1-D-Coupled Model User`s Manual
Contents
1. This file contains the time profile of the photolysis rate constants At the present time the file is called SOLARTC IN and can be created by running the program SOLAR FOR Program SOLAR calculates the photolysis rate constants for different species according to the geographical area and time of the day by calculating the solar radiation intensity for a given point in space and time and using a table of quantum yields for species The content of the file SOLARTC IN is Line 1 Comment line Line 2 Starting time Ending time Time increment Starting local time is in 2400 format Ending time is also in 2400 format except that this is the accumulated time thus for a four day simulation 96 Hrs the Starting time is 600 and the Ending time is 10200 Time increment is in minutes Line 3 From line 3 to the end of the file the same format for each of the species will follow The header line contains the reaction label and the name of the species in the same form as in the permanent reaction library The header line is followed by several lines of data Each of these lines have three elements the Time solar zenith angle and the photochemical reaction first order rate constant for the species in the header line at the time indicated The unit for the rate constant is 1 Sec 7 Initialization file initial concentration data file This file contains the initial values for species concentrations This file is an ASCH file and be created2. update time TUPDATE time interval If PVFLAG FALSE then pressure profile is set to a constant value and the next line in the input file must be the constant pressure value LINE 8 VARIABLE NAME IUPDATE VARIABLE TYPE INTEGER _ IUPDATE USAGE IUPDATE is the update indicator it determines the value of logical name NOUPDATE If IUPDATE 0 then NOUPDATE TRUE and the subroutine UPDATE is bypassed If IUPDATE 1 then NOUPDATE FALSE and the subroutine UPDATE is being called every TUPDATE time interval LINE 9 February 17 2009 VARIABLE NAME TUPDATE VARIABLE TYPE REAL 8 TUPDATE USAGE Time interval for updating the variable data such as pressure temperature and boundary fluxes LINE 10 to the END OF FILE From here to the end of the file inputs are in a block format Each block starts with a comment line followed by as many line of input as necessary The block ends with the symbol END in a separate line by itself indicating the end of the data A block with only the comment line followed by a line with END means that the block does not contain any data Blocks are as follows BLOCK 1 This block contains the name of the species to be printed Species names must be in exact form and spelling as they appear in the permanent library file The names are separated by a space between them Each line can contain as many names as the user wishes to write Subroutine RDSPEC reads this block BLOCK 2 This block contain
3. 4 and cc 15x10 12 D 0 5 NREV 22 gt fs is CASE 6 Special CASE 1 Individual calculation for O3P 02 gt 03 February 17 2009 15 T 2 3 K PRES 6 0110 300 CASE 7 Special CASE 2 Individual calculation for HO2 HO2 gt H202 620 a K EN AA EON j CASE 8 Special CASE 3 Individual calculation for HO2 HO2 H20 gt H202 2820 3180 K 30840 WA HN CASE 9 Special CASE 4 Individual calculation for HO HNO3 gt NO3 H2O KO 7 2E 15 EXP 785 T K2 4 1E 16 EXP 1440 T K3 1 9E 33 EXP 725 T PRES K KO K3 1 K3 K2 CASE 10 Special CASE 5 Individual calculation for CO HO gt HO2 CO2 K 1 5E 13 1 2 439E 20 PRES CASE 11 Special CASE 6 Individual calculation for HO HO2 gt 416 Un Ja K 1 7 10 e TA 4 3 0 10 PRES t e February 17 2009 16 4 Meteorological data file This file contains the necessary meteorological data This file is created by running the Mesoscale Boundary Layer in 1_D mode The contents of this file are as follows Line 1 Number of vertical grid points KZ followed by the delta t time increment used in mesoscale model These values are read only once by subroutine INITDIF Line 2 through line 2 KZ The height of the vertical levels The heights are in centimeter CM Line KZ 2 1 Time of the output This is the mesoscale model simulation time in minutes Line KZ 2 2 USTAR PHISTAR an
