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alexxy/gromacs.git
2019-06-30
Kevin Boyd
Remove group scheme checks from runner
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2019-06-30
Magnus Lundborg
Cleaning up the GPU bonded kernel
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2019-06-28
Szilárd Páll
Separate CPU NB kernel and buffer clearing subcounters
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2019-06-28
Christian Blau
Add copy and move operations to density similarity
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2019-06-28
Magnus Lundborg
Fused GPU bonded kernels
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2019-06-28
Christian Blau
Add class to look up density fitting amplitudes
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2019-06-27
Szilárd Páll
Remove already resolved post-submit matrix TODO
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2019-06-27
Kevin Boyd
Use random water removal in gmx solvate
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2019-06-27
M. Eric Irrgang
Add helpful note about gmxpai docker notebook server.
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2019-06-26
Berk Hess
Remove tabulation from free-energy kernel
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2019-06-24
Szilárd Páll
Only use AVX512 in own-FFTW if GROMACS also uses it
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2019-06-24
Pascal Merz
Make global topology constant in trajectory writing
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2019-06-24
M. Eric Irrgang
Add a docker layer with a jupyter notebook server.
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2019-06-20
Paul Bauer
Use ISerializer for TPR file IO
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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
Berk Hess
Remove unnecessary #if GMX_MPI in pme code
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2019-06-20
Berk Hess
Template free-energy kernel on soft-core
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2019-06-20
Christian Blau
Add BasicVector scaling, max, min and toIvec
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2019-06-19
Berk Hess
Refactor PME atom handling
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2019-06-19
Paul Bauer
Split tpr header reading reading from tpr body
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2019-06-19
Berk Hess
Removed unused code paths in the NB FE kernel
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2019-06-19
M. Eric Irrgang
Updates to gmxapi docker entry points.
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2019-06-18
Paul Bauer
Fix gmx dump
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2019-06-18
Mark Abraham
Move code handling mdrun -gpu_id to taskassignment...
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2019-06-18
Berk Hess
Make forcerec const in dispatchNonbondedKernel()
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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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2019-06-18
Paul Bauer
Extend ISerializer functionality
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2019-06-18
Artem Zhmurov
Combine CUDA Leap-Frog, LINCS and SETTLE. I.
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2019-06-18
M. Eric Irrgang
Reduce docker image size for gmxapi CI.
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2019-06-18
Artem Zhmurov
Bug fix: Constraints tests are not instantiated with...
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2019-06-17
Berk Hess
Simplify GPU nbnxm x conversion
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2019-06-17
Berk Hess
Remove unused nbnxm include files
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2019-06-12
Mark Abraham
Fix pygments detection for sphinx for docs build
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2019-06-11
Mark Abraham
Use RAII approaches for hardware information detection
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2019-06-11
Mark Abraham
Clean up multisim, communication, and REMD code
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2019-06-09
Erik Lindahl
More quotes
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2019-05-29
Szilárd Páll
Template x buffer ops call on whether GPU is used
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2019-05-27
Pascal Merz
Clean up renamed simulator.h file
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2019-05-25
Pascal Merz
Remove dependence of mdoutf_write_to_trajectory_files...
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2019-05-25
Pascal Merz
Rename Integrator class
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2019-05-24
Artem Zhmurov
Clarify which of the main energy terms are printed.
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2019-05-24
Artem Zhmurov
Clarify the EnergyOutput III
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2019-05-24
Artem Zhmurov
Clarify the EnergyOutput II
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2019-05-24
Mark Abraham
Reorder code before thread-MPI spawns threads
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2019-05-23
Szilárd Páll
Fix mulitple link refs in dev-manual
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2019-05-23
Mark Abraham
Teach ArrayRefWithPadding to make a const flavour
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2019-05-22
Mark Abraham
Rewrite starting behavior
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2019-05-22
Mark Abraham
Introduce tri-state enums for restarts
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2019-05-22
Alan Gray
Pin X buffer with DD and use proper abstraction in...
