Merge pull request #3 from bschrag620/dev

Version 1.1

Author: bschrag620

main.py

@@ -7,23 +7,13 @@
 To create a plot, the first object that is needed is a Layer object. A layer has attributes of 
 (depth in cm, temperature in Kelvin, pressure in mBars, minimum window range in wavenumber cm-1, 
 maximum window range in wavenumber cm-1)
-# var_name = pyrad.Layer(10, 296, 1013.25, 600, 700
-Next, define the molecules that make up the layer. This can be done in 2 ways. Either method will
-require the same attributes to be defined, which are a (text name, HITRAN molecule ID - see table below,
-molecular weight, concentration). Concentration can be defined using ppm=, ppb=, percentage=, or concentration=,
-the app will adjust accordingly. You will get a warning if total concentrations exceed 1. First method for adding
-molecules, add them one at a time directly to the layer using .addMolecule. It's also a good idea if you want to 
-change properties of the molecules to set this equal to a molecule variable name. For ease, use the same variable
-name as description:
-####    UPDATE      ####
-ONLY USE THE TEXT NAME OF THE MOLECULE, NO NEED TO GIVE THE MOLECULE ID ANYMORE
+# var_name = pyrad.Layer(10, 296, 1013.25, 600, 700)
+Next, define the molecules that make up the layer. To do so, use layer.addMolecule(text name or molecule ID, 
+concentration, isotopeDepth) 
+
 # co2 = your_layer_name_here.addMolecule('co2', 44, ppm=350)
 # h2o = your_layer_name_here.addMolecule('h2o', 18, percentage=.4)
-The second method involves defining the molecules individually, then adding them to the layer using 
-.addMolecules (note the 's' on the end)
-# co2 = pyrad.Molecule('co2', 2, 44, ppm=350)
-# h2o = pyrad.Molecule('h2o, 1, 18, concentration=.004)
-# layer.addMolecules(co2, h2o)
+
 With the layer properties and composition defined, choose what to plot:
 # pyrad.plot(object, plotchoice)
 
@@ -32,19 +22,22 @@
 'absorption coefficient'
 'absorbance'
 'cross section'
-Personal favorite add-on is to set individualColors=True in the plot command. This will plot up to
-6 molecules individually by color as well as the total in white. There is also a choice to set 
-fill=False if you prefer to see just the outline.
+'emissivity'
+
+Personal favorite add-on is to set individualColors=True in the plot command. This will plot the base object in white
+and up to 6 of the objects that make it up in individual colors. Example, define co2 to have an isotope depth of 3,
+plotting the transmittance will show each isotope in it's own color with the total transmittance in white. There is 
+also a choice to set fill=False if you prefer to see just the outline.
 Questions or bugs, email brad.schrag@gmail.com
 """
 
-layer = pyrad.Layer(10, 300, 101.325, 640, 670)
-co2 = pyrad.Molecule('co2', 44, ppm=400)
-h2o = pyrad.Molecule('h2o', 18, percentage=.4)
-ozone = pyrad.Molecule('o3', 48, ppb=10)
+layer = pyrad.Layer(10, 300, 1013.25, 635, 640)
+co2 = layer.addMolecule('co2', ppm=400, isotopeDepth=3)
+h2o = layer.addMolecule('h2o', percentage=.4)
+ozone = layer.addMolecule('o3', ppb=10)
 
-layer.addMolecules(co2, h2o, ozone)
-pyrad.plot(co2, 'transmittance', individualColors=True)
+layer.createCrossSection()
+pyrad.plot(layer, 'transmittance', individualColors=True)
 
 """
 MOLECULE_ID = {'h2o': 1, 'co2': 2, 'o3': 3, 'n2o': 4, 'co': 5,