URAC User`s Manual
Contents
1. 24 Plotted Sensitivities to Initial NO Mixing Ratio 24 Selected Computed Mixing Ratios from Default Mode Execution of Code Augmented by Ethene and Higher Olefin Emissions 27 Computed Mixing Ratio Sensitivities of Selected Compounds to Ethene Emissions Resulting From Code Execution Under the Conditions of Figure 4 4 28 LIST OF TABLES Table Page 1 1 Parameters Read by Subroutine cntrlprm 5 4 1 4 Parameter List 13 4 2 SAPRC 90 Parameter List 14 4 3 SAPRC 97 Parameter List 15 User s Guide to URAC Calculations 1 Introduction This report describes operation of the User s Reactivity Analysis Code URAC a tropospheric chemistry calculation facility which is based on a box model description of the pollutant containing air parcel shown schematically in Figure 1 1 The box s contents are presumed to be well mixed and subjected to solar insolation which varies with geographical location date and time of day Based on this conceptual framework the code simulates chemical reaction inflow outflow emissions deposition and ventilation calculating chemical species concentrations and associated sensitivity coefficients as functions2. Figure 4 1 Simplified Schematic of Interacting Reaction Chemistry Components Because of Figure 4 1 s simplified nature it provides only a loose representation of the chemical components contained in CB 4 SAPRC 90 and SAPRC 97 VOC in Figure 4 1 for example represents the totality of volatile organic compounds whereas the three parameterization schemes treat some of these compounds individually and lump others Into several different categories Tables 4 1 4 3 indicate the chemical species and species groups included in the three schemes Table 4 1 CB 4 Parameter List Index h2o o3 no no2 no3 n2o5 c2o3 xo2 pna cro hno3 hono pan h2o2 par eth ole tol xyl ISOp meoh CO form ald2 cres mgly open etoh ntr ho2 ror Chemical Species or Lumped ParameterName water ozone nitric oxide nitrogen dioxide nitrate radical dinitrogen pentoxide peroxy acyl radical lumped peroxy radicals oxidizing NO to NO2 higher peroxyacyl nitrates cresol oxidation intermediate nitric acid nitrous acid peroxy acetyl nitrate hydrogen peroxide parafins alkanes ethene olefins alkenes toluene xylene isoprene methanol carbon monoxide formaldehyde higher aldehydes cresol methyl glyoxal open ethanol organic nitrates hydroperoxy radical ethers 13 Default Initial Condition ppm 20000 0 0 0 045 0 005 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 025 0 025 0 0
3. inss ld pue y idui 591 0 02 ind l AR ADE Aq SWNIOA ul uonenu osuoo s lnduioo UIADE xeyap ny nduno ApE un Iduu 1 y u n p ds pulu s nduioo 1 n pulm 1 L oe si lupeluupAul uun Suohlpuo Azepunoq pue suolssiuu p ds pulA aly D S 151 no UH 1p days auu 10 uoll96 1 YM payelsosse abueyo u lolH o9 MAnisu s s ind lo2 SU S lulSU S 10 09 Un un un Josey L Sues AAnisu s WU S8 OW suonenu oSuoo o sonel Bux SUBAUOD o dud dwa XeWSU doo7 uonenduluo2 ulen JO URU Z aniy SIIE yu nb sqns ul asn 40 S lQELEA pos S 10 S ABSI ACS1 LUOOISS 1p 8 10 uonoe 1 Aq eGueYo onenu ouo s lnduoo pos H o Siu loly o lbei euui u1 s nduioo I JOO Siu l lH o 515 0100 s ind lo2 yudmeu udd song Bulxiw SUONes UBDUOD slu Auoo o dud Iseju Z oneuxuuouoo 09 1 09 41 ULE s ss oo1d fE lS Ud 10 Suollpe noje5 AHAR SU S S UBADV Ip zell p xell p o dsou su s o nu d
4. volatile organic compound VOC mix Quite obviously a profusion of other reactivity definitions can be and have been posed Even if one accepts the definition given above as a standard it is obvious that a wide range of associated numerical values can arise depending on which reaction parameterization is employed what VOC mix is chosen and what environmental conditions of solar insolation humidity temperature dilution and so forth are imposed GUI code version 2 Type the command startmodel This will initiate execution for the basic model system via the graphical user interface To install software see Appendix A The computational procedure described in this report takes a neutral approach to this issue by providing a versatile platform which enables the user to stipulate whichever reactivity definition he or she prefers In essence the code computes sensitivity coefficients L q 1 where c is the concentration of species i and o the parameter selected for the sensitivity test e g initial abundance of precursor j solar insolation a specific reaction rate coefficient deposition flux Given this the user may select conditions appropriate to MIR or an alternate reactivity definition of choice execute the code and obtain the desired result The following sections of this report instruct the potential user on procedures for applying the code to this end 2 Governing Equations
5. 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 025 0 00375 0 0016625 0 0 0 0015 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 025 0 0 0 0 0 0 1 79 0 0675568 Table 4 3 SAPRC 97 Parameter List Continued Index Chemical Species or Lumped Parameter Name Default Initial Condition ppm alk2 more reactive alkanes 0 0374675 aro1 monoalkyl benzenes 0 0214286 aro2 more reactive aromatics 0 0125 ole1 other terminal alkenes 0 0125 ole2 internal alkenes 0 0025955 ole3 terpenes 0 0035 hcooh formic acid 0 0 ccooh acetic acid 0 0 etoh ethanol 0 0 mtbe methyl tertiary butyl ether 0 0 mbut methyl butenol 0 0 Cxo2 mtbe reaction product 0 0 tbuo mtbe reaction product 0 0 prod mtbe reaction product 0 0 Inert mtbe reaction product 0 0 hc2h methyl butenol reaction product 0 0 rc2h methyl butenol reaction product 0 0 ispd lumped isoprene reaction products 0 0 isop isoprene 0 0 bhcho2 lumped isoprene and ispd reaction products 0 0 c303 lumped isoprene and ispd reaction products 0 0 hc204 lumped reaction product 0 0 These schemes compute a number of additional species notabiy several of the radicals shown in Figure 4 1 as steady states Within the FCM based representation these steady states are computed explicitly within subroutines chmslo and chmist These are not normally output as computed results however they can be channeled to output by appropriate modification of these subroutines Programs associated with the bat
6. 0 0 0 0 025 0 00375 0 0016625 0 0015 0 0 0 0 0 0 0 0 0 0 0 025 0 0125 0 0025955 0 0035 0 00075 0 0675568 0 0374675 0 0214286 0 0125 0 0 0 0 0 0 0 0 0 0 Table 4 3 SAPRC 97 Parameter List Index h2o o3 no no2 n2o5 n2o5 no3 ho2 ro2 rco3 hno3 hono hno4 pan ppn nphe gpan pbzn CO co2 h202 xooh hcho ccho rcho acet mek rno3 gly mgly phen cres bald afg1 afg2 ethe h2 XC xn ch4 alk1 Chemical Species or Lumped Parameter Name water ozone nitric oxide nitrogen dioxide dinitrogen pentoxide dinitrogen pentoxide nitrate radicals hydroperoxy radical total organic peroxy radicals total acyl peroxy radicals nitric acid nitrous acid peroxynitric acid peroxyacetyi nitrate higher peroxyacyl nitrates nitrophenols PAN analog formed from glyoxal PAN analogs formed from aromatc aldehydes carbon monoxide carbon dioxide hydrogen peroxide total hydroperoxide groups formaldehyde acetaldehyde higher aldehydes acetone ketones and higher oxygenated products organic nitrates glyoxal methyl glyoxal and other alpha dicarbonyls phenols cresols and other aromatic oxygenates benzaldehyde uncharacterized fragmentation products uncharacterized fragmentation products ethene hydrogen lost carbon lost nitrogen methane less reactive alkanes 15 Default Initial Condition ppm 20000 0 0 0 045 0 005 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7. and altered via mouse and keyboard Entries are made by clicking in the chosen text input block deleting and adding text and ending with a lt return gt Once the user is satisfied with all entries clicking on Continue will initiate the next step by opening a new window Figure 5 4 which allows entry of initial mixing ratios for all chemical species With this window in the same manner as in the previous window the 20 s a R A bd apa 121 em hve s a a a d n pong val x LS E L rr s Pa R TE 2 R 7 T K 3 F ae d beth Sine L Rz m Sa Parameter initialization default pau or delete defaults and enter initial values Defaults L 2 L a ae E e Enter initial species concentrati r r Figure 5 4 Initial Chemical Species Mixing Ratios user can edit each text block or use the default values for the chemical species and again click on Continue to proceed to the next step A plotting routine provides visual representation of the model output results Figure 5 5 shows the form in which the user via several clickable buttons may select chemical species to be plotted over the time period of the model run In the interest of keeping plots legible no more than 5 species may be chosen p
