Changeset 47d041 for src/Actions/MoleculeAction

Timestamp:

Nov 3, 2011, 7:44:01 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:

41a467

Parents:

50e4e5

git-author:

Frederik Heber <heber@…> (10/27/11 11:53:58)

git-committer:

Frederik Heber <heber@…> (11/03/11 19:44:01)

Message:

HUGE: Removed all calls to Log(), eLog(), replaced by LOG() and ELOG().

• Replaced DoLog(.) && (Log() << Verbose(.) << ... << std::endl) by Log(., ...).
• Replaced Log() << Verbose(.) << .. << by Log(., ...)
• on multiline used stringstream to generate and message which was finally used in LOG(., output.str())
• there should be no more occurence of Log(). LOG() and ELOG() must be used instead.
• Eventually, this will allow for storing all errors and re-printing them on program exit which would be very helpful to ascertain error-free runs for the user.

Location:

src/Actions/MoleculeAction

Files:

• FillVoidWithMoleculeAction.cpp (modified) (4 diffs)
• FillWithMoleculeAction.cpp (modified) (4 diffs)
• LoadAction.cpp (modified) (4 diffs)
• RotateAroundSelfByAngleAction.cpp (modified) (3 diffs)
• RotateToPrincipalAxisSystemAction.cpp (modified) (1 diff)
• SaveAdjacencyAction.cpp (modified) (1 diff)
• SaveBondsAction.cpp (modified) (1 diff)
• SaveSelectedMoleculesAction.cpp (modified) (3 diffs)
• SaveTemperatureAction.cpp (modified) (2 diffs)
• SuspendInWaterAction.cpp (modified) (1 diff)
• VerletIntegrationAction.cpp (modified) (2 diffs)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -51 +51 @@
 
   if (!boost::filesystem::exists(params.fillername)) {
-    DoeLog(1) && (eLog() << Verbose(1) << "File with filler molecule " << params.fillername << " does not exist!" << endl);
+    ELOG(1, "File with filler molecule " << params.fillername << " does not exist!");
     return Action::failure;
   }
 
-  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
+  LOG(1, "INFO: Filling Box with water molecules, "
       << " minimum distance to molecules" << params.boundary
       << ", random atom displacement " << params.RandAtomDisplacement
@@ -61 +61 @@
       << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
       << "), MinDistance " << params.MinDistance
-      << ", DoRotate " << params.DoRotate << "." << endl);
+      << ", DoRotate " << params.DoRotate << ".");
   // construct water molecule
   std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
-//  DoLog(0) && (Log() << Verbose(0) << presentmolecules.size() << " molecules initially are present." << std::endl);
+//  LOG(0, presentmolecules.size() << " molecules initially are present.");
   std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
   ifstream input;
@@ -95 +95 @@
   // (we can in general remove more quickly from a list than a vector)
   std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules are present." << std::endl);
+//  LOG(0, fillermolecules.size() << " molecules are present.");
   std::list<molecule *> fillermolecules_list;
   std::copy( fillermolecules.begin(),  fillermolecules.end(), std::back_inserter( fillermolecules_list ));
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules have been copied." << std::endl);
+//  LOG(0, fillermolecules_list.size() << " molecules have been copied.");
   for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
       iter != presentmolecules.end();
@@ -104 +104 @@
     fillermolecules_list.remove(*iter);
   }
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules left after removal." << std::endl);
+//  LOG(0, fillermolecules_list.size() << " molecules left after removal.");
   fillermolecules.clear();
   std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));
 
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules have been inserted." << std::endl);
+//  LOG(0, fillermolecules.size() << " molecules have been inserted.");
 
   return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,params));

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -49 +49 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
+  LOG(1, "INFO: Filling Box with water molecules, "
       << " minimum distance to molecules" << params.boundary
       << ", random atom displacement " << params.RandAtomDisplacement
@@ -55 +55 @@
       << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
       << "), MinDistance " << params.MaxDistance
-      << ", DoRotate " << params.DoRotate << "." << endl);
+      << ", DoRotate " << params.DoRotate << ".");
   // construct water molecule
   std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
-//  DoLog(0) && (Log() << Verbose(0) << presentmolecules.size() << " molecules initially are present." << std::endl);
+//  LOG(0, presentmolecules.size() << " molecules initially are present.");
   std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
   ifstream input;
@@ -113 +113 @@
   // (we can in general remove more quickly from a list than a vector)
   std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules are present." << std::endl);
+//  LOG(0, fillermolecules.size() << " molecules are present.");
   std::list<molecule *> fillermolecules_list;
   std::copy( fillermolecules.begin(),  fillermolecules.end(), std::back_inserter( fillermolecules_list ));
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules have been copied." << std::endl);
+//  LOG(0, fillermolecules_list.size() << " molecules have been copied.");
   for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
       iter != presentmolecules.end();
@@ -122 +122 @@
     fillermolecules_list.remove(*iter);
   }
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules left after removal." << std::endl);
+//  LOG(0, fillermolecules_list.size() << " molecules left after removal.");
   fillermolecules.clear();
   std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));
 
