source: tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at@ 45f4b6b

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator 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_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion GeometryObjects Gui_displays_atomic_force_velocity IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks RotateToPrincipalAxisSystem_UndoRedo StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps Ubuntu_1604_changes stable
Last change on this file since 45f4b6b was ff7ac6, checked in by Frederik Heber <heber@…>, 9 years ago

BREAKS: Summation and OrthogonalSummation both now allow to set a specific "ZeroInstance".

  • this replaces then the default ZeroInstance<T> used and may be used to enforce specific parameters in the summation, e.g. a smaller grid when summing SamplingGrid.
  • Note that this breaks all long-range results for the moment. The reason is that so far the ZeroInstance was effectively the first result/contribution upon which all others were summed. This worked because each fragment used the same grid size, namely the one of the global grid. With the independent fragment grids this will no longer be possible, which is why we introduce the possibility to set a specific ZeroInstance, i.e. providing the global grid to sum onto externally.
  • to be absolutely precise: The reasons why the tests break is that the little change in ::Sum(): sum =.. -> sum +=..
  • TESTS: Setting regression tests AnalyseFragmentResults to failed.
  • Property mode set to 100644
File size: 11.3 KB
Line 
1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2013 University of Bonn
4# Copyright (C) 2013 Frederik Heber
5#
6# This program is free software: you can redistribute it and/or modify
7# it under the terms of the GNU General Public License as published by
8# the Free Software Foundation, either version 3 of the License, or
9# (at your option) any later version.
10#
11# This program is distributed in the hope that it will be useful,
12# but WITHOUT ANY WARRANTY; without even the implied warranty of
13# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14# GNU General Public License for more details.
15#
16# You should have received a copy of the GNU General Public License
17# along with this program. If not, see <http://www.gnu.org/licenses/>.
18#
19### fragment the molecule and check the number of configs
20#
21# BondFragmentShortRangeResults.dat is created like this:
22# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 0 --server-address 127.0.0.1 --server-port 1026 --fragment-resultfile BondFragmentShortRangeResults.dat
23
24AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
25AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
26
27file=BondFragmentShortRangeResults.dat
28AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
29AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
30AT_CHECK([../../molecuilder --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [ignore])
31AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
32AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
33AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
34AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
35AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
36AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
37
38AT_CLEANUP
39
40AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
41AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces])
42
43file=BondFragmentShortRangeResults.dat
44AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
45AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
46AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [ignore])
47AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
48
49AT_CLEANUP
50
51#
52# BondFragmentLongRangeResults.dat is created like this:
53# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --save-fragment-results BondFragmentLongRangeResults.dat
54
55AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC])
56AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
57AT_XFAIL_IF([/bin/true])
58
59file=BondFragmentLongRangeResults_OBC.dat
60AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
61AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
62AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
63#AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
64AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
65AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
66AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
67AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
68AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
69AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
70AT_CHECK([grep "File contains long-range information but long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
71 AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
72 ])
73
74AT_CLEANUP
75
76AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC and forces])
77AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
78AT_XFAIL_IF([/bin/true])
79
80file=BondFragmentLongRangeResults_OBC.dat
81AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
82AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
83AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
84AT_CHECK([grep "File contains long-range information but long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
85 AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data], 0, [ignore], [ignore])
86 ])
87
88AT_CLEANUP
89
90#
91# BondFragmentLongRangeResults.dat is created like this:
92# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Wrap Wrap Wrap --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --save-fragment-results BondFragmentLongRangeResults.dat
93
94AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC])
95AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
96AT_XFAIL_IF([/bin/true])
97
98file=BondFragmentLongRangeResults_PBC.dat
99AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
100AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
101AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
102#AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
103AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
104AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
105AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
106AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
107AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
108AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
109AT_CHECK([grep "File contains long-range information but long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
110 AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
111 ])
112
113AT_CLEANUP
114
115AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC and forces])
116AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
117AT_XFAIL_IF([/bin/true])
118
119file=BondFragmentLongRangeResults_PBC.dat
120AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
121AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
122AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb -o tremolo --set-tremolo-atomdata "Id type x=3 u=3 F=3" --reset 1 --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [stderr])
123AT_CHECK([grep "File contains long-range information but long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
124 AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data], 0, [ignore], [ignore])
125 ])
126
127AT_CLEANUP
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