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Polyphemus 1.1α User's Guide

1. 3 7 INITIAL CONDITIONS Ic 59 To download any data from the NCAR Community Data Portal you need to register This is quite easy and fast but there is a second step You also have to ask for an access to Mozart data specifically This takes longer as the application has to be reviewed by someone but it should go without problems if you say that you need Mozart data to generate initial and boundary conditions for a CTM The data can be found in ACD Atmospheric Chemistry Models Data Set and Visualization Tools If you registered in this section of the site you should be able to access MOZART Model for OZone And Related chemical Tracers This opens a page with various informations about Mozart and in particular in Nested Collections a link named MOZART 2 MACCM3 Standard Simulation v2 1 Click on this link At the time the direct link is http cdp ucar edu browse browse htm uri http dataportal ucar edu metadata acd mozart mozart2 mozart _v2_1_maccm3 thredds xml but if this changes a search for MOZART MACCM3 should lead you to the page There are 38 files available in NCAR Community Data Portal from hc0040 nc to hc0077 nc One file gathers data for ten consecutive days File hc0040 nc start at 26 December Data in those files have been generated for a typical year which means they can be use to generate boundary conditions for any year See Equation 3 1to know how to determine the file you need given
2. bio bio cfg 2001 04 22 bio bio cfg 2001 01 22 2001 04 23 bio general cfg bio cfg 2001 04 22 The first three calls are equivalent The fourth one involves two configuration files The program bio behaves as if these two configuration files were merged It means that the fields required by the program may be put in any of these two files Markups defined in one file can be expanded in the other file The only constraint is that each section should appear in a single file only 2 3 3 Sharing Configuration The command line bio general cfg bio cfg 2001 04 22 1d with the two configuration files general cfg and meteo cfg is the advocated line The configuration file general cfg gathers information that may be needed by several programs in the preprocessing directory meteo attenuation luc usgs etc Such a configuration file is provided with Polyphemus preprocessing general cfg general Home u cergrene 0 bordas Directory_computed_fields lt Home gt B data Directory_ground_data lt Directory_computed_fields gt ground Programs lt Home gt codes Polyphemus HEAD domain Date 2001 01 02 Delta_t 3 0 2 3 RUNNING PROGRAMS 23 x_min 10 0 Delta_x 0 5 Nx 65 y_min 40 5 Delta_y 0 5 Ny 33 Nz 5 Vertical_levels lt Programs gt levels dat The simulation domain and the simulation dates are defined In addition markups Directory_computed_fields Directory_ground_data and Programs are introduc
3. e North South surface stress accumulated 181 e Evaporation accumulated 182 e Low cloud cover 186 e Medium cloud cover 187 34 e High cloud cover 188 e Skin temperature 235 e Forecast albedo 243 CHAPTER 2 USING POLYPHEMUS e Cloud liquid water content 3D 246 e Cloud ice water content 3D 247 e Cloud cover 3D 248 Not all data may be required depending on the programs you actually run 2 5 4 Mandatory Data for Models The table below presents all variables needed by various models and the name under which they appear in the data configuration files Note that additional data can be necessary to add initial conditions boundary conditions source terms volume emissions surface emissions or loss terms deposition velocities scavenging In the table Gaussian represents any Gaussian model GaussianPlume GaussianPuff GaussianPlume_aer or GaussianPuff_aer as they all need the same data Table 2 1 Mandatory data for each models Model Data necessary Castor Transport Temperature Pressure Altitude AirDensity Meridional Wind ZonalWind VerticalDiffusion CastorChemistry The same as Castor Transport and SpecificHumidity Liquid WaterContent Attenuation Polair3DTransport MeridionalWind for advection ZonalWind for advection VerticalDiffusion for diffusion Horizontal_diffusion if Isotropic_diffusion is set to no this value
