Ignore:
Timestamp:
Apr 22, 2010, 2:00:03 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:
299554
Parents:
6613ec
Message:

Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) << ...);

Most of the files are affected, but this is necessary as if DoLog() says verbosity is not enough, all the stream operators won"t get executed which saves substantial amount of computation time.

Signed-off-by: Frederik Heber <heber@…>

File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/moleculelist.cpp

    r6613ec ra67d19  
    3636MoleculeListClass::~MoleculeListClass()
    3737{
    38   Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl;
     38  DoLog(3) && (Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl);
    3939  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
    40     Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl;
     40    DoLog(4) && (Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl);
    4141    delete (*ListRunner);
    4242  }
    43   Log() << Verbose(4) << "Freeing ListOfMolecules." << endl;
     43  DoLog(4) && (Log() << Verbose(4) << "Freeing ListOfMolecules." << endl);
    4444  ListOfMolecules.clear(); // empty list
    4545};
    … …  
    145145
    146146  // header
    147   Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
    148   Log() << Verbose(0) << "-----------------------------------------------" << endl;
     147  DoLog(0) && (Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl);
     148  DoLog(0) && (Log() << Verbose(0) << "-----------------------------------------------" << endl);
    149149  if (ListOfMolecules.size() == 0)
    150     Log() << Verbose(0) << "\tNone" << endl;
     150    DoLog(0) && (Log() << Verbose(0) << "\tNone" << endl);
    151151  else {
    152152    Origin.Zero();
    … …  
    165165      }
    166166      // output Index, Name, number of atoms, chemical formula
    167       Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
     167      DoLog(0) && (Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t");
    168168      Elemental = (*ListRunner)->elemente->end;
    169169      while(Elemental->previous != (*ListRunner)->elemente->start) {
    170170        Elemental = Elemental->previous;
    171171        if (Counts[Elemental->Z] != 0)
    172           Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z];
     172          DoLog(0) && (Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z]);
    173173      }
    174174      // Center and size
    175       Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     175      DoLog(0) && (Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl);
    176176    }
    177177  }
    … …  
    339339  while (Walker->next != srcmol->end) {
    340340    Walker = Walker->next;
    341     Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl;
     341    DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl);
    342342    if (!TesselStruct->IsInnerPoint(Walker->x, LCList)) {
    343343      CopyAtoms[Walker->nr] = new atom(Walker);
    … …  
    348348    }
    349349  }
    350   Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.";
     350  DoLog(1) && (Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.");
    351351
    352352  // go through all bonds and add as well
    … …  
    354354  while(Binder->next != srcmol->last) {
    355355    Binder = Binder->next;
    356     Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl;
     356    DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl);
    357357    mol->AddBond(CopyAtoms[Binder->leftatom->nr], CopyAtoms[Binder->rightatom->nr], Binder->BondDegree);
    358358  }
    … …  
    366366void MoleculeListClass::Output(ofstream *out)
    367367{
    368   Log() << Verbose(1) << "MoleculeList: ";
     368  DoLog(1) && (Log() << Verbose(1) << "MoleculeList: ");
    369369  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    370     Log() << Verbose(0) << *ListRunner << "\t";
    371   Log() << Verbose(0) << endl;
     370    DoLog(0) && (Log() << Verbose(0) << *ListRunner << "\t");
     371  DoLog(0) && (Log() << Verbose(0) << endl);
    372372};
    373373
    … …  
    395395  char *FragmentNumber = NULL;
    396396
    397   Log() << Verbose(1) << "Saving hydrogen saturation correction ... ";
     397  DoLog(1) && (Log() << Verbose(1) << "Saving hydrogen saturation correction ... ");
    398398  // 0. parse in fit constant files that should have the same dimension as the final energy files
    399399  // 0a. find dimension of matrices with constants
    … …  
    405405  input.open(line.c_str());
    406406  if (input == NULL) {
    407     Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
     407    DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
    408408    return false;
    409409  }
    … …  
    422422    b++;
    423423  }
    424   Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ";
     424  DoLog(0) && (Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ");
    425425  input.close();
    426426
    … …  
    465465  }
    466466  for (int k = 0; k < 3; k++) {
    467     Log() << Verbose(0) << "Constants " << k << ":" << endl;
