Changeset 065574 for src/Jobs

Timestamp:

Dec 10, 2012, 10:10:56 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:

de84ef

Parents:

758e56

git-author:

Frederik Heber <heber@…> (08/29/12 13:09:08)

git-committer:

Frederik Heber <heber@…> (12/10/12 10:10:56)

Message:

Added level and near_field_cells as options to FragmentationAutomationAction.

• new options are grid-level and near-field-cells that allow setting the precision of the electron charge density sampling (and potentil calculation) and the smearing out of nuclei charge density on the command-line.

Location:

src/Jobs

Files:

• VMGJob.cpp (modified) (2 diffs)
• VMGJob.hpp (modified) (3 diffs)

src/Jobs/VMGJob.cpp

@@ -78 +78 @@
     const SamplingGrid &_density_grid,
     const std::vector< std::vector< double > > &_particle_positions,
-    const std::vector< double > &_particle_charges) :
+    const std::vector< double > &_particle_charges,
+    const size_t _near_field_cells) :
   FragmentJob(_JobId),
   density_grid(_density_grid),
   particle_positions(_particle_positions),
   particle_charges(_particle_charges),
+  near_field_cells(_near_field_cells),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid))
 {}
 
 VMGJob::VMGJob() :
-  FragmentJob(JobId::IllegalJob)
+  FragmentJob(JobId::IllegalJob),
+  near_field_cells(5)
 {}
 
@@ -129 +132 @@
   // TODO: As a matter of fact should use open boundary conditions
   const Boundary boundary(Periodic, Periodic, Periodic);
-  int near_field_cells = 10;
 
   /*

src/Jobs/VMGJob.hpp

@@ -36 +36 @@
    *
    * @param _JobId id of the job
-   * @param _begin offset of the domain
-   * @param _size edge length of the cubic(!) domain
-   * @param _level level is \f$2^{\text{level}}\f$ grid points
-   * @param _sampled_input vector of sampled points of the grid as right-hand side
+   * @param _density_grid sampled electron charge density from short-range solutions
+   * @param _particle_positions position per nuclei
+   * @param _particle_charges charges per nuclei
+   * @param _near_field_cells number of grid-points used to smear our nuclei charge
    */
   VMGJob(const JobId_t _JobId,
       const SamplingGrid &density_grid,
       const std::vector< std::vector< double > > &_particle_positions,
-      const std::vector< double > &_particle_charges);
+      const std::vector< double > &_particle_charges,
+      const size_t _near_field_cells);
   virtual ~VMGJob();
 
@@ -59 +60 @@
   //!> charges of all nuclei
   const std::vector< double > particle_charges;
+  //!> near field cells used in smearing out core charge density
+  const size_t near_field_cells;
 
 private:
@@ -78 +81 @@
     ar & const_cast< std::vector< std::vector< double > > &>(particle_positions);
     ar & const_cast< std::vector< double > &>(particle_charges);
+    ar & const_cast< size_t &>(near_field_cells);
     ar & returndata;
   }