passagemath-polyhedra 10.6.31rc3__cp314-cp314-musllinux_1_2_x86_64.whl

sage/schemes/toric/ideal.py

@@ -0,0 +1,451 @@
+# sage_setup: distribution = sagemath-polyhedra
+# sage.doctest: needs sage.geometry.polyhedron sage.graphs sage.libs.singular
+r"""
+Toric ideals
+
+A toric ideal (associated to an integer matrix `A`) is an ideal of the
+form
+
+.. MATH::
+
+    I_A = \left<
+        x^u - x^v
+        : u,v \in \ZZ_\geq^n
+        , u-v \in \ker(A)
+        \right>
+
+In other words, it is an ideal generated by irreducible "binomials",
+that is, differences of monomials without a common factor. Since the
+Buchberger algorithm preserves this property, any Groebner basis is
+then also generated by binomials.
+
+EXAMPLES::
+
+    sage: A = matrix([[1,1,1], [0,1,2]])
+    sage: IA = ToricIdeal(A)
+    sage: IA.ker()
+    Free module of degree 3 and rank 1 over Integer Ring
+    User basis matrix:
+    [-1  2 -1]
+    sage: IA
+    Ideal (-z1^2 + z0*z2) of Multivariate Polynomial
+    Ring in z0, z1, z2 over Rational Field
+
+Here, the "naive" ideal generated by `z_0 z_2 - z_1^2` does already
+equal the toric ideal. But that is not true in general! For example,
+this toric ideal ([Stu1997]_, Example 1.2) is the twisted
+cubic and cannot be generated by `2=\dim \ker(A)` polynomials::
+
+    sage: A = matrix([[3,2,1,0], [0,1,2,3]])
+    sage: IA = ToricIdeal(A)
+    sage: IA.ker()
+    Free module of degree 4 and rank 2 over Integer Ring
+    User basis matrix:
+    [-1  1  1 -1]
+    [-1  2 -1  0]
+    sage: IA
+    Ideal (-z1*z2 + z0*z3, -z1^2 + z0*z2, z2^2 - z1*z3) of
+    Multivariate Polynomial Ring in z0, z1, z2, z3 over Rational Field
+
+The following family of toric ideals is from Example 4.4 of
+[Stu1997]_. One can show that `I_d` is generated by one
+quadric and `d` binomials of degree `d`::
+
+    sage: def I(d):
+    ....:     return ToricIdeal(matrix([[1,1,1,1,1], [0,1,1,0,0], [0,0,1,1,d]]))
+    sage: I(2)
+    Ideal (-z3^2 + z0*z4,
+           z0*z2 - z1*z3,
+           z2*z3 - z1*z4) of
+    Multivariate Polynomial Ring in z0, z1, z2, z3, z4 over Rational Field
+    sage: I(3)
+    Ideal (-z3^3 + z0^2*z4,
+           z0*z2 - z1*z3,
+           z2*z3^2 - z0*z1*z4,
+           z2^2*z3 - z1^2*z4) of
+    Multivariate Polynomial Ring in z0, z1, z2, z3, z4 over Rational Field
+    sage: I(4)
+    Ideal (-z3^4 + z0^3*z4,
+           z0*z2 - z1*z3,
+           z2*z3^3 - z0^2*z1*z4,
+           z2^2*z3^2 - z0*z1^2*z4,
+           z2^3*z3 - z1^3*z4) of
+    Multivariate Polynomial Ring in z0, z1, z2, z3, z4 over Rational Field
+
+Finally, the example in [SH1995b]_ ::
+
+    sage: A = matrix(ZZ, [ [15,  4, 14, 19,  2,  1, 10, 17],
+    ....:                  [18, 11, 13,  5, 16, 16,  8, 19],
+    ....:                  [11,  7,  8, 19, 15, 18, 14,  6],
+    ....:                  [17, 10, 13, 17, 16, 14, 15, 18] ])
+    sage: IA = ToricIdeal(A)     # long time
+    sage: IA.ngens()             # long time
+    213
+
+TESTS::
+
+    sage: A = matrix(ZZ, [[1, 1, 0, 0, -1,  0,  0, -1],
+    ....:                 [0, 0, 1, 1,  0, -1, -1,  0],
+    ....:                 [1, 0, 0, 1,  1,  1,  0,  0],
+    ....:                 [1, 0, 0, 1,  0,  0, -1, -1]])
+    sage: IA = ToricIdeal(A)
+    sage: R = IA.ring()
+    sage: R.inject_variables()
+    Defining z0, z1, z2, z3, z4, z5, z6, z7
+    sage: IA == R.ideal([z4*z6-z5*z7, z2*z5-z3*z6, -z3*z7+z2*z4,
+    ....:     -z2*z6+z1*z7, z1*z4-z3*z6, z0*z7-z3*z6, -z1*z5+z0*z6, -z3*z5+z0*z4,
+    ....:     z0*z2-z1*z3])  # Computed with Maple 12
+    True
+