     467    DoLog(0) && (Log() << Verbose(0) << "Constants " << k << ":" << endl);
    468468    for (int j = 0; j < b; j++) {
    469469      for (int i = 0; i < a; i++) {
    470         Log() << Verbose(0) << FitConstant[k][i][j] << "\t";
     470        DoLog(0) && (Log() << Verbose(0) << FitConstant[k][i][j] << "\t");
    471471      }
    472       Log() << Verbose(0) << endl;
    473     }
    474     Log() << Verbose(0) << endl;
     472      DoLog(0) && (Log() << Verbose(0) << endl);
     473    }
     474    DoLog(0) && (Log() << Verbose(0) << endl);
    475475  }
    476476
    … …  
    560560  }
    561561  Free(&FitConstant);
    562   Log() << Verbose(0) << "done." << endl;
     562  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
    563563  return true;
    564564};
    … …  
    580580
    581581  // open file for the force factors
    582   Log() << Verbose(1) << "Saving  force factors ... ";
     582  DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
    583583  line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
    584584  ForcesFile.open(line.str().c_str(), ios::out);
    … …  
    608608    }
    609609    ForcesFile.close();
    610     Log() << Verbose(1) << "done." << endl;
     610    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    611611  } else {
    612612    status = false;
    613     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     613    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    614614  }
    615615  ForcesFile.close();
    … …  
    663663    sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    664664    outputFragment.open(FragmentName, ios::out);
    665     Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...";
     665    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
    666666    if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
    667       Log() << Verbose(0) << " done." << endl;
     667      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
    668668    else
    669       Log() << Verbose(0) << " failed." << endl;
     669      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
    670670    result = result && intermediateResult;
    671671    outputFragment.close();
    … …  
    673673
    674674    // list atoms in fragment for debugging
    675     Log() << Verbose(2) << "Contained atoms: ";
     675    DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
    676676    Walker = (*ListRunner)->start;
    677677    while (Walker->next != (*ListRunner)->end) {
    678678      Walker = Walker->next;
    679       Log() << Verbose(0) << Walker->Name << " ";
    680     }
    681     Log() << Verbose(0) << endl;
     679      DoLog(0) && (Log() << Verbose(0) << Walker->Name << " ");
     680    }
     681    DoLog(0) && (Log() << Verbose(0) << endl);
    682682
    683683    // center on edge
    … …  
    703703    // and save as config
    704704    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    705     Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...";
     705    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
    706706    if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
    707       Log() << Verbose(0) << " done." << endl;
     707      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
    708708    else
    709       Log() << Verbose(0) << " failed." << endl;
     709      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
    710710    result = result && intermediateResult;
    711711
    … …  
    715715    // and save as mpqc input file
    716716    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    717     Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...";
     717    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
    718718    if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
    719       Log() << Verbose(2) << " done." << endl;
     719      DoLog(2) && (Log() << Verbose(2) << " done." << endl);
    720720    else
    721       Log() << Verbose(0) << " failed." << endl;
     721      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
    722722
    723723    result = result && intermediateResult;
    … …  
    726726    Free(&FragmentNumber);
    727727  }
    728   Log() << Verbose(0) << " done." << endl;
     728  DoLog(0) && (Log() << Verbose(0) << " done." << endl);
    729729
    730730  // printing final number
    731   Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl;
     731  DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
    732732
    733733  // restore cell_size
    … …  
    768768      Walker = Advancer;
    769769      Advancer = Advancer->next;
    770       Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
     770      DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
    771771      unlink(Walker);
    772772      Walker->father = Walker;
    … …  
    819819      strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
    820820    }
    821     Log() << Verbose(1) << "MolName is " << molecules[i]->name << endl;
     821    DoLog(1) && (Log() << Verbose(1) << "MolName is " << molecules[i]->name << endl);
