From b08c822a9bc738edc4c594d48a0136229b9889b9 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Thu, 16 Jan 2020 11:58:39 -0700 Subject: [PATCH 1/8] Update documentation based on #58 This commit contains minor text updates; it doesn't include the reorg or updates to the CMF page suggested in #58; since those are bigger, I'll handle them separately. --- docs/source/bmi.getter_setter.rst | 8 ++++---- docs/source/bmi.grid_funcs.rst | 4 ++-- docs/source/bmi.implementation.rst | 5 +++++ docs/source/bmi.info_funcs.rst | 4 +++- docs/source/bmi.time_funcs.rst | 8 +++++--- docs/source/bmi.var_funcs.rst | 3 +++ docs/source/model_grids.rst | 8 ++++---- 7 files changed, 26 insertions(+), 14 deletions(-) diff --git a/docs/source/bmi.getter_setter.rst b/docs/source/bmi.getter_setter.rst index 9a832f8..311f04c 100644 --- a/docs/source/bmi.getter_setter.rst +++ b/docs/source/bmi.getter_setter.rst @@ -27,8 +27,8 @@ state variable can be changed or check the new data for validity. int get_value(in string name, in array<> dest); The `get_value` function takes a variable name and copies values into a -provided buffer. -The type and size of the buffer depend on the variable, +provided array parameter. +The type and size of the array parameter depend on the variable, and can be determined through :ref:`get_var_type`, :ref:`get_var_nbytes`, etc. Recall that arrays are always flattened in BMI, @@ -39,7 +39,7 @@ even if the model uses dimensional variables. * The *dest* argument must be defined and allocated before calling `get_value`. Whatever values it contains are overwritten in the call to `get_value`. -* In Python, the buffer is a :term:`numpy` array. +* In Python, the array parameter is a :term:`numpy` array. * In C++, `get_value` is a void function. * Depending on how a model is written, a variable may not be accessible until after the call to :ref:`initialize`. Likewise, the @@ -59,7 +59,7 @@ even if the model uses dimensional variables. The `get_value_ptr` function takes a variable name and returns a reference to a variable. -Unlike the buffer returned from :ref:`get_value`, +Unlike the array parameter returned from :ref:`get_value`, the reference always points to the current values of the variable, even if the model's state has changed. diff --git a/docs/source/bmi.grid_funcs.rst b/docs/source/bmi.grid_funcs.rst index 885082a..98b8958 100644 --- a/docs/source/bmi.grid_funcs.rst +++ b/docs/source/bmi.grid_funcs.rst @@ -49,7 +49,6 @@ is given in the :ref:`model_grids` section. **Implementation notes** -* This function is needed for every :ref:`grid type `. * In C++ and Python, the *type* argument is omitted and the grid type name is returned from the function. @@ -66,7 +65,8 @@ is given in the :ref:`model_grids` section. /* SIDL */ int get_grid_rank(in int grid, out int rank); -Given a :term:`grid identifier`, get the :term:`rank` of that grid as an integer. +Given a :term:`grid identifier`, get the :term:`rank` (the number of +dimensions) of that grid as an integer. A grid's rank determines the length of the return value of many of the following grid functions. diff --git a/docs/source/bmi.implementation.rst b/docs/source/bmi.implementation.rst index 0a51fd4..adc799b 100644 --- a/docs/source/bmi.implementation.rst +++ b/docs/source/bmi.implementation.rst @@ -34,6 +34,11 @@ here are some tips to help when writing a BMI for a model. responsibility to ensure that array information is flattened/redimensionalized in the correct order. +* Recall that models can have mulitple grids. This can be particularly + useful for defining :term:`exchange items ` that + don't vary over the model domain; e.g., a diffusivity -- just define + the variable on a separate :ref:`scalar grid `. + * Avoid using global variables, if possible. This isn't strictly a BMI requirement, but if a model only uses local variables, its BMI will be self-contained. This may allow multiple instances of the model to diff --git a/docs/source/bmi.info_funcs.rst b/docs/source/bmi.info_funcs.rst index 5ceab74..ed50df5 100644 --- a/docs/source/bmi.info_funcs.rst +++ b/docs/source/bmi.info_funcs.rst @@ -43,6 +43,7 @@ but it should be unique to prevent conflicts with other components. The number of variables the model can use from other models implementing a BMI. +Also the number of variables that can be set with :ref:`set_value`. **Implementation notes** @@ -64,6 +65,7 @@ implementing a BMI. The number of variables the model can provide other models implementing a BMI. +Also the number