Merge branch 'devel_branch' into cleanup

CMakeLists.txt

@@ -61,11 +61,12 @@ set(USE_DYN_TN false)
 # Set compiler versions for Cmake
 #  Intel
 if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
+    add_definitions(-DPPIFORT)
     set(compiler_name "ifort")
     add_definitions(-DPPIFORT)
 #  GNU
 elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
-    add_definitions(-DPPGFOFTRAN)
+    add_definitions(-DPPGFORTRAN)
     set(compiler_name "gfortran")
 endif ()
 find_program(WHICH NAMES which)

LICENSE

@@ -631,8 +631,8 @@ to attach them to the start of each source file to most effectively
 state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
+    {one line to give the program's name and a brief idea of what it does.}
+    Copyright (C) {year}  {name of author}
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    <program>  Copyright (C) <year>  <name of author>
+    {project}  Copyright (C) {year}  {fullname}
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.

docs/Gemfile

@@ -0,0 +1,25 @@
+source "https://rubygems.org"
+ruby RUBY_VERSION
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+# gem "jekyll", "3.3.0"
+
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.0"
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+gem "github-pages", group: :jekyll_plugins
+gem "jekyll-theme-minimal"
+
+# If you have any plugins, put them here!
+# group :jekyll_plugins do
+#    gem "jekyll-feed", "~> 0.6"
+# end

docs/README.md

@@ -0,0 +1,35 @@
+LESGO solves the filtered Navier-Stokes equations in the high-Reynolds number
+limit on a Cartesian mesh. Originally designed to simulate flow in the
+atmospheric boundary layer, LESGO has been extended and used to simulate flow
+over tree canopies, wall-mounted cubes, and wind turbine arrays, among other things.
+At its core is the LES flow solver. Built on top of the solver are modules that provide
+additional functionality such as immersed boundary methods, wind farm modeling, and so on.
+
+LESGO was originally based on the code presented in John D. Albertson's PhD Thesis "Large
+eddy simulation of land-atmosphere interaction" (University of California, Davis
+1996). In the intervening years, many researchers have [contributed](contributors.html)
+to LESGO's code base and used LESGO in dozens of scientific [publications](publications.html).
+
+If you use LESGO for any purpose, please [cite](citing.html) appropriately.
+
+LESGO is distributed without any warranty or technical support.
+
+## Features
+* [Flow solver](solver.html)
+* [Subgrid scale models](subgrid.html)
+* [Wall models](wall-model.html)
+* [Level set immersed boundary method](levelset.html)
+* [Wind turbine modeling](wind.html)
+* [Concurrent precursor simulations](precursor.html)
+
+## Getting started
+To [get started](start.html), download the code using the buttons on the left.
+You'll need a modern Fortran compiler that supports C preprocessor directives,
+[CMake](https://cmake.org/), and [FFTW3](http://www.fftw.org/).
+
+## Licensing
+LESGO is a free, open-source tool published under the
+[GNU General Public License Version 3](http://www.gnu.org/licenses/)
+
+## Acknowledgements
+Development of LESGO has been supported in part by the National Science Foundation.

docs/_config.yml

@@ -0,0 +1,16 @@
+# Site settings
+title: LESGO
+email: [email protected]
+description:  # this means to ignore newlines until "baseurl:"
+  LESGO is a parallel pseudo-spectral large-eddy simulation code.
+show_downloads: "true"
+
+# Build settings
+theme: jekyll-theme-minimal
+markdown: kramdown
+repository: lesgo_jhu/lesgo-pages
+exclude:
+  - Gemfile
+  - Gemfile.lock
+
+

