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Use refactored weas #47

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Apr 5, 2024
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Use refactored weas #47

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508f8de
use_refactored_weas
superstar54 Mar 18, 2024
f9942c8
add python_task and update data.objects
superstar54 Mar 19, 2024
f8ed009
add camear and instancedMshPrimitive
superstar54 Mar 22, 2024
4303f88
use WidgetWrapper and install weas locally
superstar54 Mar 23, 2024
bc9e2cc
add tests on camera, ops
superstar54 Mar 23, 2024
3f21133
update doc
superstar54 Mar 24, 2024
2a7a0c1
split operator to another PR
superstar54 Mar 24, 2024
f11931d
update README
superstar54 Mar 24, 2024
ca43fbc
support ipywidget 7.x
superstar54 Mar 25, 2024
922ba3a
split data API to another PR
superstar54 Mar 29, 2024
31f0da2
update ui-test
superstar54 Mar 29, 2024
b529861
convert the positions (NumPy array) into a list (#51)
superstar54 Apr 3, 2024
e11b146
Merge branch 'main' into use_refactored_weas
superstar54 Apr 3, 2024
d211d70
fix snake style class name
superstar54 Apr 4, 2024
053e16b
update camera doc to include two settings:
superstar54 Apr 4, 2024
557883c
convert the positions (NumPy array) into a list (#51)
superstar54 Apr 3, 2024
68c092e
Merge branch 'main' into use_refactored_weas
superstar54 Apr 4, 2024
f69bf9a
Merge branch 'main' into use_refactored_weas
superstar54 Apr 4, 2024
d283898
fix camera
superstar54 Apr 5, 2024
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54 changes: 46 additions & 8 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -112,10 +112,10 @@ For a nice visualization of a crystal, show
from weas_widget import WeasWidget
viewer1 = WeasWidget()
viewer1.load_example("tio2.cif")
viewer1.modelStyle = 2
viewer1.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]
viewer1.showBondedAtoms = True
viewer1.colorType = "VESTA"
viewer1.avr.model_style = 2
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just pointing out that the meaning of avr is not intuitively clear to me

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It's AtomsViewer 😆 . I am thinking of three names:

  • viewer.avr.model_style=1
  • viewer.atoms_viewer.model_style=1
  • viewer.atoms.model_style=1
    Which one do you think is better? Or any other names?

BTW, tor the moment, the widget has three top-level attributes:

  • avr: AtomsViewer,
  • camera
  • imp: InstancedMeshPrimitive
    In the future, we will add
  • light
  • ops: Operators, e.g., viewer.ops.objects.delete()
  • scene, access all objects in the scene.

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@ltalirz ltalirz Apr 4, 2024 •
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I would vote for the option viewer.atoms in that case

camera, scene and light are self-explanatory.
imp is not - perhaps mesh?
ops is also not so clear to me (it would usually stand for "operations" as in FLOPS) - will there be other properties besides objects? (if not, objects could be a top-level attribute)

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Thanks! I need to think about this more; Most names come directly from the JavaScript part. I need to make sure the names are good on both sides.

viewer1.avr.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]
viewer1.avr.show_bonded_atoms = True
viewer1.avr.color_type = "VESTA"
viewer1
```

Expand All @@ -131,8 +131,8 @@ from ase.io.cube import read_cube_data
volume, atoms = read_cube_data("h2o-homo.cube")
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.volumetricData = {"values": volume}
viewer.isoSettings = [{"isovalue": 0.0001, "mode": 0}]
viewer.avr.iso.volumetric_data = {"values": volume}
viewer.avr.iso.settings = [{"isovalue": 0.0001, "mode": 0}]
viewer
```
<img src="docs/source/_static/images/example-isosurface.png" width="300px"/>
Expand All @@ -150,7 +150,7 @@ atoms*=[2, 2, 1]
atoms.set_array("moment", np.ones(len(atoms)))
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.modelStyle = 1
viewer.avr.model_style = 1
viewer
```
<img src="docs/source/_static/images/example-magnetic-moment.png" width="300px"/>
Expand All @@ -171,14 +171,52 @@ trajectory = generate_phonon_trajectory(atoms, eigenvector, repeat=[4, 4, 1])
viewer = WeasWidget()
viewer.from_ase(trajectory)
# set a vector field to show the arrow
viewer.vectorField = [{"origins": "positions", "vectors": "movement", "radius": 0.1}]
viewer.avr.vf.settings = [{"origins": "positions", "vectors": "movement", "radius": 0.1}]
viewer.avr.vf.show = True
viewer
```

<img src="docs/source/_static/images/example-phonon.gif" width="300px"/>



## Test

### Unit test

```console
pytest
```

### End-to-end test

The e2e test is similar to [ipywidgets](https://ipywidgets.readthedocs.io/en/latest/dev_testing.html).

