Changeset 244a84 for src/parser.cpp

Timestamp:

Jan 26, 2010, 12:52:31 PM (16 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, 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:

04b6f9, 481601

Parents:

315164

Message:

GetDistanceToSurface() separated, filling now with water instead of boron, DissectMoleculeIntoConnectedSubgraphs() now working on list of molecules instead of single one.

• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() so far was working on a single molecule (given by parameter) instead of the list already contained in the list of its class.
• Tesselation::GetDistanceSquaredToSurface() is split up into function of same name, which calls finds the closest triangle and calls Tesselation::GetDistanceSquaredToTriangle() which contains the former code.
• PeriodicCorrelationToSurface() was adapted to the above split.
• in tesselation.cpp lots of list<> and set<>s were replaced by the already present and appropriate define's.

• small verbosity changes in: MatrixContainer::ParseMatrix(), TesselPoint::TesselPoint(), TesselPoint::~TesselPoint(), PointCloud::PointCloud(), PointCloud::~PointCloud(), Tesselation::GuessStartingTriangle(), BondGraph::LoadBondLengthTable() (status of parsing gives appropriate message).

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

File:

• src/parser.cpp (modified) (4 diffs)

src/parser.cpp

@@ -158 +158 @@
 
   input.open(name, ios::in);
-  //Log() << Verbose(0) << "Opening " << name << " ... "  << input << endl;
+  //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
   if (input == NULL) {
     eLog() << Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl;
@@ -181 +181 @@
   }
   //Log() << Verbose(0) << line.str() << endl;
-  //Log() << Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
+  //Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
   if (ColumnCounter[MatrixNr] == 0) {
     eLog() << Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl;
@@ -197 +197 @@
     }
   }
-  //Log() << Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
+  //Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
   if (RowCounter[MatrixNr] == 0) {
     eLog() << Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl;
@@ -220 +220 @@
       input.getline(filename, 1023);
       stringstream lines(filename);
-      //Log() << Verbose(0) << "Matrix at level " << j << ":";// << filename << endl;
+      //Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
       for(int k=skipcolumns;k--;)
         lines >> filename;
       for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
         lines >> Matrix[MatrixNr][j][k];
-        //Log() << Verbose(0) << " " << setprecision(2) << Matrix[MatrixNr][j][k];;
+        //Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
       }
-      //Log() << Verbose(0) << endl;
       Matrix[MatrixNr][ RowCounter[MatrixNr] ] = Malloc<double>(ColumnCounter[MatrixNr], "MatrixContainer::ParseMatrix: *Matrix[RowCounter[MatrixNr]][]");
       for(int j=ColumnCounter[MatrixNr];j--;)