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NEKO v0.8.0 #1229

Merged
merged 1,005 commits into from
Jul 7, 2024
Merged

NEKO v0.8.0 #1229

merged 1,005 commits into from
Jul 7, 2024
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Commits on Mar 20, 2024

  1. Update src/bc/field_dirichlet.f90

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Commits on Mar 21, 2024

  1. Import field_ptr_t to the main module

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  2. Facelift for field registry, add optional to add_field

    @timofeymukha
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  3. Rename optional argument to add_field

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  4. Add field_writer

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  5. Disable CI checks on drafts.

    @timfelle
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  6. Change argument inent in field_list append

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  7. Merge pull request #1191 from timfelle/cicd/disable_on_draft 

    Disable CI checks on drafts.
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  8. Update doc/pages/simcomps.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
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    timofeymukha and timfelle authored Mar 21, 2024
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  9. Update doc/pages/simcomps.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
    @timofeymukha @timfelle
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  10. Small fixes

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  11. Remove unused variables

    @timofeymukha
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  12. pass case_t%params instead of case_t as constuctor of time_step_contr… 

    …oller; pass time_step_controller_t to subroutine step() of _scheme_t and their inherit types
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  13. minor changes

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  14. minor changes

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  15. Merge pull request #1192 from ExtremeFLOW/feature/field_writer 

    Add field_writer simcomp
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  16. Update src/fluid/fluid_pnpn.f90 

    Co-authored-by: Timofey Mukha <[email protected]>
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  17. Merge branch 'develop' of github.com:ExtremeFLOW/neko into feature/fi… 

    …eld_bcs
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  18. Moved the min distance to the node rather than the aabb.

    @timfelle
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  19. Increase robustness when box is uninitialized.

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  20. Moved padding away from element specific operator.

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  21. Added support for meshes

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  22. Crude implementation of the mesh transform for brinkman.

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  23. Transform the bunny instead of the domain.

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  24. Fix bug where distance function still used aabb fro min_distance even… 

    … though it was moved to aabb_node.
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  25. Fixed dependencies.

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Commits on Mar 22, 2024

  1. wrap up projection pre- and post-equation-solving

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  2. delete mistakenly copied files

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  3. solving problem on ubuntu gfortran-10 compiler

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  4. Added getters for min and max corners

    @timfelle
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  5. Update example for new ksp interface

    @njansson
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  6. Merge remote-tracking branch 'upstream/develop' into f2py_coupling

    @adperezm
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  7. Merge pull request #1174 from ExtremeFLOW/projection 

    Projection
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  8. Merge pull request #1195 from adperezm/f2py_coupling 

    F2py coupling
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  9. Merge pull request #1194 from ExtremeFLOW/fix/poisson_example 

    Update example for new ksp interface
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  10. Fixed missing initialization in aabb 

    Ensure number of elements are up to date in tri_mesh
    @timfelle
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  11. Brinkman terms updates.

    @timfelle
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  12. Update documentation

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  13. Update doc/pages/case-file.md 

    Co-authored-by: Timofey Mukha <[email protected]>
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  14. Update doc/pages/case-file.md 

    Co-authored-by: Timofey Mukha <[email protected]>
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  15. Merge commit 'd16c23db721af1d5d470b0f70b98310b0293090b' into enhancem… 

    …ent/stl_transform
    @timfelle
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  16. Fix dangling pointers

    @njansson
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  17. Merge with develop

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  18. debug projection to make simulation work without projection and remov… 

    …e some dummy stuffs
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Commits on Mar 23, 2024

  1. remove ifs in projection objects' construction

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  2. Ensure bc_inflow is allocated before resolving its type

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  3. Merge pull request #1198 from ExtremeFLOW/projection_debug 

    debug on projection
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  4. Merge remote-tracking branch 'origin/develop' into fix/dangling_ptrs

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  5. Merge remote-tracking branch 'origin/develop' into fix/fluid_validate

    @njansson
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  6. Cleanup

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  7. Fix danling pointers in usr_neko

