source: tests/testsuite.at@ f37746

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
Last change on this file since f37746 was 4eb4fe, checked in by Frederik Heber <heber@…>, 15 years ago

"-e <db path>" not necessary anymore.

Removed necessity of specifying path to databases (this was one check of molecuilder/test/testsuite.at which cannot be fulfilled anymore with boost::program_options)
For this to work a great number of small changes have been necessary:

class periodentafel:

  • all .db files merged into const char * arrays in elements_db.cpp
  • periodentafel rewritten:
  • FindElement(), AskElement() and EnterElement return element * const instead of const element * (i.e. the contents of the pointer is const (the element) not the pointer itself which is very vexatious (i.e. FindElement() yields const element * which can subsequently not be used for RemoveElement(), ...)
  • parsedElems is not needed anymore. Instead we operate on map elements directly
  • new unittest periodentafelTest which is made friend of periodentafel to be able to access private loading functions directly

A number of unit tests had to be changed (all that create elements during setUp() which is now unnecessary)

Some of the analysis_bonds function's signatures were changed in the process:

Finally, the respective tests are removed from molecuilder/tests/testsuite.at.
  • Property mode set to 100755
File size: 11.0 KB
RevLine 
[f3cba6]1# Process with autom4te to create an -*- Autotest -*- test suite.
[ebcade]2#
3# see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir.
4# In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.
[f3cba6]5
6AT_INIT([Molecular Builder])
7
8# Checking if command line options are parsed correctly
9AT_BANNER([MoleCuilder - standard options])
10AT_SETUP([Standard Options])
[ebcade]11AT_KEYWORDS([options])
[f3cba6]12AT_CHECK([pwd],[ignore],[ignore])
13AT_CHECK([../../molecuilder -v], 0, [stdout], [ignore])
[482373]14AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
[f3cba6]15AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
16AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
[2a5eb7]17AT_CHECK([../../molecuilder -e], 134, [ignore], [stderr])
[f00693]18AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
[f3cba6]19AT_CLEANUP
20
[ebcade]21
[ab3a0e]22AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
[ebcade]23# 1. create some simplest molecular geometry
24AT_SETUP([Simple configuration - xyz file generation])
[2a5eb7]25AT_KEYWORDS([Atom handling])
[f3cba6]26AT_DATA([test.xyz], [[1
27 # test configuration, created by molecuilder test suite
28H 10. 10. 10.
29]])
[ebcade]30AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
31AT_CLEANUP
32
33# 2. parsing an xyz
34AT_SETUP([Simple configuration - parsing xyz file])
35AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/pre/test.xyz .], 0)
36AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
[c26f44]37AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
[f3cba6]38], [ignore])
[ebcade]39AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
40AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
41AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
42
43# 3. add atom
44AT_CLEANUP
45AT_SETUP([Simple configuration - adding atom])
46AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
47AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
48AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
49AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
50AT_CLEANUP
51
52# 4. change the element
53AT_SETUP([Simple configuration - Changing element])
54AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/pre/test.conf test.conf], 0)
55AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
56AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
57AT_CLEANUP
58
59# 5. remove atom
60AT_SETUP([Simple configuration - Atom removal])
61AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/pre/test.conf .], 0)
62AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
63AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
64AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
65AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
66AT_CLEANUP
67
68# 6. test some more configuration that all desire parameters and count how many complain
69AT_SETUP([Simple configuration - invalid commands on empty configs])
70AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
71AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
72], [ignore])
73AT_CLEANUP
74
75# 7. test some more configuration that all need parameters and count how many complain
76AT_SETUP([Simple configuration - invalid commands on present configs])
77AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/7/pre/test.conf .], 0)
[482373]78AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
79AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
80AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
81AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
82AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
83AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
84AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
85AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
86AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
87AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
88AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
89AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
90AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
91AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
92AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
93AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
94AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
95AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
96AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
97AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
[f3cba6]98AT_CLEANUP
99
[ebcade]100
101AT_BANNER([MoleCuilder - Graph routines test])
102AT_SETUP([Graph - DFS analysis])
[2a5eb7]103AT_KEYWORDS([graph])
[ebcade]104AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Graph/1/pre/test.conf .], 0)
[482373]105AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -vvv -D 2.], 0, [stdout], [stderr])
[ebcade]106AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
107], [ignore])
108AT_CLEANUP
109
[ab3a0e]110AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
[ebcade]111# 1. check config
112AT_SETUP([Fragmentation - Checking present config])
[2a5eb7]113AT_KEYWORDS([fragmentation])
[ebcade]114AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/1/pre/test.conf .], 0)
[c26f44]115AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
[3c1dfb]116], [ignore])
117AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
[ebcade]118AT_CLEANUP
119# 2. fragment the molecule and check the number of configs
120AT_SETUP([Fragmentation - Fragmentation])
121AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/2/pre/test.conf .], 0)
122AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
[3c1dfb]123AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
124AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
125], [ignore])
[ebcade]126AT_CLEANUP
127# 3. check whether parsing of BondFragment files and re-rwriting config files is working (exit code is 2 as we don't need to continue wrt to ...OrderAtSite)
128AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
129AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/3/pre/* .], 0)
130AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
[3c1dfb]131AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
132AT_CLEANUP
[f3cba6]133
[ebcade]134
135AT_BANNER([MoleCuilder - Tesselation test])
136# 1. Non convex tesselation
137AT_SETUP([Tesselation - Non-Convex Envelope])
[2a5eb7]138AT_KEYWORDS([Tesselation])
[ebcade]139AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/pre/* .], 0)
140AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
141AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
142AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
143AT_CLEANUP
144
145# 2. convex tesselation (where the non-convex is already convex)
146AT_SETUP([Tesselation - Convex Envelope])
147AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/pre/* .], 0)
148AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
149AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
150AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
[482373]151AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
[ebcade]152AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
153AT_CLEANUP
154
155# 3. Big Non convex tesselation
156AT_SETUP([Tesselation - Big non-Convex Envelope])
157AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/pre/* .], 0)
158AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
159AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
160AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
161AT_CLEANUP
162
163# 4. Big convex tesselation - is not working yet
164#AT_SETUP([Tesselation - big convex Envelope])
165#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/pre/* .], 0)
166#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
167#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
168#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
[482373]169#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
[ebcade]170#AT_CLEANUP
171
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