Changeset ad7270 for src

Timestamp:

Dec 16, 2010, 5:32:23 PM (14 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:

2a0a9e3

Parents:

f4d063

git-author:

Frederik Heber <heber@…> (12/15/10 16:26:52)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:23)

Message:

Reduced initial verbosity of code.

FIX:

• initUI() - no more admonishing of missing bond length table.

The following messages have been placed in comments:

• Registering of Action/Options.
• Looking for KnownTypes.
• Stating MenuNames, Separators and submenu creations.
• No more listing of parsed elements.
• No more listing of thermostats.

The following messages have been added:

• prepended scanning arguments in CommandLineParser::scan...().
• prepended running arguments in CommandLineWindow::display().
• additional new line after ProgamHeader().
• correct CommandLine UI setting to occur before arguments are parsed.
• changed verbosity levels of CommandLineParser::scanforSequenceOfArguments(), also all use DoLog(), i.e. global verbosity makes them be listed again.

NOTE:

• MemDebug: as delete NULL is safe, we do not warn when this occurs. Also, in Qt this happens a lot.

TESTFIX:

• setting global verbosity to 1, messed with Standard_Options/1. There we set verbosity to 9 to avoid this in the future.

Location:

src

Files:

• Actions/CommandAction/BondLengthTableAction.cpp (modified) (1 diff)
• Helpers/MemDebug.cpp (modified) (1 diff)
• ThermoStatContainer.cpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineParser.cpp (modified) (5 diffs)
• UIElements/CommandLineUI/CommandLineWindow.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) (3 diffs)
• UIElements/Menu/Menu.cpp (modified) (3 diffs)
• UIElements/Menu/MenuDescription.cpp (modified) (1 diff)
• UIElements/Menu/Qt4/QtMenu.hpp (modified) (2 diffs)
• builder_init.cpp (modified) (3 diffs)
• periodentafel.cpp (modified) (3 diffs)

src/Actions/CommandAction/BondLengthTableAction.cpp

@@ -47 +47 @@
   if (configuration->BG == NULL) {
     configuration->BG = new BondGraph(configuration->GetIsAngstroem());
-    if ((!params.BondGraphFileName.empty()) && (configuration->BG->LoadBondLengthTable(params.BondGraphFileName.string()))) {
+    if ((!params.BondGraphFileName.empty())
+        && boost::filesystem::exists(params.BondGraphFileName)
+        && (configuration->BG->LoadBondLengthTable(params.BondGraphFileName.string()))) {
       DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
       return Action::success;

src/Helpers/MemDebug.cpp

@@ -509 +509 @@
 void operator delete(void *ptr) throw() {
   if(!ptr){
-    cerr << "Warning: Deleting NULL pointer" << endl;
+    //cerr << "Warning: Deleting NULL pointer" << endl;
     return;
   }

src/ThermoStatContainer.cpp

@@ -54 +54 @@
   ThermostatTraits<Thermostat> *WoodcockTrait = new ThermostatTraits<Woodcock>();
   availThermostats[WoodcockTrait->getName()] = WoodcockTrait;
-  for(traitsMap::iterator iter = availThermostats.begin();iter!=availThermostats.end();++iter){
-    cout << iter->first << endl;
-  }
+
+  // for debugging: list all thermostats
+//  cout << "List of known thermostats: ";
+//  for(traitsMap::iterator iter = availThermostats.begin();iter!=availThermostats.end();++iter){
+//    cout << iter->first << " ";
+//  }
+//  cout << endl;
+
   ASSERT(availThermostats.size()==6,"Not all implemented thermostats referenced!\nDid you check the names in the traits?");
   activeThermostat=new Berendsen();

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -97 +97 @@
       const OptionTrait* const currentOption = OptionRegistry::getInstance().getOptionByName(optioniter->first);
       // add the option
-      std::cout << "Registering Option "
-          << currentOption->getName()
-          << " with type '" << currentOption->getTypeName() << "' "
-          << " with description '" << currentOption->getDescription() << "' ";
-      if (currentOption->hasShortForm())
-        std::cout << ", with short form " << currentOption->getShortForm();
-      else
-        std::cout << ", with no short form ";
-      if (currentOption->hasDefaultValue())
-        std::cout << ", with default value " << currentOption->getDefaultValue();
-      else
-        std::cout << ", with no default value ";
-      std::cout << std::endl;
+//      std::cout << "Registering Option "
+//          << currentOption->getName()
+//          << " with type '" << currentOption->getTypeName() << "' "
+//          << " with description '" << currentOption->getDescription() << "' ";
+//      if (currentOption->hasShortForm())
+//        std::cout << ", with short form " << currentOption->getShortForm();
+//      else
+//        std::cout << ", with no short form ";
+//      if (currentOption->hasDefaultValue())
+//        std::cout << ", with default value " << currentOption->getDefaultValue();
+//      else
+//        std::cout << ", with no default value ";
+//      std::cout << std::endl;
 
       AddOptionToParser(currentOption, (CmdParserLookup["options"]));
@@ -116 +116 @@
     if (!ActionAlreadyAdded_flag) {
       // add the action
-      std::cout << "Registering Action "
-          << currentAction->Traits.getName()
-          << " in menu " << currentAction->Traits.getMenuName()
-          << " with type '" << currentAction->Traits.getTypeName() << "' "
-          << " with description '" << currentAction->Traits.getDescription() << "' ";
-      if (currentAction->Traits.hasShortForm())
-        std::cout << ", with short form " << currentAction->Traits.getShortForm();
-      else
-        std::cout << ", with no short form ";
-      if (currentAction->Traits.hasDefaultValue())
-        std::cout << ", with default value " << currentAction->Traits.getDefaultValue();
-      else
-        std::cout << ", with no default value ";
-      std::cout  << std::endl;
+//      std::cout << "Registering Action "
+//          << currentAction->Traits.getName()
+//          << " in menu " << currentAction->Traits.getMenuName()
+//          << " with type '" << currentAction->Traits.getTypeName() << "' "
+//          << " with description '" << currentAction->Traits.getDescription() << "' ";
+//      if (currentAction->Traits.hasShortForm())
+//        std::cout << ", with short form " << currentAction->Traits.getShortForm();
+//      else
+//        std::cout << ", with no short form ";
+//      if (currentAction->Traits.hasDefaultValue())
+//        std::cout << ", with default value " << currentAction->Traits.getDefaultValue();
+//      else
+//        std::cout << ", with no default value ";
+//      std::cout  << std::endl;
 
       ASSERT(CmdParserLookup.find(currentAction->Traits.getMenuName()) != CmdParserLookup.end(),
@@ -156 +156 @@
   ASSERT(currentOption != NULL, "CommandLineParser::AddOptionToParser() - currentOption is NULL!");
   // add other options
-  std::cout << "Adding Action " << currentOption->getName() << " with type " << currentOption->getType()->name() << " and KeyandShortform " << currentOption->getKeyAndShortForm() << " to CommandLineParser." << std::endl;
+  //std::cout << "Adding Action " << currentOption->getName() << " with type " << currentOption->getType()->name() << " and KeyandShortform " << currentOption->getKeyAndShortForm() << " to CommandLineParser." << std::endl;
   switch(TypeToEnums.getEnumforType(currentOption->getType())) {
     default:
@@ -369 +369 @@
 {
   std::map <std::string, std::string> ShortFormToActionMap = getShortFormToActionMap();
+  DoLog(0) && (Log() << Verbose(0) << "Scanning command line arguments and recognizing Actions." << std::endl);
   // go through all arguments
   for (int i=1;i<argc;i++) {
-    (std::cout << Verbose(1) << "Checking on " << argv[i] << std::endl);
+    DoLog(2) && (Log() << Verbose(2) << "Checking on " << argv[i] << std::endl);
     // check whether they
     if (argv[i][0] == '-') { // .. begin with -
-      (cout << Verbose(1) << "Possible argument: " << argv[i] << endl);
+      DoLog(2) && (Log() << Verbose(2) << "Possible argument: " << argv[i] << endl);
       if (argv[i][1] == '-') { // .. or --
-        (cout << Verbose(1) << "Putting " << argv[i] << " into the sequence." << endl);
+        DoLog(1) && (Log() << Verbose(1) << "Putting " << argv[i] << " into the sequence." << endl);
         SequenceOfActions.push_back(&(argv[i][2]));
         //  .. and check that next letter is not numeric, if so insert
@@ -382 +383 @@
         std::map <std::string, std::string>::iterator iter = ShortFormToActionMap.find(&(argv[i][1]));
         if (iter != ShortFormToActionMap.end()) {
-          (cout << Verbose(1) << "Putting " << iter->second << " for " << iter->first << " into the sequence." << endl);
+          DoLog(1) && (Log() << Verbose(1) << "Putting " << iter->second << " for " << iter->first << " into the sequence." << endl);
           SequenceOfActions.push_back(iter->second);
         }

