Changeset 3f9eba

Timestamp:

Feb 3, 2011, 9:51:19 AM (14 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:

c9bc2b7

Parents:

1f91f4

git-author:

Frederik Heber <heber@…> (01/01/11 22:27:54)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:19)

Message:

New classes for random number generation.

• we use boost::random as a basis. It implements a lot of pseudo-random engines and various distributions. However, everything is templated and there are no base classes to store prototypes of the instances in a map. We need these such that we are able to offer the user at run-time every choice possible.
• Hence, we need to encapsulate all engines, distributions and (engine, distribution) tuples: RandomNumber..._Encapsulation classes.
• each with an abstract base class as the interface: RandomNumber... classes.
• RandomNumberGeneratorFactory is then a singleton that contains all the Maps and tables:
  • from string (user input is string) to enum (storing enum is more efficient that a lengthy string)
  • from enum to instance (of the abstract class).
• RandomNumberGeneratorFactory is a singleton to allow for global control of what kind of numbers are generated, hence there are also two new Actions:
  • SetRandomNumbersDistributionAction
  • SetRandomNumbersEngineAction to specify which (engine,distribution) tuple to use. There are two new regression tests for these Actions.
• The user in the end only uses two classes: RandomNumberGeneratorFactory and RandomNumberGenerator. The first only for obtaining a specific variant of the latter and the latter to generate the numbers (operator() is passed on to boost::variate_generator::operator()).
• There is a unit test on the RandomNumberGeneratorFactory that checks some of the table entries and whether one of the RandomNumberGenerator is working (uniform_smallint so far).

Details:

• As there are ~25 engines and ~15 distributions this makes an enormous amount of possible combinations. To automatically construct these, we use some stuff from boost::preprocessor in order to generate enums, tables and maps automatically just from a sequence of the typenames.
• we have be-friended the unit test a lot to allow for easier testing, e.g. we need access to internal ..._type to test whether their type is correct.
• cleanUp() purges the instance of RandomNumberGeneratorFactory.
• in RandomNumber..._Encapsulation::name() functions are only used for the unit tests.
• this all resides in its own subfolder RandomNumbers. So far, it is completely independent of everything else.

Files:

• configure.ac (modified) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (added)
• src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.def (added)
• src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.hpp (added)
• src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (added)
• src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.def (added)
• src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.hpp (added)
• src/Makefile.am (modified) (3 diffs)
• src/RandomNumbers/RandomNumberDistribution.hpp (added)
• src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (added)
• src/RandomNumbers/RandomNumberEngine.hpp (added)
• src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (added)
• src/RandomNumbers/RandomNumberGenerator.cpp (added)
• src/RandomNumbers/RandomNumberGenerator.hpp (added)
• src/RandomNumbers/RandomNumberGeneratorFactory.cpp (added)
• src/RandomNumbers/RandomNumberGeneratorFactory.def (added)
• src/RandomNumbers/RandomNumberGeneratorFactory.hpp (added)
• src/RandomNumbers/RandomNumberGeneratorFactory.undef (added)
• src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (added)
• src/RandomNumbers/TemplatePowerSetGenerator.hpp (added)
• src/RandomNumbers/unittests/Makefile.am (added)
• src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (added)
• src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp (added)
• src/builder_init.cpp (modified) (2 diffs)
• src/unittests/Makefile.am (modified) (1 diff)
• tests/regression/Makefile.am (modified) (2 diffs)
• tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (added)
• tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (added)
• tests/regression/RandomNumbers/testsuite-randomnumbers.at (added)
• tests/regression/testsuite.at (modified) (1 diff)

configure.ac

@@ -229 +229 @@
         src/LinearAlgebra/unittests/Makefile
         src/Parser/unittests/Makefile
+  src/RandomNumbers/unittests/Makefile
   src/Shapes/unittests/Makefile
         src/UIElements/Menu/unittests/Makefile

