def GraphIsomorphism(G1, G2):
"""Graph Isomorphism formula
The formula is the CNF encoding of the statement that two simple
graphs G1 and G2 are isomorphic.
Parameters
----------
G1 : networkx.Graph
an undirected graph object
G2 : networkx.Graph
an undirected graph object
Returns
-------
A CNF formula which is satiafiable if and only if graphs G1 and G2
are isomorphic.
"""
F = CNF()
F.header = "Graph Isomorphism problem between graphs " +\
G1.name + " and " + G2.name + "\n" + F.header
F.mode_strict()
U=enumerate_vertices(G1)
V=enumerate_vertices(G2)
var = _graph_isomorphism_var
for (u, v) in product(U,V):
F.add_variable(var(u, v))
# Defined on both side
for u in U:
F.add_clause([(True, var(u, v)) for v in V])
for v in V:
F.add_clause([(True, var(u, v)) for u in U])
# Injective on both sides
for u in U:
for v1, v2 in combinations(V, 2):
F.add_clause([(False, var(u, v1)),
(False, var(u, v2))])
for v in V:
for u1, u2 in combinations(U, 2):
F.add_clause([(False, var(u1, v)),
(False, var(u2, v))])
# Edge consistency
for u1, u2 in combinations(U, 2):
for v1, v2 in combinations(V, 2):
if G1.has_edge(u1, u2) != G2.has_edge(v1, v2):
F.add_clause([(False, var(u1, v1)),
(False, var(u2, v2))])
F.add_clause([(False, var(u1, v2)),
(False, var(u2, v1))])
return F
def GraphIsomorphism(G1, G2):
"""Graph Isomorphism formula
The formula is the CNF encoding of the statement that two simple
graphs G1 and G2 are isomorphic.
Parameters
----------
G1 : networkx.Graph
an undirected graph object
G2 : networkx.Graph
an undirected graph object
Returns
-------
A CNF formula which is satiafiable if and only if graphs G1 and G2
are isomorphic.
"""
F = CNF()
F.header = "Graph Isomorphism problem between graphs " +\
G1.name + " and " + G2.name + "\n" + F.header
U = enumerate_vertices(G1)
V = enumerate_vertices(G2)
var = _graph_isomorphism_var
for (u, v) in product(U, V):
F.add_variable(var(u, v))
# Defined on both side
for u in U:
F.add_clause([(True, var(u, v)) for v in V], strict=True)
for v in V:
F.add_clause([(True, var(u, v)) for u in U], strict=True)
# Injective on both sides
for u in U:
for v1, v2 in combinations(V, 2):
F.add_clause([(False, var(u, v1)), (False, var(u, v2))],
strict=True)
for v in V:
for u1, u2 in combinations(U, 2):
F.add_clause([(False, var(u1, v)), (False, var(u2, v))],
strict=True)
# Edge consistency
for u1, u2 in combinations(U, 2):
for v1, v2 in combinations(V, 2):
if G1.has_edge(u1, u2) != G2.has_edge(v1, v2):
F.add_clause([(False, var(u1, v1)), (False, var(u2, v2))],
strict=True)
F.add_clause([(False, var(u1, v2)), (False, var(u2, v1))],
strict=True)
return F
def GraphAutomorphism(G):
"""Graph Automorphism formula
The formula is the CNF encoding of the statement that a graph G
has a nontrivial automorphism, i.e. an automorphism different from
the idential one.
Parameter
---------
G : a simple graph
Returns
-------
A CNF formula which is satiafiable if and only if graph G has a
nontrivial automorphism.
"""
tmp = CNF()
header = "Graph automorphism formula for graph " + G.name + "\n" + tmp.header
F = GraphIsomorphism(G, G)
F.header = header
var = _graph_isomorphism_var
F.add_clause([(False, var(u, u)) for u in enumerate_vertices(G)],
strict=True)
return F
def GraphAutomorphism(G):
"""Graph Automorphism formula
The formula is the CNF encoding of the statement that a graph G
has a nontrivial automorphism, i.e. an automorphism different from
the idential one.
Parameter
---------
G : a simple graph
Returns
-------
A CNF formula which is satiafiable if and only if graph G has a
nontrivial automorphism.
"""
tmp = CNF()
header = "Graph automorphism formula for graph "+ G.name +"\n"+ tmp.header
F = GraphIsomorphism(G, G)
F.header = header
var = _graph_isomorphism_var
F.add_clause([(False, var(u, u)) for u in enumerate_vertices(G)], strict=True)
return F
def PerfectMatchingPrinciple(G):
"""Generates the clauses for the graph perfect matching principle.
The principle claims that there is a way to select edges to such
that all vertices have exactly one incident edge set to 1.
Parameters
----------
G : undirected graph
"""
cnf = CNF()
# Describe the formula
name = "Perfect Matching Principle"
if hasattr(G, 'name'):
cnf.header = name + " of graph:\n" + G.name + "\n" + cnf.header
else:
cnf.header = name + ".\n" + cnf.header
def var_name(u, v):
if u <= v:
return 'x_{{{0},{1}}}'.format(u, v)
else:
return 'x_{{{0},{1}}}'.format(v, u)
# Each vertex has exactly one edge set to one.
for v in enumerate_vertices(G):
edge_vars = [var_name(u, v) for u in neighbors(G, v)]
cnf.add_equal_to(edge_vars, 1)
return cnf
def PerfectMatchingPrinciple(G):
"""Generates the clauses for the graph perfect matching principle.
The principle claims that there is a way to select edges to such
that all vertices have exactly one incident edge set to 1.
Parameters
----------
G : undirected graph
"""
cnf=CNF()
# Describe the formula
name="Perfect Matching Principle"
if hasattr(G,'name'):
cnf.header=name+" of graph:\n"+G.name+"\n"+cnf.header
else:
cnf.header=name+".\n"+cnf.header
def var_name(u,v):
if u<=v:
return 'x_{{{0},{1}}}'.format(u,v)
else:
return 'x_{{{0},{1}}}'.format(v,u)
# Each vertex has exactly one edge set to one.
for v in enumerate_vertices(G):
edge_vars = [var_name(u,v) for u in neighbors(G,v)]
cnf.add_equal_to(edge_vars,1)
return cnf
def TseitinFormula(graph,charges=None):
"""Build a Tseitin formula based on the input graph.
Odd charge is put on the first vertex by default, unless other
vertices are is specified in input.
Arguments:
- `graph`: input graph
- `charges': odd or even charge for each vertex
"""
V=enumerate_vertices(graph)
if charges==None:
charges=[1]+[0]*(len(V)-1) # odd charge on first vertex
else:
charges = [bool(c) for c in charges] # map to boolean
if len(charges)<len(V):
charges=charges+[0]*(len(V)-len(charges)) # pad with even charges
# init formula
tse=CNF()
for e in sorted(graph.edges(),key=sorted):
tse.add_variable(edgename(e))
# add constraints
for v,c in zip(V,charges):
# produce all clauses and save half of them
names = [ edgename((u,v)) for u in neighbors(graph,v) ]
for cls in parity_constraint(names,c):
tse.add_clause(list(cls),strict=True)
return tse
def EvenColoringFormula(G):
"""Even coloring formula
The formula is defined on a graph :math:`G` and claims that it is
possible to split the edges of the graph in two parts, so that
each vertex has an equal number of incident edges in each part.
The formula is defined on graphs where all vertices have even
degree. The formula is satisfiable only on those graphs with an
even number of vertices in each connected component [1]_.
Arguments
---------
G : networkx.Graph
a simple undirected graph where all vertices have even degree
Raises
------
ValueError
if the graph in input has a vertex with odd degree
Returns
-------
CNF object
References
----------
.. [1] Locality and Hard SAT-instances, Klas Markstrom
Journal on Satisfiability, Boolean Modeling and Computation 2 (2006) 221-228
"""
F = CNF()
F.mode_strict()
F.header = "Even coloring formula on graph " + G.name + "\n" + F.header
def var_name(u, v):
if u <= v:
return 'x_{{{0},{1}}}'.format(u, v)
else:
return 'x_{{{0},{1}}}'.format(v, u)
for (u, v) in enumerate_edges(G):
F.add_variable(var_name(u, v))
# Defined on both side
for v in enumerate_vertices(G):
if G.degree(v) % 2 == 1:
raise ValueError(
"Markstrom formulas requires all vertices to have even degree."
)
edge_vars = [var_name(u, v) for u in neighbors(G, v)]
# F.add_exactly_half_floor would work the same
F.add_exactly_half_ceil(edge_vars)
return F
def EvenColoringFormula(G):
"""Even coloring formula
The formula is defined on a graph :math:`G` and claims that it is
possible to split the edges of the graph in two parts, so that
each vertex has an equal number of incident edges in each part.
The formula is defined on graphs where all vertices have even
degree. The formula is satisfiable only on those graphs with an
even number of vertices in each connected component [1]_.
Arguments
---------
G : networkx.Graph
a simple undirected graph where all vertices have even degree
Raises
------
ValueError
if the graph in input has a vertex with odd degree
Returns
-------
CNF object
References
----------
.. [1] Locality and Hard SAT-instances, Klas Markstrom
Journal on Satisfiability, Boolean Modeling and Computation 2 (2006) 221-228
"""
F = CNF()
F.header = "Even coloring formula on graph " + G.name + "\n" + F.header
def var_name(u,v):
if u<=v:
return 'x_{{{0},{1}}}'.format(u,v)
else:
return 'x_{{{0},{1}}}'.format(v,u)
for (u, v) in enumerate_edges(G):
F.add_variable(var_name(u, v))
# Defined on both side
for v in enumerate_vertices(G):
if G.degree(v) % 2 == 1:
raise ValueError("Markstrom formulas requires all vertices to have even degree.")
edge_vars = [ var_name(u,v) for u in neighbors(G,v) ]
for cls in CNF.equal_to_constraint(edge_vars,
len(edge_vars)/2):
F.add_clause(cls,strict=True)
return F
def PebblingFormula(digraph):
"""Pebbling formula
Build a pebbling formula from the directed graph. If the graph has
an `ordered_vertices` attribute, then it is used to enumerate the
vertices (and the corresponding variables).
Arguments:
- `digraph`: directed acyclic graph.
"""
if not is_dag(digraph):
raise ValueError(
"Pebbling formula is defined only for directed acyclic graphs")
peb = CNF()
peb.mode_unchecked()
if hasattr(digraph, 'name'):
peb.header = "Pebbling formula of: "+digraph.name+"\n\n"+peb.header
else:
peb.header = "Pebbling formula\n\n"+peb.header
# add variables in the appropriate order
vertices = enumerate_vertices(digraph)
position = dict((v, i) for (i, v) in enumerate(vertices))
for v in vertices:
peb.add_variable(
v, description="There is a pebble on vertex ${}$".format(v))
# add the clauses
for v in vertices:
# If predecessors are pebbled the vertex must be pebbled
pred = sorted(digraph.predecessors(v), key=lambda x: position[x])
peb.add_clause([(False, p) for p in pred]+[(True, v)])
if digraph.out_degree(v) == 0: # the sink
peb.add_clause([(False, v)])
return peb
def PebblingFormula(digraph):
"""Pebbling formula
Build a pebbling formula from the directed graph. If the graph has
an `ordered_vertices` attribute, then it is used to enumerate the
vertices (and the corresponding variables).
Arguments:
- `digraph`: directed acyclic graph.
"""
if not is_dag(digraph):
raise ValueError("Pebbling formula is defined only for directed acyclic graphs")
peb=CNF()
peb.mode_unchecked()
if hasattr(digraph,'name'):
peb.header="Pebbling formula of: "+digraph.name+"\n\n"+peb.header
else:
peb.header="Pebbling formula\n\n"+peb.header
# add variables in the appropriate order
vertices=enumerate_vertices(digraph)
position=dict((v,i) for (i,v) in enumerate(vertices))
for v in vertices:
peb.add_variable(v,description="There is a pebble on vertex ${}$".format(v))
# add the clauses
for v in vertices:
# If predecessors are pebbled the vertex must be pebbled
pred=sorted(digraph.predecessors(v),key=lambda x:position[x])
peb.add_clause([(False,p) for p in pred]+[(True,v)])
if digraph.out_degree(v)==0: #the sink
peb.add_clause([(False,v)])
return peb
def TseitinFormula(graph,charges=None):
"""Build a Tseitin formula based on the input graph.
Odd charge is put on the first vertex by default, unless other
vertices are is specified in input.
Arguments:
- `graph`: input graph
- `charges': odd or even charge for each vertex
"""
V=enumerate_vertices(graph)
if charges==None:
charges=[1]+[0]*(len(V)-1) # odd charge on first vertex
else:
charges = [bool(c) for c in charges] # map to boolean
if len(charges)<len(V):
charges=charges+[0]*(len(V)-len(charges)) # pad with even charges
# init formula
tse=CNF()
edgename = { }
for (u,v) in sorted(graph.edges(),key=sorted):
edgename[(u,v)] = "E_{{{0},{1}}}".format(u,v)
edgename[(v,u)] = "E_{{{0},{1}}}".format(u,v)
tse.add_variable(edgename[(u,v)])
# add constraints
for v,c in zip(V,charges):
# produce all clauses and save half of them
names = [ edgename[(u,v)] for u in neighbors(graph,v) ]
for cls in CNF.parity_constraint(names,c):
tse.add_clause(list(cls),strict=True)
return tse
def VertexCover(G, d):
F = CNF()
def D(v):
return "x_{{{0}}}".format(v)
def N(v):
return tuple(sorted([e for e in G.edges(v)]))
# Fix the vertex order
V = enumerate_vertices(G)
# Create variables
for v in V:
F.add_variable(D(v))
# Not too many true variables
F.add_less_or_equal([D(v) for v in V], d)
# Every edge must have a true D variable
for e in G.edges():
F.add_clause([(True, D(v)) for v in e])
return F
def DominatingSetOPB(G,d,tiling,seed):
F=CNF()
def D(v):
return "x_{{{0}}}".format(v)
def N(v):
return tuple(sorted([ v ] + [ u for u in G.neighbors(v) ]))
# Fix the vertex order
V=enumerate_vertices(G)
#avgdegree=sum(len(set(N(v))) for v in V)/len(V)
#d=len(V)/(avgdegree+1)
# Create variables
for v in V:
F.add_variable(D(v))
# Not too many true variables
if not tiling:
F.add_less_or_equal([D(v) for v in V],d)
# Every neighborhood must have a true D variable
neighborhoods = sorted( set(N(v) for v in V) )
for N in neighborhoods:
if tiling:
F.add_equal_to([D(v) for v in N], 1)
else:
F.add_clause([(True,D(v)) for v in N])
# Set some vertex to true
if seed:
F.add_clause([(True,D(V[0]))])
return F
def VertexCover(G,d):
F=CNF()
def D(v):
return "x_{{{0}}}".format(v)
def N(v):
return tuple(sorted([ e for e in G.edges(v) ]))
# Fix the vertex order
V=enumerate_vertices(G)
# Create variables
for v in V:
F.add_variable(D(v))
# Not too many true variables
F.add_less_or_equal([D(v) for v in V],d)
# Every edge must have a true D variable
for e in G.edges():
F.add_clause([ (True,D(v)) for v in e])
return F
def GraphOrderingPrinciple(graph,
total=False,
smart=False,
plant=False,
knuth=0):
"""Generates the clauses for graph ordering principle
Arguments:
- `graph` : undirected graph
- `total` : add totality axioms (i.e. "x < y" or "x > y")
- `smart` : "x < y" and "x > y" are represented by a single variable (implies `total`)
- `plant` : allow last element to be minimum (and could make the formula SAT)
- `knuth` : Don Knuth variants 2 or 3 of the formula (anything else suppress it)
"""
gop = CNF()
# Describe the formula
if total or smart:
name = "Total graph ordering principle"
else:
name = "Ordering principle"
if smart:
name = name + "(compact representation)"
if hasattr(graph, 'name'):
gop.header = name + "\n on graph " + graph.name + ".\n\n" + gop.header
else:
gop.header = name + ".\n\n" + gop.header
# Fix the vertex order
V = enumerate_vertices(graph)
# Add variables
iterator = combinations if smart else permutations
for v1, v2 in iterator(V, 2):
gop.add_variable(varname(v1, v2))
