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add entire arguments of gaussian style #830

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Aug 1, 2022
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add entire arguments of gaussian style #830

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4fc8dbb
add entire arguments of gaussian style
njzjz Jul 30, 2022
67f3948
add args for relative model deviation
njzjz Jul 30, 2022
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52 changes: 45 additions & 7 deletions dpgen/generator/arginfo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,6 +139,10 @@ def model_devi_lmp_args() -> List[Argument]:
doc_model_devi_nopbc = 'Assume open boundary condition in MD simulations.'
doc_model_devi_activation_func = 'Set activation functions for models, length of the list should be the same as numb_models, and two elements in the list of string respectively assign activation functions to the embedding and fitting nets within each model. Backward compatibility: the orginal "list of String" format is still supported, where embedding and fitting nets of one model use the same activation function, and the length of the list should be the same as numb_models.'
doc_shuffle_poscar = 'Shuffle atoms of each frame before running simulations. The purpose is to sample the element occupation of alloys.'
doc_use_relative = 'Calculate relative force model deviation.'
doc_epsilon = 'The level parameter for computing the relative force model deviation.'
doc_use_relative_v = 'Calculate relative virial model deviation.'
doc_epsilon_v = 'The level parameter for computing the relative virial model deviation.'

return [
model_devi_jobs_args(),
Expand Down Expand Up @@ -173,6 +177,10 @@ def model_devi_lmp_args() -> List[Argument]:
Argument("model_devi_activation_func", list, optional=True,
doc=doc_model_devi_activation_func),
Argument("shuffle_poscar", bool, optional=True, default=False, doc=doc_shuffle_poscar),
Argument("use_relative", bool, optional=True, default=False, doc=doc_use_relative),
Argument("epsilon", float, optional=True, doc=doc_epsilon),
Argument("use_relative_v", bool, optional=True, default=False, doc=doc_use_relative_v),
Argument("epsilon_v", float, optional=True, doc=doc_epsilon_v),
]


Expand Down Expand Up @@ -204,30 +212,60 @@ def fp_style_vasp_args() -> List[Argument]:

# gaussian
def fp_style_gaussian_args() -> List[Argument]:
doc_keywords = 'Keywords for Gaussian input.'
doc_multiplicity = 'Spin multiplicity for Gaussian input. If set to auto, the spin multiplicity will be detected automatically. If set to frag, the "fragment=N" method will be used.'
"""Gaussian fp style arguments.

Returns
-------
list[dargs.Argument]
list of Gaussian fp style arguments
"""
doc_keywords = 'Keywords for Gaussian input, e.g. force b3lyp/6-31g**. If a list, run multiple steps.'
doc_multiplicity = ('Spin multiplicity for Gaussian input. If `auto`, multiplicity will be detected automatically, '
'with the following rules: when fragment_guesses=True, multiplicity will +1 for each radical, '
'and +2 for each oxygen molecule; when fragment_guesses=False, multiplicity will be 1 or 2, '
'but +2 for each oxygen molecule.')
doc_nproc = 'The number of processors for Gaussian input.'
doc_charge = 'Molecule charge. Only used when charge is not provided by the system.'
doc_fragment_guesses = 'Initial guess generated from fragment guesses. If True, `multiplicity` should be `auto`.'
doc_basis_set = 'Custom basis set.'
doc_keywords_high_multiplicity = ('Keywords for points with multiple raicals. `multiplicity` should be `auto`. '
'If not set, fallback to normal keywords.')

args = [
Argument("keywords", [str or list],
Argument("keywords", [str, list],
optional=False, doc=doc_keywords),
Argument("multiplicity", [int or str],
optional=False, doc=doc_multiplicity),
Argument("multiplicity", [int, str],
optional=True, default="auto", doc=doc_multiplicity),
Argument("nproc", int, optional=False, doc=doc_nproc),
Argument("charge", int, optional=True, default=0, doc=doc_nproc),
Argument("fragment_guesses", bool, optional=True, default=False, doc=doc_fragment_guesses),
Argument("basis_set", str, optional=True, doc=doc_fragment_guesses),
Argument("keywords_high_multiplicity", str, optional=True, doc=doc_keywords_high_multiplicity),
]

doc_use_clusters = 'If set to true, clusters will be taken instead of the whole system. This option does not work with DeePMD-kit 0.x.'
doc_cluster_cutoff = 'The cutoff radius of clusters if use_clusters is set to true.'
doc_use_clusters = 'If set to true, clusters will be taken instead of the whole system.'
doc_cluster_cutoff = ('The soft cutoff radius of clusters if `use_clusters` is set to true. Molecules will be taken '
'as whole even if part of atoms is out of the cluster. Use `cluster_cutoff_hard` to only '
'take atoms within the hard cutoff radius.')
doc_cluster_cutoff_hard = ('The hard cutoff radius of clusters if `use_clusters` is set to true. Outside the hard cutoff radius, '
'atoms will not be taken even if they are in a molecule where some atoms are within the cutoff radius.')
doc_cluster_minify = ('If enabled, when an atom within the soft cutoff radius connects a single bond with '
'a non-hydrogen atom out of the soft cutoff radius, the outer atom will be replaced by a '
'hydrogen atom. When the outer atom is a hydrogen atom, the outer atom will be '
'kept. In this case, other atoms out of the soft cutoff radius will be removed.')
doc_fp_params_gaussian = 'Parameters for Gaussian calculation.'

return [
Argument("use_clusters", bool, optional=True, default=False, doc=doc_use_clusters),
Argument("cluster_cutoff", float,
optional=True, doc=doc_cluster_cutoff),
Argument("cluster_cutoff_hard", float, optional=True, doc=doc_cluster_cutoff_hard),
Argument("cluster_minify", bool, optional=True, default=False, doc=doc_cluster_minify),
Argument("fp_params", dict, args, [],
optional=False, doc=doc_fp_params_gaussian),
]


# siesta
def fp_style_siesta_args() -> List[Argument]:
doc_ecut = 'Define the plane wave cutoff for grid.'
Expand Down