chemparseplot.plot.landscape

Sketch-map landscape figures over minima databases.

A campaign of quenched minima becomes one figure: a sketch-map plane (lab-cosmo dimlandmark/dimred binaries) over a permutation-invariant descriptor, a filled-contour energy surface with thin contour lines, per-arm scatter overlays, pinned reference markers, and rendered structure insets in the figure margins tied to their map points.

The default descriptor is the sorted smoothed-coordination-number vector, the discriminant of the sketch-map literature for Lennard-Jones clusters: it separates the fcc funnel from the icosahedral one. SOAP power spectra (through featomic) remain available for molecular systems where coordination alone degenerates.

Added in version 1.10.0.

Module Contents

Functions

cn_matrix	Sorted smoothed coordination numbers, permutation invariant.
soap_matrix	Structure-averaged SOAP power spectra through featomic.
median_sigma	The sketch-map switching scale: median pairwise descriptor distance.
run_sketchmap	Landmark selection and the published sketch-map projection schedule.
plot_landscape_surface	Filled-contour energy surface with thin contour lines.
margin_inset_slots	Axes-fraction slots down the left and right figure margins.
place_margin_insets	Structure insets at margin slots, arrowed to their map points.

Data

ARM_MARKERS
SOAP_HYPERS

API

chemparseplot.plot.landscape.ARM_MARKERS

[‘o’, ‘^’, ‘s’, ‘P’, ‘X’]

chemparseplot.plot.landscape.SOAP_HYPERS

None

chemparseplot.plot.landscape.cn_matrix(structures, symbols, cutoff=1.5, cn_species=None)

Sorted smoothed coordination numbers, permutation invariant.

A Fermi switching function at the cutoff keeps the vector continuous, so near-degenerate minima do not collapse onto identical rows.

Parameters

structures : sequence of array-like Flat 3N coordinate rows. symbols : list of str One chemical symbol per atom. cutoff : float Coordination cutoff in the coordinate units. cn_species : str, optional Restrict the descriptor to atoms of one species.

Added in version 1.10.0.

chemparseplot.plot.landscape.soap_matrix(structures, symbols, cutoff=4.0, hypers=None)

Structure-averaged SOAP power spectra through featomic.

Added in version 1.10.0.

chemparseplot.plot.landscape.median_sigma(matrix, rng, sample=400)

The sketch-map switching scale: median pairwise descriptor distance.

Added in version 1.10.0.

chemparseplot.plot.landscape.run_sketchmap(matrix, smbin, lapack_lib, n_landmark, sigma, workdir, n_pinned=0)

Landmark selection and the published sketch-map projection schedule.

dimlandmark picks minmax landmarks (the first n_pinned rows are pinned); dimred runs sigmoid exponents 8,8 against 2,8, conjugate gradient pre-optimization, then the pointwise global grid stage. No -pi: descriptor space is not periodic.

Returns

coords, idx : ndarray Projected landmark coordinates and their row indices in matrix.

Added in version 1.10.0.

chemparseplot.plot.landscape.plot_landscape_surface(ax, coords, energies, cmap=None, levels=20)

Filled-contour energy surface with thin contour lines.

Returns the contour set for colorbar wiring.

Added in version 1.10.0.

chemparseplot.plot.landscape.margin_inset_slots(n)

Axes-fraction slots down the left and right figure margins.

Added in version 1.10.0.

chemparseplot.plot.landscape.place_margin_insets(fig, ax, entries, zoom=0.14, renderer='xyzrender')

Structure insets at margin slots, arrowed to their map points.

Parameters

entries : list of dict Each carries atoms (ASE Atoms), xy (map point), and optionally label drawn under the slot.

Added in version 1.10.0.