#
# Non minimality axioms
#
# Clause is generated in such a way that if totality is enforces,
# every pair occurs with a specific orientation.
# Allow minimum on last vertex if 'plant' options.
for med in xrange(len(V) - (plant and 1)):
clause = []
for lo in xrange(med):
if graph.has_edge(V[med], V[lo]):
clause += [(True, varname(V[lo], V[med]))]
for hi in xrange(med + 1, len(V)):
if not graph.has_edge(V[med], V[hi]):
continue
elif smart:
clause += [(False, varname(V[med], V[hi]))]
else:
clause += [(True, varname(V[hi], V[med]))]
gop.add_clause(clause, strict=True)
#
# Transitivity axiom
#
if len(V) >= 3:
if smart:
# Optimized version if smart representation of totality is used
for (v1, v2, v3) in combinations(V, 3):
gop.add_clause([(True, varname(v1, v2)),
(True, varname(v2, v3)),
(False, varname(v1, v3))],
strict=True)
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v3)),
(True, varname(v1, v3))],
strict=True)
elif total:
# With totality we still need just two axiom per triangle
for (v1, v2, v3) in combinations(V, 3):
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v3)),
(False, varname(v3, v1))],
strict=True)
gop.add_clause([(False, varname(v1, v3)),
(False, varname(v3, v2)),
(False, varname(v2, v1))],
strict=True)
else:
for (v1, v2, v3) in permutations(V, 3):
# knuth variants will reduce the number of
# transitivity axioms
if knuth == 2 and ((v2 < v1) or (v2 < v3)):
continue
if knuth == 3 and ((v3 < v1) or (v3 < v2)):
continue
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v3)),
(True, varname(v1, v3))],
strict=True)
if not smart:
# Antisymmetry axioms (useless for 'smart' representation)
for (v1, v2) in combinations(V, 2):
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v1))],
strict=True)
# Totality axioms (useless for 'smart' representation)
if total:
for (v1, v2) in combinations(V, 2):
gop.add_clause([(True, varname(v1, v2)),
(True, varname(v2, v1))],
strict=True)
return gop
def StoneFormula(D, nstones):
"""Stone formulas
The stone formulas have been introduced in [2]_ and generalized in
[1]_. They are one of the classic examples that separate regular
resolutions from general resolution [1]_.
A \"Stones formula\" from a directed acyclic graph :math:`D`
claims that each vertex of the graph is associated with one on
:math:`s` stones (not necessarily in an injective way).
In particular for each vertex :math:`v` in :math:`V(D)` and each
stone :math:`j` we have a variable :math:`P_{v,j}` that claims
that stone :math:`j` is associated to vertex :math:`v`.
Each stone can be either red or blue, and not both.
The propositional variable :math:`R_j` if true when the stone
:math:`j` is red and false otherwise.
The clauses of the formula encode the following constraints.
If a stone is on a source vertex (i.e. a vertex with no incoming
edges), then it must be red. If all stones on the predecessors of
a vertex are red, then the stone of the vertex itself must be red.
The formula furthermore enforces that the stones on the sinks
(i.e. vertices with no outgoing edges) are blue.
.. note:: The exact formula structure depends by the graph and on
its topological order, which is determined by the
``enumerate_vertices(D)``.
Parameters
----------
D : a directed acyclic graph
it should be a directed acyclic graph.
nstones : int
the number of stones.
Raises
------
ValueError
if :math:`D` is not a directed acyclic graph
ValueError
if the number of stones is negative
References
----------
.. [1] M. Alekhnovich, J. Johannsen, T. Pitassi and A. Urquhart
An Exponential Separation between Regular and General Resolution.
Theory of Computing (2007)
.. [2] R. Raz and P. McKenzie
Separation of the monotone NC hierarchy.
Combinatorica (1999)
"""
if not is_dag(D):
raise ValueError(
"Stone formulas are defined only for directed acyclic graphs.")
if nstones < 0:
raise ValueError("There must be at least one stone.")
cnf = CNF()
if hasattr(D, 'name'):
cnf.header = "Stone formula of: " + D.name + "\nwith " + str(
nstones) + " stones\n" + cnf.header
else:
cnf.header = "Stone formula with " + str(
nstones) + " stones\n" + cnf.header
# Add variables in the appropriate order
vertices = enumerate_vertices(D)
position = dict((v, i) for (i, v) in enumerate(vertices))
stones = list(range(1, nstones + 1))
# Caching variable names
color_vn = {}
stone_vn = {}
# Stones->Vertices variables
for v in vertices:
for j in stones:
stone_vn[(v, j)] = "P_{{{0},{1}}}".format(v, j)
cnf.add_variable(stone_vn[(v, j)],
description="Stone ${1}$ on vertex ${0}$".format(
v, j))
# Color variables
for j in stones:
color_vn[j] = "R_{{{0}}}".format(j)
cnf.add_variable(color_vn[j],
description="Stone ${}$ is red".format(j))
# Each vertex has some stone
for v in vertices:
cnf.add_clause_unsafe([(True, stone_vn[(v, j)]) for j in stones])
# If predecessors have red stones, the sink must have a red stone
for v in vertices:
for j in stones:
pred = sorted(D.predecessors(v), key=lambda x: position[x])
for stones_tuple in product([s for s in stones if s != j],
repeat=len(pred)):
cnf.add_clause_unsafe([(False, stone_vn[(p, s)])
for (p, s) in zip(pred, stones_tuple)] +
[(False, stone_vn[(v, j)])] +
[(False, color_vn[s])
for s in _uniqify_list(stones_tuple)] +
[(True, color_vn[j])])
if D.out_degree(v) == 0: #the sink
for j in stones:
cnf.add_clause_unsafe([(False, stone_vn[(v, j)]),
(False, color_vn[j])])
return cnf
def DominatingSet(G,d, alternative = False):
r"""Generates the clauses for a dominating set for G of size <= d
The formula encodes the fact that the graph :math:`G` has
a dominating set of size :math:`d`. This means that it is possible
to pick at most :math:`d` vertices in :math:`V(G)` so that all remaining
vertices have distance at most one from the selected ones.
Parameters
----------
G : networkx.Graph
a simple undirected graph
d : a positive int
the size limit for the dominating set
alternative : bool
use an alternative construction that
is provably hard from resolution proofs.