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -25 +25 @@
 #include "CommandLineUI/CommandLineStatusIndicator.hpp"
 
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
+
 #include "Actions/Action.hpp"
 #include "Actions/ActionRegistry.hpp"
@@ -50 +53 @@
 
   // go through all possible actions
+  DoLog(0) && (Log() << Verbose(0) << "Calling Actions ... " << std::endl);
   for (std::list<std::string>::iterator CommandRunner = CommandLineParser::getInstance().SequenceOfActions.begin(); CommandRunner != CommandLineParser::getInstance().SequenceOfActions.end(); ++CommandRunner) {
-    cout << "Checking presence of " << *CommandRunner << ": ";
     if (ActionRegistry::getInstance().isActionPresentByName(*CommandRunner)) {
-      cout << "calling " << *CommandRunner << endl;
+      DoLog(1) && (Log() << Verbose(1)
+          << "Checking presence of " << *CommandRunner << ": "
+          << "calling " << *CommandRunner << endl);
       ActionRegistry::getInstance().getActionByName(*CommandRunner)->call();
     } else {
-      cout << "absent." << endl;
+      DoLog(1) && (Log() << Verbose(1)
+          << "Checking presence of " << *CommandRunner << ": "
+          << "absent." << endl);
     }
   }

src/UIElements/CommandLineUI/TypeEnumContainer.cpp

@@ -64 +64 @@
   TypeEnumMap[&typeid(std::vector<const element *>)] = ListOfElementsType;
 
-  ListAllKnownTypes();
+  // for debugging: list all stored types
+  //ListAllKnownTypes();
 };
 
@@ -83 +84 @@
     std::cout << " Known type is " << (iter->first)->name() << " or enum " << iter->second << std::endl;
   }
-  std::cout << "BoxVector type is " << typeid(BoxVector).name() << std::endl;
-  std::cout << "Vector type is " << typeid(Vector).name() << std::endl;
-  std::cout << "VectorValue type is " << typeid(VectorValue).name() << std::endl;
 }
 
@@ -94 +92 @@
 enum TypeEnumContainer::EnumOfTypes TypeEnumContainer::getEnumforType(const std::type_info *_type)
 {
-  std::cout << "Looking for type " << _type->name() << std::endl;
+  //std::cout << "Looking for type " << _type->name() << std::endl;
   ASSERT(TypeEnumMap.find(_type) != TypeEnumMap.end(),
       "CommandLineParser::getEnumforType() - cannot find the type as enum!.");

src/UIElements/Menu/Menu.cpp

@@ -76 +76 @@
         const std::string &TopName = iter->second.first;
         const int &MenuPosition = iter->second.second;
-        std::cout << "MenuName is " << MenuName
-            << ", TopName is " << TopName
-            << " and Position is " << MenuPosition
-            << std::endl;
+//        std::cout << "MenuName is " << MenuName
+//            << ", TopName is " << TopName
+//            << " and Position is " << MenuPosition
+//            << std::endl;
 
