Added ability to check for the NeutPy main configuration file before …

…trying to run it.

Updated README.md
Uploading shot 144977_3000 for reference.

GT3/Neutrals/neutrals.py

@@ -9,6 +9,7 @@
 from neutpy import neutrals
 from collections import namedtuple
 import json
+import os.path
 from GT3.Core.Processors import NumpyEncoder
 
 
@@ -17,6 +18,7 @@ class Neutrals:
 
     def __init__(self, inp, core, cpus=False):
 
+
         if abs(1.0 - core.sep_val) > .0001:
             print "The separatrix value has been overwritten. Cannot run Neutrals calculation"
             return
@@ -36,9 +38,12 @@ def __init__(self, inp, core, cpus=False):
         except:
             # Run NeutPy
             print "Neutrals data not found. Running NeutPy"
+            if not self._check_conf("neutpy.conf"):
+                raise IOError("No NeutPy main configuration file found.")
             self.npi = neutrals()
             if cpus:
                 self.npi.set_cpu_cores(cpus)
+
             self.npi.from_gt3(core, inp)
             self.data = self.NeutralDataNT(self.npi.midpts[:, 0],
                                     self.npi.midpts[:, 1],
@@ -56,6 +61,8 @@ def __init__(self, inp, core, cpus=False):
 
     def reRun(self, cpus=False):
         print ("Manually re-running NeutPy")
+        if not self._check_conf("neutpy.conf"):
+            raise IOError("No NeutPy main configuration file found.")
         self.npi = neutrals()
         if cpus:
             self.npi.set_cpu_cores(cpus)
@@ -87,4 +94,11 @@ def _save_data(self):
         except Exception as e:
             print "Unable to save NeutPy data to file: %s" % str(e)
 
+    def _check_conf(self, f):
+        """
+        Checks to see if a neutpy.conf file exists
+        :return: A boolean of whether the file exists.
+        :rtype: bool
+        """
+        return os.path.isfile(f)
 

README.md

@@ -1,4 +1,4 @@
-The Georgia Tech Tokamak Transport Code (GT3)
+The Georgia Tech Tokamak Transport Code (GT3). Also known as GTEDGE2.
 
 **Installation**
 
@@ -36,3 +36,41 @@ To install NeutPy:
 
 `$ pip install neutpy`
 
+**Usage**
+
+GT3 can be run in 2 different ways: via a config file and profiles or via a test data class.
+
+- **From Files**
+
+The primary method of running GT3 is via the gt3 class
+
+```python
+from GT3 import gt3
+```
+
+If `neutpy` is installed, you'll see a message indicating that it is being imported. Otherwise, a warning 
+will be given. If you will be running `neutpy`, the main configuration file needs to be placed in the
+CWD. A sample configuration file can be found on the neutpy github as `neutpy.conf`
+
+GT3 is instantiated in this manner by providing an input file.
+
+```python
+myPlasma = gt3(inputFile="myInputFile")
+```
+
+See the `/inputs` directory for example input files (generally called `togt3_d3d_shotid_timeid`).
+The `inputFile` argument takes a file relative to the current working directory (CWD). An input file will
+include some plasma parameters and meshing information. In addition, the locations of 1D and 2D
+profile data are entered into this file. The locations also must be relative to the CWD. See the
+`inputs` directory for an example with DIII-D shot 144977.3000.
+
+GT3 includes various modules that provide information and calculations about the plasma. Running `gt3()`
+with the `mode` argument will run different sets of modules (see `gt3.py` for a list of modes).
+Modules can also be run using the various arguments (`run_IOL()`, `run_NBI()`, `run_radial_transport()`, etc.).
+
+To run the full radial transport code, use the `mode='radialtrans'` argument in `gt3()` or run 
+`myPlasma.run_radial_transport()`.
+
+- **From A Class**
+
+*Documentation Coming Soon*

inputs/144977_3000/gt3_144977_3000_Te.dat

@@ -0,0 +1,201 @@
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