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testsuite-fragmentation.at@ 11428f

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Last change on this file since 11428f was 35b698, checked in by Frederik Heber <heber@…>, 15 years ago

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

FragmentMolecule() - configuration is not needed anymore, but a path (including prefix)
class molecule:
- lots of changes from char * to std:string (due to above): LinearInterpolationBetweenConfiguration(), CheckOrderAtSite(), StoreBondsToFile(), StoreAdjacencyToFile(), CheckAdjacencyFileAgainstMolecule(), CheckAdjacencyFileAgainstMolecule_Init(), ParseOrderAtSiteFromFile(), StoreOrderAtSiteFile(), StoreForcesFile(), ScanAdaptiveFileIntoMap(), StoreForcesFile(), AddHydrogenCorrection(), OutputConfigForListOfFragments()
- in all above functions, also stringstreams have been replaced by simple strings and file != NULL by file.good()
- no more CalculateOrbitals(), shifted to class PcpParser
FragmentationAction: argument of -f is now the prefix, molecule is obtained by molecule-by-id
no more strcpy needed in: MoleculeLinearInterpolationofTrajectoriesAction, MoleculeSaveAdjacencyAction, MoleculeSaveBondsAction
oldmenu::FragmentAtoms() - needs to ask for path with prefix now
config: RetrieveConfigPathAndName() and configpath removed (replaced by above path with prefix)
changes due to this removal: SaveConfig(), config::Load(), config::LoadOld()

FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)

ParseCommandLineOptions()
- new parameter BondGraphFileName and creation of bond graph is done in main()
- no more config::load, just parser->load(), ConfigFileName is set extra and we always set configPresent to present.
- FIX: filename is only set when no molecule was allocated before
- FIX: case 't' and 'f' had wrong argc checks
main()
- FormatParserStorage is set with mpqc, pcp and xyz
- BondGraph is constructed from new string BondGrapghFileName

new Libparser.a
all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

testsuite-fragmentation - changes to due to different -f calling syntax.
most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

Signed-off-by: Frederik Heber <heber@…>

Property mode set to 100644

File size: 1.6 KB

Rev	Line
[8c574b]	1	AT_BANNER([MoleCuilder - Fragmentation and Re-fragmentation test])
	2	# 1. check config
	3	AT_SETUP([Fragmentation - Checking present config])
	4	AT_KEYWORDS([fragmentation])
	5	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/1/pre/test.conf .], 0)
	6	AT_CHECK([fgrep "Ion_Type1_4" test.conf], 0, [Ion_Type1_4 8.532785963 4.787886018 2.645886050 0 # molecule nr 6
	7	], [ignore])
	8	AT_CHECK([fgrep "Ion_Type2_4" test.conf], 1, [ignore], [ignore])
	9	AT_CLEANUP
	10
	11	# 2. fragment the molecule and check the number of configs
	12	AT_SETUP([Fragmentation - Fragmentation])
	13	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/2/pre/test.conf .], 0)
[35b698]	14	AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f ./BondFragment --molecule-by-id 0 --distance 1.55 --order 2], 0, [ignore], [ignore])
[0de7e8]	15	AT_CHECK([ls -l BondFragment*.conf \| wc -l], 0, [5
[8c574b]	16	], [ignore])
	17	AT_CLEANUP
	18
	19	# 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)
[756b53]	20	# NOTE: Result code of 2 is not returned if "-v 1" is missing, then sequence of atoms is changed all the time and Adjacency files never match.
	21	AT_SETUP([Fragmentation - BROKEN: Fragmentation is at MaxOrder])
[e4b5de]	22	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Fragmentation/3/pre/test.conf .], 0)
[35b698]	23	AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f ./BondFragment --molecule-by-id 0 --distance 1.55 --order 2], 0, [ignore], [ignore])
	24	AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 1 -f ./BondFragment --molecule-by-id 0 --distance 1.55 --order 2], [ignore], [ignore], [ignore])
[8c574b]	25	AT_CLEANUP

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