diff --git a/docs/auto_update_fops.py b/docs/auto_update_fops.py new file mode 100644 index 00000000..5690f7c9 --- /dev/null +++ b/docs/auto_update_fops.py @@ -0,0 +1,64 @@ +from dptb.utils.argcheck import common_options, train_options, data_options, model_options +from dptb.utils.argcheck import run_options, set_info_options +from dargs.dargs import Argument + +def gen_doc_list(arglist, make_anchor=False, make_link=False): + + if isinstance(arglist, Argument): + arglist = [arglist] + assert isinstance(arglist, list) + + ptr = [] + for arg in arglist: + ptr.append(arg.gen_doc(make_anchor=make_anchor, make_link=make_link)) + + return "\n\n".join(ptr) + + +# 1. common_options +ops = common_options() +docstr = gen_doc_list(ops, make_anchor=True, make_link=True) +with open("./input_params/common_options.rst", "w") as of: + print('========================================\nCommon Options\n========================================', file=of) + print(docstr, file=of) +print("1. updated common_options.rst") + +# 2. train_options +ops = train_options() +docstr = gen_doc_list(ops, make_anchor=True, make_link=True) +with open("./input_params/train_options.rst", "w") as of: + print('========================================\nTrain Options\n========================================', file=of) + print(docstr, file=of) +print("2. updated train_options.rst") + +# 3. model_options +ops = model_options() +docstr = gen_doc_list(ops, make_anchor=True, make_link=True) +with open("./input_params/model_options.rst", "w") as of: + print('========================================\nModel Options\n========================================', file=of) + print(docstr, file=of) +print("3. updated model_options.rst") + +# 4. data_options +ops = data_options() +docstr = gen_doc_list(ops, make_anchor=True, make_link=True) +with open("./input_params/data_options.rst", "w") as of: + print('========================================\nData Options\n========================================', file=of) + print(docstr, file=of) +print("4. updated data_options.rst") + +# 5. run_options +ops = run_options() +docstr = gen_doc_list(ops, make_anchor=True, make_link=True) +with open("./input_params/run_options.rst", "w") as of: + print('========================================\nRun Options\n========================================', file=of) + print(docstr, file=of) +print("5. updated run_options.rst") + +# 6. set_info_options +ops = set_info_options() +docstr = gen_doc_list(ops, make_anchor=True, make_link=True) +with open("./input_params/set_info.rst", "w") as of: + print('========================================\nSet Info\n========================================', file=of) + print(docstr, file=of) +print("6. updated set_info.rst") diff --git a/docs/input_params/data_options.rst b/docs/input_params/data_options.rst index 7893209c..95443cba 100644 --- a/docs/input_params/data_options.rst +++ b/docs/input_params/data_options.rst @@ -9,6 +9,30 @@ data_options: The options for dataset settings in training. + .. _`data_options/r_max`: + + r_max: + | type: ``str`` | ``float`` | ``int``, optional, default: ``5.0`` + | argument path: ``data_options/r_max`` + + r_max + + .. _`data_options/oer_max`: + + oer_max: + | type: ``str`` | ``float`` | ``int``, optional, default: ``5.0`` + | argument path: ``data_options/oer_max`` + + oer_max + + .. _`data_options/er_max`: + + er_max: + | type: ``str`` | ``float`` | ``int``, optional, default: ``5.0`` + | argument path: ``data_options/er_max`` + + er_max + .. _`data_options/train`: train: diff --git a/docs/input_params/model_options.rst b/docs/input_params/model_options.rst index 766d970b..d9662809 100644 --- a/docs/input_params/model_options.rst +++ b/docs/input_params/model_options.rst @@ -25,7 +25,7 @@ model_options: method: | type: ``str`` (flag key), default: ``se2`` | argument path: ``model_options/embedding/method`` - | possible choices: |code:model_options/embedding[se2]|_, |code:model_options/embedding[baseline]|_, |code:model_options/embedding[deeph-e3]|_, |code:model_options/embedding[e3baseline_0]|_, |code:model_options/embedding[e3baseline_1]|_, |code:model_options/embedding[e3baseline_2]|_, |code:model_options/embedding[e3baseline_3]|_, |code:model_options/embedding[e3baseline_4]|_, |code:model_options/embedding[e3baseline_5]|_, |code:model_options/embedding[e3baseline_6]|_, |code:model_options/embedding[e3baseline_nonlocal]|_ + | possible choices: |code:model_options/embedding[se2]|_, |code:model_options/embedding[baseline]|_, |code:model_options/embedding[deeph-e3]|_, |code:model_options/embedding[e3baseline_5]|_, |code:model_options/embedding[e3baseline_6]|_, |code:model_options/embedding[slem]|_, |code:model_options/embedding[lem]|_, |code:model_options/embedding[e3baseline_nonlocal]|_ The parameters to define the embedding model. @@ -35,20 +35,14 @@ model_options: .. _`code:model_options/embedding[baseline]`: `model_options/embedding[baseline]`_ .. |code:model_options/embedding[deeph-e3]| replace:: ``deeph-e3`` .. _`code:model_options/embedding[deeph-e3]`: `model_options/embedding[deeph-e3]`_ - .. |code:model_options/embedding[e3baseline_0]| replace:: ``e3baseline_0`` - .. _`code:model_options/embedding[e3baseline_0]`: `model_options/embedding[e3baseline_0]`_ - .. |code:model_options/embedding[e3baseline_1]| replace:: ``e3baseline_1`` - .. _`code:model_options/embedding[e3baseline_1]`: `model_options/embedding[e3baseline_1]`_ - .. |code:model_options/embedding[e3baseline_2]| replace:: ``e3baseline_2`` - .. _`code:model_options/embedding[e3baseline_2]`: `model_options/embedding[e3baseline_2]`_ - .. |code:model_options/embedding[e3baseline_3]| replace:: ``e3baseline_3`` - .. _`code:model_options/embedding[e3baseline_3]`: `model_options/embedding[e3baseline_3]`_ - .. |code:model_options/embedding[e3baseline_4]| replace:: ``e3baseline_4`` - .. _`code:model_options/embedding[e3baseline_4]`: `model_options/embedding[e3baseline_4]`_ .. |code:model_options/embedding[e3baseline_5]| replace:: ``e3baseline_5`` .. _`code:model_options/embedding[e3baseline_5]`: `model_options/embedding[e3baseline_5]`_ .. |code:model_options/embedding[e3baseline_6]| replace:: ``e3baseline_6`` .. _`code:model_options/embedding[e3baseline_6]`: `model_options/embedding[e3baseline_6]`_ + .. |code:model_options/embedding[slem]| replace:: ``slem`` + .. _`code:model_options/embedding[slem]`: `model_options/embedding[slem]`_ + .. |code:model_options/embedding[lem]| replace:: ``lem`` + .. _`code:model_options/embedding[lem]`: `model_options/embedding[lem]`_ .. |code:model_options/embedding[e3baseline_nonlocal]| replace:: ``e3baseline_nonlocal`` .. _`code:model_options/embedding[e3baseline_nonlocal]`: `model_options/embedding[e3baseline_nonlocal]`_ @@ -253,605 +247,466 @@ model_options: | argument path: ``model_options/embedding[deeph-e3]/n_layer`` - .. _`model_options/embedding[e3baseline_0]`: + .. _`model_options/embedding[e3baseline_5]`: - When |flag:model_options/embedding/method|_ is set to ``e3baseline_0``: + When |flag:model_options/embedding/method|_ is set to ``e3baseline_5``: - .. _`model_options/embedding[e3baseline_0]/irreps_hidden`: + .. _`model_options/embedding[e3baseline_5]/irreps_hidden`: irreps_hidden: - | type: ``str``, optional, default: ``64x0e+32x1o+16x2e+8x3o+8x4e+4x5o`` - | argument path: ``model_options/embedding[e3baseline_0]/irreps_hidden`` + | type: ``str`` + | argument path: ``model_options/embedding[e3baseline_5]/irreps_hidden`` - .. _`model_options/embedding[e3baseline_0]/lmax`: + .. _`model_options/embedding[e3baseline_5]/lmax`: lmax: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_0]/lmax`` + | type: ``int`` + | argument path: ``model_options/embedding[e3baseline_5]/lmax`` - .. _`model_options/embedding[e3baseline_0]/avg_num_neighbors`: + .. _`model_options/embedding[e3baseline_5]/avg_num_neighbors`: avg_num_neighbors: - | type: ``float`` | ``int``, optional, default: ``50`` - | argument path: ``model_options/embedding[e3baseline_0]/avg_num_neighbors`` + | type: ``float`` | ``int`` + | argument path: ``model_options/embedding[e3baseline_5]/avg_num_neighbors`` - .. _`model_options/embedding[e3baseline_0]/r_max`: + .. _`model_options/embedding[e3baseline_5]/r_max`: r_max: | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_0]/r_max`` + | argument path: ``model_options/embedding[e3baseline_5]/r_max`` - .. _`model_options/embedding[e3baseline_0]/n_layers`: + .. _`model_options/embedding[e3baseline_5]/n_layers`: n_layers: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_0]/n_layers`` + | type: ``int`` + | argument path: ``model_options/embedding[e3baseline_5]/n_layers`` - .. _`model_options/embedding[e3baseline_0]/n_radial_basis`: + .. _`model_options/embedding[e3baseline_5]/n_radial_basis`: n_radial_basis: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_0]/n_radial_basis`` + | type: ``int``, optional, default: ``10`` + | argument path: ``model_options/embedding[e3baseline_5]/n_radial_basis`` - .. _`model_options/embedding[e3baseline_0]/PolynomialCutoff_p`: + .. _`model_options/embedding[e3baseline_5]/PolynomialCutoff_p`: PolynomialCutoff_p: | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_0]/PolynomialCutoff_p`` + | argument path: ``model_options/embedding[e3baseline_5]/PolynomialCutoff_p`` The order of polynomial cutoff function. Default: 6 - .. _`model_options/embedding[e3baseline_0]/latent_kwargs`: - - latent_kwargs: - | type: ``dict`` | ``NoneType``, optional, default: ``None`` - | argument path: ``model_options/embedding[e3baseline_0]/latent_kwargs`` - - .. _`model_options/embedding[e3baseline_0]/env_embed_multiplicity`: - - env_embed_multiplicity: - | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_0]/env_embed_multiplicity`` - - .. _`model_options/embedding[e3baseline_0]/linear_after_env_embed`: - - linear_after_env_embed: - | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_0]/linear_after_env_embed`` - - .. _`model_options/embedding[e3baseline_0]/latent_resnet_update_ratios_learnable`: - - latent_resnet_update_ratios_learnable: - | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_0]/latent_resnet_update_ratios_learnable`` - - - .. _`model_options/embedding[e3baseline_1]`: - - When |flag:model_options/embedding/method|_ is set to ``e3baseline_1``: - - .. _`model_options/embedding[e3baseline_1]/irreps_hidden`: - - irreps_hidden: - | type: ``str``, optional, default: ``64x0e+32x1o+16x2e+8x3o+8x4e+4x5o`` - | argument path: ``model_options/embedding[e3baseline_1]/irreps_hidden`` - - .. _`model_options/embedding[e3baseline_1]/lmax`: - - lmax: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_1]/lmax`` - - .. _`model_options/embedding[e3baseline_1]/avg_num_neighbors`: - - avg_num_neighbors: - | type: ``float`` | ``int``, optional, default: ``50`` - | argument path: ``model_options/embedding[e3baseline_1]/avg_num_neighbors`` - - .. _`model_options/embedding[e3baseline_1]/r_max`: - - r_max: - | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_1]/r_max`` - - .. _`model_options/embedding[e3baseline_1]/n_layers`: - - n_layers: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_1]/n_layers`` - - .. _`model_options/embedding[e3baseline_1]/n_radial_basis`: - - n_radial_basis: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_1]/n_radial_basis`` - - .. _`model_options/embedding[e3baseline_1]/PolynomialCutoff_p`: - - PolynomialCutoff_p: - | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_1]/PolynomialCutoff_p`` - - The order of polynomial cutoff function. Default: 6 + .. _`model_options/embedding[e3baseline_5]/cutoff_type`: - .. _`model_options/embedding[e3baseline_1]/latent_kwargs`: + cutoff_type: + | type: ``str``, optional, default: ``polynomial`` + | argument path: ``model_options/embedding[e3baseline_5]/cutoff_type`` - latent_kwargs: - | type: ``dict`` | ``NoneType``, optional, default: ``None`` - | argument path: ``model_options/embedding[e3baseline_1]/latent_kwargs`` + The type of cutoff function. Default: polynomial - .. _`model_options/embedding[e3baseline_1]/env_embed_multiplicity`: + .. _`model_options/embedding[e3baseline_5]/env_embed_multiplicity`: env_embed_multiplicity: | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_1]/env_embed_multiplicity`` - - .. _`model_options/embedding[e3baseline_1]/linear_after_env_embed`: - - linear_after_env_embed: - | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_1]/linear_after_env_embed`` + | argument path: ``model_options/embedding[e3baseline_5]/env_embed_multiplicity`` - .. _`model_options/embedding[e3baseline_1]/latent_resnet_update_ratios_learnable`: + .. _`model_options/embedding[e3baseline_5]/tp_radial_emb`: - latent_resnet_update_ratios_learnable: + tp_radial_emb: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_1]/latent_resnet_update_ratios_learnable`` - - - .. _`model_options/embedding[e3baseline_2]`: - - When |flag:model_options/embedding/method|_ is set to ``e3baseline_2``: - - .. _`model_options/embedding[e3baseline_2]/irreps_hidden`: - - irreps_hidden: - | type: ``str``, optional, default: ``64x0e+32x1o+16x2e+8x3o+8x4e+4x5o`` - | argument path: ``model_options/embedding[e3baseline_2]/irreps_hidden`` - - .. _`model_options/embedding[e3baseline_2]/lmax`: + | argument path: ``model_options/embedding[e3baseline_5]/tp_radial_emb`` - lmax: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_2]/lmax`` + Whether to use tensor product radial embedding. - .. _`model_options/embedding[e3baseline_2]/avg_num_neighbors`: + .. _`model_options/embedding[e3baseline_5]/tp_radial_channels`: - avg_num_neighbors: - | type: ``float`` | ``int``, optional, default: ``50`` - | argument path: ``model_options/embedding[e3baseline_2]/avg_num_neighbors`` + tp_radial_channels: + | type: ``list``, optional, default: ``[128, 128]`` + | argument path: ``model_options/embedding[e3baseline_5]/tp_radial_channels`` - .. _`model_options/embedding[e3baseline_2]/r_max`: + The number of channels in tensor product radial embedding. - r_max: - | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_2]/r_max`` + .. _`model_options/embedding[e3baseline_5]/latent_channels`: - .. _`model_options/embedding[e3baseline_2]/n_layers`: + latent_channels: + | type: ``list``, optional, default: ``[128, 128]`` + | argument path: ``model_options/embedding[e3baseline_5]/latent_channels`` - n_layers: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_2]/n_layers`` + The number of