Add ase_interface with support for optimization and md #176

JunnHuo · 2025-07-10T06:54:52Z

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CLAassistant · 2025-07-10T06:54:58Z

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leeleolay · 2025-07-11T03:37:29Z

ppmat/calculators/base_calculator.py

此文件内容重点抽象了predictor，建议进一步抽象为predictor组件，新建一个ppmat/predictor文件下，放到该目录下，可兼容加载属性预测模型，机器学习势函数模型的多个任务的predictor

已修改为predict组件中

leeleolay · 2025-07-11T03:40:14Z

interatomic_potentials/applications/md.py

此文件放到calculator下面会不会更好一点，calculator支持md的计算功能

已修改为task组件中

不建议使用task，和场景的计算“任务”概念冲突

leeleolay · 2025-07-11T03:41:46Z

ppmat/calculators/ase_calculator.py

这里修改为ase_engine会不会更合适一点，方便后面兼容多个计算软件库，从calculor的功能层面，支持md，dft任务，从支持这些任务的引擎来说，包括了ase，或者以后添加的其他软件库

leeleolay · 2025-07-11T03:49:41Z

interatomic_potentials/applications/relax_structure.py

这个同md，是不是也可以迁移到calculator中

leeleolay · 2025-07-11T03:51:10Z

interatomic_potentials/applications/md_ase_case.py

md_ase_case这里的代码看起来和md有些重复，功能区分和调用逻辑上是不是可以再优化一下

已删除，合并到一个文件中

leeleolay · 2025-07-11T03:51:24Z

interatomic_potentials/applications/relax_structure_ase_case.py

这里同md_case

已删除，合并到一个文件中

leeleolay · 2025-07-11T03:52:28Z

predictor和calculator建议取消掉ppmat，和trainer保持类似的命名一致性规则

zhiminzhang0830 · 2025-07-11T06:06:13Z

interatomic_potentials/applications/md.py

+import sys
+
+__dir__ = os.path.dirname(os.path.abspath(__file__))  # ruff: noqa
+sys.path.insert(0, os.path.abspath(os.path.join(__dir__, "../../")))  # ruff: noqa


使用新的安装方式后，不需要动态引入路径了，可以删除这两行代码了

zhiminzhang0830 · 2025-07-11T06:10:31Z

ppmat/calculators/ase_calculator.py

+            if "energy_per_atom" in label_names and "energy" not in label_names:
+                label_names.append("energy")
+        else:
+            raise NotImplementedError(


最好也支持一下mattersim

这版pr后支持mattersim

zhiminzhang0830

辛苦后续需修改模型readme中关于predict部分的运行命令，其他说明文件中如涉及predict部分辛苦也一并修改

zhiminzhang0830 · 2025-07-17T06:00:04Z

ppmat/predict/property_interface.py

+                    out = self.model.predict(data)
+            else:
+                out = self.model.predict(data)
+            out = self.post_process(out)


建议将此处的model.predict、post_process等操作整合到一个新的函数内，并在此处调用，也方便在ase_interface中调用

zhiminzhang0830 · 2025-07-17T06:04:18Z

ppmat/predict/base.py

+            save_load.load_pretrain(model, self.checkpoint_path)
+        else:
+            logger.info("Since model_name is given, downloading it...")
+            model, config = build_model_from_name(self.model_name, self.weights_name)


if分支中对chgnet修改了其is_intensive参数，但else分支中未做处理，可能会导致此处产生的模型不符合预期

zhiminzhang0830 · 2025-07-17T06:06:26Z

ppmat/predict/base.py

+    def load_inference_model(
+        self,
+        ase_calc: bool = False,
+        device: Optional[str] = "cpu",


device参数在以下的代码中未使用，需要增加使用该参数的代码

zhiminzhang0830 · 2025-07-17T06:19:56Z

ppmat/predict/base.py

+            all_files = [
+                osp.join(file_path, f)
+                for f in os.listdir(file_path)
+                if f.endswith(".cif")


此处与注释中的不太一致，应修改注释或增加其他文件类型的支持

Supported formats include: CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT, vasprun.xml, CSSR, Netcdf and pymatgen's JSON-serialized structures.

