User`s Manual
Contents
1. CHAPTER 3 INPUT AND OUTPUT input txt The user should also provide an input file similar to the following table interest t_init t_end max_bp tau_lifetime max_path f min global kin where 1 0 0 1 0e 3 0 9e 5 1500 1 e interest an index of the species of interest Sinterest if the user is interested in the production and or consumption of Sinterest Otherwise the user should specify interest as a non positive number e t_init t init a time interval t_init t_init C 0 7 where PumpKin will perform the analysis e max_bp if positive the maximum number of branching points considered otherwise it is disregarded e tau lifetime if positive a lifetime threshold with units of s otherwise it is disre garded e max_path if positive the maximum number of pathways considered per branching point treatment i e only the first max_path pathways with higher rate will be considered otherwise it is disregarded e f min if positive pathway rate threshold in units of mol cm s7 i e pathways with a rate smaller than f min will be deleted otherwise it is disregarded e global_kin boolean parameter If 1 or true PumpKin will interpret the input files as from Global_Kin otherwise from ZDPlaskin The order of parameters in the input file should be exactly like in the table The names of parameters are not important On the other hand the names of input files are very import2. 2000 9 R Dorai and M J Kushner A model for plasma modification of polypropylene using atmo spheric pressure discharges J Phys D 36 666 2003 6 Rajesh Dorai and Mark J Kushner Repetitively pulsed plasma remediation of no x in soot laden exhaust using dielectric barrier discharges Journal of Physics D Applied Physics 35 22 2954 2002 6 A Flitti and S Pancheshnyi Gas heating in fast pulsed discharges in N2 O2 mixtures European Physical Journal Applied Physics 45 2 021001 2009 6 9 R Lehmann An algorithm for the determination of all significant pathways in chemical reaction systems Journal of Atmospheric Chemistry 47 1 45 78 2004 A Luque Computer code QPlaskin http www trappa es content software 6 9 A Makhorin GNU Linear Programming Kit 4 9 http www gnu org software glpk S Pancheshnyi B Eismann G J M Hagelaar and L C Pitchford Computer code ZDPlasKin University of Toulouse LAPLACE CNRS UPS INP Toulouse France 2008 zdplaskin laplace univ tlse fr 6 9 R Schuster and S Schuster Refined algorithm and computer program for calculating all non negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed Computer applications in the biosciences CABIOS 9 1 79 85 1993 S Schuster C Hilgetag J H Woods and D A Fell Reaction routes in biochemical reaction systems Algebraic properties validated calculation
3. j Mok G 1 NR A 16 Equation ensures that the constructed pathway P fully recycles Sp that is it has no net production or consumption of Sp The rate f of the new pathway P is calculated using the branching probabilities discussed in 5 and reads tx fi In T D A 17 A 2 DESCRIPTION OF THE ALGORITHM 19 e If Ac 0 we store the contribution of P to Ac by introducing a new pathway P that is identical to Pk but has a rate I Ds if Ac gt 0 fn fk l amp l Dr if Ac lt 0 A 18 e We remove all the pathways that have been connected with all partners Pathways that neither produce nor consume Sp are not affected A 2 4 Deletion of Insignificant Pathways Even when the total number of reactions is relatively low PumpKin may generate an excessive number of pathways To avoid this combinatorial explosion we delete a newly formed pathway P if its rate fn is less than the user specified threshold fmin To keep track of the contribution from the deleted pathways we update equations A 7 A 9 in the following way Tj FP HZ gmc fn j 1l nr A 19 Di Di Min fn Min gt 0 i 1 ns A 20 di di Min fa Min lt 0 i l ng A 21 where is the multiplicity of reaction R in Pa and Min is the number of molecules of S produced by Pa More details are discussed in 5 A 2 5 Sub Pathways In section A 2 4 we discussed the procedure to limit the growth of total number of pat
4. parameters discussed in the section 3 1 will also affect the runtime For typical use cases we estimate runtime in the order of minutes Chapter 3 Input and Output 3 1 Input To determine the chemical pathways PumpKin requires from the user the stoichiometric matrix and kinetic data for the full chemical reaction system namely e chemical reactions Rj j 1 nR involving between species S i 1 ng where nr and ng are the number of chemical reactions and species respectively e stoichiometric coefficients s which represent the number of molecules of species S produced or negative number of molecules of S consumed by reaction Rj e a time evolution of concentrations c t and reactions rate r t where l 1 n7 and to t lt S tne tend The code is independent of the units chosen by the user Conventionally c t is specified in units of mol em and r in units of mol cm s71 PumpKin expects that user stores data in the following files qt_species_list txt Contains the names of species included in the model qt_reactions_list txt Contains human readable reaction signatures qt_conditions txt Contains the time steps t see A 1 resulting from the simulation qt_matrix txt Contains the stoichiometric matrix of the chemical model qt_densities txt Contains the time dependent densities of each species at times t qt_rates txt Contains the time dependent rates of each reaction at times t
