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Clean up nbnxm bounding boxes
2019-03-06
Berk Hess
Clean up nbnxm bounding boxes
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2019-03-06
Berk Hess
Convert nbnxm bounding box to a struct
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2019-03-05
Berk Hess
Fix post-submit warnings
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2019-03-05
Berk Hess
Move nbnxm atomdata types to atomdata.h
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2019-03-05
Berk Hess
Turn nbnxn_grid_t into a class
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2019-02-28
Berk Hess
Use unique_ptr in nonbonded_verlet_t
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2019-02-27
Berk Hess
Use new/delete for t_forcerec
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2019-02-27
Berk Hess
Clean up dispersioncorrection.cpp
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2019-02-27
Berk Hess
Fix 4 compilers warnings
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2019-02-27
Berk Hess
Collect dispersion correction code
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2019-02-26
Berk Hess
Correct grompp index file error message
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2019-02-26
Berk Hess
Clean up mtop pbc functions
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2019-02-23
Berk Hess
Move all nbnxm pruning details into module
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2019-02-23
Berk Hess
Hide internals of nbnxm parlist
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2019-02-22
Berk Hess
Formalize dynamic pruning with GPU emulation
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2019-02-21
Berk Hess
Move free-energy kernel dispatch into nbnxm module
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2019-02-21
Berk Hess
Minor nbnxm cleanup
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2019-02-21
Berk Hess
Clean up nbnxm enums
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2019-02-21
Berk Hess
Simplify make_pairlist() call signature
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2019-02-20
Berk Hess
Add havePPDomainDecomposition()
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2019-02-20
Berk Hess
Refactor DLB region handling
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2019-02-17
Berk Hess
Use enum class for nbnxm locality
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2019-02-17
Berk Hess
Extract nbnxm grid.h and pairlistwork.h
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2019-02-17
Berk Hess
Fix compiler warnings
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2019-02-17
Berk Hess
Move nbnxm details from sim_util.cpp to module
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2019-02-16
Berk Hess
Move nbnxn files to nbnxm directory
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2019-02-15
Berk Hess
Fix mass Delta H double counting
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2019-02-09
Berk Hess
Disallow rerun with perturbed masses or constraints
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2019-02-06
Berk Hess
Fix segfault with EM, DD and group scheme
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2019-02-01
Berk Hess
Fix incorrect LJ repulsion force switching on GPUs
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2019-01-25
Berk Hess
Fix LINCS bug from recent commit 211039fc
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2019-01-23
Berk Hess
Fix error with 2D/3D DLB
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2019-01-22
Berk Hess
Add utility method to NbnxnPairlistGpu
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2019-01-22
Berk Hess
Remove now usused GPU alloc/free functions
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2019-01-22
Berk Hess
Convert NbnxnPairlistGpu to C++
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2019-01-21
Berk Hess
Convert nbnxn_atomdata_t to C++
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2019-01-16
Berk Hess
Rename HostVector to PaddedHostVector
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2019-01-10
Berk Hess
Split nbnxn_atomdata_init()
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2019-01-10
Berk Hess
Change grid pointers in nbnxn search to references
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2019-01-10
Berk Hess
Split nbnxn_list_work_t and change to C++
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2019-01-10
Berk Hess
Use std::vector in NbnxnPairlistCpu
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2019-01-09
Berk Hess
Fix gcc-8 release warnings in tng_io
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2019-01-09
Berk Hess
Added DefaultInitializationAllocator
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2019-01-04
Berk Hess
Split nbnxn pairlist types for CPU and GPU
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2019-01-04
Berk Hess
Replace NBNXN_CPU_CLUSTER_I_SIZE by c_nbnxnCpuIClusterSize
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2019-01-03
Berk Hess
Fix segmentation fault in DD code
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2018-12-27
Berk Hess
Use AtomPair for LINCS indexing
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2018-12-27
Berk Hess
Use arrayref in LINCS
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2018-12-21
Berk Hess
Improve nbnxn cjFromCi() function
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2018-12-18
Berk Hess
