Changeset d067d45 for src/joiner.cpp

Timestamp:

Jul 23, 2009, 1:45:24 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, 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:

51c910

Parents:

ce5ac3 (diff), 437922 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• src/joiner.cpp (modified) (5 diffs)

src/joiner.cpp

@@ -2 +2 @@
  *
  * Takes evaluated fragments (energy and forces) and by reading the factors files determines total energy
- * and each force for the whole molecule. 
- *    
+ * and each force for the whole molecule.
+ *
  */
 
 //============================ INCLUDES ===========================
 
-#include "datacreator.hpp" 
-#include "helpers.hpp" 
-#include "parser.hpp" 
-#include "periodentafel.hpp" 
+#include "datacreator.hpp"
+#include "helpers.hpp"
+#include "parser.hpp"
+#include "periodentafel.hpp"
 
 //============================== MAIN =============================
@@ -46 +46 @@
   cout << "Joiner" << endl;
   cout << "======" << endl;
-  
+
   // Get the command line options
   if (argc < 3) {
@@ -63 +63 @@
     periode->LoadPeriodentafel(argv[3]);
   }
-  
+
   // Test the given directory
   if (!TestParams(argc, argv))
     return 1;
-  
+
   // +++++++++++++++++ PARSING +++++++++++++++++++++++++++++++
-  
+
   // ------------- Parse through all Fragment subdirs --------
   if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return 1;
@@ -124 +124 @@
     if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
   }
-  
+
   // ----------- Resetting last matrices (where full QM values are stored right now)
   if(!Energy.SetLastMatrix(0., 0)) return 1;
@@ -237 +237 @@
   }
 
-  // exit  
+  // exit
   delete(periode);
   Free((void **)&dir, "main: *dir");