snappy 3.2__cp310-cp310-macosx_10_12_x86_64.whl

snappy/snap/__init__.py

@@ -0,0 +1,114 @@
+from .shapes import polished_tetrahedra_shapes
+from ..sage_helper import _within_sage, sage_method
+from .polished_reps import polished_holonomy
+from . import nsagetools, interval_reps, slice_obs_HKL
+from .character_varieties import character_variety, character_variety_ideal
+
+if _within_sage:
+    from .find_field import ListOfApproximateAlgebraicNumbers
+
+
+@sage_method
+def tetrahedra_field_gens(manifold):
+    """
+    The shapes of the tetrahedra as ApproximateAlgebraicNumbers. Can be
+    used to compute the tetrahedra field, where the first two parameters
+    are bits of precision and maximum degree of the field::
+
+        sage: M = Manifold('m015')
+        sage: tets = M.tetrahedra_field_gens()
+        sage: tets.find_field(100, 10, optimize=True)    # doctest: +NORMALIZE_WHITESPACE +NUMERIC9
+        (Number Field in z with defining polynomial x^3 - x - 1
+         with z = -0.6623589786223730? - 0.5622795120623013?*I,
+        <ApproxAN: -0.662358978622 - 0.562279512062*I>, [-z, -z, -z])
+    """
+    if manifold.is_orientable():
+        def func(prec):
+            return polished_tetrahedra_shapes(manifold, bits_prec=prec)
+    else:
+        double_cover = manifold.orientation_cover()
+
+        def func(prec):
+            return polished_tetrahedra_shapes(double_cover, bits_prec=prec)[::2]
+    return ListOfApproximateAlgebraicNumbers(func)
+
+
+@sage_method
+def trace_field_gens(manifold, fundamental_group_args=[]):
+    """
+    The generators of the trace field as ApproximateAlgebraicNumbers. Can be
+    used to compute the tetrahedra field, where the first two parameters
+    are bits of precision and maximum degree of the field::
+
+        sage: M = Manifold('m125')
+        sage: traces = M.trace_field_gens()
+        sage: traces.find_field(100, 10, optimize=True)    # doctest: +NORMALIZE_WHITESPACE
+        (Number Field in z with defining polynomial x^2 + 1
+         with z = -1*I,
+        <ApproxAN: -1.0*I>, [z + 1, z, z + 1])
+    """
+    def func(prec):
+        return polished_holonomy(manifold, prec,
+                                 fundamental_group_args).trace_field_generators()
+    return ListOfApproximateAlgebraicNumbers(func)
+
+
+@sage_method
+def invariant_trace_field_gens(manifold, fundamental_group_args=[]):
+    """
+    The generators of the trace field as ApproximateAlgebraicNumbers. Can be
+    used to compute the tetrahedra field, where the first two parameters
+    are bits of precision and maximum degree of the field::
+
+        sage: M = Manifold('m007(3,1)')
+        sage: K = M.invariant_trace_field_gens().find_field(100, 10, optimize=True)[0]
+        sage: L = M.trace_field_gens().find_field(100, 10, optimize=True)[0]
+        sage: K.polynomial(), L.polynomial()
+        (x^2 - x + 1, x^4 - 2*x^3 + x^2 + 6*x + 3)
+    """
+    def func(prec):
+        return polished_holonomy(manifold, prec,
+                                 fundamental_group_args).invariant_trace_field_generators()
+    return ListOfApproximateAlgebraicNumbers(func)
+
+
+@sage_method
+def holonomy_matrix_entries(manifold,
+                            fundamental_group_args=[],
+                            match_kernel=True):
+    """
+    The entries of the matrices of the holonomy as list of ApproximateAlgebraicNumbers
+    (four consecutive numbers per matrix). The numbers are guaranteed to lie in the
+    trace field only if match_kernel = False::
+
+        sage: M = Manifold("m004")
+        sage: mat_entries = M.holonomy_matrix_entries(match_kernel = False) # doctest: +NORMALIZE_WHITESPACE +NUMERIC9
+        sage: mat_entries
+        <SetOfAAN: [0.5 + 0.8660254037844386*I, 0.5 - 0.8660254037844386*I, 0.5 + 0.8660254037844386*I, 1.0 - 1.7320508075688772*I, 1.0 - 3.4641016151377544*I, -2.0 + 1.7320508075688772*I, -1.0 - 1.7320508075688772*I, 1.7320508075688772*I]>
