Changeset bc55c9

Timestamp:

Dec 19, 2012, 3:25:54 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:

eb1efe

Parents:

56c5de4

git-author:

Frederik Heber <heber@…> (10/10/12 22:37:55)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:25:54)

Message:

Added NaN check to Tersoff's parameter_derivative().

File:

• src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) (6 diffs)

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -308 +308 @@
     case n:
     {
-      const double temp =
-          pow(params[beta]*function_zeta(r_ij), params[n]);
-      const double cutoff = function_cutoff(r_ij.distance);
-      result += (cutoff == 0.) ?
+      const double zeta = function_zeta(r_ij);
+      const double temp = pow( params[beta]*zeta , params[n]);
+      const double cutoff = function_cutoff(r_ij.distance);
+      const double tempres = ((cutoff == 0.) || (zeta == 0.)) ? // zeta must be caught if zero due to log
           0. : .5 * cutoff *
           function_smoother(
@@ -324 +324 @@
               /(params[n]*(1.+temp)))
           ;
+//      if (tempres != tempres)
+//      LOG(2, "DEBUG: tempres is NaN."); 
+//      LOG(2, "DEBUG: Adding " << tempres << " for p.d. w.r.t n, temp=" << temp << ", cutoff=" << cutoff);
+      result += tempres;
       break;
     }
@@ -346 +350 @@
       double factor = function_derivative_c(r_ij);
       result += tempres*factor;
+      if (result != result)
+        ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
       break;
     }
@@ -366 +372 @@
       double factor = function_derivative_d(r_ij);
       result += tempres*factor;
+      if (result != result)
+        ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
       break;
     }
@@ -386 +394 @@
       double factor = function_derivative_h(r_ij);
       result += tempres*factor;
+      if (result != result)
+        ELOG(1, "result is NaN, zeta=" << zeta << ", temp=" << temp << ", cutoff=" << cutoff << ", tempres=" << tempres << ", factor=" << factor);
       break;
     }
@@ -394 +404 @@
       break;
   }
+  if (result != result)
+    ELOG(1, "result is NaN.");
   }
   return results_t(1,-result);