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2019-07-31	Szilárd Páll	Fixes for F buffer ops change	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Remove need for GROMOS FF in test	commit \| commitdiff \| tree
2019-07-31	Pascal Merz	Rename Simulator to LegacySimulator	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Move cycle counting into the GPU bonded module	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Report when development feature flags are used	commit \| commitdiff \| tree
2019-07-31	Szilárd Páll	Move end of step GPU task launches to a function	commit \| commitdiff \| tree
2019-07-30	Paul Bauer	Add wrapper for outputadapter methods	commit \| commitdiff \| tree
2019-07-28	Berk Hess	Convert Ewald correction tables to C++	commit \| commitdiff \| tree
2019-07-26	Berk Hess	Add default initialization to interaction_const_t	commit \| commitdiff \| tree
2019-07-26	Christian Blau	Fix failing check-source target on python3.6	commit \| commitdiff \| tree
2019-07-25	Berk Hess	Split canDetectGpus()	commit \| commitdiff \| tree
2019-07-25	Szilárd Páll	Only stop the CUDA profiler if there are devices	commit \| commitdiff \| tree
2019-07-24	Paul Bauer	Fix doxygen in coordianteio files	commit \| commitdiff \| tree
2019-07-24	Paul Bauer	Add outputadapters (3/3)	commit \| commitdiff \| tree
2019-07-24	M. Eric Irrgang	Fix gmxapi notebook image and sample_restraint docker...	commit \| commitdiff \| tree
2019-07-24	M. Eric Irrgang	Improve gmxapi docker testing environment.	commit \| commitdiff \| tree
2019-07-23	M. Eric Irrgang	Don't install sample restraint package by default.	commit \| commitdiff \| tree
2019-07-23	Kevin Boyd	Modernize syntax of enable_if and traits to use _t...	commit \| commitdiff \| tree
2019-07-09	M. Eric Irrgang	Incorporate sample_restraint repository.	commit \| commitdiff \| tree
2019-07-09	M. Eric Irrgang	Begin CMake front-end for Python packaging machinery.	commit \| commitdiff \| tree
2019-07-08	Szilárd Páll	Eliminate a use of double precision in the GPU bonded...	commit \| commitdiff \| tree
2019-07-08	Berk Hess	Store nbnxm gridSet data in GridSetData	commit \| commitdiff \| tree
2019-07-05	Mark Abraham	Modernize FindHwloc.cmake	commit \| commitdiff \| tree
2019-07-05	M. Eric Irrgang	Python bindings for mdrun.	commit \| commitdiff \| tree
2019-07-04	Mark Abraham	Further clang-tidy-7 fix	commit \| commitdiff \| tree
2019-07-03	Artem Zhmurov	Combine CUDA Leap-Frog, LINCS and SETTLE. II.	commit \| commitdiff \| tree
2019-07-03	Kevin Boyd	Updates to math/vec.h	commit \| commitdiff \| tree
2019-07-02	Berk Hess	Re-enable affinity diagonostics with MPI	commit \| commitdiff \| tree
2019-07-02	Kevin Boyd	Add function for calculating 3x3 matrix determinant	commit \| commitdiff \| tree
2019-07-02	Kevin Boyd	Remove references to ecutsGROUP	commit \| commitdiff \| tree
2019-07-01	Pascal Merz	Fix module detection for physical validation	commit \| commitdiff \| tree
2019-07-01	Szilárd Páll	Refactor tracking of GPU short-range work/skipping	commit \| commitdiff \| tree
2019-07-01	Berk Hess	Fix MPI deadlock in affinity setting	commit \| commitdiff \| tree
2019-07-01	M. Eric Irrgang	gmxapi Python package documentation infrastructure.	commit \| commitdiff \| tree
2019-06-30	Szilárd Páll	Create dedicated subcounter for nonbonded FEP	commit \| commitdiff \| tree
2019-06-30	Kevin Boyd	Remove group scheme checks from runner	commit \| commitdiff \| tree
2019-06-30	Magnus Lundborg	Cleaning up the GPU bonded kernel	commit \| commitdiff \| tree
2019-06-20	Paul Bauer	Use ISerializer for TPR file IO	commit \| commitdiff \| tree
2019-06-20	Berk Hess	Template free-energy kernel on soft-core	commit \| commitdiff \| tree
2019-06-20	Christian Blau	Add BasicVector scaling, max, min and toIvec	commit \| commitdiff \| tree
2019-06-19	Berk Hess	Refactor PME atom handling	commit \| commitdiff \| tree
2019-06-19	Paul Bauer	Split tpr header reading reading from tpr body	commit \| commitdiff \| tree
2019-06-19	Berk Hess	Removed unused code paths in the NB FE kernel	commit \| commitdiff \| tree
2019-06-18	Paul Bauer	Fix gmx dump	commit \| commitdiff \| tree
2019-06-18	Mark Abraham	Move code handling mdrun -gpu_id to taskassignment...	commit \| commitdiff \| tree
2019-06-18	Berk Hess	Make forcerec const in dispatchNonbondedKernel()	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
2019-06-18	M. Eric Irrgang	Reduce docker image size for gmxapi CI.	commit \| commitdiff \| tree
2019-06-18	Artem Zhmurov	Bug fix: Constraints tests are not instantiated with...	commit \| commitdiff \| tree
