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Add function calls to MdModules to sign up for notifications
2020-03-05
Christian Blau
Add function calls to MdModules to sign up for notifications
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2020-03-05
Christian Blau
Split off implementation details of MdModuleNotification
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2020-03-04
Christian Blau
Save excluded non-bonded interactions in .tpr file
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2020-03-04
Christian Blau
Add classhelper macro to forbid copy, move and any...
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2020-02-25
Christian Blau
Document density-fit cross-correlation in .mdp options
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2020-02-18
Christian Blau
Split MdModuleNotifications into topics
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2020-02-12
Christian Blau
Introduce readXvgData to read xvg data into std::vector
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2020-01-31
Christian Blau
Documentation fix for local atom set data
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2019-12-20
Christian Blau
Remove problematic output of gmx angle
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2019-12-15
Christian Blau
Fix densityfitting stalling and energies
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2019-12-12
Christian Blau
Densityfitting - enforce similarity increase with adaptive...
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2019-12-06
Christian Blau
Change arbitrary units to counts in RMSD distance distributi...
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2019-12-05
Christian Blau
Relax cross-correlation test precision
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2019-12-04
Christian Blau
Remove cutoff-scheme group from default mdout.mdp output
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2019-12-02
Christian Blau
Relax test tolerance for cross correlation measure...
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2019-11-28
Christian Blau
Fix check-pointing for density guided simulations
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2019-11-25
Christian Blau
Fix duplicate CONNECT records in pdb files
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2019-11-25
Christian Blau
Read mrc density map format with all endianesses.
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2019-11-25
Christian Blau
Check mrc header for sanity
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2019-11-24
Christian Blau
InMemorySerializer with endianess swap.
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2019-11-07
Christian Blau
Stochastic dynamics - document that nsttcouple is ignored
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2019-11-01
Christian Blau
Fix cross-correlation calculation instability
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2019-10-22
Christian Blau
Fix nst in density-fitting module
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2019-10-18
Christian Blau
Manual entry and .mdp option for adaptive force scaling
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2019-10-18
Christian Blau
genion: prohibit ion placement close to non-solvent
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2019-10-18
Christian Blau
Basic refactoring genion and adding test
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2019-10-18
Christian Blau
Adaptive force scaling for densityfitting
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2019-10-16
Christian Blau
Exponential moving average
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2019-09-23
Christian Blau
Grompp error for mismatching nst for energy calulation...
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2019-09-23
Christian Blau
Amendments to density fitting manual section
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2019-09-22
Christian Blau
Add cross-correlation as density simlarity measure
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2019-09-19
Christian Blau
Check input record also in tests
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2019-09-19
Christian Blau
Consistently change densityfitting spreading weight...
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2019-09-18
Christian Blau
Add mdp option documentation for density fitting.
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2019-09-12
Christian Blau
Manual entry for density guided simulations
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2019-09-12
Christian Blau
Add release note for density fitting.
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2019-09-11
Christian Blau
Add comments to grompp generated .mdp output for densityfitting
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2019-09-11
Christian Blau
End to end test for density fitting
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2019-09-11
Christian Blau
Densityfitting write int64_t indices instead of gmx...
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2019-09-10
Christian Blau
Use the current mass instead of massA in density fitting...
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2019-09-10
Christian Blau
Account for reference density origin shift in pbc correction
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2019-09-09
Christian Blau
Relative entropy as density similarity measure
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2019-09-09
Christian Blau
Add option to normalize densities prior to density...
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2019-09-09
Christian Blau
Adding every N-steps option to densityfitting
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2019-09-06
Christian Blau
Adding energy output field for density fitting
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2019-09-06
Christian Blau
Periodic boundary correction for density fitting
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2019-09-05
Christian Blau
Add reference density file option to densityfitting
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2019-09-04
Christian Blau
Fix double overload in LocalAtomSet code when gmx:...
