| 1 | # Process with autom4te to create an -*- Autotest -*- test suite.
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| 2 | #
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| 3 | # see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir.
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| 4 | # In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.
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| 5 |
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| 6 | AT_INIT([Molecular Builder])
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| 7 |
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| 8 | # Checking if command line options are parsed correctly
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| 9 | AT_BANNER([MoleCuilder - standard options])
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| 10 | AT_SETUP([Standard Options])
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| 11 | AT_KEYWORDS([options])
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| 12 | AT_CHECK([pwd],[ignore],[ignore])
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| 13 | AT_CHECK([../../molecuilder -v 1], 0, [stdout], [ignore])
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| 14 | AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
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| 15 | AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
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| 16 | AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
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| 17 | AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
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| 18 | AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
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| 19 | AT_CLEANUP
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| 20 |
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| 21 |
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| 22 | AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
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| 23 | # 1. create some simplest molecular geometry
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| 24 | AT_SETUP([Simple configuration - xyz file generation])
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| 25 | AT_KEYWORDS([Atom handling])
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| 26 | AT_DATA([test.xyz], [[1
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| 27 | # test configuration, created by molecuilder test suite
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| 28 | H 10. 10. 10.
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| 29 | ]])
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| 30 | AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
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| 31 | AT_CLEANUP
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| 32 |
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| 33 | # 2. parsing an xyz
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| 34 | AT_SETUP([Simple configuration - parsing xyz file])
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| 35 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/pre/test.xyz .], 0)
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| 36 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
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| 37 | AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
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| 38 | ], [ignore])
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| 39 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
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| 40 | AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
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| 41 | AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
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| 42 |
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| 43 | # 3. add atom
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| 44 | AT_CLEANUP
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| 45 | AT_SETUP([Simple configuration - adding atom])
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| 46 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
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| 47 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
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| 48 | AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
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| 49 | AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
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| 50 | AT_CLEANUP
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| 51 |
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| 52 | # 4. change the element
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| 53 | AT_SETUP([Simple configuration - Changing element])
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| 54 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/pre/test.conf test.conf], 0)
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| 55 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
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| 56 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
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| 57 | AT_CLEANUP
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| 58 |
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| 59 | # 5. remove atom
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| 60 | AT_SETUP([Simple configuration - Atom removal])
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| 61 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/pre/test.conf .], 0)
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| 62 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
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| 63 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
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| 64 | AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
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| 65 | AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
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| 66 | AT_CLEANUP
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| 67 |
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| 68 | # 6. test some more configuration that all desire parameters and count how many complain
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| 69 | AT_SETUP([Simple configuration - invalid commands on empty configs])
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| 70 | AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
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| 71 | AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
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| 72 | ], [ignore])
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| 73 | AT_CLEANUP
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| 74 |
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| 75 | # 7. test some more configuration that all need parameters and count how many complain
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| 76 | AT_SETUP([Simple configuration - invalid commands on present configs])
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| 77 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Simple_configuration/7/pre/test.conf .], 0)
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| 78 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
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| 79 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 80 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
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| 81 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 82 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
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| 83 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 84 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
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| 85 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 86 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
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| 87 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 88 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
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| 89 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 90 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
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| 91 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 92 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
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| 93 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 94 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
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| 95 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 96 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
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| 97 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
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| 98 | AT_CLEANUP
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| 99 |
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| 100 |
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| 101 | AT_BANNER([MoleCuilder - molecular config creation])
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| 102 | # 1. check box setting
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| 103 | AT_SETUP([Domain - defining simulation domain])
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| 104 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
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| 105 | AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
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| 106 | AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Domain/1/post/test.conf], 0, [stdout], [stderr])
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| 107 | AT_KEYWORDS([domain])
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| 108 | AT_CLEANUP
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| 109 |
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| 110 |
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| 111 | AT_BANNER([MoleCuilder - Graph routines test])
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| 112 | AT_SETUP([Graph - DFS analysis])
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| 113 | AT_KEYWORDS([graph])
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| 114 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Graph/1/pre/test.conf .], 0)
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| 115 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
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| 116 | AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
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| 117 | ], [ignore])
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| 118 | AT_CLEANUP
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| 119 |
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| 120 | AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
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| 121 | # 1. check config
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| 122 | AT_SETUP([Fragmentation - Checking present config])
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| 123 | AT_KEYWORDS([fragmentation])
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| 124 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/1/pre/test.conf .], 0)
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| 125 | AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
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| 126 | ], [ignore])
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| 127 | AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
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| 128 | AT_CLEANUP
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| 129 | # 2. fragment the molecule and check the number of configs
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| 130 | AT_SETUP([Fragmentation - Fragmentation])
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| 131 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/2/pre/test.conf .], 0)
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| 132 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
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| 133 | AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
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| 134 | AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
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| 135 | ], [ignore])
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| 136 | AT_CLEANUP
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| 137 | # 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)
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| 138 | AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
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| 139 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Fragmentation/3/pre/* .], 0)
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| 140 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
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| 141 | AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
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| 142 | AT_CLEANUP
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| 143 |
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| 144 |
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| 145 | AT_BANNER([MoleCuilder - Tesselation test])
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| 146 | # 1. Non convex tesselation
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| 147 | AT_SETUP([Tesselation - Non-Convex Envelope])
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| 148 | AT_KEYWORDS([Tesselation])
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| 149 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/pre/* .], 0)
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| 150 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
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| 151 | AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
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| 152 | AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/1/post/$file], 0, [ignore], [ignore])
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| 153 | AT_CLEANUP
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| 154 |
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| 155 | # 2. convex tesselation (where the non-convex is already convex)
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| 156 | AT_SETUP([Tesselation - Convex Envelope])
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| 157 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/pre/* .], 0)
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| 158 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
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| 159 | AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
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| 160 | AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/2/post/$file], 0, [ignore], [ignore])
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| 161 | AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
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| 162 | AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
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| 163 | AT_CLEANUP
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| 164 |
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| 165 | # 3. Big Non convex tesselation
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| 166 | AT_SETUP([Tesselation - Big non-Convex Envelope])
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| 167 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/pre/* .], 0)
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| 168 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
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| 169 | AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
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| 170 | AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/3/post/$file], 0, [ignore], [ignore])
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| 171 | AT_CLEANUP
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| 172 |
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| 173 | # 4. Big convex tesselation - is not working yet
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| 174 | #AT_SETUP([Tesselation - big convex Envelope])
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| 175 | #AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/pre/* .], 0)
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| 176 | #AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
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| 177 | #AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
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| 178 | #AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Tesselation/4/post/$file], 0, [ignore], [ignore])
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| 179 | #AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
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| 180 | #AT_CLEANUP
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| 181 |
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