Changeset e2037e

Timestamp:

Aug 9, 2013, 2:20:37 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:

a74a96

Parents:

484e2a

git-author:

Frederik Heber <heber@…> (07/08/13 07:37:04)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:37)

Message:

Added FourBodyPotential_Torsion.

• also added regression test to torsion potential.

Files:

• src/Potentials/Makefile.am (modified) (2 diffs)
• src/Potentials/PotentialFactory.cpp (modified) (2 diffs)
• src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (added)
• src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (added)
• src/Potentials/Specifics/PotentialTypes.def (modified) (1 diff)
• src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (added)
• src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp (added)
• src/Potentials/Specifics/unittests/Makefile.am (modified) (4 diffs)
• tests/regression/Fragmentation/FitPotential/pre/torsion_homology.dat (added)
• tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) (1 diff)

src/Potentials/Makefile.am

@@ -14 +14 @@
   Potentials/SerializablePotential.cpp \
   Potentials/Specifics/ConstantPotential.cpp \
+  Potentials/Specifics/FourBodyPotential_Torsion.cpp \
   Potentials/Specifics/ManyBodyPotential_Tersoff.cpp \
   Potentials/Specifics/PairPotential_Harmonic.cpp \
@@ -42 +43 @@
 SPECIFICPOTENTIALSHEADER = \
   Potentials/Specifics/ConstantPotential.hpp \
+  Potentials/Specifics/FourBodyPotential_Torsion.hpp \
   Potentials/Specifics/ManyBodyPotential_Tersoff.hpp \
   Potentials/Specifics/PairPotential_Harmonic.hpp \

src/Potentials/PotentialFactory.cpp

@@ -115 +115 @@
   case lennardjones:
       return new PairPotential_LennardJones(types);
+  case torsion:
+      return new FourBodyPotential_Torsion(types);
   default:
     ASSERT(0, "PotentialFactory::createInstance() - unknown potential desired to create.");
@@ -147 +149 @@
     potential = new PairPotential_LennardJones();
     break;
+  case torsion:
+    potential = new FourBodyPotential_Torsion();
+    break;
   default:
     ASSERT(0, "PotentialFactory::createInstance() - unknown potential desired to create.");

src/Potentials/Specifics/PotentialTypes.def

@@ -1 +1 @@
 //!> preprocessor sequence of all known potential types. Just add new parser here
-#define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)(lennardjones)
+#define POTENTIALSEQUENCE (constant)(tersoff)(morse)(harmonic)(harmonic_angle)(lennardjones)(torsion)
 //!> Number of enumerations calculate automatically
 #define PotentialTypes_END BOOST_PP_SEQ_SIZE(POTENTIALSEQUENCE)

src/Potentials/Specifics/unittests/Makefile.am

@@ -4 +4 @@
 POTENTIALSSPECIFICSTESTSSOURCES = \
         ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp \
+        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp \
         ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp \
         ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp \
@@ -12 +13 @@
 POTENTIALSSPECIFICSTESTSHEADERS = \
         ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp \
+        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp \
         ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp \
         ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.hpp \
@@ -20 +22 @@
 POTENTIALSSPECIFICSTESTS = \
         ConstantPotentialUnitTest \
+        FourBodyPotential_TorsionUnitTest \
         ManyBodyPotential_TersoffUnitTest \
         PairPotential_HarmonicUnitTest \
@@ -44 +47 @@
         ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp
 ConstantPotentialUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
+
+FourBodyPotential_TorsionUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp \
+        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp
+FourBodyPotential_TorsionUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
 
 ManyBodyPotential_TersoffUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \

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

@@ -49 +49 @@
 AT_CLEANUP
 
+AT_SETUP([Fragmentation - Fit torsion potential to butane])
+AT_KEYWORDS([fragmentation parse-homologies fit-potential torsion])
+AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
+
+file=torsion_homology.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "torsion" --potential-charges 6 6 6 6 --fragment-charges 6 6 6 6 1 1 1 1 1 1 1 1 1 1 --set-threshold 9e-12], 0, [stdout], [ignore])
+# check that L_2 error is below 9e-12
+AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 9e-12) exit 1}'], 0, [ignore], [ignore])
+AT_CHECK([grep "torsion:.*particle_type1=6,.*particle_type2=6,.*particle_type3=6,.*particle_type4=6,.*spring_constant=0.001.*,.*equilibrium_distance=0.99.*;" stdout], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
 AT_SETUP([Fragmentation - Fit LJ potential to argon])
 AT_KEYWORDS([fragmentation parse-homologies fit-potential lennardjones])