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@68fbb5
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18 years |
FrederikHeber |
Revert "some new functions: vector::vector(), …
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@c4a0a2
|
18 years |
FrederikHeber |
enabled fast parsing (-n)
config::Load(): the repetition and thereby …
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@d11f22
|
18 years |
FrederikHeber |
some new functions: vector::vector(), vector::ProjectOntoPlane(), …
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@32b6dc
|
18 years |
FrederikHeber |
Working version of PAS transformation (tested on C-S-H cluster) and …
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@a89a22
|
18 years |
FrederikHeber |
these are all smaller fixes due to extensively enabled compiler …
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@75793b2
|
18 years |
FrederikHeber |
these are all smaller fixes due to extensively enabled compiler …
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@02bc3c
|
18 years |
FrederikHeber |
new aclocal macro with controles all the …
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@0cc323
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18 years |
FrederikHeber |
<string.h> needed for strncat and companions for gcc-4.3.0
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@807e8a
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18 years |
FrederikHeber |
libblas needed for libgsl is now found via AC_SEARCH_LIB and list blas …
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@eefb8e
|
18 years |
FrederikHeber |
OutputConfigForListOfFragments(): return of …
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@bdba3c
|
18 years |
FrederikHeber |
AM_CFLAGS thrown out as warnings are added to CFLAGS in …
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@328544
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18 years |
FrederikHeber |
LoadPeriodentafel() mixup of cat and cpy orders prevented loading of …
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@9e831e
|
18 years |
FrederikHeber |
main(): periode is not printed anymore after parsing cmd options, …
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@9bfb34
|
18 years |
FrederikHeber |
for bigger molecules listing of found keywords slows things done (yet, …
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@cfaf42
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18 years |
FrederikHeber |
renamed ElementsFileName to PathToDatabases, -e now gives path to …
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@8b486e
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18 years |
FrederikHeber |
renamed ElementsFileName to PathToDatabases, -e now gives path to …
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@8dc9b3
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18 years |
FrederikHeber |
BUGFIX: config files' path in the current working directory would not …
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@3b1427
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18 years |
FrederikHeber |
BUGFIX: single letter FragmentNumbers gave "\n" as return string.
…
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@51483b
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18 years |
FrederikHeber |
Some sensible starting values for element class construct
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@38c017
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18 years |
FrederikHeber |
new define LocalPath being the local path for pointers to set to (like …
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@5063f1
|
18 years |
FrederikHeber |
bit more verbosity on the FragmentNumber
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@23c207
|
18 years |
FrederikHeber |
fragmentation no more has various methods (dropped ... A)
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@94b458
|
18 years |
FrederikHeber |
BUGFIX: line.erase() threw exception with illegal line end
Found by …
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@5eb05a
|
18 years |
FrederikHeber |
molecule::CreateAdjacencyList() now needs IsAngstroem as parameter
…
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@44fa6a
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18 years |
FrederikHeber |
removed specialised CFLAGS for general AM_C(PP)FLAGS that just enable …
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@f75030
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18 years |
FrederikHeber |
Lots of for loops now count in reverse order where it does not matter, …
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@a6e314
|
18 years |
FrederikHeber |
ParseMatrix(): char * to string, Contains() hat KeySetContainer:: …
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@3ce105
|
18 years |
FrederikHeber |
command line parsing outsourced to ParseCommandLineOptions(), cases in …
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@927aba
|
18 years |
FrederikHeber |
new function CenterInBox, some char* converted to string
CenterInBox …
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@06feff
|
18 years |
FrederikHeber |
new vector header added to molecuilder_SOURCES
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@33c05d
|
18 years |
FrederikHeber |
one lousy space added
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@725869
|
18 years |
FrederikHeber |
new header file for the vector class, new operators +=,*=,*,+
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@0e348e
|
18 years |
FrederikHeber |
main(): typo in Usage message, BUGFIX - command line arguments did not …
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@cc6dfb
|
18 years |
FrederikHeber |
CyclicStructureAnalysis(): forget to check whether we actually have …
|
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@0716ff4
|
18 years |
FrederikHeber |
MinimumRingSize is now an array over all atoms
Each entry in …
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@2700f5e
|
18 years |
FrederikHeber |
TranslateIndicesToGlobalIDs() did not check whether FragmentList.. …
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@59ddad
|
18 years |
FrederikHeber |
joiner now writes ENERGYPERFRAGMENT file for adaptive BOSSANOVA
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@0421a3
|
18 years |
FrederikHeber |
CreateDataFragment(): endline after datum in header
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@c84895
|
18 years |
FrederikHeber |
ENERGYPERFRAGMENT without ".dat"
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@310b25
|
18 years |
FrederikHeber |
some comments for where "F" and where "E" terms are created
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@a3ff7b2
|
18 years |
FrederikHeber |
molecule::CheckOrderAtSite() now interprets negative Orders as …
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@461e93
|
18 years |
FrederikHeber |
molecule::CheckOrderAtSite() returns bool and used as threshold …
|
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@d88597
|
18 years |
FrederikHeber |
new function molecule::CreateMappingLabelsToConfigSequence() creates …
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@2b79c3
|
18 years |
FrederikHeber |
new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in …
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@169b24
|
18 years |
FrederikHeber |
new functions MoleculeLeafClass::AssignKeySetsToFragment() and …
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@ea84ed
|
18 years |
FrederikHeber |
FragmentMolecule(): abstractized AssignKeySetsToFragments() and …
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@84e88a
|
18 years |
FrederikHeber |
new function FillListOfLocalAtoms() checks whether List needs filling …
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@08fd83
|
18 years |
FrederikHeber |
MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling of …
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@7b80a5
|
18 years |
FrederikHeber |
new functions MoleculeLeafClass::Count() and …
|
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@255d13
|
18 years |
FrederikHeber |
FillBondStructureFromReference: previous == NULL was bad idea, new …
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@9c3496
|
18 years |
FrederikHeber |
new function molecule::CheckOrderAtSite and …
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@b8eb3a
|
18 years |
FrederikHeber |
new function MoleculeLeafClass::FillBondStructureFromReference that …
|
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@c901e3
|
18 years |
FrederikHeber |
new function CreateFatherLookupTable
Creates a lookup table for true …
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@7afa7e
|
18 years |
FrederikHeber |
Matrix::ParseMatrix()L: comment makes it clearer at what fragment with …
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@a01955
|
18 years |
FrederikHeber |
rewritten CyclicStructureAnalysis(): uses DFS spanning tree and …
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@d50d2a
|
18 years |
FrederikHeber |
AtomStackClass -> template <typename T> StackClass<T> change in new …
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@417bb5
|
18 years |
FrederikHeber |
changed comments a bit
|
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@48efc3
|
18 years |
FrederikHeber |
MatrixContainer::MatrixContainer() debug message fixes only, …
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@0e8321
|
18 years |
FrederikHeber |
KeySetFile is stored without an additional last tab on each line
|
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@8449ed
|
18 years |
FrederikHeber |
joiner crashed due to incorrect destructing of MatrixContainer, …
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@115bf4
|
18 years |
FrederikHeber |
ForcesFile and TEFactors are _needed_, reincorporated. UniqueFragments …
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@38fc0d
|
18 years |
FrederikHeber |
Free(): only set to NULL if it was free'd otherwise it is already
|
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@cffff8
|
18 years |
FrederikHeber |
~MatrixContainer(): Bugfix - Free if Matrix[MatrixCounter] would also …
|
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@30fda2
|
18 years |
FrederikHeber |
commenting in header changed for the four main functions that …
|
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|
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@c75363
|
18 years |
FrederikHeber |
HUGE REWRITE to allow for adaptive increase of the bond order, first …
|
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|
|
@e936b3
|
18 years |
FrederikHeber |
Velocities were not correctly handled, also not in fragments
First …
non_adaptive_molecuilder
|
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|
@c510a7
|
18 years |
FrederikHeber |
char lengths of 255 and MAXDUMMYSTRING replaced with define …
|
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|
@307fd1
|
18 years |
FrederikHeber |
Store/CheckAdj...() now also incorporate bond order to check against.
|
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@16b0c8
|
18 years |
FrederikHeber |
config file is again first argument and implemented test of …
|
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@9bd230
|
18 years |
FrederikHeber |
changed config file to first argument again and standard config name …
|
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@7e2c5c
|
18 years |
FrederikHeber |
bugfix: configpath and -name are not set to empty string.
|
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@584691
|
18 years |
FrederikHeber |
bugfix in main: without arguments, code would crash due to access of …
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|
@2456db
|
18 years |
FrederikHeber |
Full test for fragmentation procedure with readin of the adjacency …
|
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|
@7b1cea
|
18 years |
FrederikHeber |
configname is also stored in config structure, GetDefaultPath by …
|
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@36b128
|
18 years |
FrederikHeber |
Comply with test again: help and version command options exit at once
…
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@f5306f
|
18 years |
FrederikHeber |
config::Load..() now get filename instead of pointer to file, bugfix …
|
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|
|
@661288
|
18 years |
FrederikHeber |
Atoms in the fragments in the configs are again ordered as first …
|
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|
@e565a8
|
18 years |
FrederikHeber |
removed some output lines (commented-out) mostly in …
|
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@8efbfc
|
18 years |
FrederikHeber |
FragmentMolecule(): status variable used when checking adjacency file …
|
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|
@d982bb
|
18 years |
FrederikHeber |
All filenames (const char *) have been transferred to defs.hpp
…
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@34d37c
|
18 years |
FrederikHeber |
storing and comparing Adjacency outsourced into two new functions.
…
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@2614f83
|
18 years |
FrederikHeber |
FragmentMolecule(): Adjacency store/check and parsing of KeySetFile …
|
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|
@bd8439
|
18 years |
FrederikHeber |
main(): thrown out unused stringstreams prefix and line
|
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|
@23409a
|
18 years |
FrederikHeber |
OutputConfigForListOfFragments(): various ofstream gathered into a …
|
|
|
|
@1ddebb
|
18 years |
FrederikHeber |
forgot to commit the actual autotest files listed during last commit, …
|
|
|
|
@b5279f0
|
18 years |
FrederikHeber |
Complete test kit (make check) for the three parts: pcp, molecuilder, …
|
|
|
|
@16cd31
|
18 years |
FrederikHeber |
AddXYZFile(): Bugfix - if element could not be parsed (e.g. elements …
|
|
|
|
@c72cbe
|
18 years |
FrederikHeber |
Load/StorePeriodentafel(): filename as parameter, if NULL default name …
|
|
|
|
@a829d1
|
18 years |
FrederikHeber |
new elementsdb-switch and command line options parsing parts moved …
|
|
|
|
@b021e4
|
18 years |
FrederikHeber |
Load/StorePeriodentafel(): filename as parameter, if NULL default name …
|
|
|
|
@8129de
|
18 years |
FrederikHeber |
Huge rewrite of initial command line parsing
config file argument is …
|
|
|
|
@370060
|
18 years |
FrederikHeber |
added VERSIONSTRING
|
|
|
|
@941b66
|
18 years |
FrederikHeber |
LoadPeriodentafel(): no more outputs of parsed elements
|
|
|
|
@201832
|
18 years |
FrederikHeber |
normal blas (e.g. prefered gotoblas) instead of gslcblas is used in linking
|
|
|
|
@77da65
|
18 years |
FrederikHeber |
ADDHYDROGEN and HAVE_DEBUG fix: config.h was not yet included
…
|
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|
|
@e58fcb7
|
18 years |
FrederikHeber |
FragmentMolecule(): debug messages removed for ADDHYDROGEN
|
|
|
|
@bd7b85
|
18 years |
FrederikHeber |
AC_MSG_WARN if both optimization and debug present removed
As …
|
|
|
|
@da83f8
|
18 years |
FrederikHeber |
added --enable-optimization, thrown -g -O specifics out of …
|
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|
|
@090299
|
18 years |
FrederikHeber |
molecuilder reads and stored ion velocities
Class atom has new …
|
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|
|
@a0bcf1
|
18 years |
FrederikHeber |
-initial commit
-Minimum set of files needed from ESPACK SVN …
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