From 728e60c147ca1bb72e1a872b95a3237b2bbbbf24 Mon Sep 17 00:00:00 2001 From: fschuch Date: Mon, 13 Sep 2021 15:51:19 -0300 Subject: [PATCH] adjusting documentation --- README.md | 5 +- docs/index.rst | 8 +- docs/tutorial/parameters.ipynb | 3089 +++++++++++++++--------------- xcompact3d_toolbox/array.py | 4 +- xcompact3d_toolbox/gui.py | 3 +- xcompact3d_toolbox/mesh.py | 24 +- xcompact3d_toolbox/parameters.py | 4 +- xcompact3d_toolbox/sandbox.py | 5 +- 8 files changed, 1557 insertions(+), 1585 deletions(-) diff --git a/README.md b/README.md index e3fe718..13cfb7c 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ In addition to [ipywidgets](https://ipywidgets.readthedocs.io/en/latest/) for an Data structure is provided by [xarray](http://xarray.pydata.org/en/stable/) (see [Why xarray?](http://xarray.pydata.org/en/stable/why-xarray.html)), that introduces labels in the form of dimensions, coordinates and attributes on top of raw [NumPy](https://numpy.org/)-like arrays, which allows for a more intuitive, more concise, and less error-prone developer experience. It integrates tightly with [dask](https://dask.org/) for parallel computing and [hvplot](https://hvplot.holoviz.org/user_guide/Gridded_Data.html) for interactive data visualization. -Finally, Xcompact3d Toolbox is fully integrated with the new *Sandbox Flow Configuration*. +Finally, Xcompact3d-toolbox is fully integrated with the new *Sandbox Flow Configuration*. The idea is to easily provide everything that XCompact3d needs from a [Jupyter Notebook](https://jupyter.org/), like initial conditions, solid geometry, boundary conditions, and the parameters ([see examples](https://xcompact3d-toolbox.readthedocs.io/en/latest/tutorial.html#sandbox-examples)). It makes life easier for beginners, that can run any new flow configuration without worrying about Fortran and [2decomp](http://www.2decomp.org/). For developers, it works as a rapid prototyping tool, to test concepts and then compare results to validate any future Fortran implementation. @@ -142,8 +142,7 @@ Now, any change you make at the source code will be available at your local inst * [Documentation](https://xcompact3d-toolbox.readthedocs.io/); * [Suggestions for new features and bug report](https://github.com/fschuch/xcompact3d_toolbox/issues); * [See what is coming next (Project page)](https://github.com/fschuch/xcompact3d_toolbox/projects/1); -* [Xcompact3d's repository](https://github.com/xcompact3d/Incompact3d); -* [My fork from Xcompact3d's repository](https://github.com/fschuch/Xcompact3d/); +* [Xcompact3d's repository](https://github.com/xcompact3d/Incompact3d). ## Try it Online diff --git a/docs/index.rst b/docs/index.rst index f823f88..d540abb 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,9 +19,10 @@ In addition to ipywidgets_ for an user friendly interface. Data structure is provided by xarray_ (see `Why xarray?`_), that introduces labels in the form of dimensions, coordinates and attributes on top of raw NumPy_-like arrays, which allows for a more intuitive, more concise, and less error-prone -developer experience. It integrates tightly with dask_ for parallel computing. +developer experience. It integrates tightly with dask_ for parallel computing and +hvplot_ for interactive data visualization. -Finally, Xcompact3d Toolbox is fully integrated with the new *Sandbox Flow Configuration*. +Finally, Xcompact3d-toolbox is fully integrated with the new *Sandbox Flow Configuration*. The idea is to easily provide everything