diff --git a/.gitignore b/.gitignore
index feac29bf0dc2a0c0ce9af09a2085e4cd718891ce..e090b1d87d5c4921b7bd12087cccd1b157c9cf07 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,5 @@ distribute*egg
distribute*tar.gz
a.out
*.vtu
+
+.cache
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bc7599d4ce9d16f916e91e1bb109ac4f426023ff..7c2f2c973ec844128cbbe291a6008a1b894344a0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -34,3 +34,12 @@ Python 3.5 POCL:
- pocl
except:
- tags
+Documentation:
+ script:
+ - EXTRA_INSTALL="numpy"
+ - curl -L -O -k https://gitlab.tiker.net/inducer/ci-support/raw/master/build-docs.sh
+ - ". ./build-docs.sh"
+ tags:
+ - python3.5
+ only:
+ - master
diff --git a/doc/index.rst b/doc/index.rst
index f652d1ba9f72dffe21584f07737ebf1a7b40c4a9..4bde9b27731468d2d65b2fe35c3ee887242debea 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -8,6 +8,7 @@ Contents:
mesh
discretization
+ misc
Indices and tables
==================
diff --git a/doc/misc.rst b/doc/misc.rst
new file mode 100644
index 0000000000000000000000000000000000000000..488262acbc29882a93c25d4ba137d77ac37e8660
--- /dev/null
+++ b/doc/misc.rst
@@ -0,0 +1,79 @@
+.. _installation:
+
+Installation
+============
+
+This command should install :mod:`meshmode`::
+
+ pip install meshmode
+
+(Note the extra "."!)
+
+You may need to run this with :command:`sudo`.
+If you don't already have `pip <https://pypi.python.org/pypi/pip>`_,
+run this beforehand::
+
+ curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
+ python get-pip.py
+
+For a more manual installation, `download the source
+<http://pypi.python.org/pypi/meshmode>`_, unpack it, and say::
+
+ python setup.py install
+
+You may also clone its git repository::
+
+ git clone --recursive git://github.com/inducer/meshmode
+ git clone --recursive http://git.tiker.net/trees/meshmode.git
+
+User-visible Changes
+====================
+
+Version 2016.1
+--------------
+.. note::
+
+ This version is currently under development. You can get snapshots from
+ meshmode's `git repository <https://github.com/inducer/meshmode>`_
+
+.. _license:
+
+Licensing
+=========
+
+:mod:`meshmode` is licensed to you under the MIT/X Consortium license:
+
+Copyright (c) 2014-16 Andreas Klöckner and Contributors.
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+
+Acknowledgments
+===============
+
+Andreas Klöckner's work on :mod:`meshmode` was supported in part by
+
+* US Navy ONR grant number N00014-14-1-0117
+* the US National Science Foundation under grant numbers DMS-1418961 and CCF-1524433.
+
+AK also gratefully acknowledges a hardware gift from Nvidia Corporation. The
+views and opinions expressed herein do not necessarily reflect those of the
+funding agencies.
diff --git a/doc/upload-docs.sh b/doc/upload-docs.sh
index 25c97f52894584dfd72f3955c20026f475136e39..2c219a8c84b8f6b1835a9fb6ffb25b2274461616 100755
--- a/doc/upload-docs.sh
+++ b/doc/upload-docs.sh
@@ -1,3 +1,3 @@
#! /bin/sh
-rsync --progress --verbose --archive --delete _build/html/* doc-upload:doc/meshmode
+rsync --verbose --archive --delete _build/html/* doc-upload:doc/meshmode
diff --git a/meshmode/discretization/connection/refinement.py b/meshmode/discretization/connection/refinement.py
index 75604ec05dd945cde45e0e6cdd55724f88083c3f..4477a9bfd0fdbf4e24659c059997e1e6156fb894 100644
--- a/meshmode/discretization/connection/refinement.py
+++ b/meshmode/discretization/connection/refinement.py
@@ -161,7 +161,9 @@ def make_refinement_connection(refiner, coarse_discr, group_factory):
coarse_mesh = refiner.get_previous_mesh()
fine_mesh = refiner.last_mesh
- assert coarse_discr.mesh is coarse_mesh
+ if coarse_discr.mesh != coarse_mesh:
+ raise ValueError(
+ "course_discr must live on the same mesh given to the refiner!")