5. a linear optimization problem 5 which we solve by the simplex method employing the GPLK package 7 Then we search for the sub pathways Pj k 1 npr in the list of pathways constructed so far by the main part of the algorithm If Pj is contained in that list then we add fj to its rate otherwise we add Py as a new entry with rate fy GNU General Public License Version 2 June 1991 Copyright 1989 1991 Free Software Foundation Inc http fsf org Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed Preamble The licenses for most software are designed to take away your freedom to share and change it By contrast the GNU General Public License is intended to guarantee your freedom to share and change free software to make sure the software is free for all its users This General Public License applies to most of the Free Software Foundation s software and to any other program whose authors commit to using it Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead You can apply it to your programs too When we speak of free software we are referring to freedom not price Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software and charge for this service if you wish that you receive source code or can get it if you want it that you can change
6. ensure that we don t violate the balance between the production consumption and concentration change of a species A 4 and the following holds at any point Ac pi d At A 10 The mean rate 6 of the concentration change of species S is defined as Ac At Besides we also need the auxiliary variable D defined as Sn gt D max p d Pi di di if Aci u 0 A 11 d pot 6 if Ac lt 0 A reaction sequence Py is called sub pathway of a pathway P if all intermediate species cor responding to the branching points are at steady state and the set of all reactions from Py is a subset of the set of reactions of P i e R P C R P A 12 where R P j 1 nr lxy 0 A pathway is called elementary if it does not contain sub pathways condition C3 from 10 A 2 Description of the Algorithm Algorithm 1 summarizes in pseudo code the steps in the PumpKin code A 2 1 Initialization The algorithm starts with a list of pathways each containing only one reaction 1 ifj k A TA k l A l Tjk 0 else J gt NR 3 To each pathway we assign the rate of the corresponding reaction i e fk rp k 1 nr The book keeping variables 7 p and d are set equal to zero 18 APPENDIX A PUMPKIN ALGORITHM Algorithm 1 PumpKin algorithm 1 begin 2 read input files Section 3 initialize pathways individual pathways Section 4 chose branching point Sp Sectio
7. is interactive but does not normally print such an announcement your work based on the Program is not required to print an announcement These requirements apply to the modified work as a whole If identifiable sections of that work are not derived from the Program and can be reasonably considered independent and separate works in themselves then this License and its terms do not apply to those sections when you distribute them as separate works But when you distribute the same sections as part of a whole which is a work based on the Program the distribution of the whole must be on the terms of this License whose permissions for other licensees extend to the entire whole and thus to each and every part regardless of who wrote it Thus it is not the intent of this section to claim rights or contest your rights to work written entirely by you rather the intent is to exercise the right to control the distribution of derivative or collective works based on the Program In addition mere aggregation of another work not based on the Program with the Program or with a work based on the Program on a volume of a storage or distribution medium does not bring the other work under the scope of this License 3 You may copy and distribute the Program or a work based on it under Section 2 in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following A 2 DESCRIPTION OF THE ALGORITH
