Changeset edac7c

Timestamp:

Feb 25, 2013, 5:28:58 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:

d94e7e

Parents:

dd8094

git-author:

Frederik Heber <heber@…> (11/19/12 14:25:29)

git-committer:

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

Message:

DEBUG: LevMartester now looks for the oxygen atom in water as HomologyGraph.

File:

• src/LevMartester.cpp (modified) (4 diffs)

src/LevMartester.cpp ¶

@@ -213 +213 @@
   {
     // then we ought to pick the right HomologyGraph ...
-    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,6,3);
+    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,8,1);
     if (graph != HomologyGraph()) {
       LOG(1, "First representative graph containing three saturated carbons is " << graph << ".");
 
       // Afterwards we go through all of this type and gather the distance and the energy value
+      Fragment::charges_t h2o;
+      h2o += 8,1,1;
       TrainingData AngleData(
           boost::bind(&Extractors::reorderArgumentsByIncreasingDistance,
               boost::bind(&Extractors::gatherAllSymmetricDistanceArguments,
                   boost::bind(&Extractors::gatherPositionOfTuples,
-                      _1, Fragment::charges_t(3,6.)
+                      _1, boost::cref(h2o)
                   ), _2 // gather carbon triples
               )
@@ -256 +258 @@
   {
     // then we ought to pick the right HomologyGraph ...
-    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,6,2);
+    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,8,1);
     if (graph != HomologyGraph()) {
       LOG(1, "First representative graph containing two saturated carbons is " << graph << ".");
 
       // Afterwards we go through all of this type and gather the distance and the energy value
+      Fragment::charges_t h2o;
+      h2o += 8,1;
       TrainingData MorseData(
           boost::bind(&Extractors::gatherAllSymmetricDistanceArguments,
               boost::bind(&Extractors::gatherPositionOfTuples,
-                  _1, Fragment::charges_t(2,6.)
+                  _1, boost::cref(h2o)
               ), _2 // gather first carbon pair
             )
@@ -299 +303 @@
   {
     // then we ought to pick the right HomologyGraph ...
-    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,6,1);
+    const HomologyGraph graph = getFirstGraphwithTimesSpecificElement(homologies,8,1);
     if (graph != HomologyGraph()) {
       LOG(1, "First representative graph containing one saturated carbon is " << graph << ".");
@@ -305 +309 @@
       // Afterwards we go through all of this type and gather the distance and the energy value
       Fragment::charges_t SaturatedCarbon;
-      SaturatedCarbon += 6.,1.;
+      SaturatedCarbon += 8.,1.;
       TrainingData TersoffData(
 //          boost::bind(&Extractors::gatherAllSymmetricDistanceArguments,