source: tests/regression/testsuite.at@ afd01c

# Process with autom4te to create an -*- Autotest -*- test suite.
#
# see regression/... subdirs wherein for each of the cases and each check (enumerated) is a pre and post dir. 
# In pre initial files are placed, in post results can be found to be checked by diff in this testsuite.

AT_INIT([Molecular Builder])


AT_BANNER([MoleCuilder - standard options])
# 1. verbosity
AT_SETUP([Standard Options - verbosity])
AT_KEYWORDS([options])
AT_CHECK([pwd],[ignore],[ignore])
AT_CHECK([../../molecuilder -v 1], 0, [stdout], [ignore])
AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
AT_CLEANUP

# 2. help screen
AT_SETUP([Standard Options - help screen])
AT_KEYWORDS([options])
AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
AT_CHECK([fgrep "Give this help screen" stdout], 0, [ignore], [ignore])
AT_CLEANUP

# 3. no element database
AT_SETUP([Standard Options - no element database])
AT_KEYWORDS([options])
AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
AT_CLEANUP

# 4. element database
AT_SETUP([Standard Options - element database])
AT_KEYWORDS([options])
AT_DATA([elements.db], [[#      Covalent        radius  of      each    element in      Angstroem       from    CSD     (binding        is:     [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t]   with    t       =       0.4A
#Element        Name    Symbol  Period  Group   Block   Atomic  Number  AtomicWeight    Covalent        Radius  vdW     Radius
Hydrogen        H       1       1       s       1       1.008   0.23    1.09
Helium  He      1       18      p       2       4.003   1.5     1.4
]])
AT_CHECK([../../molecuilder test.conf -e ./], 0, [stdout], [stderr])
AT_CHECK([grep -E "Using.*as elements database." stdout], 0, [ignore], [ignore])
AT_CHECK([fgrep "Element list loaded successfully." stdout], 0, [ignore], [ignore])
AT_CHECK([fgrep "Something went wrong while parsing the other databases!" stderr], 0, [ignore], [ignore])
AT_CLEANUP

# 5. bond length database
AT_SETUP([Standard Options - bond length table])
AT_KEYWORDS([options])
AT_DATA([bondlength.db], [[# bond length database
        1       2
1       1.      0.
2       0.      0.
]])
AT_CHECK([../../molecuilder test.conf -g bondlength.db], 0, [stdout], [stderr])
AT_CHECK([grep -E "Using.*as bond length table." stdout], 0, [ignore], [ignore])
AT_CLEANUP

# 6. fast trajectories
AT_SETUP([Standard Options - fast trajectories])
AT_KEYWORDS([options])
AT_CHECK([../../molecuilder test.conf -n], 0, [stdout], [stderr])
AT_CHECK([fgrep "I won't parse trajectories" stdout], 0, [ignore], [ignore])
AT_CLEANUP

# 7. molecule default name
AT_SETUP([Standard Options - molecule default name])
AT_KEYWORDS([options])
AT_CHECK([../../molecuilder test.conf -X test], 0, [stdout], [stderr])
AT_CHECK([fgrep "Default name of new molecules set to test." stdout], 0, [ignore], [ignore])
AT_CLEANUP

AT_BANNER([MoleCuilder - Specifics])
# 1. MPQC basis
AT_SETUP([Specifics - MPQC basis])
AT_KEYWORDS([options])
AT_CHECK([pwd],[ignore],[ignore])
AT_CHECK([../../molecuilder test.conf -v 1 -M test], 0, [stdout], [ignore])
AT_CHECK([fgrep "Setting MPQC basis to test." stdout], 0, [ignore], [ignore])
AT_CLEANUP


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 test.conf -e ${abs_top_srcdir}/src/ -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.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/post/$file], 0, [ignore], [ignore])
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])
AT_CLEANUP