Returns
-------
CNF
the CNF encoding for dominating of size :math:`\leq d` for graph :math:`G`
"""
F=CNF()
if not isinstance(d,int) or d<1:
ValueError("Parameter \"d\" is expected to be a positive integer")
# Describe the formula
name="{}-dominating set".format(d)
if hasattr(G,'name'):
F.header=name+" of graph:\n"+G.name+".\n\n"+F.header
else:
F.header=name+".\n\n"+F.header
# Fix the vertex order
V=enumerate_vertices(G)
def D(v):
return "x_{{{0}}}".format(v)
def M(v,i):
return "g_{{{0},{1}}}".format(v,i)
def N(v):
return tuple(sorted([ v ] + [ u for u in G.neighbors(v) ]))
# Create variables
for v in V:
F.add_variable(D(v))
for i,v in product(range(1,d+1),V):
F.add_variable(M(v,i))
# No two (active) vertices map to the same index
if alternative:
for u,v in combinations(V,2):
for i in range(1,d+1):
F.add_clause( [ (False,D(u)),(False,D(v)), (False,M(u,i)), (False,M(v,i)) ])
else:
for i in range(1,d+1):
for c in CNF.less_or_equal_constraint([M(v,i) for v in V],1):
F.add_clause(c)
# (Active) Vertices in the sequence are not repeated
if alternative:
for v in V:
for i,j in combinations(range(1,d+1),2):
F.add_clause([(False,D(v)),(False,M(v,i)),(False,M(v,j))])
else:
for i,j in combinations_with_replacement(range(1,d+1),2):
i,j = min(i,j),max(i,j)
for u,v in combinations(V,2):
u,v = max(u,v),min(u,v)
F.add_clause([(False,M(u,i)),(False,M(v,j))])
# D(v) = M(v,1) or M(v,2) or ... or M(v,d)
if not alternative:
for i,v in product(range(1,d+1),V):
F.add_clause([(False,M(v,i)),(True,D(v))])
for v in V:
F.add_clause([(False,D(v))] + [(True,M(v,i)) for i in range(1,d+1)])
# Every neighborhood must have a true D variable
neighborhoods = sorted( set(N(v) for v in V) )
for N in neighborhoods:
F.add_clause([ (True,D(v)) for v in N])
return F
def SubgraphFormula(graph,templates, symmetric=False):
"""Test whether a graph contains one of the templates.
Given a graph :math:`G` and a sequence of template graphs
:math:`H_1`, :math:`H_2`, ..., :math:`H_t`, the CNF formula claims
that :math:`G` contains an isomorphic copy of at least one of the
template graphs.
E.g. when :math:`H_1` is the complete graph of :math:`k` vertices
and it is the only template, the formula claims that :math:`G`
contains a :math:`k`-clique.
Parameters
----------
graph : networkx.Graph
a simple graph
templates : list-like object
a sequence of graphs.
symmetric:
all template graphs are symmetric wrt permutations of
vertices. This allows some optimization in the search space of
the assignments.
induce:
force the subgraph to be induced (i.e. no additional edges are allowed)
Returns
-------
a CNF object
"""
F=CNF()
# One of the templates is chosen to be the subgraph
if len(templates)==0:
return F
elif len(templates)==1:
selectors=[]
elif len(templates)==2:
selectors=['c']
else:
selectors=['c_{{{}}}'.format(i) for i in range(len(templates))]
for s in selectors:
F.add_variable(s)
if len(selectors)>1:
for cls in F.equal_to_constraint(selectors,1):
F.add_clause( cls , strict=True )
# comment the formula accordingly
if len(selectors)>1:
F.header=dedent("""\
CNF encoding of the claim that a graph contains one among
a family of {0} possible subgraphs.
""".format(len(templates))) + F.header
else:
F.header=dedent("""\
CNF encoding of the claim that a graph contains an induced
copy of a subgraph.
""".format(len(templates))) + F.header
# A subgraph is chosen
N=graph.order()
k=max([s.order() for s in templates])
var_name = lambda i,j: "S_{{{0},{1}}}".format(i,j)
for i,j in product(range(k),range(N)):
F.add_variable( var_name(i,j) )
if symmetric:
gencls = F.unary_mapping(range(k),range(N),var_name=var_name,
functional=True,injective=True,
nondecreasing=True)
else:
gencls = F.unary_mapping(range(k),range(N),var_name=var_name,
functional=True,injective=True)
for cls in gencls:
F.add_clause( cls, strict=True )
# The selectors choose a template subgraph. A mapping must map
# edges to edges and non-edges to non-edges for the active
# template.
if len(templates)==1:
activation_prefixes = [[]]
elif len(templates)==2:
activation_prefixes = [[(True,selectors[0])],[(False,selectors[0])]]
else:
activation_prefixes = [[(True,v)] for v in selectors]
# maps must preserve the structure of the template graph
gV = enumerate_vertices(graph)
for i in range(len(templates)):
k = templates[i].order()
tV = enumerate_vertices(templates[i])
if symmetric:
# Using non-decreasing map to represent a subset
localmaps = product(combinations(range(k),2),
combinations(range(N),2))
else:
localmaps = product(combinations(range(k),2),
permutations(range(N),2))
for (i1,i2),(j1,j2) in localmaps:
# check if this mapping is compatible
tedge=templates[i].has_edge(tV[i1],tV[i2])
gedge=graph.has_edge(gV[j1],gV[j2])
if tedge == gedge:
continue
# if it is not, add the corresponding
F.add_clause(activation_prefixes[i] + \
[(False,var_name(i1,j1)),
(False,var_name(i2,j2)) ],strict=True)
return F
def SparseStoneFormula(D,B):
"""Sparse Stone formulas
This is a variant of the :py:func:`StoneFormula`. See that for
a description of the formula. This variant is such that each
vertex has only a small selection of which stone can go to that
vertex. In particular which stones are allowed on each vertex is
specified by a bipartite graph :math:`B` on which the left
vertices represent the vertices of DAG :math:`D` and the right
vertices are the stones.
If a vertex of :math:`D` correspond to the left vertex :math:`v`
in :math:`B`, then its neighbors describe which stones are allowed
for it.
The vertices in :math:`D` do not need to have the same name as the
one on the left side of :math:`B`. It is only important that the
number of vertices in :math:`D` is the same as the vertices in the
left side of :math:`B`.
In that case the element at position :math:`i` in the ordered
sequence ``enumerate_vertices(D)`` corresponds to the element of
rank :math:`i` in the sequence of left side vertices of
:math:`B` according to the output of ``Left, Right =
bipartite_sets(B)``.
Standard :py:func:`StoneFormula` is essentially equivalent to
a sparse stone formula where :math:`B` is the complete graph.
Parameters
----------
D : a directed acyclic graph
it should be a directed acyclic graph.
B : bipartite graph
Raises
------
ValueError
if :math:`D` is not a directed acyclic graph
ValueError
if :math:`B` is not a bipartite graph
ValueError
when size differs between :math:`D` and the left side of
:math:`B`
See Also
--------
StoneFormula
"""
if not is_dag(D):
raise ValueError("Stone formulas are defined only for directed acyclic graphs.")
if not has_bipartition(B):
raise ValueError("Vertices to stones mapping must be specified with a bipartite graph")
Left, Right = bipartite_sets(B)
nstones = len(Right)
if len(Left) != D.order():
raise ValueError("Formula requires the bipartite left side to match #vertices of the DAG.")
cnf = CNF()
if hasattr(D, 'name'):
cnf.header = "Sparse Stone formula of: " + D.name + "\nwith " + str(nstones) + " stones\n" + cnf.header
else:
cnf.header = "Sparse Stone formula with " + str(nstones) + " stones\n" + cnf.header
# add variables in the appropriate order
vertices=enumerate_vertices(D)
stones=range(1,nstones+1)
mapping = cnf.unary_mapping(vertices,stones,sparsity_pattern=B)
stone_formula_helper(cnf,D,mapping)
return cnf
def stone_formula_helper(F,D,mapping):
"""Stones formulas helper
Builds the clauses of a stone formula given the mapping object
between stones and vertices of the DAG. THis is not supposed to be
called by user code, and indeed this function assumes the following facts.
