[Refine] Fix several bugs on custom device

README.md

@@ -300,6 +300,7 @@ python -c "import paddle; paddle.utils.run_check()"
 | [Open3D](https://github.com/PFCCLab/Open3D.git) | 三维图形库 | 全量支持 |
 | [neuraloperator](https://github.com/PFCCLab/neuraloperator) | 神经算子库 | 全量支持 |
 | [paddle_scatter](https://github.com/PFCCLab/paddle_scatter) | 张量稀疏聚合库 | 全量支持 |
+| [paddle_cluster](https://github.com/PFCCLab/paddle_cluster) | 几何采样聚合库 | 全量支持 |
 | [paddle_sparse](https://github.com/PFCCLab/paddle_sparse) | 张量稀疏计算库 | 全量支持 |
 | [paddle_harmonics](https://github.com/PFCCLab/paddle_harmonics.git) | 球面谐波变换库 | 全量支持 |
 | [deepali](https://github.com/PFCCLab/deepali) | 图像、点云配准库 | 全量支持 |

docs/index.md

@@ -142,7 +142,7 @@
     | 问题类型 | 案例名称 | 优化算法 | 模型类型 | 训练方式 | 数据集 | 参考资料 |
     |-----|---------|-----|---------|----|---------|---------|
     | 材料设计 | [散射板设计(反问题)](./zh/examples/hpinns.md) | 机理驱动 | Transformer | 无监督学习 | [Train Data](https://paddle-org.bj.bcebos.com/paddlescience/datasets/hPINNs/hpinns_holo_train.mat)<br>[Eval Data](https://paddle-org.bj.bcebos.com/paddlescience/datasets/hPINNs/hpinns_holo_valid.mat) | [Paper](https://arxiv.org/pdf/2102.04626.pdf) |
-    | 晶体材料属性预测 | [CGCNN](./zh/examples/cgcnn.md) | 数据驱动 | GNN | 监督学习 | [MP](https://next-gen.materialsproject.org/) / [Perovskite](https://cmr.fysik.dtu.dk/cubic_perovskites/cubic_perovskites.html) / [C2DB](https://cmr.fysik.dtu.dk/c2db/c2db.html) / [test](https://paddle-org.bj.bcebos.com/paddlescience%2Fdatasets%2Fcgcnn%2Fcgcnn-test.zip) | [Paper](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.145301) |
+    | 晶体材料属性预测 | [CGCNN](./zh/examples/cgcnn.md) | 数据驱动 | GNN | 监督学习 | [MP](https://next-gen.materialsproject.org/) / [Perovskite](https://cmr.fysik.dtu.dk/cubic_perovskites/cubic_perovskites.html) / [C2DB](https://cmr.fysik.dtu.dk/c2db/c2db.html) / [test](https://paddle-org.bj.bcebos.com/paddlescience/datasets/cgcnn/cgcnn-test.zip) | [Paper](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.145301) |
     | 二维材料生成与数据库 | [ML2DDB](./en/examples/ml2ddb.md) | 数据驱动 | GNN/Diffusion | 监督学习 | Coming Soon | [Paper](https://arxiv.org/pdf/2507.00584) |
 
 === "地球科学"

docs/zh/api/arch.md

@@ -4,11 +4,12 @@
     handler: python
     options:
       members:
+        - Arch
         - AFNONet
         - AMGNet
-        - Arch
         - AutoEncoder
         - ChipDeepONets
+        - Climateformer
         - CrystalGraphConvNet
         - CuboidTransformer
         - CVit1D
@@ -21,31 +22,30 @@
         - FNO1d
         - Generator
         - HEDeepONets
+        - IFMMLP
         - KAN
         - LatentNO
+        - LNO
         - LorenzEmbedding
+        - Meteoformer
         - MLP
         - ModelList
         - ModifiedMLP
+        - MoleculeModel
         - NowcastNet
+        - Preformer
+        - RegDGCNN
+        - RegPointNet
         - SFNONet
         - SPINN
         - STAFNet
         - TFNO1dNet
         - TFNO2dNet
         - TFNO3dNet
+        - TGCN
         - Transformer
         - UNetEx
         - UNONet
         - USCNN
-        - LNO
-        - TGCN
-        - RegDGCNN
-        - RegPointNet
-        - IFMMLP
-        - Meteoformer
-        - Climateformer
-        - MoleculeModel
-        - Preformer
       show_root_heading: true
       heading_level: 3

docs/zh/api/geometry.md

@@ -11,10 +11,10 @@
         - Hypersphere
         - Interval
         - Mesh
-        - SDFMesh
         - PointCloud
         - Polygon
         - Rectangle
+        - SDFMesh
         - Sphere
         - TimeDomain
         - TimeXGeometry

docs/zh/api/metric.md

@@ -10,10 +10,10 @@
         - LatitudeWeightedACC
         - LatitudeWeightedRMSE
         - MAE
+        - MaxAE
         - MeanL2Rel
         - MSE
-        - RMSE
-        - MaxAE
         - R2Score
+        - RMSE
       show_root_heading: true
       heading_level: 3

docs/zh/examples/CNN_UTS.md

@@ -3,7 +3,7 @@
 === "模型训练命令"
 
     ``` sh
-    python main.py mode=train
+    python main.py
     ```
 
 === "模型评估命令"
@@ -15,10 +15,10 @@
 ## 下载预训练模型
 
 | [resnet18-v5-fold1](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
- [resnet18-v5-fold2](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
- [resnet18-v5-fold3](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
- [resnet18-v5-fold4](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
- [resnet18-v5-fold5](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) ||
+[resnet18-v5-fold2](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
+[resnet18-v5-fold3](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
+[resnet18-v5-fold4](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
+[resnet18-v5-fold5](https://paddle-org.bj.bcebos.com/paddlescience/models/CNN_UTS/resnet18-v5-fold1.pdparams) |
 
 ## 下载模型必要参数
 
@@ -37,19 +37,19 @@
 ```
 CNN_UTS/
 │
-├─ conf/  
+├─ conf/
 │    └─ resnet.yaml
-├─ data_utils.py  
-├─ model_utils.py  
-├─ main.py  
-├─ requirements.txt  
-├─ readme.md  
-├─ resnet18-v5-finetune/  
-├─ outputs/  
-├─ Saved_Output/  
-└─ Dataset/  
-     ├─ Train_val/  
-     └─ Test/  
+├─ data_utils.py
+├─ model_utils.py
+├─ main.py
+├─ requirements.txt
+├─ readme.md
+├─ resnet18-v5-finetune/
+├─ outputs/
+├─ Saved_Output/
+└─ Dataset/
+     ├─ Train_val/
+     └─ Test/
 ```
 
 ## 2. 模型原理

docs/zh/examples/MLP_LI.md

@@ -12,8 +12,8 @@
 
 | 数据集名称 | 下载链接 |
 |-----------|---------|
-| 训练集 + 验证集 | [MP_data_down_loading(train+validate).csv](https://paddle-org.bj.bcebos.com/paddlescience%2Fdocs%2FMP_data_down_loading(train%2Bvalidate).csv) |
-| 训练集 + 验证集 + 测试集 | [MP_data_down_loading(train+validate+test).csv](https://paddle-org.bj.bcebos.com/paddlescience%2Fdocs%2FMP_data_down_loading(train%2Bvalidate%2Btest).csv) |
+| 训练集 + 验证集 | [MP_data_down_loading(train+validate).csv](https://paddle-org.bj.bcebos.com/paddlescience/docs/MP_data_down_loading(train+validate).csv) |
+| 训练集 + 验证集 + 测试集 | [MP_data_down_loading(train+validate+test).csv](https://paddle-org.bj.bcebos.com/paddlescience/docs/MP_data_down_loading(train+validate+test).csv) |
 
 数据读取需要额外安装依赖 `bayesian-optimization`，请运行安装命令 `pip install bayesian-optimization`。
 
@@ -28,7 +28,7 @@
 
 | 预训练模型                        |
 |-----------------------------------|
-| [MLP_LI_pretrained.pdparams]( https://paddle-org.bj.bcebos.com/paddlescience%2Fmodels%2FMLP_LI_pretrained.pdparams) |
+| [MLP_LI_pretrained.pdparams](https://paddle-org.bj.bcebos.com/paddlescience/models/MLP_LI_pretrained.pdparams) |
 
 
 ## 模型训练命令

docs/zh/examples/cgcnn.md

@@ -11,6 +11,7 @@
     ``` sh
     python CGCNN.py TRAIN_DIR="Your train dataset path" VALID_DIR="Your evaluate dataset path"
     ```
+
 === "模型评估命令"
 
