Changeset 48d20d for src/Actions

Timestamp:

May 3, 2013, 11:58:26 AM (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:

661d2d

Parents:

57f14c

git-author:

Frederik Heber <heber@…> (04/09/13 07:44:29)

git-committer:

Frederik Heber <heber@…> (05/03/13 11:58:26)

Message:

Added new action FitPotentialAction to fit empirical potentials.

• moved functionality from levmartester into new Action.
• removed levmartester.
• needs both enable-levmar and path to libs/include with-levmar. This allows checking as distinct enable switch.
• added regression test Fragmentation/FitPotential for morse and harmonic_angle fit to water molecule. Using awk to check on L2 error.
• added take-best-of option such that fits is done as many times and best (in terms of l2 error) is used. This should make regression test FitPotential more stable (right now we take best of 5).
• DOCU: extended construct documentation due to new PotentialTypes construct.
• DOCU: made construct lists items appear alphabetically.
• DOCU: extended installation documentation with VTK and levmar.
• DOCU: also URLs for scafacos, VTK, and levmar.

Location:

src/Actions

Files:

• FragmentationAction/FitPotentialAction.cpp (added)
• FragmentationAction/FitPotentialAction.def (added)
• FragmentationAction/FitPotentialAction.hpp (added)
• GlobalListOfActions.hpp (modified) (3 diffs)
• Makefile.am (modified) (2 diffs)

src/Actions/GlobalListOfActions.hpp

@@ -122 +122 @@
   (SelectionNotAllShapes) \
   (SelectionNotShapeByName) \
+  (FragmentationAnalyseFragmentationResults) \
   (FragmentationFragmentation) \
-  (FragmentationAnalyseFragmentationResults) \
   (FragmentationStoreSaturatedFragment) \
   (FillRegularGrid) \
@@ -136 +136 @@
 // we need to append the automation action in case we have the JobMarket
 #ifdef HAVE_JOBMARKET
-#define GLOBALLISTOFACTIONS \
+#define GLOBALLISTOFACTIONS_JOBMARKET \
     BOOST_PP_SEQ_PUSH_BACK( \
         BOOST_PP_SEQ_PUSH_BACK( \
@@ -145 +145 @@
     )
 #else
-#define GLOBALLISTOFACTIONS \
+#define GLOBALLISTOFACTIONS_JOBMARKET \
     GLOBALLISTOFACTIONS_initial
 #endif /* HAVE_JOBMARKET */
 
+#ifdef HAVE_LEVMAR
+#define GLOBALLISTOFACTIONS_LEVMAR \
+    BOOST_PP_SEQ_PUSH_BACK( \
+        GLOBALLISTOFACTIONS_JOBMARKET, \
+        FragmentationFitPotential \
+    )
+#else
+#define GLOBALLISTOFACTIONS_LEVMAR \
+    GLOBALLISTOFACTIONS_JOBMARKET
+#endif /* HAVE_LEVMAR */
+
+// define final list
+#define GLOBALLISTOFACTIONS GLOBALLISTOFACTIONS_LEVMAR
+
 #endif /* GLOBALLISTOFACTIONS_HPP_ */
 

src/Actions/Makefile.am

@@ -234 +234 @@
   Actions/FragmentationAction/ParseFragmentJobsAction.def
 endif
+
+if CONDLEVMAR
+FRAGMENTATIONACTIONSOURCE += \
+  Actions/FragmentationAction/FitPotentialAction.cpp
+FRAGMENTATIONACTIONHEADER += \
+  Actions/FragmentationAction/FitPotentialAction.hpp
+FRAGMENTATIONACTIONDEFS += \
+  Actions/FragmentationAction/FitPotentialAction.def
+endif
+
 
 GRAPHACTIONSOURCE = \
@@ -543 +553 @@
 libMolecuilderActionPrototypes_la_CPPFLAGS += $(JobMarket_CFLAGS)
 endif
+if CONDLEVMAR
+libMolecuilderActionPrototypes_la_CPPFLAGS += $(LEVMAR_CPPFLAGS)
+endif
 libMolecuilderActions_la_includedir = $(includedir)/MoleCuilder/
 libMolecuilderActionPrototypes_la_includedir = $(includedir)/MoleCuilder/