Skip to content

core

Core recipes for the NewtonNet code.

has_newtonnet module-attribute 

has_newtonnet = bool(find_spec('newtonnet'))

has_sella module-attribute 

has_sella = bool(find_spec('sella'))

freq_job 

freq_job(
    atoms: Atoms,
    temperature: float = 298.15,
    pressure: float = 1.0,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs
) -> VibThermoSchema

Perform a frequency calculation using the given atoms object.

Parameters:

  • atoms (Atoms) –

    The atoms object representing the system.

  • temperature (float, default: 298.15 ) –

    The temperature for the thermodynamic analysis.

  • pressure (float, default: 1.0 ) –

    The pressure for the thermodynamic analysis.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Additional fields to add to the results dictionary.

  • **calc_kwargs –

    Custom kwargs for the NewtonNet calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the newtonnet.utils.ase_interface.MLAseCalculator calculator.

Returns:

  • VibThermoSchema –

    Dictionary of results. See the type-hint for the data structure.

Source code in quacc/recipes/newtonnet/core.py 
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
@job
@requires(
    has_newtonnet, "NewtonNet must be installed. Refer to the quacc documentation."
)
def freq_job(
    atoms: Atoms,
    temperature: float = 298.15,
    pressure: float = 1.0,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs,
) -> VibThermoSchema:
    """
    Perform a frequency calculation using the given atoms object.

    Parameters
    ----------
    atoms
        The atoms object representing the system.
    temperature
        The temperature for the thermodynamic analysis.
    pressure
        The pressure for the thermodynamic analysis.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    additional_fields
        Additional fields to add to the results dictionary.
    **calc_kwargs
        Custom kwargs for the NewtonNet calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the `newtonnet.utils.ase_interface.MLAseCalculator` calculator.

    Returns
    -------
    VibThermoSchema
        Dictionary of results. See the type-hint for the data structure.
    """
    settings = get_settings()
    calc_defaults = {
        "model_path": settings.NEWTONNET_MODEL_PATH,
        "settings_path": settings.NEWTONNET_CONFIG_PATH,
        "hess_method": "autograd",
    }
    calc_flags = recursive_dict_merge(calc_defaults, calc_kwargs)

    calc = NewtonNet(**calc_flags)
    final_atoms = Runner(atoms, calc, copy_files=copy_files).run_calc()

    summary = Summarize(
        additional_fields={"name": "NewtonNet Frequency"} | (additional_fields or {})
    ).run(final_atoms, atoms)

    vib = VibrationsData(final_atoms, summary["results"]["hessian"])
    return VibSummarize(
        vib,
        directory=summary["dir_name"],
        additional_fields={"name": "ASE Vibrations and Thermo Analysis"},
    ).vib_and_thermo(
        "ideal_gas",
        energy=summary["results"]["energy"],
        temperature=temperature,
        pressure=pressure,
    )

relax_job 

relax_job(
    atoms: Atoms,
    opt_params: OptParams | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs
) -> OptSchema

Relax a structure.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • opt_params (OptParams | None, default: None ) –

    Dictionary of custom kwargs for the optimization process. For a list of available keys, refer to quacc.runners.ase.Runner.run_opt.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Additional fields to add to the results dictionary.

  • **calc_kwargs –

    Dictionary of custom kwargs for the NewtonNet calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the newtonnet.utils.ase_interface.MLAseCalculator calculator.

Returns:

Source code in quacc/recipes/newtonnet/core.py 
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
@job
@requires(
    has_newtonnet, "NewtonNet must be installed. Refer to the quacc documentation."
)
def relax_job(
    atoms: Atoms,
    opt_params: OptParams | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs,
) -> OptSchema:
    """
    Relax a structure.

    Parameters
    ----------
    atoms
        Atoms object
    opt_params
        Dictionary of custom kwargs for the optimization process. For a list
        of available keys, refer to [quacc.runners.ase.Runner.run_opt][].
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    additional_fields
        Additional fields to add to the results dictionary.
    **calc_kwargs
        Dictionary of custom kwargs for the NewtonNet calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the `newtonnet.utils.ase_interface.MLAseCalculator` calculator.

    Returns
    -------
    OptSchema
        Dictionary of results, specified in [quacc.schemas.ase.Summarize.opt][].
        See the type-hint for the data structure.
    """
    settings = get_settings()
    calc_defaults = {
        "model_path": settings.NEWTONNET_MODEL_PATH,
        "settings_path": settings.NEWTONNET_CONFIG_PATH,
    }
    opt_defaults = {"optimizer": Sella} if has_sella else {}

    calc_flags = recursive_dict_merge(calc_defaults, calc_kwargs)
    opt_flags = recursive_dict_merge(opt_defaults, opt_params)

    calc = NewtonNet(**calc_flags)
    dyn = Runner(atoms, calc, copy_files=copy_files).run_opt(**opt_flags)

    return _add_stdev_and_hess(
        Summarize(
            additional_fields={"name": "NewtonNet Relax"} | (additional_fields or {})
        ).opt(dyn)
    )

static_job 

static_job(
    atoms: Atoms,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs
) -> RunSchema

Carry out a single-point calculation.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Additional fields to add to the results dictionary.

  • **calc_kwargs –

    Custom kwargs for the NewtonNet calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the newtonnet.utils.ase_interface.MLAseCalculator calculator.

Returns:

Source code in quacc/recipes/newtonnet/core.py 
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
@job
@requires(
    has_newtonnet, "NewtonNet must be installed. Refer to the quacc documentation."
)
def static_job(
    atoms: Atoms,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs,
) -> RunSchema:
    """
    Carry out a single-point calculation.

    Parameters
    ----------
    atoms
        Atoms object
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    additional_fields
        Additional fields to add to the results dictionary.
    **calc_kwargs
        Custom kwargs for the NewtonNet calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the `newtonnet.utils.ase_interface.MLAseCalculator` calculator.

    Returns
    -------
    RunSchema
        Dictionary of results, specified in [quacc.schemas.ase.Summarize.run][].
        See the type-hint for the data structure.
    """
    settings = get_settings()
    calc_defaults = {
        "model_path": settings.NEWTONNET_MODEL_PATH,
        "settings_path": settings.NEWTONNET_CONFIG_PATH,
    }
    calc_flags = recursive_dict_merge(calc_defaults, calc_kwargs)

    calc = NewtonNet(**calc_flags)
    final_atoms = Runner(atoms, calc, copy_files=copy_files).run_calc()

    return Summarize(
        additional_fields={"name": "NewtonNet Static"} | (additional_fields or {})
    ).run(final_atoms, atoms)