Changeset 6ff62c for src/Fragmentation/Automation

Timestamp:

May 1, 2013, 7:52:55 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:

b6b21a

Parents:

53c579

git-author:

Frederik Heber <heber@…> (03/27/13 11:26:13)

git-committer:

Frederik Heber <heber@…> (05/01/13 07:52:55)

Message:

Added DoValenceOnly has new option to FragmentationAutomationAction.

• this carries over to MPQCData, MPQCJob, MPQCFragmentController, and VMGFragmentController, that need to pass on the option.
• Changes to MPQCData have been caught by increasing serialization version.
• TESTFIX: Redid files for regression test AnalyseFragmentResults.

Location:

src/Fragmentation/Automation

Files:

• MPQCFragmentController.cpp (modified) (2 diffs)
• MPQCFragmentController.hpp (modified) (1 diff)
• VMGFragmentController.cpp (modified) (2 diffs)
• VMGFragmentController.hpp (modified) (1 diff)

src/Fragmentation/Automation/MPQCFragmentController.cpp

@@ -51 +51 @@
 #include "World.hpp"
 
-bool MPQCFragmentController::addJobsFromQueue(const MPQCData::DoLongrange_t _DoLongrange)
+bool MPQCFragmentController::addJobsFromQueue(
+    const MPQCData::DoLongrange_t _DoLongrange,
+    const MPQCData::DoValenceOnly_t _DoValenceOnly
+    )
 {
   // give them all valid ids
@@ -60 +63 @@
     MPQCJob *job = boost::polymorphic_downcast<MPQCJob *>(jobiter->get());
     job->DoLongrange = _DoLongrange;
+    job->DoValenceOnly = _DoValenceOnly;
     changeJobId((*jobiter), getAvailableId());
   }

src/Fragmentation/Automation/MPQCFragmentController.hpp

@@ -42 +42 @@
    *
    * \param _DoSampleDensity whether to actually sample the resulting electronic density
+   * \param _DoValenceOnly whether to sample just the valence or the total elctron and nuclei density
    * \return true - jobs obtained, false - queue empty
    */
-  bool addJobsFromQueue(const MPQCData::DoLongrange_t _DoLongrange);
+  bool addJobsFromQueue(
+      const MPQCData::DoLongrange_t _DoLongrange,
+      const MPQCData::DoValenceOnly_t _DoValenceOnly
+      );
 
   /** Get results map of calculated jobs.

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -48 +48 @@
 #include "World.hpp"
 
+/** Helper function for the number of core electrons of a given element \a z.
+ *
+ * \param z atomic number of element
+ * \return number of core electrons for this element
+ */
+static int getCoreElectrons(const int z)
+{
+  int n=0;
+  if (z > 2) n += 2;
+  if (z > 10) n += 8;
+  if (z > 18) n += 8;
+  if (z > 30) n += 10;
+  if (z > 36) n += 8;
+  if (z > 48) n += 10;
+  if (z > 54) n += 8;
+  return n;
+}
+
 bool VMGFragmentController::createLongRangeJobs(
     const std::map<JobId_t, MPQCData> &fragmentData,
     const std::vector<SamplingGrid> &full_sampled_grid,
     const size_t near_field_cells,
-    const size_t interpolation_degree)
+    const size_t interpolation_degree,
+    const MPQCData::DoValenceOnly_t _DoValenceOnly)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -82 +101 @@
       for (size_t i=0;i<3;++i) position[i] = pos[i]/AtomicLengthToAngstroem;
       positions.push_back(position);
-      charges.push_back((double)((*iter)->getElement().getAtomicNumber()));
+      int charge = (*iter)->getElement().getAtomicNumber();
+      // subtract core electron charge from nuclei charge if only valence sampled
+      if (_DoValenceOnly == MPQCData::DoSampleValenceOnly)
+        charge -= getCoreElectrons(charge);
+      charges.push_back((double)charge);
     }
   }

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -39 +39 @@
   {}
 
+  /** Creates the long range jobs from finished short-range jobs.
+   *
+   * \param fragmentData finished short-range results
+   * \param full_sampled_grid sampled electron densities from finished short-range jobs
+   * \param near_field_cells radius of b-splines for interpolation charges onto grid
+   * \param interpolation_degree interpolation degree for newton interpolation from grid
+   * \param _DoValenceOnly whether to neglect core electron and nuclei charges
+   */
   bool createLongRangeJobs(
       const std::map<JobId_t, MPQCData> &fragmentData,
       const std::vector<SamplingGrid> &full_sampled_grid,
       const size_t near_field_cells,
-      const size_t interpolation_degree);
+      const size_t interpolation_degree,
+      const MPQCData::DoValenceOnly_t _DoValenceOnly);
+
+  /** Get results of finished long-range jobs.
+   *
+   * \param fragmentData contains results on return
+   */
   void getResults(std::map<JobId_t, VMGData> &fragmentData) {
     SpecificFragmentController::getResults<VMGData>(fragmentData);