- :math:`D` is equal to `mapping.domain()`
- :math:`D` is a DAG
Parameters
----------
F : CNF
the CNF which will contain the clauses of the stone formula
D : a directed acyclic graph
it should be a directed acyclic graph.
mapping : unary_mapping object
mapping between stones and graph vertices
See Also
--------
StoneFormula : the classic stone formula
SparseStoneFormula : stone formula with sparse mapping
"""
# add variables in the appropriate order
vertices=enumerate_vertices(D)
# Stones->Vertices variables
for v in mapping.variables():
F.add_variable(v)
# Color variables
for stone in mapping.range():
F.add_variable("R_{{{0}}}".format(stone),
description="Stone ${}$ is red".format(stone))
# Each vertex has some stone
for cls in mapping.clauses():
F.add_clause_unsafe(cls)
# If predecessors have red stones, the sink must have a red stone
for v in vertices:
for j in mapping.images(v):
pred=sorted(D.predecessors(v),key=lambda x:mapping.RankDomain[x])
for stones_tuple in product(*tuple( [s for s in mapping.images(v) if s!=j ] for v in pred)):
F.add_clause([(False, mapping.var_name(p,s)) for (p,s) in zip(pred,stones_tuple)] +
[(False, mapping.var_name(v,j))] +
[(False, "R_{{{0}}}".format(s)) for s in _uniqify_list(stones_tuple)] +
[(True, "R_{{{0}}}".format(j))],
strict=True)
if D.out_degree(v)==0: #the sink
for j in mapping.images(v):
F.add_clause([ (False, mapping.var_name(v,j)),
(False,"R_{{{0}}}".format(j))],
strict = True)
return F
def GraphOrderingPrinciple(graph,total=False,smart=False,plant=False,knuth=0):
"""Generates the clauses for graph ordering principle
Arguments:
- `graph` : undirected graph
- `total` : add totality axioms (i.e. "x < y" or "x > y")
- `smart` : "x < y" and "x > y" are represented by a single variable (implies `total`)
- `plant` : allow last element to be minimum (and could make the formula SAT)
- `knuth` : Don Knuth variants 2 or 3 of the formula (anything else suppress it)
"""
gop = CNF()
# Describe the formula
if total or smart:
name = "Total graph ordering principle"
else:
name = "Ordering principle"
if smart:
name = name + "(compact representation)"
if hasattr(graph, 'name'):
gop.header = name+"\n on graph "+graph.name+".\n\n"+gop.header
else:
gop.header = name+".\n\n"+gop.header
# Fix the vertex order
V = enumerate_vertices(graph)
# Add variables
iterator = combinations if smart else permutations
for v1,v2 in iterator(V,2):
gop.add_variable(varname(v1,v2))
#
# Non minimality axioms
#
# Clause is generated in such a way that if totality is enforces,
# every pair occurs with a specific orientation.
# Allow minimum on last vertex if 'plant' options.
for med in xrange(len(V) - (plant and 1)):
clause = []
for lo in xrange(med):
if graph.has_edge(V[med], V[lo]):
clause += [(True, varname(V[lo], V[med]))]
for hi in xrange(med+1, len(V)):
if not graph.has_edge(V[med], V[hi]):
continue
elif smart:
clause += [(False, varname(V[med], V[hi]))]
else:
clause += [(True, varname(V[hi], V[med]))]
gop.add_clause(clause, strict=True)
#
# Transitivity axiom
#
if len(V) >= 3:
if smart:
# Optimized version if smart representation of totality is used
for (v1, v2, v3) in combinations(V, 3):
gop.add_clause([(True, varname(v1, v2)),
(True, varname(v2, v3)),
(False, varname(v1, v3))],
strict=True)
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v3)),
(True, varname(v1, v3))],
strict=True)
elif total:
# With totality we still need just two axiom per triangle
for (v1, v2, v3) in combinations(V, 3):
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v3)),
(False, varname(v3, v1))],
strict=True)
gop.add_clause([(False, varname(v1, v3)),
(False, varname(v3, v2)),
(False, varname(v2, v1))],
strict=True)
else:
for (v1, v2, v3) in permutations(V, 3):
# knuth variants will reduce the number of
# transitivity axioms
if knuth == 2 and ((v2 < v1) or (v2 < v3)):
continue
if knuth == 3 and ((v3 < v1) or (v3 < v2)):
continue
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v3)),
(True, varname(v1, v3))],
strict=True)
if not smart:
# Antisymmetry axioms (useless for 'smart' representation)
for (v1, v2) in combinations(V, 2):
gop.add_clause([(False, varname(v1, v2)),
(False, varname(v2, v1))],
strict=True)
# Totality axioms (useless for 'smart' representation)
if total:
for (v1, v2) in combinations(V, 2):
gop.add_clause([(True, varname(v1, v2)),
(True, varname(v2, v1))],
strict=True)
return gop
def StoneFormula(D,nstones):
"""Stone formulas
The stone formulas have been introduced in [2]_ and generalized in
[1]_. They are one of the classic examples that separate regular
resolutions from general resolution [1]_.
A \"Stones formula\" from a directed acyclic graph :math:`D`
claims that each vertex of the graph is associated with one on
:math:`s` stones (not necessarily in an injective way).
In particular for each vertex :math:`v` in :math:`V(D)` and each
stone :math:`j` we have a variable :math:`P_{v,j}` that claims
that stone :math:`j` is associated to vertex :math:`v`.
Each stone can be either red or blue, and not both.
The propositional variable :math:`R_j` if true when the stone
:math:`j` is red and false otherwise.
The clauses of the formula encode the following constraints.
If a stone is on a source vertex (i.e. a vertex with no incoming
edges), then it must be red. If all stones on the predecessors of
a vertex are red, then the stone of the vertex itself must be red.
The formula furthermore enforces that the stones on the sinks
(i.e. vertices with no outgoing edges) are blue.
.. note:: The exact formula structure depends by the graph and on
its topological order, which is determined by the
``enumerate_vertices(D)``.
Parameters
----------
D : a directed acyclic graph
it should be a directed acyclic graph.
nstones : int
the number of stones.
Raises
------
ValueError
if :math:`D` is not a directed acyclic graph
ValueError
if the number of stones is negative
References
----------
.. [1] M. Alekhnovich, J. Johannsen, T. Pitassi and A. Urquhart
An Exponential Separation between Regular and General Resolution.
Theory of Computing (2007)
.. [2] R. Raz and P. McKenzie
Separation of the monotone NC hierarchy.