4. 20 8 0e 01 B 0e 23 6 0e 01 6 0e 23 4 0e 01 4 0e 23 2 0e 01 2 0e 23 0 0e 00 o 0 0e 00 c Situation 3 Concentration at t 0s t 0 5s and d Situation 4 Concentration at t 0s t 0 5s and t 2 5s t 2 5s Figure B 2 Evolution of the puff for the various meteorological situations 138 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE 8 0e 03 8 0e 03 25 7 0e 03 7 0e 03 207 6 0e 03 6 0e 03 5 0e 03 5 0e 03 isk 4 4 0e 03 4 0e 03 10 3 0e 03 3 0e 03 2 0e 03 2 0e 03 Se 1 0e 03 1 0e 03 0 0 10 20 30 40 50 a Situation 1 b Situation 2 8 0e 03 2st 25L 1 4e 02 7 0e 03 1 2e 02 20 6 0e 03 20 1 0e 02 5 0e 03 a Tr 8 0e 01 4 0e 03 6 0e 01 10 3 0e 03 10 4 0e 01 2 0e 03 Se Se 1 0e 03 2 0e 01 o o o 10 20 30 40 50 o 10 20 30 40 50 c Situation 3 d Situation 4 Figure B 3 Concentration at t 4s for the various meteorological situations Bibliography Arstila H Korhonen P and Kulmala M 1999 Ternary nucleation kinetics and application to water ammonia hydrochloric acid system J Aer Sci 30 2 131 138 Debry E Fahey K M Sartelet K Sportisse B and Tombette M 2006 Technical Note A new SIze REsolved Aerosol Model SIREAM Technical Report 37 CEREA Fahey K M and Pandis S N 2003 Size resolved aqueous phase atmospheric chemistry in a three dimensional chemical transport mode
5. Database_MM5_meteo Directory_meteo Directory_attenuation tmin Delta_t Nt xmin Delta_x Nx ymin Delta_y Ny Nz projection_type Prev_accumulated_rain Type Min_height Min Max Apply_vert paths Directory in which MM5 input files may be found If amp D appears in the file name it is replaced by MM5 YYYY MM DD where YYYY is the year MM the month and DD the day Directory where output meteorological files are stored Directory where the output of program attenuation is stored MM5 First hour stored in every MM5 file Time step in hour of data stored in every MM5 file Number of time steps stored in every MM5 file Index in MM5 coordinates of the center of the lower left cell in MM5 grid This is most likely 0 5 Index MM5 coordinates increase along longitude of MM5 grid This is most likely 1 Number of cells or dot points along longitude integer in MM5 grid Index in MM5 coordinates of the center of the lower left cell in MM5 grid This is most likely 0 5 Index MM5 coordinates increase along latitude of MM5 grid This is most likely 1 Number of cells or dot points along latitude integer in MM5 grid Number of vertical layers integer in MM5 grid Type of projection 1 corresponds to Lambert conformal conic 2 to Mercator and 3 to stereographic accumulated_rain Is the rain accumulated from the previous day attenuation Parameterization to be used to compute cloud attenuation Pu
6. Step Space step in meters lon_origin_ea Longitude of the center of lower right cell for Eurasia lat_origin_ea Latitude of the center of the lower right cell for Eurasia lon origin af Longitude of the center of the lower right cell for Africa lat origin af Latitude of the center of the lower right cell for Eurasia lon upper left_ea Longitude of the center of the upper left cell for Eurasia lat_upper_left_ea Latitude of the center of the upper left cell for Eurasia lon upper left_af Longitude of the center of the upper left cell for Africa lat_ upper left_af Latitude of the center of the upper left cell for Africa Nx_ea Number of cells along longitude in the input file for Eurasia Nx_af Number of cells along longitude in the input file for Africa Ny_ea Number of cells along latitude in the input file for Eurasia Ny_af Number of cells along latitude in the input file for Africa Nc Number of land categories Sea_index Index of the sea in land categories Remember that indices start at 0 The output land cover file is in format c y xj where c stands for land use category Program luc usgs does not require any date as an input in command line To launch luc usgs just type 42 CHAPTER 3 PREPROCESSING luc usgs general cfg luc usgs cfg 3 3 3 Conversions luc convert The output of luc glcf or luc usgs are land use cover described with GLCF or USGS cat egories It is often useful to convert these descriptions to
7. luc usgs TestCase config luc usgs cfg TestCase config general cfg The output on screen will be A 4 COMPUTING METEOROLOGICAL DATA 127 Reading configuration files done Memory allocation for data fields done Reading LUC data done Building LUC data on output grid done Writing output data done A 3 2 Roughness The preprocessing program roughness needs as input data the results of luc usgs The file roughness cfg in Polyphemus preprocessing ground should be ready to use just check that the markup LUC_origin is set to usgs Then compile and execute roughness make roughness roughness roughness cfg TestCase config general cfg The output on screen will be Reading configuration files done Reading roughness data done Writing roughness binary done A 4 Computing Meteorological Data No modification to configuration file MM5 meteo cfg should be necessary but make sure to use the version of this file included in directory TestCase and not in directory Polyphemus You can open the file and check that Database MM5 meteo is the path to the file MM5 2004 08 09 where the date is represented by amp D For details about the other options available in the config uration file see Section 3 4 5 Then compile MM5 meteo cd meteo make MM5 meteo and execute it MM5 meteo TestCase config MM5 meteo cfg TestCase config general cfg 20040809 The output on screen will be Reading
