From 1e9c1fd5e4011349eb72e51f720cf8a0459fddd6 Mon Sep 17 00:00:00 2001 From: Deepak Rangarajan Date: Mon, 29 Jan 2024 18:43:55 +0000 Subject: [PATCH 1/2] add codespell to ci --- .gitlab-ci.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a9d958c..ce991b9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -27,6 +27,15 @@ docs:userguide: tags: - docker +docs:codespell: + image: sphinxdoc/sphinx:latest + script: + - pip install codespell + - codespell --enable-colors --quiet-level 2 docs/source_docs/ docs/picvva/ + stage: build-docs + tags: + - docker + ################################################################################ # Deploy ################################################################################ -- GitLab From ebe69e8cd0cda4c4877df17cdc6f40b76eec0edb Mon Sep 17 00:00:00 2001 From: Deepak Rangarajan Date: Mon, 29 Jan 2024 19:11:45 +0000 Subject: [PATCH 2/2] fix spellings --- docs/picvva/conf.py | 2 +- docs/source_docs/eb/EBWalls.rst | 2 +- docs/source_docs/particles/ParticleBasics.rst | 2 +- docs/source_docs/qb/single_bubble.rst | 2 +- docs/source_docs/references/hpc.rst | 4 ++-- docs/source_docs/references/hpc/Bridges2.rst | 2 +- docs/source_docs/references/hpc/Crusher.rst | 8 ++++---- docs/source_docs/references/hpc/Delta.rst | 6 +++--- docs/source_docs/references/hpc/Frontier.rst | 2 +- docs/source_docs/references/hpc/Joule2.rst | 2 +- docs/source_docs/references/hpc/Perlmutter.rst | 4 ++-- docs/source_docs/references/hpc/Polaris.rst | 2 +- docs/source_docs/references/hpc/Summit.rst | 4 ++-- docs/source_docs/user_guide/inputs/geometry.rst | 2 +- docs/source_docs/user_guide/inputs/initialization.rst | 2 +- docs/source_docs/user_guide/inputs/model_options.rst | 2 +- docs/source_docs/user_guide/inputs/output/monitors.rst | 2 +- docs/source_docs/user_guide/inputs/output/plotfiles.rst | 2 +- docs/source_docs/user_guide/inputs/time-stepping.rst | 2 +- docs/source_docs/user_guide/quick_start/BuildingMFIX.rst | 2 +- 20 files changed, 28 insertions(+), 28 deletions(-) diff --git a/docs/picvva/conf.py b/docs/picvva/conf.py index 9c59623..ff404dc 100644 --- a/docs/picvva/conf.py +++ b/docs/picvva/conf.py @@ -170,6 +170,6 @@ man_pages = [ # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'picvva', u'MFIX-Exa PIC VVA Manual', - author, 'MFIX-Exa Team', "MFIX-Exa Particle-in-Cell Verification, Validation and Applicaiton Manual", + author, 'MFIX-Exa Team', "MFIX-Exa Particle-in-Cell Verification, Validation and Application Manual", 'Technical Report'), ] diff --git a/docs/source_docs/eb/EBWalls.rst b/docs/source_docs/eb/EBWalls.rst index ec59de0..cd1675e 100644 --- a/docs/source_docs/eb/EBWalls.rst +++ b/docs/source_docs/eb/EBWalls.rst @@ -60,7 +60,7 @@ geometries depending on the value of the :cpp:`mfix.geometry` setting in the | | cf. note 1 below | +------------------------------+----------------------+ -1. ``Generic`` geometry specification requires user implemenation +1. ``Generic`` geometry specification requires user implementation inside ``src/eb.mfix_eb_generic.cpp``. Also see the `AMReX geometry documentation`_ for information on how to construct new geometries using the method of constructive solid geometry. diff --git a/docs/source_docs/particles/ParticleBasics.rst b/docs/source_docs/particles/ParticleBasics.rst index 0e3f215..3725539 100644 --- a/docs/source_docs/particles/ParticleBasics.rst +++ b/docs/source_docs/particles/ParticleBasics.rst @@ -53,7 +53,7 @@ method. It's structure is: updateNeighbors(lev); } - // Itterate over particles + // Iterate over particles for (MFIXParIter pti(*this, lev); pti.isValid(); ++pti) { // Forces and torques due to particle-wall collisions diff --git a/docs/source_docs/qb/single_bubble.rst b/docs/source_docs/qb/single_bubble.rst index 85da9fa..8311348 100644 --- a/docs/source_docs/qb/single_bubble.rst +++ b/docs/source_docs/qb/single_bubble.rst @@ -6,7 +6,7 @@ Single Bubble Injection Another variation on bubbling typically observed in bubbling fluidized beds is the detailed single-bubble study of Boyce and coworkers [BPLPM19]_. In the experiment, a cylinderical bed is brought to incipient fluidization -(just *under* minimum fluidization) by a uniform disributor. Then, an +(just *under* minimum fluidization) by a uniform distributor. Then, an additional volume of gas is abruptly injected from a nozzle located in the center of the bed causing a single bubble to form and rise