README file for directory GECKO-A/SCRIPTS
=========================================

RUNNING ON CHEYENNE:

All scripts invoke cheyenne_scripting_functions.bash (contains functions write_cheyenne_*script) which writes GENERATED_SCRIPTS specific to particular run.  THESE are what is sent to cheyenne.

1) generate mechanism from scratch & interpret it:
./generate_scheme_cheyenne.bash -i {cheminput.dat file} -m {mechname} -s {settings file}
invokes: 
	launch_generator_cheyenne.bash
	postprocess_generator_cheyenne.bash >> write_akparameter.bash
	run_interp_cheyenne.bash


2) add to existing mechanism:
./generate_scheme_cheyenne.bash -i {cheminput.dat file} -m {mechname} -x {existing mechanism} -s {settings file}
invokes: 
	postprocess_generator_cheyenne.bash >> write_akparameter.bash
	run_interp_cheyenne.bash

3) interpret existing mechanism (eg if you edited/added to it):
./gen_finish_scheme.bash {mechname}
invokes: 
	postprocess_generator_cheyenne.bash >> write_akparameter.bash
	run_interp_cheyenne.bash

4) run box model: 
./run_boxmod_cheyenne.bash -m {mechname} -k {keyfile} -p {photfile} -c {conc_file}
invokes:
	compile_boxmod.bash 
	launch_boxmod_cheyenne.bash 
	run_postproc_cheyenne.bash

5) run box model continuation:
./run_boxmod_cheyenne.bash -m {mechname} -k {keyfile} -p {photfile} -c {conc_file} -v {previous runname} 
invokes:
	compile_boxmod.bash 
	launch_boxmod_cheyenne.bash 
	run_postproc_cheyenne.bash

NOTES:
- boxmod must be recompiled for each specific akparameter_module.f90 file
