Create a Package subclass for handling CP2K CHARMM forcefields

[BvB93]

• The current CP2K class is heavily tailored towards density functional theory-calculations (DFT).
• Either alter the existing CP2K class or create a separate Package subclass for handling classical molecular mechanics (MM) calculations (something along the line of CP2K_MM ?).
• The initial focus should be to ensure compatiblity with CHARMM-type forcefields. Depending on user-demand (and the required amount of work) this can later be expanded.

Example input

>>> from qmflows import Settings, cp2k_mm, geometry
>>> from scm.plams import Molecule

>>> mol = Molecule(...)

# The charges; these will override anything specified in the .psf file
>>> charge = Settings({'param': 'charge'})
>>> charge.Cd = 0.9768
>>> charge.Se = -0.9768

# The Lennard-Jones epsilon and sigma paramters
>>> lj = Settings({'param': 'epsilon', 'sigma'})
>>> lj.unit = 'kcalmol', 'angstrom'
>>> lj['Cd Cd'] = 0.0741, 1.2340
>>> lj['Cd Se'] = 0.3639, 2.9400
>>> lj['Se Se'] = 0.1020, 4.8520

# Combine the settings
>>> s = Settings()
>>> s.periodic = 'NONE'  # This is the default
>>> s.psf = '/path/to/my/psf/file'
>>> s.prm = '/path/to/my/prm/file'
>>> s.lennard_jones = lj
>>> s.charge = charge

# Apply the geometry template
>>> s.specific.cp2k += geometry.specific.cp2k_mm

>>> job = cp2k_mm(settings=s, mol=mol)
>>> result = run(job)

[BvB93]

Proposed syntax for forcefield parameters as inspired by those in Auto-FOX:

>>> from qmflows import Settings

>>> s = Settings()
>>> s.specific.cp2k.sigma = Settings({
... 'key_path': ('specific', 'cp2k', 'force_eval', 'mm', 'forcefield', 'nonbonded', 'lennard-jones')
... 'unit': 'angstrom'
... 'Cd': '3.0'
... 'Se': 2.5
... 'O': 2
... })
>>> s.specific.cp2k.epsilon = Settings({
... 'key_path': ('specific', 'cp2k', 'force_eval', 'mm', 'forcefield', 'nonbonded', 'lennard-jones')
... 'Cd': '12.0'
... 'Se': 3.5
... 'O': 8
... })

In the proposed syntax each parameter block consists of three different type of keys:

• "key_path": A path of nested keys leading to the setting of interest. The "key_path" provided in the example above corresponds to the CP2K FORCE_EVAL/MM/FORCEFIELD/NONBONDED/LENNARD-JONES section. This keyword is mandatory and a value must be assigned by the user. Alternatively, a user can provide a string ("lennard-jones" in this case) serving as one of the in qmflows-defined aliases for the actual key path; for a comprehensive overview of available aliases see: https://github.com/SCM-NV/qmflows/blob/666f326a76de0f88f35b0f75071e1db2aa1d1508/src/qmflows/packages/cp2k_mm.py#L207-L238
• "unit": The unit that will be assigned to all parameters within a particular parameter block; see https://manual.cp2k.org/trunk/units.html for a comprehensive overview of all available units. Supplying this value will, for example, internally transform "O": 2 into "O": "[angstrom] 2". This is an optional keyword.
• "Cd", "Se", "O", etc.: The values of the actual parameters of interest. The name of the block (in combination with "key_path") will finally determine in where block these values will be assigned, e.g. under SIGMA and EPSILON.

[BvB93]

Open question: what would be best name for the "key_path" keyword (tentative name) as described above? Solved as of https://github.com/SCM-NV/qmflows/issues/148#issuecomment-596585344.

[BvB93]

Updated the parameter syntax in https://github.com/SCM-NV/qmflows/commit/4f086061d9454f834f208913bf8bdc00356739a3: Moved "key_path" to the main key and moved the specific CP2K keys to "param". Dictionary values can now be supplied as a either scalars or sequences but cannot be freely mixed.

>>> lennard_jones = {  # Example 1
...     'param': ('epsilon', 'sigma'),
...     'unit': ('kcalmol', 'angstrom'),  # An optional key
...     'Cs': (1, 1),
...     'Cd': (2, 2),
...     'O': (3, 3),
...     'H': (4, 4)
... }

>>> lennard_jones = [  # Example 2
... {'param': 'epsilon',
...  'unit': 'kcalmol',  # An optional key
...  'Cs': 1,
...  'Cd': 2,
...  'O': 3,
...  'H': 4},
... {'param': 'sigma',
...  'unit': 'angstrom',  # An optional key
...  'Cs': 1,
...  'Cd': 2,
...  'O': 3,
...  'H': 4}
... ]

Note that both examples result in equivalent settings.

[BvB93]

Introduced in https://github.com/SCM-NV/qmflows/pull/150. See https://github.com/SCM-NV/qmflows/issues/159 for further updates and new features.