# 3. add atom
AT_SETUP([Simple configuration - adding atom])
AT_KEYWORDS([configuration])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 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.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
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])
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.conf test.conf], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E 0 6], 0, [ignore], [ignore])
AT_CHECK([file=test.conf; 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 test.conf -e ${abs_top_srcdir}/src/ -r 0], 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.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
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])
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 empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "Not enough or invalid" stderr], 0, [1
], [ignore])
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 test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
AT_CHECK([fgrep -c "CRITICAL: Not enough or invalid" stderr], 0, [ignore], [ignore])
AT_CLEANUP

# 8. Removing sphere of atoms
AT_SETUP([Simple configuration - BROKEN: 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 test.conf -e ${abs_top_srcdir}/src/ -R 2 7.], 134, [stdout], [stderr])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/$file], 0, [ignore], [ignore])
AT_CLEANUP


AT_BANNER([MoleCuilder - simulation domain])
# 1. define box setting
AT_SETUP([Domain - defining simulation domain])
AT_KEYWORDS([domain])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
AT_CLEANUP

# 2. center atoms in defined domain
AT_SETUP([Domain - setting and centering in domain])
AT_KEYWORDS([domain])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b 15 0 15 0 0 15], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/2/post/test.conf], 0, [stdout], [stderr])
AT_CLEANUP

# 3. center atoms with defined boundary
AT_SETUP([Domain - centering with defined boundary])
AT_KEYWORDS([domain])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c 5 10 15], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/3/post/test.conf], 0, [stdout], [stderr])
AT_CLEANUP

# 4. center atoms and adjusting boundary
AT_SETUP([Domain - centering and setting domain])
AT_KEYWORDS([domain])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -O], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/4/post/test.conf], 0, [stdout], [stderr])
AT_CLEANUP

# 5. scaling box
AT_SETUP([Domain - scaling box])
AT_KEYWORDS([domain])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/5/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s 0.5 1. 0.9], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/5/post/test.conf], 0, [stdout], [stderr])
AT_CLEANUP

# 6. duplicating box
AT_SETUP([Domain - duplicating box])
AT_KEYWORDS([domain])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -d 1 1 1], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/test.conf], 0, [stdout], [stderr])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -d 2 1 1], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/test-x.conf], 0, [stdout], [stderr])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -d 1 2 1], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/test-y.conf], 0, [stdout], [stderr])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -d 1 1 2], 0, [stdout], [stderr])
AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/test-z.conf], 0, [stdout], [stderr])
AT_CLEANUP


AT_BANNER([MoleCuilder - Graph routines test])
# 1. DFS analysis
AT_SETUP([Graph - DFS analysis])
AT_KEYWORDS([graph])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/1/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
], [ignore])
AT_CLEANUP

AT_SETUP([Graph - subgraph dissection])
AT_KEYWORDS([graph])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Graph/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -I], 0, [stdout], [stderr])
AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
AT_CLEANUP


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], 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], 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], 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], 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 0 1 teststep 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], 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.], 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.], 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. Periodic translation
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 1], 0, [stdout], [stderr])
#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
AT_CLEANUP


AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
# 1. check config
AT_SETUP([Fragmentation - Checking present config])
AT_KEYWORDS([fragmentation])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4       8.532785963     4.787886018     2.645886050     0 # molecule nr 6
], [ignore])
AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
AT_CLEANUP

# 2. fragment the molecule and check the number of configs
AT_SETUP([Fragmentation - Fragmentation])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 0, [ignore], [ignore], [mkdir std; mv BondFragment*.conf* std/])
AT_CHECK([mkdir std; mv BondFragment*.conf* std/], 0)
AT_CHECK([ls -l std/BondFragment*.conf | wc -l], 0, [5
], [ignore])
AT_CLEANUP

# 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)
AT_SETUP([Fragmentation - Fragmentation is at MaxOrder])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -f 1.55 2], 2, [ignore], [ignore], [mkdir new; mv BondFragment*.conf* new/])
AT_CHECK([mkdir new; mv BondFragment*.conf* new/], 0)
AT_CLEANUP


