Changeset f5724f for tests

Timestamp:

Aug 12, 2013, 11:30:33 AM (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:

93909a

Parents:

24e19e

git-author:

Frederik Heber <heber@…> (07/26/13 09:08:31)

git-committer:

Frederik Heber <heber@…> (08/12/13 11:30:33)

Message:

Moved all FragmentationActions related to potentials into own menu and folder.

• changed class names Fragmentation... -> Potential...
• changed tokens in GlobalListOfActions.
• added menu entry "potential" and CommandLineParser program_options variable.
• moved regression tests into own folder as well and renamed folder in files.

Location:

tests/regression

Files:

• Fragmentation/testsuite-fragmentation.at (modified) (1 diff)
• Makefile.am (modified) (3 diffs)
• Potential/FitParticleCharges/pre/homology_grid.dat (moved) (moved from tests/regression/Fragmentation/FitParticleCharges/pre/homology_grid.dat )
• Potential/FitParticleCharges/pre/water.pdb (moved) (moved from tests/regression/Fragmentation/FitParticleCharges/pre/water.pdb )
• Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at (moved) (moved from tests/regression/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at ) (2 diffs)
• Potential/FitPotential/pre/angle_homology.dat (moved) (moved from tests/regression/Fragmentation/FitPotential/pre/angle_homology.dat )
• Potential/FitPotential/pre/harmonic_homology.dat (moved) (moved from tests/regression/Fragmentation/FitPotential/pre/harmonic_homology.dat )
• Potential/FitPotential/pre/improper_homology.dat (moved) (moved from tests/regression/Fragmentation/FitPotential/pre/improper_homology.dat )
• Potential/FitPotential/pre/length_homology.dat (moved) (moved from tests/regression/Fragmentation/FitPotential/pre/length_homology.dat )
• Potential/FitPotential/pre/lj_homology.dat (moved) (moved from tests/regression/Fragmentation/FitPotential/pre/lj_homology.dat )
• Potential/FitPotential/pre/torsion_homology.dat (moved) (moved from tests/regression/Fragmentation/FitPotential/pre/torsion_homology.dat )
• Potential/FitPotential/testsuite-potential-fit-potential.at (moved) (moved from tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at ) (6 diffs)
• Potential/testsuite-potential.at (added)
• testsuite.at (modified) (1 diff)

tests/regression/Fragmentation/testsuite-fragmentation.at

@@ -30 +30 @@
 # check storing saturated fragment
 m4_include([Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at])
-
-# fitting potential to fragment results
-m4_include([Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at])
-
-# fitting particle charges to fragment results
-m4_include([Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at])

tests/regression/Makefile.am

@@ -17 +17 @@
         Options \
         Parser \
+        Potential \
         RandomNumbers \
         Selection \
@@ -73 +74 @@
         $(srcdir)/Fragmentation/testsuite-fragmentation.at \
         $(srcdir)/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at \
-        $(srcdir)/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at \
-        $(srcdir)/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at \
         $(srcdir)/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at \
         $(srcdir)/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at \
@@ -161 +160 @@
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at \
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-save.at \
+        $(srcdir)/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at \
+        $(srcdir)/Potential/FitPotential/testsuite-potential-fit-potential.at \
         $(srcdir)/RandomNumbers/testsuite-randomnumbers.at \
         $(srcdir)/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at \

tests/regression/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at

@@ -21 +21 @@
 # ./molecuilder -i pre/water.pdb --center-in-box "8,0,8,0,0,8" --select-all-atoms --fragment-molecule BondFragment --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 4 --DoPrintDebug 1 --DoValenceOnly 0 --analyse-fragment-results --store-grids 1 --save-homologies homology_grid_4_full.dat
 
-AT_SETUP([Fragmentation - Fit particle charges to water])
-AT_KEYWORDS([fragmentation parse-homologies fit-particle-charges])
+AT_SETUP([Potential - Fit particle charges to water])
+AT_KEYWORDS([potential parse-homologies fit-particle-charges])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-particle-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
@@ -28 +28 @@
 # molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --analyse-fragment-results --save-homologies homology_grid.dat
 file=homology_grid.dat
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitParticleCharges/pre/$file $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitParticleCharges/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder --parse-homologies $file --fit-particle-charges --potential-file water.particles --fragment-charges 8 1 1 --radius 1.5], 0, [stdout], [ignore])

tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at

@@ -19 +19 @@
 ### fit some potentials
 
-AT_SETUP([Fragmentation - Fit morse potential to water])
-AT_KEYWORDS([fragmentation parse-homologies fit-potential morse])
+AT_SETUP([Potential - Fit morse potential to water])
+AT_KEYWORDS([potential parse-homologies fit-potential morse])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
 file=length_homology.dat
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "morse" --potential-charges 8 1 --fragment-charges 1 8 1 --set-threshold 1e-6], 0, [stdout], [ignore])
@@ -34 +34 @@
 AT_CLEANUP
 
-AT_SETUP([Fragmentation - Fit harmonic potential to water])
-AT_KEYWORDS([fragmentation parse-homologies fit-potential harmonic])
+AT_SETUP([Potential - Fit harmonic potential to water])
+AT_KEYWORDS([potential parse-homologies fit-potential harmonic])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
 file=harmonic_homology.dat
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "harmonic_bond" --potential-charges 8 1 --fragment-charges 1 8 1 --set-threshold 1e-6], 0, [stdout], [ignore])
@@ -49 +49 @@
 AT_CLEANUP
 
-AT_SETUP([Fragmentation - Fit harmonic_angle potential to water])
-AT_KEYWORDS([fragmentation parse-homologies fit-potential harmonic_angle])
+AT_SETUP([Potential - Fit harmonic_angle potential to water])
+AT_KEYWORDS([potential parse-homologies fit-potential harmonic_angle])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
 file=angle_homology.dat
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "harmonic_angle" --potential-charges 1 8 1 --fragment-charges 1 8 1 --set-threshold 1e-6], 0, [stdout], [ignore])
@@ -64 +64 @@
 AT_CLEANUP
 
-AT_SETUP([Fragmentation - Fit torsion potential to butane])
-AT_KEYWORDS([fragmentation parse-homologies fit-potential torsion])
+AT_SETUP([Potential - Fit torsion potential to butane])
+AT_KEYWORDS([potential 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([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$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])
@@ -78 +78 @@
 AT_CLEANUP
 
-AT_SETUP([Fragmentation - Fit improper potential to ammonia])
-AT_KEYWORDS([fragmentation parse-homologies fit-potential improper])
+AT_SETUP([Potential - Fit improper potential to ammonia])
+AT_KEYWORDS([potential parse-homologies fit-potential improper])
 AT_XFAIL_IF([/bin/true])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
 file=improper_homology.dat
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_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])
@@ -94 +94 @@
 AT_CLEANUP
 
-AT_SETUP([Fragmentation - Fit LJ potential to argon])
-AT_KEYWORDS([fragmentation parse-homologies fit-potential lennardjones])
+AT_SETUP([Potential - Fit LJ potential to argon])
+AT_KEYWORDS([potential parse-homologies fit-potential lennardjones])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
 file=lj_homology.dat
-AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
 AT_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])

tests/regression/testsuite.at

@@ -54 +54 @@
 m4_include(Fragmentation/testsuite-fragmentation.at)
 
+m4_include(Potential/testsuite-potential.at)
+
 m4_include(Tesselation/testsuite-tesselation.at)