Merge branch 'master' of https://github.com/AMReX-Codes/MFIX-Exa

.github/workflows/build.yml

@@ -0,0 +1,41 @@
+name: Build-and-Deploy
+
+# Run this workflow every time a new commit pushed to your repository
+on: push
+
+jobs:
+  # Set the job key. The key is displayed as the job name
+  # when a job name is not provided
+  publish:
+    # Name the Job
+    name: Build Sphinx manual HTML target
+    # Set the type of machine to run on
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Install Doxygen
+        run: sudo apt install doxygen
+
+      - name: Install Sphinx
+        run: pip install sphinx sphinx-rtd-theme
+
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Build MFiX-Exa HTML manual
+        run: make -C docs
+        env:
+          DEFAULT_BRANCH: main
+          GITLAB_TOKEN: ${{ secrets.GITLAB_TOKEN }}
+
+      - name: Deploy to GitHub Pages
+        if: success()
+        uses: crazy-max/ghaction-github-pages@v2
+        with:
+          target_branch: gh-pages
+          build_dir: docs/webroot
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

docs/source/Inputs_Chapter.rst

@@ -38,7 +38,7 @@ keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc.
 .. toctree::
    :maxdepth: 1
 
-   Units, mesh, geometry, species, fluid, DEM, regions, inital and boundary conditions <inputs/InputsProblemDefinition>
+   Units, mesh, geometry, species, fluid, DEM, regions, initial and boundary conditions <inputs/InputsProblemDefinition>
    Particle drag <inputs/InputsDrag>
    inputs/InputsTimeStepping
    inputs/InputsInitialization

docs/source/eb/EBWalls.rst

@@ -139,7 +139,7 @@ The :cpp:`mfix` class stores the following EB data:
 
 As discussed in the previous sub-section, the difference between
 :cpp:`mfix::eb_levels` and :cpp:`mfix::particle_eb_levels` enables the user to
-specify a modfied EB geometry for particles only. Whereas the fluid sees the EB
+specify a modified EB geometry for particles only. Whereas the fluid sees the EB
 geometry in :cpp:`mfix::eb_levels`. If no addition particle EB geometry is
 specified (point 4 in the previous section), then
 :cpp:`mfix::particle_eb_levels` points to :cpp:`mfix::eb_levels`.
@@ -229,7 +229,7 @@ calling :cpp:`mfix::Init`. The recommended procedure therefore is
 Also note that mfix defines boundary conditions in Fortran also (via the
 mfix.dat). Since these are potentially needed to build EB walls,
 :cpp:`mfix::make_eb_geometry` also calls :cpp:`mfix_set_bc_type`.
- 
+
 The grids for each level are build in the :cpp:`mfix::Init` by invoking the
 initialization functions inherited from :cpp:`amrex::AmrCore`.
 
@@ -305,4 +305,4 @@ There are two special cases involving level-sets:
 
 .. _AMReX EB documentation: https://amrex-codes.github.io/amrex/docs_html/EB_Chapter.html
 .. _AMReX Level-Set documentation: https://amrex-codes.github.io/amrex/docs_html/EB.html#level-sets
-.. _AMReX geometry documentation: https://amrex-codes.github.io/amrex/docs_html/EB.html#initializing-the-geometric-database 
+.. _AMReX geometry documentation: https://amrex-codes.github.io/amrex/docs_html/EB.html#initializing-the-geometric-database

docs/source/inputs/InputsDrag.rst

@@ -9,21 +9,21 @@ The following inputs must be preceded by "mfix."
 | drag_type         | Which drag model to use                                               | String      | None      |
 +-------------------+-----------------------------------------------------------------------+-------------+-----------+
 
-The options currently supported in mfix are :cpp:`WenYu`, :cpp:`Gidaspow`, :cpp:`BVK2`, or :cpp:`UserDrag`. 
+The options currently supported in mfix are :cpp:`WenYu`, :cpp:`Gidaspow`, :cpp:`BVK2`, or :cpp:`UserDrag`.
 
-If one of these is not specified, the code will abort with 
+If one of these is not specified, the code will abort with
 
 .. highlight:: c++
 
 ::
 
-   amrex::Abort::0::"Don't know this drag type!!! 
+   amrex::Abort::0::"Don't know this drag type!!!
 
