Fix cvit (#1244)

* fix cvit coords_dim and shapenet_car.py

* update requirements.txt

* fix

* fix docstring style for chemprop_molecule_utils.py

* fix

Author: HydrogenSulfate

docs/zh/examples/transolver.md

@@ -2,7 +2,7 @@
 
 !!! note
 
-    第一次运行时，会对 mlcfd_data 进行预处理，大约需要一小时，请耐心等待
+    运行本案例前请先安装相关依赖库: `pip install -r requirements.txt`
 
 === "模型训练命令"
 
@@ -15,6 +15,10 @@
     python main.py
     ```
 
+    !!! note
+
+        第一次运行时，会对 mlcfd_data 进行预处理，大约需要一小时，请耐心等待
+
 === "模型评估命令"
 
     ``` sh
@@ -26,6 +30,10 @@
     python main.py mode=eval EVAL.pretrained_model_path=https://paddle-org.bj.bcebos.com/paddlescience/models/transolver/transolver_pretrained.pdparams
     ```
 
+    !!! note
+
+        第一次运行时，会对 mlcfd_data 进行预处理，大约需要一小时，请耐心等待
+
 === "模型导出命令"
 
     ``` sh
@@ -43,6 +51,10 @@
     python main.py mode=infer
     ```
 
+    !!! note
+
+        第一次运行时，会对 mlcfd_data 进行预处理，大约需要一小时，请耐心等待
+
 | 预训练模型  | 指标 |
 |:--| :--|
 | [transolver_pretrained.pdparams](https://paddle-org.bj.bcebos.com/paddlescience/models/transolver/transolver_pretrained.pdparams) | rho_d:, 0.99314<br>c_d: 0.01136<br>relative l2 error of press: 0.07829<br>relative l2 error of velocity: 0.02304<br>press: 4.95888<br>velocity: [0.12163974 0.14851639 0.41583335] 0.26443 |

examples/transolver/requirements.txt

@@ -0,0 +1,2 @@
+-e git+https://github.com/PFCCLab/paddle_geometric.git@main#egg=paddle_geometric
+vtk

examples/transolver/shapenet_car.py

@@ -24,7 +24,13 @@
 
 try:
     from paddle_geometric import nn as nng
+except ModuleNotFoundError:
+    pass
+try:
     from paddle_geometric.data import Data
+except ModuleNotFoundError:
+    pass
+try:
     from paddle_geometric.utils import k_hop_subgraph
 except ModuleNotFoundError:
     pass
@@ -362,7 +368,9 @@ def get_shape(data, max_n_point=8192, normalize=True, use_height=False):
     return shape_pc
 
 
-def create_edge_index_radius(data, r, max_neighbors=32) -> "torch.Tensor":  # noqa: F821
+def create_edge_index_radius(
+    data, r, max_neighbors=32
+) -> "paddle.Tensor":  # noqa: F821
     data.edge_index = nng.radius_graph(
         x=data.pos, r=r, loop=True, max_num_neighbors=max_neighbors
     )
@@ -410,23 +418,23 @@ def __len__(self):
     def __getitem__(self, idx):
         sample = self.datalist[idx]
         shape = get_shape(sample, use_height=self.use_height)
-        velo_press = paddle.from_dlpack(sample.y)
+        velo_press = sample.y
 
         inp = {
-            "x": paddle.from_dlpack(sample.x),
-            # "pos": paddle.from_dlpack(sample.pos),
+            "x": sample.x,
+            # "pos": (sample.pos),
         }
         lab = {
             "velo_vec": velo_press[..., 0:3],  # x,y,z
             "press": velo_press[..., 3:],  # p
-            "surf": paddle.from_dlpack(sample.surf),
+            "surf": sample.surf,
         }
         wei = {}
         # lab["sdf"] = inp["x"][:, 3:4]
         # lab["normal_vec"] = inp["x"][:, 4:]
 
         if not self.training:
-            lab["shape"] = paddle.from_dlpack(shape)
+            lab["shape"] = shape
 
         return inp, lab, wei