8. atmospheric chemistry but it should useful as an instructional tool to a variety of other interested persons as well 2 Persons involved with policy analysis and air quality management decision processes While the limitations of this simple box model approach are obvious it is nevertheless valuable as a scoping tool for evaluating alternative control scenarios prior to selection implementation and or more detailed modeling analysis One particular application of this code is its use as a tool for calculating reactivities of air pollution constituents and at the outset it is important to note that a diversity of definitions of the term reactivity is applied throughout the published literature As an example Carter 1995 defines maximum incremental reactivity MIR of species j as Os Ox where O3 is the calculated ozone concentration at the time of its diurnal maximum and XI Is the amount of a specific precursor j admitted to the system through its initial and boundary conditions This definition is further constrained by selecting the concurrently existing NO nu one can execute tHe code immediately as follows abundance to maximize the peak ozone reactivity when calculated characterizing xj as the concentration of the concurrently existing Jump Start For systems with this software 1 Open a Unix terminal X Window and change to the directory containing the
9. derivative d dj d alpha is unity C thus the time derivative of the sensitivity coefficient is 1 0 deltaz C accordingly C sens J sens 29 5 dt d function l1 d alpha j C include senscommon com include chdata cmd include chparm cmd include jmhdata cmd real advinCnsmax advoutCnsmax emissCnsmax depCnsmax entrCnsmax cCnsmax sensCnsmax C C user supplied sensitivity derivative input C sensCketh sensCketh 0 5 dt deltaz return end Ozone X 1 NO o EE NO2_ o WA 1110 o HNO3 2 PAN Ethene of AL Zoot X of VA 1 MAL EAN 6 8 10 12 14 16 18 Time of Day Figure 6 1 Selected Computed Mixing Ratios from Default Mode Execution of Code Augmented by Ethene and Higher Olefin Emissions Using CB 4 Parameterization Zi Figure 6 2 shows a plot of the computed sensitivities for this case using the same initial concentrations and ethene emissions that were applied for Figure 6 1 Also for this calculation the original file sensinit f was modified to remove sensitivity calculations for NO Initial conditions Here the ethene mixing ratios exhibit a monotonic sensitivity to ethene emissions as should be expected Ozone shows an early strong and positive sensitivity to ethene emissions which later decays to negative values reflecting exhaustion of the NO reactant and the influence of the direct ozone olefin r
10. interface the chemical schemes with the three dimensional SAI Urban Airshed Model UAM 4 Partly as a consequence of this fact the present code has made liberal use of a few UAM 4 subroutines notably those involving nighttime chemistry and solar insolation In addition this software applies a modified version of the Gear ordinary differential equation solver published by Hindmarsh 1983 as well some Linpack matrix processing routines included with the Gear code distribution The origins of these incorporated codes are indicated by comment statements in the associated subroutines 1 Several variants of the basic CB 4 scheme are in current use The version employed here is that supplied with the FCM preprocessor software 7 Numerous small modifications to the published FCM code were necessary to enable operation on the Sun and Macintosh operating systems 11 For users with limited experience with tropospheric chemistry it is useful at the outset to consider a simplified schematic chemical representation indicating the interactions between nitrogen species organic species and various oxidants such as that shown in Figure 4 1 Consulting this figure when viewing graphical output from the code is often useful in facilitating insights with regard to the interacting chemical processes i PAN PPN u b 2 HNO RO HO o z HO2NO gt z RHO H O HNO fho 3 RO a yoo Oz U CO lt gt cO
11. p SSIWO INOAPe UIADe SUessAUd L Suasi AyAIsues 1Ip S 85 O g ucuu s ouu n ululenu Aq SUWINIOA ul ayes uopeuaovuoo s indulo 41U9 2 U uu S loul uonisod p Aq SWNIOA ul ayes Bueu2 uonenu uo Sayndwo0y dap zeyjap uonisodep InoApe jndjno AR APE Aq SWNIOA ul uollenu ouoo s lnduioo INOApe xeyap n d indinoyosape ug uu s ouu ssiuu jndul uolssiul Aq uun oA ul BBueYO uopeiuaouoo s nduoo ssituu 2 18514 UIApe ind l AHD ADE Aq SWNIOA ul ayes uoljenu ouoo Sayndwoy xeyap n indundeape u 1 OUI ye edu dud inss id pue uduu s ind lo2 dud dwa in ei duu y w n p ds pulu sayndwoy 1 n puim 1 G L oHe si lupeuupAu uin Suonlpuo Aepunoq pue suolssiuu p ds pulA 31y t e u nb s uonezileniul wo nulluoo If sensitivity calculations are desired the code performs a numerical integration of equation 4 by calling subroutine
12. 214286 0 0125 0 0005 0 0 1 0 0 025 0 0125 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Table 4 2 SAPRC 90 Parameter List Index h20 03 no no2 no3 n2o5 hno3 hono hno4 ho2 CO ho2h ro2 ooh c2co3 pan ppn hcho ccho rcho mek rno3 cres mgly afg2 so2 ethe ole1 ole2 ole3 ole4 alk1 alk2 aro1 aro2 sulf hcooh ccooh aux1 aux2 Chemical Species or Lumped Parameter Name vvater ozone nitric oxide nitrogen dioxide nitrate radicals dinitrogen pentoxide nitric acid nitrous acid peroxynitric acid hydroperoxy radical carbon monoxide hydrogen peroxide alkyperoxy radical total hydroperoxide groups acetyl peroxy radicals higher acylperoxy radicals peroxyacetyl nitrate higher peroxyacyl nitrates formaldehyde acetaldehyde higher aldehydes ketones and higher oxygenated products organic nitrates cresols phenols and other aromatic oxygenates methyl glyoxal and other alpha dicarbonyls uncharacterized fragmentation products sulfur dioxide ethene other terminal alkenes internal alkenes isoprene terpenes less reactive alkanes more reactive alkanes monoalkyl benzenes more reactive aromatics sulfate formic acid acetic acid auxiliary species 1 reacts only with OH auxiliary species 2 reacts with OH O3 O NOS and hv 14 Default Initial Condition ppm 20000 0 0 0 045 0 005 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
13. A 1 Appendix B Description of Source Code Files B 1 LIST OF ILLUSTRATIONS Figure Page 1 1 Schematic of Computational Domain 1 3 1 Flow Chart for Code Initialization 6 3 2 Flow Chart for Main Computation Loop 8 3 3 Flow Chart for Subroutine derivative 10 3 4 Flow Chart for Subroutine sensint 10 4 1 Simplified Schematic of Interacting Reaction Chemistry 4 2 4 3 5 1 5 2 5 3 5 4 5 5 5 6 5 7 5 8 6 1 6 2 Componen is aaa ay r c 12 Selected Output from Default Mode Execution of Code 18 Computed Mixing Ratio Sensitivities of Selected Compounds to Initial Mixing Ratio Sum of Non aromatic Hydrocarbons 19 Initial X Window for SAPRC90 Startup 19 Reaction Parameterization Listing 20 Control Parameter Initialization 21 Initial Chemical Species Concentrations 21 Species for Plotting 22 Sensitivity Species UU 23 Plotted Results for Species Mixing Ratios
14. ENVAIR 05 001 February 2005 User s Guide to URAC Calculations Kenneth M Busness KB Consulting Kennewick Washington Jeremy M Hales Envair Pasco Washington Prepared for Argonne National Laboratory under Contract No 2F 00871 by Envair 12507 Eagle Reach Pasco Washington 99301 DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government Neither the United States Government nor any agency thereof nor Argonne National Laboratory nor Envair nor any of their employees or subcontractors makes any warranty expressed or implied or assumes any legal liability for the accuracy completeness or usefulness of any information apparatus product or process disclosed or represents that Its use would not infringe privately owned rights Reference herein to any specific commercial product process or service by trade name trademark manufacturer or othervvise does not necessarily constitute or impiy its endorsement recommendation or favoring by the United States Government or any agency thereof or Argonne National Laboratory or Envair The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof ENVAIR for the UNITED STATES DEPARTMENT OF ENERGY under ANL Contract No 2F 00871 ENVAIR 05 001 February 2005 User s Guide to URAC Calculations Kenneth M Busness deremy M H