4. constant during the course of the simulation This means that a differential equation regarding the chemical reaction of these species will not be set but they will be treated for vertical diffusion and transport They also will be updated if necessary Subroutine RDNDIS This subroutine is here for historical reason It may be used later February 17 2009 4 Subroutine RDDIS This subroutine is here for historical reason It may be used later Subroutine REORDR This subroutine reorders the species array so that the species with the constant concentration will be moved to the end of the array This is useful since it adds to the efficiency of the model when solving for stiff differential equations Subroutine RDNAMES This subroutine reads the name of the files containing the time series of meteorological data and boundary and incoming flux data The first file contains the meteorological data The second file contains the boundary fluxes species deposition velocities and flux of the pollutants at different vertical levels Subroutine RDFLUXA This subroutine reads species with a flux at the boundary from the parameter input file The name and order of the species here must match the data in the chemistry update file The flux unit right now is CM 3 CM S which can easily be changed to PPM CM S by a little modification to the code Subroutine RDFLUXB This subroutine reads species with a deposition velocity at the
5. contain as many names as the user wishes to write Subroutine RDREAC February 17 2009 3 This subroutine reads reaction specifications The subroutine first reads the reaction labels from parameter input file These are the reactions that user wishes to include in the simulation Then the permanent reaction library is searched for the reaction lists with these labels If they are found they will be included in the simulation otherwise an error message will be displayed By inclusion we mean that the subroutine RDREAC reads the complete list of the reaction This include the reactants and the products of the reaction and rate constants or the parameters necessary to calculate the rate constants Subroutine CALCR calculates the rate constants that need to be calculated every update time Subroutine RDRKA This subroutine reads reaction rate constants from the parameter input file It reads reaction labels followed by a reaction rate constant This option allows the user specify reaction rate constants different from that of the permanent library Subroutine RDSOLAR This subroutine reads the time profile of the photolysis rates from the file called SOLARTC IN Photolysis rate constants are read only once at the beginning of the simulation and stored in an array called SRATE Then each update interval subroutine UPDATEB6 updates the rate constants by interpolation Subroutine RDCCON This subroutine reads species whose concentrations are
6. of the method number of steps in the multi step method changes internally to achieve the required accuracy METHOD USED 12 Line 8 Line 9 VARIABLE NAME VARIABLE TYPE USAGE VARIABLE NAME VARIABLE TYPE USAGE An ADAMS Predictor Corrector is used ADAMS method is a multistep method It can be both implicit and explicit If the implicit method is used to improve the approximation obtained by an explicit method the combination is called Predictor Corrector method Thus with choice of MF 0 the ADAMS explicit method is used to predict the approximation then ADAMS implicit method is used to correct it A multi step method suitable for stiff system is used It will also work for non stiff systems However the user must provide a subroutine PEDERV which evaluates the partial derivatives of the differential equations with respect to the YC s This is done by call PEDERV XTIME YC PW M Where PW isan N by N working array which must be set to the partial of the i th eguation with respect to the j th dependent variable in PW i j PW is actually an M by M array where M is the value of N used on the first call to DIFSUB The same as case I except that this subroutine computes the partial derivatives by numerical differencing of the derivatives Hence PEDERV is not called NLARGE INTEGER NLARGE This parameter indicates the method of matrix inversion for the matrix of partial derivatives If NLARGE lt 0 then t
7. One Dimensional Coupled Model User s Manual Prepared By Arastoo P Biazar Atmospheric Science Program University of Alabama in Huntsville Huntsville Alabama January 13 1994 February 17 2009 Section I PROGRAM DESCRIPTION What follows is the description of the main program routine the subroutines that it calls and their main function and model requirements in general Main routine The main routine is called UAHIDMDL and it consists of calls to 16 different subroutines The main function of the first 15 subroutines is to provide the necessary input parameters and to do preparation for the model run The 16th subroutine called UAHMDL is the main body of the model and will do the required simulation Subroutine names and arguments are SETU Pi ee UG opens the i o files and library file STAMP ISTAMP prints out the current date and time to the unit ISTAMP RDINPT XTIMBPB reads title and gear parameters RDSPEC Si i otarrain reads optional list of species to define order in printout RDREAC Mi Tno reads reaction specifications optional rate constants RDRKA oiae anaa reads reaction rate constants from the input file RDSOLAR i Gw reads photolysis rate constants RDCCON egnet dw oodd reads species whose concentrations are constant RONDE sii GY egd I o a not used read species not subject to dispersion RD DISP debyd sg ed not used read species subject to dispersion REORDER Sr
8. boundary from the parameter input file The name and the order of the species should match that of the chemistry update file The unit is cm s February 17 2009 5 Subroutine RDFLUXC This subroutine reads the name of the species with an incoming flux between two vertical levels in the model The name and the order of the species should match that of the chemistry update file The two vertical levels are also included in the update file Subroutine UAHMDL This subroutine is the main body of the model It integrate the model equations and will terminate after the time period specified by the user February 17 2009 6 Section II DESCRIPTION OF THE INPUT AND OUTPUT FILES There are eight input files used by this model and three output files created by the model These files are A Input files 1 Interactive input file 2 Control parameter input file 3 Permanent library file 4 Meteorological data file 5 Chemistry data file 6 Photolysis rate constants file solar file 7 Initialization file initial concentration data file 8 Restart binary data file B Output files 1 Information output file 2 Concentration output file 3 Restart binary data file End of the run concentration file 1 Interactive input file This an optional file The information requested by the model interactively can be provided in several ways One way to furnish the required information is to write them into a file and then assign t
9. d ROOF USTAR is the friction velocity in CM S PHISTAR another friction quantity which is not being used at the present time ROOF is the planetary boundary layer height in CM Line KZ 2 3 through KZ 2 3 KZ Each of the following lines contains THETAP PIP QVP and ALPHA for each vertical grid point THETAP is the potential temperature in degrees Kelvin it will be converted to temperature by the function THETATOT Since potential temperature is calculated according to Poisson s equation THETA T PO P R CP thus T THETA P PO R CP Units of input must be as follows THETA IN DEGREES K P IN MILIBARS Units of output is as follows THETATOT In degrees Kelvin Constants used PO 1000 MILIBARS CP 1 005E 03 J KG K 1 005E 07 CM 2 S 2 K RD 287 J KG K RD CP 286 Therefore the equation for the conversion will be T THETA P 1000 0 286 February 17 2009 17 PIP is scaled pressure PI use the EXNER function to get the unscaled pressure in MILIBARS P PO PIP CP 10000 CP RD WHERE CP 1004 M 2 S 2 K CP RD 3 4965 PO 1013 25 MB and 10000 is the unit correction factor for M 2 to CM 2 QVP is specific humidity MV APOR MMOIST AIR IN G G ALPHA is the diffusion coefficient in CM 2 S The last KZ 2 line of this file will be repeated When it is time to update the meteorological data this file is being read again to update the values 5 Chemistry data file This file co
10. en a 000 O occurs which means the end of the data line has been reached the next line is read Rate constants for each type is calculated in the following way CASE 1 Reactions that are dependent on solar intensity Rate constant calculated elsewhere and are inputted from SOLARTC IN file CASE 2 Reactions which have constant rate constants Read 1 subseguent number that is the rate constant CASE 3 Reactions which are temperature dependent Need 2 subseguent numbers Ist one is A pre exponential factor 2nd one is E activation energy The calculation is according to the ARRHENIUS EOUATION K A exp E RT CASE 4 Pressure dependent reactions set of 5 with common equation Need 4 subsequent numbers IST KO 300 2ND N 3RD KI 300 4TH M KA K0300 KB N KC KI300 KD M T N KO T KO 5 300 300 T a KI T KT 5 February 17 2009 14 a fufas Cu KO T PRES F a a rae ih SOs m KIT i a CASE 5 These are unimolecular reactions Read 3 subsequent numbers 1ST number of reaction that this is the reverse of 2ND A 3RD B 7 K KR A e where l l r Una k KO T PRES AY ork UT LD 1 KIT J and E CT BB KO T AA ago T DD KI T CC 2 300 The values of AA BB CC and DD depend on the value of the first input parameter We let the first parameter to be named NREV Then 1 81073 NREV 20 gt 32 B c 4 7x10 12 1D 1
