Implement penalty BC

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
     - name: Install apt packages
       run: |
         sudo apt-get update
-        sudo apt-get install gfortran libopenmpi-dev
+        sudo apt-get install gfortran libopenmpi-dev ccache
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1

.gitignore

@@ -4,7 +4,7 @@
 # Compiled Object files
 *.slo
 *.lo
-*.o
+# *.o
 *.obj
 
 # Precompiled Headers
@@ -23,7 +23,7 @@
 # Compiled Static libraries
 *.lai
 *.la
-*.a
+# *.a
 *.lib
 
 # Executables
@@ -63,6 +63,7 @@ src/*/_version.py
 pip-wheel-metadata
 build/
 .nox
+.coverage
 
 # Jupyter
 .ipynb_checkpoints

README.md

@@ -7,15 +7,25 @@
 
 ## Quick start
 
+Install using Python 3.6+ as follows:
+
+    git clone --recursive https://github.com/exabl/snek5000-abl.git
+    cd snek5000-abl
+    pip install -e .
+
+Activate necessary environment variables
+
+    source activate.sh
+
+Use the command line tool to launch / set / inspect the simulation parameters
+
+    abl --help
+
+## Tests
 ```sh
 pip install -e '.[tests]'
 # Run simple tests: including compilation
 pytest
 # Run slow tests: launches simulation
 pytest --runslow
 ```
-# Authors
-
-* [Ashwin Vishnu Mohanan](mailto:[email protected])
-* [Geert Brethouwer](mailto:[email protected]) 
-* [Luigi Antonialli](mailto:[email protected])

Snakefile

@@ -1,4 +1,8 @@
+import os
 from glob import iglob
+from pathlib import Path
+
+import snek5000
 from snek5000.util.archive import tar_name, archive
 
 PYTHON_DIRECTORIES = ["docs", "src", "tests"]
@@ -55,6 +59,8 @@ rule ctags:
     input:
         nek5000="lib/Nek5000/core",
         abl="src/abl",
+        snek=Path(snek5000.__file__).parent,
+        py_env=os.getenv("VIRTUAL_ENV", os.getenv("CONDA_PREFIX", ""))
     output:
         ".tags",
     params:
@@ -68,13 +74,15 @@ rule ctags:
                     "logs",
                     "*.tar.gz",
                     "*.f?????",
+                    "*.py",
                 )
             )
         ),
     shell:
         """
         ctags --verbose -f {output} --language-force=Fortran -R {input.nek5000}
         ctags --verbose -f {output} {params.excludes} --append --language-force=Fortran -R {input.abl}
+        ctags -f {output} --append --languages=Python -R {input.abl} {input.snek} {input.py_env}/lib
         """
 
 

activate.sh

@@ -1,6 +1,6 @@
-DIR="$(pwd)"
+DIR="$(pwd -P)"
 export NEK_SOURCE_ROOT="$DIR/lib/Nek5000"
-export PATH="$PATH:$NEK_SOURCE_ROOT/bin"
+export PATH="$PATH:$NEK_SOURCE_ROOT/bin:$DIR/bin"
 
 alias smake="snakemake"
 # tarball utilities

bin/abl.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+# MESH=11; ROUGH=0.1
+# MESH=212; ROUGH=0.1
+# MESH=222; ROUGH=0.0001
+MESH=12; ROUGH=0.0001
+
+abl -d penalty -m $MESH -n penalty -o 1 -w 7-00:00:00 --in-place False \
+  -fw 0.05 -fc 0.75 -ft False -sb False \
+  -s mixing_len \
+  -b noslip \
+  -zw $ROUGH -z0 $ROUGH \
+  -p 1.0 \
+  $@

bin/submit.py

@@ -5,50 +5,56 @@
 from snek5000.clusters import Cluster
 
 cluster = Cluster()
-sub_dir = "november"
-base_name_run = "hi"
+sub_dir = "21march"
+base_name_run = "pen"
 sub_command = "launch"
 #  sub_command = "launch compile"
 # sub_command = "launch release"; cluster.cmd_run = "echo"
 # sub_command = "debug"
 # sub_command = "show box"
-dry_run = False
+dry_run = True
 
