| [dd6c07] | 1 | #
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| 2 | # MoleCuilder - creates and alters molecular systems
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| 3 | # Copyright (C) 2013 University of Bonn
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| 4 | # Copyright (C) 2013 Frederik Heber
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| 5 | #
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| 6 | # This program is free software: you can redistribute it and/or modify
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| 7 | # it under the terms of the GNU General Public License as published by
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| 8 | # the Free Software Foundation, either version 3 of the License, or
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| 9 | # (at your option) any later version.
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| 10 | #
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| 11 | # This program is distributed in the hope that it will be useful,
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| 12 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 13 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 14 | # GNU General Public License for more details.
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| 15 | #
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| 16 | # You should have received a copy of the GNU General Public License
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| 17 | # along with this program. If not, see <http://www.gnu.org/licenses/>.
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| 18 | #
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| 19 | ### fragment the molecule and check the number of configs
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| 20 | #
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| 21 | # BondFragmentShortRangeResults.dat is created like this:
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| [d50b91] | 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 --save-fragment-results BondFragmentShortRangeResults.dat
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| [dd6c07] | 23 |
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| 24 | AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
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| [d50b91] | 25 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
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| [dd6c07] | 26 |
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| 27 | file=BondFragmentShortRangeResults.dat
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| 28 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 29 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 30 | AT_CHECK([../../molecuilder --dry-run --parse-fragment-results $file --analyse-fragment-results --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [ignore])
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| [dd6c07] | 31 | AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| 32 | AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| 33 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 34 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 35 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 36 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 37 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 38 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
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| 39 |
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| 40 | AT_CLEANUP
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| 41 |
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| 42 | AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
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| [d50b91] | 43 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces])
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| [dd6c07] | 44 |
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| 45 | file=BondFragmentShortRangeResults.dat
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| 46 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 47 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 48 | AT_CHECK([../../molecuilder --dry-run -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 --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [ignore])
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| [dd6c07] | 49 | AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| 50 | AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| 51 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
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| 52 |
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| 53 | AT_CLEANUP
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| 54 |
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| 55 | #
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| 56 | # BondFragmentLongRangeResults.dat is created like this:
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| [d50b91] | 57 | # ./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_OBC.dat
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| [dd6c07] | 58 |
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| 59 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC])
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| [d50b91] | 60 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
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| [dd6c07] | 61 |
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| 62 | file=BondFragmentLongRangeResults_OBC.dat
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| 63 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 64 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 65 | AT_CHECK([../../molecuilder --dry-run -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 --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [stderr])
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| [dd6c07] | 66 | AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| 67 | AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [stderr])
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| 68 | #AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
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| 69 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 70 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 71 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 72 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 73 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 74 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| [d50b91] | 75 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [dd6c07] | 76 | AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
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| 77 | ])
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| 78 |
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| 79 | AT_CLEANUP
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| 80 |
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| [af340c] | 81 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC and forces])
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| [d50b91] | 82 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
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| [af340c] | 83 |
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| 84 | file=BondFragmentLongRangeResults_OBC.dat
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| 85 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 86 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 87 | AT_CHECK([../../molecuilder --dry-run -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 --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [stderr])
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| [af340c] | 88 | AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| [835b53] | 89 | AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [stderr])
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| [d50b91] | 90 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [835b53] | 91 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data], 0, [ignore], [ignore])
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| 92 | ])
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| [af340c] | 93 |
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| 94 | AT_CLEANUP
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| 95 |
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| [dd6c07] | 96 | #
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| 97 | # BondFragmentLongRangeResults.dat is created like this:
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| [d50b91] | 98 | # ./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_PBC.dat
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| [dd6c07] | 99 |
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| 100 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC])
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| [d50b91] | 101 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
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| [dd6c07] | 102 |
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| 103 | file=BondFragmentLongRangeResults_PBC.dat
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| 104 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 105 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 106 | AT_CHECK([../../molecuilder --dry-run -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 --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [stderr])
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| [dd6c07] | 107 | AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| 108 | AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [stderr])
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| 109 | #AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
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| 110 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 111 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 112 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 113 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 114 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 115 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| [d50b91] | 116 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [dd6c07] | 117 | AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
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| 118 | ])
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| 119 |
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| 120 | AT_CLEANUP
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| [af340c] | 121 |
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| 122 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC and forces])
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| [d50b91] | 123 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
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| [af340c] | 124 |
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| 125 | file=BondFragmentLongRangeResults_PBC.dat
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| 126 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
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| 127 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
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| [d50b91] | 128 | AT_CHECK([../../molecuilder --dry-run -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 --no-dry-run --store-session session-fragmentation-analyse-fragment-results.py --session-type python], 0, [ignore], [stderr])
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| [af340c] | 129 | AT_CHECK([grep -v "Command.*DryRun" session-fragmentation-analyse-fragment-results.py >session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [ignore])
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| [835b53] | 130 | AT_CHECK([../../molecuilderguitest session-fragmentation-analyse-fragment-results_new.py], 0, [ignore], [stderr])
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| [d50b91] | 131 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
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| [835b53] | 132 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data], 0, [ignore], [ignore])
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| 133 | ])
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| [af340c] | 134 |
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| 135 | AT_CLEANUP
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