Changeset bae7bc for src/Fragmentation/Automation/FragmentationChargeDensity.hpp

Timestamp:

Apr 15, 2013, 10:28:25 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:

503acc1

Parents:

4f44ae

git-author:

Frederik Heber <heber@…> (03/04/13 14:14:10)

git-committer:

Frederik Heber <heber@…> (04/15/13 10:28:25)

Message:

Outsourced parsing of fragment files into ParseFragmentJobsAction from FragmentationAutomationAction.

• We now solely rely on the job queue to contain all the information we need.
• FragmentationAutomationAction now clears queue after calculation.

File:

• src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) (4 diffs)

src/Fragmentation/Automation/FragmentationChargeDensity.hpp

@@ -16 +16 @@
 
 #include <map>
-#include <string>
 #include <vector>
 
@@ -27 +26 @@
 #include "Jobs/Grid/SamplingGrid.hpp"
 
+class KeySetsContainer;
+
 /** This structure is a container for the summed up charge density per level.
  *
@@ -35 +36 @@
    *
    * @param fragmentData MPQCData resulting from the jobs, each associated to a job
-   * @param KeySetFilename filename with keysets to associate forces correctly
+   * @param KeySet KeySets of all (non-hydrogen) atoms
    */
   FragmentationChargeDensity(
       const std::map<JobId_t,MPQCData> &fragmentData,
-      const std::string &KeySetFilename);
+      const KeySetsContainer& KeySet);
 
   std::vector<SamplingGrid> getFullSampledGrid();
@@ -54 +55 @@
   //!> results per IndexSet of summed up fragment positions and charges
   std::map<IndexSet::ptr, std::pair<MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> > Result_perIndexSet_Fragment;
+
+private:
+  /** Helper function to call OrthogonalSummation.
+   *
+   * \param fragmentData map of calculated jobs
+   * \param KeySet container of all keysets
+   * \param MatrixNrLookup map with enumerated job ids
+   */
+  void sumUp(
+      const std::map<JobId_t,MPQCData> &fragmentData,
+      const KeySetsContainer &KeySet,
+      const std::map< JobId_t, size_t > &MatrixNrLookup);
+
 };