AtChem on–line

version 1.1

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About AtChem on–line

AtChem on–line is a tool for running simulations of Master Chemical Mechanism using just your web browser, no installation is required. The user needs to supply two files: one with the chemical reactions and one with initial concentrations, change other parameters if necessary and press “Submit”. A link to a zip file with the results should appear soon.

Currently there is one login for everyone – this will be changed in the future and users will need to register to receive an individual login. Until then, remember that everyone can access your data.

On the home page you can find links to example input files. The set “simplest” describes a very simple model with one reaction. The set “allfiles” defines a larger model and contains all possible types of input file. The format of input files is described in detail below.

There is an online tutorial designed to lead you through the features of the AtChem on-line tool. It is available on the MCM website

Input data files

Mechanism file

Mandatory. This file contains the chemical mechanism you wish to use. It must have extension “.fac”. All the reactions must be described in facsimile format, i.e. reaction rate, substrates and products, separated by signs “% : = ;”, i.e.
% k : A + B + ... = C + D + ... ;
The file must also contain the peroxy radical sum, i.e.
RO2 = RO2a + RO2b +...;
If there are no peroxy radicals, an empty sum should be used. Lines which do not start with “%” nor with “RO2=” are ignored.

Below is an example of a very simple mechanism file. The mechanism described contains only one reaction, A–>C occuring with reaction rate 1E-4 and there are no peroxy radicals.

* ------------------------------------------------------------------- *;
* SIMPLEST MECHANISM                                                  *;
* ------------------------------------------------------------------- *;
RO2 =;
% 1e-4 : A = C ;

A more complex example of mechanism file can be viewed here. Subset mechanisms from the MCM website should be downloaded in Facsimile format and are suitable for direct input to the model.

Initial concentration file

Mandatory. This file must have extension “.config”. It should contain two columns: first with MCM names of the species and second with the concentration in molecules cm-3. Concentration of -1 means end of input – anything following will be ignored. An example of initial concentration file is below.

 O          2192.515962496984
 O3         5.356756840167577E+11
 NO3        14010.124722567038
end         -1
all below is ignored
 NO         1.0992718929324424E+8
 NO2        1.8473660738403264E+09

Any species not included in this file will initialize with a default value of 0. It is not necessary to initialize species which are going to be constrained. Environmental variables have separate input fields below and should not be included in this file.

Constraints

There are two types of constraints: species constraints and environmental constraints. These are provided as two zip files which contain a separate file for each constraint. Constraints can be provided on different timescales e.g. data every minute for NO and every hour for VOCs. The solver will interpolate between data points for less frequent data.

Important: When using constraining data the model start and stop time must be within the range of the constraining data to avoid undefined solver behaviour. The model start time is set in the model parameters section and the end time is determined by the size and number of steps.

Species constraints file

Optional. This is a zip file containing data for any species you wish to constrain. The data for each species is contained in a separate file which is named with the MCM name for the species e.g. CH3COCH3. The first line of each file should be the number of data points contained in the file. Following this each line should have 2 numbers separated by spaces; the first number is the time that the data point occurs at in seconds, the second number is the species concentration in molecules cm-3.

All the data files should be placed in 1 zipped file with the file extension “.zip”

Environmental constraints file

Optional. This is a zip file containing data for any environmental parameter you wish to constrain and the files have the same format as the species constraints. The environmental constraints are temperature, H2O, relative humidity (RH) (NB only 1 of H2O and RH should be provided to the model), pressure, M, dilution rate (DILUTE), declination angle (DEC), boundary layer height, JFAC, ROOFOPEN and photolysis rates. With the exception of the photolysis rates if these parameters are being constrained then the appropriate input in the Environment variables section should be set to CONSTRAINED

Concentration output file

Optional. This is a file specifying which species concentrations you would like outputting from the model. It should be a list of MCM species names, 1 per line. This file should have the file extension “.config”

If this file is not provided by the user then the output will default to the same species as those in the initial concentrations file. The frequency of the output can be set in the model parameters section.

Photolysis rates

Optional. This file allows the user to specify a different photolysis rate parameterization to the default parameterization used in the MCM. The format should use the same 3 parameter configuration (J = l*cosX@m*EXP(-n*secX) ) and the file should have the extension'.rates'

Example file: https://atchem.leeds.ac.uk/run/exdata/allfiles/photolysis_rates.rates

The photolysis rates file can also be used to specify a constant rate for each photolysis rate. The format for this file is number, rate coefficeint and name and the file should have the extension '.const'

Example file: https://atchem.leeds.ac.uk/run/exdata/allfiles/photolysis_rates.const

Environment variables

These can be given a fixed value or constrained to a data file provided in the environmental constraints zip file (set value to CONSTRAINED). Some variables (specified below) can be ignored (set value to NOTUSED). Some environmental variables can also be calculated by the model. To use this feature the value should be set to CALC and the necessary additional inputs must be given; details of required inputs are given below.

M: Number of air molecules (molecules cm-3)

Can be calculated, requires temperature and pressure to be provided

Cannot be NOTUSED

Default value=2.60e+19

TEMP: Temperature (K)

Must be provided as a fixed value or constrained. CANNOT be calculated or NOTUSED Default value=281.95

Pressure: Torr

Cannot be calculated. Default value= NOTUSED

RH: Relative humidity

Cannot be calculated but can be NOTUSED provided H2O is given (%) Default value= NOTUSED

H2O: Water concentration (molecules cm-3)

Can be calculated, requires relative humidity to be provided

Can be NOTUSED provided RH is given

Default value=3.06e+17

DEC: Declination of the sun (radians)

Can be calculated, requires date to be provided

Cannot be set to "NOTUSED", must be fixed, constrained or calculated.

Default value=0.28782328e+00

BOUNDARYLAYERHEIGHT: Allows user to set the boundary layer height

Cannot be calculated. Default value= NOTUSED

DILUTE: Dilution rate (s-1)

Cannot be calculated. Can be NOTUSED Default value= 6.77E-6

JFAC: Factor used to correct calculated photolysis rates e.g. to adjust for cloudiness

Can be calculated by comparing a measured photolysis rate to that calculated by the model (currently only works for JNO2) requires JFAC species to be set and constraining data for this photolysis rate to be provided

Default value=NOTUSED

ROOFOPEN: Flag to turn photolysis rates on or off 0=off, 1=on.

Cannot be calculated. Can be NOTUSED. Default value is 1

Model Parameters

Number of steps and step size: The total time of the model run is determined by the number of steps and the step size. The step size controls how often the concentration output is produced. To run a model for 2 hours with output every 5 minutes would require a step size 300s and 24 steps

Max nr. of constrained species and Max. nr of constrained species:

These control the maximum size of a constraint file and maximum number of constrained species and can usually be left as the default values

Rates output step size: Frequency of output for the production and loss rates (seconds)

Model start time: Seconds. If using constraining data the model start time must be within the range of the constraint data and the total run time of the model (determined by the number of steps and the step size) must give a model end time which is also within the range of the constraining data.

Jacobian output step size: As this output is not commonly used it defaults to twice the model run time so it isn’t produced. This should only be altered if it is required and will produce very large files so should not be output too frequently as this may cause large models to crash.

Latitude and longitude: Should be set to the location of the experiment

Day, month and year: Should be set to the date of the experiment

Inst. Rates output step size: Frequency of output for the instantaneous rates for every reaction in the model (seconds). The output is produced as 1 file for each step and the name of the file corresponds to the time in seconds

Other

Job name – Only use A-Z0-9_– characters and do not use spaces. The server will append an integer to the name to ensure that each job has a unique ID.

Description – this can be used to record any information you like about the model and is optional.

JFAC species: Used to compare a constrained photolysis rate to the photolysis rate calculated by the model. The factor by which they differ is used to correct the other calculated photolysis rates.

Production and Loss rates output: These are used to specify which species the production and loss rates should be output for.

Further help

This application is still under development and any feedback you have will be appreciated.

If you have any problems then please contact us with the job name as this will help us to trace the problem.

Katarzyna Borońska
E–mail: k.boronska@leeds.ac.uk
Telephone: +44 113 343 5324
Jenny Young
E–mail: J.C.Young@leeds.ac.uk
Telephone: +44 113 343 6486