Merge remote-tracking branch 'upstream/master' into CodeTidying

Author: XZTian64

.github/workflows/frontier/build.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 build_opts=""
-if [ "$1" == "gpu" ]; then
+if [ "$1" = "gpu" ]; then
     build_opts="--gpu"
 fi
 

.github/workflows/frontier/submit.sh

@@ -13,10 +13,10 @@ else
     exit 1
 fi
 
-if [ "$2" == "cpu" ]; then
+if [ "$2" = "cpu" ]; then
     sbatch_device_opts="\
 #SBATCH -n 32                       # Number of cores required"
-elif [ "$2" == "gpu" ]; then
+elif [ "$2" = "gpu" ]; then
     sbatch_device_opts="\
 #SBATCH -n 8                       # Number of cores required"
 else

.github/workflows/frontier/test.sh

@@ -3,7 +3,7 @@
 gpus=`rocm-smi --showid | awk '{print $1}' | grep -Eo '[0-9]+' | uniq | tr '\n' ' '`
 ngpus=`echo "$gpus" | tr -d '[:space:]' | wc -c`
 
-if [ "$job_device" == "gpu" ]; then
+if [ "$job_device" = "gpu" ]; then
     ./mfc.sh test --max-attempts 3 -j $ngpus -- -c frontier
 else
     ./mfc.sh test --max-attempts 3 -j 32 -- -c frontier

.github/workflows/phoenix/bench.sh

@@ -2,19 +2,26 @@
 
 n_ranks=12
 
-if [ "$job_device" == "gpu" ]; then
+if [ "$job_device" = "gpu" ]; then
     n_ranks=$(nvidia-smi -L | wc -l)        # number of GPUs on node
     gpu_ids=$(seq -s ' ' 0 $(($n_ranks-1))) # 0,1,2,...,gpu_count-1
     device_opts="--gpu -g $gpu_ids"
 fi
 
-mkdir -p /storage/scratch1/6/sbryngelson3/mytmp_build
-export TMPDIR=/storage/scratch1/6/sbryngelson3/mytmp_build
+tmpbuild=/storage/scratch1/6/sbryngelson3/mytmp_build
+currentdir=$tmpbuild/run-$(( RANDOM % 900 ))
+mkdir -p $tmpbuild
+mkdir -p $currentdir
 
-if ["$job_device" == "gpu"]; then
+export TMPDIR=$currentdir
+
+if [ "$job_device" = "gpu" ]; then
     ./mfc.sh bench --mem 12 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix-bench $device_opts -n $n_ranks
 else
     ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix-bench $device_opts -n $n_ranks
 fi
 
+sleep 10
+rm -rf "$currentdir" || true
+
 unset TMPDIR

.github/workflows/phoenix/submit-bench.sh

@@ -25,9 +25,9 @@ sbatch_gpu_opts="\
 #SBATCH -G2\
 "
 
-if [ "$2" == "cpu" ]; then
+if [ "$2" = "cpu" ]; then
     sbatch_device_opts="$sbatch_cpu_opts"
-elif [ "$2" == "gpu" ]; then
+elif [ "$2" = "gpu" ]; then
     sbatch_device_opts="$sbatch_gpu_opts"
 else
     usage

.github/workflows/phoenix/submit.sh

@@ -25,9 +25,9 @@ sbatch_gpu_opts="\
 #SBATCH -G2\
 "
 
-if [ "$2" == "cpu" ]; then
+if [ "$2" = "cpu" ]; then
     sbatch_device_opts="$sbatch_cpu_opts"
-elif [ "$2" == "gpu" ]; then
+elif [ "$2" = "gpu" ]; then
     sbatch_device_opts="$sbatch_gpu_opts"
 else
     usage

.github/workflows/phoenix/test.sh

@@ -1,15 +1,15 @@
 #!/bin/bash
 
 build_opts=""
-if [ "$job_device" == "gpu" ]; then
+if [ "$job_device" = "gpu" ]; then
     build_opts="--gpu"
 fi
 
 ./mfc.sh test --dry-run -j 8 $build_opts
 
 n_test_threads=8
 
-if [ "$job_device" == "gpu" ]; then
+if [ "$job_device" = "gpu" ]; then
     gpu_count=$(nvidia-smi -L | wc -l)        # number of GPUs on node
     gpu_ids=$(seq -s ' ' 0 $(($gpu_count-1))) # 0,1,2,...,gpu_count-1
     device_opts="-g $gpu_ids"

.typos.toml

@@ -17,6 +17,7 @@ gam = "gam"
 Gam = "Gam"
 strang = "strang"
 Strang = "Strang"
+TKE = "TKE"
 