from meshmode.discretization import Discretization
fine_discr = Discretization(
diff --git a/meshmode/discretization/visualization.py b/meshmode/discretization/visualization.py
index 956e301533b3222db7d50916ed381222b26e416a..d68ec0c58078e68417721c8205fc3f24021d0bad 100644
--- a/meshmode/discretization/visualization.py
+++ b/meshmode/discretization/visualization.py
@@ -291,7 +291,7 @@ def write_nodal_adjacency_vtk_file(file_name, mesh, compressor=None,):
nconnections = len(adj.neighbors)
connections = np.empty((nconnections, 2), dtype=np.int32)
- nb_starts = adj.neighbor_starts
+ nb_starts = adj.neighbors_starts
for iel in range(mesh.nelements):
connections[nb_starts[iel]:nb_starts[iel+1], 0] = iel
diff --git a/meshmode/mesh/__init__.py b/meshmode/mesh/__init__.py
index 4e2f1f0ace6ddf7ca50ca0d95fde980414563dcb..da0fdfe242536997dc3dc2f71c465f2eddf07560 100644
--- a/meshmode/mesh/__init__.py
+++ b/meshmode/mesh/__init__.py
@@ -490,6 +490,7 @@ class Mesh(Record):
face_id_dtype = np.int8
def __init__(self, vertices, groups, skip_tests=False,
+ node_vertex_consistency_tolerance=None,
nodal_adjacency=False,
facial_adjacency_groups=False,
boundary_tags=None,
@@ -500,6 +501,9 @@ class Mesh(Record):
:arg skip_tests: Skip mesh tests, in case you want to load a broken
mesh anyhow and then fix it inside of this data structure.
+ :arg node_vertex_consistency_tolerance: If *False*, do not check
+ for consistency between vertex and nodal data. If *None*, use
+ the (small, near FP-epsilon) tolerance.
:arg nodal_adjacency: One of three options:
*None*, in which case this information
will be deduced from vertex adjacency. *False*, in which case
@@ -576,15 +580,16 @@ class Mesh(Record):
)
if not skip_tests:
- assert _test_node_vertex_consistency(self)
+ assert _test_node_vertex_consistency(
+ self, node_vertex_consistency_tolerance)
for g in self.groups:
assert g.vertex_indices.dtype == self.vertex_id_dtype
if nodal_adjacency:
- assert nodal_adjacency.neighbor_starts.shape == (self.nelements+1,)
+ assert nodal_adjacency.neighbors_starts.shape == (self.nelements+1,)
assert len(nodal_adjacency.neighbors.shape) == 1
- assert nodal_adjacency.neighbor_starts.dtype == self.element_id_dtype
+ assert nodal_adjacency.neighbors_starts.dtype == self.element_id_dtype
assert nodal_adjacency.neighbors.dtype == self.element_id_dtype
if facial_adjacency_groups:
@@ -691,7 +696,7 @@ class Mesh(Record):
# {{{ node-vertex consistency test
-def _test_node_vertex_consistency_simplex(mesh, mgrp):
+def _test_node_vertex_consistency_simplex(mesh, mgrp, tol):
if mgrp.nelements == 0:
return True
@@ -710,7 +715,8 @@ def _test_node_vertex_consistency_simplex(mesh, mgrp):
np.sum((map_vertices - grp_vertices)**2, axis=0),
axis=-1))
- tol = 1e3 * np.finfo(per_element_vertex_errors.dtype).eps
+ if tol is None:
+ tol = 1e3 * np.finfo(per_element_vertex_errors.dtype).eps
from meshmode.mesh.processing import find_bounding_box
@@ -723,14 +729,17 @@ def _test_node_vertex_consistency_simplex(mesh, mgrp):
return True
-def _test_node_vertex_consistency(mesh):
+def _test_node_vertex_consistency(mesh, tol):
"""Ensure that order of by-index vertices matches that of mapped
unit vertices.
"""
+ if tol is False:
+ return
+
for mgrp in mesh.groups:
if isinstance(mgrp, SimplexElementGroup):
- assert _test_node_vertex_consistency_simplex(mesh, mgrp)
+ assert _test_node_vertex_consistency_simplex(mesh, mgrp, tol)
else:
from warnings import warn
warn("not implemented: node-vertex consistency check for '%s'"
diff --git a/meshmode/mesh/generation.py b/meshmode/mesh/generation.py
index 65761586e01c8b0aa60f82d6f8b4bc00941eeed7..ce2a5f236d0ec524a411c78c87b7904abd423db6 100644
--- a/meshmode/mesh/generation.py
+++ b/meshmode/mesh/generation.py
@@ -175,7 +175,10 @@ def qbx_peanut(t):
# {{{ make_curve_mesh
-def make_curve_mesh(curve_f, element_boundaries, order):
+def make_curve_mesh(curve_f, element_boundaries, order,
+ unit_nodes=None,
+ node_vertex_consistency_tolerance=None,
+ return_parametrization_points=False):
"""
:arg curve_f: A callable representing a parametrization for a curve,
accepting a vector of point locations and returning
@@ -183,15 +186,20 @@ def make_curve_mesh(curve_f, element_boundaries, order):
:arg element_boundaries: a vector of element boundary locations in
:math:`[0,1]`, in order. 0 must be the first entry, 1 the
last one.
- :returns: a :class:`meshmode.mesh.Mesh`
+ :arg unit_nodes: if given, the unit nodes to use. Must have shape
+ ``(dim, nnoodes)``.
+ :returns: a :class:`meshmode.mesh.Mesh`, or if *return_parametrization_points*
+ is True, a tuple ``(mesh, par_points)``, where *par_points* is an array of
+ parametrization points.
"""
assert element_boundaries[0] == 0
assert element_boundaries[-1] == 1
nelements = len(element_boundaries) - 1
- unodes = mp.warp_and_blend_nodes(1, order)
- nodes_01 = 0.5*(unodes+1)
+ if unit_nodes is None:
+ unit_nodes = mp.warp_and_blend_nodes(1, order)
+ nodes_01 = 0.5*(unit_nodes+1)
vertices = curve_f(element_boundaries)
@@ -200,7 +208,8 @@ def make_curve_mesh(curve_f, element_boundaries, order):
# (el_nr, node_nr)
t = el_starts[:, np.newaxis] + el_lengths[:, np.newaxis]*nodes_01
- nodes = curve_f(t.ravel()).reshape(vertices.shape[0], nelements, -1)
+ t = t.ravel()
+ nodes = curve_f(t).reshape(vertices.shape[0], nelements, -1)
from meshmode.mesh import Mesh, SimplexElementGroup
egroup = SimplexElementGroup(
@@ -210,12 +219,18 @@ def make_curve_mesh(curve_f, element_boundaries, order):
np.arange(1, nelements+1, dtype=np.int32) % nelements,
]).T,
nodes=nodes,
- unit_nodes=unodes)
+ unit_nodes=unit_nodes)
- return Mesh(
+ mesh = Mesh(
vertices=vertices, groups=[egroup],
nodal_adjacency=None,
- facial_adjacency_groups=None)
+ facial_adjacency_groups=None,
+ node_vertex_consistency_tolerance=node_vertex_consistency_tolerance)
+
+ if return_parametrization_points:
+ return mesh, t
+ else:
+ return mesh
# }}}
diff --git a/meshmode/mesh/io.py b/meshmode/mesh/io.py
index a5bbe20492ae25d59b6cf7a4a3cf2e2e2df4d4f4..f3cdaea853d0f9441d7d463f2155ba8d95004d1e 100644
--- a/meshmode/mesh/io.py
+++ b/meshmode/mesh/io.py
@@ -43,6 +43,7 @@ __doc__ = """
.. autofunction:: generate_gmsh
.. autofunction:: from_meshpy
.. autofunction:: from_vertices_and_simplices
+.. autofunction:: to_json
"""
@@ -314,4 +315,57 @@ def from_vertices_and_simplices(vertices, simplices, order=1, fix_orientation=Fa
# }}}
+# {{{ to_json
+
+def to_json(mesh):
+ """Return a JSON-able Python data structure for *mesh*. The structure directly
+ reflects the :class:`Mesh` data structure."""
