Changeset 1413f4


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:
484e2a
Parents:
4792ab
git-author:
Frederik Heber <heber@…> (07/05/13 08:12:49)
git-committer:
Frederik Heber <heber@…> (08/09/13 14:20:37)
Message:

Added LennardJones pair potential.

  • this is for later fitting between order-1 fragments.
  • also added regression test for LJ fitting.
Files:
5 added
5 edited

Legend:

Unmodified
Added
Removed

  • src/Potentials/Makefile.am

    r4792ab r1413f4  
    1717  Potentials/Specifics/PairPotential_Angle.cpp \
    1818  Potentials/Specifics/PairPotential_Harmonic.cpp \
     19  Potentials/Specifics/PairPotential_LennardJones.cpp \
    1920  Potentials/Specifics/PairPotential_Morse.cpp \
    2021  Potentials/Specifics/PotentialTypes.cpp
    … …  
    4445  Potentials/Specifics/PairPotential_Angle.hpp \
    4546  Potentials/Specifics/PairPotential_Harmonic.hpp \
     47  Potentials/Specifics/PairPotential_LennardJones.hpp \
    4648  Potentials/Specifics/PairPotential_Morse.hpp
    4749 

  • src/Potentials/PotentialFactory.cpp

    r4792ab r1413f4  
    113113  case harmonic_angle:
    114114      return new PairPotential_Angle(types);
     115  case lennardjones:
     116      return new PairPotential_LennardJones(types);
    115117  default:
    116118    ASSERT(0, "PotentialFactory::createInstance() - unknown potential desired to create.");
    … …  
    142144    potential = new PairPotential_Angle();
    143145    break;
     146  case lennardjones:
     147    potential = new PairPotential_LennardJones();
     148    break;
    144149  default:
    145150    ASSERT(0, "PotentialFactory::createInstance() - unknown potential desired to create.");

  • src/Potentials/Specifics/PotentialTypes.def

    r4792ab r1413f4  
    11//!> preprocessor sequence of all known potential types. Just add new parser here
    2 #define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)
     2#define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)(lennardjones)
    33//!> Number of enumerations calculate automatically
    44#define PotentialTypes_END BOOST_PP_SEQ_SIZE(POTENTIALSEQUENCE)

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

    r4792ab r1413f4  
    77        ../Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp \
    88        ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp \
     9        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp \
    910        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp
    1011
    … …  
    1415        ../Potentials/Specifics/unittests/PairPotential_AngleUnitTest.hpp \
    1516        ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.hpp \
     17        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp \
    1618        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.hpp
    1719
    … …  
    2123        PairPotential_AngleUnitTest \
    2224        PairPotential_HarmonicUnitTest \
     25        PairPotential_LennardJonesUnitTest \
    2326        PairPotential_MorseUnitTest
    2427
    … …  
    5760PairPotential_HarmonicUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    5861
     62PairPotential_LennardJonesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     63        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp \
     64        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp
     65PairPotential_LennardJonesUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
     66
    5967PairPotential_MorseUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    6068        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp \

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

    r4792ab r1413f4  
    4848
    4949AT_CLEANUP
     50
     51AT_SETUP([Fragmentation - Fit LJ potential to argon])
     52AT_KEYWORDS([fragmentation parse-homologies fit-potential lennardjones])
     53AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
     54
     55file=lj_homology.dat
     56AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
     57AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
     58AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "lennardjones" --potential-charges 18 18 --fragment-charges 18 18 --set-threshold 7e-11], 0, [stdout], [ignore])
     59# check that L_2 error is below 7e-11
     60AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 7e-11) exit 1}'], 0, [ignore], [ignore])
     61# check parameters to printed precision
     62AT_CHECK([grep "lennardjones:.*particle_type1=18,.*particle_type2=18,.*epsilon=1.*e-05,.*sigma=8.2.*;" stdout], 0, [ignore], [ignore])
     63
     64AT_CLEANUP
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