+The next example first appeared in Example 12.7 in [Stu1995]_. It is also
+used by the Maple 12 help system as example::
+
+    sage: A = matrix(ZZ, [[1, 2, 3, 4, 0, 1, 4, 5],
+    ....:                 [2, 3, 4, 1, 1, 4, 5, 0],
+    ....:                 [3, 4, 1, 2, 4, 5, 0, 1],
+    ....:                 [4, 1, 2, 3, 5, 0, 1, 4]])
+    sage: IA = ToricIdeal(A, 'z1, z2, z3, z4, z5, z6, z7, z8')
+    sage: R = IA.ring()
+    sage: R.inject_variables()
+    Defining z1, z2, z3, z4, z5, z6, z7, z8
+    sage: IA == R.ideal([z4^4-z6*z8^3, z3^4-z5*z7^3, -z4^3+z2*z8^2,
+    ....:     z2*z4-z6*z8, -z4^2*z6+z2^2*z8, -z4*z6^2+z2^3, -z3^3+z1*z7^2,
+    ....:     z1*z3-z5*z7, -z3^2*z5+z1^2*z7, z1^3-z3*z5^2])
+    True
+
+AUTHORS:
+
+- Volker Braun (2011-01-03): Initial version
+"""
+
+# ****************************************************************************
+#       Copyright (C) 2010 Volker Braun <vbraun.name@gmail.com>
+#
+#  Distributed under the terms of the GNU General Public License (GPL)
+#  as published by the Free Software Foundation; either version 2 of
+#  the License, or (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
+
+# TODO:
+#   * Implement the Di Biase & Urbanke algorithm
+#   * Implement the Conti & Traverso algorithm (for educational purposes)
+#   * Cythonize the Buchberger algorithm for toric ideals
+#   * Use the (multiple) weighted homogeneity during Groebner basis computations
+
+
+from sage.rings.polynomial.polynomial_ring_constructor import PolynomialRing
+from sage.misc.misc_c import prod
+from sage.matrix.constructor import matrix
+from sage.rings.integer_ring import ZZ
+from sage.rings.rational_field import QQ
+from sage.rings.polynomial.multi_polynomial_ideal import MPolynomialIdeal
+
+
+class ToricIdeal(MPolynomialIdeal):
+    r"""
+    This class represents a toric ideal defined by an integral matrix.
+
+    INPUT:
+
+    - ``A`` -- integer matrix; the defining matrix of the toric ideal
+
+    - ``names`` -- string (optional); names for the variables. By
+      default, this is ``'z'`` and the variables will be named ``z0``,
+      ``z1``, ...
+
+    - ``base_ring`` -- a ring (default: `\QQ`); the base
+      ring of the ideal. A toric ideal uses only coefficients `\pm 1`.
+
+    - ``polynomial_ring`` -- a polynomial ring (optional); the
+      polynomial ring to construct the ideal in
+
+      You may specify the ambient polynomial ring via the
+      ``polynomial_ring`` parameter or via the ``names`` and
+      ``base_ring`` parameter. A :exc:`ValueError` is raised if you
+      specify both.
+
+    - ``algorithm`` -- string (optional); the algorithm to use. For
+      now, must be ``'HostenSturmfels'`` which is the algorithm
+      proposed by Hosten and Sturmfels in [SH1995b]_.
+
+    EXAMPLES::
+
+        sage: A = matrix([[1,1,1], [0,1,2]])
+        sage: ToricIdeal(A)
+        Ideal (-z1^2 + z0*z2) of Multivariate Polynomial Ring
+        in z0, z1, z2 over Rational Field
+
+    First way of specifying the polynomial ring::
+
+        sage: ToricIdeal(A, names='x,y,z', base_ring=ZZ)
+        Ideal (-y^2 + x*z) of Multivariate Polynomial Ring
+        in x, y, z over Integer Ring
+
+    Second way of specifying the polynomial ring::
+
+        sage: R.<x,y,z> = ZZ[]
+        sage: ToricIdeal(A, polynomial_ring=R)
+        Ideal (-y^2 + x*z) of Multivariate Polynomial Ring
+        in x, y, z over Integer Ring
+
+    It is an error to specify both::
+
+        sage: ToricIdeal(A, names='x,y,z', polynomial_ring=R)
+        Traceback (most recent call last):
+        ...
