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firedrakeproject · Jan 30, 2023 · 12ab3a0 · 12ab3a0
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diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -66,7 +66,7 @@ Colin Cotter..................<http://www.imperial.ac.uk/people/colin.cotter>
 
 Joshua Coutinho
 
-Patrick E. Farrell............<https://www.maths.ox.ac.uk/people/patrick.farrell>
+Patrick E. Farrell............<https://pefarrell.org>
 
 Simon Funke...................<http://www.simonfunke.com>
 
@@ -84,8 +84,6 @@ David Ham.....................<http://www.imperial.ac.uk/people/david.ham>
 
 Christopher Hawkes
 
-Reuben Hill...................<https://www.imperial.ac.uk/people/reuben.hill10>
-
 Miklós Homolya
 
 Christian Jacobs
@@ -126,7 +124,7 @@ Lawrence Mitchell
 
 Eike Mueller
 
-Reuben W. Nixon-Hill
+Reuben Nixon-Hill.............<https://www.imperial.ac.uk/people/reuben.hill10>
 
 Alberto Paganini..............<https://www2.le.ac.uk/departments/mathematics/extranet/staff-material/staff-profiles/alberto-paganini>
 

diff --git a/demos/benney_luke/benney_luke.py.rst b/demos/benney_luke/benney_luke.py.rst
@@ -53,10 +53,18 @@ Note that the Neumann boundary conditions have been used to remove every surface
 
 .. math::
 
-  \int_{\Omega} \frac{\phi^{n+1/2}-\phi^n}{\frac{1}{2}\!dt}\,v + \frac{\mu}{2}\nabla\left(\frac{\phi^{n+1/2}-\phi^n}{\frac{1}{2}\!dt}\right)\cdot\nabla v + \eta^n\,v + \frac{\epsilon}{2}\nabla\phi^{n+1/2}\cdot\nabla\phi^{n+1/2}\,v \,dx\,dy &= 0 \\
-  \int_{\Omega} q^{n+1/2}\,v - \frac{2}{3}\nabla\phi^{n+1/2}\cdot\nabla v \,dx\,dy &= 0 \\
-  \int_{\Omega} \frac{\eta^{n+1}-\eta^n}{dt}\,v + \frac{\mu}{2}\nabla\left(\frac{\eta^{n+1}-\eta^n}{dt}\right)\cdot\nabla v - \frac{1}{2}\Bigl( \left(1+\epsilon\eta^{n+1}\right) + \left(1+\epsilon\eta^n\right) \Bigr)\nabla\phi^{n+1/2}\cdot\nabla v - \mu\nabla q^{n+1/2}\cdot\nabla v \,dx\,dy &= 0 \\
-  \int_{\Omega} \frac{\phi^{n+1}-\phi^{n+1/2}}{\frac{1}{2}\!dt}\,v + \frac{\mu}{2}\nabla\left(\frac{\phi^{n+1}-\phi^{n+1/2}}{\frac{1}{2}\!dt}\right)\cdot\nabla v + \eta^{n+1}\,v + \frac{\epsilon}{2}\nabla\phi^{n+1/2}\cdot\nabla\phi^{n+1/2}\,v \,dx\,dy &= 0 \\
+  \int_{\Omega} \frac{\phi^{n+1/2}-\phi^n}{\frac{1}{2}\!dt}\,v + \frac{\mu}{2}\nabla\left(\frac{\phi^{n+1/2}-\phi^n}{\frac{1}{2}\!dt}\right)\cdot\nabla v \hspace{8em}\\
+  + \eta^n\,v + \frac{\epsilon}{2}\nabla\phi^{n+1/2}\cdot\nabla\phi^{n+1/2}\,v \,dx\,dy &= 0 \\\\
+  %
+  \int_{\Omega} q^{n+1/2}\,v - \frac{2}{3}\nabla\phi^{n+1/2}\cdot\nabla v \,dx\,dy &= 0 \\\\
+  %
+  \int_{\Omega} \frac{\eta^{n+1}-\eta^n}{dt}\,v + \frac{\mu}{2}\nabla\left(\frac{\eta^{n+1}-\eta^n}{dt}\right)\cdot\nabla v \hspace{8em}\\
+  - \frac{1}{2}\Bigl( \left(1+\epsilon\eta^{n+1}\right) + \left(1+\epsilon\eta^n\right) \Bigr)\nabla\phi^{n+1/2}\cdot\nabla v \hspace{4em}\\
+  - \mu\nabla q^{n+1/2}\cdot\nabla v \,dx\,dy &= 0 \\\\
+  %
+  \int_{\Omega} \frac{\phi^{n+1}-\phi^{n+1/2}}{\frac{1}{2}\!dt}\,v + \frac{\mu}{2}\nabla\left(\frac{\phi^{n+1}-\phi^{n+1/2}}{\frac{1}{2}\!dt}\right)\cdot\nabla v \hspace{8em}\\
+  + \eta^{n+1}\,v + \frac{\epsilon}{2}\nabla\phi^{n+1/2}\cdot\nabla\phi^{n+1/2}\,v \,dx\,dy &= 0 \\\\
+  %
   \int_{\Omega} q^{n+1}\,v - \frac{2}{3}\nabla\phi^{n+1}\cdot\nabla v \,dx\,dy &= 0.
 
 Furthermore, we note that the Benney-Luke equations admit asymptotic solutions (correct up to order :math:`\epsilon`). The "exact" solutions can be found by assuming one-dimensional travelling waves of the type

diff --git a/demos/linear_fluid_structure_interaction/linear_fluid_structure_interaction.py.rst b/demos/linear_fluid_structure_interaction/linear_fluid_structure_interaction.py.rst
@@ -39,13 +39,18 @@ After numerous manipulations (described in detail in :cite:`Salwa:2017`) and eva
 .. math::
 
     \begin{aligned}
-    & \int v \phi^{n+1} \, {\mathrm d} S_f = \int v (\phi^n - \Delta t \eta^n) \, {\mathrm d} S_f \\
-    & \int \rho_0 {\bf v} \cdot {\bf U}^{n+1} \, {\mathrm d} x_S \underline{ + \int {\bf n} \cdot {\bf v} \, \phi^{n+1} \, {\mathrm d} s_s} = \rho_0 \int {\bf v} \cdot {\bf U}^n \, {\mathrm d} x_S \nonumber\\
-    & \hspace{5cm}  - \Delta t \int \left( \lambda \nabla \cdot {\bf v} \nabla \cdot {\bf X}^n + \mu \frac{\partial X^n_j}{\partial x_i}  \left( \frac{\partial v_i}{\partial x_j}  + \frac{\partial v_j}{\partial x_i} \right) \right) \, {\mathrm d} x_S \underline{ + \int {\bf n} \cdot {\bf v} \, \phi^n \, {\mathrm d} s_s }
-    \\
-    & \int \nabla v \cdot \nabla \phi^{n+1} \, {\mathrm d} x_F \underline{ - \int v {\bf n} \cdot {\bf U}^{n+1} \, {\mathrm d} s_s }= 0 \\ %\hspace{1cm} (+ \text{Dirichlet BC at } \partial \Omega_f)\\
-    & \int v \eta^{n+1} \, {\mathrm d} S_f = \int v \eta^n \, {\mathrm d} S_f + \Delta  t \int \nabla v \cdot \nabla \phi^{n+1} \, {\mathrm d} x_F   \underline{ - \Delta t \int v {\bf n} \cdot {\bf U}^{n+1}\, {\mathrm d} s_s }\\
-    & \int {\bf v} \cdot {\bf X}^{n+1} \, {\mathrm d} x_S = \int {\bf v} \cdot ( {\bf X}^n + \Delta t {\bf U}^{n+1} ) \, {\mathrm d} x_S \, .
+    \int v \phi^{n+1} \, {\mathrm d} S_f &= \int v (\phi^n - \Delta t \eta^n) \, {\mathrm d} S_f \\\\
+    %
+    \int \rho_0 {\bf v} \cdot {\bf U}^{n+1} \, {\mathrm d} x_S\ \underline{+ \int {\bf n} \cdot {\bf v} \, \phi^{n+1} \, {\mathrm d} s_s} &= \rho_0 \int {\bf v} \cdot {\bf U}^n \, {\mathrm d} x_S \nonumber\\
+    &\hspace{4em}- \Delta t \int \left( \lambda \nabla \cdot {\bf v} \nabla \cdot {\bf X}^n + \mu \frac{\partial X^n_j}{\partial x_i}  \left( \frac{\partial v_i}{\partial x_j}  + \frac{\partial v_j}{\partial x_i} \right) \right) \, {\mathrm d} x_S \\
+    &\hspace{8em}\underline{ + \int {\bf n} \cdot {\bf v} \, \phi^n \, {\mathrm d} s_s }\\\\
+    %
+    \int \nabla v \cdot \nabla \phi^{n+1} \, {\mathrm d} x_F\ \underline{- \int v {\bf n} \cdot {\bf U}^{n+1} \, {\mathrm d} s_s } &= 0 \\\\ %\hspace{1cm} (+ \text{Dirichlet BC at } \partial \Omega_f)\\
+    %
+    \int v \eta^{n+1} \, {\mathrm d} S_f &= \int v \eta^n \, {\mathrm d} S_f + \Delta  t \int \nabla v \cdot \nabla \phi^{n+1} \, {\mathrm d} x_F\\
+    &\hspace{4em}\underline{- \Delta t \int v {\bf n} \cdot {\bf U}^{n+1}\, {\mathrm d} s_s }\\\\
+    %
+    \int {\bf v} \cdot {\bf X}^{n+1} \, {\mathrm d} x_S &= \int {\bf v} \cdot ( {\bf X}^n + \Delta t {\bf U}^{n+1} ) \, {\mathrm d} x_S \, .
     \end{aligned}
 