11. he inverse of matrix is found directly if non singular If NLARGE is not zero then the program performs L U decomposition on matrix of partial derivatives TINC REAL 8 TINC This parameter indicates the TINC is the output time interval in hrs Line 10 through the end of the file Line 10 contains the comment line Following this comment line each line contains a reaction label followed by the reaction list type of the reaction and necessary parameters for calculating the rate constants There are several states in reading the reaction list The first state is when the reaction label is being read It is checked against the list of reaction labels and an error message is printed if a match is not found i e it is an undefined reaction label February 17 2009 13 mos The second state is reading reactants Reactants are read until an is encountered s which separate reactants are optional and ignored The third state is reading products s are ignored The products are followed by a which indicates the start of the fourth state In the fourth state the program reads the type of rate constant and from that determines how many more variables to read for that type of rate constant calculation It then reads that many variables and puts them into the array RKMOD Then the program reads the order of the reaction i e 1 for first order reactions 2 for 2nd order reactions and so forth The fifth state occurs wh
12. his file to be the standard input unit The format of this file is Line 1 Either y or n for the answer to debug option Line 2 Name of the control parameter input line Line 3 Name of the permanent library file 2 Control parameter input file The name of this file is given to the program interactively This file contains the definition of the input parameters for 1d coupled model The contents of the file are as follows LINE ffl VARIABLE NAME TITLE VARIABLE TYPE REAL 8 TITLE 10 COMMON GEAR TITLE USAGE An array of 10 containing the title for the run February 17 2009 7 LINE 2 VARIABLE NAME TMAX VARIABLE TYPE REAL 8 TMAX COMMON GEAR TMAX USAGE Simulation time in hours After read statement it is converted to seconds TMAX TMAX 3600 LINE 3 VARIABLE NAME XEQT VARIABLE TYPE REAL XEQT LOCAL TO SUBROUTINE RDINPT USAGE Number of species to be printed at equal time intervals in EOT file NEQT INTEGER XEQT COMMON GEAR NEQT LINE 4 VARIABLE NAME IRESTART VARIABLE TYPE INTEGER IRESTART COMMON RDINPT IRESTART USAGE Indicates how the model to be initialized IRESTART 0 gt Not a restart IRESTART 1 gt Restart with one file IRESTART 2 gt Restart with two files If IRESTART 0 then model reads the initial values from a file supplied by the user If IRESTART 1 then model reads the initial values from a file called TCRESTART BIN which is a binary file created by the model at the end of each r
13. ions of reaction rate constants The following is the line by line description of the contents of this file Line 1 VARIABLE NAME EPS VARIABLE TYPE REAL 8 EPS February 17 2009 11 USAGE Line 2 VARIABLE NAME VARIABLE TYPE USAGE Line 3 VARIABLE NAME VARIABLE TYPE USAGE Line 4 VARIABLE NAME VARIABLE TYPE USAGE Line 5 VARIABLE NAME VARIABLE TYPE USAGE Line 6 VARIABLE NAME VARIABLE TYPE USAGE Line 7 VARIABLE NAME VARIABLE TYPE USAGE February 17 2009 Tolerance for convergence in the Gear routine This tolerance can be changed internally in Gear if the convergence is not achieved within the specified iteration limit HMIN REAL 8 HMIN Minimum time step allowed in the integration Time step in the Gear routine cannot be reduced to a value less than HMIN If this value is reached the program will terminate with an error message HMAX REAL 8 HMAX Maximum integration time step to be taken in the simulation NOUT INTEGER NOUT Number of species in the output The concentration of the first NOUT members of the species list will be printed in the DAT file NTEST INTEGER NTEST For historical reasons NWRPLO INTEGER NWRPLO For historical reasons MF INTEGER MEF Method indicator for Gear routine This variable indicates what method to be used in Gear routine Notice that we use a variable order multi step method This means the order