 [files]
 extend-exclude = ["docs/documentation/references*", "tests/", "toolchain/cce_simulation_workgroup_256.sh"]

docs/documentation/case.md

@@ -825,7 +825,6 @@ When ``polytropic = 'F'``, the gas compression is modeled as non-polytropic due
 | `mixlayer_vel_profile` | Logical | Set the mean streamwise velocity to hyperbolic tangent profile |
 | `mixlayer_vel_coef`    | Real    | Coefficient for the hyperbolic tangent profile of a mixing layer |
 | `mixlayer_perturb`     | Logical | Perturb the initial velocity field by instability waves |
-| `mixlayer_domain`      | Real    | Domain size of a mixing layer for the linear stability analysis |
 
 The table lists velocity field parameters.
 The parameters are optionally used to define initial velocity profiles and perturbations.
@@ -840,15 +839,13 @@ The parameters are optionally used to define initial velocity profiles and pertu
 
 - `perturb_sph_fluid` specifies the fluid component whose partial density is to be perturbed.
 
-- `mixlayer_vel_profile` activates setting the mean streamwise velocity to a hyperbolic tangent profile. This option works only for 2D and 3D cases.
+- `mixlayer_vel_profile` activates setting the mean streamwise velocity to a hyperbolic tangent profile. This option works only for `n > 0`.
 
 - `mixlayer_vel_coef` is a parameter for the hyperbolic tangent profile of a mixing layer when `mixlayer_vel_profile = 'T'`. The mean streamwise velocity profile is given as:
 
-$$ u = patch\_icpp(1)\%vel(1) * tanh(y\_cc * mixlayer\_vel\_profile) $$
+$$ u = \mbox{patch\_icpp(1)\%vel(1)} * \tanh( y_{cc} * \mbox{mixlayer\_vel\_coef}) $$
 
-- `mixlayer_perturb` activates the perturbation of initial velocity by instability waves obtained from linear stability analysis for a mixing layer with hyperbolic tangent mean streamwise velocity profile. This option only works for `n > 0`, `bc_y%[beg,end] = -6`, `num_fluids = 1`, `model_eqns = 2` and `mixlayer_vel_profile = 'T'`.
-
-- `mixlayer_domain` defines the domain size to compute spatial eigenvalues of the linear instability analysis when `mixlayer_perturb = 'T'`. For example, the spatial eigenvalue in `x` direction in 2D problem will be $2 \pi \alpha / (mixlayer\_domain*patch\_icpp(1)\%length\_y)$ for $\alpha = 1$, $2$ and $4$.
+- `mixlayer_perturb` activates the velocity perturbation for a temporal mixing layer with hyperbolic tangent mean streamwise velocity profile, using an inverter version of the spectrum-based synthetic turbulence generation method proposed by Guo et al. (2023, JFM). This option only works for `p > 0` and `mixlayer_vel_profile = 'T'`.
 
 ### 11. Phase Change Model
 | Parameter              | Type    | Description                                    |

docs/documentation/references.md

@@ -20,6 +20,8 @@
 
 - <a id="Gottlieb98">Gottlieb, S. and Shu, C.-W. (1998). Total variation diminishing runge-kutta schemes. Mathematics of computation of the American Mathematical Society, 67(221):73–85.</a>
 
+- <a id="Guo23">Guo, H., Jiang, P., Ye, L., & Zhu, Y. (2023). An efficient and low-divergence method for generating inhomogeneous and anisotropic turbulence with arbitrary spectra. Journal of Fluid Mechanics, 970, A2.</a>
+
 - <a id="Henrick05">Henrick, A. K., Aslam, T. D., and Powers, J. M. (2005). Mapped weighted essentially nonoscillatory schemes: achieving optimal order near critical points. Journal of Computational Physics, 207(2):542–567.</a>
 
 - <a id="Borges08">Borges, R., Carmona, M., Costa, B., and Don, W. S. (2008). An improved weighted essentially non-oscillatory scheme for hyperbolic conservation laws. Journal of computational physics, 227(6):3191–3211.</a>
@@ -34,6 +36,8 @@
 
 - <a id="Meng16">Meng, J. C. C. (2016). Numerical simulations of droplet aerobreakup. PhD thesis, California Institute of Technology.</a>
 
+- <a id="Michalke64"> Michalke, A. (1964). On the inviscid instability of the hyperbolictangent velocity profile. Journal of Fluid Mechanics, 19(4), 543-556.</a>
+
 - <a id="Pirozzoli13">Pirozzoli, S., and Colonius, T. (2013). Generalized characteristic relaxation boundary conditions for unsteady compressible flow simulations. Journal of Computational Physics, 248:109-126.</a>
 
 - <a id="Preston07">Preston, A., Colonius, T., and Brennen, C. (2007). A reduced-order model of diffusive effects on the dynamics of bubbles. Physics of Fluids, 19(12):123302.</a>