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2020-10-13	Christian Blau	Add missing header in shake to fix mac clang compilation	commit \| commitdiff \| tree
2020-10-09	Christian Blau	Remove dysfunctional QMMM interface pt5	commit \| commitdiff \| tree
2020-10-02	Christian Blau	Fix FEP lambda interpolation for reruns	commit \| commitdiff \| tree
2020-10-01	Christian Blau	Fix the FEP lambda interpolation	commit \| commitdiff \| tree
2020-09-22	Christian Blau	Nelder-Mead downhill simplex optimisation	commit \| commitdiff \| tree
2020-09-16	Christian Blau	Extend user docs on affine transformations for densities	commit \| commitdiff \| tree
2020-09-15	Christian Blau	All coordinates in the density-guided-simulation group...	commit \| commitdiff \| tree
2020-09-10	Christian Blau	Simplify and fix how lambda values are set	commit \| commitdiff \| tree
2020-09-08	Christian Blau	Allow density-guided simulations to translate structure	commit \| commitdiff \| tree
2020-09-07	Christian Blau	Fix clang-format failure in coordinatetransformation.h	commit \| commitdiff \| tree
2020-09-07	Christian Blau	Implement affine coordinate transformation	commit \| commitdiff \| tree
2020-09-04	Christian Blau	String to array conversion functions	commit \| commitdiff \| tree
2020-08-13	Christian Blau	Remove superfluous math utility functions	commit \| commitdiff \| tree
2020-08-10	Christian Blau	Move density fitting checkpointing into state	commit \| commitdiff \| tree
2020-08-07	Christian Blau	Fixed the mis-fix	commit \| commitdiff \| tree
2020-07-07	Christian Blau	Move finalising routine into mtop	commit \| commitdiff \| tree
2020-07-02	Christian Blau	Coordinate transformation on single RVecs	commit \| commitdiff \| tree
2020-07-01	Christian Blau	Updated the change management documentation	commit \| commitdiff \| tree
2020-04-17	Christian Blau	proposed fix for redmine bug #3403	commit \| commitdiff \| tree
2020-03-16	Christian Blau	Remove dysfunctional QMMM interface pt4	commit \| commitdiff \| tree
2020-03-16	Christian Blau	Remove dysfunctional QMMM interface pt3	commit \| commitdiff \| tree
2020-03-16	Christian Blau	Remove dysfunctional QMMM interface pt2	commit \| commitdiff \| tree
2020-03-16	Christian Blau	Remove dysfunctional QMMM interface pt1	commit \| commitdiff \| tree
2020-03-11	Christian Blau	Amend optional documentation	commit \| commitdiff \| tree
2020-03-05	Christian Blau	Add function calls to MdModules to sign up for notifications	commit \| commitdiff \| tree
2020-03-05	Christian Blau	Split off implementation details of MdModuleNotification	commit \| commitdiff \| tree
2020-03-04	Christian Blau	Save excluded non-bonded interactions in .tpr file	commit \| commitdiff \| tree
2020-03-04	Christian Blau	Add classhelper macro to forbid copy, move and any...	commit \| commitdiff \| tree
2020-02-25	Christian Blau	Document density-fit cross-correlation in .mdp options	commit \| commitdiff \| tree
2020-02-18	Christian Blau	Split MdModuleNotifications into topics	commit \| commitdiff \| tree
2020-02-12	Christian Blau	Introduce readXvgData to read xvg data into std::vector	commit \| commitdiff \| tree
2020-01-31	Christian Blau	Documentation fix for local atom set data	commit \| commitdiff \| tree
2019-12-20	Christian Blau	Remove problematic output of gmx angle	commit \| commitdiff \| tree
2019-12-15	Christian Blau	Fix densityfitting stalling and energies	commit \| commitdiff \| tree
2019-12-12	Christian Blau	Densityfitting - enforce similarity increase with adaptive...	commit \| commitdiff \| tree
2019-12-06	Christian Blau	Change arbitrary units to counts in RMSD distance distributi...	commit \| commitdiff \| tree
2019-12-05	Christian Blau	Relax cross-correlation test precision	commit \| commitdiff \| tree
2019-12-04	Christian Blau	Remove cutoff-scheme group from default mdout.mdp output	commit \| commitdiff \| tree
2019-12-02	Christian Blau	Relax test tolerance for cross correlation measure...	commit \| commitdiff \| tree
2019-11-28	Christian Blau	Fix check-pointing for density guided simulations	commit \| commitdiff \| tree
2019-11-25	Christian Blau	Fix duplicate CONNECT records in pdb files	commit \| commitdiff \| tree
2019-11-25	Christian Blau	Read mrc density map format with all endianesses.	commit \| commitdiff \| tree
2019-11-25	Christian Blau	Check mrc header for sanity	commit \| commitdiff \| tree
2019-11-24	Christian Blau	InMemorySerializer with endianess swap.	commit \| commitdiff \| tree
2019-11-07	Christian Blau	Stochastic dynamics - document that nsttcouple is ignored	commit \| commitdiff \| tree
2019-11-01	Christian Blau	Fix cross-correlation calculation instability	commit \| commitdiff \| tree
2019-10-22	Christian Blau	Fix nst in density-fitting module	commit \| commitdiff \| tree
2019-10-18	Christian Blau	Manual entry and .mdp option for adaptive force scaling	commit \| commitdiff \| tree
2019-10-18	Christian Blau	genion: prohibit ion placement close to non-solvent	commit \| commitdiff \| tree
2019-10-18	Christian Blau	Basic refactoring genion and adding test	commit \| commitdiff \| tree