    822822    insert(molecules[i]);
    823823  }
    … …  
    848848    FragmentCounter = MolMap[Walker->nr];
    849849    if (FragmentCounter != 0) {
    850       Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
     850      DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
    851851      unlink(Walker);
    852852      molecules[FragmentCounter-1]->AddAtom(Walker);    // counting starts at 1
    … …  
    873873  Free(&MolMap);
    874874  Free(&molecules);
    875   Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl;
     875  DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
    876876};
    877877
    … …  
    982982  int AtomNo;
    983983
    984   Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl;
     984  DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
    985985  // fill ListOfLocalAtoms if NULL was given
    986986  if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
    987     Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
     987    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
    988988    return false;
    989989  }
    990990
    991991  if (status) {
    992     Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl;
     992    DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
    993993    // remove every bond from the list
    994994    bond *Binder = NULL;
    … …  
    10111011            Leaf->AddBond(Walker, OtherWalker, (*Runner)->BondDegree);
    10121012        } else {
    1013           Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl;
     1013          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl);
    10141014          status = false;
    10151015        }
    … …  
    10241024      Free(&ListOfLocalAtoms);
    10251025  }
    1026   Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl;
     1026  DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
    10271027  return status;
    10281028};
    … …  
    10571057        next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter);
    10581058    } else {
    1059       Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl;
     1059      DoLog(1) && (Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl);
    10601060      return false;
    10611061    }
    … …  
    10631063    return true;
    10641064  } else {
    1065     Log() << Verbose(1) << "Rootstack is NULL." << endl;
     1065    DoLog(1) && (Log() << Verbose(1) << "Rootstack is NULL." << endl);
    10661066    return false;
    10671067  }
    … …  
    11131113  int KeySetCounter = 0;
    11141114
    1115   Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl;
     1115  DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
    11161116  // fill ListOfLocalAtoms if NULL was given
    11171117  if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
    1118     Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
     1118    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
    11191119    return false;
    11201120  }
    … …  
    11441144    delete (TempSet);
    11451145    if (KeySetCounter == 0) {// if there are no keysets, delete the list
    1146       Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl;
     1146      DoLog(1) && (Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl);
    11471147      delete (FragmentList[FragmentCounter]);
    11481148    } else
    1149       Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl;
     1149      DoLog(1) && (Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl);
    11501150    FragmentCounter++;
    11511151    if (next != NULL)
    … …  
    11531153    FragmentCounter--;
    11541154  } else
    1155     Log() << Verbose(1) << "KeySetList is NULL or empty." << endl;
     1155    DoLog(1) && (Log() << Verbose(1) << "KeySetList is NULL or empty." << endl);
    11561156
    11571157  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
    … …  
    11611161      Free(&ListOfLocalAtoms);
    11621162  }
    1163   Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl;
     1163  DoLog(1) && (Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl);
    11641164  return status;
    11651165};
    … …  
    11741174void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
    11751175{
    1176   Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl;
     1176  DoLog(1) && (Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl);
    11771177  KeySet *TempSet = new KeySet;
    11781178  if (FragmentList[FragmentCounter] != NULL) {
    … …  
    11851185    delete (TempSet);
    11861186  } else {
    1187     Log() << Verbose(1) << "FragmentList is NULL." << endl;
     1187    DoLog(1) && (Log() << Verbose(1) << "FragmentList is NULL." << endl);
    11881188  }
    11891189  if (next != NULL)
    11901190    next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
    11911191  FragmentCounter--;
    1192   Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl;
     1192  DoLog(1) && (Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl);
    11931193};
    11941194
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