Changeset fbf143 for src/Fragmentation/Summation/Containers

Timestamp:

Apr 15, 2013, 6:13:22 PM (12 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:

a3427f

Parents:

8e84fe

git-author:

Frederik Heber <heber@…> (04/10/13 16:11:13)

git-committer:

Frederik Heber <heber@…> (04/15/13 18:13:22)

Message:

Placed Containers, Converter, and SetValues as subfolders into Summation.

• also libMolecuilderFragmentationSummation is now a shared library, easing linkage to libMolecuilderJobs, and contains all of the three convenience libraries.
• libMolecuilderFragmentationSetValues is now again convenience, as contained in ..Summation which in turn is shared.
• KeySetsContainer right now is the link between lib..Summation and lib.. Fragmentation. Hence, we had to extract the module and change it into a shared library, as it is required by libMolecuilderJobs through ..Summation but also by ..Fragmentation that heavily relies on this container.
• moved parseKeySetFile down into Fragmentation folder to KeySetsContainer, it is also contained in new shared library libMolecuilderFragmentation_ KeySetsContainer.

Location:

src/Fragmentation/Summation/Containers

Files:

• FragmentationChargeDensity.cpp (moved) (moved from src/Fragmentation/Containers/FragmentationChargeDensity.cpp ) (1 diff)
• FragmentationChargeDensity.hpp (moved) (moved from src/Fragmentation/Containers/FragmentationChargeDensity.hpp ) (1 diff)
• FragmentationLongRangeResults.cpp (moved) (moved from src/Fragmentation/Containers/FragmentationLongRangeResults.cpp ) (1 diff)
• FragmentationLongRangeResults.hpp (moved) (moved from src/Fragmentation/Containers/FragmentationLongRangeResults.hpp ) (1 diff)
• FragmentationShortRangeResults.cpp (moved) (moved from src/Fragmentation/Containers/FragmentationShortRangeResults.cpp ) (1 diff)
• FragmentationShortRangeResults.hpp (moved) (moved from src/Fragmentation/Containers/FragmentationShortRangeResults.hpp ) (1 diff)
• MPQCData.cpp (moved) (moved from src/Fragmentation/Containers/MPQCData.cpp )
• MPQCData.hpp (moved) (moved from src/Fragmentation/Containers/MPQCData.hpp ) (1 diff)
• MPQCDataFused.hpp (moved) (moved from src/Fragmentation/Containers/MPQCDataFused.hpp )
• MPQCDataMap.hpp (moved) (moved from src/Fragmentation/Containers/MPQCDataMap.hpp ) (1 diff)
• MPQCData_printKeyNames.hpp (moved) (moved from src/Fragmentation/Containers/MPQCData_printKeyNames.hpp )
• Makefile.am (moved) (moved from src/Fragmentation/Containers/Makefile.am ) (1 diff)
• VMGData.cpp (moved) (moved from src/Fragmentation/Containers/VMGData.cpp )
• VMGData.hpp (moved) (moved from src/Fragmentation/Containers/VMGData.hpp ) (1 diff)
• VMGDataFused.hpp (moved) (moved from src/Fragmentation/Containers/VMGDataFused.hpp )
• VMGDataMap.hpp (moved) (moved from src/Fragmentation/Containers/VMGDataMap.hpp ) (1 diff)
• VMGData_printKeyNames.hpp (moved) (moved from src/Fragmentation/Containers/VMGData_printKeyNames.hpp )
• createMatrixNrLookup.cpp (moved) (moved from src/Fragmentation/Containers/createMatrixNrLookup.cpp )
• createMatrixNrLookup.hpp (moved) (moved from src/Fragmentation/Containers/createMatrixNrLookup.hpp )
• extractJobIds.hpp (moved) (moved from src/Fragmentation/Containers/extractJobIds.hpp )
• unittests/MPQCDataUnitTest.cpp (moved) (moved from src/Fragmentation/Containers/unittests/MPQCDataUnitTest.cpp ) (1 diff)
• unittests/MPQCDataUnitTest.hpp (moved) (moved from src/Fragmentation/Containers/unittests/MPQCDataUnitTest.hpp )
• unittests/Makefile.am (moved) (moved from src/Fragmentation/Containers/unittests/Makefile.am ) (3 diffs)

src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp

@@ -46 +46 @@
 
 #include "Fragmentation/KeySetsContainer.hpp"
-#include "Fragmentation/Containers/createMatrixNrLookup.hpp"
-#include "Fragmentation/Containers/extractJobIds.hpp"
-#include "Fragmentation/Containers/parseKeySetFile.hpp"
+#include "Fragmentation/parseKeySetFile.hpp"
+#include "Fragmentation/Summation/Containers/createMatrixNrLookup.hpp"
+#include "Fragmentation/Summation/Containers/extractJobIds.hpp"
 #include "Fragmentation/Summation/IndexSetContainer.hpp"
 #include "Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp"

src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp

@@ -24 +24 @@
 #endif
 
-#include "Fragmentation/Containers/MPQCData.hpp"
-#include "Fragmentation/Containers/MPQCDataMap.hpp"
-#include "Fragmentation/SetValues/Fragment.hpp"
-#include "Fragmentation/SetValues/SamplingGrid.hpp"
+#include "Fragmentation/Summation/Containers/MPQCData.hpp"
+#include "Fragmentation/Summation/Containers/MPQCDataMap.hpp"
+#include "Fragmentation/Summation/SetValues/Fragment.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
 #include "Fragmentation/Summation/IndexSet.hpp"
 

