Changeset 649aaa for src/Actions/MoleculeAction

Timestamp:

Jun 13, 2012, 5:39:12 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:

8453b3

Parents:

301723

git-author:

Frederik Heber <heber@…> (05/09/12 16:17:57)

git-committer:

Frederik Heber <heber@…> (06/13/12 17:39:12)

Message:

All Actions' .def files now have a paramvalids that is used to for validators of their Parameters.

• the structure ActionParameters contains Parameter<> instances per required parameter of the Action.
• these Parameter<> contain a validation functionality if given a Validator.
• right now via boost::preprocessor magic (new defines valid_print and validcopy_print) we create the cstor of the derived ActionParameters class and create a DummyValidator of the correct type for each parameter.
• TODO: We have to go through each .def file and replace DummyValidator by the correct Validator.
• added src/Actions/test.sh which is the shell script to make these changes.

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)
• LoadAction.def (modified) (1 diff)
• RotateAroundSelfByAngleAction.def (modified) (1 diff)
• RotateToPrincipalAxisSystemAction.def (modified) (1 diff)
• SaveAdjacencyAction.def (modified) (1 diff)
• SaveBondsAction.def (modified) (1 diff)
• SaveSelectedMoleculesAction.def (modified) (1 diff)
• SaveTemperatureAction.def (modified) (1 diff)
• SuspendInWaterAction.def (modified) (1 diff)
• VerletIntegrationAction.def (modified) (1 diff)

src/Actions/MoleculeAction/BondFileAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)(unsigned int)(unsigned int)
+#define paramvalids (DummyValidator< boost::filesystem::path >())(DummyValidator< unsigned int >())(DummyValidator< unsigned int >())
 #define paramtokens ("bond-file")("skiplines")("offset")
 #define paramdescriptions ("name of the bond file")("number of header lines to skip")("offset to add to each id")

src/Actions/MoleculeAction/ChangeNameAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (std::string)
+#define paramvalids (DummyValidator< std::string >())
 #define paramtokens ("change-molname")
 #define paramdescriptions ("new name of molecule")

src/Actions/MoleculeAction/CopyAction.def

@@ -9 +9 @@
 #include <vector>
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (Vector)
+#define paramvalids (DummyValidator< Vector >())
 #define paramtokens ("position")
 #define paramdescriptions ("position in R^3 space")

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def

@@ -10 +10 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)(Vector)(double)(double)(double)(double)(bool)
+#define paramvalids (DummyValidator< boost::filesystem::path >())(DummyValidator< Vector >())(DummyValidator< double >())(DummyValidator< double >())(DummyValidator< double >())(DummyValidator< double >())(DummyValidator< bool >())
 #define paramtokens ("fill-void")("distances")("distance-to-molecule")("random-atom-displacement")("random-molecule-displacement")("distance-to-boundary")("DoRotate")
 #define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("minimum distance to present molecules")("magnitude of random atom displacement")("magnitude of random molecule displacement")("minimum distance to boundary")("whether to rotate or not")

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -11 +11 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)(Vector)(double)(double)(double)(double)(bool)
+#define paramvalids (DummyValidator< boost::filesystem::path >())(DummyValidator< Vector >())(DummyValidator< double >())(DummyValidator< double >())(DummyValidator< double >())(DummyValidator< double >())(DummyValidator< bool >())
 #define paramtokens ("fill-molecule")("distances")("distance-to-molecule")("random-atom-displacement")("random-molecule-displacement")("MaxDistance")("DoRotate")
 #define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("minimum distance to present molecules")("magnitude of random atom displacement")("magnitude of random molecule displacement")("maximum spatial distance")("whether to rotate or not")

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (unsigned int)(unsigned int)(unsigned int)(bool)
+#define paramvalids (DummyValidator< unsigned int >())(DummyValidator< unsigned int >())(DummyValidator< unsigned int >())(DummyValidator< bool >())
 #define paramtokens ("start-step")("interpolation-steps")("end-step")("id-mapping")
 #define paramdescriptions ("first or start step")("number of steps to interpolate in between start and end step")("last or end step")("whether the identity shall be used in mapping atoms onto atoms or not")

src/Actions/MoleculeAction/LoadAction.def

@@ -11 +11 @@
 #include <boost/shared_ptr.hpp>
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
+#define paramvalids (DummyValidator< boost::filesystem::path >())
 #define paramtokens ("load")
 #define paramdescriptions ("name of molecule file")

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

@@ -10 +10 @@
 class Vector;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (double)(Vector)
+#define paramvalids (DummyValidator< double >())(DummyValidator< Vector >())
 #define paramtokens ("rotate-around-self")("axis")
 #define paramdescriptions ("rotation angle in degrees")("direction rotation of rotation axis relative to molecule's center of gravity")

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

@@ -12 +12 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (Vector)
+#define paramvalids (DummyValidator< Vector >())
 #define paramtokens ("rotate-to-principal-axis-system")
 #define paramdescriptions ("vector to which to align the biggest eigenvector with")

src/Actions/MoleculeAction/SaveAdjacencyAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
+#define paramvalids (DummyValidator< boost::filesystem::path >())
 #define paramtokens ("save-adjacency")
 #define paramdescriptions ("name of the adjacency file to write to")

src/Actions/MoleculeAction/SaveBondsAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
+#define paramvalids (DummyValidator< boost::filesystem::path >())
 #define paramtokens ("save-bonds")
 #define paramdescriptions ("name of the bonds file to write to")

src/Actions/MoleculeAction/SaveSelectedMoleculesAction.def

@@ -9 +9 @@
 
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
+#define paramvalids (DummyValidator< boost::filesystem::path >())
 #define paramtokens ("save-selected-molecules")
 #define paramdescriptions ("file name of file")

src/Actions/MoleculeAction/SaveTemperatureAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
+#define paramvalids (DummyValidator< boost::filesystem::path >())
 #define paramtokens ("save-temperature")
 #define paramdescriptions ("name of the temperature file to write to")

src/Actions/MoleculeAction/SuspendInWaterAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (double)
+#define paramvalids (DummyValidator< double >())
 #define paramtokens ("suspend-in-water")
 #define paramdescriptions ("desired final density")

src/Actions/MoleculeAction/VerletIntegrationAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
+
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)(double)(unsigned int)(bool)
+#define paramvalids (DummyValidator< boost::filesystem::path >())(DummyValidator< double >())(DummyValidator< unsigned int >())(DummyValidator< bool >())
 #define paramtokens ("verlet-integration")("deltat")("MDSteps")("keep-fixed-CenterOfMass")
 #define paramdescriptions ("perform verlet integration of a given force file")("time step width")("number of MDSteps to integrate")("whether forces and velocities shall be corrected such that center of mass remains at rest")