Archive for the ‘Kinetics’ Category
Where to publish non-physics preprints? or where to find a chemistry preprint server without the arxiv.org like endorsement system?
A good friend, and former follow graduate student, and I recently finished a scientific manuscript we have been working for some years now. Since we are both out of academia, and busy with other things, putting an article into peer review is not our top priority at the moment. Nevertheless, we would still like the world (or at least a few people) know about our work, and also secure our intellectual property, by not letting others publish the exact same ideas. We came up with the idea of publishing it on a pre-print server, and then time should tell if we would submit to a peer-reviewed journal. The best known (physics) pre-print server is the arxiv.org hosted by Cornell University Library. Although our work probably could be classified into some subtopic physics category, strictly speaking, chemistry would be more appropriate, chemical kinetics and catalysis to be more accurate. Furthermore, the endorsement system used by arxiv.org is also frustrating, to put it mildly. Once you’re out of research it seems very difficult to get endorsement. I consider my scientific network to be quite broad and large, however I do not know a single soul who can endorse me. Thus, arxiv.org seemed out of the question. Then, where to find a chemistry pre-print server with a less strict endorsement system? It turns out that Nature has started their own pre-print service known as Nature precedings, and they are embracing chemistry. Thank you. So now our manuscript is public available. As a note to those wanting to publish physics preprints without endorsement (and chemistry as well), the so-called vixra.org (arxiv reversed) is an option. However, I have not been able to really judge the quality of the content being published. Well to be honest the same goes to Nature precedings, but since Nature Scientific Publishing is behind, it sounds better in my ears.
The presentation accompanying paper no. 39 is available
Years ago I made some on-line material available on my (old) website in order to supplement some of my publications. In the meantime I have closed down the old website, and guess what, now the material has been requested (cough!). What to do now? Use the the internet archive/waybackmachine.
“Browse through over 150 billion web pages archived from 1996 to a few months ago. To start surfing the Wayback, type in the web address of a site or page where you would like to start, and press enter. Then select from the archived dates available. The resulting pages point to other archived pages at as close a date as possible. Keyword searching is not currently supported.”
This page contains supplementary material to some of my publications
|Table of contents [showhide]|
Linux gazette 114
In order to try out Example 3 in the article Python for scientific use. Part I: Data visualization in Linux Gazette 114 (2005) (http://linuxgazette.net/114/andreasen.html) a number of data files are needed.
tar xvfz 3ddata.tar.gz
in the directory from which the python script is run.
Linux gazette 115
In order to try out Example 3 in the article Python for scientific use. Part II: Data analysis in Linux Gazette 115 (2005) (http://linuxgazette.net/115/andreasen.html) a number of data files are needed.
tar xvfz 3dtdata.tar.gz
in the directory from which the python script is run.
The kinetic models published in Simplified kinetic models of methanol oxidation on silver are all implemented in a number of octave (http://www.octave.org) scripts. You can see all individual files in the table below. All files can be obtained either by downloading octavefiles.tar.gz (http://andr.dk/octavefiles/octavefiles.tar.gz) or by
wget -i FILELIST.txt
|MeOH_test.m (http://andr.dk/octavefiles/MeOH_test.m)||Main file|
|Keqsel.m (http://andr.dk/octavefiles/Keqsel.m)||Reaction step equilibrium constants calculated using statistical thermodynamics|
|K_HandS.m (http://andr.dk/octavefiles/K_HandS.m)||Reaction step equilibrium constants calculated using enthalpies and entropies|
|fullrateorig.m (http://andr.dk/octavefiles/fullrateorig.m)||The original rate law from quasi equilibrium approximation and stat. therm. with a plug-flow reactor model included|
|fullrate.m (http://andr.dk/octavefiles/fullrate.m)||The original rate law from quasi equilibrium approximation and classical thermodynamics with a plug-flow reactor model included|
|marirate.m (http://andr.dk/octavefiles/marirate.m)||The MARI approximation|
|israte.m (http://andr.dk/octavefiles/israte.m)||The IS approximation|
|powerlawrate.m (http://andr.dk/octavefiles/powerlawrate.m)||The clean surface approximation|
|qtransA.m (http://andr.dk/octavefiles/qtransA.m)||Calculation of the translational partition function|
|qvibA.m (http://andr.dk/octavefiles/qvibA.m)||Calculation of the vibrational partition function for a single vibration (cm-1)|
|qvibAJ.m (http://andr.dk/octavefiles/qvibAJ.m)||Calculation of the vibrational partition function for a single vibration (J/mol)|
|qrotA2D.m (http://andr.dk/octavefiles/qrotA2D.m)||Calculation of the 2-D rotational partition function (cm-1)|