+        sage: K = mat_entries.find_field(100, 10, optimize = True)[0]
+        sage: K.polynomial()
+        x^2 - x + 1
+    """
+
+    def func(prec):
+        G = polished_holonomy(manifold,
+                              prec,
+                              fundamental_group_args=fundamental_group_args,
+                              match_kernel=match_kernel)
+        return sum( [G.SL2C(g).list() for g in G.generators()], [])
+    return ListOfApproximateAlgebraicNumbers(func)
+
+
+def add_methods(mfld_class, hyperbolic=True):
+    mfld_class.alexander_polynomial = nsagetools.alexander_polynomial
+    mfld_class.homological_longitude = nsagetools.homological_longitude
+    mfld_class.slice_obstruction_HKL = slice_obs_HKL.slice_obstruction_HKL
+    if hyperbolic:
+        mfld_class.polished_holonomy = polished_holonomy
+        mfld_class.tetrahedra_field_gens = tetrahedra_field_gens
+        mfld_class.trace_field_gens = trace_field_gens
+        mfld_class.invariant_trace_field_gens = invariant_trace_field_gens
+        mfld_class.holonomy_matrix_entries = holonomy_matrix_entries
+        mfld_class.hyperbolic_torsion = nsagetools.hyperbolic_torsion
+        mfld_class.hyperbolic_adjoint_torsion = nsagetools.hyperbolic_adjoint_torsion
+        mfld_class.hyperbolic_SLN_torsion = nsagetools.hyperbolic_SLN_torsion

snappy/snap/character_varieties.py

@@ -0,0 +1,375 @@
+"""
+Computing the defining equations of the SL(2, C) character variety
+in terms of the trace coordinates.
+
+Code contributed by Jean-Philippe Burelle
+
+based on: https://arxiv.org/abs/1703.08241
+"""
+
+from ..pari import pari
+import string
+from itertools import combinations, combinations_with_replacement, product
+
+
+def cycle_sort(l):
+    """
+    Utility function which takes a list l and returns the minimum
+    for the alphabetical order among all cyclic permutations of the list.
+    """
+    s = l
+    for i in range(0,len(l)):
+        temp = l[i:] + l[0:i]
+        if temp < s:
+            s = temp
+    return s
+
+
+def pari_poly_variable(variable_name):
+    """
+    Ensures that PARI has the requested polynomial variable defined.
+    If "variable_name" is already defined in PARI as something else,
+    an exception is raised.
+
+    >>> val = 3*pari_poly_variable('silly')**2; val
+    3*silly^2
+    >>> ten = pari('silly = 10')
+    >>> pari_poly_variable('silly')
+    Traceback (most recent call last):
+    ...
+    RuntimeError: In PARI, "silly" is already defined
+    """
+    p = pari(variable_name)
+    success = p.type() == 't_POL' and p.variables() == [p]
+    if not success:
+        raise RuntimeError('In PARI, "%s" is already defined' % variable_name)
+    return p
+
+
+class TracePolynomialRing():
+    """
+    >>> S = TracePolynomialRing('ab')
+    >>> S.var_names
+    ['Ta', 'Tb', 'Tab']
+    >>> R = TracePolynomialRing('abc')
+    >>> R.var_names
+    ['Ta', 'Tb', 'Tc', 'Tab', 'Tac', 'Tbc', 'Tabc']
+    >>> R('Ta*Tb')
+    Tb*Ta
+    """
+    def __init__(self, gens):
+        self._set_var_names(gens)
+        self.vars = [pari_poly_variable(v) for v in self.var_names]
+
+    def _set_var_names(self, gens):
+        if (len(set(gens)) != len(gens) or
+            not set(gens).issubset(string.ascii_lowercase)):
+            raise ValueError('Generators are unsuitable')
+        poly_vars = list(gens) + list(combinations(gens, 2))
+        poly_vars += list(combinations(gens, 3))
+        self.var_names = ['T' + ''.join(v) for v in poly_vars]
+
+    def __call__(self, poly):
+        return pari(poly)
+
+
+class Word():
+    """
+    The Word class is used to make objects which represent words in a
+    free group. The words are represented by a string of letters, with
+    capital letters standing for inverses. ex: 'abAB'. The string is
+    contained in the 'letters' attribute of the class.
+    """
+
+    def __init__(self,letters):
+        """Creates a Word from a string, automatically reduces"""
+        if isinstance(letters, Word):
+            s = letters.letters
+        else:
+            s = letters
+            # As long as the word is not reduced, delete all substrings xX or Xx
+            while not self.is_reduced(s):
+                for i,j in zip(s,s[1:]):
+                    if i != j and (i == j.upper() or i == j.lower()):
+                        s = s.replace(i + j,"")
+        self.letters = s
+
+    def __repr__(self):
+        return self.letters
+
+    def __mul__(self,other):
+        return Word(self.letters+other.letters)
+
+    def inverse(self):
+        return Word(self.letters.swapcase()[::-1])
+
+    def is_reduced(self,s):
+        """Returns true if and only if the string s represents a reduced word"""
+        for i,j in zip(s,s[1:]):
+            if i != j and (i == j.upper() or i == j.lower()):
+                break
+        else:
+            return True
+        return False
+
+    def SL2_trace(self):
+        """
+        Returns the simplified SL(2) trace of the Word represented by this
+        object. The format of the output is a Pari polynomial in the
+        variables Tw where w is a word of length 3 or less
+
+        Examples:
+        >>> Word("a").SL2_trace()
+        Ta
+        >>> Word("A").SL2_trace()
+        Ta
+        >>> Word("aa").SL2_trace()
+        Ta^2 - 2
+        >>> Word("abAB").SL2_trace()
+        Ta^2 - Tab*Tb*Ta + (Tb^2 + (Tab^2 - 2))
+        >>> Word("abca").SL2_trace()
+        Tabc*Ta - Tbc
+        """
+        if self.letters == "":
+            return pari("2") # The SL(2,C) trace of the identity word is 2.
+
+        # Cyclically permute the letters until they are minimal for the
+        # lexicographic ordering.
+        s = cycle_sort(self.letters)
+
+        # Reduction of traces when there is a repeated letter
+        for L in sorted(set(s)):
+            i = s.find(L)
+            j = s.find(L, i + 1)
+            if j > i:
+                w1 = s[i:j]
+                w2 = s[j: ] + s[:i]
+                return tr(Word(w1))*tr(Word(w2)) - tr(Word(w1).inverse()*Word(w2))
+
+        # Reduction of traces with inverses
+        for i in s:
+            if i.isupper():
+                [w1,c,w2] = s.partition(i)
+                return (Word(i.lower()).SL2_trace()*Word(w2+w1).SL2_trace()
+                - Word(w1+i.lower()+w2).SL2_trace())
+
+        # Reductions of traces of length larger than 4
+        if len(s) >= 4:
+            [x,y,z,w] = [s[0],s[1],s[2],s[3:]]
+            return (pari("1/2")*(tr(Word(x))*tr(Word(y))*tr(Word(z))*tr(Word(w))
+            + tr(Word(x))*tr(Word(y+z+w)) + tr(Word(y))*tr(Word(x+z+w))
+            + tr(Word(z))*tr(Word(x+y+w)) + tr(Word(w))*tr(Word(x+y+z))
+            - tr(Word(x+z))*tr(Word(y+w)) + tr(Word(x+w))*tr(Word(y+z))
+            + tr(Word(x+y))*tr(Word(z+w))
+            - tr(Word(x))*tr(Word(y))*tr(Word(z+w))
+            - tr(Word(x))*tr(Word(w))*tr(Word(y+z))
+            - tr(Word(y))*tr(Word(z))*tr(Word(x+w))
+            - tr(Word(z))*tr(Word(w))*tr(Word(x+y))))
+
+        # If the word is length 3 but not lexicographically sorted, we use a
+        # trace identity to express it in terms of lexicographically
+        # ordered words
+        if len(s) == 3 and s != ''.join(sorted(s)):
+            [x,y,z] = s
+            return (-Word(x+z+y).SL2_trace()
+            + Word(x).SL2_trace()*Word(y+z).SL2_trace()
+            + Word(y).SL2_trace()*Word(x+z).SL2_trace()
+            + Word(z).SL2_trace()*Word(x+y).SL2_trace()
+            - Word(x).SL2_trace()*Word(y).SL2_trace()*Word(z).SL2_trace())
+
+        # Output the trace if is one of the generators (length 3 or less,
+        # alphabetical order)
+        if len(s) <= 3 and s.islower():
+            return pari("T"+s)
+
+
+def tr(w):
+    """Shortcut for the SL2_trace method of a word object"""
+    return w.SL2_trace()
+
+
+class Presentation():
+    """
+    Class representing a presentation of a finitely presented group.
