{"action":"created","comment":{"url":"https://api.github.com/repos/mit-crpg/openmc/pulls/comments/109689916","pull_request_review_id":30808205,"id":109689916,"diff_hunk":"@@ -0,0 +1,353 @@\n+.. _usersguide_geometry:\n+\n+=================\n+Defining Geometry\n+=================\n+\n+.. currentmodule:: openmc\n+\n+--------------------\n+Surfaces and Regions\n+--------------------\n+\n+The geometry of a model in OpenMC is defined using `constructive solid\n+geometry`_ (CSG), also sometimes referred to as combinatorial geometry. CSG\n+allows a user to create complex regions using Boolean operators (intersection,\n+union, and complement) on simpler regions. In order to define a region that we\n+can assign to a cell, we must first define surfaces which bound the region. A\n+surface is a locus of zeros of a function of Cartesian coordinates\n+:math:`x,y,z`, e.g.\n+\n+- A plane perpendicular to the :math:`x` axis: :math:`x − x_0 = 0`\n+- A cylinder perpendicular to the :math:`z` axis: :math:`(x − x_0)^2 + (y −\n+  y_0)^2 − R^2 = 0`\n+- A sphere: :math:`(x − x_0)^2 + (y − y_0)^2 + (z − z_0)^2 − R^2 = 0`\n+\n+Defining a surface alone is not sufficient to specify a volume -- in order to\n+define an actual volume, one must reference the *half-space* of a surface. A\n+surface half-space is the region whose points satisfy a positive of negative\n+inequality of the surface equation. For example, for a sphere of radius one\n+centered at the origin, the surface equation is :math:`f(x,y,z) = x^2 + y^2 +\n+z^2 − 1 = 0`. Thus, we say that the negative half-space of the sphere, is\n+defined as the collection of points satisfying :math:`f(x,y,z) < 0`, which one\n+can reason is the inside of the sphere. Conversely, the positive half-space of\n+the sphere would correspond to all points outside of the sphere, satisfying\n+:math:`f(x,y,z) > 0`.\n+\n+In the Python API, surfaces are created via subclasses of\n+:class:`openmc.Surface`. The available surface types and their corresponding\n+classes are listed in the following table.\n+\n+.. table:: Surface types available in OpenMC.\n+\n+    +----------------------+------------------------------+---------------------------+\n+    | Surface              | Equation                     | Class                     |\n+    +======================+==============================+===========================+\n+    | Plane perpendicular  | :math:`x - x_0 = 0`          | :class:`openmc.XPlane`    |\n+    | to :math:`x`-axis    |                              |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Plane perpendicular  | :math:`y - y_0 = 0`          | :class:`openmc.YPlane`    |\n+    | to :math:`y`-axis    |                              |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Plane perpendicular  | :math:`z - z_0 = 0`          | :class:`openmc.ZPlane`    |\n+    | to :math:`z`-axis    |                              |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Arbitrary plane      | :math:`Ax + By + Cz = D`     | :class:`openmc.Plane`     |\n+    +----------------------+------------------------------+---------------------------+\n+    | Infinite cylinder    | :math:`(y-y_0)^2 + (z-z_0)^2 | :class:`openmc.XCylinder` |\n+    | parallel to          | - R^2 = 0`                   |                           |\n+    | :math:`x`-axis       |                              |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Infinite cylinder    | :math:`(x-x_0)^2 + (z-z_0)^2 | :class:`openmc.YCylinder` |\n+    | parallel to          | - R^2 = 0`                   |                           |\n+    | :math:`y`-axis       |                              |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Infinite cylinder    | :math:`(x-x_0)^2 + (y-y_0)^2 | :class:`openmc.ZCylinder` |\n+    | parallel to          | - R^2 = 0`                   |                           |\n+    | :math:`z`-axis       |                              |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Sphere               | :math:`(x-x_0)^2 + (y-y_0)^2 | :class:`openmc.Sphere`    |\n+    |                      | + (z-z_0)^2 - R^2 = 0`       |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Cone parallel to the | :math:`(y-y_0)^2 + (z-z_0)^2 | :class:`openmc.XCone`     |\n+    | :math:`x`-axis       | - R^2(x-x_0)^2 = 0`          |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Cone parallel to the | :math:`(x-x_0)^2 + (z-z_0)^2 | :class:`openmc.YCone`     |\n+    | :math:`y`-axis       | - R^2(y-y_0)^2 = 0`          |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | Cone parallel to the | :math:`(x-x_0)^2 + (y-y_0)^2 | :class:`openmc.ZCone`     |\n+    | :math:`z`-axis       | - R^2(z-z_0)^2 = 0`          |                           |\n+    +----------------------+------------------------------+---------------------------+\n+    | General quadric      | :math:`Ax^2 + By^2 + Cz^2 +  |  :class:`openmc.Quadric`  |\n+    | surface              | Dxy + Eyz + Fxz \\\\+Gx + Hy + |                           |\n+    |                      | Jz + K = 0`                  |                           |\n+    +----------------------+------------------------------+---------------------------+\n+\n+Each surface is characterized by several parameters. As one example, the\n+parameters for a sphere are the :math:`x,y,z` coordinates of the center of the\n+sphere and the radius of the sphere. All of these parameters can be set either\n+as optional keyword arguments to the class constructor or via attributes::\n+\n+  sphere = openmc.Sphere(R=10.0)\n+\n+  # ..or..\n+  sphere = openmc.Sphere()\n+  sphere.r = 10.0\n+\n+Once a surface has been created, half-spaces can be obtained by applying the\n+unary ``-`` or ``+`` operators, corresponding to the negative and positive\n+half-spaces, respectively. For example::\n+\n+   >>> sphere = openmc.Sphere(R=10.0)\n+   >>> inside_sphere = -sphere\n+   >>> outside_sphere = +sphere\n+   >>> type(inside_sphere)\n+   <class 'openmc.surface.Halfspace'>\n+\n+Instances of :class:`openmc.Halfspace` can be combined together using the\n+Boolean operators ``&`` (intersection), ``|`` (union), and ``~`` (complement)::\n+\n+  >>> inside_sphere = -openmc.Sphere()\n+  >>> above_plane = +openmc.ZPlane()\n+  >>> northern_hemisphere = inside_sphere & above_plane\n+  >>> type(northern_hemisphere)\n+  <class 'openmc.region.Intersection'>\n+\n+For many regions, a bounding-box can be determined automatically::\n+\n+  >>> northern_hemisphere.bounding_box\n+  (array([-1., -1., 0.]), array([1., 1., 1.]))\n+\n+Boundary Conditions\n+-------------------\n+\n+When a surface is created, by default particles that pass through the surface\n+will consider it to be transmissive, i.e., they pass through the surface\n+freely. If your model does not extend to infinity in all spatial dimensions, you\n+may want to specify different behavior for particles passing through a\n+surface. To specify a vacuum boundary condition, simply change the\n+:attr:`Surface.boundary_type` attribute to 'vacuum'::\n+\n+   outer_surface = openmc.Sphere(R=100.0, boundary_type='vacuum')\n+\n+   # ..or..\n+   outer_surface = openmc.Sphere(R=100.0)\n+   outer_surface.boundary_type = 'vacuum'\n+\n+Reflective and periodic boundary conditions can be set with the strings\n+'reflective' and 'periodic'. Vacuum and reflective boundary conditions can be\n+applied to any type of surface. Periodic boundary conditions can only be applied\n+to pairs of axis-aligned planar surfaces.\n+\n+.. _usersguide_cells:\n+\n+-----\n+Cells\n+-----\n+\n+Once you have a material created and a region of space defined, you need to\n+define a *cell* that assigns the material to the region. Cells are created using\n+the :class:`openmc.Cell` class::\n+\n+  fuel = openmc.Cell(fill=uo2, region=pellet)\n+\n+  # ..or..\n+  fuel = openmc.Cell()\n+  fuel.fill = uo2\n+  fuel.region = pellet\n+\n+In this example, an instance of :class:`openmc.Material` is assigned to the\n+:attr:`Cell.fill` attribute. One can also fill a cell with a :ref:`universe\n+<usersguide_universes>` or :ref:`lattice <usersguide_lattices>`.