Changeset 691be4 for src/FunctionApproximation/Extractors.cpp

Timestamp:

Feb 25, 2013, 5:28:58 PM (13 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, Candidate_v1.7.0, 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:

1f3b2a

Parents:

d94e7e

git-author:

Frederik Heber <heber@…> (11/26/12 22:23:13)

git-committer:

Frederik Heber <heber@…> (02/25/13 17:28:58)

Message:

FunctionArgument now contains charges, too, and rewrote Extractors accordingly.

• gatherDistancesFromFragment is now what we mostly want: Returns exactly the arguments in the way we specify.
• PairPotential_AngleUnitTest now has gives additional types to potential's cstor.

File:

• src/FunctionApproximation/Extractors.cpp (modified) (8 diffs)

src/FunctionApproximation/Extractors.cpp

@@ -52 +52 @@
 FunctionModel::arguments_t
 Extractors::gatherAllDistanceArguments(
-    const Fragment::positions_t &positions,
+    const Fragment::positions_t& positions,
+    const Fragment::charges_t& charges,
     const size_t globalid)
 {
@@ -68 +69 @@
       const Vector secondtemp((*secondpositer)[0],(*secondpositer)[1],(*secondpositer)[2]);
       arg.distance = firsttemp.distance(secondtemp);
+      arg.types = std::make_pair(
+          charges[ std::distance(positions.begin(), firstpositer) ],
+          charges[ std::distance(positions.begin(), secondpositer) ]
+          );
       arg.indices = std::make_pair(
           std::distance(
@@ -84 +89 @@
 FunctionModel::arguments_t
 Extractors::gatherAllSymmetricDistanceArguments(
-    const Fragment::positions_t &positions,
+    const Fragment::positions_t& positions,
+    const Fragment::charges_t& charges,
     const size_t globalid)
 {
@@ -100 +106 @@
       const Vector secondtemp((*secondpositer)[0],(*secondpositer)[1],(*secondpositer)[2]);
       arg.distance = firsttemp.distance(secondtemp);
+      arg.types = std::make_pair(
+          charges[ std::distance(positions.begin(), firstpositer) ],
+          charges[ std::distance(positions.begin(), secondpositer) ]
+          );
       arg.indices = std::make_pair(
           std::distance(
@@ -114 +124 @@
 }
 
-Fragment::positions_t Extractors::_detail::gatherPositionsFromCharges(
-    const Fragment::positions_t &positions,
-    const Fragment::charges_t &charges,
-    const chargeiters_t targets
+Fragment::positions_t Extractors::_detail::gatherPositionsFromTargets(
+    const Fragment::positions_t& positions,
+    const Fragment::charges_t& charges,
+    const chargeiters_t &targets
     )
 {
@@ -129 +139 @@
   }
   return filtered_positions;
+}
+
+FunctionModel::arguments_t Extractors::_detail::gatherDistancesFromTargets(
+    const Fragment::positions_t& positions,
+    const Fragment::charges_t& charges,
+    const chargeiters_t &targets,
+    const size_t globalid
+    )
+{
+  Fragment::positions_t filtered_positions;
+  Fragment::charges_t filtered_charges;
+  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);
+    filtered_positions.push_back(*positer);
+    filtered_charges.push_back(**firstpairiter);
+  }
+  return Extractors::gatherAllSymmetricDistanceArguments(
+      filtered_positions,
+      filtered_charges,
+      globalid);
 }
 
@@ -218 +251 @@
 }
 
-Fragment::positions_t
-Extractors::gatherPositionOfTuples(
-    const Fragment& fragment,
+Extractors::chargeiters_t
+Extractors::_detail::gatherTargetsFromFragment(
+    const Fragment::charges_t& charges,
     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,
@@ -248 +281 @@
       ++chargeiter)
     ASSERT( *chargeiter != charges.end(),
-        "Extractors::gatherDistanceOfTuples() - we have not found enough targets?!");
+        "Extractors::gatherTargetsFromFragment() - we have not found enough targets?!");
 #endif
+
+  return targets;
+}
+
+Fragment::positions_t
+Extractors::gatherPositionsFromFragment(
+    const Fragment::positions_t positions,
+    const Fragment::charges_t charges,
+    const Fragment::charges_t& elements
+    )
+{
+  // 1.-3. gather correct charge positions
+  chargeiters_t targets =
+      Extractors::_detail::gatherTargetsFromFragment(charges, elements);
   // 4. convert position_t to Vector
-  return Extractors::_detail::gatherPositionsFromCharges(
-          fragment.getPositions(),
+  return Extractors::_detail::gatherPositionsFromTargets(
+          positions,
           charges,
           targets);
+}
+
+FunctionModel::arguments_t
+Extractors::gatherDistancesFromFragment(
+    const Fragment::positions_t positions,
+    const Fragment::charges_t charges,
+    const Fragment::charges_t& elements,
+    const size_t globalid
+    )
+{
+  // 1.-3. gather correct charge positions
+  chargeiters_t targets =
+      Extractors::_detail::gatherTargetsFromFragment(charges, elements);
+  // 4. convert position_t to Vector
+  return Extractors::_detail::gatherDistancesFromTargets(
+          positions,
+          charges,
+          targets,
+          globalid);
 }