Changeset 065574 for src/Fragmentation/Automation

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/Fragmentation/Automation

Files:

• MPQCFragmentController.cpp (modified) (2 diffs)
• MPQCFragmentController.hpp (modified) (3 diffs)
• VMGFragmentController.cpp (modified) (3 diffs)
• VMGFragmentController.hpp (modified) (1 diff)

src/Fragmentation/Automation/MPQCFragmentController.cpp

@@ -48 +48 @@
 #include "World.hpp"
 
-const int MPQCFragmentController::LEVEL = 5;
-
 bool MPQCFragmentController::addJobsFromFiles(
     const std::string &executable,
@@ -98 +96 @@
   ASSERT( M.determinant() == size*size*size,
       "parsejob() - current domain matrix "+toString(M)+" is not cubic.");
-  const int level = LEVEL;
   FragmentJob::ptr testJob( new MPQCJob(nextid, output, begin, size, level) );
   jobs.push_back(testJob);

src/Fragmentation/Automation/MPQCFragmentController.hpp

@@ -34 +34 @@
 public:
   MPQCFragmentController(boost::asio::io_service &io_service) :
-    SpecificFragmentController(io_service)
+    SpecificFragmentController(io_service),
+    level(5)
   {}
   virtual ~MPQCFragmentController()
@@ -46 +47 @@
   }
 
+  void setLevel(const size_t _level) { level = _level; }
+
 private:
   void parsejob(
@@ -55 +58 @@
 private:
   //!> resolution of sampled electron density as \f$2^{\text{level}}\f$
-  static const int LEVEL;
+  size_t level;
 };
 

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -50 +50 @@
     const std::map<JobId_t, MPQCData> &fragmentData,
     const SamplingGrid &full_sampled_grid,
-    const Fragment &full_fragment)
+    const Fragment &full_fragment,
+    const size_t near_field_cells)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -62 +63 @@
         << " gridpoints and " << data.charges.size() << " particle charges.");
     FragmentJob::ptr testJob(
-        new VMGJob(next_id, data.sampled_grid, data.positions, data.charges) );
+        new VMGJob(next_id, data.sampled_grid, data.positions, data.charges, near_field_cells) );
     jobs.push_back(testJob);
   }
@@ -84 +85 @@
         << " gridpoints and " << charges.size() << " particle charges.");
     FragmentJob::ptr testJob(
-        new VMGJob(next_id, full_sampled_grid, positions, charges) );
+        new VMGJob(next_id, full_sampled_grid, positions, charges, near_field_cells) );
     jobs.push_back(testJob);
   }

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -39 +39 @@
       const std::map<JobId_t, MPQCData> &fragmentData,
       const SamplingGrid &full_sampled_grid,
-      const Fragment &full_fragment);
+      const Fragment &full_fragment,
+      const size_t near_field_cells);
   void getResults(std::map<JobId_t, VMGData> &fragmentData) {
     SpecificFragmentController::getResults<VMGData>(fragmentData);