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@3d4088
|
17 years |
FrederikHeber |
Included missing silicon and took more or lesss sensible values for …
|
|
|
|
@67f102
|
17 years |
FrederikHeber |
config::Save() and config::Load() parse MD steps into and out of …
|
|
|
|
@8f8621
|
17 years |
FrederikHeber |
Rename of class vector to Vector to avoid conflict with vector from STL.
|
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|
@0a08df
|
17 years |
FrederikHeber |
Scaffold of new function: VerletForceIntegration() - does MD step by …
|
|
|
|
@e8dd4d
|
17 years |
FrederikHeber |
pcp.speed is parsed and analyzed again (Time matrices).
This was …
|
|
|
|
@e6372f
|
17 years |
FrederikHeber |
The entries in the Header of ForceMatrix are now separated by tabs, …
|
|
|
|
@7670cab
|
17 years |
FrederikHeber |
new test function CheckForConnectedSubgraph() and bigger rewrite of …
|
|
|
|
@ec947b
|
17 years |
FrederikHeber |
CyclicStructureAnalysis(): BUGFIX - BFSStack may be empty if we can't …
|
|
|
|
@d49416
|
17 years |
FrederikHeber |
2 BUGFIXES: CreateAdjacencyList() and CyclicStructureAnalysis()
…
|
|
|
|
@126934
|
17 years |
FrederikHeber |
CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms …
|
|
|
|
@3f805d
|
17 years |
FrederikHeber |
CyclicStructureAnalysis: BUGFIX - MinimumRingSize was not set …
|
|
|
|
@39651f
|
17 years |
FrederikHeber |
Removed Output of parsed elements db (does work well, so not necessary …
|
|
|
|
@747b10
|
17 years |
FrederikHeber |
CheckOrderAtSite: BUGFIX - Added MinimumRingSize to parameter list, as …
|
|
|
|
@db3ea3
|
17 years |
FrederikHeber |
BIG change: Hcorrection included and bugfix of analyzer (wrt forces)
…
JoinAnalysis_works_for_forces
|
|
|
|
@b3eb8e
|
17 years |
FrederikHeber |
adding atom: element is now first, not last parameter and output …
|
|
|
|
@0f7a85
|
17 years |
FrederikHeber |
BUGFIX: elements.db is now using path instead of file
elements …
|
|
|
|
@ed5f58
|
17 years |
FrederikHeber |
class vector was wrongly still in molecules.hpp instead of vector.hpp
|
|
|
|
@23b4aa
|
17 years |
FrederikHeber |
StoreKeySetFile(): removed unncessary iterator "ende" storing
|
|
|
|
@6beb99
|
17 years |
FrederikHeber |
changed verbosity a bit
|
|
|
|
@375dcf
|
17 years |
FrederikHeber |
introduced shieldings to analyzer and joiner
both now handle …
|
|
|
|
@d7b1bf
|
17 years |
FrederikHeber |
ParseCommandLineOptions(): new option 'O' centers system at origin
…
|
|
|
|
@329d0f
|
17 years |
FrederikHeber |
StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond …
|
|
|
|
@7a40c8
|
17 years |
FrederikHeber |
ParseCommandLineOptions(): BUGFIX - break was missing for case 'n' …
|
|
|
|
@cccac6
|
17 years |
FrederikHeber |
Merge branch 'bisect' into AdaptiveMolecuilder
|
|
|
|
@42bdb2
|
17 years |
FrederikHeber |
MatrixContainer::ParseMatrix(): BUGFIX - line_s_.eof()
Bug was …
|
|
|
|
@b73d28
|
17 years |
FrederikHeber |
OutputConfigForListOfFragments(): boundary is now 2.5 Angstroem …
|
|
|
|
@1f9f1b
|
17 years |
FrederikHeber |
BUGFIX: If other databases could not be loaded, no error was produced, …
|
|
|
|
@0779a9
|
17 years |
FrederikHeber |
some mor changes to fine-tune the cluster generation.
Sadly, …
|
|
|
|
@3f0c46
|
17 years |
FrederikHeber |
Final touches for Create Clusters in water
repetition in …
|
|
|
|
@7fcea6
|
17 years |
FrederikHeber |
Smaller fixes
CreateClustersinWater is now PrepareClustersinWater (as …
|
|
|
|
@e292c10
|
17 years |
FrederikHeber |
VolumeOfConvexEnvelope: Works!
