AT_BANNER([MoleCuilder - Molecules])
# 1. Bonds from file
AT_SETUP([Molecules - Bonds from file])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/1/pre/test.* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 4 -A test.dbond --molecule-by-id 0], 0, [stdout], [stderr])
AT_CHECK([fgrep "Looking for atoms 2 and 9." stdout], 0, [ignore], [ignore])
AT_CLEANUP

# 2. Storing adjacency info
AT_SETUP([Molecules - Storing bond info])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -j test.dbond --molecule-by-id 0], 0, [stdout], [stderr])
AT_CHECK([file=test.dbond; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -J test.adj --molecule-by-id 0], 0, [stdout], [stderr])
AT_CHECK([file=test.adj; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/2/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 3. Storing temperature
AT_SETUP([Molecules - Storing temperature])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -S test.ekin --molecule-by-id 0], 0, [stdout], [stderr])
AT_CHECK([file=test.ekin; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/3/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 4. linear interpolation
AT_SETUP([Molecules - BROKEN: Linear interpolation])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/4/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -L teststep --start-step 0 --end-step 1 --molecule-by-id 0 --id-mapping 1], 0, [stdout], [stderr])
AT_CLEANUP

# 5. Verlet force integration
AT_SETUP([Molecules - BROKEN: Verlet force integration])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/pre/test.* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -P test.forces --molecule-by-id 0], 134, [stdout], [stderr])
#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 6. Translation
AT_SETUP([Molecules - Translation])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/pre/test.* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t 1. 1. 1. --molecule-by-id 0 --periodic 0], 0, [stdout], [stderr])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/6/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 7. Periodic translation
AT_SETUP([Molecules - Periodic translation])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/pre/test.* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t 12. 12. 12. --molecule-by-id 0 --periodic 1], 0, [stdout], [stderr])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/7/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 8. Rotate to PAS
AT_SETUP([Molecules - BROKEN: Rotate to PAS])
AT_KEYWORDS([Molecules])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/pre/test.* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -m 0], 0, [stdout], [stderr])
#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
AT_CLEANUP