│ │ ├── type.raw │ │ └── type_map.raw │ └── validation_data │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ └── force.npy │ ├── type.raw │ └── type_map.raw ├── input.json └── dpmd.slurm 其...
"type_map": ["Ge", "Te"] } 参数定义如下: nvnmd模型的多个版本对应于不同的网络结构(后面也会根据需要新增版本)。nvnmd-v0和nvnmd-v1在以下方面不同: nvnmd-v0和nvnmd-v1分别使用se_a描述符和se_atten描述符。 nvnmd-v0中每种元素有一组参数,最多支持4种元素类型,nvnmd-v1中所有元素共享一...
self.type_map = type_map self.ntypes = len(type_map) self.rcut = r_max @@ -692,14 +718,30 @@ def forward_lower_common(def serialize(self) -> dict: """Serialize the model.""" msg = "not implemented" raise NotImplementedError(msg) ...
Thetype_mapis optional, which provide the element names (but not restricted to) for corresponding atom types. The construction of the descriptor is given by optiondescriptor. Thetypeof the descriptor is set to"se_a", which means smooth-edition, angular infomation. Thercutis the cut-off radius...
"type_map": ["O","H"], "descriptor": { "type": "se_uni", "sel": [40], "rcut_smth": 0.5, "rcut": 4.0, "nlayers": 3, "g1_dim": 128, "g2_dim": 32, "attn2_hidden": 32, "attn2_nhead": 4, "attn1_hidden": 128, "attn1_nhead": 4, "axis_dim": 4, "updat...
The type_map is optional, which provide the element names (but not restricted to) for corresponding atom types. The construction of the descriptor is given by option descriptor. The type of the descriptor is set to "se_a", which means smooth-edition, angular infomation. The rcut is the ...
"type_map":["O","H"], DeepMD-kit中对每个原子类型是按从0开始的整数编号的。这个参数给了这样的编号系统中每个原子类型一个元素名。这里我们照写data/type_map.raw的内容就好。比如我们改成 : "type_map":["A","B","C"], 其次,我们修改一下近邻搜索参数 : ...
Type embedding net type_map Mapping atom type to the name (str) of the type. For example type_map[1] gives the name of the type 1. data_stat_nbatch Number of frames used for data statistic data_stat_protect Protect parameter for atomic energy regression Methods build(coord_, atype_, ...
neighbor_stat(*, system: str, rcut: float, type_map: List[str], one_type: bool = False, **kwargs)[source] Calculate neighbor statistics. Parameters systemstr system to stat rcutfloat cutoff radius type_maplist[str] type map one_typebool, optional, default=False treat all types as...
ms = dpdata.System(type_map=type_map) ms.from_deepmd_npy(system_path, labeled=False) nframe = ms.get_nframes() # nframes x natoms x 3 coord = ms['coords'] # nframes x 9 cell = ms['cells'].reshape([nframe, -1]) # List[int] ...