8. 6 1 where T 2 is the species half life time in days and to is a reference time If a species has no decay its half life time is set to 0 and this is interpreted by Decay as the fact that concentration does not vary due to decay C t C to exp Ge 6 1 The parameters needed are provided in species dat as follow species Spl Sp2 Sp3 Sp4 aerosol_species Aer1 Aer2 half_life Half lives in days put O for species without decay 6 2 CHEMISTRY MODULES 111 Sp1 300 Sp2 216 Sp3 0 Sp4 41 half_life_aerosol Half lives in days put O for species without decay Aeri 250 Aer2 120 Use of Two Values of Decay Another option is that each species has two values of T y2 one for the day and one for the night This is in particular the case for species which have a biological effect As before for a species without decay both half life times are set to 0 The equation involved is very similar to equation 6 1 except that the value of T y2 can vary In that case With_time_dependence is set to yes and With_filiation_matrix to no The parameters needed are provided in species dat species Spl Sp2 Sp3 Sp4 aerosol_species Aer1 Aer2 half_life_time Half lives in days put O for species without decay First value for day second for night Sp1 300 500 Sp2 216 300 Sp3 0 0 Sp4 41 72 half_life_time_aerosol Half lives in days put O for species without decay First value for day second for nig
9. Filename Comments If initial conditions are activated With_initial_condition and not inter polated Interpolated_initial_condition set to no If boundary conditions With_boundary_condition Required fields are Temperature Pressure Altitude AirDensity ZonalWind and VerticalDiffusion If deposition is activated With deposition are activated MeridionalWind If volume emissions are activated With_volume_emission Nz is the num ber of levels in which pollutants are emitted 5 9 3 Vertical Levels and Species A file containing vertical levels similar to the one for Polair models is read but is not useful Give any such file Species file has two sections e species which contains all species managed by the simulation e species_ppm which contains all species for which an upwind scheme is not used 5 10 CASTORCHEMISTRY 105 5 10 CastorChemistry Model CastorChemistry is derived from CastorTransport and all data presented in Section 5 9 are necessary for this model too In addition some other parameters are needed 5 10 1 Main Configuration File castor cfg options With_chemistry Is chemistry taken into account chemistry Reaction file Data file containing the reactions Stoichiometry file Data file containing the stoichiometry of the reactions Photolysis_file Rates file 5 10 2 Data Description and Species Data Description The only difference with what is desc
10. GroundObservationManager see Section 4 8 1 and to observation sim cfg if you use SimObservationManager see Section 4 8 2 The data assimilation experiments are controlled by the following options domain Nt Number of time steps for the whole simulation assimilation and prediction data assimilation Nt_assimilation Number of time steps for the assimilation period Nt is supposed to be greater than or equal to Nt_assimilation From time step 0 to time 4 5 DATA ASSIMILATION DRIVERS 77 step Nt_assimilation 1 assimilation is performed and from step Nt_assimilation to step Nt 1 prediction is performed In many cases such as data assimilation and ensemble prediction perturbed model simula tions are needed Perturbations are managed by PerturbationManager see Section 4 9 reading an additional section perturbation management Configuration_file Name of the file that contains perturbation configurations 4 5 2 OptimalInterpolationDriver It is the driver dedicated to data assimilation applications using optimal interpolation algorithm The optimal interpolation algorithm estimates model state status by minimizing the error vari ance of the estimation called analysis in data assimilation terminology It searches for a linear combination between background state model simulations and the background departures The background departures are defined as the discrepancies between observations and