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2019-05-22
Jinke Fan
Add support for Hygon Dhyana processor
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2019-05-22
Alan Gray
Code quality improvements for CUDA position buffer ops
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2019-05-22
Mark Abraham
Move functionality to mdrunutility
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2019-05-20
Szilárd Páll
Improve X buffer ops kernel
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2019-05-16
Erik Lindahl
Added more quotes
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2019-05-16
M. Eric Irrgang
Fix typos regarding GMX_PHYSICAL_VALIDATION CMake variable.
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2019-05-16
Pascal Merz
Use Python 3
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2019-05-14
Berk Hess
Make all do_force_lowlevel() input const
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2019-05-14
Mark Abraham
Update infrastructure needed for restart rewrite
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2019-05-13
Artem Zhmurov
Clarify the EnergyOutput I
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2019-05-13
Paul Bauer
Fix math formatting in reference manual
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2019-05-12
Artem Zhmurov
CUDA version of Leap-Frog integrator with basic tests
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2019-05-10
Alan Gray
Position buffer ops in CUDA
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2019-05-10
Paul Bauer
Remove more manual memory management
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2019-05-09
M. Eric Irrgang
More Python testing infrastructure for gmxapi.
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2019-05-09
M. Eric Irrgang
Add gmxapi._logging submodule.
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2019-05-09
M. Eric Irrgang
Update I/O handling in gmxapi.commandline.
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2019-05-09
M. Eric Irrgang
Expand gmxapi.operation tools to support the data flow...
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2019-05-09
M. Eric Irrgang
Fix formatting and typos.
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2019-05-09
M. Eric Irrgang
Support basic command line wrapper in gmxapi
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2019-05-08
Mark Abraham
Provide hook for forks of GROMACS to describe themselves
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2019-05-07
Mark Abraham
Provide better help for using libc++
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2019-05-06
Artem Zhmurov
Fixing minor memory issues in MDLib
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2019-05-06
Mark Abraham
Improve how mdrun -noappend names output files
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2019-05-04
Berk Hess
Remove PME exclusion correction
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2019-05-03
Mark Abraham
More tests for how mdrun -cpi restarts handle files
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2019-05-03
Paul Bauer
Add outputadapters (2/3)
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2019-05-03
Paul Bauer
Replace t_grps with std::vector
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2019-05-03
Berk Hess
Convert manage_threading_t and gmx_enerdata_t to C++
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2019-05-02
Paul Bauer
Add outputadapters (1/3)
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2019-05-02
M. Eric Irrgang
Infrastructure updates for dependent changes.
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2019-05-02
Artem Zhmurov
Use test with parameters for EnergyOutput
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2019-05-02
Paul Bauer
Add builder for TrajectoryFileWriter
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2019-05-02
Berk Hess
Change nbnxm FEP pointer to unique_ptr
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2019-05-02
Mark Abraham
Enhance path search functions
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2019-04-30
Artem Zhmurov
CUDA version of SETTLE algorithm with basic tests
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2019-04-30
Mark Abraham
Test the output of "gmx mdrun help"
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2019-04-30
Berk Hess
Add con/destructor for t_forcetable
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2019-04-30
Berk Hess
Convert DispersionCorrection to a class
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2019-04-29
Artem Zhmurov
Fix for the CUDA version of LINCS
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2019-04-28
Artem Zhmurov
CUDA version of LINCS constraints.
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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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2019-04-26
Paul Bauer
Add C++ coordinate file writing method.
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2019-04-25
Szilárd Páll
Fix clang warning about NULL use
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2019-04-25
Szilárd Páll
Avoid using AtomLocality::Count as a valid value
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2019-04-25
Christian Blau
density fitting forces
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2019-04-25
Artem Zhmurov
Improvements for energy output test.
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2019-04-25
Paul Bauer
Add Interface to change coordinate file info
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