of variables that can be retrieved with :ref:`get_value`. **Implementation notes** @@ -101,7 +103,7 @@ Standard Names do not have to be used within the model. function in a vector, a standard container in the language. * In Python, the argument is omitted and the names are returned from the function in a tuple, a standard container in the language. -* A model may have no input variables. +* A model might have no input variables. [:ref:`info_funcs` | :ref:`basic_model_interface`] diff --git a/docs/source/bmi.time_funcs.rst b/docs/source/bmi.time_funcs.rst index 9ce26a5..51d4d95 100644 --- a/docs/source/bmi.time_funcs.rst +++ b/docs/source/bmi.time_funcs.rst @@ -61,8 +61,9 @@ The end time of the model. **Implementation notes** -* If the model doesn't define an end time, a large number (e.g., - 1.0e6) is typically chosen. +* If the model doesn't define an end time, a large number (e.g., the + largest floating point number supported on a platform) is typically + chosen. * In C++ and Python, the argument is omitted and the time is returned from the function. @@ -87,7 +88,8 @@ It's recommended to use `time unit conventions`_ from Unidata's **Implementation notes** * Avoid using `years` as a unit, if possible, since a year is - difficult to define precisely. + difficult to define precisely. UDUNITS defines a year as 365.2422 + days or 31556926 seconds. * In C++ and Python, the argument is omitted and the units are returned from the function. diff --git a/docs/source/bmi.var_funcs.rst b/docs/source/bmi.var_funcs.rst index 6f42c2d..24c93b8 100644 --- a/docs/source/bmi.var_funcs.rst +++ b/docs/source/bmi.var_funcs.rst @@ -160,6 +160,9 @@ element the variable is defined. Valid return values are: * In C++ and Python, the *location* argument is omitted and the location is returned from the function. +* If the given variable is a scalar (i.e., defined on a :ref:`scalar + grid `), the return from this function is + ignored. [:ref:`var_funcs` | :ref:`basic_model_interface`] diff --git a/docs/source/model_grids.rst b/docs/source/model_grids.rst index c4d422e..53045b5 100644 --- a/docs/source/model_grids.rst +++ b/docs/source/model_grids.rst @@ -33,10 +33,10 @@ its length would be listed first. .. note:: - The grid shape is the number of :term:`nodes ` in the - coordinate directions, not the number of cells or - elements. It is possible for grid values to be - associated with the nodes or with the cells. + The grid shape is the number of rows and columns of :term:`nodes + `, as opposed to other types of element (such as cells or + faces). It is possible for grid values to be associated with the + nodes or with the cells. .. _uniform_rectilinear: From 0b2dc35c00d1e099e9207bd83cf89e2d7ce3b320 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Thu, 16 Jan 2020 14:43:50 -0700 Subject: [PATCH 2/8] Revise the Additional Topics section * Talk about *pymt* instead of the CMF * Moved advice on Standard Names to best practices doc * Added Help section * Added sentence in main body linking to best practices doc --- docs/source/bmi.implementation.rst | 13 +++++ docs/source/bmi.spec.rst | 3 ++ docs/source/csdms.rst | 85 +++++++++++------------------- docs/source/index.rst | 15 ++++++ 4 files changed, 62 insertions(+), 54 deletions(-) diff --git a/docs/source/bmi.implementation.rst b/docs/source/bmi.implementation.rst index adc799b..345f1ae 100644 --- a/docs/source/bmi.implementation.rst +++ b/docs/source/bmi.implementation.rst @@ -25,6 +25,18 @@ here are some tips to help when writing a BMI for a model. the BMI specifies are the names of the functions, their arguments, and their return values. +* :term:`Standard Names` are not required for naming a model's + :term:`exchange items `. However, the use of + standardized names makes it easier for a framework (or a human) to + match input and output variables between models. + +* Don't change the variable names you currently use within your model + to :term:`Standard Names`. Standard Names are too long and + cumbersome to be used within a model code. Instead, you find a + `matching`_ Standard Name for each variable in your model and then + write your BMI functions to accept the Standard Names and map them + to your model's internal names. + * Constructs and features that are natural for the language should be used when implementing a BMI. BMI strives to be developer-friendly. @@ -78,3 +90,4 @@ here are some tips to help when writing a BMI for a model. .. _C++: https://github.com/csdms/bmi-example-cxx .. _Fortran: https://github.com/csdms/bmi-example-fortran .. _Python: https://github.com/csdms/bmi-example-python +.. _matching: https://github.com/csdms/standard_names_registry diff --git a/docs/source/bmi.spec.rst b/docs/source/bmi.spec.rst index 1e53744..9a471cb 100644 --- a/docs/source/bmi.spec.rst +++ b/docs/source/bmi.spec.rst @@ -59,6 +59,9 @@ Following the table is a detailed description of each function, including the function prototype in SIDL, grouped by functional category. +Be sure to check out the collected wisdom of our :ref:`best practices +document ` for tips on implementing a BMI. + .. table:: **Table 2:** Summary of BMI functions. :align: center :widths: 30, 70 diff --git a/docs/source/csdms.rst b/docs/source/csdms.rst index 012d081..11e3a46 100644 --- a/docs/source/csdms.rst +++ b/docs/source/csdms.rst @@ -1,26 +1,24 @@ -.. _cmf: - -The CSDMS Modeling Framework -============================ - -Any model that provides the BMI functions can be easily converted -to a CSDMS plug-and-play component within the CSDMS Modeling -Framework (CMF). This conversion/wrapping process can be done -automatically using the CSDMS Babelizer tool, which generates -bindings for all of the CSDMS supported languages, so that the -model becomes a plug-in for within the CSDMS framework. - -.. - "becomes a plug-in for"? I don't understand. - -Any model that provides the BMI functions should also be -straightforward to ingest as a component into other component-based -modeling frameworks. For example, all model coupling frameworks -use Model Control Functions very similar to those of the BMI, -so providing them helps get a model ready for *plug-and-play* into -any framework. - -Within the CMF, a component automatically gains many +.. _pymt: + +The Python Modeling Toolkit (*pymt*) +==================================== + +Any model that provides the BMI functions can be converted +to a plug-and-play component +that runs in the CSDMS `Python Modeling Toolkit`_ (*pymt*). +This conversion process can be done +automatically with the CSDMS Babelizer tool, which generates +a Python package from any of the CSDMS supported languages +(currently C, C++, Fortran, and Python). +Some additional metadata is also required, +describes such things as: + +* the model author(s), license, description, web page, etc. +* how the model is built and how it can be linked +* template input files +* description of input parameters (description, units, ranges, etc.) + +Within *pymt*, a component automatically gains many new capabilities. This includes the ability to be coupled to other models even if their (1) programming language, (2) variable names, (3) variable units, (4) time-stepping scheme or (5) @@ -28,39 +26,18 @@ computational grid is different. It also gains: * the ability to write output variables to standardized NetCDF files, -* a graphical user interface (GUI), * unit conversion tools, -* time interpolation - - -CSDMS Standard Names --------------------- - -Note that the *name* parameter in many of the BMI functions -refers to a standardized variable name from the -`CSDMS_Standard_Names `_. -These names are not *required* by the BMI to be CSDMS Standard Names, -however, the use of standardized names makes it possible for a -framework (or a human) to more easily match components' input and -output variables. - -.. note: - - Note you **do not** change the variable names that you currently - use within your model. The standard names are too long to be - used within your model code. Instead, you find a matching CSDMS - Standard Name for each variable in your model and then write your - BMI functions to accept the standard names and map them to your - model's internal names. +* time interpolation, +* all the data analysis and visualization tools available in Python, +* the ability to run in a Jupyter Notebook +If you have a model with a BMI, +and would like to componentize it and add it to *pymt*, +please contact us through the `CSDMS Help Desk`_. +We'd be happy (and excited) to help! -Model metadata --------------- -For a model to be incorporated into the CSDMS framework, some additional -metadata is required. This metadata describes such things as: +.. Links: -* The model author(s), license, description, web page, etc. -* How the model is built and how it can be linked -* Template input files -* Description of input parameters (description, units, ranges, etc.) +.. _Python Modeling Toolkit: https://pymt.readthedocs.io +.. _CSDMS Help Desk: https://github.com/csdms/help-desk