Changeset 301dbf

Timestamp:

Feb 24, 2013, 12:58:53 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:

bc6705

Parents:

4a77be7

git-author:

Frederik Heber <heber@…> (10/22/12 13:38:33)

git-committer:

Frederik Heber <heber@…> (02/24/13 12:58:53)

Message:

Refactored gatherDistanceOfTuples().

• it is now able to work on arbitrary vectors of elements, not just tuples of two.

Location:

src

Files:

• FunctionApproximation/Extractors.cpp (modified) (2 diffs)
• FunctionApproximation/Extractors.hpp (modified) (3 diffs)
• LevMartester.cpp (modified) (1 diff)

src/FunctionApproximation/Extractors.cpp ¶

@@ -40 +40 @@
 #include <boost/assign.hpp>
 
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 
@@ -81 +82 @@
 }
 
-FunctionModel::arguments_t
-Extractors::gatherFirstDistance(
-    const Fragment& fragment,
-    const size_t index,
-    const size_t firstelement,
-    const size_t secondelement
-    ) {
-  const Fragment::charges_t charges = fragment.getCharges();
-  const Fragment::positions_t positions = fragment.getPositions();
-  typedef Fragment::charges_t::const_iterator chargeiter_t;
-  std::vector< chargeiter_t > firstpair;
-  firstpair.reserve(2);
-  firstpair +=
-      std::find(charges.begin(), charges.end(), firstelement),
-      std::find(charges.begin(), charges.end(), secondelement);
-  if ((firstpair[0] == charges.end()) || (firstpair[1] == charges.end())) {
-    // complain if tuple not found
-    ELOG(1, "Could not find pair " << firstelement << "," << secondelement
-        << " in fragment " << fragment);
-    return FunctionModel::arguments_t();
-  }
-  // convert position_t to Vector
-  std::vector< std::pair<Vector, size_t> > DistancePair;
-  for (std::vector<chargeiter_t>::const_iterator firstpairiter = firstpair.begin();
-      firstpairiter != firstpair.end(); ++firstpairiter) {
+Fragment::positions_t Extractors::_detail::gatherPositionsFromCharges(
+    const Fragment::positions_t &positions,
+    const Fragment::charges_t &charges,
+    const chargeiters_t targets
+    )
+{
+  Fragment::positions_t filtered_positions;
+  for (chargeiters_t::const_iterator firstpairiter = targets.begin();
+      firstpairiter != targets.end(); ++firstpairiter) {
     Fragment::positions_t::const_iterator positer = positions.begin();
     const size_t steps = std::distance(charges.begin(), *firstpairiter);
     std::advance(positer, steps);
-    DistancePair.push_back(
-        std::make_pair(Vector((*positer)[0], (*positer)[1], (*positer)[2]),
-            steps));
-  }
-  // finally convert Vector pair to distance-like argument
-  argument_t arg;
-  arg.indices.first = DistancePair[0].second;
-  arg.indices.second = DistancePair[1].second;
-  arg.distance = DistancePair[0].first.distance(DistancePair[1].first);
-  arg.globalid = index;
-
-  return FunctionModel::arguments_t(1, arg);
-}
+    filtered_positions.push_back(*positer);
+  }
+  return filtered_positions;
+}
+
+Fragment::positions_t
+Extractors::gatherDistanceOfTuples(
+    const Fragment& fragment,
+    const Fragment::charges_t elements
+    ) {
+  const Fragment::charges_t charges = fragment.getCharges();
+  /// The main problem here is that we have to know how many same
+  /// elements (but different atoms!) we are required to find. Hence,
+  /// we first have to count same elements, then get different targets
+  /// for each and then associated them in correct order back again.
+
+  // 1. we have to make elements unique with counts, hence convert to map
+  elementcounts_t elementcounts;
+  for (Fragment::charges_t::const_iterator elementiter = elements.begin();
+      elementiter != elements.end(); ++elementiter) {
+    // insert new element
+    std::pair< elementcounts_t::iterator, bool> inserter =
+        elementcounts.insert( std::make_pair( *elementiter, 1) );
+    // if already present, just increase its count
+    if (!inserter.second)
+      ++(inserter.first->second);
+  }
+
+  // 2. then for each element we need as many targets (chargeiters) as counts
+  elementtargets_t elementtargets;
+  for (elementcounts_t::const_iterator countiter = elementcounts.begin();
+      countiter != elementcounts.end();
+      ++countiter) {
+    chargeiter_t chargeiter = charges.begin();
+    const element_t &element = countiter->first;
+    const count_t &count = countiter->second;
+    for (count_t i = 0; i < count; ++i) {
+      chargeiter_t tempiter = std::find(chargeiter, charges.end(), element);
+      if (tempiter != charges.end()) {
+        // try to insert new list
+        std::pair< elementtargets_t::iterator, bool> inserter =
+          elementtargets.insert( std::make_pair( countiter->first, chargeiters_t(1, tempiter)) );
+        // if already present, append to it
+        if (!inserter.second) {
+          inserter.first->second.push_back(tempiter);
+        } else { // if created, increase vector's reserve to known size
+          inserter.first->second.reserve(countiter->second);
+        }
+        // search from this element onwards then
+        chargeiter = ++tempiter;
+      } else {
+        ELOG(1, "Could not find desired number of elements " << elements << " in fragment.");
+        return Fragment::positions_t();
+      }
+    }
+  }
+
+  // 3. we go again through elements and use one found target for each count
+  // in that order
+  elementcounts_t counts; // how many chargeiters of this element have been used
+  chargeiters_t targets;
+  targets.reserve(elements.size());
+  for (Fragment::charges_t::const_iterator elementiter = elements.begin();
+      elementiter != elements.end(); ++elementiter) {
+    const element_t &element = *elementiter;
+    count_t &count = counts[element]; // if not present, std::map creates instances with default of 0
+#ifndef NDEBUG
+    {
+      elementcounts_t::const_iterator testiter = elementcounts.find(element);
+      ASSERT( (testiter != elementcounts.end()) && (count < testiter->second),
+          "Extractors::gatherDistanceOfTuples() - we want to use more chargeiters for element "
+          +toString(element)+" than we counted initially.");
+    }
+#endif
+    elementtargets_t::iterator targetiter = elementtargets.find(element);
+    ASSERT (targetiter != elementtargets.end(),
+        "Extractors::gatherDistanceOfTuples() - not enough chargeiters for element "
+        +toString(element)+".");
+    chargeiters_t &chargeiters = targetiter->second;
+    const chargeiter_t &chargeiter = chargeiters[count++];
+    targets.push_back(chargeiter);
+  }
+#ifndef NDEBUG
+  // check all for debugging
+  for (chargeiters_t::const_iterator chargeiter = targets.begin();
+      chargeiter != targets.end();
+      ++chargeiter)
+    ASSERT( *chargeiter != charges.end(),
+        "Extractors::gatherDistanceOfTuples() - we have not found enough targets?!");
+#endif
+  // 4. convert position_t to Vector
+  return Extractors::_detail::gatherPositionsFromCharges(
+          fragment.getPositions(),
+          charges,
+          targets);
+}
+
+FunctionModel::arguments_t Extractors::reorderArgumentsByIncreasingDistance(
+    const FunctionModel::arguments_t &args
+    )
+{
+  FunctionModel::arguments_t returnargs(args);
+  std::sort(returnargs.begin(), returnargs.end(), argument_t::DistanceComparator);
+  return returnargs;
+}
+

