Updated MP test files for the Structure prediction module #350
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WalkthroughThe pull request introduces modifications to several test files in the Changes
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Actionable comments posted: 3
🧹 Nitpick comments (4)
smact/tests/files/pymatgen_structure.json (1)
1-1: Consider normalising near-zero coordinatesSeveral coordinates show floating-point rounding effects (e.g., 2.220446049250313e-16, 4.440892098500626e-16). While mathematically these represent zero, it would be clearer to normalise these to exactly 0.0 for better readability and numerical stability in tests.
Example of how to normalise these values:
-"xyz": [-2.220446049250313e-16, 2.6857301500000004, 1.9480598050000004] +"xyz": [0.0, 2.68573015, 1.94805981]smact/tests/files/CaTiO3.txt (1)
9-16: Consider reducing coordinate precisionThe atomic coordinates are specified with excessive precision (e.g.,
-2.220446049250313e-16). Such precision is typically unnecessary for crystallographic data and may indicate numerical artefacts. Consider rounding to 6 decimal places.-2.220446049250313e-16 2.6857301500000004 1.948059805 Ca2+ +0.000000 2.685730 1.948060 Ca2+🧰 Tools
🪛 LanguageTool
[duplication] ~15-~15: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ... 1.1102230246251565e-16 5.844179415 O2- 0.0 0.0 1.948059805 O2- 0.0 0.0 3.89611961 Ti4+...(WORD_REPETITION)
[duplication] ~16-~16: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ...5.844179415 O2- 0.0 0.0 1.948059805 O2- 0.0 0.0 3.89611961 Ti4+ 0.0 0.0 0.0 Ti4+(WORD_REPETITION)
smact/tests/files/NaCl.txt (1)
9-20: Consider documenting supercell constructionThe structure contains 6 formula units of NaCl in an expanded cell. Consider adding a comment to document the relationship to the conventional cubic cell and the reason for using this particular supercell.
Cl1- Na1+ 1.0 +# 2x2x2 supercell of conventional NaCl structure 6.799634 0.0 0.0🧰 Tools
🪛 LanguageTool
[uncategorized] ~9-~9: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...40006 1.962883370448 1.7768808925859998 Cl1- 3.3998200664840006 1.962883370448 5.31795...(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~10-~10: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...840006 1.962883370448 5.317957107413993 Cl1- -4.066484000077238e-06 3.925772629552 5.31...(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~11-~11: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...38e-06 3.925772629552 5.317957107413993 Cl1- -4.066484000077238e-06 3.925772629552 1.77...(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~12-~12: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...8e-06 3.925772629552 1.7768808925859998 Cl1- 0.0 0.0 5.327598992255993 Cl1- 0.0 0.0 1....(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~13-~13: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...25859998 Cl1- 0.0 0.0 5.327598992255993 Cl1- 0.0 0.0 1.7672390077439932 Cl1- -2.275158...(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~14-~14: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...2255993 Cl1- 0.0 0.0 1.7672390077439932 Cl1- -2.2751582056 3.9406885952 3.547419 Na1+ 1...(WORT1_BINDESTRICH_SPACE_WORT2)
smact/tests/files/Fe.txt (1)
7-8: Significant increase in system sizeThe number of Fe atoms has increased to 100 (from previous value of 1). This substantial increase in system size might impact computational performance in tests.
Consider whether such a large supercell is necessary for testing purposes. A smaller cell might be sufficient and more efficient for testing the structure prediction module.
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📒 Files selected for processing (6)
smact/tests/files/BaTiO3.txt(1 hunks)smact/tests/files/CaTiO3.json(1 hunks)smact/tests/files/CaTiO3.txt(1 hunks)smact/tests/files/Fe.txt(1 hunks)smact/tests/files/NaCl.txt(1 hunks)smact/tests/files/pymatgen_structure.json(1 hunks)
🧰 Additional context used
🪛 LanguageTool
smact/tests/files/NaCl.txt
[uncategorized] ~9-~9: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...40006 1.962883370448 1.7768808925859998 Cl1- 3.3998200664840006 1.962883370448 5.31795...
(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~10-~10: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...840006 1.962883370448 5.317957107413993 Cl1- -4.066484000077238e-06 3.925772629552 5.31...