11. Nchamberlain Configuration_file 93 Ordinate in meter of the center of the lower left cell Step length along y in m Number of cells along y integer Number of vertical levels integer Path to the file that defines vertical levels heights Land category choose between rural and urban Choose whether it is nighttime night or daytime day Relevant only when there is biological decay Path to the file that defines involved species gaussian Is radioactive decay taken into account Is biological decay taken into account Is scavenging taken into account Is dry deposition taken into account Path to the file containing the meteorological data Path to the file that contains the puff data deposition Model used to take dry deposition into account Chamberlain for Chamberlain model Overcamp for Overcamp model Number of points to calculate the Chamberlain integral integer Relevant only when dry deposition with Chamberlain model is taken into account output Path to the configuration for the output saver 5 3 2 Puff Description puff dat Puffs are described in a single configuration file containing as many sections as there are puffs Each section named source is associated with a new source Each section contains the following information 1 the time when the puff is released s from the beginning of the simulation 2 the total mass emitted in mass unit the mass unit does not matter th
12. The whole Polyphemus directory should not be modified except maybe makefiles Copy the configuration files you need in a dedicated directory modify the new configuration files in this directory and run Polyphemus programs from this directory Your directory tree may look like Polyphemus version driver include postprocessing preprocessing utils MyStudy configuration data emissions meteo Al results reference new_emissions A where MyStudy contains Polyphemus configurations files set for the study configuration with general cfg meteo cfg init data generated by preprocessing programs directory data and output results from the chemistry transport model results with results from different runs Notice that Polyphemus directory includes the version number or the date This is very useful in order to properly track simulations In directory MyStudy you should add a file called version which should contain Polyphemus version and maybe the version of other tools You may also want to copy configuration files in your output directory For instance you may copy meteo cfg in directory MyStudy data meteo so as to know with which configuration your meteorological data were generated 32 CHAPTER 2 USING POLYPHEMUS 2 5 2 Roadmaps Roadmaps with Eulerian Models In short the main steps to set up an Eulerian simulation are 1 generation of ground data land use cover roughness height preprocessing
13. at m s the specific humidity in kg kg SpecificHumidity bin the surface relative humidity SurfaceRelativeHumidity bin the liquid water content in kg kg LiquidWaterContent bin the cloud attenuation coefficients Attenuation bin the soil moisture SoilMoisture bin the aerodynamic resistance AerodynamicResistance bin the friction velocity in ms FrictionModule bin Deposition Velocities Deposition velocities are generated on the basis of meteorological fields and land data The programs must be launched after meteorological and ground preprocessing The computation of deposition velocities for Gaussian models is presented in Section 3 9 2 3 5 1 Program dep The program dep computes deposition velocities according to Wesely 1989 or Zhang et al 2003 In addition to general cfg the program reads the configuration in dep cfg In this file paths to several files generated by programs meteo or MM5 meteo are given 52 CHAPTER 3 PREPROCESSING SurfaceTemperature SurfaceRichardson SolarRadiation WindModule PAR PARdiff PARdir SpecificHumidity SurfacePressure FrictionVelocity CanopyWetness Rain RoughnessHeight Type Data Directory_dep Ns CellRoughness Ra Rb Re Save_resistance paths File where surface temperature is stored File where surface Richardson number is stored File where solar radiation is stored File where wind module is stored File where photo
