Changeset 47d041 for src/moleculelist.cpp

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, Candidate_v1.7.0, Candidate_v1.7.1, 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.

File:

• src/moleculelist.cpp (modified) (21 diffs)

src/moleculelist.cpp

@@ -56 +56 @@
 MoleculeListClass::~MoleculeListClass()
 {
-  DoLog(4) && (Log() << Verbose(4) << "Clearing ListOfMolecules." << endl);
+  LOG(4, "Clearing ListOfMolecules.");
   for(MoleculeList::iterator MolRunner = ListOfMolecules.begin(); MolRunner != ListOfMolecules.end(); ++MolRunner)
     (*MolRunner)->signOff(this);
@@ -111 +111 @@
 
   // sort each atom list and put the numbers into a list, then go through
-  //Log() << Verbose(0) << "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << "." << endl;
+  //LOG(0, "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << ".");
   // Yes those types are awkward... but check it for yourself it checks out this way
   molecule *const *mol1_ptr= static_cast<molecule *const *>(a);
@@ -238 +238 @@
 void MoleculeListClass::Output(std::ostream *out)
 {
-  DoLog(1) && (Log() << Verbose(1) << "MoleculeList: ");
-  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    DoLog(0) && (Log() << Verbose(0) << *ListRunner << "\t");
-  DoLog(0) && (Log() << Verbose(0) << endl);
+  if (DoLog(1)) {
+    std::stringstream output;
+    output << "MoleculeList: ";
+    for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
+      output << *ListRunner << "\t";
+      LOG(1, output.str());
+  }
 };
 
@@ -257 +260 @@
     number = (int)floor(((double)number / 10.));
     order++;
-    //Log() << Verbose(0) << "Number is " << number << ", order is " << order << "." << endl;
+    //LOG(0, "Number is " << number << ", order is " << order << ".");
   }
   // allocate string
@@ -268 +271 @@
     number = (int)floor(((double)number / 10.));
   }
-  //Log() << Verbose(0) << returnstring << endl;
+  //LOG(0, returnstring);
   return returnstring;
 };
@@ -292 +295 @@
   char *FragmentNumber = NULL;
 
-  DoLog(1) && (Log() << Verbose(1) << "Saving hydrogen saturation correction ... ");
+  LOG(1, "Saving hydrogen saturation correction ... ");
   // 0. parse in fit constant files that should have the same dimension as the final energy files
   // 0a. find dimension of matrices with constants
@@ -300 +303 @@
   input.open(line.c_str());
   if (input.fail()) {
-    DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
+    LOG(1, endl << "Unable to open " << line << ", is the directory correct?");
     return false;
   }
@@ -317 +320 @@
     b++;
   }
-  DoLog(0) && (Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ");
+  LOG(0, "I recognized " << a << " columns and " << b << " rows, ");
   input.close();
 
@@ -341 +344 @@
     input.open(line.c_str());
     if (input.fail()) {
-      DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
+      ELOG(0, endl << "Unable to open " << line << ", is the directory correct?");
       performCriticalExit();
       return false;
@@ -348 +351 @@
     while ((!input.eof()) && (k < b)) {
       input.getline(ParsedLine, 1023);
-      //Log() << Verbose(0) << "Current Line: " << ParsedLine << endl;
+      //LOG(1, "INFO: Current Line: " << ParsedLine);
       zeile.str(ParsedLine);
       zeile.clear();
       l = 0;
+      //std::stringstream output;
       while ((!zeile.eof()) && (l < a)) {
         zeile >> FitConstant[i][l][k];
-        //Log() << Verbose(0) << FitConstant[i][l][k] << "\t";
+        //output << FitConstant[i][l][k] << "\t";
         l++;
       }
-      //Log() << Verbose(0) << endl;
+      //LOG(1, "INFO: fit constant are " << output.str());
       k++;
     }
     input.close();
   }
-  for (int k = 0; k < 3; k++) {
-    DoLog(0) && (Log() << Verbose(0) << "Constants " << k << ":" << endl);
-    for (int j = 0; j < b; j++) {
-      for (int i = 0; i < a; i++) {
-        DoLog(0) && (Log() << Verbose(0) << FitConstant[k][i][j] << "\t");
-      }
-      DoLog(0) && (Log() << Verbose(0) << endl);
-    }
-    DoLog(0) && (Log() << Verbose(0) << endl);
+  if (DoLog(1)) {
+    for (int k = 0; k < 3; k++) {
+      std::stringstream output;
+      output << "Constants " << k << ": ";
+      for (int j = 0; j < b; j++) {
+        for (int i = 0; i < a; i++) {
+          output << FitConstant[k][i][j] << "\t";
+        }
+        output << std::endl;
+      }
+      LOG(0, output.str());
+    }
   }
 
