Pathway Plot

 

Manual

Anders Broe Bendtsen

15 March 1999

What does the program do?

Pathway Plot is a program, which automatically will plot the dominant reaction paths, in a detailed chemical kinetic model, based on simulation output from a SENKIN simulation. 

Pathway Plot is a postprocessor to SENKIN. From one or more initial key species and a binary output file from a SENKIN simulation, the program defines the set of important key species and plots the significant reactions between these species. You may choose to view only species containing a defined element, and at any time you may take over control of the plots.  

Installation

Click here to register for Downloading PP_INST.EXE The downloaded file will be 800K. 

Run PP_INST.EXE 

This will prompt you for a new directory and unpack PP.EXE, an example CKLINK and SAVE.BIN and a required SALFLIBC.DLL system file. For information the ASCII mechanism, CK.MEC and SENKIN input and output SK.INP and SK.OUT are also unpacked to the directory, but these files are not needed. 

Pahway Plot example

Pathway Plot manual

Running Pathway Plot

Pathway Plot Display

Pathway Plot setup

Printing Pathway Plots

System Requirements

Trouble shooting

About Pathway Plot

Running Pathway Plot

First run your SENKIN simulation to generate a SAVE.BIN binary output file.

Ensure that the binary SAVE.BIN and CKLINK. files of the reaction set is in the same directory as PP.EXE

If your binary files have other names use the DOS command SET as follows:
SET CHEMKIN=CHEM.BIN
(for defining the binary file of the reaction set to be "CHEM.BIN")
SET SENKIN=SENKIN.BIN
(for defining the binary file of the SENKIN simulation to be "SENKIN.BIN")

Call PP.EXE

If you do not have a default setup (found in a ROPCONT.INP file) you will be prompted to setup Pathway Plot. You may select Setup from the File menu to obtain the same dialogue boxes. You must select one key species, and subsequently press Continue.

When the set-up is sufficiently defined, you must press the OK button to see the Pathway Plot of the next time step. Unmark Pause in the File menu to see a continuous "movie" of the reaction.

To exit select Exit from the File menu.

Introduction 

Pathway Plot's displayPathway Plot Screen. Click to see full screen.

In the centre of the display, will be the Pathway Plot, with arrows between species. The width and colour of arrows will be proportional to the activity of the path between the species. The species will be followed by a circle. The colour of the circle will correspond to the total reaction of the species, and the size of the circle to the logarithm of the concentration of the species.

To the right on the plot is a scale translating the colours of arrows and circles to rates of progress (units are defined in your CHEMKIN-II reaction set). The rate of progress is the net production (or removal) of a species through a reaction, but for a Pathway Plot arrow from species A to P

Introduction it may be the sum of several reaction, with one reactant (A) and product (P) in common.

To the left are the active species which have been defined as unwanted on the plot.

In the top left corner is an OK button which is used to show the pathway plot at the next time step.

Introduction 

Pathway Plot setup

In setup you choose which species to display and you define the display here. Setup is chosen from the File menu. The setup window has three parts, "Key Species", "Drawing" and "Position of species" as defined below.
To continue plotting from the setup, select 'Continue'. If no species are selected you will prompted if you want to exit.

Selection of key species

You will be prompted for an initial set of key species. Select by clicking the species.

To avoid cluttering of your display you may choose to select some "Ignored" species. If you do not want Pathway Plot to expand your set of active species, remove the mark in the box next to "Expand key species".

If you want to start from scratch you may want to clear the selection of key species and/or ignored species.

To see species which must contain a single element select this element in the active element box. This will force all species not containing the active element to be ignored. You may select several active species, and you may subsequently deselect the "active elements" and manually select or deselect igored species.

Drawing of pathways

This setup makes it possible to select the active range of your pathway plots. You may define the colour range of your plot, and you may select the Relative production/removal limit, which is the level of contribution needed for an arrow to be included (and thus for expansion of species).
You may also choose how the reactions should be described; without text, by reactants and products or by reaction numbers. You may select a colour scale (Note that the flame scale is best for black and white printers).