+    gens is a list of Word objects representing the generators
+    rels is a list of Word objects representing the relations.
+    """
+    def __init__(self,G,R):
+        """Creates a Presentation from G:generators and R:relations"""
+        self.gens = G
+        self.rels = R
+
+    def __repr__(self):
+        r = ''
+        for w in self.rels:
+            r += ('\n' + str(w))
+        return "Generators\n" + str(self.gens) + "\n"+"Relations" + r
+
+
+############################
+# Relations in the character variety
+
+def mult_traceless(a1,a2,a3=None):
+    """
+    Takes 2 or 3 words and returns the trace of their product after
+    making them traceless via M-> M-1/2tr(M)*I.
+    """
+    if a3 is None:
+        return tr(a1*a2)-pari("1/2")*tr(a1)*tr(a2)
+    else:
+        return (pari("5/8")*tr(a1)*tr(a2)*tr(a3) - pari("1/2")*tr(a3)*tr(a1*a2)
+                - pari("1/2")*tr(a2)*tr(a1*a3) - pari("1/2")*tr(a1)*tr(a2*a3)
+                + tr(a1*a2*a3))
+
+
+def s3(a1,a2,a3):
+    """
+    Accessory function to sum (with sign) "mult_traceless" over all
+    permutations of three arguments. Used in defining rel1.
+    """
+    return (mult_traceless(a1,a2,a3) + mult_traceless(a2,a3,a1)
+            + mult_traceless(a3,a1,a2) - mult_traceless(a1,a3,a2)
+            - mult_traceless(a3,a2,a1) - mult_traceless(a2,a1,a3))
+
+
+def det(M):
+    """Determinant of a 3x3 matrix"""
+    return (M[0][0]*M[1][1]*M[2][2] + M[0][1]*M[1][2]*M[2][0]
+            + M[1][0]*M[2][1]*M[0][2] - M[0][2]*M[1][1]*M[2][0]
+            - M[0][1]*M[1][0]*M[2][2] - M[0][0]*M[1][2]*M[2][1])
+
+
+def rel1(i):
+    """Generates type 1 relations for generators (words) i1,i2,i3 j1,j2,j3"""
+    [[i1,i2,i3],[j1,j2,j3]] = i
+    return (s3(i1,i2,i3)*s3(j1,j2,j3) + 18*det(
+        [[mult_traceless(i1,j1),mult_traceless(i1,j2),mult_traceless(i1,j3)],
+         [mult_traceless(i2,j1),mult_traceless(i2,j2),mult_traceless(i2,j3)],
+         [mult_traceless(i3,j1),mult_traceless(i3,j2),mult_traceless(i3,j3)]]))
+
+
+def rel2(j):
+    """Generates type 2 relations for generators (words) i,p0,p1,p2,p3"""
+    [i,[p0,p1,p2,p3]] = j
+    return (mult_traceless(i,p0)*s3(p1,p2,p3)
+            - mult_traceless(i,p1)*s3(p0,p2,p3)
+            + mult_traceless(i,p2)*s3(p0,p1,p3) - mult_traceless(i,p3)*s3(p0,p1,p2))
+
+
+def rels_from_rel(R, G):
+    """
+    Returns the relations in the character variety coming from a relation
+    in the group presentation. The input is:
+
+    R - a word object, the relation in the group
+    G - a list of words, the set of generators of the group
+    """
+    relations = [tr(R*g)-tr(g) for g in G]
+    relations = relations + [tr(R)-tr(Word(""))]
+    return [r for r in relations if r != 0]
+
+
+def character_variety(gens, rels=None):
+    """
+    Takes a list of generators and relators, either as Words or as
+    plain strings, and returns a Presentation object containing
+    generators and relations for the SL(2, C) character variety of the
+    group generated by gens and with relations rels. You can also give
+    a SnapPy fundamental group as the sole argument.
