Changeset d03292

Timestamp:

Dec 19, 2012, 3:26:11 PM (13 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:

17b3598

Parents:

f48ad3

git-author:

Frederik Heber <heber@…> (10/05/12 19:18:28)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:26:11)

Message:

Implemented box constraints for FunctionModel, using a feature of LevMar.

• we need lower and upper bounds for each parameter. These can be passed on to specific function of LevMar.
• LevMartester checks whether isBoxConstraints apply and requires parameter derivatives in this case.

Location:

src

Files:

• FunctionApproximation/FunctionApproximation.cpp (modified) (1 diff)
• FunctionApproximation/FunctionModel.hpp (modified) (1 diff)
• LevMartester.cpp (modified) (2 diffs)
• Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) (2 diffs)
• Potentials/Specifics/PairPotential_Harmonic.hpp (modified) (2 diffs)
• Potentials/Specifics/PairPotential_Morse.hpp (modified) (2 diffs)

src/FunctionApproximation/FunctionApproximation.cpp

@@ -169 +169 @@
     // give this pointer as additional data to construct function pointer in
     // LevMarCallback and call
-    if (mode == FiniteDifferences) {
-      ret=dlevmar_dif(
-          &FunctionApproximation::LevMarCallback,
-          p, x, m, n, 1000, opts, info, work, covar, this); // no Jacobian, caller allocates work memory, covariance estimated
-    } else if (mode == ParameterDerivative) {
-      ret=dlevmar_der(
-          &FunctionApproximation::LevMarCallback,
-          &FunctionApproximation::LevMarDerivativeCallback,
-          p, x, m, n, 1000, opts, info, work, covar, this); // no Jacobian, caller allocates work memory, covariance estimated
+    if (model.isBoxConstraint()) {
+      FunctionModel::parameters_t lowerbound = model.getLowerBoxConstraints();
+      FunctionModel::parameters_t upperbound = model.getUpperBoxConstraints();
+      double *lb = new double[m];
+      double *ub = new double[m];
+      for (size_t i=0;i<m;++i) {
+        lb[i] = lowerbound[i];
+        ub[i] = upperbound[i];
+      }
+      if (mode == FiniteDifferences) {
+        ret=dlevmar_bc_dif(
+            &FunctionApproximation::LevMarCallback,
+            p, x, m, n, lb, ub, NULL, 1000, opts, info, work, covar, this); // no Jacobian, caller allocates work memory, covariance estimated
+      } else if (mode == ParameterDerivative) {
+        ret=dlevmar_bc_der(
+            &FunctionApproximation::LevMarCallback,
+            &FunctionApproximation::LevMarDerivativeCallback,
+            p, x, m, n, lb, ub, NULL, 1000, opts, info, work, covar, this); // no Jacobian, caller allocates work memory, covariance estimated
+      } else {
+        ASSERT(0, "FunctionApproximation::operator() - Unknown jacobian method chosen.");
+      }
+      delete[] lb;
+      delete[] ub;
     } else {
       ASSERT(0, "FunctionApproximation::operator() - Unknown jacobian method chosen.");
+      if (mode == FiniteDifferences) {
+        ret=dlevmar_dif(
+            &FunctionApproximation::LevMarCallback,
+            p, x, m, n, 1000, opts, info, work, covar, this); // no Jacobian, caller allocates work memory, covariance estimated
+      } else if (mode == ParameterDerivative) {
+        ret=dlevmar_der(
+            &FunctionApproximation::LevMarCallback,
+            &FunctionApproximation::LevMarDerivativeCallback,
+            p, x, m, n, 1000, opts, info, work, covar, this); // no Jacobian, caller allocates work memory, covariance estimated
+      } else {
+        ASSERT(0, "FunctionApproximation::operator() - Unknown jacobian method chosen.");
+      }
     }
 

src/FunctionApproximation/FunctionModel.hpp

@@ -78 +78 @@
    */
   virtual results_t parameter_derivative(const arguments_t &arguments, const size_t index) const=0;
+
+  /** States whether lower and upper boundaries should be used to constraint
+   * the parameter search for this function model.
+   *
+   * \return true - constraints should be used, false - else
+   */
+  virtual bool isBoxConstraint() const=0;
+
+  /** Returns a vector which are the lower boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling lowest allowed values
+   */
+  virtual parameters_t getLowerBoxConstraints() const=0;
+
+  /** Returns a vector which are the upper boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling highest allowed values
+   */
+  virtual parameters_t getUpperBoxConstraints() const=0;
 };
 

src/LevMartester.cpp

@@ -318 +318 @@
     FunctionApproximation approximator(1, 1, model);
     approximator.setTrainingData(DistanceEnergyVector.first,DistanceEnergyVector.second);
-    approximator(FunctionApproximation::ParameterDerivative);
+    if (model.isBoxConstraint() && approximator.checkParameterDerivatives())
+      approximator(FunctionApproximation::ParameterDerivative);
+    else
+      ELOG(0, "We require parameter derivatives for a box constraint minimization.");
     params = model.getParameters();
 
@@ -392 +395 @@
         model); // CH4 has 5 atoms, hence 5*4/2 distances
     approximator.setTrainingData(DistanceEnergyVector.first,DistanceEnergyVector.second);
-    approximator(FunctionApproximation::FiniteDifferences);
+    if (model.isBoxConstraint() && approximator.checkParameterDerivatives())
+      approximator(FunctionApproximation::ParameterDerivative);
+    else
+      ELOG(0, "We require parameter derivatives for a box constraint minimization.");
     params = model.getParameters();
 

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -16 +16 @@
 #include <boost/function.hpp>
 #include <cmath>
+#include <limits>
 
 #include "CodePatterns/Assert.hpp"
@@ -120 +121 @@
    */
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
+
+  /** States whether lower and upper boundaries should be used to constraint
+   * the parameter search for this function model.
+   *
+   * \return true - constraints should be used, false - else
+   */
+  bool isBoxConstraint() const {
+    return true;
+  }
+
+  /** Returns a vector which are the lower boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling lowest allowed values
+   */
+  parameters_t getLowerBoxConstraints() const {
+    parameters_t lowerbound(getParameterDimension(), -std::numeric_limits<double>::max());
+//    lowerbound[R] = 0.;
+//    lowerbound[S] = 0.;
+//    lowerbound[lambda3] = 0.;
+//    lowerbound[alpha] = 0.;
+    lowerbound[beta] = std::numeric_limits<double>::min();
+    lowerbound[n] = std::numeric_limits<double>::min();
+    lowerbound[c] = std::numeric_limits<double>::min();
+    lowerbound[d] = std::numeric_limits<double>::min();
+    return lowerbound;
+  }
+
+  /** Returns a vector which are the upper boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling highest allowed values
+   */
+  parameters_t getUpperBoxConstraints() const {
+    return parameters_t(getParameterDimension(), std::numeric_limits<double>::max());
+  }
 
 private:

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -14 +14 @@
 #include <config.h>
 #endif
+
+#include <limits>
 
 #include "CodePatterns/Assert.hpp"
@@ -98 +100 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** States whether lower and upper boundaries should be used to constraint
+   * the parameter search for this function model.
+   *
+   * \return true - constraints should be used, false - else
+   */
+  bool isBoxConstraint() const {
+    return true;
+  }
+
+  /** Returns a vector which are the lower boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling lowest allowed values
+   */
+  parameters_t getLowerBoxConstraints() const {
+    parameters_t lowerbounds(getParameterDimension(), -std::numeric_limits<double>::max());
+    lowerbounds[equilibrium_distance] = 0.;
+    return lowerbounds;
+  }
+
+  /** Returns a vector which are the upper boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling highest allowed values
+   */
+  parameters_t getUpperBoxConstraints() const {
+    return parameters_t(getParameterDimension(), std::numeric_limits<double>::max());
+  }
+
   enum parameter_enum_t {
     spring_constant=0,

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -14 +14 @@
 #include <config.h>
 #endif
+
+#include <limits>
 
 #include "CodePatterns/Assert.hpp"
@@ -99 +101 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
+  /** States whether lower and upper boundaries should be used to constraint
+   * the parameter search for this function model.
+   *
+   * \return true - constraints should be used, false - else
+   */
+  bool isBoxConstraint() const {
+    return true;
+  }
+
+  /** Returns a vector which are the lower boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling lowest allowed values
+   */
+  parameters_t getLowerBoxConstraints() const {
+    parameters_t lowerbound(getParameterDimension(), -std::numeric_limits<double>::max());
+    lowerbound[equilibrium_distance] = 0.;
+    return lowerbound;
+  }
+
+  /** Returns a vector which are the upper boundaries for each parameter_t
+   * of this FunctionModel.
+   *
+   * \return vector of parameter_t resembling highest allowed values
+   */
+  parameters_t getUpperBoxConstraints() const {
+    return parameters_t(getParameterDimension(), std::numeric_limits<double>::max());
+  }
+
   enum parameter_enum_t {
     spring_constant=0,