Changeset 9b7db1

Timestamp:

May 30, 2010, 4:51:45 PM (15 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:

5d12d2

Parents:

c7a473

Message:

Added case '-R' (removing atoms outside of sphere) to testsuite.

• basically works, but molecuilder crashes with SIGABT when destroying world.

Files:

• src/builder.cpp (modified) (1 diff)
• tests/regression/Simple_configuration/8/post/test.conf (added)
• tests/regression/Simple_configuration/8/pre/test.conf (added)
• tests/regression/testsuite.at (modified) (6 diffs)

src/builder.cpp

@@ -2134 +2134 @@
                     first = second;
                     second = first->next;
-                    if (first->x.DistanceSquared(third->x) > tmp1*tmp1) // distance to first above radius ...
+                    if (first->x.DistanceSquared(third->x) > tmp1*tmp1) {// distance to first above radius ...
                       mol->RemoveAtom(first);
+                    }
                   }
                 } else {

tests/regression/testsuite.at

@@ -158 +158 @@
 AT_CLEANUP
 
+# 8. Removing sphere of atoms
+AT_SETUP([Molecules - BROKEN: Removing sphere of atoms])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -R 2 7.], 134, [stdout], [stderr])
+AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
+AT_CLEANUP
+
 
 AT_BANNER([MoleCuilder - simulation domain])
@@ -221 +229 @@
 
 # 2. Storing adjacency info
-AT_SETUP([Graph - Storing bond info])
+AT_SETUP([Molecules - Storing bond info])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/pre/test.conf .], 0)
@@ -231 +239 @@
 
 # 3. Storing temperature
-AT_SETUP([Graph - Storing temperature])
+AT_SETUP([Molecules - Storing temperature])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/pre/test.conf .], 0)
@@ -239 +247 @@
 
 # 4. linear interpolation
-AT_SETUP([Graph - Linear interpolation])
+AT_SETUP([Molecules - BROKEN: Linear interpolation])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/4/pre/test.conf .], 0)
@@ -246 +254 @@
 
 # 5. Verlet force integration
-AT_SETUP([Graph - Verlet force integration])
+AT_SETUP([Molecules - BROKEN: Verlet force integration])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/pre/test.* .], 0)
@@ -252 +260 @@
 #AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
-
 
 AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])