### Example: Using Unit Conversions with Equation of State

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Utility.md

Demonstrates how to use the MKS to CGS and CGS to MKS unit conversion aliases when calling an equation of state function. This example calculates density using mixed units.

```rst
auto eos = pele::physics::PhysicsType::eos();
amrex::Real P_mean = 101325.0_rt; // Pressure in Pa (MKS)
amrex::Real massfrac[NUM_SPECIES]; // Mass fractions tracked by PeleLM(eX)
amrex::Real Temp = 300.0_rt; // Temp in K
amrex::Real rho_cgs = 0.0_rt; // Density in g/cm^3 (CGS)

// Calculate density in CGS units, then convert to MKS
eos.PYT2R(m2c::P(P_mean), massfrac, Temp, rho_cgs);
amrex::Real rho = c2m::Rho(rho_cgs); // Convert eos density to MKS
```

--------------------------------

### CMake Project Setup

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/CMakeLists.txt

Sets the minimum required CMake version and initializes the project. It also appends a custom module path for CMake modules.

```cmake
cmake_minimum_required (VERSION 3.10)
project(PelePhysics-Docs NONE)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
```

--------------------------------

### Example: Direct CEPTR Usage for Homogeneous Mechanisms

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

An example of directly using CEPTR for homogeneous mechanisms, executed from the CEPTR directory.

```bash
cd ${PELE_PHYSICS_HOME}/Support/ceptr
poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/LiDryer/mechanism.yaml
```

--------------------------------

### Generate HIT IC Example

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

Example command to generate an initial condition file for isotropic turbulence using the gen_hit_ic.py script with a specified resolution.

```rst
./gen_hit_ic.py -N 16
```

--------------------------------

### Spray Injection Initialization Example

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Spray.md

Illustrates how to modify the InitSprayParticles() function in SprayParticleInitInsert.cpp to create a jet in the domain for spray injection.

```cpp
// Example of how to initialize spray particles
// This is a placeholder and needs to be implemented based on specific needs.
void InitSprayParticles() {
    // Logic to initialize spray particles goes here.
    // This might involve setting initial positions, velocities, temperatures, etc.
    // For example:
    // spray.SetNumParticles(1000);
    // spray.SetParticleProperties(0, {x, y, z}, {vx, vy, vz}, temp, mass); 
}
```

--------------------------------

### Display Regression Test Help

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Regression/README.md

Display verbose usage and setup information for the regtest.py script, including available options.

```bash
./regtest.py -h
```

--------------------------------

### Input File Parameters for CVODE Reactor

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

Configure ODE solver settings, including time step, reactor type, and tolerances. Specify CVODE solver type and Jacobian evaluation method. This example uses a dense direct solver without an analytical Jacobian.

```rst
#ODE solver options
# REACTOR mode
ode.dt = 1.e-05
ode.ndt = 10
# Reactor formalism: 1=full e, 2=full h
ode.reactor_type = 1
# Tolerances for ODE solve
ode.rtol = 1e-9
ode.atol = 1e-9
# Select ARK/CV-ODE Jacobian eval: 0=FD 1=AJ
ode.analytical_jacobian = 0
#CVODE SPECIFICS
# Choose between sparse (5) dense (1/101) iterative (99) solver
cvode.solve_type = 1

#OTHER
# Max size of problem
max_grid_size = 2
# Choose name of output pltfile
amr.plot_file       = plt
# Fuel species
fuel_name = CH4

```

--------------------------------

### Getting Help for PMF Generator Script

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Utility.md

Display all available command-line options for the Cantera PMF generator script to customize flame simulation parameters.

```bash
poetry -C ../../../Support/ceptr/ run python cantera_pmf_generator.py --help
```

--------------------------------

### Generating a PMF File with Cantera

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Utility.md

Use the provided Python script to solve a 1D unstrained premixed flame using Cantera and save it in the format required by Pele codes. This example computes a dodecane/air flame.

```bash
poetry -C ../../../Support/ceptr/ run python cantera_pmf_generator.py -m dodecane_lu -f NC12H26 -d 0.01 -o ./ 
```

--------------------------------

### Compile PeleTurb3d Executable

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Support/TurbInflowGenerator/README.md

Compile the C++ executable for generating the turbfile. Ensure AMReX is installed and accessible.

```bash
make
```

--------------------------------

### Specify SuiteSparse Directory

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

If SuiteSparse is not found in the default path, provide its installation directory using this flag.

```makefile
SUITESPARSE_DIR=PathToSuiteSparse/
```

--------------------------------

### Clone PelePhysics Repository

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/GettingStarted.md

Use this command to clone the PelePhysics repository and its submodules. Ensure Git version 1.7.x or higher is installed. The --recursive option downloads necessary dependencies.

```bash
git clone --recursive https://github.com/AMReX-Combustion/PelePhysics.git
```

--------------------------------

### Generate Mechanisms using a Local Helper Script

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

Execute a local helper script ('convert.sh') from the directory containing the mechanism.yaml file. This may require a valid Cantera installation.

```bash
./convert.sh
```

--------------------------------

### Build and Run PelePhysics Documentation

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/index.md

Build the HTML documentation locally using Sphinx. Ensure the PELE_PHYSICS_DIR environment variable is set to your repository's location.

```default
cd ${PELE_PHYSICS_DIR}/build
sphinx-build -M html ../Docs/sphinx .

```

--------------------------------

### Create New Feature Branch

Source: https://github.com/amrex-combustion/pelephysics/blob/development/CONTRIBUTING.md

Create a new branch for your feature, starting from the 'development' branch.

```bash
git checkout development
git checkout -b AmazingNewFeature
```

--------------------------------

### Initialize and Apply Filter

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Utility.md

Demonstrates the initialization of a Filter object with specified type and grid ratio, followed by applying the filter to MultiFab data. Ensure sufficient ghost cells are present.

```rst
les_filter = Filter(les_filter_type, les_filter_fgr);
...
les_filter.apply_filter(bxtmp, flux[i], filtered_flux[i], Density, NUM_STATE);
```

--------------------------------

### Display Help for propcoeff.py

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

This command displays the help message for the 'propcoeff.py' script, outlining its usage and available options for calculating property coefficients.

```bash
$ python propcoeff.py -h
```

--------------------------------

### QSSA Help Command

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

Displays the usage and available options for the qssa command, including arguments for mechanism file, non-QSSA species list, QSSA method, and visualization.

```bash
poetry run qssa -h
```

--------------------------------

### Navigate to Test Case Directory

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/GettingStarted.md

Change the current directory to the specific test case you want to work with. Ensure the PELE_PHYSICS_HOME environment variable is set correctly.

```bash
cd ${PELE_PHYSICS_HOME}/Testing/Exec/ReactEval
```

--------------------------------

### Enable KLU Sparse Solver

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

Set this flag to TRUE in the GNUmakefile to enable the use of the KLU sparse direct linear solver, which requires the SuiteSparse package.

```makefile
PELE_USE_KLU = TRUE
```

--------------------------------

### Enable CVode and KLU in GNUmakefile

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

Set USE_SUNDIALS_PP to TRUE and PELE_USE_KLU to TRUE in the GNUmakefile to activate the CVode solver and its sparse KLU features.

```makefile
#######################
# ODE solver OPTIONS: DVODE (default) / SUNDIALS / RK explicit
#######################
# Activates use of SUNDIALS: CVODE (default) / ARKODE
USE_SUNDIALS_PP = TRUE
ifeq ($(USE_SUNDIALS_PP), TRUE)
  ...
  # use KLU sparse features -- only useful if CVODE is used
  PELE_USE_KLU = TRUE
  ...
else
  ...
endif

#######################
...
```

--------------------------------

### Format All Source Files

Source: https://github.com/amrex-combustion/pelephysics/blob/development/CONTRIBUTING.md

Use clang-format to automatically format all C++ and header files in the Source and Testing directories.

```bash
find Source Testing \( -name "*.cpp" -o -name "*.H" \) -exec clang-format -i {} +
```

--------------------------------

### Configure CVode Solver in Input File

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

Set ode.analytical_jacobian to 1 and cvode.solve_type to 99 in the input file to use a preconditioned iterative Krylov solver with sparse Jacobian evaluation for CVode.

```input
#######################
#ODE solver options
...
# Select ARK/CV-ODE Jacobian eval: 0=FD 1=AJ
ode.analytical_jacobian = 1
#CVODE SPECIFICS
# Choose between sparse (5) dense (1/101) iterative (99) solver
cvode.solve_type = 99
...
#OTHER
...
```