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  8. Fix dangling ptrs in simcomps

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  9. Merge pull request #1199 from ExtremeFLOW/fix/fluid_validate 

    Ensure bc_inflow is allocated before resolving its type
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  10. Merge pull request #1197 from ExtremeFLOW/fix/dangling_ptrs 

    Fix dangling pointers
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Commits on Mar 24, 2024

  1. Merge pull request #1187 from timfelle/fix/tests 

    Point interpolation test
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  2. Use field_writer in lambda2 and vorticity

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  3. Update depends

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  4. Cleanup dead code

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Commits on Mar 25, 2024

  1. Added specific routines for double and single array options

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  2. Merge pull request #1196 from timfelle/enhancement/stl_transform 

    Enhancement/boundary_mesh_transform
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  3. Merge pull request #1200 from ExtremeFLOW/feature/writing_simcomps 

    Use field_writer in lambda2 and vorticity
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  4. Merge branch 'develop' into feature/boussinesq_source

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  5. Update depends

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  6. Merge pull request #1154 from ExtremeFLOW/feature/boussinesq_source

    @njansson
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  7. Merge pull request #1201 from ExtremeFLOW/fix/cleanup_projection 

    Cleanup dead code
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  8. edit doc

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  9. free fields and bcs

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  10. Merge branch 'develop' of github.com:ExtremeFLOW/neko into feature/fi… 

    …eld_bcs
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  11. edit dep

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  12. Fix possible dis-cont. warnings

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Commits on Mar 26, 2024

  1. small edits

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  2. Merge pull request #1202 from ExtremeFLOW/fix/cont_arrays

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  3. Fix danling pointers in mesh

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Commits on Mar 27, 2024

  1. Harmonize factory module names

    @timofeymukha
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  2. Try to fix Intel CI

    @njansson
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  3. Debug workflow

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  4. Debug workflow

    @njansson
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  5. Debug workflow

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  6. Fixed a stochastic bug where the type would sometimes not be read cor… 

    …rectly from the json file.
    @timfelle
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  7. Update develop.yml

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  8. Merge pull request #1208 from ExtremeFLOW/fix/ci-intel 

    Try to fix Intel CI
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  9. Merge branch 'develop' into fix/mesh_dangling_ptrs

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  10. Merge pull request #1206 from ExtremeFLOW/fix/mesh_dangling_ptrs 

    Fix danling pointers in mesh
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  11. update example

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  12. add global flag for max length of boundary labels

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  13. add extra parameter to check if dirichlet_update is called from fluid… 

    … or scalar
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  14. Move dirichlet_update inside fluid and scalar

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  15. update depends

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  16. Merge branch 'develop' of github.com:ExtremeFLOW/neko into feature/fi… 

    …eld_bcs
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  17. make CI happY

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  18. Update user_intf.f90

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Commits on Mar 28, 2024

  1. Some doc and example update

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  2. Merge branch 'feature/field_bcs' of github.com:ExtremeFLOW/neko into … 

    …feature/field_bcs
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Commits on Mar 29, 2024

  1. Use proper abscmp to check for 0.0_rp

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Commits on Mar 30, 2024

  1. Merge pull request #1211 from ExtremeFLOW/fix/krylov_abscmp_checks

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Commits on Mar 31, 2024

  1. Merge commit 'e2f5f6ad7bc038b1d59ce7522f69200677549608' into fix/brin… 

    …kman_term
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  2. Add "only" to places

    @timofeymukha
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  3. Modernize advection

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  4. Fix module docstring

    @timofeymukha
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  5. Copyright year

    @timofeymukha
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Commits on Apr 1, 2024

  1. Merge branch 'develop' into fix/factory_modules

    @timofeymukha
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  2. Promote coef to bc_t

    @timofeymukha
    timofeymukha committed Apr 1, 2024
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  3. Trim down Dong bc constructor interface

    @timofeymukha
    timofeymukha committed Apr 1, 2024
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  4. Small fix in dong_outflow

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    timofeymukha committed Apr 1, 2024
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Commits on Apr 2, 2024

  1. Update src/fluid/fluid_pnpn.f90 

    Co-authored-by: Tim Felle Olsen <[email protected]>
    @timofeymukha @timfelle
    timofeymukha and timfelle authored Apr 2, 2024
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  2. Update src/fluid/fluid_pnpn.f90 

    Co-authored-by: Tim Felle Olsen <[email protected]>
    @timofeymukha @timfelle
    timofeymukha and timfelle authored Apr 2, 2024
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  3. Merge pull request #1209 from timfelle/fix/brinkman_term 

    Fix bug in reading type from json file
    @timofeymukha
    timofeymukha authored Apr 2, 2024
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  4. Add mising imports

    @timofeymukha
    timofeymukha committed Apr 2, 2024
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  5. fix bugs in average_field_in_space: allow avg on multiple time steps

    @Shiyu-Sandy-Du
    Shiyu-Sandy-Du committed Apr 2, 2024
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  6. Remove unused shmem variable

    @njansson
    njansson committed Apr 2, 2024
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  7. Finalize doc

    @vbaconnet
    vbaconnet committed Apr 2, 2024
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  8. Merge pull request #1212 from ExtremeFLOW/fix/more_only 

    Add "only" to fluid_pnpn and some related types
    @timofeymukha
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  9. Fix invalid, expensive sync in gmres

    @njansson
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Commits on Apr 3, 2024

  1. Introduction of a probe header. 

    Header contains number of probes, number of fields, and a list of the fields probed in order.
    @timfelle
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  2. Updated documentation of probes to include output format

    @timfelle
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  3. Merge pull request #1221 from ExtremeFLOW/fix/gmres_gs_sync

    @njansson
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  4. Merge branch 'develop' into feature/json_advection

    @timofeymukha
    timofeymukha committed Apr 3, 2024
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  5. Fix use conflict

    @timofeymukha
    timofeymukha committed Apr 3, 2024
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  6. Add field%size

    @timofeymukha
    timofeymukha committed Apr 3, 2024
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  7. Merge pull request #1223 from ExtremeFLOW/feature/field_size 

    Add a wrapper for dofmap%size in the field_t type
    @njansson
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  8. Merge pull request #1220 from ExtremeFLOW/fix/cleanup_cdtp 

    Remove unused shmem variable
    @njansson
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  9. Fix pressure dirichlet bc not added to the bc_list

    @vbaconnet
    vbaconnet committed Apr 3, 2024
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  10. finalize example

    @vbaconnet
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  11. edit doc

    @vbaconnet
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  12. Merge branch 'develop' of github.com:ExtremeFLOW/neko into feature/fi… 

    …eld_bcs
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  13. Throw errors in scalar/vector apply

    @vbaconnet
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  14. Update src/fluid/fluid_scheme.f90

    @njansson
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  15. Apply suggestions from code review

    @njansson
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Commits on Apr 4, 2024

  1. Merge pull request #1171 from ExtremeFLOW/fix/pc_jacobi_vector 

    Refactor pc_jacobi (CPU) to allow for vectorisation
    @njansson
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  2. Merge pull request #1222 from timfelle/enhancement/probe_header 

    Introduce probe header and update probe documentation
    @timofeymukha
    timofeymukha authored Apr 4, 2024
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  3. Merge branch 'develop' into feature/bc_interface

    @timofeymukha
    timofeymukha committed Apr 4, 2024
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  4. Merge pull request #985 from ExtremeFLOW/feature/field_bcs 

    Feature user dirichlet bcs
    @njansson
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  5. Merge branch 'develop' into feature/bc_interface

    @timofeymukha
    timofeymukha committed Apr 4, 2024
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  6. Merge

    @timofeymukha
    timofeymukha committed Apr 4, 2024
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  7. Merge pull request #1215 from ExtremeFLOW/feature/bc_interface 

    Promote coef component to bc_t
    @timofeymukha
    timofeymukha authored Apr 4, 2024
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  8. Merge pull request #1218 from ExtremeFLOW/fix/averaging_field_in_space 

    fix bugs in average_field_in_space: allow avg on multiple time steps
    @njansson
    njansson authored Apr 4, 2024
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  9. Resolve merge conflicts

    @njansson
    njansson committed Apr 4, 2024
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  10. Fix build issues

    @njansson
    njansson committed Apr 4, 2024
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  11. Merge branch 'develop' into feature/json_advection

    @timofeymukha
    timofeymukha committed Apr 4, 2024
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  12. Fix leftover from merge

    @njansson
    njansson committed Apr 4, 2024
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  13. Merge pull request #1213 from ExtremeFLOW/feature/json_advection 

    Modernize advection types to use json
    @njansson
    njansson authored Apr 4, 2024
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  14. Merge pull request #1207 from ExtremeFLOW/fix/factory_modules 

    Harmonize factory module filenames
    @timofeymukha
    timofeymukha authored Apr 4, 2024
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  15. Merge pull request #1216 from ExtremeFLOW/feature/slim_dong 

    Remove u, v, w fron Dong outflow constructor
    @njansson
    njansson authored Apr 4, 2024
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Commits on Apr 5, 2024

  1. Restructure lambda2 routine, and fix calculation on SX

    @njansson
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  2. Add missing file

    @njansson
    njansson committed Apr 5, 2024
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  3. Make flint happy

    @njansson
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  4. Merge pull request #1224 from ExtremeFLOW/fix/lambda2_sx 

    Restructure lambda2 routine, and fix calculation on SX
    @njansson
    njansson authored Apr 5, 2024
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  5. Updated cff file to include all authors

    @njansson
    njansson committed Apr 5, 2024
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  6. Update doi

    @njansson
    njansson committed Apr 5, 2024
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  7. Merge pull request #1225 from ExtremeFLOW/fix/citation_authors 

    Updated cff file to include all authors
    @njansson
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Commits on Apr 6, 2024

  1. Update publist, fixes #1188

    @njansson
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  2. Merge pull request #1227 from ExtremeFLOW/fix/publist 

    Update publist
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Commits on Apr 8, 2024

  1. Migrate authors info

    @njansson
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  2. Create release branch for 0.8, with first release candidate

    @njansson
    njansson committed Apr 8, 2024
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  3. Sync with master

    @njansson
    njansson committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. Fixes from previous merge

    @njansson
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  2. More fixes after bad merge

    @njansson
    njansson committed Apr 9, 2024
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Commits on Apr 12, 2024

  1. Remove explicit mention of KTH 

    (cherry picked from commit 341a9f1)
    @njansson
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Commits on Apr 13, 2024

  1. Update release CI

    @njansson
    njansson committed Apr 13, 2024
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  2. Update release CI

    @njansson
    njansson committed Apr 13, 2024
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  3. Update release workflow

    @njansson
    njansson committed Apr 13, 2024
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  4. Fix typo

    @njansson
    njansson committed Apr 13, 2024
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  5. Fix OpenCL build

    @njansson
    njansson committed Apr 13, 2024
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  6. Fix math rendering for Brinkmann source term 

    (cherry picked from commit eff5cc3)
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Commits on Apr 15, 2024

  1. reformat links for doxygen

    @vbaconnet
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  2. Merge pull request #1233 from ExtremeFLOW/doc/fix-user-file-links 

    reformat links for doxygen
    @njansson
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  3. add TOC

    @vbaconnet
    vbaconnet committed Apr 15, 2024
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  4. fix links

    @vbaconnet
    vbaconnet committed Apr 15, 2024
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  5. Add contributing.md to pages

    @vbaconnet
    vbaconnet committed Apr 15, 2024
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  6. fix link

    @vbaconnet
    vbaconnet committed Apr 15, 2024
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  7. Change title to html tags due to known Doxygen bug not resolving code… 

    … span in markdown tags. doxygen/doxygen#6998
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Commits on Apr 16, 2024

  1. Revamping the documentation. 

    The landing page now contains links into the full list of pages.