 for (
     mesh_nb_nodes_walltime,
     filter_weight,
     filter_cutoff,
     filter_temporal,
-    sgs_model,
     sgs_boundary,
+    sgs_model,
+    boundary_cond,
     z_wall,
+    z0,
+    pen_tiamp,
 ) in itertools.product(
-    zip([111], [1] * 1, [f"{days}-00:00:00" for days in (7,) * 1]),
+    zip([222], [1] * 1, [f"{days}-00:00:00" for days in (1,) * 1]),
     [0.05],
     [0.75],
     # [0.], [1.],
     [False],
-    ["vreman", "constant", "shear_imp"],
-    # "dynamic"],
     [False],
-    [0.1],
+    ["mixing_len"],
+    #  ["vreman", "constant", "shear_imp"],
+    # "dynamic"],
+    ["noslip"],
+    [0.0001],
+    [0.001],
+    [-(10 ** p) for p in range(6)],
 ):
     mesh, nb_nodes, walltime = mesh_nb_nodes_walltime
 
-
-    name_run = (
-        f"{base_name_run}-{sgs_model}-ft{int(filter_temporal)}-sb{int(sgs_boundary)}"
-    )
+    name_run = f"{base_name_run}-{sgs_model}-{pen_tiamp:07d}"
     if filter_temporal and sgs_boundary:
         print(f"skipping ... {name_run}")
         continue
 
     cmd = (
-        f"\n{sys.executable} ./simul.py "
+        f"\n{sys.executable} -m abl.cli "
         f"-d {sub_dir} -m {mesh} -n {name_run} -o {nb_nodes} -w {walltime} "
         f"-fw {filter_weight} -fc {filter_cutoff} -ft {filter_temporal} "
         f"-s {sgs_model} -sb {sgs_boundary} "
-        f"-zw {z_wall} "
+        f"-b {boundary_cond} "
+        f"-zw {z_wall} -z0 {z0} "
+        f"-p {pen_tiamp} "
         f"{sub_command}"
     )
     if dry_run:
@@ -66,6 +72,6 @@
             email="[email protected]",
             interactive=True,
             omp_num_threads=None,  # do not set
+            # NOTE: for small simulations
+            nb_cores_per_node=16,
         )
-
-# ./simple.py -m 2 -n geert -o 1 -w 7-00:00:00 -zw 0 -fw 0.05 -fc 0.75 show size

docs/Doxyfile

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "eTurb"
+PROJECT_NAME           = "abl"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -790,7 +790,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = .. ../lib/Nek5000/core ../src/abl ../src/abl/toolbox ../src/abl/sgs
+INPUT                  = .. ../lib/Nek5000/core ../src/abl ../src/abl/toolbox ../src/abl/sgs ../src/abl/bc ../src/abl/forcing
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -909,7 +909,12 @@ FILE_PATTERNS          = *.c \
                          MNTRLOGD \
                          MNTRTMRD \
                          RPRMD \
-                         STATD
+                         STATD \
+                         PENALTY \
+                         DYN \
+                         SGS \
+                         SGS_BC \
+                         WMLES
                          # *.py \
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
@@ -925,7 +930,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = ../lib/Nek5000/core/makenek.inc
+EXCLUDE                = ../lib/Nek5000/core/makenek.inc ../src/abl/forcing/penalty.f
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

docs/conf.py

@@ -50,7 +50,7 @@ def root(module):
 
 version = ".".join(abl.__version__.split(".")[:3])
 # The full version, including alpha/beta/rc tags
-release = abl.__version__
+release = version
 
 
 # -- General configuration ---------------------------------------------------
@@ -157,14 +157,57 @@ def root(module):
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_material"
+
+
+# Set link name generated in the top bar.
+html_title = "main docs"
+
+html_sidebars = {
+    "*[!index]*": [
+        "logo-text.html",
+        "globaltoc.html",
+        "localtoc.html",
+        "searchbox.html",
+    ]
+}
+
+html_favicon = "_static/favicon.ico"
+
+# Material theme options (see theme.conf for more information)
+html_theme_options = {
+    # Set the name of the project to appear in the navigation.
+    "nav_title": f"{project} documentation",
+    # ??
+    "touch_icon": html_favicon,
+    # Logo to the left of the title
+    "logo_icon": "&#x1F30A",  # https://emojipedia.org/water-wave/
+    #
+    "nav_links": [
+        {"href": "doxygen/modules", "title": "fortran docs", "internal": True}
+    ],
+    # Specify a base_url used to generate sitemap.xml. If not
+    # specified, then no sitemap will be built.
+    "base_url": f"https://exabl.github.io/{project}",
+    # Set the color and the accent color
+    "color_primary": "teal",
+    "color_accent": "dark-green",
+    # Set the repo location to get a badge with stats
+    "repo_url": f"https://github.com/exabl/{project}/",
+    "repo_name": project,
+    # Visible levels of the global TOC; -1 means unlimited
+    "globaltoc_depth": 1,
+    # If False, expand all TOC entries
+    "globaltoc_collapse": True,
+    # If True, show hidden TOC entries
+    "globaltoc_includehidden": False,
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-html_favicon = "_static/favicon.ico"
 
 # -- Options for Intersphinx -------------------------------------------------
 

docs/index.rst

@@ -1,11 +1,15 @@
-.. eturb documentation master file, created by
+.. snek5000-abl documentation master file, created by
    sphinx-quickstart on Wed Dec 25 01:55:26 2019.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
 Welcome to snek5000-*abl*'s documentation!
 ===========================================
 
+The ABL_ project is an interdisciplinary effort to model the atmospheric
+boundary layer using Nek5000_. This documentation describes the Fortran user
+code and its Python interface made using snek5000_'s API.
+
 .. raw:: html
 
 
@@ -58,9 +62,9 @@ Links
 .. * :ref:`Upstream documentation for Nek5000 <nek:genindex>`
 .. Strange intersphinx bug: WARNING: undefined label: nek:genindex (if the link has no caption the label must precede a section header)
 
-* `Nek5000 documentation <https://nek5000.github.io/NekDoc/appendix.html>`_
+* Nek5000_ documentation
 * `KTH framework documentation <https://kth-nek5000.github.io/KTH_Framework>`_
-* `snek5000 documentation <https://exabl.github.io/snek5000>`_
+* snek5000_ documentation
 * `pymech documentation <https://pymech.readthedocs.io>`_
 
 Indices and tables
@@ -71,3 +75,6 @@ Indices and tables
 * :ref:`search`
 * `Documentation produced with Doxygen <doxygen/modules.html>`_
 
+.. _ABL: https://e-science.se/people-and-research/projects/exabl/
+.. _Nek5000: https://nek5000.github.io/NekDoc/appendix.html
+.. _snek5000: https://snek5000.readthedocs.io

noxfile.py

@@ -3,4 +3,4 @@
 
 @nox.session(python=["3.6", "3.7", "3.8"])
 def tests(session):
-    session.run("pytest")
+    session.run("pytest", "tests")

setup.cfg

@@ -21,15 +21,23 @@ packages=find:
 install_requires =
     snek5000 >= 0.4.0b1
     pymech >= 1.3.0.post0
+    click
     zstandard
 setup_requires =
     setuptools_scm
 
+[options.entry_points]
+console_scripts =
+    abl = abl.cli:main
+
+snek5000.solvers =
+    abl = abl.solver
+
 [options.extras_require]
 docs =
     sphinx
     recommonmark
-    sphinx_rtd_theme
+    sphinx-material
     breathe
     setuptools_scm
 

src/.editorconfig

@@ -0,0 +1,3 @@
+[*.f]
+indent_size = 3
+trim_trailing_whitespace = true