| [f3cba6] | 1 | # Process with autom4te to create an -*- Autotest -*- test suite.
|
|---|
| [ebcade] | 2 | #
|
|---|
| 3 | # see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir.
|
|---|
| 4 | # In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.
|
|---|
| [f3cba6] | 5 |
|
|---|
| 6 | AT_INIT([Molecular Builder])
|
|---|
| 7 |
|
|---|
| 8 | # Checking if command line options are parsed correctly
|
|---|
| 9 | AT_BANNER([MoleCuilder - standard options])
|
|---|
| 10 | AT_SETUP([Standard Options])
|
|---|
| [ebcade] | 11 | AT_KEYWORDS([options])
|
|---|
| [f3cba6] | 12 | AT_CHECK([pwd],[ignore],[ignore])
|
|---|
| [6670a97] | 13 | AT_CHECK([../../molecuilder -v 1], 0, [stdout], [ignore])
|
|---|
| [482373] | 14 | AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
|
|---|
| [f3cba6] | 15 | AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
|
|---|
| 16 | AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
|
|---|
| [60f50a] | 17 | AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
|
|---|
| [f00693] | 18 | AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
|
|---|
| [f3cba6] | 19 | AT_CLEANUP
|
|---|
| 20 |
|
|---|
| [ebcade] | 21 |
|
|---|
| [ab3a0e] | 22 | AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
|
|---|
| [ebcade] | 23 | # 1. create some simplest molecular geometry
|
|---|
| 24 | AT_SETUP([Simple configuration - xyz file generation])
|
|---|
| [2a5eb7] | 25 | AT_KEYWORDS([Atom handling])
|
|---|
| [f3cba6] | 26 | AT_DATA([test.xyz], [[1
|
|---|
| 27 | # test configuration, created by molecuilder test suite
|
|---|
| 28 | H 10. 10. 10.
|
|---|
| 29 | ]])
|
|---|
| [b2b47f] | 30 | AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 31 | AT_CLEANUP
|
|---|
| 32 |
|
|---|
| 33 | # 2. parsing an xyz
|
|---|
| 34 | AT_SETUP([Simple configuration - parsing xyz file])
|
|---|
| [b2b47f] | 35 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
|
|---|
| [ebcade] | 36 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
|
|---|
| [c26f44] | 37 | AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1 10.000000000 10.000000000 10.000000000 0 # molecule nr 0
|
|---|
| [f3cba6] | 38 | ], [ignore])
|
|---|
| [b2b47f] | 39 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
|
|---|
| 40 | AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
|
|---|
| 41 | AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 42 |
|
|---|
| 43 | # 3. add atom
|
|---|
| 44 | AT_CLEANUP
|
|---|
| 45 | AT_SETUP([Simple configuration - adding atom])
|
|---|
| 46 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 10. 10. 10.], 0, [ignore], [ignore])
|
|---|
| [b2b47f] | 47 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
|
|---|
| 48 | AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
|
|---|
| 49 | AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 50 | AT_CLEANUP
|
|---|
| 51 |
|
|---|
| 52 | # 4. change the element
|
|---|
| 53 | AT_SETUP([Simple configuration - Changing element])
|
|---|
| [b2b47f] | 54 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.conf test.conf], 0)
|
|---|
| [ebcade] | 55 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
|
|---|
| [b2b47f] | 56 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 57 | AT_CLEANUP
|
|---|
| 58 |
|
|---|
| 59 | # 5. remove atom
|
|---|
| 60 | AT_SETUP([Simple configuration - Atom removal])
|
|---|
| [b2b47f] | 61 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
|
|---|
| [ebcade] | 62 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
|
|---|
| [b2b47f] | 63 | AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
|
|---|
| 64 | AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
|
|---|
| 65 | AT_CHECK([file=test.conf.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 66 | AT_CLEANUP
|
|---|
| 67 |
|
|---|
| 68 | # 6. test some more configuration that all desire parameters and count how many complain
|
|---|
| 69 | AT_SETUP([Simple configuration - invalid commands on empty configs])
|
|---|
| 70 | AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 71 | AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
|
|---|
| 72 | ], [ignore])
|
|---|
| 73 | AT_CLEANUP
|
|---|
| 74 |
|
|---|
| 75 | # 7. test some more configuration that all need parameters and count how many complain
|
|---|
| 76 | AT_SETUP([Simple configuration - invalid commands on present configs])
|
|---|
| [b2b47f] | 77 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
|
|---|
| [482373] | 78 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
|
|---|
| 79 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 80 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 81 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 82 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 83 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 84 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 85 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 86 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 87 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 88 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 89 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 90 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
|
|---|
| 91 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 92 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
|
|---|
| 93 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 94 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
|
|---|
| 95 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| 96 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
