From fc8d4b52648dbcc64ad7d9f79f22cd53ce036166 Mon Sep 17 00:00:00 2001 From: Rohit Kakodkar Date: Mon, 4 Nov 2024 09:54:52 -0500 Subject: [PATCH] Fixed example03 | added copybutton --- docs/conf.py | 1 + docs/cookbooks/example_02.rst | 2 +- docs/cookbooks/example_03.rst | 90 ++-- docs/meshfem2d/internal_mesher.rst | 2 +- docs/parameter_documentation/receivers.rst | 4 +- docs/requirements.txt | 1 + poetry.lock | 533 +++++++++++++++++---- pyproject.toml | 4 + 8 files changed, 502 insertions(+), 135 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 2010471b..38557d48 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -43,6 +43,7 @@ "sphinx_sitemap", "sphinx.ext.inheritance_diagram", "breathe", + "sphinx_copybutton", ] # Add any paths that contain templates here, relative to this directory. diff --git a/docs/cookbooks/example_02.rst b/docs/cookbooks/example_02.rst index eaf541b2..d94b1f78 100644 --- a/docs/cookbooks/example_02.rst +++ b/docs/cookbooks/example_02.rst @@ -252,7 +252,7 @@ To execute the mesher run Make sure either your are in the build directory of SPECFEM2D kokkos or the build directory is added to your ``PATH``. -Note the path of the database file and :ref:`stations_file` generated after successfully running the mesher. +Note the path of the database file and a stations file generated after successfully running the mesher. Defining the source ~~~~~~~~~~~~~~~~~~~ diff --git a/docs/cookbooks/example_03.rst b/docs/cookbooks/example_03.rst index ec6809ce..2e4b9a9d 100644 --- a/docs/cookbooks/example_03.rst +++ b/docs/cookbooks/example_03.rst @@ -296,21 +296,21 @@ To store the wavefield at the last time step, we need to set the following param Lastly we define the source: .. code-block:: yaml - :caption: sources.yaml - - number-of-sources: 1 - sources: - - force: - x: 50000 - z: 40000 - source_surf: false - angle: 270.0 - vx: 0.0 - vz: 0.0 - Ricker: - factor: 0.75e+10 - tshift: 0.0 - f0: 0.42 + :caption: forward_sources.yaml + + number-of-sources: 1 + sources: + - force: + x: 50000 + z: 40000 + source_surf: false + angle: 270.0 + vx: 0.0 + vz: 0.0 + Ricker: + factor: 0.75e+10 + tshift: 0.0 + f0: 0.42 With the above input files, we can run the forward simulation. @@ -355,36 +355,36 @@ Now finally we can run the adjoint simulation. We use the same mesh database as 1. The adjoint sources are added to the sources file. .. code-block:: yaml - :caption: sources.yaml - - number-of-sources: 2 - sources: - - force: - x: 50000 - z: 40000 - source_surf: false - angle: 270.0 - vx: 0.0 - vz: 0.0 - Ricker: - factor: 0.75e+10 - tshift: 0.0 - f0: 0.42 - - - adjoint-source: - station_name: AA - network_name: S0001 - x: 150000 - z: 40000 - source_surf: false - angle: 0.0 - vx: 0.0 - vz: 0.0 - External: - format: ascii - stf: - X-component: OUTPUT_FILES/adjoint_sources/S0001AA.BXX.adj - Z-component: OUTPUT_FILES/adjoint_sources/S0001AA.BXZ.adj + :caption: adjoint_sources.yaml + + number-of-sources: 2 + sources: + - force: + x: 50000 + z: 40000 + source_surf: false + angle: 270.0 + vx: 0.0 + vz: 0.0 + Ricker: + factor: 0.75e+10 + tshift: 0.0 + f0: 0.42 + + - adjoint-source: + station_name: AA + network_name: S0001 + x: 150000 + z: 40000 + source_surf: false + angle: 0.0 + vx: 0.0 + vz: 0.0 + External: + format: ascii + stf: + X-component: OUTPUT_FILES/adjoint_sources/S0001AA.BXX.adj + Z-component: OUTPUT_FILES/adjoint_sources/S0001AA.BXZ.adj The adjoint sources require an external source time function generated during the previous step. The source time function is stored as a trace in ASCII format. Where the ``BXX`` is the X-component of the adjoint source and ``BXZ`` is the Z-component of the adjoint source. diff --git a/docs/meshfem2d/internal_mesher.rst b/docs/meshfem2d/internal_mesher.rst index 29925fa4..cf476f73 100644 --- a/docs/meshfem2d/internal_mesher.rst +++ b/docs/meshfem2d/internal_mesher.rst @@ -96,4 +96,4 @@ The region is described using a string. - ``nxmax``: Integer value describing the x-coordinate of the spectral element at the top right corner of the region. - ``nzmin``: Integer value describing the z-coordinate of the spectral element at the bottom left corner of the region. - ``nzmax``: Integer value describing the z-coordinate of the spectral element at the top right corner of the region. - - ``material_number``: Integer value describing the type of material in the region. This value references the material number in the :ref:`velocity_model` section. + - ``material_number``: Integer value describing the type of material in the region. This value references the material number in the ``velocity_model``. diff --git a/docs/parameter_documentation/receivers.rst b/docs/parameter_documentation/receivers.rst index 816d48d3..4e28af9e 100644 --- a/docs/parameter_documentation/receivers.rst +++ b/docs/parameter_documentation/receivers.rst @@ -5,7 +5,7 @@ Receivers section defines receiver information required to calculate seismograms .. note:: - Please note that the :ref:`stations_file` is generated using SPECFEM2D mesh generator i.e. xmeshfem2d + Please note that the ``stations_file`` is generated using SPECFEM2D mesh generator i.e. xmeshfem2d **Parameter Name** : ``receivers`` ----------------------------------- @@ -23,7 +23,7 @@ Receivers section defines receiver information required to calculate seismograms **possible values** : [string] -**documentation** : Path to :ref:`stations_file` +**documentation** : Path to ``stations_file`` **Parameter Name** : ``receivers.angle`` ****************************************************** diff --git a/docs/requirements.txt b/docs/requirements.txt index dfc206a9..b55aacb5 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ breathe furo +sphinx-copybutton sphinx-sitemap diff --git a/poetry.lock b/poetry.lock index 0d3ecee7..cdaa792b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,6 +11,17 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] + [[package]] name = "babel" version = "2.16.0" @@ -215,6 +226,20 @@ files = [ {file = "clang_format-14.0.6-py2.py3-none-win_amd64.whl", hash = "sha256:d780c04334bca80f2b60d25bf53c37bd0618520ee295a7888a11f25bde114ac4"}, ] +[[package]] +name = "click" +version = "8.1.7" +description = "Composable command line interface toolkit" +optional = false +python-versions = ">=3.7" +files = [ + {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, + {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + [[package]] name = "colorama" version = "0.4.6" @@ -237,6 +262,23 @@ files = [ {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"}, ] +[[package]] +name = "doc8" +version = "0.11.2" +description = "Style checker for Sphinx (or other) RST documentation" +optional = false +python-versions = ">=3.6" +files = [ + {file = "doc8-0.11.2-py3-none-any.whl", hash = "sha256:9187da8c9f115254bbe34f74e2bbbdd3eaa1b9e92efd19ccac7461e347b5055c"}, + {file = "doc8-0.11.2.tar.gz", hash = "sha256:c35a231f88f15c204659154ed3d499fa4d402d7e63d41cba7b54cf5e646123ab"}, +] + +[package.dependencies] +docutils = "*" +Pygments = "*" +restructuredtext-lint = ">=0.7" +stevedore = "*" + [[package]] name = "docutils" version = "0.18.1" @@ -337,74 +379,109 @@ MarkupSafe = ">=2.0" [package.extras] i18n = ["Babel (>=2.7)"] +[[package]] +name = "markdown-it-py" +version = "3.0.0" +description = "Python port of markdown-it. 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