     ``` sh

docs/zh/examples/fourcastnet.md

@@ -41,14 +41,16 @@
 
     ``` sh
     # 下载风速预测小样本数据
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience%2Fdatasets%2FFourcastNet%2F2018-04-04_n6_precip.npy -P ./datasets/era5/test/
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience%2Fdatasets%2FFourcastNet%2F2018-04-04_n6.npy -P ./datasets/era5/test/
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/FourcastNet/global_stds.npy -P ./datasets/era5/stat/
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/FourcastNet/global_means.npy -P ./datasets/era5/stat/
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/FourcastNet/2018-04-04_n6_precip.npy -P ./datasets/era5/test/
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/FourcastNet/2018-04-04_n6.npy -P ./datasets/era5/test/
+    # 下载降水量预测小样本数据
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/FourcastNet/2018-09-08_n32.npy -P ./datasets/era5/test/
     # 风速预训练模型推理
     python train_pretrain.py mode=infer
     # 风速微调模型推理
     python train_finetune.py mode=infer
-    # 下载降水量预测小样本数据
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience%2Fdatasets%2FFourcastNet%2F2018-09-08_n32.npy -P ./datasets/era5/test/
     # 降水量模型推理
     python train_precip.py mode=infer
     ```

docs/zh/examples/ifm.md

@@ -11,7 +11,7 @@
     ``` sh
     # 在tox21/sider/hiv/bace/bbbp等数据上训练模型MLP-IFM,embed_name可选IFM/None
     # mode/data_label/MODEL.embed_name 等参数可在conf/ifm.yaml进行配置
-    python ifm.py mode=train data_label=tox21 MODEL.embed_name='IFM'
+    python ifm.py data_label=tox21 MODEL.embed_name='IFM'
     ```
 
 === "模型评估命令"

docs/zh/examples/nsfnet.md

@@ -2,39 +2,39 @@
 
 <a href="https://aistudio.baidu.com/projectdetail/7305373" class="md-button md-button--primary" style>AI Studio快速体验</a>
 
-=== "模型评估命令"
+=== "模型训练命令"
 
     ``` sh
     # VP_NSFNet1
-    python VP_NSFNet1.py    mode=eval  pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet1.pdparams
+    python VP_NSFNet1.py
 
     # VP_NSFNet2
     # linux
     wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/NSFNet/cylinder_nektar_wake.mat -P ./data/
     # windows
     # curl https://paddle-org.bj.bcebos.com/paddlescience/datasets/NSFNet/cylinder_nektar_wake.mat --create-dirs -o ./data/cylinder_nektar_wake.mat
-
-    python VP_NSFNet2.py    mode=eval  data_dir=./data/cylinder_nektar_wake.mat  pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet2.pdparams
+    python VP_NSFNet2.py data_dir=./data/cylinder_nektar_wake.mat
 
     # VP_NSFNet3
-    python VP_NSFNet3.py    mode=eval  pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet3.pdparams
+    python VP_NSFNet3.py
     ```
 
-=== "模型训练命令"
+=== "模型评估命令"
 
     ``` sh
     # VP_NSFNet1
-    python VP_NSFNet1.py
+    python VP_NSFNet1.py mode=eval pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet1.pdparams
 
     # VP_NSFNet2
     # linux
     wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/NSFNet/cylinder_nektar_wake.mat -P ./data/
     # windows
     # curl https://paddle-org.bj.bcebos.com/paddlescience/datasets/NSFNet/cylinder_nektar_wake.mat --create-dirs -o ./data/cylinder_nektar_wake.mat
-    python VP_NSFNet2.py data_dir=./data/cylinder_nektar_wake.mat
+
+    python VP_NSFNet2.py mode=eval data_dir=./data/cylinder_nektar_wake.mat pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet2.pdparams
 
     # VP_NSFNet3
-    python VP_NSFNet3.py
+    python VP_NSFNet3.py mode=eval pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet3.pdparams
     ```
 
 

docs/zh/examples/nsfnet4.md

@@ -2,7 +2,7 @@
 
 <a href="https://aistudio.baidu.com/projectdetail/7305374" class="md-button md-button--primary" style>AI Studio快速体验</a>
 
-=== "模型评估命令"
+=== "模型训练命令"
 
