additional broken test cases

docs/documentation/case.md

@@ -522,6 +522,9 @@ To restart the simulation from $k$-th time step, see [Restarting Cases](running.
 | `probe_wrt`          | Logical | Write the flow chosen probes data files for each time step	|
 | `num_probes`         | Integer | Number of probes	|
 | `probe(i)%[x,y,z]`   | Real	 | Coordinates of probe $i$	|
+| `output_partial_domain` | Logical | Output part of the domain |
+| `[x,y,z]_output%beg` | Real    | Beginning of the output domain in the [x,y,z]-direction |
+| `[x,y,z]_output%end` | Real    | End of the output domain in the [x,y,z]-direction |
 
 The table lists formatted database output parameters. The parameters define variables that are outputted from simulation and file types and formats of data as well as options for post-processing.
 
@@ -549,6 +552,11 @@ If `file_per_process` is true, then pre_process, simulation, and post_process mu
 
 - `probe_wrt` activates the output of state variables at coordinates specified by `probe(i)%[x;y,z]`.
 
+- `output_partial_domain` activates the output of part of the domain specified by `[x,y,z]_output%beg` and `[x,y,z]_output%end`.
+This is useful for large domains where only a portion of the domain is of interest.
+It is not supported when `precision = 1` and `format = 1`. 
+It also cannot be enabled with `flux_wrt`, `heat_ratio_wrt`, `pres_inf_wrt`, `c_wrt`, `omega_wrt`, `ib`, `schlieren_wrt`, or `qm_wrt`.
+
 ### 8. Acoustic Source {#acoustic-source}
 
 | Parameter                             | Type    | Description |

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/2D_triple_point/case.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+import math
+import json
+
+eps = 1e-8
+Nx = 699
+Ny = 299
+
+print(json.dumps({
+    # Logistics ================================================
+    'run_time_info'                : 'F',
+    # ==========================================================
+
+    # Computational Domain Parameters ==========================
+    'x_domain%beg'                 :  0,
+    'x_domain%end'                 :  7,
+    'y_domain%beg'                 :  0,
+    'y_domain%end'                 :  3,
+    'm'                            : int(Nx),
+    'n'                            : int(Ny),
+    'p'                            : 0,
+    'cfl_adap_dt'                  : 'T',
+    'cfl_target'                   : 0.8,
+    'n_start'                      : 0,
+    't_stop'                       : 4.0,
+    't_save'                       : 0.04,
+    # ==========================================================
+
+    # Simulation Algorithm Parameters ==========================
+    'num_patches'                  : 3,
+    'model_eqns'                   : 2,
+    'alt_soundspeed'               : 'F',
+    'num_fluids'                   : 2,
+    'mpp_lim'                      : 'T',
+    'mixture_err'                  : 'T',
+    'time_stepper'                 : 3,
+    'weno_order'                   : 7,
+    'weno_eps'                     : 1.E-16,
+    'weno_Re_flux'                 : 'F',  
+    'weno_avg'                     : 'F',
+    'mapped_weno'                  : 'T',
+    'null_weights'                 : 'F',
+    'mp_weno'                      : 'F',
+    'riemann_solver'               : 2,
+    'wave_speeds'                  : 1,
+    'avg_state'                    : 2,
+    'bc_x%beg'                     : -3,#11,
+    'bc_x%end'                     : -3,#12
+    'bc_y%beg'                     : -3,
+    'bc_y%end'                     : -3,
+    # ==========================================================
+
+    # Formatted Database Files Structure Parameters ============
+    'format'                       : 1,
+    'precision'                    : 2,
+    'prim_vars_wrt'                :'T',
+    'schlieren_wrt'                :'T',
+    'fd_order'                     : 4,
+    'schlieren_alpha(1)'           : 0.5,
+    'schlieren_alpha(2)'           : 0.5,
+    'parallel_io'                  :'T',
+    # ==========================================================
+
+    # Patch 1: Left state   ====================================
+    'patch_icpp(1)%geometry'       : 3,
+    'patch_icpp(1)%x_centroid'     : 0.5,
+    'patch_icpp(1)%y_centroid'     : 3,
+    'patch_icpp(1)%length_x'       : 1,
+    'patch_icpp(1)%length_y'       : 6,
+    'patch_icpp(1)%vel(1)'         : 0.,
+    'patch_icpp(1)%vel(2)'         : 0.,
+    'patch_icpp(1)%pres'           : 1.,
+    'patch_icpp(1)%alpha_rho(1)'   : (1 - eps)*1.,
+    'patch_icpp(1)%alpha_rho(2)'   : eps,
+    'patch_icpp(1)%alpha(1)'       : 1 - eps,
+    'patch_icpp(1)%alpha(2)'       : eps,
+    # ==========================================================
+
+    # Patch 2: Top right state  ================================
+    'patch_icpp(2)%geometry'       : 3,
+    'patch_icpp(2)%alter_patch(1)' : 'T',
+    'patch_icpp(2)%x_centroid'     : 4,
+    'patch_icpp(2)%y_centroid'     : 2.25,
+    'patch_icpp(2)%length_x'       : 6,
+    'patch_icpp(2)%length_y'       : 1.5,
+    'patch_icpp(2)%vel(1)'         : 0.,
+    'patch_icpp(2)%vel(2)'         : 0.,
+    'patch_icpp(2)%pres'           : 0.1,
+    'patch_icpp(2)%alpha_rho(1)'   : (1-eps)*0.125,
+    'patch_icpp(2)%alpha_rho(2)'   : eps,
+    'patch_icpp(2)%alpha(1)'       : 1 - eps,
+    'patch_icpp(2)%alpha(2)'       : eps,
+    # ==========================================================
+
+    # Patch 3: Bottom right state  =============================
+    'patch_icpp(3)%geometry'       : 3,
+    'patch_icpp(3)%alter_patch(1)' : 'T',
+    'patch_icpp(3)%x_centroid'     : 4,
+    'patch_icpp(3)%y_centroid'     : 0.75,
+    'patch_icpp(3)%length_x'       : 6,
+    'patch_icpp(3)%length_y'       : 1.5,
+    'patch_icpp(3)%vel(1)'         : 0.,
+    'patch_icpp(3)%vel(2)'         : 0.,
+    'patch_icpp(3)%pres'           : 0.1,
+    'patch_icpp(3)%alpha_rho(1)'   : eps,
+    'patch_icpp(3)%alpha_rho(2)'   : (1 - eps)*1.,
+    'patch_icpp(3)%alpha(1)'       : eps,# 0.95
+    'patch_icpp(3)%alpha(2)'       : 1 - eps,#0.05,
+    # ==========================================================
+
+    # Fluids Physical Parameters ===============================
+    'fluid_pp(1)%gamma'            : 1./(1.5 - 1.),
+    'fluid_pp(1)%pi_inf'           : 0,
+    'fluid_pp(2)%gamma'            : 1./(1.4 - 1.),
+    'fluid_pp(2)%pi_inf'           : 0.,
+    # ==========================================================
+}))

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"/>