src/FunctionApproximation/Extractors.hpp ¶

@@ -23 +23 @@
  */
 namespace Extractors {
+  typedef Fragment::charges_t::const_iterator chargeiter_t;
+  typedef std::vector<chargeiter_t> chargeiters_t;
+
+  typedef size_t count_t;
+  typedef Fragment::charge_t element_t;
+  typedef std::map< element_t, count_t> elementcounts_t;
+  typedef std::map< element_t, chargeiters_t > elementtargets_t;
+
   /** Namespace for some internal helper functions.
    *
@@ -37 +45 @@
         const Fragment::positions_t &positions,
         const size_t globalid);
+
+    /** Gather all positions from the same aligned vector of charges.
+     *
+     * Basically, we filter the positions indicated by the targets but
+     * from a different vector that has the same layout.
+     *
+     * \param positions positions to search
+     * \param charges charges to match with \targets
+     * \param targets iterators on charges
+     * \return filtered positions
+     */
+    Fragment::positions_t gatherPositionsFromCharges(
+        const Fragment::positions_t &positions,
+        const Fragment::charges_t &charges,
+        const chargeiters_t targets
+        );
   }
 
@@ -53 +77 @@
   }
 
-  /** Gather first distance for the two matching charges.
+  /** Gather all positions associated to the matching \a elements.
    *
    * \param fragment fragment with all nuclei positions
-   * \param index index refers to the index within the global set of configurations
-   * \param firstelement first element of pair
-   * \param secondelement second element of pair, order is reflected in indices of return argument_t
-   * \return vector of of argument_t containing all found distances
+   * \param elements tuple of desired elements
+   * \return vector of positions_t containing
    */
-  FunctionModel::arguments_t gatherFirstDistance(
+  Fragment::positions_t gatherDistanceOfTuples(
       const Fragment& fragment,
-      const size_t index,
-      const size_t firstelement,
-      const size_t secondelement
+      const Fragment::charges_t elements
+      );
+
+  /** Reorder arguments by increasing distance.
+   *
+   * \param args arguments to reorder
+   * \return reordered args
+   */
+  FunctionModel::arguments_t reorderArgumentsByIncreasingDistance(
+      const FunctionModel::arguments_t &args
       );
 

src/LevMartester.cpp ¶

@@ -364 +364 @@
     // Afterwards we go through all of this type and gather the distance and the energy value
     TrainingData MorseData(
-        boost::bind(&Extractors::gatherFirstDistance, _1, _2, 6, 6) // gather first carbon pair
+        boost::bind(&Extractors::_detail::gatherAllDistanceArguments,
+            boost::bind(&Extractors::gatherDistanceOfTuples,
+                _1, Fragment::charges_t(2,6.)
+            ), _2 // gather first carbon pair
+          )
         );
     MorseData(homologies.getHomologousGraphs(graph));