Changeset a504946 for src

Timestamp:

Jul 8, 2013, 2:22:04 PM (12 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:

a315e8

Parents:

49dcf7

git-author:

Frederik Heber <heber@…> (06/11/13 12:07:24)

git-committer:

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

Message:

Training data can now be written to optional file.

Location:

src/Actions/FragmentationAction

Files:

• FitPotentialAction.cpp (modified) (1 diff)
• FitPotentialAction.def (modified) (1 diff)

src/Actions/FragmentationAction/FitPotentialAction.cpp

@@ -249 +249 @@
 
       // print table
-      LOG(3, "DEBUG: I gathered the following training data:\n" <<
-          _detail::writeDistanceEnergyTable(data.getDistanceEnergyTable()));
+      if (params.training_file.get().string().empty()) {
+        LOG(3, "DEBUG: I gathered the following training data:\n" <<
+            _detail::writeDistanceEnergyTable(data.getDistanceEnergyTable()));
+      } else {
+        std::ofstream trainingstream(params.training_file.get().string().c_str());
+        if (trainingstream.good()) {
+          LOG(3, "DEBUG: Writing training data to file " <<
+              params.training_file.get().string() << ".");
+          trainingstream << _detail::writeDistanceEnergyTable(data.getDistanceEnergyTable());
+        }
+        trainingstream.close();
+      }
     }
 

src/Actions/FragmentationAction/FitPotentialAction.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 (boost::filesystem::path)(std::string)(boost::filesystem::path)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)
-#define paramtokens ("homology-file")("fit-potential")("potential-file")("potential-charges")("fragment-charges")("take-best-of")
-#define paramdescriptions ("homology file to parse")("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)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))
-#define paramreferences (homology_file)(potentialtype)(potential_file)(charges)(fragment)(best_of_howmany)
+#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 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))
+#define paramreferences (homology_file)(training_file)(potentialtype)(potential_file)(charges)(fragment)(best_of_howmany)
 #define paramvalids \
 (FilePresentValidator()) \
+(DummyValidator<boost::filesystem::path>()) \
 (PotentialTypeValidator()) \
 (DummyValidator<boost::filesystem::path>()) \