Add zinc protein #3
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Support virial forward run on gpu with cpu kernel
Deepmd in Paddle for example, just 'water_se_a' model
…a_cpu fix error in cpu mode
…load support jist save load
HydrogenSulfate
changed the base branch from
zinc_protein
to
add_water_tensor_dipole
HydrogenSulfate
requested changes
Jan 3, 2024
deepmd/descriptor/se_a_mask.py
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| @@ -115,6 +117,8 @@ def __init__( | |||
| precision: str = "default", | |||
| uniform_seed: bool = False, | |||
| ) -> None: | |||
| paddle.nn.Layer.__init__(self) | |||
There was a problem hiding this comment.
- 把上面的
@Descriptor.register("se_a_mask")装饰器去掉 - 使用
super().__init__()
deepmd/descriptor/se_a_mask.py
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| self.place_holders[ii] = tf.placeholder( | ||
| GLOBAL_NP_FLOAT_PRECISION, [None, None], name=name_pfx + "t_" + ii | ||
| # self.nei_type = tf.constant(nei_type, dtype=tf.int32) | ||
| self.nei_type = paddle.to_tensor(nei_type, dtype="int32") |
There was a problem hiding this comment.
self.register_buffer("nei_type", paddle.to_tensor(nei_type, dtype="int32"))，注册为buffer代替to_tensor
deepmd/descriptor/se_a_mask.py
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| # avg_zero = np.zeros([self.ntypes, self.ndescrpt]).astype( | ||
| # GLOBAL_NP_FLOAT_PRECISION | ||
| # ) | ||
| # std_ones = np.ones([self.ntypes, self.ndescrpt]).astype( | ||
| # GLOBAL_NP_FLOAT_PRECISION | ||
| # ) | ||
| # sub_graph = tf.Graph() | ||
| # with sub_graph.as_default(): | ||
| # name_pfx = "d_sea_mask_" | ||
| # for ii in ["coord", "box"]: | ||
| # self.place_holders[ii] = tf.placeholder( | ||
| # GLOBAL_NP_FLOAT_PRECISION, [None, None], name=name_pfx + "t_" + ii | ||
| # ) | ||
| # self.place_holders["type"] = tf.placeholder( | ||
| # tf.int32, [None, None], name=name_pfx + "t_type" | ||
| # ) | ||
| # self.place_holders["mask"] = tf.placeholder( | ||
| # tf.int32, [None, None], name=name_pfx + "t_aparam" | ||
| # ) # named aparam for inference compatibility in c++ interface. | ||
|
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| # self.place_holders["natoms_vec"] = tf.placeholder( | ||
| # tf.int32, [self.ntypes + 2], name=name_pfx + "t_natoms" | ||
| # ) # Not used in se_a_mask. For compatibility with c++ interface. | ||
| # self.place_holders["default_mesh"] = tf.placeholder( | ||
| # tf.int32, [None], name=name_pfx + "t_mesh" | ||
| # ) # Not used in se_a_mask. For compatibility with c++ interface. | ||
|
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| # self.stat_descrpt, descrpt_deriv, rij, nlist = op_module.descrpt_se_a_mask( | ||
| # self.place_holders["coord"], | ||
| # self.place_holders["type"], | ||
| # self.place_holders["mask"], | ||
| # self.place_holders["box"], | ||
| # self.place_holders["natoms_vec"], | ||
| # self.place_holders["default_mesh"], | ||
| # ) | ||
| # self.sub_sess = tf.Session(graph=sub_graph, config=default_tf_session_config) |
deepmd/train/trainer.py
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| @@ -126,8 +126,12 @@ def _init_param(self, jdata): | |||
| descrpt_param["multi_task"] = True | |||
| if descrpt_param["type"] in ["se_e2_a", "se_a", "se_e2_r", "se_r", "hybrid"]: | |||
| descrpt_param["spin"] = self.spin | |||
| descrpt_param.pop("type") | |||
| self.descrpt = deepmd.descriptor.se_a.DescrptSeA(**descrpt_param) | |||
| if descrpt_param["type"]=="se_a_mask": | |||
| self.mask = paddle.to_tensor(self.mask, place="cpu") | ||
| box_ = paddle.to_tensor(box_, place="cpu") | ||
| natoms = paddle.to_tensor(natoms, place="cpu") | ||
| mesh = paddle.to_tensor(mesh, place="cpu") |
| } | ||
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| void DescrptSeAMaskCPUKernel(int n_descrpt, |
There was a problem hiding this comment.
将DescrptSeAMaskCPUKernel从普通函数改造成模板函数，可参考其他文件，否则浮点类型会被固定为double
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| descrpt[kk*total_atom_num * total_atom_num * n_descrpt+ ii * total_atom_num * 4 + jj] = 0.; | ||
| } | ||
| for (int jj = 0; jj < natoms * 4 * 3; ++jj) { | ||
| descrpt_deriv[kk*total_atom_num * total_atom_num * n_descrpt * 3+ ii * total_atom_num * 4 * 3 + jj] = 0.; |
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| // int nloc = total_atom_num; | ||
| // int ndescrpt = nloc > 0 ? nframes * nloc * 3 / net_deriv.shape()[1] : 0; | ||
| // int ndescrpt = nloc * 4; | ||
| // int nnei = total_atom_num; | ||
| // int nnei = nloc > 0 ? nlist_tensor.shape()[1] / nloc : 0; |
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| // int ndescrpt = nloc > 0 ? net_deriv_tensor.shape()[1] / nloc : 0; | ||
| // int nnei = total_atom_num; |
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| .Inputs({paddle::Grad("force"), "net_deriv", "in_deriv", "mask", "nlist"}) | ||
| .Attrs({"total_atom_num: int"}) | ||
| .Outputs({paddle::Grad("net_deriv")}) | ||
| .SetKernelFn(PD_KERNEL(ProdForceSeAMaskBackward)); |
HydrogenSulfate
changed the base branch from
add_water_tensor_dipole
to
paddle2
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