Changeset 0932c2 for src/Potentials

Timestamp:

Jun 27, 2014, 11:43:27 AM (11 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:

1dbbeb

Parents:

7e3e41

git-author:

Frederik Heber <heber@…> (06/26/14 07:41:59)

git-committer:

Frederik Heber <heber@…> (06/27/14 11:43:27)

Message:

FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype.

• this caused all engines to always start with default seed of 1, irrespective of the set parameter. The engine is always cloned from prototypes in the factory that can be manipulated to change their parameters. Hence, clone needs to set the seed (the engine's only parameter).
• EmpiricalPotentials now use RandomNumberGenerator to obtain random starting values.
• TESTFIX: fit-potential regression tests now use fixed seed in order to always take the same amount of time (some test runs in debug mode take very long because of ill-chosen random values).

Location:

src/Potentials

Files:

• Specifics/FourBodyPotential_Torsion.cpp (modified) (2 diffs)
• Specifics/ManyBodyPotential_Tersoff.cpp (modified) (2 diffs)
• Specifics/PairPotential_Harmonic.cpp (modified) (2 diffs)
• Specifics/PairPotential_LennardJones.cpp (modified) (2 diffs)
• Specifics/PairPotential_Morse.cpp (modified) (2 diffs)
• Specifics/ThreeBodyPotential_Angle.cpp (modified) (2 diffs)
• Specifics/unittests/Makefile.am (modified) (1 diff)
• unittests/Makefile.am (modified) (1 diff)

src/Potentials/Specifics/FourBodyPotential_Torsion.cpp

@@ -51 +51 @@
 #include "Potentials/InternalCoordinates/FourBody_TorsionAngle.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 class Fragment;
 
-// static definitions
+// static definitions1
 const FourBodyPotential_Torsion::ParameterNames_t
 FourBodyPotential_Torsion::ParameterNames =
@@ -254 +256 @@
     const TrainingData &data)
 {
-  params[FourBodyPotential_Torsion::spring_constant] = 2.*rand()/(double)RAND_MAX;
-  params[FourBodyPotential_Torsion::equilibrium_distance] = -.5+1.*rand()/(double)RAND_MAX;
-}
-
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
+  params[FourBodyPotential_Torsion::spring_constant] = 2.*(random()/(rng_max-rng_min));
+  params[FourBodyPotential_Torsion::equilibrium_distance] = 2.*(random()/(rng_max-rng_min));
+}
+

src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp

@@ -54 +54 @@
 #include "Potentials/InternalCoordinates/OneBody_Constant.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 class Fragment;
@@ -713 +715 @@
     const TrainingData &data)
 {
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
 //  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::A] = 1e+4*(random()/(rng_max-rng_min));//1.393600e+03;
+  params[ManyBodyPotential_Tersoff::B] = 1e+4*(random()/(rng_max-rng_min));//3.467000e+02;
+  params[ManyBodyPotential_Tersoff::lambda] = 1e+1*(random()/(rng_max-rng_min));//3.487900e+00;
+  params[ManyBodyPotential_Tersoff::mu] = 1e+1*(random()/(rng_max-rng_min));//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::beta] = 1e-1*(random()/(rng_max-rng_min));//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::n] = 1e+1*(random()/(rng_max-rng_min));//7.275100e-01;
+  params[ManyBodyPotential_Tersoff::c] = 1e+1*(random()/(rng_max-rng_min));//3.804900e+04;
+  params[ManyBodyPotential_Tersoff::d] = 1e+1*(random()/(rng_max-rng_min));//4.384000e+00;
+  params[ManyBodyPotential_Tersoff::h] = 1e+1*(random()/(rng_max-rng_min));//-5.705800e-01;
+}
+

src/Potentials/Specifics/PairPotential_Harmonic.cpp

@@ -52 +52 @@
 #include "Potentials/InternalCoordinates/TwoBody_Length.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 class Fragment;
@@ -213 +215 @@
     const TrainingData &data)
 {
-  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;
-}
-
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
+  params[PairPotential_Harmonic::equilibrium_distance] = 3e+0*(random()/(rng_max-rng_min)) + .5;// 1.;
+  params[PairPotential_Harmonic::spring_constant] = 1e+0*(random()/(rng_max-rng_min));// 0.2;
+}
+

src/Potentials/Specifics/PairPotential_LennardJones.cpp

@@ -52 +52 @@
 #include "Potentials/InternalCoordinates/TwoBody_Length.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 class Fragment;
@@ -222 +224 @@
     const TrainingData &data)
 {
-  params[PairPotential_LennardJones::epsilon] = 1e-2*rand()/(double)RAND_MAX;
-  params[PairPotential_LennardJones::sigma] = (3.+10.*rand()/(double)RAND_MAX);// 0.5;
-}
-
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
+  params[PairPotential_LennardJones::epsilon] = 1e-2*(random()/(rng_max-rng_min));
+  params[PairPotential_LennardJones::sigma] = (3.+10.*(random()/(rng_max-rng_min)));// 0.5;
+}
+

src/Potentials/Specifics/PairPotential_Morse.cpp

@@ -53 +53 @@
 #include "Potentials/InternalCoordinates/TwoBody_Length.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 class Fragment;
@@ -242 +244 @@
     const TrainingData &data)
 {
-  params[PairPotential_Morse::dissociation_energy] = 1e+0*rand()/(double)RAND_MAX;// 0.5;
-  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;
-}
-
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
+  params[PairPotential_Morse::dissociation_energy] = 1e+0*(random()/(rng_max-rng_min));// 0.5;
+  params[PairPotential_Morse::spring_constant] = 1e+0*(random()/(rng_max-rng_min));// 1.;
+  params[PairPotential_Morse::equilibrium_distance] =  3e+0*(random()/(rng_max-rng_min));//2.9;
+}
+

src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp

@@ -52 +52 @@
 #include "Potentials/InternalCoordinates/ThreeBody_Angle.hpp"
 #include "Potentials/ParticleTypeCheckers.hpp"
+#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
+#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 class Fragment;
@@ -240 +242 @@
     const TrainingData &data)
 {
-  params[ThreeBodyPotential_Angle::spring_constant] = 1e+0*rand()/(double)RAND_MAX;// 0.2;
-  params[ThreeBodyPotential_Angle::equilibrium_distance] = -0.3;//2e+0*rand()/(double)RAND_MAX - 1.;// 1.;
-}
-
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
+  params[ThreeBodyPotential_Angle::spring_constant] = 1e+0*(random()/(rng_max-rng_min));// 0.2;
+  params[ThreeBodyPotential_Angle::equilibrium_distance] = -0.3;//2e+0*(random()/(rng_max-rng_min)) - 1.;// 1.;
+}
+

src/Potentials/Specifics/unittests/Makefile.am

@@ -41 +41 @@
         ../libMolecuilderFragmentation.la \
         ../libMolecuilderFunctionApproximation.la \
+        ../libMolecuilderRandomNumbers.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \

src/Potentials/unittests/Makefile.am

@@ -37 +37 @@
         ../libMolecuilderFunctionApproximation.la \
         ../libMolecuilderFragmentation_getFromKeysetStub.la \
+        ../libMolecuilderRandomNumbers.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \