Merge pull request #52 from LLNL/jouleheating_bugfix

Implements a bugfix for Joule heating terms
- Adds option to include y-direction pressure gradient (oldseec=0) --> Warning if not used
- jhswitch=0 should always be used --> Warning if not used
- Added override-variable that must be set to 1 by users to allow using old models

.gitignore

@@ -5,14 +5,9 @@ build/
 .idea/
 .DS_Store
 *~
-*.swp
 a.out
-PyUEDGE_tutorial/*
-*.swo
-*.egg
 pyscripts/__src__.py
-uedge.egg-info/
 dist/uedge-8.0.0-py3.7-macosx-10.9-x86_64.egg
 uedge.egg-info
+*.egg
 *.c
-*.f

INSTALL

@@ -1,44 +1,50 @@
 
-UEDGE is in a transitional phase from running in the BASIS environment, 
-developed at LLNL, to Python. This version, tagged $Name:  $, can 
-run in both environments. If you have interest in the Basis version of 
-UEDGE contact Bill Meyer ([email protected]). New installations of the 
-Basis version are discouraged as there is no longer any official support 
-for the Basis software. Unless you know otherwise, assume this checkout 
-is intended for building the Python UEDGE module. The remainder of these 
-installation instructions apply only to the Python version of UEDGE. The 
-Python version of UEDGE has been build on several Linux distributions and 
-on MacOSX High Sierra and Mojave. 
+Uedge was originally developed to run in the Basis environment developed 
+at LLNL. It has since been ported to run as a Python module. The Python
+module Uedge has been built on several Linux distributions and MacOSX versions.
 
+The Basis version of Uedge is deprecated. If you have interest in 
+the Basis version of Uedge contact Bill Meyer ([email protected]).  There 
+is no longer any official support for the Basis software. The capability
+to build the Basis version is maintained for legacy installations and
+may be removed from the repository at any time.
 
-Building Python UEDGE (pyUedge).
+
+Building Python Uedge (pyUedge).
 
     Prerequisites:
-        - Python 2.7
-              We recommend the Anaconda (2) Python data science distribution. 
-              This includes many useful packages. Besides the base Python 
-              packages pyUedge includes Python scripts that utilize the 
-              matplotlib and hdf5 packages. Numpy is a required package to 
-              build pyUedge.
+        - Python 3.x
+              Should work with all Python 3 versions.
+
+              Anaconda3 is a useful Python distribution but puts constraints
+              on the compiler version that may be used to build pyUedge. The 
+              compiler must be compatible with the libraries that come included
+              with Anaconda. Anaconda will report the gcc version that was used
+              to build the included libraries. The compiler used must at least 
+              use the same C runtime library version.
 
         - Fortran/C compilers
-              Only gfortran and gcc have been tested. 
+              Only gfortran and gcc have been tested and supported. 
 
-    Requisites:
         - Forthon 
-           Generates link between UEDGE Fortran and Python.
-           pip install forthon
-        - MPPL (More Productive Programming Language)
-           MPPL is a Fortran preprocessor
-           pip install mppl
+           Generates link between Uedge Fortran and Python.
+           "pip install forthon"
+
+    Requisites:
+        - matplotlib
+           pyUedge includes Python scripts that import maplotlib
+        - h5py
+           pyUedge includes Python scripts for saving/restoring results
+           in hdf5 files.
 
 
      Install with pip:
         pip install uedge
 
-        ****Note that there was a version numbering change. If a 
-        "pip show uedge" reports version 7.6 then a "pip uninstall uedge" 
-        and "pip install --no-cache-dir uedge" will be nesseccary.
+        If pyUedge reports that an update is available then a 
+        "pip install uedge --upgrade" can be executed. If that results in
+        multiple versions a "pip uninstall uedge" and 
+        "pip install --no-cache-dir uedge" will be nesseccary.
 
      Install from git clone:
        python setup.py build

aph/Package

@@ -3,6 +3,6 @@ POINTER = cray
 
 VDF = aph.v
 
-NVDF = ../com/com_basis.v
+NVDF = ../com/com.v
 
 SM = aphrates.m aphread.m

api/Package

@@ -1,9 +1,9 @@
 PKG = api
 POINTER = cray
 
-VDF = api_basis.v
+VDF = api.v
 
-NVDF = ../com/com_basis.v ../bbb/bbb_basis.v
+NVDF = ../com/com.v
 
 SM = apifcn.m apip93.m apisorc.m fimp.m inelrates.m fmombal.m sputt.m
 

api/api.v

@@ -16,6 +16,10 @@ KMXZ=KXA*MXMINZ
 NBA=5		# used in fmombal
 }
 
+***** Com_Dim_Vars hidden:    
+dim_vars_hidden     integer    # Do not edit this group. It is used to build
+                               # the Basis version of the code. 
+
 ***** Physical_constants2:
 # Add the 2 to distinquish from same constants in package bbb
 ev2	real	/1.6022e-19/   # 1 electron volt in Joules