Additionally the documentation have been sectioned into 3 main parts.

- A user guide, with all pages related to code usage and installation.
- Developer guide for all information regarding code style and conventions.
- Appendices, which contain all the remaining information. This is kinda a catch-all until enough appendices are related and can become a new section.

Additionally the Doxyfile have been update to make sure new pages are always added to the documentation without manual insertion into the file.
    @timfelle
    timfelle committed Apr 16, 2024
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  2. Adding a few more table of contents

    @timfelle
    timfelle committed Apr 16, 2024
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  3. Fix links on landing page

    @timfelle
    timfelle committed Apr 16, 2024
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  4. Update documentation.yml

    @njansson
    njansson authored Apr 16, 2024
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  5. Update documentation.yml

    @njansson
    njansson authored Apr 16, 2024
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  6. Update documentation.yml

    @njansson
    njansson authored Apr 16, 2024
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  7. Update documentation.yml

    @njansson
    njansson authored Apr 16, 2024
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  8. Link to headings instead of files

    @timfelle
    timfelle committed Apr 16, 2024
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  9. Update links to publications

    @njansson
    njansson authored Apr 16, 2024
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  10. fixed mistake in appendices

    @timfelle
    timfelle committed Apr 16, 2024
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  11. Update index.md with ref instead if md references

    @njansson
    njansson authored Apr 16, 2024
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  12. Update appendices.md, fixed ref

    @njansson
    njansson authored Apr 16, 2024
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  13. Update appendices.md

    @njansson
    njansson authored Apr 16, 2024
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  14. Merge branch 'release/0.8' into doc/reformat-index-and-contrib

    @njansson
    njansson authored Apr 16, 2024
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  15. add small extra explanations

    @vbaconnet
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  16. Updated Makefile.am

    @timfelle
    timfelle committed Apr 16, 2024
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  17. Don't do blank line

    @timfelle
    timfelle committed Apr 16, 2024
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  18. Fix indentation bug

    @timfelle
    timfelle committed Apr 16, 2024
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  19. add link to statistics page

    @vbaconnet
    vbaconnet committed Apr 16, 2024
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  20. remove blank causing table to not render

    @vbaconnet
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  21. Merge pull request #1235 from ExtremeFLOW/doc/reformat-index-and-contrib 

    Reformat documentation and contributing guide
    @njansson
    njansson authored Apr 16, 2024
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  22. Update main.yml

    @njansson
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Commits on Apr 17, 2024

  1. Update README.md

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Commits on Apr 19, 2024

  1. Add marker for serial files, and fix deadlock, fixes #1239 

    (cherry picked from commit 44b96e4)
    @njansson
    njansson committed Apr 19, 2024
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  2. Update rocm version

    @njansson
    njansson committed Apr 19, 2024
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Commits on Apr 22, 2024

  1. Add missing call to padded version of Axhelm 

    (cherry picked from commit fc62f28)
    @njansson
    njansson committed Apr 22, 2024
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  2. Cleanup pnpn res device from invalid chars... 

    (cherry picked from commit f4560f6)
    @njansson
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Commits on Apr 23, 2024

  1. modify apply_vector to account for optional args

    @vbaconnet
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  2. Merge pull request #1249 from ExtremeFLOW/fix/field-dirichlet-optiona… 

    …l-args

modify apply_vector to account for optional args
    @timofeymukha
    timofeymukha authored Apr 23, 2024
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  3. Fix plot script in scalar_mms 

    (cherry picked from commit e4a0bb2)
    @timofeymukha @njansson
    timofeymukha authored and njansson committed Apr 23, 2024
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Commits on Apr 26, 2024

  1. Fix invalid conversion when naming members of a field series 

    (cherry picked from commit 4c47ab1)
    @njansson
    njansson committed Apr 26, 2024
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Commits on Apr 29, 2024

