documentation update #1012
documentation update #1012
Conversation
📝 WalkthroughWalkthroughA new Markdown documentation file on Adaptive Mesh Refinement (AMR) was added, containing detailed explanations including the Toth and Roe divergence-preserving refinement method. Simultaneously, an existing reStructuredText documentation file covering the same AMR topics was removed. Additionally, a new Markdown file on spatial discretization was added, replacing a minimal reStructuredText file. No code or public API changes were made. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Doc_AMR_MD as AMR Markdown Doc
participant Doc_AMR_RST as AMR reST Doc
participant Doc_Spatial_MD as Spatial Discretization Markdown Doc
participant Doc_Spatial_RST as Spatial Discretization reST Doc
participant Doc_Toth2002_MD as Toth and Roe Method Doc
User->>Doc_AMR_MD: Add detailed AMR documentation (Markdown)
User->>Doc_AMR_RST: Remove old AMR documentation (reST)
User->>Doc_Spatial_MD: Add new spatial discretization doc (Markdown)
User->>Doc_Spatial_RST: Remove old spatial discretization doc (reST)
User->>Doc_Toth2002_MD: Add Toth and Roe refinement method doc (Markdown)
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Actionable comments posted: 1
🔭 Outside diff range comments (1)
doc/source/theory/amr.md (1)
1-32: 🛠️ Refactor suggestionPopulate section placeholders with content
This file currently only lists section titles. To provide value, each header should include an introduction, algorithm description, key equations or pseudocode, and references. Consider adding at least a brief summary under each heading before merging.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integrati...(BASED_HYPHEN)
🧹 Nitpick comments (1)
doc/source/theory/amr.md (1)
6-6: Standardize header style
The section headings use inconsistent capitalization, hyphenation, and pluralization. Please:
- Convert to Title Case (e.g.
## Patch-Based Approach,## Recursive Time Integration).- Hyphenate compound adjectives (
Patch-Based).- Align singular/plural forms (e.g. use
Particles at Level Boundariesto mirrorFields at Level Boundaries).Also applies to: 10-10, 13-13, 16-16, 20-20, 24-24, 28-28
🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integrati...(BASED_HYPHEN)
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🪛 LanguageTool
doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integrati...
(BASED_HYPHEN)
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🛠️ Refactor suggestion
Include the new Markdown file in the doc build
Ensure your Sphinx setup (conf.py) is configured to parse Markdown (e.g., via MyST or recommonmark) and update the parent toctree (likely in index.rst or an adjacent MD file) to reference theory/amr.md. Otherwise this content won’t appear in the rendered documentation.
🤖 Prompt for AI Agents
In doc/source/theory/amr.md at line 2, the new Markdown file is not included in
the Sphinx documentation build. To fix this, configure your Sphinx `conf.py` to
support Markdown parsing (using MyST or recommonmark) and update the parent
toctree, such as in `index.rst` or a nearby MD file, to add a reference to
`theory/amr.md` so it appears in the rendered docs.
There was a problem hiding this comment.
Actionable comments posted: 1
♻️ Duplicate comments (1)
doc/source/theory/amr.md (1)
2-2: Include new AMR doc in Sphinx toctree
Ensureconf.pysupports Markdown (MyST or recommonmark) and addtheory/amr.mdto the parenttoctreeso this content appears in the rendered docs.
🧹 Nitpick comments (8)
doc/source/theory/amr.md (6)
6-6: Hyphenate compound term
Change “Patch based approach” to “Patch-based approach” for consistency with technical writing standards.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
12-12: Correct section heading typo
Rename “## Regriding” to “## Regridding” to use the standard term.
18-21: Fix spelling mistakes in regridding description
Apply this diff to correct typos:- Regriding is the process of changing the geometry of an existing mesh level in the - AMR hierarchy, by changing the number and geometry of some patches of that level. + Regridding is the process of changing the geometry of an existing mesh level in the + AMR hierarchy by changing the number and geometry of some patches of that level. - Concretely, regriding means removing an entired level from the AMR hierachy and replacing - it by a new one. The so-called "new" leveel will be initialized by copying values - from the old level wherever they overlap, and by refininig values from coarser levels + Concretely, regridding means removing an entire level from the AMR hierarchy and replacing + it with a new one. The so-called "new" level will be initialized by copying values + from the old level wherever they overlap and by refining values from coarser levels
40-46: Improve grammar and hyphenation
- Change “risking to break” to “risking breaking” or “risk of breaking” for clarity.
- Hyphenate “coarse-fine boundaries” instead of “coarse fine boundaries.”
🧰 Tools
🪛 LanguageTool
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...(ADMIT_ENJOY_VB)
48-56: Review image usage and alt text
The same image (coarse_fine_boundary2.png) appears twice. Confirm if this duplication is intentional or replace the second instance with the correct figure or a clarifying caption.
74-74: Correct spelling in divergence context
Change “divergnce” to “divergence” in “preserve a zero divergnce of the magnetic field.”🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
doc/source/theory/toth2002.md (2)
1-2: Enhance document title for clarity
Consider updating the title to include the year and method context, e.g.:# Tóth and Roe (2002) Divergence-Preserving Refinement Method
30-30: Remove question mark in equation
The equation ends with a question mark (= \frac{D}{r^{3}} ?). Replace it with a statement (= \frac{D}{r^{3}}) or move the query into the surrounding text.
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🪛 LanguageTool
doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
doc/source/theory/toth2002.md
[duplication] ~6-~6: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^...
(WORD_REPEAT_RULE)
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^...
(WORD_REPEAT_RULE)
[duplication] ~8-~8: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...
(WORD_REPEAT_RULE)
[duplication] ~14-~14: Možný preklep: zopakovali ste slovo
Context: ...end{align} $$ with: $$ \begin{align} U_{x x} &= \frac{1}{8} \sum_{ijk=\pm } ijv^{i,...
(WORD_REPEAT_RULE)
[duplication] ~15-~15: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } ijv^{i,j,k} + ikw^{i,j,k}\ V_{y y} &= \frac{1}{8} \sum_{ijk=\pm } iju^{i,...
(WORD_REPEAT_RULE)
[duplication] ~16-~16: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } iju^{i,j,k} + jkw^{i,j,k}\ W_{z z} &= \frac{1}{8} \sum_{ijk=\pm } iku^{i,...
(WORD_REPEAT_RULE)
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🔇 Additional comments (1)
doc/source/theory/amr.md (1)
77-80: Verify cross-reference syntax
The syntax[[toth2002|Toth and Roe formulas]]may not be supported by all Markdown parsers. Consider using a standard MyST link or Sphinx role, for example:See [Toth and Roe formulas](toth2002.md)
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Actionable comments posted: 3
♻️ Duplicate comments (1)
doc/source/theory/amr.md (1)
1-1: Include the new AMR Markdown file in the Sphinx toctree
Ensure thatdoc/source/theory/amr.mdis referenced in the parenttoctree(e.g.,index.rstor an adjacent.md), and confirm that the Sphinxconf.pyis configured with MyST or recommonmark to parse Markdown files.
🧹 Nitpick comments (7)
doc/source/theory/amr.md (7)
6-6: Add hyphen to heading for consistency
Change "## Patch based approach" to "## Patch-based approach" to correctly use a hyphenated compound adjective.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
23-26: Add missing article and clarify text
Revise "depending on whether particle data is refined, or field is." to "depending on whether particle data is refined or the field is refined."🧰 Tools
🪛 LanguageTool
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...(AI_EN_LECTOR_MISSING_DETERMINER_THE)
40-42: Adjust phrasing for fluency
Replace "so to preserve a zero divergnce of the magnetic field" with "so as to preserve a zero divergence of the magnetic field".
44-47: Improve grammar and preposition use
Change "imposing its face value blindly to the other without risking to break the divergence-free condition" to:imposing its face value blindly on the other without risking breaking the divergence-free condition🧰 Tools
🪛 LanguageTool
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...(ADMIT_ENJOY_VB)
66-66: Fix subject–verb agreement
Update "if the refinement of the new blue components only consider values" to:if the refinement of the new blue components only considers values🧰 Tools
🪛 LanguageTool
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
71-71: Clarify spatial relation and punctuation
Revise "cells just left to the former boundary" to "cells just to the left of the former boundary", and add a comma before "since" for readability.🧰 Tools
🪛 LanguageTool
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...(AI_HYDRA_LEO_MISSING_COMMA)
74-74: Correct typo in "divergence" and add missing hyphens
Change "preserve a zero divergnce of the magnetic field at the coarse fine boundary is to ensure" to:preserve a zero divergence of the magnetic field at the coarse-fine boundary is to ensure🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
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✅ Files skipped from review due to trivial changes (1)
- doc/source/conf.py
🧰 Additional context used
🪛 LanguageTool
doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
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🔇 Additional comments (1)
doc/source/theory/amr.md (1)
92-98: Check MyST admonition syntax
Verify that the:::{seealso}directive is recognized by your MyST configuration. If not, consider using the fenced directive syntax:```{seealso} Toth and Roe 2002 Divergence- and Curl-Preserving Prolongation and Restriction Formulas Volume 180, Issue 2, 10 August 2002, Pages 736-750 https://doi.org/10.1006/jcph.2002.7120</details> </blockquote></details> </details> <!-- This is an auto-generated comment by CodeRabbit for review status -->
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Actionable comments posted: 4
♻️ Duplicate comments (3)
doc/source/theory/amr.md (3)
2-2: Include new Markdown in Sphinx toctree
Ensuredoc/source/theory/amr.mdis added to your Sphinx toctree (e.g., inindex.rst) and that the MyST parser is enabled inconf.py, so this document is rendered.
77-77:⚠️ Potential issueFix broken hyperlink reference
Update the link to match the actual filename:- (see [Toth and Roe formulas](toth2022)) + (see [Toth and Roe formulas](toth2002))
14-21:⚠️ Potential issueFix multiple typos in regridding section
Correct the following typos to improve clarity:
- "entired" → "entire"
- "hierachy" → "hierarchy"
- "leveel" → "level"
- "refininig" → "refining"
Example diff:
- Concretely, regriding means removing an entired level from the AMR hierachy and replacing + Concretely, regridding means removing an entire level from the AMR hierarchy and replacing it by a new one. The so-called "new" leveel will be initialized by copying values - from the old level wherever they overlap, and by refininig values from coarser levels + from the old level wherever they overlap, and by refining values from coarser levels where they do not.
🧹 Nitpick comments (14)
doc/source/theory/amr.md (14)
6-6: Hyphenate compound adjective
"Patch based" should be "Patch-based" to correctly hyphenate the compound adjective.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
29-29: Use title case for section heading
Capitalize key words for consistency:- ## Field refinement + ## Field Refinement
31-31: Use title case for subsection heading
Use consistent title casing for headings:- ### divergence-free magnetic refinement + ### Divergence-Free Magnetic Refinement
45-46: Improve phrasing for clarity
Consider rephrasing to:- We cannot have one mesh imposing its face value blindly to the other without risking to break the divergence-free condition. + We cannot have one mesh blindly impose its face value on the other without risking the divergence-free condition.🧰 Tools
🪛 LanguageTool
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition.  + 
56-56: Improve image alt text
Provide a more descriptive alt text:-  + 
66-67: Fix subject-verb agreement
Change "only consider values" to "only considers values":- In the first case, if the refinement of the new blue components only consider values + In the first case, if the refinement of the new blue components only considers values🧰 Tools
🪛 LanguageTool
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
71-71: Clarify spatial relation
Revise for grammar and clarity:- will create a non-zero divergence in cells just left to the former boundary since + will create a non-zero divergence in cells just to the left of the former boundary, since🧰 Tools
🪛 LanguageTool
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...(AI_HYDRA_LEO_MISSING_COMMA)
75-75: Clarify redundancy
Remove the repeated word "flux":- ensure that newly refined faces account for the flux at fine fluxes at the coarse-fine boundary + ensure that newly refined faces account for the fine fluxes at the coarse-fine boundary
90-90: Align alt text with image file
Update the alt text to match the PNG filename:-  + 
101-101: Use title case for section heading- ## Particle refinement + ## Particle Refinement
105-105: Use title case for section heading- ## Field coarsening + ## Field Coarsening
109-109: Use title case for section heading- ## Fields at level boundaries + ## Fields at Level Boundaries
113-113: Use title case for section heading- ## Particle at level boundaries + ## Particle at Level Boundaries
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doc/source/theory/amr.md(1 hunks)
🧰 Additional context used
🪛 LanguageTool
doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
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🔇 Additional comments (1)
doc/source/theory/amr.md (1)
9-9: The heading "## Recursive time integration" is clear and well-formed.
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Actionable comments posted: 2
♻️ Duplicate comments (1)
doc/source/theory/amr.md (1)
2-2: Ensure inclusion in Sphinx toctree
This new Markdown file won’t appear in the built docs unless it’s referenced in your Sphinxtoctree(e.g., inindex.rst) and yourconf.pyis configured to parse MD (MyST or recommonmark).