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp

@@ -46 +46 @@
 
 #include "Fragmentation/KeySetsContainer.hpp"
-#include "Fragmentation/Converter/DataConverter.hpp"
-#include "Fragmentation/Containers/createMatrixNrLookup.hpp"
-#include "Fragmentation/Containers/extractJobIds.hpp"
-#include "Fragmentation/Containers/parseKeySetFile.hpp"
+#include "Fragmentation/parseKeySetFile.hpp"
+#include "Fragmentation/Summation/Converter/DataConverter.hpp"
+#include "Fragmentation/Summation/Containers/createMatrixNrLookup.hpp"
+#include "Fragmentation/Summation/Containers/extractJobIds.hpp"
 #include "Fragmentation/Summation/AllLevelOrthogonalSummator.hpp"
 #include "Fragmentation/Summation/IndexSetContainer.hpp"

src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp

@@ -29 +29 @@
 #include "Fragmentation/Summation/SubsetMap.hpp"
 
-#include "Fragmentation/Containers/MPQCData.hpp"
-#include "Fragmentation/Containers/MPQCDataMap.hpp"
-#include "Fragmentation/Containers/VMGData.hpp"
-#include "Fragmentation/Containers/VMGDataMap.hpp"
-#include "Fragmentation/SetValues/SamplingGrid.hpp"
+#include "Fragmentation/Summation/Containers/MPQCData.hpp"
+#include "Fragmentation/Summation/Containers/MPQCDataMap.hpp"
+#include "Fragmentation/Summation/Containers/VMGData.hpp"
+#include "Fragmentation/Summation/Containers/VMGDataMap.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
 
 /** FragmentationLongRangeResults contains the summed up results per level resulting

src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp

@@ -46 +46 @@
 
 #include "Fragmentation/KeySetsContainer.hpp"
-#include "Fragmentation/Converter/DataConverter.hpp"
-#include "Fragmentation/Containers/createMatrixNrLookup.hpp"
-#include "Fragmentation/Containers/extractJobIds.hpp"
-#include "Fragmentation/Containers/parseKeySetFile.hpp"
+#include "Fragmentation/parseKeySetFile.hpp"
+#include "Fragmentation/Summation/Converter/DataConverter.hpp"
+#include "Fragmentation/Summation/Containers/createMatrixNrLookup.hpp"
+#include "Fragmentation/Summation/Containers/extractJobIds.hpp"
 #include "Fragmentation/Summation/AllLevelOrthogonalSummator.hpp"
 #include "Fragmentation/Summation/IndexSetContainer.hpp"

src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp

@@ -29 +29 @@
 #include "Fragmentation/Summation/SubsetMap.hpp"
 
-#include "Fragmentation/Containers/MPQCData.hpp"
-#include "Fragmentation/Containers/MPQCDataMap.hpp"
+#include "Fragmentation/Summation/Containers/MPQCData.hpp"
+#include "Fragmentation/Summation/Containers/MPQCDataMap.hpp"
 
 /** FragmentationShortRangeResults contains the summed up results per level resulting

src/Fragmentation/Summation/Containers/MPQCData.hpp

@@ -20 +20 @@
 #include <vector>
 
-#include "Fragmentation/SetValues/SamplingGrid.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
 
 class MPQCCommandJob;

src/Fragmentation/Summation/Containers/MPQCDataMap.hpp

@@ -17 +17 @@
 #include <boost/mpl/list.hpp>
 
-#include "Fragmentation/Containers/MPQCDataFused.hpp"
+#include "Fragmentation/Summation/Containers/MPQCDataFused.hpp"
 
 class Fragment;

src/Fragmentation/Summation/Containers/Makefile.am

@@ -3 +3 @@
 
 FRAGMENTATIONCONTAINERSOURCE = \
-        Fragmentation/Containers/createMatrixNrLookup.cpp \
-        Fragmentation/Containers/FragmentationChargeDensity.cpp \
-        Fragmentation/Containers/FragmentationLongRangeResults.cpp \
-        Fragmentation/Containers/FragmentationShortRangeResults.cpp \
-        Fragmentation/Containers/MPQCData.cpp \
-        Fragmentation/Containers/parseKeySetFile.cpp
+        Fragmentation/Summation/Containers/createMatrixNrLookup.cpp \
+        Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp \
+        Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp \
+        Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp \
+        Fragmentation/Summation/Containers/MPQCData.cpp
         
 if CONDVMG
 FRAGMENTATIONCONTAINERSOURCE += \
-        Fragmentation/Containers/VMGData.cpp
+        Fragmentation/Summation/Containers/VMGData.cpp
 endif
 