 The drag models are defined in src/src_des/des_drag_K.H
 
 If the user wishes to use their own drag model, they must
 
-  * specify :cpp:`mfix.drag_type = UserDrag` in the inputs file 
+  * specify :cpp:`mfix.drag_type = UserDrag` in the inputs file
 
   * provide the code in the ComputeDragUser routine in a local usr_drag.cpp file.
     An example can be found in tests/DEM06-x.
@@ -39,7 +39,7 @@ With the variables defined as follows:
      *    Mug     - gas laminar viscosity
      *    ROpg    - gas density * EP_g
      *    vrel    - magnitude of gas-solids relative velocity
-     *    DPM     - particle diamater of solids phase M
+     *    DPM     - particle diameter of solids phase M
      *    DPA     - average particle diameter
      *    PHIS    - solids volume fraction of solids phases
      *    fvelx   - x component of the fluid velocity at the particle position
@@ -49,7 +49,7 @@ With the variables defined as follows:
      *    pid     - particle id number
      */
 
-The WenYu model is defined as 
+The WenYu model is defined as
 
    .. code:: shell
 
@@ -67,7 +67,7 @@ The WenYu model is defined as
      if (RE < DEMParams::eps) return 0.0;
      return 0.75 * C_d * vrel * ROPg * std::pow(EPg, -2.65) / DPM;
 
-The Gidaspow model is defined as 
+The Gidaspow model is defined as
 
    .. code:: shell
 
@@ -97,7 +97,7 @@ The Gidaspow model is defined as
       if (RE < DEMParams::eps) return 0.0;
       return (1.0 - PHI_gs)*Ergun + PHI_gs*WenYu;
 
-The Gidaspow model is defined as 
+The Gidaspow model is defined as
 
    .. code:: shell
 

docs/source/inputs/InputsProblemDefinition.rst

@@ -660,7 +660,7 @@ tridimensional). We recall that, on the remaining part of the EBs, homogeneous
 Neumann boundary conditions are assumed by default.
 
 In the following table there is a list of the possible entries for EB boundary
-conditions. Each entry must be preceeded by `bc.[region0].`
+conditions. Each entry must be preceded by `bc.[region0].`
 
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
 |                     | Description                                                           |   Type      | Default   |

docs/source/qb/granRT.rst

@@ -67,7 +67,7 @@ numerical results for roughly the first half of the transien: an initially flat
 interface gives way to many fingers falling into the gas which merge and form 
 a semi-stable bubble pattern. However, the simulated bubbles appear to be less
 stable than those in the lab, which rise uniformily to the surface. However, in 
-the simulations the center bubble rises slighlty faster than the one on the 
+the simulations the center bubble rises slightly faster than the one on the 
 left, which shifts more weight over the left-hand bubble, which further impedes 
 its rise and eventually "squishes" the left-hand bubble into the center bubble
 as it breaks the surface. Later, the right hand bubble also merges with (what 
@@ -77,7 +77,7 @@ significantly accelerates the second half of the transient (notice the
 different times between experiment and simulation). Several different 
 variations of this setup were performed: different drag laws, slower inversion 
 time, different combinations of particle restitution and friction coefficients, 
-inclusion of front and back walls. Although all tests were slighlty different, 
+inclusion of front and back walls. Although all tests were slightly different, 
 none were able to match the stability of the later time bubble pattern observed 
 experimentally.  
 

docs/source/qb/hcs.rst

@@ -1,52 +1,52 @@
 .. _Chap:QB:hcs:
 