+
+    Examples:
+
+    >>> character_variety([Word("a"),Word("b")],[Word("aba")])
+    Generators
+    [Ta, Tb, Tab]
+    Relations
+    Tab*Ta^2 + (-Tb - 1)*Ta - Tab
+    -Tb + (Tab^2 - 2)
+    Tab*Ta + (-Tb - 2)
+    >>> character_variety(["a","b"],["abAB"])
+    Generators
+    [Ta, Tb, Tab]
+    Relations
+    Ta^3 - Tab*Tb*Ta^2 + (Tb^2 + (Tab^2 - 4))*Ta
+    Ta^2 - Tab*Tb*Ta + (Tb^2 + (Tab^2 - 4))
+    >>> character_variety("abc",[])
+    Generators
+    [Ta, Tb, Tc, Tab, Tac, Tbc, Tabc]
+    Relations
+    36*Ta^2 + ((-36*Tab + 36*Tabc*Tc)*Tb + (-36*Tac*Tc - 36*Tabc*Tbc))*Ta + (36*Tb^2 + (-36*Tbc*Tc - 36*Tabc*Tac)*Tb + (36*Tab^2 + (-36*Tabc*Tc + 36*Tbc*Tac)*Tab + (36*Tc^2 + (36*Tac^2 + (36*Tbc^2 + (36*Tabc^2 - 144))))))
+    >>> len(character_variety("abcd",[]).rels)
+    14
+
+    >>> character_variety("xy",["xy"])
+    Generators
+    [Tx, Ty, Txy]
+    Relations
+    (Txy - 1)*Tx - Ty
+    -Tx + (Txy - 1)*Ty
+    Txy - 2
+
+    >>> H = Manifold('dLQacccbjkg')        # Hopf link exterior.
+    >>> character_variety(H.fundamental_group())  # Answer copied from above.
+    Generators
+    [Ta, Tb, Tab]
+    Relations
+    Ta^3 - Tab*Tb*Ta^2 + (Tb^2 + (Tab^2 - 4))*Ta
+    Ta^2 - Tab*Tb*Ta + (Tb^2 + (Tab^2 - 4))
+
+    >>> G = Manifold('L6a5').fundamental_group()
+    >>> V = character_variety(G)
+    >>> len(V.gens), len(V.rels)
+    (7, 9)
+
+    """
+    if rels is None:  # SnapPy group
+        G = gens
+        gens, rels = G.generators(), G.relators()
+    gens = [Word(gen) for gen in gens]
+    rels = [Word(R) for R in rels]
+    ring = TracePolynomialRing([g.letters for g in gens])
+
+    # Type 1
+    triples = list(combinations(gens,3))
+    pairsoftriples = list(combinations_with_replacement(triples,2))
+
+    t1 = [rel1(i) for i in pairsoftriples]
+
+    # Type 2
+    fours = list(combinations(gens,4))
+    indices = product(gens,fours)
+
+    t2 = [rel2(j) for j in indices]
+
+    # Relations from relations
+    r = []
+    for R in rels:
+        r += rels_from_rel(R,gens)
+
+    return Presentation(ring.vars, t1+t2+r)
+
+
+def character_variety_ideal(gens, rels=None):
+    """
+    sage: M = Manifold('m004')
+    sage: I = character_variety_ideal(M.fundamental_group())
+    sage: I.dimension()
+    1
+    sage: len(I.radical().primary_decomposition())
+    2
+    """
+    presentation = character_variety(gens, rels)
+    from ..sage_helper import PolynomialRing, QQ
+    R = PolynomialRing(QQ, [repr(v) for v in presentation.gens])
+    return R.ideal([R(p) for p in presentation.rels])
+
+
+def total_answer_length(I):
+    return sum([len(list(p)) for p in I.gens()])
+
+
+if __name__ == "__main__":
+    from snappy.testing import doctest_modules
+    import sys
+    current_module = sys.modules[__name__]
+    doctest_modules([current_module])