Changeset c0e28c for tests

Timestamp:

Jan 6, 2012, 2:02:08 PM (13 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:

d08ab3

Parents:

fbbcde

git-author:

Frederik Heber <heber@…> (01/04/12 18:34:22)

git-committer:

Frederik Heber <heber@…> (01/06/12 14:02:08)

Message:

FIX: One could not load another pdb file due to local ids messing up.

• We enhanced FormatParser_common now contains two maps to go from local to global and back again. Thi is necessary, as ids in a file only make sense within that file. We added the following functions: resetIdAssociations(), associateLocaltoGlobalId(), getGlobalId(), getLocalId().
• adapted TremoloParser and PdbParser because they are the only formats that also contain bond information and where the associations are needed to translate the local connections into global ones.
• removed SerialSet entirely from PdbParser, is replaced by new construct, in similar manner AtomIdMap for TremoloParser.
• TEST: Added regression tests for all Parser to check for loading twice the same file.

Location:

tests/regression

Files:

• Makefile.am (modified) (5 diffs)
• Parser/Mpqc/post/doublewater.in (added)
• Parser/Mpqc/pre/water.in (added)
• Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (added)
• Parser/Pcp/post/doubletest.conf (added)
• Parser/Pcp/post/doublewater.conf (added)
• Parser/Pcp/pre/water.conf (added)
• Parser/Pcp/testsuite-parser-pcp-load-multiply.at (added)
• Parser/Pdb/post/doublewater.pdb (added)
• Parser/Pdb/pre/water.pdb (added)
• Parser/Pdb/testsuite-parser-pdb-load-multiply.at (added)
• Parser/Psi3/post/doublewater.psi (added)
• Parser/Psi3/pre/water.psi (added)
• Parser/Psi3/testsuite-parser-psi3-load-multiply.at (added)
• Parser/Tremolo/post/doublewater.data (added)
• Parser/Tremolo/pre/water.data (added)
• Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (added)
• Parser/Xyz/post/doublewater.xyz (added)
• Parser/Xyz/pre/water.xyz (added)
• Parser/Xyz/testsuite-parser-xyz-load-multiply.at (added)
• Parser/testsuite-parser.at (modified) (6 diffs)

tests/regression/Makefile.am

@@ -96 +96 @@
         $(srcdir)/Parser/Mpqc/testsuite-parser-mpqc-empty.at \
         $(srcdir)/Parser/Mpqc/testsuite-parser-mpqc-load.at \
+        $(srcdir)/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at \
         $(srcdir)/Parser/Mpqc/testsuite-parser-mpqc-save.at \
         $(srcdir)/Parser/Pcp/testsuite-parser-pcp-empty.at \
         $(srcdir)/Parser/Pcp/testsuite-parser-pcp-load.at \
+        $(srcdir)/Parser/Pcp/testsuite-parser-pcp-load-multiply.at \
         $(srcdir)/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at \
         $(srcdir)/Parser/Pcp/testsuite-parser-pcp-save.at \
@@ -105 +107 @@
         $(srcdir)/Parser/Pdb/testsuite-parser-pdb-empty.at \
         $(srcdir)/Parser/Pdb/testsuite-parser-pdb-load.at \
+        $(srcdir)/Parser/Pdb/testsuite-parser-pdb-load-multiply.at \
         $(srcdir)/Parser/Pdb/testsuite-parser-pdb-load-various.at \
         $(srcdir)/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at \
@@ -111 +114 @@
         $(srcdir)/Parser/Psi3/testsuite-parser-psi3-empty.at \
         $(srcdir)/Parser/Psi3/testsuite-parser-psi3-load.at \
+        $(srcdir)/Parser/Psi3/testsuite-parser-psi3-load-multiply.at \
         $(srcdir)/Parser/Psi3/testsuite-parser-psi3-save.at \
         $(srcdir)/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at \
@@ -120 +124 @@
         $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo-empty.at \
         $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo-load.at \
+        $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at \
         $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo-save.at \
         $(srcdir)/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at \
@@ -127 +132 @@
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-empty.at \
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-load.at \
+        $(srcdir)/Parser/Xyz/testsuite-parser-xyz-load-multiply.at \
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at \
         $(srcdir)/Parser/Xyz/testsuite-parser-xyz-save.at \

tests/regression/Parser/testsuite-parser.at

@@ -5 +5 @@
 m4_include([Parser/Mpqc/testsuite-parser-mpqc-empty.at])
 m4_include([Parser/Mpqc/testsuite-parser-mpqc-load.at])
+m4_include([Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at])
 m4_include([Parser/Mpqc/testsuite-parser-mpqc-save.at])
 
@@ -16 +17 @@
 m4_include([Parser/Pcp/testsuite-parser-pcp-empty.at])
 m4_include([Parser/Pcp/testsuite-parser-pcp-load.at])
+m4_include([Parser/Pcp/testsuite-parser-pcp-load-multiply.at])
 m4_include([Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at])
 m4_include([Parser/Pcp/testsuite-parser-pcp-save.at])
@@ -22 +24 @@
 m4_include([Parser/Pdb/testsuite-parser-pdb-empty.at])
 m4_include([Parser/Pdb/testsuite-parser-pdb-load.at])
+m4_include([Parser/Pdb/testsuite-parser-pdb-load-multiply.at])
 m4_include([Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at])
 m4_include([Parser/Pdb/testsuite-parser-pdb-save.at])
@@ -35 +38 @@
 m4_include([Parser/Pdb/testsuite-parser-pdb-load-various.at])
 
-# parsing mpqc
+# parsing psi3
 m4_include([Parser/Psi3/testsuite-parser-psi3-empty.at])
 m4_include([Parser/Psi3/testsuite-parser-psi3-load.at])
+m4_include([Parser/Psi3/testsuite-parser-psi3-load-multiply.at])
 m4_include([Parser/Psi3/testsuite-parser-psi3-save.at])
 
@@ -43 +47 @@
 m4_include([Parser/Tremolo/testsuite-parser-tremolo-empty.at])
 m4_include([Parser/Tremolo/testsuite-parser-tremolo-load.at])
+m4_include([Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at])
 m4_include([Parser/Tremolo/testsuite-parser-tremolo-save.at])
 
@@ -56 +61 @@
 m4_include([Parser/Xyz/testsuite-parser-xyz-empty.at])
 m4_include([Parser/Xyz/testsuite-parser-xyz-load.at])
+m4_include([Parser/Xyz/testsuite-parser-xyz-load-multiply.at])
 m4_include([Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at])
 m4_include([Parser/Xyz/testsuite-parser-xyz-save.at])