15. The governing equations associated with this code are in aloft c UC _ UC m m c d AZ 2 _ Wi d r 2 ot Ax Ax Az dt Az Az Az where t the independent variable time u the advection velocity m s c the concentration of component i in the volume element moles m the concentration of component i entering the volume element moles m5 GO the concentration of component i immediately above the volume element moles m q the emission flux of component i moles m hr w the wet deposition flux of component i moles m hr d the dry deposition flux of component i moles m hr the chemical production rate of component i moles m3 hr Ax Ay Az dimensions of the model box in the x y and z directions respectively m The corresponding sensitivity equations are aloft d AZ in oL C C D a men _ r fac ua o c c AZ do t 1 aq ow a0 N ar 96 AZ da da E where 5 the change in the dependent variable induced by a change in the parameter a i e the sensitivity of c to a a the parameter being subjected to the sensitivity test The partial derivatives on the right hand side of 3 impiy that t is constrained but do not r impose constraints on c or other parameters in the equations In particular a J is calculated in the code in terms o
16. Windows platform because It provided a means of migrating the associated codes to a Unix environment FCM s unified approach is an attractive concept t suffers however from three significant drawbacks First considerable effort is required to adapt a reaction parameterization to the FCM framework and as a result only a few reaction parameterizations exist under this format Second documentation in the FCM user s manual is rather obscure and the code has some machine dependencies making operation of this software a somewhat challenging proposition Finally FCM is designed to serve as a set up facility for operations with the three dimensional model UAM 4 and so doing it produces a number of artifacts that are extraneous for other applications As noted previously several of these artifacts have migrated to the code presented in this report As a consequence we suggest that a more direct approach not involving FCM be applied in adapting future parameterizations to this computational framework As noted in Section 3 subroutine derivative serves as the main portal between the chemical mechanism and the remaining code and all attempts to expand this software to include additional chemistry parameterizations must begin by making appropriate modifications to this subroutine and Its subsidiary subroutines as well as providing suitable replacements for the subroutines newphk and newrk The flow charts given in Section 3 are intended to aid in e
17. ales Prepared for Argonne National Laboratory and the U S Department of Energy under Contract No 2F 00871 Envair Pasco VVashington 99301 KB Consulting Kennevvick VVashington Blank Page Abstract The User s Reactivity Analysis Code URAC is computation facility which allows a user with minimum effort or knowledge of atmospheric chemistry and computation techniques to simulate and display atmospheric chemistry interactions on desktop and laptop computers It is based on a simple box model approach and is designed primarily for two user communities 1 Persons wishing to increase their understanding of tropospheric chemistry in a straightforward and convenient manner without the burden of acquiring prior knowledge of the computational basis A primary target audience for this application consists of college level students of atmospheric chemistry but it should useful as an instructional tool to a variety of other interested persons as well 2 Persons involved with policy analysis and air quality management decision processes While the limitations of code s box model approach are obvious it is nevertheless valuable as a scoping tool for evaluating alternative control scenarios prior to selection implementation and or more detailed modeling analysis The current computational system accommodates three different reaction parameterizations Carbon Bond 4 SAPRC 90 and SAPRC 97 These parameterizations were prepared els
18. and oxygen are held constant Water vapor concentration is adjustable in the code s initialization process Click below for a listing of reactions in this parameterization Figure 5 1 Initial X Window for SAPRC90 Startup 19 If the user chooses to display the reaction parameterizations for the model mechanism clicking on the Listing button displays a browser window shown in Figure 5 2 containing those parameterizations SF H SO Reaction Parameterization MOZ HV 0 U U2 M lt 035 M tl NU2 NU 02 U 02 MNOS M 03 NO M Z 02 05 NOZ 02 M S H WOS 2 NOZ H NO 02 2 NOZ H z W205 M205 02 NOS M205 H20 2 HNOS H z AOS NU NO2 UZ H Hi NU z M s H 02 03 H D 02 O3 0102 02 0102 H20 2 H 01D2 M 0 H H HONO HONO Hv HO NO H MH z HNOJ H HNO3 H20 NO3 5 HV HO NOZ H CO HO2 H O03 H Z 02 FL WL f 5 77 Figure 5 2 Reaction Parameterization Listing Selecting the Continue button causes the next window to be displayed With this display Figure 5 3 the user is able to interactively set initial conditions for several control time and geographic variables e g latitude longitude year month day start end times Initial default values are displayed which can be used for testing the model and which can all be edited
19. ates for each species by summing over all relevant reactions These values are returned to the calling routine via the vector a4 and applied as input to the numerical integration process Subroutines rates chmslo and chmfst in the version of derivative supplied with this software were prepared by executing a modified version of the Flexible Chemical Mechanism FCM code and contain some artifacts associated with FCM Most importantly the published FCM package applies an ordinary differential equation solver that depends on the chemical species being segregated into two classes slow and fast As noted previously the code included with the present system uses a modified Gear solver where segregation into slow and fast species is not required The coding in subroutine derivative controls input and output to and from chmslo and chmfst in a manner that is compatible with the Gear based integrator Subroutine sensint which integrates that portion of the sensitivity equation that is associated with chemical transformation processes is shown schematically in Figure 3 5 From equations 3 and 4 this can be written as chem _ an fon D nl la Laal aln 5 Upon interrogation by its calling routine subroutine sensint activates a Jacobian matrix generator subroutine fdjac to compute the array of concentration derivatives in equation 5 Subsequent to this step it sets up the matrices for the implicit finite difference equa
20. ch mode code version are contained in the directory Batch_Codes dir within the subdirectories cb4 dir saprc90 dir saprc97 dir and com dir com dir contains the source code used by all three mechanisms while the remaining directorles contain mechanism specific code as vvell as common files Default mode batch execution for any one of the three mechanisms is accomplished by entering the directory for the chosen mechanism executing the sf macro by typing sf to create the executable code and then typing program The code execution resulting from this process writes computed results to the file AAoutput These default calculations correspond to a location of 47 5N 122 3VV beginning at 6 00 on July 3 1998 with the initial mixing ratios shown in Tables 4 1 4 3 Simulations for other times locations and initial mixing ratios can be performed by making appropriate changes to the files simcontrol init f and initsens f and then recompiling with the sf command 16 Figure 4 2 shows plots of mixing ratios and sensitivity coefficients obtained from the AAoutput file of selected pollutants corresponding to the default conditions and the CB 4 parameterization The mixing ratios indicate typical behavior of photochemical ozone production with simultaneous reduction of NO and ethene plus the buildup of reaction products such as nitric acid and PAN The lower plot shows the sensitivity of these same species to initial NO mixing ratio Ozone
21. ckly during early hours compared to the zero emission case shown in Figure 4 2 it maximizes at about 11 00 and then declines behavior that stems largely from the direct reaction between ethene and additional olefins and ozone cf Figure 4 1 Sensitivity calculations associated with physical processes are performed by appropriate modification of the file physsense f in conformance with the sensitivity equation 3 If for example one wishes to assess sensitivity of selected species including ethene to ethene emissions the resulting version of equation 3 is re 7 Seren xi _ 1 2 ethene emission a ot Az ethene emission rate and the corresponding version of physsense f for the half time step is 26 subroutine physsens Cadvin advout emiss dep entr c sens deltax deltaz dt C C called from main program C C this subroutine updates those sensitivity coefficients associated with C non reactlon parameters e g emission deposition advective terms C entrainment and ls intended for modification by the user as appropriate C the operative return variables ar the updated sensitivity coefficients C sens 1 corresponding to a chosen sensitivity parameter alpha C C as an example say our sensitivity parameter alpha ls a dry deposition C velocity of species j referring to the sensitivity equation given in the C user s manual the only term directly influenced by this parameter ls the C deposition rate of species jJ dj The