Combinatorica (1999)
"""
if not is_dag(D):
raise ValueError("Stone formulas are defined only for directed acyclic graphs.")
if nstones<0:
raise ValueError("There must be at least one stone.")
cnf = CNF()
if hasattr(D, 'name'):
cnf.header = "Stone formula of: " + D.name + "\nwith " + str(nstones) + " stones\n" + cnf.header
else:
cnf.header = "Stone formula with " + str(nstones) + " stones\n" + cnf.header
# Add variables in the appropriate order
vertices=enumerate_vertices(D)
position=dict((v,i) for (i,v) in enumerate(vertices))
stones=range(1,nstones+1)
# Caching variable names
color_vn = {}
stone_vn = {}
# Stones->Vertices variables
for v in vertices:
for j in stones:
stone_vn[(v,j)] = "P_{{{0},{1}}}".format(v,j)
cnf.add_variable(stone_vn[(v,j)],
description="Stone ${1}$ on vertex ${0}$".format(v,j))
# Color variables
for j in stones:
color_vn[j] = "R_{{{0}}}".format(j)
cnf.add_variable(color_vn[j],
description="Stone ${}$ is red".format(j))
# Each vertex has some stone
for v in vertices:
cnf.add_clause_unsafe([(True,stone_vn[(v,j)]) for j in stones])
# If predecessors have red stones, the sink must have a red stone
for v in vertices:
for j in stones:
pred=sorted(D.predecessors(v),key=lambda x:position[x])
for stones_tuple in product([s for s in stones if s!=j],repeat=len(pred)):
cnf.add_clause_unsafe([(False, stone_vn[(p,s)]) for (p,s) in zip(pred,stones_tuple)] +
[(False, stone_vn[(v,j)])] +
[(False, color_vn[s]) for s in _uniqify_list(stones_tuple)] +
[(True, color_vn[j])])
if D.out_degree(v)==0: #the sink
for j in stones:
cnf.add_clause_unsafe([ (False,stone_vn[(v,j)]), (False,color_vn[j])])
return cnf
def DominatingSet(G, d, alternative=False):
r"""Generates the clauses for a dominating set for G of size <= d
The formula encodes the fact that the graph :math:`G` has
a dominating set of size :math:`d`. This means that it is possible
to pick at most :math:`d` vertices in :math:`V(G)` so that all remaining
vertices have distance at most one from the selected ones.
Parameters
----------
G : networkx.Graph
a simple undirected graph
d : a positive int
the size limit for the dominating set
alternative : bool
use an alternative construction that
is provably hard from resolution proofs.
Returns
-------
CNF
the CNF encoding for dominating of size :math:`\leq d` for graph :math:`G`
"""
F = CNF()
if not isinstance(d, int) or d < 1:
ValueError("Parameter \"d\" is expected to be a positive integer")
# Describe the formula
name = "{}-dominating set".format(d)
if hasattr(G, 'name'):
F.header = name + " of graph:\n" + G.name + ".\n\n" + F.header
else:
F.header = name + ".\n\n" + F.header
# Fix the vertex order
V = enumerate_vertices(G)
def D(v):
return "x_{{{0}}}".format(v)
def M(v, i):
return "g_{{{0},{1}}}".format(v, i)
def N(v):
return tuple(sorted([v] + [u for u in G.neighbors(v)]))
# Create variables
for v in V:
F.add_variable(D(v))
for i, v in product(list(range(1, d + 1)), V):
F.add_variable(M(v, i))
# No two (active) vertices map to the same index
if alternative:
for u, v in combinations(V, 2):
for i in range(1, d + 1):
F.add_clause([(False, D(u)), (False, D(v)), (False, M(u, i)),
(False, M(v, i))])
else:
for i in range(1, d + 1):
for c in CNF.less_or_equal_constraint([M(v, i) for v in V], 1):
F.add_clause(c)
# (Active) Vertices in the sequence are not repeated
if alternative:
for v in V:
for i, j in combinations(list(range(1, d + 1)), 2):
F.add_clause([(False, D(v)), (False, M(v, i)), (False, M(v,
j))])
else:
for i, j in combinations_with_replacement(list(range(1, d + 1)), 2):
i, j = min(i, j), max(i, j)
for u, v in combinations(V, 2):
u, v = max(u, v), min(u, v)
F.add_clause([(False, M(u, i)), (False, M(v, j))])
# D(v) = M(v,1) or M(v,2) or ... or M(v,d)
if not alternative:
for i, v in product(list(range(1, d + 1)), V):
F.add_clause([(False, M(v, i)), (True, D(v))])
for v in V:
F.add_clause([(False, D(v))] + [(True, M(v, i))
for i in range(1, d + 1)])
# Every neighborhood must have a true D variable
neighborhoods = sorted(set(N(v) for v in V))
for N in neighborhoods:
F.add_clause([(True, D(v)) for v in N])
return F
def VertexCover(G,k, alternative = False):
r"""Generates the clauses for a vertex cover for G of size <= k
Parameters
----------
G : networkx.Graph
a simple undirected graph
k : a positive int
the size limit for the vertex cover
Returns
-------
CNF
the CNF encoding for vertex cover of size :math:`\leq k` for graph :math:`G`
"""
F=CNF()
if not isinstance(k,int) or k<1:
ValueError("Parameter \"k\" is expected to be a positive integer")
# Describe the formula
name="{}-vertex cover".format(k)
if hasattr(G,'name'):
F.header=name+" of graph:\n"+G.name+".\n\n"+F.header
else:
F.header=name+".\n\n"+F.header
# Fix the vertex order
V=enumerate_vertices(G)
E=enumerate_edges(G)
def D(v):
return "x_{{{0}}}".format(v)
def M(v,i):
return "g_{{{0},{1}}}".format(v,i)
def N(v):
return tuple(sorted([ v ] + [ u for u in G.neighbors(v) ]))
# Create variables
for v in V:
F.add_variable(D(v))
for i,v in product(range(1,k+1),V):
F.add_variable(M(v,i))
# No two (active) vertices map to the same index
for i in range(1,k+1):
for c in CNF.less_or_equal_constraint([M(v,i) for v in V],1):
F.add_clause(c)
# (Active) Vertices in the sequence are not repeated
for i,j in combinations_with_replacement(range(1,k+1),2):
i,j = min(i,j),max(i,j)
for u,v in combinations(V,2):
u,v = max(u,v),min(u,v)
F.add_clause([(False,M(u,i)),(False,M(v,j))])
# D(v) = M(v,1) or M(v,2) or ... or M(v,k)
for i,v in product(range(1,k+1),V):
F.add_clause([(False,M(v,i)),(True,D(v))])
for v in V:
F.add_clause([(False,D(v))] + [(True,M(v,i)) for i in range(1,k+1)])
# Every neighborhood must have a true D variable
for v1,v2 in E:
F.add_clause([(True,D(v1)), (True,D(v2))])
return F
def SparseStoneFormula(D, B):
"""Sparse Stone formulas
This is a variant of the :py:func:`StoneFormula`. See that for
a description of the formula. This variant is such that each
vertex has only a small selection of which stone can go to that
vertex. In particular which stones are allowed on each vertex is
specified by a bipartite graph :math:`B` on which the left
vertices represent the vertices of DAG :math:`D` and the right
vertices are the stones.
If a vertex of :math:`D` correspond to the left vertex :math:`v`
in :math:`B`, then its neighbors describe which stones are allowed
for it.
The vertices in :math:`D` do not need to have the same name as the
one on the left side of :math:`B`. It is only important that the
number of vertices in :math:`D` is the same as the vertices in the
left side of :math:`B`.
In that case the element at position :math:`i` in the ordered
sequence ``enumerate_vertices(D)`` corresponds to the element of
rank :math:`i` in the sequence of left side vertices of
:math:`B` according to the output of ``Left, Right =
bipartite_sets(B)``.
Standard :py:func:`StoneFormula` is essentially equivalent to
a sparse stone formula where :math:`B` is the complete graph.
Parameters
----------
D : a directed acyclic graph
it should be a directed acyclic graph.
B : bipartite graph
Raises
------
ValueError
if :math:`D` is not a directed acyclic graph
ValueError
if :math:`B` is not a bipartite graph
ValueError
when size differs between :math:`D` and the left side of
:math:`B`
See Also
--------
StoneFormula
"""
if not is_dag(D):
raise ValueError(
"Stone formulas are defined only for directed acyclic graphs.")
if not has_bipartition(B):
raise ValueError(
"Vertices to stones mapping must be specified with a bipartite graph"
)
Left, Right = bipartite_sets(B)
nstones = len(Right)
if len(Left) != D.order():
raise ValueError(
"Formula requires the bipartite left side to match #vertices of the DAG."
