Changeset 0f5956 for src/Actions/FragmentationAction/FragmentationAction.def

Timestamp:

Sep 6, 2016, 2:36:46 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, Candidate_v1.7.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, 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, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

c6f2c5

Parents:

d21933

git-author:

Frederik Heber <heber@…> (08/31/16 10:45:35)

git-committer:

Frederik Heber <heber@…> (09/06/16 14:36:46)

Message:

Added "parse-state-files" option to fragment-molecule which is off by default.

• this prevents accidental parsing of stale keysets, adjacency, or orderatsite files. These hard to find errors ever and again cause failing fragmentation because e.g. some hydrogen is suddenly in the keysets although hydrogens are excluded.

File:

• src/Actions/FragmentationAction/FragmentationAction.def (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.def

@@ -21 +21 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::string)(double)(int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)(bool)
-#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")("DoCyclesFull")
-#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")("always calculate (aromatic) rings fully, even beyond desired order")
-#define paramdefaults (PARAM_DEFAULT("BondFragment"))(PARAM_DEFAULT(3.))(PARAM_DEFAULT(3))(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))(PARAM_DEFAULT(false))
-#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)(DoCyclesFull)
+#define paramtypes (std::string)(double)(int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)(bool)(bool)
+#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")("DoCyclesFull")("parse-state-files")
+#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")("always calculate (aromatic) rings fully, even beyond desired order")("whether to parse keysets, orderatsite, adjacency from state files")
+#define paramdefaults (PARAM_DEFAULT("BondFragment"))(PARAM_DEFAULT(3.))(PARAM_DEFAULT(3))(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))(PARAM_DEFAULT(false))(PARAM_DEFAULT(false))
+#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)(DoCyclesFull)(ParseStateFiles)
 #define paramvalids \
 (DummyValidator< std::string >()) \
@@ -35 +35 @@
 (RangeValidator< unsigned int >(1, 10)) \
 (DummyValidator< unsigned int >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >())