Changeset 255829

Timestamp:

Apr 6, 2011, 1:50:41 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:

3bfd78

Parents:

8766e72

git-author:

Frederik Heber <heber@…> (04/01/11 19:26:03)

git-committer:

Frederik Heber <heber@…> (04/06/11 13:50:41)

Message:

Removed Helpers.hpp, deleted Helpers.cpp and libMoleCuilderHelpers.la is history.

• defs.cpp is now compiled into libmolecuilder.la.
• ShapeUnitTest alone needs defs.cpp.
• Most changes are removal of Helpers/helpers.hpp.
• performCriticalExit() now inline function in Helpers/helpers.hpp.
• also inclusion possible where performCriticalExit() is needed.
• Helpers/helpers.hpp does not include defs.hpp anymore and this causes lots of missing Helpers/defs.hpp, CodePatterns/Log.hpp and alikes.
• removed src/Helpers from configure.ac.

Files:

• configure.ac (modified) (1 diff)
• src/BoundaryPolygonSet.cpp (modified) (1 diff)
• src/ConfigFileBuffer.cpp (modified) (1 diff)
• src/Dynamics/MinimiseConstrainedPotential.cpp (modified) (1 diff)
• src/Dynamics/OutputTemperature.hpp (modified) (1 diff)
• src/Dynamics/VerletForceIntegration.hpp (modified) (1 diff)
• src/Formula.hpp (modified) (1 diff)
• src/Graph/CheckAgainstAdjacencyFile.cpp (modified) (1 diff)
• src/Helpers/Makefile.am (deleted)
• src/Helpers/defs.hpp (modified) (1 diff)
• src/Helpers/helpers.cpp (deleted)
• src/Helpers/helpers.hpp (modified) (1 diff)
• src/Makefile.am (modified) (9 diffs)
• src/Parser/unittests/ParserPcpUnitTest.cpp (modified) (1 diff)
• src/Parser/unittests/ParserPdbUnitTest.cpp (modified) (1 diff)
• src/Parser/unittests/ParserXyzUnitTest.cpp (modified) (1 diff)
• src/Shapes/unittests/Makefile.am (modified) (2 diffs)
• src/Thermostats/Berendsen.cpp (modified) (1 diff)
• src/Thermostats/GaussianThermostat.cpp (modified) (1 diff)
• src/Thermostats/Langevin.cpp (modified) (1 diff)
• src/Thermostats/NoseHoover.cpp (modified) (1 diff)
• src/Thermostats/Woodcock.cpp (modified) (1 diff)
• src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) (1 diff)
• src/analysis_correlation.hpp (modified) (1 diff)
• src/analyzer.cpp (modified) (1 diff)
• src/atom.hpp (modified) (1 diff)
• src/boundary.cpp (modified) (1 diff)
• src/config.cpp (modified) (1 diff)
• src/datacreator.cpp (modified) (1 diff)
• src/joiner.cpp (modified) (1 diff)
• src/linkedcell.cpp (modified) (1 diff)
• src/molecule.cpp (modified) (1 diff)
• src/molecule.hpp (modified) (1 diff)
• src/molecule_geometry.cpp (modified) (1 diff)
• src/molecule_graph.cpp (modified) (1 diff)
• src/parser.cpp (modified) (2 diffs)
• src/periodentafel.cpp (modified) (1 diff)
• src/tesselation.hpp (modified) (1 diff)
• src/triangleintersectionlist.cpp (modified) (1 diff)
• src/unittests/ListOfBondsUnitTest.cpp (modified) (1 diff)
• src/unittests/Makefile.am (modified) (1 diff)
• src/unittests/TesselationUnitTest.cpp (modified) (1 diff)
• src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) (1 diff)
• src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) (1 diff)

configure.ac

@@ -228 +228 @@
         src/Exceptions/Makefile
   src/Graph/Makefile
-  src/Helpers/Makefile
         src/LinearAlgebra/Makefile
         src/Parser/Makefile

src/BoundaryPolygonSet.cpp

@@ -30 +30 @@
 
 #include "CodePatterns/Assert.hpp"
-#include "Helpers/helpers.hpp"
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/Plane.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "CodePatterns/Verbose.hpp"
 
 using namespace std;

src/ConfigFileBuffer.cpp

@@ -25 +25 @@
 
 #include "ConfigFileBuffer.hpp"
-#include "Helpers/helpers.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
+#include "Helpers/helpers.hpp"
 #include "World.hpp"
 

