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Merged
aligfellow merged 10 commits into from
Mar 13, 2026
Merged

Vector bugfix #48

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4f6226e
draw axis vectors when custom vec also provided
scohenjanes5 Mar 12, 2026
67c5626
rotate axis and custom vectors on equal footing
scohenjanes5 Mar 12, 2026
aaebe65
Redo crystal tests to use canonical rotations
scohenjanes5 Mar 12, 2026
cb1d899
rotate Vectors and Lattice with same mechanism
scohenjanes5 Mar 12, 2026
ec788e5
Merge branch 'aligfellow:main' into vector-bugfix
scohenjanes5 Mar 12, 2026
a09c32b
dos2unix
scohenjanes5 Mar 12, 2026
72c3324
Merge branch 'vector-bugfix' of https://github.com/scohenjanes5/xyzre…
scohenjanes5 Mar 12, 2026
582339c
dos2unix
scohenjanes5 Mar 12, 2026
ea157b0
Merge branch 'main' of github.com:aligfellow/xyzrender into vector-bu…
aligfellow Mar 13, 2026
bffbfbe
Added is_axis flag, scale annotation only. Changed flag to vector fro…
aligfellow Mar 13, 2026
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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -844,7 +844,7 @@ Overlay arbitrary 3D vectors as arrows on the rendered image via a JSON file. Us


```bash
xyzrender ethanol.xyz --vectors ethanol_dip.json -o ethanol_dip.svg
xyzrender ethanol.xyz --vector ethanol_dip.json -o ethanol_dip.svg
```

Each entry in the JSON array defines one arrow:
Expand Down Expand Up @@ -1153,7 +1153,7 @@ Available rotation axes: `x`, `y`, `z`, `xy`, `xz`, `yz`, `yx`, `zx`, `zy`. Pref
| `--label-size PT` | Label font size (overrides preset) |
| `--cmap FILE` | Per-atom property colormap (Viridis, 1-indexed) |
| `--cmap-range VMIN VMAX` | Explicit colormap range (default: auto from file) |
| `--vectors FILE` | JSON file of vector arrows to overlay (see Vector arrows section) |
| `--vector FILE` | JSON file of vector arrows to overlay (see Vector arrows section) |
| `--vector-scale FACTOR` | Global length scale for all vector arrows (default: 1.0) |
| **Crystal** | |
| `--crystal [{vasp,qe}]` | Load as crystal via phonopy; format auto-detected or specify explicitly |
Expand Down
2 changes: 1 addition & 1 deletion docs/source/cli_reference.md
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Expand Up @@ -102,7 +102,7 @@ Full flag reference for `xyzrender`. See also `xyzrender --help`.

| Flag | Description |
|------|-------------|
| `--vectors FILE` | Path to a JSON file defining 3D vector arrows for overlay |
| `--vector FILE` | Path to a JSON file defining 3D vector arrows for overlay |
| `--vector-scale` | Global length multiplier for all vector arrows |

## GIF animations
Expand Down
2 changes: 1 addition & 1 deletion docs/source/examples/annotations.md
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Expand Up @@ -92,7 +92,7 @@ Overlay arbitrary 3D vectors as arrows on the rendered image via a JSON file. Us


```bash
xyzrender ethanol.xyz --vectors ethanol_dip.json -o ethanol_dip.svg
xyzrender ethanol.xyz --vector ethanol_dip.json -o ethanol_dip.svg
```

Each entry in the JSON array defines one arrow:
Expand Down
117 changes: 7 additions & 110 deletions examples/examples.ipynb
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Expand Up @@ -1360,122 +1360,19 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"id": "c2cb9dfe",
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
"<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" viewBox=\"0 0 800 500\" width=\"500\" height=\"auto\">\n",
" <rect width=\"100%\" height=\"100%\" fill=\"#ffffff\"/>\n",
" <defs>\n",
" <g id=\"x6a0\"><radialGradient id=\"x6g0\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#c3c3c3\"/><stop offset=\"100%\" stop-color=\"#888888\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"59.0\" fill=\"url(#x6g0)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x6a1\"><radialGradient id=\"x6g1\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#c3c3c3\"/><stop offset=\"100%\" stop-color=\"#888888\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"59.0\" fill=\"url(#x6g1)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x6a2\"><radialGradient id=\"x6g2\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ff5555\"/><stop offset=\"100%\" stop-color=\"#cc0a0a\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"52.9\" fill=\"url(#x6g2)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x6a8\"><radialGradient id=\"x6g8\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#cccccc\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x6g8)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" </defs>\n",
" <use x=\"573.1\" y=\"411.9\" xlink:href=\"#x6a2\"/>\n",
" <line x1=\"617.7\" y1=\"395.1\" x2=\"694.9\" y2=\"366.0\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"543.7\" y1=\"374.4\" x2=\"462.4\" y2=\"270.6\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"298.4\" y1=\"480.1\" x2=\"404.8\" y2=\"134.5\" stroke=\"#b22222\" stroke-width=\"15.6\" stroke-linecap=\"round\"/>\n",
" <polygon points=\"420.9,82.3 424.7,140.6 385.0,128.4\" fill=\"#b22222\"/>\n",
" <text x=\"439.7\" y=\"43.0\" font-size=\"62.4\" fill=\"#b22222\" font-family=\"Arial,sans-serif\" text-anchor=\"middle\" font-weight=\"bold\">μ</text>\n",
" <use x=\"721.0\" y=\"356.2\" xlink:href=\"#x6a8\"/>\n",
" <use x=\"429.7\" y=\"228.8\" xlink:href=\"#x6a1\"/>\n",
" <line x1=\"379.3\" y1=\"245.5\" x2=\"245.9\" y2=\"289.6\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <use x=\"195.5\" y=\"306.3\" xlink:href=\"#x6a0\"/>\n",
"</svg>"
],
"text/plain": [
"<xyzrender.api.SVGResult at 0x7e746c0764e0>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from xyzrender import load, render\n",
"\n",
"etoh = load(\"structures/ethanol.xyz\")\n",
"vec = {\n",
" \"anchor\": \"center\",\n",
" \"vectors\": [\n",
" {\n",
" \"origin\": \"com\",\n",
" \"vector\": [1.0320170291976951, -0.042708195030485986, -1.332397645862797],\n",
" \"color\": \"firebrick\",\n",
" \"label\": \"μ\",\n",
" }\n",
" ],\n",
"}\n",
"render(etoh, vectors=vec, vector_scale=1.5)"
]
"outputs": [],
"source": "from xyzrender import load, render\n\netoh = load(\"structures/ethanol.xyz\")\nvec = {\n \"anchor\": \"center\",\n \"vectors\": [\n {\n \"origin\": \"com\",\n \"vector\": [1.0320170291976951, -0.042708195030485986, -1.332397645862797],\n \"color\": \"firebrick\",\n \"label\": \"μ\",\n }\n ],\n}\nrender(etoh, vector=vec, vector_scale=1.5)"
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"id": "4fa885ba",
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
"<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" viewBox=\"0 0 800 554\" width=\"500\" height=\"auto\">\n",
" <rect width=\"100%\" height=\"100%\" fill=\"#ffffff\"/>\n",
" <defs>\n",
" <g id=\"x9a0\"><radialGradient id=\"x9g0\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#c3c3c3\"/><stop offset=\"100%\" stop-color=\"#888888\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"59.0\" fill=\"url(#x9g0)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a1\"><radialGradient id=\"x9g1\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#c3c3c3\"/><stop offset=\"100%\" stop-color=\"#888888\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"59.0\" fill=\"url(#x9g1)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a2\"><radialGradient id=\"x9g2\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ff5555\"/><stop offset=\"100%\" stop-color=\"#cc0a0a\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"52.9\" fill=\"url(#x9g2)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a3\"><radialGradient id=\"x9g3\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#d6d6d6\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x9g3)\" stroke=\"#494949\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a4\"><radialGradient id=\"x9g4\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#cccccc\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x9g4)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a5\"><radialGradient id=\"x9g5\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#cccccc\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x9g5)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a6\"><radialGradient id=\"x9g6\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#d5d5d5\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x9g6)\" stroke=\"#414141\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a7\"><radialGradient id=\"x9g7\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#cccccc\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x9g7)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" <g id=\"x9a8\"><radialGradient id=\"x9g8\" cx=\".5\" cy=\".5\" fx=\".33\" fy=\".33\" r=\".66\"><stop offset=\"0%\" stop-color=\"#ffffff\"/><stop offset=\"100%\" stop-color=\"#cccccc\"/></radialGradient><circle cx=\"0\" cy=\"0\" r=\"31.0\" fill=\"url(#x9g8)\" stroke=\"#000000\" stroke-width=\"10.4\"/></g>\n",
" </defs>\n",
" <use x=\"159.2\" y=\"352.5\" xlink:href=\"#x9a3\"/>\n",
" <line x1=\"164.8\" y1=\"338.7\" x2=\"184.9\" y2=\"288.8\" stroke=\"#0a0a0a\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <use x=\"458.2\" y=\"80.5\" xlink:href=\"#x9a6\"/>\n",
" <line x1=\"453.8\" y1=\"96.6\" x2=\"438.1\" y2=\"154.4\" stroke=\"#090909\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"426.4\" y1=\"534.1\" x2=\"683.6\" y2=\"243.0\" stroke=\"#b22222\" stroke-width=\"15.6\" stroke-linecap=\"round\"/>\n",
" <use x=\"573.1\" y=\"368.1\" xlink:href=\"#x9a2\"/>\n",
" <line x1=\"617.7\" y1=\"351.3\" x2=\"694.9\" y2=\"322.3\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"543.7\" y1=\"330.6\" x2=\"462.4\" y2=\"226.8\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"241.1\" y1=\"276.3\" x2=\"426.3\" y2=\"215.6\" stroke=\"#4682b4\" stroke-width=\"15.6\" stroke-linecap=\"round\"/>\n",
" <use x=\"721.0\" y=\"312.4\" xlink:href=\"#x9a8\"/>\n",
" <line x1=\"333.5\" y1=\"293.4\" x2=\"489.6\" y2=\"117.6\" stroke=\"#b22222\" stroke-width=\"15.6\" stroke-linecap=\"round\"/>\n",
" <use x=\"429.7\" y=\"185.1\" xlink:href=\"#x9a1\"/>\n",
" <line x1=\"379.3\" y1=\"201.7\" x2=\"245.9\" y2=\"245.8\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"436.1\" y1=\"154.1\" x2=\"448.5\" y2=\"95.2\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"222.9\" y1=\"190.8\" x2=\"187.5\" y2=\"283.2\" stroke=\"#b22222\" stroke-width=\"15.6\" stroke-linecap=\"round\"/>\n",
" <polygon points=\"168.0,334.2 168.1,275.8 206.9,290.7\" fill=\"#b22222\"/>\n",
" <use x=\"195.5\" y=\"262.5\" xlink:href=\"#x9a0\"/>\n",
" <line x1=\"161.2\" y1=\"222.0\" x2=\"97.0\" y2=\"146.3\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <line x1=\"187.7\" y1=\"294.9\" x2=\"173.3\" y2=\"354.9\" stroke=\"#000000\" stroke-width=\"26.0\" stroke-linecap=\"round\"/>\n",
" <use x=\"79.0\" y=\"125.0\" xlink:href=\"#x9a5\"/>\n",
" <use x=\"169.2\" y=\"372.0\" xlink:href=\"#x9a4\"/>\n",
" <use x=\"451.9\" y=\"78.9\" xlink:href=\"#x9a7\"/>\n",
" <polygon points=\"525.8,76.7 505.1,131.3 474.1,103.8\" fill=\"#b22222\"/>\n",
" <polygon points=\"719.8,202.1 699.2,256.8 668.1,229.3\" fill=\"#b22222\"/>\n",
" <polygon points=\"478.2,198.6 432.8,235.3 419.8,195.9\" fill=\"#4682b4\"/>\n",
" <text x=\"538.9\" y=\"200.5\" font-size=\"62.4\" fill=\"#4682b4\" font-family=\"Arial,sans-serif\" text-anchor=\"middle\" font-weight=\"bold\">E</text>\n",
"</svg>"
],
"text/plain": [
"<xyzrender.api.SVGResult at 0x7e74403ee780>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"render(etoh, hy=True, vectors=\"structures/ethanol_forces_efield.json\", vector_scale=2)"
]
"outputs": [],
"source": "render(etoh, hy=True, vector=\"structures/ethanol_forces_efield.json\", vector_scale=2)"
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -3681,4 +3578,4 @@
},
"nbformat": 4,
"nbformat_minor": 5
}
}
4 changes: 2 additions & 2 deletions examples/generate.sh
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Expand Up @@ -75,8 +75,8 @@ xyzrender "$DIR/bimp.out" -o "$IMG/bimp_ts_nci.svg" --ts --gif-trj --vdw 84-169
xyzrender "$DIR/bimp.out" -o "$IMG/bimp_ts_nci.svg" --gif-ts --gif-rot --vdw 84-169 --nci -go "$IMG/bimp_nci_ts.gif"

echo "=== Vector arrows ==="
xyzrender "$DIR/ethanol.xyz" --vectors "$DIR/ethanol_dip.json" -o "$IMG/ethanol_dip.svg" --gif-rot -go "$IMG/ethanol_dip.gif" # dipole at center of mass, with rotation
xyzrender "$DIR/ethanol.xyz" --hy --vectors "$DIR/ethanol_forces_efield.json" --vector-scale 1.5 -o "$IMG/ethanol_forces_efield.svg" -go "$IMG/ethanol_forces_efield.gif" --gif-rot # per-atom forces, with rotation
xyzrender "$DIR/ethanol.xyz" --vector "$DIR/ethanol_dip.json" -o "$IMG/ethanol_dip.svg" --gif-rot -go "$IMG/ethanol_dip.gif" # dipole at center of mass, with rotation
xyzrender "$DIR/ethanol.xyz" --hy --vector "$DIR/ethanol_forces_efield.json" --vector-scale 1.5 -o "$IMG/ethanol_forces_efield.svg" -go "$IMG/ethanol_forces_efield.gif" --gif-rot # per-atom forces, with rotation

echo "=== Crystal / unit cell ==="
xyzrender "$DIR/caffeine_cell.xyz" --cell -o "$IMG/caffeine_cell.svg" --no-orient --gif-rot -go "$IMG/caffeine_cell.gif"
Expand Down
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