8. neutral interactions are calculated using the BOL SIG solver built in into the ZDPlasKin As initial value of the electron density we use n 0 20 100 The list of species and reactions was automatically converted into a system of ordinary differ ential equations and solved numerically using the ZDPlasKin tool The user can visualize the results of ZDPlasKin using the open source software QtPlaskin 6 y 4 1 4 2 Global Kin Examples Available soon CHAPTER 4 EXAMPLES Table 4 1 Species considered in the model Ground neutrals N Na O Oz Oz NO NO2 NO3 N20 N205 Positive ions 4 NOt N20 NOF OF No Excited neutrals Na AFEF BL C I a dy N 2D P O D tS Oz a Ag b Lf 4 5 eV O2 X v 1 4 No X v 1 8 Negative ions e O7 03 03 Oz NO NO3 NO3 N3O Acknowledgements The authors acknowledge the support from STW project 10751 part of the Netherlands s Or ganization for Scientific Research NWO The authors also acknowledge the support from the European Science Foundation ESF for short visit grants 5297 5697 and 5698 within the ESF Research Network Program RNP entitled Thunderstorm effects on the atmosphere ionosphere system TEA IS 11 12 CHAPTER 4 EXAMPLES Bibliography 9 10 M Capitelli Ferreira C M Gordiets B F and Osipov A I Plasma Kinetics in Atmospheric Gases Springer Verlag Berlin Germany
9. notice and disclaimer of warranty keep intact all the notices that refer to this License and to the absence of any warranty and give any other recipients of the Program a copy of this License along with the Program You may charge a fee for the physical act of transferring a copy and you may at your option offer warranty protection in exchange for a fee 2 You may modify your copy or copies of the Program or any portion of it thus forming a work based on the Program and copy and distribute such modifications or work under the terms of Section 1 above provided that you also meet all of these conditions a You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change b You must cause any work that you distribute or publish that in whole or in part contains or is derived from the Program or any part thereof to be licensed as a whole at no charge to all third parties under the terms of this License c If the modified program normally reads commands interactively when run you must cause it when started running for such interactive use in the most ordinary way to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty or else saying that you provide a warranty and that users may redistribute the program under these conditions and telling the user how to view a copy of this License Exception if the Program itself
10. procedure and example from nucleotide metabolism Journal of Mathematical Biology 45 2 153 181 2002 13 14 BIBLIOGRAPHY Appendix A PumpKin Algorithm In this section we briefly describe the algorithm proposed by Lehmann 5 and used in the package PumpKin For a more detailed description and discussion about the algorithm we refer to 5 A l Basic Definitions We assume the chemical reactions Rj j 1 nR involving species S i 1 ng Beside of R it is assumed that the stoichiometric coefficients s which represent the number of molecules of species S produced or negative number of molecules of S consumed by reaction Rj are given For simplicity PumpKin assumes only unidirectional reactions and in case of reversible reactions it is the responsibility of the user to split them into forward and backward steps incorporating external sources and sinks as pseudo reactions We assume that the user has already integrated the chemical model following the temporal evolution of species S during the time interval 0 7 which was divided in general non uniformly into nr parts That is for every species S and reaction R we know the concentrations c t and the reaction rates r 4 where l 1 nr For a given time interval to tena E 0 7 we can calculate Aci elena ci to i 1 NS A 1 1 tend ex f di Y dm 4 2 1 tend naar ff ri t dt j 1 NR A 3 where At tena t
11. the software or use pieces of it in new free programs and that you know you can do these things To protect your rights we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights These restrictions translate to certain responsibilities for you if you distribute copies of the software or if you modify it For example if you distribute copies of such a program whether gratis or for a fee you must give the recipients all the rights that you have You must make sure that they too receive or can get the source code And you must show them these terms so they know their rights We protect your rights with two steps 1 copyright the software and 2 offer you this license which gives you legal permission to copy distribute and or modify the software Also for each author s protection and ours we want to make certain that everyone understands that there is no warranty for this free software If the software is modified by someone else and passed on we want its recipients to know that what they have is not the original so that any problems introduced by others will not reflect on the original authors reputations Finally any free program is threatened constantly by software patents We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses in effect making the program proprietary To prevent this we have made it clear that any patent mus