leeleolay

建议模块从ppmat/predict修改为ppmat/predictor

leeleolay · 2025-07-18T07:04:37Z

predictor和calculator逻辑拆分的还是有点问题

…iction script

leeleolay

文件名Applications 建议修改为 “Data–Mechanics Integrated Scientific Computing”

leeleolay · 2025-09-17T11:21:35Z

applications/application_configs/potential.yaml

+hydra:
+  job:
+    name: potential
+    chdir: True                                            # 是否切换工作目录到 run.dir


中文注释辛苦切换为英文

leeleolay · 2025-09-17T11:22:32Z

tests/dataset_jarvis.py

test下的文件如果不是必须的辛苦不要提交了

leeleolay · 2025-09-17T11:27:18Z

applications/structure_generation.py

这个文件是不是提交错了

Data_Mechanics_Integrated_Scientific_Computing/structure_generation.py

leeleolay

新增的training yaml建议都放到Training_test里面

leeleolay · 2025-09-28T06:05:36Z

Data_Mechanics_Integrated_Scientific_Computing/example_data/cifs/results_pred_property.csv

这个文件的作用是什么？如果是结果文件的话可以删除掉，或者在readme文件里注明参考结果文件，相关文件放到网上存储

leeleolay · 2025-09-28T06:06:53Z

Data_Mechanics_Integrated_Scientific_Computing/structure_generation.py

这个文件可以删除

leeleolay · 2025-09-28T06:08:53Z

Data_Mechanics_Integrated_Scientific_Computing/application_configs/property.yaml

这个地方的property是用在哪个地方的？

leeleolay · 2025-09-28T06:10:28Z

experiments/structure_generation/configs/Sample/by_chemical_formula.yaml

sample这块的都可以先删掉

leeleolay · 2025-09-28T06:13:13Z

ppmat/datasets/mptrj_dataset.py

            path (str): Path to the data.
        """
        json_data = read_json(path)
+


这个地方的改动是为什么？

leeleolay · 2025-09-28T06:15:19Z

ppmat/predictor/__init__.py

predictor里面为什么要暴露StructureSampler

leeleolay · 2025-09-28T06:16:26Z

ppmat/predictor/sample.py

这个可以删掉的

leeleolay · 2025-09-28T06:18:03Z

tests/dataset_jarvis.py

这几个文件如果没有改变辛苦可以不提交

leeleolay · 2025-09-28T06:21:36Z

experiments/interatomic_potentials/configs/task_chgnet/README.md

这里和mattersim为什么出现了两个readme文件？

leeleolay · 2025-09-28T12:40:03Z

辛苦提供一个readme文档，怎么运行；requirement里添加hydra

leeleolay · 2025-10-16T02:11:45Z

docs/multi_device.md

这个地方还原吧

leeleolay · 2025-10-16T02:12:30Z

README.md

这里请还原

leeleolay · 2025-10-16T02:16:04Z

interatomic_potentials/configs/chgnet/chgnet_mptrj.yaml

这个文件夹应该还原不改动

leeleolay · 2025-10-16T02:17:55Z

property_prediction/configs/comformer/comformer_jarvis_alex_pbe_2d_train_e_form.yaml

这个文件夹请还原

leeleolay · 2025-10-16T02:18:52Z

structure_generation/configs/mattergen/mattergen_alex_mp20.yaml

这个文件夹请还原

leeleolay · 2025-10-16T02:19:46Z

ppmat/predictor/sample.py

leeleolay · 2025-10-23T12:38:10Z

ppmat/models/dimenetpp/dimenetpp.py

        property_names (Optional[str], optional): A comma-separated list of
            target property names to predict. Defaults to "formation_energy_per_atom".
-        data_norm_mean (float, optional): The mean used for normalizing target values.
+        data_mean (float, optional): The mean used for normalizing target values.