)
cnf = CNF()
if hasattr(D, 'name'):
cnf.header = "Sparse Stone formula of: " + D.name + "\nwith " + str(
nstones) + " stones\n" + cnf.header
else:
cnf.header = "Sparse Stone formula with " + str(
nstones) + " stones\n" + cnf.header
# add variables in the appropriate order
vertices = enumerate_vertices(D)
stones = list(range(1, nstones + 1))
mapping = cnf.unary_mapping(vertices, stones, sparsity_pattern=B)
stone_formula_helper(cnf, D, mapping)
return cnf
def SubgraphFormula(graph,templates):
"""Test whether a graph contains one of the templates.
Given a graph :math:`G` and a sequence of template graphs
:math:`H_1`, :math:`H_2`, ..., :math:`H_t`, the CNF formula claims
that :math:`G` contains an isomorphic copy of at least one of the
template graphs.
E.g. when :math:`H_1` is the complete graph of :math:`k` vertices
and it is the only template, the formula claims that :math:`G`
contains a :math:`k`-clique.
Parameters
----------
graph : networkx.Graph
a simple graph
templates : list-like object
a sequence of graphs.
Returns
-------
a CNF object
"""
F=CNF()
# One of the templates is chosen to be the subgraph
if len(templates)==0:
return F
elif len(templates)==1:
selectors=[]
elif len(templates)==2:
selectors=['c']
else:
selectors=['c_{{{}}}'.format(i) for i in range(len(templates))]
for s in selectors:
F.add_variable(s)
if len(selectors)>1:
# Exactly one of the graphs must be selected as subgraph
F.add_clause([(True,v) for v in selectors],strict=True)
for (a,b) in combinations(selectors):
F.add_clause( [ (False,a), (False,b) ], strict=True )
# comment the formula accordingly
if len(selectors)>1:
F.header=dedent("""\
CNF encoding of the claim that a graph contains one among
a family of {0} possible subgraphs.
""".format(len(templates))) + F.header
else:
F.header=dedent("""\
CNF encoding of the claim that a graph contains an induced
copy of a subgraph.
""".format(len(templates))) + F.header
# A subgraph is chosen
N=graph.order()
k=max([s.order() for s in templates])
for i,j in product(range(k),range(N)):
F.add_variable("S_{{{0},{1}}}".format(i,j))
# each vertex has an image...
for i in range(k):
F.add_clause([(True,"S_{{{0},{1}}}".format(i,j)) for j in range(N)],strict=True)
# ...and exactly one
for i,(a,b) in product(range(k),combinations(range(N),2)):
F.add_clause([(False,"S_{{{0},{1}}}".format(i,a)),
(False,"S_{{{0},{1}}}".format(i,b)) ], strict = True)
# Mapping is strictly monotone increasing (so it is also injective)
localmaps = product(combinations(range(k),2),
combinations_with_replacement(range(N),2))
for (a,b),(i,j) in localmaps:
F.add_clause([(False,"S_{{{0},{1}}}".format(min(a,b),max(i,j))),
(False,"S_{{{0},{1}}}".format(max(a,b),min(i,j))) ],strict=True)
# The selectors choose a template subgraph. A mapping must map
# edges to edges and non-edges to non-edges for the active
# template.
if len(templates)==1:
activation_prefixes = [[]]
elif len(templates)==2:
activation_prefixes = [[(True,selectors[0])],[(False,selectors[0])]]
else:
activation_prefixes = [[(True,v)] for v in selectors]
# maps must preserve the structure of the template graph
gV = enumerate_vertices(graph)
for i in range(len(templates)):
k = templates[i].order()
tV = enumerate_vertices(templates[i])
localmaps = product(combinations(range(k),2),
combinations(range(N),2))
for (i1,i2),(j1,j2) in localmaps:
# check if this mapping is compatible
tedge=templates[i].has_edge(tV[i1],tV[i2])
gedge=graph.has_edge(gV[j1],gV[j2])
if tedge == gedge: continue
# if it is not, add the corresponding
F.add_clause(activation_prefixes[i] + \
[(False,"S_{{{0},{1}}}".format(min(i1,i2),min(j1,j2))),
(False,"S_{{{0},{1}}}".format(max(i1,i2),max(j1,j2))) ],strict=True)
return F
def GraphColoringFormula(G,colors,functional=True):
"""Generates the clauses for colorability formula
The formula encodes the fact that the graph :math:`G` has a coloring
with color set ``colors``. This means that it is possible to
assign one among the elements in ``colors``to that each vertex of
the graph such that no two adjacent vertices get the same color.
Parameters
----------
G : networkx.Graph
a simple undirected graph
colors : list or positive int
a list of colors or a number of colors
Returns
-------
CNF
the CNF encoding of the coloring problem on graph ``G``
"""
col=CNF()
col.mode_strict()
if isinstance(colors,int) and colors>=0:
colors = range(1,colors+1)
if not isinstance(list, collections.Iterable):
ValueError("Parameter \"colors\" is expected to be a iterable")
# Describe the formula
name="graph colorability"
if hasattr(G,'name'):
col.header=name+" of graph:\n"+G.name+".\n\n"+col.header
else:
col.header=name+".\n\n"+col.header
# Fix the vertex order
V=enumerate_vertices(G)
# Create the variables
for vertex in V:
for color in colors:
col.add_variable('x_{{{0},{1}}}'.format(vertex,color))
# Each vertex has a color
for vertex in V:
clause = []
for color in colors:
clause += [(True,'x_{{{0},{1}}}'.format(vertex,color))]
col.add_clause(clause)
# unique color per vertex
if functional:
for (c1,c2) in combinations(colors,2):
col.add_clause([
(False,'x_{{{0},{1}}}'.format(vertex,c1)),
(False,'x_{{{0},{1}}}'.format(vertex,c2))])
# This is a legal coloring
for (v1,v2) in enumerate_edges(G):
for c in colors:
col.add_clause([
(False,'x_{{{0},{1}}}'.format(v1,c)),
(False,'x_{{{0},{1}}}'.format(v2,c))])
return col
def stone_formula_helper(F, D, mapping):
"""Stones formulas helper
Builds the clauses of a stone formula given the mapping object
between stones and vertices of the DAG. THis is not supposed to be
called by user code, and indeed this function assumes the following facts.
- :math:`D` is equal to `mapping.domain()`
- :math:`D` is a DAG
Parameters
----------
F : CNF
the CNF which will contain the clauses of the stone formula
D : a directed acyclic graph
it should be a directed acyclic graph.
mapping : unary_mapping object
mapping between stones and graph vertices
See Also
--------
StoneFormula : the classic stone formula
SparseStoneFormula : stone formula with sparse mapping
"""
# add variables in the appropriate order
vertices = enumerate_vertices(D)
# Stones->Vertices variables
for v in mapping.variables():
F.add_variable(v)
# Color variables
for stone in mapping.range():
F.add_variable("R_{{{0}}}".format(stone),
description="Stone ${}$ is red".format(stone))
# Each vertex has some stone
for cls in mapping.clauses():
F.add_clause_unsafe(cls)
# If predecessors have red stones, the sink must have a red stone
for v in vertices:
for j in mapping.images(v):
pred = sorted(D.predecessors(v),
key=lambda x: mapping.RankDomain[x])
for stones_tuple in product(*tuple(
[s for s in mapping.images(v) if s != j] for v in pred)):
F.add_clause([(False, mapping.var_name(p, s))
for (p, s) in zip(pred, stones_tuple)] +
[(False, mapping.var_name(v, j))] +
[(False, "R_{{{0}}}".format(s))
for s in _uniqify_list(stones_tuple)] +
[(True, "R_{{{0}}}".format(j))],
strict=True)
if D.out_degree(v) == 0: #the sink
for j in mapping.images(v):
F.add_clause([(False, mapping.var_name(v, j)),
(False, "R_{{{0}}}".format(j))],
strict=True)
return F
def SubgraphFormula(graph, templates, symmetric=False):
"""Test whether a graph contains one of the templates.