🧹 Nitpick comments (7)
doc/source/theory/amr.md (7)
6-6: Use hyphen in heading
Change "Patch based approach" to "Patch-based approach" for correct compound adjective spelling.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
9-9: Use hyphen in heading
Change "Recursive time integration" to "Recursive time-integration" to maintain consistency with compound modifier style.
12-12: Fix typo in heading
Correct the heading from "## Regriding " to "## Regridding".
18-21: Correct multiple typos
- "entired" → "entire"
- "hierachy" → "hierarchy"
- "leveel" → "level"
- "refininig" → "refining"
23-24: Add missing article
Update "or field is" to "or the field is" for grammatical completeness.🧰 Tools
🪛 LanguageTool
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...(AI_EN_LECTOR_MISSING_DETERMINER_THE)
46-46: Adjust preposition for clarity
Change "imposing its face value blindly to the other" to "imposing its face value blindly on the other".🧰 Tools
🪛 LanguageTool
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...(ADMIT_ENJOY_VB)
74-74: Fix typo and hyphenation
Change "divergnce" to "divergence" and "coarse fine" to "coarse-fine".🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
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doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
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doc/source/theory/amr.md (1)
1-3: Include the new Markdown file in the Sphinx docs
Ensure that your Sphinxconf.pyis configured to support Markdown parsing (e.g., via MyST or recommonmark) and that the parent toctree (such as inindex.rst) includestheory/amr.mdso this content appears in the rendered documentation.
🧹 Nitpick comments (8)
doc/source/theory/amr.md (8)
6-6: Add hyphen for compound adjective
The heading "Patch based approach" should be "Patch-based approach" to improve readability.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
12-12: Fix heading typo
Change "## Regriding" to "## Regridding" (correct the spelling and remove trailing space).
14-21: Correct typos in regridding description
Replace "entired" → "entire", "hierachy" → "hierarchy", "leveel" → "level", and "refininig" → "refining" within this paragraph.
23-24: Add missing article and fix spelling
Replace "regriding" with "regridding" and change "or field is" to "or the field is" for grammatical correctness.🧰 Tools
🪛 LanguageTool
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...(AI_EN_LECTOR_MISSING_DETERMINER_THE)
46-46: Use proper preposition
Consider revising "imposing its face value blindly to the other" to "imposing its face value blindly on the other" for idiomatic phrasing.🧰 Tools
🪛 LanguageTool
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...(ADMIT_ENJOY_VB)
66-66: Ensure subject-verb agreement
Change "refinement of the new blue components only consider" to "refinement of the new blue components only considers" to match singular subject.🧰 Tools
🪛 LanguageTool
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
74-74: Fix typo and hyphenation
Correct "divergnce" → "divergence" and hyphenate "coarse fine" → "coarse-fine".🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
92-97: Correct MyST admon syntax
Use::: seealsoto open the admonition instead of:::{seealso}, and close with:::for proper MyST formatting.
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doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
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♻️ Duplicate comments (5)
doc/source/theory/amr.md (5)
1-3: Include in Sphinx toctree
Ensure this Markdown file is referenced in the parent toctree (e.g., inindex.rstor a nearby MD) and verify that MyST or a similar parser is enabled inconf.pyso the content is rendered.
92-92: 🛠️ Refactor suggestionUse correct MyST admon syntax
Change the opening seealso block to::: seealsoinstead of:::{seealso}.Apply this diff:
-:::{seealso} +::: seealso
23-24: 🛠️ Refactor suggestionCorrect spelling and add missing article
Fix "regriding" → "regridding" and add "the" before "field" for clarity.Apply this diff:
-Technically, regriding involves different methods depending on whether particle data -is refined, or field is. The specific operation performed also depends on the type +Technically, regridding involves different methods depending on whether particle data +is refined, or the field is. The specific operation performed also depends on the type🧰 Tools
🪛 LanguageTool
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...(AI_EN_LECTOR_MISSING_DETERMINER_THE)
74-74: 🛠️ Refactor suggestionFix typo and hyphenation
Correct "divergnce" → "divergence" and hyphenate "coarse-fine".Apply this diff:
-The only way to preserve a zero divergnce of the magnetic field at the coarse fine boundary +The only way to preserve a zero divergence of the magnetic field at the coarse-fine boundary🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
18-21: 🛠️ Refactor suggestionCorrect typos in 'Regridding' description
Several words are misspelled.Apply this diff:
-Concretely, regriding means removing an entired level from the AMR hierachy and replacing -it by a new one. The so-called "new" leveel will be initialized by copying values -from the old level wherever they overlap, and by refininig values from coarser levels +Concretely, regridding means removing an entire level from the AMR hierarchy and replacing +it with a new one. The so-called "new" level will be initialized by copying values +from the old level wherever they overlap, and by refining values from coarser levels
🧹 Nitpick comments (3)
doc/source/theory/amr.md (3)
6-6: Hyphenate 'Patch-based approach'
Use a hyphen for the compound adjective.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
41-42: Fix spelling: 'regridding'
Correct the typo in this sentence.Apply this diff:
-Refining the magnetic field so to preserve its divergence-free character is easy in general but becomes tricky when done at the coarse-fine boundaries -during regriding. +Refining the magnetic field to preserve its divergence-free character is generally straightforward, but becomes tricky when done at the coarse-fine boundaries +during regridding.
75-75: Clarify wording
The phrase "flux at fine fluxes" is redundant. Consider simplifying to "account for the fine fluxes".
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doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~24-~24: You might be missing the article “the” here.
Context: ...on whether particle data is refined, or field is. The specific operation performed al...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
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♻️ Duplicate comments (1)
doc/source/theory/toth2002.md (1)
7-7:⚠️ Potential issueCritical: Incorrect variable in w-component formula
The averaging term forw^{i,j,0}mistakenly usesv^{i,j,±}. It should reference the w components.
Apply this diff:- w^{i,j,0}&=\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^2 V_{xyz} + w^{i,j,0}&=\frac{1}{2}(w^{i,j,+} + w^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^2 V_{xyz}🧰 Tools
🪛 LanguageTool
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...(WORD_REPEAT_RULE)
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[duplication] ~5-~5: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^...
(WORD_REPEAT_RULE)
[duplication] ~6-~6: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^...
(WORD_REPEAT_RULE)
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...
(WORD_REPEAT_RULE)
[duplication] ~13-~13: Možný preklep: zopakovali ste slovo
Context: ...z} \end{align} with: \begin{align} U_{x x} &= \frac{1}{8} \sum_{ijk=\pm } ijv^{i,...
