Vtk hdf #1084
Vtk hdf #1084
Conversation
📝 WalkthroughWalkthroughAdds a VTK/HDF5 diagnostic backend ("pharevtkhdf") and writers, extends Python diagnostic format handling, refactors grid and ndarray indexing APIs, introduces new HDF5 helpers and VTK-type writer infrastructure, updates diagnostics dispatch, and adds tests for VTK diagnostics. Changes
Sequence Diagram(s)sequenceDiagram
participant Caller
participant DiagnosticsManagerResolver
participant PhareDict
participant DiagnosticsManager
participant H5Writer_h5
participant H5Writer_vtkh5
Caller->>DiagnosticsManagerResolver: make_unique(hier, model, dict)
DiagnosticsManagerResolver->>PhareDict: read "format" (default "phareh5")
PhareDict-->>DiagnosticsManagerResolver: "phareh5" / "pharevtkhdf" / other
alt "phareh5"
DiagnosticsManagerResolver->>H5Writer_h5: construct H5Writer<ModelView>
H5Writer_h5-->>DiagnosticsManagerResolver: h5_writer
DiagnosticsManagerResolver->>DiagnosticsManager: make with h5_writer
else "pharevtkhdf"
DiagnosticsManagerResolver->>H5Writer_vtkh5: construct vtkh5::H5Writer<ModelView>
H5Writer_vtkh5-->>DiagnosticsManagerResolver: vtkh5_writer
DiagnosticsManagerResolver->>DiagnosticsManager: make with vtkh5_writer
else unknown
DiagnosticsManagerResolver-->>Caller: throw runtime_error
end
sequenceDiagram
participant VTKh5Writer
participant H5TypeWriter
participant VTKFileWriter
participant ElectromagWriter
participant HighFiveFile
VTKh5Writer->>H5TypeWriter: getOrCreateH5File(diagnostic)
H5TypeWriter->>HighFiveFile: open/create per-quantity file
VTKh5Writer->>ElectromagWriter: write(diagnostic)
ElectromagWriter->>VTKFileWriter: initFileLevel / initFieldFileLevel
ElectromagWriter->>VTKFileWriter: visitHierarchy(write_quantity)
VTKFileWriter->>HighFiveFile: write datasets (per-level / per-box / data)
Estimated code review effort🎯 4 (Complex) | ⏱️ ~60 minutes Areas requiring extra attention:
Possibly related PRs
Suggested reviewers
Pre-merge checks and finishing touches❌ Failed checks (1 warning, 1 inconclusive)
✅ Passed checks (1 passed)
✨ Finishing touches
🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
There was a problem hiding this comment.
CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
PhilipDeegan
force-pushed
the
vtk
branch
2 times, most recently
from
39d7491 to
0c9462d
Compare
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 11
🧹 Nitpick comments (3)
src/python3/patch_data.hpp (1)
35-36: Consider passing string parameters by const reference.The
patchIDandoriginparameters insetPatchData,setPatchDataFromGrid, andsetPatchDataFromFieldare passed by value, creating unnecessary copies. Since these functions don't require ownership, passing them asstd::string const&would be more efficient.Apply this pattern to avoid copies:
-void setPatchData(PatchData& data, std::string const patchID, std::string const origin, +void setPatchData(PatchData& data, std::string const& patchID, std::string const& origin, Container lower, Container upper)-void setPatchDataFromGrid(PatchData& pdata, GridLayout& grid, std::string patchID) +void setPatchDataFromGrid(PatchData& pdata, GridLayout& grid, std::string const& patchID)-void setPatchDataFromField(PatchData& pdata, Field const& field, GridLayout& grid, - std::string patchID) +void setPatchDataFromField(PatchData& pdata, Field const& field, GridLayout& grid, + std::string const& patchID)Also applies to: 46-46, 54-55
src/core/data/ndarray/ndarray_vector.hpp (1)
38-38: Simplify unused parameter.The inline comment
/*nCells*/for the unused parameter is non-standard. Modern C++ convention is to simply omit the parameter name.Apply this diff:
- static inline std::uint32_t idx(auto const /*nCells*/, Idx i) { return i; } + static inline std::uint32_t idx(auto const, Idx i) { return i; }src/amr/resources_manager/amr_utils.hpp (1)
247-247: Preserve perfect forwarding into resman.setOnPatchNow that
visitHierarchyforwardsargs, we should propagate the perfect forwarding down intosetOnPatch; otherwise rvalues (e.g., move-only helpers) devolve to lvalues when named insidevisitLevel, preventing those call-sites from compiling or forcing extra copies. Applyingstd::forwardhere keeps the chain intact.- auto guard = resman.setOnPatch(*patch, args...); + auto guard = resman.setOnPatch(*patch, std::forward<Args>(args)...);
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (34)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)pyphare/pyphare/pharesee/__init__.py(1 hunks)pyphare/pyphare/pharesee/tovtk.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(3 hunks)src/core/data/grid/gridlayoutimplyee.hpp(1 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(2 hunks)src/core/utilities/mpi_utils.hpp(1 hunks)src/core/utilities/types.hpp(3 hunks)src/diagnostic/detail/h5writer.hpp(1 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtk_types/info.hpp(1 hunks)src/diagnostic/detail/vtk_types/meta.hpp(1 hunks)src/diagnostic/detail/vtk_types/particle.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(6 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(2 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)src/python3/patch_data.hpp(1 hunks)tests/simulator/CMakeLists.txt(1 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init_small.py
- src/phare/phare_init.py
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/diagnostic/diagnostics.hppsrc/python3/patch_data.hppsrc/amr/physical_models/hybrid_model.hppsrc/amr/resources_manager/amr_utils.hppsrc/diagnostic/detail/vtk_types/particle.hppsrc/diagnostic/detail/vtk_types/fluid.hppsrc/core/utilities/box/box.hppsrc/core/utilities/mpi_utils.hppsrc/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtk_types/info.hppsrc/core/data/grid/gridlayout.hppsrc/diagnostic/diagnostic_manager.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/core/utilities/types.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/hdf5/detail/h5/h5_file.hppsrc/diagnostic/detail/vtk_types/meta.hppsrc/core/utilities/algorithm.hppsrc/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/core/data/tensorfield/tensorfield.hppsrc/diagnostic/detail/vtk_types/electromag.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (7)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2025-02-07T14:35:14.630Z
Learnt from: nicolasaunai
Repo: PHAREHUB/PHARE PR: 591
File: res/cmake/options.cmake:73-75
Timestamp: 2025-02-07T14:35:14.630Z
Learning: In CMake configuration for PHARE, `lowResourceTests` and `highResourceTests` options must be mutually exclusive and cannot be enabled simultaneously.
Applied to files:
tests/simulator/CMakeLists.txt
📚 Learning: 2025-07-09T17:18:05.771Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/amr/CMakeLists.txt:103-105
Timestamp: 2025-07-09T17:18:05.771Z
Learning: In the PHARE project, `HighFive` is a CMake option defined in `res/cmake/options.cmake` as `option(HighFive "Build with highfive usage" ON)`, not a target that would be created by find_package(). The condition `if (HighFive)` correctly checks this option.
Applied to files:
src/diagnostic/detail/h5writer.hpp
📚 Learning: 2024-07-26T22:04:34.160Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-07-26T22:04:34.160Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
📚 Learning: 2025-09-17T13:50:16.038Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/tensorfield/tensor_field_data_factory.hpp:112-112
Timestamp: 2025-09-17T13:50:16.038Z
Learning: PhilipDeegan indicated that getSizeOfMemory returning a placeholder value of 1 in TensorFieldDataFactory is acceptable for their use case, suggesting it may not be critical for PHARE's memory management needs.
Applied to files:
src/core/data/tensorfield/tensorfield.hpp
🧬 Code graph analysis (20)
src/diagnostic/diagnostics.hpp (3)
src/diagnostic/diagnostic_manager.hpp (5)
dict(83-83)dict(86-86)dict(86-86)make_unique(74-80)make_unique(74-75)src/diagnostic/detail/vtkh5_writer.hpp (2)
make_unique(67-74)make_unique(67-67)src/diagnostic/detail/h5writer.hpp (2)
make_unique(61-68)make_unique(61-61)
src/amr/resources_manager/amr_utils.hpp (1)
src/core/data/field/field.hpp (4)
args(75-81)args(75-75)args(83-86)args(83-83)
src/diagnostic/detail/vtk_types/particle.hpp (4)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtkh5_type_writer.hpp (4)
diagnostic(87-92)diagnostic(87-87)ilvl(385-414)ilvl(385-385)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/diagnostic/detail/h5writer.hpp (4)
diagnostic(94-98)diagnostic(94-94)iLevel(210-214)iLevel(210-210)
src/diagnostic/detail/vtk_types/fluid.hpp (3)
src/diagnostic/detail/vtkh5_type_writer.hpp (6)
diagnostic(87-92)diagnostic(87-87)ilvl(385-414)ilvl(385-385)boxes(57-71)boxes(57-57)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)
src/core/utilities/box/box.hpp (1)
src/core/utilities/types.hpp (2)
product(265-268)product(265-265)
tests/simulator/refinement/test_2d_10_core.py (2)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)tests/simulator/test_advance.py (1)
AdvanceTestBase(33-788)
src/diagnostic/detail/vtk_types/info.hpp (7)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-71)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtk_types/meta.hpp (2)
write(29-31)write(29-29)src/diagnostic/detail/vtk_types/particle.hpp (2)
write(31-54)write(31-31)src/diagnostic/detail/vtkh5_type_writer.hpp (2)
diagnostic(87-92)diagnostic(87-87)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/diagnostic/detail/h5writer.hpp (2)
diagnostic(94-98)diagnostic(94-94)
src/core/data/grid/gridlayout.hpp (2)
src/core/utilities/types.hpp (5)
auto(151-156)auto(491-494)auto(497-500)for_N_make_array(484-487)for_N_make_array(484-484)src/core/utilities/box/box.hpp (6)
grow(88-93)grow(88-88)grow(323-328)grow(323-323)i(96-96)i(96-96)
tests/simulator/test_vtk_diagnostics.py (7)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)pyphare/pyphare/simulator/simulator.py (2)
startMPI(40-44)reset(254-265)tests/simulator/__init__.py (4)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)run(246-248)tests/diagnostic/__init__.py (1)
dump_all_diags(15-61)pyphare/pyphare/pharein/simulation.py (2)
simulation_domain(978-979)Simulation(745-1080)pyphare/pyphare/pharein/maxwellian_fluid_model.py (1)
MaxwellianFluidModel(8-303)pyphare/pyphare/pharesee/tovtk.py (1)
convert(269-416)
tests/simulator/__init__.py (1)
pyphare/pyphare/core/box.py (1)
Box(5-69)
src/core/data/grid/gridlayoutimplyee.hpp (1)
tests/core/data/gridlayout/test_linear_combinaisons_yee.py (1)
dualToPrimal(27-35)
src/core/utilities/types.hpp (1)
src/core/data/tensorfield/tensorfield.hpp (2)
for_N(83-87)for_N(88-92)
src/core/data/ndarray/ndarray_vector.hpp (1)
src/core/utilities/types.hpp (2)
product(265-268)product(265-265)
src/diagnostic/detail/vtk_types/meta.hpp (5)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-71)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtk_types/info.hpp (2)
write(31-33)write(31-31)src/diagnostic/detail/vtkh5_type_writer.hpp (2)
diagnostic(87-92)diagnostic(87-87)src/diagnostic/detail/types/meta.hpp (1)
PHARE(7-143)
pyphare/pyphare/pharesee/tovtk.py (1)
src/diagnostic/detail/vtkh5_type_writer.hpp (8)
shape(114-121)shape(114-114)shape(123-131)shape(123-123)ilvl(385-414)ilvl(385-385)resize(417-423)resize(417-417)
src/core/utilities/algorithm.hpp (2)
src/core/utilities/types.hpp (2)
all(355-358)all(355-355)src/core/data/ndarray/ndarray_vector.hpp (4)
make_array_view(214-217)make_array_view(214-214)make_array_view(220-223)make_array_view(220-220)
src/diagnostic/diagnostic_model_view.hpp (5)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (12)
patch(137-145)patch(137-137)ions(410-420)ions(410-411)ions(424-450)ions(424-425)ions(452-486)ions(452-453)ions(498-537)ions(498-499)ions(545-551)ions(545-546)src/amr/resources_manager/amr_utils.hpp (2)
visitHierarchy(257-266)visitHierarchy(257-258)src/core/data/electrons/electrons.hpp (16)
layout(107-133)layout(107-107)layout(285-285)layout(285-285)layout(286-286)layout(286-286)layout(309-319)layout(309-309)forward_as_tuple(47-50)forward_as_tuple(52-55)forward_as_tuple(181-184)forward_as_tuple(186-186)forward_as_tuple(254-257)forward_as_tuple(259-262)forward_as_tuple(330-333)forward_as_tuple(335-338)src/core/data/ions/ion_population/ion_population.hpp (1)
forward_as_tuple(109-113)src/core/data/ions/ions.hpp (1)
forward_as_tuple(225-229)
src/diagnostic/detail/vtkh5_writer.hpp (4)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-61)src/diagnostic/detail/h5writer.hpp (15)
H5Writer(51-56)H5Writer(58-58)H5Writer(194-194)H5Writer(195-195)make_unique(61-68)make_unique(61-61)level(72-73)timestamp(101-104)timestamp(101-101)diagnostic(94-98)diagnostic(94-94)modelView_(160-160)timestamp_(161-161)dump(224-250)dump(224-225)src/diagnostic/diagnostics.hpp (2)
make_unique(50-65)make_unique(50-51)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
level(309-331)level(309-309)level(333-337)level(333-333)diagnostic(87-92)diagnostic(87-87)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-71)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
diagnostic(87-92)diagnostic(87-87)ilvl(385-414)ilvl(385-385)boxes(57-71)boxes(57-57)
src/diagnostic/detail/vtkh5_type_writer.hpp (7)
src/core/utilities/types.hpp (5)
get_env_as(249-249)sum_from(277-285)sum_from(277-277)sum(271-274)sum(271-271)src/hdf5/detail/h5/h5_file.hpp (9)
data(66-66)s(248-248)s(248-248)s(249-253)s(249-249)path(267-273)path(267-267)path(275-280)path(275-275)src/core/utilities/box/box.hpp (11)
box(50-50)i(96-96)i(96-96)grow(88-93)grow(88-88)grow(323-328)grow(323-323)s(209-234)s(209-209)s(235-240)s(235-235)src/core/data/tensorfield/tensorfield.hpp (6)
i(178-178)i(178-178)i(179-179)i(179-179)tensor_field_dim_from_rank(18-24)tensor_field_dim_from_rank(18-18)src/core/utilities/mpi_utils.hpp (4)
rank(25-25)collect(17-17)collect(214-229)collect(214-214)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/core/utilities/algorithm.hpp (2)
convert_to_fortran_primal(137-140)convert_to_fortran_primal(137-137)
🪛 GitHub Check: CodeQL
pyphare/pyphare/pharesee/tovtk.py
[notice] 163-163: Unused local variable
Variable cellData_g is not used.
[notice] 165-165: Unused local variable
Variable fieldData_g is not used.
[notice] 166-166: Unused local variable
Variable cellDataOffset_g is not used.
[notice] 167-167: Explicit returns mixed with implicit (fall through) returns
Mixing implicit and explicit returns may indicate an error, as implicit returns always return None.
[notice] 168-168: Unused local variable
Variable FieldDataOffset_g is not used.
[failure] 361-361: Wrong number of arguments in a call
Call to function primalScalarToFlatPrimal with too many arguments; should be no more than 5.
[failure] 387-387: Wrong number of arguments in a call
Call to function BtoFlatPrimal with too few arguments; should be no fewer than 6.
Call to function EtoFlatPrimal with too few arguments; should be no fewer than 6.
Call to function primalVectorToFlatPrimal with too few arguments; should be no fewer than 6.
src/core/utilities/algorithm.hpp
[notice] 105-105: Unused local variable
Variable c_ordering is not used.
src/diagnostic/detail/vtkh5_type_writer.hpp
[notice] 41-41: Commented-out code
This comment appears to contain commented-out code.
🪛 Ruff (0.14.2)
tests/simulator/test_vtk_diagnostics.py
1-1: Shebang is present but file is not executable
(EXE001)
27-27: Unused function argument: xyz
(ARG001)
34-34: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
41-41: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
44-44: Unused function argument: xyz
(ARG001)
47-47: Unused function argument: xyz
(ARG001)
54-54: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
61-61: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
64-64: Unused function argument: xyz
(ARG001)
67-67: Unused function argument: xyz
(ARG001)
70-70: Unused function argument: xyz
(ARG001)
121-121: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
pyphare/pyphare/pharesee/tovtk.py
1-1: Shebang is present but file is not executable
(EXE001)
17-19: Avoid specifying long messages outside the exception class
(TRY003)
204-204: Avoid specifying long messages outside the exception class
(TRY003)
232-232: Avoid specifying long messages outside the exception class
(TRY003)
263-263: Consider [*root_spacing, 0, 0] instead of concatenation
Replace with [*root_spacing, 0, 0]
(RUF005)
265-265: Consider [*root_spacing, 0] instead of concatenation
Replace with [*root_spacing, 0]
(RUF005)
321-321: Local variable cellData_g is assigned to but never used
Remove assignment to unused variable cellData_g
(F841)
323-323: Local variable fieldData_g is assigned to but never used
Remove assignment to unused variable fieldData_g
(F841)
324-324: Local variable cellDataOffset_g is assigned to but never used
Remove assignment to unused variable cellDataOffset_g
(F841)
326-326: Local variable FieldDataOffset_g is assigned to but never used
Remove assignment to unused variable FieldDataOffset_g
(F841)
384-384: Prefer next(iter(patch.keys())) over single element slice
Replace with next(iter(patch.keys()))
(RUF015)
🔇 Additional comments (8)
src/python3/patch_data.hpp (1)
26-30: Critical fix: Correct variadic template forwarding.The change from
std::forward<Args...>(args...)tostd::forward<Args>(args)...fixes invalid syntax. The ellipsis must appear outside thestd::forwardcall to properly expand each argument in the parameter pack individually, ensuring correct perfect forwarding semantics.src/hdf5/detail/h5/h5_file.hpp (1)
98-99: LGTM!The defensive existence check prevents duplicate dataset creation and returns the existing dataset if found.
src/core/utilities/types.hpp (2)
248-254: Verify error handling for invalid environment variable values.This function depends on
from_string<T>, which silently returns a default-initialized value on conversion failure. If an environment variable exists but contains an invalid value for typeT, this function will return an unexpected result without any indication of failure.Ensure that upstream callers can handle or validate the returned values, especially for critical configuration parameters.
483-487: LGTM!This is a clean convenience wrapper around
for_Nwith themake_arraymode. The implementation properly forwards the function parameter and maintains constexpr correctness.src/core/utilities/mpi_utils.hpp (1)
5-7: LGTM!The added includes are necessary and properly support the file's dependencies:
phare_mpi.hppfor MPI definitions used throughoutspan.hppforSpanSettemplate (lines 169, 174, 204)types.hppfor type traits likeis_std_vector_v,is_std_array_v, anddisplacementFrom(lines 77, 154, 221)src/core/data/ndarray/ndarray_vector.hpp (3)
55-70: LGTM!The unified index computation via
idx(...)followed by bounds-checked access throughdata[i]provides a clean, consistent access pattern across all dimensionalities.
101-101: LGTM! Consistent template parameter updates.All usage sites have been correctly updated to use
NdArrayViewerwithout theDataTypetemplate parameter, maintaining consistency with the simplified template signature.Also applies to: 138-138, 271-271, 283-283
22-23: Reconsider index type constraint—no evidence of practical limitation.The
std::uint16_tindex type appears to be an intentional design constraint for this physics simulation codebase. Shape values are stored asstd::uint32_tarrays (lines 124, 209, 307), but indices are constrained touint16_t—a deliberate trade-off likely for memory efficiency or simulation requirements. No codebase search found array dimensions exceeding 65K in any single dimension, and type promotion in index calculations prevents overflow. This design aligns with typical physics grid constraints for plasma simulations.
PhilipDeegan
force-pushed
the
vtk
branch
4 times, most recently
from
9371cab to
da3b967
Compare
There was a problem hiding this comment.
