[Example] Add TADF材料分子的光电性质预测

docs/zh/examples/TADF.md

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+# 化学领域-分子性质预测
+
+| 预训练模型  | 指标 |
+|:--| :--|
+| [Est.pdparams](https://paddle-org.bj.bcebos.com/paddlescience/models/TADF/Est/Est_pretrained.pdparams) | loss(MAE): 0.045 |
+| [f.pdparams](https://paddle-org.bj.bcebos.com/paddlescience/models/TADF/f/f_pretrained.pdparams) | loss(MAE): 0.036 |
+| [angle.pdparams](https://paddle-org.bj.bcebos.com/paddlescience/models/TADF/angle/angle_pretrained.pdparams) | loss(MAE): 0.041 |
+
+
+=== "模型训练命令"
+
+    ``` sh
+    #Est预测：
+    python Est.py mode=train
+
+    #f 预测
+    python f.py mode=train
+
+    # angle 预测
+    python angle.py mode=train
+
+    ```
+=== "模型评估命令"
+
+    ``` sh
+     #Est 评估：
+    python Est.py
+
+    #f 评估
+    python f.py
+
+    # angle 评估
+    python angle.py
+
+
+
+# 化学领域-分子性质预测
+## 1.背景简介
+有机发光二极管（OLED）具有高效率、结构灵活和低成本的优势，在先进显示和照明技术中受到广泛关注。在有机发光二极管器件中，电注入载流子以1：3的比例形成单线态和三线态激子。以纯荧光材料为发光材料构建的OLED发光效率IQE理论极限为25%。另一方面，有机金属复合物发光材料通过引入稀有金属（Ir，Pt等）带来强自旋轨道耦合（SOC），可以将单线态激子通过系间窜越过程转化成三线态激子，从而利用三线态激子发出磷光，其IQE可达100%，但是稀有金属价格昂贵，为推广使用带来了阻碍。热活化延迟荧光材料（TADF）为解决这些问题提供了新思路，并引起了广泛关注。在TADF中，三线态通过逆系间窜越过程（RISC）转化成单重态并发出荧光，从而实现100%的IQE，而RISC过程很大程度上取决于最低单线态（S1）和最低三线态（T1） 之间的能隙（ΔEST）。根据量子力学理论，ΔEST相当于HOMO和LUMO之间的交换积分的两倍。因此TADF分子的常见设计策略是将电子供体（D）和电子受体（A）以明显扭曲的二面角结合以实现HOMO和LUMO在空间上明显的分离。然而，与ΔEST相反，振子强度（f）需要较大的HOMO和LUMO之间的重叠积分，这二者之间的矛盾需要进一步平衡。
+
+## 论文信息：
+Yufei Bu, Qian Peng*, Designing Promising Thermally Activated Delayed Fluroscence Emitters via Machine Learning-Assisted High-Throughput Virtual Screening. J. Phys. Chem. C. 2023. DOI: 10.1021/acs.jpcc.3c05337
+
+##  2.功能目标
+通过高通量计算构建数据集，使用分子指纹作为模型输入，实现对于TADF材料分子性质的无计算预测。
+
+## 3.数据库构建
+我们选择常用的49个受体和50个受体以单键相连的方式进行组合，通过穷举所有可能的组合位点我们得到了44470个分子。通过MMFF94力场优化得到分子的初始结构。从44470个分子中随机提取5136个分子，在B3LYP/6-31G（d）水平下对5136个分子进行基态结构优化，采用TDDFT方法在基态构型下进行激发态性质计算。
+
+## 4.模型构建
+对于三个预测对象，设计了相同的深度神经网络，网络结构为含有两层隐藏层的神经网络，第一层隐藏层含有587个神经元，第二层隐藏层含有256个神经元，隐藏层之间加入Dropout。本文档以angle预测为例介绍
+
+```
+model = ppsci.arch.DNN(
+    input_keys=tuple(x.keys()),
+    hidden_size=hidden_size,
+    num_layers=num_layers,
+    **cfg.MODEL,
+)
+```
+
+## 5.约束构建
+本研究采用监督学习，直接构建'SupervisedConstraint'
+
+```
+ bc_sup = ppsci.constraint.SupervisedConstraint(
+        dataloader_cfg={
+            "dataset": {
+                "input": x,
+                "label": {"u": y_train},
+                "weight": {"W": param},
+                "name": "IterableNamedArrayDataset",
+            },
+            "batch_size": cfg.TRAIN.batch_size,
+        },
+        loss=ppsci.loss.MSELoss("mean"),
+        name="bc_sup",
+    )
+```
+
+## 6. 优化器构建
+训练器采用Adam优化器
+
+```
+ optimizer = ppsci.optimizer.optimizer.Adam(
+        cfg.TRAIN.learning_rate,
+        beta1=(0.9, 0.99)[0],
+        beta2=(0.9, 0.99)[1],
+        weight_decay=cfg.TRAIN.weight_decay,
+    )(model)
+
+```
+
+## 7. 模型训练
+完成上述设置之后，只需要将上述实例化的对象按顺序传递给'ppsci.solver.Solver'，然后启动训练
+
+```
