AtChem Online

Outline

We run the AtChem code as a web service, thus making the Master Chemical Mechanism simulation of atmosphere chemistry phenomena accessible to other members of the EUROCHAMP group.

Current version

Run AtChem online

Version 2.1 (2022-12)

• The application has undergone a major migration between hosting locations.
• Log in with user 'atchem', usual password. Please report any issues or request the password by contacting Andrew Rickard, CC Killian Murphy.

Version 2.0

• User and session management.
• User "outsider" partially deactivated (cannot run jobs, but you can use his credentials to create your own user account).

Version 1.5

• Option to alter O2 and N2 concentrations - see help page for further details.

Version 1.4

• Evolution of the concentration is plotted for several species.
• Output is less verbose.

Version 1.3

• Generic rates can be defined in the mechanism file.
• Number of photolysis rates can vary (was hard-coded 35).
• Photolysis constants can be provided in a file with extension “.const” (see below).
• Extension “.config” is no longer accepted for photolysis rates – please use “.rates”.
• RO2 sum is saved in file envVar.output.
• Output is less verbose.
• Header of photolysis rates output file is fixed.
• Instantaneous rates are output at correct intervals.

Warning! Instead of photolysisRates.config you should now provide either photolysisRates.rates (format unchanged) or photolysisRates.const with J/L/N columns (number/rate/name).

Sample data

• allfiles: a large set of data, containing all input files
• simplest: dataset describing reaction A - > C with rate coefficient 1e-4

Source code

The core code is written by Chris Martin in Fortran 90 and uses an open-source library CVODE, providing rapid solvers of ODE systems. The Python wrapper, written by Kasia Borońska, takes care of converting the input data, running the simulation on the server and displaying links to zipped output files. You can download a current version of AtChem from this link.

Documentation

Using the online version is straightforward. User uploads the mechanism file (in FACSIMILE format), initial concentrations file and, optionally, some configuration files, set environment variables and model parameters. It is also possible to enter the job name and a short description. After pressing "submit", the simulation will be run on the server and links to input and output files will be displayed, along with a unique job ID.

People involved

• Kasia Borońsa
• Peter Jimack
• Mike Pilling
• Andrew Rickard
• Monica Vázquez Moreno
• David Waller
• Jennifer Young
• Killian Murphy