22. datory in configuring the installation PATHs The distributions typically install by default in usr local bin usr local include usr local lib and usr local man The Sun may prefer these files in usr bin usr include etc Even with specific paths included in compiler options the compiler may insist on finding libraries in other places It may be necessary to copy the installed files from usr local lib to usr lib for example if the configuration files in the A 3 distribution are executed as provided It should be possible to target the correct installation locations by editing the configuration or makefile provided to force files to be installed in usr See the documentation Readme or Install included with the distributions On both Macintosh and Sun systems it typically is necessary to edit file permissions to enable these installations A 4 Other Useful Image Capture Resources Several applications that facilitate capturing X Windows graphic images are available as part of the X Windows distribution xwd will generate a graphics file from a screen displayed image and save it as an xwd file xwud will recapture a previously saved xwd file and display it on the screen Another useful utility is xwd2ps which will generate color images of X Window dumps in PostScript from an xwd file This utility can be downloaded as a zipped tar file from ftp x org R5contrib xwd2ps tar Z and is free to use in the public domain In
23. downloaded from the Fink VVebsite for these purposes The makefiles given here with the GUI code designate fort77 as the Fortran compiler To compile and link the code one executes the script files by typing the command sf in each of the three directories cb4 dir saprc90 dir and saprc97 dir This creates the executables startCB4 start90 and start97 The easiest way to launch the code is to type the command startmodel in the next lower directory and indicated by the Jump Start box on page 2 Computations for conditions other than the base case can be performed by modifying the appropriate subroutines and re compiling in a manner similar to that for the batch codes A 3 Software Distributions Required for the Graphical User Interface X Windows must be installed on the user s computer in order to operate the graphical user interface version of this code This interface was generated using standard C code and Xforms 1 0 90 a GUI toolkit for X Window systems The Xforms Library is free software licensed under the GNU Lesser General Public License version 2 1 It must be installed on the user s system in order to compile and run the models with the supporting GUI A 2 The Xforms distribution compiling instructions for standard Unix systems plus any recent update information is available at http VVVVV nOngnu org xforms Xforms also relies on other libraries which may or may not already be installed on the us
24. eaction Upon studying the examples shown in Figures 4 2 4 3 6 1 and 6 2 the reader should be well prepared to expand his or her usage of the code to encompass all features In so doing we recommend that the user make an archive copy of the original codes for future reference to help avoid any forgotten subroutine changes in the working versions We also recommend executing all three code versions in default mode and archiving the results for possible use as downstream backchecks on code integrity Ozone NO NO2 T N HNO3 TN le PAN J deki Ethene X 1 Sensitivity to Ethene Emission Rate h m O O O O 6 8 10 12 14 16 18 Time of Day Figure 6 2 Computed Mixing Ratio Sensitivities of Selected Compounds to Ethene Emis sions Resulting From Code Execution Under the Conditions of Figure 4 4 Using CB 4 Parameterization 7 Future Extensions Given the evolution of new chemical parameterization schemes and the variety of additional schemes in current existence it is of some interest to question whether and how the procedure described here should be extended to include other reaction parameterizations As noted above the codes given in this report were developed using the FCM software which is centered on the idea of a unified approach to a variety of reaction parameterizatons FCM was particularly useful for implementing the SAPRAC 28 parameterizations which were developed originally on a DOS
25. enscommon com Sf simcontrol titrat f 1 Directory Batch_ Codes dir saprc97 dir BLCKDATA f filcon cmd specid f CHEMPARM init f Steady f SAPRC97 f initsens f print 1 airquality jmhdata cmd calib emd makefile sf chdata cmd mscal cmd simcontrol chparm cmd nitbal f titrat f cntrol cmd plotfile Senscommon com GUI codes for the MacIntosh and Sun are in the directory 1 Codes dir As noted in Appendix A these should operate on other Unix or Linux based systems but some configuration effort should be expected depending on specific system characteristics Subdirectories and codes within GUI Codes dir are listed as follows Directory GUI Codes dir com dir accumulate f advectinput f advectoutput f chread f cntrlorm f concmxratio f deposition f Directory GUL Codes dir cb4 BLCKDATA f CB4621 f CBIV_ Parameterization CHEMPARM airquality calib cmd chdata cmd chemplot c chemplot1 dat chemplot2 dat chemplots dat chemplot4 dat chemplot5 dat chparm cmd cntrol cmd derivative f emission f entrain f fdjac f main f newphk f newrk f dir initenviron main c Initparams dat initsens f jmhdata cmd main f makefile mscal cmd nitbal f paramsCB dat plotCB dat plotmaxmin dat plotparamCB c plotparamCB fd plotparamCB h plotparamCB_main c B 2 physsens f sensint f slsodec f solarz f temperature f timespan f wind f sensparamCB h sensparamCB_main c sensplot c sensplot1 dat sensplot2 dat sensplo
26. er plot Following these selections clicking on Continue advances to the next step Initial parameters were previously selected in the variables entered as initial conditions Figure 5 3 One of these control variables determines if sensitivity calculations are to be performed If the sensitivity control variable is set to 1 an additional plot is generated showing the effects of the sensitivity species on the species chosen for plotting In this instance when Continue is clicked following selection of the species to be plotted Figure 5 5 an additional window is displayed to enable user selection of sensitivity species see Figure 5 6 If the sensitivity control variable was set to this step is not executed Select 5 species for plotting 2 ROZ ANOS OOH CRES CEOS MGL Y LLC U 2 202 CCHO x zx x Zx x Vv x x lt lt Figure 5 5 Species for Plotting 22 Select sensitivity parameters H zH MER FL QOH LEO C2C U PFN x gt x x x x x x x 4 lt Figure 5 6 Sensitivity Species When all available selections have been completed all variables are passed to the Fortran reacti
27. er s system libXpm version 4 7 or newer X PixMap a format for storing and retrieving X pixmaps to from files libjpeg version 6 0b or newer A C code library to read and write JPEG compressed image files All new XPM releases with installation instructions can be obtained via ftp on ftp x org contrib libraries Boston USA koala inria fr 138 96 24 30 pub xpm Sophia Antipolis France This is copyrighted software for which free use is granted by Groupe Bull The jpeg libraries and installation instructions can be found at ftp uu net graphics jpeg This is free to use software generated by the IJG Independent JPEG Group In Macintosh systems these distributions can be installed in a straightforward manner by following the included instructions For Xforms and the jpeg library the binary library include and manual files install in usr local bin usr local lib usr local include and usr local man directories respectively The Xpm libraries install in usr X11R6 lib along with all the standard X libraries The Xpm include file xpm h installs in usr X11 R6 include X11 Installation on Sun Solaris is similar but may be a bit more difficult Several filenames may be corrupted by unexpected changes from upper to lower case or lower to upper case Compiler designation is likely to differ from the typical cc e g c89 but this may be changed appropriately in the configuration or makefile Caution is man
