py_utils.core.to_networkx Namespace Reference

Functions
str	vertex (Population pop, int n)
range	_sizes (Population pop, int n_max)
	to_networkx (ReactionAdmissibilityGraph rag, int n_max=40, bool include_binary=True)
None	write_graphml (G, path)
str	structural_report (ReactionAdmissibilityGraph rag, int n_max=40)

Variables
	ap
	type
	int
	default
	help
	choices
	action
	Path
	a = ap.parse_args()
	inp
	rag
	_
	equations
	cascade
str	report = structural_report(rag, n_max=a.n_max)
	encoding
	G

Detailed Description

core/to_networkx.py — explicit materialization of a RAG for diagnostics.

Host-independent.  The production path keeps the reaction admissibility
graph *implicit*: an :class:`Edge` is a size-parameterized family, and the
graph walker never instantiates a vertex.  That is the right choice for the
inner loop (see the paper, Section "Implementation"), but it means the
standard structural queries — connectivity, reachability from the monomer
pools, orphaned vertices, cycle structure — are not available for free.

This module supplies them by exporting the declared graph, truncated at a
chosen size cut-off, into an explicit ``networkx.MultiDiGraph``.  It is a
DIAGNOSTIC path only: nothing in the solver imports it, and NetworkX is an
optional dependency.

Typical use::

    from py_utils.materials import build_eurofer_rag
    from py_utils.core.to_networkx import to_networkx, structural_report

    rag, layout = build_eurofer_rag(inp, rr)
    G = to_networkx(rag, n_max=40)
    print(structural_report(rag, n_max=40))

Cite as: NetworkX, Hagberg, Schult & Swart, Proc. SciPy 2008.

Function Documentation

_sizes()

range py_utils.core.to_networkx._sizes ( Population  pop, int  n_max  )

protected

Definition at line 44 of file to_networkx.py.

structural_report()

str py_utils.core.to_networkx.structural_report	(	ReactionAdmissibilityGraph	rag,
		int	n_max = 40
	)

Human-readable structural audit of a declared RAG.

Reports vertex/edge counts, weak connectivity, the set of vertices not
reachable from the monomer pools (a declaration bug: population with no
production channel), and the set with no outgoing edge (a sink-only
trap).  Intended to be run once per host declaration and quoted in the
paper, not called during integration.

Definition at line 205 of file to_networkx.py.

to_networkx()

py_utils.core.to_networkx.to_networkx	(	ReactionAdmissibilityGraph	rag,
		int	n_max = 40,
		bool	include_binary = True
	)

Materialize ``rag`` up to size ``n_max`` as a ``networkx.MultiDiGraph``.

Parameters
----------
rag : ReactionAdmissibilityGraph
    The host's declared graph.
n_max : int
    Size cut-off.  Keep it small (tens): the binary edge classes are
    O(n_max**2) per family, which is exactly why the production path
    does not materialize the graph at all.
include_binary : bool
    Expand COALESCENCE and ANNIHILATION families.  These are directed
    *hyperedges* (two precursors); NetworkX has no hyperedge type, so
    each is represented by its two tail->head arcs, both tagged
    ``hyperedge=True`` and sharing a ``hyper_id``.  Set False for a
    cleaner drawing.

Returns
-------
networkx.MultiDiGraph
    Node attributes: ``polarity``, ``population``, ``size``.
    Edge attributes: ``edge_class``, ``label``, ``kernel``,
    ``hyperedge``, ``hyper_id``.

Definition at line 51 of file to_networkx.py.

vertex()

str py_utils.core.to_networkx.vertex	(	Population	pop,
		int	n
	)

Canonical string key for the vertex (polarity, size, population).

Definition at line 39 of file to_networkx.py.

write_graphml()

None py_utils.core.to_networkx.write_graphml	(		G,
			path
	)

Write ``G`` to GraphML, dropping attributes GraphML cannot represent.

``to_networkx`` tags every arc with ``hyper_id``, which is ``None`` on
the unary edge classes because they are not hyperedge members, and
``kernel`` is ``None`` for any edge the host declared without one.
The GraphML writer rejects ``None`` outright ("GraphML writer does not
support <class 'NoneType'> as data values"), so exporting the graph
unmodified always fails.  Attributes are dropped rather than coerced:
an absent ``hyper_id`` is what "not a hyperedge" means, and writing a
sentinel would invite a reader to treat it as an id.

The input graph is not modified.

Definition at line 176 of file to_networkx.py.

Variable Documentation

_

py_utils.core.to_networkx._

protected

Definition at line 292 of file to_networkx.py.

a

py_utils.core.to_networkx.a = ap.parse_args()

Definition at line 288 of file to_networkx.py.

action

py_utils.core.to_networkx.action

Definition at line 281 of file to_networkx.py.

ap

py_utils.core.to_networkx.ap

Initial value:

=  argparse.ArgumentParser(
        description="Materialize and audit the EUROFER-97 reaction "
                    "admissibility graph.")

Definition at line 270 of file to_networkx.py.

cascade

py_utils.core.to_networkx.cascade

Definition at line 293 of file to_networkx.py.

choices

py_utils.core.to_networkx.choices

Definition at line 278 of file to_networkx.py.

default

py_utils.core.to_networkx.default

Definition at line 273 of file to_networkx.py.

encoding

py_utils.core.to_networkx.encoding

Definition at line 298 of file to_networkx.py.

equations

py_utils.core.to_networkx.equations

Definition at line 293 of file to_networkx.py.

G

py_utils.core.to_networkx.G

Initial value:

=  to_networkx(rag, n_max=a.n_max,
                        include_binary=not a.no_binary)

Definition at line 301 of file to_networkx.py.

help

py_utils.core.to_networkx.help

Definition at line 274 of file to_networkx.py.

inp

py_utils.core.to_networkx.inp

Initial value:

=  InputData(I=a.I, V=a.V,
                    physics_option=f"full_CD_{a.cascade}")

Definition at line 290 of file to_networkx.py.

int

py_utils.core.to_networkx.int

Definition at line 273 of file to_networkx.py.

Path

py_utils.core.to_networkx.Path

Definition at line 284 of file to_networkx.py.

rag

py_utils.core.to_networkx.rag

Definition at line 292 of file to_networkx.py.

report

str py_utils.core.to_networkx.report = structural_report(rag, n_max=a.n_max)

Definition at line 295 of file to_networkx.py.

type

py_utils.core.to_networkx.type

Definition at line 273 of file to_networkx.py.