2019-06-12	Mark Abraham	Fix pygments detection for sphinx for docs build	commit \| commitdiff \| tree
2019-06-11	Mark Abraham	Use RAII approaches for hardware information detection	commit \| commitdiff \| tree
2019-06-11	Mark Abraham	Clean up multisim, communication, and REMD code	commit \| commitdiff \| tree
2019-05-29	Szilárd Páll	Template x buffer ops call on whether GPU is used	commit \| commitdiff \| tree
2019-05-27	Pascal Merz	Clean up renamed simulator.h file	commit \| commitdiff \| tree
2019-05-25	Pascal Merz	Remove dependence of mdoutf_write_to_trajectory_files...	commit \| commitdiff \| tree
2019-05-25	Pascal Merz	Rename Integrator class	commit \| commitdiff \| tree
2019-05-24	Artem Zhmurov	Clarify the EnergyOutput III	commit \| commitdiff \| tree
2019-05-24	Artem Zhmurov	Clarify the EnergyOutput II	commit \| commitdiff \| tree
2019-05-24	Mark Abraham	Reorder code before thread-MPI spawns threads	commit \| commitdiff \| tree
2019-05-23	Szilárd Páll	Fix mulitple link refs in dev-manual	commit \| commitdiff \| tree
2019-05-23	Mark Abraham	Teach ArrayRefWithPadding to make a const flavour	commit \| commitdiff \| tree
2019-05-22	Mark Abraham	Rewrite starting behavior	commit \| commitdiff \| tree
2019-05-22	Mark Abraham	Introduce tri-state enums for restarts	commit \| commitdiff \| tree
2019-05-22	Alan Gray	Pin X buffer with DD and use proper abstraction in...	commit \| commitdiff \| tree
2019-05-22	Jinke Fan	Add support for Hygon Dhyana processor	commit \| commitdiff \| tree
2019-05-22	Mark Abraham	Move functionality to mdrunutility	commit \| commitdiff \| tree
2019-05-16	Erik Lindahl	Added more quotes	commit \| commitdiff \| tree
2019-05-14	Mark Abraham	Update infrastructure needed for restart rewrite	commit \| commitdiff \| tree
2019-05-10	Paul Bauer	Remove more manual memory management	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	More Python testing infrastructure for gmxapi.	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	Add gmxapi._logging submodule.	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	Update I/O handling in gmxapi.commandline.	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	Expand gmxapi.operation tools to support the data flow...	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	Fix formatting and typos.	commit \| commitdiff \| tree
2019-05-09	M. Eric Irrgang	Support basic command line wrapper in gmxapi	commit \| commitdiff \| tree
2019-05-03	Mark Abraham	More tests for how mdrun -cpi restarts handle files	commit \| commitdiff \| tree
2019-05-03	Paul Bauer	Add outputadapters (2/3)	commit \| commitdiff \| tree
2019-05-02	Paul Bauer	Add outputadapters (1/3)	commit \| commitdiff \| tree
2019-05-02	M. Eric Irrgang	Infrastructure updates for dependent changes.	commit \| commitdiff \| tree
2019-05-02	Paul Bauer	Add builder for TrajectoryFileWriter	commit \| commitdiff \| tree
2019-05-02	Berk Hess	Change nbnxm FEP pointer to unique_ptr	commit \| commitdiff \| tree
2019-05-02	Mark Abraham	Enhance path search functions	commit \| commitdiff \| tree
2019-04-30	Mark Abraham	Test the output of "gmx mdrun help"	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
2019-04-26	Paul Bauer	Add C++ coordinate file writing method.	commit \| commitdiff \| tree
2019-04-25	Christian Blau	density fitting forces	commit \| commitdiff \| tree
2019-04-25	Paul Bauer	Add Interface to change coordinate file info	commit \| commitdiff \| tree
2019-04-25	Mark Abraham	Update style guide about class enums	commit \| commitdiff \| tree
2019-04-23	Mark Abraham	Clarify pushing of interaction types	commit \| commitdiff \| tree
2019-04-18	Berk Hess	Remove nbnxm kernel type from pairlist generation	commit \| commitdiff \| tree
2019-04-18	Berk Hess	Remove charge groups from domdec and localtop	commit \| commitdiff \| tree
2019-04-18	Mark Abraham	Create gmx::compat::optional	commit \| commitdiff \| tree
2019-04-17	Paul Bauer	Enable printing of known issues in commandline	commit \| commitdiff \| tree
2019-04-17	Mark Abraham	Fix post-submit	commit \| commitdiff \| tree
2019-04-17	Berk Hess	Reduce nbnxm CPU kernel arguments	commit \| commitdiff \| tree
2019-04-17	Berk Hess	Simplify nbnxm shift force handling	commit \| commitdiff \| tree
2019-04-16	Szilárd Páll	Move functions operating on enerdata out of force.cpp	commit \| commitdiff \| tree
2019-04-16	Berk Hess	Simplify nbnxm buffer clearing	commit \| commitdiff \| tree
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