28. ewhere and were processed for use in URAC using software provided by the Flexible Chemical Mechanism system developed by Kumar and his coworkers In addition to computing time series of pollutant concentrations the code performs sensitivity calculations which can be used for interpreting reaction behavior and component dependencies as well as for computing reactivity scales of arbitrary definition Codes presented in this report are intended for Unix systems and were prepared using Macintosh and Sun platforms They can be operated in a simple batch mode or through the use of an X Windows based graphical user interface CONTENTS Section Page 1 TMIOECI UD u a mi a inad 1 2 Governing Equations c e e e 3 3 Code Description 4 N OVON CN rennene RENEE EEEE EE EE EE E 4 3 2 Code Initialization 4 3 3 Main Computation Loop 7 4 Basic Code Operation and Interpretation Bal 100 b yaram r 11 5 Basic Code Operation and Interpretation ere ms 17 6 Advanced Operations 25 7 Future Extensions 28 HET b 30 Appendix A Software Installation nstructions
29. ewphk to determine for the current time and location rate coefficients for all photolysis reactions newphrk in turn calls subroutine solarz to determine the solar angle at the current time and location This is used in turn in conjunction with the photolysis look up tables to determine photolysis rate coefficients coef i for each photolytic Species i Subsequent to setting rate coefficients for all photolysis reactions the program proceeds to interrogate subroutine newrk to determine rate coefficients rk i for the system s thermal reactions The code then performs initial steady state calculations as dictated by the specific reaction parameterization in use and proceeds to print the system s initial conditions to the file AAoutput Subroutine print used for this purpose is user supplied and should be modified for use with different chemical mechanisms as appropriate for the constituents contained in these parameterizations The above operations complete initialization required for chemical reaction calculations These are followed immediately by initial operations for non reaction processes within the model volume deltax deltay deltaz including emission and advection The first step in these operations is to convert all chemical mixing ratios to their concentration equivalents in units of gram moles per cubic meter using subroutine concmxratio followed by interrogation of subroutines advectinput and emission to determine associated contr
30. exhibits a negative sensitivity to initial NO in the first few hours ovving to nitric oxide titration of ozone and ozone producing radicals As expected the sensitivity of NO to its own initial condition is initially unity Sensitivity coefficients can be computed for the initial conditions of multiple species For example if one vvishes to compute sensitivitles to the total non aromatic hydrocarbon mix par eth ole isop in the CB 4 parameterization one could simply set the corresponding initial sensitivity coefficients to unity in file sensinit f Figure 4 5 shows selected output resulting from this action As can be noted from this figure ozone sensitivities show a rapid initial rise with a subsequent falloff resulting from competing effects of hydrocarbon reaction products 5 Basic Code Operation and Interpretation GUI Mode Graphical user interface GUI operation is the simplest way to execute the code One simply moves to the directory containing the code for a specific reaction parameterization and if compilation to create an executable code is required types the command sf Once the executable codes for all parameterizations exist moving to the next highest directory and typing startmodel presents the user with a choice of parameterizations and a consecutive series of windows that allow selection of simulation location date and time as well as initial mixing ratios and sensitivity parameters The GUI also allows execution u
31. f ODE Solvers in Scientific Computing R S Stepleman et al eds North Holland Amsterdam 1983 vol 1 of IMACS Transactions on Scientific Computation pp 55 64 30 Appendix A Software Installation Procedures The codes described in this manual have been installed and tested on the Macintosh OSX version 10 3 and the Sun operating OS Release 5 8 They should be operable on other Unix and Linux platforms as well although system specific features of X Window applications may necessitate some adjustment when using the GUI based codes on these computers Appendix B gives source code listings for the MacIntosh and Sun platforms which are presented individually for batch and GUI based applications In each case the codes are segregated into four directories One for each reaction paramaterization cb4 dir saprc90 dir and saprc97 dir and one com dir that contains code common to all parameterizations This arrangement permits convenient compilation and linking of the codes using shell scripts To compile and link code associated with a particular parameterization one simply moves to the directory for that parameterization and executes the script file by typing sf which in turn executes a makefile controlling the compilation and linking process resulting in the desired executable code The procedure described to this point results in executable code corresponding to the base case conditions described in the previous sections of
32. f its constrained counterparts on ys 28 oo J do taza Co 2 k ac 5040 4 3 Code Description 3 1 Overview Appendix B provides the Fortran and C source codes for the calculation system The code s algorithms approximate solutions to equations 2 and 3 using the method of fractional steps which separates the reaction related terms from their non reaction counterparts over short time intervals of length dt hours integrates these terms individually and then recombines the results to compute dependent variable values at the intervals ends The time variable t hours is incremented at each step and the process continues until it exceeds the pre set variable tstop hours whereupon a normal exit occurs Instructions for executing this code in both GUI and batch modes are given in Section 4 3 2 Code Initialization Figure 3 1 is a schematic for initializing batch mode operation of the basic code GUI based operation is similar except for provisions for interactive input and online plotting As indicated by this schematic primary control of the code s execution occurs in the main 4 program main through sequential interrogation of a number of subroutines The first of these cntrlprm reads data from the user supplied simcontrol file to establish several basic geographic and control variables including position start and stop dates and times print controls the bypass toggles istatic a
33. ibutions to the rates of change in pollutant concentration within the model volume This information is stored in units of gram moles per cubic meter hour in arrays emiss i and advin i for emission and advection respectively This concludes program initialization 3 3 Main Computation Loop Figure 3 2 shows the sequence of the code s main computation loop Upon completing initialization operations the code updates the wind temperature emissions and inflow boundary conditions as required followed by updates for concentration change rates associated with advective output wet and or dry deposition and entrainment of air from aloft These steps are followed immediately by integration of the physical process contributions to the concentration variables for one half time step If sensitivity calculations are desired the code then interrogates subroutine physsens to provide a similar integration for the chosen sensitivity parameters Subsequently the concentrations are converted back into mixing ratios and photolysis and thermal reaction rate coefficients are updated in preparation for chemical reaction computations which are coordinated through the numerical integration scheme slsodec slsodec is a standard Gear integration package modified to store historical concentration values for subsequent use in the sensitivity coefficient integration In contrast to the half time step integrations described above for the physical processes one call t