+        ValueError: you must not specify both variable names and a polynomial ring
+    """
+
+    def __init__(self, A,
+                 names='z', base_ring=QQ,
+                 polynomial_ring=None,
+                 algorithm='HostenSturmfels'):
+        r"""
+        Create an ideal and a multivariate polynomial ring containing it.
+
+        See the :mod:`module documentation
+        <sage.schemes.toric.ideal>` for an introduction to
+        toric ideals.
+
+        INPUT:
+
+        See the :class:`class-level documentation <ToricIdeal>` for
+        input values.
+
+        EXAMPLES::
+
+            sage: A = matrix([[1,1,1], [0,1,2]])
+            sage: ToricIdeal(A)
+            Ideal (-z1^2 + z0*z2) of Multivariate Polynomial Ring
+            in z0, z1, z2 over Rational Field
+            sage: ToricIdeal(A, names='x', base_ring=GF(101))
+            Ideal (-x1^2 + x0*x2) of Multivariate Polynomial Ring
+            in x0, x1, x2 over Finite Field of size 101
+            sage: ToricIdeal(A, names='x', base_ring=FractionField(QQ['t']))
+            Ideal (-x1^2 + x0*x2) of
+            Multivariate Polynomial Ring in x0, x1, x2 over
+             Fraction Field of Univariate Polynomial Ring in t over Rational Field
+        """
+        self._A = matrix(ZZ, A)
+        if polynomial_ring:
+            if names != 'z' or base_ring is not QQ:
+                raise ValueError('you must not specify both variable names and a polynomial ring')
+            self._names = [str(g) for g in polynomial_ring.gens()]
+            self._base_ring = polynomial_ring.base_ring()
+            ring = polynomial_ring
+        else:
+            self._names = names
+            self._base_ring = base_ring
+            ring = self._init_ring('degrevlex')
+
+        if algorithm == 'HostenSturmfels':
+            ideal = self._ideal_HostenSturmfels()
+        else:
+            raise ValueError(f'algorithm = {algorithm} is not known')
+
+        gens = [ring(x) for x in ideal.gens()]
+        MPolynomialIdeal.__init__(self, ring, gens, coerce=False)
+
+    def A(self):
+        """
+        Return the defining matrix.
+
+        OUTPUT: integer matrix
+
+        EXAMPLES::
+
+            sage: A = matrix([[1,1,1], [0,1,2]])
+            sage: IA = ToricIdeal(A)
+            sage: IA.A()
+            [1 1 1]
+            [0 1 2]
+        """
+        return self._A
+
+    def ker(self):
+        """
+        Return the kernel of the defining matrix.
+
+        OUTPUT: the kernel of ``self.A()``.
+
+        EXAMPLES::
+
+            sage: A = matrix([[1,1,1], [0,1,2]])
+            sage: IA = ToricIdeal(A)
+            sage: IA.ker()
+            Free module of degree 3 and rank 1 over Integer Ring
+             User basis matrix: [-1  2 -1]
+        """
+
+        if '_ker' in self.__dict__:
+            return self._ker
+        self._ker = self.A().right_kernel(basis='LLL')
+        return self._ker
+
+    def nvariables(self):
+        r"""
+        Return the number of variables of the ambient polynomial ring.
+
+        OUTPUT: integer; the number of columns of the defining matrix :meth:`A`
+
+        EXAMPLES::
+
+            sage: A = matrix([[1,1,1], [0,1,2]])
+            sage: IA = ToricIdeal(A)
+            sage: IA.nvariables()
+            3
+        """
+        return self.A().ncols()
+
+    def _init_ring(self, term_order):
+        r"""
+        Construct the ambient polynomial ring.
+
+        INPUT:
+
+        - ``term_order`` -- string; the order of the variables, for
+          example ``'neglex'`` and ``'degrevlex'``
+
+        OUTPUT: a polynomial ring with the given term order
+
+        .. NOTE::
+
+            Reverse lexicographic ordering is equivalent to negative
+            lexicographic order with the reversed list of
+            variables. We are using the latter in the implementation
+            of the Hosten/Sturmfels algorithm.
+
+        EXAMPLES::
+
+            sage: A = matrix([[1,1,1], [0,1,2]])
+            sage: IA = ToricIdeal(A)
+            sage: R = IA._init_ring('neglex');  R
+            Multivariate Polynomial Ring in z0, z1, z2 over Rational Field
+            sage: R.term_order()
+            Negative lexicographic term order
+            sage: R.inject_variables()
+            Defining z0, z1, z2
+            sage: z0 < z1 and z1 < z2
+            True
+        """
+        return PolynomialRing(self._base_ring, self._names,
+                              self.nvariables(), order=term_order)
+
+    def _naive_ideal(self, ring):
+        r"""
+        Return the "naive" subideal.