AT_BANNER([MoleCuilder - Tesselation test])
# 1. Non convex tesselation
AT_SETUP([Tesselation - Non-Convex Envelope])
AT_KEYWORDS([Tesselation])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/1/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 2. convex tesselation (where the non-convex is already convex)
AT_SETUP([Tesselation - Convex Envelope])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
AT_CHECK([diff ConvexEnvelope.dat NonConvexEnvelope.dat], 0, [ignore], [ignore])
AT_CLEANUP

# 3. Big Non convex tesselation
AT_SETUP([Tesselation - Big non-Convex Envelope])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/pre/* .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -N 4. NonConvexEnvelope], 0, [stdout], [stderr])
AT_CHECK([file=NonConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=NonConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/3/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 4. Big convex tesselation - is not working yet 
#AT_SETUP([Tesselation - big convex Envelope])
#AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
#AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
#AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
#AT_CHECK([fgrep "tesselated volume area is 16.4016 angstrom^3" stdout], 0, [ignore], [ignore])
#AT_CLEANUP


AT_BANNER([MoleCuilder - Filling in molecules])
# 1. filling box
AT_SETUP([Filling - filling empty box])
AT_KEYWORDS([filling])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/pre/test.conf .], 0)
AT_DATA([water.xyz], [[3
 # test configuration, created by molecuilder test suite
O       0.      0.      0.
H       0.758602 0.     0.504284 
H       0.758602 0.     -0.504284 
]])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -F water.xyz 3.1 3.1 3.1 2.1 0. 0. 0], 0, [stdout], [stderr])
AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/1/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 2. suspend in water with certain density
AT_SETUP([Filling - BROKEN: suspend in water])
AT_KEYWORDS([filling])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -u 1.3], 0, [stdout], [stderr])
#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/2/post/$file], 0, [ignore], [ignore])
AT_CLEANUP


AT_BANNER([MoleCuilder - Analysis])
# 1. pair correlation analysis
AT_SETUP([Analysis - pair correlation])
AT_KEYWORDS([analysis])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output.csv bin_output.csv 0 20], 0, [stdout], [stderr])
AT_CHECK([fgrep "Begin of PairCorrelation" stdout], 0, [ignore], [ignore])
AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/1/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 2. pair correlation analysis - range test
AT_SETUP([Analysis - pair correlation range test])
AT_KEYWORDS([analysis])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output-5.csv bin_output-5.csv 0 5], 0, [stdout], [stderr])
AT_CHECK([file=output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=bin_output-5.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output-10.csv bin_output-10.csv 5 10], 0, [stdout], [stderr])
AT_CHECK([file=output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=bin_output-10.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C E 1 8 output-20.csv bin_output-20.csv 10 20], 0, [stdout], [stderr])
AT_CHECK([file=output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=bin_output-20.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/2/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 3. pair correlation analysis to point
AT_SETUP([Analysis - point correlation])
AT_KEYWORDS([analysis])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -C P 1 10. 10. 10. output.csv bin_output.csv 0 20], 0, [stdout], [stderr])
AT_CHECK([fgrep "Begin of CorrelationToPoint" stdout], 0, [ignore], [ignore])
AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/3/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 4. pair correlation analysis to surface
AT_SETUP([Analysis - surface correlation])
AT_KEYWORDS([analysis])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -I -C S 1 output.csv bin_output.csv 1. 0 20], 0, [stdout], [stderr])
AT_CHECK([fgrep "Begin of CorrelationToSurface" stdout], 0, [ignore], [ignore])
AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/4/post/$file], 0, [ignore], [ignore])
AT_CLEANUP

# 4. principal axis system
AT_SETUP([Analysis - principal axis system])
AT_KEYWORDS([analysis])
AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/5/pre/test.conf .], 0)
AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -m 0], 0, [stdout], [stderr])
AT_CHECK([fgrep "eigenvalue = 4382.53," stdout], 0, [ignore], [ignore])
AT_CHECK([fgrep "eigenvalue = 4369.24," stdout], 0, [ignore], [ignore])
AT_CHECK([fgrep "eigenvalue = 28.9359," stdout], 0, [ignore], [ignore])
AT_CLEANUP