Loading .travis.yml +4 −6 Original line number Diff line number Diff line dist: xenial language: generic python: - 3.6 install: - pip install --user sphinx # sphinx_rtd_theme # pypi's sphinx_rtd_theme is outdated. Internet recommends using current # master. Note: at some point, it will be OK to add `sphinx_rtd_theme` to # the `pip install` above => remove line below: - python -m pip install --user https://github.com/rtfd/sphinx_rtd_theme/archive/master.zip -U - python -m pip install --user sphinx sphinx-rtd-theme script: bash ./build_and_deploy.sh Loading @@ -24,7 +22,7 @@ addons: deploy: provider: pages target-branch: gh-pages local-dir: docs/build local-dir: docs/webroot skip-cleanup: true github-token: $GITHUB_TOKEN # Set in travis-ci.org dashboard, marked secure keep-history: true Loading build_and_deploy.sh +3 −41 Original line number Diff line number Diff line #!/bin/bash #!/bin/bash -ex set -e # Exit with nonzero exit code if anything fails # Then we build and deploy the sphinx / doxygen documentation Loading @@ -16,43 +16,5 @@ fi #SSH_REPO=${REPO/https:\/\/github.com\//git@github.com:} #SHA=`git rev-parse --verify HEAD` # Change working directory to /docs cd docs # ..................................... now we're in /docs ############################# DOXYGEN ######################################## cd doxygen # ..................................... now we're in /docs/doxygen # create temporary clone of MFiX-Exa SOURCE_BRANCH git clone https://gitlab-ci-token:$GITLAB_TOKEN@mfix.netl.doe.gov/gitlab/exa/mfix.git # build the Doxygen documentation doxygen doxygen.conf cd .. # ..................................... now we're in /docs # move it to the deploy directory: /docs/build mkdir build mv doxygen/html build/doxygen ############################# SPHINX ######################################## # now do sphinx make html cd build # ..................................... now we're in /docs/build mv html docs_html ############################# WEB SERVER STUFF ################################ # Sphinx is set up to treat build/html (and by mv, build/docs_html) as the # webroot. Hence the .nojekyll file is in the wrong place mv docs_html/.nojekyll . # PWD is currently /docs/build, we want to move /docs/webroot into /docs/build mv ../webroot/* . # build Doxygen docs and Sphinx docs make -C docs docs/Makefile +12 −6 Original line number Diff line number Diff line # Minimal makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = python -msphinx SPHINXPROJ = amrex SOURCEDIR = source BUILDDIR = build BUILDDIR = webroot all: html webroot/doxygen mv webroot/html webroot/docs_html # Sphinx is set up to treat its build directory as the webroot, hence the # .nojekyll file is in the wrong place mv webroot/docs_html/.nojekyll webroot # Put it first so that "make" without argument is like "make help". help: @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) Loading @@ -18,3 +19,8 @@ help: # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) webroot/doxygen: git clone "https://gitlab-ci-token:$(GITLAB_TOKEN)@mfix.netl.doe.gov/gitlab/exa/mfix.git" doxygen/mfix cd doxygen && doxygen doxygen.conf mv doxygen/html $@ docs/source/BuildingMacVelocities.rst 0 → 100644 +62 −0 Original line number Diff line number Diff line Creating the MAC velocities ~~~~~~~~~~~~~~~~~~~~~~~~~~~ To create the normal velocities on faces, we first extrapolate from the cell centers on each side using the slopes as computed earlier, and upwind the face value to define :math:`U^{pred}` . To compute the x-velocity on the x-faces of regular (ie not cut) cells, we call .. code:: shell AMREX_CUDA_HOST_DEVICE_FOR_3D(ubx, i, j, k, { // X-faces Real upls = ccvel_fab(i ,j,k,0) - 0.5 * xslopes_fab(i ,j,k,0); Real umns = ccvel_fab(i-1,j,k,0) + 0.5 * xslopes_fab(i-1,j,k,0); if ( umns < 0.0 && upls > 0.0 ) { umac_fab(i,j,k) = 0.0; } else { Real avg = 0.5 * ( upls + umns ); if ( std::abs(avg) < small_vel) { umac_fab(i,j,k) = 0.0; } else if (avg >= 0) { umac_fab(i,j,k) = umns; } else { umac_fab(i,j,k) = upls; } } }); For cut cells we test on whether the area fraction is non-zero: .. code:: shell AMREX_CUDA_HOST_DEVICE_FOR_3D(ubx, i, j, k, { // X-faces if (ax_fab(i,j,k) > 0.0) { Real upls = ccvel_fab(i ,j,k,0) - 0.5 * xslopes_fab(i ,j,k,0); Real umns = ccvel_fab(i-1,j,k,0) + 0.5 * xslopes_fab(i-1,j,k,0); if ( umns < 0.0 && upls > 0.0 ) { umac_fab(i,j,k) = 0.0; } else { Real avg = 0.5 * ( upls + umns ); if ( std::abs(avg) < small_vel) { umac_fab(i,j,k) = 0.0; } else if (avg >= 0) { umac_fab(i,j,k) = umns; } else { umac_fab(i,j,k) = upls; } } } else { umac_fab(i,j,k) = huge_vel; } }); We then perform a MAC projection on the face-centered velocities to enforce that they satisfy .. math:: \nabla \cdot (\varepsilon_g U^{MAC}) = 0 We do this by solving .. math:: \nabla \cdot \frac{\varepsilon_g}{\rho_g} \nabla \phi^{MAC} = \nabla \cdot \left( \varepsilon_g U^{pred} \right) then defining .. math:: U^{MAC} = U^{pred} - \frac{1}{\rho_g} \nabla \phi^{MAC} docs/source/CITests.rst 0 → 100644 +107 −0 Original line number Diff line number Diff line .. _Chap:CITesting : Continuous Integration ====================== The following regression tests are run every time a commit is pushed to the main MFiX-Exa repository on the NETL gitlab. For each of the tests in the chart below, there are three directional variations; these are identified in the repository as, for example, FLD01-x, FLD01-y, and FLD01-z. For each direction, where appropriate, there are multiple versions, with the following notations: * SGS: single grid serial * MGS: multiple grid serial * TGS: tiled grid serial * MGP: multiple grid parallel Below Ng = number of grids, Npa = number of particles, Np = number of MPI ranks. All the FLD cases are fluid-only and steady state. All the DEM cases are particle-only except for DEM06 and DEM07 which are fluid and particles; these both use the "BVK2" drag type. In all cases the particle data were read in from "particle_input.dat" None of these tests have non-rectangular geometry. "NSW" means "No Slip Wall" and "Per" is "periodic." "MI/PO" refers to Mass Inflow at the low end of the domain and Pressure Outflow at the high end. "PI/PO" refers to Pressure Inflow at the low end of the domain and Pressure Outflow at the high end. Additional detail about these problems is given in tests/README.md Single-grid, single-process (SGS) particle-only tests: +-------+----+----+----+------+------+-------+-----+--------------------+ | Test | nx | ny | nz | bc_x | bc_y | bc_z | Npa | Description | +=======+====+====+====+======+======+=======+=====+====================+ | DEM01 | 2 | 5 | 5 | NSW | Per | Per | 1 | Freely falling | | | | | | | | | | particle with | | | | | | | | | | wall collision | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM02 | 2 | 5 | 5 | NSW | Per | Per | 1 | Multiple bounces | | | | | | | | | | with bounce height | | | | | | | | | | measured | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM03 | 2 | 5 | 5 | NSW | Per | Per | 2 | Two stacked | | | | | | | | | | compressed | | | | | | | | | | particles | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM04 | 4 | 4 | 4 | NSW | Per | Per | 1 | Single particle | | | | | | | | | | slipping on a | | | | | | | | | | rough surface | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM05 | 5 | 2 | 5 | Per | Per | Per | 93 | Oblique particle | | | | | | | | | | collisions | | | | | | | | | | | +-------+----+----+----+------+------+-------+-----+--------------------+ Steady-state fluid-only tests: +-------+-----+----+----+----+-------+------+------+-----+----------------------+ | Test | | nx | ny | nz | bc_x | bc_y | bc_z | Ng | Np | +=======+=====+====+====+====+=======+======+======+=====+======================+ | FLD01 | | 8 | 8 | 4 | Per | NSW | Per | Poiseuille flow | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | | SGS | | | | | | | 1 | 1 | | | | MGS | | | | | | | 4 | 1 | | | | MGP | | | | | | | 4 | 8 | | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | FLD02 | | 80 |16 | 16 | MI/PO | NSW | NSW | Couette flow | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | | SGS | | | | | | | 1 | 1 | | | | MGS | | | | | | | 40 | 1 | | | | MGP | | | | | | | 40 | 8 | | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | FLD03 | | 8 | 8 | 4 | PI/PO | NSW | Per | Poiseuille flow | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | | SGS | | | | | | | 1 | 1 | | | | MGS | | | | | | | 4 | 1 | | | | MGP | | | | | | | 4 | 8 | | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ Coupled particle/fluid tests: +-------+-----+----+----+----+------+------+------+------+----+--------------------+ | Test | | nx | ny | nz | bc_x | bc_y | bc_z | Npa | Ng | Np | +=======+=====+====+====+====+======+======+======+======+====+====================+ | DEM06 | | 50 | 5 | 5 | NSW | NSW | NSW | 1 | Single particle falling | | | | | | | | | | | under gravity | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ | | SGS | | | | | | | | 1 | 1 | | | | MGS | | | | | | | | 10 | 1 | | | | MGP | | | | | | | | 10 | 8 | | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ | DEM07 | | 20 | 20 | 20 | Per | Per | Per | 1222 | Homogeneous cooling | | | | | | | | | | | system | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ | | SGS | | | | | | | | 1 | 1 | | | | MGS | | | | | | | | 8 | 1 | | | | MGP | | | | | | | | 8 | 8 | | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ Loading
.travis.yml +4 −6 Original line number Diff line number Diff line dist: xenial language: generic python: - 3.6 install: - pip install --user sphinx # sphinx_rtd_theme # pypi's sphinx_rtd_theme is outdated. Internet recommends using current # master. Note: at some point, it will be OK to add `sphinx_rtd_theme` to # the `pip install` above => remove line below: - python -m pip install --user https://github.com/rtfd/sphinx_rtd_theme/archive/master.zip -U - python -m pip install --user sphinx sphinx-rtd-theme script: bash ./build_and_deploy.sh Loading @@ -24,7 +22,7 @@ addons: deploy: provider: pages target-branch: gh-pages local-dir: docs/build local-dir: docs/webroot skip-cleanup: true github-token: $GITHUB_TOKEN # Set in travis-ci.org dashboard, marked secure keep-history: true Loading
build_and_deploy.sh +3 −41 Original line number Diff line number Diff line #!/bin/bash #!/bin/bash -ex set -e # Exit with nonzero exit code if anything fails # Then we build and deploy the sphinx / doxygen documentation Loading @@ -16,43 +16,5 @@ fi #SSH_REPO=${REPO/https:\/\/github.com\//git@github.com:} #SHA=`git rev-parse --verify HEAD` # Change working directory to /docs cd docs # ..................................... now we're in /docs ############################# DOXYGEN ######################################## cd doxygen # ..................................... now we're in /docs/doxygen # create temporary clone of MFiX-Exa SOURCE_BRANCH git clone https://gitlab-ci-token:$GITLAB_TOKEN@mfix.netl.doe.gov/gitlab/exa/mfix.git # build the Doxygen documentation doxygen doxygen.conf cd .. # ..................................... now we're in /docs # move it to the deploy directory: /docs/build mkdir build mv doxygen/html build/doxygen ############################# SPHINX ######################################## # now do sphinx make html cd build # ..................................... now we're in /docs/build mv html docs_html ############################# WEB SERVER STUFF ################################ # Sphinx is set up to treat build/html (and by mv, build/docs_html) as the # webroot. Hence the .nojekyll file is in the wrong place mv docs_html/.nojekyll . # PWD is currently /docs/build, we want to move /docs/webroot into /docs/build mv ../webroot/* . # build Doxygen docs and Sphinx docs make -C docs
