adding analysis documentation

docs/source/userGuide/models/color/analysis/basic.rst

@@ -0,0 +1,38 @@
+======================================
+Color model -- Basic Analysis
+======================================
+
+The basic analysis routine for the LBPM color model logs a time series
+of averaged information to the space-delimited CSV file ``timelog.csv``.
+The ``analysis_interval`` key should be specified to control the interval at
+to perform basic analysis, which corresponds to the number of simulation timesteps
+to perform between analyses. The basic analysis routine is designed to
+be lightweight so that it can be performed frequently, and it is almost always
+useful to enable it. Results  will be immediately logged
+to ``timelog.csv`` which can be used to assess whether or not the simulation is
+behaving as expected. Furthermore, the analysis framework will check
+simulation measures to verfiy that no ``NaN`` are detected for the fluid
+pressure and flow rate.
+
+The list of measures logged to ``timelog.csv`` are defined as follows.
+The region of space occupied by the wetting fluid is determined from the
+phase indicator field, :math:`\Omega_w:\phi<0` 
+
+
+* ``sw`` -- water saturation (fluid component 2)
+* ``krw`` -- water effective permeability 
+* ``krn`` -- non-wetting fluid effective permeability
+* ``krn`` -- non-wetting fluid effective permeability
+* ``krwf`` -- non-wetting fluid effective permeability
+* ``krnf`` -- non-wetting fluid effective permeability
+
+  
+More comprehensive analysis is performed in the ``subphase`` analysis module. 
+
+.. code-block:: bash
+
+Analysis {
+    analysis_interval = 1000
+    visualization_interval = 20000
+ }
+

docs/source/userGuide/models/color/index.rst

@@ -37,6 +37,16 @@ that can be over-ridden to develop customized simulations.
 
    protocols/*
 
+****************************
+Analysis capabilities
+****************************
+   
+.. toctree::
+   :glob:
+   :maxdepth: 2
+
+   analysis/*
+
 
 ***************************
 Model parameters
@@ -44,10 +54,12 @@ Model parameters
 
 The essential model parameters for the color model are
 
-- :math:`\alpha` -- control the interfacial tension between fluids with key ``alpha``
-- :math:`\beta`  -- control the width of the interface with key ``beta``
-- :math:`\tau_A` -- control the viscosity of fluid A with key ``tauA``
-- :math:`\tau_B` -- control the viscosity of fluid B with key ``tauB``
+- ``alpha`` -- control the interfacial tension between fluids with :math:`0 < \alpha < 0.01`
+- ``beta`` -- control the width of the interface with key :math:`\beta < 1`
+- ``tauA`` -- control the viscosity of fluid A with :math:`0.7 < \tau_A < 1.5`
+- ``tauB`` -- control the viscosity of fluid B with :math:`0.7 < \tau_B < 1.5`
+- ``rhoA`` -- control the viscosity of fluid A with :math:`0.05 < \rho_A < 1.0`
+- ``rhoB`` -- control the viscosity of fluid B with :math:`0.05 < \rho_B < 1.0`
 
 ****************************
 Model Formulation