 The underlined terms are the coupling terms. Note that the first equation for :math:`\phi` at the free surface is solved on the free surface only, the last equation for :math:`{\bf X}` in the structure domain, while the others are solved in both domains. Moreover, the second and third equations for :math:`\phi` and :math:`{\bf U}` need to be solved simultaneously. The geometry of the system with initial condition is shown below.

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,21 +23,23 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.graphviz',
-              'sphinxcontrib.youtube',
-              'sphinxcontrib.bibtex',
-              'sphinxcontrib.inkscapeconverter',
-              'numpydoc']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.graphviz',
+    'sphinxcontrib.youtube',
+    'sphinxcontrib.bibtex',
+    'sphinxcontrib.inkscapeconverter',
+    'numpydoc'
+]
 
 mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-chtml.min.js'
 
 mathjax3_config = {
-  'loader': {'load': ['[tex]/mathtools']},
-  'tex': {'packages': {'[+]': ['mathtools']}}
+    'loader': {'load': ['[tex]/mathtools']},
+    'tex': {'packages': {'[+]': ['mathtools']}}
 }
 
 # Both the class’ and the __init__ method’s docstring are concatenated and
@@ -197,12 +199,9 @@
 
 # -- Options for LaTeX output --------------------------------------------
 
-# ~ latex_engine = 'lualatex'
-# ~ latex_use_xindy = False
-
 latex_additional_files = [
-        '_static/sphinxpoptitle.sty'
-    ]
+    '_static/sphinxpoptitle.sty'
+]
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
@@ -245,14 +244,15 @@
 
     'extrapackages': r'''\usepackage{mathtools}''',
 
-    'maketitle' : r'\sphinxpoptitlepages'
+    'maketitle': r'\sphinxpoptitlepages',
+
+    'makeindex': r'\usepackage[columns=1]{idxlayout}\makeindex'
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ('book', 'Firedrake.tex', u'User Manual',
-     ' \\and '.join(author_list), 'manual'),
+    ('book', 'Firedrake.tex', u'User Manual', r' \and '.join(author_list), 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -261,7 +261,7 @@
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = True
+#latex_use_parts = False
 
 # If true, show page references after internal links.
 #latex_show_pagerefs = False
@@ -282,8 +282,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'firedrake', u'Firedrake Documentation',
-     author, 1)
+    ('index', 'firedrake', u'Firedrake Documentation', author, 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -295,11 +294,15 @@
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
-texinfo_documents = [
-    ('index', 'Firedrake', u'Firedrake Documentation',
-     author, 'Firedrake', 'One line description of project.',
-     'Miscellaneous'),
-]
+texinfo_documents = [(
+    'index',
+    'Firedrake',
+    u'Firedrake Documentation',
+    author,
+    'Firedrake',
+    'One line description of project.',
+    'Miscellaneous'
+),]
 
 # Documents to append as an appendix to all manuals.
 #texinfo_appendices = []

diff --git a/docs/source/team.ini b/docs/source/team.ini
@@ -1,4 +1,5 @@
 [a]
+# A section for short links
 icl: http://www.imperial.ac.uk
 gh: https://github.com
 
