Tutorial Updates

source/user/tutorial/add_arche.rst

@@ -46,7 +46,7 @@ to model facilities that may be at the peripheral of a problem.  The Cycamore
 facility archetypes are:
 
 * **Source:** `Source <http://fuelcycle.org/user/cycamoreagents.html#cycamore-source>`_ 
-  is a generic source of material may fill the role of any
+  is a generic source of material that may fill the role of any
   facility that produces fresh material.  Depending on how much of the fuel
   cycle a user wants to model explicitly, this could fill the role of a uranium
   mine, an enrichment facility, a fuel fabrication facility, import of a commodity from 
@@ -70,16 +70,23 @@ facility archetypes are:
   that permanently holds used nuclear material.  Depending on how much of the
   fuel cycle a user wants to model explicitly, this could fill the role of a
   geologic repository, an interim storage facility, export of a commodity to outside simulated facilities, etc.
+* **Mixer:** `Mixer <https://fuelcycle.org/user/cycamoreagents.html#cycamore-mixer>`_ is 
+* **Storage:** `Storage <https://fuelcycle.org/user/cycamoreagents.html#cycamore-storage>`_
+* 
 
 
 Activity: Discover the Available Archetypes
 ===========================================
 If using |Cyclus| on your machine, the archetypes available to you are only those that you have downloaded. 
-To check which archetypes are downloaded on your machine run the command ``cyclus -a`` from your terminal.
+To check which archetypes are downloaded on your machine run the command ``cyclus -a`` from your terminal. You will notice that there are more archetypes listed than the ones we 
+have discussed. This is because we have only discussed the facility archetypes so far, 
+and Cycamore also has `region and institution archetypes <https://fuelcycle.org/user/tutorial/add_reg_inst.html#concept-regions-institutions>`_, which we will discuss later. 
+
+Note: using this command will only show the 
+`C++-based archetypes <https://fuelcycle.org/arche/tutorial_cpp/index.html>`_ that 
+are available. It will not show any `python-based archetypes <https://fuelcycle.org/arche/tutorial_py/index.html>`_. 
+
 
-If you are not running |Cyclus| on your machine, the archetypes available to you include those in Cycamore, which 
-can be found on the `archetypes
-<http://fuelcycle.org/user/cycamoreagents.html>`_ webpage.
 
 
 What archetypes can you see yourself using in your research?
@@ -125,10 +132,13 @@ The ``archetype`` block is located after the simulation control block and takes
           <lib>lib2</lib>
           <name>arch_2</name>
         </spec>
+        ...
     </archetypes>
 
 where ``lib`` is the library in which the archetype came from and ``name`` is
-the archetype name. Let's build our archetypes!
+the archetype name. You need one `spec` block in the archetypes section 
+for each archetype you use in your simulation. 
+Let's build the archetypes block in our input file. 
 Using the template below and the table below,
 fill in the template with the variables listed in the table below.
 
@@ -200,7 +210,7 @@ Once complete, your ``archetypes`` block should look like:
       </spec>
     </archetypes>
 
-Once complete, append the archetypes section under the control section of input file [#f1]_.
+The order of the archetypes in this block is of no consequence. Once complete, append the archetypes section under the control section of input file [#f1]_.
 
 .. rubric:: Footnotes
 

source/user/tutorial/add_arche_commod_recipe.rst

@@ -2,30 +2,30 @@ Getting Started on Recycle
 ============================
 
 This exercise will start with some simple activities based on what you learned
-in the first exercise.
+in the first exercise, using the second input file you made.
 
 Activity: Adding Archetypes
 -----------------------------
 
 We will need two additional archetypes:
 
-1. Add the *cycamore FuelFab* archetype
-2. Add the *cycamore Separations* archetype
+1. Add the ``Cycamore::FuelFab`` archetype
+2. Add the ``Cycamore::Separations`` archetype
 
 Activity: Adding Commodities
 -----------------------------
 
 We will need 4 additional commodities:
 
-1. Fresh-MOX-Fuel
-2. Used-MOx-Fuel
-3. Separated-Fissile
-4. Separated-Waste
+1. fresh_mox
+2. used_mox
+3. Separated_Fissile
+4. Separated_Waste
 
 Activity: Adding Recipes
 --------------------------
 
-We'll continue with very approximate recipes by adding a single recipe for Used-MOX-Fuel-4:
+We'll continue with very approximate recipes by adding a single recipe for Used-MOX-Fuel:
 
 +------------+-----------------+
 |  U-235     |   0.002         |

source/user/tutorial/add_commod_recipe.rst

@@ -5,7 +5,8 @@ Concept: Commodities
 ++++++++++++++++++++
 
 |Cyclus| exchanges resources between facilities using a market-like mechanism
-called the **dynamic resource exchange (DRE)**.  The concept of a **commodity** is
+called the `**dynamic resource exchange (DRE)** <https://fuelcycle.org/arche/dre.html>`_.  
+The concept of a **commodity** is
 used to simply indicate which facilities may be interested in trading with
 each other through the DRE. A commodity is therefore nothing more than a
 unique name that is used to define a set of producers and consumers of a
@@ -22,18 +23,15 @@ Any potential resource transfer (i.e., a bid or a request) may be
 denoted as **exclusive**. An exclusive transfer excludes partial fulfillment;
 it must either be met fully or not at all. This mode supports concepts
 such as the trading of individual reactor assemblies. In combination
-with the notion of mutual requests, complex instances of supply and
+with the notion of mutual requests (one request that can be met through multiple 
+commodities), complex instances of supply and
 demand are enabled. 
 
-Finally, requesting facilities, institutions and
-regions may apply **preferences** to each potential request-bid pairing
+Finally, requesting facilities may apply **preferences** to each potential request-bid pairing
 based on the proposed resource transfer. Facilities can apply arbitrary
 complex logic to **rank the bids** that they have received, whether based on
 the quantity available in each bid or on the quality of each bid, and
-the consequent implications of the physics behavior of that facility. In
-addition, an institution can apply a higher preference to a partner to
-which it is congenial; similarly, a region may negate any transfers of
-material which have a higher uranium enrichment than is allowable.
+the consequent implications of the physics behavior of that facility. 
 
 For example, the flow graph below shows three suppliers (left) and two
 consumers (right), and the potential flows of various commodities among
@@ -167,7 +165,7 @@ Concept: Recipes
 Most commodities are materials, which have a quantity and an
 isotopic composition.
 Recipes are the isotopic composition of a certain material. For
-example, u_ore has an isotropic composition of 0.711% :math:`^{235}`\ U and
+example, u_ore has an isotopic composition of 0.711% :math:`^{235}`\ U and
 99.284% :math:`^{238}`\ U. The recipe section of a |Cyclus| input file is
 typically located at the end of the input and is of the form:
 
@@ -199,9 +197,10 @@ For example, :math:`^{235}`\ U can be expressed as:
 For more details, reference the `Recipe definition
 <../input_specs/recipe.html>`_ page.
 
-First, we can declare the isotopic compositions of the fresh and spent
-fuel. We'll be using simple recipes: fresh fuel is 4.0% :math:`^{235}`\ U by mass,
-remainder U-238. Spent fuel is 1.1% :math:`^{235}`\ U, 94.0% :math:`^{238}`\ U, 0.9% :math:`^{239}`\ Pu, and
+For this input file, we need to define three recipes: natural uranium, fresh fuel, 
+and spent fuel. We'll be using simple recipes: natural uranium is 0.711% 
+:math:`^{235}`\ U by mass, remainder :math:`^{238}`\ U, fresh fuel is 4.0% :math:`^{235}`\ U by mass,
+remainder U-238, and spent fuel is 1.1% :math:`^{235}`\ U, 94.0% :math:`^{238}`\ U, 0.9% :math:`^{239}`\ Pu, and
 4.0% :math:`^{137}`\ Cs.
 
 Activity: Creating a Recipe

source/user/tutorial/add_deploy.rst

@@ -2,8 +2,8 @@ Deploying New Facilities
 ==========================
 
 Often in fuel cycle analysis, transition scenarios are considered. These ask 
-questins like: "How does the 
-commissioning and decommissioning of reactors affect electrity production or 
+questions like: "How does the 
+commissioning and decommissioning of reactors affect electricity production or 
 material transactions?". Transition analysis will
 require an institution that can deploy additional facilities at given time 
 steps: the ``cycamore DeployInst`` archetype.  This is the simplest institution 
@@ -12,7 +12,8 @@ new facilities, in which the user simply defines the times at which new agents
 should be deployed as copies of available prototypes.
 
 In this case, we will keep the current institutions and add another
-institution that will deploy more facilities over time.
+institution that will deploy more facilities over time, which can be used 
+to meet a growing electricity demand in a simulation.
 
 Example: DeployInst
 --------------------------------
@@ -66,27 +67,27 @@ We will now use this to add the institution for ``DeployInst``.
 
 where:
 
-* prototype: Ordered list of prototypes to build
+* prototypes: Ordered list of prototypes to build
 * build_times: Time step on which to deploy agents given in prototype list
 * n_build: Number of each prototype given in prototype list to build
 
 Activity: Add a New Institution 
-++++++++++++++++++++++++++++++++++++++++++
+--------------------------------
 
 Using the table below and the DeployInst template above, fill out the commodities
 template.
 