(WORD_REPEAT_RULE)
[duplication] ~14-~14: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } ijv^{i,j,k} + ikw^{i,j,k}\ V_{y y} &= \frac{1}{8} \sum_{ijk=\pm } iju^{i,...
(WORD_REPEAT_RULE)
[duplication] ~15-~15: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } iju^{i,j,k} + jkw^{i,j,k}\ W_{z z} &= \frac{1}{8} \sum_{ijk=\pm } iku^{i,...
(WORD_REPEAT_RULE)
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♻️ Duplicate comments (2)
doc/source/theory/toth2002.md (2)
12-16: Wrap secondary and tertiary align blocks in math delimiters
Both the refinement terms (U_{x x},V_{y y},W_{z z}) and the mixed derivatives (U_{xyz},V_{xyz},W_{xyz}) are defined in separatealignenvironments that need enclosing$$for correct Markdown rendering.+$$ \begin{align} U_{x x} &= \dots \\ V_{y y} &= \dots \\ W_{z z} &= \dots \end{align} +$$ +$$ \begin{align} U_{xyz}&=\dots \\ V_{xyz}&=\dots \\ W_{xyz}&=\dots \end{align} +$$Also applies to: 20-24
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[duplication] ~13-~13: Možný preklep: zopakovali ste slovo
Context: ...z} \end{align} with: \begin{align} U_{x x} &= \frac{1}{8} \sum_{ijk=\pm } ijv^{i,...(WORD_REPEAT_RULE)
[duplication] ~14-~14: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } ijv^{i,j,k} + ikw^{i,j,k}\ V_{y y} &= \frac{1}{8} \sum_{ijk=\pm } iju^{i,...(WORD_REPEAT_RULE)
[duplication] ~15-~15: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } iju^{i,j,k} + jkw^{i,j,k}\ W_{z z} &= \frac{1}{8} \sum_{ijk=\pm } iku^{i,...(WORD_REPEAT_RULE)
4-8:⚠️ Potential issueFix w-component formula and wrap align in math delimiters
The third equation mistakenly averages the v-components instead of the w-components, and thealignblock isn’t wrapped in$$.Apply this diff:
+$$ \begin{align} - u^{0,j,k}&=\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^2 W_{xyz} \\ - v^{i,0,k}&=\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^2 U_{xyz}\\ - w^{i,j,0}&=\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^2 V_{xyz} + u^{0,j,k}&=\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^2 W_{xyz} \\ + v^{i,0,k}&=\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^2 U_{xyz}\\ + w^{i,j,0}&=\frac{1}{2}(w^{i,j,+} + w^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^2 V_{xyz} \end{align} +$$🧰 Tools
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[duplication] ~5-~5: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^...(WORD_REPEAT_RULE)
[duplication] ~6-~6: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^...(WORD_REPEAT_RULE)
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...(WORD_REPEAT_RULE)
🧹 Nitpick comments (2)
doc/source/theory/toth2002.md (2)
28-31: Clarify the divergence verification equation
The inline equation ends with a?, which may be unintended or denote a placeholder. Remove the?or add explanatory text to clarify its purpose.
34-53: Enclose all subsequentalignenvironments in math delimiters
Throughout the divergence verification section, multiplealignblocks (lines 34–53, 57–76, 81–95, 100–103, 108–111, 115–119) are unwrapped. Wrap each in$$to ensure proper LaTeX rendering in Markdown.Also applies to: 57-76, 81-95, 100-103, 108-111, 115-119
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doc/source/theory/toth2002.md
[duplication] ~5-~5: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^...
(WORD_REPEAT_RULE)
[duplication] ~6-~6: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^...
(WORD_REPEAT_RULE)
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + v^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...
(WORD_REPEAT_RULE)
[duplication] ~13-~13: Možný preklep: zopakovali ste slovo
Context: ...z} \end{align} with: \begin{align} U_{x x} &= \frac{1}{8} \sum_{ijk=\pm } ijv^{i,...
(WORD_REPEAT_RULE)
[duplication] ~14-~14: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } ijv^{i,j,k} + ikw^{i,j,k}\ V_{y y} &= \frac{1}{8} \sum_{ijk=\pm } iju^{i,...
(WORD_REPEAT_RULE)
[duplication] ~15-~15: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } iju^{i,j,k} + jkw^{i,j,k}\ W_{z z} &= \frac{1}{8} \sum_{ijk=\pm } iku^{i,...
(WORD_REPEAT_RULE)
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🔇 Additional comments (1)
doc/source/theory/toth2002.md (1)
1-2: Heading is clear
The document title succinctly describes the content.
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Actionable comments posted: 8
♻️ Duplicate comments (4)
doc/source/theory/amr.md (2)
2-2: Includeamr.mdin the Sphinx toctree
Ensuredoc/source/index.rst(or the appropriate parent) referencestheory/amr.mdand confirm that MyST or recommonmark is enabled inconf.pyso this document appears in the rendered output.
92-97: Fix MyST admonition syntax
Use the correct MyST syntax for a seealso admonition:::: seealso Toth and Roe 2002 Divergence- and Curl-Preserving Prolongation and Restriction Formulas … :::instead of the current
::: {seealso}notation.doc/source/theory/toth2002.md (2)
4-8: 🛠️ Refactor suggestionEnclose primary align block in math delimiters
Wrap the\begin{align}…\end{align}block with$$to ensure it renders properly:+ $$ \begin{align} u^{0,j,k}&=… \\ v^{i,0,k}&=… \\ w^{i,j,0}&=… \end{align} + $$🧰 Tools
🪛 LanguageTool
[duplication] ~5-~5: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^...(WORD_REPEAT_RULE)
[duplication] ~6-~6: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^...(WORD_REPEAT_RULE)
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + w^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...(WORD_REPEAT_RULE)
12-17: 🛠️ Refactor suggestionWrap secondary align block with math delimiters
Enclose the equations at lines 12–16 in$$and remove any stray$$to render correctly:+ $$ \begin{align} U_{xx} &= … \\ V_{yy} &= … \\ W_{zz} &= … \end{align} + $$🧰 Tools
🪛 LanguageTool
[duplication] ~13-~13: Možný preklep: zopakovali ste slovo
Context: ...z} \end{align} with: \begin{align} U_{x x} &= \frac{1}{8} \sum_{ijk=\pm } ijv^{i,...(WORD_REPEAT_RULE)
[duplication] ~14-~14: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } ijv^{i,j,k} + ikw^{i,j,k}\ V_{y y} &= \frac{1}{8} \sum_{ijk=\pm } iju^{i,...(WORD_REPEAT_RULE)
[duplication] ~15-~15: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } iju^{i,j,k} + jkw^{i,j,k}\ W_{z z} &= \frac{1}{8} \sum_{ijk=\pm } iku^{i,...(WORD_REPEAT_RULE)
🧹 Nitpick comments (8)
doc/source/theory/amr.md (8)
6-6: Hyphenate 'Patch based approach'
Change the heading to “## Patch-based approach” for correct hyphenation.🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
12-12: Capitalize and trim heading 'regridding'
Update the heading to “## Regridding” (capital R, no trailing space) for consistency.
