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Add -maxtau option to gmx msd
2021-10-26
Joe Jordan
Use correct c0 parameter in Me2PO4 in OPLSAA
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2021-10-26
Joe Jordan
Add missing parameter to dihedral docs
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2021-10-21
Joe Jordan
Expand signatures for nblib listed forces calculator
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2021-10-21
Joe Jordan
Add helper functions for setting up Nbnxm gpu object...
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2021-10-08
Joe Jordan
Add nblib tpr reading
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2021-10-07
Joe Jordan
Introduce nblib nonbonded force calculator impl class
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2021-08-26
Joe Jordan
Add several more listed forces interaction types to...
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2021-08-18
Joe Jordan
Simplify nblib listed forces type tests
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2021-08-17
Joe Jordan
Add Urey-Bradley listed interaction to nblib
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2021-08-16
Joe Jordan
Updates to nblib listed forces kernels
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2021-08-16
Joe Jordan
Rework nblib kernel checks and setup code
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2021-06-28
Joe Jordan
Add nblib virials function with test
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2021-06-16
Joe Jordan
Use unique_ptr<ListedForcesGpu> in forcerec
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2021-06-11
Joe Jordan
Add createNbnxmCPU, usage, and test
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2021-06-09
Joe Jordan
Move nbnxm setup responsibility to its own files and...
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2021-06-09
Joe Jordan
Expose and test getVdwKernelType
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2021-06-09
Joe Jordan
Extend nblib listed pbc holder and template kernels
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2021-06-08
Joe Jordan
CoulombKernelType enum, lookup function, and tests
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2021-06-07
Joe Jordan
Miscellaneous updates from nblib
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2021-06-06
Joe Jordan
Updates to nblib test infra and tests
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2021-05-26
Joe Jordan
Move t_forcetable and table enums to forcetable header
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2021-05-25
Joe Jordan
Only Pass needed data to nonbonded param setup in forcerec
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2021-05-24
Joe Jordan
Remove dead members from gmx_pme_t
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2021-05-24
Joe Jordan
Remove forcerec from dispatchFreeEnergyKernel signature
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2021-05-20
Joe Jordan
Localize variables in gmx_pme_do
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2021-05-20
Joe Jordan
Localize variables in ewald_LRcorrection
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2021-05-19
Joe Jordan
Clean up some headers in mdlib
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2021-05-18
Joe Jordan
Fix several doxygen errors
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2021-05-10
Joe Jordan
Fix harmless bug in nonbonded FEP tests
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2021-05-05
Joe Jordan
Apply clang-tidy11 to tools
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2021-05-05
Joe Jordan
Pass ArrayRefs to dispatchNonbondedKernel
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2021-05-05
Joe Jordan
Remove mdatoms from coupling code and use more ArrayRef
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2021-05-04
Joe Jordan
Apply clang-tidy11 to statistics
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2021-05-03
Joe Jordan
ArrayRef in pme
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2021-04-27
Joe Jordan
Apply clang-tidy11 to mdrun
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2021-04-27
Joe Jordan
Unify constructor of nbnxn_atomdata_t
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2021-04-27
Joe Jordan
Constructor for t_mde_delta_h_coll
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2021-04-26
Joe Jordan
Remove inputrec from initialize_lambdas signature
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2021-04-22
Joe Jordan
Vectors in history_t
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2021-04-21
Joe Jordan
Mostly remove t_mdatoms from update signatures
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2021-04-21
Joe Jordan
clang-tidy-11 fixes for gmxpreprocess
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2021-04-21
Joe Jordan
Rename some enum names in ModuleMultiThread
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2021-04-20
Joe Jordan
clang-tidy-11 fixes for topology, gpu_utils, and selection
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2021-04-20
Joe Jordan
Use enum class for gmx_omp_nthreads
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2021-04-20
Joe Jordan
clang-tidy-11 fixes for utils
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2021-04-14
Joe Jordan
Pass forcerec arguments instead of forcerec to gmx_nb_free_e...
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2021-04-13
Joe Jordan
Use array for term and foreign_term in gmx_enerdata_t
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2021-04-12
Joe Jordan
Pass cFREEZE and cTC to update after DD partitioning
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2021-04-12
Joe Jordan
Expose init_interaction_const and move to correct header...