--------------------------------

### Create Symbolic Links for Testing

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Regression/README.md

Create symbolic links to the regression testing script and the PelePhysics test configuration file within the current directory. Assumes regression_testing and PelePhysics are cloned into REGTEST_SCRATCH.

```bash
ln -s ${REGTEST_SCRATCH}/regression_testing/regtest.py .
ln -s ${REGTEST_SCRATCH}/PelePhysics/Testing/Regression/PelePhysics-tests.ini .
```

--------------------------------

### Configure PelePhysics to Use SUNDIALS (CVODE)

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

Modify the GNUmakefile to set USE_SUNDIALS_PP to TRUE to activate the SUNDIALS library, which provides CVODE.

```makefile
USE_SUNDIALS_PP = FALSE
...
#######################
# ODE solver OPTIONS: DVODE (default) / SUNDIALS / RK explicit
#######################
# Activates use of SUNDIALS: CVODE (default) / ARKODE
USE_SUNDIALS_PP = TRUE
...

#######################
...
```

--------------------------------

### GNUmakefile Configuration for PelePhysics with CUDA

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

This GNUmakefile configures PelePhysics for GPU acceleration using CUDA and enables the CVODE ODE solver with SUNDIALS. It specifies models for equation of state, chemistry, and transport.

```makefile
PRECISION  = DOUBLE
PROFILE    = FALSE

DEBUG      = FALSE

DIM        = 3

COMP       = gcc
FCOMP      = gfortran

USE_MPI    = FALSE
USE_OMP    = FALSE

FUEGO_GAS  = TRUE

USE_CUDA   = TRUE

TINY_PROFILE = TRUE

# define the location of the PELE_PHYSICS top directory
PELE_PHYSICS_HOME    := ../../..

#######################
# this flag activates the subcycling mode in the D/Cvode routines
DEFINES  += -DMOD_REACTOR

#######################
# ODE solver OPTIONS on GPU: SUNDIALS
#######################
# Activates use of SUNDIALS: CVODE (default)
USE_SUNDIALS_PP = TRUE

##############################################
ifeq ($(FUEGO_GAS), TRUE)
  Eos_Model       = Fuego
  Chemistry_Model = drm19
  Reactions_dir   = Fuego
  Transport_Model   = Simple
else
  Eos_Model       = GammaLaw
  Reactions_dir = Null
  Transport_Model = Constant
endif

Bpack   := ./Make.package
Blocs   := .

include $(PELE_PHYSICS_HOME)/Testing/Exec/Make.PelePhysics

```

--------------------------------

### Setting PMF Runtime Parameters

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Utility.md

Configure Premixed Flame (PMF) initialization by specifying the data file and whether to perform cell averaging. These parameters are set in the input file.

```rst
pmf.datafile = pmf.dat
pmf.do_cellAverage = 1
```

--------------------------------

### QSS Input Configuration for Analytical Jacobian

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Tutorials.md

Recommended TOML configuration for generating QSS mechanisms with analytical Jacobians, specifying readability, arithmetic, replacement, recycle, and character settings.

```toml
[Readability]
hformat =                       "gpu"

[Arithmetic]
remove_1 =                      true
remove_pow =                    true
remove_pow10 =                  true

[Replacement]
min_op_count =                  0
min_op_count_all =              10
gradual_op_count =              true
remove_single_symbols_cse =     true

[Recycle]
store_in_jacobian =             true
recycle_cse =                   true

[Characters]
round_decimals =                true
```

--------------------------------

### Run TurbInflow Utility

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

Execute the built TurbInflow utility. Running without arguments displays available options.

```bash
./PeleTurb3d.gnu.ex
```

--------------------------------

### Run HIT IC Generation with Poetry

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

Demonstrates how to run the gen_hit_ic.py script using poetry to manage dependencies, ensuring correct versions of SciPy and Matplotlib are used.

```rst
poetry run -C ../ceptr/ python gen_hit_ic.py -N 16
```

--------------------------------

### Run PelePhysics Test Case

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/GettingStarted.md

Execute the compiled PelePhysics program with the specified input file. This command runs the ReactEval executable using the 'inputs.3d-regt_GPU' configuration.

```bash
./Pele3d.gnu.ex inputs.3d-regt_GPU
```

--------------------------------

### Create Test Directory Structure

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Regression/README.md

Navigate to the regression test run directory and create the expected directory structure for PelePhysics test data. Ensure REGTEST_RUNDIR environment variable is set.

```bash
cd ${REGTEST_RUNDIR}; mkdir -p TestData/PelePhysics
```

--------------------------------

### Generate Benchmark Solutions

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Regression/README.md

Generate the initial benchmark solutions for all tests defined in the PelePhysics-tests.ini configuration file. This command overwrites existing benchmarks.

```bash
./regtest.py --make_benchmarks "<a useful comment>" PelePhysics-tests.ini
```

--------------------------------

### Generate HIT IC Help

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

Displays help information for the gen_hit_ic.py script, outlining available options for generating isotropic turbulence velocity fields.

```rst
./gen_hit_ic.py --help
usage: gen_hit_ic.py [-h] [-k0 K0] [-N N] [-Nk NK] [-s SEED] [-p]

Generate the velocity fluctuations for the HIT IC

options:
  -h, --help            show this help message and exit
  -k0 K0                Wave number containing highest energy
  -N N                  Resolution
  -Nk NK                Resolution in wavenumber space for intermediate step
  -s SEED, --seed SEED  Random number generator seed
  -p, --plot            Save a plot of the x-velocity
```

--------------------------------

### Build PelePhysics Executable

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/GettingStarted.md

Compile the main executable for the test case. The `-j 4` option allows for parallel compilation using 4 processors to speed up the build process.

```bash
make -j 4
```

--------------------------------

### Run TurbInflow with Input File

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

Execute the TurbInflow utility with a specified input file. Adjust 'hit_file' and 'input_ncell' as needed.

```bash
./PeleTurb3d.gnu.ex input
```

--------------------------------

### Generate All Mechanisms

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

Executes commands to generate both non-reduced and reduced chemistry mechanisms in batch. This includes converting mechanism lists and generating QSS YAML files.

```bash
poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
```

--------------------------------

### GNUmakefile Configuration for CVODE

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

Set USE_SUNDIALS_PP to TRUE to enable CVODE integration. Ensure FUEGO_GAS is TRUE and the chemistry model is set appropriately. This configuration is for direct C++ calls to CVODE.

```makefile
PRECISION  = DOUBLE
PROFILE    = FALSE

DEBUG      = FALSE

DIM        = 3

COMP       = gcc
FCOMP      = gfortran

USE_MPI    = TRUE
USE_OMP    = FALSE

FUEGO_GAS  = TRUE

TINY_PROFILE = TRUE

# define the location of the PELE_PHYSICS top directory
PELE_PHYSICS_HOME    := ../../../..

#######################
DEFINES  += -DMOD_REACTOR

#######################
# ODE solver OPTIONS: DVODE (default) / SUNDIALS / RK explicit
#######################
# Activates use of SUNDIALS: CVODE (default) / ARKODE
USE_SUNDIALS_PP = TRUE
ifeq ($(USE_SUNDIALS_PP), TRUE)
  # provide location of sundials lib if needed
  SUNDIALS_LIB_DIR=$(PELE_PHYSICS_HOME)/ThirdParty/sundials/instdir/lib/
  # use KLU sparse features -- only useful if CVODE is used
  PELE_USE_KLU = FALSE
  ifeq ($(PELE_USE_KLU), TRUE)
    # provide location of KLU lib if needed
    SUITESPARSE_DIR=$(PELE_PHYSICS_HOME)/ThirdParty/SuiteSparse/
  endif
endif

#######################
ifeq ($(FUEGO_GAS), TRUE)
  Eos_Model       = Fuego
  Chemistry_Model = drm19
  Reactions_dir   = Fuego
  Transport_Model = Simple
else
  Eos_Model       = GammaLaw
  Reactions_dir   = Null
  Transport_Model = Constant
endif

Bpack   := ./Make.package
Blocs   := .

include $(PELE_PHYSICS_HOME)/Testing/Exec/Make.PelePhysics

```

--------------------------------

### Build and Run Single Drop Evaporation Tests

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Spray.md

Use Validate.py to build new executables and run single droplet evaporation test cases with specified liquid properties and pressure saturation methods.

```bash
python Validate.py -b -c WongLin
```

```bash
python Validate.py -b -c WongLin -l mp -p CC
```

```bash
python Validate.py -b -c RungeJP8 -m --cmlm_path <local-path-to-cmlm>
```

```bash
python Validate.py -b -c RungeJP8-H
```

--------------------------------

### Convert Reduced Mechanisms in Batch

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

Converts a list of qssa.yaml and qssa_input.toml files for reduced chemistries in batch. This process also uses multiprocessing for parallel generation.

```bash
cd ${PELE_PHYSICS_HOME}/Support/ceptr
poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
```

--------------------------------

### Clone Required Repositories

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Regression/README.md

Clone the amrex, regression_testing, and PelePhysics repositories into a designated scratch area. Ensure REGTEST_SCRATCH environment variable is set.

```bash
git clone git@github.com:AMReX-Codes/amrex.git ${REGTEST_SCRATCH}/amrex
git clone git@github.com:AMReX-Codes/regression_testing ${REGTEST_SCRATCH}/regression_testing
git clone git@github.com:AMReX-Combustion/PelePhysics.git ${REGTEST_SCRATCH}/PelePhysics
```

--------------------------------

### Build TurbInflow Utility

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Support.md

Build the TurbInflow utility using make. Ensure AMReX is available or specify AMREX_HOME if not recursively cloned.

```bash
make -j
```

--------------------------------

### Build Dependencies for PelePhysics

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/GettingStarted.md

Compile necessary third-party libraries (TPL) required by PelePhysics. This step is essential before building the main executable and may need to be repeated if compile-time options change.

```bash
make TPL
```

--------------------------------

### Generate QSS Mechanism with Analytical Jacobian

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Tutorials.md

Generates a QSS mechanism with an analytical Jacobian using the qssa tool. Requires skeletal mechanism and non-QSS species list.

```bash
cd ${PELE_PHYSICS_HOME}/Support/ceptr
poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml
```

```bash
cd ${PELE_PHYSICS_HOME}/Support/ceptr
poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian
```

--------------------------------

### Copy Radiation Data Files

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Exec/Radiation/CMakeLists.txt

Copies necessary data files for radiation testing to the build directory. Ensure the 'kpDB' file exists in the source directory.

```cmake
file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/kpDB" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
```

--------------------------------

### Generate Turbfile

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Support/TurbInflowGenerator/README.md

Execute the compiled program to generate the turbfile. Adapt the input file to your specific simulation needs, including the path to the generated HIT data and the input cell count.

```bash
./PeleTurb3d.gnu.ex input hit_file=hit_ic_4_128.dat input_ncell=128
```

--------------------------------

### Configure ANSYS Fluent DPM Spray Injection

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Spray.md

Set up spray particle injection using data from ANSYS Fluent DPM solution files. Ensure the DPM file name and periodic behavior are correctly specified.

```input
spray.jetnames=jet_dpm
spray.jet_dpm.read_from_dpm_file=true
spray.jet_dpm.dpm_filename=<filename>
spray.jet_dpm.is_dpm_periodic=true
spray.jet_dpm.initial_injection_dpm_time=<DPM time stamp>
spray.jet_dpm.initial_injection_flow_time=<flow time>
spray.jet_dpm.trans_matrix=<3x3 matrix>
spray.jet_dpm.translation=<dx,dy,dz>
```

--------------------------------

### Turbulent Inflow Input File Options

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Utility.md

Configuration options for setting up turbulent inflow patches. These parameters control the source of turbulence data, its application on domain boundaries, and scaling factors.

```rst
turbinflows=low high                                    # Names of injections (can provide any number)

turbinflow.low.turb_file      = TurbFileHIT/TurbTEST    # Path to directory created in previous step
turbinflow.low.dir            = 1                       # Boundary normal direction (0,1, or 2) for patch
turbinflow.low.side           = "low"                   # Boundary side (low or high) for patch
turbinflow.low.turb_scale_loc = 633.151                 # Factor by which to scale the spatial coordinate between the data file and simulation
turbinflow.low.turb_scale_vel = 1.0                     # Factor by which to scale the velocity between the data file and simulation
turbinflow.low.turb_center    = 0.005 0.005             # Center point where turbulence patch will be applied
turbinflow.low.turb_conv_vel  = 5.                      # Velocity to move through the 3rd dimension to simulate time evolution
turbinflow.low.turb_nplane    = 32                      # Number of planes to read and store at a time
turbinflow.low.time_offset    = 0.0                     # Offset in time for reading through the 3rd dimension
turbinflow.low.verbose        = 0                       # Verbosity level
turbinflow.low.extrap_nonperiodic = 0                   # Allow interpolation near edges of inflow patch where stencil may touch ghost cells
turbinflow.low.tile_periodic  = 0                       # Cover the entire inflow face by periodically repeating/tiling the inflow patch
turbinflow.low.interp_type    = quadratic               # Either quadratic (default) or linear (required if there are nonperiodic directions)
turbinflow.low.time_periodic  = 0                       # Specify if the turbinflow data should be repeated in time, only valid for time varying turbinflow of type "istimeplanes"

turbinflow.high.turb_file      = TurbFileHIT/TurbTEST   # All same as above, but for second injection patch
turbinflow.high.dir            = 1
turbinflow.high.side           = "high"
turbinflow.high.turb_scale_loc = 633.151
turbinflow.high.turb_scale_vel = 1.0
turbinflow.high.turb_center    = 0.005 0.005
turbinflow.high.turb_conv_vel  = 5.
turbinflow.high.turb_nplane    = 32
turbinflow.high.time_offset    = 0.0006
turbinflow.high.verbose        = 2
```

--------------------------------

### Citation for PeleMP and PeleRad Capabilities in PelePhysics

Source: https://github.com/amrex-combustion/pelephysics/blob/development/README.md

Use this BibTeX entry to cite the multi-physics capabilities (soot, spray, radiation) within PelePhysics, which were imported from PeleMP and PeleRad. This citation is for specific components and their associated publication.

```bibtex
@article{owen2023pelemp,
  title={PeleMP: The Multiphysics Solver for the Combustion Pele Adaptive Mesh Refinement Code Suite},
  author={Owen, Landon D and Ge, Wenjun and Rieth, Martin and Arienti, Marco and Esclapez, Lucas and S Soriano, Bruno and Mueller, Michael E and Day, Marc and Sankaran, Ramanan and Chen, Jacqueline H},
  journal={Journal of Fluids Engineering},
  pages={1--41},
  year={2023}
}
```

--------------------------------

### Generate QSS Chemistry YAML

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

Generates a QSS chemistry YAML file from a skeletal YAML and a list of non-QSS species. Ensure you are in the correct directory and have the necessary input files.

```bash
cd ${PELE_PHYSICS_HOME}/Support/ceptr
poetry run qssa -f ${PATH_TO_YAML}/skeletal.yaml -n ${PATH_TO_YAML}/non_qssa_list.yaml
```

--------------------------------

### Generate Mechanisms using a Mechanisms Directory Helper Script

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/Ceptr.md

Use a bash script located in the Mechanisms directory to convert a specified YAML mechanism file.

```bash
bash ${PELE_PHYSICS_HOME}/Mechanisms/converter.sh -f ./LiDryer/mechanism.yaml
```

--------------------------------

### Run Regression Tests

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Testing/Regression/README.md

Execute the regression tests defined in the PelePhysics-tests.ini configuration file. Results will be formatted in HTML and available at TestData/PelePhysics/web/index.html.

```bash
./regtest.py PelePhysics-tests.ini
```

--------------------------------

### Specify CVODE Library Directory

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Docs/sphinx/CvodeInPP.md

If Sundials is not found in the default path, provide the directory containing the Sundials libraries using this flag.

```makefile
CVODE_LIB_DIR=PathToSundials/instdir/lib/
```

--------------------------------

### Generate Input File for PeleC using FuelLib

Source: https://github.com/amrex-combustion/pelephysics/blob/development/Mechanisms/liquid_fuels_nonreacting/README.md

Use this command to generate the required input file for PeleC when using the MP liquid property model. Ensure the FUELLIB_DIR environment variable is set.

```bash
cd $FUELLIB_DIR/source
python Export4Pele.py --fuel_name posf10264 --units cgs --export_mix True --liq_prop_model mp
```