\n+\n+The classes :class:`Halfspace`, :class:`Intersection`, :class:`Union`, and\n+:class:`Complement` and all instances of :class:`openmc.Region` and can be\n+assigned to the :attr:`Cell.region` attribute.","path":"docs/source/usersguide/geometry.rst","position":165,"original_position":165,"commit_id":"973b66c1d065c730e1a56e4c5400157e87b4435a","original_commit_id":"973b66c1d065c730e1a56e4c5400157e87b4435a","user":{"login":"wbinventor","id":209492,"avatar_url":"https://avatars1.githubusercontent.com/u/209492?v=3","gravatar_id":"","url":"https://api.github.com/users/wbinventor","html_url":"https://github.com/wbinventor","followers_url":"https://api.github.com/users/wbinventor/followers","following_url":"https://api.github.com/users/wbinventor/following{/other_user}","gists_url":"https://api.github.com/users/wbinventor/gists{/gist_id}","starred_url":"https://api.github.com/users/wbinventor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wbinventor/subscriptions","organizations_url":"https://api.github.com/users/wbinventor/orgs","repos_url":"https://api.github.com/users/wbinventor/repos","events_url":"https://api.github.com/users/wbinventor/events{/privacy}","received_events_url":"https://api.github.com/users/wbinventor/received_events","type":"User","site_admin":false},"body":"It seems that class attributes can't be referenced via a hyperlink.","created_at":"2017-04-04T15:08:29Z","updated_at":"2017-04-04T15:08:30Z","html_url":"https://github.com/mit-crpg/openmc/pull/850#discussion_r109689916","pull_request_url":"https://api.github.com/repos/mit-crpg/openmc/pulls/850","_links":{"self":{"href":"https://api.github.com/repos/mit-crpg/openmc/pulls/comments/109689916"},"html":{"href":"https://github.com/mit-crpg/openmc/pull/850#discussion_r109689916"},"pull_request":{"href":"https://api.github.com/repos/mit-crpg/openmc/pulls/850"}}},"pull_request":{"url":"https://api.github.com/repos/mit-crpg/openmc/pulls/850","id":114063321,"html_url":"https://github.com/mit-crpg/openmc/pull/850","diff_url":"https://github.com/mit-crpg/openmc/pull/850.diff","patch_url":"https://github.com/mit-crpg/openmc/pull/850.patch","issue_url":"https://api.github.com/repos/mit-crpg/openmc/issues/850","number":850,"state":"open","locked":false,"title":"Big documentation update","user":{"login":"paulromano","id":743095,"avatar_url":"https://avatars2.githubusercontent.com/u/743095?v=3","gravatar_id":"","url":"https://api.github.com/users/paulromano","html_url":"https://github.com/paulromano","followers_url":"https://api.github.com/users/paulromano/followers","following_url":"https://api.github.com/users/paulromano/following{/other_user}","gists_url":"https://api.github.com/users/paulromano/gists{/gist_id}","starred_url":"https://api.github.com/users/paulromano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paulromano/subscriptions","organizations_url":"https://api.github.com/users/paulromano/orgs","repos_url":"https://api.github.com/users/paulromano/repos","events_url":"https://api.github.com/users/paulromano/events{/privacy}","received_events_url":"https://api.github.com/users/paulromano/received_events","type":"User","site_admin":false},"body":"This pull request is a big update of our user's guide and related documentation (closes #842). To summarize the documentation changes:\r\n\r\n- The user's guide is now written with the Python API in mind. The intimate details of the XML formats are now found in the 'File Format Specifications' area. A lot of it has been gutted and new sections were added (parallelism, volume calculations, scripts).\r\n- Three new example notebooks were added (TRISO, CANDU, and pin cell)\r\n- The MDGXS part II notebook was fixed (closes #845)\r\n- The nuclear data notebook was updated to show some of the ENDF-related capabilities as well as basic use of physical data (atomic masses, etc).\r\n\r\nThere are a few non-documentation changes as well:\r\n\r\n- `openmc-plot-mesh-tally` was not in a working state. It has now been fixed.\r\n- `Settings.output_path` was combined into `Settings.output`\r\n- If no spatial distribution is given for a source, a point source at the origin is assumed.\r\n- If no source is given at all, an isotropic, point source with a Watt fission spectrum is assumed.