14. by certain reference run of Polair3D amp s in path names is replaced by species name Date min Starting date for the simulation results in data files Delta_t Time step in seconds for the simulation results in data files Levels Levels for the simulated data in files Initial_concentration Flag that indicates whether initial concentrations are included in data file 4 9 Perturbation Manager The PerturbationManager is dedicated to perturbation managements It reads the perturbation configurations and performs perturbations The concerning fields are then updated according to perturbation results for new model simulations in diverse applications such as data assimilation and ensemble predictions Library NewRan is needed for random number generations The perturbation fields are defined in configuration file of which the name can be read from section perturbation management in the driver configuration file general Fields Perturbation field list that depends on species e g Deposition Ve locity PhotolysisRate SurfaceEmission and BoundaryCondition Rand_seed Seed assignment for NewRan library either a given seed number in JO 1 or name of the directory that contains NewRan seed files or a random seed number in JO 1 that depends on the current CPU time Field maximum_spread Every random number for field perturbations cannot exceed the mean plus or minus Field_maximum_spread times the standard de
15. gaussian deposition except that there are some more information specific to the aerosol species The input and output files are the same as described in the section about gaussian deposition so in this section we will only describe the data that are added to the files described previously One input file is needed in addition to the meteorological data and species data files It is the diameter file reference diameter dat which contains the diameters of the aerosol particles Configuration File In the configuration file the following information are added data Diameter Path to the data file that contains the particle diameters scavenging 70 CHAPTER 3 PREPROCESSING Type_aer Parameterization to be used to calculate the scavenging coefficients for aerosol species Value Values to be used for a Slinn parameterization choose between best_estimate and conservative deposition Type_aer Parameterization to be used to calculate the deposition velocities for aerosol species The parameterization type for the scavenging coefficient of aerosol species can be chosen between e none the scavenging coefficient is set to 0 for all aerosol species e constant the scavenging coefficient is constant for one given diameter and entered in the species file e slinn the scavenging coefficient is calculated with a Slinn parameterization In that case the only input data that are used are the rainfall rate and the particl
16. gt gt from pylab import Loads Matplotlib gt gt gt x arange 10 dtype d gt gt gt y xx x gt gt gt plot y gt gt gt plot x y gt gt gt figure New figure gt gt gt plot x y k k for black for a solid line gt gt gt figure 1 Comes back to the first figure gt gt gt plot x y k for a discontinuous line gt gt gt close Closes current figure gt gt gt plot x y k for a dotted line gt gt gt clf Clears the figure gt gt gt plot x y k label Simple label is for the legend gt gt gt plot x 2 y k label Double gt gt gt legend gt gt gt xlabel Abscissa gt gt gt ylabel Ordinate gt gt gt savefig plot_example eps Saves the figure in EPS could be PNG or JPG 7 1 7 1 GRAPHICAL OUTPUT 117 3 Visualization with AtmoPy AtmoPy provides functions to use Basemap easily and to process data mainly statistics It is first used to load binary files generated in preprocessing or output of a model or a driver Configuration File disp cfg In order to load and process data in a binary file it is convenient to use AtmoPy with a small configuration file often called disp cfg This file describes the data to be read input optional Nt Number of time steps to be read in the binary file It can be less than the total number of time steps in the file