  1. Update main.yml

    @njansson
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  2. Update main.yml

    @njansson
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  3. Update documentation.yml

    @njansson
    njansson authored Apr 29, 2024
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  4. Update main.yml

    @njansson
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Commits on May 1, 2024

  1. Update README.md 

    (cherry picked from commit 1ebfb16)
    @MartinKarp @njansson
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  2. Update README.md 

    (cherry picked from commit 7bbba1e)
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  3. Update README.md 

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  4. Update README.md 

    (cherry picked from commit 520de26)
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  5. Update README.md 

    (cherry picked from commit 76b7a95)
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  6. Update README.md 

    (cherry picked from commit 5387dc6)
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  7. Update README.md 

    (cherry picked from commit a8d04a4)
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  8. Update README.md 

    (cherry picked from commit 16bf88f)
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  9. Update README.md 

    (cherry picked from commit 0f1d781)
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  10. Update README.md 

    (cherry picked from commit 9dda1d2)
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  11. Update README.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
(cherry picked from commit 23e8758)
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  12. Update README.md 

    Co-authored-by: Niclas Jansson <[email protected]>
(cherry picked from commit e33916a)
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  13. Update README.md 

    (cherry picked from commit a4cf357)
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  14. Update README.md 

    (cherry picked from commit bf97e70)
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  15. Update README.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
(cherry picked from commit bc7de12)
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  16. Update doc workflow

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Commits on May 2, 2024

  1. Prevent memory issues during bc mark zones from list

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Commits on May 3, 2024

  1. Fix regression in interface

    @njansson
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  2. Add missing logic for 

    (cherry picked from commit c65cfc2)
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  3. fixes

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Commits on May 9, 2024

  1. Fix invalid logic, preventing contrib from being built 

    (cherry picked from commit 765219c)
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Commits on May 22, 2024

  1. Fix invalid dimension specification (overriden by array declaration) 

    (cherry picked from commit 051847c)
    @njansson
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  2. Update release CI

    @njansson
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Commits on May 30, 2024

  1. Fix reporting of ARM Neoverse V2 (eg. Nvidia Grace)

    @njansson
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  2. Use standard language constructs to guide vectorisation

    @njansson
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  3. Fix some more loops 

    (cherry picked from commit c74cefc)
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Commits on Jun 2, 2024

  1. Bump version

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Commits on Jun 13, 2024

  1. some initial draft 

    (cherry picked from commit d8709f9)
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  2. add little text 

    (cherry picked from commit 777a8e2)
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  3. Update doc/pages/user-guide/statistics-guide.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
(cherry picked from commit b4b9c7f)
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  4. Update doc/pages/user-guide/statistics-guide.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
(cherry picked from commit 74f528c)
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  5. Update doc/pages/user-guide/statistics-guide.md 

    Co-authored-by: Tim Felle Olsen <[email protected]>
(cherry picked from commit 854a6a1)
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  6. typos 

    (cherry picked from commit 8bf163b)
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  7. fix roccm version

    @timfelle
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  8. Remove release from main cI again. we do not want to run the document… 

    …ation here.
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  9. develop CI must also be updated to the new rocm to be able to merge i… 

    …t in.
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  10. Fix the dist steps as well

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  11. Merge pull request #1309 from timfelle/fix/main-ci 

    Fix/main-ci
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Commits on Jun 27, 2024

  1. Fix typo in code snippet 

    (cherry picked from commit 9ce9d87)
    @vbaconnet @njansson
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  2. Fix more typo in code snippet 

    (cherry picked from commit c6743c6)
    @vbaconnet @njansson
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  3. Backport CI fixes for Intel

    @njansson
    njansson committed Jun 27, 2024
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Commits on Jul 5, 2024

  1. Bump version

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Commits on Jul 7, 2024

  1. Fix invalid links in documentation

    @njansson
    njansson committed Jul 7, 2024
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  2. Fix order in cff file

    @njansson
    njansson committed Jul 7, 2024
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