Changeset a315e8

Timestamp:

Jul 8, 2013, 2:22:04 PM (11 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:

62164d

Parents:

a504946

git-author:

Frederik Heber <heber@…> (06/26/13 18:33:00)

git-committer:

Frederik Heber <heber@…> (07/08/13 14:22:04)

Message:

Potential type is given via extra option not "fit-potential".

• also "potential-type" is optional and "potential-file" can be given as well.
• added EmptyStringValidator.
• TESTFIX: Regression test FitPotential adapted to option "potential-type".

Files:

• src/Actions/FragmentationAction/FitPotentialAction.def (modified) (3 diffs)
• src/Parameters/Makefile.am (modified) (1 diff)
• src/Parameters/Validators/Specific/EmptyStringValidator.hpp (added)
• tests/Python/AllActions/options.dat (modified) (2 diffs)
• tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) (2 diffs)

src/Actions/FragmentationAction/FitPotentialAction.def

@@ -12 +12 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
 #include "Parameters/Validators/RangeValidator.hpp"
 #include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/ElementValidator.hpp"
+#include "Parameters/Validators/Specific/EmptyStringValidator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 #include "Parameters/Validators/Specific/PotentialTypeValidator.hpp"
@@ -22 +24 @@
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)(boost::filesystem::path)(std::string)(boost::filesystem::path)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)
-#define paramtokens ("homology-file")("training-file")("fit-potential")("potential-file")("potential-charges")("fragment-charges")("take-best-of")
+#define paramtokens ("homology-file")("training-file")("potential-type")("potential-file")("potential-charges")("fragment-charges")("take-best-of")
 #define paramdescriptions ("homology file to parse")("optional file to write training data to")("potential type to fit")("potential file specifying multiple potentials to fit")("charges specifying the potential")("charges specifying the fragment")("take the best among this many approximations")
 #define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))
@@ -29 +31 @@
 (FilePresentValidator()) \
 (DummyValidator<boost::filesystem::path>()) \
-(PotentialTypeValidator()) \
+(EmptyStringValidator() || PotentialTypeValidator()) \
 (DummyValidator<boost::filesystem::path>()) \
 (STLVectorValidator< std::vector<const element *> >(0,99, ElementValidator())) \

src/Parameters/Makefile.am

@@ -50 +50 @@
         Parameters/Validators/Specific/BoxVectorValidator.hpp \
         Parameters/Validators/Specific/ElementValidator.hpp \
+        Parameters/Validators/Specific/EmptyStringValidator.hpp \
         Parameters/Validators/Specific/FilePresentValidator.hpp \
         Parameters/Validators/Specific/FileSuffixValidator.hpp \

tests/Python/AllActions/options.dat

@@ -75 +75 @@
 fill-void       "water.data"
 fill-void       "water.xyz"
-fit-potential   "morse"
 forces-file     "test.forces"
 fragment-charges        "1 1"
@@ -135 +134 @@
 potential-charges       "1 1"
 potential-file  "test.potentials"
+potential-type  "morse"
 radius  "20."
 random-atom-displacement        "0."

tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at

@@ -26 +26 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder --fit-potential "morse" --homology-file $file --potential-charges 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
+AT_CHECK([../../molecuilder --fit-potential --potential-type "morse" --homology-file $file --potential-charges 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
 # check that L_2 error is below 1e-6
 AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-6) exit 1}'], 0, [ignore], [ignore])
@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder --fit-potential "harmonic_angle" --homology-file $file --potential-charges 1 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
+AT_CHECK([../../molecuilder --fit-potential --potential-type "harmonic_angle" --homology-file $file --potential-charges 1 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
 # check that L_2 error is below 1e-6
 AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])