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -31 +31 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/helpers.hpp"
 #include "molecule.hpp"
 #include "parser.hpp"

src/Dynamics/OutputTemperature.hpp

@@ -13 +13 @@
 #include <config.h>
 #endif
+
+#include "Helpers/defs.hpp"
 
 template <class T>

src/Dynamics/VerletForceIntegration.hpp

@@ -21 +21 @@
 #include "CodePatterns/Verbose.hpp"
 #include "Dynamics/MinimiseConstrainedPotential.hpp"
+#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "parser.hpp"

src/Formula.hpp

@@ -22 +22 @@
 
 #include "types.hpp"
-#include "Helpers/helpers.hpp"
 
 #include "CodePatterns/enumeration.hpp"

src/Graph/CheckAgainstAdjacencyFile.cpp

@@ -27 +27 @@
 #include "Bond/bond.hpp"
 #include "CodePatterns/Assert.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "Helpers/defs.hpp"
 
 CheckAgainstAdjacencyFile::CheckAgainstAdjacencyFile() :

src/Helpers/defs.hpp

@@ -33 +33 @@
 
 //enum BondOrderScheme { NoScheme, BottomUp, TopDown, ANOVA, Combined }; //!< Fragmentation scheme used in BOSS
-
-
 
 //enum CutCyclicBond { KeepBond,  SaturateBond }; //!< Saturation scheme either atom- or bondwise 

src/Helpers/helpers.hpp

@@ -16 +16 @@
 #endif
 
-#include <fstream>
-
-#include "Helpers/defs.hpp"
-#include "CodePatterns/Log.hpp"
-
-/********************************************** definitions *********************************/
-
-/********************************************** helpful functions *********************************/
-
-void performCriticalExit();
+#include <cstdlib>
 
 /********************************************** helpful template functions *********************************/
 
+
+inline void performCriticalExit()
+{
+  exit(255);
+}
 
 

src/Makefile.am

@@ -3 +3 @@
 
 SUBDIRS = \
-  Helpers \
         Exceptions \
         RandomNumbers \
@@ -144 +143 @@
   Graph/BondGraph.hpp
 
+HELPERSSOURCE = \
+        Helpers/defs.cpp
+
+HELPERSHEADER = \
+        Helpers/defs.hpp \
+        Helpers/helpers.hpp
+
 THERMOSTATSOURCE = \
   Thermostats/Berendsen.cpp \
@@ -192 +198 @@
   ${DYNAMICSSOURCE} \
   ${GRAPHSOURCE} \
+  ${HELPERSSOURCE} \
   ${RANDOMSOURCE} \
   ${THERMOSTATSOURCE} \
@@ -227 +234 @@
   ${DYNAMICSHEADER} \
   ${GRAPHHEADER} \
+  ${HELPERSHEADER} \
   ${RANDOMSOURCE} \
   ${THERMOSTATHEADER} \
@@ -254 +262 @@
         LinearAlgebra/libMolecuilderLinearAlgebra.la \
         Graph/libMolecuilderGraph.la \
-        Helpers/libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
         ${BOOST_PROGRAM_OPTIONS_LIB}
@@ -324 +331 @@
         Exceptions/libMolecuilderExceptions.la \
         RandomNumbers/libMolecuilderRandomNumbers.la \
-        Helpers/libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
         $(BOOST_LIB)
@@ -347 +353 @@
         Exceptions/libMolecuilderExceptions.la \
         RandomNumbers/libMolecuilderRandomNumbers.la \
-        Helpers/libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
         $(BOOST_LIB) \
@@ -363 +368 @@
         Exceptions/libMolecuilderExceptions.la \
         RandomNumbers/libMolecuilderRandomNumbers.la \
-        Helpers/libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
         $(BOOST_LIB)
@@ -378 +382 @@
         Exceptions/libMolecuilderExceptions.la \
         RandomNumbers/libMolecuilderRandomNumbers.la \
-        Helpers/libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
         $(BOOST_LIB)

