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@a4644b
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16 years |
FrederikHeber |
Extended the testsuite to encompass the vital areas of molecuilder.
- …
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@f92d00
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16 years |
FrederikHeber |
class molecule implementation split up into six separate parts.
- …
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@58808e
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16 years |
FrederikHeber |
Fixed testsuite, removed some minor bugs.
- …
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@8afe31
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16 years |
FrederikHeber |
Merge branch 'ConcaveHull' into ConvexHull
Conflicts:
.gitignore …
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@39d983
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16 years |
Saskia Metzler |
#19 Observe memory usage
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@606dfb
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16 years |
FrederikHeber |
Implemenation of embedding merge, untested. LinearInterpolation now …
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@8b7e0a
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16 years |
FrederikHeber |
New function RemoveAllBoundaryPoints() for sequentially removing all …
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@84b811
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16 years |
FrederikHeber |
Merge branch 'ConcaveHull' of …
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@66ce7a
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16 years |
FrederikHeber |
Replaced Vector::Projection() by Vector::ScalarProduct()
- Projection …
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@48cd93
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16 years |
Saskia Metzler |
Ticket 14: Rename .._.. functions in boundary.cpp
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@844cf5
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16 years |
FrederikHeber |
Sorted the menu list in ParseCommandLineParamaters() and print volume …
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@70c4567
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16 years |
FrederikHeber |
New function ConvexizeNonconvexEnvelope() to calculate the volume of a …
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@51abbe
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16 years |
FrederikHeber |
ParseCommandLineOptions(), NonConvex tesselation is now clocked.
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@0fc0b5
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16 years |
FrederikHeber |
Test case of filling a simulation domain with water included.
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@d93bb24
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16 years |
FrederikHeber |
FillWithMolecule() for testing built into ParseCommandLine()
JansCluster_water
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@834ff3
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16 years |
FrederikHeber |
Huge refactoring of Tesselation routines, but not finished yet.
- new …
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@4e4940
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16 years |
FrederikHeber |
We are one step further in fixing the convex hull: There are two …
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@78b45a
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16 years |
FrederikHeber |
ConvexTesselation working again.
- File was not written, as NULL was …
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@a0fb02
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16 years |
FrederikHeber |
BUGFIX: ManipulateAtoms() had mol = NULL
- in ManipulateAtoms() the …
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@53d153
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16 years |
FrederikHeber |
Split VolumeOfConvexEnvelope() into find_convex_border() and …
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@c3a303
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16 years |
FrederikHeber |
Merge branch 'master' into ConcaveHull
Conflicts:
…
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@a048fa
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16 years |
FrederikHeber |
fixed indentation from tabs to two spaces.
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@47548d
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16 years |
FrederikHeber |
Merge branch 'AtomRemoval'
Conflicts:
molecuilder/src/builder.cpp …
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@1f6efb
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16 years |
FrederikHeber |
fixed indentation from tabs to two spaces.
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@f39735
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16 years |
FrederikHeber |
Merge branch 'MultipleMolecules'
Conflicts:
…
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@560995
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16 years |
FrederikHeber |
Fix indentation from tabs to two spaces to prepare merging with …
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@1b2aa1
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16 years |
FrederikHeber |
Fix indentation from tab to two spaces.
The trouble was caused at the …
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@3b470f
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16 years |
FrederikHeber |
Merge branch 'Thermostat'
Conflicts:
.gitignore
Makefile.am …
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@6fb785
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16 years |
FrederikHeber |
molecule::CenterInBox puts atoms now periodically into the given box, …
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@ab7b5e7
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16 years |
FrederikHeber |
Memory leak fix: ParseCommandLineOptions() and main() free'd mol twice …
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@bd86e8
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16 years |
FrederikHeber |
Changed the unsatisfactory PathToDatabases construct, removing warning …
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@61e92a
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16 years |
FrederikHeber |
Removed unneeded variables
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@d98327
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16 years |
FrederikHeber |
BUGFIX: LinkedCell list had to created with 2.*RADIUS of sphere
Some …
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@eeae5b
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16 years |
FrederikHeber |
Cosmetical changes in Find_third_point_for_tesselation() and …
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@ea9696
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16 years |
FrederikHeber |
Removing of atoms via command line possible
-R switchs allows for the …
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@378e87
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16 years |
FrederikHeber |
BUGFIX: RemoveAtom() would remove the iterator, molecule::RemoveAtom() …
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@bb12e7
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16 years |
FrederikHeber |
removed lots of warnings due to unused variables
This arose due to …
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@37a050
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16 years |
FrederikHeber |
fixes due to changes in molecule structure (Center...()) and merge …
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@3021d93
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16 years |
FrederikHeber |
simple switched order for edit molecule to be in alphabetical ordering
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@c830e8e
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16 years |
FrederikHeber |
Basic implementation of Multiple molecules.
builder.cpp:
- …
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@451d7a
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17 years |
FrederikHeber |
Gaussian basis for MPQC input files can now be specified with -B …
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@f23d7d
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17 years |
FrederikHeber |
Basis for MPQC can now be specified via command line switch
* -B is …
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@e08f45
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17 years |
FrederikHeber |
Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull
Conflicts:
…
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@848729
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17 years |
FrederikHeber |
Just a temporary commit
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@eec6c8
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17 years |
FrederikHeber |
Now we also produce Raster3D output files additionally to TecPlot ones …
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@735468
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17 years |
neuen |
Another update w.r.t. the Tesselation.