For the first time, one needs to install the dependence.

```
cd tests/notebooks/
yarn install
```

Then run in a terminal:

```
yarn start
```

In another terminal:

```
yarn test
```

If the snapshots need to be updated:

```
yarn test:update
```

## Contact
* Xing Wang <xingwang1991@gmail.com>

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10 changes: 4 additions & 6 deletions docs/source/boundary.rst
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Expand Up @@ -21,15 +21,13 @@ Show the atoms on the unit cell:

.. code-block:: python

viewer.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]
viewer.modelStyle = 1
viewer.drawModels()
viewer.avr.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]
viewer.avr.model_style = 1


Create a supercell:

.. code-block:: python

viewer.boundary = [[-1, 2], [-1, 2], [-1, 2]]
viewer.modelStyle = 1
viewer.drawModels()
viewer.avr.boundary = [[-1, 2], [-1, 2], [-1, 2]]
viewer.avr.model_style = 1
28 changes: 24 additions & 4 deletions docs/source/camera.rst
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Expand Up @@ -2,15 +2,35 @@
Camera
===================

Setting
=============
The camera can be configured in two ways:

Direct Camera Settings
=======================

The camera has three direct settings:

- **zoom**: Controls the zoom level of the camera.
- **position**: Specifies the camera's position in 3D space.
- **look_at**: Determines the point in space the camera is oriented towards.

One can set the direction and zoom of the camera:
Example usage:

.. code-block:: python

viewer.cameraSetting = {"direction": [0, 5, 1], "zoom": 2}
viewer.camera.zoom = 2
viewer.camera.position = [0, 0, 100]
viewer.camera.look_at = [0, 0, 0]

Viewpoint-Centric Settings
===========================
This approach is useful for orienting the camera towards a subject, like the center of atoms or a bounding box, based on direction and distance from the subject.
This method automatically calculates the appropriate `position` and `look_at`` values.

.. code-block:: python

# Direction is relative to the center of atoms or bounding box.
# Distance specifies how far the camera is from the look_at point.
viewer.camera.setting = {"direction": [0, 5, 1], "distance": 50, "zoom": 2}
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Camera Type
=============
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6 changes: 3 additions & 3 deletions docs/source/color.rst
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Expand Up @@ -44,9 +44,9 @@ Here we show how to color the atoms by their forces.

viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.colorBy = "Force"
viewer.colorRamp = ["red", "yellow", "blue"]
viewer.modelStyle = 1
viewer.avr.color_by = "Force"
viewer.avr.color_ramp = ["red", "yellow", "blue"]
viewer.avr.model_style = 1
viewer


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4 changes: 2 additions & 2 deletions docs/source/isosurface.rst
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Expand Up @@ -16,8 +16,8 @@ Here is an example of drawing isosurfaces for HOMO of H2O molecule.
volume, atoms = read_cube_data("h2o-homo.cube")
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.volumetricData = {"values": volume}
viewer.isoSettings = [{"isovalue": 0.0001, "mode": 0}]
viewer.avr.iso.volumetric_data = {"values": volume}
viewer.avr.iso.settings = [{"isovalue": 0.0001, "mode": 0}]
viewer

.. figure:: _static/images/example-isosurface.png
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2 changes: 1 addition & 1 deletion docs/source/mesh_primitive.rst
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Expand Up @@ -63,7 +63,7 @@ The following example shows how to use the mesh primitive to draw two cubes and
},
]