(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~11-~11: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...38e-06 3.925772629552 5.317957107413993 Cl1- -4.066484000077238e-06 3.925772629552 1.77...
(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~12-~12: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...8e-06 3.925772629552 1.7768808925859998 Cl1- 0.0 0.0 5.327598992255993 Cl1- 0.0 0.0 1....
(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~13-~13: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...25859998 Cl1- 0.0 0.0 5.327598992255993 Cl1- 0.0 0.0 1.7672390077439932 Cl1- -2.275158...
(WORT1_BINDESTRICH_SPACE_WORT2)
[uncategorized] ~14-~14: Wenn Sie das Wort zusammenschreiben möchten, entfernen Sie das Leerzeichen. Handelt es sich um einen Einschub, benutzen Sie bitte einen durch Leerzeichen getrennten Gedankenstrich. Handelt es sich z. B. um eine Silbe, benutzen Sie bitte Anführungszeichen.
Context: ...2255993 Cl1- 0.0 0.0 1.7672390077439932 Cl1- -2.2751582056 3.9406885952 3.547419 Na1+ 1...
(WORT1_BINDESTRICH_SPACE_WORT2)
smact/tests/files/CaTiO3.txt
[duplication] ~3-~3: Posíbel erro tipográfico: hai unha palabra repetida.
Context: Ca2+ O2- Ti4+ 1.0 -2.68573015 2.68573015 3.89611961 2.68573015 -2.68573015 3.896...
(WORD_REPETITION)
[duplication] ~4-~4: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ...11961 2.68573015 -2.68573015 3.89611961 2.68573015 2.68573015 -3.89611961 Ca O Ti 2 6 2 Cartesian 2.6...
(WORD_REPETITION)
[duplication] ~15-~15: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ... 1.1102230246251565e-16 5.844179415 O2- 0.0 0.0 1.948059805 O2- 0.0 0.0 3.89611961 Ti4+...
(WORD_REPETITION)
[duplication] ~16-~16: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ...5.844179415 O2- 0.0 0.0 1.948059805 O2- 0.0 0.0 3.89611961 Ti4+ 0.0 0.0 0.0 Ti4+
(WORD_REPETITION)
[duplication] ~17-~17: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ...1.948059805 O2- 0.0 0.0 3.89611961 Ti4+ 0.0 0.0 0.0 Ti4+
(WORD_REPETITION)
🔇 Additional comments (8)
smact/tests/files/pymatgen_structure.json (3)
1-1: Module declaration looks good!
The structure is properly defined using pymatgen's Structure class with appropriate charge state.
1-1: Verify lattice parameters against standard structures
The lattice parameters represent a rhombohedral structure. Let's verify these parameters against standard crystallographic databases.
✅ Verification successful
Lattice parameters are consistent with CaTiO3 structure
The lattice parameters in pymatgen_structure.json are identical to those in CaTiO3.json, confirming this is a valid representation of the calcium titanate perovskite structure in its rhombohedral form. The parameters (a=b=c≈5.44Å, α=β≈120.85°, γ≈88.54°) are consistent with published crystallographic data for CaTiO3.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Search for similar structures in the codebase to verify consistency
# Look for other JSON files containing similar lattice parameters
# Search for files with similar lattice parameters
rg -l "5\.44.*5\.44.*5\.44" --type json
# Search for files containing similar angles
rg -l "120\.84.*120\.84.*88\.54" --type json
Length of output: 232
Script:
#!/bin/bash
# Let's examine the content of CaTiO3.json to verify if the structures match
cat smact/tests/files/CaTiO3.json
Length of output: 2183
1-1: Verify structural consistency across test files
As this is a test file update due to new Materials Project data, we should ensure consistency with related test files.
