Changeset a88452

Timestamp:

Mar 30, 2012, 9:18:17 AM (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:

5a4cbc

Parents:

d505a3

git-author:

Frederik Heber <heber@…> (01/20/12 01:29:57)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:18:17)

Message:

Added new Action subfolder, menu, and CommandLine options map, and FillRegularGrid Action in it.

• counts, offset and min-distance as parameters that determine the filling.
• we find bounding sphere for the selected set of atoms.
• CopyAtoms_withBonds is used in cloning the cluster.
• libMolecuilderFilling added to libMolecuilderUI.

Files:

• src/Actions/FillAction/FillRegularGridAction.cpp (added)
• src/Actions/FillAction/FillRegularGridAction.def (added)
• src/Actions/FillAction/FillRegularGridAction.hpp (added)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (4 diffs)
• src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) (1 diff)
• src/UIElements/Makefile.am (modified) (1 diff)
• src/UIElements/Menu/MenuDescription.cpp (modified) (3 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/GlobalListOfActions.hpp

@@ -105 +105 @@
         (SelectionNotAllAtomsInsideCuboid) \
         (SelectionAtomById) \
-        (FragmentationFragmentation)
+        (FragmentationFragmentation) \
+        (FillRegularGrid)
 
 #endif /* GLOBALLISTOFACTIONS_HPP_ */

src/Actions/Makefile.am

@@ -52 +52 @@
   ${ATOMACTIONSOURCE} \
   ${CMDACTIONSOURCE} \
+  ${FILLACTIONSOURCE} \
   ${FRAGMENTATIONACTIONSOURCE} \
   ${GRAPHACTIONSOURCE} \
@@ -67 +68 @@
   ${ATOMACTIONHEADER} \
   ${CMDACTIONHEADER} \
+  ${FILLACTIONHEADER} \
   ${FRAGMENTATIONACTIONHEADER} \
   ${GRAPHACTIONHEADER} \
@@ -82 +84 @@
   ${ATOMACTIONDEFS} \
   ${CMDACTIONDEFS} \
+  ${FILLACTIONDEFS} \
   ${FRAGMENTATIONACTIONDEFS} \
   ${GRAPHACTIONDEFS} \
@@ -173 +176 @@
   Actions/CommandAction/VersionAction.def \
   Actions/CommandAction/WarrantyAction.def
+
+FILLACTIONSOURCE = \
+        Actions/FillAction/FillRegularGridAction.cpp
+FILLACTIONHEADER = \
+        Actions/FillAction/FillRegularGridAction.hpp
+FILLACTIONDEFS = \
+        Actions/FillAction/FillRegularGridAction.def
+
 
 FRAGMENTATIONACTIONSOURCE = \

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -51 +51 @@
   atom("Atom options"),
   command("Command options"),
+  fill("fill options"),
   fragmentation("Fragmentation options"),
   graph("Graph options"),
@@ -65 +66 @@
   CmdParserLookup["command"] = &command;
   CmdParserLookup["edit"] = &edit;
+  CmdParserLookup["fill"] = &fill;
   CmdParserLookup["fragmentation"] = &fragmentation;
   CmdParserLookup["graph"] = &graph;

src/UIElements/CommandLineUI/CommandLineParser.hpp

@@ -58 +58 @@
   po::options_description command;
   po::options_description edit;
+  po::options_description fill;
   po::options_description fragmentation;
   po::options_description graph;

src/UIElements/Makefile.am

@@ -263 +263 @@
         libMolecuilderAnalysis.la \
         libMolecuilderGraph.la \
+        libMolecuilderFilling.la \
         libMolecuilder.la \
         libMolecuilderFragmentation.la \

src/UIElements/Menu/MenuDescription.cpp

@@ -49 +49 @@
   MenuPositionMap->insert(std::make_pair("command",TopPosition("",3)));
   MenuPositionMap->insert(std::make_pair("edit",TopPosition("",2)));
+  MenuPositionMap->insert(std::make_pair("fill",TopPosition("tools",5)));
   MenuPositionMap->insert(std::make_pair("fragmentation",TopPosition("tools",3)));
   MenuPositionMap->insert(std::make_pair("graph",TopPosition("tools",4)));
@@ -63 +64 @@
   MenuDescriptionsMap->insert(std::make_pair("command","Configuration"));
   MenuDescriptionsMap->insert(std::make_pair("edit","Edit"));
+  MenuDescriptionsMap->insert(std::make_pair("fill","Fill"));
   MenuDescriptionsMap->insert(std::make_pair("fragmentation","Fragmentation"));
   MenuDescriptionsMap->insert(std::make_pair("graph","Graph"));
@@ -77 +79 @@
   MenuNameMap->insert(std::make_pair("command","Configuration"));
   MenuNameMap->insert(std::make_pair("edit","Edit"));
+  MenuNameMap->insert(std::make_pair("fill","Fill"));
   MenuNameMap->insert(std::make_pair("fragmentation","Fragmentation"));
   MenuNameMap->insert(std::make_pair("graph","Graph"));

tests/Python/AllActions/options.dat

@@ -74 +74 @@
 MaxDistance     "-1"
 MDSteps "1"
+mesh-offset     "0.5,0.5,0.5"
+mesh-size       "10,10,10"
+min-distance    "1."
 molecule-by-id  "0"
 nonconvex-envelope      "25"