Changeset 56c5de4 for src

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:

bc55c9

Parents:

2e9486

git-author:

Frederik Heber <heber@…> (10/10/12 22:35:53)

git-committer:

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

Message:

Added an offset to the Tersoff potential.

Location:

src/Potentials/Specifics

Files:

• ManyBodyPotential_Tersoff.cpp (modified) (5 diffs)
• ManyBodyPotential_Tersoff.hpp (modified) (3 diffs)

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -77 +77 @@
     const double &_d,
     const double &_h,
+    const double &_offset,
     boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
   params(parameters_t(MAXPARAMS, 0.)),
@@ -103 +104 @@
   params[d] = _d;
   params[h] = _h;
+  params[offset] = _offset;
 }
 
@@ -139 +141 @@
   }
 //  LOG(2, "DEBUG: operator()(" << r_ij.distance << ") = " << result);
-  return std::vector<result_t>(1, result);
+  return std::vector<result_t>(1, params[offset]+result);
 }
 
@@ -160 +162 @@
 //  ASSERT( arguments.size() == 1,
 //      "ManyBodyPotential_Tersoff::parameter_derivative() - requires exactly one argument.");
+  if (index == offset)
+    return results_t(1, 1.);
+
   double result = 0.;
   for(arguments_t::const_iterator argiter = arguments.begin();
@@ -383 +388 @@
       break;
     }
+    case offset:
+      result += 1.;
+      break;
     default:
       break;

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -67 +67 @@
    * @param d
    * @param h
+   * @param offset
    * @param _triplefunction function that returns a list of triples (i.e. the
    *        two remaining distances) to a given pair of points (contained as
@@ -87 +88 @@
       const double &_d,
       const double &_h,
+      const double &_offset,
       boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction);
 
@@ -212 +214 @@
     d,
     h,
+    offset,
 //    R,
 //    S,