source: tests/Fragmentations/testsuite.at@ ec7511

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 ec7511 was ec7511, checked in by Frederik Heber <heber@…>, 11 years ago

FIX: CyclicStructureAnalysis falsely used DFS, skipped some cycles.

  • FIX: CyclicStructureAnalysis did use DFS instead of BFS for finding cycles. Note that CyclicStructureAnalysis with coronene would find supercycles and not the smaller interconnected ones.
  • FIX: Cycles were skipped when all bonds marked cyclic, not enough. In interconnected aromatic rings, bonds may very well be marked as cyclic from earlier extraction of cycles and yet the specific cycle might not have been found yet (e.g. coronene). In this case we now check whether this particular cycle has already been extracted and only skip if so.
  • TESTFIX: added new fragmentation regression tests on some metallic systems.
  • this is mainly for regression on bond graph detection and cycle analysis.
  • Property mode set to 100644
File size: 11.1 KB
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1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2008-2012 University of Bonn
4#
5# This program is free software: you can redistribute it and/or modify
6# it under the terms of the GNU General Public License as published by
7# the Free Software Foundation, either version 3 of the License, or
8# (at your option) any later version.
9#
10# This program is distributed in the hope that it will be useful,
11# but WITHOUT ANY WARRANTY; without even the implied warranty of
12# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13# GNU General Public License for more details.
14#
15# You should have received a copy of the GNU General Public License
16# along with this program. If not, see <http://www.gnu.org/licenses/>.
17#
18#
19# MoleCuilder - creates and alters molecular systems
20# Copyright (C) 2008-2012 University of Bonn
21#
22# This program is free software: you can redistribute it and/or modify
23# it under the terms of the GNU General Public License as published by
24# the Free Software Foundation, either version 3 of the License, or
25# (at your option) any later version.
26#
27# This program is distributed in the hope that it will be useful,
28# but WITHOUT ANY WARRANTY; without even the implied warranty of
29# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
30# GNU General Public License for more details.
31#
32# You should have received a copy of the GNU General Public License
33# along with this program. If not, see <http://www.gnu.org/licenses/>.
34#
35# Process with auto#m4te to create an -*- Autotest -*- test suite.
36#
37# see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir.
38# In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.
39
40AT_INIT([Molecular Builder - Fragmentation])
41AT_TESTED(diff grep egrep fgrep)
42
43# Use colored output with new-enough Autotest.
44#m4_ifdef([AT_COLOR_TESTS], [AT_COLOR_TESTS])
45
46# fragmentation of 1_2-dimethoxyethane
47m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at)
48m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at)
49m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at)
50m4_include(Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at)
51
52# fragmentation of 1_2-dimethylbenzene
53m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at)
54m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at)
55m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at)
56m4_include(Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at)
57
58# fragmentation of 2-methylcyclohexanone
59m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at)
60m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at)
61m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at)
62m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at)
63
64# fragmentation of anthracene
65m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at)
66m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at)
67m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at)
68m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at)
69m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at)
70m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at)
71
72# fragmentation of benzene
73m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at)
74m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at)
75m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at)
76m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at)
77m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at)
78m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at)
79
80# fragmentation of cholesterol
81m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at)
82m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at)
83m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at)
84m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at)
85
86# fragmentation of coronene
87m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at)
88m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at)
89m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at)
90m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at)
91m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at)
92m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at)
93
94# fragmentation of cycloheptane
95m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at)
96m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at)
97m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at)
98m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at)
99m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at)
100m4_include(Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at)
101
102# fragmentation of dimethyl_bromomalonate
103m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at)
104m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at)
105m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at)
106m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at)
107m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at)
108m4_include(Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at)
109
110# fragmentation of glucose
111m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at)
112m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at)
113m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at)
114m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at)
115m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at)
116m4_include(Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at)
117
118# fragmentation of heptan
119m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at)
120m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at)
121m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at)
122m4_include(Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at)
123
124# fragmentation of isoleucine
125m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at)
126m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at)
127m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at)
128m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at)
129m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at)
130m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at)
131
132# fragmentation of naphthalene
133m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at)
134m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at)
135m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at)
136m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at)
137m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at)
138m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at)
139
140# fragmentation of neohexane
141m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at)
142m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at)
143m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at)
144m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at)
145m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at)
146m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at)
147
148# fragmentation of N_N-dimethylacetamide
149m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at)
150m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at)
151m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at)
152m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at)
153m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at)
154m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at)
155
156# fragmentation of phenanthrene
157m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at)
158m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at)
159m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at)
160m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at)
161m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at)
162m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at)
163
164# fragmentation of proline
165m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order1.at)
166m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order2.at)
167m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order3.at)
168m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order4.at)
169m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order5.at)
170m4_include(Fragmenting/proline/testsuite-fragmenting-proline-order6.at)
171
172# fragmentation of putrescine
173m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at)
174m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at)
175m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at)
176m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at)
177m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at)
178m4_include(Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at)
179
180# fragmentation of tartaric_acid
181m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at)
182m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at)
183m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at)
184m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at)
185m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at)
186m4_include(Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at)
187
188# Joining of heptan
189m4_include(Joining/heptan/testsuite-joining-heptan.at)
190
191# Analyzing of heptan
192m4_include(Analyzing/heptan/testsuite-analyzing-heptan.at)
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