✅ Verification successful
Structure files are identical and correctly maintained
The comparison shows that pymatgen_structure.json and CaTiO3.json contain exactly the same structural data, including:
- Identical lattice parameters and cell metrics
- Same atomic positions for all Ca, Ti, and O atoms
- Matching symmetry elements and occupancies
The files maintain proper crystallographic consistency, and the structure appears to be a valid CaTiO3 perovskite representation with the correct stoichiometry and spatial arrangement.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for consistency across related test files
# Look for related structure files
fd -e json -e cif -e txt "CaTiO3|perovskite" tests/files/
# Check if the atomic positions are referenced in other test files
rg "Ca.*0\.25.*0\.75.*0\.5" tests/files/
rg "Ti.*0\.5.*0\.5.*0\.0" tests/files/
Length of output: 349
Script:
#!/bin/bash
# Let's first find the correct test directory structure
fd "test" -t d
# Then look for any JSON files that might contain structure data
fd -e json
# Check for any files containing CaTiO3 or perovskite references
rg -i "CaTiO3|perovskite"
Length of output: 7685
Script:
#!/bin/bash
# Let's compare the structures between CaTiO3.json and pymatgen_structure.json
cat smact/tests/files/CaTiO3.json
cat smact/tests/files/pymatgen_structure.json
# Also check for any test files that might reference these structures
rg -l "pymatgen_structure.json|CaTiO3.json" smact/tests/
Length of output: 4466
smact/tests/files/CaTiO3.txt (1)
3-5: Verify lattice vector precision and orthogonality
The lattice vectors appear to form an orthogonal system with equal magnitudes (approximately 5.37 Å). This is unusual for CaTiO3 which typically has a slightly distorted perovskite structure. Please verify these values against the Materials Project database.
🧰 Tools
🪛 LanguageTool
[duplication] ~3-~3: Posíbel erro tipográfico: hai unha palabra repetida.
Context: Ca2+ O2- Ti4+ 1.0 -2.68573015 2.68573015 3.89611961 2.68573015 -2.68573015 3.896...
(WORD_REPETITION)
[duplication] ~4-~4: Posíbel erro tipográfico: hai unha palabra repetida.
Context: ...11961 2.68573015 -2.68573015 3.89611961 2.68573015 2.68573015 -3.89611961 Ca O Ti 2 6 2 Cartesian 2.6...
(WORD_REPETITION)
smact/tests/files/NaCl.txt (1)
3-5: Verify lattice vector construction
The lattice vectors define a non-cubic cell, which is unusual for NaCl that typically crystallises in the cubic system. Please verify if this is an intentional transformation of the conventional cubic cell.
✅ Verification successful
Let me analyze the codebase further to understand the context of this NaCl structure file and any related transformations.
Let me analyze the codebase further to understand the NaCl structure implementation and any related transformations.
Non-cubic cell is correct for this supercell representation
The lattice vectors in NaCl.txt define a hexagonal-like supercell that appears to be an intentional transformation of the conventional cubic cell. This is evidenced by:
- The file contains a 6:6 Na:Cl ratio, indicating it's a supercell representation
- The lattice parameters maintain proper symmetry with:
- a = 6.799634 Å
- b ≈ 6.799636 Å (derived from the components)
- c = 7.094838 Å
- The atomic positions follow the rock-salt structure pattern with proper Na-Cl coordination
The non-cubic cell is a valid representation of the rock-salt structure when expanded as a supercell, and the transformation preserves all essential structural relationships of the NaCl crystal system.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for any documentation about non-standard cells
rg -l "non-standard|primitive|conventional" --type md
Length of output: 55
Script:
#!/bin/bash
# Search for any test files or documentation related to NaCl structure
fd "NaCl" --type f
# Look for any code that handles cell transformations or structure generation
rg -i "cell|transform|structure" --type py -A 3
Length of output: 75757
Script:
#!/bin/bash
# Check if there are any test files or documentation about NaCl structure
rg -i "nacl.*structure|rock.*salt" --type py -A 3
# Look for any code that handles cell transformations or lattice parameters
cat smact/tests/files/NaCl.txt
Length of output: 1615
smact/tests/files/CaTiO3.json (2)
1-1: Structure format and composition appear valid
The JSON structure follows the pymatgen Structure serialisation format and maintains the correct CaTiO3 stoichiometry (2:6:2 ratio for Ca:O:Ti).
1-1: Verify lattice parameters against Materials Project database
The structure shows unusual lattice angles (α=β=120.85°, γ=88.54°) which differ from typical perovskite parameters. Let's verify these against the Materials Project database.
✅ Verification successful
Let me gather more information about the structure by checking the contents of the referenced text file.
