source: molecuilder/src

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Diff Rev Age Author Log Message
(edit) @725869   17 years FrederikHeber new header file for the vector class, new operators +=,*=,*,+
(edit) @0e348e   17 years FrederikHeber main(): typo in Usage message, BUGFIX - command line arguments did not …
(edit) @cc6dfb   17 years FrederikHeber CyclicStructureAnalysis(): forget to check whether we actually have …
(edit) @0716ff4   17 years FrederikHeber MinimumRingSize is now an array over all atoms Each entry in …
(edit) @2700f5e   17 years FrederikHeber TranslateIndicesToGlobalIDs() did not check whether FragmentList.. …
(edit) @59ddad   17 years FrederikHeber joiner now writes ENERGYPERFRAGMENT file for adaptive BOSSANOVA
(edit) @0421a3   17 years FrederikHeber CreateDataFragment(): endline after datum in header
(edit) @c84895   17 years FrederikHeber ENERGYPERFRAGMENT without ".dat"
(edit) @310b25   17 years FrederikHeber some comments for where "F" and where "E" terms are created
(edit) @a3ff7b2   17 years FrederikHeber molecule::CheckOrderAtSite() now interprets negative Orders as …
(edit) @461e93   17 years FrederikHeber molecule::CheckOrderAtSite() returns bool and used as threshold …
(edit) @d88597   17 years FrederikHeber new function molecule::CreateMappingLabelsToConfigSequence() creates …
(edit) @2b79c3   17 years FrederikHeber new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in …
(edit) @169b24   17 years FrederikHeber new functions MoleculeLeafClass::AssignKeySetsToFragment() and …
(edit) @ea84ed   17 years FrederikHeber FragmentMolecule(): abstractized AssignKeySetsToFragments() and …
(edit) @84e88a   17 years FrederikHeber new function FillListOfLocalAtoms() checks whether List needs filling …
(edit) @08fd83   17 years FrederikHeber MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling of …
(edit) @7b80a5   17 years FrederikHeber new functions MoleculeLeafClass::Count() and …
(edit) @255d13   17 years FrederikHeber FillBondStructureFromReference: previous == NULL was bad idea, new …
(edit) @9c3496   17 years FrederikHeber new function molecule::CheckOrderAtSite and …
(edit) @b8eb3a   17 years FrederikHeber new function MoleculeLeafClass::FillBondStructureFromReference that …
(edit) @c901e3   17 years FrederikHeber new function CreateFatherLookupTable Creates a lookup table for true …
(edit) @7afa7e   17 years FrederikHeber Matrix::ParseMatrix()L: comment makes it clearer at what fragment with …
(edit) @a01955   17 years FrederikHeber rewritten CyclicStructureAnalysis(): uses DFS spanning tree and …
(edit) @d50d2a   17 years FrederikHeber AtomStackClass -> template <typename T> StackClass<T> change in new …
(edit) @417bb5   17 years FrederikHeber changed comments a bit
(edit) @48efc3   17 years FrederikHeber MatrixContainer::MatrixContainer() debug message fixes only, …
(edit) @0e8321   17 years FrederikHeber KeySetFile is stored without an additional last tab on each line
(edit) @8449ed   17 years FrederikHeber joiner crashed due to incorrect destructing of MatrixContainer, …
(edit) @115bf4   17 years FrederikHeber ForcesFile and TEFactors are _needed_, reincorporated. UniqueFragments …
(edit) @38fc0d   17 years FrederikHeber Free(): only set to NULL if it was free'd otherwise it is already
(edit) @cffff8   17 years FrederikHeber ~MatrixContainer(): Bugfix - Free if Matrix[MatrixCounter] would also …
(edit) @30fda2   17 years FrederikHeber commenting in header changed for the four main functions that …
(edit) @c75363   17 years FrederikHeber HUGE REWRITE to allow for adaptive increase of the bond order, first …
(edit) @e936b3   17 years FrederikHeber Velocities were not correctly handled, also not in fragments First … non_adaptive_molecuilder
(edit) @c510a7   17 years FrederikHeber char lengths of 255 and MAXDUMMYSTRING replaced with define …
(edit) @307fd1   17 years FrederikHeber Store/CheckAdj...() now also incorporate bond order to check against.
(edit) @9bd230   17 years FrederikHeber changed config file to first argument again and standard config name …
(edit) @7e2c5c   17 years FrederikHeber bugfix: configpath and -name are not set to empty string.
(edit) @584691   17 years FrederikHeber bugfix in main: without arguments, code would crash due to access of …
(edit) @7b1cea   17 years FrederikHeber configname is also stored in config structure, GetDefaultPath by …
(edit) @36b128   17 years FrederikHeber Comply with test again: help and version command options exit at once …
(edit) @f5306f   17 years FrederikHeber config::Load..() now get filename instead of pointer to file, bugfix …
(edit) @661288   17 years FrederikHeber Atoms in the fragments in the configs are again ordered as first …
(edit) @e565a8   17 years FrederikHeber removed some output lines (commented-out) mostly in …
(edit) @8efbfc   17 years FrederikHeber FragmentMolecule(): status variable used when checking adjacency file …
(edit) @d982bb   17 years FrederikHeber All filenames (const char *) have been transferred to defs.hpp …
(edit) @34d37c   17 years FrederikHeber storing and comparing Adjacency outsourced into two new functions. …
(edit) @2614f83   17 years FrederikHeber FragmentMolecule(): Adjacency store/check and parsing of KeySetFile …
(edit) @bd8439   17 years FrederikHeber main(): thrown out unused stringstreams prefix and line
(edit) @23409a   17 years FrederikHeber OutputConfigForListOfFragments(): various ofstream gathered into a …
(edit) @16cd31   17 years FrederikHeber AddXYZFile(): Bugfix - if element could not be parsed (e.g. elements …
(edit) @c72cbe   17 years FrederikHeber Load/StorePeriodentafel(): filename as parameter, if NULL default name …
(edit) @a829d1   17 years FrederikHeber new elementsdb-switch and command line options parsing parts moved …
(edit) @b021e4   17 years FrederikHeber Load/StorePeriodentafel(): filename as parameter, if NULL default name …
(edit) @8129de   17 years FrederikHeber Huge rewrite of initial command line parsing config file argument is …
(edit) @370060   17 years FrederikHeber added VERSIONSTRING
(edit) @941b66   17 years FrederikHeber LoadPeriodentafel(): no more outputs of parsed elements
(edit) @77da65   17 years FrederikHeber ADDHYDROGEN and HAVE_DEBUG fix: config.h was not yet included …
(edit) @e58fcb7   17 years FrederikHeber FragmentMolecule(): debug messages removed for ADDHYDROGEN
(edit) @da83f8   17 years FrederikHeber added --enable-optimization, thrown -g -O specifics out of …
(edit) @090299   17 years FrederikHeber molecuilder reads and stored ion velocities Class atom has new …
(add) @a0bcf1   17 years FrederikHeber -initial commit -Minimum set of files needed from ESPACK SVN …
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