| [55e1bc] | 1 | #
|
|---|
| 2 | # MoleCuilder - creates and alters molecular systems
|
|---|
| 3 | # Copyright (C) 2013 University of Bonn
|
|---|
| [5aaa43] | 4 | # Copyright (C) 2013 Frederik Heber
|
|---|
| [55e1bc] | 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
|
|---|
| [6ff62c] | 20 | #
|
|---|
| [e2925fd] | 21 | # BondFragmentShortRangeResults.dat is created like this:
|
|---|
| [ea63cb] | 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
|
|---|
| [55e1bc] | 23 |
|
|---|
| [e2925fd] | 24 | AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
|
|---|
| [d203350] | 25 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
|
|---|
| [55e1bc] | 26 |
|
|---|
| [e2925fd] | 27 | file=BondFragmentShortRangeResults.dat
|
|---|
| [55e1bc] | 28 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
|
|---|
| 29 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
|
|---|
| [d203350] | 30 | AT_CHECK([../../molecuilder --parse-fragment-results $file --analyse-fragment-results], 0, [ignore], [ignore])
|
|---|
| [e2925fd] | 31 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
|
|---|
| 32 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
|
|---|
| 33 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
|
|---|
| 34 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
|
|---|
| 35 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
|
|---|
| [47cee7] | 36 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
|
|---|
| [e2925fd] | 37 |
|
|---|
| 38 | AT_CLEANUP
|
|---|
| 39 |
|
|---|
| [e5ebaf] | 40 | AT_SETUP([Fragmentation - Analyse short-range fragmentation results with forces])
|
|---|
| [d203350] | 41 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces])
|
|---|
| [e5ebaf] | 42 |
|
|---|
| 43 | file=BondFragmentShortRangeResults.dat
|
|---|
| 44 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
|
|---|
| 45 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
|
|---|
| [d203350] | 46 | AT_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])
|
|---|
| [e5ebaf] | 47 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
|
|---|
| 48 |
|
|---|
| 49 | AT_CLEANUP
|
|---|
| 50 |
|
|---|
| [e2925fd] | 51 | #
|
|---|
| 52 | # BondFragmentLongRangeResults.dat is created like this:
|
|---|
| [ea63cb] | 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_OBC.dat
|
|---|
| [e2925fd] | 54 |
|
|---|
| [6531a7] | 55 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC])
|
|---|
| [d203350] | 56 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
|
|---|
| [e2925fd] | 57 |
|
|---|
| [6531a7] | 58 | file=BondFragmentLongRangeResults_OBC.dat
|
|---|
| [e2925fd] | 59 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
|
|---|
| 60 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
|
|---|
| [d203350] | 61 | AT_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])
|
|---|
| [6531a7] | 62 | #AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
|
|---|
| 63 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| 64 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| 65 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| 66 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| 67 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| 68 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| [72b467] | 69 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
|
|---|
| [6531a7] | 70 | AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/$output], 0, [ignore], [ignore])
|
|---|
| 71 | ])
|
|---|
| 72 |
|
|---|
| 73 | AT_CLEANUP
|
|---|
| 74 |
|
|---|
| [d93d2c] | 75 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with OBC and forces])
|
|---|
| [d203350] | 76 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
|
|---|
| [d93d2c] | 77 |
|
|---|
| 78 | file=BondFragmentLongRangeResults_OBC.dat
|
|---|
| 79 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
|
|---|
| 80 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
|
|---|
| [d203350] | 81 | AT_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])
|
|---|
| [72b467] | 82 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
|
|---|
| [835b53] | 83 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data], 0, [ignore], [ignore])
|
|---|
| 84 | ])
|
|---|
| [d93d2c] | 85 |
|
|---|
| 86 | AT_CLEANUP
|
|---|
| 87 |
|
|---|
| [6531a7] | 88 | #
|
|---|
| 89 | # BondFragmentLongRangeResults.dat is created like this:
|
|---|
| [ea63cb] | 90 | # ./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
|
|---|
| [6531a7] | 91 |
|
|---|
| 92 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC])
|
|---|
| [d203350] | 93 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results])
|
|---|
| [6531a7] | 94 |
|
|---|
| 95 | file=BondFragmentLongRangeResults_PBC.dat
|
|---|
| 96 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
|
|---|
| 97 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
|
|---|
| [d203350] | 98 | AT_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])
|
|---|
| [6531a7] | 99 | #AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data], 0, [ignore], [ignore])
|
|---|
| 100 | AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| 101 | AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| 102 | AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| 103 | AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| 104 | AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| 105 | AT_CHECK([output=BondFragment_IndexedEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| [72b467] | 106 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
|
|---|
| [6531a7] | 107 | AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/$output], 0, [ignore], [ignore])
|
|---|
| [e2925fd] | 108 | ])
|
|---|
| [55e1bc] | 109 |
|
|---|
| 110 | AT_CLEANUP
|
|---|
| [d93d2c] | 111 |
|
|---|
| 112 | AT_SETUP([Fragmentation - Analyse long-range fragmentation results with PBC and forces])
|
|---|
| [d203350] | 113 | AT_KEYWORDS([fragmentation parse-fragment-results analyse-fragment-results forces longrange])
|
|---|
| [d93d2c] | 114 |
|
|---|
| 115 | file=BondFragmentLongRangeResults_PBC.dat
|
|---|
| 116 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
|
|---|
| 117 | AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
|
|---|
| [d203350] | 118 | AT_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])
|
|---|
| [72b467] | 119 | AT_CHECK([grep "long-range analysis capability not compiled in" stderr], 0, [ignore], [ignore], [
|
|---|
| [835b53] | 120 | AT_CHECK([diff alkane-3.data ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data], 0, [ignore], [ignore])
|
|---|
| 121 | ])
|
|---|
| [d93d2c] | 122 |
|
|---|
| 123 | AT_CLEANUP
|
|---|