34. l specid f species90 c species90 fd species90 h species90 main c start90 c start90 fd start90 h start90 main c steady f titrat f sensparamCB h sensparamCB_main c sensplot c sensplot1 dat sensplot2 dat sensplot3 dat sensplot4 dat sensplot5 dat setgrid f sf chemplot3 dat chemplot4 dat chemplot5 dat chparm cmd cntrol cmd compfort forowse1 c filcon cmd init f initenviron c initenviron fd initenviron h plotmaxmin dat plotparamCB c plotparamCB fd plotparamCB h plotparamCB_main c plotsensCB dat print f scale f senscommon com sensitivity f sensparamCB c sensparamCB fd B 4 simcontrol specid f species97 c species9 fd species97 h species97 _main c start97 c start97 fd start97 h start9 7 main c steady 1 titrat f
35. lic domain but is free to use in non commercial and not for profit purposes 17 Ozone X 1 NO NO2 HNO3 PAN Ethene Mixing Ratio ppm 6 8 10 12 14 16 18 Time of Day NO NO2_ HNO3 PAN Ethene Sensitivity to Initial NO Mixing Ratio 6 8 10 12 14 16 18 Time of Day Figure 4 2 Selected Output from Default Mode Execution of Code Using CB 4 Parameter ization Top Computed Mixing Ratios Bottom Computed Mixing Ratio Sensitivities to Initial NO Mixing Ratio sus REED aN T O L A t Z 6 8 10 12 14 16 18 Time of Day Sensitivity to Combined Olefin Paraffin Mixing Ratio Figure 4 3 Computed Mixing Ratio Sensitivities of Selected Compounds to Initial Mixing Ratio Sum of Non aromatic Hydrocarbons Resulting from Default Mode Execution of Code Using CB 4 Parameterization As shown in Figure 5 1 an initial window provides a brief description of the reaction parameterization for the selected chemistry scheme and allows the user to evoke a listing of the relevant reactions in a subsequent browser window SAPRC 90 Reaction Parameterization This FCM produced version of s amp PRC 30 contains 131 reactions H has 54 active species which are computed by the conventional integration routine and 10 steady state species Of1D OH ROZA ROZ ROZ HOCOO B40 HOHE and 02 which are computed algebraically Other reactants including water vapor methane
36. nd isens and various control parameters for the ordinary differential equation solver Table 1 1 Subsequent to this the main program interrogates subroutine timespan which calculates the simulation time in hours from the start and stop times and dates read in through cntrlprm Next in the calling sequence is subroutine chread which was taken directly from the FCM code and modified only slightly for present use This subroutine reads the FCM generated CHEMPARM file to obtain chemical species names and associated chemical reaction rate parameters Within this process the code establishes lookup tables of photolysis coefficients as functions of solar zenith angle phorate angle species which will be interpolated to determine photolysis rates as functions of time later in the code This is followed by interrogation of user supplied subroutine init which sets initial conditions for the chemical species mixing ratios parts per million which are placed in the one dimensional array c The code allows sensitivity calculations to be performed or bypassed at the user s discretion by setting the control toggle isens to 1 or 0 respectively Under conditions when isens 1 the main program calls subroutine initsens to supply initial conditions for the sensitivity equations equations 3 above Table 1 1 Parameters Read by Subroutine cntrlprm mrunid iprint 1 istatic isens lat long iy im id Z nbd ned tbeg tend nste
37. nduioo YIMOU uozLou wo sejos s induujoo Au n p oul i 1 J 09 siu rolH o siskjo OUd s indulo2 pi Al Z UO S e s zie os yydm u ql ow ye edy dyd inss ld pue y yJ pduu sunyesedwa s ind lo2 dud uonezieniul 40 HEYD MOJA 7176 aniy ay 1 S lQEL A YOo O euu lui pue 1y 101 1 uun Jofew uu 2 Aeyap wnjoa 149 18S su s S USIDIY9O09 AHAH SU S s zi ellu su s su sylu L SU S suonein re AHAHISU S o Kene ul wdd sone Sulxiui 6111 s s o z leniui Uy s lpul s r ds yeul lul s s 6 nun li NHYd NIHO 94 Buipe i q unoo s r ds pue 1580 5199 pio ds pe lu dols pue ues wo 40151 sinou u aw uni s ind lo2 ueds uun 8 Hun lli fONuoouls WO e ep spe y suone no e5 AHAHISU S 40 9 660 si91 uueied 0 1400 1 AlOS S lep 2018 PEJS hih uni s1 9 uueied jonuoo olseq spe ki 4 1 HEIS Upon setting the element dimensions and time increment and initializing the run clock the code interrogates subroutine temperature to compute the local temperature and pressure It then calls subroutine n
38. o subroutine slsodec results in chemical integrations over a full time step dt Subsequent to completion of integration for the current time step the code proceeds to check for and perform simplified operations for nighttime chemistry and also calculates total odd nitrogen abundance for later use in material balance adjustments 7 dol dols1 p p x 1101 nil 1 Uhuudi lqELEA olluo5 luud Aq se sins l indino s ss oo1d jeaisAud 10 suol p no e5 Sau RAD Ip zell p xell p Nedsou suas o ulesjue dep ssituu noApe ulApe su ss ud su s suone no je5 AHAnIsu S ID S 1 1 Ssiwa InNoApe UIAPe 10 57 TL jo Dau i d p yewu s jow ju uuurenu Aq ul Sucu uonenu osuoo s lnduioo nu 2 dap uonisod p Aq p lnqilluoo un oA ul s ind lo2 d p zeq p uoni sod p U uu S loul InoApe indino AH APE Aq uun oA ul Byes s ind lo2 INOApe xeyap n olindinol2 ADE ug uu s ouu ssiuu jndul uolssiul Aq SWNIOA ul uollenueouoo s lnduioo ssitu ze p uolssiuu ye edu dud
39. o the sensitivity calculatios associated with reaction processes include any sensitivity paramenters other than initial concentrations f chmslo a0 rk a2 coef a4 a5 cst t nsmax Compute associated partial derivatives as user supplied block Load matrix elements numerical integration of equation 4 Applies throughput rates to compute reaction rates for each chemical species chmfst a0 rk a2 coef ahold a5 cst t nsmax Solve matrix equation to obtain implicit numerical integration of equation 4 sgefa concjac nsmax 1 nsmax 1 indx d sgesl concjac nsmax 1 nsmax 1 indx sens 0 Applies throughput rates to compute reaction rates for each chemical species Move ahold array contents into high side of a4 array a4 array now holds updated reaction rates ppm min n x isteps m Return Return n n 1 Figure 3 3 Flow Chart for Subroutine Figure 3 4 Flow Chart for Subroutine derivative sensint 10 Completion of the reaction chemistry block in the main program results in an integration of chemical processes and associated sensitivity coefficients for one time step The program Figure 3 2 subsequently converts all mixing ratios to concentrations and embarks on a half time step integration for physical processes in a manner identical to that shown on the left hand side of the diagram completing a full integration of all processes over a time step dt Finally the code outputs the re
40. of elapsed time The original intent of this project was to render the computational framework sufficiently adaptable to accommodate a variety of chemical parameterization schemes While this is Indeed the case in principal the current software allows chemical conversion within the parcel to be simulated using three chemistry parameterizations only CB 4 SAPRC 90 and SAPRC 97 Adaptation of these schemes for this code was performed using the Flexible Chemical Mechanism FCM software produced by Kumar Lurmann and Carter 1995 This procedure as well as required steps for adaptation of additional schemes is discussed later in this report Figure 1 1 Schematic of Computational Domain The software associated with this code is written for Unix operating systems and allows execution in batch mode as well as through a graphical user interface GUI As such it provides a convenient facility for executing the reaction codes which requires little prior knowledge of atmospheric chemistry or the intricacies of formulating and solving the associated equations These features reflect the primary intent of this software which is to serve the following two groups of users 1 Persons wishing to increase their understanding of tropospheric chemistry in a straightforward and convenient manner without the burden of acquiring prior knowledge of the computational basis A primary target audience for this application consists of college level students of
