Changeset 58bbd3 for src/Actions

Timestamp:

Jun 9, 2010, 3:08:46 PM (15 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:

31b09e

Parents:

1e6913

Message:

Cases 'C' are now handled by CommandLineUI.

• TESTFIX: Analysis/3/post/bin_output.csv was wrong, bins had max around 10, not 5. (which must be the max, as the box of water molecules is from 5:15 centered at 10 for each axis)
• PeriodicPairCorrelartion(): Old commented-out block removed.
• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() - MolName and id is printed.

File:

• src/Actions/MapOfActions.cpp (modified) (14 diffs)

src/Actions/MapOfActions.cpp

@@ -50 +50 @@
   v = boost::any(BoxValue(BV));
 }
-
 
 /** Constructor of class MapOfActions.
@@ -85 +84 @@
   DescriptionMap["nonconvex-envelope"] = "create the non-convex envelope for a molecule";
   DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
-  DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements";
-  DescriptionMap["pair-correlation-point"] = "pair correlation analysis between atoms of a element to a given point";
-  DescriptionMap["pair-correlation-surface"] = "pair correlation analysis between atoms of a given element and a surface";
+  DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
   DescriptionMap["principal-axis-system"] = "calculate the principal axis system of the specified molecule";
@@ -113 +110 @@
   DescriptionMap["distances"] = "list of three of distances in space, one for each axis direction";
   DescriptionMap["DoRotate"] = "whether to rotate or just report angles";
-  DescriptionMap["element"] = "set of elements";
+  DescriptionMap["element"] = "single element";
+  DescriptionMap["elements"] = "set of elements";
   DescriptionMap["end-mol"] = "last or end step";
   DescriptionMap["input"] = "name of input file";
@@ -120 +118 @@
   DescriptionMap["MaxDistance"] = "maximum distance in space";
   DescriptionMap["molecule-by-id"] = "index of a molecule";
+  DescriptionMap["molecule-by-name"] = "name of a molecule";
   DescriptionMap["order"] = "order of a discretization, dissection, ...";
   DescriptionMap["output-file"] = "name of the output file";
@@ -146 +145 @@
   ShortFormMap["linear-interpolate"] = "L";
   ShortFormMap["nonconvex-envelope"] = "N";
-  ShortFormMap["pair-correlation"] = "CE";
-  ShortFormMap["pair-correlation-point"] = "CP";
-  ShortFormMap["pair-correlation-surface"] = "CS";
+  ShortFormMap["pair-correlation"] = "C";
   ShortFormMap["parse-xyz"] = "p";
   ShortFormMap["remove-atom"] = "r";
@@ -188 +185 @@
   TypeMap["nonconvex-envelope"] = Molecule;
   TypeMap["parse-xyz"] = String;
+  TypeMap["pair-correlation"] = String;
   TypeMap["principal-axis-system"] = Axis;
   TypeMap["remove-atom"] = Atom;
@@ -208 +206 @@
   TypeMap["bin-end"] = Double;
   TypeMap["bin-start"] = Double;
+  TypeMap["bin-width"] = Double;
   TypeMap["distance"] = Double;
   TypeMap["distances"] = Vector;
@@ -217 +216 @@
   TypeMap["MaxDistance"] = Double;
   TypeMap["molecule-by-id"] = Molecule;
+  TypeMap["molecule-by-name"] = Molecule;
   TypeMap["order"] = Integer;
   TypeMap["output-file"] = String;
@@ -224 +224 @@
   // default values for any action that needs one (always string!)
   DefaultValue["molecule-by-id"] = "-1";
+  DefaultValue["bin-width"] = "0.5";
+  DefaultValue["periodic"] = "0";
 
 
@@ -240 +242 @@
 //      generic.insert("default-molname");
         generic.insert("depth-first-search");
-//      generic.insert("element-db");
+//      generic.insert("element-d<b");
 //      generic.insert("fastparsing");
   generic.insert("fill-molecule");
@@ -248 +250 @@
 //  generic.insert("molecular-volume");
 //  generic.insert("nonconvex-envelope");
-//      generic.insert("pair-correlation");
-//      generic.insert("pair-correlation-point");
-//      generic.insert("pair-correlation-surface");
+        generic.insert("pair-correlation");
 //      generic.insert("parse-xyz");
 //  generic.insert("principal-axis-system");
@@ -269 +269 @@
         generic.insert("version");
 //      // list of generic values
-//      generic.insert("bin-output-file");
-//  generic.insert("bin-end");
-//  generic.insert("bin-start");
 //  generic.insert("distance");
 //  generic.insert("distances");
@@ -278 +275 @@
     generic.insert("input");
 //  generic.insert("length");
-//  generic.insert("output-file");
-//  generic.insert("periodic");
-//  generic.insert("position");
 //  generic.insert("start-mol");
 
@@ -287 +281 @@
 
     // hidden arguments
+  generic.insert("bin-end");
+  generic.insert("bin-output-file");
+  generic.insert("bin-start");
+  generic.insert("bin-width");
   generic.insert("distance");
   generic.insert("DoRotate");
   generic.insert("distances");
+  generic.insert("element");
+  generic.insert("elements");
   generic.insert("lengths");
   generic.insert("MaxDistance");
   generic.insert("molecule-by-id");
+  generic.insert("molecule-by-name");
   generic.insert("order");
+  generic.insert("output-file");
+  generic.insert("periodic");
+  generic.insert("position");
 }