src/Parser/unittests/ParserPcpUnitTest.cpp

@@ -29 +29 @@
 #include "element.hpp"
 #include "periodentafel.hpp"
+#include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"
 

src/Parser/unittests/ParserPdbUnitTest.cpp

@@ -29 +29 @@
 #include "element.hpp"
 #include "periodentafel.hpp"
+#include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"
 

src/Parser/unittests/ParserXyzUnitTest.cpp

@@ -29 +29 @@
 #include "element.hpp"
 #include "periodentafel.hpp"
+#include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"
 

src/Shapes/unittests/Makefile.am

@@ -19 +19 @@
         ../../LinearAlgebra/libMolecuilderLinearAlgebra.la \
         ../../Exceptions/libMolecuilderExceptions.la \
-        ../../Helpers/libMolecuilderHelpers.la \
         ${CodePatterns_LIBS} \
         $(BOOST_LIB)
@@ -25 +24 @@
 ShapeUnittest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ShapeUnitTest.cpp \
-        ShapeUnitTest.hpp
+        ShapeUnitTest.hpp \
+        ../../Helpers/defs.cpp
 ShapeUnittest_LDADD = $(SHAPELIBS)
 

src/Thermostats/Berendsen.cpp

@@ -18 +18 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"

src/Thermostats/GaussianThermostat.cpp

@@ -14 +14 @@
 
 #include "GaussianThermostat.hpp"
-#include "LinearAlgebra/Vector.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Helpers/defs.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "AtomSet.hpp"
 #include "element.hpp"

src/Thermostats/Langevin.cpp

@@ -18 +18 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
 #include "ThermoStatContainer.hpp"
 

src/Thermostats/NoseHoover.cpp

@@ -19 +19 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"

src/Thermostats/Woodcock.cpp

@@ -19 +19 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Helpers/defs.hpp"
 #include "ThermoStatContainer.hpp"
 

src/UIElements/Views/Qt4/QtStatusBar.cpp

@@ -29 +29 @@
 
 #include "World.hpp"
-#include "Helpers/helpers.hpp"
 #include "Actions/Process.hpp"
 

src/analysis_correlation.hpp

@@ -32 +32 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Helpers/helpers.hpp"
 
 /****************************************** forward declarations *****************************/

src/analyzer.cpp

@@ -23 +23 @@
 
 #include <cstring>
+#include <cmath>
 
 #include "datacreator.hpp"
-#include "Helpers/helpers.hpp"
 #include "parser.hpp"
 #include "periodentafel.hpp"
+#include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
 

src/atom.hpp

@@ -22 +22 @@
 #include <vector>
 
-#include "Helpers/helpers.hpp"
 #include "atom_atominfo.hpp"
 #include "atom_bondedparticle.hpp"

src/boundary.cpp

@@ -31 +31 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/Plane.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"

src/config.cpp

@@ -35 +35 @@
 #include "ConfigFileBuffer.hpp"
 #include "element.hpp"
+#include "Graph/BondGraph.hpp"
 #include "Helpers/helpers.hpp"
-#include "Graph/BondGraph.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"

src/datacreator.cpp

@@ -21 +21 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <fstream>
+#include <sstream>
+#include <iomanip>
+
+#include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "LinearAlgebra/defs.hpp"
-#include "Helpers/helpers.hpp"
+#include "Helpers/defs.hpp"
 #include "datacreator.hpp"
 #include "parser.hpp"
 
-#include <iomanip>
+using namespace std;
 