Some signs switched, but atom …
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@db177a
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17 years |
neuen |
several changes, now output is created, quality unknown
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@59f86c
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17 years |
FrederikHeber |
VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and …
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@f89a9e
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17 years |
FrederikHeber |
config::Save() and config::SaveMPQC() now take string for filename, …
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@136e89
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17 years |
FrederikHeber |
ParseCommandLineOptions(): All cases now make thorough checks …
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@5a78f5
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17 years |
FrederikHeber |
BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected …
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@b86de7
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17 years |
FrederikHeber |
BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected …
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@556157
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17 years |
FrederikHeber |
thermostats enumerator, necessary variables included in class config, …
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@63b5c31
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17 years |
FrederikHeber |
Implemented molecule::LinearInterpolationBetweenConfiguration().
…
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@909610
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17 years |
FrederikHeber |
Basic implementation of Constrained MD is done, missing testing.
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@c99adf
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17 years |
FrederikHeber |
Constrained Molecular Dynamics: two new functions …
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@55ebd0
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17 years |
FrederikHeber |
ParseCommandLineOptions(): Command line option "-E" for changing an …
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@79cd79
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17 years |
FrederikHeber |
new function: molecule::OutputTemperatureFromTrajectories() stores …
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@f9cd68
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17 years |
FrederikHeber |
BUGFIX: Moved case 'a' in ParseCommandLineOptions() to the …
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@5887ed
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17 years |
FrederikHeber |
SaveConfig() now also stores an MPQC input file.
…
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@55e916
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17 years |
FrederikHeber |
FIX: ExitFlag not defaults to 0, and set specifically to 1 in the …
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@644ba1
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17 years |
FrederikHeber |
Adaptivity fixes, MD by VerletForceIntegration introduced, MD …
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@8f8621
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17 years |
FrederikHeber |
Rename of class vector to Vector to avoid conflict with vector from STL.
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@0a08df
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17 years |
FrederikHeber |
Scaffold of new function: VerletForceIntegration() - does MD step by …
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@39651f
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17 years |
FrederikHeber |
Removed Output of parsed elements db (does work well, so not necessary …
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@b3eb8e
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17 years |
FrederikHeber |
adding atom: element is now first, not last parameter and output …
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@375dcf
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17 years |
FrederikHeber |
introduced shieldings to analyzer and joiner
both now handle …
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@d7b1bf
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17 years |
FrederikHeber |
ParseCommandLineOptions(): new option 'O' centers system at origin
…
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@7a40c8
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17 years |
FrederikHeber |
ParseCommandLineOptions(): BUGFIX - break was missing for case 'n' …
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@1f9f1b
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17 years |
FrederikHeber |
BUGFIX: If other databases could not be loaded, no error was produced, …
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@0779a9
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17 years |
FrederikHeber |
some mor changes to fine-tune the cluster generation.
Sadly, …
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@3f0c46
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17 years |
FrederikHeber |
Final touches for Create Clusters in water
repetition in …
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@7fcea6
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17 years |
FrederikHeber |
Smaller fixes
CreateClustersinWater is now PrepareClustersinWater (as …
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@e292c10
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17 years |
FrederikHeber |
VolumeOfConvexEnvelope: Works!
VolumeOfConvexEnvelope has been …
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@ffcf49
|
17 years |
FrederikHeber |
fastparse enabled by "-n"
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@32b6dc
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17 years |
FrederikHeber |
Working version of PAS transformation (tested on C-S-H cluster) and …
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@9e831e
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17 years |
FrederikHeber |
main(): periode is not printed anymore after parsing cmd options, …
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@8b486e
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17 years |
FrederikHeber |
renamed ElementsFileName to PathToDatabases, -e now gives path to …
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@5eb05a
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17 years |
FrederikHeber |
molecule::CreateAdjacencyList() now needs IsAngstroem as parameter
…
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@f75030
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17 years |
FrederikHeber |
Lots of for loops now count in reverse order where it does not matter, …
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@3ce105
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17 years |
FrederikHeber |
command line parsing outsourced to ParseCommandLineOptions(), cases in …
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@0e348e
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17 years |
FrederikHeber |
main(): typo in Usage message, BUGFIX - command line arguments did not …
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@0716ff4
|
17 years |
FrederikHeber |
MinimumRingSize is now an array over all atoms
Each entry in …
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@c75363
|
17 years |
FrederikHeber |
HUGE REWRITE to allow for adaptive increase of the bond order, first …
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@e936b3
|
17 years |
FrederikHeber |
Velocities were not correctly handled, also not in fragments
First …
non_adaptive_molecuilder
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@c510a7
|
17 years |
FrederikHeber |
char lengths of 255 and MAXDUMMYSTRING replaced with define …
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@9bd230
|
17 years |
FrederikHeber |
changed config file to first argument again and standard config name …
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@584691
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17 years |
FrederikHeber |
bugfix in main: without arguments, code would crash due to access of …
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@36b128
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17 years |
FrederikHeber |
Comply with test again: help and version command options exit at once
…
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@f5306f
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17 years |
FrederikHeber |
config::Load..() now get filename instead of pointer to file, bugfix …
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@a829d1
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17 years |
FrederikHeber |
new elementsdb-switch and command line options parsing parts moved …
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@8129de
|
17 years |
FrederikHeber |
Huge rewrite of initial command line parsing
config file argument is …
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@a0bcf1
|
17 years |
FrederikHeber |
-initial commit
-Minimum set of files needed from ESPACK SVN …
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