From d94b9f3b5da95b5da00b47263a304a7300fdb505 Mon Sep 17 00:00:00 2001 From: yanghan234 Date: Tue, 3 Dec 2024 03:50:21 +0000 Subject: [PATCH] deploy: b57447fd5bdb451ceed70e413adf51e1752b494e --- ..._3.png => examples_phonon_example_7_3.png} | Bin ..._4.png => examples_phonon_example_7_4.png} | Bin _sources/examples/phonon_example.ipynb | 17 ++---- _sources/user_guide/getting_started.rst | 5 +- _sources/user_guide/installation.rst | 5 +- examples/phonon_example.html | 14 ++--- examples/phonon_example.ipynb | 17 ++---- searchindex.js | 2 +- user_guide/getting_started.html | 51 +++++++++--------- user_guide/installation.html | 5 +- 10 files changed, 55 insertions(+), 61 deletions(-) rename _images/{examples_phonon_example_8_3.png => examples_phonon_example_7_3.png} (100%) rename _images/{examples_phonon_example_8_4.png => examples_phonon_example_7_4.png} (100%) diff --git a/_images/examples_phonon_example_8_3.png b/_images/examples_phonon_example_7_3.png similarity index 100% rename from _images/examples_phonon_example_8_3.png rename to _images/examples_phonon_example_7_3.png diff --git a/_images/examples_phonon_example_8_4.png b/_images/examples_phonon_example_7_4.png similarity index 100% rename from _images/examples_phonon_example_8_4.png rename to _images/examples_phonon_example_7_4.png diff --git a/_sources/examples/phonon_example.ipynb b/_sources/examples/phonon_example.ipynb index 4653aa9..bab2964 100644 --- a/_sources/examples/phonon_example.ipynb +++ b/_sources/examples/phonon_example.ipynb @@ -27,18 +27,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "
\n", - " If you see the error information that the ``phonopy`` package is missing, you can install it with\n", - "
" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - " ``conda install phonopy -c conda-forge``\n", - "
" + "> 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", + "> ```" ] }, { diff --git a/_sources/user_guide/getting_started.rst b/_sources/user_guide/getting_started.rst index 5088487..3703b26 100644 --- a/_sources/user_guide/getting_started.rst +++ b/_sources/user_guide/getting_started.rst @@ -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 @@ -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) diff --git a/_sources/user_guide/installation.rst b/_sources/user_guide/installation.rst index 4fc33be..7f575f6 100644 --- a/_sources/user_guide/installation.rst +++ b/_sources/user_guide/installation.rst @@ -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 `_, +and the `uv `_ package manager. .. code-block:: console diff --git a/examples/phonon_example.html b/examples/phonon_example.html index bdeba00..3fbf5bb 100644 --- a/examples/phonon_example.html +++ b/examples/phonon_example.html @@ -343,12 +343,12 @@

2. Phonon Dispersion -

If you see the error information that the phonopy package is missing, you can install it with

- -
-

conda install phonopy -c conda-forge

+
+

If you see the error that the phonopy package is missing, you can install it with