12. type cd pumpkin X Y src make Advanced users may want to modify the Makefile to change compiler or the location of GLPK 2 1 3 Execution Instructions The user can run PumpKin by typing the following command pumpkin input folder where input folder is the location of the input folder If the user doesn t specify the location of input folder PumpKin by default will look it in the current folder i e pumpkin X Y src Input 2 1 4 Running Built in Examples The most current version of PumpKin versions 1 1 and higher is coming with a native support of ZDPlasKin and Global_Kin modeling platforms PumpKin is distributed with the following example folders which are discussed in section Examples are located in the following folders pumpkin X Y src Examples ZDPlasKin Input_10 pumpkin X Y src Examples ZDPlasKin Input_20 The user can run PumpKin with the examples by pumpkin Examples ZDPlasKin Input_10 pumpkin Examples ZDPlasKin Input_20 or by pumpkin Examples Global_Kin 2 1 5 Typical Running Time The typical running time of the examples from the section is around 30 seconds on the MacBook Pro 15 inch Mid 2010 with a CPU Intel Core i5 at 2 4 GHz 4 GB 1067 MHz DDR3 of RAM memory and the operating system Mac OS X 10 9 Generally speaking PumpKin runtime depends on problem size as loading large input files into the computer memory might be time consuming On the other hand the user s choice of the input
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15. User s Manual Software Version 1 5 Date Dec 18 2015 Pumpkin Tool Aram H Markosyan Copyright 2013 2015 Aram H Markosyan All rights reserved PumpKin A tool to find principal pathways in plasma chemical models Copyright c 2013 2015 Aram H Markosyan This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program if not write to the Free Software Foundation Inc 51 Franklin Street Fifth Floor Boston MA 02110 1301 USA Permission to use PumpKin under the license GNU GPL version 2 is hereby granted provided that proper reference is made in publications reporting results obtained using this software At present the preferred way to reference PumpKin is as follows A H Markosyan A Luque F J Gordillo Vzquez U Ebert PumpKin A tool to find principal pathways in plasma chemical models Computer Physics Communications 185 pp 2697 2702 2014 doi 10 1016 j cpc 2014 05 019 Point of Contact Dr Aram H Markos
16. ant In order to keep compatibility with VMS VAX systems the input files can be all in capitals except the input txt Currently PumpKin is fully compatible with the output formats of ZDPlasKin 8 4 6 and Global Kin 3 2 The PumpKin package is distributed examples of input files 3 2 Output Depending on whether the user has specified the interest parameter as a positive integer the index of the species of interest or as a non positive number the user does not have any species of interest one of the following results will be printed 3 2 OUTPUT 7 interest gt 0 PumpKin will output all the pathways and their rates producing or consuming the species of interest Sinterest as well as the relative production or consumption compared with the initial concentration of Sinterest The output will also contain information such as how much Sinterest has been produced or consumed by the pathways that are deleted by PumpKin using parameters f_min or max path interest lt 0 PumpKin will output all the pathways and their rates sorted by rate In some cases this number can be very large so we decided to limit it by 100 which of course can be easily changed inside the PumpKin source code The output will also contain information such as the amount of a certain species that has been produced or consumed by the pathways that are deleted by PumpKin according to the parameters f min or max_path After successful first run PumpKin will as
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18. erms and conditions either of that version or of any later version published by the Free Software Foundation If the Program does not specify a version number of this License you may choose any version ever published by the Free Software Foundation If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different write to the author to ask for permission For software which is copyrighted by the Free Software Foundation write to the Free Software Foundation we sometimes make exceptions for this Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally NO WARRANTY 11 12 BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE PRO GRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUD ING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER
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20. hways in our algorithm On the other hand when two pathways are connected it may happen that the resulting reaction sequence is unnecessarily complicated i e it contains other pathways as sub pathways As described in section A 2 4 we often eliminate insignificant pathways so it is not enough to check whether other pathways constructed so far are sub pathways of P Instead for a given pathway P we determine all elementary sub pathways Pj k 1 np using the algorithm by Schuster and Schuster 9 5 This method has a limitation namely it requires that all intermediate species i e branching points are at steady state NR y Zin Sij Ofor all for which S has been a branching point A 22 j 1 The condition A 22 can be enforced by adding pseudo reactions to the pathway P with mul tiplicity m n for all previous branching points S Si gt if Mim gt 0 A 23 20 APPENDIX A PUMPKIN ALGORITHM Sit if Min lt 0 A 24 Once we have the sub pathways Py k 1 np of a pathway Pa then we represent P as a linear combination with non negative wights wx of these sub pathways i e np n wer j 1 NR A 25 k 1 where x and Tik are the multiplicities of reaction Rj in pathway P and subpathway P re spectively Such representation is justified in 10 The rate fn of Pa will be distributed to the sub pathways according to fi wk fn k 1 np A 26 The equation leads to
21. k user to enter a new species of interest In this case PumpKin will not perform any actual pathway analysis and save a lot of time but only will print for a given input file with a new species of interest the production consumption of the new species of interest User can type O to see the dominant pathways or a negative number to terminate execution CHAPTER 3 INPUT AND OUTPUT Chapter 4 Examples The most current version of PumpKin versions 1 1 and higher is coming with a native support of ZDPlasKin and Global_Kin modeling platforms 4 1 ZDPlasKin Examples PumpKin is distributed with two sets of input files from ZDPlasKin pumpkin X Y src Examples ZDPlasKin Input_10 pumpkin X Y src Examples ZDPlasKin Input_20 Both examples are the outputs of the zero dimensional plasma kinetic solver ZDPlasKin We use a zero dimensional model to describe the dynamics of species under a constant electric field The following system of ordinary differential equations ODEs is used to describe the interaction between the species d n dt where the source term S is the total production and destruction rate of species 7 in various processes The adapted version of the kinetic file for N2 O2 mixtures dry air from ZDPlasKin 8 4 is used which consists of 650 reactions and 53 species from the table A complete list of plasma chemical precesses in N2 O2 mixtures is taken mainly from 1 Trans port parameters and constant rates for electron
22. mir fr where e xj is the multiplicity of reaction R in the pathway P zero if Rj does not occur in Py j 1 nr k 1 np e mix is the positive negative number of molecules of S produced consumed by the pathway Pr i 1 ns k 1 np e fi is the rate of pathway Pp k 1 np Then by the definition of x and the stoichiometric coefficients s we have nr Mik gt Sij Tjk A 5 j 1 If we multiply both sides of A 5 by fk we get Mik fk gt ar law Je A 6 j l which illustrates that z 4 fk is the portion of the rate r of reaction R associated with the pathway Pr We take into account the effects of deleted pathways with small rates in next section For this we introduce the additional variables 7 which represent the part of the rate of reaction Rj associated with the deleted pathways and p and d representing the rate of the production and destruction of species S by deleted pathways In this case the rate of each reaction will be totally distributed to pathways including the effect of the deleted ones np k 1 A 2 DESCRIPTION OF THE ALGORITHM 17 On the other hand the total rate of production p and destruction d of a species S by all pathways including the effect of deleted pathways are Pi Pi gt Mik fk A 8 k mi gt 0 di di gt Mak fk A 9 k mir lt 0 Although p di p and d are changed at different steps inside the algorithm we always
23. n 5 repeat 6 merge pathways producing S with pathways consuming Sp Section 7 delete pathways with a rate less than fmin Section 8 determine and split sub pathways Section 9 until the new branching point S is found 10 ouput Section A 2 5 11 end A 2 2 Branching Points Depending on the time scale of interest and the lifetime of species of interest the user might need to exclude certain species from the list of branching points For this user can define lifetime threshold Tmin In this case the species with lifetime greater than Tmin are considered as long lived species and not used as branching points Then for every species S with a lifetime shorter than Tmin and that has not been a branching point yet we calculate its lifetime 7 with respect to the pathways constructed so far 5 m FR A 14 with c from and d from A 9 As the next branching point we choose the species with the shortest lifetime 7 A 2 3 Merging Pathways Let us assume that we are given branching point species S and that so far we have constructed pathways Pk k 1 np Then we perform the following steps e Every pathway Py producing the species Sp is connected with each pathway PF consuming Sp Let us denote the resulting pathway by Pa The number of molecules Min of S and the corresponding multiplicities zjn of the reactions R in the pathway P can be calculated as Min Me Mal Mi Mok i 1 NnS A 15 Lin Tjk Mp
