7.3.1.3. SCC-DFTB repulsive potential

Important

This class cannot be stored in .yaml format and so cannot be used through the ParAMS GUI nor with the ParAMSJob Python class.

The DFTBSplineRepulsivePotentialParameters class provides an interface to reading and writing the two-body repulsive potential contained in the SCC-DFTB Slater-Koster parameter files. An analytical form of the repulsive function is represented, for example, by a TaperedDoubleExponential instance, or any other instance inheriting from RepulsiveFunction.

Note

Some DFTB parameter sets (e.g., QUASINANO2015) in the Amsterdam Modeling Suite are encrypted. The encrypted parameters cannot be reparameterized with ParAMS.

See also

Tutorial: DFTB repulsive potential

To use this interface, the Slater-Koster files must already contain the electronic parameters, as well as some repulsive function represented by cubic splines. When writing a parameter set, the DFTBSplineRepulsivePotentialParameters instance will write out all Slater-Koster files, keeping the electronic parts but overwriting the repulsive potentials.

The names of parameters are of the form Element1-Element2:p0, e.g., O-Zn:p0 is the first parameter of the analytical repulsive function written as splines to O-Zn.skf, O-Zn:p1 is the second parameter, etc. For a TaperedDoubleExponential, there are four parameters per element pair. Note: The element names must be sorted alphabetically. The function defined for the element pair O-Zn will also be written to Zn-O.skf. The parameters Zn-O:p0 etc. are ignored.

Slater-Koster files that have no active parameters associated with them will be copied, i.e., the original repulsive potential is used.

Example:

# Make an interface to the SCC-DFTB repulsive potential parametrization.
interface = DFTBSplineRepulsivePotentialParameters(
  folder='/amshome/atomicdata/DFTB/DFTB.org/znorg-0-1', # use electronic parameters from znorg-0-1
  repulsive_function=TaperedDoubleExponential(cutoff=5.67), #repulsive potential defined by four parameters
  r_range=np.arange(0., 5.87, 0.1), # distances (in bohr) for which to center the cubic splines
  other_settings=dftb_s # Settings object defining e.g. k-point sampling
)

# Refit only the O-Zn and Zn-O repulsive potential parameters
# All other repulsive potentials from znorg-0-1 (e.g. as defined in C-C.skf)
# will be kept in their original form
for p in interface:
    p.is_active = p.name.startswith('O-Zn')

7.3.1.3.1. DFTBSplineRepulsivePotentialParameters API

class DFTBSplineRepulsivePotentialParameters(folder, repulsive_function, r_range, other_settings=None)

Interface to the parameterization of the SCC-DFTB two-body repulsive potential in the AMS DFTB engine.

__init__(folder, repulsive_function, r_range, other_settings=None)

Create a new instance based on the parameterization in folder.

Parameters:

folderstr

The folder from which the original .skf files are read. They must include Spline repulsive potentials. The electronic parts of the .skf files will be copied to the new (reparametrized) .skf files. The repulsive potential part will be overwritten. Note: The repulsive function to be parametrized is not initialized from the .skf files.

repulsive_function: RepulsiveFunction (e.g. TaperedDoubleExponential)

An analytical repulsive function containing parmeters to be optimized.

r_rangelist of floats corresponding to distances for which to write cubic splines

The unit must be bohr

other_settingsSettings

A settings instance with other settings to be used for the engine. Should start at normal root level of Settings instances used with the AMS driver, i.e. DFTB engine input should be in other_settings.input.dftb.

yaml_store(*args, **kwargs)

Overrides the base class method to do nothing. This parameter interface cannot be written to YAML.

_get_spline_string_list(repulsive_function, params, r_range)

return a list of strings that can be written as the Spline repulsive potential in a .skf file

write(folder, parameters=None)

Writes the current parameterization to disk.

If folder does not exist, it will be created. If folder exists the files in it will be overwritten if necessary.

pickle_dump(fname)

Stores the parameter interface instance in a binary format to fname. Loading it with pickle_load() will restore values, ranges and active settings. If fname does not end with the .pkl extension, it will be added.

classmethod pickle_load(fname)

Loads the parameter interface from a binary file stored with pickle_dump().

get_engine(parameters=None, path=None, write=True)

Returns

Engine for an SCC-DFTB engine matching the passed params.

If path is not set (should be a directory), the parameter files will be created in a temporary directory that is deleted when the returned Engine is garbage collected.

7.3.1.3.2. TaperedDoubleExponential API

class TaperedDoubleExponential(cutoff=7.0)

Tapered double exponential function of the form

0.5*[cos(pi*r/cutoff)+1]*[A*exp(-B*r)+C*exp(-D*r)]

where A, B, C, D are the parameters.

__init__(cutoff=7.0)

Initialize self. See help(type(self)) for accurate signature.

__call__(x, params)

x : a numpy array containing the values for which to evaluate the function params : a list or 1D numpy array with self.npar (=4) elements

Returns a numpy array with the same shape as x containing the function value for each evaluated point