\r\n\r\nWord of advice to the reviewer -- you might want to just build the documentation and go through it rather than trying to figure things out based on the diff that github shows since a lot of files were moved.","created_at":"2017-04-04T03:16:02Z","updated_at":"2017-04-04T15:08:30Z","closed_at":null,"merged_at":null,"merge_commit_sha":"a3ad2fa0c8b06943aef5298e8622aaf93017567b","assignee":{"login":"wbinventor","id":209492,"avatar_url":"https://avatars1.githubusercontent.com/u/209492?v=3","gravatar_id":"","url":"https://api.github.com/users/wbinventor","html_url":"https://github.com/wbinventor","followers_url":"https://api.github.com/users/wbinventor/followers","following_url":"https://api.github.com/users/wbinventor/following{/other_user}","gists_url":"https://api.github.com/users/wbinventor/gists{/gist_id}","starred_url":"https://api.github.com/users/wbinventor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wbinventor/subscriptions","organizations_url":"https://api.github.com/users/wbinventor/orgs","repos_url":"https://api.github.com/users/wbinventor/repos","events_url":"https://api.github.com/users/wbinventor/events{/privacy}","received_events_url":"https://api.github.com/users/wbinventor/received_events","type":"User","site_admin":false},"assignees":[{"login":"wbinventor","id":209492,"avatar_url":"https://avatars1.githubusercontent.com/u/209492?v=3","gravatar_id":"","url":"https://api.github.com/users/wbinventor","html_url":"https://github.com/wbinventor","followers_url":"https://api.github.com/users/wbinventor/followers","following_url":"https://api.github.com/users/wbinventor/following{/other_user}","gists_url":"https://api.github.com/users/wbinventor/gists{/gist_id}","starred_url":"https://api.github.com/users/wbinventor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wbinventor/subscriptions","organizations_url":"https://api.github.com/users/wbinventor/orgs","repos_url":"https://api.github.com/users/wbinventor/repos","events_url":"https://api.github.com/users/wbinventor/events{/privacy}","received_events_url":"https://api.github.com/users/wbinventor/received_events","type":"User","site_admin":false}],"milestone":null,"commits_url":"https://api.github.com/repos/mit-crpg/openmc/pulls/850/commits","review_comments_url":"https://api.github.com/repos/mit-crpg/openmc/pulls/850/comments","review_comment_url":"https://api.github.com/repos/mit-crpg/openmc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/mit-crpg/openmc/issues/850/comments","statuses_url":"https://api.github.com/repos/mit-crpg/openmc/statuses/973b66c1d065c730e1a56e4c5400157e87b4435a","head":{"label":"paulromano:usersguide","ref":"usersguide","sha":"973b66c1d065c730e1a56e4c5400157e87b4435a","user":{"login":"paulromano","id":743095,"avatar_url":"https://avatars2.githubusercontent.com/u/743095?v=3","gravatar_id":"","url":"https://api.github.com/users/paulromano","html_url":"https://github.com/paulromano","followers_url":"https://api.github.com/users/paulromano/followers","following_url":"https://api.github.com/users/paulromano/following{/other_user}","gists_url":"https://api.github.com/users/paulromano/gists{/gist_id}","starred_url":"https://api.github.com/users/paulromano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paulromano/subscriptions","organizations_url":"https://api.github.com/users/paulromano/orgs","repos_url":"https://api.github.com/users/paulromano/repos","events_url":"https://api.github.com/users/paulromano/events{/privacy}","received_events_url":"https://api.github.com/users/paulromano/received_events","type":"User","site_admin":false},"repo":{"id":6039026,"name":"openmc","full_name":"paulromano/openmc","owner":{"login":"paulromano","id":743095,"avatar_url":"https://avatars2.githubusercontent.com/u/743095?v=3","gravatar_id":"","url":"https://api.github.com/users/paulromano","html_url":"https://github.com/paulromano","followers_url":"https://api.github.com/users/paulromano/followers","following_url":"https://api.github.com/users/paulromano/following{/other_user}","gists_url":"https://api.github.com/users/paulromano/gists{/gist_id}","starred_url":"https://api.github.com/users/paulromano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paulromano/subscriptions","organizations_url":"https://api.github.com/users/paulromano/orgs","repos_url":"https://api.github.com/users/paulromano/repos","events_url":"https://api.github.com/users/paulromano/events{/privacy}","received_events_url":"https://api.github.com/users/paulromano/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/paulromano/openmc","description":"OpenMC 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