CEPTR: Chemistry Evaluation for Pele Through Recasting
We use CEPTR to generate C++ mechanism files from Cantera yaml chemistry files. CEPTR is a python package part of the PelePhysics source code.
Software requirements
The CEPTR package uses poetry to manage the Python dependencies. Poetry is therefore required to use CEPTR and can typically be installed through system package managers (e.g. HomeBrew) or following the instructions in poetry’s documentation.
To install CEPTR dependencies:
$ cd ${PELE_PHYSICS_HOME}/Support/ceptr
$ poetry update
Usage
Generating for a single chemistry
There are three ways to use CEPTR to generate C++ mechanism files for a given chemistry
Using CEPTR directly:
Executed from the
${PELE_PHYSICS_HOME}/Support/ceptr
directory, the most general usage of CEPTR is:$ poetry run convert -f ${PELEPHYSICS_HOME}/Mechanisms/${chemistry}/mechanism.yaml \ --chemistry {chemistry-type} \ --gas_name {gas-name} \ --interface_name {interface-name}
The
--chemistry
, or equivalently-c
, argument allows users to convey if the${chemistry}
of interest is either one of two valid options, namely,homogeneous
orheterogeneous
. Similarly, the--gas_name
and--interface_name
arguments allow users to specify the names of the homogeneous phase and gas-solid interface prescribed in the correspondingmechanism.yaml
file.The default
chemistry-type
,gas-name
arehomogeneous
andgas
respectively while that forinterface-name
isNone
. Note that if aheterogeneous
chemistry-type
is specified, the user must necessarily specify a correspondinginterface-name
.An example of directly using CEPTR for homogeneous mechanisms is:
$ cd ${PELE_PHYSICS_HOME}/Support/ceptr $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/LiDryer/mechanism.yaml
Note
CEPTR interpretations of heterogeneous mechanisms is currently a work in progress.
Using a helper script in the directory containing the
mechanism.yaml
file:$ ./convert.sh
Using a helper script in the
Models
directory:$ bash ${PELE_PHYSICS_HOME}/Mechanisms/converter.sh -f ./LiDryer/mechanism.yaml
Batched generation
Note
If you are using batched generation as outlined here, it will automatically use multiprocessing to generate the files in parallel using all CPUs detected on the machine. If you want to change that you can pass the optional argument -n NPCU
, wheren NCPU
is an integer indicating the number of processes you want to use.
For non-reduced chemistries, CEPTR can take a file with a list of mechanism.yaml
files to convert:
$ cd ${PELE_PHYSICS_HOME}/Support/ceptr
$ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
For reduced chemistries, CEPTR can take a file with a list of qssa.yaml
and qssa_input.toml
to convert:
$ cd ${PELE_PHYSICS_HOME}/Support/ceptr
$ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
For generating qssa.yaml
for reduced chemistries, CEPTR can take a file with a list of skeletal.yaml
and non_qssa_list.yaml
:
$ cd ${PELE_PHYSICS_HOME}/Support/ceptr
$ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
To generate all mechanisms:
$ 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
Converting CHEMKIN files
We rely on Cantera’s ck2yaml
utility to convert CHEMKIN files to the Cantera yaml format (and proceed as above with CEPTR on the resulting yaml file):
$ cd ${PELE_PHYSICS_HOME}/Support/ceptr
$ poetry run ck2yaml --input=${PATH_TO_CHEMKIN_DIR}/mechanism.inp --thermo=${PATH_TO_CHEMKIN_DIR}/therm.dat --transport=${PATH_TO_CHEMKIN_DIR}/tran.dat --permissive
The files tran.dat
and therm.dat
are optional if already included in the .inp
file.
Generating a QSS chemistry file
To generate a QSS chemistry yaml file from another yaml file, one executes:
$ poetry run qssa -f ${PATH_TO_YAML}/skeletal.yaml -n ${PATH_TO_YAML}/non_qssa_list.yaml
The full list of options is:
$ poetry run qssa -h
usage: qssa [-h] -f FNAME -n NQSSA [-m {0,1,2}] [-v]
Mechanism converter
optional arguments:
-h, --help show this help message and exit
-f FNAME, --fname FNAME
Mechanism file
-n NQSSA, --nqssa NQSSA
Non-QSSA species list
-m {0,1,2}, --method {0,1,2}
QSSA method (default: 2)
-v, --visualize Visualize quadratic coupling and QSSA dependencies
For a detailed description of these options and a further information on the way QSS mechanism are treated in CEPTR the reader may consult the QSS section.
See Tutorials (Generating NC12H26 QSS mechanism with analytical jacobian and Generating NC12H26 QSS mechanism without analytical jacobian) for generating QSS mechanisms from the .yaml
files.