+
conda install phonopy -c conda-forge
+
+

2.1. Set up the atomic structure with attached MatterSim Calculator#

@@ -454,14 +454,14 @@

2.2. Set up the phonon workflow

-../_images/examples_phonon_example_8_3.png +../_images/examples_phonon_example_7_3.png
-../_images/examples_phonon_example_8_4.png +../_images/examples_phonon_example_7_4.png
diff --git a/examples/phonon_example.ipynb b/examples/phonon_example.ipynb index 4653aa9..bab2964 100644 --- a/examples/phonon_example.ipynb +++ b/examples/phonon_example.ipynb @@ -27,18 +27,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "
\n", - " If you see the error information that the ``phonopy`` package is missing, you can install it with\n", - "
" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - " ``conda install phonopy -c conda-forge``\n", - "
" + "> 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", + "> ```" ] }, { diff --git a/searchindex.js b/searchindex.js index c4292a4..d31d11d 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"A minimal example using ASE calculator": [[5, "a-minimal-example-using-ase-calculator"]], "Batch prediction using the Potential class": [[5, "batch-prediction-using-the-potential-class"]], "Bibliography": [[4, "bibliography"]], "Compile the docs": [[0, "compile-the-docs"]], "Examples": [[1, null]], "Frequently Asked Questions": [[4, "frequently-asked-questions"]], "Getting Started": [[5, null]], "Import the necessary modules": [[3, "import-the-necessary-modules"]], "Install from PyPI": [[6, "install-from-pypi"]], "Install from source code": [[6, "install-from-source-code"]], "Installation": [[6, null]], "MatterSim Documentations": [[0, null]], 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Structure Optimization", "Welcome to the MatterSim Documentation!", "Getting Started", "Installation"], "titleterms": {"A": 5, "ASE": 5, "ask": 4, "atom": 2, "attach": 2, "batch": 5, "bibliographi": 4, "calcul": [2, 5], "checkpoint": 6, "class": 5, "code": 6, "compil": 0, "dispers": 2, "doc": 0, "document": [0, 4], "exampl": [1, 5], "frequent": 4, "from": 6, "get": 5, "import": 3, "instal": 6, "mattersim": [0, 2, 4], "minim": 5, "model": [4, 6], "modul": 3, "necessari": 3, "optim": 3, "overview": 4, "phonon": 2, "potenti": 5, "pre": 4, "predict": 5, "prerequisit": 0, "pypi": 6, "question": 4, "relax": 3, "run": 3, "set": [2, 3], "sourc": 6, "start": 5, "structur": [2, 3], "train": 4, "up": [2, 3], "us": 5, "welcom": 4, "workflow": 2}}) \ No newline at end of file diff --git a/user_guide/getting_started.html b/user_guide/getting_started.html index cb190cd..6d5ae24 100644 --- a/user_guide/getting_started.html +++ b/user_guide/getting_started.html @@ -360,32 +360,35 @@

Batch prediction using the predict_properties method. In the following example, we demonstrate how to predict the properties of a list of structures using the Potential class.

-
 1import numpy as np
- 2from ase.build import bulk
- 3from ase.units import GPa
- 4from mattersim.forcefield.potential import Potential
- 5from mattersim.datasets.utils.build import build_dataloader
- 6
- 7# set up the structure
- 8si = bulk("Si", "diamond", a=5.43)
- 9
-10# replicate the structures to form a list
-11structures = [si] * 10
-12
-13# load the model
-14potential = Potential.load(load_path="/path/to/checkpoint", device="cuda:0")
-15
-16# build the dataloader that is compatible with MatterSim
-17dataloader = build_dataloader(structures, only_inference=True)
+
 1import torch
+ 2import numpy as np
+ 3from ase.build import bulk
+ 4from ase.units import GPa
+ 5from mattersim.forcefield.potential import Potential
+ 6from mattersim.datasets.utils.build import build_dataloader
+ 7
+ 8# set up the structure
+ 9si = bulk("Si", "diamond", a=5.43)
+10
+11# replicate the structures to form a list
+12structures = [si] * 10
+13
+14# load the model
+15device = "cuda" if torch.cuda.is_available() else "cpu"
+16print(f"Running MatterSim on {device}")
+17potential = Potential.load(device=device)
 18
-19# make predictions
-20predictions = potential.predict_properties(dataloader, include_forces=True, include_stresses=True)
+19# build the dataloader that is compatible with MatterSim
+20dataloader = build_dataloader(structures, only_inference=True)
 21
-22# print the predictions
-23print(f"Total energy in eV: {predictions[0]}")
-24print(f"Forces in eV/Angstrom: {predictions[1]}")
-25print(f"Stresses in GPa: {predictions[2]}")
-26print(f"Stresses in eV/A^3: {np.array(predictions[2])*GPa}")
+22# make predictions
+23predictions = potential.predict_properties(dataloader, include_forces=True, include_stresses=True)
+24
+25# print the predictions
+26print(f"Total energy in eV: {predictions[0]}")
+27print(f"Forces in eV/Angstrom: {predictions[1]}")
+28print(f"Stresses in GPa: {predictions[2]}")
+29print(f"Stresses in eV/A^3: {np.array(predictions[2])*GPa}")
 

 

 

diff --git a/user_guide/installation.html b/user_guide/installation.html
index 3b5b505..df0fc21 100644
--- a/user_guide/installation.html
+++ b/user_guide/installation.html
@@ -348,8 +348,9 @@ 
Install from source codehttps://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,
+and the uv package manager.

 
mamba env create -f environment.yaml
 mamba activate mattersim
 uv pip install -e .