Changeset 752dc7 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:

f904d5

Parents:

990a62

git-author:

Frederik Heber <heber@…> (10/05/12 20:27:13)

git-committer:

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

Message:

FIX: Made R and S also fixed parameters, this is in accordance with [Malshe].

Location:

src/Potentials/Specifics

Files:

• ManyBodyPotential_Tersoff.cpp (modified) (7 diffs)
• ManyBodyPotential_Tersoff.hpp (modified) (2 diffs)
• unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) (3 diffs)

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -51 +51 @@
     ) :
     params(parameters_t(MAXPARAMS, 0.)),
+    R(3.2),
+    S(3.5),
     lambda3(0.),
     alpha(0.),
@@ -76 +78 @@
     boost::function< std::vector<arguments_t>(const argument_t &, const double)> &_triplefunction) :
   params(parameters_t(MAXPARAMS, 0.)),
+  R(_R),
+  S(_S),
   lambda3(_lambda3),
   alpha(_alpha),
@@ -83 +87 @@
 {
 //  Info info(__func__);
-  params[R] = _R;
-  params[S] = _S;
+//  R = _R;
+//  S = _S;
   params[A] = _A;
   params[B] = _B;
@@ -151 +155 @@
   const argument_t &r_ij = arguments[0];
   switch (index) {
-    case R:
-    {
-      const double result = 0.;
-      return results_t(1, result);
-      break;
-    }
-    case S:
-    {
-      const double result = 0.;
-      return results_t(1, result);
-      break;
-    }
+//    case R:
+//    {
+//      const double result = 0.;
+//      return results_t(1, result);
+//      break;
+//    }
+//    case S:
+//    {
+//      const double result = 0.;
+//      return results_t(1, result);
+//      break;
+//    }
     case A:
     {
@@ -311 +315 @@
 //  Info info(__func__);
   double result = 0.;
-  if (distance < params[R])
+  if (distance < R)
     result = 1.;
-  else if (distance > params[S])
+  else if (distance > S)
     result = 0.;
   else {
-    result = (0.5 + 0.5 * cos( M_PI * (distance - params[R])/(params[S]-params[R])));
+    result = (0.5 + 0.5 * cos( M_PI * (distance - R)/(S-R)));
   }
 //  LOG(2, "DEBUG: function_cutoff(" << distance << ") = " << result);
@@ -358 +362 @@
 
   // get all triples within the cutoff
-  std::vector<arguments_t> triples = triplefunction(r_ij, params[S]);
+  std::vector<arguments_t> triples = triplefunction(r_ij, S);
   for (std::vector<arguments_t>::const_iterator iter = triples.begin();
       iter != triples.end(); ++iter) {
@@ -381 +385 @@
 
   // get all triples within the cutoff
-  std::vector<arguments_t> triples = triplefunction(r_ij, params[S]);
+  std::vector<arguments_t> triples = triplefunction(r_ij, S);
   for (std::vector<arguments_t>::const_iterator iter = triples.begin();
       iter != triples.end(); ++iter) {

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -180 +180 @@
 private:
   enum parameter_enum_t {
-    R=0,
-    S=1,
-    A=2,
-    B=3,
-    lambda=4,
-    mu=5,
-    beta=6,
-    n=7,
-    c=8,
-    d=9,
-    h=10,
-//    lambda3=11,
-//    alpha=12,
-//    chi=13,
-//    omega=14,
+    A,
+    B,
+    lambda,
+    mu,
+    beta,
+    n,
+    c,
+    d,
+    h,
+//    R,
+//    S,
+//    lambda3,
+//    alpha,
+//    chi,
+//    omega,
     MAXPARAMS
   };
@@ -200 +200 @@
   parameters_t params;
 
+public:
   // some internal parameters which are fixed
+  const double R;
+  const double S;
   const double lambda3;
   const double alpha;

src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp

@@ -128 +128 @@
   // [Tersoff, '89]
   params.resize(ManyBodyPotential_Tersoff::MAXPARAMS,0.);
-  params[ManyBodyPotential_Tersoff::R] = 1.800000e+00;
-  params[ManyBodyPotential_Tersoff::S] = 2.100000e+00;
+//  params[ManyBodyPotential_Tersoff::R] = 1.800000e+00;
+//  params[ManyBodyPotential_Tersoff::S] = 2.100000e+00;
   params[ManyBodyPotential_Tersoff::A] = 1.393600e+03;
   params[ManyBodyPotential_Tersoff::B] = 3.467000e+02;
@@ -289 +289 @@
   ManyBodyPotential_Tersoff tersoff(fct);
   tersoff.setParameters(params);
+  const_cast<double &>(tersoff.R) = 1.8;
+  const_cast<double &>(tersoff.S) = 2.1;
   for (size_t index = 0; index < configurations.size(); ++index) {
     CurrentConfiguration = &(configurations[index]);
@@ -307 +309 @@
     // of the first and second position for the second configuration is easy to
     // see as 1.119779. However, tremolo obtains 1.1197792 for unknown reasons.
-    // Maybe, there is some float floating around in the code ...
+    // Maybe, there is some float floating around in the code ... see strtod() bugs
+//    LOG(2, "Comparing " << output[index] << " and " << .5*temp);
     CPPUNIT_ASSERT(
         Helpers::isEqual(