docs/Makefile +12 −6 Original line number Diff line number Diff line # Minimal makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = python -msphinx SPHINXPROJ = amrex SOURCEDIR = source BUILDDIR = build BUILDDIR = webroot all: html webroot/doxygen mv webroot/html webroot/docs_html # Sphinx is set up to treat its build directory as the webroot, hence the # .nojekyll file is in the wrong place mv webroot/docs_html/.nojekyll webroot # Put it first so that "make" without argument is like "make help". help: @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) Loading @@ -18,3 +19,8 @@ help: # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) webroot/doxygen: git clone "https://gitlab-ci-token:$(GITLAB_TOKEN)@mfix.netl.doe.gov/gitlab/exa/mfix.git" doxygen/mfix cd doxygen && doxygen doxygen.conf mv doxygen/html $@
docs/source/BuildingMacVelocities.rst 0 → 100644 +62 −0 Original line number Diff line number Diff line Creating the MAC velocities ~~~~~~~~~~~~~~~~~~~~~~~~~~~ To create the normal velocities on faces, we first extrapolate from the cell centers on each side using the slopes as computed earlier, and upwind the face value to define :math:`U^{pred}` . To compute the x-velocity on the x-faces of regular (ie not cut) cells, we call .. code:: shell AMREX_CUDA_HOST_DEVICE_FOR_3D(ubx, i, j, k, { // X-faces Real upls = ccvel_fab(i ,j,k,0) - 0.5 * xslopes_fab(i ,j,k,0); Real umns = ccvel_fab(i-1,j,k,0) + 0.5 * xslopes_fab(i-1,j,k,0); if ( umns < 0.0 && upls > 0.0 ) { umac_fab(i,j,k) = 0.0; } else { Real avg = 0.5 * ( upls + umns ); if ( std::abs(avg) < small_vel) { umac_fab(i,j,k) = 0.0; } else if (avg >= 0) { umac_fab(i,j,k) = umns; } else { umac_fab(i,j,k) = upls; } } }); For cut cells we test on whether the area fraction is non-zero: .. code:: shell AMREX_CUDA_HOST_DEVICE_FOR_3D(ubx, i, j, k, { // X-faces if (ax_fab(i,j,k) > 0.0) { Real upls = ccvel_fab(i ,j,k,0) - 0.5 * xslopes_fab(i ,j,k,0); Real umns = ccvel_fab(i-1,j,k,0) + 0.5 * xslopes_fab(i-1,j,k,0); if ( umns < 0.0 && upls > 0.0 ) { umac_fab(i,j,k) = 0.0; } else { Real avg = 0.5 * ( upls + umns ); if ( std::abs(avg) < small_vel) { umac_fab(i,j,k) = 0.0; } else if (avg >= 0) { umac_fab(i,j,k) = umns; } else { umac_fab(i,j,k) = upls; } } } else { umac_fab(i,j,k) = huge_vel; } }); We then perform a MAC projection on the face-centered velocities to enforce that they satisfy .. math:: \nabla \cdot (\varepsilon_g U^{MAC}) = 0 We do this by solving .. math:: \nabla \cdot \frac{\varepsilon_g}{\rho_g} \nabla \phi^{MAC} = \nabla \cdot \left( \varepsilon_g U^{pred} \right) then defining .. math:: U^{MAC} = U^{pred} - \frac{1}{\rho_g} \nabla \phi^{MAC}
docs/source/CITests.rst 0 → 100644 +107 −0 Original line number Diff line number Diff line .. _Chap:CITesting : Continuous Integration ====================== The following regression tests are run every time a commit is pushed to the main MFiX-Exa repository on the NETL gitlab. For each of the tests in the chart below, there are three directional variations; these are identified in the repository as, for example, FLD01-x, FLD01-y, and FLD01-z. For each direction, where appropriate, there are multiple versions, with the following notations: * SGS: single grid serial * MGS: multiple grid serial * TGS: tiled grid serial * MGP: multiple grid parallel Below Ng = number of grids, Npa = number of particles, Np = number of MPI ranks. All the