Changeset 24fbf3 for src/Actions/MoleculeAction

Timestamp:

Oct 30, 2010, 6:44:29 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, Candidate_v1.7.0, 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:

fc192f

Parents:

2a6a2c

git-author:

Frederik Heber <heber@…> (10/26/10 10:43:36)

git-committer:

Frederik Heber <heber@…> (10/30/10 18:44:29)

Message:

All specialization of ActionTraits now contain specific information.

• new defines in Action_impl_header.hpp: DEFAULTVALUE, DESCRiPTION, SHORTFORM, TYPEINFO.
• i.e. removed the MapOfActions' short-wiring.
• script used for extraction is in src/Actions/convert.sh.
• we cause a compilation error if DESCRIPTION or TYPEINFO are missing.
• FIX: added some typeinfos as void where missing.

Location:

src/Actions/MoleculeAction

Files:

• BondFileAction.def (modified) (1 diff)
• ChangeNameAction.def (modified) (1 diff)
• CopyAction.def (modified) (1 diff)
• FillVoidWithMoleculeAction.def (modified) (1 diff)
• FillWithMoleculeAction.def (modified) (1 diff)
• LinearInterpolationofTrajectoriesAction.def (modified) (1 diff)
• RotateAroundSelfByAngleAction.def (modified) (1 diff)
• RotateToPrincipalAxisSystemAction.def (modified) (2 diffs)
• SaveAdjacencyAction.def (modified) (1 diff)
• SaveBondsAction.def (modified) (1 diff)
• SaveTemperatureAction.def (modified) (1 diff)
• SuspendInWaterAction.def (modified) (1 diff)
• VerletIntegrationAction.def (modified) (1 diff)

src/Actions/MoleculeAction/BondFileAction.def

@@ -24 +24 @@
 #define TOKEN "bond-file"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "name of the bond file"
+#define SHORTFORM "A"
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/ChangeNameAction.def

@@ -24 +24 @@
 #define TOKEN "change-molname"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "change the name of a molecule"
+#undef SHORTFORM
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/CopyAction.def

@@ -24 +24 @@
 #define TOKEN "copy-molecule"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "copies a molecule with all atoms and bonds"
+#undef SHORTFORM
+#define TYPEINFO &typeid(molecule)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def

@@ -25 +25 @@
 #define TOKEN "fill-void"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "fill void space of box with a filler molecule"
+#undef SHORTFORM
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -25 +25 @@
 #define TOKEN "fill-molecule"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "fill around molecules' surface with a filler molecule"
+#define SHORTFORM "F"
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

@@ -24 +24 @@
 #define TOKEN "linear-interpolate"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "linear interpolation in discrete steps between start and end position of a molecule"
+#define SHORTFORM "L"
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

@@ -25 +25 @@
 #define TOKEN "rotate-self"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "rotates molecules by a specific angle around own center of gravity"
+#undef SHORTFORM
+#define TYPEINFO &typeid(double)

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include "Actions/Values.hpp"
 #include "LinearAlgebra/Vector.hpp"
+
 class MoleculeListClass;
 
@@ -25 +27 @@
 #define TOKEN "rotate-to-pas"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "calculate the principal axis system of the specified molecule and rotate specified axis to align with main axis"
+#define SHORTFORM "m"
+#define TYPEINFO &typeid(VectorValue)

src/Actions/MoleculeAction/SaveAdjacencyAction.def

@@ -24 +24 @@
 #define TOKEN "save-adjacency"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "name of the adjacency file to write to"
+#define SHORTFORM "J"
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/SaveBondsAction.def

@@ -24 +24 @@
 #define TOKEN "save-bonds"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "name of the bonds file to write to"
+#define SHORTFORM "j"
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/SaveTemperatureAction.def

@@ -24 +24 @@
 #define TOKEN "save-temperature"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "name of the temperature file to write to"
+#define SHORTFORM "S"
+#define TYPEINFO &typeid(std::string)

src/Actions/MoleculeAction/SuspendInWaterAction.def

@@ -24 +24 @@
 #define TOKEN "suspend-in-water"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "suspend the given molecule in water such that in the domain the mean density is as specified"
+#define SHORTFORM "u"
+#define TYPEINFO &typeid(double)

src/Actions/MoleculeAction/VerletIntegrationAction.def

@@ -24 +24 @@
 #define TOKEN "verlet-integrate"
 
+
+// finally the information stored in the ActionTrait specialization
+#undef DEFAULTVALUE
+#define DESCRIPTION "perform verlet integration of a given force file"
+#define SHORTFORM "P"
+#define TYPEINFO &typeid(std::string)