14-15: Capitalize sentence and remove comma
Start with “Regridding is the process…” and remove the comma after “hierarchy”:Regridding is the process of changing the geometry of an existing mesh level in the AMR hierarchy by changing the number and geometry of some patches of that level.
48-48: Add descriptive alt text for image
Provide meaningful alt text instead of “coarse_fine_boundary” to improve accessibility.
56-56: Add descriptive alt text for image
Enhance accessibility by giving “coarse_fine_boundary2.png” a concise, descriptive alt string.
74-74: Hyphenate 'coarse fine boundary'
Use “coarse-fine boundary” to maintain consistent hyphenation.🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
77-77: Explicitly include file extension in link
Consider using[Toth and Roe formulas](toth2002.md)so the link matches the actual Markdown filename.
90-90: Add descriptive alt text for image
Provide a clear alt description for “tothandroe2002.png” (e.g., “Toth & Roe interpolation schematic”).
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doc/source/theory/coarse_fine_boundary.pngis excluded by!**/*.pngdoc/source/theory/coarse_fine_boundary2.pngis excluded by!**/*.pngdoc/source/theory/tothDivVerif.pngis excluded by!**/*.pngdoc/source/theory/tothandroe2002.pngis excluded by!**/*.png
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.gitignore(0 hunks)doc/source/conf.py(1 hunks)doc/source/index.rst(1 hunks)doc/source/theory/amr.md(1 hunks)doc/source/theory/amr.rst(0 hunks)doc/source/theory/spatial_discretization.md(1 hunks)doc/source/theory/spatial_discretization.rst(0 hunks)doc/source/theory/toth2002.md(1 hunks)
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✅ Files skipped from review due to trivial changes (1)
- doc/source/index.rst
🚧 Files skipped from review as they are similar to previous changes (2)
- doc/source/theory/spatial_discretization.md
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🧰 Additional context used
🪛 LanguageTool
doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~117-~117: Possible missing preposition found.
Context: ...ypes of fields: - the electric field - the ion total density and bulk velocity #...
(AI_HYDRA_LEO_MISSING_OF)
doc/source/theory/toth2002.md
[duplication] ~5-~5: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^...
(WORD_REPEAT_RULE)
[duplication] ~6-~6: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^...
(WORD_REPEAT_RULE)
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + w^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...
(WORD_REPEAT_RULE)
[duplication] ~13-~13: Možný preklep: zopakovali ste slovo
Context: ...z} \end{align} with: \begin{align} U_{x x} &= \frac{1}{8} \sum_{ijk=\pm } ijv^{i,...
(WORD_REPEAT_RULE)
[duplication] ~14-~14: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } ijv^{i,j,k} + ikw^{i,j,k}\ V_{y y} &= \frac{1}{8} \sum_{ijk=\pm } iju^{i,...
(WORD_REPEAT_RULE)
[duplication] ~15-~15: Možný preklep: zopakovali ste slovo
Context: ...jk=\pm } iju^{i,j,k} + jkw^{i,j,k}\ W_{z z} &= \frac{1}{8} \sum_{ijk=\pm } iku^{i,...
(WORD_REPEAT_RULE)
⏰ Context from checks skipped due to timeout of 90000ms (7)
- GitHub Check: build (macos-14)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-13)
- GitHub Check: build (ubuntu-latest, gcc)
- GitHub Check: build (ubuntu-latest, clang)
- GitHub Check: Analyze (python)
- GitHub Check: Analyze (cpp)
| \begin{align} | ||
| &2(bx^{+++}+bx^{+ --} - bx^{- ++} - bx^{---} \\ | ||
| &+ by^{- ++}+by^{++ -} - by^{-- +} - by^{+ --} \\ | ||
| &+ bz^{- ++} + bz^{+ - +} - bz^{- + -} - bz^{+ --}) | ||
| \end{align} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Wrap first/second order align block with $$
Ensure the \begin{align} block is enclosed in $$ to display as math.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 101 to 105, the LaTeX align
environment is not enclosed within double dollar signs, which is required to
properly display the block as math. Wrap the entire \begin{align} ...
\end{align} block with $$ at the start and end to ensure correct math rendering.
| \begin{align} | ||
| &4bx^{+++}-4bx^{- ++}+by^{+++}+bz^{+++}-by^{-++}-bz^{-++}-by^{+-+}+bz^{+-+}+by^{++-}-bz^{++-} \\ | ||
| &-by^{+--}-bz^{+--}-by^{-+-}+bz^{-+-}+by^{--+}-bz^{--+}+by^{---}+bz^{---} \\ | ||
| &4by^{-++}-4by^{- -+}-bx^{+++}-bz^{+++}+bx^{-++}-bz^{-++}+bx^{+-+}+bz^{+-+}-bx^{++-}+bz^{++-}\\ | ||
| &+bx^{+--}-bz^{+--}+bx^{-+-}+bz^{-+-}-bx^{--+}+bz^{--+}-bx^{---}-bz^{---} \\ | ||
| &4bz^{-++}-4bz^{- +-}-bx^{+++}-by^{+++}+bx^{-++}-by^{-++}-bx^{+-+}+by^{+-+}+bx^{++-}+by^{++-}\\ | ||
| &+bx^{+--}-by^{+--}-bx^{-+-}+by^{-+-}+bx^{--+}+by^{--+}-bx^{---}-by^{---} \\ \\ \\ | ||
|
|
||
| &+\frac{ \Delta z^2}{(\Delta x)^2 + (\Delta z)^2}(by^{+++}-by^{- ++} - by^{+ - +} - by^{++ -}+ by^{+ --} + by^{- + -} + by^{-- +} - by^{---}) \\ | ||
| &+ \frac{\Delta y^2}{\Delta x^2 + \Delta y^2}(bz^{+++}-bz^{- ++} - bz^{+ - +} - bz^{++ -} + bz^{+ --} + bz^{- + -} + bz^{-- +} - bz^{---}) \\ \\ | ||
| &+ \frac{ \Delta x^2}{(\Delta x)^2 + (\Delta y)^2}(bz^{+++}-bz^{- ++} - bz^{+ - +} - bz^{++ -} + bz^{+ --} + bz^{- + -} + bz^{-- +} - bz^{---}) \\ | ||
| &- \frac{\Delta z^2}{\Delta y^2 + \Delta z^2}(bx^{+++}-bx^{- ++} - bx^{+ - +} - bx^{++ -} + bx^{+ --} + bx^{- + -} + bx^{-- +} - bx^{---}) \\ | ||
| &-\frac{ \Delta y^2}{(\Delta y)^2 + (\Delta z)^2}(bx^{+++}-bx^{- ++} - bx^{+ - +} - bx^{++ -} + bx^{+ --} + bx^{- + -} + bx^{-- +} - bx^{---}) \\ | ||
| &+ \frac{\Delta x^2}{\Delta x^2 + \Delta z^2}(by^{+++}-by^{- ++} - by^{+ - +} - by^{++ -} + by^{+ --} + by^{- + -} + by^{-- +} - by^{---}) | ||
| \end{align} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Enclose multiplication result block in math delimiters
Add $$ before and after lines 83–97 to render this LaTeX section correctly.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 83 to 97, the LaTeX block
containing the multiplication results is not enclosed in math delimiters,
causing rendering issues. Add double dollar signs ($$) before line 83 and after
line 97 to properly delimit the entire LaTeX block for correct rendering.