41. on entrain f physsens f temperature f wind f Documentation contained within these files makes modifications for this purpose a reasonably straightforward process and here we demonstrate this procedure by imposing 2 X 107 moles m emissions of ethene eth and higher olefins ole within the construct of the CB 4 based model using the default parameters for initial mixing ratios time and location The modified emission subroutine is given as follows 25 Subroutine emission deltaz emiss called from main program subroutine to calculate gain in chemical content by model volume from emission em1ss 13 has units of moles Ccubic meter hour areal emission rate in box moles square meter hr deltaz Cmeters rn n rn include chparm cmd include chdata cmd include jmhdata cmd real emissCnsmax do 10 1 1 nospec emiss 1 0 10 contlnue emissCketh 0002 deltaz emissCkole 0002 deltaz return end One should note that this modified subroutine holds the emission rate constant for the total simulation period One could easily accommodate time variant emission rates if desired using the clock variable taftrmn hours after midnight of initial run day which is supplied via the jmhdata cmd include file Figure 6 1 shows the resulting computed mixing ratios for selected pollutants including ethene whose general upward trend reflects addition by emissions Although ozone rises somewhat more qui
42. ps dtmin tslin relerr abserr frdark alowlmt run title printing interval control variable 1 for non variable meteorology 0 otherwise control variable sensitivity calculations done if 1 latitude degrees longitude degrees year month day time zone begin day day of start month end day day of end month begin time hrs since mindnight of start day end time hrs since midnight of stop day max steps in integration smallest time increment hr max time increment hr relative error absolute error dark criterion lower limit for species concentrations g u S ouu suonenu oSuoo o sonel Bux 5 2 o dud XBLUSU L doo uone1nduuoo urew p3950o1d suonpuoo Sud su s o Pund ssiuu ndui uoissiwa Aq u Bueu2o uonenu ouo s lnduioo ssiuu ze j p uoissiuui s jqenen lu pu d p i ulo A qissod pue pioe snopu uozo s l1els Ape 1s 10119 0 oIss Apeals uiape Indu Aq p iq nuoo uun oA ul BHueYO uone nu uo s indulo2 UIADE xeyap n indunosape SUOHIPUOD peu 5109 5495 9 Pund n p ds pulu s jndwop U DH o s u lolH o euu u s
43. se case results in file AAoutput described in this user s manual Computations for conditions other than the base case can be performed by modifying the appropriate subroutines re compiling and executing as noted above A 2 GUI Operations on the Macintosh and the Sun As with the batch system the GUI based code is Installed by creating a directory given some arbitrary name at the user s discretion containing four subdirectories cb4 dir saprc90 dir saprc97 dir and com dir and loading these with the codes listed in Appendix B2 along with the script file startmodel In addition to the Fortran files these codes contain several C c files and accompanying include h and Xforms fd files are required As with the batch case described in A 1 the com dir directory contains Fortran code common to all three model mechanisms In addition to setting the correct Fortran compiler designation it will be necessary for the user to designate the C compiler name appropriate for his or her system in the makefiles Also it may be necessary to edit the linking paths to include and library files For example a typical link line in the Macintosh makefile is usr X11R nclude L usr X11R6 lib lforms X11 IXpm Caution An apparent bug in the gnu g77 compiler prevents linking to form executable programs for the GUI code on Macintosh computers Because of this vve recom mend using the fort77 compiler vvhich can be
44. sensint sensint uses a fully implicit numerical scheme which is made possible by the linearity of equation 4 Subsequently the code performs an integration of the physical process components for a second half step in a manner identical to that used for the first half step updates all computed values and proceeds to the next time step Figure 3 3 shows a progression of subroutine calls within subroutine derivative which is interrogated at various points by slsodec and its subservient routines prepi and stode as well as by fdiac a Jacobian matrix generator used in the sensitivity coefficient integration Upon successful execution derivative returns the chemical transformation rates for each of the chemical species units of ppm min in the vector argument a4 As such derivative serves as the main portal between the chemical mechanism and the remaining code All attempts to expand this softvvare to include additional chemistry parameterizations must begin by making appropriate modifications to this subroutine and its subsidiary subroutines as well as providing suitable replacements for the subroutines newphk and newrk Subroutine rates accepts information on concentrations and chemical reaction rate coefficients and calculates the individual reaction rate of each species pertaining to each individual reaction Subroutines chmfst and chmslo accept individual reaction rate information generated by rates and proceed to compute collective reaction r
45. sing default parameters which are identical to those described above for batch operation Computed results take the form of plots similar to those shown in Figures 4 2 and 4 3 The user interface to facilitate user access to the Fortran based chemical reactivity codes is written in the C programming language and implemented in X Windows It is generic and independent of the user s Unix platform providing the platform contains the requisite X Windows drivers which are all available for public use with some limitations The application makes extensive use of XForms a powerful graphical user interface toolkit for X Windows This GUI was developed on Mac OSX version 10 3 and Sun OS Release 5 8 using X11R6 in a Unix environment Simplicity of operation through the use of interactive graphics makes execution of the chemical reactivity calculation codes a very user friendly process The user is presented with a series of windows relevant to the chemistry parameterization selected CBIV SAPRC90 SAPRC97 which enable input of initial environmental conditions initial chemical species concentrations and the ability to select groups of species for plotting along with species to be used as sensitivity parameters 1 Xforms Version 1 0 90 is the Free Software distribution of the Xforms Library t is licensed under the GNU Lesser General Public License version 2 1 Xforms was developed and copyrighted by T C Zhao and Mark Overmars It is not pub
46. sor to the plot window and clicking one writes the contents of the window to the specified file To recall the xvvd file to the screen one can use the xvvud utility which is also part of the X11 distribution This is done by typing the command xwud in filename while in the appropriate directory Subsequentiy there are several applications which can convert the xvvd file into post script pdf or some other format that can be printed One such conversion application is xvvd2ps which will convert the xvvd file to PostScript To perform such a conversion one moves to an X terminal window navigates to the directory containing the xwd file and executes the command xwd2ps filename xwd gt filename ps This file can be printed to a PostScript printer 6 Advanced Operations Although the graphical user interface allows convenient manipulation of all variables associated vvith files init f initsens f and simcontrol it does itself not accommodate calculations of physical processes such as emission deposition advection and entrainment n fact each of these processes is inactive in the code s default version resulting essentially in a batch reactor simulation One can activate these additional processes in a straightforvvard manner using either the GUI or batch software by making appropriate changes to the following files and recompiling the code advectinput f advectoutput f deposition f emissi
47. stallation difficulties with the provided makefile on Sun systems can be circumvented by manually compiling the C files into the executable xwd2ps and installing the executable include and man files into locations indicated in the makefile usr local bin usr local include and usr local man man1 A 4 Appendix B Description of Source Code Files All source codes are listed in the Codes folder on the CD Batch codes for the Macintosh and Sun are in the directory Batch Codes dir These codes should operate on other Unix or Linux based systems vvith little or no modification Subdirectories and codes within Batch Codes dir are listed as follows Directory Batch_Codes dir com dir accumulate f derivative f advectinput f emission f advectoutput f entrain f chread f fdjac f cntrlorm f main f concmxratio f newphk f deposition f newrk f Directory Batch Codes dir cb4 dir BLCKDATA f filcon cmd CB4621 f init f CHEMPARM initsens f airquality jmhdata cmd calib cmd makefile chdata cmd mscal cmd chparm cmd nitbal f cntrol cmd plottile Directory Batch Codes dir saprc90 dir BLCKDATA f init f CHEMPARM initsens f airquality jmhdata cmd calib cmd makefile chdata cmd mscal cmd chparm cmd nitbal f cntrol cmd plottile filcon cmd sarmap f physsens f sensint f slsodec f solarz f temperature f timespan f wind f specid f steady 1 orint f senscommon com Sf simcontrol titrat f specid f steady 1 print f s
