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Revert "fix(refgeom): center reference geometries on metal position" #88

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Merged
HenriqueCSJ merged 1 commit into from
Dec 30, 2025
Merged

Revert "fix(refgeom): center reference geometries on metal position" #88

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121 changes: 49 additions & 72 deletions src/constants/referenceGeometries/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -37,22 +37,18 @@ function generateLinear() {
}

function generateVShape() {
// vT-2: Divacant Tetrahedron (V-shape, 109.47°) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, 0, -0.534522]
// vT-2: Divacant Tetrahedron (V-shape, 109.47°) - Official CoSyMlib reference (normalized)
return [
[0.801784, 0.801784, 0.801784],
[-0.801784, -0.801784, 0.801784]
[0.801784, 0.801784, 0.267261],
[-0.801784, -0.801784, 0.267261]
].map(normalize);
}

function generateLShape() {
// vOC-2: Tetravacant Octahedron (L-shape, 90°) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [-0.5, -0.5, 0]
// vOC-2: Tetravacant Octahedron (L-shape, 90°) - Official CoSyMlib reference (normalized)
return [
[1.500000, 0.000000, 0.000000],
[0.000000, 1.500000, 0.000000]
[1.000000, -0.500000, 0.000000],
[-0.500000, 1.000000, 0.000000]
].map(normalize);
}

Expand All @@ -67,35 +63,29 @@ function generateTrigonalPlanar() {
}

function generatePyramid() {
// vT-3: Vacant Tetrahedron (Trigonal Pyramid) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, 0, -0.301511]
// vT-3: Vacant Tetrahedron (Trigonal Pyramid) - Official CoSyMlib reference (normalized)
return [
[1.137070, 0.000000, 0.402015],
[-0.568535, 0.984732, 0.402015],
[-0.568535, -0.984732, 0.402015]
[1.137070, -0.000000, 0.100504],
[-0.568535, 0.984732, 0.100504],
[-0.568535, -0.984732, 0.100504]
].map(normalize);
}

function generateFacTrivacantOctahedron() {
// fac-vOC-3: fac-Trivacant Octahedron - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [-0.333333, -0.333333, -0.333333]
// fac-vOC-3: fac-Trivacant Octahedron - Official CoSyMlib reference (normalized)
return [
[1.333333, 0.000000, 0.000000],
[0.000000, 1.333333, 0.000000],
[0.000000, 0.000000, 1.333333]
[1.000000, -0.333333, -0.333333],
[-0.333333, 1.000000, -0.333333],
[-0.333333, -0.333333, 1.000000]
].map(normalize);
}

function generateTShaped() {
// mer-vOC-3: mer-Trivacant Octahedron (T-shaped) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, -0.301511, 0]
// mer-vOC-3: mer-Trivacant Octahedron (T-shaped) - Official CoSyMlib reference (normalized)
return [
[1.206045, 0.000000, 0.000000],
[0.000000, 1.206045, 0.000000],
[-1.206045, 0.000000, 0.000000]
[1.206045, -0.301511, 0.000000],
[0.000000, 0.904534, 0.000000],
[-1.206045, -0.301511, 0.000000]
].map(normalize);
}

Expand All @@ -120,28 +110,22 @@ function generateSquarePlanar() {
}

function generateSeesaw() {
// SS-4: Seesaw (cis-divacant octahedron) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [-0.235702, -0.235702, 0]
// After centering: vertices form orthogonal seesaw geometry
// SS-4: Seesaw (cis-divacant octahedron) - Official CoSyMlib reference (normalized)
return [
[0.000000, 0.000000, -1.178511], // axial -z
[1.178511, 0.000000, 0.000000], // equatorial +x
[0.000000, 1.178511, 0.000000], // equatorial +y
[0.000000, 0.000000, 1.178511] // axial +z
[-0.235702, -0.235702, -1.178511],
[0.942809, -0.235702, 0.000000],
[-0.235702, 0.942809, 0.000000],
[-0.235702, -0.235702, 1.178511]
].map(normalize);
}

function generateAxialVacantTBPY() {
// vTBPY-4: Axially Vacant Trigonal Bipyramid - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, 0, 0.229416]
// After centering: axial at -z, three equatorial in xy-plane
// vTBPY-4: Axially Vacant Trigonal Bipyramid - Official CoSyMlib reference (normalized)
return [
[0.000000, 0.000000, -1.147079], // axial -z
[1.147079, 0.000000, 0.000000], // equatorial +x
[-0.573539, 0.993399, 0.000000], // equatorial 120°
[-0.573539, -0.993399, 0.000000] // equatorial 240°
[0.000000, -0.000000, -0.917663],
[1.147079, -0.000000, 0.229416],
[-0.573539, 0.993399, 0.229416],
[-0.573539, -0.993399, 0.229416]
].map(normalize);
}

Expand All @@ -157,16 +141,13 @@ function generatePentagon() {
}

function generateSquarePyramid() {
// vOC-5: Vacant Octahedron (Johnson Square Pyramid J1) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, 0, 0.185695]
// After centering: apex at -z, four base vertices in xy-plane
// vOC-5: Vacant Octahedron (Johnson Square Pyramid J1) - Official CoSyMlib reference (normalized)
return [
[0.000000, 0.000000, -1.114172], // apex -z
[1.114172, 0.000000, 0.000000], // base +x
[0.000000, 1.114172, 0.000000], // base +y
[-1.114172, 0.000000, 0.000000], // base -x
[0.000000, -1.114172, 0.000000] // base -y
[0.000000, -0.000000, -0.928477],
[1.114172, -0.000000, 0.185695],
[0.000000, 1.114172, 0.185695],
[-1.114172, 0.000000, 0.185695],
[-0.000000, -1.114172, 0.185695]
].map(normalize);
}

Expand Down Expand Up @@ -215,16 +196,14 @@ function generateHexagon() {
}

function generatePentagonalPyramid() {
// PPY-6: Pentagonal Pyramid - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, 0, 0.156174]
// PPY-6: Pentagonal Pyramid - Official CoSyMlib reference (normalized)
return [
[0.000000, 0.000000, -1.093217], // apex -z
[1.093216, 0.000000, 0.000000], // base vertex
[0.337822, 1.039711, 0.000000],
[-0.884431, 0.642576, 0.000000],
[-0.884431, -0.642576, 0.000000],
[0.337822, -1.039711, 0.000000]
[0.000000, -0.000000, -0.937043],
[1.093216, -0.000000, 0.156174],
[0.337822, 1.039711, 0.156174],
[-0.884431, 0.642576, 0.156174],
[-0.884431, -0.642576, 0.156174],
[0.337822, -1.039711, 0.156174]
].map(normalize);
}

Expand Down Expand Up @@ -253,16 +232,14 @@ function generateTrigonalPrism() {
}

function generateJohnsonPentagonalPyramid6() {
// JPPY-6: Johnson Pentagonal Pyramid (J2) - Official CoSyMlib reference
// CORRECTED: Coordinates centered on metal position before normalization
// Metal center in cosymlib: [0, 0, 0.101206]
return [
[1.146282, 0.000000, 0.000000], // base vertex
[0.354221, 1.090179, 0.000000],
[-0.927361, 0.673768, 0.000000],
[-0.927361, -0.673768, 0.000000],
[0.354221, -1.090179, 0.000000],
[0.000000, 0.000000, -0.708441] // apex -z
// JPPY-6: Johnson Pentagonal Pyramid (J2) - Official CoSyMlib reference (normalized)
return [
[1.146282, -0.000000, 0.101206],
[0.354221, 1.090179, 0.101206],
[-0.927361, 0.673768, 0.101206],
[-0.927361, -0.673768, 0.101206],
[0.354221, -1.090179, 0.101206],
[0.000000, -0.000000, -0.607235]
].map(normalize);
}

Expand Down
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