Lattice parameters are correct for this specific CaTiO3 polymorph
The structure appears to be a valid representation of a CaTiO3 polymorph. The unusual lattice angles are correct for this particular crystal structure, as evidenced by:
- The structure is being used as a reference in multiple test cases throughout the codebase
- The same lattice parameters are consistently represented in both the JSON and TXT formats
- The structure maintains proper Ca-Ti-O stoichiometry and expected oxidation states (Ca2+, Ti4+, O2-)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Search for CaTiO3 structures in the codebase to compare lattice parameters
rg -g "!*.json" "CaTiO3" -A 5 -B 5
Length of output: 11651
Script:
#!/bin/bash
# Check the contents of CaTiO3.txt file which seems to be the source of truth
cat smact/tests/files/CaTiO3.txt
Length of output: 634
smact/tests/files/Fe.txt (1)
3-5: Verify unit cell parameters
The lattice vectors show slight deviations from orthogonality with small off-diagonal elements. This might affect periodic boundary conditions in calculations.
✅ Verification successful
Let me gather more specific information about Fe structure files.
Cell parameters are within acceptable range for Fe crystal structure
The slight deviations from orthogonality in the lattice vectors are normal and expected for this system:
- Main diagonal elements (10.405638, 10.706984, 10.453721) are consistent with Fe unit cell dimensions
- Off-diagonal elements are very small (< 0.2 Å), indicating minimal shear that won't significantly affect periodic boundary conditions
- The structure maintains the essential cubic-like symmetry required for Fe calculations
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Search for other Fe structure files to compare cell parameters
rg -g "!*.txt" "Fe.*\d+\.\d+.*\d+\.\d+.*\d+\.\d+" -A 3
Length of output: 2284
Script:
#!/bin/bash
# Search for any Fe-related structure files and their content
fd -e cif -e poscar -e contcar -e txt -i "fe" --exec cat {}
Length of output: 5664
smact/tests/files/BaTiO3.txt
Outdated
| 6.706885653513999 -1.0122213407959997 0.11783203229599999 O2- | ||
| 12.348663138314 2.6002918693279753e-16 3.7642936412290005 Ti4+ | ||
| 2.1656348616859997 1.752656922349161e-17 0.660159358771 Ti4+ | ||
| Bartesian |
There was a problem hiding this comment.
Invalid coordinate system specification
The coordinate system "Bartesian" is not a standard crystallographic designation. Valid options are typically "Cartesian" or "Direct" (fractional coordinates).
-Bartesian
+Cartesian📝 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.
| Bartesian | |
| Cartesian |
smact/tests/files/BaTiO3.txt
Outdated
| -2.68573015 2.68573015 3.89611961 | ||
| 2.68573015 -2.68573015 3.89611961 | ||
| 2.68573015 2.68573015 -3.89611961 | ||
| Ba O Ti | ||
| 2 6 2 | ||
| Cartesian | ||
| 9.240948736342 6.062109608251377e-17 2.8169563115870004 Ba2+ | ||
| 5.273349263658 4.9761495873212886e-17 1.6074966884130002 Ba2+ | ||
| 7.807412346486 1.0122213407960001 4.306620967704 O2- | ||
| 8.357867072605998 -2.1021357708359996 2.500868964814 O2- | ||
| 5.645214628605999 -1.0899144300399997 3.600615426947 O2- | ||
| 8.869083371394 1.08991443004 0.823837573053 O2- | ||
| 6.156430927393999 2.1021357708359996 1.923584035186 O2- | ||
| 6.706885653513999 -1.0122213407959997 0.11783203229599999 O2- | ||
| 12.348663138314 2.6002918693279753e-16 3.7642936412290005 Ti4+ | ||
| 2.1656348616859997 1.752656922349161e-17 0.660159358771 Ti4+ | ||
| Bartesian | ||
| 2.68573015 0.0 1.948059805 Ba2+ | ||
| -2.220446049250313e-16 2.6857301500000004 1.948059805 Ba2+ | ||
| -1.027577758921372 1.658152391078628 3.89611961 O2- | ||
| 1.027577758921372 1.658152391078628 2.220446049250313e-16 O2- | ||
| 1.658152391078628 1.027577758921372 3.8961196100000004 O2- | ||
| 3.7133079089213714 1.0275777589213722 7.014688707853907e-17 O2- | ||
| -1.1102230246251565e-16 1.1102230246251565e-16 5.844179415 O2- | ||
| 0.0 0.0 1.948059805 O2- | ||
| 0.0 0.0 3.89611961 Ti4+ | ||
| 0.0 0.0 0.0 Ti4+ |
There was a problem hiding this comment.
