diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a9d958c0697435717197425536a938ccf450ce8e..ce991b9030afab48e9a943dfe90a64e00062eaa3 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 ################################################################################ diff --git a/docs/picvva/conf.py b/docs/picvva/conf.py index 9c596235d7a62a230d794bfe8b791ffea3bfa81a..ff404dcc69f9393a99eda9e6acfe1d7c288ea681 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 ec59de031fef18417b4023866dd894bb71a7b91d..cd1675ece2e1cd926766bbc2d0294a6a1cf10b55 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 0e3f215ea146f8c7a1f6be30cf9e394036fd8ce1..3725539866f29d9a8abd3a96d86ba097ca42d972 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 85da9fa7340d2b729608d243a191816f5387ac9d..83113481d0fd07d832094a7ecd265da1ceffd3cc 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 cd56c6fe5a12b2824dd8a02004adea6173f57fc0..2fc47c7a4f3b32752514e84460b8f71be79d8704 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 ac4ca1036aac04dc589d2a213c20cd2aa9630696..d26fbebcd2bf9bb06f200e35dd91b602962937e9 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 fa6c4115540b5d262329d7674d41dc6e3482922b..965f98080d30b9e7f15a428575b68925947d8968 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 ceb0cc72fb4abd0d1844c53a3293eaf5392c1820..6b7e5e69f7d62fbbaab85e8d76970ce34cf78678 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 86c73c90125f3dcd0a92e47d485f48b849cf5d15..beadfb7b3386826141701c30b74014f55fa7173f 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 b004c456ccc5faefea10e83c11d779b3701841cc..bf5232cf5dcffa47c463e09c1cf8d61a7ba5f4cc 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 833a0f6251b69455029fd718d04fecb1808c5eda..2f615d96b6ec2342bc0881fd809c76badbdc773f 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 aab7a030d797ceaeaff059f7ffb20329d0c2c0ee..7737701d37155ca83229fc5a6278b4046aebc539 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 99cfce96d49e17689ff67fae7cb2e283903b4ba8..808f752d316816a448ef8e80816921e596058047 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 eb69e51ada05253ceefd57e3dbe2ed9b47f4090c..1f9b21ea435d7e4c034d008f177c6aa3f63e169d 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 d57f102a1a0baf450a5f570fe339292d06275973..cd8a24aec090abde1418fd4b221db09b850313bf 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 63cc06c93402561328c24665e54ae1a84de12d1c..afa74e3c08ea3bf86a81a2bc4cd2fa8a8856406e 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 d2ac4cb3ad44d44070a11b96503696b7b81974d4..6a5bda130e8ec281009fa527443da481d42778ce 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 6418c80a97a723c2c9ecc8ab1e4ea4df62cdcb9f..83c0d0585099cb8b01e26e6aeb980a10e19d7147 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 afec60b33d1817861086e134cf0f5d4b5a0189ef..97dc7ea13724701df7643d1774ea49ec24943125 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 d8ddb2df91e7e9d29fa52d7e069257cd2fa14cfb..362342337a8cf9bf0f48a8bc60f41417317d25a3 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