Add LSTMDoubleFit model for low-dimensional perovskite design

.clang_format.hook

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# Copyright (c) 2024 PaddlePaddle Authors. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -e
+
+readonly VERSION="13.0.0"
+
+version=$(clang-format -version)
+
+if ! [[ $(python -V 2>&1 | awk '{print $2}' | awk -F '.' '{print $1$2}') -ge 36 ]]; then
+    echo "clang-format installation by pip need python version great equal 3.6,
+          please change the default python to higher version."
+    exit 1
+fi
+
+if ! [[ $version == *"$VERSION"* ]]; then
+    # low version of pip may not have the source of clang-format whl
+    pip install --upgrade pip
+    pip install clang-format==13.0.0
+fi
+
+clang-format $@

.gitignore

@@ -136,4 +136,38 @@ ppsci/_version.py
 __pycache__/
 stability_prediction/data_bak/*
 stability_prediction/log/*
-stability_prediction/checkpoints/*
+stability_prediction/checkpoints/*
+
+structure_prediction/data/*
+structure_prediction/data_bak/*
+structure_prediction/log/*
+structure_prediction/checkpoints/*
+
+data/*
+log/*
+
+output/*
+experimental/output/*
+experimental/output
+experimental/data
+experimental/log/
+experimental/log2/
+
+output/*experimental/data/
+experimental/output/
+experimental/
+log2/
+log3/
+log_step2/
+log_step3/
+nohup.out
+ppmat/models/mattersim/threebody_indices.c
+step2_latest.log_nobug
+step3_15_H_without_formular.ckpt
+pretrained/
+result*
+spectrum_elucidation/retrival_database
+test/samplers
+outputs
+
+

.pre-commit-config.yaml

@@ -3,45 +3,61 @@ repos:
     rev: 5.11.5
     hooks:
       - id: isort
-        args: ["--multi-line=7", "--sl"]
+        args: ["--multi-line=7", "--sl", "--profile", "black", "--filter-files"]
+        exclude: '(jointContribution|legacy)/.*'
 
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
       - id: black
+        exclude: '(jointContribution|legacy)/.*'
 
-  # - repo: https://github.com/charliermarsh/ruff-pre-commit
-  #   rev: "v0.0.272"
-  #   hooks:
-  #     - id: ruff
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.272"
+    hooks:
+      - id: ruff
+        exclude: '(jointContribution|legacy)/.*'
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: a11d9314b22d8f8c7556443875b731ef05965464
     hooks:
       - id: check-merge-conflict
+        exclude: '(jointContribution|legacy)/.*'
       - id: check-symlinks
+        exclude: '(jointContribution|legacy)/.*'
       - id: detect-private-key
+        exclude: '(jointContribution|legacy)/.*'
         files: (?!.*paddle)^.*$
       - id: end-of-file-fixer
+        exclude: '(jointContribution|legacy)/.*'
       - id: trailing-whitespace
+        exclude: '(jointContribution|legacy)/.*'
       - id: check-case-conflict
+        exclude: '(jointContribution|legacy)/.*'
       - id: check-yaml
-        exclude: "mkdocs.yml"
+        # exclude: "mkdocs.yml"
+        exclude: (^jointContribution/.* | "mkdocs.yml" | ^legacy/.*)
       - id: pretty-format-json
+        exclude: '(jointContribution|legacy)/.*'
         args: [--autofix]
       - id: requirements-txt-fixer
+        exclude: '(jointContribution|legacy)/.*'
 
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.0.1
     hooks:
       - id: forbid-crlf
         files: \.md$
+        exclude: '(jointContribution|legacy)/.*'
       - id: remove-crlf
         files: \.md$
+        exclude: '(jointContribution|legacy)/.*'
       - id: forbid-tabs
         files: \.md$
+        exclude: '(jointContribution|legacy)/.*'
       - id: remove-tabs
         files: \.md$
+        exclude: '(jointContribution|legacy)/.*'
 
   - repo: local
     hooks:
@@ -51,3 +67,6 @@ repos:
         entry: bash .clang_format.hook -i
         language: system
         files: \.(c|cc|cxx|cpp|cu|h|hpp|hxx|cuh|proto)$
+        exclude: '(jointContribution|legacy)/.*'
+
+exclude: '(jointContribution|legacy)/.*'