| \begin{align} | ||
| bx^{0++}-bx^{- ++}&=\frac{1}{2}(bx^{+++}-bx^{- ++})+\frac{1}{8}(by^{+++}+bz^{+++}-by^{-++}-bz^{-++}-by^{+-+}+bz^{+-+}+by^{++-}-bz^{++-}\\ | ||
| &-by^{+--}-bz^{+--}-by^{-+-}+bz^{-+-}+by^{--+}-bz^{--+}+by^{---}+bz^{---}) \\ | ||
| &+\frac{1}{8} \frac{ \Delta z^2}{(\Delta x)^2 + (\Delta z)^2}(by^{+++}-by^{- ++} - by^{+ - +} - by^{++ -} \\ | ||
| &+ by^{+ --} + by^{- + -} + by^{-- +} - by^{---}) \\ | ||
| &+ \frac{1}{8} \frac{\Delta y^2}{\Delta x^2 + \Delta y^2}(bz^{+++}-bz^{- ++} - bz^{+ - +} - bz^{++ -} \\ | ||
| &+ bz^{+ --} + bz^{- + -} + bz^{-- +} - bz^{---}) \\ | ||
| by^{- ++} - by^{-0+}&=\frac{1}{2}(by^{-++}-by^{- -+})-\frac{1}{8}(bx^{+++}+bz^{+++}-bx^{-++}+bz^{-++}-bx^{+-+}-bz^{+-+}+bx^{++-}-bz^{++-}\\ | ||
| &-bx^{+--}+bz^{+--}-bx^{-+-}-bz^{-+-}+bx^{--+}-bz^{--+}+bx^{---}+bz^{---}) \\ | ||
| &+\frac{1}{8} \frac{ \Delta x^2}{(\Delta x)^2 + (\Delta y)^2}(bz^{+++}-bz^{- ++} - bz^{+ - +} - bz^{++ -} \\ | ||
| &+ bz^{+ --} + bz^{- + -} + bz^{-- +} - bz^{---}) \\ | ||
| &- \frac{1}{8} \frac{\Delta z^2}{\Delta y^2 + \Delta z^2}(bx^{+++}-bx^{- ++} - bx^{+ - +} - bx^{++ -} \\ | ||
| &+ bx^{+ --} + bx^{- + -} + bx^{-- +} - bx^{---})\\ | ||
| bz^{- ++}-bz^{- +0}&=\frac{1}{2}(bz^{-++}-bz^{- +-})-\frac{1}{8}(bx^{+++}+by^{+++}-bx^{-++}+by^{-++}+bx^{+-+}-by^{+-+}-bx^{++-}-by^{++-}\\ | ||
| &-bx^{+--}+by^{+--}+bx^{-+-}-by^{-+-}-bx^{--+}-by^{--+}+bx^{---}+by^{---}) \\ | ||
| &-\frac{1}{8} \frac{ \Delta y^2}{(\Delta y)^2 + (\Delta z)^2}(bx^{+++}-bx^{- ++} - bx^{+ - +} - bx^{++ -} \\ | ||
| &+ bx^{+ --} + bx^{- + -} + bx^{-- +} - bx^{---}) \\ | ||
| &+ \frac{1}{8} \frac{\Delta x^2}{\Delta x^2 + \Delta z^2}(by^{+++}-by^{- ++} - by^{+ - +} - by^{++ -} \\ | ||
| &+ by^{+ --} + by^{- + -} + by^{-- +} - by^{---}) | ||
| \end{align} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Wrap 'differences' align block in math delimiters
Surround the multi-line \begin{align}…\end{align} section with $$ for proper formatting.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 59 to 78, the multi-line LaTeX
align environment is not wrapped in math delimiters, which can cause formatting
issues. Fix this by enclosing the entire \begin{align}...\end{align} block
within double dollar signs ($$) to ensure it is properly rendered as a displayed
math block.
| \begin{align} | ||
| &by^{+++} - by^{- ++} - by^{+ - +} - by^{++ -} + by^{+ --} + by^{- + -} + by^{-- +} - by^{---} \\ | ||
| +&bz^{+++} - bz^{- ++} - bz^{+ - +} - bz^{++ -} + bz^{+ --} + bz^{- + -} + bz^{-- +} - bz^{---} \\ | ||
| -&bx^{+++} + bx^{- ++} + bx^{+ - +} + bx^{++ -} - bx^{+ --} - bx^{- + -} - bx^{-- +} + bx^{---} | ||
| \end{align} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Wrap third order align block with math delimiters
Add $$ around the equations at lines 109–113 for proper Markdown rendering.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 109 to 113, the third order align
block is missing math delimiters, causing improper Markdown rendering. Wrap the
entire align environment with double dollar signs ($$) before line 109 and after
line 113 to ensure it is correctly recognized and rendered as a math block.
| \begin{align} | ||
| bx^{0++}&=\frac{1}{2}(bx^{+++}+bx^{- ++})+\frac{1}{8}(by^{+++}+bz^{+++}-by^{-++}-bz^{-++}-by^{+-+}+bz^{+-+}+by^{++-}-bz^{++-}\\ | ||
| &-by^{+--}-bz^{+--}-by^{-+-}+bz^{-+-}+by^{--+}-bz^{--+}+by^{---}+bz^{---}) \\ | ||
| &+\frac{1}{8} \frac{ \Delta z^2}{(\Delta x)^2 + (\Delta z)^2}(by^{+++}-by^{- ++} - by^{+ - +} - by^{++ -} \\ | ||
| &+ by^{+ --} + by^{- + -} + by^{-- +} - by^{---}) \\ | ||
| &+ \frac{1}{8} \frac{\Delta y^2}{\Delta x^2 + \Delta y^2}(bz^{+++}-bz^{- ++} - bz^{+ - +} - bz^{++ -} \\ | ||
| &+ bz^{+ --} + bz^{- + -} + bz^{-- +} - bz^{---}) \\ | ||
| by^{-0+}&=\frac{1}{2}(by^{-++}+by^{- -+})+\frac{1}{8}(bx^{+++}+bz^{+++}-bx^{-++}+bz^{-++}-bx^{+-+}-bz^{+-+}+bx^{++-}-bz^{++-}\\ |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Enclose divergence verification equations in $$
The \begin{align} block under “Divergence verification” needs $$ wrappers to render as math.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 36 to 43, the LaTeX align
environment for divergence verification equations is missing enclosing `$$`
delimiters, which are required for proper math rendering. Add `$$` before the
`\begin{align}` and after the `\end{align}` to ensure the entire block is
correctly recognized and rendered as a math environment.
| \begin{align} | ||
| U_{xyz}&=\frac{1}{8}\sum_{ijk=\pm} \frac{ijku^{i,j,k}}{(\Delta y)^2+(\Delta z)^2} \\ | ||
| V_{xyz}&=\frac{1}{8}\sum_{ijk=\pm} \frac{ijkv^{i,j,k}}{(\Delta x)^2+(\Delta z)^2} \\ | ||
| W_{xyz}&=\frac{1}{8}\sum_{ijk=\pm} \frac{ijkw^{i,j,k}}{(\Delta x)^2+(\Delta y)^2} | ||
| \end{align} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Wrap tertiary align block with math delimiters
Ensure the third \begin{align}…\end{align} block is surrounded by $$.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 20 to 24, the tertiary align block
is not wrapped with math delimiters. Surround the entire
\begin{align}...\end{align} block with double dollar signs ($$) to properly
format it as a displayed math block in the markdown.
| \begin{align} | ||
| &bx^{+++}+bx^{+- +}+bx^{++-}+bx^{+ - -}-bx^{- + +} -bx^{- + -}-bx^{-- +} -bx^{- --}\\ | ||
| +&by^{+++}+by^{- + +}+by^{++ -}+by^{-+-}-by^{+ - +}-by^{- - +} -by^{+ --} -by^{-- -} \\ | ||
| +&bz^{+++}+bz^{- + +}+bz^{+- +}+bz^{--+}-bz^{+ + -}-bz^{- + -} -bz^{+ --} -bz^{-- -} | ||
| \end{align} |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Enclose final expression align block in $$
Surround the last \begin{align}…\end{align} environment with $$ for correct display.
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md around lines 117 to 121, the final expression
inside the align environment is not enclosed within double dollar signs, which
is required for proper display in the rendered document. To fix this, wrap the
entire \begin{align}...\end{align} block with $$ at the start and end to ensure
correct mathematical formatting.
| \begin{align} | ||
| u^{0,j,k}&=\frac{1}{2}(u^{+,j,k} + u^{-,j,k}) + U_{x x} + k(\Delta z)^2 V_{xyz} + j(\Delta y)^2 W_{xyz} \\ | ||
| v^{i,0,k}&=\frac{1}{2}(v^{i,+,k} + v^{i,-,k}) + V_{y y} + i(\Delta x)^2 W_{xyz} + k(\Delta z)^2 U_{xyz}\\ | ||
| w^{i,j,0}&=\frac{1}{2}(v^{i,j,+} + w^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^2 V_{xyz} |
There was a problem hiding this comment.
Fix variable in w-component averaging
The average term uses v^{i,j,+} instead of w^{i,j,+}. Update to:
\frac{1}{2}\bigl(w^{i,j,+} + w^{i,j,-}\bigr)🧰 Tools
🪛 LanguageTool
[duplication] ~7-~7: Možný preklep: zopakovali ste slovo
Context: ...\frac{1}{2}(v^{i,j,+} + w^{i,j,-}) + W_{z z} + j(\Delta y)^2 U_{xyz} + i(\Delta x)^...
(WORD_REPEAT_RULE)
🤖 Prompt for AI Agents
In doc/source/theory/toth2002.md at line 7, the averaging term for the
w-component incorrectly uses v^{i,j,+} instead of w^{i,j,+}. Replace v^{i,j,+}
with w^{i,j,+} so the term reads \frac{1}{2}\bigl(w^{i,j,+} + w^{i,j,-}\bigr) to
correctly average the w-component values.
There was a problem hiding this comment.
Actionable comments posted: 0
♻️ Duplicate comments (2)
doc/source/theory/amr.md (2)
92-97:⚠️ Potential issueFix invalid MyST admon syntax.
MyST uses
::: seealsorather than:::{seealso}:-:::{seealso} +::: seealso Toth and Roe 2002 ... :::
1-5: 💡 Verification agent🧩 Analysis chain
Verify inclusion in Sphinx toctree.
Ensure
theory/amr.mdis referenced in your toctree so it appears in the built docs:
🏁 Script executed:
#!/bin/bash # Search for amr.md in the index rg -n "amr.md" -n doc/source/index.rst || echo "Please add 'theory/amr.md' to your toctree."Length of output: 141
Add
theory/amr.mdto the Sphinx toctreeThe file
doc/source/theory/amr.mdisn’t referenced indoc/source/index.rst, so it won’t be included in the built documentation. Please update your toctree:• File:
doc/source/index.rst
• Insert under the existing.. toctree::directiveSuggested diff:
.. toctree:: :maxdepth: 2 + theory/amr.md
🧹 Nitpick comments (16)
doc/source/theory/amr.md (16)
6-6: Hyphenate compound adjective in heading.Use a hyphen for “Patch-based approach” to follow standard English:
-## Patch based approach +## Patch-based approach🧰 Tools
🪛 LanguageTool
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...(BASED_HYPHEN)
12-12: Capitalize and normalize heading ‘regridding’.Make it title-case and remove trailing space:
-## regridding +## Regridding
14-15: Sentence case and capitalize the first word.Every section intro should start with a capital letter:
-regridding is the process of changing the geometry of an existing mesh level in the +Regridding is the process of changing the geometry of an existing mesh level in the
23-24: Streamline conditional phrasing.Remove the comma and clarify the comparison:
-Technically, regridding involves different methods depending on whether particle data -is refined, or field data is. +Technically, regridding involves different methods depending on whether particle data or field data is being refined.
