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doc: update docs and fix bugs #35

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merged 3 commits into from
Dec 3, 2024
Merged

doc: update docs and fix bugs #35

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5aa4de6
fix hyperlink
yanghan-microsoft Dec 3, 2024
5ef0cf3
update warning
yanghan-microsoft Dec 3, 2024
225a5b2
update the second example for getting started
yanghan-microsoft Dec 3, 2024
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17 changes: 5 additions & 12 deletions docs/examples/phonon_example.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -27,18 +27,11 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"<div class=\"alert alert-info\">\n",
" If you see the error information that the ``phonopy`` package is missing, you can install it with\n",
"</div>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<div class=\"alert alert-info\">\n",
" ``conda install phonopy -c conda-forge``\n",
"</div>"
"> If you see the error that the ``phonopy`` package is missing, you can install it with\n",
"> \n",
"> ```bash\n",
"> conda install phonopy -c conda-forge\n",
"> ```"
]
},
{
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5 changes: 4 additions & 1 deletion docs/user_guide/getting_started.rst
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Expand Up @@ -43,6 +43,7 @@ a list of structures using the ``Potential`` class.
.. code-block:: python
:linenos:

import torch
import numpy as np
from ase.build import bulk
from ase.units import GPa
Expand All @@ -56,7 +57,9 @@ a list of structures using the ``Potential`` class.
structures = [si] * 10

# load the model
potential = Potential.load(load_path="/path/to/checkpoint", device="cuda:0")
device = "cuda" if torch.cuda.is_available() else "cpu"
print(f"Running MatterSim on {device}")
potential = Potential.load(device=device)

# build the dataloader that is compatible with MatterSim
dataloader = build_dataloader(structures, only_inference=True)
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5 changes: 3 additions & 2 deletions docs/user_guide/installation.rst
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Expand Up @@ -33,8 +33,9 @@ To install the package, run the following command under the root of the folder:


Please note that the installation process may take a while due to the installation of the dependencies.
For faster installation, we recommend the users to install with [mamba or micromamba](https://mamba.readthedocs.io/en/latest/index.html),
and the [uv](https://docs.astral.sh/uv/) package manager.
For faster installation, we recommend the users to install with
`mamba or micromamba <https://mamba.readthedocs.io/en/latest/index.html>`_,
and the `uv <https://docs.astral.sh/uv/>`_ package manager.

.. code-block:: console

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