Changeset dbf8c8

Timestamp:

Feb 27, 2013, 12:39:03 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:

caa00e9

Parents:

b760bc3

git-author:

Frederik Heber <heber@…> (11/30/12 08:41:39)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:39:03)

Message:

FIX: Now default parameters are present for every potential and used for check_derivatives.

• checking derivatives with exp() is numerically very unstable as large numbers may easily occur. Hence, rather check the derivatives at some fixed but nicely behaved spot that is probably not the minimum.

Location:

src

Files:

• LevMartester.cpp (modified) (3 diffs)
• Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Angle.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Harmonic.cpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Morse.cpp (modified) (1 diff)
• Potentials/Specifics/SaturationPotential.cpp (modified) (1 diff)

src/LevMartester.cpp ¶

@@ -249 +249 @@
       FunctionModel &model = angle;
       FunctionApproximation approximator(AngleData, model);
-      if (model.isBoxConstraint() && approximator.checkParameterDerivatives())
+      if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
+        // we set parameters here because we want to test with default ones
+        angle.setParameters(params);
         approximator(FunctionApproximation::ParameterDerivative);
-      else {
+      } else {
         ELOG(0, "We require parameter derivatives for a box constraint minimization.");
         return 1;
@@ -300 +302 @@
       FunctionModel &model = morse;
       FunctionApproximation approximator(MorseData, model); // we only give CC distance, hence 1 input dim
-      if (model.isBoxConstraint() && approximator.checkParameterDerivatives())
+      if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
+        // we set parameters here because we want to test with default ones
+        morse.setParameters(params);
         approximator(FunctionApproximation::ParameterDerivative);
-      else {
+      } else {
         ELOG(0, "We require parameter derivatives for a box constraint minimization.");
         return 1;
@@ -365 +369 @@
 
       SaturationPotential saturation(types, 2.5, triplefunction);
-      saturation.setParameters(params);
       FunctionModel &model = saturation;
       FunctionApproximation approximator(TersoffData, model); // CH4 has 5 atoms, hence 5*4/2 distances
-      if (model.isBoxConstraint() && approximator.checkParameterDerivatives())
+      if (model.isBoxConstraint() && approximator.checkParameterDerivatives()) {
+        // we set parameters here because we want to test with default ones
+        saturation.setParameters(params);
         approximator(FunctionApproximation::ParameterDerivative);
-      else {
+      } else {
         ELOG(0, "We require parameter derivatives for a box constraint minimization.");
         return 1;

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp ¶

@@ -87 +87 @@
     omega(1.),
     triplefunction(_triplefunction)
-{}
+{
+  // have some decent defaults for parameter_derivative checking
+  params[A] = 3000.;
+  params[B] = 300.;
+  params[lambda] = 5.;
+  params[mu] = 3.;
+  params[beta] = 2.;
+  params[n] = 1.;
+  params[c] = 0.01;
+  params[d] = 1.;
+  params[h] = 0.01;
+  params[offset] = 0.01;
+}
 
 ManyBodyPotential_Tersoff::ManyBodyPotential_Tersoff(

src/Potentials/Specifics/PairPotential_Angle.cpp ¶

@@ -62 +62 @@
   SerializablePotential(_ParticleTypes),
   params(parameters_t(MAXPARAMS, 0.))
-{}
+{
+  // have some decent defaults for parameter_derivative checking
+  params[spring_constant] = 1.;
+  params[equilibrium_distance] = 0.1;
+  params[energy_offset] = 0.1;
+}
 
 PairPotential_Angle::PairPotential_Angle(

src/Potentials/Specifics/PairPotential_Harmonic.cpp ¶

@@ -61 +61 @@
     SerializablePotential(_ParticleTypes),
   params(parameters_t(MAXPARAMS, 0.))
-{}
+{
+  // have some decent defaults for parameter_derivative checking
+  params[spring_constant] = 1.;
+  params[equilibrium_distance] = 1.;
+  params[energy_offset] = 0.1;
+}
 
 PairPotential_Harmonic::PairPotential_Harmonic(

src/Potentials/Specifics/PairPotential_Morse.cpp ¶

@@ -64 +64 @@
   SerializablePotential(_ParticleTypes),
   params(parameters_t(MAXPARAMS, 0.))
-{}
+{
+  // have some decent defaults for parameter_derivative checking
+  params[spring_constant] = 1.;
+  params[equilibrium_distance] = 1.;
+  params[dissociation_energy] = 0.1;
+  params[energy_offset] = 0.1;
+}
 
 PairPotential_Morse::PairPotential_Morse(

src/Potentials/Specifics/SaturationPotential.cpp ¶

@@ -71 +71 @@
   SerializablePotential(_ParticleTypes),
   morse(_ParticleTypes),
-  angle(_ParticleTypes),
+  angle(symmetrizeTypes(_ParticleTypes)),
   energy_offset(0.),
   triplefunction(_triplefunction),