source: tests/regression/testsuite.at@ 8048a4

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 8048a4 was 8048a4, checked in by Frederik Heber <heber@…>, 15 years ago

Added case '-s' (scaling box) to testsuite.
  • Property mode set to 100755
File size: 22.5 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# 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
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
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
81
82AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
83# 1. create some simplest molecular geometry
84AT_SETUP([Simple configuration - xyz file generation])
85AT_KEYWORDS([Atom handling])
86AT_DATA([test.xyz], [[1
87 # test configuration, created by molecuilder test suite
88H 10. 10. 10.
89]])
90AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
91AT_CLEANUP
92
93# 2. parsing an xyz
94AT_SETUP([Simple configuration - parsing xyz file])
95AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
96AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
97AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
98], [ignore])
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])
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])
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])
110AT_CLEANUP
111
112# 4. change the element
113AT_SETUP([Simple configuration - Changing element])
114AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
115AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
116AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
117AT_CLEANUP
118
119# 5. remove atom
120AT_SETUP([Simple configuration - Atom removal])
121AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
122AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
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])
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])
137AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
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])
158AT_CLEANUP
159
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
168
169AT_BANNER([MoleCuilder - simulation domain])
170# 1. define box setting
171AT_SETUP([Domain - defining simulation domain])
172AT_KEYWORDS([domain])
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])
175AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
176AT_CLEANUP
177
178# 2. center atoms in defined domain
179AT_SETUP([Domain - setting and centering in domain])
180AT_KEYWORDS([domain])
181AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/pre/test.conf .], 0)
182AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b 15 0 15 0 0 15], 0, [stdout], [stderr])
183AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/post/test.conf], 0, [stdout], [stderr])
184AT_CLEANUP
185
186# 3. center atoms with defined boundary
187AT_SETUP([Domain - centering with defined boundary])
188AT_KEYWORDS([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
194# 4. center atoms and adjusting boundary
195AT_SETUP([Domain - centering and setting domain])
196AT_KEYWORDS([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
202# 5. scaling box
203AT_SETUP([Domain - scaling box])
204AT_KEYWORDS([domain])
205AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/5/pre/test.conf .], 0)
206AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s 0.5 1. 0.9], 0, [stdout], [stderr])
207AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/5/post/test.conf], 0, [stdout], [stderr])
208AT_CLEANUP
209
210
211AT_BANNER([MoleCuilder - Graph routines test])
212# 1. DFS analysis
213AT_SETUP([Graph - DFS analysis])
214AT_KEYWORDS([graph])
215AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/1/pre/test.conf .], 0)
216AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
217AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
218], [ignore])
219AT_CLEANUP
220
221AT_SETUP([Graph - subgraph dissection])
222AT_KEYWORDS([graph])
223AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/2/pre/test.conf .], 0)
224AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -I], 0, [stdout], [stderr])
225AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
226AT_CLEANUP
227
228
229AT_BANNER([MoleCuilder - Molecules])
230# 1. Bonds from file
231AT_SETUP([Graph - Bonds from file])
232AT_KEYWORDS([Molecules])
233AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/1/pre/test.* .], 0)
234AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 4 -A test.dbond], 0, [stdout], [stderr])
235AT_CHECK([fgrep "Looking for atoms 2 and 9." stdout], 0, [ignore], [ignore])
236AT_CLEANUP
237
238# 2. Storing adjacency info
239AT_SETUP([Molecules - Storing bond info])
240AT_KEYWORDS([Molecules])
241AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/pre/test.conf .], 0)
242AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -j test.dbond], 0, [stdout], [stderr])
243AT_CHECK([file=test.dbond; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
244AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -J test.adj], 0, [stdout], [stderr])
245AT_CHECK([file=test.adj; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
246AT_CLEANUP
247
248# 3. Storing temperature
249AT_SETUP([Molecules - Storing temperature])
250AT_KEYWORDS([Molecules])
251AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/pre/test.conf .], 0)
252AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -S test.ekin], 0, [stdout], [stderr])
253AT_CHECK([file=test.ekin; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/post/$file], 0, [ignore], [ignore])
254AT_CLEANUP
255
256# 4. linear interpolation
257AT_SETUP([Molecules - BROKEN: Linear interpolation])
258AT_KEYWORDS([Molecules])
259AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/4/pre/test.conf .], 0)
260AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -L 0 1 teststep 1], 0, [stdout], [stderr])
261AT_CLEANUP
262
263# 5. Verlet force integration
264AT_SETUP([Molecules - BROKEN: Verlet force integration])
265AT_KEYWORDS([Molecules])
266AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/pre/test.* .], 0)
267AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -P test.forces], 134, [stdout], [stderr])
268#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/post/$file], 0, [ignore], [ignore])
269AT_CLEANUP
270
271# 6. Translation
272AT_SETUP([Molecules - Translation])
273AT_KEYWORDS([Molecules])
274AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/pre/test.* .], 0)
275AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t 1. 1. 1.], 0, [stdout], [stderr])
276AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/post/$file], 0, [ignore], [ignore])
277AT_CLEANUP
278
279# 6. Periodic translation
280AT_SETUP([Molecules - Periodic translation])
281AT_KEYWORDS([Molecules])
282AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/pre/test.* .], 0)
283AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T 12. 12. 12.], 0, [stdout], [stderr])
284AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/post/$file], 0, [ignore], [ignore])
285AT_CLEANUP
286
287
288AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
289# 1. check config
290AT_SETUP([Fragmentation - Checking present config])
291AT_KEYWORDS([fragmentation])
292AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
293AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
294], [ignore])
295AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
296AT_CLEANUP
297
298# 2. fragment the molecule and check the number of configs
299AT_SETUP([Fragmentation - Fragmentation])
300AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
301AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
302AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
303AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
304], [ignore])
305AT_CLEANUP
306
307# 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)
308AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
309AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/* .], 0)
310AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
311AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
312AT_CLEANUP
313
314
315AT_BANNER([MoleCuilder - Tesselation test])
316# 1. Non convex tesselation
317AT_SETUP([Tesselation - Non-Convex Envelope])
318AT_KEYWORDS([Tesselation])
319AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
320AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
321AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
322AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
323AT_CLEANUP
324
325# 2. convex tesselation (where the non-convex is already convex)
326AT_SETUP([Tesselation - Convex Envelope])
327AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
328AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
329AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
330AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
331AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
332AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
333AT_CLEANUP
334
335# 3. Big Non convex tesselation
336AT_SETUP([Tesselation - Big non-Convex Envelope])
337AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
338AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
339AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
340AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
341AT_CLEANUP
342
343# 4. Big convex tesselation - is not working yet
344#AT_SETUP([Tesselation - big convex Envelope])
345#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
346#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
347#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
348#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
349#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
350#AT_CLEANUP
351
352
353AT_BANNER([MoleCuilder - Filling in molecules])
354# 1. filling box
355AT_SETUP([Analysis - filling empty box])
356AT_KEYWORDS([analysis])
357AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/pre/test.conf .], 0)
358AT_DATA([water.xyz], [[3
359 # test configuration, created by molecuilder test suite
360O 0. 0. 0.
361H 0.758602 0. 0.504284
362H 0.758602 0. -0.504284
363]])
364AT_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])
365AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/post/$file], 0, [ignore], [ignore])
366AT_CLEANUP
367
368
369AT_BANNER([MoleCuilder - Analysis])
370# 1. pair correlation analysis
371AT_SETUP([Analysis - pair correlation])
372AT_KEYWORDS([analysis])
373AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/pre/test.conf .], 0)
374AT_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])
375AT_CHECK([fgrep "Begin of PairCorrelation" stdout], 0, [ignore], [ignore])
376AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
377AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
378AT_CLEANUP
379
380# 2. pair correlation analysis - range test
381AT_SETUP([Analysis - pair correlation range test])
382AT_KEYWORDS([analysis])
383AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/pre/test.conf .], 0)
384AT_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])
385AT_CHECK([file=output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
386AT_CHECK([file=bin_output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
387AT_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])
388AT_CHECK([file=output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
389AT_CHECK([file=bin_output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
390AT_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])
391AT_CHECK([file=output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
392AT_CHECK([file=bin_output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
393AT_CLEANUP
394
395# 3. pair correlation analysis to point
396AT_SETUP([Analysis - point correlation])
397AT_KEYWORDS([analysis])
398AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/pre/test.conf .], 0)
399AT_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])
400AT_CHECK([fgrep "Begin of CorrelationToPoint" stdout], 0, [ignore], [ignore])
401AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
402AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
403AT_CLEANUP
404
405# 4. pair correlation analysis to surface
406AT_SETUP([Analysis - surface correlation])
407AT_KEYWORDS([analysis])
408AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/pre/test.conf .], 0)
409AT_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])
410AT_CHECK([fgrep "Begin of CorrelationToSurface" stdout], 0, [ignore], [ignore])
411AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
412AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
413AT_CLEANUP
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