3.2.2. horton.espfit.cost – ESP cost functions for estimating and testing charges¶
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class
horton.espfit.cost.ESPCost(A, B, C, natom)¶ Bases:
object-
classmethod
from_grid_data(coordinates, ugrid, vref, weights, rcut=20.0, alpha=None, gcut=None)¶
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classmethod
from_hdf5(grp)¶
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gradient(x)¶
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solve(qtot=None, ridge=0.0)¶
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to_hdf5(grp)¶
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value(x)¶
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value_charges(charges)¶
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worst(qtot=0.0)¶ Return a worst-case value for the cost function
Optional arguments:
- qtot
- The total charge of the molecule/crystal
Higher values for the cost function are still possible but if that happens, it is better not to use charges at all.
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classmethod
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horton.espfit.cost.setup_weights(coordinates, numbers, grid, dens=None, near=None, far=None)¶ Define a weight function for the ESPCost
Arguments:
- coordinates
- An array with shape (N, 3) containing atomic coordinates.
- numbers
- A vector with shape (N,) containing atomic numbers.
- grid
- A UniformGrid object.
Optional arguments:
- dens
The density-based criterion. This is a three-tuple with rho, lnrho0 and sigma. rho is the atomic or the pro-atomic electron density on the same grid as the ESP data. lnrho0 and sigma are parameters defined in JCTC, 3, 1004 (2007), DOI:10.1021/ct600295n. The weight function takes the form:
exp(-sigma*(ln(rho) - lnrho0)**2)
Note that the density, rho, should not contain depletions in the atomic cores, as is often encountered with pseudo-potential computations. In that case it is recommended to construct a promolecular density as input for this option.
- near
- Exclude points near the nuclei. This is a dictionary with as items (number, (R0, gamma)).
- far
- Exclude points far away. This is a two-tuple: (R0, gamma).