|qrotA2DJ.m (http://andr.dk/octavefiles/qrotA2DJ.m)||Calculation of the 2-D rotational partition function for a single vibration (J/mol)|
|qrotA3D.m (http://andr.dk/octavefiles/qrotA3D.m)||Calculation of the 3-D rotational partition function (cm-1)|
|qvibtotA.m (http://andr.dk/octavefiles/qvibtotA.m)||Calculation of the total vibrational partition function for a molecule (cm-1)|
|HvibA.m (http://andr.dk/octavefiles/HvibA.m)||Calculation of the vibrational enthalpy of a single vibration (cm-1)|
|HvibAJ.m (http://andr.dk/octavefiles/HvibAJ.m)||Calculation of the vibrational enthalpy of a single vibration (J/mol)|
|HvibtotA.m (http://andr.dk/octavefiles/HvibtotA.m)||Calculation of the total vibrational enthalpy for a molecule (cm-1)|
Full text available for CIMAC paper no. 39 2010: Modelling of the oxidation of fuel sulfur in low speed two-stroke engines
In large marine two stroke Diesel engines during combustion of sulfur containing fuel, the sulfur is oxidised to SO2 , mainly, although substantial amounts of SO3 and H2SO4 will form as well. These latter species may cause corrosional wear of the cylinder liner if not neutralised by lube oil additives. Potential attacks is due to either condensation of sulfuric acid on the cylinder liner lube oil film or direct dissolution of oxidised sulfur species in the lube oil film in which reaction with dissolved water may be the source of acidic species. In order to evaluate and predict corrosional wear of the liner material, it is pivotal to have realistic estimates of the distribution/concentration of oxidised sulfur species as well as a reliable model of
formation, transport and destruction of acidic species in the oil film. This paper addresses the former part by invoking a detailed reaction mechanism in order to simulate the oxidation of fuel bound sulfur and predicting the concentration of SO2 as well as the conversion fraction into SO3 and H2 SO4 . The reaction mechanism is coupled to a realistic model of the combustion process in which the air entrainment into the combustion zone is accounted for. The results of the simulation are evaluated with respect to previously applied models as well as existing data on the conversion fraction of SO2 to SO3 and H2 SO4 . The conversion fraction is found to be in a range of 2.6-6.7 %.
A pivotal part for the creation of the above paper has been the usage of the Cantera software for handling thermodynamics and integration of kinetic rate equations.
I have authored a paper entitled “Modelling of the oxidation of fuel sulfur in low speed two-stroke Diesel engines ” in collaboration with my colleague Stefan Mayer from the Process Development Department, Marine Low-Speed, MAN Diesel in Copenhagen. The paper has just been accepted for publication for the 2010 CIMAC congress held in Bergen, Norway, and will be presented by myself at the congress on Wednesday 16th of June in the morning between 8.30 and 10.00 in Room C (according to the preliminary programme).
In the paper a detailed a detailed reaction mechanism is used in order to simulate the oxidation of fuel bound sulfur and predicting the concentration of SO2 as well as the conversion fraction into SO3 and H2SO4 . The reaction mechanism is coupled to a realistic model of the combustion process in which the air entrainment into the combustion zone is accounted for. The results of the simulation are evaluated with respect to previously applied models as well as existing data on the conversion fraction of SO2 to SO3 and H2SO4. The conversion fraction is found to be in a range of 2.6-6.7 %.
Note: I just checked that the procedure (svn) given below also works for Ubuntu 10.10, and it does.
Here’s a brief description on how I managed to compile and install cantera 1.8 on Ubuntu 9.10 (32 bit), with the full python interface. However, first a little description of what cantera is (taken from the website):
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.
Cantera is written in C++, and can be interfaced also from python, matlab and Fortran.
- First step is to install any dependencies. This is handled by apt-get:
sudo apt-get install subversion g++ gfortran python2.6-dev python-numpy libsundials* graphviz
- Next step is to get the source for cantera. This can be done by either downloading the cantera-1.8.0-beta-tar.gz from the cantera site our checking the latest version from svn
svn checkout http://cantera.googlecode.com/svn/cantera18/trunk/ cantera
- change to the cantera directory (either the svn checkout or the untarred/gunzipped cantera-1.8.0)
- Edit the file named preconfig and make sure the following lines are included by uncommenting/editing
- The entire preconfig file can be viewed here
- then in a terminal run the following commands
sudo make install
- If everything went well you should be able to import the Cantera module in python:
>>>from Cantera import *
Nørskov et al. recently wrote a perspective in Science Magazine entitled “Rate Control and Reaction Engineering” with a short description “A concept for evaluating. the relative importance of steps in complex reactions may guide the development of better catalysts”. The article also addresses our recently published paper “Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates” in JACS. Thanks guys!