Use std::vector in LINCS
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2018-12-14
Berk Hess
Fix LINCS triangle constraining with OpenMP
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2018-12-14
Berk Hess
Fixed nullptr derefence in LINCS error
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2018-12-14
Berk Hess
Fix LINCS triangle constraining with OpenMP
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2018-12-12
Berk Hess
Temporary fix for OpenCL PME gather
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2018-12-11
Berk Hess
Fix update groups with 2D/3D DLB
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2018-12-11
Berk Hess
Make large PME grids work on GPU
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2018-12-11
Berk Hess
Document mdrun mdp option modification
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2018-12-05
Berk Hess
Add update groups to parallelization docs
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2018-12-05
Berk Hess
Make large PME grids work on GPU
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2018-11-26
Berk Hess
Fix FP exception in pull code
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2018-11-16
Berk Hess
grompp now checks tau-p>=2*tau-t with NH+PR
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2018-11-08
Berk Hess
Fix bug with DD for dims without PBC
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2018-11-01
Berk Hess
Fix broken update groups
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2018-10-31
Berk Hess
Limit auto assignment of bondeds to GPUs
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2018-10-31
Berk Hess
Pin important buffers in CUDA bondeds
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2018-10-31
Berk Hess
Work around expanded ensemble issues
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2018-10-31
Berk Hess
Fix FP exception in energy reduction
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2018-10-31
Berk Hess
Correct VV integrator nstcalcenergy use
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2018-10-31
Berk Hess
Correct grompp nstexpanded/nstcalcenergy check
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2018-10-26
Berk Hess
Add missing mass term to deltaH
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2018-10-23
Berk Hess
Add missing constraint term to deltaH
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2018-10-21
Berk Hess
Fix mdrun start/end time print
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2018-10-18
Berk Hess
Add env.var. to disable update groups
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2018-10-12
Berk Hess
Implement assigning bondeds to the GPU
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2018-10-10
Berk Hess
Move pull output functions to output.cpp
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2018-10-10
Berk Hess
Minor refactoring in bonded threading
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2018-10-09
Berk Hess
Fix compiler warning
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2018-10-08
Berk Hess
Enable update groups
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2018-10-05
Berk Hess
Add update groups to DD atom displacement
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2018-10-04
Berk Hess
Make AVX2 pass TSAN
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2018-10-04
Berk Hess
Add note to avoid constraints=all-bonds
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2018-10-03
Berk Hess
Remove unnecessary clearing in gmxcpp
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2018-10-03
Berk Hess
Convert gmx_cpp to C++
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2018-10-02
Berk Hess
Update DD cutoffs for update groups
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2018-09-30
Berk Hess
Correct update group angle param type
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2018-09-29
Berk Hess
Refactoring in calc_verletbuf.cpp
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2018-09-29
Berk Hess
Add UpdateGroupsCog to DD
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2018-09-27
Berk Hess
Move maxReferenceTemperature() to inputrec
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2018-09-27
Berk Hess
Improve update group radii
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2018-09-27
Berk Hess
Reorganize RVec scaling functions
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2018-09-26
Berk Hess
Extract settle test water coordinates
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2018-09-26
Berk Hess
Support atom groups in nbnxn_search
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2018-09-25
Berk Hess
Add UpdateGroupsCog class
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2018-09-24
Berk Hess
Fix performance report when init_step!=0
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2018-09-22
Berk Hess
Add update groups boolean to DD
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2018-09-22
Berk Hess
Rename DD constraint booleans
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2018-09-22
Berk Hess
Add update groups
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2018-09-20
Berk Hess
Change pull buffers to std::vector
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2018-09-20
Berk Hess
Fix type bug in trilinic DD code
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2018-09-19
Berk Hess
Convert gmx_cmap_t to C++
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