Changeset dbf8c8 for src/Potentials/Specifics

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/Potentials/Specifics

Files:

• ManyBodyPotential_Tersoff.cpp (modified) (1 diff)
• PairPotential_Angle.cpp (modified) (1 diff)
• PairPotential_Harmonic.cpp (modified) (1 diff)
• PairPotential_Morse.cpp (modified) (1 diff)
• SaturationPotential.cpp (modified) (1 diff)

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),