48. sults to file or to the GUI as required Provided the desired time limit has not been exceeded the program loops back to perform operations for the subsequent time step Otherwise the program performs a normal termination Depending on whether the batch mode or GUI versions are used the code outputs computed variables on an hourly basis as dictated by the user interface or by the user modifiable subroutine print In both cases the code writes selected output to the diagnostic file tracefile which is intended for debugging purposes in the event of failed execution 4 Basic Code Operation and Interpretation Batch Mode As noted in the previous section the current code version allows the choice between three different chemical parameterization schemes as implemented through the Flexible Chemical Mechanism FCM preprocessing code FCM is documented in a report by Kumar et al 1995 and the associated software is available on the Internet www arb ca gov eos research research htm Documentation for the three chemistry parameterization schemes is given as follows CB IV Gery et al 1989 SAPRC 90 Carter 1990 SAPRC 97 Carter et al 1997 Because this documentation exists this report will not provide a detailed discussion of these parameterizations or of the FCM preprocessor other than to note some FCM adaptations necessary for present purposes The most important of these adaptations reflects the fact that the FCM was prepared mainly to
49. t3 dat sensplot4 dat sensplot5 dat setgrid f sf simcontrol specid f speciesCB c speciesCB fd speciesCB h compfort forowse1 c filcon cmd Init f Initenviron c initenviron fd initenviron h plotsensCB dat orint f scale f senscommon com sensitivity f sensparamCB c sensparamCB fd Directory GUI Codes dir saprc90 dir BLCKDATA f SAPRC90_ Parameterization CHEMPARM airquality calib emd chdata cmd chemplot c chemplot1 dat chemplot2 dat chemplot3 dat chemplot4 dat chemplot5 dat chparm cmd cntrol cmd compfort forowse1 c filcon cmd Init f initenviron c initenviron fd initenviron h initenviron main c initparams dat initsens f jmhdata cmd main f makefile mscal cmd nitbal 1 paramsCB dat plotCB dat plotmaxmin dat plotparamCB c plotparamCB fd plotparamCB h plotparamCB_main c plotsensCB dat print f sarmap f scale f senscommon com sensitivity f sensparamCB c sensparamCB fd Directory GUI Codes dir saprc97 dir BLCKDATA f initenviron main c CHEMPARM initparams dat SAPRC97 f initsens f SAPRC97 Parameterization jmhdata cmd airquality main f calib cmd makefile chdata cmd mscal cmd chemplot c nitbal f chemplot1 dat paramsCB dat chemplot2 dat plotCB dat B 3 speciesCB_main c StartCB c StartCB fd StartCB h startCB main c steady f titrat f sensparamCB h sensparamCB_main c sensplot c sensplot1 dat sensplot2 dat sensplot3 dat sensplot4 dat sensplot5 dat setgrid f Sf simcontro
50. this manual Computations for non base case conditions require modifications of the appropriate Fortran subroutines and re compilation as noted in Section 6 The GUI source code listings include numerous files containing code written in C Although these C code files are compiled and linked by the makefiles along with the Fortran source code they should not require modification by the user A 1 Batch Operations on the MacIntosh and Sun Section B 1 lists the batch code which is identical for the Macintosh and the Sun To install this code one creates four directories cb4 dir saprc90 dir saprc97 dir and com dir and loads the files as indicated in Section B 1 Next one checks to ensure that permissions for these files are set appropriately and that the Fortran compiler designation in the makefiles Included in directories cb4 dir saprc90 dir and saprc97 dir is correct In the listed versions this designation appears in the first lines of the makefiles COMPILER f77 If a different compiler designation is used such for example 077 or fort77 then these lines should be changed as appropriate see text box in Section A 2 for a cautionary note regarding operation of the GUI codes using the gnu g77 compiler This completes the installation process To compile and link the code one simply executes the script file by typing the command sf This creates an executable file named program which can be run immediately to produce the ba
51. tion f srn ls sr A 6 J ta 0 j C1 Co aes where the two dimensional Jacobian matrix J represents the array of concentration derivatives and solves this system of equations using the Linpack matrix processing routines sgefa and sgesl As discussed previously the right hand term in equation 6 pertains to active sensitivity components that affect the reaction portion of equation 3 but are not associated with the initial concentrations e g reaction rate coefficients This is accommodated by a block within sensint which is intended for user modification in cases where such components are included Entry from call to subroutine sensint sens s Set index of historical time step n 1 Entry from call to internal function f derivative from subroutine slsodec prepj and stode as well sa from subroutine fdjac derivative neq t y a4 rdt reciprocal of historical time increment Store mixing ratio arrays in a0 and a5 working arrays y n average of end point mixing ratios for historical time increment rates a0 rk a2 coef a4 a5 cst t nsmax Calculates throughput rates for the individual reaction species combinations For example the thoughput rate for species A the reaction A B C D equals the production rate of A by this reaction fdjac nsmax nsmax y concjac Computes jacobian derivatives of rxn rate wrt concentration at historical step n D
52. vity calculation algorithms as described in Section 4 Following execution of the Fortran routines data are passed back to the GUI C code plotting routine where the computed mixing ratios and sensitivities time sequenced plots are generated and displayed as in Figures 5 7 and 5 8 As shown in Figure 5 7 the user can select Done and terminate the run or Next Plot which causes the sensitivity plot to be displayed The model run is now completed and the user can terminate the program by selecting Done or initiate another run by clicking Next Run which will activate the control initialization display Figure 5 3 This action will start another run using the same model mechanism e g SAPRC90 To execute a different model mechanism SAPRC9Q7 or CBIV it is necessary to terminate and restart selecting the desired model scheme To capture the screen image of the plot the xvvd utility which is part of the X11 distribution can be used to retain the image in a xwd file To save the image the user opens another X terminal window navigates to the executing model directory and executes 23 selected Chemical species O m n m wm x E a Hrs since start n t V t 5 6 0 4 0 Hrs since start Figure 5 8 Plotted Sensitivities to Initial NO Mixing Ratio 24 the command xwd gt filename xwd The cursor will turn into a crosshair By moving the cur
53. xtension processes of this type SAPRC99 is an additional parameterization currently included in the FCM package SAPRC99 s FCM implementation had not attained sufficient maturity at the time of this development effort to be included with the codes given in this report 29 References Carter W P L 1995 Computer modeling of environmental chamber measurements of maximum incremental reactivities of volatile organic compounds Atmospheric Environment 29 2513 2527 Kumar N F W Lurmann and W P L Carter 1995 Development of the Flexible Chemical Mechanism Version of the Urban Airshed Model Final report to California Air Resources Board ST1 94470 1508 FR Sonoma Technology Inc Petaluma California Gery M W G Z Whitten J P Killus and M C Dodge 1989 A Photochemical Kinetics Mechanism for Urban and Regional Scale Computer Modeling J Geophys Res 94 12925 12956 Carter VV P L 1990 A Detailed Mechanism for the Gas Phase Atmospheric Reactions of Organic Compounds Atmos Environ 24A 481 518 Carter W P L D Luo and L Malkina 1997a Environmental Chamber Studies for Development of an Updated Photochemical Mechanism for VOC Reactivity Assessment final report to California Air Resources Board Contract 92 345 Coordinating Research Council Project M 9 and National Renevvable Energy Laboratory Contract ZF 2 12252 07 November 26 A C Hindmarsh ODEPACK A Systematized Collection o
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