14. nput file with an extension of IN File 2 an output file with an extension of OUT File 3 an output file with an extension of EOT For example if user supplies the name TEST then a file named TEST IN will be opened as input file and must contain all the required input parameters A file named TEST OUT will be opened to deliver the output information This file will contain specific information about the simulation The third file to be opened is called TEST EOT which is an output file and will contain the concentration values at equal time periods The user is prompted for the reaction library filename This name should be the complete filename This file is an input file and must be supplied by the user This file contains some of the Gear parameters plus a complete list of the reactions and their type and reaction rate constants We will refer to this file as the permanent library file Subroutine RDINPT XTIME This subroutine reads in the title of the run and other input parameters from both input files i e parameter input file and permanent library file Description of each will follow in the section describing the input output files Subroutine RDSPEC This subroutine reads optional list of species from the parameter input file to define order in printout Species names must be in exact form and spelling as they appear in the permanent library file The names are separated by a space between them Each line can
15. ntains the information about the chemical species and their fluxes The file can be created with the help of a preprocessor The preprocessor program is called CHEMBLD for The chemistry data file contains 1 the flux of species at the boundary 2 the deposition velocities and 3 flux of the species between levels 1 and 2 of the model Each of these three elements can be and must omitted according to the specification in the parameter input file For example if there is no species with incoming flux between two model levels the control parameter data file does not have any entry in the corresponding section Thus chemistry data file also should not contain any entry In another word control parameter data file contains the list of the species whose values are read from chemistry data file For the same reason the order of the values in the chemistry data file must match the order of the species list in the control parameter data file The elements of the chemistry data file are as follows 1 A A HEADER LINE FOR SPECIES WITH FLUXES AT THE BOUNDARY B VALUE OF THE FLUX IN CM 3 CM S 2 A A HEADER LINE FOR DEPOSITION VELOCITIES B VALUES IN CM S 3 A A HEADER LINE FOR SPECIES WITH FLUX TO THE LEVELS I TO 2 B VALUES IN CM 3 S The number of entries lines for each block depends on the number of species specified in the control parameter data file February 17 2009 18 6 Photolysis rate constants file solar file
16. s the reaction labels Only the reactions with these labels will be included in the simulation The program reads the permanent reaction library and includes the reactions with matching labels The labels here must be in exact form as they appear in the permanent library Subroutine RDREAC reads this block BLOCK 3 This block contains the list of reaction labels followed by a reaction rate constant This block is used if there are reactions with rate constants different from that of the permanent library Subroutine RDRKA reads this block BLOCK 4 This block contains the name of species which have constant concentration during the simulation This means that a differential equation regarding the chemical reaction of these species will not be set But they will be treated for vertical diffusion and transport They also will be updated if necessary Subroutine RDCCON reads this block BLOCK 5 This block is here for historical reasons It may be used later Subroutine RDNDIS reads this block BLOCK 6 This block is here for historical reasons It may be used later Subroutine RDDIS reads this block BLOCK 7 February 17 2009 10 This block contains the name of the files containing the time series of meteorological data and boundary and incoming flux data The first line of this block starts with integer number 1 followed by a space and the name of the file containing the meteorological data The second line starts wi