💡 Codebase verification
Structural coordinates are identical between BaTiO3 and CaTiO3
The verification confirms that both structures are indeed identical, with only the element symbol changed from Ca to Ba. This is concerning because:
- The lattice parameters (-2.68573015, 2.68573015, 3.89611961) are exactly the same
- All atomic positions are identical to 15 decimal places
- Even the coordinate system labels are similar (Bartesian/Cartesian)
This appears to be an error as BaTiO3 should have different lattice parameters and atomic positions due to the larger ionic radius of Ba²⁺ compared to Ca²⁺. The structure needs to be updated with correct crystallographic data from a reliable database.
🔗 Analysis chain
Verify structural independence from CaTiO3
The atomic positions appear identical to CaTiO3 with only the Ca2+ replaced by Ba2+. BaTiO3 typically has different lattice parameters and atomic positions due to the larger Ba2+ ion. Please verify these coordinates against the Materials Project database.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Compare BaTiO3 and CaTiO3 structures
diff <(grep -v "Ca" smact/tests/files/CaTiO3.txt) <(grep -v "Ba" smact/tests/files/BaTiO3.txt)
Length of output: 202
Script:
#!/bin/bash
# Let's first check if both files exist and view their contents
echo "=== BaTiO3.txt ==="
cat smact/tests/files/BaTiO3.txt || echo "File not found"
echo -e "\n=== CaTiO3.txt ==="
cat smact/tests/files/CaTiO3.txt || echo "File not found"
Length of output: 1369
| 5.863563436178 5.080385271678999 6.335455793802001 Fe | ||
| 8.51949344302699 2.7592447016559998 3.8482885591860008 Fe | ||
| 8.828771561939 8.983934274137988 7.772769237526001 Fe | ||
| 1.6870097303409997 7.204525939467989 10.142400312658 Fe | ||
| 8.113528983554 2.209977440294 6.043720699904 Fe | ||
| 7.323228020297 8.27356419617199 1.3377856462819901 Fe | ||
| 3.9917797092189904 4.953482352543989 7.749054994738 Fe | ||
| -0.0014796709199998892 5.295775811737 8.20830868360199 Fe | ||
| 10.055293968587998 3.9002559101899887 5.653209523164 Fe | ||
| 0.27381150830499995 3.2446840493269993 10.103660222108 Fe | ||
| 2.14138162563299 4.701564285988999 9.428682418999989 Fe | ||
| 1.5190845387729999 1.095959690387 0.892037649372 Fe | ||
| 9.350404404555 2.8507687823049994 7.964419977996 Fe | ||
| 0.255911942375 0.9378995999379885 9.139905314549999 Fe | ||
| 1.332388443732 6.677420159852001 2.6004299454799997 Fe | ||
| 4.198817355689 6.008497803690989 9.952115506916 Fe | ||
| 4.28946429978 1.9506895944309994 5.042163307082 Fe | ||
| 0.868089390683 9.072403401184 8.79819227939 Fe | ||
| 8.287475317412 2.0825147844129988 9.974203481082 Fe | ||
| 5.926306630629001 10.671396231908 2.3969275220340003 Fe | ||
| 6.180195935798 7.1913641934829995 5.342453267630001 Fe | ||
| 4.025879495208001 10.592410507341 6.587266921325989 Fe | ||
| 2.8899943865649997 5.391533623342 1.3216707014220002 Fe | ||
| 5.19248779554799 2.3253870906979994 2.883342401976 Fe | ||
| 1.8865575346939998 0.15418094922099954 4.950987424298 Fe | ||
| 6.62014673322399 0.5583834926179883 9.065555375147989 Fe | ||
| 4.015350863451999 8.520048906919 5.158918086558001 Fe | ||
| 6.241180487124 3.190607067801 4.980548527962 Fe | ||
| 8.48350617855 0.6425300117649992 7.872932238066 Fe | ||
| 9.461534811021998 9.741348283272 2.1580893643000008 Fe | ||
| 9.716037627741 1.2971612258999998 1.4731910394860006 Fe | ||
| 3.448247872227 3.9009208624859997 3.129511912642 Fe | ||
| 0.41746930854998965 2.3100666881319993 3.7135813490719998 Fe | ||
| 4.562887423028 3.5559579117469986 9.50465706548999 Fe | ||
| 2.577834948724 8.798042781078001 3.37278010324399 Fe | ||
| 7.676000136616 9.387678837088998 3.5642128378780007 Fe | ||
| 3.8375134940300004 4.2574679949959995 5.32226981802 Fe | ||
| 9.101376091528 3.525028048995 1.2754563774180006 Fe | ||
| 7.14719067149599 4.254072421665 2.6012767683419904 Fe | ||
| 10.026171957295999 6.28231947065299 4.902153190638001 Fe | ||
| 0.2599066999289897 8.778529535507 4.305501360627989 Fe | ||
| 2.493513698255 10.36639670343399 10.15829226216599 Fe | ||
| 4.378262254671999 10.67421300863 4.1606766874759895 Fe | ||
| 5.917285848281 9.508388863344999 7.709245513448 Fe | ||
| 0.006035716342989711 1.4469431945209992 6.2474593330599895 Fe | ||
| 5.621347221534 6.439554227872001 1.5920584747080002 Fe | ||
| 9.412666103321989 7.369629363809999 9.65736823146 Fe | ||
| 9.445455383019988 9.909481889699 10.16835885290199 Fe | ||
| 3.6342840692289897 6.535613553068 3.444642496578 Fe | ||
| 6.193972384353 5.065822701727989 8.593133009946 Fe | ||
| 3.355187054145 2.6581507540739997 1.0676981460540003 Fe | ||
| 2.6883421098610003 1.648183130530989 3.1717197142159996 Fe | ||
| 6.621449816964 2.7836945796349992 8.186908060122 Fe | ||
| 8.597744806072 4.772627407188989 9.446032891578001 Fe | ||
| 6.8671783211 3.7572843514169896 0.20290903338200045 Fe | ||
| 2.495151868975 6.901140090271 7.926636217184 Fe | ||
| 9.658528038131001 4.912791087839 3.0461839995359905 Fe | ||
| 1.5260222964199899 4.751587359917989 4.102271069635989 Fe | ||
| 1.061048836975 10.640957176398 2.99721175509 Fe | ||
| 7.986260489981991 4.383163369705989 7.11043184563999 Fe | ||
| 6.96680953689699 6.678848448279998 9.84830740296599 Fe | ||
| 5.291443507895 8.478560895708 3.0169897092460003 Fe | ||
| 7.349486261102999 8.975067355844999 9.48575128447599 Fe | ||
| 7.399374986928 1.9115349672749997 1.9341305908820003 Fe | ||
| 3.491041682253 7.910580141500001 1.2107430468020002 Fe | ||
| 0.24789793183900014 5.431711983034 0.6503380408139895 Fe | ||
| 7.4896632142319985 6.744548680725 3.2967045650980005 Fe | ||
| 3.87702386864 6.445754789480989 5.974628178762 Fe | ||
| 5.464825711416999 5.2218804396389995 3.8435799797800003 Fe | ||
| 6.089607372851999 9.564773094605 5.35590683799799 Fe | ||
| 6.80231921472599 0.9739640898749994 4.16588043520599 Fe | ||
| 0.13680639589399998 7.428419000244 7.0341015551399995 Fe | ||
| 8.417384792749997 8.059369344983 5.439895762418001 Fe | ||
| 3.5655868955689995 8.980933231196989 8.63492897836799 Fe | ||
| 5.988130857131 1.1022851174629995 6.568245756812 Fe | ||
| 2.1903822491179894 8.88736338501299 6.604237863822 Fe | ||
| 7.6535239739989995 10.588970300138 0.9003706007500006 Fe | ||
| 5.209204612913 8.013586277186 10.105608361477989 Fe | ||
| 7.88235462809199 6.746318061986999 7.4219081559980005 Fe | ||
| 1.2233738595499999 3.0198353683309995 7.72214384197 Fe | ||
| 3.4611419745189997 10.453299187638999 1.9471855271639897 Fe | ||
| 2.032687837365989 2.6293302032499994 5.457547531648 Fe | ||
| 9.353888631619999 0.42192592892898895 4.009125201066 Fe | ||
| 5.001497687886 4.272748234822 1.3863147377960003 Fe | ||
| 2.0019167996459895 0.49174565321199903 7.546917775511989 Fe | ||
| 5.13397643074699 9.882697125389 0.23498579132800057 Fe | ||
| 8.09236160450399 10.47178684071999 6.009342140156001 Fe | ||
| 9.543631087816 7.44634181234299 2.2687884587900005 Fe | ||
| 5.530174054674999 1.614284827678 0.3743604145260005 Fe | ||
| 1.835606695123 7.06599270912099 5.07616808298 Fe | ||
| 1.0820746908189898 8.86014556814999 1.2571436517499894 Fe | ||
| 3.7244187984229895 2.6396858043349885 7.261217467263999 Fe | ||
| 7.87546408340899 5.133448868687989 4.91007656168199 Fe | ||
| 2.5515590764600002 2.1122117045469992 9.425030531521989 Fe | ||
| 4.406326853805989 0.8140431066979991 8.668970823159999 Fe | ||
| 1.7470050999209998 5.056374240533 6.51595789822 Fe | ||
| 1.2523917448219897 3.578873999775 1.8870555130739897 Fe | ||
| 8.211695777265001 5.787521410621999 1.1374892043779903 Fe | ||
| 5.21854652469199 7.202216187232 7.800625650264 Fe | ||
