refactor(data preprocess): remove the cut off options from info.json #200
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…and collect the values from input.json
Previous the ase data will be transferred into text file and then loaded by the _TrajData. now i refactor the function. both text and ase data are treated equally. will works as a class funtion to initial the _TrajData class.
…om_model_options .
…g96. For powerlaw and varTang96, the rs is not exactly the hard cutoff. so when extract the r_max for data. we have to use rs + 5 * w; but for other method just use rs.
…s instance and add from_model class function. note, compared to the previous build_dataset, this one is more flexible. previous build_dataset is a function. now i define a class DataBuilder and re-defined __call__ function. then build_dataset is an instance of DataBuilder class. so i can use build_dataset.from_model() to build dataset from model. at the same time the previous way to use build_dataset is still available. like build_dataset(...).
| @@ -500,7 +500,7 @@ def from_points( | |||
| def from_ase( | |||
| cls, | |||
| atoms, | |||
| r_max, | |||
| r_max: Union[float, int, dict], | |||
| er_max: Optional[float] = None, | |||
| # same cell size, then copy it to all frames. | ||
| cell = np.expand_dims(cell, axis=0) | ||
| data["cell"] = np.broadcast_to(cell, (info["nframes"], 3, 3)) | ||
| elif cell.shape[0] == info["nframes"] * 3: |
| pos = np.loadtxt(os.path.join(root, "positions.dat")) | ||
| if len(pos.shape) == 1: | ||
| pos = pos.reshape(1,3) | ||
| natoms = info["natoms"] |
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ok看起来nframes和natoms的逻辑是没动的
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nframes natoms 如果想去掉。就必须修改文本数据的存储格式。比如一帧结构存为一行这样。不然没办法从数据中提取这个信息。因此我没办法去掉。
| @@ -170,7 +170,7 @@ def __init__(self, model:torch.nn.Module, results_path: str=None, use_gui: bool= | |||
| self.results_path = results_path | |||
| self.use_gui = use_gui | |||
|
|
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| def get_bands(self, data: Union[AtomicData, ase.Atoms, str], kpath_kwargs: dict, AtomicData_options: dict={}): | |||
| def get_bands(self, data: Union[AtomicData, ase.Atoms, str], kpath_kwargs: dict, pbc:Union[bool,list]=None, AtomicData_options:dict=None): | |||
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这里为啥单加pbc，以及，前面数据部分AtomicData_options 被info取代掉了，这里为啥保留？
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单加pbc 是因为这信息不一定能从给的结构文件中提取到。需要支持外部的指定。 这里支持AtomicData_options 是为了兼容以前的一些存档。这个后续使用是可以不提供。但是对于一些旧存档，就必须加上，不然存档不能用。
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而数据部分取消，是因为以后做训练任务，我们就不需要这个了。以后新训练下来的模型，后处理算能带的时候，也可以不提供这个。这个参数现在是 optional的。
这一切都是为了软件的兼容性，所不得不做的设置。
floatingCatty
approved these changes
Aug 13, 2024
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refactor(data preprocess): remove the cut off options from info.json and collect the values from input.json. when run model no need to supply the atomicdata options.
Fix: #155