这里为什么这么改

leeleolay · 2025-10-23T12:39:30Z

ppmat/models/dimenetpp/dimenetpp.py

-            tensor=paddle.to_tensor(data_norm_std), name="data_norm_std"
-        )
+        self.register_buffer(tensor=paddle.to_tensor(data_mean), name="data_mean")
+        self.register_buffer(tensor=paddle.to_tensor(data_std), name="data_std")


这里为什么取消锁进

leeleolay · 2025-10-24T07:09:32Z

property_prediction/configs/comformer/comformer_mp2018_train_60k_band_gap.yaml

-  formation_energy_per_atom:
+  band_gap:
    __class_name__: paddle.nn.L1Loss #MAEMetric
    __init_params__: {}


这里为什么要修改

leeleolay · 2025-10-24T07:10:46Z

ppmat/predictor/__init__.py

@@ -0,0 +1,21 @@
+# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserved.


2023 改为2025

leeleolay · 2025-10-24T07:12:27Z

ppmat/predictor/base.py

@@ -0,0 +1,245 @@
+# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserved.


修改为2025

leeleolay · 2025-10-24T07:21:31Z

ppmat/predictor/sample.py

这个文件是不是可以还原

leeleolay · 2025-10-24T07:22:11Z

ppmat/predictor/structures.py

添加paddle 权利说明注释

leeleolay · 2025-10-24T07:23:02Z

ppmat/calculator/ase.py

@@ -0,0 +1,452 @@
+# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserved.


leeleolay

dataset的代码还原一下吧或者为什么要修改，之前的问题回复一下

leeleolay · 2025-10-24T11:48:38Z

ppmat/datasets/matbench_dataset.py

-    from different matbench JSON files and processing them for materials property prediction.
+        science benchmark datasets.
+    The implementation supports loading multiple properties from different
+        matbench JSON files and processing them for materials property prediction.


leeleolay self-requested a review July 11, 2025 03:31

leeleolay reviewed Jul 11, 2025

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zhiminzhang0830 reviewed Jul 11, 2025

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zhiminzhang0830 reviewed Jul 17, 2025

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leeleolay reviewed Jul 18, 2025

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JunnHuo added 8 commits September 1, 2025 07:00

Add ase_interface with support for optimization and md

69aa46b

Keep the from_structures func in base_calculator

deea169

Add predict and tasks modules; update ASE interface and property pred…

37ed942

…iction script

Add example usage

1c75f1d

WIP: save local changes

06c3c3e

modify err

ee55f16

Remove tests from tracking

0226096

Save local changes before rebase

c32fabd

JunnHuo force-pushed the develop branch from cd05a95 to c32fabd Compare September 1, 2025 07:07

JunnHuo added 7 commits September 1, 2025 07:13

Sync missing files from upstream/develop

6023fe5

modify train config

0d3354f

revise train config (2nd version)

9a2dc78

revise train config (3rd version)

f8b5710

Update training config (4th version)

24d6b70

Update training config (5th version)

a34fef1

Update training config

59614f5

leeleolay requested changes Sep 17, 2025

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JunnHuo added 2 commits September 18, 2025 11:33

small fix

6eeafb6

small fix: correct structure generation

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leeleolay reviewed Sep 19, 2025

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Data_Mechanics_Integrated_Scientific_Computing/structure_generation.py Outdated Show resolved Hide resolved

leeleolay reviewed Sep 28, 2025

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save local changes before merge upstream

52f050a

merge upstream develop

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leeleolay added the enhancement New feature or request label Sep 30, 2025

change configs and README

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leeleolay requested changes Oct 16, 2025

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JunnHuo added 6 commits October 16, 2025 10:02

resolve config bug in predict.py

e8ce0be

keep previous content

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keep previous content

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keep previous content

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keep previous content

578522a

fix: correct commit message for ppmatSim README

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leeleolay reviewed Oct 23, 2025

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JunnHuo added 2 commits October 24, 2025 03:48

revert

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remove experiments directory for PR review

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leeleolay reviewed Oct 24, 2025

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JunnHuo added 2 commits October 24, 2025 08:06

correct

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correct

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leeleolay reviewed Oct 24, 2025

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		@@ -0,0 +1,21 @@
		# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserved.

		@@ -0,0 +1,245 @@
		# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserved.

		@@ -0,0 +1,452 @@
		# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserved.

Add ase_interface with support for optimization and md #176

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Add ase_interface with support for optimization and md #176

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leeleolay commented Jul 11, 2025

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leeleolay commented Jul 18, 2025

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CLAassistant commented Jul 10, 2025 •

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