     ``` sh
     # VP_NSFNet4
@@ -12,10 +12,11 @@
     # windows
     # curl https://paddle-org.bj.bcebos.com/paddlescience/datasets/NSFNet/NSF4_data.zip --create-dirs -o ./data/NSF4_data.zip
     # unzip ./data/NSF4_data.zip
-    python VP_NSFNet4.py    mode=eval  data_dir=./data/  EVAL.pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet4.pdparams
+    python VP_NSFNet4.py data_dir=./data/
+
     ```
 
-=== "模型训练命令"
+=== "模型评估命令"
 
     ``` sh
     # VP_NSFNet4
@@ -25,8 +26,7 @@
     # windows
     # curl https://paddle-org.bj.bcebos.com/paddlescience/datasets/NSFNet/NSF4_data.zip --create-dirs -o ./data/NSF4_data.zip
     # unzip ./data/NSF4_data.zip
-    python VP_NSFNet4.py data_dir=./data/
-
+    python VP_NSFNet4.py mode=eval data_dir=./data/ EVAL.pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/nsfnet/nsfnet4.pdparams
     ```
 
 === "模型导出命令"

docs/zh/examples/perovskite_solar_cells_nn.md

@@ -9,7 +9,7 @@
 === "模型训练命令"
 
     ``` sh
-    python psc_nn.py mode=train
+    python psc_nn.py
     ```
 
 === "模型评估命令"
@@ -20,7 +20,7 @@
     ```
 
     ``` sh
-    # 或使用远程预训练模型
+    # 或使用提供的预训练模型
     python psc_nn.py mode=eval eval.pretrained_model_path="https://paddle-org.bj.bcebos.com/paddlescience/models/PerovskiteSolarCells/solar_cell_pretrained.pdparams"
     ```
 
@@ -59,7 +59,7 @@
 
 ### 3.1 数据集介绍
 
-本案例使用的数据集包含 [Perovskite Database Project(PDP) 数据](https://paddle-org.bj.bcebos.com/paddlescience%2Fdatasets%2Fpsc%2Fdata.zip)。数据集分为以下几个部分：
+本案例使用的数据集包含 [Perovskite Database Project(PDP) 数据](https://paddle-org.bj.bcebos.com/paddlescience/datasets/psc/data.zip)。数据集分为以下几个部分：
 
 1. 训练集：
    - 特征数据：`data/cleaned/training.csv`

docs/zh/examples/phygeonet.md

@@ -25,8 +25,8 @@
     # curl https://paddle-org.bj.bcebos.com/paddlescience/datasets/PhyGeoNet/heat_equation_bc_test.npz --create-dirs -o ./data/heat_equation.npz
 
     python heat_equation_with_bc.py
-
     ```
+
 === "模型评估命令"
 
     ``` sh

docs/zh/examples/synthemol.md

@@ -11,7 +11,7 @@
     ``` sh
     # 使用antibiotics等数据训练模型chemprop模型,实现Property Predict
     # 配置可在conf/synthemol.yaml进行修改
-    python main.py mode=train
+    python main.py
     ```
 
 === "Property Predictor模型评估命令"

docs/zh/examples/tadf.md

@@ -16,17 +16,17 @@
     ``` sh
     # Est 预测:  
     cd TADF_Est
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/Est/Est.dat  https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/Est/Est.dat https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
     python Est.py mode=train
 
-    #f 预测:
+    # f 预测:
     cd TADF_f
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/f/f.dat  https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/f/f.dat https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
     python f.py mode=train
 
     # angle 预测:
     cd TADF_angle
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/angle/angle.dat  https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/angle/angle.dat https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
     python angle.py mode=train
     ```
 
@@ -35,17 +35,17 @@
     ``` sh
     # Est 评估：
     cd TADF_Est
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/Est/Est.dat  https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/Est/Est.dat https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
     python Est.py mode=eval EVAL.pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/TADF/Est/Est_model.pdparams
 
     # f 评估:
     cd TADF_f
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/f/f.dat  https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/f/f.dat https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
     python f.py mode=eval EVAL.pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/TADF/f/f_model.pdparams
 
     # angle 评估:
     cd TADF_angle
-    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/f/f.dat  https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
+    wget -nc https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/f/f.dat https://paddle-org.bj.bcebos.com/paddlescience/datasets/TADF/smis.txt
     python angle.py mode=eval EVAL.pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/TADF/angle/angle_model.pdparams
     ```