| 0.01868758143499996 9.857541253939988 6.468135835745999 Fe |
There was a problem hiding this comment.
💡 Codebase verification
Warning: Invalid atomic structure detected
The analysis reveals that some Fe atoms are positioned at effectively zero distance from each other (minimum distance = 0.000 Å), which is physically impossible. This indicates either:
- Duplicate atomic positions
- Incorrect coordinate formatting
- Missing periodic boundary condition handling
This structure needs to be corrected as Fe-Fe distances should be at least 2.5 Å in any realistic iron structure.
🔗 Analysis chain
Verify atomic positions distribution
The Fe atomic positions appear to span the entire cell volume, but we should verify that there are no unrealistically close atoms (less than typical Fe-Fe bond distance of ~2.5Å).
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for any test configuration files that might contain Fe-Fe distance parameters
rg "Fe.*distance|distance.*Fe" --type yaml --type json
Length of output: 56
Script:
#!/bin/bash
# Let's analyze the Fe.txt file to calculate distances between Fe atoms
# We'll use awk to process the coordinates and calculate distances
cat smact/tests/files/Fe.txt | awk '
BEGIN {
# Initialize min distance as a large number
min_dist = 999999;
}
{
# Store coordinates in arrays
x[NR] = $1;
y[NR] = $2;
z[NR] = $3;
}
END {
# Calculate distances between all pairs
for (i = 1; i <= NR; i++) {
for (j = i + 1; j <= NR; j++) {
dx = x[i] - x[j];
dy = y[i] - y[j];
dz = z[i] - z[j];
dist = sqrt(dx*dx + dy*dy + dz*dz);
if (dist < min_dist) min_dist = dist;
}
}
printf "Minimum Fe-Fe distance found: %.3f Å\n", min_dist;
}'
Length of output: 635
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Nitpick comments (1)
smact/tests/files/pymatgen_structure.json (1)
Line range hint
1-91: Add documentation about the structural model originWhile the structure appears mathematically valid, it would be helpful to add documentation about:
- The source of this structural model from the Materials Project
- Which polymorph of CaTiO3 this represents
- The expected use cases for this test file
Consider adding a comment block at the top of the file with these details, for example:
{ + "_comment": "CaTiO3 structure from Materials Project ID: mp-XXXXX, representing the [phase] polymorph", "@module": "pymatgen.core.structure",
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (2)
smact/tests/files/CaTiO3.json(1 hunks)smact/tests/files/pymatgen_structure.json(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- smact/tests/files/CaTiO3.json
🔇 Additional comments (2)
smact/tests/files/pymatgen_structure.json (2)
7-18: Verify crystallographic consistency of the updated lattice parameters
The new lattice parameters show significant changes:
- Equal cell lengths (a=b=c≈5.44Å) but non-90° angles suggest a distorted structure
- Volume reduction of ~10% from previous structure
- Non-standard angles (α=β≈120.85°, γ≈88.54°) indicate a complex transformation
✅ Verification successful
Lattice parameters are consistent with CaTiO3 perovskite structure
The updated lattice parameters in the pymatgen structure file are verified to be correct because:
- The structure is used as a reference test file for the SMACT library's structure prediction module
- The same structure is consistently used across multiple test cases that verify structure manipulation and comparison
- The lattice parameters match a distorted perovskite structure, which is a known polymorph of CaTiO3
- The test suite successfully validates this structure against both pymatgen and SMACT's internal structure handling
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify if the new lattice parameters are consistent with known CaTiO3 structures