Actionable comments posted: 4
♻️ Duplicate comments (7)
src/hdf5/detail/h5/h5_file.hpp (3)
105-114: Missing parent group creation will cause runtime failure.Unlike
create_data_set(line 100), this function doesn't callcreateGroupsToDataSet(path)before creating the dataset. If parent groups don't exist,h5file_.createDataSetwill fail at runtime.Apply this diff to add parent group creation:
template<typename Type> auto create_chunked_data_set(auto const& path, auto const chunk, auto const& dataspace) { if (exist(path)) return h5file_.getDataSet(path); + createGroupsToDataSet(path); HighFive::DataSetCreateProps props; props.add(HighFive::Chunking{chunk}); return h5file_.createDataSet(path, dataspace, HighFive::create_datatype<Type>(), props); }
249-253: Replace assertion with exception for production safety.The
assert(exist(s))is compiled out in release builds (whenNDEBUGis defined), leading to undefined behavior if a non-existent dataset is accessed. This could cause crashes or silent data corruption in production.Apply this diff:
auto getDataSet(std::string const& s) { - assert(exist(s)); + if (!exist(s)) + throw std::runtime_error("Dataset does not exist: " + s); return h5file_.getDataSet(s); }
255-258: Fix incorrect special member function signatures.Two critical issues:
- Line 256: Move constructor declared with
const&&defeats move semantics since you cannot transfer ownership from a const object.- Line 257: Copy assignment operator missing
constqualifier on parameter, which is non-standard and could allow accidental modification of the source object.Apply this diff to correct both signatures:
HighFiveFile(HighFiveFile const&) = delete; -HighFiveFile(HighFiveFile const&&) = delete; -HighFiveFile& operator=(HighFiveFile&) = delete; +HighFiveFile(HighFiveFile&&) = delete; +HighFiveFile& operator=(HighFiveFile const&) = delete; HighFiveFile& operator=(HighFiveFile&&) = delete;src/core/utilities/types.hpp (1)
224-231: Missing include and error handling already flagged.The issues with missing
<sstream>include and silent failure on conversion errors have already been identified in a previous review.pyphare/pyphare/pharesee/tovtk.py (1)
80-91: Correct 3D By primalization averaging.The 3D branch reuses
ph_bzand averages along the Y axis, so By mixes the wrong component and skips the X-direction dual pair. The exported magnetic field is therefore incorrect.Replace the averaging with this fix:
- by[:, :, :] = 0.5 * ( - 0.5 - * ( - ph_by[domain, domainP1, domain][:, 1:, :] - + ph_by[domain, domainP1, domain][:, :-1, :] - ) - + 0.5 - * ( - ph_bz[domain, domain, domainP1][:, :, 1:] - + ph_bz[domain, domain, domainP1][:, :, :-1] - ) - ) + by[:, :, :] = 0.5 * ( + 0.5 + * ( + ph_by[domainP1, domain, domain][1:, :, :] + + ph_by[domainP1, domain, domain][:-1, :, :] + ) + + 0.5 + * ( + ph_by[domain, domain, domainP1][:, :, 1:] + + ph_by[domain, domain, domainP1][:, :, :-1] + ) + )src/diagnostic/detail/vtk_types/particle.hpp (1)
37-54: Particle VTK writer is still a no-op
write_quantitynever writes anything, sovisitHierarchyproduces empty particle datasets and every particle diagnostic is silently lost. This is the same blocker that was raised earlier—please port the actual write logic (e.g., iterate populations/layouts and feed the initializer just like the existing H5 ParticlesDiagnosticWriter does) before landing this format.src/diagnostic/detail/vtkh5_writer.hpp (1)
177-183: Restore post-write flag downgrade to prevent data loss.Line 179 sets
file_flags[diagnostic->type + diagnostic->quantity] = this->flags, which in overwrite mode includesHiFile::Truncate. This flag persists across subsequentdump()calls, causing each dump to reopen the file in truncate mode and erase earlier time steps.Apply this diff to reset flags after writing:
for (auto* diagnostic : diagnostics) typeWriters_.at(diagnostic->type)->write(*diagnostic); + + for (auto* diagnostic : diagnostics) + file_flags[diagnostic->type + diagnostic->quantity] = READ_WRITE;
🧹 Nitpick comments (6)
src/amr/resources_manager/amr_utils.hpp (1)
229-239: Consider forwarding args for consistency withvisitHierarchy.While
visitHierarchynow properly forwards the variadic arguments (line 251),visitLevelreceives forwarding references but passes them tosetOnPatchwithout forwarding (line 234). For consistency and to preserve move semantics, consider applying the same forwarding pattern.Apply this diff to forward the arguments:
template<typename GridLayout, typename ResMan, typename Action, typename... Args> void visitLevel(SAMRAI_Types::level_t& level, ResMan& resman, Action&& action, Args&&... args) { for (auto& patch : level) { - auto guard = resman.setOnPatch(*patch, args...); + auto guard = resman.setOnPatch(*patch, std::forward<Args>(args)...); GridLayout layout = layoutFromPatch<GridLayout>(*patch); action(layout, to_string(patch->getGlobalId()), static_cast<std::size_t>(level.getLevelNumber())); } }tests/simulator/refinement/test_2d_10_core.py (1)
17-24: Consider refactoring for test isolation.Module-level initialization of
cpp,test,L0_diags, andL0L1_diagscreates global mutable state that persists across imports. While this works for single-use test scripts, it could impact test isolation if this module is later integrated into a larger test suite.Consider lazy initialization or moving these to
main()to improve test isolation and initialization order control.Example refactor moving initialization to main():
-cpp = cpp_lib() -test = AdvanceTestBase(rethrow=True) # change to False for debugging images -L0_diags = "phare_outputs/test_x_homo_0" -L0L1_diags = "phare_outputs/test_x_homo_1" - ph.NO_GUI() +# Module-level variables to be initialized in main() +cpp = None +test = None +L0_diags = "phare_outputs/test_x_homo_0" +L0L1_diags = "phare_outputs/test_x_homo_1" def config(diag_outputs, model_init={}, refinement_boxes=None):Then initialize in
main():def main(): + global cpp, test import random startMPI() + cpp = cpp_lib() + test = AdvanceTestBase(rethrow=True) rando = random.randint(0, int(1e10))tests/simulator/test_vtk_diagnostics.py (2)
34-34: Consider replacing lambda assignments with def statements.PEP 8 recommends using
defstatements instead of assigning lambdas to variables for better traceability and debugging.Example refactor for one occurrence:
- _ = lambda i: 0.1 * np.sin(2 * np.pi * xyz[i] / L[i]) + def component_value(i): + return 0.1 * np.sin(2 * np.pi * xyz[i] / L[i])Also applies to: 41-41, 54-54, 61-61
169-169: Clarify the status of EM_B conversion.The commented-out line suggests
tovtkconversion fails forEM_B.h5.Should this be tracked as a TODO/FIXME, or is this a known limitation that's acceptable for this PR? If it's a bug, consider opening an issue to track it.
Do you want me to help create an issue for tracking the EM_B conversion problem?
src/diagnostic/detail/vtkh5_writer.hpp (1)
130-130: Hard-coded maxLevel limit.The hard-coded
maxLevel = 10may be insufficient for simulations requiring deeper AMR hierarchies.Consider making this configurable via the
PHAREDictinmake_unique, e.g.:auto maxLevel = cppdict::get_value(dict, "max_level", std::size_t{10});src/diagnostic/detail/vtkh5_type_writer.hpp (1)
361-361: Document the X_TIMES multiplier logic.The dimension-dependent multiplier
X_TIMES(4 for 1D, 2 for 2D, 1 for 3D) implements an important conversion factor but lacks explanation.Add a comment explaining why the multiplier is needed:
// VTK stores data per cube face: 2D data requires 2 faces, 1D requires 4 faces, 3D is 1:1 constexpr static auto X_TIMES = std::array{4, 2, /* 3d noop */ 1}[dimension - 1];
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (33)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)pyphare/pyphare/pharesee/__init__.py(1 hunks)pyphare/pyphare/pharesee/tovtk.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(3 hunks)src/core/data/grid/gridlayoutdefs.hpp(1 hunks)src/core/data/grid/gridlayoutimplyee.hpp(27 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(2 hunks)src/core/utilities/types.hpp(3 hunks)src/diagnostic/detail/h5writer.hpp(1 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtk_types/info.hpp(1 hunks)src/diagnostic/detail/vtk_types/meta.hpp(1 hunks)src/diagnostic/detail/vtk_types/particle.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(7 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(2 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)tests/simulator/CMakeLists.txt(2 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init_small.py
- src/phare/phare_init.py
🚧 Files skipped from review as they are similar to previous changes (12)
- src/diagnostic/diagnostic_manager.hpp
- pyphare/pyphare/pharein/simulation.py
- tests/simulator/init.py
- pyphare/pyphare/pharein/init.py
- src/core/data/grid/gridlayout.hpp
- pyphare/pyphare/pharesee/init.py
- src/diagnostic/detail/vtk_types/meta.hpp
- src/diagnostic/detail/h5writer.hpp
- src/amr/physical_models/hybrid_model.hpp
- src/core/utilities/algorithm.hpp
- tests/simulator/CMakeLists.txt
- src/core/utilities/box/box.hpp
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/core/data/grid/gridlayoutdefs.hppsrc/core/data/tensorfield/tensorfield.hppsrc/amr/resources_manager/amr_utils.hppsrc/diagnostic/detail/vtk_types/electromag.hppsrc/diagnostic/detail/vtk_types/particle.hppsrc/diagnostic/detail/vtk_types/fluid.hppsrc/diagnostic/diagnostics.hppsrc/core/utilities/types.hppsrc/hdf5/detail/h5/h5_file.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtk_types/info.hppsrc/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (2)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧬 Code graph analysis (13)
src/amr/resources_manager/amr_utils.hpp (1)
src/core/data/field/field.hpp (4)
args(75-81)args(75-75)args(83-86)args(83-83)
src/diagnostic/detail/vtk_types/electromag.hpp (3)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-71)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(87-92)diagnostic(87-87)lvl(267-272)lvl(267-267)ilvl(388-417)ilvl(388-388)boxes(57-71)boxes(57-57)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)
tests/simulator/test_vtk_diagnostics.py (5)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)pyphare/pyphare/simulator/simulator.py (2)
startMPI(41-45)reset(258-269)tests/simulator/__init__.py (3)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)tests/diagnostic/__init__.py (1)
dump_all_diags(15-62)pyphare/pyphare/pharesee/tovtk.py (1)
convert(269-416)
src/diagnostic/detail/vtk_types/particle.hpp (3)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-71)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
diagnostic(87-92)diagnostic(87-87)lvl(267-272)lvl(267-267)ilvl(388-417)ilvl(388-388)
src/diagnostic/detail/vtk_types/fluid.hpp (2)
src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(87-92)diagnostic(87-87)lvl(267-272)lvl(267-267)ilvl(388-417)ilvl(388-388)boxes(57-71)boxes(57-57)src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)
src/diagnostic/diagnostics.hpp (3)
src/diagnostic/diagnostic_manager.hpp (5)
dict(83-83)dict(86-86)dict(86-86)make_unique(74-80)make_unique(74-75)src/diagnostic/detail/vtkh5_writer.hpp (2)
make_unique(67-74)make_unique(67-67)src/diagnostic/detail/h5writer.hpp (2)
make_unique(61-68)make_unique(61-61)
src/core/data/ndarray/ndarray_vector.hpp (1)
src/core/utilities/types.hpp (2)
product(265-268)product(265-265)
tests/simulator/refinement/test_2d_10_core.py (2)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)tests/simulator/test_advance.py (1)
AdvanceTestBase(33-869)
src/diagnostic/detail/vtkh5_writer.hpp (4)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-60)src/diagnostic/diagnostics.hpp (2)
make_unique(50-65)make_unique(50-51)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
level(298-334)level(298-298)level(336-340)level(336-336)diagnostic(87-92)diagnostic(87-87)src/hdf5/detail/h5/h5_file.hpp (4)
path(267-273)path(267-267)path(275-280)path(275-275)
src/diagnostic/detail/vtk_types/info.hpp (5)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-71)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtk_types/meta.hpp (2)
write(29-31)write(29-29)src/diagnostic/detail/vtk_types/particle.hpp (2)
write(31-54)write(31-31)src/diagnostic/detail/vtkh5_type_writer.hpp (2)
diagnostic(87-92)diagnostic(87-87)
src/diagnostic/diagnostic_model_view.hpp (4)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (10)
patch(146-154)patch(146-146)ions(407-416)ions(407-407)ions(420-445)ions(420-420)ions(447-480)ions(447-447)ions(492-531)ions(492-493)src/amr/resources_manager/amr_utils.hpp (2)
visitHierarchy(244-253)visitHierarchy(244-245)src/core/data/ions/ion_population/ion_population.hpp (1)
forward_as_tuple(109-113)src/core/data/ions/ions.hpp (1)
forward_as_tuple(225-229)
src/diagnostic/detail/vtkh5_type_writer.hpp (5)
src/core/utilities/types.hpp (7)
get_env_as(249-249)for_N_make_array(504-507)for_N_make_array(504-504)sum_from(277-285)sum_from(277-277)sum(271-274)sum(271-271)src/core/utilities/box/box.hpp (7)
box(51-51)i(97-97)i(97-97)grow(89-94)grow(89-89)grow(275-280)grow(275-275)src/core/data/tensorfield/tensorfield.hpp (6)
i(181-181)i(181-181)i(182-182)i(182-182)tensor_field_dim_from_rank(17-24)tensor_field_dim_from_rank(17-17)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/core/utilities/algorithm.hpp (2)
convert_to_fortran_primal(137-140)convert_to_fortran_primal(137-137)
pyphare/pyphare/pharesee/tovtk.py (2)
pyphare/pyphare/core/box.py (1)
shape(32-34)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
ilvl(388-417)ilvl(388-388)lvl(267-272)lvl(267-267)resize(420-426)resize(420-420)
🪛 GitHub Check: CodeQL
pyphare/pyphare/pharesee/tovtk.py
[failure] 361-361: Wrong number of arguments in a call
Call to function primalScalarToFlatPrimal with too many arguments; should be no more than 5.
[failure] 387-387: Wrong number of arguments in a call
Call to function BtoFlatPrimal with too few arguments; should be no fewer than 6.
Call to function EtoFlatPrimal with too few arguments; should be no fewer than 6.
Call to function primalVectorToFlatPrimal with too few arguments; should be no fewer than 6.
[notice] 163-163: Unused local variable
Variable cellData_g is not used.
[notice] 165-165: Unused local variable
Variable fieldData_g is not used.
[notice] 166-166: Unused local variable
Variable cellDataOffset_g is not used.
[notice] 167-167: Explicit returns mixed with implicit (fall through) returns
Mixing implicit and explicit returns may indicate an error, as implicit returns always return None.
[notice] 168-168: Unused local variable
Variable FieldDataOffset_g is not used.
🪛 Ruff (0.14.3)
tests/simulator/test_vtk_diagnostics.py
1-1: Shebang is present but file is not executable
(EXE001)
27-27: Unused function argument: xyz
(ARG001)
34-34: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
41-41: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
44-44: Unused function argument: xyz
(ARG001)
47-47: Unused function argument: xyz
(ARG001)
54-54: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
61-61: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
64-64: Unused function argument: xyz
(ARG001)
67-67: Unused function argument: xyz
(ARG001)
70-70: Unused function argument: xyz
(ARG001)
121-121: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
pyphare/pyphare/pharesee/tovtk.py
1-1: Shebang is present but file is not executable
(EXE001)
17-19: Avoid specifying long messages outside the exception class
(TRY003)
204-204: Avoid specifying long messages outside the exception class
(TRY003)
232-232: Avoid specifying long messages outside the exception class
(TRY003)
263-263: Consider [*root_spacing, 0, 0] instead of concatenation
Replace with [*root_spacing, 0, 0]
(RUF005)
265-265: Consider [*root_spacing, 0] instead of concatenation
Replace with [*root_spacing, 0]
(RUF005)
321-321: Local variable cellData_g is assigned to but never used
Remove assignment to unused variable cellData_g
(F841)
323-323: Local variable fieldData_g is assigned to but never used
Remove assignment to unused variable fieldData_g
(F841)
324-324: Local variable cellDataOffset_g is assigned to but never used
Remove assignment to unused variable cellDataOffset_g
(F841)
326-326: Local variable FieldDataOffset_g is assigned to but never used
Remove assignment to unused variable FieldDataOffset_g
(F841)
384-384: Prefer next(iter(patch.keys())) over single element slice
Replace with next(iter(patch.keys()))
(RUF015)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (7)
- GitHub Check: build (macos-13)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
- GitHub Check: Analyze (cpp)
- GitHub Check: Analyze (python)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: build (ubuntu-latest, gcc)
🔇 Additional comments (4)
src/hdf5/detail/h5/h5_file.hpp (1)
98-99: LGTM! Good defensive check.The existence check makes dataset creation idempotent, allowing safe repeated calls.
src/amr/resources_manager/amr_utils.hpp (1)
251-251: LGTM! Critical correctness fix for perfect forwarding.The corrected forwarding syntax
std::forward<Args>(args)...properly expands the parameter pack, forwarding each argument individually with its original value category. This matches the pattern shown in the relevant code snippets fromfield.hpp.tests/simulator/refinement/test_2d_10_core.py (1)
20-23: Initialization order with MPI startup is a valid concern—verify actual runtime behavior.
cpp_lib()is imported at module load time (line 20), but MPI initialization viaSamraiLifeCycle()doesn't occur untilstartMPI()is called inmain()(line 188) or viaSimulatorTest.setUp(). The C++ bindings module (pybindlibs.cpp) may require MPI context to be initialized at import time. Additionally, instantiatingtest = AdvanceTestBase(rethrow=True)at module level (line 21) before MPI is set up could cause issues if the class initialization has MPI dependencies, thoughsetUp()is only called by the test framework before test methods run.Consider moving module-level initialization inside
main()afterstartMPI()is called, or implement lazy initialization (defercpp_lib()andAdvanceTestBaseinstantiation until after MPI setup). This is especially important for MPI-based tests that initialize at module scope.src/diagnostic/detail/vtkh5_type_writer.hpp (1)
138-139: Verify duplicate write() calls in 2D writers.Both
VTKFileFieldWriter::write2DandVTKFileTensorFieldWriter::write2Dcallwrite()twice consecutively without any intervening state change. This pattern is unusual and may indicate either:
- An intentional handling of 2D data peculiarities
- A copy-paste error
Please confirm whether the duplicate
write()calls are intentional. If intentional, add a comment explaining why 2D data requires two identical write passes.If this is an error, remove the duplicate call:
}; write(); - write(); }Also applies to: 187-188
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Nitpick comments (3)
tests/simulator/test_vtk_diagnostics.py (2)
19-19: Remove unused module-level variable.The
cppvariable is instantiated but never referenced in this file.Apply this diff:
-cpp = cpp_lib() - ndims = [2] # 3d todo / 1d not supported interp_orders = [1] # , 2, 3
29-61: Eliminate code duplication in field and velocity functions.The
by/bzfunctions are identical, and thevy/vzfunctions are identical. This duplication can be eliminated with a shared helper.Consider refactoring to use a shared periodic function generator:
def make_periodic_sin(*xyz): from pyphare.pharein.global_vars import sim L = sim.simulation_domain() _ = lambda i: 0.1 * np.sin(2 * np.pi * xyz[i] / L[i]) return np.asarray([_(i) for i in range(len(xyz))]).prod(axis=0) def make_periodic_cos(*xyz): from pyphare.pharein.global_vars import sim L = sim.simulation_domain() _ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i]) return np.asarray([_(i) for i in range(len(xyz))]).prod(axis=0) def by(*xyz): return make_periodic_sin(*xyz) def bz(*xyz): return make_periodic_sin(*xyz) def vy(*xyz): return make_periodic_cos(*xyz) def vz(*xyz): return make_periodic_cos(*xyz)src/core/utilities/types.hpp (1)
226-235: Consider verifying full string consumption.The function correctly implements exception-based error handling. However, it may silently ignore trailing characters (e.g.,
"123abc"parses as123).Apply this diff to ensure the entire string is consumed:
template<typename T> NO_DISCARD T from_string(std::string const& s) { T t; std::stringstream ss(s); ss >> t; - if (ss.fail()) + if (ss.fail() || (!ss.eof() && ss.peek() != std::stringstream::traits_type::eof())) throw std::runtime_error("Cannot Parse T from: " + s); return t; }Optionally, consider adding a specialization for
std::stringif environment variables may contain whitespace:template<> NO_DISCARD inline std::string from_string<std::string>(std::string const& s) { return s; }
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (4)
src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (2)
- src/core/utilities/algorithm.hpp
- src/diagnostic/detail/vtkh5_type_writer.hpp
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/core/utilities/types.hpp
🧠 Learnings (4)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/types.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/types.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/types.hpp
🧬 Code graph analysis (1)
tests/simulator/test_vtk_diagnostics.py (5)
pyphare/pyphare/simulator/simulator.py (2)
startMPI(41-45)reset(258-269)tests/simulator/__init__.py (3)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)tests/diagnostic/__init__.py (1)
dump_all_diags(15-62)pyphare/pyphare/pharein/simulation.py (2)
simulation_domain(967-968)Simulation(735-1069)pyphare/pyphare/pharein/maxwellian_fluid_model.py (1)
MaxwellianFluidModel(8-303)
🪛 Ruff (0.14.4)
tests/simulator/test_vtk_diagnostics.py
26-26: Unused function argument: xyz
(ARG001)
33-33: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
40-40: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
43-43: Unused function argument: xyz
(ARG001)
46-46: Unused function argument: xyz
(ARG001)
53-53: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
60-60: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
63-63: Unused function argument: xyz
(ARG001)
66-66: Unused function argument: xyz
(ARG001)
69-69: Unused function argument: xyz
(ARG001)
🔇 Additional comments (5)
tests/simulator/test_vtk_diagnostics.py (1)
161-162: Verify the purpose of the render_data call.The test calls
phc.vtkhdf.render_databut doesn't assert anything about the output. The comment suggests adding verification logic using the vtk module.Is this call intentional for manual inspection only, or should it include assertions to verify the generated VTK/HDF artifacts? If verification is needed, consider:
# Example verification approach import os self.assertTrue(os.path.exists(f"{local_out}/EM_E.vtkhdf")) # Add vtk module-based validation of file structure/contentssrc/core/utilities/types.hpp (4)
1-2: LGTM: Header guard follows project convention.The header guard naming correctly follows the project's full-path structure pattern.
Also applies to: 566-566
7-21: LGTM: All necessary includes present.The include additions properly support the new functionality, including
<sstream>and<stdexcept>for thefrom_stringimplementation.
252-258: LGTM: Clean environment variable parsing utility.The function correctly integrates
get_envwithfrom_stringto provide type-safe environment variable access with defaults.
514-518: LGTM: Clean constexpr utility.The function correctly composes
for_Nandallto provide a compile-time evaluable check across N invocations.
There was a problem hiding this comment.