-//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules have been inserted." << std::endl);
+//  LOG(0, fillermolecules.size() << " molecules have been inserted.");
 
   return Action::state_ptr(new MoleculeFillWithMoleculeState(fillermolecules,params));

src/Actions/MoleculeAction/LoadAction.cpp

@@ -48 +48 @@
   // parsing file if present
   if (!boost::filesystem::exists(params.filename)) {
-    DoLog(1) && (Log() << Verbose(1) << "Specified input file " << params.filename << " not found." << endl);
+    LOG(1, "Specified input file " << params.filename << " not found.");
     return Action::failure;
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "Specified input file found, parsing ... ");
+    LOG(1, "Specified input file found, parsing ... ");
 
     // extract suffix
@@ -66 +66 @@
 #endif
     } else {
-      DoeLog(1) && (eLog() << Verbose(1) << "Input file does not have a suffix, cannot recognize format." << endl);
+      ELOG(1, "Input file does not have a suffix, cannot recognize format.");
       return Action::failure;
     }
@@ -89 +89 @@
     MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
     (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
-    DoLog(0) && (Log() << Verbose(0) << "Chemical formula is " << (*iter)->getFormula() << std::endl);
+    LOG(0, "Chemical formula is " << (*iter)->getFormula());
 
     return Action::state_ptr(
@@ -136 +136 @@
   (*iter)->SetNameFromFilename(state->FilenamePrefix.c_str());
   (*iter)->setId(state->molId);
-  DoLog(0) && (Log() << Verbose(0) << "Chemical formula is " << (*iter)->getFormula() << std::endl);
+  LOG(0, "Chemical formula is " << (*iter)->getFormula());
 
   return Action::state_ptr(

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp

@@ -59 +59 @@
     // Creation Line that is the rotation axis
     Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
-    DoLog(0) && (Log() << Verbose(0) <<  "Center of gravity is " << *CenterOfGravity << "." << std::endl);
+    LOG(0,  "Center of gravity is " << *CenterOfGravity << ".");
     Line RotationAxis(*CenterOfGravity, params.Axis);
     delete(CenterOfGravity);
-    DoLog(0) && (Log() << Verbose(0) << "Rotate " << mol->getName() << " around self by " << params.angle << " radian around axis " << RotationAxis << "." << endl);
+    LOG(0, "Rotate " << mol->getName() << " around self by " << params.angle << " radian around axis " << RotationAxis << ".");
 
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
       (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), params.angle));
     }
-    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
+    LOG(0, "done.");
   }
 
@@ -78 +78 @@
   BOOST_FOREACH(molecule *mol, state->selectedMolecules) {
     Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
-    DoLog(0) && (Log() << Verbose(0) <<  "Center of gravity is " << *CenterOfGravity << "." << std::endl);
+    LOG(0,  "Center of gravity is " << *CenterOfGravity << ".");
     Line RotationAxis(*CenterOfGravity, state->params.Axis);
     delete(CenterOfGravity);
-    DoLog(0) && (Log() << Verbose(0) << "Rotate " << mol->getName() << " around self by " << -state->params.angle << " radian around axis " << RotationAxis << "." << endl);
+    LOG(0, "Rotate " << mol->getName() << " around self by " << -state->params.angle << " radian around axis " << RotationAxis << ".");
 
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
@@ -96 +96 @@
   BOOST_FOREACH(molecule *mol, state->selectedMolecules) {
     Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
-    DoLog(0) && (Log() << Verbose(0) <<  "Center of gravity is " << *CenterOfGravity << "." << std::endl);
+    LOG(0,  "Center of gravity is " << *CenterOfGravity << ".");
     Line RotationAxis(*CenterOfGravity, state->params.Axis);
     delete(CenterOfGravity);
-    DoLog(0) && (Log() << Verbose(0) << "Rotate " << mol->getName() << " around self by " << state->params.angle << " radian around axis " << RotationAxis << "." << endl);
+    LOG(0, "Rotate " << mol->getName() << " around self by " << state->params.angle << " radian around axis " << RotationAxis << ".");
 
     for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

@@ -48 +48 @@
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
-    DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
+    LOG(0, "Converting to prinicipal axis system.");
 