 FRAGMENTATIONCONTAINERHEADER = \
-        Fragmentation/Containers/createMatrixNrLookup.hpp \
-        Fragmentation/Containers/extractJobIds.hpp \
-        Fragmentation/Containers/FragmentationChargeDensity.hpp \
-        Fragmentation/Containers/FragmentationLongRangeResults.hpp \
-        Fragmentation/Containers/FragmentationShortRangeResults.hpp \
-        Fragmentation/Containers/MPQCData.hpp \
-        Fragmentation/Containers/MPQCDataFused.hpp \
-        Fragmentation/Containers/MPQCDataMap.hpp \
-        Fragmentation/Containers/MPQCData_printKeyNames.hpp \
-        Fragmentation/Containers/parseKeySetFile.hpp
+        Fragmentation/Summation/Containers/createMatrixNrLookup.hpp \
+        Fragmentation/Summation/Containers/extractJobIds.hpp \
+        Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp \
+        Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp \
+        Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp \
+        Fragmentation/Summation/Containers/MPQCData.hpp \
+        Fragmentation/Summation/Containers/MPQCDataFused.hpp \
+        Fragmentation/Summation/Containers/MPQCDataMap.hpp \
+        Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp
         
 if CONDVMG
 FRAGMENTATIONCONTAINERHEADER += \
-        Fragmentation/Containers/VMGData.hpp \
-        Fragmentation/Containers/VMGDataFused.hpp \
-        Fragmentation/Containers/VMGDataMap.hpp \
-        Fragmentation/Containers/VMGData_printKeyNames.hpp
+        Fragmentation/Summation/Containers/VMGData.hpp \
+        Fragmentation/Summation/Containers/VMGDataFused.hpp \
+        Fragmentation/Summation/Containers/VMGDataMap.hpp \
+        Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp
 endif
 
 noinst_LTLIBRARIES += libMolecuilderFragmentationContainers.la
-libMolecuilderFragmentationContainers_la_includedir = $(includedir)/MoleCuilder/Fragmentation/Containers/
+libMolecuilderFragmentationContainers_la_includedir = $(includedir)/MoleCuilder/Fragmentation/Summation/Containers/
 libMolecuilderFragmentationContainers_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
 libMolecuilderFragmentationContainers_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
 libMolecuilderFragmentationContainers_la_LIBADD = \
+  libMolecuilderHelpers.la \
         ${CodePatterns_LIBS}
 

src/Fragmentation/Summation/Containers/VMGData.hpp

@@ -22 +22 @@
 #include <vector>
 
-#include "Fragmentation/SetValues/SamplingGrid.hpp"
+#include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
 
 /** This struct contains all returned data from an VMGJob

src/Fragmentation/Summation/Containers/VMGDataMap.hpp

@@ -18 +18 @@
 #include <boost/mpl/list.hpp>
 
-#include "Fragmentation/Containers/VMGDataFused.hpp"
+#include "Fragmentation/Summation/Containers/VMGDataFused.hpp"
 
 class SamplingGrid;

src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp

@@ -46 +46 @@
 #include "MPQCDataUnitTest.hpp"
 
-#include "Fragmentation/Containers/MPQCData.hpp"
+#include "Fragmentation/Summation/Containers/MPQCData.hpp"
 
 #include "CodePatterns/Assert.hpp"

src/Fragmentation/Summation/Containers/unittests/Makefile.am

@@ -3 +3 @@
 
 FRAGMENTATIONCONTAINERTESTSSOURCES = \
-  ../Fragmentation/Containers/unittests/MPQCDataUnitTest.cpp
+  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp
   
 FRAGMENTATIONCONTAINERTESTSHEADERS = \
-  ../Fragmentation/Containers/unittests/MPQCDataUnitTest.hpp
+  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp
 
 FRAGMENTATIONCONTAINERTESTS = \
@@ -17 +17 @@
 
 FRAGMENTATIONCONTAINERLIBS = \
-  ../libMolecuilderFragmentationContainers.la \
-        ../libMolecuilderFragmentationSetValues.la \
+  ../libMolecuilderFragmentationSummation.la \
   $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
   $(BOOST_THREAD_LDFLAGS) $(BOOST_THREAD_LIBS) \
@@ -27 +26 @@
 MPQCDataUnitTest_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
 MPQCDataUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
-  ../Fragmentation/Containers/unittests/MPQCDataUnitTest.cpp \
-  ../Fragmentation/Containers/unittests/MPQCDataUnitTest.hpp
+  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp \
+  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp
 MPQCDataUnitTest_LDADD = ${FRAGMENTATIONCONTAINERLIBS}