Changeset 6efcae

Timestamp:

Feb 25, 2013, 5:29:09 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:

ed2551

Parents:

67cd3a

git-author:

Frederik Heber <heber@…> (11/25/12 06:37:09)

git-committer:

Frederik Heber <heber@…> (02/25/13 17:29:09)

Message:

SerializablePotential is new type to be stored in PotentialRegistry.

• added new class SerializablePotential with operator<<() and ..>>() and a a set of virtual functions to be implemented in deriving classes.
• added unit test SerializablePotentialUnitTest and mock implementation of such a SerializablePotential.
• added exceptions, thrown when parsing of potential containing line fails.
• NOTE: empty name/key of a parameter are not printed on output.

Location:

src

Files:

• LevMartester.cpp (modified) (1 diff)
• Potentials/EmpiricalPotential.hpp (modified) (1 diff)
• Potentials/Exceptions.hpp (added)
• Potentials/Makefile.am (modified) (2 diffs)
• Potentials/PotentialRegistry.cpp (modified) (1 diff)
• Potentials/PotentialRegistry.hpp (modified) (2 diffs)
• Potentials/SerializablePotential.cpp (added)
• Potentials/SerializablePotential.hpp (added)
• Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Angle.hpp (modified) (1 diff)
• Potentials/Specifics/PairPotential_Harmonic.hpp (modified) (2 diffs)
• Potentials/Specifics/PairPotential_Morse.hpp (modified) (1 diff)
• Potentials/Specifics/SaturationPotential.hpp (modified) (1 diff)
• Potentials/unittests/Makefile.am (added)
• Potentials/unittests/SerializablePotentialUnitTest.cpp (added)
• Potentials/unittests/SerializablePotentialUnitTest.hpp (added)
• Potentials/unittests/stubs/SerializablePotentialMock.cpp (added)
• Potentials/unittests/stubs/SerializablePotentialMock.hpp (added)
• unittests/Makefile.am (modified) (1 diff)

src/LevMartester.cpp

@@ -40 +40 @@
 
 #include <boost/assign.hpp>
+#include <boost/assign/list_of.hpp>
 #include <boost/bind.hpp>
 #include <boost/filesystem.hpp>

src/Potentials/EmpiricalPotential.hpp

@@ -66 +66 @@
    */
   virtual derivative_components_t derivative(const arguments_t &arguments) const=0;
-
-  /** Return the name of this specific potential.
-   *
-   * This is required for storage in a Registry.
-   *
-   * \return name of the potential
-   */
-  virtual const std::string getName() const=0;
 };
 
-
 #endif /* EMPIRICALPOTENTIAL_HPP_ */

src/Potentials/Makefile.am

@@ -5 +5 @@
   Potentials/Specifics/ManyBodyPotential_Tersoff.cpp \
   Potentials/PotentialRegistry.cpp \
+  Potentials/SerializablePotential.cpp \
   Potentials/Specifics/PairPotential_Angle.cpp \
   Potentials/Specifics/PairPotential_Harmonic.cpp \
@@ -12 +13 @@
 POTENTIALSHEADER = \
   Potentials/EmpiricalPotential.hpp \
+  Potentials/Exceptions.hpp \
   Potentials/helpers.hpp \
   Potentials/PotentialRegistry.hpp \
+  Potentials/SerializablePotential.hpp \
   Potentials/Specifics/ManyBodyPotential_Tersoff.hpp \
   Potentials/Specifics/PairPotential_Angle.hpp \

src/Potentials/PotentialRegistry.cpp

@@ -40 +40 @@
 
 CONSTRUCT_SINGLETON(PotentialRegistry)
-CONSTRUCT_REGISTRY(EmpiricalPotential)
+CONSTRUCT_REGISTRY(SerializablePotential)

src/Potentials/PotentialRegistry.hpp

@@ -16 +16 @@
 #include "CodePatterns/Registry.hpp"
 #include "CodePatterns/Singleton.hpp"
-#include "Potentials/EmpiricalPotential.hpp"
+#include "Potentials/SerializablePotential.hpp"
 
 /** Potential Registry.
@@ -29 +29 @@
  * ones.
  */
-class PotentialRegistry : public Singleton<PotentialRegistry>, public Registry<EmpiricalPotential>
+class PotentialRegistry : public Singleton<PotentialRegistry>, public Registry<SerializablePotential>
 {
   friend class Singleton<PotentialRegistry>;
-  //friend class Registry<EmpiricalPotential>;
+  //friend class Registry<SerializablePotential>;
 
 public:

src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp

@@ -120 +120 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
-  /** Return the name of this specific potential.
-   *
-   * This is required for storage in a Registry.
-   *
-   * \return name of the potential
-   */
-  const std::string getName() const {
+  /** Return the token name of this specific potential.
+   *
+   * \return token name of the potential
+   */
+  const std::string getToken() const {
     return std::string("tersoff");
   }

src/Potentials/Specifics/PairPotential_Angle.hpp

@@ -93 +93 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
-  /** Return the name of this specific potential.
+  /** Return the token name of this specific potential.
    *
-   * This is required for storage in a Registry.
-   *
-   * \return name of the potential
+   * \return token name of the potential
    */
-  const std::string getName() const {
+  const std::string getToken() const {
     return std::string("harmonic_angle");
   }

src/Potentials/Specifics/PairPotential_Harmonic.hpp

@@ -93 +93 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
-  /** Return the name of this specific potential.
-   *
-   * This is required for storage in a Registry.
-   *
-   * \return name of the potential
-   */
-  const std::string getName() const {
-    return std::string("harmonic_bond");
-  }
-
   /** States whether lower and upper boundaries should be used to constraint
    * the parameter search for this function model.
@@ -132 +122 @@
   }
 
+  /** Return the token name of this specific potential.
+   *
+   * \return token name of the potential
+   */
+  const std::string getToken() const {
+    return std::string("harmonic_bond");
+  }
+
   enum parameter_enum_t {
     spring_constant=0,

src/Potentials/Specifics/PairPotential_Morse.hpp

@@ -94 +94 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
-  /** Return the name of this specific potential.
+  /** Return the token name of this specific potential.
    *
-   * This is required for storage in a Registry.
-   *
-   * \return name of the potential
+   * \return token name of the potential
    */
-  const std::string getName() const {
+  const std::string getToken() const {
     return std::string("morse");
   }

src/Potentials/Specifics/SaturationPotential.hpp

@@ -96 +96 @@
   results_t parameter_derivative(const arguments_t &arguments, const size_t index) const;
 
-  /** Return the name of this specific potential.
+  /** Return the token name of this specific potential.
    *
-   * This is required for storage in a Registry.
-   *
-   * \return name of the potential
+   * \return token name of the potential
    */
-  const std::string getName() const {
+  const std::string getToken() const {
     return std::string("saturation");
   }

src/unittests/Makefile.am

@@ -30 +30 @@
 include ../../src/Parameters/unittests/Makefile.am
 include ../../src/Parser/unittests/Makefile.am
+include ../../src/Potentials/unittests/Makefile.am
 include ../../src/Potentials/Specifics/unittests/Makefile.am
 include ../../src/RandomNumbers/unittests/Makefile.am