through the bed. Measurement of the evolution of the bubble formation, rise and diff --git a/docs/source_docs/references/hpc.rst b/docs/source_docs/references/hpc.rst index cd56c6f..2fc47c7 100644 --- a/docs/source_docs/references/hpc.rst +++ b/docs/source_docs/references/hpc.rst @@ -1,7 +1,7 @@ .. _GettingStarted:HPC: -Building on HPC Sytems -====================== +Building on HPC Systems +======================= On selected high-performance computing (HPC) systems MFIX-Exa has specific building instructions. Follow the guide here instead of the generic instructions. diff --git a/docs/source_docs/references/hpc/Bridges2.rst b/docs/source_docs/references/hpc/Bridges2.rst index ac4ca10..d26fbeb 100644 --- a/docs/source_docs/references/hpc/Bridges2.rst +++ b/docs/source_docs/references/hpc/Bridges2.rst @@ -5,7 +5,7 @@ If this is your first time building MFIX-Exa on Bridges-2, please review the general notes below and `Basics`_ section first. * To access Delta-2, you will need PSC account which can be administered - by the NSF ACCESS allocation managment system. + by the NSF ACCESS allocation management system. * You can find the name of your account(s) and the current balance with the ``accounts`` command. * These instructions build MFIX-Exa on the login nodes using `-j8` CPUs. diff --git a/docs/source_docs/references/hpc/Crusher.rst b/docs/source_docs/references/hpc/Crusher.rst index fa6c411..965f980 100644 --- a/docs/source_docs/references/hpc/Crusher.rst +++ b/docs/source_docs/references/hpc/Crusher.rst @@ -7,7 +7,7 @@ review the general notes below and `Basics`_ section first. * To access Summit, you will need an `OLCF account `_ and an RSA token. -* The name of hte MFIX-Exa account is ``cfd122`` +* The name of the MFIX-Exa account is ``cfd122`` * These instructions build MFIX-Exa on the login nodes using ``-j8`` CPUs. You may have to decrease this value if there is high traffic or you may want to increase this value if you are on a compute @@ -346,7 +346,7 @@ prior to following any of the full build instructions above. .. warning:: For some reason, something in PEGTL does not set the experimental - filesytem when installing in ``PrgEnv-gnu`` (but it does in ``PrgEnv-cray``). + filesystem when installing in ``PrgEnv-gnu`` (but it does in ``PrgEnv-cray``). So you you have to force that manually. One hack to do so is shown below. Make sure that "experimental" precedes filesystem on or near lines 47 and 51 in @@ -491,7 +491,7 @@ Example run scripts: export OMP_NUM_THREADS=$omp export MPICH_GPU_SUPPORT_ENABLED=1 # remove for cpu only #export FI_MR_CACHE_MAX_COUNT=0 # libfabric disable caching - export FI_MR_CACHE_MONITOR=memhooks # alt cashe monitor + export FI_MR_CACHE_MONITOR=memhooks # alt cache monitor export FI_CXI_RX_MATCH_MODE=software export FI_CXI_REQ_BUF_SIZE=12582912 export FI_CXI_REQ_BUF_MIN_POSTED=6 @@ -531,7 +531,7 @@ Example run scripts: export OMP_NUM_THREADS=$omp export MPICH_GPU_SUPPORT_ENABLED=1 # remove for cpu only #export FI_MR_CACHE_MAX_COUNT=0 # libfabric disable caching - export FI_MR_CACHE_MONITOR=memhooks # alt cashe monitor + export FI_MR_CACHE_MONITOR=memhooks # alt cache monitor export FI_CXI_RX_MATCH_MODE=software export FI_CXI_REQ_BUF_SIZE=12582912 export FI_CXI_REQ_BUF_MIN_POSTED=6 diff --git a/docs/source_docs/references/hpc/Delta.rst b/docs/source_docs/references/hpc/Delta.rst index ceb0cc7..6b7e5e6 100644 --- a/docs/source_docs/references/hpc/Delta.rst +++ b/docs/source_docs/references/hpc/Delta.rst @@ -10,7 +10,7 @@ If this is your first time building MFIX-Exa on Delta, please review the general notes below and `Basics`_ section first. * To access Delta, you will need an NCSA account which can be administered - by the NSF ACCESS allocation managment system. + by the NSF ACCESS allocation management system. * You can find the name of your account(s) and the current balance with the ``accounts`` command. * These instructions build MFIX-Exa on the login nodes using `-j8` CPUs. @@ -69,7 +69,7 @@ you need to load boost, such as module load boost/1.80.0 -There is a known incompatability with AMReX and the pre-loaded cuda version 11.6.1. +There is a known incompatibility with AMReX and the pre-loaded cuda version 11.6.1. To build with GPU support you will need to downgrade or upgrade versions, such as .. code:: bash @@ -90,7 +90,7 @@ you first need to build and install these libraries and their dependencies. Instructions on building the necessary dependencies are below and should be successfully installed first. There are two primary methods of building the code ``cmake`` and ``gmake`` which are provided -seperately below. +separately below. cmake ~~~~~ diff --git a/docs/source_docs/references/hpc/Frontier.rst b/docs/source_docs/references/hpc/Frontier.rst index 86c73c9..beadfb7 100644 --- a/docs/source_docs/references/hpc/Frontier.rst +++ b/docs/source_docs/references/hpc/Frontier.rst @@ -7,7 +7,7 @@ review the general notes below and `Basics`_ section first. * To access Summit, you will need an `OLCF account `_ and an RSA token. -* The name of hte MFIX-Exa account is ``cfd122`` +* The name of the MFIX-Exa account is ``cfd122`` * These instructions build MFIX-Exa on the login nodes using ``-j8`` CPUs. You may have to decrease this value if there is high traffic or you may want to increase this value if you are on a compute diff --git a/docs/source_docs/references/hpc/Joule2.rst b/docs/source_docs/references/hpc/Joule2.rst index b004c45..bf5232c 100644 --- a/docs/source_docs/references/hpc/Joule2.rst +++ b/docs/source_docs/references/hpc/Joule2.rst @@ -78,7 +78,7 @@ you first need to build and install these libraries and their dependencies. Instructions on building the necessary dependencies are below and should be successfully installed first. There are two primary methods of building the code ``cmake`` and ``gmake`` which are provided -seperately below. +separately below. cmake ~~~~~ diff --git a/docs/source_docs/references/hpc/Perlmutter.rst b/docs/source_docs/references/hpc/Perlmutter.rst index 833a0f6..2f615d9 100644 --- a/docs/source_docs/references/hpc/Perlmutter.rst +++ b/docs/source_docs/references/hpc/Perlmutter.rst @@ -12,7 +12,7 @@ review the general notes below and `Basics`_ section first. ssh @perlmutter-p1.nersc.gov ssh @saul-p1.nersc.gov - Login with your Iris password + (Google) Aunthenticator passcode. + Login with your Iris password + (Google) Authenticator passcode. * These instructions build MFIX-Exa on the login nodes using `-j8` CPUs. You may have to decrease this value if there is high traffic @@ -98,7 +98,7 @@ you first need to build and install these libraries and their dependencies. Instructions on building the necessary dependencies are below and should be successfully installed first. There are two primary methods of building the code `cmake` and `gmake` which are provided -seperately below. +separately below. cmake ~~~~~ diff --git a/docs/source_docs/references/hpc/Polaris.rst b/docs/source_docs/references/hpc/Polaris.rst index aab7a03..7737701 100644 --- a/docs/source_docs/references/hpc/Polaris.rst +++ b/docs/source_docs/references/hpc/Polaris.rst @@ -85,7 +85,7 @@ you first need to build and install these libraries and their dependencies. Instructions on building the necessary dependencies are below and should be successfully installed first. There are two primary methods of building the code `cmake` and `gmake` which are provided -seperately below. +separately below. cmake ~~~~~ diff --git a/docs/source_docs/references/hpc/Summit.rst b/docs/source_docs/references/hpc/Summit.rst index 99cfce9..808f752 100644 --- a/docs/source_docs/references/hpc/Summit.rst +++ b/docs/source_docs/references/hpc/Summit.rst @@ -7,7 +7,7 @@ review the general notes below and `Basics`_ section first. * To access Summit, you will need an `OLCF account `_ and an RSA token. -* The name of hte MFIX-Exa account is ``cfd122`` +* The name of the MFIX-Exa account is ``cfd122`` * These instructions build MFIX-Exa on the login nodes using ``-j8`` CPUs. You may have to decrease this value if there is high traffic or you may want to increase this value if you are on a compute @@ -79,7 +79,7 @@ you first need to build and install these libraries and their dependencies. Instructions on building the necessary dependencies are below and should be successfully installed first. There are two primary methods of building the code ``cmake`` and ``gmake`` which are provided -seperately below. +separately below. cmake ~~~~~ diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index eb69e51..1f9b21e 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -260,7 +260,7 @@ the EB ``cylinder`` are *covered* and thereby excluded from calculations. The ``generic`` geometry option is used to select the user-programed embedded boundary geometry. -* A custom embedded boundary geometry is programed by the user in ``src/eb/mfixeb_generic.cpp`` +* A custom embedded boundary geometry is programmed by the user in ``src/eb/mfixeb_generic.cpp`` using ``AMReX`` native implicit functions and operations. * An executable containing the geometry modifications is compiled. * The geometry is accessed using the ``generic`` input. diff --git a/docs/source_docs/user_guide/inputs/initialization.rst b/docs/source_docs/user_guide/inputs/initialization.rst index d57f102..cd8a24a 100644 --- a/docs/source_docs/user_guide/inputs/initialization.rst +++ b/docs/source_docs/user_guide/inputs/initialization.rst @@ -8,7 +8,7 @@ The following inputs must be preceded by ``mfix`` and determine how we initializ +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +======================+=======================================================================+=============+==============+ -| do_initial_proj | Preform an initial projection | Bool | True | +| do_initial_proj | Perform an initial projection | Bool | True | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | initial_iterations | Number of pressure iterations to execute before time-marching | Int | 3 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 63cc06c..afa74e3 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -377,7 +377,7 @@ The following inputs must be preceded by "mfix." +-------------------+---------------------------------+-------------+--------------+ The options currently supported in mfix are :cpp:`RanzMarshall` (default) and :cpp:`Gunn`. -In both models the HTC is determined from a Nusslet number corelation. +In both models the HTC is determined from a Nusslet number correlation. The RanzMarshall Nusselt number correlation is defined as: diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index d2ac4cb..6a5bda1 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -601,7 +601,7 @@ Flow rates For Lagrangian monitors of type FlowRate, the flow plane must be specified in the inputs and it must be defined by one of the regions defined in the regions inputs. The following input for a monitor [monitor] of type FlowRate can be -used, preceeded by the "mfix.monitors" prefix. +used, preceded by the "mfix.monitors" prefix. +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/output/plotfiles.rst b/docs/source_docs/user_guide/inputs/output/plotfiles.rst index 6418c80..83c0d05 100644 --- a/docs/source_docs/user_guide/inputs/output/plotfiles.rst +++ b/docs/source_docs/user_guide/inputs/output/plotfiles.rst @@ -130,7 +130,7 @@ All these parameters are user-defined. +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plot_int | Specify timestep frequency for plotting the file | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plot_per_approx | Specify time interval frequency for ploting the file | Real | 0 | +| [region].plot_per_approx | Specify time interval frequency for plotting the file | Real | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plt_regtest | Save all variables to plot file (overrides all other IO flags) | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/time-stepping.rst b/docs/source_docs/user_guide/inputs/time-stepping.rst index afec60b..97dc7ea 100644 --- a/docs/source_docs/user_guide/inputs/time-stepping.rst +++ b/docs/source_docs/user_guide/inputs/time-stepping.rst @@ -15,7 +15,7 @@ step is computed based on the advective CFL condition. .. caution:: **The adaptive time step based on the advective CFL condition is always computed - and is stronly recommended for most cases.** + and is strongly recommended for most cases.** * For a fixed time step simiulation, if the computed step size is smaller than ``mfix.fixed_dt`` for a fixed, the simulation aborts with the message: diff --git a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst index d8ddb2d..3623423 100644 --- a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst +++ b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst @@ -5,7 +5,7 @@ This page gives the generic instructions for building MFIX-Exa using gmake and c The instructions assume you have already downloaded and unpacked the MFIX-Exa code into a local ``mfix`` directory. If not, please visit the `download page `_ first. -For HPC cluser specific instructions, please refer to :ref:`GettingStarted:HPC`. +For HPC cluster specific instructions, please refer to :ref:`GettingStarted:HPC`. Building with gmake -- GitLab