Changeset ee9018 for src

Timestamp:

Aug 15, 2013, 8:41:17 AM (11 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:

f6c19d

Parents:

d9d028

git-author:

Frederik Heber <heber@…> (04/15/13 19:03:31)

git-committer:

Frederik Heber <heber@…> (08/15/13 08:41:17)

Message:

InterfaceVMGJob now may also use open boundary (FAS instead of CS).

• so far, according to Julian, only order 2 is implemented correctly.
• we choose between open and periodic boundary conditions by a parameter in VMGJob.
• VMGFragmentController uses the parameter when instantating VMGJobs.

Location:

src

Files:

• Fragmentation/Automation/VMGFragmentController.cpp (modified) (3 diffs)
• Fragmentation/Automation/VMGFragmentController.hpp (modified) (2 diffs)
• Jobs/InterfaceVMGJob.hpp (modified) (1 diff)
• Jobs/VMGJob.cpp (modified) (7 diffs)
• Jobs/VMGJob.hpp (modified) (2 diffs)

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -75 +75 @@
     const TreatGrid_t _TreatGrid,
     const MPQCData::DoValenceOnly_t _DoValenceOnly,
-    const bool _DoPrintDebug)
+    const bool _DoPrintDebug,
+    const bool _OpenBoundaryConditions)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -97 +98 @@
             interpolation_degree,
             _SampleParticles == DoSampleParticles,
-            _DoPrintDebug) );
+            _DoPrintDebug,
+            _OpenBoundaryConditions) );
     jobs.push_back(testJob);
   }
@@ -143 +145 @@
             interpolation_degree,
             _SampleParticles == DoSampleParticles,
-            _DoPrintDebug) );
+            _DoPrintDebug,
+            _OpenBoundaryConditions) );
     jobs.push_back(testJob);
   }

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -61 +61 @@
    * \param _DoValenceOnly whether to neglect core electron and nuclei charges
    * \param _DoPrintDebug whether we do print grid for debug visualization or not
+   * \param _OpenBoundaryConditions whether we have open (true) or periodic (false)
+   *        boundary conditions
    */
   bool createLongRangeJobs(
@@ -70 +72 @@
       const TreatGrid_t _TreatGrid,
       const MPQCData::DoValenceOnly_t _DoValenceOnly,
-      const bool _DoPrintDebug);
+      const bool _DoPrintDebug,
+      const bool _OpenBoundaryConditions = false);
 
   /** Get results of finished long-range jobs.

src/Jobs/InterfaceVMGJob.hpp

@@ -53 +53 @@
       const ImportParticles_t _ImportParticles=DoImportParticles,
       const bool _DoPrintDebug=false,
-      int coarseningSteps=0,
+      int coarseningSteps=9,
       double alpha=1.6
       );

src/Jobs/VMGJob.cpp

@@ -54 +54 @@
 #include "comm/comm_serial.hpp"
 #endif
+// periodic boundary conditions
 #include "cycles/cycle_cs_periodic.hpp"
 #include "discretization/discretization_poisson_fd.hpp"
+#include "level/level_operator_cs.hpp"
+#include "smoother/gsrb_poisson_4.hpp"
+#include "solver/solver_singular.hpp"
+// open boundary conditions
+#include "cycles/cycle_fas_dirichlet.hpp"
+#include "discretization/discretization_poisson_fv.hpp"
 #include "grid/multigrid.hpp"
 //#include "grid/tempgrid.hpp"
-#include "level/level_operator_cs.hpp"
+#include "level/level_operator_fas.hpp"
 #include "level/stencils.hpp"
-#include "smoother/gsrb_poisson_4.hpp"
+#include "smoother/gsrb_poisson_2.hpp"
 #include "solver/givens.hpp"
-//#include "solver/solver_regular.hpp"
-#include "solver/solver_singular.hpp"
+#include "solver/solver_regular.hpp"
 #include "units/particle/comm_mpi_particle.hpp"
 
@@ -85 +91 @@
     const size_t _interpolation_degree,
     const bool _DoImportParticles,
-    const bool _DoPrintDebug) :
+    const bool _DoPrintDebug,
+    const bool _OpenBoundaryConditions) :
   FragmentJob(_JobId),
   density_grid(_density_grid),
@@ -94 +101 @@
   DoImportParticles(_DoImportParticles),
   DoPrintDebug(_DoPrintDebug),
+  OpenBoundaryConditions(_OpenBoundaryConditions),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
   particles()
@@ -104 +112 @@
   DoImportParticles(true),
   DoPrintDebug(false),
+  OpenBoundaryConditions(false),
   particles()
 {}
@@ -201 +210 @@
 void VMGJob::InitVMG()
 {
-  // TODO: As a matter of fact should use open boundary conditions
-  const Boundary boundary(Periodic, Periodic, Periodic);
+  Boundary *boundary = NULL;
+  if (OpenBoundaryConditions)
+    boundary = new Boundary(Open, Open, Open);
+  else
+    boundary = new Boundary(Periodic, Periodic, Periodic);
 
   /*
    * Choose multigrid components (self-registering)
    */
+
 #ifdef HAVE_MPI
-  new Particle::CommMPI(boundary, new DomainDecompositionMPI());
+  new Particle::CommMPI(*boundary, new DomainDecompositionMPI());
 #else
-  new CommSerial(boundary);
-#endif
-  new DiscretizationPoissonFD(4);
+  new CommSerial(*boundary);
+#endif
+  if (OpenBoundaryConditions)
+    new DiscretizationPoissonFV(2);
+  else
+    new DiscretizationPoissonFD(4);
   new VMGInterfaces::InterfaceVMGJob(
       density_grid,
@@ -218 +234 @@
       particle_positions,
       particle_charges,
-      boundary,
+      *boundary,
       2,
       density_grid.level,
@@ -228 +244 @@
           : VMGInterfaces::InterfaceVMGJob::DontImportParticles,
       DoPrintDebug);
-  new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);
-  new Givens<SolverSingular>();
   const int cycle_type = 1; // V-type
-  new CycleCSPeriodic(cycle_type);
-  new GaussSeidelRBPoisson4();
+  if (OpenBoundaryConditions) {
+    new LevelOperatorFAS(Stencils::RestrictionFullWeight, Stencils::Injection, Stencils::InterpolationTrilinear);
+    new Givens<SolverRegular>();
+    new CycleFASDirichlet(cycle_type);
+    new GaussSeidelRBPoisson2();
+  } else {
+    new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);
+    new Givens<SolverSingular>();
+    new CycleCSPeriodic(cycle_type);
+    new GaussSeidelRBPoisson4();
+  }
+  delete boundary;
 
   /*

src/Jobs/VMGJob.hpp

@@ -52 +52 @@
       const size_t _interpolation_degree,
       const bool _DoImportParticles=true,
-      const bool _DoPrintDebug=false
+      const bool _DoPrintDebug=false,
+      const bool _OpenBoundaryConditions=false
       );
   virtual ~VMGJob();
@@ -78 +79 @@
   //!> whether we do print grid for debug visualization or not
   const bool DoPrintDebug;
+  //!> whether we have open (true) boundary conditions or periodic (false)
+  const bool OpenBoundaryConditions;
 
 private: