source: tests/regression/testsuite.at@ 9b7db1

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 9b7db1 was 9b7db1, checked in by Frederik Heber <heber@…>, 16 years ago

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

  • basically works, but molecuilder crashes with SIGABT when destroying world.
  • Property mode set to 100755
File size: 21.3 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
[a97f55]8
[f3cba6]9AT_BANNER([MoleCuilder - standard options])
[a97f55]10# 1. verbosity
11AT_SETUP([Standard Options - verbosity])
[ebcade]12AT_KEYWORDS([options])
[f3cba6]13AT_CHECK([pwd],[ignore],[ignore])
[6670a97]14AT_CHECK([../../molecuilder -v 1], 0, [stdout], [ignore])
[482373]15AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
[a97f55]16AT_CLEANUP
17
18# 2. help screen
19AT_SETUP([Standard Options - help screen])
20AT_KEYWORDS([options])
[f3cba6]21AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
22AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
[a97f55]23AT_CLEANUP
24
[2f0c42]25# 3. no element database
26AT_SETUP([Standard Options - no element database])
[a97f55]27AT_KEYWORDS([options])
[60f50a]28AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
[f00693]29AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
[f3cba6]30AT_CLEANUP
31
[2f0c42]32# 4. element database
33AT_SETUP([Standard Options - element database])
34AT_KEYWORDS([options])
[ff73a2]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
[2f0c42]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]])
[ff73a2]40AT_CHECK([../../molecuilder test.conf -e ./], 0, [stdout], [stderr])
[2f0c42]41AT_CHECK([grep -E "Using.*as elements database." stdout], 0, [ignore], [ignore])
[ff73a2]42AT_CHECK([fgrep "Element list loaded successfully." stdout], 0, [ignore], [ignore])
[2f0c42]43AT_CHECK([fgrep "Something went wrong while parsing the other databases!" stderr], 0, [ignore], [ignore])
44AT_CLEANUP
45
[403637]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
[e8e48ab]58# 6. fast trajectories
59AT_SETUP([Standard Options - fast trajectories])
60AT_KEYWORDS([options])
61AT_CHECK([../../molecuilder test.conf -n], 0, [stdout], [stderr])
62AT_CHECK([fgrep "I won't parse trajectories" stdout], 0, [ignore], [ignore])
63AT_CLEANUP
64
[93d732b]65# 7. molecule default name
66AT_SETUP([Standard Options - molecule default name])
67AT_KEYWORDS([options])
68AT_CHECK([../../molecuilder test.conf -X test], 0, [stdout], [stderr])
69AT_CHECK([fgrep "Default name of new molecules set to test." stdout], 0, [ignore], [ignore])
70AT_CLEANUP
71
[5188f5]72AT_BANNER([MoleCuilder - Specifics])
73# 1. MPQC basis
74AT_SETUP([Specifics - MPQC basis])
75AT_KEYWORDS([options])
76AT_CHECK([pwd],[ignore],[ignore])
77AT_CHECK([../../molecuilder test.conf -v 1 -M test], 0, [stdout], [ignore])
78AT_CHECK([fgrep "Setting MPQC basis to test." stdout], 0, [ignore], [ignore])
79AT_CLEANUP
80
[ebcade]81
[ab3a0e]82AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
[ebcade]83# 1. create some simplest molecular geometry
84AT_SETUP([Simple configuration - xyz file generation])
[2a5eb7]85AT_KEYWORDS([Atom handling])
[f3cba6]86AT_DATA([test.xyz], [[1
87 # test configuration, created by molecuilder test suite
88H 10. 10. 10.
