Changeset eb1efe for src/Potentials/Specifics

Timestamp:

Dec 19, 2012, 3:26:11 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:

f48ad3

Parents:

bc55c9

git-author:

Frederik Heber <heber@…> (10/05/12 14:02:07)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:26:11)

Message:

Extended LevMartester to fit a Tersoff potential to the first order fragments.

• this required adding a globalid to argument_t for the triplefunction to work, i.e. in order to get at possible neighbouring atoms and their distances. This requires some global information.
• TESTFIX: We don't need static variable CurrentConfiguration in ManyBodyPotential_TersoffTest anymore as we have the index to the current configuration now stored in each argument_t.

Location:

src/Potentials/Specifics/unittests

Files:

• ManyBodyPotential_TersoffUnitTest.cpp (modified) (5 diffs)
• ManyBodyPotential_TersoffUnitTest.hpp (modified) (1 diff)

src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp

@@ -65 +65 @@
 
 ManyBodyPotential_TersoffTest::configurations_t ManyBodyPotential_TersoffTest::configurations;
-ManyBodyPotential_TersoffTest::configuration_t *ManyBodyPotential_TersoffTest::CurrentConfiguration = NULL;
 
 /** This function looks up all distances ik and jk to a given ij and
@@ -73 +72 @@
 triplefunction(const argument_t &arguments, const double cutoff)
 {
+  const ManyBodyPotential_TersoffTest::configuration_t &CurrentConfiguration =
+      ManyBodyPotential_TersoffTest::configurations[arguments.globalid];
   std::vector<FunctionModel::arguments_t> result;
   // go through current configuration and gather all other distances
   ManyBodyPotential_TersoffTest::configuration_t::const_iterator firstiter =
-      ManyBodyPotential_TersoffTest::CurrentConfiguration->begin();
+      CurrentConfiguration.begin();
   std::advance(firstiter, arguments.indices.first);
   ManyBodyPotential_TersoffTest::configuration_t::const_iterator seconditer =
-      ManyBodyPotential_TersoffTest::CurrentConfiguration->begin();
+      CurrentConfiguration.begin();
   std::advance(seconditer, arguments.indices.second);
   for (ManyBodyPotential_TersoffTest::configuration_t::const_iterator iter =
-      ManyBodyPotential_TersoffTest::CurrentConfiguration->begin();
-      iter != ManyBodyPotential_TersoffTest::CurrentConfiguration->end();
+      CurrentConfiguration.begin();
+      iter != CurrentConfiguration.end();
       ++iter) {
     // skip k==i and k==j
@@ -92 +93 @@
     args[0].distance = firstiter->distance(*iter);
     args[0].indices = std::make_pair(
-        std::distance( // enforce const_iterator return from begin()
-            const_cast<const ManyBodyPotential_TersoffTest::configuration_t *>(
-                ManyBodyPotential_TersoffTest::CurrentConfiguration
-                )->begin(), firstiter),
-        std::distance( // enforce const_iterator return from begin()
-            const_cast<const ManyBodyPotential_TersoffTest::configuration_t *>(
-                ManyBodyPotential_TersoffTest::CurrentConfiguration
-                )->begin(), iter)
+        std::distance(CurrentConfiguration.begin(), firstiter),
+        std::distance(CurrentConfiguration.begin(), iter)
     );
+    args[0].globalid = arguments.globalid;
     // jk
     args[1].distance = seconditer->distance(*iter);
     args[1].indices = std::make_pair(
-        std::distance( // enforce const_iterator return from begin()
-            const_cast<const ManyBodyPotential_TersoffTest::configuration_t *>(
-                ManyBodyPotential_TersoffTest::CurrentConfiguration
-                )->begin(), seconditer),
-        std::distance( // enforce const_iterator return from begin()
-            const_cast<const ManyBodyPotential_TersoffTest::configuration_t *>(
-                ManyBodyPotential_TersoffTest::CurrentConfiguration
-                )->begin(), iter)
+        std::distance(CurrentConfiguration.begin(), seconditer),
+        std::distance(CurrentConfiguration.begin(), iter)
     );
+    args[1].globalid = arguments.globalid;
     result.push_back(args);
   }
@@ -276 +267 @@
 {
   configurations.clear();
-  CurrentConfiguration = NULL;
 }
 
@@ -292 +282 @@
   const_cast<double &>(tersoff.S) = 2.1;
   for (size_t index = 0; index < configurations.size(); ++index) {
-    CurrentConfiguration = &(configurations[index]);
+    const configuration_t &CurrentConfiguration = configurations[index];
     double temp = 0.;
-    for (size_t i=0; i < CurrentConfiguration->size(); ++i)
-      for (size_t j=0; j < CurrentConfiguration->size(); ++j) {
+    for (size_t i=0; i < CurrentConfiguration.size(); ++i)
+      for (size_t j=0; j < CurrentConfiguration.size(); ++j) {
         if (i == j)
           continue;
         argument_t arg;
         arg.indices = std::make_pair(i,j);
-        arg.distance = (*CurrentConfiguration)[i].distance((*CurrentConfiguration)[j]);
+        arg.distance = CurrentConfiguration[i].distance(CurrentConfiguration[j]);
+        arg.globalid = index; // this is needed for the triplefunction to the configuration
         FunctionModel::arguments_t args(1,arg);
         const ManyBodyPotential_Tersoff::results_t res = tersoff(args);

src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp

@@ -45 +45 @@
       typedef std::vector<configuration_t> configurations_t;
       static configurations_t configurations;
-      static configuration_t *CurrentConfiguration;
 private:
       FunctionModel::parameters_t params;