VolumeOfConvexEnvelope has been …
|
|
|
|
@9185c8
|
17 years |
FrederikHeber |
cosmetics
|
|
|
|
@dcf51d
|
17 years |
FrederikHeber |
StorePeriodentafel(): BUGFIX - there still was elements.db instead of …
|
|
|
|
@364fc0
|
17 years |
FrederikHeber |
fastparse was not yet working for more than one ion type
moved …
|
|
|
|
@2259f4
|
17 years |
FrederikHeber |
VolumeOfConvexEnvelope() finished and tested with SiOH4, …
|
|
|
|
@ffcf49
|
17 years |
FrederikHeber |
fastparse enabled by "-n"
|
|
|
|
@b9a995
|
17 years |
FrederikHeber |
some new functions: vector::vector(), vector::ProjectOntoPlane(), …
|
|
|
|
@68fbb5
|
17 years |
FrederikHeber |
Revert "some new functions: vector::vector(), …
|
|
|
|
@c4a0a2
|
17 years |
FrederikHeber |
enabled fast parsing (-n)
config::Load(): the repetition and thereby …
|
|
|
|
@d11f22
|
17 years |
FrederikHeber |
some new functions: vector::vector(), vector::ProjectOntoPlane(), …
|
|
|
|
@32b6dc
|
17 years |
FrederikHeber |
Working version of PAS transformation (tested on C-S-H cluster) and …
|
|
|
|
@a89a22
|
17 years |
FrederikHeber |
these are all smaller fixes due to extensively enabled compiler …
|
|
|
|
@75793b2
|
17 years |
FrederikHeber |
these are all smaller fixes due to extensively enabled compiler …
|
|
|
|
@0cc323
|
17 years |
FrederikHeber |
<string.h> needed for strncat and companions for gcc-4.3.0
|
|
|
|
@eefb8e
|
17 years |
FrederikHeber |
OutputConfigForListOfFragments(): return of …
|
|
|
|
@bdba3c
|
17 years |
FrederikHeber |
AM_CFLAGS thrown out as warnings are added to CFLAGS in …
|
|
|
|
@328544
|
17 years |
FrederikHeber |
LoadPeriodentafel() mixup of cat and cpy orders prevented loading of …
|
|
|
|
@9e831e
|
17 years |
FrederikHeber |
main(): periode is not printed anymore after parsing cmd options, …
|
|
|
|
@9bfb34
|
17 years |
FrederikHeber |
for bigger molecules listing of found keywords slows things done (yet, …
|
|
|
|
@cfaf42
|
17 years |
FrederikHeber |
renamed ElementsFileName to PathToDatabases, -e now gives path to …
|
|
|
|
@8b486e
|
17 years |
FrederikHeber |
renamed ElementsFileName to PathToDatabases, -e now gives path to …
|
|
|
|
@8dc9b3
|
17 years |
FrederikHeber |
BUGFIX: config files' path in the current working directory would not …
|
|
|
|
@3b1427
|
17 years |
FrederikHeber |
BUGFIX: single letter FragmentNumbers gave "\n" as return string.
…
|
|
|
|
@51483b
|
17 years |
FrederikHeber |
Some sensible starting values for element class construct
|
|
|
|
@38c017
|
17 years |
FrederikHeber |
new define LocalPath being the local path for pointers to set to (like …
|
|
|
|
@5063f1
|
17 years |
FrederikHeber |
bit more verbosity on the FragmentNumber
|
|
|
|
@94b458
|
17 years |
FrederikHeber |
BUGFIX: line.erase() threw exception with illegal line end
Found by …
|
|
|
|
@5eb05a
|
17 years |
FrederikHeber |
molecule::CreateAdjacencyList() now needs IsAngstroem as parameter
…
|
|
|
|
@44fa6a
|
17 years |
FrederikHeber |
removed specialised CFLAGS for general AM_C(PP)FLAGS that just enable …
|
|
|
|
@f75030
|
17 years |
FrederikHeber |
Lots of for loops now count in reverse order where it does not matter, …
|
|
|
|
@a6e314
|
17 years |
FrederikHeber |
ParseMatrix(): char * to string, Contains() hat KeySetContainer:: …
|
|
|
|
@3ce105
|
17 years |
FrederikHeber |
command line parsing outsourced to ParseCommandLineOptions(), cases in …
|
|
|
|
@927aba
|
17 years |
FrederikHeber |
new function CenterInBox, some char* converted to string
CenterInBox …
|
|
|
|
@06feff
|
17 years |
FrederikHeber |
new vector header added to molecuilder_SOURCES
|
|
|
|
@33c05d
|
17 years |
FrederikHeber |
one lousy space added
|
|
|
|
@725869
|
17 years |
FrederikHeber |
new header file for the vector class, new operators +=,*=,*,+
