Changeset 9445081 for src/Fragmentation/Automation/FragmentJobQueue.hpp

Timestamp:

Nov 4, 2016, 9:37:51 AM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, 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_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, 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_IntegrationTest, 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, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

ea63cb

Parents:

041a79

git-author:

Frederik Heber <heber@…> (10/04/16 08:06:18)

git-committer:

Frederik Heber <heber@…> (11/04/16 09:37:51)

Message:

FragmentJobQueue additionally stores the bond graph as an edge set per fragment/job.

• added SaturatedFragment::getEdges() that returns the set of edges, indices rewritten (starting at 0), and hydrogens included, i.e. matching with the lines in the output config.
• ExportGraph_ToJobs::operator() additionally queries for the edge set and places it in the JobQueue.

File:

• src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) (6 diffs)

src/Fragmentation/Automation/FragmentJobQueue.hpp

@@ -20 +20 @@
 #include "CodePatterns/Singleton.hpp"
 
+#include "Fragmentation/EdgesPerFragment.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
 #include "Fragmentation/parseKeySetFile.hpp"
 #include "Jobs/MPQCJob.hpp"
+#include "types.hpp"
 
 /** FragmentJobQueue is a static instance to contain all present fragment
@@ -45 +47 @@
 
 public:
+  typedef FragmentationEdges::edges_per_fragment_t edges_per_fragment_t;
 
   /** Pushes a vector of jobs into the queue.
    *
    * \param _jobs new jobs to push
-   * \param KeySet KeySet of all (non-hydrogen) atoms
-   * \param FullKeySet KeySet of all atoms except saturation hydrogens
+   * \param _KeySet KeySet of all (non-hydrogen) atoms
+   * \param _FullKeySet KeySet of all atoms except saturation hydrogens
+   * \param _edges_per_fragment edges of bond graph of all fragments
    */
   void addJobs(
       std::vector<FragmentJob::ptr> &_jobs,
       const KeySetsContainer &_KeySets,
-      const KeySetsContainer &_FullKeySets);
+      const KeySetsContainer &_FullKeySets,
+      const edges_per_fragment_t &_edges_per_fragment);
 
   /** Returns ref to jobs.
@@ -96 +101 @@
       );
 
+  /** Adds edges after fragments have been added by file.
+   *
+   */
+  bool addEdgesPerFragmentFromFiles(
+      const boost::filesystem::path &path
+      );
+
   /** Getter for the container of all KeySets to the jobs.
    *
@@ -107 +119 @@
    */
   const KeySetsContainer& getFullKeySets() const { return FullKeySets; }
+
+  /** Getter for the container of all edges of the bond graph over all jobs.
+   *
+   * \return const ref to container
+   */
+  const edges_per_fragment_t& getEdgesPerFragment() const { return edges_per_fragment; }
 
   /* Empties contained jobs and all KeySets.
@@ -130 +148 @@
   //!> container for all KeySet's with all except saturation hydrogen to the jobs
   KeySetsContainer FullKeySets;
+  //!> container for all edges of the bond graph of each fragments
+  edges_per_fragment_t edges_per_fragment;
 };
 
@@ -136 +156 @@
     std::vector<FragmentJob::ptr> &_jobs,
     const KeySetsContainer &_KeySets,
-    const KeySetsContainer &_FullKeySets)
+    const KeySetsContainer &_FullKeySets,
+    const edges_per_fragment_t &_edges_per_fragment)
 {
   jobs.insert(jobs.end(), _jobs.begin(), _jobs.end());
   KeySets.insert(_KeySets);
   FullKeySets.insert(_FullKeySets);
+  edges_per_fragment.reserve(edges_per_fragment.size()+_edges_per_fragment.size());
+  edges_per_fragment.insert(
+      edges_per_fragment.end(),
+      _edges_per_fragment.begin(), _edges_per_fragment.end());
 }