Changeset cd2591

Timestamp:

Dec 10, 2012, 10:11:00 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:

db6f7d

Parents:

67fec1

git-author:

Frederik Heber <heber@…> (09/13/12 08:26:14)

git-committer:

Frederik Heber <heber@…> (12/10/12 10:11:00)

Message:

Added interpolation-degree as parameter to FragmentationAutomationAction.

• this allows setting the interpolation-degree without recompilation.
• this is now required as we have to calculate the nuclei energy whose precision depends on the interpolation degree from the potential grid.

Files:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (1 diff)
• src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) (2 diffs)
• src/Fragmentation/Automation/VMGFragmentController.cpp (modified) (3 diffs)
• src/Fragmentation/Automation/VMGFragmentController.hpp (modified) (1 diff)
• src/Jobs/VMGJob.cpp (modified) (4 diffs)
• src/Jobs/VMGJob.hpp (modified) (4 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -432 +432 @@
     // Phase Five: create VMGJobs
     const size_t near_field_cells = params.near_field_cells.get();
+    const size_t interpolation_degree = params.interpolation_degree.get();
     if (!vmgcontroller.createLongRangeJobs(
         fragmentData,
         full_sample,
-        summedChargeDensity.getFragment(), near_field_cells))
+        summedChargeDensity.getFragment(),
+        near_field_cells,
+        interpolation_degree))
       return Action::failure;
 

src/Actions/FragmentationAction/FragmentationAutomationAction.def

@@ -21 +21 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::vector< boost::filesystem::path >)(std::string)(std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(bool)
-#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("DoLongrange")
-#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("whether to calculate long-range contributions")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(5))(PARAM_DEFAULT("0"))
-#define paramreferences (jobfiles)(path)(host)(port)(executable)(level)(near_field_cells)(DoLongrange)
+#define paramtypes (std::vector< boost::filesystem::path >)(std::string)(std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)
+#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")
+#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))
+#define paramreferences (jobfiles)(path)(host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)
 #define paramvalids \
 (STLVectorValidator< std::vector< boost::filesystem::path > >(ParserFileValidator() && FilePresentValidator())) \
@@ -33 +33 @@
 (DummyValidator< boost::filesystem::path >()) \
 (RangeValidator< unsigned int >(1, 10)) \
-(RangeValidator< unsigned int >(0, 20)) \
+(RangeValidator< unsigned int >(1, 20)) \
+(RangeValidator< unsigned int >(1, 10)) \
 (DummyValidator< bool >())
 

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -52 +52 @@
     const std::vector<SamplingGrid> &full_sampled_grid,
     const Fragment &full_fragment,
-    const size_t near_field_cells)
+    const size_t near_field_cells,
+    const size_t interpolation_degree)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -64 +65 @@
         << " gridpoints and " << data.charges.size() << " particle charges.");
     FragmentJob::ptr testJob(
-        new VMGJob(next_id, data.sampled_grid, data.positions, data.charges, near_field_cells) );
+        new VMGJob(next_id, data.sampled_grid, data.positions, data.charges, near_field_cells, interpolation_degree) );
     jobs.push_back(testJob);
   }
@@ -92 +93 @@
         << " gridpoints and " << charges.size() << " particle charges.");
     FragmentJob::ptr testJob(
-        new VMGJob(next_id, *iter, positions, charges, near_field_cells) );
+        new VMGJob(next_id, *iter, positions, charges, near_field_cells, interpolation_degree) );
     jobs.push_back(testJob);
   }

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -43 +43 @@
       const std::vector<SamplingGrid> &full_sampled_grid,
       const Fragment &full_fragment,
-      const size_t near_field_cells);
+      const size_t near_field_cells,
+      const size_t interpolation_degree);
   void getResults(std::map<JobId_t, VMGData> &fragmentData) {
     SpecificFragmentController::getResults<VMGData>(fragmentData);

src/Jobs/VMGJob.cpp

@@ -81 +81 @@
     const std::vector< std::vector< double > > &_particle_positions,
     const std::vector< double > &_particle_charges,
-    const size_t _near_field_cells) :
+    const size_t _near_field_cells,
+    const size_t _interpolation_degree) :
   FragmentJob(_JobId),
   density_grid(_density_grid),
@@ -87 +88 @@
   particle_charges(_particle_charges),
   near_field_cells(_near_field_cells),
+  interpolation_degree(_interpolation_degree),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
   num_particles(0),
@@ -97 +99 @@
 VMGJob::VMGJob() :
   FragmentJob(JobId::IllegalJob),
-  near_field_cells(5),
+  near_field_cells(3),
+  interpolation_degree(3),
   num_particles(0),
   f(NULL),
@@ -218 +221 @@
   new ObjectStorage<int>("MAX_ITERATION", 15);
   new ObjectStorage<int>("PARTICLE_NEAR_FIELD_CELLS", near_field_cells);
-  new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", 3);
+  new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", interpolation_degree);
 
   // first initialize f,x,p,q,... from STL vectors

src/Jobs/VMGJob.hpp

@@ -40 +40 @@
    * @param _particle_charges charges per nuclei
    * @param _near_field_cells number of grid-points used to smear our nuclei charge
+   * @param _interpolation_degree degree of interpolation polynomial for getting nuclei
+   *        potential from grid
    */
   VMGJob(const JobId_t _JobId,
@@ -45 +47 @@
       const std::vector< std::vector< double > > &_particle_positions,
       const std::vector< double > &_particle_charges,
-      const size_t _near_field_cells);
+      const size_t _near_field_cells,
+      const size_t _interpolation_degree
+      );
   virtual ~VMGJob();
 
@@ -64 +68 @@
   //!> near field cells used in smearing out core charge density
   const size_t near_field_cells;
+  //!> interpolation degree used in sampling the potential of the nuclei
+  const size_t interpolation_degree;
 
 private:
@@ -95 +101 @@
     ar & const_cast< std::vector< double > &>(particle_charges);
     ar & const_cast< size_t &>(near_field_cells);
+    ar & const_cast< size_t &>(interpolation_degree);
     ar & returndata;
   }

tests/Python/AllActions/options.dat

@@ -78 +78 @@
 id-mapping      "1"
 input   "test.data"
+interpolation-degree    "5"
 interpolation-steps     "9"
 keep-fixed-CenterOfMass "0"