+
+        INPUT:
+
+        - ``ring`` -- the ambient ring of the ideal
+
+        OUTPUT: a subideal of the toric ideal in the polynomial ring ``ring``
+
+        EXAMPLES::
+
+            sage: A = matrix([[1,1,1], [0,1,2]])
+            sage: IA = ToricIdeal(A)
+            sage: IA.ker()
+            Free module of degree 3 and rank 1 over Integer Ring
+             User basis matrix: [-1  2 -1]
+            sage: IA._naive_ideal(IA.ring())
+            Ideal (z1^2 - z0*z2) of Multivariate Polynomial Ring in z0, z1, z2 over Rational Field
+        """
+        x = ring.gens()
+        binomials = []
+        for row in self.ker().matrix().rows():
+            xpos = prod(x[i]**max(row[i], 0) for i in range(len(x)))
+            xneg = prod(x[i]**max(-row[i], 0) for i in range(len(x)))
+            binomials.append(xpos - xneg)
+        return ring.ideal(binomials)
+
+    def _ideal_quotient_by_variable(self, ring, ideal, n):
+        r"""
+        Return the ideal quotient `(J:x_n^\infty)`.
+
+        INPUT:
+
+        - ``ring`` -- the ambient polynomial ring in neglex order
+
+        - ``ideal`` -- the ideal `J`
+
+        - ``n`` -- integer; the index of the next variable to divide by
+
+        OUTPUT: the ideal quotient `(J:x_n^\infty)`
+
+        ALGORITHM:
+
+        Proposition 4 of [SH1995b]_.
+
+        EXAMPLES::
+
+            sage: A = lambda d: matrix([[1,1,1,1,1],[0,1,1,0,0],[0,0,1,1,d]])
+            sage: IA = ToricIdeal(A(3))
+            sage: R = PolynomialRing(QQ, 5, 'z', order='neglex')
+            sage: J0 = IA._naive_ideal(R)
+            sage: IA._ideal_quotient_by_variable(R, J0, 0)
+            Ideal (z2*z3^2 - z0*z1*z4, z1*z3 - z0*z2,
+                   z2^2*z3 - z1^2*z4, z1^3*z4 - z0*z2^3)
+             of Multivariate Polynomial Ring in z0, z1, z2, z3, z4 over Rational Field
+        """
+        N = self.nvariables()
+        y = list(ring.gens())
+        x = [y[i - n] for i in range(N)]
+        y_to_x = dict(zip(x, y))
+        x_to_y = dict(zip(y, x))
+        # swap variables such that the n-th variable becomes the last one
+        J = ideal.subs(y_to_x)
+
+        # TODO: Can we use the weighted homogeneity with respect to
+        # the rows of self.A() when computing the Groebner basis, see
+        # [SH1995b]?
+        basis = J.groebner_basis()
+
+        # x_n = y[0]   # the cheapest variable in the revlex order
+        def subtract(e, power):
+            l = list(e)
+            return tuple([l[0] - power] + l[1:])
+
+        def divide_by_x_n(p):
+            d_old = p.monomial_coefficients()
+            power = min(e[0] for e in d_old)
+            d_new = {subtract(exponent, power): coefficient
+                     for exponent, coefficient in d_old.items()}
+            return p.parent()(d_new)
+        basis = [divide_by_x_n(b) for b in basis]
+        quotient = ring.ideal(basis)
+        return quotient.subs(x_to_y)
+
+    def _ideal_HostenSturmfels(self):
+        r"""
+        Compute the toric ideal by Hosten and Sturmfels' algorithm.
+
+        OUTPUT:
+
+        The toric ideal as an ideal in the polynomial ring
+        ``self.ring()``.
+
+        EXAMPLES::
+
+            sage: A = matrix([[3,2,1,0], [0,1,2,3]])
+            sage: IA = ToricIdeal(A);  IA
+            Ideal (-z1*z2 + z0*z3, -z1^2 + z0*z2, z2^2 - z1*z3)
+             of Multivariate Polynomial Ring in z0, z1, z2, z3 over Rational Field
+            sage: R = IA.ring()
+            sage: IA == IA._ideal_HostenSturmfels()
+            True
+
+        TESTS::
+
+            sage: I_2x2 = identity_matrix(ZZ, 2)
+            sage: ToricIdeal(I_2x2)
+            Ideal (0) of Multivariate Polynomial Ring in z0, z1 over Rational Field
+        """
+        ring = self._init_ring('neglex')
+        J = self._naive_ideal(ring)
+        if J.is_zero():
+            return J
+        for i in range(self.nvariables()):
+            J = self._ideal_quotient_by_variable(ring, J, i)
+        return J