diff --git a/docs/source/index.rst b/docs/source/index.rst index 64b68e9..4ab6152 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -21,6 +21,16 @@ Additional Topics glossary references +Help +==== + +Adding a BMI to a model can be a daunting task. +If you'd like assistance, +CSDMS can help. +Depending on your need, we can provide advice or consulting services. +Feel free to contact us through the `CSDMS Help Desk`_. + + Project Information =================== @@ -31,3 +41,8 @@ Project Information contributing conduct credits + + +.. Links: + +.. _CSDMS Help Desk: https://github.com/csdms/help-desk From 5fc7766382a0a17b1c41806cdb9debe3ce6d5a8f Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Thu, 30 Jan 2020 15:56:55 -0700 Subject: [PATCH 3/8] Fix incorrect signature on connectivity functions The connectivity functions should take as input a 1d array of the correct size to hold the connectivity list. The array parameter had been listed as output. --- bmi.sidl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/bmi.sidl b/bmi.sidl index 9023196..950451a 100644 --- a/bmi.sidl +++ b/bmi.sidl @@ -62,9 +62,9 @@ package csdms version 2.0 { int get_grid_node_count(in int grid, out int count); int get_grid_edge_count(in int grid, out int count); int get_grid_face_count(in int grid, out int count); - int get_grid_edge_nodes(in int grid, out array edge_nodes); - int get_grid_face_edges(in int grid, out array face_edges); - int get_grid_face_nodes(in int grid, out array face_nodes); - int get_grid_nodes_per_face(in int grid, out array nodes_per_face); + int get_grid_edge_nodes(in int grid, in array edge_nodes); + int get_grid_face_edges(in int grid, in array face_edges); + int get_grid_face_nodes(in int grid, in array face_nodes); + int get_grid_nodes_per_face(in int grid, in array nodes_per_face); } } From e1e1ffb7780005e2f9cd67ceb3d27bc31788acf4 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Thu, 30 Jan 2020 15:59:03 -0700 Subject: [PATCH 4/8] Update docs to show correct signature for connectivity functions Also added a more detail to the descriptions for these functions. --- docs/source/bmi.grid_funcs.rst | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/docs/source/bmi.grid_funcs.rst b/docs/source/bmi.grid_funcs.rst index 98b8958..ffa39fd 100644 --- a/docs/source/bmi.grid_funcs.rst +++ b/docs/source/bmi.grid_funcs.rst @@ -366,12 +366,13 @@ Get the number of :term:`faces ` in the grid. .. code-block:: java /* SIDL */ - int get_grid_edge_nodes(in int grid, out array edge_nodes); + int get_grid_edge_nodes(in int grid, in array edge_nodes); Get the edge-node connectivity. For each edge, connectivity is given as node at edge tail, followed by -node at edge head. +node at edge head. The total length of the array is +2 * :ref:`get_grid_edge_count`. **Implementation notes** @@ -391,7 +392,7 @@ node at edge head. .. code-block:: java /* SIDL */ - int get_grid_face_edges(in int grid, out array face_edges); + int get_grid_face_edges(in int grid, in array face_edges); Get the face-edge connectivity. @@ -413,12 +414,14 @@ Get the face-edge connectivity. .. code-block:: java /* SIDL */ - int get_grid_face_nodes(in int grid, out array face_nodes); + int get_grid_face_nodes(in int grid, in array face_nodes); Get the face-node connectivity. For each face, the nodes (listed in a counter-clockwise direction) that form the boundary of the face. +For a grid of quadrilaterals, +the total length of the array is 4 * :ref:`get_grid_face_count`. **Implementation notes** @@ -438,10 +441,12 @@ that form the boundary of the face. .. code-block:: java /* SIDL */ - int get_grid_nodes_per_face(in int grid, out array nodes_per_face); + int get_grid_nodes_per_face(in int grid, in array nodes_per_face); Get the number of nodes for each face. +The number of edges per face is equal to the number of nodes per face. + **Implementation notes** * This function is used for describing :ref:`unstructured From d9a51a2b7ef4444915ba383cdcff44b1224c694b Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Tue, 11 Feb 2020 12:16:59 -0700 Subject: [PATCH 5/8] Add section on how to start writing a BMI (#63) * Add section on how to start writing a BMI This was a request from Michael Young (UT-Austin), and it was written by @gregtucker. * Link how to start guide into main text * Use sensible file and link names for getting started and best practices docs * Add getting started and best practices docs to sidebar links * Call out getting started and best practices