Changeset e9cfc4 for src

Timestamp:

Nov 13, 2012, 11:11:38 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:

8a8c8c

Parents:

d2a0f6d

git-author:

Frederik Heber <heber@…> (07/15/12 11:22:16)

git-committer:

Frederik Heber <heber@…> (11/13/12 11:11:38)

Message:

Added rudimentarily complete structure of interface to VMG and VMGJob that uses VMG.

• interface is adapted from interface_particles.cpp.
• VMGJob is adapted from interface_fcs.cpp.
• this is a test whether we may compile solidly against VMG component.
• so far, the grid is initialized to zero, the MG solver is called and the potential should return as zero.

Location:

src/Jobs

Files:

• InterfaceVMGJob.cpp (added)
• InterfaceVMGJob.hpp (added)
• Makefile.am (modified) (2 diffs)
• VMGJob.cpp (modified) (2 diffs)
• VMGJob.hpp (modified) (1 diff)

src/Jobs/Makefile.am

@@ -7 +7 @@
         Jobs/MPQCJob.cpp
 if CONDVMG
-JOBSSOURCE += Jobs/VMGJob.cpp
+JOBSSOURCE += \
+        Jobs/InterfaceVMGJob.cpp \
+        Jobs/VMGJob.cpp
 endif
 
@@ -18 +20 @@
         Jobs/MPQCJob.hpp 
 if CONDVMG
-JOBSSOURCE += Jobs/VMGJob.hpp
+JOBSHEADER += \
+        Jobs/InterfaceVMGJob.hpp \
+        Jobs/VMGJob.hpp
 endif
 

src/Jobs/VMGJob.cpp

@@ -43 +43 @@
 #include "Jobs/VMGJob.hpp"
 
-#include "grid/tempgrid.hpp"
+#include "mg.hpp"
+#include "base/object.hpp"
+#include "base/defs.hpp"
+#include "comm/comm_serial.hpp"
+#include "cycles/cycle_cs_periodic.hpp"
+#include "grid/multigrid.hpp"
+//#include "grid/tempgrid.hpp"
+#include "level/level_operator_cs.hpp"
+#include "level/stencils.hpp"
+#include "samples/discretization_poisson_fd.hpp"
+#include "smoother/gsrb_poisson_4.hpp"
+#include "solver/givens.hpp"
+//#include "solver/solver_regular.hpp"
+#include "solver/solver_singular.hpp"
+//#include "units/particle/comm_mpi_particle.hpp"
+
+#include "LinearAlgebra/defs.hpp"
+#include "Jobs/InterfaceVMGJob.hpp"
+
+using namespace VMG;
 
 VMGJob::VMGJob(const JobId_t _JobId, const std::vector< double > &_sampled_input) :
@@ -59 +78 @@
 FragmentResult::ptr VMGJob::Work()
 {
-  VMG::TempGrid *grid = new VMG::TempGrid();
+  // initialize VMG library solver
+  InitVMG();
+
+  /*
+   * Start the multigrid solver
+   */
+  MG::Solve();
+
+  /// create and fill result object
   FragmentResult::ptr ptr( new FragmentResult(getId()) );
-  delete grid;
+
+  /*
+   * Delete all data.
+   */
+  MG::Destroy();
+
   return ptr;
+}
+
+/** Initialization of VMG library.
+ *
+ * The contents is heavily inspired from interface_fcs.cpp: VMG_fcs_init() of
+ * the ScaFaCoS project.
+ *
+ */
+void VMGJob::InitVMG()
+{
+  // TODO: As a matter of fact should use open boundary conditions
+  const Boundary boundary(Periodic, Periodic, Periodic);
+  int level = 7;
+  double box_offset[NDIM] = { 0., 0., 0. };
+  double box_size = 1;
+//  int near_field_cells = 10;
+
+  /*
+   * Choose multigrid components (self-registering)
+   */
+  new CommSerial(boundary);
+  new DiscretizationPoissonFD(4);
+  new VMGInterfaces::InterfaceVMGJob(
+      sampled_input,
+      boundary,
+      2,
+      level,
+      Vector(box_offset),
+      box_size);
+  new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);
+  new Givens<SolverSingular>();
+  const int cycle_type = 1; // V-type
+  new CycleCSPeriodic(cycle_type);
+  new GaussSeidelRBPoisson4();
+
+  /*
+   * Register required parameters
+   */
+  new ObjectStorage<int>("PRESMOOTHSTEPS", 3);
+  new ObjectStorage<int>("POSTSMOOTHSTEPS", 3);
+  new ObjectStorage<vmg_float>("PRECISION", 1.0e-10);
+  new ObjectStorage<int>("MAX_ITERATION", 15);
+//  new ObjectStorage<int>("PARTICLE_NEAR_FIELD_CELLS", near_field_cells);
+//  new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", 3);
+
+  /*
+   * Post init
+   */
+  MG::PostInit();
+
+  /*
+   * Check whether the library is correctly initialized now.
+   */
+  MG::IsInitialized();
 }
 

src/Jobs/VMGJob.hpp

@@ -42 +42 @@
 
 private:
+  void InitVMG();
+
+private:
   //!> contents of the input file
   const std::vector< double > sampled_input;