Install.md

@@ -0,0 +1,56 @@
+# Installation 🔧
+
+[简体中文](./Install_cn.md)
+
+## 1. Installation Instructions
+
+We recommend using a conda virtual environment to manage dependencies. You can install conda via [Miniforge](https://github.com/conda-forge/miniforge).
+
+### 1.1 Create Virtual Environment
+Create and activate a new conda virtual environment:
+
+    conda create -n ppmat python=3.10
+    conda activate ppmat
+
+We currently develop under Python 3.10 environment and recommend using Python 3.10 or newer.
+
+### 1.2 Install PaddlePaddle
+Install the appropriate PaddlePaddle version based on your CUDA version. Refer to the [PaddlePaddle Official Website](https://www.paddlepaddle.org.cn/install/quick) for installation commands. We recommend installing PaddlePaddle version >= 3.1 or the develop version.
+
+For example, in a CUDA 12.6 environment, install the paddlepaddle-gpu version:
+
+    python -m pip install paddlepaddle-gpu==3.1.0 -i https://www.paddlepaddle.org.cn/packages/stable/cu126/
+
+After installation, verify the installation with:
+
+    python -c "import paddle; paddle.utils.run_check()"
+
+If you see "PaddlePaddle is installed successfully! Let's start deep learning with PaddlePaddle now.", the installation was successful.
+
+### 1.3 Install PaddleMaterials from Source:
+
+    # Clone PaddleMaterials repository
+    git clone https://github.com/PaddlePaddle/PaddleMaterials.git
+
+    # Navigate to PaddleMaterials directory
+    cd PaddleMaterials
+
+    # Install dependencies
+    pip install --upgrade pip setuptools wheel
+    pip install setuptools_scm
+    pip install Cython
+
+    # Install in editable mode
+    pip install -e .
+
+## 2. Run Examples
+
+Predict material properties using the MegNet model:
+
+    python property_prediction/predict.py --model_name='megnet_mp2018_train_60k_e_form' --weights_name='best.pdparams' --cif_file_path='./property_prediction/example_data/cifs/'
+
+Predict energy and forces using the MatterSim model:
+
+    python interatomic_potentials/predict.py --model_name='mattersim_1M' --weights_name='mattersim-v1.0.0-1M_model.pdparams' --cif_file_path='./interatomic_potentials/example_data/cifs/'
+
+For more usage instructions, refer to the [Get Started](./get_started.md) documentation.

Install_cn.md

@@ -0,0 +1,58 @@
+
+# Installation 🔧
+
+[English](./Install.md)
+
+## 1. 安装说明
+
+我们推荐使用conda虚拟环境来管理依赖包，你可以通过安装[Miniforge](https://github.com/conda-forge/miniforge)使用conda。
+
+### 1.1 创建虚拟环境
+创建一个新的conda虚拟环境，并激活环境：
+
+    conda create -n ppmat python=3.10
+    conda activate ppmat
+
+目前我们在python 3.10环境下进行开发，因此建议使用python 3.10或者更高的版本。
+
+### 1.2 安装PaddlePaddle
+根据你的cuda版本安装对应版本的PaddlePaddle，具体安装命令可参考[PaddlePaddle官网](https://www.paddlepaddle.org.cn/install/quick)。我们推荐安装PaddlePaddle >= 3.1或者develop版本。
+
+例如，对于cuda12.6环境，安装paddlepaddle-gpu版本：
+
+     python -m pip install paddlepaddle-gpu==3.1.0 -i https://www.paddlepaddle.org.cn/packages/stable/cu126/
+
+安装完毕之后，运行以下命令，验证 Paddle 是否安装成功。
+
+    python -c "import paddle; paddle.utils.run_check()"
+
+如果出现 PaddlePaddle is installed successfully! Let's start deep learning with PaddlePaddle now. 信息，说明已成功安装。
+
+### 1.3 源码安装PaddleMaterials：
+
+    # clone PaddleMaterials
+    git clone https://github.com/PaddlePaddle/PaddleMaterials.git
+
+    # 切换到PaddleMaterials目录
+    cd PaddleMaterials
+
+    # 安装依赖
+    pip install --upgrade pip setuptools wheel
+    pip install setuptools_scm
+    pip install Cython
+
+    # 以可编辑模式安装PaddleMaterials
+    pip install -e .
+
+
+## 2. 运行示例
+
+使用 MegNet 模型预测材料属性：
+
+    python property_prediction/predict.py --model_name='megnet_mp2018_train_60k_e_form' --weights_name='best.pdparams' --cif_file_path='./property_prediction/example_data/cifs/'
+
+使用 MatterSim 模型预测能量和力：
+
+    python interatomic_potentials/predict.py --model_name='mattersim_1M' --weights_name='mattersim-v1.0.0-1M_model.pdparams' --cif_file_path='./interatomic_potentials/example_data/cifs/'
+
+更多的使用说明可以参考[Get Started](./get_started.md)。