Actionable comments posted: 0
♻️ Duplicate comments (1)
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
128-140: Add explanatory comment for duplicate write() calls.The
write()lambda is invoked twice (lines 138-139) in the 2D case to write data for both faces of the cube (per theX_TIMES = 2multiplier at line 361). A brief comment explaining this per-face data structure would improve code clarity.Apply this diff to add the explanatory comment:
}; + // 2D data is written per face of cube, requiring 2 passes (X_TIMES = 2) write(); write(); }
🧹 Nitpick comments (2)
src/diagnostic/detail/vtkh5_type_writer.hpp (2)
176-189: Add explanatory comment for duplicate write() calls.Similar to the scalar field writer, the tensor field
write()lambda is invoked twice (lines 187-188) for 2D per-face data. Add a comment for consistency and clarity.Apply this diff:
}; + // 2D data is written per face of cube, requiring 2 passes (X_TIMES = 2) write(); write(); }
102-121: Consider clarifying the primal_qty sentinel usage.The
primal_qtyis hardcoded torhoat line 104 and used to query the primal grid layout. While this works (all primal quantities share the same centering), the intent—usingrhoas a representative primal quantity—could be clearer with a brief comment.Consider adding a comment:
- auto static constexpr primal_qty = physical_quantity_type::rho; + // Use rho as representative primal quantity (all primal quantities share same centering) + auto static constexpr primal_qty = physical_quantity_type::rho;
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (3)
src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/core/utilities/algorithm.hppsrc/core/utilities/types.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (7)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2024-10-22T10:05:54.014Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-10-22T10:05:54.014Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-11-10T09:37:57.021Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1084
File: src/diagnostic/diagnostic_model_view.hpp:219-221
Timestamp: 2025-11-10T09:37:57.021Z
Learning: In PHARE, temporary fields like tmpField_, tmpVec_, and tmpTensor_ in src/diagnostic/diagnostic_model_view.hpp use a name-based resource allocation pattern. Fields with names "PHARE_sumField", "PHARE_sumVec", and "PHARE_sumTensor" are allocated globally elsewhere in the resources manager (e.g., in src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp), and components reference the same storage through identically-named field objects. These do not require local allocation via rm.enumerate().
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/algorithm.hppsrc/core/utilities/types.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/types.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/detail/vtkh5_type_writer.hpp
🧬 Code graph analysis (1)
src/core/utilities/algorithm.hpp (3)
src/core/data/electrons/electrons.hpp (8)
layout(107-133)layout(107-107)layout(285-285)layout(285-285)layout(286-286)layout(286-286)layout(309-319)layout(309-309)src/core/utilities/types.hpp (4)
all(365-369)all(365-366)all(376-379)all(376-376)src/core/data/ndarray/ndarray_vector.hpp (4)
make_array_view(214-217)make_array_view(214-214)make_array_view(220-223)make_array_view(220-220)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (7)
- GitHub Check: Analyze (python)
- GitHub Check: Analyze (cpp)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
- GitHub Check: build (macos-13)
🔇 Additional comments (8)
src/core/utilities/types.hpp (3)
226-235: LGTM! Error handling properly implemented.The
from_stringfunction now includes proper error handling by throwingstd::runtime_erroron parse failure, addressing the concern raised in the previous review. The approach aligns with the author's preference for explicit error signaling.
252-258: LGTM! Clean environment variable utility.The
get_env_asfunction provides a clean, type-safe interface for reading environment variables with defaults, properly leveraging thefrom_stringutility.
514-518: LGTM! Consistent with existing patterns.The
for_N_allfunction cleanly integrates with the existingfor_Ninfrastructure, providing a convenient compile-time predicate evaluation utility.src/core/utilities/algorithm.hpp (3)
98-123: LGTM! Variable usage is correct.The
c_orderingvariable at line 105 is correctly used as a template parameter inmake_array_view<c_ordering>at line 109. The static analysis warning about it being unused is a false positive—the variable is used in a constant expression context to specify Fortran (row-major) ordering for the array view.The conversion logic properly handles both all-primal and mixed-centering cases with an appropriate optimization path.
Based on learnings: Variable c_ordering is used to create an array view for handling Fortran-ordered data layout.
125-140: LGTM! Clean recursive implementation.The TensorField specialization correctly applies field-level primal conversion to each tensor component, and the wrapper provides a clean public interface.
71-96: <!-- [scratchpad_start]
[task review_file_2/3 review_segment_1/3]
Verify limited PhysicalQuantity support - FINAL CONCLUSION[observations]
- Physical quantities exist: Bx, By, Bz, Ex, Ey, Ez, Jx, Jy, Jz, rho, Vx, Vy, Vz, P, Mxx, Mxy, Mxz, Myy, Myz, Mzz (from gridlayoutimplyee.hpp:111-112)
- HybridQuantity::Scalar defines rho, Vx, Vy, Vz and more
- VTK-HDF5 diagnostics output: charge_density (rho), mass_density (rho), bulkVelocity (V tensor)
- Fluid quantities flow through: writeTensorField/writeField → convert_to_fortran_primal → convert_to_primal
- convert_to_primal throws runtime_error for ANY quantity outside {Bx, By, Bz, Ex, Ey, Ez}
- Vx, Vy, Vz shown with all-primal centering in gridlayoutimplyee.hpp lines 87-92
- BUT: gridlayoutimplyee.hpp has full centering array for all 20 quantities, suggesting they CAN have different centerings
[analysis]
- Review concern is VALID: function only handles EM fields but may receive fluid quantities
- Evidence suggests Vx/Vy/Vz are typically primal, but centering system is flexible
- If ANY fluid quantity can be dual-centered and flows to diagnostic output, runtime error occurs
- Code structure suggests this is either: (a) incomplete bug, (b) untested edge case, or (c) guaranteed safe by external constraints not visible here
[pending]
Verification needed: Can rho, Vx, Vy, Vz ever have dual centering? If yes, is there test coverage?[decision]
Review comment is LEGITIMATE but cannot be definitively proven as bug without runtime/behavioral analysis.
Tag:
I have gathered sufficient information to evaluate the review comment. The verification reveals that:
- The
convert_to_primalfunction handles only electromagnetic field components (Bx, By, Bz, Ex, Ey, Ez)- The codebase defines many additional physical quantities: rho, Vx, Vy, Vz, P, Jx, Jy, Jz, and tensor components (Mxx, Mxy, etc.)
- The VTK-HDF5 diagnostic writer outputs fluid quantities (charge density, mass density, bulk velocity) alongside electromagnetic fields
- Both fluid and electromagnetic fields flow through the same
convert_to_fortran_primal→convert_to_primalconversion path- The function throws
std::runtime_errorfor any unsupported quantityWhile evidence suggests velocity components (Vx, Vy, Vz) are typically primal-centered, the grid layout system supports configurable centering for all quantities, and the code provides no guarantee that fluid quantities cannot be dual-centered in certain configurations.
The review comment identifies a legitimate concern: the function is incomplete for the full set of physical quantities it may receive at runtime. Whether this manifests as an actual bug depends on whether dual-centered fluid fields can occur in practice, which cannot be determined from static analysis alone.
src/diagnostic/detail/vtkh5_type_writer.hpp (2)
355-385: LGTM! MPI coordination logic is correct.The
resize_datafunction properly coordinates parallel HDF5 writes using MPI collective operations. Each rank computes its write offset by summing the data sizes of all preceding ranks, ensuring non-overlapping writes to the shared dataset.
388-417: LGTM! Consistent MPI coordination pattern.The
resize_boxesfunction follows the same correct MPI coordination pattern asresize_data, ensuring each rank writes its box metadata to non-overlapping regions of the shared HDF5 dataset.
| Field tmpField_{"PHARE_sumField", core::HybridQuantity::Scalar::rho}; | ||
| VecField tmpVec_{"PHARE_sumVec", core::HybridQuantity::Vector::V}; | ||
| TensorFieldT tmpTensor_{"PHARE_sumTensor", core::HybridQuantity::Tensor::M}; |
There was a problem hiding this comment.
during PGL these were only doing a sum, but perhaps they should be renamed generally, to PHARE_tmpX or similar
|
wheel available for python3.14. see https://gitlab.kitware.com/vtk/vtk/-/issues/19845#note_1729163 I had to rename it to |
There was a problem hiding this comment.
Actionable comments posted: 1
♻️ Duplicate comments (2)
src/core/data/grid/gridlayout.hpp (1)
5-14: Use a signed ghost width inAMRGhostBoxForto avoid signed/unsigned underflow.
AMRGhostBoxForcurrently does:auto AMRGhostBoxFor(auto const& field) const { auto const centerings = centering(field); return grow(AMRBoxFor(field), for_N_make_array<dimension>([&](auto i) { return nbrGhosts(centerings[i]); })); }
nbrGhostsreturnsstd::uint32_t, whileBox<int, dimension>::growsubtracts this value fromlower. That mixes signed and unsigned arithmetic; for smallAMRBox_.lower[i](e.g., 0),lower -= sizecan underflow in the unsigned domain and then be converted back toint, which is undefined behavior.Casting the ghost count to a signed type when building the array keeps all arithmetic in the signed domain:
- auto AMRGhostBoxFor(auto const& field) const - { - auto const centerings = centering(field); - return grow(AMRBoxFor(field), for_N_make_array<dimension>( - [&](auto i) { return nbrGhosts(centerings[i]); })); - } + auto AMRGhostBoxFor(auto const& field) const + { + auto const centerings = centering(field); + return grow( + AMRBoxFor(field), + for_N_make_array<dimension>([&](auto i) { + return static_cast<int>(nbrGhosts(centerings[i])); + })); + }This preserves the intended semantics (grow the field box by the ghost width on all sides) while avoiding undefined behavior from signed/unsigned underflow. The new
amr_lcl_idxhelpers built on these boxes then remain safe.Also applies to: 1027-1046, 1180-1194, 1220-1226
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
128-139: Add inline comment for duplicate write() in 2D.The duplicate
write()call at lines 137-138 is intentional (per X_TIMES multiplier logic at line 358) but lacks inline documentation. Add a brief comment explaining that 2D data is written per face of a cube and requires two passes.Based on past review comments.
🧹 Nitpick comments (14)
src/core/utilities/types.hpp (1)
1-2: New utility helpers are consistent and well-scoped
- The expanded includes and updated guard match the new usages (
std::stringstream,std::optional, algorithms, exceptions).from_stringandget_env_asare straightforward and make the env/config handling clearer; throwing on parse failure is a reasonable, explicit policy.for_N_all/for_N_anycorrectly reuse the existingfor_N+ containerall/anyhelpers, keeping the implementation minimal.If you expect
from_stringto be used only for a narrow set of types (e.g., arithmetic), you could later add astatic_assertto document that constraint, but it’s not required now.Also applies to: 12-21, 226-235, 252-258, 514-519, 566-566
src/core/data/ndarray/ndarray_vector.hpp (1)
19-24: ReworkedNdArrayViewerindexing fixes the 16‑bit issue and centralizes layout logic
- Using
Id = std::uint32_tand routing all access through the newidxhelpers addresses the previous 16‑bit overflow risk and keeps C/Fortran ordering logic in one place.- The
at(...)helpers with theproduct(nCells, std::uint32_t{1})assertion give a clear bound check and are used consistently byMaskedView,NdArrayView, andNdArrayVector.If you ever need arrays with more than ~4e9 elements, consider switching
Idand theproductaccumulator tostd::size_tto avoid 32‑bit overflow; for current realistic grid sizes this is fine.Also applies to: 25-37, 38-53, 55-63, 65-70, 101-102, 130-139, 288-292, 300-304
src/diagnostic/diagnostics.hpp (1)
27-29: Format‑driven writer selection is clear and backward‑compatibleThe resolver cleanly adds a
"format"switch:
- Defaults to
"phareh5"to preserve existing behavior.- Selects the new
vtkh5::H5Writerwhen"pharevtkhdf"is requested.- Throws with a clear message on unknown formats.
You might later want a slightly more descriptive log (e.g., prefixing
"diagnostics format=") instead of logging the raw string, but the current behavior is acceptable.Also applies to: 53-62
src/diagnostic/detail/vtk_types/electromag.hpp (1)
12-55: Electromag VTKHDF writer follows the existing fluid writer patternThe new
ElectromagDiagnosticWriter:
- Uses
VTKFileWriterandmodelView.onLevelsin the same way as the fluid writer, initializing per‑level datasets and then writing viavisitHierarchy.- Filters electromag fields by matching
diagnostic.quantityto"/" + vecField->name(), which keeps the selection logic straightforward.Minor nits, purely optional:
- You already bind
auto& modelViewat the top;write_quantitycould reuse it instead of re‑callingthis->h5Writer_.modelView().- The header‑guard end comment still says
PHARE_DIAGNOSTIC_DETAIL_TYPES_ELECTROMAG_H; consider updating it to match the actual guard macro for consistency.Also applies to: 60-62
src/diagnostic/detail/vtk_types/info.hpp (1)
11-33:InfoDiagnosticWriteris currently a no‑op stub
InfoDiagnosticWriteris wired into the vtkh5 infrastructure but bothwriteandcomputeare empty. That’s safe ifinfodiagnostics aren’t yet meant to produce VTKHDF output, but it may be surprising to users who configure such diagnostics and see no data.Consider either:
- Adding a TODO/comment to make the stub status explicit, or
- Implementing a minimal
writethat populates basic run metadata once you know the desired content.You could also mark the
diagnosticparameter[[maybe_unused]]in the stub to silence unused‑parameter warnings, and update the#endifcomment to match the guard macro.Also applies to: 38-38
tests/simulator/test_vtk_diagnostics.py (1)
105-129: Avoid reusing the samesimInputdict across parameter combinations.
permutemutates a singledicand then passes that same dict object assimInputfor every(ndim, interp_order)pair. With only one combination today this is harmless, but as soon as you uncomment moreinterp_ordersorndims, later tests will see the mutated state from earlier ones.Consider building a fresh config per case:
-def permute(dic): - dic.update(simArgs.copy()) - return [ - dict( - ndim=ndim, - interp=interp_order, - simInput=dic, - ) - for ndim, interp_order in itertools.product(ndims, interp_orders) - ] +def permute(overrides): + base = simArgs.copy() + base.update(overrides) + return [ + dict( + ndim=ndim, + interp=interp_order, + simInput=base.copy(), + ) + for ndim, interp_order in itertools.product(ndims, interp_orders) + ]The rest of the test (model setup,
tearDown, and diagnostic run) looks sound; Ruff’sARG001/E731hints insetup_modelare stylistic and can be addressed later if you want a clean lint run.Also applies to: 144-159
src/diagnostic/detail/vtk_types/fluid.hpp (1)
13-97: Fluid VTK/HDF writer wiring matches the existing Electromag patterns.The
isActiveDiagchecks, per-level initialization, and per-population handling (density, charge_density, flux) are consistent with the H5/VTK writer design and should correctly gate which fields are emitted for a givenDiagnosticProperties. Only a tiny nit: the#endifcomment uses...FLUID_Hwhile the guard macro is...FLUID_HPP; you may want to align those for clarity.Also applies to: 100-104
src/diagnostic/diagnostic_model_view.hpp (1)
33-39: Model view tmp-field plumbing and hierarchy helpers are coherent.The switch to
tmpTensor_(withrm.enumerate-based allocation), the updatedvisitHierarchycall, and the new utilities (localLevelBoxes,tmpField/tmpVecField/tmpTensorField,getCompileTimeResourcesViewList) all line up with the existing name-based resource pattern (PHARE_sumField/Vec/Tensor) and the vtkh5 writers’ needs. Behavior should remain unchanged while making the temporary storage more explicit. Renaming the tmp resources away from"*sum*"is purely cosmetic and can be deferred if you want to preserve resource-manager conventions.
Based on learningsAlso applies to: 62-81, 93-99, 145-172, 179-195, 218-221
src/diagnostic/detail/vtkh5_writer.hpp (1)
130-130: Document or parametrize the hardcoded level bounds.The TODO indicates
minLevelandmaxLevelare hardcoded. Consider documenting why these specific values (0 and 10) were chosen, or add a constructor parameter or dict entry to allow configuration.src/diagnostic/detail/vtkh5_type_writer.hpp (5)
38-38: Document the FloatType override rationale.
FloatTypeis hardcoded tofloat, ignoringWriter::FloatType. Based on past comments, this is due to ParaView VTK reader limitations with doubles. Consider adding a more detailed comment explaining this constraint and referencing the ParaView limitation.
164-164: Clarify ownership comment.The comment "NOT OWNED HERE" could be more explicit. Consider: "References parent VTKFileWriter's data_offset member" for clarity.
211-211: Clarify ownership comment.The comment "NOT OWNED HERE" could be more explicit. Consider: "References parent VTKFileWriter's data_offset member" for clarity.
352-359: Expand documentation for X_TIMES dimension mapping.The X_TIMES calculation is clever but cryptic. The comment mentions "per face of a cube" but doesn't explain why 2D is ×2 or 1D is ×4. Consider expanding the comment to clarify that this accounts for converting lower-dimensional data into 3D cube faces for VTK compatibility.
417-419: Document in-place modification of boxes parameter.Line 418 modifies
boxes.upper += 1in place to convert to primal indexing. Sinceboxesis passed by non-const reference, this side effect may not be obvious to callers. Add a comment documenting this intentional mutation or consider returning a copy if the modification isn't required by the caller.
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (31)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(4 hunks)src/core/data/grid/gridlayoutdefs.hpp(1 hunks)src/core/data/grid/gridlayoutimplyee.hpp(27 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(6 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/h5writer.hpp(2 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtk_types/info.hpp(1 hunks)src/diagnostic/detail/vtk_types/meta.hpp(1 hunks)src/diagnostic/detail/vtk_types/particle.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(7 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(2 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)tests/simulator/CMakeLists.txt(2 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init.py
- src/phare/phare_init_small.py
🚧 Files skipped from review as they are similar to previous changes (10)
- pyphare/pyphare/pharein/simulation.py
- src/core/data/grid/gridlayoutdefs.hpp
- src/core/data/tensorfield/tensorfield.hpp
- src/diagnostic/detail/vtk_types/particle.hpp
- src/amr/physical_models/hybrid_model.hpp
- pyphare/pyphare/pharein/init.py
- tests/simulator/refinement/test_2d_10_core.py
- src/diagnostic/detail/vtk_types/meta.hpp
- tests/simulator/init.py
- tests/simulator/CMakeLists.txt
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/diagnostic/detail/vtk_types/electromag.hppsrc/diagnostic/diagnostic_manager.hppsrc/core/utilities/algorithm.hppsrc/diagnostic/detail/vtk_types/fluid.hppsrc/diagnostic/diagnostics.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/amr/resources_manager/amr_utils.hppsrc/diagnostic/detail/vtk_types/info.hppsrc/core/data/grid/gridlayout.hppsrc/diagnostic/detail/h5writer.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/diagnostic/diagnostic_model_view.hppsrc/core/utilities/types.hppsrc/hdf5/detail/h5/h5_file.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hppsrc/core/utilities/box/box.hpp
🧠 Learnings (11)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2024-10-22T10:05:54.014Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-10-22T10:05:54.014Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/algorithm.hppsrc/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2025-11-10T09:37:57.021Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1084
File: src/diagnostic/diagnostic_model_view.hpp:219-221
Timestamp: 2025-11-10T09:37:57.021Z
Learning: In PHARE, temporary fields like tmpField_, tmpVec_, and tmpTensor_ in src/diagnostic/diagnostic_model_view.hpp use a name-based resource allocation pattern. Fields with names "PHARE_sumField", "PHARE_sumVec", and "PHARE_sumTensor" are allocated globally elsewhere in the resources manager (e.g., in src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp), and components reference the same storage through identically-named field objects. These do not require local allocation via rm.enumerate().
Applied to files:
src/core/utilities/algorithm.hppsrc/diagnostic/detail/h5writer.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/algorithm.hppsrc/core/utilities/types.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/core/data/grid/gridlayout.hpp:805-821
Timestamp: 2024-10-09T08:32:15.667Z
Learning: In the `AMRToLocal` function, before converting to `uint32_t`, assert that `local >= 0` to ensure values are valid.
Applied to files:
src/core/data/grid/gridlayout.hpp
📚 Learning: 2025-07-09T17:18:05.771Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/amr/CMakeLists.txt:103-105
Timestamp: 2025-07-09T17:18:05.771Z
Learning: In the PHARE project, `HighFive` is a CMake option defined in `res/cmake/options.cmake` as `option(HighFive "Build with highfive usage" ON)`, not a target that would be created by find_package(). The condition `if (HighFive)` correctly checks this option.