2019-10-18	Christian Blau	Adaptive force scaling for densityfitting	commit \| commitdiff \| tree
2019-10-16	Christian Blau	Exponential moving average	commit \| commitdiff \| tree
2019-09-23	Christian Blau	Grompp error for mismatching nst for energy calulation...	commit \| commitdiff \| tree
2019-09-23	Christian Blau	Amendments to density fitting manual section	commit \| commitdiff \| tree
2019-09-22	Christian Blau	Add cross-correlation as density simlarity measure	commit \| commitdiff \| tree
2019-09-19	Christian Blau	Check input record also in tests	commit \| commitdiff \| tree
2019-09-19	Christian Blau	Consistently change densityfitting spreading weight...	commit \| commitdiff \| tree
2019-09-18	Christian Blau	Add mdp option documentation for density fitting.	commit \| commitdiff \| tree
2019-09-12	Christian Blau	Manual entry for density guided simulations	commit \| commitdiff \| tree
2019-09-12	Christian Blau	Add release note for density fitting.	commit \| commitdiff \| tree
2019-09-11	Christian Blau	Add comments to grompp generated .mdp output for densityfitting	commit \| commitdiff \| tree
2019-09-11	Christian Blau	End to end test for density fitting	commit \| commitdiff \| tree
2019-09-11	Christian Blau	Densityfitting write int64_t indices instead of gmx...	commit \| commitdiff \| tree
2019-09-10	Christian Blau	Use the current mass instead of massA in density fitting...	commit \| commitdiff \| tree
2019-09-10	Christian Blau	Account for reference density origin shift in pbc correction	commit \| commitdiff \| tree
2019-09-09	Christian Blau	Relative entropy as density similarity measure	commit \| commitdiff \| tree
2019-09-09	Christian Blau	Add option to normalize densities prior to density...	commit \| commitdiff \| tree
2019-09-09	Christian Blau	Adding every N-steps option to densityfitting	commit \| commitdiff \| tree
2019-09-06	Christian Blau	Adding energy output field for density fitting	commit \| commitdiff \| tree
2019-09-06	Christian Blau	Periodic boundary correction for density fitting	commit \| commitdiff \| tree
2019-09-05	Christian Blau	Add reference density file option to densityfitting	commit \| commitdiff \| tree
2019-09-04	Christian Blau	Fix double overload in LocalAtomSet code when gmx:...	commit \| commitdiff \| tree
2019-09-04	Christian Blau	Read mrc file using file name	commit \| commitdiff \| tree
2019-09-01	Christian Blau	Add checkpointing for MdModules	commit \| commitdiff \| tree
2019-08-30	Christian Blau	Constructing local atom sets for density fitting	commit \| commitdiff \| tree
2019-08-30	Christian Blau	LocalAtomSet construction with vectors of gmx::index	commit \| commitdiff \| tree
2019-08-30	Christian Blau	Implementing the density fitting force provider	commit \| commitdiff \| tree
2019-08-27	Christian Blau	Add density fitting parameters	commit \| commitdiff \| tree
2019-08-27	Christian Blau	Access to GaussTransform3D data	commit \| commitdiff \| tree
2019-08-27	Christian Blau	Add index group option to density fitting	commit \| commitdiff \| tree
2019-08-26	Christian Blau	Activation of density fitting and move of module notifications	commit \| commitdiff \| tree
2019-08-25	Christian Blau	Index groups for MdModules from grompp	commit \| commitdiff \| tree
2019-08-17	Christian Blau	Fix segfault with old tprs processing internal parameters	commit \| commitdiff \| tree
2019-08-15	Christian Blau	Move densityfitting options and output into seperate...	commit \| commitdiff \| tree
2019-08-14	Christian Blau	Info class to name and generate the densityfitting...	commit \| commitdiff \| tree
2019-08-14	Christian Blau	Internal parameter storage for IMDModules	commit \| commitdiff \| tree
2019-08-08	Christian Blau	Harmonize mrc density format extents with rest of code.	commit \| commitdiff \| tree
2019-08-08	Christian Blau	Provide callbacks/notifications for MDModules	commit \| commitdiff \| tree
2019-07-26	Christian Blau	Fix failing check-source target on python3.6	commit \| commitdiff \| tree
2019-07-24	Christian Blau	Fix HTML source documenation error caused by GaussTransform3D	commit \| commitdiff \| tree
2019-06-28	Christian Blau	Add copy and move operations to density similarity	commit \| commitdiff \| tree
2019-06-28	Christian Blau	Add class to look up density fitting amplitudes	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Add coordinate scaling class and extend TranslateAndScale	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Allow non-uniform Gaussians	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Add BasicVector scaling, max, min and toIvec	commit \| commitdiff \| tree
2019-06-18	Christian Blau	Mrc format header to lattice coordinate transform	commit \| commitdiff \| tree
2019-06-18	Christian Blau	Density similarity measure and gradient	commit \| commitdiff \| tree
2019-04-27	Christian Blau	mrc density map reading/writing	commit \| commitdiff \| tree
2019-04-27	Christian Blau	Three dimensional coordiante transformation.	commit \| commitdiff \| tree
2019-04-25	Christian Blau	density fitting forces	commit \| commitdiff \| tree
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