-+-------------+-------------+---------------------+
++-----------------------+-------------+-----------+
 | Prototype             | build_times | n_build   |
-+=============+=============+=====================+
++=======================+=============+===========+
 | UraniumMine           | 1           | 1         |
-+-------------+-------------+---------------------+
++-----------------------+-------------+-----------+
 | FuelFab               | 1           | 1         |
-+-------------+-------------+---------------------+
++-----------------------+-------------+-----------+
 | 1178MWe BRAIDWOOD_1   | 2           | 1         |
-+-------------+-------------+---------------------+
++-----------------------+-------------+-----------+
 | 1000MWe LIGHTWATER_1  | 3           | 1         |
-+-------------+-------------+---------------------+
++-----------------------+-------------+-----------+
 
 Using the prototype facilities already created, the new institution should
 look like the following:
@@ -121,16 +122,16 @@ look like the following:
       </config>
     </institution>
 
-The above institution will create 1 ``UraniumMine`` and 1 ``FuelFab`` facility on
+The above institution will deploy 1 ``UraniumMine`` and 1 ``FuelFab`` facility on
 time step 1. The next time step will deploy the ``1178MWe BRAIDWOOD_1`` reactor
 prototype. And finally, at time step 3, the ``1000We LIGHTWATER_1`` will be deployed.
 This institution block goes inside the Region block, with the previously created 
-insitutions blocks. 
+institution blocks. 
 
-**ExampleInstitution** is a placeholder for your institution name, and in this scenario
+``ExampleInstitution`` is a placeholder for your institution name, and in this scenario
 only one of each prototype will be deployed since ``n_build`` has a value of 1 for each.
 
 This example is now complete. Save your file as the desired file name (with ``.xml`` 
 extension) and run your code through |Cyclus|. If your simulation runs into errors, 
 sample files can be found `here <https://doi.org/10.5281/zenodo.4557613>`_ under 
-``input_deployinst.xml`` or ``ouput_deployinst.sqlite``.
+``input_deployinst.xml`` or ``output_deployinst.sqlite``.

source/user/tutorial/add_fab.rst

@@ -1,7 +1,7 @@
 Adding a Stream Mixing Fuel Fabrication Facility
 ==================================================
 
-The cycamore FuelFab archetype uses the _equivalence method_ to mix streams of
+The cycamore FuelFab archetype uses the *equivalence method* to mix streams of
 fissile material with so-called "filler" material in an attempt to match 
 neutronics of the
 requested material. More details about the archetype and the state
@@ -19,17 +19,17 @@ archetype:
     <config>
       <FuelFab>
         <fill_commods> 
-            <val>_______</val> 
+            <val>[string]</val> 
         </fill_commods>
-        <fill_recipe>_______</fill_recipe>
-        <fill_size>_______</fill_size>
+        <fill_recipe>[string]</fill_recipe>
+        <fill_size>[double]</fill_size>
         <fiss_commods>
-            <val>_______</val>
+            <val>[string]</val>
         </fiss_commods>
-        <fiss_size>_______</fiss_size>
-        <spectrum>_______</spectrum>
-        <outcommod>_______</outcommod>
-        <throughput>_______</throughput>
+        <fiss_size>[double]</fiss_size>
+        <spectrum>[string (`fission_spectrum_ave` or `thermal`)]</spectrum>
+        <outcommod>[string]</outcommod>
+        <throughput>[double]</throughput>
       </FuelFab>
     </config>
   </facility>
@@ -42,11 +42,11 @@ plutonium and natural uranium into MOX fuel:
 * Filler stream commodity: ``u_ore``
 * Filler stream recipe: ``nat_u``
 * Filler stream inventory capacity: 1000 tonnes
-* Fissile stream commodity: Separated_Fissile
+* Fissile stream commodity: ``Separated_Fissile``
 * Fissile stream inventory capacity: 5 tonnes
-* Output Commodity: Fresh_MOX_Fuel
+* Output Commodity: ``fresh_mox``
 * Maximum Throughput: 2 tonnes/timestep
-* Specturm type: "thermal"
+* Spectrum type: ``thermal``
 
 Filling in the template, the input block looks like:
 
@@ -62,7 +62,7 @@ Filling in the template, the input block looks like:
         <fiss_commods><val>Separated_Fissile</val></fiss_commods>
         <fiss_size>5000</fiss_size>
         <spectrum>thermal</spectrum>
-        <outcommod>Fresh_MOX_Fuel</outcommod>
+        <outcommod>fresh_mox</outcommod>
         <throughput>2000</throughput>
       </FuelFab>
     </config>