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2021-04-12
Joe Jordan
Replace defines with constexpr in ishift
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2021-04-12
Joe Jordan
Add a fourth coordinate to virial tests
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2021-04-11
Joe Jordan
Pass ref_t to initialize_lambdas
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2021-03-31
Joe Jordan
ArrayRefs and const refs in global_stat
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2021-03-31
Joe Jordan
Use more ArrayRefs in signatures of update impl class
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2021-03-29
Joe Jordan
Add tests for calcvir
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2021-03-29
Joe Jordan
Move nsgrid header/source from mdlib to domdec
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2021-03-26
Joe Jordan
Use ArrayRefs instead of mdatoms in gmx_nb_free_energy_kerne...
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2021-03-25
Joe Jordan
Use more vectors for EnergyOutput private members
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2021-03-25
Joe Jordan
Constructor for t_tabledata
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2021-03-25
Joe Jordan
Use ArrayRef in special forces
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2021-03-25
Joe Jordan
Use ArrayRef in signatures of constraints and some...
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2021-03-23
Joe Jordan
Modernize t_nrnb
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2021-03-23
Joe Jordan
Use ArrayRef in calc_mu
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2021-03-19
Joe Jordan
Use more arrayref in listed forces sigatures
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2021-03-19
Joe Jordan
Use ArrayRef in ewald_LRcorrection
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2021-03-19
Joe Jordan
Make non bonded energy terms enum class
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2021-03-16
Joe Jordan
Use RVec and std::array in gmx_domdec_comm_t
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2021-03-16
Joe Jordan
Remove conditional assignemnt of cell sizes from domdec...
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2021-03-10
Joe Jordan
Remove param fillLocal, which was always false, from...
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2021-03-09
Joe Jordan
Use constexpr for physical constants and move them...
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2021-03-08
Joe Jordan
Correct the dependencies of nblib tests
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2021-03-01
Joe Jordan
Use const ref for mtop and inputrec in EnergyOutput...
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2021-02-28
Joe Jordan
Use more const ref in domdec API
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2021-02-26
Joe Jordan
Only use const ref for mtop and inputrec in domdec
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2021-02-23
Joe Jordan
Use verbose names in init_forcerec
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2021-02-22
Joe Jordan
Hold unique_ptr to gmx_ewald_tab_t in forcerec
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2021-02-22
Joe Jordan
Hold unique_ptr for interaction_const in forcerec
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2021-02-20
Joe Jordan
Remove unsed structs from nblist and use vector in...
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2021-02-19
Joe Jordan
Revome unused code from nsgrid
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2021-02-19
Joe Jordan
Use const refs in init_nb_verlet
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2021-02-19
Joe Jordan
Rename and add doxygen to reaction field params in...
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2021-02-18
Joe Jordan
Use unique_ptr for forcerec in runner
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2021-02-16
Joe Jordan
Use const ref to inputrec in do_force
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2021-02-11
Joe Jordan
Use unique_ptr for tables
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2021-02-05
Joe Jordan
Use raw strings instead of format in docker build script
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2021-01-25
Joe Jordan
Check availability of compile flags at cmake time
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2020-11-17
Joe Jordan
Remove some extraneous compiler flags from nblib
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2020-11-09
Joe Jordan
Add backend for nblib listed forces API
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2020-11-04
Joe Jordan
NBLIB listed forces API update
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2020-10-30
Joe Jordan
Introduce nblib versioning
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2020-10-13
Joe Jordan
Fix segfault in pull reading
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2020-10-02
Joe Jordan
Add tests for setStringEntry
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2020-09-30
Joe Jordan
Add nblib sample script
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2020-09-29
Joe Jordan
Add nblib backend: Part 2 of 2
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2020-09-28
Joe Jordan
Add nblib backend: Part 1 of 2
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2020-09-28
Joe Jordan
Add initial nblib public API
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2020-09-10
Joe Jordan
Replace GMX_ASSERT with assert in vectypes.h
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2020-07-03
Joe Jordan
Use vector in atoms2md instead of pointer
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2020-06-23
Joe Jordan
Remove some headers from install targets
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2018-11-19
Joe Jordan
fix unused variable warning from gmxapi compilation
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