Changeset cee9e8

Timestamp:

Oct 13, 2015, 8:14:32 PM (9 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:

92232f

Parents:

b1c5f46

git-author:

Frederik Heber <heber@…> (09/01/15 13:47:28)

git-committer:

Frederik Heber <heber@…> (10/13/15 20:14:32)

Message:

Added Interfragmenter::findLargestCutoff() to find largest Rcut not causing additional inter-fragments.

• so far, the function is only used in FragmentationAction by merely printing the distance.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• Fragmentation/Interfragmenter.cpp (modified) (2 diffs)
• Fragmentation/Interfragmenter.hpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp ¶

@@ -259 +259 @@
         << params.InterOrder.get() << " and distance of "
         << params.distance.get() << ".");
+    const enum HydrogenTreatment treatment =
+        params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+    const double UpperBound = std::max(10., params.distance.get());
     Interfragmenter fragmenter(TotalGraph);
-    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+
+    // check the largest Rcut that causes no additional inter-fragments
+    const double Min_Rcut =
+        fragmenter.findLargestCutoff(params.InterOrder.get(), UpperBound, treatment);
+
+    // then add fragments
     fragmenter(params.InterOrder.get(), params.distance.get(), treatment);
+
     LOG(0, "STATUS: There are now " << TotalGraph.size() << " fragments after interfragmenting.");
   }

src/Fragmentation/Interfragmenter.cpp ¶

@@ -42 +42 @@
 #include "LinearAlgebra/Vector.hpp"
 
+#include "Descriptors/AtomDescriptor.hpp"
 #include "Element/element.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -234 +235 @@
   TotalGraph.InsertGraph(InterFragments, counter);
 }
+
+double Interfragmenter::findLargestCutoff(
+    const size_t _MaxOrder,
+    const double _upperbound,
+    const enum HydrogenTreatment _treatment) const
+{
+  double Rcut = _upperbound*_upperbound;
+  std::pair<atomId_t, atomId_t> ClosestPair;
+  // place all atoms into LC grid with some upper bound
+  const LinkedCell::LinkedCell_View view = World::getInstance().getLinkedCell(_upperbound);
+
+  atomkeyset_t atomkeyset = getAtomKeySetMap(_MaxOrder);
+
+  // go through each atom and find closest atom not in the same keyset
+  for (Graph::const_iterator keysetiter = TotalGraph.begin();
+      keysetiter != TotalGraph.end(); ++keysetiter) {
+    const KeySet &keyset = keysetiter->first;
+    LOG(2, "DEBUG: Current keyset is " << keyset);
+    const AtomIdSet atoms(keyset);
+
+    // get neighboring atoms outside the current molecule
+    const candidates_t candidates = getNeighborsOutsideMolecule(atoms, _upperbound, _treatment);
+    const Vector center = getAtomIdSetCenter(atoms);
+
+    for (candidates_t::const_iterator candidateiter = candidates.begin();
+        candidateiter != candidates.end(); ++candidateiter) {
+      atom const * const Walker = *candidateiter;
+      // go through each atom in set and pick minimal distance
+      for (AtomIdSet::const_iterator setiter = atoms.begin(); setiter != atoms.end(); ++setiter) {
+        const double distanceSquared = Walker->getPosition().DistanceSquared(center);
+        // pick the smallest compared to current Rcut if smaller
+        if (distanceSquared < Rcut) {
+          Rcut = distanceSquared;
+          ClosestPair.first = (*setiter)->getId();
+          ClosestPair.second = Walker->getId();
+        }
+      }
+    }
+  }
+  LOG(1, "INFO: Largest inter-fragment distance to cause no additional fragments: " << Rcut);
+
+  return Rcut;
+}

src/Fragmentation/Interfragmenter.hpp ¶

@@ -56 +56 @@
       const double Rcut,
       const enum HydrogenTreatment treatment);
+
+  /** This finds the largest cut off distance (\a Rcut) such that when running
+   * operator() no additional inter-fragments would be produced.
+   *
+   * \param MaxOrder maximum order for fragments to interrelate
+   * \param _upperbound upper bound on \a Rcut above which we do not look
+   * \param treatment whether hydrogens are treated specially or not
+   * \return largest cutoff distance to cause no additional inter-fragments
+   */
+  double findLargestCutoff(
+      const size_t _MaxOrder,
+      const double _upperbound,
+      const enum HydrogenTreatment _treatment) const;
 
 private: