Merge pull request #13 from jaclark5/update

Add 'adding an eos' section to setting up page and links to eos and c…

Author: jaclark5

docs/eos.rst

@@ -6,6 +6,9 @@ Here we list list the available equations of state and the function used to acce
 
 .. autofunction:: despasito.equations_of_state.eos
 
+
+.. _eos-types:
+
 Available EOS
 -------------
 

docs/getting_started.rst

@@ -5,7 +5,7 @@ Install Package
 ---------------
 .. note:: DESPASITO is not yet available on pip or conda-forge, but it is a package that can be installed in your python environment.
 
-**Step 1:** Download the master branch from our github page as a zip file, or clone it with gitand save in your desired directory.
+**Step 1:** Download the master branch from our github page as a zip file, or clone it with git and save in your desired directory.
 
 **Step 2:** Install with ``pip install .``
 

docs/index.rst

@@ -12,7 +12,7 @@ First open-source application for thermodynamic calculations and parameter fitti
 
 The first facet is a means to evaluate the SAFT-:math:`\gamma`-Mie EOS for binary vapor-liquid equilibria (VLE). This framework allows easy implementation of more advanced thermodynamic calculations as well as additional forms of SAFT or other equations of state. Feel free to contribute!
 
-The second facet is parameterization, not only of the equation of state (EOS) but also for simulations. The SAFT-:math:`\gamma`-Mie formalism is an attractive source of simulation parameters as it offers a means to directly link the intermolecular potential with thermodynamic properties. This application has the ability to fit EOS parameters to experimental thermodynamic data in a top down approach for self and cross interaction parameters. Once published, we will also provide an scripts to estimate cross interaction parameters for SAFT-:math:`\gamma`-Mie from DFT calculations. It should be noted that it is recommended to additionally fine tune simulation parameters in an iterative fashion, but previous works have found close agreement with those fit to the EOS.
+The second facet is parameterization, not only of the equation of state (EOS) but also for simulations. The SAFT-:math:`\gamma`-Mie formalism is an attractive source of simulation parameters as it offers a means to directly link the intermolecular potential with thermodynamic properties. This application has the ability to fit EOS parameters to experimental thermodynamic data in a top down approach for self and cross interaction parameters. Once published, we will also provide scripts to estimate cross interaction parameters for SAFT-:math:`\gamma`-Mie from DFT calculations. It should be noted that it is recommended to additionally fine tune simulation parameters in an iterative fashion, but previous works have found close agreement with those fit to the EOS.
 
 .. toctree::
    :maxdepth: 1

docs/settingup.rst

@@ -2,6 +2,8 @@
 Setting Up a Thermodynamic Calculation
 ======================================
 
+.. contents:: :local:
+
 Basic Use
 #########
 In this tutorial we will assume the user is creating the necessary files for the python module use of this package (rather than as an imported library). A basic calculation requires 2 files:
@@ -29,6 +31,8 @@ The first three lines are used in producing our EOS object. The `bead_config` li
 
 The last 4 lines for thermodynamic calculation instructions, although only `calculation_type` is actually required. The other lines depend on the calculation type being used. In this case, defining the pressure is optional, if it was missing DESPASITO would assume atmospheric pressure.
 
+See :ref:`calc-types` for a list of available types of thermodynamic calculations.
+
 `EOSgroup.json`::
     
     {
@@ -80,3 +84,17 @@ If you checked our examples folder in DESPASITO, you might have noticed that the
  #. In the command line, include the `-p` option to define the absolute or relative path.
 
 Other options for controlling the output are also available in the command line implementation. Type `python -m despasito -h` to discover more.
+
+Specifying Equation of State (EOS)
+##################################
+
+By default, DESPASITO used the SAFT-:math:`\gamma`-Mie equation of state. However, you can change the EOS by adding the "eos" option to the `input.json` file. This option is passed to the :func:`~despasito.equations_of_state.eos` function, an example of this can be found in the Peng-Robinson calculations in the `examples` directory. The syntax for an equation of state is module.eos, where module is the family the eos belongs to, and eos is the equation of state. For Peng-Robinson this entry would be,
+
+    "eos": "cubic.peng_robinson"
+
+and for SAFT-:math:`\gamma`-Mie,
+
+    "eos": "saft.gamma_mie"
+
+See :ref:`eos-types` for a list of available equations of state.
+

docs/thermo.rst

@@ -4,9 +4,13 @@ Thermodynamic Calculations
 
 .. autofunction:: despasito.thermodynamics.thermo
 
+.. _calc-types:
+
 Available Calculation Types
 ---------------------------
 
+Click below!
+
 .. currentmodule:: despasito
 .. autosummary::
    :toctree: _autosummary
@@ -15,6 +19,9 @@ Available Calculation Types
 
 Supporting Thermodynamic Functions
 ----------------------------------
+
+Click below!
+
 .. autosummary::
    :toctree: _autosummary