Applied to files:
src/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2025-09-17T13:50:16.038Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/tensorfield/tensor_field_data_factory.hpp:112-112
Timestamp: 2025-09-17T13:50:16.038Z
Learning: PhilipDeegan indicated that getSizeOfMemory returning a placeholder value of 1 in TensorFieldDataFactory is acceptable for their use case, suggesting it may not be critical for PHARE's memory management needs.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/types.hppsrc/core/utilities/box/box.hpp
🧬 Code graph analysis (14)
src/diagnostic/detail/vtk_types/electromag.hpp (3)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-97)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(87-92)diagnostic(87-87)lvl(261-266)lvl(261-261)ilvl(382-411)ilvl(382-382)boxes(57-71)boxes(57-57)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)
src/diagnostic/diagnostic_manager.hpp (1)
src/amr/resources_manager/amr_utils.hpp (2)
to_string(222-227)to_string(222-222)
src/core/utilities/algorithm.hpp (3)
src/core/utilities/types.hpp (4)
all(365-369)all(365-366)all(376-379)all(376-376)src/core/data/ndarray/ndarray_vector.hpp (4)
make_array_view(214-217)make_array_view(214-214)make_array_view(220-223)make_array_view(220-220)src/amr/data/field/field_geometry.hpp (4)
box(136-179)box(136-137)box(198-207)box(198-198)
tests/simulator/test_vtk_diagnostics.py (7)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)pyphare/pyphare/simulator/simulator.py (2)
startMPI(41-45)reset(258-269)tests/simulator/__init__.py (4)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)run(246-248)tests/diagnostic/__init__.py (1)
dump_all_diags(15-62)pyphare/pyphare/pharein/simulation.py (2)
simulation_domain(967-968)Simulation(735-1069)pyphare/pyphare/pharein/maxwellian_fluid_model.py (1)
MaxwellianFluidModel(8-303)pyphare/pyphare/pharein/electron_model.py (1)
ElectronModel(22-35)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(87-92)diagnostic(87-87)lvl(261-266)lvl(261-261)ilvl(382-411)ilvl(382-382)boxes(57-71)boxes(57-57)src/diagnostic/detail/h5writer.hpp (4)
diagnostic(94-98)diagnostic(94-94)iLevel(210-214)iLevel(210-210)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)
src/diagnostic/diagnostics.hpp (3)
src/diagnostic/diagnostic_manager.hpp (5)
dict(83-83)dict(86-86)dict(86-86)make_unique(74-80)make_unique(74-75)src/diagnostic/detail/h5writer.hpp (2)
make_unique(61-68)make_unique(61-61)src/diagnostic/detail/vtkh5_writer.hpp (2)
make_unique(67-74)make_unique(67-67)
src/amr/resources_manager/amr_utils.hpp (1)
src/core/data/field/field.hpp (4)
args(75-81)args(75-75)args(83-86)args(83-83)
src/diagnostic/detail/vtk_types/info.hpp (7)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-97)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtk_types/meta.hpp (2)
write(29-31)write(29-29)src/diagnostic/detail/vtk_types/particle.hpp (2)
write(31-33)write(31-31)src/diagnostic/detail/vtkh5_type_writer.hpp (2)
diagnostic(87-92)diagnostic(87-87)src/diagnostic/detail/h5writer.hpp (2)
diagnostic(94-98)diagnostic(94-94)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)
src/core/data/grid/gridlayout.hpp (4)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (4)
field(929-956)field(929-930)field(958-964)field(958-958)src/core/utilities/types.hpp (2)
for_N_make_array(508-511)for_N_make_array(508-508)src/amr/resources_manager/amr_utils.hpp (5)
AMRToLocal(45-46)AMRToLocal(53-54)AMRToLocal(62-62)AMRToLocal(77-90)AMRToLocal(77-78)src/amr/resources_manager/amr_utils.cpp (6)
AMRToLocal(34-40)AMRToLocal(34-35)AMRToLocal(47-54)AMRToLocal(47-48)AMRToLocal(62-66)AMRToLocal(62-62)
src/core/data/ndarray/ndarray_vector.hpp (1)
src/core/utilities/types.hpp (2)
product(269-272)product(269-269)
src/diagnostic/diagnostic_model_view.hpp (5)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (10)
patch(146-154)patch(146-146)ions(407-416)ions(407-407)ions(420-445)ions(420-420)ions(447-480)ions(447-447)ions(492-531)ions(492-493)src/amr/messengers/refiner.hpp (8)
rm(276-281)rm(276-276)rm(284-290)rm(284-285)rm(293-299)rm(293-293)rm(302-312)rm(302-303)src/amr/resources_manager/amr_utils.hpp (2)
visitHierarchy(244-253)visitHierarchy(244-245)src/core/data/ions/ions.hpp (1)
forward_as_tuple(225-229)src/core/data/ions/ion_population/ion_population.hpp (1)
forward_as_tuple(109-113)
src/diagnostic/detail/vtkh5_writer.hpp (5)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-60)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
level(292-328)level(292-292)level(330-337)level(330-330)diagnostic(87-92)diagnostic(87-87)src/amr/resources_manager/amr_utils.hpp (2)
to_string(222-227)to_string(222-222)src/hdf5/detail/h5/h5_file.hpp (4)
path(270-276)path(270-270)path(278-283)path(278-278)src/core/data/tensorfield/tensorfield.hpp (2)
size(208-208)size(208-208)
src/diagnostic/detail/vtkh5_type_writer.hpp (5)
src/core/utilities/types.hpp (7)
get_env_as(253-253)for_N_make_array(508-511)for_N_make_array(508-508)sum_from(281-289)sum_from(281-281)sum(275-278)sum(275-275)src/hdf5/detail/h5/h5_file.hpp (5)
data(66-66)path(270-276)path(270-270)path(278-283)path(278-278)src/core/utilities/box/box.hpp (9)
box(53-53)i(99-99)i(99-99)grow(91-96)grow(91-91)grow(328-333)grow(328-328)size(78-88)size(78-78)src/core/data/tensorfield/tensorfield.hpp (8)
i(181-181)i(181-181)i(182-182)i(182-182)size(208-208)size(208-208)tensor_field_dim_from_rank(17-24)tensor_field_dim_from_rank(17-17)src/core/utilities/algorithm.hpp (2)
convert_to_fortran_primal(149-152)convert_to_fortran_primal(149-149)
src/core/utilities/box/box.hpp (2)
src/core/utilities/point/point.hpp (4)
i(68-68)i(68-68)i(69-69)i(69-69)src/core/utilities/types.hpp (7)
product(269-272)product(269-269)for_N(467-498)for_N(467-467)for_N(501-504)for_N(501-501)for_N_any(521-521)
🪛 Ruff (0.14.5)
tests/simulator/test_vtk_diagnostics.py
25-25: Unused function argument: xyz
(ARG001)
32-32: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
39-39: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
42-42: Unused function argument: xyz
(ARG001)
45-45: Unused function argument: xyz
(ARG001)
52-52: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
59-59: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
62-62: Unused function argument: xyz
(ARG001)
65-65: Unused function argument: xyz
(ARG001)
68-68: Unused function argument: xyz
(ARG001)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (5)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: Analyze (cpp)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
🔇 Additional comments (6)
src/amr/resources_manager/amr_utils.hpp (1)
244-252: Corrected forwarding invisitHierarchySwitching to
std::forward<Action>(action), std::forward<Args>(args)...is the right fix for propagating value categories intovisitLevel; this aligns with the rest of the templated call sites. No further changes needed here.src/diagnostic/detail/h5writer.hpp (1)
6-8: Header wiring and non-assignableH5Writerlook goodThe new diagnostic-type includes correctly match the
typeWriters_instantiations, and the header ordering remains sane.Replacing the bogus deleted
operator&with deleted copy/move assignment operators is the right way to makeH5Writernon-assignable while keeping intent clear.Also applies to: 12-17, 176-198
src/diagnostic/diagnostic_manager.hpp (1)
23-37: CosmeticdiagNamedeclaration change onlySwitching to
std::string const diagNameis a style-only change with no behavioral impact; the registration loop remains unchanged.src/core/data/grid/gridlayoutimplyee.hpp (1)
413-537: Bx/By/Bz-to-moments stencils and updated moments↔field helpers look correct.The new
BxToMoments/ByToMoments/BzToMomentsimplementations cover all required dual combinations in 2D and 3D with properly normalized weights, and the updatedmomentsToE*/*ToMomentshelpers usingstd::array{...}via CTAD preserve the existing stencils with cleaner syntax. The patterns are consistent with the existing Yee layout projections and previous fixes to the B→moment offsets.Also applies to: 575-603
src/hdf5/detail/h5/h5_file.hpp (1)
95-117: HDF5 dataset helpers now handle existence and chunking robustly.Reusing existing datasets in
create_data_set/create_chunked_data_set, addingexist/checkedgetDataSet, and fixing the special-member declarations all look correct and improve safety without adding complexity.Also applies to: 250-261
src/core/utilities/box/box.hpp (1)
29-31: Box iterator alias, shape/size helpers, andboxes_iteratorlook solid.The added
iteratoralias,shape/sizehelpers,boxes_iteratorzipper, and freegrowall integrate cleanly with existing Box semantics and support the new AMR and Fortran-ordering utilities without adding complexity.Also applies to: 99-102, 160-203, 209-259, 327-333
There was a problem hiding this comment.
Actionable comments posted: 1
♻️ Duplicate comments (1)
src/core/utilities/algorithm.hpp (1)
102-135: Fix invalid dereference ofBox::shape()return value.Line 117 dereferences
lcl_box.shape()when constructingdst_view. IfBox::shape()returns a value (not a pointer), this dereference is ill-formed and will cause compilation errors or undefined behavior. Themake_array_viewfunction expects astd::array<std::uint32_t, dim>-like shape.Build an explicit shape array from the box extents:
auto const lcl_box = layout.AMRToLocal(layout.AMRBoxFor(dst)); - auto dst_view = make_array_view<c_ordering>(dst.data(), *lcl_box.shape()); + + std::array<std::uint32_t, dim> shape{}; + for (std::size_t d = 0; d < dim; ++d) + shape[d] = static_cast<std::uint32_t>(lcl_box.shape(d)); + + auto dst_view = make_array_view<c_ordering>(dst.data(), shape);This same fix should also be applied if
shape()is dereferenced elsewhere in the conversion functions.
🧹 Nitpick comments (2)
src/diagnostic/diagnostics.hpp (1)
28-29: Format-based writer selection cleanly introduces VTK/HDF diagnostics.
- Reading
formatfrom the dict (defaulting to"phareh5") keeps the old HDF5 path as the default while allowing"pharevtkhdf"to select the new VTK writer.- The explicit runtime error for unknown formats plus the log line make configuration issues easy to diagnose and keep the resolver logic simple to extend later.
Also applies to: 53-62
src/diagnostic/detail/vtk_types/electromag.hpp (1)
12-55: Electromagnetic VTK/HDF writer integrates correctly with the existing type-writer pattern.
ElectromagDiagnosticWritermirrors the other type writers: per‑diagnostic filtering onquantity,initFileLevelandinitTensorFieldFileLevel<1>per level, thenvisitHierarchydrivingwriteTensorField<1>for matching electromag fields.- Using a no‑op
computeis appropriate when the fields are already available from the model view and no extra preprocessing is required.One tiny nit: the
#endifcomment guard name doesn’t match the#ifndefmacro, but it’s purely cosmetic.Also applies to: 60-62
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (31)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(4 hunks)src/core/data/grid/gridlayoutdefs.hpp(1 hunks)src/core/data/grid/gridlayoutimplyee.hpp(27 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(6 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/h5writer.hpp(2 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtk_types/info.hpp(1 hunks)src/diagnostic/detail/vtk_types/meta.hpp(1 hunks)src/diagnostic/detail/vtk_types/particle.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(7 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(2 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)tests/simulator/CMakeLists.txt(2 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init_small.py
- src/phare/phare_init.py
🚧 Files skipped from review as they are similar to previous changes (11)
- tests/simulator/CMakeLists.txt
- tests/simulator/test_vtk_diagnostics.py
- src/core/data/grid/gridlayoutdefs.hpp
- pyphare/pyphare/pharein/init.py
- src/diagnostic/detail/vtk_types/particle.hpp
- src/diagnostic/detail/vtk_types/meta.hpp
- src/diagnostic/detail/vtk_types/fluid.hpp
- pyphare/pyphare/pharein/simulation.py
- tests/simulator/refinement/test_2d_10_core.py
- src/amr/physical_models/hybrid_model.hpp
- src/diagnostic/detail/vtk_types/info.hpp
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/amr/resources_manager/amr_utils.hppsrc/diagnostic/detail/vtk_types/electromag.hppsrc/core/data/tensorfield/tensorfield.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/diagnostic/diagnostic_manager.hppsrc/diagnostic/diagnostics.hppsrc/diagnostic/detail/h5writer.hppsrc/core/utilities/box/box.hppsrc/core/utilities/types.hppsrc/hdf5/detail/h5/h5_file.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/core/utilities/algorithm.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hppsrc/core/data/grid/gridlayout.hppsrc/diagnostic/diagnostic_model_view.hpp
🧠 Learnings (11)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2025-07-09T17:18:05.771Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/amr/CMakeLists.txt:103-105
Timestamp: 2025-07-09T17:18:05.771Z
Learning: In the PHARE project, `HighFive` is a CMake option defined in `res/cmake/options.cmake` as `option(HighFive "Build with highfive usage" ON)`, not a target that would be created by find_package(). The condition `if (HighFive)` correctly checks this option.
Applied to files:
src/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2025-11-10T09:37:57.021Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1084
File: src/diagnostic/diagnostic_model_view.hpp:219-221
Timestamp: 2025-11-10T09:37:57.021Z
Learning: In PHARE, temporary fields like tmpField_, tmpVec_, and tmpTensor_ in src/diagnostic/diagnostic_model_view.hpp use a name-based resource allocation pattern. Fields with names "PHARE_sumField", "PHARE_sumVec", and "PHARE_sumTensor" are allocated globally elsewhere in the resources manager (e.g., in src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp), and components reference the same storage through identically-named field objects. These do not require local allocation via rm.enumerate().
Applied to files:
src/diagnostic/detail/h5writer.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/box/box.hppsrc/core/utilities/types.hpp
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/types.hppsrc/core/utilities/algorithm.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/algorithm.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-10-22T10:05:54.014Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-10-22T10:05:54.014Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/core/data/grid/gridlayout.hpp:805-821
Timestamp: 2024-10-09T08:32:15.667Z
Learning: In the `AMRToLocal` function, before converting to `uint32_t`, assert that `local >= 0` to ensure values are valid.
Applied to files:
src/core/data/grid/gridlayout.hpp
📚 Learning: 2025-09-17T13:50:16.038Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/tensorfield/tensor_field_data_factory.hpp:112-112
Timestamp: 2025-09-17T13:50:16.038Z
Learning: PhilipDeegan indicated that getSizeOfMemory returning a placeholder value of 1 in TensorFieldDataFactory is acceptable for their use case, suggesting it may not be critical for PHARE's memory management needs.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
🔇 Additional comments (15)
src/amr/resources_manager/amr_utils.hpp (1)
243-252: Corrected perfect-forwarding of variadic argumentsUsing
std::forward<Args>(args)...here is the correct pattern for forwarding a parameter pack intovisitLevel; the previousstd::forward<Args...>(args...)form would be ill-formed and break perfect forwarding. No further changes needed around this call site.src/core/data/grid/gridlayoutimplyee.hpp (1)
413-603: Yee B↔moment stencils and CTAD refactor look consistent.
- The new
BxToMoments/ByToMoments/BzToMomentsimplementations correctly cover all dual directions: 2 points in 1D, 2 points for single-dual 2D cases, and 4-point averages for 3D where two directions are dual, with weights summing to 1 in each stencil and offsets aligned with the centering comments.- The switch from
std::array<WeightPoint<dimension>, N>{...}tostd::array{...}is a pure CTAD cleanup and keeps the existing interpolation behavior unchanged acrossmomentsTo*,*ToMoments, and the various B↔E mappings.Also applies to: 784-924
src/hdf5/detail/h5/h5_file.hpp (2)
95-117: Chunked dataset helper and parent-group handling are sound.
create_data_setandcreate_chunked_data_setnow both:
- Reuse an existing dataset when
exist(path)is true, and- Call
createGroupsToDataSet(path)before creation, ensuring parent groups exist.This aligns the chunked path with the non‑chunked API and avoids group-creation failures while keeping the interface compact.
250-261: Existence wrapper and stricter ownership semantics are appropriate.
exist(std::string const&) constandgetDataSet(std::string const&)add a clear, checked access path; throwing on missing datasets avoids the previous release‑build assert hole.- Deleting copy and move operations for
HighFiveFileis a good safeguard around the underlying HDF5 handle and simplifies lifetime reasoning.src/core/utilities/box/box.hpp (2)
29-32: Box iterator alias and shape/size helpers are clear and idiomatic.
- Exposing
using iterator = box_iterator<Type, dim>;alignsBoxwith standard container conventions and enables the new higher‑level iterators.shape(i),shape(), andsize()make the “inclusive upper bound” convention explicit and keepsize()readable viacore::product(shape(), std::size_t{1}).- The free
grow(Box, size)thin wrapper is a useful utility without adding complexity.Also applies to: 99-102, 327-333
160-203: box_iterator and boxes_iterator semantics look correct for multi-box traversal.
box_iterator::operator!=now checks bothbox_andindex_, which matches the sentinel construction inBox::end()and gives expected STL-style loop semantics.boxes_iterator<Boxes...>:
- Stores the boxes by value in a tuple and uses
Boxes::iteratorto derive the iterator tuple type.iterator::operator++advances all underlying iterators, andoperator!=usesfor_N_anyso iteration stops when any component reaches its ownend().operator*aggregates*itper box viafor_N, which is a compact way to yield per-box indices in lockstep.Assuming
for_N/for_N_anybehave as in the rest of the codebase (tuple/any-style reducers), this design is consistent and efficient.Also applies to: 209-259
src/diagnostic/diagnostic_manager.hpp (1)
31-37: Const placement change fordiagNameis harmless.Using
std::string const diagNameis equivalent to the previous declaration and keeps the loop logic unchanged.src/core/data/tensorfield/tensorfield.hpp (1)
206-209: Qualifier reordering onsize()has no behavioral effect.Swapping
constexpr statictostatic constexpris purely cosmetic; the function remains a constexpr static size helper returningN.src/diagnostic/detail/h5writer.hpp (1)
6-7: LGTM! Include reorganization and operator deletion fix are correct.The include reordering and additions support the new VTK-HDF5 writer architecture, and fixing the operator deletions from
operator&(address-of) tooperator=(assignment) is the correct approach for a non-copyable, non-movable class.Also applies to: 12-17, 196-197
src/core/utilities/types.hpp (1)
226-235: LGTM! New utility functions are well-designed.The new functions provide clean interfaces:
from_string<T>throws on parse failure, avoiding silent errorsget_env_as<T>provides type-safe environment variable access with defaultsfor_N_allandfor_N_anyare convenient wrappers over the existingfor_NinfrastructureAlso applies to: 252-258, 514-524
src/core/data/grid/gridlayout.hpp (1)
1027-1045: LGTM! Grid layout extensions support primal projections.The new
BxToMoments,ByToMoments, andBzToMomentsaccessors, along with the updatedAMRBoxFor/AMRGhostBoxFormethods andamr_lcl_idxhelpers, provide the necessary infrastructure for the VTK-HDF5 primal conversions introduced elsewhere in the PR.Also applies to: 1180-1194, 1220-1226
src/diagnostic/diagnostic_model_view.hpp (1)
37-37: LGTM! Temporary storage and helper accessors support VTK-HDF5 diagnostics.The new
Fieldalias, updatedvisitHierarchysignature, and temporary storage accessors (tmpField(),tmpVecField(),tmpTensorField()) provide the necessary infrastructure for primal conversion and VTK-HDF5 output. The temporary fields use name-based resource allocation patterns that are managed globally.Based on learnings
Also applies to: 96-98, 145-172, 219-221
src/core/data/ndarray/ndarray_vector.hpp (1)
19-70: LGTM! NdArrayViewer refactoring and index type fix are correct.The template signature simplification (removing the
DataTypeparameter) and the fix to usestd::uint32_tfor indices (instead of the previous 16-bit type) correctly addresses the wraparound concern for large grids.src/diagnostic/detail/vtkh5_writer.hpp (1)
52-74: LGTM! VTK-HDF5 writer implementation is well-structured.The new
H5Writer<ModelView>class correctly implements:
- Non-copyable/non-movable semantics via deleted assignment operators
- Per-diagnostic file management with proper flag handling (including reset to
READ_WRITEafter the first dump to prevent truncation)- Level-based dump control via
dump_level- Type-writer registry for per-diagnostic-type output
Also applies to: 77-186
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
1-348: LGTM! VTK-HDF5 type writer base provides comprehensive infrastructure.The
H5TypeWriter<Writer>base class and its nested helper structures (VTKFileFieldInfo,VTKFileWriter, etc.) provide well-organized support for:
- Per-level dataset initialization and resizing
- Field and tensor field writing with primal conversion
- AMR box and offset management
- Configurable chunk sizes via environment variable
The
X_TIMESmultiplier logic for lower-dimensional data replication in 3D views is clearly documented.
There was a problem hiding this comment.
Actionable comments posted: 0
♻️ Duplicate comments (2)
src/core/utilities/algorithm.hpp (1)
102-135: Fix the shape construction formake_array_viewcalls.Line 117 dereferences
lcl_box.shape(), butBox::shape()now returns a value (not a pointer), so*lcl_box.shape()is ill-formed. Additionally,make_array_viewexpects astd::array<std::uint32_t, dim>.Build an explicit shape array from the box instead:
auto const lcl_box = layout.AMRToLocal(layout.AMRBoxFor(dst)); -auto dst_view = make_array_view<c_ordering>(dst.data(), *lcl_box.shape()); + +std::array<std::uint32_t, dim> shape{}; +for (std::size_t d = 0; d < dim; ++d) + shape[d] = static_cast<std::uint32_t>(lcl_box.shape()[d]); + +auto dst_view = make_array_view<c_ordering>(dst.data(), shape);src/diagnostic/detail/vtk_types/particle.hpp (1)
12-26: Particle VTK diagnostics never write anything (emptywrite)
ParticlesDiagnosticWriter::writeis empty, so selecting this backend for particle diagnostics will silently generate VTKHDF files with no particle data. That’s a functional break compared to the existing HDF writer.Either implement the actual write path (mirroring
ParticlesDiagnosticWriterinsrc/diagnostic/detail/types/particle.hpp) or explicitly disable/register particle diagnostics as unsupported forpharevtkhdfso this can’t be selected by configuration.Also applies to: 30-33
🧹 Nitpick comments (5)
src/diagnostic/detail/vtk_types/fluid.hpp (1)
1-2: Align#endifcomment with header guard nameThe guard macro is
PHARE_DIAGNOSTIC_DETAIL_VTK_TYPES_FLUID_HPPbut the trailing#endifcomment uses...FLUID_H. For consistency and grep-ability, consider updating the comment to match the macro name.Also applies to: 100-104
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
162-174: Avoid copying the Fortran-primal buffers returned byconvert_to_fortran_primal
convert_to_fortran_primalreturns a reference to the temporary workspace, but here it’s bound by value:auto const frimal = core::convert_to_fortran_primal(...);This copies the entire field/tensor before every write. You can keep the same semantics and avoid the copy by binding a const reference instead:
- auto const frimal = core::convert_to_fortran_primal( + auto const& frimal = core::convert_to_fortran_primal( typewriter->h5Writer_.modelView().tmpField(), field, layout); ... - auto const frimal = core::convert_to_fortran_primal( + auto const& frimal = core::convert_to_fortran_primal( typewriter->h5Writer_.modelView().template tmpTensorField<rank>(), tf, layout);This should reduce memory traffic noticeably on large grids without changing behavior.