+solver = ppsci.solver.Solver(
+        model,
+        constraint={
+            "bc_sup": bc_sup,
+        },
+        optimizer=optimizer,
+        epochs=cfg.TRAIN.epochs,
+        eval_during_train=False,
+        iters_per_epoch=cfg.TRAIN.iters_per_epoch,
+        seed=cfg.seed,
+    )
+```
+
+## 8. 完整代码
+
+```
+import os
+
+import hydra
+import matplotlib.pyplot as plt
+import numpy as np
+import paddle
+import rdkit.Chem as Chem
+from omegaconf import DictConfig
+from rdkit.Chem import AllChem
+from sklearn.decomposition import PCA
+from sklearn.metrics import r2_score
+from sklearn.model_selection import train_test_split
+
+import ppsci
+
+os.environ["HYDRA_FULL_ERROR"] = "1"
+os.environ["KMP_DUPLICATE_LIB_OK"] = "True"
+plt.rcParams["axes.unicode_minus"] = False
+plt.rcParams["font.sans-serif"] = ["DejaVu Sans"]
+
+# 加载数据集
+data = []
+for line in open("./angle.dat"):
+    num = float(line.strip())
+    num = num / 90
+    data.append(num)
+smis = []
+for line in open("./smis.txt"):
+    smis.append(line.strip())
+vectors = []
+del_mol = []
+for num in smis:
+    mol = Chem.MolFromSmiles(num)
+    try:
+        fp = AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048)
+        _input = np.array(list(map(float, fp.ToBitString())))
+        vectors.append(_input)
+    except Exception:
+        del_mol.append(num)
+pca = PCA(n_components=0.99)
+pca.fit(vectors)
+Xlist = paddle.to_tensor(pca.transform(vectors))
+
+
+def train(cfg: DictConfig):
+    # 划分数据集
+    def k_fold(k, i, X, Y):
+        fold_size = tuple(X.shape)[0] // k
+        val_start = i * fold_size
+        if i != k - 1:
+            val_end = (i + 1) * fold_size
+            x_val, y_val = X[val_start:val_end], Y[val_start:val_end]
+            x_train = np.concatenate((X[0:val_start], X[val_end:]), axis=0)
+            y_train = np.concatenate((Y[0:val_start], Y[val_end:]), axis=0)
+        else:
+            x_val, y_val = X[val_start:], Y[val_start:]
+            x_train = X[0:val_start]
+            y_train = Y[0:val_start]
+        return x_train, y_train, x_val, y_val
+
+    x_train, y_train, x_test, y_test = k_fold(cfg.TRAIN.k, cfg.TRAIN.i, Xlist, data)
+    # 处理数据集
+    x_train = paddle.to_tensor(x_train, dtype="float32")
+    x = {
+        "key_{}".format(i): paddle.unsqueeze(
+            paddle.to_tensor(x_train[:, i], dtype="float32"), axis=1
+        )
+        for i in range(x_train.shape[1])
+    }
+    y_train = paddle.unsqueeze(paddle.to_tensor(y_train, dtype="float32"), axis=1)
+
+    param = paddle.empty((len(x["key_0"]), len(x_train)), "float32")
+    param = ppsci.utils.initializer.xavier_normal_(param)
+    # 构建约束
+    bc_sup = ppsci.constraint.SupervisedConstraint(
+        dataloader_cfg={
+            "dataset": {
+                "input": x,
+                "label": {"u": y_train},
+                "weight": {"W": param},
+                "name": "IterableNamedArrayDataset",
+            },