 //=========================== FUNCTIONS============================

src/joiner.cpp

@@ -23 +23 @@
 
 #include <cstring>
+#include <cmath>
 
 #include "datacreator.hpp"
-#include "Helpers/helpers.hpp"
 #include "parser.hpp"
 #include "periodentafel.hpp"
+#include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
 

src/linkedcell.cpp

@@ -20 +20 @@
 
 #include "atom.hpp"
-#include "Helpers/helpers.hpp"
 #include "linkedcell.hpp"
 #include "CodePatterns/Verbose.hpp"

src/molecule.cpp

@@ -36 +36 @@
 #include "graph.hpp"
 #include "Graph/BondGraph.hpp"
-#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/leastsquaremin.hpp"
 #include "LinearAlgebra/Plane.hpp"

src/molecule.hpp

@@ -28 +28 @@
 #include "CodePatterns/ObservedIterator.hpp"
 #include "CodePatterns/Cacheable.hpp"
+#include "Helpers/defs.hpp"
 #include "Formula.hpp"
 #include "AtomSet.hpp"

src/molecule_geometry.cpp

@@ -28 +28 @@
 #include "element.hpp"
 #include "Graph/BondGraph.hpp"
-#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/leastsquaremin.hpp"
 #include "LinearAlgebra/Line.hpp"

src/molecule_graph.cpp

@@ -34 +34 @@
 #include "Graph/BondGraph.hpp"
 #include "Helpers/defs.hpp"
-#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "linkedcell.hpp"

src/parser.cpp

@@ -22 +22 @@
 
 #include <cstring>
+#include <fstream>
 #include <iomanip>
 
+#include "parser.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "Helpers/defs.hpp"
 #include "Helpers/helpers.hpp"
-#include "parser.hpp"
-#include "CodePatterns/Verbose.hpp"
+
+using namespace std;
 
 // ======================================= FUNCTIONS ==========================================
@@ -287 +292 @@
     }
   } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl); 
+    DoeLog(1) && (eLog()<< Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl);
   }
   return true;

src/periodentafel.cpp

@@ -27 +27 @@
 #include "element.hpp"
 #include "elements_db.hpp"
-#include "Helpers/helpers.hpp"
 #include "CodePatterns/Log.hpp"
 #include "periodentafel.hpp"

src/tesselation.hpp

@@ -29 +29 @@
 #include "BoundaryMaps.hpp"
 #include "BoundaryPointSet.hpp"
-#include "Helpers/helpers.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "TesselPoint.hpp"

src/triangleintersectionlist.cpp

@@ -27 +27 @@
 #include "triangleintersectionlist.hpp"
 
-#include "CodePatterns/Info.hpp"
+#include "tesselation.hpp"
 #include "BoundaryMaps.hpp"
 #include "BoundaryPointSet.hpp"
 #include "BoundaryLineSet.hpp"
 #include "BoundaryTriangleSet.hpp"
-#include "tesselation.hpp"
+#include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "Helpers/defs.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "CodePatterns/Verbose.hpp"
 
 /** Constructor for class TriangleIntersectionList.

src/unittests/ListOfBondsUnitTest.cpp

@@ -26 +26 @@
 #include <cstring>
 
-
+#include "CodePatterns/Log.hpp"
 #include "World.hpp"
 #include "atom.hpp"

src/unittests/Makefile.am

@@ -44 +44 @@
         ../Exceptions/libMolecuilderExceptions.la \
         ../RandomNumbers/libMolecuilderRandomNumbers.la \
-        ../Helpers/libMolecuilderHelpers.la \
         $(BOOST_LIB)
 ALLLIBS = \

src/unittests/TesselationUnitTest.cpp

@@ -29 +29 @@
 #include "BoundaryTriangleSet.hpp"
 #include "CandidateForTesselation.hpp"
+#include "CodePatterns/Log.hpp"
 #include "Helpers/defs.hpp"
 #include "PointCloudAdaptor.hpp"

src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp

@@ -27 +27 @@
 #include <iostream>
 
+#include "CodePatterns/Log.hpp"
 #include "Helpers/defs.hpp"
 #include "TesselPoint.hpp"

src/unittests/Tesselation_InsideOutsideUnitTest.cpp

@@ -30 +30 @@
 #include "BoundaryTriangleSet.hpp"
 #include "CandidateForTesselation.hpp"
+#include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "Helpers/defs.hpp"