89]])
[b2b47f]90AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
[ebcade]91AT_CLEANUP
92
93# 2. parsing an xyz
94AT_SETUP([Simple configuration - parsing xyz file])
[b2b47f]95AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
[ebcade]96AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
[c26f44]97AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
[f3cba6]98], [ignore])
[b2b47f]99AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
100AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
101AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
[ebcade]102
103# 3. add atom
104AT_CLEANUP
105AT_SETUP([Simple configuration - adding atom])
106AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
[b2b47f]107AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
108AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
109AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
[ebcade]110AT_CLEANUP
111
112# 4. change the element
113AT_SETUP([Simple configuration - Changing element])
[b2b47f]114AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
[ebcade]115AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
[b2b47f]116AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
[ebcade]117AT_CLEANUP
118
119# 5. remove atom
120AT_SETUP([Simple configuration - Atom removal])
[b2b47f]121AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
[ebcade]122AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
[b2b47f]123AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
124AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
125AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
[ebcade]126AT_CLEANUP
127
128# 6. test some more configuration that all desire parameters and count how many complain
129AT_SETUP([Simple configuration - invalid commands on empty configs])
130AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
131AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
132], [ignore])
133AT_CLEANUP
134
135# 7. test some more configuration that all need parameters and count how many complain
136AT_SETUP([Simple configuration - invalid commands on present configs])
[b2b47f]137AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
[482373]138AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
139AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
140AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
141AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
142AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
143AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
144AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
145AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
146AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
147AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
148AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
149AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
150AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
151AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
152AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
153AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
154AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
155AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
156AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
157AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
[f3cba6]158AT_CLEANUP
159
[9b7db1]160# 8. Removing sphere of atoms
161AT_SETUP([Molecules - BROKEN: Removing sphere of atoms])
162AT_KEYWORDS([Molecules])
163AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
164AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -R 2 7.], 134, [stdout], [stderr])
165AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
166AT_CLEANUP
167
[ebcade]168
[e3989a]169AT_BANNER([MoleCuilder - simulation domain])
170# 1. define box setting
[c82720]171AT_SETUP([Domain - defining simulation domain])
[e3989a]172AT_KEYWORDS([defining domain])
[c82720]173AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
174AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
[b2b47f]175AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
[c82720]176AT_CLEANUP
177
[e3989a]178# 2. center atoms in defined domain
179AT_SETUP([Domain - setting and centering in domain])
180AT_KEYWORDS([setting domain])
[b2b47f]181AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/pre/test.conf .], 0)
[e3989a]182AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b 15 0 15 0 0 15], 0, [stdout], [stderr])
[b2b47f]183AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/post/test.conf], 0, [stdout], [stderr])
[e3989a]184AT_CLEANUP
[c82720]185
[0335a2]186# 3. center atoms with defined boundary
187AT_SETUP([Domain - centering with defined boundary])
188AT_KEYWORDS([setting domain])
189AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/pre/test.conf .], 0)
190AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c 5 10 15], 0, [stdout], [stderr])
191AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/post/test.conf], 0, [stdout], [stderr])
192AT_CLEANUP
193
[745874]194# 4. center atoms and adjusting boundary
195AT_SETUP([Domain - centering and setting domain])
196AT_KEYWORDS([setting domain])
197AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/pre/test.conf .], 0)
198AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -O], 0, [stdout], [stderr])
199AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/post/test.conf], 0, [stdout], [stderr])
200AT_CLEANUP
201
[0335a2]202
[ebcade]203AT_BANNER([MoleCuilder - Graph routines test])
[046a1e]204# 1. DFS analysis
[ebcade]205AT_SETUP([Graph - DFS analysis])
[2a5eb7]206AT_KEYWORDS([graph])
[b2b47f]207AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/1/pre/test.conf .], 0)
[6670a97]208AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
[ebcade]209AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
210], [ignore])
211AT_CLEANUP
212
[046a1e]213AT_SETUP([Graph - subgraph dissection])
214AT_KEYWORDS([graph])
215AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/2/pre/test.conf .], 0)
216AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -I], 0, [stdout], [stderr])
217AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
218AT_CLEANUP
219
220
[c68c90]221AT_BANNER([MoleCuilder - Molecules])
222# 1. Bonds from file
223AT_SETUP([Graph - Bonds from file])
[13bfeb]224AT_KEYWORDS([Molecules])
[c68c90]225AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/1/pre/test.* .], 0)
226AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 4 -A test.dbond], 0, [stdout], [stderr])
227AT_CHECK([fgrep "Looking for atoms 2 and 9." stdout], 0, [ignore], [ignore])
228AT_CLEANUP
229
[72e36f]230# 2. Storing adjacency info
[9b7db1]231AT_SETUP([Molecules - Storing bond info])
[13bfeb]232AT_KEYWORDS([Molecules])
233AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/pre/test.conf .], 0)
[72e36f]234AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -j test.dbond], 0, [stdout], [stderr])
235AT_CHECK([file=test.dbond; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
236AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -J test.adj], 0, [stdout], [stderr])
237AT_CHECK([file=test.adj; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
238AT_CLEANUP
239
[13bfeb]240# 3. Storing temperature
[9b7db1]241AT_SETUP([Molecules - Storing temperature])
[13bfeb]242AT_KEYWORDS([Molecules])
243AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/pre/test.conf .], 0)
244AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -S test.ekin], 0, [stdout], [stderr])
245AT_CHECK([file=test.ekin; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/post/$file], 0, [ignore], [ignore])
246AT_CLEANUP
247
[f8f14d]248# 4. linear interpolation
[9b7db1]249AT_SETUP([Molecules - BROKEN: Linear interpolation])
[f8f14d]250AT_KEYWORDS([Molecules])
251AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/4/pre/test.conf .], 0)
252AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -L 0 1 teststep 1], 0, [stdout], [stderr])
253AT_CLEANUP
254
[c7a473]255# 5. Verlet force integration
[9b7db1]256AT_SETUP([Molecules - BROKEN: Verlet force integration])
[c7a473]257AT_KEYWORDS([Molecules])
258AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/pre/test.* .], 0)
259AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -P test.forces], 134, [stdout], [stderr])
260#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/post/$file], 0, [ignore], [ignore])
261AT_CLEANUP
262
[ab3a0e]263AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
[ebcade]264# 1. check config
265AT_SETUP([Fragmentation - Checking present config])
[2a5eb7]266AT_KEYWORDS([fragmentation])
[b2b47f]267AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
[c26f44]268AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
[3c1dfb]269], [ignore])
270AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
[ebcade]271AT_CLEANUP
[06f8ee]272
[ebcade]273# 2. fragment the molecule and check the number of configs
274AT_SETUP([Fragmentation - Fragmentation])
[b2b47f]275AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
[ebcade]276AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
[3c1dfb]277AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
278AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
279], [ignore])
[ebcade]280AT_CLEANUP
[06f8ee]281
[ebcade]282# 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)
283AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
[b2b47f]284AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/* .], 0)
[ebcade]285AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
[3c1dfb]286AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
287AT_CLEANUP
[f3cba6]288
[ebcade]289
290AT_BANNER([MoleCuilder - Tesselation test])
291# 1. Non convex tesselation
292AT_SETUP([Tesselation - Non-Convex Envelope])
[2a5eb7]293AT_KEYWORDS([Tesselation])
[b2b47f]294AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
[ebcade]295AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
[b2b47f]296AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
297AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
[ebcade]298AT_CLEANUP
299
300# 2. convex tesselation (where the non-convex is already convex)
301AT_SETUP([Tesselation - Convex Envelope])
[b2b47f]302AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
[ebcade]303AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
[b2b47f]304AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
305AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
[482373]306AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
[ebcade]307AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
308AT_CLEANUP
309
310# 3. Big Non convex tesselation
311AT_SETUP([Tesselation - Big non-Convex Envelope])
[b2b47f]312AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
[ebcade]313AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
[b2b47f]314AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
315AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
[ebcade]316AT_CLEANUP
317
318# 4. Big convex tesselation - is not working yet
319#AT_SETUP([Tesselation - big convex Envelope])
[b2b47f]320#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
[ebcade]321#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
[b2b47f]322#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
323#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
[482373]324#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
[ebcade]325#AT_CLEANUP
326
[06f8ee]327
[1325ba]328AT_BANNER([MoleCuilder - Filling in molecules])
329# 1. filling box
330AT_SETUP([Analysis - filling empty box])
331AT_KEYWORDS([analysis])
332AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/pre/test.conf .], 0)
333AT_DATA([water.xyz], [[3
334 # test configuration, created by molecuilder test suite
335O 0. 0. 0.
336H 0.758602 0. 0.504284
337H 0.758602 0. -0.504284
338]])
339AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -F water.xyz 3.1 3.1 3.1 2.1 0. 0. 0], 0, [stdout], [stderr])
340AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/post/$file], 0, [ignore], [ignore])
341AT_CLEANUP
342
343
[06f8ee]344AT_BANNER([MoleCuilder - Analysis])
345# 1. pair correlation analysis
346AT_SETUP([Analysis - pair correlation])
347AT_KEYWORDS([analysis])
348AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/pre/test.conf .], 0)
349AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output.csv bin_output.csv 0 20], 0, [stdout], [stderr])
350AT_CHECK([fgrep "Begin of PairCorrelation" stdout], 0, [ignore], [ignore])
351AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
352AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
353AT_CLEANUP
354
[08f6ff]355# 2. pair correlation analysis - range test
[06f8ee]356AT_SETUP([Analysis - pair correlation range test])
357AT_KEYWORDS([analysis])
358AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/pre/test.conf .], 0)
359AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output-5.csv bin_output-5.csv 0 5], 0, [stdout], [stderr])
360AT_CHECK([file=output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
361AT_CHECK([file=bin_output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
362AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output-10.csv bin_output-10.csv 5 10], 0, [stdout], [stderr])
363AT_CHECK([file=output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
364AT_CHECK([file=bin_output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
365AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output-20.csv bin_output-20.csv 10 20], 0, [stdout], [stderr])
366AT_CHECK([file=output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
367AT_CHECK([file=bin_output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
368AT_CLEANUP
[08f6ff]369
370# 3. pair correlation analysis to point
[ef2b39]371AT_SETUP([Analysis - point correlation])
[08f6ff]372AT_KEYWORDS([analysis])
373AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/pre/test.conf .], 0)
374AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C P 1 10. 10. 10. output.csv bin_output.csv 0 20], 0, [stdout], [stderr])
375AT_CHECK([fgrep "Begin of CorrelationToPoint" stdout], 0, [ignore], [ignore])
376AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
377AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
378AT_CLEANUP
[ef2b39]379
380# 4. pair correlation analysis to surface
381AT_SETUP([Analysis - surface correlation])
382AT_KEYWORDS([analysis])
383AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/pre/test.conf .], 0)
384AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -I -C S 1 output.csv bin_output.csv 1. 0 20], 0, [stdout], [stderr])
385AT_CHECK([fgrep "Begin of CorrelationToSurface" stdout], 0, [ignore], [ignore])
386AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
387AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
388AT_CLEANUP
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