+            "batch_size": cfg.TRAIN.batch_size,
+        },
+        loss=ppsci.loss.MSELoss("mean"),
+        name="bc_sup",
+    )
+    hidden_size = [587, 256]
+    num_layers = None
+    # 实例化模型
+    model = ppsci.arch.DNN(
+        input_keys=tuple(x.keys()),
+        hidden_size=hidden_size,
+        num_layers=num_layers,
+        **cfg.MODEL,
+    )
+    optimizer = ppsci.optimizer.optimizer.Adam(
+        cfg.TRAIN.learning_rate,
+        beta1=(0.9, 0.99)[0],
+        beta2=(0.9, 0.99)[1],
+        weight_decay=cfg.TRAIN.weight_decay,
+    )(model)
+
+    # 构建Solver
+    solver = ppsci.solver.Solver(
+        model,
+        constraint={
+            "bc_sup": bc_sup,
+        },
+        optimizer=optimizer,
+        epochs=cfg.TRAIN.epochs,
+        eval_during_train=False,
+        iters_per_epoch=cfg.TRAIN.iters_per_epoch,
+        seed=cfg.seed,
+    )
+    try:
+        solver.train()
+    except Exception as ex:
+        print(ex)
+    paddle.save(model.state_dict(), cfg.TRAIN.save_model_path)
+
+
+# 进行测试
+def eval(cfg: DictConfig):
+    # 重新划分数据集
+    x_train, x_test, y_train, y_test = train_test_split(
+        Xlist, data, test_size=cfg.EVAL.test_size, random_state=cfg.EVAL.seed
+    )
+    x = {
+        "key_{}".format(i): paddle.unsqueeze(
+            paddle.to_tensor(x_test[:, i], "float32"), axis=1
+        )
+        for i in range(x_test.shape[1])
+    }
+    hidden_size = [587, 256]
+    num_layers = None
+    model = ppsci.arch.DNN(
+        input_keys=tuple(x.keys()),
+        hidden_size=hidden_size,
+        num_layers=num_layers,
+        **cfg.MODEL,
+    )
+    model.set_state_dict(paddle.load(cfg.EVAL.load_model_path))
+    ytest = paddle.unsqueeze(paddle.to_tensor(y_test, dtype="float32"), axis=1)
+    ypred = model(x)
+    ytest = {"u": ytest}
+
+    # 计算损失
+    loss = ppsci.metric.MAE()
+    MAE = loss(ypred, ytest).get("u").numpy()
+    loss = ppsci.metric.RMSE()
+    RMSE = loss(ypred, ytest).get("u").numpy()
+    ypred = ypred.get("u").numpy()
+    ytest = ytest.get("u").numpy()
+    R2 = r2_score(ytest, ypred)
+    print("MAE", MAE)
+    print("RMSE", RMSE)
+    print("R2", R2)
+
+    # 可视化
+    plt.scatter(ytest, ypred, s=15, color="royalblue", marker="s", linewidth=1)
+    plt.plot([ytest.min(), ytest.max()], [ytest.min(), ytest.max()], "r-", lw=1)
+    plt.legend(title="R²={:.3f}\n\nMAE={:.3f}".format(R2, MAE))
+    plt.xlabel("Test θ(°)")
+    plt.ylabel("Predicted θ(°)")
+    plt.show()
+
+
+@hydra.main(version_base=None, config_path="./config", config_name="angle.yaml")
+def main(cfg: DictConfig):
+    if cfg.mode == "train":
+        train(cfg)
+    elif cfg.mode == "eval":
+        eval(cfg)
+    else:
+        raise ValueError(f"cfg.mode should in ['train', 'eval'], but got '{cfg.mode}'")
+
+
+# if cfg.mode == "train":
+#     train(cfg)
+# elif cfg.mode == "eval":
+#     evaluate(cfg)
+
+
+if __name__ == "__main__":
+    main()
+```