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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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@307290
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16 years |
FrederikHeber |
Merge branch 'ConstrainedMolecularDynamics'
Conflicts:
…
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@59a745
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16 years |
FrederikHeber |
Merge branch 'test'
Conflicts:
molecuilder/src/analyzer.cpp …
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@3b470f
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16 years |
FrederikHeber |
Merge branch 'Thermostat'
Conflicts:
.gitignore
Makefile.am …
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@09f4dc
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16 years |
FrederikHeber |
Merge branch 'HessianMatrix'
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@2218dca
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16 years |
FrederikHeber |
Merge branch 'GraphRefactoring'
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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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17 years |
FrederikHeber |
BUGFIX: RemoveAtom() would remove the iterator, molecule::RemoveAtom() …
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@a41b50
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17 years |
FrederikHeber |
return type of MoleculeListClass::insert is now void instead of bool …
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@bb12e7
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17 years |
FrederikHeber |
removed lots of warnings due to unused variables
This arose due to …
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@37a050
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17 years |
FrederikHeber |
fixes due to changes in molecule structure (Center...()) and merge …
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@d618b5
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17 years |
FrederikHeber |
Lots of bugfixes, some name changes and new functions
BUGFIX:
- …
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@8b05c6
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17 years |
FrederikHeber |
MoleculeListClass::Enumerate() lists center and size of molecule, fix …
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@899029f
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17 years |
FrederikHeber |
Framework for embedding one molecule into another, now the embedding …
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@3021d93
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17 years |
FrederikHeber |
simple switched order for edit molecule to be in alphabetical ordering
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@c830e8e
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17 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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@97c751
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17 years |
FrederikHeber |
Chi integration had some copy&paste error
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@e08f45
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17 years |
FrederikHeber |
Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull
Conflicts:
…
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@dafe43
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17 years |
FrederikHeber |
Merge ../espack3
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@d3d15c
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17 years |
FrederikHeber |
Find_non_convex_border(): calls CreateAdjacencyList() to fill bond list
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@95183e
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17 years |
FrederikHeber |
New file and class LinkedCell that contains the linked cell algorithms …
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@848729
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17 years |
FrederikHeber |
Just a temporary commit
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@3d9045
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17 years |
FrederikHeber |
Merge branch 'ConcaveHull' of …
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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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@2ac928
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17 years |
neuen |
fancy commit
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@fe3c9a
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17 years |
FrederikHeber |
Merge branch 'ConcaveHull' of …
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@07c050
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17 years |
FrederikHeber |
Cleaned up all debugging output
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@56a489
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17 years |
neuen |
BallAngel enhanced, added new alternative direction for issues with …
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@edf4a0
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17 years |
neuen |
Switched choice process to Ball angle completely.
Problem remains. …
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@2b7a1a
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17 years |
neuen |
First change to Ball angle as criteria, however, change sucks.
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@87c8e7
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17 years |
neuen |
Solved possible problem with Second quadrant overhaul
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@313dff
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17 years |
neuen |
Tesselation starts to look good, minor discrepancies are still there …
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@5a447f
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17 years |
neuen |
Atom indices are now correctly processed.
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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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@3e20fe
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17 years |
neuen |
Parses a pdb and xyz file and decideds which atoms are in both and …
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@e0c5b1
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17 years |
neuen |
Multiple changes to boundary, currently not fully operational. …
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@f5b58e
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17 years |
neuen |
The border.cpp contains the same functions as the changes in boundary, …
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@6b3826
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17 years |
neuen |
In vector a function for calculation of the vector-(cross-)product has …
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@a709c4
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17 years |
neuen |
Construction of border triangles of non convex point set
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@6ce722
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17 years |
FrederikHeber |
Analyzer now produces data file with Frobenius norm of hessian matrix.
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@ab64f4
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17 years |
FrederikHeber |
Added some commentary to HessianMatrix::SumSubHessians to ease debugging
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@95628a
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17 years |
FrederikHeber |
Implemented Frobenius norm calculation for class HessianMatrix
…
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@f98e5a
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17 years |
FrederikHeber |
HessianMatrix implemented fully, but not yet working, probably due to …
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@002351
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17 years |
FrederikHeber |
Implemented analysis of magnetic susceptibilites.
This is very …
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@650212
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17 years |
FrederikHeber |
Begin of implementing classes Graph, SubGraph, Node and Edge.
So far …
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@d40e32
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17 years |
FrederikHeber |
Analyzer now produces data file with Frobenius norm of hessian matrix.
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@5f5df2
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17 years |
FrederikHeber |
Begin of implementing classes Graph, SubGraph, Node and Edge.
