Changeset d52819 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:

775dd1a

Parents:

7b019a

git-author:

Frederik Heber <heber@…> (11/30/12 16:35:37)

git-committer:

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

Message:

Extracted initial parameter setting per specific potential to FunctionModel::setParametersToRandomInitialValues().

• this is preparatory for generalizing potential fitting.

Location:

src/Potentials/Specifics

Files:

• ManyBodyPotential_Tersoff.cpp (modified) (2 diffs)
• ManyBodyPotential_Tersoff.hpp (modified) (2 diffs)
• PairPotential_Angle.cpp (modified) (2 diffs)
• PairPotential_Angle.hpp (modified) (2 diffs)
• PairPotential_Harmonic.cpp (modified) (2 diffs)
• PairPotential_Harmonic.hpp (modified) (2 diffs)
• PairPotential_Morse.cpp (modified) (2 diffs)
• PairPotential_Morse.hpp (modified) (2 diffs)
• SaturationPotential.cpp (modified) (2 diffs)
• SaturationPotential.hpp (modified) (2 diffs)
• unittests/Makefile.am (modified) (1 diff)

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -49 +49 @@
 
 #include "FunctionApproximation/Extractors.hpp"
+#include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
@@ -697 +698 @@
 }
 
+void
+ManyBodyPotential_Tersoff::setParametersToRandomInitialValues(
+    const TrainingData &data)
+{
+//  params[ManyBodyPotential_Tersoff::R] = 1./AtomicLengthToAngstroem;
+//  params[ManyBodyPotential_Tersoff::S] = 2./AtomicLengthToAngstroem;
+  params[ManyBodyPotential_Tersoff::A] = 1e+4*rand()/(double)RAND_MAX;//1.393600e+03;
+  params[ManyBodyPotential_Tersoff::B] = 1e+4*rand()/(double)RAND_MAX;//3.467000e+02;
+  params[ManyBodyPotential_Tersoff::lambda] = 1e+1*rand()/(double)RAND_MAX;//3.487900e+00;
+  params[ManyBodyPotential_Tersoff::mu] = 1e+1*rand()/(double)RAND_MAX;//2.211900e+00;
+  //  params[ManyBodyPotential_Tersoff::lambda3] = 0.;
+  //  params[ManyBodyPotential_Tersoff::alpha] = 0.;
+  params[ManyBodyPotential_Tersoff::beta] = 1e-1*rand()/(double)RAND_MAX;//1.572400e-07;
+  //  params[ManyBodyPotential_Tersoff::chi] = 1.;
+  //  params[ManyBodyPotential_Tersoff::omega] = 1.;
+  params[ManyBodyPotential_Tersoff::n] = 1e+1*rand()/(double)RAND_MAX;//7.275100e-01;
+  params[ManyBodyPotential_Tersoff::c] = 1e+1*rand()/(double)RAND_MAX;//3.804900e+04;
+  params[ManyBodyPotential_Tersoff::d] = 1e+1*rand()/(double)RAND_MAX;//4.384000e+00;
+  params[ManyBodyPotential_Tersoff::h] = 1e+1*rand()/(double)RAND_MAX;//-5.705800e-01;
+  params[ManyBodyPotential_Tersoff::offset] = //0.*rand()/(double)RAND_MAX;//-5.705800e-01;
+      data.getTrainingOutputAverage()[0];
+}
+

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -21 +21 @@
 #include "Potentials/SerializablePotential.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
+
+class TrainingData;
 
 /** This class is the implementation of the Tersoff potential function.
@@ -318 +320 @@
   }
 
+  /** Sets the parameter randomly within the sensible range of each parameter.
+   *
+   * \param data container with training data for guesstimating range
+   */
+  void setParametersToRandomInitialValues(const TrainingData &data);
+
   /** Getter for the number of parameters of this model function.
    *

src/Potentials/Specifics/PairPotential_Angle.cpp

@@ -46 +46 @@
 
 #include "FunctionApproximation/Extractors.hpp"
+#include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
@@ -219 +220 @@
 }
 
+void
+PairPotential_Angle::setParametersToRandomInitialValues(
+    const TrainingData &data)
+{
+  params[PairPotential_Angle::energy_offset] =
+      data.getTrainingOutputAverage()[0];// -1.;
+  params[PairPotential_Angle::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 0.2;
+  params[PairPotential_Angle::equilibrium_distance] = -0.3;//2e+0*rand()/(double)RAND_MAX - 1.;// 1.;
+}
+

src/Potentials/Specifics/PairPotential_Angle.hpp

@@ -22 +22 @@
 #include "Potentials/SerializablePotential.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
+
+class TrainingData;
 
 /** This is the implementation of a harmonic angle potential.
@@ -64 +66 @@
     return params;
   }
+
+  /** Sets the parameter randomly within the sensible range of each parameter.
+   *
+   * \param data container with training data for guesstimating range
+   */
+  void setParametersToRandomInitialValues(const TrainingData &data);
 
   /** Getter for the number of parameters of this model function.