FLD cases are fluid-only and steady state. All the DEM cases are particle-only except for DEM06 and DEM07 which are fluid and particles; these both use the "BVK2" drag type. In all cases the particle data were read in from "particle_input.dat" None of these tests have non-rectangular geometry. "NSW" means "No Slip Wall" and "Per" is "periodic." "MI/PO" refers to Mass Inflow at the low end of the domain and Pressure Outflow at the high end. "PI/PO" refers to Pressure Inflow at the low end of the domain and Pressure Outflow at the high end. Additional detail about these problems is given in tests/README.md Single-grid, single-process (SGS) particle-only tests: +-------+----+----+----+------+------+-------+-----+--------------------+ | Test | nx | ny | nz | bc_x | bc_y | bc_z | Npa | Description | +=======+====+====+====+======+======+=======+=====+====================+ | DEM01 | 2 | 5 | 5 | NSW | Per | Per | 1 | Freely falling | | | | | | | | | | particle with | | | | | | | | | | wall collision | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM02 | 2 | 5 | 5 | NSW | Per | Per | 1 | Multiple bounces | | | | | | | | | | with bounce height | | | | | | | | | | measured | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM03 | 2 | 5 | 5 | NSW | Per | Per | 2 | Two stacked | | | | | | | | | | compressed | | | | | | | | | | particles | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM04 | 4 | 4 | 4 | NSW | Per | Per | 1 | Single particle | | | | | | | | | | slipping on a | | | | | | | | | | rough surface | +-------+----+----+----+------+------+-------+-----+--------------------+ | DEM05 | 5 | 2 | 5 | Per | Per | Per | 93 | Oblique particle | | | | | | | | | | collisions | | | | | | | | | | | +-------+----+----+----+------+------+-------+-----+--------------------+ Steady-state fluid-only tests: +-------+-----+----+----+----+-------+------+------+-----+----------------------+ | Test | | nx | ny | nz | bc_x | bc_y | bc_z | Ng | Np | +=======+=====+====+====+====+=======+======+======+=====+======================+ | FLD01 | | 8 | 8 | 4 | Per | NSW | Per | Poiseuille flow | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | | SGS | | | | | | | 1 | 1 | | | | MGS | | | | | | | 4 | 1 | | | | MGP | | | | | | | 4 | 8 | | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | FLD02 | | 80 |16 | 16 | MI/PO | NSW | NSW | Couette flow | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | | SGS | | | | | | | 1 | 1 | | | | MGS | | | | | | | 40 | 1 | | | | MGP | | | | | | | 40 | 8 | | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | FLD03 | | 8 | 8 | 4 | PI/PO | NSW | Per | Poiseuille flow | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ | | SGS | | | | | | | 1 | 1 | | | | MGS | | | | | | | 4 | 1 | | | | MGP | | | | | | | 4 | 8 | | +-------+-----+----+----+----+-------+------+------+-----+----+-----------------+ Coupled particle/fluid tests: +-------+-----+----+----+----+------+------+------+------+----+--------------------+ | Test | | nx | ny | nz | bc_x | bc_y | bc_z | Npa | Ng | Np | +=======+=====+====+====+====+======+======+======+======+====+====================+ | DEM06 | | 50 | 5 | 5 | NSW | NSW | NSW | 1 | Single particle falling | | | | | | | | | | | under gravity | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ | | SGS | | | | | | | | 1 | 1 | | | | MGS | | | | | | | | 10 | 1 | | | | MGP | | | | | | | | 10 | 8 | | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ | DEM07 | | 20 | 20 | 20 | Per | Per | Per | 1222 | Homogeneous cooling | | | | | | | | | | | system | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+ | | SGS | | | | | | | | 1 | 1 | | | | MGS | | | | | | | | 8 | 1 | | | | MGP | | | | | | | | 8 | 8 | | +-------+-----+----+----+----+------+------+------+------+----+----+---------------+