@@ -386 +393 @@
     // 2. take every hydrogen that is a saturated one
     for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
-      //Log() << Verbose(1) << "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << "." << endl;
+      //LOG(1, "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
       if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->father == NULL)
           || ((*iter)->father->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
         for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
-          //Log() << Verbose(2) << "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << "." << endl;
+          //LOG(2, "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
           // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
           const BondList &bondlist = (*runner)->getListOfBonds();
@@ -397 +404 @@
             // 4. evaluate the morse potential for each matrix component and add up
             distance = (*runner)->distance(*(*iter));
-            //Log() << Verbose(0) << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":" << endl;
+            //std::stringstream output;
+            //output << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":";
             for (int k = 0; k < a; k++) {
               for (int j = 0; j < b; j++) {
@@ -408 +416 @@
                   default:
                     tmp = FitConstant[0][k][j] * pow(distance, FitConstant[1][k][j]) + FitConstant[2][k][j];
+                    break;
                 };
                 correction[k][j] -= tmp; // ground state is actually lower (disturbed by additional interaction)
-                //Log() << Verbose(0) << tmp << "\t";
+                //output << tmp << "\t";
               }
-              //Log() << Verbose(0) << endl;
+              //output << endl;
             }
-            //Log() << Verbose(0) << endl;
+            //LOG(0, output.str());
           }
         }
@@ -459 +468 @@
   }
   delete[](FitConstant);
-  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
+  LOG(0, "done.");
   return true;
 };
@@ -477 +486 @@
 
   // open file for the force factors
-  DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
+  LOG(1, "Saving  force factors ... ");
   if (!ForcesFile.fail()) {
-    //Log() << Verbose(1) << "Final AtomicForcesList: ";
     //output << prefix << "Forces" << endl;
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
@@ -488 +496 @@
             if ((*atomIter)->getType()->getNumber() == (*elemIter).first) {
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
-                //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
                 ForcesFile << SortIndex[(*atomIter)->GetTrueFather()->getNr()] << "\t";
               } else
@@ -500 +507 @@
     }
     ForcesFile.close();
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
+    LOG(1, "done.");
   } else {
     status = false;
-    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << filename << "." << endl);
+    LOG(1, "failed to open file " << filename << ".");
   }
   ForcesFile.close();
@@ -640 +647 @@
   Vector center;
   char filename[MAXSTRINGSIZE];
-  Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
+  std::cout << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
   mol = World::getInstance().createMolecule();
   do {
-    Log() << Verbose(0) << "Enter file name: ";
+    std::cout << "Enter file name: ";
     cin >> filename;
   } while (!mol->AddXYZFile(filename));
@@ -661 +668 @@
   molecule *mol = NULL;
   do {
-    Log() << Verbose(0) << "Enter index of molecule: ";
+    std::cout << "Enter index of molecule: ";
     cin >> nr;
     mol = ReturnIndex(nr);
   } while (mol == NULL);
-  Log() << Verbose(0) << "Enter name: ";
+  std::cout << "Enter name: ";
   cin >> filename;
   mol->SetNameFromFilename(filename);
@@ -676 +683 @@
   mol = NULL;
   do {
-   Log() << Verbose(0) << "Enter index of molecule: ";
+    std::cout << "Enter index of molecule: ";
    cin >> nr;
    mol = ReturnIndex(nr);
   } while (mol == NULL);
-  Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
+  std::cout << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
   do {
-   Log() << Verbose(0) << "Enter file name: ";
+    std::cout << "Enter file name: ";
    cin >> filename;
   } while (!mol->AddXYZFile(filename));
@@ -691 +698 @@
   int nr;
   molecule *mol = NULL;
-  Log() << Verbose(0) << "Enter index of molecule: ";
+  std::cout << "Enter index of molecule: ";
   cin >> nr;
   for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)