|
|
|
|
@0e348e
|
17 years |
FrederikHeber |
main(): typo in Usage message, BUGFIX - command line arguments did not …
|
|
|
|
@cc6dfb
|
17 years |
FrederikHeber |
CyclicStructureAnalysis(): forget to check whether we actually have …
|
|
|
|
@0716ff4
|
17 years |
FrederikHeber |
MinimumRingSize is now an array over all atoms
Each entry in …
|
|
|
|
@2700f5e
|
17 years |
FrederikHeber |
TranslateIndicesToGlobalIDs() did not check whether FragmentList.. …
|
|
|
|
@59ddad
|
17 years |
FrederikHeber |
joiner now writes ENERGYPERFRAGMENT file for adaptive BOSSANOVA
|
|
|
|
@0421a3
|
17 years |
FrederikHeber |
CreateDataFragment(): endline after datum in header
|
|
|
|
@c84895
|
17 years |
FrederikHeber |
ENERGYPERFRAGMENT without ".dat"
|
|
|
|
@310b25
|
17 years |
FrederikHeber |
some comments for where "F" and where "E" terms are created
|
|
|
|
@a3ff7b2
|
17 years |
FrederikHeber |
molecule::CheckOrderAtSite() now interprets negative Orders as …
|
|
|
|
@461e93
|
17 years |
FrederikHeber |
molecule::CheckOrderAtSite() returns bool and used as threshold …
|
|
|
|
@d88597
|
17 years |
FrederikHeber |
new function molecule::CreateMappingLabelsToConfigSequence() creates …
|
|
|
|
@2b79c3
|
17 years |
FrederikHeber |
new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in …
|
|
|
|
@169b24
|
17 years |
FrederikHeber |
new functions MoleculeLeafClass::AssignKeySetsToFragment() and …
|
|
|
|
@ea84ed
|
17 years |
FrederikHeber |
FragmentMolecule(): abstractized AssignKeySetsToFragments() and …
|
|
|
|
@84e88a
|
17 years |
FrederikHeber |
new function FillListOfLocalAtoms() checks whether List needs filling …
|
|
|
|
@08fd83
|
17 years |
FrederikHeber |
MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling of …
|
|
|
|
@7b80a5
|
17 years |
FrederikHeber |
new functions MoleculeLeafClass::Count() and …
|
|
|
|
@255d13
|
17 years |
FrederikHeber |
FillBondStructureFromReference: previous == NULL was bad idea, new …
|
|
|
|
@9c3496
|
17 years |
FrederikHeber |
new function molecule::CheckOrderAtSite and …
|
|
|
|
@b8eb3a
|
17 years |
FrederikHeber |
new function MoleculeLeafClass::FillBondStructureFromReference that …
|
|
|
|
@c901e3
|
17 years |
FrederikHeber |
new function CreateFatherLookupTable
Creates a lookup table for true …
|
|
|
|
@7afa7e
|
17 years |
FrederikHeber |
Matrix::ParseMatrix()L: comment makes it clearer at what fragment with …
|
|
|
|
@a01955
|
17 years |
FrederikHeber |
rewritten CyclicStructureAnalysis(): uses DFS spanning tree and …
|
|
|
|
@d50d2a
|
17 years |
FrederikHeber |
AtomStackClass -> template <typename T> StackClass<T> change in new …
|
|
|
|
@417bb5
|
17 years |
FrederikHeber |
changed comments a bit
|
|
|
|
@48efc3
|
17 years |
FrederikHeber |
MatrixContainer::MatrixContainer() debug message fixes only, …
|
|
|
|
@0e8321
|
17 years |
FrederikHeber |
KeySetFile is stored without an additional last tab on each line
|
|
|
|
@8449ed
|
17 years |
FrederikHeber |
joiner crashed due to incorrect destructing of MatrixContainer, …
|
|
|
|
@115bf4
|
17 years |
FrederikHeber |
ForcesFile and TEFactors are _needed_, reincorporated. UniqueFragments …
|
|
|
|
@38fc0d
|
17 years |
FrederikHeber |
Free(): only set to NULL if it was free'd otherwise it is already
|
|
|
|
@cffff8
|
17 years |
FrederikHeber |
~MatrixContainer(): Bugfix - Free if Matrix[MatrixCounter] would also …
|
|
|
|
@30fda2
|
17 years |
FrederikHeber |
commenting in header changed for the four main functions that …
|
|
|
|
@c75363
|
17 years |
FrederikHeber |
HUGE REWRITE to allow for adaptive increase of the bond order, first …
|
|
|
|
@e936b3
|
17 years |
FrederikHeber |
Velocities were not correctly handled, also not in fragments
First …
non_adaptive_molecuilder
|
|
|
|