channels in latent embedding. - .. _`model_options/embedding[e3baseline_2]/n_radial_basis`: + .. _`model_options/embedding[e3baseline_5]/latent_dim`: - n_radial_basis: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_2]/n_radial_basis`` + latent_dim: + | type: ``int``, optional, default: ``256`` + | argument path: ``model_options/embedding[e3baseline_5]/latent_dim`` - .. _`model_options/embedding[e3baseline_2]/PolynomialCutoff_p`: + The dimension of latent embedding. - PolynomialCutoff_p: - | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_2]/PolynomialCutoff_p`` + .. _`model_options/embedding[e3baseline_5]/res_update`: - The order of polynomial cutoff function. Default: 6 + res_update: + | type: ``bool``, optional, default: ``True`` + | argument path: ``model_options/embedding[e3baseline_5]/res_update`` - .. _`model_options/embedding[e3baseline_2]/latent_kwargs`: + Whether to use residual update. - latent_kwargs: - | type: ``dict`` | ``NoneType``, optional, default: ``None`` - | argument path: ``model_options/embedding[e3baseline_2]/latent_kwargs`` + .. _`model_options/embedding[e3baseline_5]/res_update_ratios`: - .. _`model_options/embedding[e3baseline_2]/env_embed_multiplicity`: + res_update_ratios: + | type: ``float``, optional, default: ``0.5`` + | argument path: ``model_options/embedding[e3baseline_5]/res_update_ratios`` - env_embed_multiplicity: - | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_2]/env_embed_multiplicity`` + The ratios of residual update, should in (0,1). - .. _`model_options/embedding[e3baseline_2]/linear_after_env_embed`: + .. _`model_options/embedding[e3baseline_5]/res_update_ratios_learnable`: - linear_after_env_embed: + res_update_ratios_learnable: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_2]/linear_after_env_embed`` - - .. _`model_options/embedding[e3baseline_2]/latent_resnet_update_ratios_learnable`: + | argument path: ``model_options/embedding[e3baseline_5]/res_update_ratios_learnable`` - latent_resnet_update_ratios_learnable: - | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_2]/latent_resnet_update_ratios_learnable`` + Whether to make the ratios of residual update learnable. - .. _`model_options/embedding[e3baseline_3]`: + .. _`model_options/embedding[e3baseline_6]`: - When |flag:model_options/embedding/method|_ is set to ``e3baseline_3``: + When |flag:model_options/embedding/method|_ is set to ``e3baseline_6``: - .. _`model_options/embedding[e3baseline_3]/irreps_hidden`: + .. _`model_options/embedding[e3baseline_6]/irreps_hidden`: irreps_hidden: - | type: ``str``, optional, default: ``64x0e+32x1o+16x2e+8x3o+8x4e+4x5o`` - | argument path: ``model_options/embedding[e3baseline_3]/irreps_hidden`` + | type: ``str`` + | argument path: ``model_options/embedding[e3baseline_6]/irreps_hidden`` - .. _`model_options/embedding[e3baseline_3]/lmax`: + .. _`model_options/embedding[e3baseline_6]/lmax`: lmax: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_3]/lmax`` + | type: ``int`` + | argument path: ``model_options/embedding[e3baseline_6]/lmax`` - .. _`model_options/embedding[e3baseline_3]/avg_num_neighbors`: + .. _`model_options/embedding[e3baseline_6]/avg_num_neighbors`: avg_num_neighbors: - | type: ``float`` | ``int``, optional, default: ``50`` - | argument path: ``model_options/embedding[e3baseline_3]/avg_num_neighbors`` + | type: ``float`` | ``int`` + | argument path: ``model_options/embedding[e3baseline_6]/avg_num_neighbors`` - .. _`model_options/embedding[e3baseline_3]/r_max`: + .. _`model_options/embedding[e3baseline_6]/r_max`: r_max: | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_3]/r_max`` + | argument path: ``model_options/embedding[e3baseline_6]/r_max`` - .. _`model_options/embedding[e3baseline_3]/n_layers`: + .. _`model_options/embedding[e3baseline_6]/n_layers`: n_layers: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_3]/n_layers`` + | type: ``int`` + | argument path: ``model_options/embedding[e3baseline_6]/n_layers`` - .. _`model_options/embedding[e3baseline_3]/n_radial_basis`: + .. _`model_options/embedding[e3baseline_6]/n_radial_basis`: n_radial_basis: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_3]/n_radial_basis`` + | type: ``int``, optional, default: ``10`` + | argument path: ``model_options/embedding[e3baseline_6]/n_radial_basis`` - .. _`model_options/embedding[e3baseline_3]/PolynomialCutoff_p`: + .. _`model_options/embedding[e3baseline_6]/PolynomialCutoff_p`: PolynomialCutoff_p: | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_3]/PolynomialCutoff_p`` + | argument path: ``model_options/embedding[e3baseline_6]/PolynomialCutoff_p`` The order of polynomial cutoff function. Default: 6 - .. _`model_options/embedding[e3baseline_3]/latent_kwargs`: + .. _`model_options/embedding[e3baseline_6]/cutoff_type`: - latent_kwargs: - | type: ``dict`` | ``NoneType``, optional, default: ``None`` - | argument path: ``model_options/embedding[e3baseline_3]/latent_kwargs`` + cutoff_type: + | type: ``str``, optional, default: ``polynomial`` + | argument path: ``model_options/embedding[e3baseline_6]/cutoff_type`` + + The type of cutoff function. Default: polynomial - .. _`model_options/embedding[e3baseline_3]/env_embed_multiplicity`: + .. _`model_options/embedding[e3baseline_6]/env_embed_multiplicity`: env_embed_multiplicity: | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_3]/env_embed_multiplicity`` - - .. _`model_options/embedding[e3baseline_3]/linear_after_env_embed`: - - linear_after_env_embed: - | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_3]/linear_after_env_embed`` + | argument path: ``model_options/embedding[e3baseline_6]/env_embed_multiplicity`` - .. _`model_options/embedding[e3baseline_3]/latent_resnet_update_ratios_learnable`: + .. _`model_options/embedding[e3baseline_6]/tp_radial_emb`: - latent_resnet_update_ratios_learnable: + tp_radial_emb: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_3]/latent_resnet_update_ratios_learnable`` - - - .. _`model_options/embedding[e3baseline_4]`: - - When |flag:model_options/embedding/method|_ is set to ``e3baseline_4``: - - .. _`model_options/embedding[e3baseline_4]/irreps_hidden`: - - irreps_hidden: - | type: ``str``, optional, default: ``64x0e+32x1o+16x2e+8x3o+8x4e+4x5o`` - | argument path: ``model_options/embedding[e3baseline_4]/irreps_hidden`` - - .. _`model_options/embedding[e3baseline_4]/lmax`: + | argument path: ``model_options/embedding[e3baseline_6]/tp_radial_emb`` - lmax: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_4]/lmax`` + Whether to use tensor product radial embedding. - .. _`model_options/embedding[e3baseline_4]/avg_num_neighbors`: + .. _`model_options/embedding[e3baseline_6]/tp_radial_channels`: - avg_num_neighbors: - | type: ``float`` | ``int``, optional, default: ``50`` - | argument path: ``model_options/embedding[e3baseline_4]/avg_num_neighbors`` + tp_radial_channels: + | type: ``list``, optional, default: ``[128, 128]`` + | argument path: ``model_options/embedding[e3baseline_6]/tp_radial_channels`` - .. _`model_options/embedding[e3baseline_4]/r_max`: + The number of channels in tensor product radial embedding. - r_max: - | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_4]/r_max`` + .. _`model_options/embedding[e3baseline_6]/latent_channels`: - .. _`model_options/embedding[e3baseline_4]/n_layers`: + latent_channels: + | type: ``list``, optional, default: ``[128, 128]`` + | argument path: ``model_options/embedding[e3baseline_6]/latent_channels`` - n_layers: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_4]/n_layers`` + The number of channels in latent embedding. - .. _`model_options/embedding[e3baseline_4]/n_radial_basis`: + .. _`model_options/embedding[e3baseline_6]/latent_dim`: - n_radial_basis: - | type: ``int``, optional, default: ``3`` - | argument path: ``model_options/embedding[e3baseline_4]/n_radial_basis`` + latent_dim: + | type: ``int``, optional, default: ``256`` + | argument path: ``model_options/embedding[e3baseline_6]/latent_dim`` - .. _`model_options/embedding[e3baseline_4]/PolynomialCutoff_p`: + The dimension of latent embedding. - PolynomialCutoff_p: - | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_4]/PolynomialCutoff_p`` + .. _`model_options/embedding[e3baseline_6]/res_update`: - The order of polynomial cutoff function. Default: 6 + res_update: + | type: ``bool``, optional, default: ``True`` + | argument path: ``model_options/embedding[e3baseline_6]/res_update`` - .. _`model_options/embedding[e3baseline_4]/latent_kwargs`: + Whether to use residual update. - latent_kwargs: - | type: ``dict`` | ``NoneType``, optional, default: ``None`` - | argument path: ``model_options/embedding[e3baseline_4]/latent_kwargs`` + .. _`model_options/embedding[e3baseline_6]/res_update_ratios`: - .. _`model_options/embedding[e3baseline_4]/env_embed_multiplicity`: + res_update_ratios: + | type: ``float``, optional, default: ``0.5`` + | argument path: ``model_options/embedding[e3baseline_6]/res_update_ratios`` - env_embed_multiplicity: - | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_4]/env_embed_multiplicity`` + The ratios of residual update, should in (0,1). - .. _`model_options/embedding[e3baseline_4]/linear_after_env_embed`: + .. _`model_options/embedding[e3baseline_6]/res_update_ratios_learnable`: - linear_after_env_embed: + res_update_ratios_learnable: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_4]/linear_after_env_embed`` - - .. _`model_options/embedding[e3baseline_4]/latent_resnet_update_ratios_learnable`: + | argument path: ``model_options/embedding[e3baseline_6]/res_update_ratios_learnable`` - latent_resnet_update_ratios_learnable: - | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_4]/latent_resnet_update_ratios_learnable`` + Whether to make the ratios of residual update learnable. - .. _`model_options/embedding[e3baseline_5]`: + .. _`model_options/embedding[slem]`: - When |flag:model_options/embedding/method|_ is set to ``e3baseline_5``: + When |flag:model_options/embedding/method|_ is set to ``slem``: - .. _`model_options/embedding[e3baseline_5]/irreps_hidden`: + .. _`model_options/embedding[slem]/irreps_hidden`: irreps_hidden: | type: ``str`` - | argument path: ``model_options/embedding[e3baseline_5]/irreps_hidden`` + | argument path: ``model_options/embedding[slem]/irreps_hidden`` - .. _`model_options/embedding[e3baseline_5]/lmax`: - - lmax: - | type: ``int`` - | argument path: ``model_options/embedding[e3baseline_5]/lmax`` - - .. _`model_options/embedding[e3baseline_5]/avg_num_neighbors`: + .. _`model_options/embedding[slem]/avg_num_neighbors`: avg_num_neighbors: | type: ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_5]/avg_num_neighbors`` + | argument path: ``model_options/embedding[slem]/avg_num_neighbors`` - .. _`model_options/embedding[e3baseline_5]/r_max`: + .. _`model_options/embedding[slem]/r_max`: r_max: | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_5]/r_max`` + | argument path: ``model_options/embedding[slem]/r_max`` - .. _`model_options/embedding[e3baseline_5]/n_layers`: + .. _`model_options/embedding[slem]/n_layers`: n_layers: | type: ``int`` - | argument path: ``model_options/embedding[e3baseline_5]/n_layers`` + | argument path: ``model_options/embedding[slem]/n_layers`` - .. _`model_options/embedding[e3baseline_5]/n_radial_basis`: + .. _`model_options/embedding[slem]/n_radial_basis`: n_radial_basis: | type: ``int``, optional, default: ``10`` - | argument path: ``model_options/embedding[e3baseline_5]/n_radial_basis`` + | argument path: ``model_options/embedding[slem]/n_radial_basis`` - .. _`model_options/embedding[e3baseline_5]/PolynomialCutoff_p`: + .. _`model_options/embedding[slem]/PolynomialCutoff_p`: PolynomialCutoff_p: | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_5]/PolynomialCutoff_p`` + | argument path: ``model_options/embedding[slem]/PolynomialCutoff_p`` The order of polynomial cutoff function. Default: 6 - .. _`model_options/embedding[e3baseline_5]/cutoff_type`: + .. _`model_options/embedding[slem]/cutoff_type`: cutoff_type: | type: ``str``, optional, default: ``polynomial`` - | argument path: ``model_options/embedding[e3baseline_5]/cutoff_type`` + | argument path: ``model_options/embedding[slem]/cutoff_type`` The type of cutoff function. Default: polynomial - .. _`model_options/embedding[e3baseline_5]/env_embed_multiplicity`: + .. _`model_options/embedding[slem]/env_embed_multiplicity`: env_embed_multiplicity: - | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_5]/env_embed_multiplicity`` + | type: ``int``, optional, default: ``10`` + | argument path: ``model_options/embedding[slem]/env_embed_multiplicity`` - .. _`model_options/embedding[e3baseline_5]/tp_radial_emb`: + .. _`model_options/embedding[slem]/tp_radial_emb`: tp_radial_emb: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_5]/tp_radial_emb`` + | argument path: ``model_options/embedding[slem]/tp_radial_emb`` Whether to use tensor product radial embedding. - .. _`model_options/embedding[e3baseline_5]/tp_radial_channels`: + .. _`model_options/embedding[slem]/tp_radial_channels`: tp_radial_channels: - | type: ``list``, optional, default: ``[128, 128]`` - | argument path: ``model_options/embedding[e3baseline_5]/tp_radial_channels`` + | type: ``list``, optional, default: ``[32]`` + | argument path: ``model_options/embedding[slem]/tp_radial_channels`` The number of channels in tensor product radial embedding. - .. _`model_options/embedding[e3baseline_5]/latent_channels`: + .. _`model_options/embedding[slem]/latent_channels`: latent_channels: - | type: ``list``, optional, default: ``[128, 128]`` - | argument path: ``model_options/embedding[e3baseline_5]/latent_channels`` + | type: ``list``, optional, default: ``[32]`` + | argument path: ``model_options/embedding[slem]/latent_channels`` The number of channels in latent embedding. - .. _`model_options/embedding[e3baseline_5]/latent_dim`: + .. _`model_options/embedding[slem]/latent_dim`: latent_dim: - | type: ``int``, optional, default: ``256`` - | argument path: ``model_options/embedding[e3baseline_5]/latent_dim`` + | type: ``int``, optional, default: ``64`` + | argument path: ``model_options/embedding[slem]/latent_dim`` The dimension of latent embedding. - .. _`model_options/embedding[e3baseline_5]/res_update`: + .. _`model_options/embedding[slem]/res_update`: res_update: | type: ``bool``, optional, default: ``True`` - | argument path: ``model_options/embedding[e3baseline_5]/res_update`` + | argument path: ``model_options/embedding[slem]/res_update`` Whether to use residual update. - .. _`model_options/embedding[e3baseline_5]/res_update_ratios`: + .. _`model_options/embedding[slem]/res_update_ratios`: res_update_ratios: | type: ``float``, optional, default: ``0.5`` - | argument path: ``model_options/embedding[e3baseline_5]/res_update_ratios`` + | argument path: ``model_options/embedding[slem]/res_update_ratios`` The ratios of residual update, should in (0,1). - .. _`model_options/embedding[e3baseline_5]/res_update_ratios_learnable`: + .. _`model_options/embedding[slem]/res_update_ratios_learnable`: res_update_ratios_learnable: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_5]/res_update_ratios_learnable`` + | argument path: ``model_options/embedding[slem]/res_update_ratios_learnable`` Whether to make the ratios of residual update learnable. - .. _`model_options/embedding[e3baseline_6]`: + .. _`model_options/embedding[lem]`: - When |flag:model_options/embedding/method|_ is set to ``e3baseline_6``: + When |flag:model_options/embedding/method|_ is set to ``lem``: - .. _`model_options/embedding[e3baseline_6]/irreps_hidden`: + .. _`model_options/embedding[lem]/irreps_hidden`: irreps_hidden: | type: ``str`` - | argument path: ``model_options/embedding[e3baseline_6]/irreps_hidden`` + | argument path: ``model_options/embedding[lem]/irreps_hidden`` - .. _`model_options/embedding[e3baseline_6]/lmax`: - - lmax: - | type: ``int`` - | argument path: ``model_options/embedding[e3baseline_6]/lmax`` - - .. _`model_options/embedding[e3baseline_6]/avg_num_neighbors`: + .. _`model_options/embedding[lem]/avg_num_neighbors`: avg_num_neighbors: | type: ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_6]/avg_num_neighbors`` + | argument path: ``model_options/embedding[lem]/avg_num_neighbors`` - .. _`model_options/embedding[e3baseline_6]/r_max`: + .. _`model_options/embedding[lem]/r_max`: r_max: | type: ``dict`` | ``float`` | ``int`` - | argument path: ``model_options/embedding[e3baseline_6]/r_max`` + | argument path: ``model_options/embedding[lem]/r_max`` - .. _`model_options/embedding[e3baseline_6]/n_layers`: + .. _`model_options/embedding[lem]/n_layers`: n_layers: | type: ``int`` - | argument path: ``model_options/embedding[e3baseline_6]/n_layers`` + | argument path: ``model_options/embedding[lem]/n_layers`` - .. _`model_options/embedding[e3baseline_6]/n_radial_basis`: + .. _`model_options/embedding[lem]/n_radial_basis`: n_radial_basis: | type: ``int``, optional, default: ``10`` - | argument path: ``model_options/embedding[e3baseline_6]/n_radial_basis`` + | argument path: ``model_options/embedding[lem]/n_radial_basis`` - .. _`model_options/embedding[e3baseline_6]/PolynomialCutoff_p`: + .. _`model_options/embedding[lem]/PolynomialCutoff_p`: PolynomialCutoff_p: | type: ``int``, optional, default: ``6`` - | argument path: ``model_options/embedding[e3baseline_6]/PolynomialCutoff_p`` + | argument path: ``model_options/embedding[lem]/PolynomialCutoff_p`` The order of polynomial cutoff function. Default: 6 - .. _`model_options/embedding[e3baseline_6]/cutoff_type`: + .. _`model_options/embedding[lem]/cutoff_type`: cutoff_type: | type: ``str``, optional, default: ``polynomial`` - | argument path: ``model_options/embedding[e3baseline_6]/cutoff_type`` + | argument path: ``model_options/embedding[lem]/cutoff_type`` The type of cutoff function. Default: polynomial - .. _`model_options/embedding[e3baseline_6]/env_embed_multiplicity`: + .. _`model_options/embedding[lem]/env_embed_multiplicity`: env_embed_multiplicity: - | type: ``int``, optional, default: ``1`` - | argument path: ``model_options/embedding[e3baseline_6]/env_embed_multiplicity`` + | type: ``int``, optional, default: ``10`` + | argument path: ``model_options/embedding[lem]/env_embed_multiplicity`` - .. _`model_options/embedding[e3baseline_6]/tp_radial_emb`: + .. _`model_options/embedding[lem]/tp_radial_emb`: tp_radial_emb: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_6]/tp_radial_emb`` + | argument path: ``model_options/embedding[lem]/tp_radial_emb`` Whether to use tensor product radial embedding. - .. _`model_options/embedding[e3baseline_6]/tp_radial_channels`: + .. _`model_options/embedding[lem]/tp_radial_channels`: tp_radial_channels: - | type: ``list``, optional, default: ``[128, 128]`` - | argument path: ``model_options/embedding[e3baseline_6]/tp_radial_channels`` + | type: ``list``, optional, default: ``[32]`` + | argument path: ``model_options/embedding[lem]/tp_radial_channels`` The number of channels in tensor product radial embedding. - .. _`model_options/embedding[e3baseline_6]/latent_channels`: + .. _`model_options/embedding[lem]/latent_channels`: latent_channels: - | type: ``list``, optional, default: ``[128, 128]`` - | argument path: ``model_options/embedding[e3baseline_6]/latent_channels`` + | type: ``list``, optional, default: ``[32]`` + | argument path: ``model_options/embedding[lem]/latent_channels`` The number of channels in latent embedding. - .. _`model_options/embedding[e3baseline_6]/latent_dim`: + .. _`model_options/embedding[lem]/latent_dim`: latent_dim: - | type: ``int``, optional, default: ``256`` - | argument path: ``model_options/embedding[e3baseline_6]/latent_dim`` + | type: ``int``, optional, default: ``64`` + | argument path: ``model_options/embedding[lem]/latent_dim`` The dimension of latent embedding. - .. _`model_options/embedding[e3baseline_6]/res_update`: + .. _`model_options/embedding[lem]/res_update`: res_update: | type: ``bool``, optional, default: ``True`` - | argument path: ``model_options/embedding[e3baseline_6]/res_update`` + | argument path: ``model_options/embedding[lem]/res_update`` Whether to use residual update. - .. _`model_options/embedding[e3baseline_6]/res_update_ratios`: + .. _`model_options/embedding[lem]/res_update_ratios`: res_update_ratios: | type: ``float``, optional, default: ``0.5`` - | argument path: ``model_options/embedding[e3baseline_6]/res_update_ratios`` + | argument path: ``model_options/embedding[lem]/res_update_ratios`` The ratios of residual update, should in (0,1). - .. _`model_options/embedding[e3baseline_6]/res_update_ratios_learnable`: + .. _`model_options/embedding[lem]/res_update_ratios_learnable`: res_update_ratios_learnable: | type: ``bool``, optional, default: ``False`` - | argument path: ``model_options/embedding[e3baseline_6]/res_update_ratios_learnable`` + | argument path: ``model_options/embedding[lem]/res_update_ratios_learnable`` Whether to make the ratios of residual update learnable. @@ -1056,6 +911,30 @@ model_options: whether to shift the training target. + .. _`model_options/prediction[e3tb]/neurons`: + + neurons: + | type: ``list`` | ``NoneType``, optional, default: ``None`` + | argument path: ``model_options/prediction[e3tb]/neurons`` + + neurons in the neural network. + + .. _`model_options/prediction[e3tb]/activation`: + + activation: + | type: ``str``, optional, default: ``tanh`` + | argument path: ``model_options/prediction[e3tb]/activation`` + + activation function. + + .. _`model_options/prediction[e3tb]/if_batch_normalized`: + + if_batch_normalized: + | type: ``bool``, optional, default: ``False`` + | argument path: ``model_options/prediction[e3tb]/if_batch_normalized`` + + if to turn on batch normalization + .. _`model_options/nnsk`: nnsk: @@ -1135,11 +1014,11 @@ model_options: When |flag:model_options/nnsk/onsite/method|_ is set to ``NRL``: - .. _`model_options/nnsk/onsite[NRL]/rc`: + .. _`model_options/nnsk/onsite[NRL]/rs`: - rc: + rs: | type: ``float``, optional, default: ``6.0`` - | argument path: ``model_options/nnsk/onsite[NRL]/rc`` + | argument path: ``model_options/nnsk/onsite[NRL]/rs`` The smooth cutoff of `fc` for nrl model, rc is where fc ~ 0.0 @@ -1181,7 +1060,7 @@ model_options: method: | type: ``str`` (flag key) | argument path: ``model_options/nnsk/hopping/method`` - | possible choices: |code:model_options/nnsk/hopping[powerlaw]|_, |code:model_options/nnsk/hopping[varTang96]|_, |code:model_options/nnsk/hopping[NRL0]|_, |code:model_options/nnsk/hopping[NRL1]|_, |code:model_options/nnsk/hopping[custom]|_ + | possible choices: |code:model_options/nnsk/hopping[powerlaw]|_, |code:model_options/nnsk/hopping[poly1pow]|_, |code:model_options/nnsk/hopping[poly2pow]|_, |code:model_options/nnsk/hopping[poly3pow]|_, |code:model_options/nnsk/hopping[poly2exp]|_, |code:model_options/nnsk/hopping[varTang96]|_, |code:model_options/nnsk/hopping[NRL0]|_, |code:model_options/nnsk/hopping[NRL1]|_, |code:model_options/nnsk/hopping[custom]|_ The hopping formula. - `powerlaw`: the powerlaw formula for bond length dependence for sk integrals. @@ -1192,6 +1071,14 @@ model_options: .. |code:model_options/nnsk/hopping[powerlaw]| replace:: ``powerlaw`` .. _`code:model_options/nnsk/hopping[powerlaw]`: `model_options/nnsk/hopping[powerlaw]`_ + .. |code:model_options/nnsk/hopping[poly1pow]| replace:: ``poly1pow`` + .. _`code:model_options/nnsk/hopping[poly1pow]`: `model_options/nnsk/hopping[poly1pow]`_ + .. |code:model_options/nnsk/hopping[poly2pow]| replace:: ``poly2pow`` + .. _`code:model_options/nnsk/hopping[poly2pow]`: `model_options/nnsk/hopping[poly2pow]`_ + .. |code:model_options/nnsk/hopping[poly3pow]| replace:: ``poly3pow`` + .. _`code:model_options/nnsk/hopping[poly3pow]`: `model_options/nnsk/hopping[poly3pow]`_ + .. |code:model_options/nnsk/hopping[poly2exp]| replace:: ``poly2exp`` + .. _`code:model_options/nnsk/hopping[poly2exp]`: `model_options/nnsk/hopping[poly2exp]`_ .. |code:model_options/nnsk/hopping[varTang96]| replace:: ``varTang96`` .. _`code:model_options/nnsk/hopping[varTang96]`: `model_options/nnsk/hopping[varTang96]`_ .. |code:model_options/nnsk/hopping[NRL0]| replace:: ``NRL0`` @@ -1226,6 +1113,90 @@ model_options: The decay w in fc + .. _`model_options/nnsk/hopping[poly1pow]`: + + When |flag:model_options/nnsk/hopping/method|_ is set to ``poly1pow``: + + .. _`model_options/nnsk/hopping[poly1pow]/rs`: + + rs: + | type: ``float``, optional, default: ``6.0`` + | argument path: ``model_options/nnsk/hopping[poly1pow]/rs`` + + The cut-off for smooth function fc for powerlaw and varTang96, fc(rs)=0.5 + + .. _`model_options/nnsk/hopping[poly1pow]/w`: + + w: + | type: ``float``, optional, default: ``0.1`` + | argument path: ``model_options/nnsk/hopping[poly1pow]/w`` + + The decay w in fc + + + .. _`model_options/nnsk/hopping[poly2pow]`: + + When |flag:model_options/nnsk/hopping/method|_ is set to ``poly2pow``: + + .. _`model_options/nnsk/hopping[poly2pow]/rs`: + + rs: + | type: ``float``, optional, default: ``6.0`` + | argument path: ``model_options/nnsk/hopping[poly2pow]/rs`` + + The cut-off for smooth function fc for powerlaw and varTang96, fc(rs)=0.5 + + .. _`model_options/nnsk/hopping[poly2pow]/w`: + + w: + | type: ``float``, optional, default: ``0.1`` + | argument path: ``model_options/nnsk/hopping[poly2pow]/w`` + + The decay w in fc + + + .. _`model_options/nnsk/hopping[poly3pow]`: + + When |flag:model_options/nnsk/hopping/method|_ is set to ``poly3pow``: + + .. _`model_options/nnsk/hopping[poly3pow]/rs`: + + rs: + | type: ``float``, optional, default: ``6.0`` + | argument path: ``model_options/nnsk/hopping[poly3pow]/rs`` + + The cut-off for smooth function fc for powerlaw and varTang96, fc(rs)=0.5 + + .. _`model_options/nnsk/hopping[poly3pow]/w`: + + w: + | type: ``float``, optional, default: ``0.1`` + | argument path: ``model_options/nnsk/hopping[poly3pow]/w`` + + The decay w in fc + + + .. _`model_options/nnsk/hopping[poly2exp]`: + + When |flag:model_options/nnsk/hopping/method|_ is set to ``poly2exp``: + + .. _`model_options/nnsk/hopping[poly2exp]/rs`: + + rs: + | type: ``float``, optional, default: ``6.0`` + | argument path: ``model_options/nnsk/hopping[poly2exp]/rs`` + + The cut-off for smooth function fc for powerlaw and varTang96, fc(rs)=0.5 + + .. _`model_options/nnsk/hopping[poly2exp]/w`: + + w: + | type: ``float``, optional, default: ``0.1`` + | argument path: ``model_options/nnsk/hopping[poly2exp]/w`` + + The decay w in fc + + .. _`model_options/nnsk/hopping[varTang96]`: When |flag:model_options/nnsk/hopping/method|_ is set to ``varTang96``: @@ -1251,11 +1222,11 @@ model_options: When |flag:model_options/nnsk/hopping/method|_ is set to ``NRL0``: - .. _`model_options/nnsk/hopping[NRL0]/rc`: + .. _`model_options/nnsk/hopping[NRL0]/rs`: - rc: + rs: | type: ``float``, optional, default: ``6.0`` - | argument path: ``model_options/nnsk/hopping[NRL0]/rc`` + | argument path: ``model_options/nnsk/hopping[NRL0]/rs`` The cut-off for smooth function fc for NRL, fc(rc) = 0. @@ -1272,11 +1243,11 @@ model_options: When |flag:model_options/nnsk/hopping/method|_ is set to ``NRL1``: - .. _`model_options/nnsk/hopping[NRL1]/rc`: + .. _`model_options/nnsk/hopping[NRL1]/rs`: - rc: + rs: | type: ``float``, optional, default: ``6.0`` - | argument path: ``model_options/nnsk/hopping[NRL1]/rc`` + | argument path: ``model_options/nnsk/hopping[NRL1]/rs`` The cut-off for smooth function fc for NRL, fc(rc) = 0. @@ -1363,6 +1334,14 @@ model_options: The step size for decay factor w. + .. _`model_options/nnsk/push/ovp_thr`: + + ovp_thr: + | type: ``float`` | ``int``, optional, default: ``0.0`` + | argument path: ``model_options/nnsk/push/ovp_thr`` + + The step size for overlap reduction + .. _`model_options/nnsk/push/period`: period: @@ -1371,3 +1350,27 @@ model_options: the interval of iterations to modify the rs w values. + .. _`model_options/dftbsk`: + + dftbsk: + | type: ``dict``, optional + | argument path: ``model_options/dftbsk`` + + The parameters to define the dftb sk model. + + .. _`model_options/dftbsk/skdata`: + + skdata: + | type: ``str`` + | argument path: ``model_options/dftbsk/skdata`` + + The path to the skfile or sk database. + + .. _`model_options/dftbsk/r_max`: + + r_max: + | type: ``float`` + | argument path: ``model_options/dftbsk/r_max`` + + the cutoff values to use sk files. + diff --git a/docs/input_params/run_options.rst b/docs/input_params/run_options.rst index 6ac4cb00..f7d1d8aa 100644 --- a/docs/input_params/run_options.rst +++ b/docs/input_params/run_options.rst @@ -23,7 +23,7 @@ run_op: task: | type: ``str`` (flag key) | argument path: ``run_op/task_options/task`` - | possible choices: |code:run_op/task_options[band]|_, |code:run_op/task_options[dos]|_, |code:run_op/task_options[pdos]|_, |code:run_op/task_options[FS2D]|_, |code:run_op/task_options[FS3D]|_, |code:run_op/task_options[write_sk]|_, |code:run_op/task_options[ifermi]|_, |code:run_op/task_options[negf]|_, |code:run_op/task_options[tbtrans_negf]|_ + | possible choices: |code:run_op/task_options[band]|_, |code:run_op/task_options[dos]|_, |code:run_op/task_options[pdos]|_, |code:run_op/task_options[FS2D]|_, |code:run_op/task_options[FS3D]|_, |code:run_op/task_options[write_sk]|_, |code:run_op/task_options[ifermi]|_, |code:run_op/task_options[negf]|_, |code:run_op/task_options[tbtrans_negf]|_, |code:run_op/task_options[write_block]|_ The string define the task DeePTB conduct, includes: - `band`: for band structure plotting. @@ -55,6 +55,8 @@ run_op: .. _`code:run_op/task_options[negf]`: `run_op/task_options[negf]`_ .. |code:run_op/task_options[tbtrans_negf]| replace:: ``tbtrans_negf`` .. _`code:run_op/task_options[tbtrans_negf]`: `run_op/task_options[tbtrans_negf]`_ + .. |code:run_op/task_options[write_block]| replace:: ``write_block`` + .. _`code:run_op/task_options[write_block]`: `run_op/task_options[write_block]`_ .. |flag:run_op/task_options/task| replace:: *task* .. _`flag:run_op/task_options/task`: `run_op/task_options/task`_ @@ -1297,6 +1299,12 @@ run_op: | type: ``bool``, optional, default: ``False`` | argument path: ``run_op/task_options[tbtrans_negf]/out_lcurrent`` + + .. _`run_op/task_options[write_block]`: + + When |flag:run_op/task_options/task|_ is set to ``write_block``: + + .. _`run_op/structure`: structure: @@ -1313,6 +1321,27 @@ run_op: To use the GUI or not + .. _`run_op/device`: + + device: + | type: ``str`` | ``NoneType``, optional, default: ``None`` + | argument path: ``run_op/device`` + + The device to run the calculation, choose among `cpu` and `cuda[:int]`, Default: None. default None means to use the device seeting in the model ckpt file. + + .. _`run_op/dtype`: + + dtype: + | type: ``str`` | ``NoneType``, optional, default: ``None`` + | argument path: ``run_op/dtype`` + + The digital number's precison, choose among: + Default: None, + - `float32`: indicating torch.float32 + - `float64`: indicating torch.float64 + default None means to use the device seeting in the model ckpt file. + + .. _`run_op/AtomicData_options`: AtomicData_options: diff --git a/docs/input_params/set_info.rst b/docs/input_params/set_info.rst index 65344cac..386737f0 100644 --- a/docs/input_params/set_info.rst +++ b/docs/input_params/set_info.rst @@ -31,6 +31,14 @@ setinfo: Type of atomic position input. Can be frac / cart / ase. + .. _`setinfo/pbc`: + + pbc: + | type: ``list`` | ``bool`` + | argument path: ``setinfo/pbc`` + + The periodic condition for the structure, can bool or list of bool to specific x,y,z direction. + .. _`setinfo/bandinfo`: bandinfo: @@ -72,41 +80,3 @@ setinfo: the max energy window, emax value is respect to the min value of the band at index band_min - .. _`setinfo/AtomicData_options`: - - AtomicData_options: - | type: ``dict`` - | argument path: ``setinfo/AtomicData_options`` - - .. _`setinfo/AtomicData_options/r_max`: - - r_max: - | type: ``dict`` | ``float`` | ``int`` - | argument path: ``setinfo/AtomicData_options/r_max`` - - the cutoff value for bond considering in TB model. - - .. _`setinfo/AtomicData_options/er_max`: - - er_max: - | type: ``dict`` | ``float`` | ``int`` | ``NoneType``, optional, default: ``None`` - | argument path: ``setinfo/AtomicData_options/er_max`` - - The cutoff value for environment for each site for env correction model. should set for nnsk+env correction model. - - .. _`setinfo/AtomicData_options/oer_max`: - - oer_max: - | type: ``dict`` | ``float`` | ``int`` | ``NoneType``, optional, default: ``None`` - | argument path: ``setinfo/AtomicData_options/oer_max`` - - The cutoff value for onsite environment for nnsk model, for now only need to set in strain and NRL mode. - - .. _`setinfo/AtomicData_options/pbc`: - - pbc: - | type: ``bool`` - | argument path: ``setinfo/AtomicData_options/pbc`` - - The periodic condition for the structure, can bool or list of bool to specific x,y,z direction. - diff --git a/docs/input_params/train_options.rst b/docs/input_params/train_options.rst index 319d938a..c119ccec 100644 --- a/docs/input_params/train_options.rst +++ b/docs/input_params/train_options.rst @@ -366,7 +366,7 @@ train_options: method: | type: ``str`` (flag key) | argument path: ``train_options/loss_options/train/method`` - | possible choices: |code:train_options/loss_options/train[hamil]|_, |code:train_options/loss_options/train[eigvals]|_, |code:train_options/loss_options/train[hamil_abs]|_, |code:train_options/loss_options/train[hamil_blas]|_ + | possible choices: |code:train_options/loss_options/train[eigvals]|_, |code:train_options/loss_options/train[skints]|_, |code:train_options/loss_options/train[hamil_abs]|_, |code:train_options/loss_options/train[hamil_blas]|_ The loss function type, defined by a string like `_`, Default: `eigs_l2dsf`. supported loss functions includes: @@ -376,10 +376,10 @@ train_options: - `hamil_blas`: - .. |code:train_options/loss_options/train[hamil]| replace:: ``hamil`` - .. _`code:train_options/loss_options/train[hamil]`: `train_options/loss_options/train[hamil]`_ .. |code:train_options/loss_options/train[eigvals]| replace:: ``eigvals`` .. _`code:train_options/loss_options/train[eigvals]`: `train_options/loss_options/train[eigvals]`_ + .. |code:train_options/loss_options/train[skints]| replace:: ``skints`` + .. _`code:train_options/loss_options/train[skints]`: `train_options/loss_options/train[skints]`_ .. |code:train_options/loss_options/train[hamil_abs]| replace:: ``hamil_abs`` .. _`code:train_options/loss_options/train[hamil_abs]`: `train_options/loss_options/train[hamil_abs]`_ .. |code:train_options/loss_options/train[hamil_blas]| replace:: ``hamil_blas`` @@ -389,19 +389,6 @@ train_options: .. _`flag:train_options/loss_options/train/method`: `train_options/loss_options/train/method`_ - .. _`train_options/loss_options/train[hamil]`: - - When |flag:train_options/loss_options/train/method|_ is set to ``hamil``: - - .. _`train_options/loss_options/train[hamil]/onsite_shift`: - - onsite_shift: - | type: ``bool``, optional, default: ``False`` - | argument path: ``train_options/loss_options/train[hamil]/onsite_shift`` - - Whether to use onsite shift in loss function. Default: False - - .. _`train_options/loss_options/train[eigvals]`: When |flag:train_options/loss_options/train/method|_ is set to ``eigvals``: @@ -430,6 +417,35 @@ train_options: The weight of eigenvalue difference. Default: 0.01 + .. _`train_options/loss_options/train[eigvals]/diff_valence`: + + diff_valence: + | type: ``dict`` | ``NoneType``, optional, default: ``None`` + | argument path: ``train_options/loss_options/train[eigvals]/diff_valence`` + + set the difference of the number of valence electrons in DFT and TB. eg {'A':6,'B':7}, Default: None, which means no difference + + .. _`train_options/loss_options/train[eigvals]/spin_deg`: + + spin_deg: + | type: ``int``, optional, default: ``2`` + | argument path: ``train_options/loss_options/train[eigvals]/spin_deg`` + + The spin degeneracy of band structure. Default: 2 + + + .. _`train_options/loss_options/train[skints]`: + + When |flag:train_options/loss_options/train/method|_ is set to ``skints``: + + .. _`train_options/loss_options/train[skints]/skdata`: + + skdata: + | type: ``str`` + | argument path: ``train_options/loss_options/train[skints]/skdata`` + + The path to the skfile or sk database. + .. _`train_options/loss_options/train[hamil_abs]`: @@ -472,7 +488,7 @@ train_options: method: | type: ``str`` (flag key) | argument path: ``train_options/loss_options/validation/method`` - | possible choices: |code:train_options/loss_options/validation[hamil]|_, |code:train_options/loss_options/validation[eigvals]|_, |code:train_options/loss_options/validation[hamil_abs]|_, |code:train_options/loss_options/validation[hamil_blas]|_ + | possible choices: |code:train_options/loss_options/validation[eigvals]|_, |code:train_options/loss_options/validation[skints]|_, |code:train_options/loss_options/validation[hamil_abs]|_, |code:train_options/loss_options/validation[hamil_blas]|_ The loss function type, defined by a string like `_`, Default: `eigs_l2dsf`. supported loss functions includes: @@ -482,10 +498,10 @@ train_options: - `hamil_blas`: - .. |code:train_options/loss_options/validation[hamil]| replace:: ``hamil`` - .. _`code:train_options/loss_options/validation[hamil]`: `train_options/loss_options/validation[hamil]`_ .. |code:train_options/loss_options/validation[eigvals]| replace:: ``eigvals`` .. _`code:train_options/loss_options/validation[eigvals]`: `train_options/loss_options/validation[eigvals]`_ + .. |code:train_options/loss_options/validation[skints]| replace:: ``skints`` + .. _`code:train_options/loss_options/validation[skints]`: `train_options/loss_options/validation[skints]`_ .. |code:train_options/loss_options/validation[hamil_abs]| replace:: ``hamil_abs`` .. _`code:train_options/loss_options/validation[hamil_abs]`: `train_options/loss_options/validation[hamil_abs]`_ .. |code:train_options/loss_options/validation[hamil_blas]| replace:: ``hamil_blas`` @@ -495,19 +511,6 @@ train_options: .. _`flag:train_options/loss_options/validation/method`: `train_options/loss_options/validation/method`_ - .. _`train_options/loss_options/validation[hamil]`: - - When |flag:train_options/loss_options/validation/method|_ is set to ``hamil``: - - .. _`train_options/loss_options/validation[hamil]/onsite_shift`: - - onsite_shift: - | type: ``bool``, optional, default: ``False`` - | argument path: ``train_options/loss_options/validation[hamil]/onsite_shift`` - - Whether to use onsite shift in loss function. Default: False - - .. _`train_options/loss_options/validation[eigvals]`: When |flag:train_options/loss_options/validation/method|_ is set to ``eigvals``: @@ -536,6 +539,35 @@ train_options: The weight of eigenvalue difference. Default: 0.01 + .. _`train_options/loss_options/validation[eigvals]/diff_valence`: + + diff_valence: + | type: ``dict`` | ``NoneType``, optional, default: ``None`` + | argument path: ``train_options/loss_options/validation[eigvals]/diff_valence`` + + set the difference of the number of valence electrons in DFT and TB. eg {'A':6,'B':7}, Default: None, which means no difference + + .. _`train_options/loss_options/validation[eigvals]/spin_deg`: + + spin_deg: + | type: ``int``, optional, default: ``2`` + | argument path: ``train_options/loss_options/validation[eigvals]/spin_deg`` + + The spin degeneracy of band structure. Default: 2 + + + .. _`train_options/loss_options/validation[skints]`: + + When |flag:train_options/loss_options/validation/method|_ is set to ``skints``: + + .. _`train_options/loss_options/validation[skints]/skdata`: + + skdata: + | type: ``str`` + | argument path: ``train_options/loss_options/validation[skints]/skdata`` + + The path to the skfile or sk database. + .. _`train_options/loss_options/validation[hamil_abs]`: @@ -578,7 +610,7 @@ train_options: method: | type: ``str`` (flag key) | argument path: ``train_options/loss_options/reference/method`` - | possible choices: |code:train_options/loss_options/reference[hamil]|_, |code:train_options/loss_options/reference[eigvals]|_, |code:train_options/loss_options/reference[hamil_abs]|_, |code:train_options/loss_options/reference[hamil_blas]|_ + | possible choices: |code:train_options/loss_options/reference[eigvals]|_, |code:train_options/loss_options/reference[skints]|_, |code:train_options/loss_options/reference[hamil_abs]|_, |code:train_options/loss_options/reference[hamil_blas]|_ The loss function type, defined by a string like `_`, Default: `eigs_l2dsf`. supported loss functions includes: @@ -588,10 +620,10 @@ train_options: - `hamil_blas`: - .. |code:train_options/loss_options/reference[hamil]| replace:: ``hamil`` - .. _`code:train_options/loss_options/reference[hamil]`: `train_options/loss_options/reference[hamil]`_ .. |code:train_options/loss_options/reference[eigvals]| replace:: ``eigvals`` .. _`code:train_options/loss_options/reference[eigvals]`: `train_options/loss_options/reference[eigvals]`_ + .. |code:train_options/loss_options/reference[skints]| replace:: ``skints`` + .. _`code:train_options/loss_options/reference[skints]`: `train_options/loss_options/reference[skints]`_ .. |code:train_options/loss_options/reference[hamil_abs]| replace:: ``hamil_abs`` .. _`code:train_options/loss_options/reference[hamil_abs]`: `train_options/loss_options/reference[hamil_abs]`_ .. |code:train_options/loss_options/reference[hamil_blas]| replace:: ``hamil_blas`` @@ -601,19 +633,6 @@ train_options: .. _`flag:train_options/loss_options/reference/method`: `train_options/loss_options/reference/method`_ - .. _`train_options/loss_options/reference[hamil]`: - - When |flag:train_options/loss_options/reference/method|_ is set to ``hamil``: - - .. _`train_options/loss_options/reference[hamil]/onsite_shift`: - - onsite_shift: - | type: ``bool``, optional, default: ``False`` - | argument path: ``train_options/loss_options/reference[hamil]/onsite_shift`` - - Whether to use onsite shift in loss function. Default: False - - .. _`train_options/loss_options/reference[eigvals]`: When |flag:train_options/loss_options/reference/method|_ is set to ``eigvals``: @@ -642,6 +661,35 @@ train_options: The weight of eigenvalue difference. Default: 0.01 + .. _`train_options/loss_options/reference[eigvals]/diff_valence`: + + diff_valence: + | type: ``dict`` | ``NoneType``, optional, default: ``None`` + | argument path: ``train_options/loss_options/reference[eigvals]/diff_valence`` + + set the difference of the number of valence electrons in DFT and TB. eg {'A':6,'B':7}, Default: None, which means no difference + + .. _`train_options/loss_options/reference[eigvals]/spin_deg`: + + spin_deg: + | type: ``int``, optional, default: ``2`` + | argument path: ``train_options/loss_options/reference[eigvals]/spin_deg`` + + The spin degeneracy of band structure. Default: 2 + + + .. _`train_options/loss_options/reference[skints]`: + + When |flag:train_options/loss_options/reference/method|_ is set to ``skints``: + + .. _`train_options/loss_options/reference[skints]/skdata`: + + skdata: + | type: ``str`` + | argument path: ``train_options/loss_options/reference[skints]/skdata`` + + The path to the skfile or sk database. + .. _`train_options/loss_options/reference[hamil_abs]`: