Merge pull request #76 from festim-dev/structure

Better structure for Verification

report/_toc.yml

@@ -12,23 +12,27 @@ parts:
   - caption: Verification
     chapters:
       - file: verification/methods
-      - file: verification/cases
+      - file: verification/simple_cases
         sections:
-        - file: verification/mes/depleting_source
-        - file: verification/mms/simple
-        - file: verification/mms/simple_transient
-        - file: verification/mms/fluxes
-        - file: verification/mms/discontinuity
-        - file: verification/mms/trapping
-        - file: verification/mms/heat_transfer
-        - file: verification/mes/radioactive_decay
-        - file: verification/mms/radioactive_decay
-        - file: verification/mms/soret
-        - file: verification/mms/simple_temperature
-        - file: verification/mes/tmap_1b
-        - file: verification/mes/tmap_1c
-        - file: verification/mes/tmap_1da
-        - file: verification/mes/tmap_1db
+          - file: verification/mms/simple
+          - file: verification/mms/simple_transient
+          - file: verification/mms/simple_temperature
+      - file: verification/mms/fluxes
+      - file: verification/mms/heat_transfer
+      - file: verification/mms/discontinuity
+      - file: verification/mms/trapping
+      - file: verification/decay
+        sections:
+          - file: verification/mes/radioactive_decay
+          - file: verification/mms/radioactive_decay
+      - file: verification/mms/soret
+      - file: verification/tmap
+        sections:
+          - file: verification/mes/depleting_source
+          - file: verification/mes/tmap_1b
+          - file: verification/mes/tmap_1c
+          - file: verification/mes/tmap_1da
+          - file: verification/mes/tmap_1db
   - caption: Validation
     chapters:
       - file: validation/plasma-driven-permeation/plasma-driven-permeation

report/verification/decay.md

@@ -0,0 +1 @@
+# Radioactive decay

report/verification/mes/depleting_source.md

@@ -15,7 +15,7 @@ kernelspec:
 
 # Diffusion from a Depleting Source
 
-```{tags} 2D, MES, transient
+```{tags} 1D, MES, transient
 ```
 
 This verification case {cite}`ambrosek_verification_2008` consists of an enclosure containing an initial quantity of hydrogen gas (at an initial pressure $P_0$).

report/verification/mes/tmap_1db.md

@@ -29,8 +29,8 @@ where
 
 $\lambda \ \mathrm{(m)}$ is the lattice parameter, \
 $\nu \ (\mathrm{s}^{-1})$, the Debye frequency \
-$n$ is the trapping site fraction, \
-$c_m (\text{atom} \ \mathrm{m}^{-3})$ is the mobile atom concentration,
+$n \ (\mathrm{s}^{-1})$ is the trapping site fraction, \
+$c_\mathrm{m} \ (\text{H} \ \mathrm{m}^{-3})$ is the mobile concentration,
 
 and the effective diffusivity $\mathrm{D_\text{eff}}$ is defined by
 

report/verification/methods.md

@@ -26,7 +26,9 @@ For each case, the L2 error $E$ is calculated in the domain $\Omega$:
 \end{equation}
 where $u_\mathrm{exact}$ and $u_\mathrm{computed}$ are the exact and computed solutions, respectively.
 
-A [detailed example](mms/simple.md) is available in this book.
+```{seealso}
+[This example](mms/simple.md) details the MMS approach.
+```
 
 ## Differentiating MES and MMS
 

report/verification/mms/discontinuity.md

@@ -27,7 +27,11 @@ Two exact solutions for mobile concentration of hydrogen are manufactured for bo
     c_\mathrm{right,exact} &= \dfrac{K_{S,\mathrm{right}}}{K_{S,\mathrm{left}}} \ c_\mathrm{left,exact}
 \end{align}
 
-Note that the manufactured solutions were chosen so that the particle flux $J = -D \nabla c_\mathrm{m} \cdot \textbf{n}$ is continuous across the materials interface. 
+````{margin}
+```{note}
+The manufactured solutions were chosen so that the particle flux $J = -D \nabla c_\mathrm{m} \cdot \textbf{n}$ is continuous across the materials interface. 
+```
+````
 
 MMS sources are derived in each material: 
 

report/verification/mms/simple_temperature.md

@@ -14,7 +14,7 @@ kernelspec:
 
 # Simple diffusion with varying temperature
 
-```{tags} 2D, MMS
+```{tags} 2D, MMS, steady state
 ```
 
 This is an extension of the [simple MMS](./simple.md) example with a non-homogenous temperature gradient.

report/verification/mms/simple_transient.md

@@ -39,6 +39,10 @@ $$
 \end{equation}
 $$(c_exact_simple_transient)
 
+```{note}
+We use a manufactured solution that varies linearly with time ($t^1$), as the backward Euler scheme provides an exact solution in this case.
+```
+
 Injecting {eq}`c_exact_simple_transient` in {eq}`problem_simple_transient`, we obtain the expressions of $S$, $c_0$, and $c_\mathrm{initial}$:
 
 \begin{align}

report/verification/mms/soret.md

@@ -14,7 +14,7 @@ kernelspec:
 
 # Soret Effect
 
-```{tags} 2D, MMS, soret
+```{tags} 2D, MMS, soret, steady state
 ```
 
 This MMS case verifies the implementation of the Soret effect in FESTIM.

report/verification/simple_cases.md

@@ -0,0 +1 @@
+# Simple cases

report/verification/tmap.md

@@ -0,0 +1 @@
+# TMAP cases