Changeset 23958d for src/Actions/MoleculeAction

Timestamp:

Jun 13, 2012, 5:39:13 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:

361805

Parents:

8453b3

git-author:

Frederik Heber <heber@…> (05/10/12 13:24:59)

git-committer:

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

Message:

HUGE: All .def files now contain a useful paramvalids line.

• many specific Validators have been added but have only DummyValidator funcitonality so far.
• also some more generic (i.e. templated) validators have been added.
• TESTFIXES: Some regression tests had to be changed because they either had initial faults or now fail due to stricter validators.
  • parser-tremolo-potentials-save: lacked .potentials file in testdir (thx validator!)
  • selection-.*.at: all stored to a targetfile more than once which is not allowed by FilePresentValidator.

Location:

src/Actions/MoleculeAction

Files:

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

src/Actions/MoleculeAction/BondFileAction.def

@@ -10 +10 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +16 @@
 // "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")
 #define paramdefaults (NODEFAULT)("1")("0")
 #define paramreferences (bondfile)(skiplines)(id_offset)
+#define paramvalids \
+(FilePresentValidator()) \
+(DummyValidator< unsigned int >()) \
+(DummyValidator< unsigned int >())
 
 #undef statetypes

src/Actions/MoleculeAction/ChangeNameAction.def

@@ -15 +15 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (name)
+#define paramvalids \
+(DummyValidator< std::string >())
 
 #define statetypes (molecule*)

src/Actions/MoleculeAction/CopyAction.def

@@ -9 +9 @@
 #include <vector>
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Specific/BoxVectorValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +15 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (position)
+#define paramvalids \
+(BoxVectorValidator())
 
 #define statetypes (const std::vector<moleculeId_t>)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def

@@ -8 +8 @@
 // all includes and forward declarations necessary for non-integral types below
 #include "LinearAlgebra/Vector.hpp"
-class MoleculeListClass;
 
+#include "LinearAlgebra/defs.hpp"
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
+#include "Parameters/Validators/Specific/BoxVectorValidator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
+#include "Parameters/Validators/Specific/ParserFileValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -16 +21 @@
 // "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")
 #define paramdefaults (NODEFAULT)(NODEFAULT)("0.")("0.")("0.")("0.")("0")
 #define paramreferences (fillername)(distances)(boundary)(RandAtomDisplacement)(RandMoleculeDisplacement)(MinDistance)(DoRotate)
+#define paramvalids \
+(FilePresentValidator() && ParserFileValidator()) \
+(BoxVectorValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
+(DummyValidator< bool >())
 
 #define statetypes (std::vector<molecule *>)

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <boost/assign.hpp>
 #include <boost/filesystem/path.hpp>
+#include <vector>
 #include "LinearAlgebra/Vector.hpp"
-class MoleculeListClass;
 
+#include "Parameters/Validators/DiscreteValidator.hpp"
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
+#include "Parameters/Validators/Specific/BoxVectorValidator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
+#include "Parameters/Validators/Specific/ParserFileValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -17 +24 @@
 // "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")
 #define paramdefaults (NODEFAULT)(NODEFAULT)("0.")("0.")("0.")("0.")("0")
 #define paramreferences (fillername)(distances)(boundary)(RandAtomDisplacement)(RandMoleculeDisplacement)(MaxDistance)(DoRotate)
+#define paramvalids \
+(FilePresentValidator() && ParserFileValidator()) \
+(BoxVectorValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator() || DiscreteValidator<double>(std::vector<double>(1,-1.))) \
+(DummyValidator< bool >())
 
 #define statetypes (std::vector<molecule *>)

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

@@ -10 +10 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/GenericValidators.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +16 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (start)(interpolation_steps)(end)(IdMapping)
+#define paramvalids \
+(DummyValidator< unsigned int >()) \
+(NotZeroValidator< unsigned int >()) \
+(DummyValidator< unsigned int >()) \
+(DummyValidator< bool >())
 
 #undef statetypes

src/Actions/MoleculeAction/LoadAction.def

@@ -11 +11 @@
 #include <boost/shared_ptr.hpp>
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
+#include "Parameters/Validators/Specific/ParserFileValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -17 +19 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (filename)
+#define paramvalids \
+(FilePresentValidator() && ParserFileValidator())
 
 #define statetypes (moleculeId_t)(std::string)(std::string)(boost::shared_ptr<FormatParser_Parameters>)

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

@@ -11 +11 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Specific/RotationAngleValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -16 +17 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (angle)(Axis)
+#define paramvalids \
+(RotationAngleValidator()) \
+(DummyValidator< Vector >())
 
 #define statetypes (std::vector<molecule*>)

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

@@ -18 +18 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (Axis)
+#define paramvalids \
+(DummyValidator< Vector >())
 
 #undef statetypes

src/Actions/MoleculeAction/SaveAdjacencyAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +16 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (adjacencyfile)
+#define paramvalids \
+(!FilePresentValidator())
 
 #undef statetypes

src/Actions/MoleculeAction/SaveBondsAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +16 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (bondsfile)
+#define paramvalids \
+(!FilePresentValidator())
 
 #undef statetypes

src/Actions/MoleculeAction/SaveSelectedMoleculesAction.def

@@ -9 +9 @@
 
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
+#include "Parameters/Validators/Specific/ParserFileValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +17 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (filename)
+#define paramvalids \
+(!FilePresentValidator() && ParserFileValidator())
 
 #undef statetypes

src/Actions/MoleculeAction/SaveTemperatureAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +16 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (temperaturefile)
+#define paramvalids \
+(!FilePresentValidator())
 
 #undef statetypes

src/Actions/MoleculeAction/SuspendInWaterAction.def

@@ -9 +9 @@
 class MoleculeListClass;
 
-#include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/GenericValidators.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +15 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (density)
+#define paramvalids \
+(PositiveValidator< double >())
 
 #undef statetypes

src/Actions/MoleculeAction/VerletIntegrationAction.def

@@ -10 +10 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/GenericValidators.hpp"
+#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
@@ -15 +17 @@
 // "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")
 #undef paramdefaults
 #define paramreferences (forcesfile)(Deltat)(MDSteps)(FixedCenterOfMass)
+#define paramvalids \
+(FilePresentValidator()) \
+(PositiveValidator< double >()) \
+(NotZeroValidator< unsigned int >()) \
+(DummyValidator< bool >())
 
 #undef statetypes