Given a graph :math:`G` and a sequence of template graphs
:math:`H_1`, :math:`H_2`, ..., :math:`H_t`, the CNF formula claims
that :math:`G` contains an isomorphic copy of at least one of the
template graphs.
E.g. when :math:`H_1` is the complete graph of :math:`k` vertices
and it is the only template, the formula claims that :math:`G`
contains a :math:`k`-clique.
Parameters
----------
graph : networkx.Graph
a simple graph
templates : list-like object
a sequence of graphs.
symmetric:
all template graphs are symmetric wrt permutations of
vertices. This allows some optimization in the search space of
the assignments.
induce:
force the subgraph to be induced (i.e. no additional edges are allowed)
Returns
-------
a CNF object
"""
F = CNF()
# One of the templates is chosen to be the subgraph
if len(templates) == 0:
return F
elif len(templates) == 1:
selectors = []
elif len(templates) == 2:
selectors = ['c']
else:
selectors = ['c_{{{}}}'.format(i) for i in range(len(templates))]
for s in selectors:
F.add_variable(s)
if len(selectors) > 1:
for cls in F.equal_to_constraint(selectors, 1):
F.add_clause(cls, strict=True)
# comment the formula accordingly
if len(selectors) > 1:
F.header = dedent("""\
CNF encoding of the claim that a graph contains one among
a family of {0} possible subgraphs.
""".format(len(templates))) + F.header
else:
F.header = dedent("""\
CNF encoding of the claim that a graph contains an induced
copy of a subgraph.
""".format(len(templates))) + F.header
# A subgraph is chosen
N = graph.order()
k = max([s.order() for s in templates])
var_name = lambda i, j: "S_{{{0},{1}}}".format(i, j)
if symmetric:
mapping = F.unary_mapping(range(k),
range(N),
var_name=var_name,
functional=True,
injective=True,
nondecreasing=True)
else:
mapping = F.unary_mapping(range(k),
range(N),
var_name=var_name,
functional=True,
injective=True,
nondecreasing=False)
for v in mapping.variables():
F.add_variable(v)
for cls in mapping.clauses():
F.add_clause(cls, strict=True)
# The selectors choose a template subgraph. A mapping must map
# edges to edges and non-edges to non-edges for the active
# template.
if len(templates) == 1:
activation_prefixes = [[]]
elif len(templates) == 2:
activation_prefixes = [[(True, selectors[0])], [(False, selectors[0])]]
else:
activation_prefixes = [[(True, v)] for v in selectors]
# maps must preserve the structure of the template graph
gV = enumerate_vertices(graph)
for i in range(len(templates)):
k = templates[i].order()
tV = enumerate_vertices(templates[i])
if symmetric:
# Using non-decreasing map to represent a subset
localmaps = product(combinations(range(k), 2),
combinations(range(N), 2))
else:
localmaps = product(combinations(range(k), 2),
permutations(range(N), 2))
for (i1, i2), (j1, j2) in localmaps:
# check if this mapping is compatible
tedge = templates[i].has_edge(tV[i1], tV[i2])
gedge = graph.has_edge(gV[j1], gV[j2])
if tedge == gedge:
continue
# if it is not, add the corresponding
F.add_clause(activation_prefixes[i] + \
[(False,var_name(i1,j1)),
(False,var_name(i2,j2)) ],strict=True)
return F
def TseitinFormula(graph, charges=None, encoding=None):
"""Build a Tseitin formula based on the input graph.
Odd charge is put on the first vertex by default, unless other
vertices are is specified in input.
Arguments:
- `graph`: input graph
- `charges': odd or even charge for each vertex
"""
V = enumerate_vertices(graph)
if charges == None:
charges = [1] + [0] * (len(V) - 1) # odd charge on first vertex
else:
charges = [bool(c) for c in charges] # map to boolean
if len(charges) < len(V):
charges = charges + [0] * (len(V) - len(charges)
) # pad with even charges
# init formula
tse = CNF()
edgename = {}
for (u, v) in sorted(graph.edges(), key=sorted):
edgename[(u, v)] = "E_{{{0},{1}}}".format(u, v)
edgename[(v, u)] = "E_{{{0},{1}}}".format(u, v)
tse.add_variable(edgename[(u, v)])
tse.mode_strict()
# add constraints
for v, charge in zip(V, charges):
# produce all clauses and save half of them
names = [edgename[(u, v)] for u in neighbors(graph, v)]
if encoding == None:
tse.add_parity(names, charge)
else:
def toArgs(listOfTuples, operator, degree):
return list(sum(listOfTuples, ())) + [operator, degree]
terms = list(map(lambda x: (1, x), names))
w = len(terms)
k = w // 2
if encoding == "extendedPBAnyHelper":
for i in range(k):
helper = ("xor_helper", i, v)
tse.add_variable(helper)
terms.append((2, helper))
elif encoding == "extendedPBOneHelper":
helpers = list()
for i in range(k):
helper = ("xor_helper", i, v)
helpers.append(helper)
tse.add_variable(helper)
terms.append(((i + 1) * 2, helper))
tse.add_linear(*toArgs([(1, x) for x in helpers], "<=", 1))
elif encoding == "extendedPBExpHelper":
for i in range(math.ceil(math.log(k, 2)) + 1):
helper = ("xor_helper", i, v)
tse.add_variable(helper)
terms.append((2**i * 2, helper))
else:
raise ValueError("Invalid encoding '%s'" % encoding)
degree = 2 * k + (charge % 2)
tse.add_linear(*toArgs(terms, "==", degree))
return tse
def GraphColoringFormula(G, colors, functional=True):
"""Generates the clauses for colorability formula
The formula encodes the fact that the graph :math:`G` has a coloring
with color set ``colors``. This means that it is possible to
assign one among the elements in ``colors``to that each vertex of
the graph such that no two adjacent vertices get the same color.
Parameters
----------
G : networkx.Graph
a simple undirected graph
colors : list or positive int
a list of colors or a number of colors
Returns
-------
CNF
the CNF encoding of the coloring problem on graph ``G``
"""
col = CNF()
if isinstance(colors, int) and colors >= 0:
colors = range(1, colors + 1)
if not isinstance(list, collections.Iterable):
ValueError("Parameter \"colors\" is expected to be a iterable")
# Describe the formula
name = "graph colorability"
if hasattr(G, 'name'):
col.header = name + " of graph:\n" + G.name + ".\n\n" + col.header
else:
col.header = name + ".\n\n" + col.header
# Fix the vertex order
V = enumerate_vertices(G)
# Each vertex has a color
for vertex in V:
clause = []
for color in colors:
clause += [(True, 'x_{{{0},{1}}}'.format(vertex, color))]
col.add_clause(clause)
# unique color per vertex
if functional:
for (c1, c2) in combinations(colors, 2):
col.add_clause([(False, 'x_{{{0},{1}}}'.format(vertex, c1)),
(False, 'x_{{{0},{1}}}'.format(vertex, c2))],
strict=True)
# This is a legal coloring
for (v1, v2) in enumerate_edges(G):
for c in colors:
col.add_clause([(False, 'x_{{{0},{1}}}'.format(v1, c)),
(False, 'x_{{{0},{1}}}'.format(v2, c))],
strict=True)
return col