+
+ def btag_to_json(btag):
+ if isinstance(btag, str):
+ return btag
+ else:
+ return btag.__name__
+
+ def group_to_json(group):
+ return {
+ "type": type(group).__name__,
+ "order": group.order,
+ "vertex_indices": group.vertex_indices.tolist(),
+ "nodes": group.nodes.tolist(),
+ "unit_nodes": group.unit_nodes.tolist(),
+ "element_nr_base": group.element_nr_base,
+ "node_nr_base": group.node_nr_base,
+ "dim": group.dim,
+ }
+
+ from meshmode import DataUnavailable
+
+ def nodal_adjacency_to_json(mesh):
+ try:
+ na = mesh.nodal_adjacency
+ except DataUnavailable:
+ return None
+
+ return {
+ "neighbors_starts": na.neighbors_starts.tolist(),
+ "neighbors": na.neighbors.tolist(),
+ }
+
+ return {
+ "version": 0,
+ "vertices": mesh.vertices.tolist(),
+ "groups": [group_to_json(group) for group in mesh.groups],
+ "nodal_adjacency": nodal_adjacency_to_json(mesh),
+ # not yet implemented
+ "facial_adjacency_groups": None,
+ "boundary_tags": [btag_to_json(btag) for btag in mesh.boundary_tags],
+ "btag_to_index": dict(
+ (btag_to_json(btag), value)
+ for btag, value in six.iteritems(mesh.btag_to_index)),
+ }
+
+# }}}
+
+
# vim: foldmethod=marker
diff --git a/meshmode/mesh/refinement/__init__.py b/meshmode/mesh/refinement/__init__.py
index 2154d45195412c6c012a54ace9b8fbcb07561055..cb001e3266192a9280e313ae95ef6b93ff988d7d 100644
--- a/meshmode/mesh/refinement/__init__.py
+++ b/meshmode/mesh/refinement/__init__.py
@@ -348,6 +348,10 @@ class Refiner(object):
indicating which elements should be split.
"""
+ if len(refine_flags) != self.last_mesh.nelements:
+ raise ValueError("length of refine_flags does not match "
+ "element count of last generated mesh")
+
#vertices and groups for next generation
nvertices = len(self.last_mesh.vertices[0])
@@ -845,7 +849,7 @@ class Refiner(object):
assert neighbors_starts[-1] == len(neighbors)
from meshmode.mesh import NodalAdjacency
- return NodalAdjacency(neighbor_starts=neighbors_starts, neighbors=neighbors)
+ return NodalAdjacency(neighbors_starts=neighbors_starts, neighbors=neighbors)
# }}}
diff --git a/meshmode/mesh/refinement/utils.py b/meshmode/mesh/refinement/utils.py
index 9a78c31d6cd2dbe5bdb2f3729815b06630c96c7f..0d0476f3454a7079ebd4df3b1ace1b604355edde 100644
--- a/meshmode/mesh/refinement/utils.py
+++ b/meshmode/mesh/refinement/utils.py
@@ -64,7 +64,7 @@ def check_nodal_adj_against_geometry(mesh, tol=1e-12):
for igrp, grp in enumerate(mesh.groups):
for iel_grp in range(grp.nelements):
iel_g = group_and_iel_to_global_iel(igrp, iel_grp)
- nb_starts = nadj.neighbor_starts
+ nb_starts = nadj.neighbors_starts
for nb_iel_g in nadj.neighbors[nb_starts[iel_g]:nb_starts[iel_g+1]]:
connected_to_element_connectivity[iel_g].add(nb_iel_g)
diff --git a/meshmode/mesh/visualization.py b/meshmode/mesh/visualization.py
index caa9c1beb3cdb7123a3c9798ce04a3c882b14f93..601086c1570e1b2a87f57b68361010774a78aeb7 100644
--- a/meshmode/mesh/visualization.py
+++ b/meshmode/mesh/visualization.py
@@ -1,6 +1,4 @@
-from __future__ import division
-from __future__ import absolute_import
-from six.moves import range
+from __future__ import division, absolute_import
__copyright__ = "Copyright (C) 2014 Andreas Kloeckner"
@@ -25,6 +23,7 @@ THE SOFTWARE.
"""
import numpy as np
+from six.moves import range
# {{{ draw_2d_mesh
diff --git a/meshmode/version.py b/meshmode/version.py
index 1da70a1e09bc16f4b7e677505af6cf4dd4502b86..d26fbc2f9341a880b1119e7e6079bd51e59e11b9 100644
--- a/meshmode/version.py
+++ b/meshmode/version.py
@@ -1,2 +1,2 @@
-VERSION = (2015, 1)
+VERSION = (2016, 1)
VERSION_TEXT = ".".join(str(i) for i in VERSION)