Changeset 7cdf58 for src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

Timestamp:

Apr 8, 2013, 11:56:08 AM (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:

830b3e

Parents:

c39675

git-author:

Frederik Heber <heber@…> (03/03/13 21:19:22)

git-committer:

Frederik Heber <heber@…> (04/08/13 11:56:08)

Message:

ExportGraph_ToFiles now uses one-by-one procedure to store fragments.

• we took MoleculeListClass::OutputConfigForListOfFragments() and also StoreForcesFile and adapted them.

File:

• src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) (1 diff)

src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

@@ -47 +47 @@
 
 private:
+        /** Helper function to store a fragment for all desired types to file.
+         *
+         * \param CurrentFragment SaturatedFragment to store to file
+         * \param FragmentNumber number padded with zeros used in filename
+         * \param FragmentCounter enumeration of this fragment
+         * \return true - file written successfully, false - writing failed
+         */
+        bool storeFragmentForAllTypes(
+            SaturatedFragment_ptr &CurrentFragment,
+            char *FragmentNumber,
+            size_t FragmentCounter) const;
+
+        /** Helper function to append the key sets in this SaturatedFragment without
+         * added hydrogens to an open stream.
+         *
+         * \param CurrentFragment fragment whose indices to write
+   * \param ForcesFile open stream to write to
+   * \param SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
+   * \return true - file written successfully, false - writing failed
+   */
+        bool appendToForcesFile(
+            SaturatedFragment_ptr &CurrentFragment,
+            std::ostream &ForcesFile,
+            const SortIndex_t &SortIndex) const;
+
+private:
         //!> prefix for fragment files
         std::string prefix;