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2019-09-04
Christian Blau
Read mrc file using file name
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2019-09-01
Christian Blau
Add checkpointing for MdModules
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2019-08-30
Christian Blau
Constructing local atom sets for density fitting
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2019-08-30
Christian Blau
LocalAtomSet construction with vectors of gmx::index
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2019-08-30
Christian Blau
Implementing the density fitting force provider
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2019-08-27
Christian Blau
Add density fitting parameters
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2019-08-27
Christian Blau
Access to GaussTransform3D data
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2019-08-27
Christian Blau
Add index group option to density fitting
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2019-08-26
Christian Blau
Activation of density fitting and move of module notifications
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2019-08-25
Christian Blau
Index groups for MdModules from grompp
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2019-08-17
Christian Blau
Fix segfault with old tprs processing internal parameters
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2019-08-15
Christian Blau
Move densityfitting options and output into seperate...
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2019-08-14
Christian Blau
Info class to name and generate the densityfitting...
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2019-08-14
Christian Blau
Internal parameter storage for IMDModules
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2019-08-08
Christian Blau
Harmonize mrc density format extents with rest of code.
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2019-08-08
Christian Blau
Provide callbacks/notifications for MDModules
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2019-07-26
Christian Blau
Fix failing check-source target on python3.6
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2019-07-24
Christian Blau
Fix HTML source documenation error caused by GaussTransform3D
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2019-06-28
Christian Blau
Add copy and move operations to density similarity
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2019-06-28
Christian Blau
Add class to look up density fitting amplitudes
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2019-06-20
Christian Blau
Add coordinate scaling class and extend TranslateAndScale
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2019-06-20
Christian Blau
Allow non-uniform Gaussians
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2019-06-20
Christian Blau
Add BasicVector scaling, max, min and toIvec
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2019-06-18
Christian Blau
Mrc format header to lattice coordinate transform
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2019-06-18
Christian Blau
Density similarity measure and gradient
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2019-04-27
Christian Blau
mrc density map reading/writing
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2019-04-27
Christian Blau
Three dimensional coordiante transformation.
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2019-04-25
Christian Blau
density fitting forces
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2019-04-22
Christian Blau
Three dimensional gauss transform
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2019-04-22
Christian Blau
One dimensional Gaussian function on lattice.
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2019-04-05
Christian Blau
densityfitting - MDModule declaration
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2019-03-22
Christian Blau
densityfitting - serializer for mrc header data.
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2019-03-19
Christian Blau
densityfitting - density file format (mrc) header.
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2019-02-12
Christian Blau
3x3 matrices
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2019-02-11
Christian Blau
view on MultiDimArray
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2019-02-07
Christian Blau
mdspan - add bracket operator slicing
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2019-02-04
Christian Blau
mdspan - free begin and end functions
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2019-02-04
Christian Blau
multidimensional array - bugfix swap
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2019-01-24
Christian Blau
Remove extra semicolons causing clang warnings.
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2019-01-23
Christian Blau
Multidimensional data in canonical layout.
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2018-12-26
Christian Blau
mdspan - basic_mdspan and mdspan declaration
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2018-12-20
Christian Blau
mdspan - basic accessor policy
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2018-12-20
Christian Blau
mdspan - mapping for right layout
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2018-12-04
Christian Blau
mdspan - extents of multidimensional arrays.
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2018-11-22
Christian Blau
mdspan - basic infrastructure
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2018-08-30
Christian Blau
Convert essential dynamics C-structs to C++ pt1.
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2018-08-30
Christian Blau
Store essential dynamics parameters as vectors instead...
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2018-08-21
Christian Blau
Add test for structural similarity measures rmsd and...
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2018-08-09
Christian Blau
Remove Debug Helpers from Essential Dynamics code.
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2018-08-08
Christian Blau
Local atom sets in rotational pulling.
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2018-08-08
Christian Blau
Essential dynamics functions use const-ref for input...
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2018-08-08
Christian Blau
Split essential dynamics eigenvector reading.
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