Changeset 791a12


Ignore:
Timestamp:
Aug 9, 2013, 2:20:37 PM (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:
ff90e3
Parents:
a74a96
git-author:
Frederik Heber <heber@…> (07/10/13 13:47:38)
git-committer:
Frederik Heber <heber@…> (08/09/13 14:20:37)
Message:

Added improper potential based on torsion potential with flipped arguments.

  • added unit test.
  • also added regression test to improper potential, is set to XFAIL for the moment.
Files:
5 added
5 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Makefile.am

    ra74a96 r791a12  
    1414  Potentials/SerializablePotential.cpp \
    1515  Potentials/Specifics/ConstantPotential.cpp \
     16  Potentials/Specifics/FourBodyPotential_Improper.cpp \
    1617  Potentials/Specifics/FourBodyPotential_Torsion.cpp \
    1718  Potentials/Specifics/ManyBodyPotential_Tersoff.cpp \
    … …  
    4344SPECIFICPOTENTIALSHEADER = \
    4445  Potentials/Specifics/ConstantPotential.hpp \
     46  Potentials/Specifics/FourBodyPotential_Improper.hpp \
    4547  Potentials/Specifics/FourBodyPotential_Torsion.hpp \
    4648  Potentials/Specifics/ManyBodyPotential_Tersoff.hpp \

  • src/Potentials/PotentialFactory.cpp

    ra74a96 r791a12  
    117117  case torsion:
    118118      return new FourBodyPotential_Torsion(types);
     119  case improper:
     120      return new FourBodyPotential_Improper(types);
    119121  default:
    120122    ASSERT(0, "PotentialFactory::createInstance() - unknown potential desired to create.");
    … …  
    152154    potential = new FourBodyPotential_Torsion();
    153155    break;
     156  case improper:
     157    potential = new FourBodyPotential_Improper();
     158    break;
    154159  default:
    155160    ASSERT(0, "PotentialFactory::createInstance() - unknown potential desired to create.");

  • src/Potentials/Specifics/PotentialTypes.def

    ra74a96 r791a12  
    11//!> preprocessor sequence of all known potential types. Just add new parser here
    2 #define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)(lennardjones)(torsion)
     2#define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)(lennardjones)(torsion)(improper)
    33//!> Number of enumerations calculate automatically
    44#define PotentialTypes_END BOOST_PP_SEQ_SIZE(POTENTIALSEQUENCE)

  • src/Potentials/Specifics/unittests/Makefile.am

    ra74a96 r791a12  
    44POTENTIALSSPECIFICSTESTSSOURCES = \
    55        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp \
     6        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp \
    67        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp \
    78        ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp \
    … …  
    1314POTENTIALSSPECIFICSTESTSHEADERS = \
    1415        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp \
     16        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp \
    1517        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp \
    1618        ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp \
    … …  
    2224POTENTIALSSPECIFICSTESTS = \
    2325        ConstantPotentialUnitTest \
     26        FourBodyPotential_ImproperUnitTest \
    2427        FourBodyPotential_TorsionUnitTest \
    2528        ManyBodyPotential_TersoffUnitTest \
    … …  
    4750        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp
    4851ConstantPotentialUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
     52
     53FourBodyPotential_ImproperUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     54        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp \
     55        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp
     56FourBodyPotential_ImproperUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    4957
    5058FourBodyPotential_TorsionUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \

  • tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at

    ra74a96 r791a12  
    6363AT_CLEANUP
    6464
     65AT_SETUP([Fragmentation - Fit improper potential to ammonia])
     66AT_KEYWORDS([fragmentation parse-homologies fit-potential improper])
     67AT_XFAIL_IF([/bin/true])
     68AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
     69
     70file=improper_homology.dat
     71AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
     72AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
     73AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "improper" --potential-charges 1 7 1 1 --fragment-charges 7 1 1 1 --set-threshold 3e-4], 0, [stdout], [ignore])
     74# check that L_2 error is below 3e-4
     75AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 3e-4) exit 1}'], 0, [ignore], [ignore])
     76# check parameters to printed precision
     77AT_CHECK([grep "improper:.*particle_type1=1,.*particle_type2=1,.*particle_type3=7,.*particle_type4=1,.*spring_constant=1.02.*,.*equilibrium_distance=0.85.*;" stdout], 0, [ignore], [ignore])
     78
     79AT_CLEANUP
     80
    6581AT_SETUP([Fragmentation - Fit LJ potential to argon])
    6682AT_KEYWORDS([fragmentation parse-homologies fit-potential lennardjones])
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