     RealSpaceMatrix InertiaTensor = mol->getInertiaTensor();

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -47 +47 @@
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
-    DoLog(0) && (Log() << Verbose(0) << "Storing adjacency to path " << params.adjacencyfile << "." << endl);
+    LOG(0, "Storing adjacency to path " << params.adjacencyfile << ".");
     // TODO: sollte stream nicht filename benutzen, besser fuer unit test
 #if BOOST_VERSION >= 104600

src/Actions/MoleculeAction/SaveBondsAction.cpp

@@ -47 +47 @@
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
-    DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << params.bondsfile << "." << endl);
+    LOG(0, "Storing bonds to path " << params.bondsfile << ".");
     // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
 #if BOOST_VERSION >= 104600

src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp

@@ -41 +41 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Storing world to file " << params.filename << "." << endl);
+  LOG(1, "Storing world to file " << params.filename << ".");
 
   // extract suffix
@@ -56 +56 @@
 #endif
   } else {
-    DoeLog(1) && (eLog() << Verbose(1) << "Output file does not have a suffix, cannot recognize format." << endl);
+    ELOG(1, "Output file does not have a suffix, cannot recognize format.");
     return Action::failure;
   }
@@ -67 +67 @@
     FormatParserStorage::getInstance().saveSelectedMolecules(output, FilenameSuffix);
   } else {
-    DoeLog(1) && (eLog() << Verbose(1) << "Could not open file " << params.filename << "." << endl);
+    ELOG(1, "Could not open file " << params.filename << ".");
   }
   output.close();

src/Actions/MoleculeAction/SaveTemperatureAction.cpp

@@ -45 +45 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Storing temperatures in " << params.temperaturefile << "." << endl);
+  LOG(1, "Storing temperatures in " << params.temperaturefile << ".");
   ofstream output;
   output.open(params.temperaturefile.string().c_str(), ios::trunc);
@@ -52 +52 @@
   OutputTemperature<std::vector<atom *> > writer(set);
   if (output.fail() || !writer((ofstream * const) &output, 0, MDSteps))
-    DoLog(2) && (Log() << Verbose(2) << "File could not be written." << endl);
+    LOG(2, "File could not be written.");
   else
-    DoLog(2) && (Log() << Verbose(2) << "File stored." << endl);
+    LOG(2, "File stored.");
   output.close();
   return Action::success;

src/Actions/MoleculeAction/SuspendInWaterAction.cpp

@@ -46 +46 @@
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
-    DoLog(0) && (Log() << Verbose(0) << "Evaluating necessary cell volume for a cluster suspended in water.");
+    LOG(0, "Evaluating necessary cell volume for a cluster suspended in water.");
     if (params.density < 1.0) {
-      DoeLog(1) && (eLog()<< Verbose(1) << "Density must be greater than 1.0g/cm^3!" << endl);
+      ELOG(1, "Density must be greater than 1.0g/cm^3!");
     } else {
       PrepareClustersinWater(World::getInstance().getConfig(), mol, volume, params.density);  // if volume == 0, will calculate from ConvexEnvelope

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -46 +46 @@
 
 
-  DoLog(1) && (Log() << Verbose(1) << "Parsing forces file and Verlet integrating." << endl);
+  LOG(1, "Parsing forces file and Verlet integrating.");
   // TODO: sollte besser stream nutzen, nicht filename direkt (es sei denn, ist prefix), besser fuer unit test
   char outputname[MAXSTRINGSIZE];
@@ -54 +54 @@
     VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat, step, false);
     if (!Verlet(outputname, 1, 0, params.FixedCenterOfMass))
-      DoLog(2) && (Log() << Verbose(2) << "File " << params.forcesfile << " not found." << endl);
+      LOG(2, "File " << params.forcesfile << " not found.");
     else
-      DoLog(2) && (Log() << Verbose(2) << "File " << params.forcesfile << " found and parsed." << endl);
+      LOG(2, "File " << params.forcesfile << " found and parsed.");
   }