Changeset e089fb for src/Jobs

Timestamp:

Feb 14, 2013, 12:26:12 PM (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:

3d9a8d

Parents:

1b01e9

git-author:

Frederik Heber <heber@…> (12/03/12 12:43:00)

git-committer:

Frederik Heber <heber@…> (02/14/13 12:26:12)

Message:

Moved particle arrays into a new struct in VMGJob.

• also the docu now states that we don't need to serialize it.

Location:

src/Jobs

Files:

• VMGJob.cpp (modified) (6 diffs)
• VMGJob.hpp (modified) (1 diff)

src/Jobs/VMGJob.cpp

@@ -90 +90 @@
   interpolation_degree(_interpolation_degree),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
+  particles()
+{}
+
+VMGJob::VMGJob() :
+  FragmentJob(JobId::IllegalJob),
+  near_field_cells(3),
+  interpolation_degree(3),
+  particles()
+{}
+
+VMGJob::~VMGJob()
+{
+}
+
+
+VMGJob::particle_arrays::particle_arrays() :
   num_particles(0),
   f(NULL),
@@ -97 +113 @@
 {}
 
-VMGJob::VMGJob() :
-  FragmentJob(JobId::IllegalJob),
-  near_field_cells(3),
-  interpolation_degree(3),
-  num_particles(0),
-  f(NULL),
-  x(NULL),
-  p(NULL),
-  q(NULL)
-{}
-
-VMGJob::~VMGJob()
+VMGJob::particle_arrays::~particle_arrays()
 {
   delete[] f;
@@ -116 +121 @@
 }
 
-void VMGJob::InitVMGArrays()
-{
-  num_particles = particle_charges.size();
+void VMGJob::particle_arrays::init(const size_t _num_particles)
+{
+  num_particles = _num_particles;
   f = new double[num_particles*3];
   x = new double[num_particles*3];
   p = new double[num_particles];
   q = new double[num_particles];
+}
+
+void VMGJob::InitVMGArrays()
+{
+  particles.init(particle_charges.size());
 
   {
@@ -130 +140 @@
       for (std::vector< double >::const_iterator positer = (*iter).begin();
           positer != (*iter).end(); ++positer) {
-        f[index] = 0.;
-        x[index++] = *positer;
+        particles.f[index] = 0.;
+        particles.x[index++] = *positer;
       }
     }
-    ASSERT( index == num_particles*3,
+    ASSERT( index == particles.num_particles*3,
         "VMGJob::VMGJob() - too many particles or components in particle_positions.");
   }
@@ -141 +151 @@
     for (std::vector< double >::const_iterator iter = particle_charges.begin();
         iter != particle_charges.end(); ++iter) {
-      p[index] = 0.;
-      q[index++] = *iter;
+      particles.p[index] = 0.;
+      particles.q[index++] = *iter;
     }
-    ASSERT( index == num_particles,
+    ASSERT( index == particles.num_particles,
         "VMGJob::VMGJob() - too many charges in particle_charges.");
   }
@@ -226 +236 @@
   InitVMGArrays();
   // then initialize as objects with VMG's storage
-  new ObjectStorage<vmg_float*>("PARTICLE_POS_ARRAY", x);
-  new ObjectStorage<vmg_float*>("PARTICLE_CHARGE_ARRAY", q);
-  new ObjectStorage<vmg_float*>("PARTICLE_POTENTIAL_ARRAY", p);
-  new ObjectStorage<vmg_float*>("PARTICLE_FIELD_ARRAY", f);
-  new ObjectStorage<vmg_int>("PARTICLE_NUM_LOCAL", num_particles);
+  new ObjectStorage<vmg_float*>("PARTICLE_POS_ARRAY", particles.x);
+  new ObjectStorage<vmg_float*>("PARTICLE_CHARGE_ARRAY", particles.q);
+  new ObjectStorage<vmg_float*>("PARTICLE_POTENTIAL_ARRAY", particles.p);
+  new ObjectStorage<vmg_float*>("PARTICLE_FIELD_ARRAY", particles.f);
+  new ObjectStorage<vmg_int>("PARTICLE_NUM_LOCAL", particles.num_particles);
 
   /*

src/Jobs/VMGJob.hpp

@@ -75 +75 @@
   VMGData returndata;
 
-  //!> number of particles
-  size_t num_particles;
-  //!> forces array
-  double *f;
-  //!> position array
-  double *x;
-  //!> potential array
-  double *p;
-  //!> charge array
-  double *q;
+  /** This structure stores particle values per particle.
+   *
+   * \note This structure contains temporary information needed during solving
+   * with VMG.
+   * \warning It is specifically not serialized!
+   *
+   */
+  struct particle_arrays {
+    particle_arrays();
+    ~particle_arrays();
+
+    /** Initializes arrays.
+     *
+     * @param _num_particles size of array per dimension
+     */
+    void init(const size_t _num_particles);
+
+    //!> number of particles
+    size_t num_particles;
+    //!> forces array
+    double *f;
+    //!> position array
+    double *x;
+    //!> potential array
+    double *p;
+    //!> charge array
+    double *q;
+  } particles;
 
 private: