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Fixes #16
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Ray Speth 2018-08-24 21:46:11 -04:00
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README.md
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@ -1,16 +1,16 @@
# cantera-jupyter
[Cantera](http://cantera.org) examples in the form of [Jupyter](http://jupyter.org)
[Cantera](https://cantera.org) examples in the form of [Jupyter](http://jupyter.org)
notebooks. To see the rendered notebooks, browse the directories above or visit the
links in the list of examples below.
**Existing Cantera users**: If you have [Cantera](http://cantera.org) and
**Existing Cantera users**: If you have [Cantera](https://cantera.org) and
[Jupyter](http://jupyter.org) installed on your local machine, simply download
any Jupyter notebook and you should be able to run it.
**New Cantera Users**: If you don't have an exiting Cantera installation, you
can either
[download and install Cantera](http://cantera.github.io/docs/sphinx/html/install.html)
[download and install Cantera](https://cantera.org/install/index.html)
or give Cantera a test drive in the cloud. Click on the Binder link below to
launch an interactive environment where you can run these examples. For this,
there is no installation required.
@ -49,10 +49,10 @@ there is no installation required.
**How do I use Cantera with Python?**
To learn how to use Cantera with Python, click
[here](http://cantera.github.io/docs/sphinx/html/cython/index.html). For more
An introduction to the Cantera Python interface is available
[here](https://cantera.org/tutorials/python-tutorial.html). For more
advanced uses of Cantera, the complete documentation can be found
[here](http://cantera.github.io/docs/sphinx/html/index.html).
[here](https://cantera.org/documentation/index.html).
**Can I forgo installing Cantera locally and just use Cantera in the cloud every
time?**

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python_tutorial.ipynb
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@ -457,7 +457,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Many properties of a [`Solution`](http://cantera.github.io/docs/sphinx/html/cython/importing.html#cantera.Solution) provide values for each species present in the phase. If you want to get values only for a subset of these species, you can use Python's \"slicing\" syntax to select data for just the species of interest. To get the mole fractions of just the major species in `gas1`, in the order specified, you can write:"
"Many properties of a [`Solution`](https://cantera.org/documentation/dev/sphinx/html/cython/importing.html#cantera.Solution) provide values for each species present in the phase. If you want to get values only for a subset of these species, you can use Python's \"slicing\" syntax to select data for just the species of interest. To get the mole fractions of just the major species in `gas1`, in the order specified, you can write:"
]
},
{
@ -511,7 +511,7 @@
"source": [
"In the previous example, we created an object that models an ideal gas mixture with the species and reactions of GRI-Mech 3.0, using the `gri30.xml` input file included with Cantera. This is a \"pre-processed\" XML input file written in a format that is easy for Cantera to parse, but hard for humans to write. Cantera also supports an input file format that is easier for humans to write, called *CTI*. Several reaction mechanism files in this format are included with Cantera, including ones that model high-temperature air, a hydrogen/oxygen reaction mechanism, and a few surface reaction mechanisms. These files are usually located in the `data` subdirectory of the Cantera installation directory, e.g. `C:\\\\Program Files\\\\Cantera\\\\data` on Windows or `/usr/local/cantera/data/` on Unix/Linux/Mac OS X machines, depending on how you installed Cantera and the options you specified.\n",
"\n",
"If, for some reason, Cantera has difficulty finding where these files are on your system, set environment variable `CANTERA_DATA` to the directory or directories (separated using `;` on Windows or `:` on other operating systems) where they are located. Alternatively, you can call function [`add_directory`](http://cantera.github.io/docs/sphinx/html/cython/importing.html#cantera.add_directory) to add a directory to the Cantera search path:"
"If, for some reason, Cantera has difficulty finding where these files are on your system, set environment variable `CANTERA_DATA` to the directory or directories (separated using `;` on Windows or `:` on other operating systems) where they are located. Alternatively, you can call function [`add_directory`](https://cantera.org/documentation/dev/sphinx/html/cython/importing.html#cantera.add_directory) to add a directory to the Cantera search path:"
]
},
{
@ -529,7 +529,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Cantera input files are plain text files, and can be created with any text editor. See the document *[Defining Phases](http://cantera.github.io/docs/sphinx/html/cti/index.html#sec-defining-phases)* for more information.\n",
"Cantera input files are plain text files, and can be created with any text editor. See the guide *[Defining Phases](https://cantera.org/tutorials/cti/defining-phases.html)* for more information.\n",
"\n",
"A Cantera input file may contain more than one phase specification, or may contain specifications of interfaces (surfaces). Here, we import definitions of two bulk phases and the interface between them from the file `diamond.cti`:"
]
@ -551,7 +551,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Note that the bulk (i.e., 3D or homogenous) phases that participate in the surface reactions must also be passed as arguments to [`Interface`](http://cantera.github.io/docs/sphinx/html/cython/importing.html#cantera.Interface)."
"Note that the bulk (i.e., 3D or homogenous) phases that participate in the surface reactions must also be passed as arguments to [`Interface`](https://cantera.org/documentation/dev/sphinx/html/cython/importing.html#cantera.Interface)."
]
},
{
@ -565,7 +565,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"See *[Converting CK-format files](http://cantera.github.io/docs/sphinx/html/cti/input-files.html#sec-ck-format-conversion)* in the *[Working with Input Files](http://cantera.github.io/docs/sphinx/html/cti/input-files.html#sec-input-files)* documentation."
"See *[Converting CK-format files](https://cantera.org/tutorials/ck2cti-tutorial.html)* in the *[Working with Input Files](https://cantera.org/tutorials/input-files.html)* documentation."
]
},
{
@ -579,7 +579,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"In addition to the Sphinx-generated *[Python Module Documentation](http://cantera.github.io/docs/sphinx/html/cython/index.html#sec-cython-documentation)*, documentation of the Python classes and their methods can be accessed from within the Python interpreter as well.\n",
"In addition to the *[Python Module Documentation](https://cantera.org/documentation/index.html)*, documentation of the Python classes and their methods can be accessed from within the Python interpreter as well.\n",
"\n",
"Suppose you have created a Cantera object and want to know what methads are avialable for it, and get help on using the methods:"
]
@ -1322,7 +1322,7 @@
"\n",
"You might be wondering how `equilibrate` works. (Then again, you might not.) Method `equilibrate` invokes Cantera's chemical equilibrium solver, which uses an element potential method. The element potential method is one of a class of equivalent *nonstoichiometric* methods that all have the characteristic that the probelm reduces to solving a set of $M$ nonlinear algebraic equations, where $M$ is the number of elements (not species). The so-called *stoichiometric* methods, on the other hand (including the Gibbs minimization), require solving $K$ nonlinear equations, where $K$ is the number of species (usually $K >> M$). See Smith and Missen's \"Chemical Reaction Equilibrium Analysis\" for more information on the various algorithms and their characteristics.\n",
"\n",
"Cantera uses a damped Newton method to solve these equations, and does a few other things to generate a good starting guess and to produce a reasonably robust algorithm. If you want to know more about the details, look at the on-line documentated source code of Cantera C++ class [`ChemEquil.h`](http://cantera.org/docs/doxygen/html/ChemEquil_8h.html)."
"Cantera uses a damped Newton method to solve these equations, and does a few other things to generate a good starting guess and to produce a reasonably robust algorithm. If you want to know more about the details, look at the on-line documentated source code of Cantera C++ class [`ChemEquil`](https://cantera.org/documentation/dev/doxygen/html/da/d0e/classCantera_1_1ChemEquil.html)."
]
},
{
@ -1336,9 +1336,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"[`Solution`](http://cantera.github.io/docs/sphinx/html/cython/importing.html#cantera.Solution) objects are also [`Kinetics`](http://cantera.github.io/docs/sphinx/html/cython/kinetics.html#cantera.Kinetics) objects, and provide all of the methods necessary to compute the thermodynamic quantities associated with each reaction, reaction rates, and species creation and destruction rates. They also provide methods to inspect the quantities that define each reaction, such as the rate constants and the stoichiometric coefficients. The rate calculation functions are used extensively within Cantera's *[reactor network model](http://cantera.github.io/docs/sphinx/html/cython/zerodim.html#sec-cython-zerodim)* and *[1D flame model](http://cantera.github.io/docs/sphinx/html/cython/onedim.html#sec-cython-onedim)*.\n",
"[`Solution`](https://cantera.org/documentation/dev/sphinx/html/cython/importing.html#cantera.Solution) objects are also [`Kinetics`](https://cantera.org/documentation/dev/sphinx/html/cython/kinetics.html#cantera.Kinetics) objects, and provide all of the methods necessary to compute the thermodynamic quantities associated with each reaction, reaction rates, and species creation and destruction rates. They also provide methods to inspect the quantities that define each reaction, such as the rate constants and the stoichiometric coefficients. The rate calculation functions are used extensively within Cantera's *[reactor network model](https://cantera.org/documentation/dev/sphinx/html/cython/zerodim.html#sec-cython-zerodim)* and *[1D flame model](https://cantera.org/documentation/dev/sphinx/html/cython/onedim.html#sec-cython-onedim)*.\n",
"\n",
"Information about individual reactions that are independent of the thermodynamic state can be obtained by accessing [`Reaction`](http://cantera.github.io/docs/sphinx/html/cython/kinetics.html#cantera.Reaction) objects with the [`Kinetics.reaction`](http://cantera.github.io/docs/sphinx/html/cython/kinetics.html#cantera.Kinetics.reaction) method:"
"Information about individual reactions that are independent of the thermodynamic state can be obtained by accessing [`Reaction`](https://cantera.org/documentation/dev/sphinx/html/cython/kinetics.html#cantera.Reaction) objects with the [`Kinetics.reaction`](https://cantera.org/documentation/dev/sphinx/html/cython/kinetics.html#cantera.Kinetics.reaction) method:"
]
},
{