Introduction

Position of species

Pathway Plot attempts to position the species, but at better plot may be obtained by manually moving the species.

This may be done in the setup, but a simpler method will be by clicking on a species. This will bring up two open circles around the species, and a number of closed circles in the available positions. Click on a closed circle to move the species. If you regret moving the species click on the original position of the species.
The benefit of moving species in the setup is the possibility to exactly define the position.

Working with saved setups

You may save the setup by selecting Save or Save Default in the setup box. Save Default will force the name to be ROPCONT.INP while Save will allow you select any name. If a file is called ROPCONT.INP in the directory PP.EXE will use this setup.

Load will allow you to select a saved setup. Format of setup files

Introduction 

Printing

To print the Pathway Plots, you must select Print from the File menu. This will have the inadvertent effect of clearing the clipboard.

Alternatively you may choose to copy the plot to a drawing program and modify the plot there. You do this by selecting "Copy" from the menu. The Pathway Plots are copied as vector drawings, allowing you full freedom in modification of the plots.

Introduction 

Tips for trouble shooting

File name errors
Your output files must be named CKLINK. and SAVE.BIN
If your files have other names use the DOS command SET as follows:
SET CHEMKIN=CHEM.BIN
(for defining the binary file of the reaction set to be "CHEM.BIN")
SET SENKIN=SENKIN.BIN
(for defining the binary file of the SENKIN simulation to be "SENKIN.BIN")

No expansion of species set is seen
Select Expand key Species in Setup
If you have only one species select manual limit definitions
Is the Relative Limit set too low?

Introduction 

Program Requirements

Windows 95 or Windows NT 4.0 (not tested with Windows 98).

Binary output from SENKIN, compiled with CKLIB vers. 3.3.

CKLINK. and SAVE.BIN file from SENKIN-simulation (output from sensitivity analysis not needed)

If your files have other names use the DOS command SET as follows: 


SET CHEMKIN=CHEM.BIN 


(for defining the binary file of the reaction set to be "CHEM.BIN") 


SET SENKIN=SENKIN.BIN 


(for defining the binary file of the SENKIN simulation to be "SENKIN.BIN")

Preferably 65536 colour high resolution display, but 640 by 480 in 256 colours is acceptable.

Introduction 

Format of ROPCONT.INP



 

Keyword

Explanation

KSPEC CH4 CO2 

! Defines key species to be plotted 

ISPEC OH O H 

! Ignores specific species 

ELEM C 

! Ignores all species without C 

POSI CH4 0.5 0.0 

! Positions CH4 in the centre at the bottom (x=0.5, y=0) 

POSI CO2 0.5 1.0 

! Positions CO2 in the centre at the top (x=0.5, y=1) 

LEVL CH4 1 

! Put CH4 at the bottom 

LEVL CO2 10 

! Put CO2 at the top 

MINF 1E-12 

! Scaling of flux'es. Minimum 1E-12 

MAXF 1E-8 

! Scaling of flux'es. Maximum 1E-12 

 


POSI and LEVL keywords may be used for all species in the mechanism, also ignored species. If species not included in the mechanism are listed an error will be seen.

Introduction 

About Pathway Plot

Copyright Anders Broe Bendtsen 1999

This program was developed during the PhD study of Anders Broe Bendtsen.

Supervisors of the project were Professor Kim Dam-Johansen and Associate Professor Peter Glarborg.

The PhD project was made under the CHEC research programme at the Dept. of Chemical Engineering at the Technical University of Denmark. (E-mail: chec@kt.dtu.dk)

Pathway Plot is provided for public use, provided that you register with the authors, and that credit is given by referring to the following paper:
Bendtsen, A.B.; Glarborg, P., and Dam-Johansen, K.: "Visualization methods in analysis of detailed chemical kinetics modelling." Comp. Chem. 25, 161, 2001

Introduction
 

 

Author Anders Broe Bendtsen, andbbdk@gmail.com

Last updated: February 16th 2001