Also applies to: 176-192
src/diagnostic/detail/vtk_types/particle.hpp (1)
7-7: Tidy up comment and header-guard comment for particles header
- The comment
// not sure this makes senseis vague and likely stale; consider either removing it or replacing with a concrete TODO if there’s a known limitation.- The guard macro is
PHARE_DIAGNOSTIC_DETAIL_VTK_TYPES_PARTICLE_HPPbut the#endifcomment usesPHARE_DIAGNOSTIC_DETAIL_TYPES_PARTICLE_H. Aligning the comment with the macro name keeps headers easier to navigate and grep. Based on learningsAlso applies to: 1-2, 37-39
src/diagnostic/detail/vtk_types/electromag.hpp (1)
1-2: Normalize header-guard comment for electromag headerSimilar to the other vtk type headers, the guard macro (
PHARE_DIAGNOSTIC_DETAIL_VTK_TYPES_ELECTROMAG_HPP) and the trailing#endifcomment (...TYPES_ELECTROMAG_H) don’t match. Consider updating the comment to mirror the macro for consistency across headers. Based on learningsAlso applies to: 60-62
tests/simulator/test_vtk_diagnostics.py (1)
119-128: Avoid sharing a single mutablesimInputacross parameterized tests
permuteupdates a singledicwithsimArgs.copy()and then reuses that same dict assimInputfor all (ndim, interp) combinations. This is harmless with the current single(2, 1)combo, but if you uncomment more dimensions/orders, later tests will see state mutated by earlier tests (e.g.,cellsbecoming nested lists).Consider returning an independent
simInputper case, e.g.:-def permute(dic): - dic.update(simArgs.copy()) - return [ - dict( - ndim=ndim, - interp=interp_order, - simInput=dic, - ) - for ndim, interp_order in itertools.product(ndims, interp_orders) - ] +def permute(overrides): + return [ + dict( + ndim=ndim, + interp=interp_order, + simInput={**simArgs, **overrides}, + ) + for ndim, interp_order in itertools.product(ndims, interp_orders) + ]This keeps each test case isolated and makes it safe to expand
ndims/interp_orders.
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (31)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(4 hunks)src/core/data/grid/gridlayoutdefs.hpp(1 hunks)src/core/data/grid/gridlayoutimplyee.hpp(27 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(6 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/h5writer.hpp(2 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtk_types/info.hpp(1 hunks)src/diagnostic/detail/vtk_types/meta.hpp(1 hunks)src/diagnostic/detail/vtk_types/particle.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(7 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(3 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)tests/simulator/CMakeLists.txt(2 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init_small.py
- src/phare/phare_init.py
🚧 Files skipped from review as they are similar to previous changes (12)
- pyphare/pyphare/pharein/simulation.py
- src/diagnostic/diagnostic_manager.hpp
- src/diagnostic/detail/vtk_types/info.hpp
- tests/simulator/init.py
- pyphare/pyphare/pharein/init.py
- src/amr/physical_models/hybrid_model.hpp
- src/diagnostic/detail/vtk_types/meta.hpp
- tests/simulator/refinement/test_2d_10_core.py
- src/core/utilities/box/box.hpp
- src/hdf5/detail/h5/h5_file.hpp
- src/core/data/grid/gridlayoutdefs.hpp
- src/amr/resources_manager/amr_utils.hpp
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/core/data/tensorfield/tensorfield.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/diagnostic/detail/vtk_types/electromag.hppsrc/diagnostic/diagnostics.hppsrc/core/utilities/types.hppsrc/diagnostic/detail/vtk_types/particle.hppsrc/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtk_types/fluid.hppsrc/diagnostic/diagnostic_model_view.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/core/data/grid/gridlayout.hppsrc/core/utilities/algorithm.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (12)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2025-02-07T14:35:14.630Z
Learnt from: nicolasaunai
Repo: PHAREHUB/PHARE PR: 591
File: res/cmake/options.cmake:73-75
Timestamp: 2025-02-07T14:35:14.630Z
Learning: In CMake configuration for PHARE, `lowResourceTests` and `highResourceTests` options must be mutually exclusive and cannot be enabled simultaneously.
Applied to files:
tests/simulator/CMakeLists.txt
📚 Learning: 2025-07-09T17:18:05.771Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/amr/CMakeLists.txt:103-105
Timestamp: 2025-07-09T17:18:05.771Z
Learning: In the PHARE project, `HighFive` is a CMake option defined in `res/cmake/options.cmake` as `option(HighFive "Build with highfive usage" ON)`, not a target that would be created by find_package(). The condition `if (HighFive)` correctly checks this option.
Applied to files:
tests/simulator/CMakeLists.txtsrc/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/types.hppsrc/core/utilities/algorithm.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/types.hppsrc/diagnostic/diagnostic_model_view.hppsrc/core/utilities/algorithm.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/types.hpp
📚 Learning: 2025-11-10T09:37:57.021Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1084
File: src/diagnostic/diagnostic_model_view.hpp:219-221
Timestamp: 2025-11-10T09:37:57.021Z
Learning: In PHARE, temporary fields like tmpField_, tmpVec_, and tmpTensor_ in src/diagnostic/diagnostic_model_view.hpp use a name-based resource allocation pattern. Fields with names "PHARE_sumField", "PHARE_sumVec", and "PHARE_sumTensor" are allocated globally elsewhere in the resources manager (e.g., in src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp), and components reference the same storage through identically-named field objects. These do not require local allocation via rm.enumerate().
Applied to files:
src/diagnostic/detail/h5writer.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2025-09-17T13:50:16.038Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/tensorfield/tensor_field_data_factory.hpp:112-112
Timestamp: 2025-09-17T13:50:16.038Z
Learning: PhilipDeegan indicated that getSizeOfMemory returning a placeholder value of 1 in TensorFieldDataFactory is acceptable for their use case, suggesting it may not be critical for PHARE's memory management needs.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/core/data/grid/gridlayout.hpp:805-821
Timestamp: 2024-10-09T08:32:15.667Z
Learning: In the `AMRToLocal` function, before converting to `uint32_t`, assert that `local >= 0` to ensure values are valid.
Applied to files:
src/core/data/grid/gridlayout.hpp
📚 Learning: 2024-10-22T10:05:54.014Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-10-22T10:05:54.014Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
🧬 Code graph analysis (11)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-97)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(74-79)diagnostic(74-74)lvl(155-160)lvl(155-155)ilvl(262-291)ilvl(262-262)boxes(51-65)boxes(51-51)
src/diagnostic/diagnostics.hpp (3)
src/diagnostic/diagnostic_manager.hpp (5)
dict(83-83)dict(86-86)dict(86-86)make_unique(74-80)make_unique(74-75)src/diagnostic/detail/h5writer.hpp (2)
make_unique(61-68)make_unique(61-61)src/diagnostic/detail/vtkh5_writer.hpp (2)
make_unique(67-74)make_unique(67-67)
src/diagnostic/detail/vtk_types/particle.hpp (7)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-97)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtk_types/info.hpp (2)
write(31-33)write(31-31)src/diagnostic/detail/vtk_types/meta.hpp (2)
write(29-31)write(29-29)src/diagnostic/detail/h5writer.hpp (2)
diagnostic(94-98)diagnostic(94-94)src/diagnostic/detail/vtkh5_type_writer.hpp (2)
diagnostic(74-79)diagnostic(74-74)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)
src/diagnostic/detail/vtk_types/fluid.hpp (3)
src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(74-79)diagnostic(74-74)lvl(155-160)lvl(155-155)ilvl(262-291)ilvl(262-262)boxes(51-65)boxes(51-51)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/diagnostic/detail/vtk_types/electromag.hpp (2)
write(30-55)write(30-30)
tests/simulator/test_vtk_diagnostics.py (6)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)pyphare/pyphare/simulator/simulator.py (2)
startMPI(41-45)reset(258-269)tests/simulator/__init__.py (3)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)tests/diagnostic/__init__.py (1)
dump_all_diags(15-62)pyphare/pyphare/pharein/simulation.py (2)
simulation_domain(967-968)Simulation(735-1069)pyphare/pyphare/pharein/maxwellian_fluid_model.py (1)
MaxwellianFluidModel(8-303)
src/diagnostic/diagnostic_model_view.hpp (4)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (10)
patch(146-154)patch(146-146)ions(407-416)ions(407-407)ions(420-445)ions(420-420)ions(447-480)ions(447-447)ions(492-531)ions(492-493)src/amr/resources_manager/amr_utils.hpp (2)
visitHierarchy(244-253)visitHierarchy(244-245)src/core/data/ions/ion_population/ion_population.hpp (1)
forward_as_tuple(109-113)src/core/data/ions/ions.hpp (1)
forward_as_tuple(225-229)
src/core/data/ndarray/ndarray_vector.hpp (1)
src/core/utilities/types.hpp (2)
product(269-272)product(269-269)
src/core/data/grid/gridlayout.hpp (3)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (4)
field(929-956)field(929-930)field(958-964)field(958-958)src/core/utilities/types.hpp (2)
for_N_make_array(508-511)for_N_make_array(508-508)src/amr/resources_manager/amr_utils.cpp (6)
AMRToLocal(34-40)AMRToLocal(34-35)AMRToLocal(47-54)AMRToLocal(47-48)AMRToLocal(62-66)AMRToLocal(62-62)
src/core/utilities/algorithm.hpp (3)
src/core/utilities/box/box.hpp (4)
dim(109-125)dim(127-142)box(53-53)boxes_iterator(214-217)src/core/utilities/types.hpp (4)
all(365-369)all(365-366)all(376-379)all(376-376)src/core/data/ndarray/ndarray_vector.hpp (4)
make_array_view(214-217)make_array_view(214-214)make_array_view(220-223)make_array_view(220-220)
src/diagnostic/detail/vtkh5_writer.hpp (6)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-60)src/diagnostic/detail/h5writer.hpp (14)
H5Writer(51-56)H5Writer(58-58)H5Writer(194-194)H5Writer(195-195)make_unique(61-68)make_unique(61-61)timestamp(101-104)timestamp(101-101)diagnostic(94-98)diagnostic(94-94)modelView_(160-160)timestamp_(161-161)dump(224-250)dump(224-225)src/diagnostic/diagnostic_manager.hpp (7)
dict(83-83)dict(86-86)dict(86-86)make_unique(74-80)make_unique(74-75)dump(172-202)dump(172-172)src/diagnostic/diagnostics.hpp (2)
make_unique(50-65)make_unique(50-51)src/diagnostic/detail/vtkh5_type_writer.hpp (2)
diagnostic(74-79)diagnostic(74-74)src/hdf5/detail/h5/h5_file.hpp (4)
path(295-301)path(295-295)path(303-308)path(303-303)
src/diagnostic/detail/vtkh5_type_writer.hpp (4)
src/core/utilities/box/box.hpp (9)
box(53-53)i(99-99)i(99-99)grow(91-96)grow(91-91)grow(328-333)grow(328-328)size(78-88)size(78-78)src/core/data/tensorfield/tensorfield.hpp (8)
i(181-181)i(181-181)i(182-182)i(182-182)size(208-208)size(208-208)tensor_field_dim_from_rank(17-24)tensor_field_dim_from_rank(17-17)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/core/utilities/algorithm.hpp (4)
convert_to_fortran_primal(103-135)convert_to_fortran_primal(103-107)convert_to_fortran_primal(138-147)convert_to_fortran_primal(138-142)
🪛 Ruff (0.14.5)
tests/simulator/test_vtk_diagnostics.py
25-25: Unused function argument: xyz
(ARG001)
32-32: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
39-39: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
42-42: Unused function argument: xyz
(ARG001)
45-45: Unused function argument: xyz
(ARG001)
52-52: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
59-59: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
62-62: Unused function argument: xyz
(ARG001)
65-65: Unused function argument: xyz
(ARG001)
68-68: Unused function argument: xyz
(ARG001)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (5)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
- GitHub Check: Analyze (cpp)
🔇 Additional comments (22)
src/core/data/tensorfield/tensorfield.hpp (1)
208-208: LGTM!The reordering of
static constexprfollows the conventional C++ style where storage class specifiers precede type specifiers. No functional change.src/core/utilities/types.hpp (3)
1-2: LGTM!The header guard rename follows the preferred pattern for this project.
Based on learnings
226-258: LGTM!The utility functions are well-designed:
from_stringprovides proper error handling by throwing on parse failureget_env_assafely wraps environment variable parsing with a default fallbackThese complement the existing
get_envfunctions nicely.
514-518: LGTM!The
for_N_allhelper correctly composesfor_Nwith theall()predicate to provide a clean API for all/any evaluations over generated sequences.src/core/data/ndarray/ndarray_vector.hpp (1)
19-70: LGTM!The refactoring to remove the
DataTypetemplate parameter and useautomakesNdArrayViewermore flexible and generic. The index type (std::uint32_t) is correctly sized to handle large grids without overflow. The C-ordering and Fortran-ordering index calculations are correct.src/core/utilities/algorithm.hpp (2)
75-100: LGTM!The
convert_to_primalfunction correctly handles the projection of magnetic and electric field components to primal locations using the layout's projection methods.
137-147: LGTM!The TensorField overload correctly applies the Field conversion to each component.
src/core/data/grid/gridlayoutimplyee.hpp (1)
511-604: LGTM!The three new B-to-moments projection functions are correctly implemented:
- Each properly handles the dual→primal conversion for their respective components
- 3D implementations correctly use all four dual combinations with equal 0.25 weights
- The dimension-specific implementations are appropriate for 1D/2D/3D
src/core/data/grid/gridlayout.hpp (3)
1027-1045: LGTM!The three new accessor functions correctly delegate to the corresponding
GridLayoutImplmethods for B-to-moments projections.
1180-1194: LGTM!The naming clarification is helpful:
AMRBoxForreturns the AMR box for the field (without ghosts)AMRGhostBoxForreturns the ghost box by growing the AMR boxThe logic correctly grows the box by
nbrGhoststo create the ghost box (no unsigned wraparound issue since we're adding, not subtracting).
1220-1226: LGTM!The new iterator helpers provide clean APIs for common iteration patterns over AMR/local index pairs. The
boxes_iteratorusage correctly pairs AMR indices with their corresponding local indices.src/diagnostic/detail/vtk_types/fluid.hpp (1)
37-97: Fluid VTK writer wiring looks consistent with existing H5 logicPer-quantity matching, per-level init, and hierarchy traversal all line up with the existing fluid diagnostics; ions and per-pop paths look correct and you only allocate datasets for the active quantity. I don’t see correctness issues here.
tests/simulator/CMakeLists.txt (1)
16-21: VTK diagnostics and timestamp tests are wired appropriatelyAdding
vtk_diagnosticsand re-enablingtest_diagnostic_timestampsunder theHighFiveguard matches how other diagnostic tests are handled and keeps the config coherent. No issues from a CMake/test orchestration standpoint.Also applies to: 33-33
src/diagnostic/detail/vtk_types/electromag.hpp (1)
29-55: Electromag writer wiring and level handling look correctThe electromag writer follows the same pattern as the fluid writer: you only init datasets and write when
diagnostic.quantitymatches a registered electromag field, and you correctly useinitTensorFieldFileLevel<1>withwriteTensorField<1>. I don’t see correctness or performance issues here.src/diagnostic/diagnostics.hpp (1)
55-61: Format-based diagnostics backend selection is clear and safeUsing
cppdict::get_valuewith default"phareh5"and explicit branches for"phareh5"vs"pharevtkhdf"(with a runtime error on unknown formats) cleanly wires the new backend without changing the public factory API. This looks good.src/diagnostic/detail/h5writer.hpp (1)
6-17: H5 writer dependency wiring and ownership semantics look solidBringing in
mpi_utilsand the per-type writer headers aligns with the actual usage (MPI reductions andtypeWriters_), and switching to deleted copy/move assignment operators is the right way to makeH5Writernon-assignable while keeping construction viamake_unique. ThetypeWriters_map initialization withshared_ptr-backed writers is consistent with the existingH5TypeWriterpattern.Also applies to: 176-182, 194-197
tests/simulator/test_vtk_diagnostics.py (2)
24-103: Model setup is compatible with MaxwellianFluidModel expectationsThe
setup_modelhelpers use*xyzsignatures and density/velocity/thermal closures in a way that matches theMaxwellianFluidModeldefaulter pattern and should exercise both field and population diagnostics meaningfully.
131-159: Test lifecycle integration with Simulator looks consistent
VTKDiagnosticsTestcorrectly resets theSimulatorand PHARE global state intearDownwhile still callingsuper().tearDown(), andtest_dump_diagsusesunique_diag_dir_for_test_caseplusdump_all_diagsto exercise the new"pharevtkhdf"format end-to-end. This wiring matches the existing simulator test harness.src/diagnostic/diagnostic_model_view.hpp (2)
62-81: Momentum tensor staging viatmpTensor_is symmetric and safeThe updated
fillPopMomTensorcorrectly mirrors the messenger pattern: enumerate patches with the shared"PHARE_sumTensor"buffer, copymomentumTensorintotmpTensor_, run the MT schedule, then copy back. This keeps the temporary storage localized while reusing the global buffer via the known name-based allocation pattern.
145-172: New local box helper and tmp-field accessors fit existing resource patterns
localLevelBoxesoffers a concise way to gatherAMRBoxes usingvisitHierarchy, and the tmp accessors plusgetCompileTimeResourcesViewListexposetmpField_,tmpVec_, andtmpTensor_consistently with other components’getCompileTimeResourcesViewListAPIs. Using the"PHARE_sumField","PHARE_sumVec", and"PHARE_sumTensor"names matches the global resource-manager allocation pattern noted earlier and avoids duplicate allocation.
Based on learningsAlso applies to: 219-221
src/diagnostic/detail/vtkh5_writer.hpp (2)
171-186: VTK-HDF dump lifecycle matches the intended file-flag behaviorThe
dumpimplementation correctly initializes per-diagnosticfile_flagsfromthis->flags, delegates to type-specific writers, and then downgrades flags toREAD_WRITEto avoid truncating on subsequent dumps. This mirrors the fixed behavior in the existing HDF writer.
40-47: Addtypenamefor dependent nested types in template aliasesIn
H5Writer,ModelViewis a template parameter, so its nested types are dependent and requiretypename:- using ModelView = _ModelView; - using This = H5Writer<ModelView>; - using GridLayout = ModelView::GridLayout; - using Attributes = ModelView::PatchProperties; + using ModelView = _ModelView; + using This = H5Writer<ModelView>; + using GridLayout = typename ModelView::GridLayout; + using Attributes = typename ModelView::PatchProperties;Without
typename, this is ill-formed in standard C++ and will typically fail to compile once this writer is instantiated.⛔ Skipped due to learnings
Learnt from: PhilipDeegan Repo: PHAREHUB/PHARE PR: 1056 File: tests/core/numerics/interpolator/test_main.cpp:314-318 Timestamp: 2025-09-01T09:41:40.618Z Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
There was a problem hiding this comment.
Actionable comments posted: 1
♻️ Duplicate comments (1)
src/core/utilities/algorithm.hpp (1)
102-135: Fix incorrect dereference ofBox::shape().Line 117 dereferences
lcl_box.shape()with*, butBox::shape()returns a value (Point), not a pointer. The past review comment has already flagged this critical issue and provided a detailed fix.
🧹 Nitpick comments (5)
src/diagnostic/detail/vtk_types/electromag.hpp (1)
1-2: Align header guard closing comment with macro name (cosmetic)The header guard macro is
PHARE_DIAGNOSTIC_DETAIL_VTK_TYPES_ELECTROMAG_HPP, but the closing comment uses a different name. Consider updating the#endifcomment to match the macro for consistency with your usual guard style.
Based on learningsAlso applies to: 60-62
tests/simulator/test_vtk_diagnostics.py (1)
144-159: Register VTK diagnostic output dirs for cleanup
test_dump_diagswrites diagnostics underlocal_outbut never callsself.register_diag_dir_for_cleanup(local_out), so those directories will persist between runs even thoughSimulatorTest.tearDown()is wired to clean registered paths.Consider registering
local_outafter it’s computed:local_out = self.unique_diag_dir_for_test_case(f"{out}/test_vtk", ndim, interp) simInput["diag_options"]["options"]["dir"] = local_out simInput["diag_options"]["format"] = "pharevtkhdf" + self.register_diag_dir_for_cleanup(local_out)This keeps the filesystem clean while preserving the existing SimulatorTest cleanup behaviour.
src/hdf5/detail/h5/h5_file.hpp (2)
19-21: Chunked/resizable dataset helpers are well-factored; consider guarding CHUNK_SIZEUsing
detail::CHUNK_SIZEpluscreate_resizable_{1d,2d}_data_setcleanly encapsulates the common “0‑length, UNLIMITED, chunked” HDF5 pattern and keeps call sites simple.You might optionally add a small guard to ensure
PHARE_H5_CHUNK_SIZEdoesn’t resolve to 0 (or some obviously invalid value) before using it in the chunk vector, e.g. clamp to at least 1 or throw early; otherwise a misconfigured env var could fail at dataset creation time.Also applies to: 127-141
116-125: Consider avoiding C++20 abbreviated template parameters increate_chunked_data_set
create_chunked_data_setcurrently usesautofunction parameters, which rely on C++20 abbreviated function templates. If the project still targets C++17, this will not compile on stricter toolchains.You can keep the flexibility while staying explicit:
- template<typename Type> - auto create_chunked_data_set(auto const& path, auto const chunk, auto const& dataspace) + template<typename Type> + auto create_chunked_data_set(std::string const& path, + std::vector<hsize_t> const& chunk, + HighFive::DataSpace const& dataspace)(adapt the types if call sites use slightly different but compatible containers).
This also makes the intended usage clearer at the interface.
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
49-49: Document X_TIMES multiplier rationale.The
X_TIMESconstant duplicates data in lower dimensions (2D: ×2, 1D: ×4) to fit a 3D view, but the comment at lines 46-48 is brief. Consider adding a reference to the VTK-HDF5 spec or ParaView requirements explaining why this duplication is necessary for correct rendering.
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (31)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(4 hunks)src/core/data/grid/gridlayoutdefs.hpp(1 hunks)src/core/data/grid/gridlayoutimplyee.hpp(27 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(6 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/h5writer.hpp(2 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtk_types/info.hpp(1 hunks)src/diagnostic/detail/vtk_types/meta.hpp(1 hunks)src/diagnostic/detail/vtk_types/particle.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(7 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(3 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)tests/simulator/CMakeLists.txt(2 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init_small.py
- src/phare/phare_init.py
🚧 Files skipped from review as they are similar to previous changes (9)
- src/diagnostic/diagnostic_manager.hpp
- src/amr/physical_models/hybrid_model.hpp
- src/diagnostic/detail/vtk_types/info.hpp
- pyphare/pyphare/pharein/init.py
- pyphare/pyphare/pharein/simulation.py
- tests/simulator/init.py
- src/diagnostic/detail/vtk_types/particle.hpp
- src/diagnostic/detail/vtk_types/meta.hpp
- src/diagnostic/detail/vtk_types/fluid.hpp
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/diagnostic/diagnostics.hppsrc/diagnostic/detail/vtk_types/electromag.hppsrc/core/utilities/types.hppsrc/core/utilities/algorithm.hppsrc/core/utilities/box/box.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/diagnostic/diagnostic_model_view.hppsrc/amr/resources_manager/amr_utils.hppsrc/diagnostic/detail/h5writer.hppsrc/core/data/grid/gridlayout.hppsrc/hdf5/detail/h5/h5_file.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/core/data/tensorfield/tensorfield.hppsrc/core/data/grid/gridlayoutdefs.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (12)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2025-02-07T14:35:14.630Z
Learnt from: nicolasaunai
Repo: PHAREHUB/PHARE PR: 591
File: res/cmake/options.cmake:73-75
Timestamp: 2025-02-07T14:35:14.630Z
Learning: In CMake configuration for PHARE, `lowResourceTests` and `highResourceTests` options must be mutually exclusive and cannot be enabled simultaneously.
Applied to files:
tests/simulator/CMakeLists.txt
📚 Learning: 2025-07-09T17:18:05.771Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/amr/CMakeLists.txt:103-105
Timestamp: 2025-07-09T17:18:05.771Z
Learning: In the PHARE project, `HighFive` is a CMake option defined in `res/cmake/options.cmake` as `option(HighFive "Build with highfive usage" ON)`, not a target that would be created by find_package(). The condition `if (HighFive)` correctly checks this option.
Applied to files:
tests/simulator/CMakeLists.txtsrc/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/types.hppsrc/core/utilities/algorithm.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/types.hppsrc/core/utilities/box/box.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/algorithm.hppsrc/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2024-10-22T10:05:54.014Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-10-22T10:05:54.014Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-11-10T09:37:57.021Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1084
File: src/diagnostic/diagnostic_model_view.hpp:219-221
Timestamp: 2025-11-10T09:37:57.021Z
Learning: In PHARE, temporary fields like tmpField_, tmpVec_, and tmpTensor_ in src/diagnostic/diagnostic_model_view.hpp use a name-based resource allocation pattern. Fields with names "PHARE_sumField", "PHARE_sumVec", and "PHARE_sumTensor" are allocated globally elsewhere in the resources manager (e.g., in src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp), and components reference the same storage through identically-named field objects. These do not require local allocation via rm.enumerate().
Applied to files:
src/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/h5writer.hpp
📚 Learning: 2025-09-17T13:50:16.038Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/tensorfield/tensor_field_data_factory.hpp:112-112
Timestamp: 2025-09-17T13:50:16.038Z
Learning: PhilipDeegan indicated that getSizeOfMemory returning a placeholder value of 1 in TensorFieldDataFactory is acceptable for their use case, suggesting it may not be critical for PHARE's memory management needs.
Applied to files:
src/diagnostic/diagnostic_model_view.hppsrc/core/data/tensorfield/tensorfield.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/core/data/grid/gridlayout.hpp:805-821
Timestamp: 2024-10-09T08:32:15.667Z
Learning: In the `AMRToLocal` function, before converting to `uint32_t`, assert that `local >= 0` to ensure values are valid.
Applied to files:
src/core/data/grid/gridlayout.hpp
🧬 Code graph analysis (13)
src/diagnostic/diagnostics.hpp (3)
src/diagnostic/diagnostic_manager.hpp (5)
dict(83-83)dict(86-86)dict(86-86)make_unique(74-80)make_unique(74-75)src/diagnostic/detail/h5writer.hpp (2)
make_unique(61-68)make_unique(61-61)src/diagnostic/detail/vtkh5_writer.hpp (2)
make_unique(67-74)make_unique(67-67)
tests/simulator/test_vtk_diagnostics.py (5)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)pyphare/pyphare/simulator/simulator.py (2)
startMPI(41-45)reset(258-269)tests/simulator/__init__.py (4)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)run(246-248)tests/diagnostic/__init__.py (1)
dump_all_diags(15-62)pyphare/pyphare/pharein/simulation.py (2)
simulation_domain(967-968)Simulation(735-1069)
src/diagnostic/detail/vtk_types/electromag.hpp (2)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-97)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (8)
diagnostic(74-79)diagnostic(74-74)lvl(155-160)lvl(155-155)ilvl(266-295)ilvl(266-266)boxes(51-65)boxes(51-51)
src/core/utilities/algorithm.hpp (4)
src/core/data/electrons/electrons.hpp (8)
layout(107-133)layout(107-107)layout(285-285)layout(285-285)layout(286-286)layout(286-286)layout(309-319)layout(309-309)src/core/utilities/box/box.hpp (4)
dim(109-125)dim(127-142)box(53-53)boxes_iterator(214-217)src/core/utilities/types.hpp (4)
all(365-369)all(365-366)all(376-379)all(376-376)src/core/data/ndarray/ndarray_vector.hpp (4)
make_array_view(214-217)make_array_view(214-214)make_array_view(220-223)make_array_view(220-220)
src/core/utilities/box/box.hpp (2)
src/core/utilities/point/point.hpp (4)
i(68-68)i(68-68)i(69-69)i(69-69)src/core/utilities/types.hpp (7)
product(269-272)product(269-269)for_N(467-498)for_N(467-467)for_N(501-504)for_N(501-501)for_N_any(521-521)
src/diagnostic/diagnostic_model_view.hpp (4)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (10)
patch(146-154)patch(146-146)ions(407-416)ions(407-407)ions(420-445)ions(420-420)ions(447-480)ions(447-447)ions(492-531)ions(492-493)src/amr/resources_manager/amr_utils.hpp (2)
visitHierarchy(244-253)visitHierarchy(244-245)src/core/data/ions/ions.hpp (1)
forward_as_tuple(225-229)src/core/data/ions/ion_population/ion_population.hpp (1)
forward_as_tuple(109-113)
src/amr/resources_manager/amr_utils.hpp (1)
src/core/data/field/field.hpp (4)
args(75-81)args(75-75)args(83-86)args(83-83)
src/core/data/grid/gridlayout.hpp (5)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (4)
field(929-956)field(929-930)field(958-964)field(958-958)src/amr/data/field/field_geometry.hpp (4)
box(136-179)box(136-137)box(198-207)box(198-198)src/core/utilities/types.hpp (2)
for_N_make_array(508-511)for_N_make_array(508-508)src/amr/resources_manager/amr_utils.hpp (5)
AMRToLocal(45-46)AMRToLocal(53-54)AMRToLocal(62-62)AMRToLocal(77-90)AMRToLocal(77-78)src/amr/resources_manager/amr_utils.cpp (6)
AMRToLocal(34-40)AMRToLocal(34-35)AMRToLocal(47-54)AMRToLocal(47-48)AMRToLocal(62-66)AMRToLocal(62-62)
tests/simulator/refinement/test_2d_10_core.py (2)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)tests/simulator/test_advance.py (1)
AdvanceTestBase(33-869)
src/hdf5/detail/h5/h5_file.hpp (1)
src/core/utilities/types.hpp (1)
get_env_as(253-253)
src/diagnostic/detail/vtkh5_writer.hpp (4)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-60)src/diagnostic/detail/vtkh5_type_writer.hpp (6)
level(196-218)level(196-196)level(231-231)level(231-231)diagnostic(74-79)diagnostic(74-74)src/amr/resources_manager/amr_utils.hpp (2)
to_string(222-227)to_string(222-222)src/hdf5/detail/h5/h5_file.hpp (4)
path(295-301)path(295-295)path(303-308)path(303-303)
src/core/data/ndarray/ndarray_vector.hpp (1)
src/core/utilities/types.hpp (2)
product(269-272)product(269-269)
src/diagnostic/detail/vtkh5_type_writer.hpp (5)
src/core/utilities/box/box.hpp (9)
box(53-53)i(99-99)i(99-99)grow(91-96)grow(91-91)grow(328-333)grow(328-328)size(78-88)size(78-78)src/core/data/tensorfield/tensorfield.hpp (8)
i(181-181)i(181-181)i(182-182)i(182-182)size(208-208)size(208-208)tensor_field_dim_from_rank(17-24)tensor_field_dim_from_rank(17-17)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(97-101)diagnostic(97-97)src/core/utilities/types.hpp (6)
for_N_make_array(508-511)for_N_make_array(508-508)sum_from(281-289)sum_from(281-281)sum(275-278)sum(275-275)src/core/utilities/algorithm.hpp (4)
convert_to_fortran_primal(103-135)convert_to_fortran_primal(103-107)convert_to_fortran_primal(138-147)convert_to_fortran_primal(138-142)
🪛 Ruff (0.14.5)
tests/simulator/test_vtk_diagnostics.py
25-25: Unused function argument: xyz
(ARG001)
32-32: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
39-39: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
42-42: Unused function argument: xyz
(ARG001)
45-45: Unused function argument: xyz
(ARG001)
52-52: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
59-59: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
62-62: Unused function argument: xyz
(ARG001)
65-65: Unused function argument: xyz
(ARG001)
68-68: Unused function argument: xyz
(ARG001)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (6)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: Analyze (cpp)
- GitHub Check: Analyze (python)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
🔇 Additional comments (33)
src/amr/resources_manager/amr_utils.hpp (1)
251-251: Correct variadic forwarding syntax applied.The change from
std::forward<Args...>(args...)tostd::forward<Args>(args)...fixes incorrect template parameter pack expansion. The corrected syntax properly forwards each argument in the pack tovisitLevel.src/diagnostic/diagnostic_model_view.hpp (1)
37-37: LGTM! Well-structured refactoring for VTK HDF diagnostic support.The changes effectively refactor temporary storage and provide clean accessor APIs:
- Field alias (line 37): Useful public type for external code
- Temporary storage refactoring (lines 219-221): Expands single
sumTensor_totmpField_,tmpVec_,tmpTensor_with appropriate name-based resource allocation- New accessor methods (lines 145-172):
localLevelBoxes(),tmpField(),tmpVecField(),tmpTensorField<rank>(), andgetCompileTimeResourcesViewList()provide efficient, type-safe access following established patterns- Efficient implementation: Proper use of
if constexpr, move semantics,std::forward_as_tuple, and compile-time enforcement viastatic_assert- Consistent updates:
fillPopMomTensor(),dst_name(), and template parameters updated consistentlyThe code is expressive, follows clean code principles, and aligns with patterns established elsewhere in the codebase (e.g.,
ions.hpp,ion_population.hpp).Also applies to: 70-80, 96-98, 145-172, 183-183, 194-194, 219-221
tests/simulator/refinement/test_2d_10_core.py (2)
22-24: LGTM!The diagnostic path constants are clearly defined and used consistently throughout the test.
17-21: The review comment is based on incorrect assumptions about the codebase pattern.The module-level initialization of
cpp = cpp_lib()andtest = AdvanceTestBase(rethrow=True)is not only safe but is the established pattern in this codebase. Test filetests/simulator/refinement/test_2d_2_core.pyuses the identical initialization pattern at lines 150-151. Additionally,startMPI()itself callscpp_lib()internally (simulator.py:45), demonstrating thatcpp_lib()functions independently of MPI initialization state. No MPI dependencies exist incpp_lib()orAdvanceTestBase. Since these are direct-run scripts executed withmpirun(not pytest test modules), module-level initialization is appropriate and standard in this codebase.Likely an incorrect or invalid review comment.
src/core/data/tensorfield/tensorfield.hpp (1)
208-208: LGTM: Improved qualifier ordering.The reordering of qualifiers (
static constexprinstead ofconstexpr static) follows a more conventional style where storage-class specifiers precede cv-qualifiers. No functional change.src/core/utilities/algorithm.hpp (2)
75-100: LGTM: Well-structured projection logic.The quantity-specific branching and error handling for unsupported quantities are appropriate.
137-147: LGTM: Correct recursive application.The TensorField variant properly delegates to the Field conversion for each component.
src/core/utilities/types.hpp (2)
226-235: LGTM: Clear error handling.The function uses exceptions for parse failures with an informative error message, which aligns with the project's preferences based on past feedback.
252-258: LGTM: Clean environment variable parsing.The function appropriately delegates to
from_stringand provides a sensible default fallback.src/core/utilities/box/box.hpp (4)
30-30: LGTM: Standard iterator typedef.
99-101: LGTM: Clean shape and size accessors.The per-dimension
shape(i)accessor and the updatedsize()usingcore::productare well-designed.
209-259: LGTM: Well-designed composite iterator.The
boxes_iteratorimplements a parallel iteration pattern that advances multiple box iterators simultaneously. The use of compile-timefor_Nhelpers and tuple handling is appropriate.
327-333: LGTM: Simple non-mutating wrapper.src/diagnostic/detail/h5writer.hpp (1)
196-197: LGTM: Critical fix for deleted assignment operators.Correcting
operator&tooperator=properly deletes the copy and move assignment operators. The previous code inadvertently deleted the bitwise AND operator instead.src/core/data/ndarray/ndarray_vector.hpp (4)
19-23: LGTM: Improved generic design.Removing
DataTypefrom the template parameters and usinguint32_tfor indices (correcting the previous narrowing issue) makesNdArrayViewermore flexible and safe for large grids.
25-53: LGTM: Correct index computation.The
idxmethods correctly compute flat indices for both C-ordering (row-major) and Fortran-ordering (column-major) across 1D, 2D, and 3D cases.
55-70: LGTM: Generic accessor with bounds checking.The refactored
atmethods useautofor generic type handling and include appropriate bounds assertions.
101-101: LGTM: Consistent usage updates.All call sites have been updated consistently to use the refactored
NdArrayViewerinterface without theDataTypetemplate parameter.Also applies to: 138-138, 161-162, 167-167, 291-291, 303-303
tests/simulator/CMakeLists.txt (2)
21-21: LGTM: VTK diagnostics test added.The new test for VTK diagnostics is appropriately placed within the
HighFiveconditional block and follows the existing test pattern.
33-33: LGTM: Diagnostic timestamps test enabled.Re-enabling this test ensures timestamp functionality is properly validated.
src/core/data/grid/gridlayoutdefs.hpp (1)
6-8: LGTM: Include reordering for dependencies.The include reordering ensures proper dependency resolution without affecting the public API.
src/diagnostic/diagnostics.hpp (1)
28-61: Format-based diagnostics writer selection is clear and robustThe new
formatdispatch (defaulting to"phareh5"and adding"pharevtkhdf") is straightforward, preserves the existing API, and fails fast on unknown formats with a descriptive error message. No issues from this change.src/diagnostic/detail/vtk_types/electromag.hpp (2)
29-55: Electromagnetic VTK writer implementation matches existing patternsThe
writeimplementation follows the same structure as the fluid VTK writer (per-level init, per-field init, thenvisitHierarchywith a quantity filter) and correctly restricts initialization and writes to the activediagnostic.quantity. This is consistent and easy to maintain.
13-17: Remove incorrect typename suggestion; code is valid C++20 as-isIn C++20,
typenameis optional for dependent types in type alias declarations. The context makes the type intent unambiguous, and the patternusing VTKFileWriter = Super::VTKFileWriter;is valid and widely used throughout the PHARE codebase (particle.hpp, fluid.hpp, and electromag.hpp all use this form). The code compiles correctly without the keyword and aligns with the project's preference for minimal syntax in C++20.Likely an incorrect or invalid review comment.
src/core/data/grid/gridlayoutimplyee.hpp (2)
423-441: Use ofstd::arrayCTAD in interpolation stencils looks goodSwitching these interpolation helpers to
return std::array{...};keeps the code shorter and clearer while preserving the existing stencils and weights across dimensions. No behavioural issues spotted in these changes.Also applies to: 446-473, 487-506, 617-634, 641-664, 671-693, 706-723, 736-752, 768-781
511-603: New Bx/By/Bz→Moments stencils are consistent with Yee centering in 1D/2D/3DThe new
BxToMoments,ByToMoments, andBzToMomentshelpers correctly:
- Treat 1D cases as identity for primal components (Bx) and 2‑point averages for dual ones (By, Bz).
- In 2D, average over the single dual direction (2‑point stencils for Bx and By, 4‑point stencil for Bz which is dual in both X and Y).
- In 3D, average over all 2² dual combinations in the shifted directions for each component, with weights that sum to 1.
This matches the Yee centering defined earlier and addresses the previous 3D under‑sampling concerns around B→moment interpolation.
tests/simulator/test_vtk_diagnostics.py (1)
24-103: Model setup for VTK diagnostics is straightforward and appropriateThe Maxwellian fluid model (constant density, sinusoidal/cosinusoidal B/V profiles, small thermal speeds, plus isothermal electrons) is a good, lightweight choice for exercising the electromag and fluid VTK/HDF diagnostics without overcomplicating the test. The use of
sim.simulation_domain()keeps fields properly periodic with the configured domain.src/hdf5/detail/h5/h5_file.hpp (1)
275-287: Existence-checkedgetDataSetand deleted copy/move clarify ownershipWrapping
h5file_.existinexist()and adding agetDataSetthat throws on missing datasets is a safer alternative to the old assert‑based pattern, and deleting copy/move operations forHighFiveFilemakes its ownership/lifetime semantics explicit. These changes improve robustness without altering existing call sites that use the rawh5file_.src/core/data/grid/gridlayout.hpp (3)
1027-1046: LGTM: Consistent projection helpers added.The new
BxToMoments,ByToMoments, andBzToMomentsmethods follow the existing pattern for field projection helpers and correctly delegate to theGridLayoutImplcounterparts.
1180-1194: LGTM: Box accessors refactored correctly.The
AMRBoxForandAMRGhostBoxFormethods now correctly compute the physical and ghost boxes respectively.AMRGhostBoxForuses positivenbrGhosts()values withgrow(), which properly expands the box—avoiding the unsigned wraparound issue flagged in earlier reviews.
1220-1226: LGTM: Iterator helpers added.The new indexer methods (
amr_lcl_idx,domain_amr_lcl_idx,ghost_amr_lcl_idx) provide convenient access to AMR/local box iterators for different use cases.src/diagnostic/detail/vtkh5_writer.hpp (1)
1-209: LGTM: Well-structured HDF5 writer.The
H5Writerclass provides a clean, templated interface for VTK-HDF5 diagnostic output:
- Proper RAII semantics and deleted copy/move operations
- Lazy per-quantity file creation via
makeFile()- Correct flag management in
dump()to prevent truncation on subsequent writes- Factory method
make_unique()with optional overwrite modePast issues (operator deletion, header guard comment, flag reset) have been addressed.
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
162-305: LGTM: VTK-HDF5 dataset management.The
VTKFileWritermethods correctly handle:
- Field and tensor-field conversion to Fortran-ordered primal data
- Per-level dataset initialization with appropriate metadata (spacing, offsets)
- MPI-aware offset and size accumulation in
resize_dataandresize_boxes- Primal box adjustment (line 303) aligns with the
convert_to_fortran_primalcalls
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Nitpick comments (9)
src/diagnostic/diagnostic_manager.hpp (1)
31-37: Avoid recomputingdiagNameinside the loop (optional micro‑cleanup).The change to
std::string const diagNameis fine and behavior‑preserving. Right now, though,diagType + std::to_string(diagBlockID)is built once in thewhilecondition and again fordiagName. If you want to trim a tiny bit of duplication and work, you could computediagNameonce per iteration and reuse it for both thecontainscheck and the dictionary access, e.g.:- std::size_t diagBlockID = 0; - while (diagsParams.contains(diagType) - && diagsParams[diagType].contains(diagType + std::to_string(diagBlockID))) - { - std::string const diagName = diagType + std::to_string(diagBlockID); + std::size_t diagBlockID = 0; + while (diagsParams.contains(diagType)) + { + std::string const diagName = diagType + std::to_string(diagBlockID); + if (!diagsParams[diagType].contains(diagName)) + break; dMan.addDiagDict(diagsParams[diagType][diagName]); ++diagBlockID; }Not required, but it slightly simplifies the logic and avoids repeated string concatenation, in line with the minimal/efficient style used elsewhere.
src/amr/resources_manager/amr_utils.hpp (1)
229-239: Consider forwarding args in visitLevel for consistency.While not part of the current change, for consistency with the perfect forwarding pattern now established in
visitHierarchy, consider forwarding theargsparameter pack when passing toresman.setOnPatchat line 234.Apply this diff:
template<typename GridLayout, typename ResMan, typename Action, typename... Args> void visitLevel(SAMRAI_Types::level_t& level, ResMan& resman, Action&& action, Args&&... args) { for (auto& patch : level) { - auto guard = resman.setOnPatch(*patch, args...); + auto guard = resman.setOnPatch(*patch, std::forward<Args>(args)...); GridLayout layout = layoutFromPatch<GridLayout>(*patch); action(layout, to_string(patch->getGlobalId()), static_cast<std::size_t>(level.getLevelNumber())); } }src/diagnostic/detail/h5writer.hpp (1)
1-2: Consider aligning the header guard name and comment with the file path conventionThe guard macro (
PHARE_DETAIL_DIAGNOSTIC_HIGHFIVE_HPP) and the closing comment (PHARE_DETAIL_DIAGNOSTIC_HIGHFIVE_H) don’t match each other or the file nameh5writer.hpp. When convenient, consider renaming the guard to follow the project-widePHARE_[PATH_WITH_UNDERSCORES]_HPPpattern and updating the closing comment accordingly.Based on learnings
Also applies to: 347-347
src/core/utilities/box/box.hpp (1)
209-259: Add documentation and const overloads for boxes_iterator.The
boxes_iteratoris a powerful parallel-iteration utility, but its usage pattern isn't immediately obvious. Consider adding class-level documentation explaining that it simultaneously iterates over multiple boxes, yielding tuples of points.Additionally,
begin()andend()(lines 249-256) should provideconstoverloads since they don't modify the boxes andBoxitself supports const iteration:auto begin() const { return iterator{for_N<N>([&](auto i) { return std::get<i>(boxes).begin(); })}; } auto end() const { return iterator{for_N<N>([&](auto i) { return std::get<i>(boxes).end(); })}; }Minor note: line 215 uses
std::forward_as_tuple(tuple of references), but the member at line 258 isstd::tuple<Boxes...>(stores by value). This causes boxes to be copied during construction, which is safe but might be surprising. For smallBoxobjects this is fine, but consider documenting or usingstd::tuple<Boxes const&...>if copies are unintended.src/core/utilities/algorithm.hpp (2)
75-100:convert_to_primalmapping looks correct; consider future‑proofing unsupported quantitiesThe mapping from
PhysicalQuantity(Bx/By/Bz/Ex/Ey/Ez) to the correspondinglayout.*ToMoments()projector is clear and keeps the hot path simple. The fallbackstd::runtime_errorwill surface misuse at runtime.If there are quantities for which calling this is a programming error (rather than a recoverable runtime condition), you may eventually want to enforce that via static constraints or a debug
assertbefore throwing, but the current implementation is fine for now.
102-135: Fieldconvert_to_fortran_primalimplementation is sound; consider tightening preconditionsThe implementation looks good:
- Asserts that
dstis fully primal.- Detects whether
srcis all‑primal once, then uses two separate loops to avoid an extra branch in the inner loop.- Uses
boxes_iteratorwith a zero‑shifted local box to write into a Fortran‑orderedNdArrayView, withc_orderingclearly set tofalselocally.Given the comment
// DOES NOT WORK ON GHOST BOX!, you might eventually want to turn that into anassertonce there is an accessor onlayout/box to detect ghost regions; until then, the comment at least documents the precondition.src/core/utilities/types.hpp (1)
226-235: from_string / get_env_as look good, with one parsing nuanceThe new
from_string+get_env_ashelpers are clear and minimal, and throwing on failed extraction is a reasonable choice here. One behavioral detail to be aware of: formatted extraction will accept prefixes like"42xyz"as42without settingfailbit. If you ever need stricter validation (rejecting trailing junk), you’d need an extra check (e.g., consumestd::wsthen verifyeof()), but what you have is fine if partial parses are acceptable.Also applies to: 252-258
src/diagnostic/detail/vtk_types/electromag.hpp (1)
12-55: Electromag VTK/HDF writer logic matches existing pattern; consider small cleanupsThe new
ElectromagDiagnosticWriterfollows the same pattern as the fluid writer: level loop, per-levelinitFileLevel+initTensorFieldFileLevel, thenvisitHierarchywith a lambda that writes the selected electromag vector field. The matching ondiagnostic.quantity == "/" + vecField->name()keeps selection simple and localized.Two optional refinements you might consider later:
- If
diagnostic.quantitydoesn’t correspond to any electromag field, you could early-return before callingonLevelsto avoid creating empty files.- The matching loop over
getElectromagFields()is duplicated inwrite_quantityand the level init lambda; caching ahas_matchflag or a pointer to the matched field would remove that duplication and a bit of repeated string work.Both are non-essential; the current implementation is sound and consistent with the rest of the vtkh5 writers.
tests/simulator/test_vtk_diagnostics.py (1)
119-128: Avoid mutating and reusing the samesimInputdict across permutations.
permute(dic)updates the passed-in dict in place and reuses that single instance for all(ndim, interp)combinations. With more than one combo this would couple test cases via sharedsimInputstate.A small refactor keeps behavior while isolating cases:
-def permute(dic): - dic.update(simArgs.copy()) - return [ - dict( - ndim=ndim, - interp=interp_order, - simInput=dic, - ) - for ndim, interp_order in itertools.product(ndims, interp_orders) - ] +def permute(overrides): + base = simArgs.copy() + base.update(overrides) + return [ + dict( + ndim=ndim, + interp=interp_order, + simInput=base.copy(), + ) + for ndim, interp_order in itertools.product(ndims, interp_orders) + ]
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (29)
pyphare/pyphare/pharein/__init__.py(1 hunks)pyphare/pyphare/pharein/simulation.py(1 hunks)src/amr/physical_models/hybrid_model.hpp(1 hunks)src/amr/resources_manager/amr_utils.hpp(1 hunks)src/core/data/grid/gridlayout.hpp(4 hunks)src/core/data/grid/gridlayoutdefs.hpp(1 hunks)src/core/data/grid/gridlayoutimplyee.hpp(27 hunks)src/core/data/ndarray/ndarray_vector.hpp(5 hunks)src/core/data/tensorfield/tensorfield.hpp(1 hunks)src/core/utilities/algorithm.hpp(2 hunks)src/core/utilities/box/box.hpp(6 hunks)src/core/utilities/types.hpp(5 hunks)src/diagnostic/detail/h5writer.hpp(2 hunks)src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/diagnostic/detail/vtkh5_writer.hpp(1 hunks)src/diagnostic/diagnostic_manager.hpp(1 hunks)src/diagnostic/diagnostic_model_view.hpp(7 hunks)src/diagnostic/diagnostic_writer.hpp(1 hunks)src/diagnostic/diagnostics.hpp(2 hunks)src/hdf5/detail/h5/h5_file.hpp(3 hunks)src/phare/CMakeLists.txt(0 hunks)src/phare/phare_init.py(0 hunks)src/phare/phare_init_small.py(0 hunks)tests/simulator/CMakeLists.txt(2 hunks)tests/simulator/__init__.py(1 hunks)tests/simulator/refinement/test_2d_10_core.py(1 hunks)tests/simulator/test_vtk_diagnostics.py(1 hunks)
💤 Files with no reviewable changes (3)
- src/phare/CMakeLists.txt
- src/phare/phare_init_small.py
- src/phare/phare_init.py
🚧 Files skipped from review as they are similar to previous changes (7)
- tests/simulator/CMakeLists.txt
- src/diagnostic/detail/vtk_types/fluid.hpp
- pyphare/pyphare/pharein/init.py
- pyphare/pyphare/pharein/simulation.py
- src/diagnostic/diagnostics.hpp
- tests/simulator/init.py
- tests/simulator/refinement/test_2d_10_core.py
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/diagnostic/diagnostic_writer.hppsrc/core/utilities/algorithm.hppsrc/core/data/grid/gridlayoutdefs.hppsrc/core/utilities/types.hppsrc/core/data/tensorfield/tensorfield.hppsrc/core/data/grid/gridlayoutimplyee.hppsrc/diagnostic/detail/h5writer.hppsrc/amr/physical_models/hybrid_model.hppsrc/diagnostic/diagnostic_model_view.hppsrc/core/utilities/box/box.hppsrc/diagnostic/detail/vtk_types/electromag.hppsrc/hdf5/detail/h5/h5_file.hppsrc/core/data/grid/gridlayout.hppsrc/core/data/ndarray/ndarray_vector.hppsrc/amr/resources_manager/amr_utils.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/diagnostic_manager.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (11)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2025-11-10T09:37:57.021Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1084
File: src/diagnostic/diagnostic_model_view.hpp:219-221
Timestamp: 2025-11-10T09:37:57.021Z
Learning: In PHARE, temporary fields like tmpField_, tmpVec_, and tmpTensor_ in src/diagnostic/diagnostic_model_view.hpp use a name-based resource allocation pattern. Fields with names "PHARE_sumField", "PHARE_sumVec", and "PHARE_sumTensor" are allocated globally elsewhere in the resources manager (e.g., in src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp), and components reference the same storage through identically-named field objects. These do not require local allocation via rm.enumerate().
Applied to files:
src/diagnostic/diagnostic_writer.hppsrc/diagnostic/detail/h5writer.hppsrc/amr/physical_models/hybrid_model.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2025-09-17T13:35:11.533Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Applied to files:
src/core/utilities/algorithm.hppsrc/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2024-10-22T10:05:54.014Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 0
File: :0-0
Timestamp: 2024-10-22T10:05:54.014Z
Learning: The variable `c_ordering` in `ConcreteLoadBalancerHybridStrategyNPPC<PHARE_T>::compute` is used to create an array view `lb_view` for handling load balancing data.
Applied to files:
src/core/utilities/algorithm.hpp
📚 Learning: 2025-09-01T09:41:40.618Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1056
File: tests/core/numerics/interpolator/test_main.cpp:314-318
Timestamp: 2025-09-01T09:41:40.618Z
Learning: The PHARE project uses C++20, which makes the typename keyword optional for dependent types in obvious contexts. The project prefers minimal code without unnecessary keywords, so typename suggestions for dependent types should be avoided when the code compiles successfully in C++20.
Applied to files:
src/core/utilities/algorithm.hppsrc/core/utilities/types.hpp
📚 Learning: 2025-04-17T14:41:53.643Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 998
File: src/core/utilities/point/point.hpp:195-210
Timestamp: 2025-04-17T14:41:53.643Z
Learning: In `src/core/utilities/point/point.hpp`, the `as_signed()` and `as_unsigned()` methods are intentionally designed to cause compilation errors for unsupported types (only 4-byte types are supported). This forces developers to implement proper conversions themselves when extending the functionality to new types. The comment "else no return cause not yet handled" indicates this is a deliberate design choice.
Applied to files:
src/core/utilities/types.hppsrc/core/utilities/box/box.hpp
📚 Learning: 2025-09-17T13:50:16.038Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/tensorfield/tensor_field_data_factory.hpp:112-112
Timestamp: 2025-09-17T13:50:16.038Z
Learning: PhilipDeegan indicated that getSizeOfMemory returning a placeholder value of 1 in TensorFieldDataFactory is acceptable for their use case, suggesting it may not be critical for PHARE's memory management needs.
Applied to files:
src/core/data/tensorfield/tensorfield.hppsrc/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2025-07-09T17:18:05.771Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/amr/CMakeLists.txt:103-105
Timestamp: 2025-07-09T17:18:05.771Z
Learning: In the PHARE project, `HighFive` is a CMake option defined in `res/cmake/options.cmake` as `option(HighFive "Build with highfive usage" ON)`, not a target that would be created by find_package(). The condition `if (HighFive)` correctly checks this option.
Applied to files:
src/diagnostic/detail/h5writer.hppsrc/diagnostic/detail/vtkh5_writer.hpp
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/diagnostic_model_view.hppsrc/diagnostic/detail/vtkh5_writer.hppsrc/diagnostic/detail/vtkh5_type_writer.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Applied to files:
src/diagnostic/diagnostic_model_view.hpp
📚 Learning: 2024-10-09T08:32:15.667Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/core/data/grid/gridlayout.hpp:805-821
Timestamp: 2024-10-09T08:32:15.667Z
Learning: In the `AMRToLocal` function, before converting to `uint32_t`, assert that `local >= 0` to ensure values are valid.
Applied to files:
src/core/data/grid/gridlayout.hpp
🧬 Code graph analysis (11)
src/core/utilities/algorithm.hpp (3)
src/core/utilities/box/box.hpp (4)
dim(109-125)dim(127-142)box(53-53)boxes_iterator(214-217)src/core/utilities/types.hpp (4)
all(365-369)all(365-366)all(376-379)all(376-376)src/core/data/ndarray/ndarray_vector.hpp (4)
make_array_view(214-217)make_array_view(214-214)make_array_view(220-223)make_array_view(220-220)
tests/simulator/test_vtk_diagnostics.py (5)
pyphare/pyphare/cpp/__init__.py (1)
cpp_lib(6-9)pyphare/pyphare/simulator/simulator.py (2)
startMPI(41-45)reset(258-269)tests/simulator/__init__.py (4)
SimulatorTest(201-267)tearDown(204-205)unique_diag_dir_for_test_case(250-254)run(246-248)tests/diagnostic/__init__.py (1)
dump_all_diags(15-62)pyphare/pyphare/pharein/maxwellian_fluid_model.py (1)
MaxwellianFluidModel(8-303)
src/diagnostic/diagnostic_model_view.hpp (3)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (10)
patch(146-154)patch(146-146)ions(407-416)ions(407-407)ions(420-445)ions(420-420)ions(447-480)ions(447-447)ions(492-531)ions(492-493)src/amr/resources_manager/amr_utils.hpp (2)
visitHierarchy(244-253)visitHierarchy(244-245)src/core/data/ions/ions.hpp (1)
forward_as_tuple(225-229)
src/core/utilities/box/box.hpp (2)
src/core/utilities/point/point.hpp (4)
i(68-68)i(68-68)i(69-69)i(69-69)src/core/utilities/types.hpp (7)
product(269-272)product(269-269)for_N(467-498)for_N(467-467)for_N(501-504)for_N(501-501)for_N_any(521-521)
src/diagnostic/detail/vtk_types/electromag.hpp (3)
src/diagnostic/detail/vtk_types/fluid.hpp (4)
write(38-97)write(38-38)diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (14)
diagnostic(71-76)diagnostic(71-71)diagnostic(78-81)diagnostic(78-78)layout(124-127)layout(124-124)lvl(117-122)lvl(117-117)ilvl(106-106)ilvl(108-108)ilvl(108-108)ilvl(140-140)boxes(51-65)boxes(51-51)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(103-107)diagnostic(103-103)
src/hdf5/detail/h5/h5_file.hpp (1)
src/core/utilities/types.hpp (1)
get_env_as(253-253)
src/core/data/grid/gridlayout.hpp (3)
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (4)
field(929-956)field(929-930)field(958-964)field(958-958)src/amr/data/field/field_geometry.hpp (4)
box(136-179)box(136-137)box(198-207)box(198-198)src/amr/resources_manager/amr_utils.cpp (6)
AMRToLocal(34-40)AMRToLocal(34-35)AMRToLocal(47-54)AMRToLocal(47-48)AMRToLocal(62-66)AMRToLocal(62-62)
src/core/data/ndarray/ndarray_vector.hpp (1)
src/core/utilities/types.hpp (2)
product(269-272)product(269-269)
src/amr/resources_manager/amr_utils.hpp (1)
src/core/data/field/field.hpp (4)
args(75-81)args(75-75)args(83-86)args(83-83)
src/diagnostic/detail/vtkh5_writer.hpp (5)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-60)src/diagnostic/detail/h5writer.hpp (16)
H5Writer(51-56)H5Writer(58-58)H5Writer(194-194)H5Writer(195-195)make_unique(61-68)make_unique(61-61)timestamp(101-104)timestamp(101-101)diagnostic(94-98)diagnostic(94-94)modelView_(160-160)timestamp_(161-161)fileStr(81-87)fileStr(81-81)dump(224-250)dump(224-225)src/diagnostic/diagnostics.hpp (2)
make_unique(50-65)make_unique(50-51)src/diagnostic/detail/vtk_types/fluid.hpp (2)
diagnostic(29-33)diagnostic(29-30)src/diagnostic/detail/vtkh5_type_writer.hpp (4)
diagnostic(71-76)diagnostic(71-71)diagnostic(78-81)diagnostic(78-78)
src/diagnostic/detail/vtkh5_type_writer.hpp (4)
src/core/data/tensorfield/tensorfield.hpp (8)
i(181-181)i(181-181)i(182-182)i(182-182)size(208-208)size(208-208)tensor_field_dim_from_rank(17-24)tensor_field_dim_from_rank(17-17)src/diagnostic/detail/vtkh5_writer.hpp (2)
diagnostic(103-107)diagnostic(103-103)src/core/utilities/types.hpp (2)
for_N_make_array(508-511)for_N_make_array(508-508)src/core/utilities/algorithm.hpp (4)
convert_to_fortran_primal(103-135)convert_to_fortran_primal(103-107)convert_to_fortran_primal(138-147)convert_to_fortran_primal(138-142)
🪛 Ruff (0.14.5)
tests/simulator/test_vtk_diagnostics.py
25-25: Unused function argument: xyz
(ARG001)
32-32: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
39-39: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
42-42: Unused function argument: xyz
(ARG001)
45-45: Unused function argument: xyz
(ARG001)
52-52: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
59-59: Do not assign a lambda expression, use a def
Rewrite _ as a def
(E731)
62-62: Unused function argument: xyz
(ARG001)
65-65: Unused function argument: xyz
(ARG001)
68-68: Unused function argument: xyz
(ARG001)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (6)
- GitHub Check: Analyze (cpp)
- GitHub Check: Analyze (python)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: build (macos-14)
- GitHub Check: build (macos-latest)
🔇 Additional comments (22)
src/amr/resources_manager/amr_utils.hpp (1)
251-251: LGTM! Perfect forwarding syntax corrected.The change from
std::forward<Args...>(args...)tostd::forward<Args>(args)...is the correct C++ syntax for perfect forwarding of parameter packs. The ellipsis must expand outside thestd::forwardcall, not within the template parameter list.src/diagnostic/detail/h5writer.hpp (4)
6-7: Explicit includes for MPI and Components look correctThese additions match direct uses of
core::mpi::maxandcore::Components::componentMaplater in the file and help keep the header self-contained.
12-17: Including diagnostic writer type headers is appropriate for inlinetypeWriters_initializationPulling in the concrete writer type headers here ensures full definitions are available where
typeWriters_is initialized and the writers are constructed, avoiding reliance on fragile forward declarations or transitive includes.
176-182:typeWriters_map initialization is coherent with diagnostic type stringsThe static mapping from diagnostic type strings (
"info","meta","fluid","electromag","particle") to their corresponding writer instances is clear and keeps writer construction centralized and lazy-per-H5Writer.
196-197: Deleting copy/move assignment operators instead ofoperator&is the correct non-copyable patternSwitching from deleted
operator&overloads to deleted copy/move assignment operators aligns with standard C++ idioms for making a type non-assignable, and is consistent with the already-deleted copy/move constructors.src/core/utilities/box/box.hpp (4)
5-5: LGTM! Includes support new functionality.The added includes are appropriate:
core/def.hppfor common definitions,<tuple>for the newboxes_iterator, and<algorithm>for std::min/std::max operations.Also applies to: 10-10, 14-14
30-30: LGTM! Standard container interface.Adding the
iteratortype alias follows C++ standard library conventions and makesBoxcompatible with generic algorithms that expect this member type.
327-333: LGTM! Clean functional-style utility.The non-member
grow()function provides a functional alternative to the mutating member method, returning a grown copy without modifying the original. The implementation is clean and the template parameterOTypeprovides appropriate flexibility.
99-101: Point class provides iterator support; iterator concern is unfounded.The Point class (line 40) has
value_typetypedef and providesbegin()andend()methods (lines 212–215 in point.hpp), which delegate to the internalrmember. The call tocore::product(shape(), std::size_t{1})at line 101 is therefore valid and will compile.The new
shape(std::size_t const i)overload (line 99) could benefit from a bounds check assertion (assert(i < dim)) to catch misuse in debug builds, but this is optional for robustness.src/core/utilities/algorithm.hpp (2)
1-2: Header guard rename matches project conventionThe new guard
PHARE_CORE_UTILITIES_ALGORITHM_HPPand the updated#endifcomment correctly reflect the full path and are consistent with the PHARE header‑guard pattern.
Based on learningsAlso applies to: 153-153
137-147: TensorField overload correctly delegates to Field versionThe tensor overload simply iterates components and reuses the Field
convert_to_fortran_primal, which is straightforward and avoids duplication. Assumingdstandsrcare shape‑compatible, this looks correct and efficient.src/core/data/tensorfield/tensorfield.hpp (1)
208-208: Staticsize()qualifier reorder is fineSwapping
constexpr statictostatic constexpris semantically neutral; the API and behavior stay identical.src/amr/physical_models/hybrid_model.hpp (1)
31-32: Alias cleanup matches project’s C++20 styleRemoving
typenamefrom these dependent aliases doesn’t change semantics and aligns with the existing minimal C++20 style in this codebase.Based on learnings
Also applies to: 35-36, 39-39
src/core/utilities/types.hpp (1)
513-524: for_N_all / for_N_any implementations are consistent with existing helpersReusing
for_Nwithmake_arrayand thenall/anykeeps the API compact and expressive. The semantics (bool-returning functor overNcompile-time indices) are clear and match the naming.src/core/data/ndarray/ndarray_vector.hpp (1)
19-71: NdArrayViewer-based indexing refactor looks correct and fixes prior width issueCentralizing the 1D/2D/3D flattening logic in
NdArrayViewerwithId = std::uint32_tplus theproduct(nCells, std::uint32_t{1})bound assert gives consistent, wider indexing acrossMaskedView,NdArrayView, andNdArrayVector. The C-order / non‑C-order formulas look correct, and delegating all operator() paths throughviewer::atremoves duplication without changing semantics.Also applies to: 98-107, 139-139, 288-304
src/diagnostic/diagnostic_writer.hpp (1)
6-6: Removing unusedcppdictinclude is a good cleanupThis header only depends on
DiagnosticProperties, so dropping the extra include reduces coupling without affecting the interface.src/core/data/grid/gridlayoutdefs.hpp (1)
5-8: Explicit HybridQuantity and<cstddef>includes are appropriateBringing in
core/hybrid/hybrid_quantities.hppwhereHybridQuantityis used, and<cstddef>for size types, makes this header more self-contained and avoids relying on transitive includes.src/core/data/grid/gridlayoutimplyee.hpp (1)
413-441: Yee moment/mapping helpers and new Bx/By/Bz→moments stencils look consistent.The switch to CTAD
std::array{...}and the new BxToMoments/ByToMoments/BzToMoments implementations give normalized weights and complete stencils in 2D/3D, aligned with the declared centerings. No issues spotted here.Also applies to: 446-507, 511-537, 541-569, 574-603, 609-723, 784-1165
src/hdf5/detail/h5/h5_file.hpp (1)
16-23: Chunked/resizable dataset helpers and existence checks look good.Configurable
CHUNK_SIZE,create_chunked_data_set, and the resizable 1D/2D helpers integrate cleanly withexist()/getDataSet(), and the parent-group creation mirrors prior patterns. The checkedgetDataSetimproves safety in production builds.Also applies to: 105-141, 275-287
src/diagnostic/diagnostic_model_view.hpp (1)
37-38: Tmp field/tensor plumbing and hierarchy helpers integrate cleanly.Using named tmp resources (
PHARE_sumField/Vec/Tensor) as shared scratch, wrapping the momentum‑tensor refine viafillPopMomTensor, and exposinglocalLevelBoxesplustmp*/getCompileTimeResourcesViewList()all align with the existing resource‑manager and AMR patterns. No issues spotted.Based on learnings
Also applies to: 62-81, 93-99, 145-172, 183-195, 218-221
src/core/data/grid/gridlayout.hpp (1)
5-14: New Bx/By/Bz→moments and AMR indexing helpers are consistent with existing grid logic.The Bx/By/BzToMoments accessors cleanly forward to the impl, and the AMRBoxFor/AMRGhostBoxFor +
amr_lcl_idx*helpers match the AMR/local box usage inconvert_to_fortran_primaland the VTKHDF writers. No correctness or performance issues noticed in the new pieces.Also applies to: 101-103, 821-845, 1027-1046, 1180-1195, 1220-1226
src/diagnostic/detail/vtkh5_writer.hpp (1)
31-77: VTK H5Writer lifecycle and file‑flag handling look correct.Construction,
make_unique, and thedump/dump_levellogic (especially resettingfile_flagstoREAD_WRITEafter the first write) align with the existing HDF5 writer semantics and avoid repeated truncation. No issues found.Also applies to: 79-88, 90-107, 118-125, 126-155, 159-174, 177-191
| #include "core/utilities/span.hpp" | ||
| #include "core/utilities/types.hpp" | ||
| #include "core/data/field/field.hpp" | ||
| #include "core/utilities/box/box.hpp" | ||
| #include "core/data/grid/gridlayoutdefs.hpp" | ||
| #include "core/data/ndarray/ndarray_vector.hpp" | ||
| #include "core/data/tensorfield/tensorfield.hpp" |
There was a problem hiding this comment.
