source: tests/regression/testsuite.at@ 2f0c42

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 2f0c42 was 2f0c42, checked in by Frederik Heber <heber@…>, 15 years ago

Added test for parsing specified element database to testsuite.
  • Property mode set to 100755
File size: 13.2 KB
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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([test.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 test.db], 0, [stdout], [stderr])
41AT_CHECK([grep -E "Using.*as elements database." stdout], 0, [ignore], [ignore])
42AT_CHECK([fgrep "Something went wrong while parsing the other databases!" stderr], 0, [ignore], [ignore])
43AT_CLEANUP
44
45
46AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
47# 1. create some simplest molecular geometry
48AT_SETUP([Simple configuration - xyz file generation])
49AT_KEYWORDS([Atom handling])
50AT_DATA([test.xyz], [[1
51 # test configuration, created by molecuilder test suite
52H 10. 10. 10.
53]])
54AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
55AT_CLEANUP
56
57# 2. parsing an xyz
58AT_SETUP([Simple configuration - parsing xyz file])
59AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
60AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
61AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
62], [ignore])
63AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
64AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
65AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
66
67# 3. add atom
68AT_CLEANUP
69AT_SETUP([Simple configuration - adding atom])
70AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
71AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
72AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
73AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
74AT_CLEANUP
75
76# 4. change the element
77AT_SETUP([Simple configuration - Changing element])
78AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
79AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
80AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
81AT_CLEANUP
82
83# 5. remove atom
84AT_SETUP([Simple configuration - Atom removal])
85AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
86AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
87AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
88AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
89AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
90AT_CLEANUP
91
92# 6. test some more configuration that all desire parameters and count how many complain
93AT_SETUP([Simple configuration - invalid commands on empty configs])
94AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
95AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
96], [ignore])
97AT_CLEANUP
98
99# 7. test some more configuration that all need parameters and count how many complain
100AT_SETUP([Simple configuration - invalid commands on present configs])
101AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
102AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
103AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
104AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
105AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
106AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
107AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
108AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
109AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
110AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
111AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
112AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
113AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
114AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
115AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
116AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
117AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
118AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
119AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
120AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
121AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
122AT_CLEANUP
123
124
125AT_BANNER([MoleCuilder - simulation domain])
126# 1. define box setting
127AT_SETUP([Domain - defining simulation domain])
128AT_KEYWORDS([defining domain])
129AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
130AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
131AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
132AT_CLEANUP
133
134# 2. center atoms in defined domain
135AT_SETUP([Domain - setting and centering in domain])
136AT_KEYWORDS([setting domain])
137AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/pre/test.conf .], 0)
138AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b 15 0 15 0 0 15], 0, [stdout], [stderr])
139AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/post/test.conf], 0, [stdout], [stderr])
140AT_CLEANUP
141
142# 3. center atoms with defined boundary
143AT_SETUP([Domain - centering with defined boundary])
144AT_KEYWORDS([setting domain])
145AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/pre/test.conf .], 0)
146AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c 5 10 15], 0, [stdout], [stderr])
147AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/post/test.conf], 0, [stdout], [stderr])
148AT_CLEANUP
149
150# 4. center atoms and adjusting boundary
151AT_SETUP([Domain - centering and setting domain])
152AT_KEYWORDS([setting domain])
153AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/pre/test.conf .], 0)
154AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -O], 0, [stdout], [stderr])
155AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/post/test.conf], 0, [stdout], [stderr])
156AT_CLEANUP
157
158
159AT_BANNER([MoleCuilder - Graph routines test])
160AT_SETUP([Graph - DFS analysis])
161AT_KEYWORDS([graph])
162AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/1/pre/test.conf .], 0)
163AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
164AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
165], [ignore])
166AT_CLEANUP
167
168AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
169# 1. check config
170AT_SETUP([Fragmentation - Checking present config])
171AT_KEYWORDS([fragmentation])
172AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
173AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
174], [ignore])
175AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
176AT_CLEANUP
177# 2. fragment the molecule and check the number of configs
178AT_SETUP([Fragmentation - Fragmentation])
179AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
180AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
181AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
182AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
183], [ignore])
184AT_CLEANUP
185# 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)
186AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
187AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/* .], 0)
188AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
189AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
190AT_CLEANUP
191
192
193AT_BANNER([MoleCuilder - Tesselation test])
194# 1. Non convex tesselation
195AT_SETUP([Tesselation - Non-Convex Envelope])
196AT_KEYWORDS([Tesselation])
197AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
198AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
199AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
200AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
201AT_CLEANUP
202
203# 2. convex tesselation (where the non-convex is already convex)
204AT_SETUP([Tesselation - Convex Envelope])
205AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
206AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
207AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
208AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
209AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
210AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
211AT_CLEANUP
212
213# 3. Big Non convex tesselation
214AT_SETUP([Tesselation - Big non-Convex Envelope])
215AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
216AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
217AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
218AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
219AT_CLEANUP
220
221# 4. Big convex tesselation - is not working yet
222#AT_SETUP([Tesselation - big convex Envelope])
223#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
224#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
225#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
226#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
227#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
228#AT_CLEANUP
229
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