How to run AtChem2

The atchem2 executable takes a number of arguments, which indicate the location of the configuration files, of the model constraints and of the model output. From version 1.2, a system of flags is used to pass the arguments to the executable (named arguments). In previous versions, the arguments have to be provided to the executable in a precise order (positional arguments).

For more information, see the AtChem2 manual in the doc/ directory.

version 1.2.*

atchem2 has 9 named arguments:

1. --model: path to the model directory - default: model/
2. --output: path to the output directory - default: model/output/
3. --configuration: path to the model configuration directory - default: model/configuration/
4. --constraints: path to the constraints directory - default: model/constraints/
5. --env_constraints: path to the environment constraints directory - default: model/constraints/environment/
6. --photo_constraints: path to the photolysis constraints directory - default: model/constraints/photolysis/
7. --spec_constraints: path to the chemical constraints directory - default: model/constraints/species/
8. --mcm: path to the MCM data files directory - default: mcm/
9. --shared_lib: path to the mechanism.so shared library - default: model/configuration/mechanism.so

In addition, the --help flag displays a help message.

The order of the flags does not matter. If a flag is not specified, AtChem2 assumes the default value for the corresponding argument, using the following hierarchical directory structure:

                                     +---------------+-------------------------+
                                     |               |                         |
                                   model/           mcm/        model/configuration/mechanism.so
                                     |
                                     | 
     +-------------------------------+-------------------------------+
     |                               |                               |
  output/                       constraints/                   configuration/
                                     |
                    +----------------+----------------+
                    |                |                |
               environment/      photolysis/       species/

For example:

• ./atchem2 --model=model/ --shared_lib=model/configuration/mechanism.so
• ./atchem2 --output=model/output/ --shared_lib=model/configuration/mechanism.so
• ./atchem2 --configuration=model/configuration/ --output=model/output/
• ./atchem2 --constraints=model/constraints/ --output=model/output/

version 1.1.*

atchem2 has 7 positional arguments:

1. path to the output directory - default = model/output/
2. path to the output reaction rates directory - default = model/output/reactionRates/
3. path to the model configuration directory - default = model/configuration/
4. path to the MCM data files directory - default = mcm/
5. path to the chemical constraints directory - default = model/constraints/species/
6. path to the environment constraints directory - default = model/constraints/environment/
7. path to the photolysis constraints directory - default = model/constraints/photolysis/

./atchem2 ./model/output/ ./model/output/reactionRates/ ./model/configuration/ ./mcm/ ./model/constraints/species/ ./model/constraints/environment/ ./model/constraints/photolysis/

version 1.0 and earlier

atchem2 has 5 positional arguments:

1. path to the output directory - default = modelOutput/
2. path to the output reaction rates directory - default = instantaneousRates/
3. path to the model configuration directory - default = modelConfiguration/
4. path to the chemical constraints directory - default = speciesConstraints/
5. path to the environment and photolysis constraints directory - default = environmentConstraints/

./atchem2 ./modelOutput/ ./instantaneousRates/ ./modelConfiguration/ ./speciesConstraints/ ./environmentConstraints/