So far …
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@25f5089
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17 years |
FrederikHeber |
Added some commentary to HessianMatrix::SumSubHessians to ease debugging
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@348b6a
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17 years |
FrederikHeber |
Implemented analysis of magnetic susceptibilites.
This is very …
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@5fd79e
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17 years |
FrederikHeber |
Implemented Frobenius norm calculation for class HessianMatrix
…
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@aa2e37
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17 years |
FrederikHeber |
HessianMatrix implemented fully, but not yet working, probably due to …
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@b4c71a
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17 years |
FrederikHeber |
ColumnCounter -> *ColumnCounter
columns of the MatrixContainer class …
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@d87482
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17 years |
FrederikHeber |
Introduced new class HessianMatrix derived from MatrixContainer, which …
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@59f86c
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17 years |
FrederikHeber |
VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and …
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@f5d7e1
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17 years |
FrederikHeber |
molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, …
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@fa2d7d
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17 years |
FrederikHeber |
Analyzer now writes usable plot and data files for shielding …
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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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@88e31c
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17 years |
FrederikHeber |
periodentafel::LoadPeriodentafel(): if other dbs fail, we just give a …
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@45105b
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17 years |
FrederikHeber |
New function IsValidNumber(): checks whether a command line argument …
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@93d0ee
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17 years |
FrederikHeber |
Analyzer now prints usable ShieldingsPAS data and plot files (so that …
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@b248ca
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17 years |
FrederikHeber |
new function AppendOutputFile() for appending to output files whereas …
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@a7e452
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17 years |
FrederikHeber |
molecule::VerletForceIntegration() different code, same algorithm …
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@7a3724
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17 years |
FrederikHeber |
new version of Tesselation::GuessStartingTriangle() seems to fix …
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@51d33c5
|
17 years |
FrederikHeber |
BUGFIX: Tesselation::AddPoint() always increased …
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@45d5cc
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17 years |
FrederikHeber |
changed basis set for mpqc from STO-3G to 3-21G (more stable with …
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@139f8c
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17 years |
FrederikHeber |
corrected number of valence orbitals for Calcium (2 -> 4) and inserted …
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@1e5e16
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17 years |
FrederikHeber |
molecule::AddHydrogenReplacementAtom() returns false on missing …
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@2bfaf8
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17 years |
FrederikHeber |
BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong place …
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@4959f1
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17 years |
FrederikHeber |
BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in output …
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@372c4cd
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17 years |
FrederikHeber |
BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong place …
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@31ed7d
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17 years |
FrederikHeber |
BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in output …
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@14178b
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17 years |
FrederikHeber |
BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong place …
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@d01f4d
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17 years |
FrederikHeber |
BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in output …
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@1bd619
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17 years |
FrederikHeber |
BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected …
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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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@a7b3b8
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17 years |
FrederikHeber |
Output of atom and bond to stream now is set to const bond/atom
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@68cfd1
|
17 years |
FrederikHeber |
corrected molecule::VerletForceIntegration() and analyzer creates data …
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@556157
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17 years |
FrederikHeber |
thermostats enumerator, necessary variables included in class config, …
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@c49678
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17 years |
FrederikHeber |
Lots of conversion factors for various units
Were taken from PCP defs.h
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@bb28e0
|
17 years |
FrederikHeber |
Some files were missing in the repository
pseudopotentials and the …
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@4a434c
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17 years |
FrederikHeber |
molecule::MinimiseConstrainedPotential(): Extension of search and …
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@9070650
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17 years |
FrederikHeber |
molecule::MinimiseConstrainedPotential() : Minimisation is fixed
Now, …
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@63b5c31
|
17 years |
FrederikHeber |
Implemented molecule::LinearInterpolationBetweenConfiguration().
…
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@909610
|
17 years |
FrederikHeber |
Basic implementation of Constrained MD is done, missing testing.
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@c99adf
|
17 years |
FrederikHeber |
Constrained Molecular Dynamics: two new functions …
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@4917ddd
|
17 years |
FrederikHeber |
config::DoWannier implemented that is parsed from config file, default is 0
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@55ebd0
|
17 years |
FrederikHeber |
ParseCommandLineOptions(): Command line option "-E" for changing an …
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@8e52aa
|
17 years |
FrederikHeber |
BUGFIX: Normalize() would try to normalize a zero vector which ended …
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@79cd79
|
17 years |
FrederikHeber |
new function: molecule::OutputTemperatureFromTrajectories() stores …
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@b21e1f
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17 years |
FrederikHeber |
BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did only …
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@d473c3
|
17 years |
FrederikHeber |
BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which …
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