that Xcompact3d needs from a `Jupyter Notebook`_, like initial conditions, solid geometry, boundary conditions, and the parameters. It makes life easier for beginners, that can run @@ -104,7 +105,7 @@ Examples Installation ------------ -It is possible to instal using pip:: +It is possible to install using pip:: pip install xcompact3d-toolbox @@ -134,6 +135,7 @@ Useful links .. _2decomp: http://www.2decomp.org/ .. _dask: https://dask.org/ +.. _hvplot: https://hvplot.holoviz.org/user_guide/Gridded_Data.html .. _ipywidgets: https://ipywidgets.readthedocs.io/en/latest/ .. _`Jupyter Notebook`: https://jupyter.org/ .. _Numpy: https://numpy.org/ diff --git a/docs/tutorial/parameters.ipynb b/docs/tutorial/parameters.ipynb index db69938..9f1e99d 100644 --- a/docs/tutorial/parameters.ipynb +++ b/docs/tutorial/parameters.ipynb @@ -1086,7 +1086,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "5aa2c0c8f2c646f5a23af992cf3adb0c", + "model_id": "651f7e2d68374818aba4c6c5628f17b0", "version_major": 2, "version_minor": 0 }, @@ -1165,7 +1165,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - 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"model_name": "BoundedIntTextModel", + "model_name": "ButtonModel", "state": { - "description": "ifirst", - "description_tooltip": "The number for the first iteration", - "layout": "IPY_MODEL_3903a55cb5da4228af35d955c11be8d6", - "max": 1000000000, - "style": "IPY_MODEL_e8a468c35812407cac2e2ebc1379752b" + "description": "Run", + "disabled": true, + "icon": "rocket", + "layout": "IPY_MODEL_5dc23d656d0f41c5976a481ec29e95a1", + "style": "IPY_MODEL_7731160a160b49eb8f7d5a9ea11dd390" } }, - "e4230588315343f699810f22a5005926": { + "d32d3ff3befc43149aba5e90088b5443": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "BoundedFloatTextModel", + "model_name": "DescriptionStyleModel", "state": { - "description": "dx", - "layout": "IPY_MODEL_0244afefa9ad485fa569477c16dc6b44", - "max": 1000000, - "step": null, - "style": "IPY_MODEL_dce07ef468aa481580a6d739d19c64a7", - "value": 0.0625 + "description_width": "" } }, - "e4f9b43d57184eb89c91eaf2cb4cffd1": { + "d3334e4e2381483ab3cd7fb82d309d33": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "HTMLModel", + "model_name": "SliderStyleModel", "state": { - "layout": "IPY_MODEL_3d01e5186b964282a57fa1845cb7bce9", - "style": "IPY_MODEL_3f12aa8b3c434312a4c5965b2f229d0b", - "value": "

Xcompact3d Parameters

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Xcompact3d Parameters

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It is fully functional with all boundary conditions available on - Xcompact3d and stretched mesh in y direction. + XCompact3d and stretched mesh in the vertical direction (y). The **atribute** ``BC`` is used to store Boundary Condition information in a dictionary (see examples), default is ``ncl1 = ncln = 2`` and ``npaire = 1``. diff --git a/xcompact3d_toolbox/gui.py b/xcompact3d_toolbox/gui.py index 30c4b9f..f58ca28 100644 --- a/xcompact3d_toolbox/gui.py +++ b/xcompact3d_toolbox/gui.py @@ -201,8 +201,7 @@ def __init__(self, **kwargs): # # # ibmstuff # - # Disabled because nobjmax is defined automatically at genepsi.py - nobjmax=widgets.IntText(disabled=True, min=0, max=1e9), + nobjmax=widgets.BoundedIntText(min=1, max=1e9), nraf=widgets.IntSlider(min=1, max=25), # # # Auxiliar for user interface, not included at the .i3d file diff --git a/xcompact3d_toolbox/mesh.py b/xcompact3d_toolbox/mesh.py index a80fc8d..edc5d54 100644 --- a/xcompact3d_toolbox/mesh.py +++ b/xcompact3d_toolbox/mesh.py @@ -262,9 +262,29 @@ def possible_grid_size(self) -> list: >>> from xcompact3d_toolbox.mesh import Coordinate >>> coordinate(is_periodic = True).possible_grid_size - [8, 10, 12, 16, 18, 20, 24, ..., 7776, 8000, 8100, 8192, 8640, 8748, 9000] + [8, 10, 12, 16, 18, 20, 24, 30, 32, 36, 40, 48, 50, 54, 60, 64, 72, 80, + 90, 96, 100, 108, 120, 128, 144, 150, 160, 162, 180, 192, 200, 216, 240, + 250, 256, 270, 288, 300, 320, 324, 360, 384, 400, 432, 450, 480, 486, + 500, 512, 540, 576, 600, 640, 648, 720, 750, 768, 800, 810, 864, 900, + 960, 972, 1000, 1024, 1080, 1152, 1200, 1250, 1280, 1296, 1350, 1440, + 1458, 1500, 1536, 1600, 1620, 1728, 1800, 1920, 1944, 2000, 2048, 2160, + 2250, 2304, 2400, 2430, 2500, 2560, 2592, 2700, 2880, 2916, 3000, 3072, + 3200, 3240, 3456, 3600, 3750, 3840, 3888, 4000, 4050, 4096, 4320, 4374, + 4500, 4608, 4800, 4860, 5000, 5120, 5184, 5400, 5760, 5832, 6000, 6144, + 6250, 6400, 6480, 6750, 6912, 7200, 7290, 7500, 7680, 7776, 8000, 8100, + 8192, 8640, 8748, 9000] >>> coordinate(is_periodic = False).possible_grid_size - [9, 11, 13, 17, 19, 21, 25, ..., 7777, 8001, 8101, 8193, 8641, 8749, 9001] + [9, 11, 13, 17, 19, 21, 25, 31, 33, 37, 41, 49, 51, 55, 61, 65, 73, 81, + 91, 97, 101, 109, 121, 129, 145, 151, 161, 163, 181, 193, 201, 217, 241, + 251, 257, 271, 289, 301, 321, 325, 361, 385, 401, 433, 451, 481, 487, + 501, 513, 541, 577, 601, 641, 649, 721, 751, 769, 801, 811, 865, 901, + 961, 973, 1001, 1025, 1081, 1153, 1201, 1251, 1281, 1297, 1351, 1441, + 1459, 1501, 1537, 1601, 1621, 1729, 1801, 1921, 1945, 2001, 2049, 2161, + 2251, 2305, 2401, 2431, 2501, 2561, 2593, 2701, 2881, 2917, 3001, 3073, + 3201, 3241, 3457, 3601, 3751, 3841, 3889, 4001, 4051, 4097, 4321, 4375, + 4501, 4609, 4801, 4861, 5001, 5121, 5185, 5401, 5761, 5833, 6001, 6145, + 6251, 6401, 6481, 6751, 6913, 7201, 7291, 7501, 7681, 7777, 8001, 8101, + 8193, 8641, 8749, 9001] """ return self._possible_grid_size diff --git a/xcompact3d_toolbox/parameters.py b/xcompact3d_toolbox/parameters.py index c92a5fb..5282a8b 100644 --- a/xcompact3d_toolbox/parameters.py +++ b/xcompact3d_toolbox/parameters.py @@ -751,13 +751,13 @@ class ParametersExtras(traitlets.HasTraits): >>> snapshot = prm.dataset[10] - * Iterate over all snapshots, loading them one by one: + * Loop through all snapshots, loading them one by one: >>> for ds in prm.dataset: ... vort = ds.uy.x3d.first_derivative("x") - ds.ux.x3d.first_derivative("y") ... prm.dataset.write(data = vort, file_prefix = "w3") - * Iterate over some snapshots, loading them one by one, with the same arguments + * Loop through some snapshots, loading them one by one, with the same arguments of a classic Python :obj:`range`, for instance, from 0 to 100 with a step of 5: >>> for ds in prm.dataset(0, 101, 5): diff --git a/xcompact3d_toolbox/sandbox.py b/xcompact3d_toolbox/sandbox.py index 15b60a2..26509e0 100644 --- a/xcompact3d_toolbox/sandbox.py +++ b/xcompact3d_toolbox/sandbox.py @@ -147,15 +147,14 @@ def init_dataset(prm): I = sum(vol_frc * ux) and them will correct streamwise velocity as ux = ux / I, so, set ``vol_frc`` properly. - After setting all values for your flow configuration, the dataset can be - written to disc with ``ds.x3d.write()``. - Examples -------- >>> prm = xcompact3d_toolbox.Parameters() >>> dataset = xcompact3d_toolbox.init_dataset(prm) + >>> # >>> # Code here your customized flow configuration + >>> # >>> prm.dataset.write(dataset) # write the files to the disc """