-Clustering in the HCS 
+Clustering in the HCS
 ======================
 
 
-The HCS is the simplest non-trivial particulate gas-solid system. The continuum 
+The HCS is the simplest non-trivial particulate gas-solid system. The continuum
 gas-phase is initially at rest. The particles are uniformily distributed in space
-and have zero momentum in all three directions. However, the particle pecular 
-velocity is non-zero, quantified by an initial *granular* temperature, 
-:math:`T_0`. The system is periodic in all direcitons and no external forces act 
-on the system. Under homogeneous conditions, the granular temperature, :math:`T`, 
-is equivalent to two-thirds of the the (massless) mean particle kinetic energy. 
-In the HCS, the Eulerian kinetic theory (KT) model of Garzo et al. [GTSH12]_ 
-reduces to: 
-
-.. math:: 
-   \frac{dT}{dt} = - \frac{2 \gamma}{m} T - \zeta_0 T 
-
-where :math:`m` is the particle mass, :math:`\gamma` is the thermal drag and 
-:math:`\zeta_0` is the zeroth-order cooling rate. The first term on the RHS 
-above represents viscous dissipation due to the interstitial gas while the 
-second term represents collisional dissipation due inelastic particle-particle 
-interactions. The ODE has an analytical solution given by Yin et al. [YZMH13]_ 
+and have zero momentum in all three directions. However, the particle pecular
+velocity is non-zero, quantified by an initial *granular* temperature,
+:math:`T_0`. The system is periodic in all directions and no external forces act
+on the system. Under homogeneous conditions, the granular temperature, :math:`T`,
+is equivalent to two-thirds of the the (massless) mean particle kinetic energy.
+In the HCS, the Eulerian kinetic theory (KT) model of Garzo et al. [GTSH12]_
+reduces to:
+
+.. math::
+   \frac{dT}{dt} = - \frac{2 \gamma}{m} T - \zeta_0 T
+
+where :math:`m` is the particle mass, :math:`\gamma` is the thermal drag and
+:math:`\zeta_0` is the zeroth-order cooling rate. The first term on the RHS
+above represents viscous dissipation due to the interstitial gas while the
+second term represents collisional dissipation due inelastic particle-particle
+interactions. The ODE has an analytical solution given by Yin et al. [YZMH13]_
 (also see [LBFHHGS16]_ for the exact model used herein which also includes a
-first-order thermal Reynolds number extension to :math:`\gamma`). In the absence 
-of clustering, the granular temperature in the HCS decays according to the 
-analytical solution, known as Haff's law [H83]_ in granular systems:  
-:math:`\gamma = 0`. However, at a critical system size [G05]_, :math:`L^*_c`, 
-(where :math:`L^* = L/d_p`), the initially homogeneous state gives way to the 
-most fundamental of gas-solid instabilities, the clustering instability, which 
-causes :math:`T` (or more accurately :math:`KE`) to deviate significantly from 
-KT solution due to regions of high and low concentration and correlated motion. 
+first-order thermal Reynolds number extension to :math:`\gamma`). In the absence
+of clustering, the granular temperature in the HCS decays according to the
+analytical solution, known as Haff's law [H83]_ in granular systems:
+:math:`\gamma = 0`. However, at a critical system size [G05]_, :math:`L^*_c`,
+(where :math:`L^* = L/d_p`), the initially homogeneous state gives way to the
+most fundamental of gas-solid instabilities, the clustering instability, which
+causes :math:`T` (or more accurately :math:`KE`) to deviate significantly from
+KT solution due to regions of high and low concentration and correlated motion.
 
 
 To test if MFiX-Exa predicts the expected clustering behavior, a system is set up
 with the following non-dimensional parameters:
-  
+
   * initial thermal Reynolds number: :math:`Re_{T_0} = \rho_g d_p \sqrt{T_0} / \mu_g = 20`
   * density ratio: :math:`\rho^* = \rho_p / \rho_g = 1000`
   * restitution coefficient: :math:`e = 0.8`
   * solids concentration: :math:`\phi = \pi N_p / 6 L^*_x L^*_y L^*_z \approx 0.05`
 
-While not specifically studied by Fullmer et al. [FLYH18]_, their results 
-indicate that :math:`L_c^*` may be as large as 100 at these conditions. 
+While not specifically studied by Fullmer et al. [FLYH18]_, their results
+indicate that :math:`L_c^*` may be as large as 100 at these conditions.
 In order to avoid the region near critical stability, we use a significnatly
-larger system size: :math:`L^*_x = L^*_y = 256`. The system is thin in the 
-depth dimension, :math:`L^*_z = 8` in order to highlight the clustering 
-phenomena. Therefore, :math:`N_p = 50000`. Because the system is hypothetical, 
+larger system size: :math:`L^*_x = L^*_y = 256`. The system is thin in the
+depth dimension, :math:`L^*_z = 8` in order to highlight the clustering
+phenomena. Therefore, :math:`N_p = 50000`. Because the system is hypothetical,
 the ideal :cpp:`BVK2` DNS drag law is applied, see [BvK07]_, [TPKKv15]_.
 
 
@@ -55,20 +55,20 @@ the ideal :cpp:`BVK2` DNS drag law is applied, see [BvK07]_, [TPKKv15]_.
    :align: center
    :alt: kinetic energy decay in the HCS
 
-   Decay of the particle mean kinetic energy compared to the KT analytical 
-   soluiton of the GTSH model. 
+   Decay of the particle mean kinetic energy compared to the KT analytical
+   soluiton of the GTSH model.
 
 
-Three replicate systems are simulated with MFiX-Exa 19.08, differing only 
-in initial particle locations and pecular velocities. The particle kinetic 
-energy is averaged in the simulations (red) and  compared to the analytical 
-granular temperature (black) of the HCS as a funciton of time in the figure 
-above. The kinetic energy :math:`KE / KE_0` decays by two to three orders of 
-magnitude in line with the HCS result until clustering and localized mean 
-motion cause a drastic deviation. The final result at :math:`t^* = 1000` 
-for one of the replicates is shown below (at right) compared to the seminal 
-result of Goldhirsch and Zanetti [GZ93]_ (true 2D), the original demonstration 
-of the clustering instability the HCS. 
+Three replicate systems are simulated with MFiX-Exa 19.08, differing only
+in initial particle locations and pecular velocities. The particle kinetic
+energy is averaged in the simulations (red) and  compared to the analytical
+granular temperature (black) of the HCS as a function of time in the figure
+above. The kinetic energy :math:`KE / KE_0` decays by two to three orders of
+magnitude in line with the HCS result until clustering and localized mean
+motion cause a drastic deviation. The final result at :math:`t^* = 1000`
+for one of the replicates is shown below (at right) compared to the seminal
+result of Goldhirsch and Zanetti [GZ93]_ (true 2D), the original demonstration
+of the clustering instability the HCS.
 
 
 .. figure:: figs/hcs_xy_1908.png
@@ -77,8 +77,4 @@ of the clustering instability the HCS.
    :alt: clustered state of the HCS
 
    Clustered state of the HCS observed by Goldhirsch and Zanetti [GZ93]_
-   (left) compared to an MFiX-Exa result (right). 
-
-
-
-
+   (left) compared to an MFiX-Exa result (right).

docs/source/qb/index.rst

@@ -3,16 +3,16 @@
 Qualitative Benchmarks
 ======================
 
-MFiX-Exa uses a three level approach to regression testing spaning from simple
+MFiX-Exa uses a three level approach to regression testing spanning from simple
 and/or short smoke tests to validation problems comparing against experimental
-data. Most of the validation benchmarks target the physics of interest to 
-MFiX-Exa's intended audience, i.e., dense bubbling, fast fluidization and 
-pneumatic transport of particulate solids by a light gas. In an effort to widen 
-the phase-space in which MFiX-Exa may be (potentially) applied, a set of 
-qualitative benchmark problems are provided below which focus more on the 
-phenomenology of a given, problem rather than averaged statistical measures. 
-Animations of numerical soluitons to several of the qualitative benchmarks 
-can be seen in the 
+data. Most of the validation benchmarks target the physics of interest to
+MFiX-Exa's intended audience, i.e., dense bubbling, fast fluidization and
+pneumatic transport of particulate solids by a light gas. In an effort to widen
+the phase-space in which MFiX-Exa may be (potentially) applied, a set of
+qualitative benchmark problems are provided below which focus more on the
+phenomenology of a given, problem rather than averaged statistical measures.
+Animations of numerical soluitons to several of the qualitative benchmarks
+can be seen in the
 `Gallery <https://amrex-codes.github.io/MFIX-Exa/gallery.html>`_
 
 
@@ -25,4 +25,3 @@ can be seen in the
    single_bubble
    biseg
    refs
-