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -46 +46 @@
 
 #include "FunctionApproximation/Extractors.hpp"
+#include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
@@ -195 +196 @@
 }
 
+void
+PairPotential_Harmonic::setParametersToRandomInitialValues(
+    const TrainingData &data)
+{
+  params[PairPotential_Harmonic::energy_offset] =
+      data.getTrainingOutputAverage()[0];// -1.;
+  params[PairPotential_Harmonic::equilibrium_distance] = 3e+0*rand()/(double)RAND_MAX + .5;// 1.;
+  params[PairPotential_Harmonic::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 0.2;
+}
+

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -22 +22 @@
 #include "Potentials/SerializablePotential.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
+
+class TrainingData;
 
 /** This is the implementation of a harmonic pair potential.
@@ -64 +66 @@
     return params;
   }
+
+  /** Sets the parameter randomly within the sensible range of each parameter.
+   *
+   * \param data container with training data for guesstimating range
+   */
+  void setParametersToRandomInitialValues(const TrainingData &data);
 
   /** Getter for the number of parameters of this model function.

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -47 +47 @@
 
 #include "FunctionApproximation/Extractors.hpp"
+#include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
@@ -224 +225 @@
 }
 
+void
+PairPotential_Morse::setParametersToRandomInitialValues(
+    const TrainingData &data)
+{
+  params[PairPotential_Morse::dissociation_energy] = 1e+0*rand()/(double)RAND_MAX;// 0.5;
+  params[PairPotential_Morse::energy_offset] =
+      data.getTrainingOutputAverage()[0];// -1.;
+  params[PairPotential_Morse::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 1.;
+  params[PairPotential_Morse::equilibrium_distance] =  3e+0*rand()/(double)RAND_MAX;//2.9;
+}
+

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -22 +22 @@
 #include "Potentials/SerializablePotential.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
+
+class TrainingData;
 
 /** This is the implementation of a harmonic pair potential.
@@ -65 +67 @@
     return params;
   }
+
+  /** Sets the parameter randomly within the sensible range of each parameter.
+   *
+   * \param data container with training data for guesstimating range
+   */
+  void setParametersToRandomInitialValues(const TrainingData &data);
 
   /** Getter for the number of parameters of this model function.

src/Potentials/Specifics/SaturationPotential.cpp

@@ -48 +48 @@
 
 #include "FunctionApproximation/Extractors.hpp"
+#include "FunctionApproximation/TrainingData.hpp"
 #include "Potentials/helpers.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
@@ -369 +370 @@
   return returnfunction;
 }
+
+void
+SaturationPotential::setParametersToRandomInitialValues(
+    const TrainingData &data)
+{
+  energy_offset = data.getTrainingOutputAverage()[0];
+  morse.setParametersToRandomInitialValues(data);
+  angle.setParametersToRandomInitialValues(data);
+}

src/Potentials/Specifics/SaturationPotential.hpp

@@ -24 +24 @@
 #include "Potentials/Specifics/PairPotential_Morse.hpp"
 #include "FunctionApproximation/FunctionModel.hpp"
+
+class TrainingData;
 
 /** This is a combination of Morse and Angle potentials for saturated elements.
@@ -77 +79 @@
   parameters_t getParameters() const;
 
+  /** Sets the parameter randomly within the sensible range of each parameter.
+   *
+   * \param data container with training data for guesstimating range
+   */
+  void setParametersToRandomInitialValues(const TrainingData &data);
+
   /** Getter for the number of parameters of this model function.
    *

src/Potentials/Specifics/unittests/Makefile.am

@@ -27 +27 @@
         ../libMolecuilderPotentials.la \
         ../libMolecuilderFragmentationSetValues.la \
+        ../libMolecuilderFragmentation.la \
         ../libMolecuilderFunctionApproximation.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \