updates top level documentation to 0.87

COPYRIGHT

@@ -1,8 +1,22 @@
 =============================================================================
-ATS: COPYRIGHT 
+ATS: COPYRIGHT
 =============================================================================
+
+Amanzi is being developed as a multi-lab open-source community code.
+Although, copyright is asserted by each lab on the contributions of
+its employees, Amanzi has a single open-source license, namely the
+three-clause BSD license.  Terms of use, redistribution and
+modification, as well as the disclaimer are given in the BSD license
+at LICENSE.
+
+----------------------------------------------
+Los Alamos National Laboratory:
+----------------------------------------------
 
-  Copyright 2011. Los Alamos National Security, LLC. This material was
+  Copyright (c) 2011-2014, Los Alamos National Security, LLC
+  All rights reserved.
+
+  Copyright 2011-2014. Los Alamos National Security, LLC. This software was
   produced under U.S. Government contract DE-AC52-06NA25396 for Los Alamos
   National Laboratory (LANL), which is operated by Los Alamos National
   Security, LLC for the U.S. Department of Energy. The U.S. Government has
@@ -13,38 +27,11 @@ ATS: COPYRIGHT
   modified software should be clearly marked, so as not to confuse it with
   the version available from LANL.
 
-  Additionally, this library is free software; redistribution and use 
-  in source and binary forms, with or without modification, are permitted 
-  provided that the following
-  conditions are met:
-
-  * Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
-
-  * Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in
-    the documentation and/or other materials provided with the
-    distribution.
-
-  * Neither the name of Los Alamos National Security, LLC, Los Alamos
-    National Laboratory, LANL, the U.S. Government, nor the names of
-    its contributors may be used to endorse or promote products
-    derived from this software without specific prior written
-    permission.
-
-  THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND
-  CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
-  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-  DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR
-  CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-  USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-  ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-  OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-  SUCH DAMAGE.
-
-=============================================================================
+  Additionally, this library is free software; you can redistribute it
+  and/or modify it under the terms of the three-clause BSD license
+  that is included at the end of this document.
 
+----------------------------------------------
+Oak Ridge National Laboratory:
+----------------------------------------------
+

INSTALL.md

@@ -1,6 +1,7 @@
-= Amanzi and ATS Installation Guide =
+ATS Installation Guide
+==================================
 
-First, a word of warning -- please be patient.  Amanzi and therefore ATS depend upon a lot of third party libraries.  This allows us to use existing, mature code to make ATS a much better software tool.  It also means installing the code and its dependencies can be quite painful and time/labor intensive.  Installation time is a very bimodal distribution -- if it "just works" this process will take 25 minutes.  If it doesn't "just work" it can take much longer.
+First, a word of warning -- please be patient.  Amanzi and therefore ATS depend upon a lot of third party libraries.  This allows us to use existing, mature code to make ATS a much better software tool.  It also means installing the code and its dependencies can be quite painful and time/labor intensive.  Installation time is a very bimodal distribution -- if it "just works" this process will take 10=20 minutes.  If it doesn't "just work" it can take much longer.
 
 The basics of the process are these.
 
@@ -11,17 +12,17 @@ The basics of the process are these.
 4. Download and install ATS.
 5. Download test problems, test ATS.
 
-All instructions assume you use bash.  Alter as needed for other shells.
+All instructions assume you use bash.  Change as needed for other shells.
 
 0. Ensure you have cmake and an MPI installation.
-  a. cmake >= 2.8.6
+  a. cmake >= 3.3
     ```
     which cmake  # this will test if you have any cmake installed
     ``` 
     If not, go to: http://www.cmake.org/cmake/resources/software.html
     To install cmake from command line see https://cmake.org/install/
 
-    Binary installations are likely fine?
+    Alternative, most binary installations are new enough, including Homebrew, Ubuntu, etc.
 
   b. MPI
     ```
@@ -50,22 +51,26 @@ All instructions assume you use bash.  Alter as needed for other shells.
     ```
     mkdir /my/path/to/atsl
     export ATS_BASE=/my/path/to/ats
+
     export ATS_SRC_DIR=${ATS_BASE}/repos/ats
-    export AMANZI_SRC_DIR=${ATS_BASE}/repos/amanzi
     export ATS_BUILD_DIR=${ATS_BASE}/ats-build
-    export AMANZI_BUILD_DIR=${ATS_BASE}/amanzi-build    
-    export AMANZI_TPLS_BUILD_DIR=${ATS_BASE}/amanzi-tpls-build    
     export ATS_DIR=${ATS_BASE}/ats-install
+
+    export AMANZI_SRC_DIR=${ATS_BASE}/repos/amanzi
+    export AMANZI_BUILD_DIR=${ATS_BASE}/amanzi-build    
     export AMANZI_DIR=${ATS_BASE}/amanzi-install    
+
+    export AMANZI_TPLS_BUILD_DIR=${ATS_BASE}/amanzi-tpls-build    
     export AMANZI_TPLS_DIR=${ATS_BASE}/amanzi-tpls-install
     export PATH=${ATS_DIR}/bin:${AMANZI_TPLS_DIR}/bin:${PATH}
+    export PYTHONPATH=${ATS_SRC_DIR}/tools/utils:${PYTHONPATH}
     ```    
-    You may want to put that line in your ~/.bashrc or similar files (~/.bash_profile on Mac OS X).
-  b. Clone the Amanzi source for the latest release.  Currently this is ``0.86``
-    ```git clone -b ats-amanzi-0.86 http://github.com/amanzi/amanzi $AMANZI_SRC_DIR```
+    You may want to put these lines in your ~/.bashrc or similar files (~/.bash_profile on Mac OS X), or better yet use Environment modules.
+  b. Clone the Amanzi source for the latest release.  Currently this is ``0.87``
+    ```git clone -b amanzi-0.87 http://github.com/amanzi/amanzi $AMANZI_SRC_DIR```
 
   c. Clone the ATS source for the latest release.
-    ```git clone -b ats-0.86 http://github.com/amanzi/ats $ATS_SRC_DIR```
+    ```git clone -b ats-0.87 http://github.com/amanzi/ats $ATS_SRC_DIR```
 
   d. Set up a directory for configuration scripts and a TPL installation directory.
     ```
@@ -137,8 +142,8 @@ All instructions assume you use bash.  Alter as needed for other shells.
     ```
   b. Run the script.
     ```. $ATS_BASE/ats-config-files/configure-amanzi-debug.sh```
-  c. Enter your T&E for the week.  This isn't as long (~3-5 minutes?)
-  d. Run Amanzi tests.  Some may not pass, but having them run means you should be in good shape.
+  c. Check your email.  This isn't as long (~3-5 minutes?)
+  d. Run Amanzi tests.  Some may not pass, but having them run with most passing means you should be in good shape.
     ```
     cd $AMANZI_BUILD_DIR
     make test
@@ -160,7 +165,7 @@ All instructions assume you use bash.  Alter as needed for other shells.
     cmake \
       -D Amanzi_DIR=${AMANZI_DIR}/lib \
       -D CMAKE_INSTALL_PREFIX=${ATS_DIR} \
-       -D CMAKE_BUILD_TYPE=Debug \
+      -D CMAKE_BUILD_TYPE=Debug \
     ${ATS_SRC_DIR}
 
     make -j8
@@ -174,7 +179,7 @@ All instructions assume you use bash.  Alter as needed for other shells.
   cd $ATS_BASE
   mkdir testing
   cd testing
-  git clone -b ats-demos-0.86 http://github.com/amanzi/ats-demos
+  git clone -b ats-demos-0.87 http://github.com/amanzi/ats-demos
   ```
   b. Run a test problem.
     ```

README.md

@@ -1,32 +1,30 @@
 ATS: The Advanced Terrestrial Simulator
 =======================================
 
-The Advanced Terrestrial Simulator (also know as the Arctic Terrestrial Simulator) is code for solving ecosystem-based, integrated, distributed hydrology.
+The Advanced Terrestrial Simulator (formerly sometimes known as the Arctic Terrestrial Simulator) is a code for solving ecosystem-based, integrated, distributed hydrology.
 
-Capabilities are largely based on solving various forms of Richards equation coupled to a surface flow equation, along with the needed sources and sinks for ecosystem and climate models.  This can (but need not) include thermal processes (especially ice for frozen soils), evapo-transpiration, albedo-driven surface energy balances, snow, biogeochemistry, plant dynamics, and much more.
+Capabilities are largely based on solving various forms of Richards equation coupled to a surface flow equation, along with the needed sources and sinks for ecosystem and climate models.  This can (but need not) include thermal processes (especially ice for frozen soils), evapo-transpiration, albedo-driven surface energy balances, snow, biogeochemistry, plant dynamics, deformation, transport, and much more.
 
 
 Getting the code
 ----------------
 
-If you just plan on using ATS and think what you want is likely in a recent release, please prefer to use the most recent [release version available here](https://github.com/amanzi/ats-dev/releases).
+If you just plan on using ATS and think what you want is likely in a recent release, please prefer to use the most recent [release version available here](https://github.com/amanzi/ats/releases).
 
-If you instead expect to do new development, please use the developer version and clone the [ats-dev repository](http://github.com/amanzi/ats-dev) using:
+If you instead expect to do new development, please use the developer version and clone the [ats repository](http://github.com/amanzi/ats) using:
 
 ```
-git clone http://github.com/amanzi/ats-dev
+git clone http://github.com/amanzi/ats
 ```
 
-NOTE: there is also an ats repository that is currently simply a placeholder for better project pages to come.  Cloning that repository will do you no good!
-
 
 Installation
 ------------
 
-Please see the [INSTALL](https://github.com/amanzi/ats-dev/blob/master/INSTALL.md) file included in the top level directory of your ATS download, or the [ats-dev wiki](https://github.com/amanzi/ats-dev/wiki).
+Please see the [INSTALL](https://github.com/amanzi/ats/blob/master/INSTALL.md) file included in the top level directory of your ATS download.
 
 
 License and Copyright
 ---------------------
 
-Please see the [LICENSE](https://github.com/amanzi/ats-dev/blob/master/LICENSE) and [COPYRIGHT](https://github.com/amanzi/ats-dev/blob/master/COPYRIGHT) files included in the top level directory of your ATS download.
+Please see the [LICENSE](https://github.com/amanzi/ats/blob/master/LICENSE) and [COPYRIGHT](https://github.com/amanzi/ats/blob/master/COPYRIGHT) files included in the top level directory of your ATS download.