AT_BANNER([MoleCuilder - molecular config creation from xyz file and atom adding])
# 1. create some simplest molecular geometry
AT_SETUP([Simple configuration - xyz file generation])
AT_KEYWORDS([configuration])
AT_DATA([test.xyz], [[1
 # test configuration, created by molecuilder test suite
H	10.	10.	10.
]])
AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/1/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 2. parsing an xyz
AT_SETUP([Simple configuration - parsing xyz file])
AT_KEYWORDS([configuration])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -p test.xyz], 0, [ignore], [ignore])
AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1	10.000000000	10.000000000	10.000000000	0 # molecule nr 0
], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 3a. add atom
AT_SETUP([Simple configuration - adding atom])
AT_KEYWORDS([configuration])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position "10., 10., 10."], 0, [ignore], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder -i test2.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position "0., 0., -1."], 134, [ignore], [ignore])
AT_CLEANUP

# 4. change the element
AT_SETUP([Simple configuration - Changing element])
AT_KEYWORDS([configuration])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/pre/test.xyz test.xyz], 0)
AT_CHECK([../../molecuilder -i test.xyz -e ${abs_top_srcdir}/src/ --select-atom-by-id 0 -E 6 ], 0, [ignore], [ignore])
AT_CHECK([file=test.xyz; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/4/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 5. remove atom
AT_SETUP([Simple configuration - Atom removal])
AT_KEYWORDS([configuration])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz --select-atom-by-id 0 -r], 0, [ignore], [ignore])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=test.xyz; diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 6. test some more configuration that all desire parameters and count how many complain
AT_SETUP([Simple configuration - invalid commands on empty configs])
AT_KEYWORDS([configuration])
AT_CHECK([../../molecuilder -i empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
AT_CLEANUP

# 7. test some more configuration that all need parameters and count how many complain
AT_SETUP([Simple configuration - invalid commands on present configs])
AT_KEYWORDS([configuration])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -t], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -T -u], 134, [ignore], [stderr])
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -u], 134, [ignore], [stderr])
AT_CLEANUP

# 8. Removing sphere of atoms
AT_SETUP([Simple configuration - Removing sphere of atoms])
AT_KEYWORDS([configuration])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
AT_CHECK([../../molecuilder -i test.conf -e ${abs_top_srcdir}/src/ -o xyz -R 7. --position "7.283585982, 3.275186040, 3.535886037"], 0, [stdout], [stderr])
AT_CHECK([sort -n test.xyz | grep -v "Created by" >test.xyz-sorted], 0, [ignore], [ignore])
AT_CHECK([sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.xyz  | grep -v "Created by" >${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.xyz-sorted], 0, [ignore], [ignore])
AT_CHECK([file=test.xyz-sorted; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
AT_CLEANUP