Joss paper md files

paper/paper.md

@@ -113,13 +113,23 @@ including common polymers, forcefields, and bulk system initialization algorithm
 
 # Recipes
 `flowerMD` offers the following two ready-to-go recipes to illustrate how the design creates
-potential for expanding the library of open-source and version-controlled workflows. The included example
-code demonstrates how the modularity of `flowerMD` allows use and re-use of workflows, using
- pre-built recipe subclasses included in the repository: `SlabSimulation`, `WeldSimulation`, and `Tensile`.
-This script creates two "slabs" of polyethylene, simulates welding at their interface, then simulates a tensile
-test of the resultant weld. Note that each of these steps can be run independently, and each simulation
+potential for expanding the library of open-source and version-controlled workflows. The example
+code included in this repository demonstrates how the modularity of `flowerMD` allows use and re-use of workflows, using
+pre-built "recipe steps" (subclasses) included in the repository: 
+`flowerMD.modules.welding.SlabSimulation`, `flowerMD.modules.welding.Interface`, `flowerMD.modules.welding.WeldSimulation`,
+and `flowerMD.library.simulations.Tensile`.
+
+We can use these four blocks to build the following recipe:
+1. `SlabSimulation` creates two "slabs" of e.g. polyethylene
+2. `Interface` joins two resultant slabs at an interface
+3. `WeldSimulation` simulates thermal welding at this interface, and
+4. `Tensile` simulates a tensile test of the resultant weld to create a stress/strain curve.
+Note that each of these steps can be run independently, and each simulation
 type is agnostic to system and force field selection, enabling easy iteration with different
-materials, force fields, etc. without replicating the workflow code itself.
+materials, force fields, etc. without replicating the workflow code itself. One example might be
+that we could instead run `SlabSimulation` on two different bulk polymers, then reuse the rest of
+the recipe unchanged. We could also iterate over new weld temperatures pending results of `Tensile` runs, etc.
+We hope this flexible and modular design will be a boon to many future molecular simulation researchers.
 
 # Availability
 `flowerMD` is freely available under the GNU General Public License (version 3)