@@ -43,7 +44,7 @@ Sophia Vorderwuelbecke: https://www.imperial.ac.uk/people/s.vorderwuelbecke18
 Tom Gregory: https://www.imperial.ac.uk/people/t.gregory18
 Jack Betteridge: https://www.imperial.ac.uk/people/j.betteridge, https://upload.wikimedia.org/wikipedia/commons/thumb/a/a1/Mallard2.jpg/632px-Mallard2.jpg
 Daniel Shapero: http://psc.apl.uw.edu/people/investigators/daniel-shapero/
-Reuben Hill: https://www.imperial.ac.uk/people/reuben.hill10
+Reuben Nixon-Hill: https://www.imperial.ac.uk/people/reuben.hill10
 Connor Ward: https://www.imperial.ac.uk/people/c.ward20
 
 [inactive-team]
@@ -110,7 +111,7 @@ Andrew McRae:
 Oliver Meister: https://www5.in.tum.de/wiki/index.php/Dipl.-Inf._Oliver_Meister
 Lawrence Mitchell:
 Eike Mueller:
-Reuben W. Nixon-Hill:
+Reuben Nixon-Hill:
 Alberto Paganini: https://www2.le.ac.uk/departments/mathematics/extranet/staff-material/staff-profiles/alberto-paganini
 Francis Poulin:
 Florian Rathgeber:

diff --git a/docs/source/team.rst_t b/docs/source/team.rst_t
@@ -1,5 +1,3 @@
-:orphan:
-
 ..
    This file is generated by team.py using the team.rst_t template and team.ini.
       DO NOT EDIT DIRECTLY

diff --git a/firedrake/preconditioners/pcd.py b/firedrake/preconditioners/pcd.py
@@ -17,8 +17,9 @@ class PCDPC(PCBase):
 
        S^{-1} \sim K^{-1} F_p M^{-1}
 
-    Where :math:`K = \\nabla^2`, :math:`M = \mathbb{I}` and
-    :math:`F_p = 1/\mathrm{Re} \\nabla^2 + u\cdot\\nabla`.
+    Where :math:`K = \nabla^2`,
+    :math:`F_p = (1/\mathrm{Re}) \nabla^2 + u\cdot\nabla`
+    and :math:`M = \mathbb{I}`.
 
     The inverse of :math:`K` is approximated by a KSP which can be
     controlled using the options prefix ``pcd_Kp_``.

diff --git a/firedrake/slate/slate.py b/firedrake/slate/slate.py
@@ -570,7 +570,7 @@ def _key(self):
 
 
 class Block(TensorBase):
-    """This class represents a tensor corresponding
+    r"""This class represents a tensor corresponding
     to particular block of a mixed tensor. Depending on
     the indices provided, the subblocks can span multiple
     test/trial spaces.
@@ -600,21 +600,21 @@ class Block(TensorBase):
 
     .. math::
 
-      \\begin{bmatrix}
+      \begin{bmatrix}
             A & B & C \\
             D & E & F \\
             G & H & J
-      \\end{bmatrix}
+      \end{bmatrix}
 
     Providing the 2-tuple ((0, 1), (0, 1)) returns a tensor
     corresponding to the upper 2x2 block:
 
     .. math::
 
-       \\begin{bmatrix}
+       \begin{bmatrix}
             A & B \\
             D & E
-       \\end{bmatrix}
+       \end{bmatrix}
 
     More generally, argument indices of the form `(idr, idc)`
     produces a tensor of block-size `len(idr)` x `len(idc)`

diff --git a/firedrake/slate/static_condensation/la_utils.py b/firedrake/slate/static_condensation/la_utils.py
@@ -454,10 +454,10 @@ def build_schur(self, rhs, non_zero_saddle_rhs=None):
 
         .. code-block:: text
 
-                A.inv = [[I, -A00.inv * A01]    *   [[A00.inv, 0    ]   *   [[I,             0]
-                        [0,  I             ]]       [0,        S.inv]]      [-A10* A00.inv,  I]]
-                        --------------------        -----------------       -------------------
-                        block1                      block2                  block3
+                A.inv=[[I, -A00.inv * A01] * [[A00.inv, 0    ] * [[I,            0]
+                      [0,  I             ]]  [0,        S.inv]]  [-A10* A00.inv, I]]
+                      --------------------   -----------------   ------------------
+                             block1                block2              block3
                 with the (inner) schur complement S = A11 - A10 * A00.inv * A01
         """