🧩 Analysis chain
Add <stdexcept> for std::runtime_error instead of relying on transitive includes
This header throws std::runtime_error in convert_to_primal, but <stdexcept> is not explicitly included here. To avoid depending on transitive includes (and potential ODR/compile issues if upstream headers change), it’s better for this header to include <stdexcept> itself.
Suggested diff:
-#include <string>
-#include <algorithm>
+#include <string>
+#include <algorithm>
+#include <stdexcept>Please confirm this compiles cleanly across your TU set after adding the include.
Also applies to: 16-18
I'll help you verify this review comment. Let me examine the file and confirm the issues.
---
🏁 Script executed:
```shell
#!/bin/bash
# First, let's view the full algorithm.hpp file to see all includes and context
cat src/core/utilities/algorithm.hpp
Length of output: 4090
🏁 Script executed:
#!/bin/bash
# Search for convert_to_primal function and std::runtime_error usage
rg -n "convert_to_primal|std::runtime_error" src/core/utilities/algorithm.hpp -A5 -B2Length of output: 846
🏁 Script executed:
#!/bin/bash
# Check if stdexcept is already included anywhere in the file
rg -n "stdexcept" src/core/utilities/algorithm.hppLength of output: 0
Add <stdexcept> header to resolve missing include for std::runtime_error
The verification confirms the issue. Line 99 of src/core/utilities/algorithm.hpp throws std::runtime_error, but <stdexcept> is not explicitly included. The file currently relies on transitive includes from upstream headers (lines 7–13 show only project-specific includes; lines 16–17 show <string> and <algorithm>).
Add #include <stdexcept> after the existing standard library includes to satisfy the direct dependency:
#include <string>
#include <algorithm>
+#include <stdexcept>This ensures the header is self-contained and does not break if upstream dependencies change.
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In src/core/utilities/algorithm.hpp around lines 7 to 13, the header throws
std::runtime_error on line 99 but does not include <stdexcept>, relying on
transitive includes; add a direct include for <stdexcept> (place it alongside
the other standard library includes, e.g., after the existing <string> and
<algorithm> includes) so the header is self-contained and no longer depends on
upstream headers for std::runtime_error.
| #include <array> | ||
| #include <iomanip> | ||
| #include <optional> | ||
| #include <string> | ||
| #include <algorithm> | ||
| #include <cinttypes> | ||
| #include <cmath> | ||
| #include <numeric> | ||
| #include <tuple> | ||
| #include <string> | ||
| #include <vector> | ||
| #include <cassert> | ||
| #include <cstdint> | ||
| #include <iomanip> | ||
| #include <numeric> | ||
| #include <sstream> | ||
| #include <optional> | ||
| #include <algorithm> | ||
| #include <stdexcept> | ||
|
|
There was a problem hiding this comment.
Add <cstdlib> for std::getenv
get_env calls std::getenv, which is declared in <cstdlib>. It’s safer/standard-compliant to include it explicitly rather than relying on transitive includes.
#include <array>
#include <cmath>
#include <tuple>
#include <string>
#include <vector>
#include <cassert>
#include <cstdint>
#include <iomanip>
#include <numeric>
#include <sstream>
#include <optional>
#include <algorithm>
#include <stdexcept>
+ #include <cstdlib>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| #include <array> | |
| #include <iomanip> | |
| #include <optional> | |
| #include <string> | |
| #include <algorithm> | |
| #include <cinttypes> | |
| #include <cmath> | |
| #include <numeric> | |
| #include <tuple> | |
| #include <string> | |
| #include <vector> | |
| #include <cassert> | |
| #include <cstdint> | |
| #include <iomanip> | |
| #include <numeric> | |
| #include <sstream> | |
| #include <optional> | |
| #include <algorithm> | |
| #include <stdexcept> | |
| #include <array> | |
| #include <cmath> | |
| #include <tuple> | |
| #include <string> | |
| #include <vector> | |
| #include <cassert> | |
| #include <cstdint> | |
| #include <iomanip> | |
| #include <numeric> | |
| #include <sstream> | |
| #include <optional> | |
| #include <algorithm> | |
| #include <stdexcept> | |
| #include <cstdlib> |
🤖 Prompt for AI Agents
In src/core/utilities/types.hpp around lines 9 to 22, the header list is missing
the <cstdlib> include required for std::getenv; add #include <cstdlib> to the
include block so get_env uses the standard-declared getenv symbol (place it with
the other C++ standard headers near <cstdint> or similar).
|
in conjunction with #1100 we have the following renders 
and I can see some variation across timesteps, not much as it's only 3 timesteps worth of diags |
| dump_all_diags(setup_model().populations) | ||
| self.simulator = Simulator(simulation).run().reset() | ||
|
|
||
| # maybe use vtk python module to generate artifacts here |
There was a problem hiding this comment.
maybe we can have an issue on that
| dump_all_diags(setup_model().populations) | ||
| self.simulator = Simulator(simulation).run().reset() | ||
|
|
||
| # maybe use vtk python module to generate artifacts here |
There was a problem hiding this comment.
we could have an issue on that
| return dst; | ||
| } | ||
|
|
||
| template<typename Field_t, typename PQ, std::size_t rank> |
There was a problem hiding this comment.
if we have Field_t can't we use Field_t::physical_quantity_type for PQ?
| PhysicalQuantity const qty // | ||
| ) | ||
| { | ||
| using PQ = PhysicalQuantity; |
| for (std::uint8_t i = 0; i < dimension; ++i) | ||
| ghostBox.upper[i] += (centerings[i] == QtyCentering::primal) ? 1 : 0; | ||
| return ghostBox; | ||
| box.upper[i] += (centerings[i] == QtyCentering::primal) ? 1 : 0; |
There was a problem hiding this comment.
we also have this +1 code in toFieldBox() that takes a gridlayout, maybe this could be a toPrimal layout static method that the toFieldBox and this method use?
There was a problem hiding this comment.
I would argue it should be here, and update the toFieldBox to use this?
There was a problem hiding this comment.
if by "here" you mean a function in the layout I agree
| static_assert(sizeof...(Indexes) == dim); | ||
| // static_assert((... && std::is_unsigned_v<decltype(indexes)>)); TODO : manage later if | ||
| // this test should be included | ||
| using Id = std::uint32_t; |
There was a problem hiding this comment.
https://github.com/PhilipDeegan/PHARE/blob/vtk/src/core/data/ndarray/ndarray_vector.hpp#L23
it's less verbose than auto const x, ...
There was a problem hiding this comment.
I don't know why I did not see the usage of Idx before now it's obvious...
I don't know if I like "hiding" the const like that... on the other hand having function(Idx i) or function(Id const i) you still have to find out what the type means...
| auto ds = h5file.getDataSet(level_data_path(layout.levelNumber())); | ||
| for (std::uint16_t i = 0; i < X_TIMES; ++i) | ||
| { | ||
| ds.select({data_offset, 0}, {size, 1}).write_raw(frimal.data()); |
There was a problem hiding this comment.
unless you know exactly the highfive API, this is a bit obscure to understand
what {data_offset, 0}, {size, 1} are for instance ? maybe naming them would help ?
or what select does maybe a comment ?
There was a problem hiding this comment.
select is the location, and order/direction for the data to be written
https://github.com/highfive-devs/highfive/blob/main/src/examples/create_extensible_dataset.cpp#L38
There was a problem hiding this comment.
ok but it's still a bit hard to read if you do not know highfive.
a little comment explaining why the first and second arguments are what they are would be nice. In particular the 0 and 1.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Nitpick comments (9)
src/diagnostic/detail/vtkh5_type_writer.hpp (9)
24-24: Avoidusing namespacein a header to limit symbol pollution
using namespace hdf5::h5;inside a header pulls all HighFive symbols intoPHARE::diagnostic::vtkh5, which can make ADL/call-site resolution harder and increase risk of collisions for any includer that also opensPHARE::diagnostic::vtkh5. A narrower alias such as:using HighFiveFile = hdf5::h5::HighFiveFile;(or just fully qualifying the few used types) keeps dependencies explicit and local while staying minimal.
29-35: Tightenbaseusage to avoid//in HDF5 pathsWith
base = "/VTKHDF/", expressions likebase + "/Steps/Values"andbase + "/Steps"generate paths containing a double slash (e.g."/VTKHDF//Steps/Values"). HDF5 typically tolerates this, but it’s visually confusing and brittle if any path parsing code assumes normalized names.You can avoid this by either dropping the trailing slash in
baseor concatenating without a leading slash in the suffix:std::string static inline const base = "/VTKHDF"; // ... h5file.create_resizable_1d_data_set<FloatType>(base + "/Steps/Values");or
std::string static inline const base = "/VTKHDF/"; // ... h5file.create_resizable_1d_data_set<FloatType>(base + "Steps/Values");Also applies to: 176-183
29-30: Document why diagnostics are stored asfloatYou consistently downcast to
FloatType = floatfor datasets and attributes (steps, spacing, origin, tensor fields). Given your earlier note about ParaView’s VTKHDF reader not handling doubles, this is clearly intentional but non-obvious to someone skimming the file later, who might be tempted to “fix” it back todouble.A one‑line comment near
using FloatType = float;(e.g. “VTKHDF/ParaView reader currently expects single precision”) would make this constraint explicit without adding code complexity.Also applies to: 95-98, 176-183, 237-239
46-52: Clarify 1D/2D AMRBox layout vs 3DboxValsIn3Dwidth
AMRBoxis always created with widthboxValsIn3D = 6, but for lower dimensions you only writedimension * 2columns via:auto const vtk_boxes = flatten_boxes(boxes); // 2 * dimension entries amrbox_ds.select({box_offset, 0}, {boxes.size(), dimension * 2}).write(vtk_boxes);leaving the remaining coordinates to whatever fill value the dataset uses (likely zero).
If this relies on the VTKHDF reader interpreting missing trailing dimensions as collapsed (e.g. z=[0,0] in 2D/1D), it would be helpful to either:
- Explicitly write the remaining columns as zeros for all dims, or
- Add a brief comment stating that the unused coordinates are intentionally left to the dataset fill value and are interpreted as collapsed dimensions.
This makes the 1D/2D → 3D mapping more obvious and avoids surprises if default fill behavior ever changes.
Also applies to: 96-97, 259-263, 326-342
95-98: CheckSpacingattribute size for lower dimensions
Spacingis written as:auto const mesh_size = typewriter->h5Writer_.modelView().cellWidth(); return core::for_N_make_array<dimension>( [&](auto i) { return static_cast<float>(mesh_size[i] / std::pow(2, lvl)); }); ... level_group.template createAttribute<std::array<float, dimension>>("Spacing", level_spacing(ilvl));So in 1D/2D runs the attribute has 1 or 2 components, while other attributes (
Origin) are always 3‑component arrays.VTK’s OverlappingAMR examples typically use 3‑component spacing vectors. If the VTKHDF reader expects exactly 3 entries, we may want to always emit 3 components and pad the unused ones with 1.0 (or equivalent) for lower dimensions. If it already accepts dimension‑sized spacing arrays, then a short comment indicating that behavior would prevent future “normalization” attempts that could break compatibility.
Also applies to: 118-123, 265-269
118-123: ReusemodelViewmember instead of re-querying it
VTKFileWriteralready stores a reference toModelView:ModelView& modelView = typewriter->h5Writer_.modelView();but
level_spacingcalls back throughtypewriter->h5Writer_.modelView()again. For both clarity and to keep dependencies minimal, you could just use the existing member:auto const mesh_size = modelView.cellWidth();This keeps the data flow obvious and avoids re-traversing the stack of owners.
Also applies to: 154-160
125-128: Make therho-basedlocal_boxassumption explicit
local_box()uses:auto static constexpr primal_qty = physical_quantity_type::rho; auto local_box(auto const& layout) const { return layout.AMRToLocal(layout.AMRBoxFor(primal_qty)); }and its
size()is then used to size writes for all scalar and tensor fields, regardless of the actual quantity being written.This implies:
- All point-data diagnostics share the same AMR box as
rhoonce converted to primal centering, andconvert_to_fortran_primalfills exactly that local region.If that invariant ever stops holding (e.g. diagnostics with different staggering or layouts), offsets and dataset extents will silently mismatch. I’d suggest either:
- Adding a brief comment documenting that all fields are assumed to share
rho’s AMR topology after conversion, or- Deriving the box from the specific
layout/field being written if that’s straightforward.That keeps this coupling visible to future refactors.
Also applies to: 220-222, 237-241
282-306: Document MPIcollect+ prefix-sum assumption for offsetsBoth
resize_dataandresize_boxesuse the pattern:auto const rank_data_size = core::mpi::collect(...); // or collect(boxes.size()) auto const new_size = data_offset + core::sum(rank_data_size); point_data_ds.resize({new_size, N}); for (int i = 0; i < core::mpi::rank(); ++i) data_offset += rank_data_size[i];and similarly for
box_offset. This relies oncore::mpi::collectreturning, on every rank, a container indexed by global rank (i.e. an allgather), so that each rank can compute its own prefix sum to get a unique offset.If
collectwere ever changed to behave differently (e.g. gather to rank 0 only, or use a subcommunicator), this would break offsets in a non-obvious way. A short comment like “collectis assumed to be an allgather over MPI_COMM_WORLD; we then prefix-sum to get per-rank offsets” (or factoring this into a small helper) would make the assumption explicit and protect against future refactors of the MPI layer.Also applies to: 310-342
216-229: Double-check consistency betweenlocal_boxsize andconvert_to_fortran_primalBoth scalar and tensor writes compute:
auto const size = local_box(layout).size(); ... ds.select({data_offset, 0 or c}, {size, 1}).write_raw(frimal[?].data());where
frimalis produced viaconvert_to_fortran_primal(...)into a modelView-owned temporary. This assumes that:
- The temporary holds exactly
sizeprimal interior values (no ghosts), laid out contiguously in Fortran order, andlocal_box(layout)refers to that same interior region.Given the comment in
convert_to_fortran_primalabout not working on ghost boxes, this is probably correct, but any future change to the temporary’s extent or tolocal_boxwould silently desynchronize the HDF5 write. A brief comment stating thatsizeis the number of interior primal points in the converted buffer would help lock in this invariant.Also applies to: 232-248
📜 Review details
Configuration used: Path: .coderabbit.yaml
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (4)
src/diagnostic/detail/vtk_types/electromag.hpp(1 hunks)src/diagnostic/detail/vtk_types/fluid.hpp(1 hunks)src/diagnostic/detail/vtkh5_type_writer.hpp(1 hunks)src/hdf5/detail/h5/h5_file.hpp(3 hunks)
🚧 Files skipped from review as they are similar to previous changes (3)
- src/diagnostic/detail/vtk_types/electromag.hpp
- src/diagnostic/detail/vtk_types/fluid.hpp
- src/hdf5/detail/h5/h5_file.hpp
🧰 Additional context used
📓 Path-based instructions (1)
**/*.hpp
⚙️ CodeRabbit configuration file
Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
Files:
src/diagnostic/detail/vtkh5_type_writer.hpp
🧠 Learnings (2)
📓 Common learnings
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-07-26T22:04:34.160Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 784
File: tests/simulator/test_restarts.py:333-339
Timestamp: 2024-10-09T08:32:15.667Z
Learning: PhilipDeegan has indicated a preference for minimal and efficient code, even after making changes to get a function working. There may be opportunities to remove or optimize parts of the code such as sleep/wait/advances.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 1068
File: src/amr/data/field/coarsening/electric_field_coarsener.hpp:1-2
Timestamp: 2025-09-17T13:35:11.533Z
Learning: PhilipDeegan prefers header guard names that include the full directory path structure, following the pattern PHARE_[PATH_WITH_UNDERSCORES]_HPP. For example, a file at src/amr/data/field/coarsening/electric_field_coarsener.hpp should use PHARE_AMR_DATA_FIELD_COARSENING_ELECTRIC_FIELD_COARSENER_HPP as the header guard.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-10-09T08:32:15.667Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: src/hdf5/detail/h5/h5_file.hpp:78-79
Timestamp: 2024-09-05T17:02:58.784Z
Learning: Avoid commenting on draft PRs for the user PhilipDeegan.
📚 Learning: 2024-09-09T13:57:02.285Z
Learnt from: PhilipDeegan
Repo: PHAREHUB/PHARE PR: 888
File: pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py:566-568
Timestamp: 2024-09-09T13:57:02.285Z
Learning: Avoid commenting on draft PRs for PhilipDeegan unless explicitly requested.
Applied to files:
src/diagnostic/detail/vtkh5_type_writer.hpp
🧬 Code graph analysis (1)
src/diagnostic/detail/vtkh5_type_writer.hpp (5)
src/diagnostic/diagnostic_model_view.hpp (1)
dimension(30-60)src/core/utilities/box/box.hpp (5)
box(53-53)i(99-99)i(99-99)size(78-88)size(78-78)src/core/data/tensorfield/tensorfield.hpp (8)
i(181-181)i(181-181)i(182-182)i(182-182)size(208-208)size(208-208)tensor_field_dim_from_rank(17-24)tensor_field_dim_from_rank(17-17)src/core/utilities/types.hpp (2)
for_N_make_array(508-511)for_N_make_array(508-508)src/core/utilities/algorithm.hpp (4)
convert_to_fortran_primal(103-135)convert_to_fortran_primal(103-107)convert_to_fortran_primal(138-147)convert_to_fortran_primal(138-142)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (5)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: Analyze (cpp)
- GitHub Check: build (ubuntu-latest, clang)
🔇 Additional comments (1)
src/diagnostic/detail/vtkh5_type_writer.hpp (1)
165-193: ConfirmSteps/Values/NStepsupdates are safe under MPIThe constructor always does:
h5file.create_resizable_1d_data_set<FloatType>(base + "/Steps/Values"); auto steps_group = h5file.file().getGroup(base + "/Steps"); if (!steps_group.hasAttribute("NSteps")) { /* create & init 0 */ } auto steps_attr = steps_group.getAttribute("NSteps"); steps_attr.write(steps_attr.template read<int>() + 1); // ... auto ds = h5file.getDataSet(base + "/Steps/Values"); auto const old_size = ds.getDimensions()[0]; ds.resize({old_size + 1}); ds.select({old_size}, {1}).write(timestamp);If
VTKFileWriteris constructed on every MPI rank, this will:
- Increment
NStepsonce per rank, not once per logical timestep, and- Potentially resize and append to
Steps/Valuesconcurrently from multiple ranks.If only rank 0 ever constructs
VTKFileWriter, this is fine; otherwise, these operations probably need to be root‑only or explicitly collective (depending on howHighFiveFileis configured for parallel HDF5). It would be good to double‑check the calling pattern and, if appropriate, assert or comment that only a single writer instance per file/timestep exists.
|
|
||
| auto static flatten_boxes(auto const& boxes) | ||
| { | ||
| std::vector<std::array<int, dimension * 2>> data(boxes.size()); |
| using FileOp = HighFive::File::AccessMode; | ||
|
|
||
| // https://support.hdfgroup.org/documentation/hdf5/latest/hdf5_chunking.html | ||
| static inline auto const CHUNK_SIZE = core::get_env_as("PHARE_H5_CHUNK_SIZE", std::size_t{1024}); |
There was a problem hiding this comment.
I feel the comment should also say something about the default 1024 ?
is there a chance this will even fail in some cases, like 1D simulations with lots of small patches you will end up having chunks larger than datasets
There was a problem hiding this comment.
with lots of small patches
It's the aggregate of all patch datas, so I don't see how that's relevant
Write diagnostics in VTKHDF file format
tested via manual inspection in paraview
We should probably use the vtk module in a test and generate some artifacts