24. o Ac and c are respectively the change of the concentration and the mean concentration of species S in the time window to teng rj is the mean rate of the reaction Rj in the time interval to tena In the rest of this paper we will use rate for rj omitting the attribute mean In this work we assume that c has units of molecules cm and that r has units of molecules em s 1 15 16 APPENDIX A PUMPKIN ALGORITHM Ideally we should have conservation of the concentration changes Ac NR AC gt Sij rj At for every i 1 ng A 4 j l but due to numerical inaccuracies in the kinetic solver and to the finite time steps the conservation A 4 will usually be violated within the user s input We take as the definition of Ac the formula A 4 instead of 4 1 One of the key questions that we want to answer is How 1 e by the interaction of which reactions are certain species produced or destroyed Obviously we can determine the reactions that produce or destroy the species directly But if such a reaction consumes or produces another specie whose chemical lifetime is shorter than the time scale of interest then it is necessary to follow the chemical fate of that species This leads to the idea of forming pathways i e reaction sequences that produce or destroy a chemical species of interest Let us denote by Pk where k 1 np the set of pathways The given pathway Py is described by the set 25
25. omponent itself accompanies the executable If distribution of executable or object code is made by offering access to copy from a designated place then offering equivalent access to copy the source code from the same place counts as distribution of the source code even though third parties are not compelled to copy the source along with the object code 4 You may not copy modify sublicense or distribute the Program except as expressly provided under this License Any attempt otherwise to copy modify sublicense or distribute the Program is void and will automatically terminate your rights under this License However parties who have received copies or rights from you under this License will not have their licenses terminated so long as such parties remain in full compliance 5 You are not required to accept this License since you have not signed it However nothing else grants you permission to modify or distribute the Program or its derivative works These actions are prohibited by law if you do not accept this License Therefore by modifying or distributing the Program or any work based on the Program you indicate your acceptance of this License to do so and all its terms and conditions for copying distributing or modifying the Program or works based on it 6 Each time you redistribute the Program or any work based on the Program the recipient automatically receives a license from the original licensor to copy distribute or mo
26. red We have tested PumpKin with the following compilers GCC and LLVM We recommend Windows users to use Cygwin www cygwin com which implements a GNU toolchain in the Windows architecture In general here are the general requirements e To build PumpKin the GNU version of make GNUmake must be installed The PumpKin makefile requires GNU make version 3 77 or later GNU software can be downloaded from many places including www gnu org software make 1 2 CHAPTER 1 INTRODUCTION e A C compiler is required PumpKin makes heavy use of the ISO IEC 14882 C Stan dard Some compilers are not fully compliant with this specification although most are PumpKin has been compiled and tested with GNU g 3 32 or higher LLVM 3 2 or higher e GLPK GNU linear programming kit must be installed 7 This allows PumpKin to solve large scale linear programming LP problems GLPK can be downloaded from org software glpk We have tested PumpKin with GLPK version higher than 4 32 The recommended system requirements depend on the choice of the input parameters and the problem size As a reference in a MacBook Pro 15 inch Mid 2010 with a CPU Intel Core i5 at 2 4 GHz 4 GB 1067 MHz DDR3 of RAM memory and the operating system Mac OS X 10 9 PumpKin runs the examples from the section 4 in about 30 seconds When the input files are large PumpKin will require more time to load them into the computer memory Chapter 2 Installa