         // does it belong to us?
@@ -125 +125 @@
 void Menu::addSeparator()
 {
-  std::cout << "Creating separator at position " << TopPosition << std::endl;
+//  std::cout << "Creating separator at position " << TopPosition << std::endl;
   ASSERT( LastItem != SeparatorItem,
       "Menu::populate() - adding another separator after a separator!");
@@ -135 +135 @@
 void Menu::addSubmenu(const std::string &MenuName, const int MenuPosition)
 {
-  std::cout << "Creating top-level menu " << MenuName
-      << " at position " << TopPosition << std::endl;
+//  std::cout << "Creating top-level menu " << MenuName
+//      << " at position " << TopPosition << std::endl;
   ASSERT (!isPresent(MenuName),
       "Menu::addSubmenu() - trying to add menu "+MenuName+" with already present token!");

src/UIElements/Menu/MenuDescription.cpp

@@ -89 +89 @@
 MenuDescription::~MenuDescription()
 {
-  std::cout << "MenuDescription: clearing maps ... " << std::endl;
+  //std::cout << "MenuDescription: clearing maps ... " << std::endl;
   for (IterableMap::iterator iter = MenuPositionMap->begin(); !MenuPositionMap->empty(); iter = MenuPositionMap->begin())
     MenuPositionMap->erase(iter);

src/UIElements/Menu/Qt4/QtMenu.hpp

@@ -72 +72 @@
         CharRunner != ActionName.end();
         ++CharRunner) {
-      std::cout << "Current char is " << *CharRunner << std::endl;
+//      std::cout << "Current char is " << *CharRunner << std::endl;
       if (!Inserted) {
         Inserter = ShortcutMap.insert(
@@ -78 +78 @@
             );
         if (Inserter.second) {
-          std::cout << "Accelerator is " << *CharRunner << std::endl;
+//          std::cout << "Accelerator is " << *CharRunner << std::endl;
           newname += '&';
           Inserted = true;

src/builder_init.cpp

@@ -67 +67 @@
   cout << "`MoleCuilder - to create and alter molecular systems." << endl;
   cout << "Copyright (C) 2010  University Bonn. All rights reserved." << endl;
+  cout << endl;
 }
 
@@ -80 +81 @@
   ProgramHeader();
 
-  setVerbosity(0);
+  setVerbosity(1);
   // need to init the history before any action is created
   ActionHistory::init();
@@ -101 +102 @@
   if (World::getInstance().getConfig()->BG == NULL) {
     World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
-    if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
-      DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
-    } else {
-      DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
+    if (boost::filesystem::exists(BondGraphFileName)) {
+      if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
+        DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
+      } else {
+        DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
+      }
     }
   }
   // handle remaining arguments by CommandLineParser
   if (argc>1) {
+    DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
     CommandLineParser::getInstance().InitializeCommandArguments();
     CommandLineParser::getInstance().Run(argc,argv);
-    DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
     UIFactory::registerFactory(new CommandLineUIFactory::description());
     UIFactory::makeUserInterface("CommandLine");

src/periodentafel.cpp

@@ -307 +307 @@
     //cout << "First header: " << header1tmp << endl;
     //cout << "Second header: " << header2tmp << endl;
-    DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
+//    DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
     while (!input.eof()) {
       element *neues = new element;
@@ -332 +332 @@
       if ((neues->getNumber() > 0) && (neues->getNumber() < MAX_ELEMENTS)) {
         parsedElements[neues->Z] = neues;
-        DoLog(0) && (Log() << Verbose(0) << " " << *neues);
+//        DoLog(0) && (Log() << Verbose(0) << " " << *neues);
       } else {
         DoeLog(2) && (eLog() << Verbose(2) << "Detected empty line or invalid element in elements db, discarding." << endl);
@@ -345 +345 @@
       }
     }
-    DoLog(0) && (Log() << Verbose(0) << endl);
+//    DoLog(0) && (Log() << Verbose(0) << endl);
   } else {
     DoeLog(1) && (eLog() << Verbose(1) << "Could not open the database." << endl);