doc and README updates

Docs/UsersGuide/GettingStarted/PeleLMGettingStarted.tex

@@ -18,10 +18,9 @@ \section{Downloading the Code}
 \end{verbatim}
 
 This will create a folder called {\tt amrex/} on your machine.
-
-\item Set the environment variable, {\tt AMREX\_HOME}, on your
-  machine to point to the path name where you have put \amrex.
-  You can add this to your {\tt .bashrc} as:
+Set the environment variable, {\tt AMREX\_HOME}, on your
+machine to point to the path name where you have put \amrex.
+You can add this to your {\tt .bashrc} as:
 \begin{verbatim}
 export AMREX_HOME="/path/to/amrex/"
 \end{verbatim}
@@ -32,6 +31,7 @@ \section{Downloading the Code}
 \end{verbatim}
 
 This will create a folder called {\tt IAMR/} on your machine.
+Set the environment variable, {\tt IAMR\_HOME}.
 
 \item Obtain an ORNL GitLab account and clone the \pele\ repositories:
 \begin{verbatim}
@@ -42,6 +42,7 @@ \section{Downloading the Code}
 \end{verbatim}
 
 This will create folders called {\tt PeleLM/} and {\tt PelePhysics/} on your machine.
+Set the environment variables, {\tt PELELM\_HOME} and {\tt PELE\_PHYSICS\_HOME}.
 
 \item You will want to periodically update each of these repositories
 by typing {\tt git pull} within each repository.

README.rst

@@ -2,13 +2,16 @@ PeleLM
 ==========================================
 *A low Mach number AMR combustion code*
 
-`PeleLM` is an adaptive-mesh low Mach number hydrodynamics code for reacting
-flows.
+`PeleLM` is an adaptive-mesh low Mach number hydrodynamics code for reacting flows.
 
 Getting Started
 ---------------
 
-* To compile and run the `Pele` suite of codes, one needs a C++ compiler that supports the C++11 standard and a Fortran compiler that supports the 2003 standard.  A hierarchical strategy for parallelism is supported, based MPI + OpenMP.  The codes work with all major MPI and OpenMP implementations.  The codes should build and run with no modifications to the `make` system if using a Linux system with the GNU compilers, version 4.8.4 and above.
+* To compile and run the `Pele` suite of codes, one needs a C++ compiler that supports 
+the C++11 standard and a Fortran compiler that supports the 2003 standard.  A hierarchical 
+strategy for parallelism is supported, based MPI + OpenMP.  The codes work with all major 
+MPI and OpenMP implementations.  The codes should build and run with no modifications to 
+the `make` system if using a Linux system with the GNU compilers, version 4.8.4 and above.
 
 To build `PeleLM` and run a sample 2D flame problem:
 
@@ -27,15 +30,21 @@ To build `PeleLM` and run a sample 2D flame problem:
     export PELELM_HOME=<location for PeleLM>
     git clone git@code.ornl.gov:Pele/PeleLM.git ${PELELM_HOME}
 
-4. Move to an example build folder, build an executable ::
+4. Set the environment variable, PELE_PHYSICS_HOME, and clone a copy of `PelePhysics` there ::
+
+    export PELE_PHYSICS_HOME=<location for PeleLM>
+    git clone git@code.ornl.gov:Pele/PelePhysics.git ${PELELM_HOME}
+
+5. Move to an example build folder, build an executable ::
 
     cd ${PELELM_HOME}/Exec/FlameInABox
     make
 
 Dependencies
 ------------
 
-`PeleLM` was created as a renamed, `LMC`, the low Mach code from CCSE (``<https://ccse.lbl.gov/index.html>``),
+`PeleLM` was created as a renamed, `LMC`, the low Mach code from CCSE 
+(``<https://ccse.lbl.gov/index.html>``),
 and is built on the `AMReX` library and the IAMR code (see above).
 
 Development model