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HenriqueCSJ merged 1 commit into from
Jan 3, 2026
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test: add XYZ fixtures for SHAPE v2.1 parity tests #90

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13 changes: 13 additions & 0 deletions tests/fixtures/shape-parity/CN10-FeL10.xyz
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11
CN=10 FeL10 hexadecahedron complex - SHAPE v2.1 parity test (HD-10 = 16.93361)
Fe -1.419400 0.000000 2.310000
C -2.178900 -1.731300 1.550800
C -0.027800 -0.383500 3.747700
C -1.156200 -1.217800 0.698000
C -3.201600 -0.741700 1.658500
C -1.291900 -0.089300 4.341300
C 0.362800 0.741700 2.961500
C -1.546800 0.089300 0.278600
C -2.810900 0.383500 0.872200
C -1.682600 1.217800 3.921900
C -0.659900 1.731300 3.069100
14 changes: 14 additions & 0 deletions tests/fixtures/shape-parity/CN11-NbL11.xyz
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CN=11 NbL11 augmented pentagonal prism complex - SHAPE v2.1 parity test (JAPPR-11 = 21.67256)
Nb -0.104400 0.077400 0.000000
C -2.020700 1.040300 1.154000
C -1.209200 2.127400 0.713200
C -1.209200 2.127400 -0.713200
C -2.020700 1.040300 -1.154000
C -2.522300 0.368600 0.000000
C 1.631700 -1.217200 -1.395700
C 0.919000 -2.194000 -0.697800
C 2.344500 -0.240300 -0.697800
C 0.919000 -2.194000 0.697800
C 2.344500 -0.240300 0.697800
C 1.631700 -1.217200 1.395700
15 changes: 15 additions & 0 deletions tests/fixtures/shape-parity/CN12-NbL12.xyz
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CN=12 NbL12 biaugmented pentagonal prism complex - SHAPE v2.1 parity test (JBAPPR-12 = 17.93587)
Nb -2.170800 0.000000 -6.069100
C -2.170800 1.512200 -7.977700
C -1.016900 0.683100 -8.102100
C -1.457600 -0.658500 -8.303100
C -2.884000 -0.658500 -8.303100
C -3.324700 0.683100 -8.102100
C -2.170800 1.396100 -4.203500
C -3.456600 0.782300 -4.287800
C -3.773800 -0.595300 -4.480200
C -2.884500 -1.700100 -4.636700
C -1.457100 -1.700100 -4.636700
C -0.567800 -0.595300 -4.480200
C -0.885100 0.782300 -4.287800
5 changes: 5 additions & 0 deletions tests/fixtures/shape-parity/CN2-CuCl2.xyz
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CN=2 CuCl2 bent dihalide - SHAPE v2.1 parity test (vT-2 = 0.10827)
Cu 0.000000 0.000000 0.000000
Cl -1.081540 1.873498 0.000000
Cl -1.081540 -1.873498 0.000000
6 changes: 6 additions & 0 deletions tests/fixtures/shape-parity/CN3-NH3.xyz
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CN=3 NH3 ammonia - SHAPE v2.1 parity test (vT-3 = 0.02875)
N -0.526500 -0.002200 -0.763300
H -0.015500 -0.875500 -0.721600
H 0.149800 0.750900 -0.732800
H -0.991500 0.038900 -1.662000
7 changes: 7 additions & 0 deletions tests/fixtures/shape-parity/CN4-CuCl4.xyz
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CN=4 CuCl4 square planar complex - SHAPE v2.1 parity test (SP-4 = 0.02657)
Cu 0.000000 0.000000 0.000000
Cl -2.067300 0.921900 -0.063600
Cl 2.067300 -0.921900 -0.063600
Cl -0.911800 -2.077700 0.003700
Cl 0.911800 2.077700 0.003700
8 changes: 8 additions & 0 deletions tests/fixtures/shape-parity/CN5-AgL5.xyz
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CN=5 Ag(I) complex 4N+1O - SHAPE v2.1 parity test (SPY-5 = 4.22501)
Ag 1.371713 4.334600 3.420395
N 0.856035 6.772996 3.832547
N 3.311115 5.508578 4.289718
N 0.425955 4.055797 1.227668
N 2.290446 2.323681 2.314340
O 0.165372 4.112289 5.476084
9 changes: 9 additions & 0 deletions tests/fixtures/shape-parity/CN6-NiN4O2.xyz
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CN=6 NiN4O2 octahedral complex - SHAPE v2.1 parity test (OC-6 = 0.21577)
Ni -0.331700 12.016500 1.246900
N -0.457700 9.773400 1.221200
N 0.436000 12.016500 3.152600
N 1.504500 12.016500 0.329200
O -2.277700 12.016500 2.201600
O -1.233100 12.016500 -0.608400
N -0.457700 14.259600 1.221200
10 changes: 10 additions & 0 deletions tests/fixtures/shape-parity/CN7-FeL7.xyz
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CN=7 FeL7 pentagonal bipyramidal complex - SHAPE v2.1 parity test (PBPY-7 = 0.00000)
Fe -0.296300 0.263100 -0.144700
F -0.204200 -1.450800 -1.354600
F -2.375000 0.352100 -0.428900
F -0.537200 0.938400 1.829100
F 1.782500 0.174100 0.139600
F -0.204200 2.361000 -0.160700
F -0.537200 -1.417500 1.091300
F 0.001600 0.884400 -2.128400
11 changes: 11 additions & 0 deletions tests/fixtures/shape-parity/CN8-FeL8.xyz
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CN=8 FeL8 square antiprism complex - SHAPE v2.1 parity test (SAPR-8 = 0.09337)
Fe 0.528800 0.000000 -2.282100
F -0.039900 -0.159600 -4.111200
F 1.647200 1.173400 -3.315000
F 2.346100 -0.528500 -1.946600
F -1.288500 -0.598500 -2.098400
F 1.097500 1.286600 -0.972300
F 0.398700 -0.859300 -0.567800
F 0.658900 -1.861500 -2.742800
F -0.589600 1.547500 -2.502900
12 changes: 12 additions & 0 deletions tests/fixtures/shape-parity/CN9-CrL9.xyz
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CN=9 CrL9 muffin complex - SHAPE v2.1 parity test (MFF-9 = 0.00000)
Cr 1.161200 13.221400 15.185000
C 2.606400 12.222300 15.545400
C 1.709900 13.567700 16.857100
C 2.436700 14.427000 14.820200
C 1.784100 12.520700 13.656000
C 0.498700 11.721200 14.458700
C 0.757800 12.063400 16.496000
C -0.618600 13.193400 15.417400
C 0.333400 14.697800 15.778500
C 0.379300 14.050700 13.800200
44 changes: 44 additions & 0 deletions tests/fixtures/shape-parity/README.md
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# SHAPE v2.1 Parity Test Structures

These XYZ files contain the molecular structures used to validate Q-Shape against SHAPE v2.1 (the reference Fortran implementation by Alvarez et al., Universitat de Barcelona).

## Test Structures

| File | CN | Metal | Best Geometry | SHAPE CShM |
|------|----|----|---------------|------------|
| CN2-CuCl2.xyz | 2 | Cu | vT-2 (V-shape) | 0.10827 |
| CN3-NH3.xyz | 3 | N | vT-3 (Pyramid) | 0.02875 |
| CN4-CuCl4.xyz | 4 | Cu | SP-4 (Square Planar) | 0.02657 |
| CN5-AgL5.xyz | 5 | Ag | SPY-5 (Square Pyramidal) | 4.22501 |
| CN6-NiN4O2.xyz | 6 | Ni | OC-6 (Octahedral) | 0.21577 |
| CN7-FeL7.xyz | 7 | Fe | PBPY-7 (Pentagonal Bipyramidal) | 0.00000 |
| CN8-FeL8.xyz | 8 | Fe | SAPR-8 (Square Antiprism) | 0.09337 |
| CN9-CrL9.xyz | 9 | Cr | MFF-9 (Muffin) | 0.00000 |
| CN10-FeL10.xyz | 10 | Fe | HD-10 (Hexadecahedron) | 16.93361 |
| CN11-NbL11.xyz | 11 | Nb | JAPPR-11 (Aug. Pent. Prism) | 21.67256 |
| CN12-NbL12.xyz | 12 | Nb | JBAPPR-12 (Biaug. Pent. Prism) | 17.93587 |

## Usage

These structures can be loaded directly into Q-Shape or used with the parity benchmark tests:

```bash
npm test -- --testPathPattern="shapeParityBenchmark"
```

## Reproducibility

All SHAPE v2.1 reference values were obtained using SHAPE v2.1 (June 2013 release) with default settings. The test structures were selected to cover:

1. **Low CN (2-4)**: Simple geometries with clear best matches
2. **Medium CN (5-8)**: Common coordination environments in transition metal chemistry
3. **High CN (9-12)**: Complex polyhedra including Johnson solids

## Validation Results

Q-Shape achieves < 0.1% relative error compared to SHAPE v2.1 for all test structures. See the main README for detailed parity tables.

## References

1. Alvarez, S. et al. *Coord. Chem. Rev.* **2005**, 249, 1693-1708. DOI: [10.1016/j.ccr.2005.03.031](https://doi.org/10.1016/j.ccr.2005.03.031)
2. SHAPE v2.1: http://www.ee.ub.edu/index.php?option=com_content&view=article&id=90&Itemid=117
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