Output Generated Mechanism
This menu combines the generated mechanism, in generated format, with a base mechanism,
in CHEMKIN format. The connection of the molecule species between the two mechanisms
is done through a molecule species list pair.
To use this menu, three sets of files are needed:
- Genenerated Mechanism These are the set of files associated with the generated mechanism on the server.
This is usually a single 'Combined' mechanism of several generated pathways.
- Base Mechanism This is the base mechanism, in CHEMKIN format, to be combined with the generated mechanism.
- Correspondences This is the set of overlapping molecule species between the generated mechanism and the
base mechanism. This file is in the form, one species per line, with the generated name listed first and the
corresponding base mechanism name listed second (separated by a space)
This set of action depends on the REACTION system, so the History window has to set up the job.
The menu consists of five tabs:
- OutputThis window contains some of the output of the tasks. It is also here where the history window
can be called if the system has not already been started.
- Options
- Generated This sets up the generated mechanism to be combined, its literature
reference and the set of molecule correspondences with the base mechanism (standard generated mechanism menu).
Using this information, the generated mechnanism
is read into the system.
- Base This sets up the base mechanism and its literature reference.
- Print The alternative nImames are set up and the combined mechanism is printed in
CHEMKIN format.
The general sequence of actions to be taken are as follows (basically working through the tabs, left to right):
- Output Tab If the REACTION job should be started, the button 'Start Remote REACTION' should
be pressed. With this the History window appears. Usually, the 'reaction' save level one should be set.
- Generated Tab
- Reference Information The 'Author', 'Source' and 'Note' fields should be filled in.
- Generated MechanismTo specify the
generated mechanism (from the server), press the 'Root Name' button. A selection of generated mechanisms
should appear and the desired chosen. The root name of the mechanism should appear in the field.
- Molecule Correspondencesthe file with the name correspondes should be read in (from the client files) by pressing 'Get Base Molecule List'.
Once read in, the fields with the species names can be modified.
- Unit Specifications The unit specifications at the bottom
should be checked (recommended to keep the defaults).
- Read InWhen all this information is entered, then the
generated mechanism can be read in with 'Read in from Server'. The output from the read will appear in the 'Output' tab.
- Lists Several buttons are supplied to view and write out the reaction and molecule lists.
- Base Tab This tab reads in the base mechanism
- File nameBy pressing 'File Name', a menu of files from the client directory is shown. The CHEMKIN
base mechanism should be chosen. The mechanism has to be relative to the default client directory.
- Root Name By pressing the 'Root Name' button, the root name of the mechanism is derived
from the full name.
- Literature Reference This is the literature reference of the base mechanism.
- Read By pressing the 'Read Mechanism' button, the base mechanism is read in. The output from the
read is shown in test field.
- Lists The reaction and molecule lists of the base mechanism can be viewed and written out.
- Print Tab This tab prints out the combined generated and base mechanism to the server (and to the
client directory).
- Names The names of the molecule correspondences of the 'Generated' tab are read in when the
'Update Alternative Names' button is pressed. All the corresponding names of the generated mechanism will
be changed to those of the base mechanism.
- Print The combined mechanism is printed out in CHEMKIN format (with the extension .ckm) when
the 'Print Mechanism to Server' is pressed. The file name is the root name with '-Out.ckm' added. The output of the job is shown in the 'Output' tab. In the
text field of the 'Print' tab is the list of molecules and reactions.
At the end of this sequence, a CHEMKIN formatted file is produced