17. ta a e reorders species list RDNAMES o reads in the name of the files met and flux data update files RDELUX Ana Y AU reads species with flux at the boundary RDELUXB A a GR reads species with deposition velocity at the boundary RDELUXC wi reads species with flux contribution to all levels UAHMDL XTIME solves eguations by gear method A description of each of these subroutines will follow Subroutine SETUP This subroutine is the only interactive part of the program The inputs can either be typed in at the terminal if the program is running interactively or can be furnished in a file assigned to the standard input unit i e unit 5 This routine reguires the answers to three guestions regarding debug option input output file names and the reaction library file name The three lines of input that satisfies this routine are Line 1 The user is prompted for the DEBUG option The answer can be either y for yes or n for no If the answer is yes then the debug option will be turned on and the model output will be dumped to the screen If February 17 2009 2 Line 2 Line 3 the answer is no then the debug option will be turned off and the output delivered to the output file The user is prompted for the input output filename The name that user supplies here with no extension will be used for both input and output files with different extensions Three files will be opened File 1 an i
18. th integer number 2 followed by a space and the name of the file containing the boundary fluxes species deposition velocities and flux of the pollutants at different vertical levels Subroutine RDNAMES reads this block BLOCK 8 This block contains the name of the species with boundary flux The name and order of the species here must match the data in the chemistry update file The flux unit right now is CM 3 CM S which can easily be changed to PPM CM S by a little modification to the code Subroutine RDFLUXA reads this block BLOCK 9 This block contains the name of the species with deposition velocity at the boundary The name and the order of the species should match that of the chemistry update file The unit is CM S Subroutine RDFLUXB reads this block BLOCK 10 This block contains the name of the species with an incoming flux between two vertical levels in the model The name and the order of the species should match that of the chemistry update file The two vertical levels are also included in the update file BLOCK 11 This block contains the name of the file containing the species initial values for all the grids in the model 3 Permanent Reaction library input file The name of this file is given to the program interactively The permanent reaction library input file contains some of the control parameters for the Gear solver and a complete list of the reactions and factors used in calculat
19. un If IRESTART 2 then model first reads the initial values from TCRESTART BIN file and then reads other values from a file supplied by the user Content of this file can be a modification of the concentration values or some other new values not presented in TCRESTART BIN file LINE 5 VARIABLE NAME RUNTYPE VARIABLE TYPE INTEGER RUNTYPE COMMON UAHGEAR RUNTYPE USAGE Indicates the type of experiment February 17 2009 RUNTYPE 1 gt DISPERSION CHEM REAC RUNTYPE 2 gt CHEM REAC ONLY RUNTYPE 3 gt DISPERSION ONLY If RUNTYPE 1 then both chemical reactions and dispersion are being considered and the full model is implemented If RUNTYPE 2 only chemical reactions are being considered and the dispersion mechanism is turned off If RUNTYPE 3 only dispersion is being considered and the chemical reactions mechanism is turned off LINE 6 VARIABLE NAME TVFLAG VARIABLE TYPE LOGICAL TVFLAG USAGE TVFLAG determines if temperature varies during the run or it is a constant If TVFLAG TRUE then temperature profile is being updated every update time TUPDATE time interval If TVFLAG FALSE then temperature profile is set to a constant value and the next line in the input file must be the constant temperature value LINE 7 VARIABLE NAME PVFLAG VARIABLE TYPE LOGICAL PVFLAG USAGE PVFLAG determines if pressure varies during the run or it is a constant If PVFLAG TRUE then pressure profile is being updated every
20. with a text editor The first line of this file is a comment line Each of the following blocks have the name of the species in a separate line followed by the species initial concentration for each grid point starting with grid point 1 at the lowest model level This file sometimes is used in conjunction with TCRESTART BIN file which is a binary file created by the model at the end of each run 8 Restart binary data file We can use the restart binary file to restart the model from the point that model was last terminated We can also change some of the concentration values when restarting the model Model automatically creates this binary file at the end of each simulation This binary file that at the present time is called TCRESTART BIN is optional and it is used if IRESTART is 1 or 2 February 17 2009 19
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