docs more strongly in main text * Add definition for SIDL to glossary, link --- AUTHORS.rst | 1 + docs/source/_templates/links.html | 6 +- ...lementation.rst => bmi.best_practices.rst} | 2 +- docs/source/bmi.getting_started.rst | 67 +++++++++++++++++++ docs/source/bmi.grid_funcs.rst | 2 +- docs/source/bmi.spec.rst | 15 +++-- docs/source/glossary.rst | 26 ++++++- docs/source/index.rst | 3 +- 8 files changed, 111 insertions(+), 11 deletions(-) rename docs/source/{bmi.implementation.rst => bmi.best_practices.rst} (99%) create mode 100644 docs/source/bmi.getting_started.rst diff --git a/AUTHORS.rst b/AUTHORS.rst index bc1f45d..25c65c3 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -19,6 +19,7 @@ Contributors * Scott Peckham * Mark Piper * Mike Taves +* Greg Tucker If you have contributed to the BMI package and your name is missing, please send an email to the coordinators, or open a pull request diff --git a/docs/source/_templates/links.html b/docs/source/_templates/links.html index 8dedb42..886e334 100644 --- a/docs/source/_templates/links.html +++ b/docs/source/_templates/links.html @@ -1,7 +1,9 @@

Useful Links

diff --git a/docs/source/bmi.implementation.rst b/docs/source/bmi.best_practices.rst similarity index 99% rename from docs/source/bmi.implementation.rst rename to docs/source/bmi.best_practices.rst index 345f1ae..dcf5209 100644 --- a/docs/source/bmi.implementation.rst +++ b/docs/source/bmi.best_practices.rst @@ -1,4 +1,4 @@ -.. _implementation: +.. _best_practices: BMI best practices ================== diff --git a/docs/source/bmi.getting_started.rst b/docs/source/bmi.getting_started.rst new file mode 100644 index 0000000..08fb683 --- /dev/null +++ b/docs/source/bmi.getting_started.rst @@ -0,0 +1,67 @@ +.. _getting_started: + +How to get started +================== + +If you want to add a Basic Model Interface (BMI) to your own model, +here are some tips on getting started. + +1. Take a look at the list of BMI +:ref:`control functions and their descriptions ` +to get an idea of what these functions are meant to do +and how they provide a standard set of controls for your model. + +2. On the theory that it's often easier to start with an example and +modify it, we recommend starting with a copy of +the :ref:`BMI example code`---look for the version +written in the language of your model---to use as a template. +Each link points to a GitHub repository that includes an +example model called "heat", and a corresponding BMI in a file called +"bmi_heat" (so, for example, the Python version is "bmi_heat.py", +the C version is "bmi_heat.c" and "bmi_heat.h", etc.). +You can grab copies by cloning the repository to your local machine +and doing a file copy from there, +or by selecting, copying, and pasting the code directly +into your favorite editor. + +3. Modify each of the BMI functions in the template file so that it works +on your model, rather than on the original "heat" example. Depending +on how your model code is structured, you may need to do some +:term:`refactoring `. +For example, if your model's initialization and main +processing are lumped together in the same body of code, you will need +to divide them into separate functions. Our experience is that codes +that are already modular usually need little or no modification, +whereas codes that are more monolithic tend to require a lot more +refactoring (but that is probably worthwhile anyway for the sake of +the quality and sustainability of the code!). +Each case is a bit different. +Be sure to check out our :ref:`BMI best practices ` document +for tips. +We encourage you to contact us with questions by posting an +issue on the `CSDMS Help Desk`_. + +4. Test it out. Try writing a program or script that initializes your +model with a simple test case using the :ref:`initialize` function, +runs it with the :ref:`update` or :ref:`update_until` functions, +and exchanges data using :ref:`get_value` and :ref:`set_value`. +Run a test to verify that you get the same output from your BMI'd model +that you got from it prior to BMI'ing. +(Note: we recommend writing a :term:`unit test` for each of your +BMI functions; to learn more about unit tests, +check out our `webinar`_). + +5. *(Optional but cool)* With a few additional steps, you can make your +model operate as a :ref:`pymt ` component, +so you can drive it directly from a Python shell, +and write Python scripts to couple it with other models. +(Learn more about *pymt* :ref:`here `, and through its `documentation`_.) +The CSDMS Integration Facility team can provide help and guidance on this +process: just contact us through the `CSDMS Help Desk`_. + + +.. Links: + +.. _CSDMS Help Desk: https://github.com/csdms/help-desk +.. _webinar: https://csdms.colorado.edu/wiki/Presenters-0478 +.. _documentation: https://pymt.readthedocs.io diff --git a/docs/source/bmi.grid_funcs.rst b/docs/source/bmi.grid_funcs.rst index ffa39fd..776f8e9 100644 --- a/docs/source/bmi.grid_funcs.rst +++ b/docs/source/bmi.grid_funcs.rst @@ -20,7 +20,7 @@ on which a constant thermal diffusivity is defined. Not all grid functions are used by each type of grid. However, all BMI grid functions must be implemented. -(See :ref:`model_grids` and :ref:`implementation`.) +(See :ref:`model_grids` and :ref:`best_practices`.) .. _get_grid_type: diff --git a/docs/source/bmi.spec.rst b/docs/source/bmi.spec.rst index 9a471cb..d51fde7 100644 --- a/docs/source/bmi.spec.rst +++ b/docs/source/bmi.spec.rst @@ -22,6 +22,8 @@ The specification for each language is given in Table 1, along with a corresponding example in which the BMI is implemented. +.. _specs_and_examples: + .. table:: **Table 1:** BMI language specifications. :align: center :widths: 20, 25, 25, 30 @@ -35,6 +37,14 @@ in which the BMI is implemented. Python `bmi.py`_ `bmi-python`_ `bmi-example-python`_ ======== ============= ============== ====================== +Along with the examples, +two documents may be particularly helpful when writing a BMI: + +* :ref:`Getting Started Guide ` --- a place to start + if you haven't written a BMI before +* :ref:`BMI Best Practices ` --- our collected wisdom on + implementing a BMI + A complete description of the functions that make up the BMI is given next. @@ -56,12 +66,9 @@ can be grouped into categories: Table 2 lists the individual BMI functions along with a brief description. Following the table is a detailed description of each function, -including the function prototype in SIDL, +including the function prototype in :term:`SIDL`, grouped by functional category. -Be sure to check out the collected wisdom of our :ref:`best practices -document ` for tips on implementing a BMI. - .. table:: **Table 2:** Summary of BMI functions. :align: center :widths: 30, 70 diff --git a/docs/source/glossary.rst b/docs/source/glossary.rst index 01a5632..7142ed9 100644 --- a/docs/source/glossary.rst +++ b/docs/source/glossary.rst @@ -16,12 +16,16 @@ A glossary of terms used with BMI. computing and a package manager. See https://www.anaconda.com/distribution for more information. - Basic Model Interface (BMI) + Basic Model Interface A set a functions that are used to interact with and control a model. See https://bmi.readthedocs.io for more information. - Community Surface Dynamics Modeling System (CSDMS) + BMI + + See :term:`Basic Model Interface`. + + Community Surface Dynamics Modeling System CSDMS is an NSF-funded program that seeks to transform the science and practice of earth-surface dynamics modeling. For @@ -56,6 +60,10 @@ A glossary of terms used with BMI. See :term:`model coupling`. + CSDMS + + See :term:`Community Surface Dynamics Modeling System`. + data Information held by an :term:`object`. @@ -161,8 +169,22 @@ A glossary of terms used with BMI. the external behaviors of the program. Refactoring is often done to clean up code and improve its performance. + Scientific Interface Definition Language + + A specification language for describing software interfaces to + scientific model codes. See :ref:`references`. + + SIDL + + See :term:`Scientific Interface Definition Language`. + Standard Names A semantic mediation technology developed at CSDMS for precisely matching variable names between models. For more information, see https://csdms.colorado.edu/wiki/CSDMS_Standard_Names. + + unit test + + A program that isolates and runs a section (a unit) of source + code to ensure that it produces an expected result. diff --git a/docs/source/index.rst b/docs/source/index.rst index 4ab6152..012a105 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -15,7 +15,8 @@ Additional Topics .. toctree:: :maxdepth: 2 - bmi.implementation + bmi.getting_started + bmi.best_practices model_grids csdms glossary From 69659d75d6e2abe720146d22b848e490083525e9 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Thu, 13 Feb 2020 14:06:38 -0700 Subject: [PATCH 6/8] Update contributor list from language specs and examples --- AUTHORS.