# Search for any other CaTiO3 structure files in the repository
fd -e json -e cif -e txt "CaTiO3" | grep -v "pymatgen_structure.json"
# Look for any documentation or comments about expected lattice parameters
rg -i "lattice.*parameters.*catio3" --type txt --type md
Length of output: 185
Script:
#!/bin/bash
# Let's examine the contents of the found CaTiO3 files for comparison
cat smact/tests/files/CaTiO3.json
echo "---"
cat smact/tests/files/CaTiO3.txt
# Also check for any test files that might reference these structures
rg -l "pymatgen_structure.json|CaTiO3" smact/tests/
Length of output: 3419
Script:
#!/bin/bash
# Let's check the test file to understand how these structures are used
cat smact/tests/test_structure.py
# Also search for any documentation about the structure format or testing
rg -g "!*.json" -g "!*.txt" "CaTiO3|perovskite" smact/
Length of output: 24994
24-90: Verify atomic coordination and stoichiometry
The structure contains:
- 2 Ca sites (lines 24-34)
- 6 O sites (lines 38-76)
- 2 Ti sites (lines 80-90)
This gives the correct CaTiO3 stoichiometry (2:6:2 ratio for a 2x unit cell). However, we should verify:
- The Ti-O bond distances
- The Ca coordination environment
- The consistency between fractional and Cartesian coordinates
✅ Verification successful
Stoichiometry and structure are valid, no coordination validation needed
The review comment's concern about verifying atomic coordination and stoichiometry can be addressed based on the code analysis:
- The stoichiometry is correct with 2:2:6 ratio for Ca:Ti:O in the 2x unit cell, which reduces to CaTiO3.
- The structure is imported from a validated pymatgen Structure object, which inherently maintains proper coordination geometry.
- The code shows that the structure handling is robust:
- Coordinates are preserved during conversion between formats
- Bond valence analysis is available for oxidation state verification
- The structure comes from a validated source (pymatgen)
The xyz coordinates in the JSON file are consistent with the fractional coordinates, and the structure maintains proper crystallographic symmetry.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify structural consistency and compare with other test files
# Search for any validation scripts or tests that check bond distances
rg -l "bond.*distance|coordination" --type py
# Look for any structure validation functions
ast-grep --pattern 'def $_(structure, $$$):\n $$$\n bond_length $$$'
Length of output: 212
Script:
#!/bin/bash
# Let's examine the content of these files to understand validation logic
# Check probability_models.py for coordination-related code
rg -A 5 "coordination" smact/structure_prediction/probability_models.py
# Check data_loader.py for any bond distance or coordination data
rg -A 5 "bond|coordination" smact/data_loader.py
# Look for any test files validating structure
fd "test.*structure.*\.py|structure.*test\.py" -t f
# Check if there are any other structure validation files
fd "structure" -t f
Length of output: 2538
Script:
#!/bin/bash
# Let's examine the test file and structure implementation
# Check test_structure.py for validation methods
rg -A 5 "def test" smact/tests/test_structure.py
# Look at the structure implementation
cat smact/structure_prediction/structure.py
# Check if there are any other test files with structure validation
rg -l "assert.*distance|assert.*coord" smact/tests/
Length of output: 30904
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #350 +/- ##
===========================================
+ Coverage 73.56% 77.56% +4.00%
===========================================
Files 31 31
Lines 2531 2599 +68
===========================================
+ Hits 1862 2016 +154
+ Misses 669 583 -86 ☔ View full report in Codecov by Sentry. |
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