Changeset 3c1dfb

Timestamp:

Apr 29, 2008, 7:06:18 AM (17 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:

6590bee

Parents:

b5ecd9

Message:

Full test for fragmentation procedure with readin of the adjacency file.

The test is still a bit of a hack (with moving BondFragment*-files and diff'ing them), but so far it works very well. A test structure is generated, till bond order 2 fragmented, the configs are moved away, fragmented again by reading adjacency, and the new configs are diff'ed against the old ones.

File:

• tests/testsuite.at (modified) (1 diff)

tests/testsuite.at

@@ -33 +33 @@
 AT_CLEANUP
 
+AT_BANNER([MoleCuilder - Fragmentation test])
+AT_SETUP([Fragmentation])
+# 1. create a fake element database with the only two elements we need
+AT_DATA([elements.db],[#  Covalent  radius  of  each  element in  Angstroem from  CSD (binding  is: [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with  t = 0.4A
+#Element  Name  Symbol  Period  Group Block Atomic  Number  AtomicWeight  Covalent  Radius  vdW Radius
+Hydrogen  H 1 1 s 1 1.008 0.23  1.09
+Carbon  C       2       14      p       6       12.011  0.68    1.70
+])
+# 2. create molecular geometry
+AT_DATA([test.xyz], [[11
+ # test configuration, created by molecuilder test suite
+C       9.782085945     3.275186040     3.535886037
+C       8.532785963     4.158586027     3.535886037
+C       7.283585982     3.275186040     3.535886037
+H       9.782085945     2.645886050     2.645886050
+H       9.782085945     2.645886050     4.425886024
+H       10.672039608    3.904536878     3.535886037
+H       8.532785963     4.787886018     2.645886050
+H       8.532785963     4.787886018     4.425886024
+H       6.393632318     3.904536877     3.535886037
+H       7.283585982     2.645886050     2.645886050
+H       7.283585982     2.645886050     4.425886024
+]])
+# 3. make sure config is empty and not remnant from last test with broken dirs
+AT_DATA([test.conf], [])
+# 4. create the config and check it
+AT_CHECK([../../molecuilder -e elements.db -p test.xyz test.conf], 0, [ignore], [ignore])
+AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4       8.532785963     4.787886018     2.645886050     0 # Number in molecule 6
+], [ignore])
+AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
+# 5. fragment the molecule and check the number of configs
+AT_CHECK([../../molecuilder -e elements.db -f 1.55 2 A test.conf], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
+AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
+AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
+], [ignore])
+AT_CHECK([../../molecuilder -e elements.db -f 1.55 2 A test.conf], 0, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
+AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
+# 6. compare both dirs by diff'ing
+AT_CHECK([diff -I '.*Created by molecuilder.*' std/ new/], 0, [], [])
+AT_CLEANUP
 
-