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/AUTHORS.rst b/AUTHORS.rst index 25c65c3..eeb7e71 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -15,11 +15,14 @@ Contributors * Michael Galloy * Julian Hofer * Eric Hutton +* Eric Morway * Boyana Norris * Scott Peckham * Mark Piper * Mike Taves * Greg Tucker +* Ben van Werkhoven +* Martijn Visser If you have contributed to the BMI package and your name is missing, please send an email to the coordinators, or open a pull request From 2545ecd211ab168debda324844b755c2870c3025 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Fri, 21 Feb 2020 09:28:29 -0700 Subject: [PATCH 7/8] Add explanation of BMI function output for unstructured grids (#64) * Make script to generate figure of unstructured grid * Tweak text locations * Adjust colors and fonts for text labels * Add unstructured grid figure * Note length of returned array * Add glossary to quick links * Add sample output from BMI functions for unstructured grid example --- docs/source/_templates/links.html | 1 + docs/source/bmi.grid_funcs.rst | 7 ++ docs/source/images/mesh_unstructured.png | Bin 0 -> 71392 bytes docs/source/images/visualize_grids.py | 81 +++++++++++++++++++++++ docs/source/model_grids.rst | 76 +++++++++++++++++++++ 5 files changed, 165 insertions(+) create mode 100644 docs/source/images/mesh_unstructured.png create mode 100644 docs/source/images/visualize_grids.py diff --git a/docs/source/_templates/links.html b/docs/source/_templates/links.html index 886e334..685977a 100644 --- a/docs/source/_templates/links.html +++ b/docs/source/_templates/links.html @@ -2,6 +2,7 @@

Useful Links

  • Getting Started Guide
  • BMI Best Practices
    • +
  • Glossary
  • BMI @ GitHub
  • Issue Tracker
  • CSDMS Homepage
    • diff --git a/docs/source/bmi.grid_funcs.rst b/docs/source/bmi.grid_funcs.rst index 776f8e9..fbaa43b 100644 --- a/docs/source/bmi.grid_funcs.rst +++ b/docs/source/bmi.grid_funcs.rst @@ -396,6 +396,9 @@ node at edge head. The total length of the array is Get the face-edge connectivity. +The length of the array returned is the sum of the values of +:ref:`get_grid_nodes_per_face`. + **Implementation notes** * This function is used for describing :ref:`unstructured @@ -422,6 +425,9 @@ For each face, the nodes (listed in a counter-clockwise direction) that form the boundary of the face. For a grid of quadrilaterals, the total length of the array is 4 * :ref:`get_grid_face_count`. +More generally, +the length of the array is the sum of the values of +:ref:`get_grid_nodes_per_face`. **Implementation notes** @@ -445,6 +451,7 @@ the total length of the array is 4 * :ref:`get_grid_face_count`. Get the number of nodes for each face. +The returned array has a length of :ref:`get_grid_face_count`. 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z+4I+o2;x^V0TS7EcgAH4A6;tKhnv)k9%(;^2p<4FvMDJ{W$hgr_C!Rp$Eo-a018vL z937}S+&@S%?6!u%tqNQc^VxHLog_aKwFi^B#F}Q&QePN0 zemHKjH%*Q*5_+hJl#}mv;QrZGXd2Yxw=oiHL>n5^d1s9@$NT(Bt)(*O-`i#vmth7-eJ$)!&>09BifBITHxs3 zJZA|X37m9Wmv%(Ua?DAmql}xoI-Py#m)leNX%*M#5PfR1zac(K05l*o zPta0!N$-czF48+Apm(aGeM9W0^W#Hj&bSA!j}AmKRZ8}V-v;Q&AvF=m6btXMC%sXl zRx$qmu%z&Fmrpr39~W;!=20gq9TL}j|87E&QX^b7@;ndvE!&lKW|VxCvKOV2y(rG( zu!I|2ju&AD8-dG_v5F1|5eo$KRI%g>BzPJ`@HOHfj8X+(v6lsJ%dDRGuYdkANBsW{ lr`YX=>;GTOWKWNdvtFFn)ob+$r` of the grid, labeled in the figure in red, +are given by coordinates + +.. code-block:: python + + x = [0, 1, 2, 1, 3, 4] + y = [3, 1, 2, 4, 0, 3] + +These will be the outputs of the :ref:`get_grid_x` and +:ref:`get_grid_y` functions, respectively. +The nodes are indexed, so +node 0 is at *(x, y) = (0, 3)*, +node 1 is at *(x, y) = (1, 1)*, etc. + +As with the grid nodes, +the grid :term:`edges ` and :term:`faces ` are indexed. +In the figure, +the edges are depicted in blue italics, +while the faces are boldfaced. +The outputs from :ref:`get_grid_node_count`, :ref:`get_grid_edge_count`, +and :ref:`get_grid_face_count` are: + +.. code-block:: python + + node_count = 6 + edge_count = 8 + face_count = 3 + +Note that the number of nodes is the length of the *x* and *y* vectors above. + +The :ref:`get_grid_nodes_per_face` function returns a vector +of length `face_count`. +The first two faces are quadrilaterals, +while the third is a triangle, so + +.. code-block:: python + + nodes_per_face = [4, 4, 3] + +The :ref:`get_grid_edge_nodes` function returns a vector +of length `2*edge_count`. +The vector is formed, pairwise, +by the node index at the tail of the edge, +followed by the node index at the head of the edge. +For the grid in the figure, this is + +.. code-block:: python + + edge_nodes = [0, 1, 1, 2, 2, 3, 3, 0, 1, 4, 4, 5, 5, 2, 5, 3] + +The :ref:`get_grid_face_edges` function returns a vector +of length `sum(nodes_per_face)`. +The vector is formed from the edge indices as displayed in the figure: + +.. code-block:: python + + face_edges = [0, 1, 2, 3, 4, 5, 6, 1, 6, 7, 2] + +Likewise, the :ref:`get_grid_face_nodes` function returns a vector +of length `sum(nodes_per_face)`. +The vector is formed from the node indices as displayed in the figure: + +.. code-block:: python + + face_nodes = [0, 1, 2, 3, 1, 4, 5, 2, 2, 5, 3] + + .. Links From 656d78fa1c87759e8debbed49b8e2123f72d2640 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Tue, 7 Apr 2020 16:55:35 -0600 Subject: [PATCH 8/8] Touch docs (#67) * Suggest use of native type names * Update intro paragraphs This excellent contribution is from @gregtucker. --- docs/source/bmi.spec.rst | 47 +++++++++++++++++++++++------------ docs/source/bmi.var_funcs.rst | 6 +++-- 2 files changed, 35 insertions(+), 18 deletions(-) diff --git a/docs/source/bmi.spec.rst b/docs/source/bmi.spec.rst index d51fde7..dbfe599 100644 --- a/docs/source/bmi.spec.rst +++ b/docs/source/bmi.spec.rst @@ -1,19 +1,34 @@ -The *Basic Model Interface* (BMI) is a library specification -created by the `Community Surface Dynamics Modeling System`_ (CSDMS) -to facilitate the conversion of a model or dataset -into a reusable, plug-and-play component. -Recall that, in this context, an interface is a named set of functions -with prescribed arguments and return values. -The BMI functions make a model self-describing and fully controllable -by a modeling framework or application. -By design, the BMI functions are straightforward to implement in -any language, using only simple data types from standard language libraries. -Also by design, the BMI functions are noninvasive. -This means that a model's BMI does not make calls to other -components or tools and is not modified to use any -framework-specific data structures. A BMI, therefore, introduces no -dependencies into a model, so the model can still be used -in a stand-alone manner. +When you climb in the driver's seat of an unfamiliar car, +you are nonetheless presented with a familiar sight. +Whatever the make or model may be, +we take it for granted that the vehicle will provide +a steering wheel, brake pedal, and speedometer, +alongside the various other controls and readouts +that are common to essentially all cars and trucks on the planet. +Although we don't usually think of it this way, +drivers across the globe benefit from a standard interface: +a set of control mechanisms and information displays +that have essentially the same design regardless of whether the vehicle +is a tiny electric two-seater or a giant stretch limousine. +This standard interface makes the job of operating a vehicle much easier +than it would be if each one presented a radically different interface. +Imagine a world where switching from a sports car to a pickup truck +required months of study and practice! +Similarly, railroads benefit from a standard for coupling rail cars together. +The result: trains can be assembled from combinations of all sorts +of different rail cars, built by different companies, +in different places, and with different purposes. + +We believe that numerical models, +and the sub-components that make up those models, +should offer a similar kind of standardization. +To this end, +the `Community Surface Dynamics Modeling System`_ (CSDMS) +has developed the *Basic Model Interface* (BMI): +a set of standard control and query functions that, +when added to a model code, +make that model both easier to learn +and easier to couple with other software elements. While a BMI can be written for any language, CSDMS currently supports four languages: diff --git a/docs/source/bmi.var_funcs.rst b/docs/source/bmi.var_funcs.rst index 24c93b8..73759db 100644 --- a/docs/source/bmi.var_funcs.rst +++ b/docs/source/bmi.var_funcs.rst @@ -52,8 +52,10 @@ A model can have one or more grids. The `get_var_type` function provides the data type of the variable as it's stored in memory by the model. -The data type is returned as a string following the :term:`numpy` convention -used by the `dtype`_ attribute; e.g., `int32`, `float`, etc. +The data type is returned as a string. +Use of native language type names is encouraged; +e.g., in C, use `int`, `float`, and `double`, +while in Fortran, use `integer`, `real`, and `double precision`. **Implementation notes**