fix examples.md figures

docs/examples.sh

@@ -1,6 +1,8 @@
 #!/bin/bash
 
-set -e
+MAX_HEIGHT=400
+
+set -e -x
 
 examples_md="$1/docs/documentation/examples.md" 
 rm "$examples_md" || true
@@ -11,11 +13,11 @@ for casedir in $(find "$1/examples/" -mindepth 1 -maxdepth 1 -type d); do
     casename="$(basename "$casedir")"
 
     if [ -f "$casedir/README.md" ]; then
-        sed -e "s/\.png/-$casename-example\.png/g" "$casedir/README.md" | sed 's/^#/##/g' >> "$examples_md"
+        sed -e "s/\.png/-$casename-example\.png/g" "$casedir/README.md" | sed 's/^#/##/g' | sed "s/MAX_HEIGHT/$MAX_HEIGHT/g" >> "$examples_md"
         echo '' >> "$examples_md"
 
         for png in $(find "$casedir" -maxdepth 1 -name '*.png'); do
             cp "$png" "$1/docs/documentation/$(basename "$png" | sed s/\.png//g)-$casename-example.png"
         done
     fi
-done
+done

examples/1D_inert_shocktube/README.md

@@ -1,12 +1,12 @@
 # 1D Multi-Component Inert Shock Tube
 
-References:
+Reference: 
 > P. J. Martínez Ferrer, R. Buttay, G. Lehnasch, and A. Mura, “A detailed verification procedure for compressible reactive multicomponent Navier–Stokes solvers”, Comput. & Fluids, vol. 89, pp. 88–110, Jan. 2014. Accessed: Oct. 13, 2024. [Online]. Available: https://doi.org/10.1016/j.compfluid.2013.10.014
 
 ## Initial Condition
 
-![Initial Condition](initial.png)
+<img src="initial.png" height="MAX_HEIGHT"/>
 
 ## Results
 
-![Results](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

examples/1D_laxshocktube/README.md

@@ -1,11 +1,12 @@
 # Lax shock tube problem (1D)
 
-Reference: P. D. Lax, Weak solutions of nonlinear hyperbolic equations and their numerical computation, Communications on pure and applied mathematics 7 (1) (1954) 159–193.
+Reference: 
+> P. D. Lax, Weak solutions of nonlinear hyperbolic equations and their numerical computation, Communications on pure and applied mathematics 7 (1) (1954) 159–193.
 
 ## Initial Condition
 
-![Initial Condition](initial.png)
+<img src="initial.png" height="MAX_HEIGHT"/>
 
 ## Result
 
-![Result](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

examples/1D_reactive_shocktube/README.md

@@ -7,8 +7,8 @@ References:
 
 ## Initial Condition
 
-![Initial Condition](initial.png)
+<img src="initial.png" height="MAX_HEIGHT"/>
 
 ## Results
 
-![Results](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

examples/1D_shuosher_old/README.md

@@ -1,11 +1,12 @@
 # Shu-Osher problem (1D)
 
-Reference: C. W. Shu, S. Osher, Efficient implementation of essentially non-oscillatory shock-capturing schemes, Journal of Computational Physics 77 (2) (1988) 439–471. doi:10.1016/0021-9991(88)90177-5.
+Reference: 
+> C. W. Shu, S. Osher, Efficient implementation of essentially non-oscillatory shock-capturing schemes, Journal of Computational Physics 77 (2) (1988) 439–471. doi:10.1016/0021-9991(88)90177-5.
 
 ## Initial Condition
 
-![Initial Condition](initial.png)
+<img src="initial.png" height="MAX_HEIGHT"/>
 
 ## Result
 
-![Result](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

examples/1D_titarevtorro/README.md

@@ -1,11 +1,12 @@
 # Titarev-Toro problem (1D)
 
-Reference: V. A. Titarev, E. F. Toro, Finite-volume WENO schemes for three-dimensional conservation laws, Journal of Computational Physics 201 (1) (2004) 238–260.
+Reference: 
+> V. A. Titarev, E. F. Toro, Finite-volume WENO schemes for three-dimensional conservation laws, Journal of Computational Physics 201 (1) (2004) 238–260.
 
 ## Initial Condition
 
-![Initial Condition](initial.png)
+<img src="initial.png" heiht="MAX_HEIGHT"/>
 
 ## Result
 
-![Result](result.png)
+<img src="result.png" heiht="MAX_HEIGHT"/>

examples/2D_hardcodied_ic/README.md

@@ -1,9 +1,6 @@
 # 2D Hardcodied IC Example
 
-## Initial Condition
+## Initial Condition and Result
 
-![Initial Condition](initial.png)
-
-## Result
-
-![Result](result.png)
+<img src="initial.png" width="45%"/>
+<img src="result.png" width="45%"/>

examples/2D_ibm_cfl_dt/README.md

@@ -2,4 +2,4 @@
 
 ## Result
 
-![Result](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

examples/2D_isentropicvortex/README.md

@@ -1,11 +1,12 @@
 # Isentropic vortex problem (2D)
 
-Reference: Coralic, V., & Colonius, T. (2014). Finite-volume Weno scheme for viscous compressible multicomponent flows. Journal of Computational Physics, 274, 95–121. https://doi.org/10.1016/j.jcp.2014.06.003
+Reference: 
+> Coralic, V., & Colonius, T. (2014). Finite-volume Weno scheme for viscous compressible multicomponent flows. Journal of Computational Physics, 274, 95–121. https://doi.org/10.1016/j.jcp.2014.06.003
 
 ## Density
 
-![Density](alpha_rho1.png)
+<img src="alpha_rho1.png" height="MAX_HEIGHT"/>
 
 ## Density Norms
 
-![Density Norms](density_norms.png)
+<img src="density_norms.png" height="MAX_HEIGHT"/>

examples/2D_lid_driven_cavity/README.md

@@ -1,16 +1,17 @@
 # Lid-Driven Cavity Problem (2D)
 
-Reference: Bezgin, D. A., & Buhendwa A. B., & Adams N. A. (2022). JAX-FLUIDS: A fully-differentiable high-order computational fluid dynamics solver for compressible two-phase flows. arXiv:2203.13760
+Reference: 
+> Bezgin, D. A., & Buhendwa A. B., & Adams N. A. (2022). JAX-FLUIDS: A fully-differentiable high-order computational fluid dynamics solver for compressible two-phase flows. arXiv:2203.13760
 
-Reference: Ghia, U., & Ghia, K. N., & Shin, C. T. (1982). High-re solutions for incompressible flow
+> Ghia, U., & Ghia, K. N., & Shin, C. T. (1982). High-re solutions for incompressible flow
 using the Navier-Stokes equations and a multigrid method. Journal of Computational Physics, 48, 387-411
 
 Video: https://youtube.com/shorts/JEP28scZrBM?feature=share
 
 ## Final Condition
 
-![Final Condition](final_condition.png)
+<img src="final_condition.png" height="MAX_HEIGHT"/>
 
 ## Centerline Velocities
 
-![Centerline Velocities](centerline_velocities.png)
+<img src="centerline_velocities.png" height="MAX_HEIGHT"/>

examples/2D_rayleigh_taylor/README.md

@@ -1,9 +1,5 @@
 # Rayleigh-Taylor Instability (2D)
 
-## Final Condition
-
-![Final Condition](final_condition.png)
-
-## Centerline Velocities
-
-![Linear Theory Comparison](linear_theory.jpg)
+## Final Condition and Linear Theory
+<img src='final_condition.png' height='MAX_HEIGHT'/>
+<img src='linear_theory.png' height='MAX_HEIGHT'/>

examples/2D_riemann_test/README.md

@@ -1,11 +1,9 @@
 # 2D Riemann Test (2D)
 
-Reference: Chamarthi, A., & Hoffmann, N., & Nishikawa, H., & Frankel S. (2023). Implicit gradients based conservative numerical scheme for compressible flows. arXiv:2110.05461 
+Reference: 
+> Chamarthi, A., & Hoffmann, N., & Nishikawa, H., & Frankel S. (2023). Implicit gradients based conservative numerical scheme for compressible flows. arXiv:2110.05461 
 
-## Density Initial Condition
+## Density Initial and Final Conditions
 
-![Density](alpha_rho1_initial.png)
-
-## Density Final Condition
-
-![Density Norms](alpha_rho1_final.png)
+<img src="alpha_rho1_initial.png" width="45%"/>
+<img src="alpha_rho1_final.png" width="45%"/>

examples/2D_shockdroplet/README.md

@@ -1,11 +1,12 @@
 # Shock Droplet (2D)
 
-Reference: Panchal et. al., A Seven-Equation Diffused Interface Method for Resolved Multiphase Flows, JCP, 475 (2023)
+Reference: 
+> Panchal et. al., A Seven-Equation Diffused Interface Method for Resolved Multiphase Flows, JCP, 475 (2023)
 
 ## Initial Condition
 
-![Initial Condition](initial.png)
+<img src="initial.png" height="MAX_HEIGHT"/>
 
 ## Result
 
-![Result](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

examples/2D_triple_point/README.md

@@ -0,0 +1,9 @@
+# 2D Triple Point (2D)
+
+Reference: 
+> Trojak, W., & Dzanic, T. Positivity-preserving discoutinous spectral element method for compressible multi-species flows. arXiv:2308.02426
+
+## Numerical Schlieren at Final Time
+
+<img src="final.png" height="MAX_HEIGHT"/>
+

examples/3D_TaylorGreenVortex/README.md

@@ -1,8 +1,10 @@
 # Taylor-Green Vortex (3D)
 
-Reference: Hillewaert, K. (2013). TestCase C3.5 - DNS of the transition of the Taylor-Green vortex, Re=1600 - Introduction and result summary. 2nd International Workshop on high-order methods for CFD.
+Reference:
+> Hillewaert, K. (2013). TestCase C3.5 - DNS of the transition of the Taylor-Green vortex, Re=1600 - Introduction and result summary. 2nd International Workshop on high-order methods for CFD.
 
 ## Final Condition
 This figure shows the isosurface with zero q-criterion.
-![Density](result.png)
+
+<img src="result.png" height="MAX_HEIGHT"/>
 

examples/3D_ibm_bowshock/README.md

@@ -2,5 +2,5 @@
 
 ## Final Condition
 
-![Density](result.png)
+<img src="result.png" height="MAX_HEIGHT">
 

examples/3D_rayleigh_taylor/README.md

@@ -1,9 +1,6 @@
 # Rayleigh-Taylor Instability (3D)
 
-## Final Condition
+## Final Condition and Linear Theory
 
-![Final Condition](final_condition.png)
-
-## Centerline Velocities
-
-![Linear Theory Comparison](linear_theory.png)
+<img src="final_condition.png" height="MAX_HEIGHT"/>
+<img src="linear_theory.png" height="MAX_HEIGHT"/>

examples/nD_perfect_reactor/README.md

@@ -1,6 +1,7 @@
 # Perfectly Stirred Reactor
 
-Reference: G. B. Skinner and G. H. Ringrose, “Ignition Delays of a Hydrogen—Oxygen—Argon Mixture at Relatively Low Temperatures”, J. Chem. Phys., vol. 42, no. 6, pp. 2190–2192, Mar. 1965. Accessed: Oct. 13, 2024. [Online]. Available: https://doi.org/10.1063/1.1696266.
+Reference:
+> G. B. Skinner and G. H. Ringrose, “Ignition Delays of a Hydrogen—Oxygen—Argon Mixture at Relatively Low Temperatures”, J. Chem. Phys., vol. 42, no. 6, pp. 2190–2192, Mar. 1965. Accessed: Oct. 13, 2024. [Online]. Available: https://doi.org/10.1063/1.1696266.
 
 ```bash
 $ python3 analyze.py
@@ -10,4 +11,4 @@ Induction Times ([OH] >= 1e-6):
  + (Che)MFC:       5.130e-05 s
 ```
 
-![Result](result.png)
+<img src="result.png" height="MAX_HEIGHT"/>

toolchain/mfc/test/cases.py

@@ -808,7 +808,7 @@ def foreach_example():
                 continue
 
             # # List of currently broken examples -> currently attempting to fix!
-            brokenCases = ["2D_ibm_cfl_dt", "1D_sodHypo", "2D_viscous", "2D_laplace_pressure_jump", "2D_bubbly_steady_shock", "2D_advection", "2D_hardcodied_ic", "2D_ibm_multiphase", "2D_acoustic_broadband", "1D_inert_shocktube", "1D_reactive_shocktube", "2D_ibm_steady_shock", "3D_performance_test", "3D_ibm_stl_ellipsoid", "3D_sphbubcollapse", "2D_ibm_stl_wedge", "3D_ibm_stl_pyramid", "3D_ibm_bowshock", "3D_turb_mixing", "2D_mixing_artificial_Ma"]
+            brokenCases = ["2D_ibm_cfl_dt", "1D_sodHypo", "2D_viscous", "2D_laplace_pressure_jump", "2D_bubbly_steady_shock", "2D_advection", "2D_hardcodied_ic", "2D_ibm_multiphase", "2D_acoustic_broadband", "1D_inert_shocktube", "1D_reactive_shocktube", "2D_ibm_steady_shock", "3D_performance_test", "3D_ibm_stl_ellipsoid", "3D_sphbubcollapse", "2D_ibm_stl_wedge", "3D_ibm_stl_pyramid", "3D_ibm_bowshock", "3D_turb_mixing", "2D_mixing_artificial_Ma", "2D_triple_point"]
             if path in brokenCases:
                 continue
             name = f"{path.split('_')[0]} -> Example -> {'_'.join(path.split('_')[1:])}"