27. software package to find all principal pathways i e the dominant reaction sequences in chemical reaction systems The goal is to analyze the production and or destruction mechanisms of a certain species of interest as well as to reduce a complex plasma chemistry models PumpKin was developed by Aram H Markosyan at CWI Centrum Wiskunde amp Informatica Amsterdam under the STW project 10751 Transient plasmas for air purification and at IAA CSIC Instituto de Astrofsica de Andaluca CSIC Granada during short visits of A H Markosyan to Dr F J Gordillo V zquez and Dr A Luque under the ESF European Science Foundation grants 5697 5698 5297 within the TEA IS Thunderstorm effects on the atmosphere ionosphere system activities A Luque contributed to the checking and validation of the code PumpKin is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 PumpKin can be downloaded from the following address You should have received a copy of the GNU General Public License along with this program if not contact Aram H Markosyan at larmarkos umi ch edu or write to the Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111 1307 USA 1 1 System Requirements PumpKin is written in the C programming language It has been tested on Mac OS X Linux OS and Microsoft Windows A C compiler is requi
28. t be licensed for everyone s free use or not licensed at all The precise terms and conditions for copying distribution and modification follow 21 22 APPENDIX A PUMPKIN ALGORITHM TERMS AND CONDITIONS FOR COPYING DISTRIBUTION AND MODIFICATION 0 This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License The Program below refers to any such program or work and a work based on the Program means either the Program or any derivative work under copyright law that is to say a work containing the Program or a portion of it either verbatim or with modifications and or translated into another language Hereinafter translation is included without limitation in the term modification Each licensee is addressed as you Activities other than copying distribution and modification are not covered by this License they are outside its scope The act of running the Program is not restricted and the output from the Program is covered only if its contents constitute a work based on the Program independent of having been made by running the Program Whether that is true depends on what the Program does 1 You may copy and distribute verbatim copies of the Program s source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright
29. tion and Execution Instructions 2 1 Installation Before installing PumpKin the user should have installed the GLPK package For this we recom mend tools like MacPorts www macports org or Fink www finkproject org for Mac OS X and package management systems for GNU Linux distributions The windows user can get installation instructions at http winglpk sourceforge net 2 1 1 Unpackaing the Distribution File The PumpKin package is distributed in the form of a packed archive a tarball It is one file named pumpkin X Y tar gz where X is the major version number and Y is the minor version number for example the archive name might be pumpkin 1 1 tar gz In order to prepare the distribution for installation you should 1 Copy the PumpKin distribution file to a working directory 2 Unpack the distribution file with the following command gzip d pumpkin X Y tar gz After unpacking the distribution file is automatically renamed to pumpkin X Y tar 3 Unarchive the distribution file with the following command tar x lt pumpkin X Y tar It automatically creates the subdirectory pumpkin X Y containing the PumpKin distribution 4 Alternatively the user can combine items 2 and 3 using tar xzf pumpkin X Y tar gz 4 CHAPTER 2 INSTALLATION AND EXECUTION INSTRUCTIONS 2 1 2 Compiling the Package After unpacking and unarchiving the PumpKin distribution you can compile build the package For this normally you should just
30. yan Address University of Michigan Electrical Engineering and Computer Science Department 1301 Beal Ave Ann Arbor MI 48109 2122 Email Tel 734 647 4840 Homepage http markosyanaram com Contents 1 Introduction 1 1 System Requirements su due d E 406 AO a au de RE A 2 Installation and Execution Instructions 21 Installation ss isis DE MN Se Oe Ecsite ee Wace ee ne 2 1 1 Unpackaing the Distribution File 2 1 2 Compiling the Parkes 44 24 2 oda wade a ia Lea A 2 1 3 Execution Instructions A 2 1 4 Running Built in Examples 2 244 4 4 eae an du eo bi ee bd A 2 1 5 Typical Running Time 2 a 2000 ae near nen A 3 Input and Output zL MIA s s on ea REA ee ea ae BSR 3 2 OUEN HIS ri aOR OLE er arena PR aR Se 6 4 Examples 9 Ad ZDPlasKin Examples Se oe a r e a AA a seu 12 Global Kin Examples cu gl e eG a ni et a Acknowledgements A PumpKin Algorithm A 1 Basic Definitions A 2 Description of the Algorithm silos oe 464 RA RE has ALL Initializations 4 2 0 se 44 es dun ea a D pu rA A 2 2 Branching Points A 2 3 Merging Pathways A 2 4 Deletion of Insignificant Pathways A 2 5 Sub Pathways Ju DE Nr ee de CHR a Bok el er a GNU General Public License CONTENTS Chapter 1 Introduction PumpKin is a user friendly
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