viewer.meshPrimitives = data
viewer.imp.settings = data
viewer


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36 changes: 18 additions & 18 deletions docs/source/quick_start.ipynb
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Expand Up @@ -121,8 +121,7 @@
"outputs": [],
"source": [
"# ball and stick\n",
"viewer.modelStyle = 1\n",
"viewer.drawModels()"
"viewer.avr.model_style = 1"
]
},
{
Expand All @@ -141,8 +140,8 @@
"outputs": [],
"source": [
"# only draw stick (bond) for first four atoms\n",
"viewer.modelSticks = [1, 1, 1, 1, 0, 0, 0, 0]\n",
"viewer.drawModels()"
"viewer.model_sticks = [1, 1, 1, 1, 0, 0, 0, 0]\n",
"viewer.avr.draw()"
]
},
{
Expand All @@ -162,8 +161,8 @@
},
"outputs": [],
"source": [
"viewer.atomScales = [1, 1, 1, 1, 1, 0.6, 0.6, 0.6, 1.5, 1.5]\n",
"viewer.drawModels()"
"viewer.avr.atom_scales = [1, 1, 1, 1, 1, 0.6, 0.6, 0.6, 1.5, 1.5]\n",
"viewer.avr.draw()"
]
},
{
Expand All @@ -184,7 +183,7 @@
},
"outputs": [],
"source": [
"viewer.selectedAtomsIndices"
"viewer.avr.selected_atoms_indices"
]
},
{
Expand All @@ -202,7 +201,7 @@
"metadata": {},
"outputs": [],
"source": [
"viewer.selectedAtomsIndices = [0, 1, 2]"
"viewer.avr.selected_atoms_indices = [0, 1, 2]"
]
},
{
Expand All @@ -229,13 +228,13 @@
"viewer1 = WeasWidget()\n",
"viewer1.load_example(\"tio2.cif\")\n",
"# show polyhedra\n",
"viewer1.modelStyle = 2\n",
"viewer1.avr.model_style = 2\n",
"# show boundary atoms\n",
"viewer1.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]\n",
"viewer1.avr.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]\n",
"# show bonded atoms outside the cell\n",
"viewer1.showBondedAtoms = True\n",
"viewer1.avr.show_bonded_atoms = True\n",
"# Change color tyoe to \"VESTA\"\n",
"viewer1.colorType = \"VESTA\"\n",
"viewer1.avr.color_type = \"VESTA\"\n",
"viewer1"
]
},
Expand Down Expand Up @@ -308,10 +307,10 @@
"volume, atoms = read_cube_data(\"../../examples/h2o-homo.cube\")\n",
"viewer = WeasWidget()\n",
"viewer.from_ase(atoms)\n",
"viewer.volumetricData = {\"values\": volume}\n",
"viewer.avr.iso.volumetric_data = {\"values\": volume}\n",
"# mode 0: plot both positive and negative isosurface for the isovalue\n",
"# mode !=0, only plot one isosurface\n",
"viewer.isoSettings = [{\"isovalue\": 0.0001, \"mode\": 0}]\n",
"viewer.avr.iso.settings = [{\"isovalue\": 0.0001, \"mode\": 0}]\n",
"viewer"
]
},
Expand Down Expand Up @@ -340,7 +339,8 @@
"atoms.set_array(\"moment\", np.ones(len(atoms)))\n",
"viewer = WeasWidget()\n",
"viewer.from_ase(atoms)\n",
"viewer.modelStyle = 1\n",
"viewer.avr.model_style = 1\n",
"viewer.camera.setting = {\"direction\": [0, -1, 0]}\n",
"viewer"
]
},
Expand All @@ -363,7 +363,7 @@
"origins = atoms.positions\n",
"# the vertor\n",
"vectors = [[0, 0, 1]]*len(atoms)\n",
"viewer.vectorField = [{\"origins\": origins, \"vectors\": vectors, \"color\": \"red\"}]"
"viewer.avr.vf.settings = [{\"origins\": origins, \"vectors\": vectors, \"color\": \"red\"}]"
]
},
{
Expand Down Expand Up @@ -395,7 +395,7 @@
"viewer = WeasWidget()\n",
"viewer.from_ase(trajectory)\n",
"# set a vector field to show the arrow\n",
"viewer.vectorField = [{\"origins\": \"positions\", \"vectors\": \"movement\", \"radius\": 0.1}]\n",
"viewer.avr.vf.settings = [{\"origins\": \"positions\", \"vectors\": \"movement\", \"radius\": 0.1}]\n",
"viewer"
]
},
Expand All @@ -420,7 +420,7 @@
"One can set the direction and zoom of the camera:\n",
"\n",
"```python\n",
"viewer.cameraSetting = {\"direction\": [0, 5, 1], \"zoom\": 2}\n",
"viewer.camera.setting = {\"direction\": [0, 5, 1], \"zoom\": 2}\n",
"```\n"
]
},
Expand Down
4 changes: 2 additions & 2 deletions docs/source/vector_field.rst
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Expand Up @@ -18,7 +18,7 @@ Show the magnetic moment as a vector field.
atoms.set_array("moment", np.ones(len(atoms)))
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.modelStyle = 1
viewer.avr.model_style = 1
viewer

.. figure:: _static/images/example-magnetic-moment.png
Expand All @@ -43,7 +43,7 @@ One can visualize the phonon dispersion via lattice vibrations. One only need to
viewer = WeasWidget()
viewer.from_ase(trajectory)
# set a vector field to show the arrow
viewer.vectorField = [{"origins": "positions", "vectors": "movement", "radius": 0.1}]
viewer.avr.vf.settings = [{"origins": "positions", "vectors": "movement", "radius": 0.1}]
viewer


Expand Down
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