src/Actions/Makefile.am

@@ -14 +14 @@
   ${MOLECULEACTIONSOURCE} \
   ${PARSERACTIONSOURCE} \
+  ${RANDONNUMBERSSOURCE} \
   ${SELECTIONATOMACTIONSOURCE} \
   ${SELECTIONMOLECULEACTIONSOURCE} \
@@ -29 +30 @@
   ${MOLECULEACTIONHEADER} \
   ${PARSERACTIONHEADER} \
+  ${RANDONNUMBERSHEADER} \
   ${SELECTIONATOMACTIONHEADER} \
   ${SELECTIONMOLECULEACTIONHEADER} \
@@ -124 +126 @@
   MoleculeAction/SuspendInWaterAction.hpp \
   MoleculeAction/VerletIntegrationAction.hpp
+
+RANDONNUMBERSSOURCE =\
+        RandomNumbersAction/SetRandomNumbersDistributionAction.cpp \
+        RandomNumbersAction/SetRandomNumbersEngineAction.cpp
+
+RANDONNUMBERSHEADER =\
+        RandomNumbersAction/SetRandomNumbersDistributionAction.hpp \
+        RandomNumbersAction/SetRandomNumbersEngineAction.hpp
                  
 SELECTIONATOMACTIONSOURCE = \

src/Makefile.am

@@ -121 +121 @@
   Descriptors/MoleculePtrDescriptor_impl.hpp \
   Descriptors/MoleculeSelectionDescriptor_impl.hpp
+
+RANDOMSOURCE = \
+        RandomNumbers/RandomNumberGeneratorFactory.cpp
+
+RANDOMHEADER = \
+        RandomNumbers/RandomNumberGenerator.hpp \
+        RandomNumbers/TemplatePowerSetGenerator.hpp \
+        RandomNumbers/RandomNumberGenerator_Encapsulation.hpp \
+        RandomNumbers/RandomNumberGeneratorFactory.hpp
   
 THERMOSTATSOURCE = \
@@ -166 +175 @@
   ${ACTIONSSOURCE} \
   ${ATOMSOURCE} \
-  ${PATTERNSOURCE} \
-  ${SHAPESOURCE} \
   ${DESCRIPTORSOURCE} \
+  ${RANDOMSOURCE} \
   ${THERMOSTATSOURCE} \
   ${TESSELATIONSOURCE} \
@@ -203 +211 @@
   ${ACTIONSHEADER} \
   ${ATOMHEADER} \
-  ${PATTERNHEADER} \
-  ${SHAPEHEADER} \
   ${DESCRIPTORHEADER} \
   ${DESCRIPTORIMPLHEADER} \
+  ${RANDOMSOURCE} \
   ${THERMOSTATHEADER} \
   ${TESSELATIONHEADER} \

src/builder_init.cpp

@@ -42 +42 @@
 #include "Actions/ActionRegistry.hpp"
 #include "Actions/ActionHistory.hpp"
+
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
 
 #include "Parser/ChangeTracker.hpp"
@@ -167 +169 @@
 void cleanUp()
 {
+  RandomNumberGeneratorFactory::purgeInstance();
   FormatParserStorage::purgeInstance();
   ChangeTracker::purgeInstance();

src/unittests/Makefile.am

@@ -7 +7 @@
         ../LinearAlgebra/unittests \
         ../Parser/unittests \
+        ../RandomNumbers/unittests \
         ../Shapes/unittests \
         ../UIElements/Menu/unittests

tests/regression/Makefile.am

@@ -11 +11 @@
         Graph \
         Molecules \
+        RandomNumbers \
         Selection \
         Simple_configuration \
@@ -34 +35 @@
         $(srcdir)/testsuite-molecules.at \
         $(srcdir)/testsuite-simple_configuration.at \
+        $(srcdir)/RandomNumbers/testsuite-randomnumbers.at \
+        $(srcdir)/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at \
+        $(srcdir)/RandomNumbers/Engine/testsuite-set-random-number-engine.at \
         $(srcdir)/Selection/testsuite-selection.at \
         $(srcdir)/Selection/Atoms/testsuite-selection-all-atoms.at \

tests/regression/testsuite.at

@@ -18 +18 @@
 m4_include(Selection/testsuite-selection.at)
 
+m4_include(RandomNumbers/testsuite-randomnumbers.at)
+
 m4_include(testsuite-domain.at)