docs/_layouts/default.html

@@ -0,0 +1,68 @@
+<!doctype html>
+<html>
+  <head>
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="chrome=1">
+    <title>{{ site.title | default: site.github.repository_name }} by {{ site.github.owner_name }}</title>
+
+    <link rel="stylesheet" href="{{ '/assets/css/style.css?v=' | append: site.github.build_revision | relative_url }}">
+    <meta name="viewport" content="width=device-width">
+
+    <script type="text/javascript"
+            src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+    </script>
+    <!--[if lt IE 9]>
+    <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
+    <![endif]-->
+  </head>
+  <body>
+    <div class="wrapper">
+      <header>
+        <h1>{{ site.title | default: site.github.repository_name }}</h1>
+        <img src="img/abl.png" alt="ABL" style="width:304px;">
+        <p>{{ site.description | default: site.github.project_tagline }}</p>
+
+        {% if site.github.is_project_page %}
+          <p class="view"><a href="{{ site.github.repository_url }}">View the Project on GitHub <small>{{ github_name }}</small></a></p>
+        {% endif %}
+
+        {% if site.github.is_user_page %}
+          <p class="view"><a href="{{ site.github.owner_url }}">View My GitHub Profile</a></p>
+        {% endif %}
+
+        {% if site.show_downloads %}
+          <ul>
+            <li><a href="{{ site.github.zip_url }}">Download <strong>ZIP File</strong></a></li>
+            <li><a href="{{ site.github.tar_url }}">Download <strong>TAR Ball</strong></a></li>
+            <li><a href="{{ site.github.repository_url }}">View On <strong>GitHub</strong></a></li>
+          </ul>
+        {% endif %}
+      </header>
+      <section>
+
+      {{ content }}
+
+      </section>
+      <footer>
+<!--         {% if site.github.is_project_page %} -->
+<!--         <p>This project is maintained by <a href="{{ site.github.owner_url }}">{{ site.github.owner_name }}</a></p> -->
+<!--         {% endif %} -->
+        <img src="img/by-sa.png" alt="by-sa" style="width:100px;">
+        <p><small>Content on this site is licensed under a <a href="https://creativecommons.org/licenses/by-sa/3.0/">Creative Commons Attribution-ShareAlike 3.0 Unported license</a>. Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
+      </footer>
+    </div>
+    <script src="{{ '/assets/js/scale.fix.js' | relative_url }}"></script>
+
+
+  {% if site.google_analytics %}
+    <script>
+        (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+        (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+        m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+        })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
+        ga('create', '{{ site.google_analytics }}', 'auto');
+        ga('send', 'pageview');
+    </script>
+  {% endif %}
+  </body>
+</html>

docs/actuator-disk.md

@@ -0,0 +1,62 @@
+# Actuator disk model
+Each turbine is represented as a drag disk with a force that depends on the
+velocity at the disk (averaged in time and space).  This force is distributed
+across several grid points that together represent the turbine.  For large arrays
+the coarse grid resolution does not allow for the modeling of individual
+blades. LESGO's implementation does not include rotation of the drag disk, and
+tangential forces are not applied to the flow.
+
+The turbine force is given by
+\\[F = -\frac{1}{2} \rho C_T' \left \langle u_d \right \rangle^2 A\\]
+where \\(\rho\\) is the fluid density, \\(C_T'\\) is the local thrust
+coefficient, \\(\left \langle u_d \right \rangle\\) is the disk and time-averaged
+velocity, and \\(A\\) is the rotor swept area.
+
+The force is distributed across grid points using an indicator function which
+is determined during code initialization. To avoid Gibbs phenomenon with sharp
+gradients, this indicator function (currently 1 inside and 0 outside a turbine)
+is smoothed with a Gaussian filter. Each grid point with a non-zero indicator
+function applies a force on the flow.
+
+## Settings
+The first settings specify the wind-turbine array geometry and orientation.
+The user can set the number of turbines in each direction as well
+as their size. Several common orientations (aligned, staggered, etc) are
+available. The user is also able to specify the thrust coefficients \\(C_T'\\).
+
+In addition to easy to use options for regularly arranged wind farms, the user
+may also specify the details for each wind turbine in the farm by writing a
+custom "input_turbines/param.dat" file. This allows for any wind farm
+configuration and allows each turbine to have its own rotor diameter,
+orientation, and thrust coefficient. The thrust coefficients and orientation of
+each turbine may also be changed in time by writing custom input files in the
+folder "input_turbines".
+
+Technical settings relating to the filtering of the indicator function, time
+averaging, and output writing are also available in "lesgo.conf". More details
+are also provided as comment in the input file.
+
+## Output
+All output files relating to the turbines can be found in the "turbine" folder.
+The following quantities are also written to file for each turbine in the files
+"turbine_#.dat".
+* current time (dimensional)
+* disk center u velocity (dimensionless)
+* disk center v velocity (dimensionless)
+* disk center w velocity (dimensionless)
+* instantaneous disk-averaged velocity (dimensionless)
+* current time and disk-averaged velocity (dimensionless)
+* counter clockwise angle, when viewed from above, from the -*x* direction \\(\theta_1\\) (degrees)
+* angle above the horizontal \\(\theta_2\\) (degrees)
+* local thrust coefficient \\(C_T'\\)
+
+The values of the time and disk-averaged velocity for each turbine as
+well as the filtering time scale are written to file "u_d_T.dat". The horizontally
+averaged streamwise velocity at the top of the domain is written to "vel_top.dat"
+
+## References
+Calaf M, Meneveau C, and Meyers J. "[Large eddy simulation study of fully developed
+wind-turbine array boundary layers](http://dx.doi.org/10.1063/1.3291077)."
+*Physics of Fluids* **22** (2010). 015110.
+
+Meyers J, Meneveau C. "[Large eddy simulations of large wind-turbine arrays in the atmospheric boundary layer](http://dx.doi.org/10.2514/6.2010-827)." *50th AIAA Aerospace Sciences Meeting*, (2010). Orlando, FL. AIAA Paper No. 2010-827.

docs/actuator-line.md

@@ -0,0 +1,68 @@
+# Actuator line/sector model
+
+The actuator line model (ALM) is implemented by applying body forces to
+the flow field. These forces are calculated by sampling the velocity field along
+the blades. At each blade point, the lift and drag forces are read from
+precomputed tables and applied to the flow field using a Gaussian filter kernel
+at a scale \\(\epsilon \\).
+
+## Settings
+The ALM in LESGO is implemented in a similar form as the [SOWFA](https://nwtc.nrel.gov/SOWFA) package from NREL, including the input
+files. Input files for the NREL 5MW reference turbine are located in "inputATM."
+The turbine array is specified in "inputATM/turbineArrayProperties." For example:
+
+
+    ! Global Properties
+    numberOfTurbines        1
+    outputInterval          1
+    updateInterval          1
+
+    ! First turbine
+    TURBINE_1 {
+    turbineType             "NREL5MWRef"
+    baseLocation            190.0, 315.0, 225.0
+    numBladePoints          60
+    epsilon                 12.5
+    sampling                "atPoint"
+    rotationDir             "cw"
+    Azimuth                 232.0105
+    RotSpeed                9.155
+    Pitch                   0
+    NacYaw                  0
+    fluidDensity            1.23
+    numAnnulusSections      1
+    annulusSectionAngle     0.
+    nacelleFlag             false
+    nacelleCd               1.
+    TSR                     6.
+    tipALMCorrection        .true.
+    optimalEpsilon          0.25
+    }
+
+Each turbine type is defined in a file that specifies basic details about the
+gemoetry of the turbine, the turbine controller, and definitions of the blades.
+The lift and drag lookup tables are located in the folder "inputATM/AeroData."
+
+## Output
+All output files relating to the turbines can be found in the "turbineOutput"
+folder. The following The following quantities are written for each turbine in the files
+"turbineOutput/TURBINE_#/...".
+* Drag coefficient
+* Drag force
+* Lift coefficient
+* Lift force
+* Thrust force
+* Tangential force
+* Axial force
+* Axial velocity
+* Relative velocity
+* Tangential velocity
+* Yaw angle
+* Pitch angle
+* Rotational speed
+* Power
+
+# References
+Martínez-Tossas LA, Churchfield M, Meneveau C. "[Large Eddy Simulation of wind turbine wakes: detailed comparisons of two codes focusing on effects of numerics and subgrid modeling](https://doi.org/10.1088/1742-6596/625/1/012024)." *Journal of Physics: Conference Series* **625** (2015). 012024.
+
+Martínez-Tossas LA, Stevens RJAM, Meneveau C. "[Wind farm large-eddy simulations on very coarse grid resolutions using an actuator line model](https://doi.org/10.2514/6.2016-1261)." *34th Wind Energy Symposium* (2016). San Diego, California. AIAA Paper No. 2016-1261.

docs/citing.md

@@ -0,0 +1,47 @@
+# Citing LESGO
+
+If you use LESGO, please cite the code appropriately. In addition to a citation
+to this website:
+
+*LESGO: A parallel pseudo-spectral large-eddy simulation code.*
+[https://lesgo-jhu.github.io/lesgo](https://lesgo-jhu.github.io/lesgo) (2017)
+
+include references to the relevant research articles. The articles that should
+be cited depend on the features used. See the list below to select the appropriate
+references for your use.
+
+## Subgrid scale models
+Bou-Zeid E, Meneveau C, Parlange MB. "[A scale-dependent Lagrangian dynamic model
+for large eddy simulation of complex turbulent flows](http://dx.doi.org/10.1063/1.1839152)."
+*Physics of Fluids* **17** (2005). 025105.
+
+Porté-Agel F, Meneveau C, Parlange MB. “[A scale-dependent dynamic model for large eddy simulation: applications to a neutral atmospheric boundary layer](https://doi.org/10.1017/S0022112000008776).” *Journal of Fluid Mechanics* **415** (2000). 261-284.
+
+Smagorinsky J. "[General circulation experiments with the primitive equations: I. The basic experiment](http://journals.ametsoc.org/doi/abs/10.1175/1520-0493%281963%29091%3C0099%3AGCEWTP%3E2.3.CO%3B2)."
+ *Monthly Weather Review* **91** (1963). 99-164.
+
+## Wall models
+Yang X, Sadique J, Mittal R, Meneveau C. "[Integral wall model for large eddy
+simulations of wall-bounded turbulent flows](http://dx.doi.org/10.1063/1.4908072)".
+*Physics of Fluids* **27** (2015). 025112.
+
+Moeng CH. "[A Large-Eddy-Simulation Model for the Study of Planetary Boundary-Layer Turbulence](https://doi.org/10.1175/1520-0469(1984)041<2052:ALESMF>2.0.CO;2)." *Journal of the Atmospheric Sciences* **41** (1984). 2052–2062.
+
+## Concurrent precursor method
+Stevens RJAM, Graham J, Meneveau C. "[A concurrent precursor inflow method for
+Large Eddy Simulations and applications to finite length wind farms](https:/doi.org/10.1016/j.renene.2014.01.024)."
+*Renewable Energy* **68** (2014). 46-50.
+
+## Wind turbines: actuator disk model
+Calaf M, Meneveau C, and Meyers J. "[Large eddy simulation study of fully developed
+wind-turbine array boundary layers.](http://dx.doi.org/10.1063/1.3291077)"
+*Physics of Fluids* **22** (2010). 015110.
+
+Meyers J, Meneveau C. "[Large eddy simulations of large wind-turbine arrays in
+the atmospheric boundary layer.](http://dx.doi.org/10.2514/6.2010-827 )" *50th
+AIAA Aerospace Sciences Meeting*, Orlando, FL, 2010. AIAA Paper No. 2010-827.
+
+## Wind turbines: actuator line model
+Martínez-Tossas LA, Churchfield M, Meneveau C. "[Large Eddy Simulation of wind turbine wakes: detailed comparisons of two codes focusing on effects of numerics and subgrid modeling](https://doi.org/10.1088/1742-6596/625/1/012024)." *Journal of Physics: Conference Series* **625** (2015). 012024.
+
+Martínez-Tossas LA, Stevens RJAM, Meneveau C. "[Wind farm large-eddy simulations on very coarse grid resolutions using an actuator line model](https://doi.org/10.2514/6.2016-1261)." *34th Wind Energy Symposium* (2016). San Diego, California. AIAA Paper No. 2016-1261.

docs/contributors.md

@@ -0,0 +1,20 @@
+# Contributors
+LESGO is the product of work by many research over many years.
+
+* William Anderson
+* Elie Bou-Zeid
+* Joel Bretheim
+* Stuart Chester
+* Jason Graham
+* Perry Johnson
+* Tony Martinez
+* Fernando Porté-Agel
+* Carl Shapiro
+* Richard Stevens
+* Yuheng Tseng
+* Claire VerHulst
+* Xiang Yang
+
+As an open source code, everyone is free to modify and add to the current LESGO
+code. If you would like to contribute to the main repository, please contact us
+with information about the contribution.