Changeset a9b86d

Timestamp:

Oct 17, 2011, 8:17:51 PM (13 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:

9758f7

Parents:

5f61dde

git-author:

Frederik Heber <heber@…> (09/15/11 16:02:17)

git-committer:

Frederik Heber <heber@…> (10/17/11 20:17:51)

Message:

Split up modules parser.[ch]pp into one module per class.

• fixed inclusion of parser.hpp in some other files.
• for the moment we have to use libMolecuilderUI for joiner and analyzer.
• Removed inline definition from FixedDigitNumber().

Location:

src

Files:

• Dynamics/LinearInterpolationBetweenSteps.hpp (modified) (1 diff)
• Dynamics/MinimiseConstrainedPotential.cpp (modified) (1 diff)
• Dynamics/VerletForceIntegration.hpp (modified) (1 diff)
• Fragmentation/EnergyMatrix.cpp (added)
• Fragmentation/EnergyMatrix.hpp (added)
• Fragmentation/ForceMatrix.cpp (added)
• Fragmentation/ForceMatrix.hpp (added)
• Fragmentation/HessianMatrix.cpp (added)
• Fragmentation/HessianMatrix.hpp (added)
• Fragmentation/KeySetsContainer.cpp (added)
• Fragmentation/KeySetsContainer.hpp (added)
• Fragmentation/Makefile.am (added)
• Fragmentation/MatrixContainer.cpp (added)
• Fragmentation/MatrixContainer.hpp (added)
• Fragmentation/analyzer.cpp (modified) (1 diff)
• Fragmentation/datacreator.cpp (modified) (1 diff)
• Fragmentation/defs.hpp (added)
• Fragmentation/helpers.cpp (added)
• Fragmentation/helpers.hpp (added)
• Fragmentation/joiner.cpp (modified) (1 diff)
• Fragmentation/parser.cpp (deleted)
• Fragmentation/parser.hpp (deleted)
• Graph/BondGraph.cpp (modified) (1 diff)
• Makefile.am (modified) (6 diffs)
• UIElements/Makefile.am (modified) (1 diff)
• 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 "Fragmentation/parser.hpp"
 #include "World.hpp"
 

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -31 +31 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Fragmentation/ForceMatrix.hpp"
 #include "Helpers/helpers.hpp"
 #include "molecule.hpp"
-#include "Fragmentation/parser.hpp"
 #include "LinearAlgebra/Plane.hpp"
 #include "World.hpp"

src/Dynamics/VerletForceIntegration.hpp

@@ -21 +21 @@
 #include "CodePatterns/Verbose.hpp"
 #include "Dynamics/MinimiseConstrainedPotential.hpp"
+#include "Fragmentation/ForceMatrix.hpp"
 #include "Helpers/helpers.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "Fragmentation/parser.hpp"
 #include "ThermoStatContainer.hpp"
 #include "Thermostats/Berendsen.hpp"

src/Fragmentation/analyzer.cpp

@@ -28 +28 @@
 
 #include "datacreator.hpp"
-#include "parser.hpp"
 #include "Element/periodentafel.hpp"
+#include "Fragmentation/defs.hpp"
+#include "Fragmentation/EnergyMatrix.hpp"
+#include "Fragmentation/ForceMatrix.hpp"
+#include "Fragmentation/helpers.hpp"
+#include "Fragmentation/HessianMatrix.hpp"
+#include "Fragmentation/KeySetsContainer.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Fragmentation/datacreator.cpp

@@ -30 +30 @@
 #include "Helpers/defs.hpp"
 #include "datacreator.hpp"
-#include "parser.hpp"
+#include "Fragmentation/EnergyMatrix.hpp"
+#include "Fragmentation/ForceMatrix.hpp"
+#include "Fragmentation/HessianMatrix.hpp"
+#include "Fragmentation/KeySetsContainer.hpp"
 
 using namespace std;

src/Fragmentation/joiner.cpp

@@ -26 +26 @@
 
 #include "datacreator.hpp"
-#include "parser.hpp"
 #include "Element/periodentafel.hpp"
+#include "Fragmentation/defs.hpp"
+#include "Fragmentation/EnergyMatrix.hpp"
+#include "Fragmentation/ForceMatrix.hpp"
+#include "Fragmentation/helpers.hpp"
+#include "Fragmentation/HessianMatrix.hpp"
+#include "Fragmentation/KeySetsContainer.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Graph/BondGraph.cpp

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

src/Makefile.am

@@ -12 +12 @@
 include Graph/Makefile.am
 include Helpers/Makefile.am
+include Fragmentation/Makefile.am
 include Parser/Makefile.am
 include RandomNumbers/Makefile.am
@@ -112 +113 @@
         Dynamics/VerletForceIntegration.hpp
 
-FRAGMENTATIONSSOURCE = \
-        Fragmentation/parser.cpp
-
-FRAGMENTATIONHEADER = \
-        Fragmentation/parser.hpp
-
 THERMOSTATSOURCE = \
   Thermostats/Berendsen.cpp \
@@ -170 +165 @@
   ${DESCRIPTORSOURCE} \
   ${DYNAMICSSOURCE} \
-  ${FRAGMENTATIONSSOURCE} \
   ${THERMOSTATSOURCE} \
   ${TESSELATIONSOURCE} \
@@ -196 +190 @@
   ${DESCRIPTORIMPLHEADER} \
   ${DYNAMICSHEADER} \
-  ${FRAGMENTATIONHEADER} \
   ${THERMOSTATHEADER} \
   ${TESSELATIONHEADER} \
@@ -300 +293 @@
 joiner_SOURCES = Fragmentation/joiner.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
 joiner_LDADD = \
-        libMolecuilder.la \
-        libMolecuilderParser.la \
-        libMolecuilderShapes.la \
+        libMolecuilderFragmentation.la \
         libMolecuilderHelpers.la \
         libMolecuilderElement.la \
@@ -311 +302 @@
 analyzer_SOURCES = Fragmentation/analyzer.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
 analyzer_LDADD = \
-        libMolecuilder.la \
-        libMolecuilderParser.la \
-        libMolecuilderShapes.la \
+        libMolecuilderFragmentation.la \
         libMolecuilderHelpers.la \
         libMolecuilderElement.la \

src/UIElements/Makefile.am

@@ -267 +267 @@
         libMolecuilderGraph.la \
         libMolecuilder.la \
+        libMolecuilderFragmentation.la \
         libMolecuilderParser.la \
         libMolecuilderShapes.la \

src/atom.cpp

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

src/atom_atominfo.cpp

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