|
|---|
| 97 | AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
|
|---|
| [f3cba6] | 98 | AT_CLEANUP
|
|---|
| 99 |
|
|---|
| [ebcade] | 100 |
|
|---|
| [e3989a] | 101 | AT_BANNER([MoleCuilder - simulation domain])
|
|---|
| 102 | # 1. define box setting
|
|---|
| [c82720] | 103 | AT_SETUP([Domain - defining simulation domain])
|
|---|
| [e3989a] | 104 | AT_KEYWORDS([defining domain])
|
|---|
| [c82720] | 105 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
|
|---|
| 106 | AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
|
|---|
| [b2b47f] | 107 | AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
|
|---|
| [c82720] | 108 | AT_CLEANUP
|
|---|
| 109 |
|
|---|
| [e3989a] | 110 | # 2. center atoms in defined domain
|
|---|
| 111 | AT_SETUP([Domain - setting and centering in domain])
|
|---|
| 112 | AT_KEYWORDS([setting domain])
|
|---|
| [b2b47f] | 113 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/pre/test.conf .], 0)
|
|---|
| [e3989a] | 114 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b 15 0 15 0 0 15], 0, [stdout], [stderr])
|
|---|
| [b2b47f] | 115 | AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/post/test.conf], 0, [stdout], [stderr])
|
|---|
| [e3989a] | 116 | AT_CLEANUP
|
|---|
| [c82720] | 117 |
|
|---|
| [ebcade] | 118 | AT_BANNER([MoleCuilder - Graph routines test])
|
|---|
| 119 | AT_SETUP([Graph - DFS analysis])
|
|---|
| [2a5eb7] | 120 | AT_KEYWORDS([graph])
|
|---|
| [b2b47f] | 121 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/1/pre/test.conf .], 0)
|
|---|
| [6670a97] | 122 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
|
|---|
| [ebcade] | 123 | AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
|
|---|
| 124 | ], [ignore])
|
|---|
| 125 | AT_CLEANUP
|
|---|
| 126 |
|
|---|
| [ab3a0e] | 127 | AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
|
|---|
| [ebcade] | 128 | # 1. check config
|
|---|
| 129 | AT_SETUP([Fragmentation - Checking present config])
|
|---|
| [2a5eb7] | 130 | AT_KEYWORDS([fragmentation])
|
|---|
| [b2b47f] | 131 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
|
|---|
| [c26f44] | 132 | AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
|
|---|
| [3c1dfb] | 133 | ], [ignore])
|
|---|
| 134 | AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
|
|---|
| [ebcade] | 135 | AT_CLEANUP
|
|---|
| 136 | # 2. fragment the molecule and check the number of configs
|
|---|
| 137 | AT_SETUP([Fragmentation - Fragmentation])
|
|---|
| [b2b47f] | 138 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
|
|---|
| [ebcade] | 139 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
|
|---|
| [3c1dfb] | 140 | AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
|
|---|
| 141 | AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
|
|---|
| 142 | ], [ignore])
|
|---|
| [ebcade] | 143 | AT_CLEANUP
|
|---|
| 144 | # 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)
|
|---|
| 145 | AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
|
|---|
| [b2b47f] | 146 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/* .], 0)
|
|---|
| [ebcade] | 147 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
|
|---|
| [3c1dfb] | 148 | AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
|
|---|
| 149 | AT_CLEANUP
|
|---|
| [f3cba6] | 150 |
|
|---|
| [ebcade] | 151 |
|
|---|
| 152 | AT_BANNER([MoleCuilder - Tesselation test])
|
|---|
| 153 | # 1. Non convex tesselation
|
|---|
| 154 | AT_SETUP([Tesselation - Non-Convex Envelope])
|
|---|
| [2a5eb7] | 155 | AT_KEYWORDS([Tesselation])
|
|---|
| [b2b47f] | 156 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
|
|---|
| [ebcade] | 157 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
|
|---|
| [b2b47f] | 158 | AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
|
|---|
| 159 | AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 160 | AT_CLEANUP
|
|---|
| 161 |
|
|---|
| 162 | # 2. convex tesselation (where the non-convex is already convex)
|
|---|
| 163 | AT_SETUP([Tesselation - Convex Envelope])
|
|---|
| [b2b47f] | 164 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
|
|---|
| [ebcade] | 165 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
|
|---|
| [b2b47f] | 166 | AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
|
|---|
| 167 | AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
|
|---|
| [482373] | 168 | AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 169 | AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
|
|---|
| 170 | AT_CLEANUP
|
|---|
| 171 |
|
|---|
| 172 | # 3. Big Non convex tesselation
|
|---|
| 173 | AT_SETUP([Tesselation - Big non-Convex Envelope])
|
|---|
| [b2b47f] | 174 | AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
|
|---|
| [ebcade] | 175 | AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
|
|---|
| [b2b47f] | 176 | AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
|
|---|
| 177 | AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 178 | AT_CLEANUP
|
|---|
| 179 |
|
|---|
| 180 | # 4. Big convex tesselation - is not working yet
|
|---|
| 181 | #AT_SETUP([Tesselation - big convex Envelope])
|
|---|
| [b2b47f] | 182 | #AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
|
|---|
| [ebcade] | 183 | #AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
|
|---|
| [b2b47f] | 184 | #AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
|
|---|
| 185 | #AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
|
|---|
| [482373] | 186 | #AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
|
|---|
| [ebcade] | 187 | #AT_CLEANUP
|
|---|
| 188 |
|
|---|
