Changeset bc28b0

Timestamp:

Oct 13, 2011, 7:00:47 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:

feb7df

Parents:

878044

git-author:

Frederik Heber <heber@…> (09/15/11 14:43:32)

git-committer:

Frederik Heber <heber@…> (10/13/11 19:00:47)

Message:

Moved modules associated with fragmentation into source subfolder Fragmentation.

Location:

src

Files:

• Dynamics/LinearInterpolationBetweenSteps.hpp (modified) (1 diff)
• Dynamics/MinimiseConstrainedPotential.cpp (modified) (1 diff)
• Dynamics/VerletForceIntegration.hpp (modified) (1 diff)
• Fragmentation/analyzer.cpp (moved) (moved from src/analyzer.cpp )
• Fragmentation/datacreator.cpp (moved) (moved from src/datacreator.cpp )
• Fragmentation/datacreator.hpp (moved) (moved from src/datacreator.hpp )
• Fragmentation/joiner.cpp (moved) (moved from src/joiner.cpp )
• Fragmentation/parser.cpp (moved) (moved from src/parser.cpp )
• Fragmentation/parser.hpp (moved) (moved from src/parser.hpp )
• Graph/BondGraph.cpp (modified) (1 diff)
• Makefile.am (modified) (7 diffs)
• atom.cpp (modified) (1 diff)
• atom_atominfo.cpp (modified) (1 diff)

src/Dynamics/LinearInterpolationBetweenSteps.hpp

@@ -25 +25 @@
 #include "Dynamics/MinimiseConstrainedPotential.hpp"
 #include "molecule.hpp"
-#include "parser.hpp"
+#include "Fragmentation/parser.hpp"
 #include "World.hpp"
 

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -33 +33 @@
 #include "Helpers/helpers.hpp"
 #include "molecule.hpp"
-#include "parser.hpp"
+#include "Fragmentation/parser.hpp"
 #include "LinearAlgebra/Plane.hpp"
 #include "World.hpp"

src/Dynamics/VerletForceIntegration.hpp

@@ -23 +23 @@
 #include "Helpers/helpers.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "parser.hpp"
+#include "Fragmentation/parser.hpp"
 #include "ThermoStatContainer.hpp"
 #include "Thermostats/Berendsen.hpp"

src/Graph/BondGraph.cpp

@@ -32 +32 @@
 #include "CodePatterns/Verbose.hpp"
 #include "molecule.hpp"
-#include "parser.hpp"
+#include "Fragmentation/parser.hpp"
 #include "periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"

src/Makefile.am

@@ -116 +116 @@
         Dynamics/VerletForceIntegration.hpp
 
+FRAGMENTATIONSSOURCE = \
+        Fragmentation/parser.cpp
+
+FRAGMENTATIONHEADER = \
+        Fragmentation/parser.hpp
+
 HELPERSSOURCE = \
         Helpers/defs.cpp
@@ -170 +176 @@
   ${DESCRIPTORSOURCE} \
   ${DYNAMICSSOURCE} \
+  ${FRAGMENTATIONSSOURCE} \
   ${HELPERSSOURCE} \
   ${THERMOSTATSOURCE} \
@@ -188 +195 @@
   molecule_geometry.cpp \
   molecule_graph.cpp \
-  parser.cpp \
   periodentafel.cpp \
   ThermoStatContainer.cpp \
@@ -204 +210 @@
   ${DESCRIPTORIMPLHEADER} \
   ${DYNAMICSHEADER} \
+  ${FRAGMENTATIONHEADER} \
   ${HELPERSHEADER} \
   ${THERMOSTATHEADER} \
@@ -218 +225 @@
   linkedcell.hpp \
   molecule.hpp \
-  parser.hpp \
   periodentafel.hpp \
   ThermoStatContainer.hpp \
@@ -313 +319 @@
         $(GUI_LIBS)
 
-joiner_SOURCES = joiner.cpp datacreator.cpp datacreator.hpp periodentafel.hpp
+joiner_SOURCES = Fragmentation/joiner.cpp Fragmentation/datacreator.cpp datacreator.hpp Fragmentation/periodentafel.hpp
 joiner_LDADD = \
         libMolecuilder.la \
@@ -323 +329 @@
         $(BOOST_THREAD_LIBS)
 
-analyzer_SOURCES = analyzer.cpp datacreator.cpp periodentafel.hpp datacreator.hpp 
+analyzer_SOURCES = Fragmentation/analyzer.cpp Fragmentation/datacreator.cpp periodentafel.hpp Fragmentation/datacreator.hpp 
 analyzer_LDADD = \
         libMolecuilder.la \

src/atom.cpp

@@ -24 +24 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "parser.hpp"
+#include "Fragmentation/parser.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/atom_atominfo.cpp

@@ -24 +24 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "parser.hpp"
+#include "Fragmentation/parser.hpp"
 #include "periodentafel.hpp"
 #include "World.hpp"