "End of ScanForPeriodicCorrection." << endl;
    35763576};
    35773577
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