31-31: Title-case subheading and hyphenate.Use consistent heading style:
-### divergence-free magnetic refinement +### Divergence-Free Magnetic Refinement
37-38: Fix spelling of “regridded”.The past-tense of “regrid” should have two d’s:
-- when a level is regrided +- when a level is regridded
40-42: Clarify prose in refinement description.Replace “so to preserve” with “to preserve” and tighten the sentence:
-Refining the magnetic field so to preserve its divergence-free character is -easy in general but becomes tricky when done at the coarse-fine boundaries -during regridding. +Refining the magnetic field to preserve its divergence-free character is straightforward in general, but becomes tricky at coarse-fine boundaries during regridding.
46-46: Correct gerund usage.Use “risking breaking” instead of “risking to break”:
-We cannot have one mesh imposing its face value blindly to the other without risking to break the divergence-free condition. +We cannot have one mesh imposing its face value blindly on the other without risking breaking the divergence-free condition.🧰 Tools
🪛 LanguageTool
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...(ADMIT_ENJOY_VB)
66-69: Fix subject-verb agreement & add missing noun.Ensure the refinement “considers” and mention the magnetic field:
-In the first case, if the refinement of the new blue components only consider values -from the coarse mesh, it cannot account for the fine flux imposed at the former -coarse-fine boundary and the divergence of the magnetic has thus no reason to be zero +In the first case, if the refinement of the new blue components only considers values from the coarse mesh, it cannot account for the fine flux imposed at the former coarse-fine boundary, and the divergence of the magnetic field therefore need not be zero🧰 Tools
🪛 LanguageTool
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
70-71: Fix typo and pronoun agreement.Correct “overwritting” and use plural pronouns:
-In the second case, the overwritting of fine faces at the former coarse-fine boundary -will create a non-zero divergence in cells just left to the former boundary since -one of the four faces of these cells see its flux changed. +In the second case, the overwriting of fine faces at the former coarse-fine boundary will create a non-zero divergence in cells just left of the former boundary since one of their four faces sees its flux changed.🧰 Tools
🪛 LanguageTool
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...(AI_HYDRA_LEO_MISSING_COMMA)
74-75: Hyphenate and remove redundancy.Combine and simplify the clause on coarse-fine boundary flux:
-The only way to preserve a zero divergence of the magnetic field at the coarse fine boundary -is to ensure that newly refined faces account for the flux at fine fluxes at the coarse-fine boundary. +The only way to preserve zero divergence of the magnetic field at the coarse-fine boundary is to ensure that newly refined faces account for the fine fluxes at that boundary.🧰 Tools
🪛 LanguageTool
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...(AI_HYDRA_LEO_MISSING_TO)
100-103: Replace placeholder with TODO or actual content.Avoid bare placeholders—either add the explanation or wrap it in a note/admon:
::: warning **TODO:** Add a detailed description of electric field refinement. :::
107-110: Correct spelling and punctuation.Fix “restriction” punctuation and “overlaped” typo:
-Coarsening, also sometimes called "restriction" is the process of projecting the -solution existing on a given level onto the region it overlaps on the next coarser level. +Coarsening, also sometimes called “restriction”, is the process of projecting the solution on a given level onto the region it overlaps on the next coarser level.
- Ensure “overlaps” is spelled with two p’s if used elsewhere.
112-118: Add missing verb in PHARE description.Insert verb to complete the sentence:
-When coarsening data between two hybrid PIC levels, PHARE three types of fields: +When coarsening data between two hybrid PIC levels, PHARE handles three types of fields:🧰 Tools
🪛 LanguageTool
[uncategorized] ~117-~117: Possible missing preposition found.
Context: ...ypes of fields: - the electric field - the ion total density and bulk velocity #...(AI_HYDRA_LEO_MISSING_OF)
141-141: Pluralize heading.Make level-boundary headings consistent:
-## Particle at level boundaries +## Particles at Level Boundaries
48-56: Enhance image alt text for accessibility.Provide descriptive alt text instead of file names:
- + - +
📜 Review details
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doc/source/theory/amr.md(1 hunks)
🧰 Additional context used
🪛 LanguageTool
doc/source/theory/amr.md
[uncategorized] ~6-~6: This expression is usually spelled with a hyphen.
Context: # Adaptive Mesh Refinement ## Patch based approach ## Recursive time integratio...
(BASED_HYPHEN)
[uncategorized] ~46-~46: The preposition “on” seems more likely in this position.
Context: ...ne mesh imposing its face value blindly to the other without risking to break the ...
(AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
[grammar] ~46-~46: The verb ‘risking’ is used with the gerund form.
Context: ...face value blindly to the other without risking to break the divergence-free condition. ![coars...
(ADMIT_ENJOY_VB)
[uncategorized] ~66-~66: This verb does not appear to agree with the subject. Consider using a different form.
Context: ...inement of the new blue components only consider values from the coarse mesh, it cannot ...
(AI_EN_LECTOR_REPLACEMENT_VERB_AGREEMENT)
[uncategorized] ~71-~71: “to the” seems less likely than “the”.
Context: ... non-zero divergence in cells just left to the former boundary since one of the four ...
(AI_HYDRA_LEO_CP_TO_THE_THE)
[uncategorized] ~71-~71: Possible missing comma found.
Context: ...rgence in cells just left to the former boundary since one of the four faces of these c...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~74-~74: Possible missing preposition found.
Context: ...nce of the magnetic field at the coarse fine boundary is to ensure that newly refine...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~88-~88: Possible missing comma found.
Context: ...es. This is illustrated in the figure below where inner new faces are represented i...
(AI_HYDRA_LEO_MISSING_COMMA)
[uncategorized] ~117-~117: Possible missing preposition found.
Context: ...ypes of fields: - the electric field - the ion total density and bulk velocity #...
(AI_HYDRA_LEO_MISSING_OF)
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still thinking about the best way to have some documentations for developpers. Stuff not useful from a user perspective but important for us, such as ghost filling, level/patch ghost particle handling, etc.
This was created because of what's in the index.rst below.
Ideally, this would be from a bridge between doxygen and sphinx.
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seems to be wip |
Just add markdown file for test and add some explanation about the refinement strategy for the magnetic field.