source: tests/regression/testsuite.at@ 403637

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 Candidate_v1.7.0 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 403637 was 403637, checked in by Frederik Heber <heber@…>, 15 years ago

Added case '-g' (load bond table) to testsuite.
  • Property mode set to 100755
File size: 13.6 KB
Line 
1# Process with autom4te to create an -*- Autotest -*- test suite.
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.
5
6AT_INIT([Molecular Builder])
7
8
9AT_BANNER([MoleCuilder - standard options])
10# 1. verbosity
11AT_SETUP([Standard Options - verbosity])
12AT_KEYWORDS([options])
13AT_CHECK([pwd],[ignore],[ignore])
14AT_CHECK([../../molecuilder -v 1], 0, [stdout], [ignore])
15AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
16AT_CLEANUP
17
18# 2. help screen
19AT_SETUP([Standard Options - help screen])
20AT_KEYWORDS([options])
21AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
22AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
23AT_CLEANUP
24
25# 3. no element database
26AT_SETUP([Standard Options - no element database])
27AT_KEYWORDS([options])
28AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
29AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
30AT_CLEANUP
31
32# 4. element database
33AT_SETUP([Standard Options - element database])
34AT_KEYWORDS([options])
35AT_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
36#Element Name Symbol Period Group Block Atomic Number AtomicWeight Covalent Radius vdW Radius
37Hydrogen H 1 1 s 1 1.008 0.23 1.09
38Helium He 1 18 p 2 4.003 1.5 1.4
39]])
40AT_CHECK([../../molecuilder test.conf -e ./], 0, [stdout], [stderr])
41AT_CHECK([grep -E "Using.*as elements database." stdout], 0, [ignore], [ignore])
42AT_CHECK([fgrep "Element list loaded successfully." stdout], 0, [ignore], [ignore])
43AT_CHECK([fgrep "Something went wrong while parsing the other databases!" stderr], 0, [ignore], [ignore])
44AT_CLEANUP
45
46# 5. bond length database
47AT_SETUP([Standard Options - bond length table])
48AT_KEYWORDS([options])
49AT_DATA([bondlength.db], [[# bond length database
50 1 2
511 1. 0.
522 0. 0.
53]])
54AT_CHECK([../../molecuilder test.conf -g bondlength.db], 0, [stdout], [stderr])
55AT_CHECK([grep -E "Using.*as bond length table." stdout], 0, [ignore], [ignore])
56AT_CLEANUP
57
58
59AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
60# 1. create some simplest molecular geometry
61AT_SETUP([Simple configuration - xyz file generation])
62AT_KEYWORDS([Atom handling])
63AT_DATA([test.xyz], [[1
64 # test configuration, created by molecuilder test suite
65H 10. 10. 10.
66]])
67AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
68AT_CLEANUP
69
70# 2. parsing an xyz
71AT_SETUP([Simple configuration - parsing xyz file])
72AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
73AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
74AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
75], [ignore])
76AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
77AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
78AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
79
80# 3. add atom
81AT_CLEANUP
82AT_SETUP([Simple configuration - adding atom])
83AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
84AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
85AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
86AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
87AT_CLEANUP
88
89# 4. change the element
90AT_SETUP([Simple configuration - Changing element])
91AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
92AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
93AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
94AT_CLEANUP
95
96# 5. remove atom
97AT_SETUP([Simple configuration - Atom removal])
98AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
99AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
100AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
101AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
102AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
103AT_CLEANUP
104
105# 6. test some more configuration that all desire parameters and count how many complain
106AT_SETUP([Simple configuration - invalid commands on empty configs])
107AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
108AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
109], [ignore])
110AT_CLEANUP
111
112# 7. test some more configuration that all need parameters and count how many complain
113AT_SETUP([Simple configuration - invalid commands on present configs])
114AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
115AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
116AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
117AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
118AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
119AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
120AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
121AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
122AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
123AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
124AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
125AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
126AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
127AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
128AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
129AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
130AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
131AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
132AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
133AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
134AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
135AT_CLEANUP
136
137
138AT_BANNER([MoleCuilder - simulation domain])
139# 1. define box setting
140AT_SETUP([Domain - defining simulation domain])
141AT_KEYWORDS([defining domain])
142AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
143AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
144AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
145AT_CLEANUP
146
147# 2. center atoms in defined domain
148AT_SETUP([Domain - setting and centering in domain])
149AT_KEYWORDS([setting domain])
150AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/pre/test.conf .], 0)
151AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b 15 0 15 0 0 15], 0, [stdout], [stderr])
152AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/post/test.conf], 0, [stdout], [stderr])
153AT_CLEANUP
154
155# 3. center atoms with defined boundary
156AT_SETUP([Domain - centering with defined boundary])
157AT_KEYWORDS([setting domain])
158AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/pre/test.conf .], 0)
159AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c 5 10 15], 0, [stdout], [stderr])
160AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/post/test.conf], 0, [stdout], [stderr])
161AT_CLEANUP
162
163# 4. center atoms and adjusting boundary
164AT_SETUP([Domain - centering and setting domain])
165AT_KEYWORDS([setting domain])
166AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/pre/test.conf .], 0)
167AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -O], 0, [stdout], [stderr])
168AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/post/test.conf], 0, [stdout], [stderr])
169AT_CLEANUP
170
171
172AT_BANNER([MoleCuilder - Graph routines test])
173AT_SETUP([Graph - DFS analysis])
174AT_KEYWORDS([graph])
175AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/1/pre/test.conf .], 0)
176AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
177AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
178], [ignore])
179AT_CLEANUP
180
181AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
182# 1. check config
183AT_SETUP([Fragmentation - Checking present config])
184AT_KEYWORDS([fragmentation])
185AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
186AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
187], [ignore])
188AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
189AT_CLEANUP
190# 2. fragment the molecule and check the number of configs
191AT_SETUP([Fragmentation - Fragmentation])
192AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
193AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
194AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
195AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
196], [ignore])
197AT_CLEANUP
198# 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)
199AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
200AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/* .], 0)
201AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
202AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
203AT_CLEANUP
204
205
206AT_BANNER([MoleCuilder - Tesselation test])
207# 1. Non convex tesselation
208AT_SETUP([Tesselation - Non-Convex Envelope])
209AT_KEYWORDS([Tesselation])
210AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
211AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
212AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
213AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
214AT_CLEANUP
215
216# 2. convex tesselation (where the non-convex is already convex)
217AT_SETUP([Tesselation - Convex Envelope])
218AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
219AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
220AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
221AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
222AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
223AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
224AT_CLEANUP
225
226# 3. Big Non convex tesselation
227AT_SETUP([Tesselation - Big non-Convex Envelope])
228AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
229AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
230AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
231AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
232AT_CLEANUP
233
234# 4. Big convex tesselation - is not working yet
235#AT_SETUP([Tesselation - big convex Envelope])
236#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
237#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
238#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
239#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
240#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
241#AT_CLEANUP
242
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