17. heat flux fm momentum flux or diag diagnostic Parameterization used to compute the quasi laminar sublayer re sistance You can choose between friction and diag Parameterization used to compute the canopy resistance Zhang et al 2003 or Wesely 1989 Should Ra Rb and Re be saved This may take a lot of storage space put no if you do not work on the deposition parameteriza tions 3 5 DEPOSITION VELOCITIES 53 Entry Type is the path to a configuration file whose entries should be File Midsummer Autumn Late_autumn Snow Spring Path to the file describing the land use cover The number of cate gories in the file is deduced from its size but it must be consistent with the data provided in the following entries Midsummer etc Data file for midsummer see below for details Data file for autumn see below for details Data file for late autumn see below for details Data file for snow see below for details Data file for spring see below for details The data files mentioned above for the five seasons must contain a column for each land use category with 22 parameters in each column You may modify these files or create new files only if you are well aware of deposition parameterizations With Polyphemus a set of 5 files is provided for convenience and any beginner should use them They are suited for land use categories as defined in Zhang et al 2002 A key step is therefore to g
18. 2 3 4 and 6 2 http docs python org documentations about Python 3 http www scipy org Tentative NumPy Tutorial introduction to NumPy 4 http matplotlib sourceforge net Matplotlib website see Sections Tutorial and Screen shots 5 http www scipy org SciPy library which includes many scientific modules linear algebra optimization etc 7 2 Postprocessing for Gaseous Species 7 2 1 Configuration File The configuration file simulation cfg is needed for disp py and evaluation py Here is a brief explanation of the various options provided in simulation cfg but more details can be found in the file itself for some options file multiple file tmin Delta_t Nt xmin Delta x Nx ymin Delta_y Ny Nz station_file station file type obs_dir station input Binary file with the results to postprocess Boolean stating whether several files are used Initial date of the binary file s in format YYYYMMDD or YYYYMMDDHH Time step in hours Number of time step in the binary file s Abscissa of the center of the lower left cell longitude in degrees Step length along x in degrees longitude Number of cells along x integer Ordinate of the center of the lower left cell latitude in degrees Step length along y usually in degrees latitude Number of cells along y integer Number of vertical levels integer File describing the stations Type of station file Emep Air
19. 2 ee 43 3 4 1 Program Meteo s sa p44 a Be i a aes St 43 3 4 2 Program attenuation a 45 Dia Program K2 lt h A JP nde x Sa eee Mega nt ee Se 45 LA Program K2sTM cise ace eto Bee Oe dee RY ee A ae eg n a 46 3 4 5 Program MM5 m te ua eg ae eae Rn Ee ae i 47 3 4 6 Program MM5 meteo castor e 49 3 5 Deposition Velocities Hu E ga t a RAe a e oS w i aa 51 3 5 1 Program dep dirae a SE eR ER aa a Se Fae a 51 3 5 2 Program dep emberson e 53 9 07 EMISSIONS i l aaa Wiad a a E oh at pe o e ad Be a a SR eR eaa ea a aai a 54 3 6 1 Mapping Two Vertical Distributions distribution 54 3 6 2 Anthropogenic Emissions EMEP emissions 54 3 6 3 Biogenic Emissions for Polair3D Models bio 57 3 6 4 Biogenic Emissions for Castor Models bio castor 57 3 6 5 Sea Salt Emissions searsalt pee ee ee 58 3 7 Initial Conditions ile 58 3 8 Boundary Conditions 444 6084 a a gs da aaa 60 3 8 1 Boundary Conditions for Gaseous Species DC o 60 3 8 2 Boundary Conditions for Aerosol Species bc gocart 61 3 9 Preprocessing for Gaussian Models e o 65 3 9 1 Program discretization o 2 en fe ke daa ra a E a 65 3 9 2 Programs gaussian deposition and gaussian deposition aer 66 4 Drivers 75 AT Base Driver sou ass o ea BOR A AA E A a as a ei S 75 4 2 Plume Driver laes haois eh 4 d
20. 5 42 er gest dere e eg ocho Bre eee Bly Beek Ha 107 6 1 2 Diffusion ROS sorat wey A at Ge alate ee OA 107 6 1 3 Tramsp tBEM oo ca Re a 107 6 2 Chemistry Modules y e sora p PEA eee PO og Re ee io eA a 107 6 21 Chemist RACM oie aca A Eo EN a eS 107 6 2 2 ChemistryRACM SIREAM 02222020004 108 6 23 ChemistryRADM uso ra ke Pe ee eee aS 110 6 2 4 ChemistryCastor soe e e moo ee 110 6 2 9 A 110 Postprocessing 113 fi Graphical Outputs gu 444 eat Bask od AE OP he ee a a 113 7 1 1 Installation and Python Modules o e e 113 7 1 2 A Very Short Introduction to Python and Matplotlib 115 7 1 3 Visualization with AtmoPy o 117 7 2 Postprocessing for Gaseous Species o 120 7 2 1 Configuration File 22 io a ea A 120 722 2 Script 6valuation pyes pe a a A Ee PS 121 23 Script diSP py 4 205 wo hos ad a ea ah as 121 7 3 Aerosol Postprocessing s am 2 2 ee 122 7 3 1 Configuration File s sceso a e eieaa da a aoe e B e ah ee 122 32 Sriptinitaerosol py 4 5445 oe eee Peek ede ob a 122 7 3 3 Script graph_aerosol py 0 a 123 Polyphemus Eulerian Test Case 125 A 1 Preparing the Test Case 2 2 a ee 125 A 2 Modifying the General Configuration File 20 126 A 3 Computing Ground Data 0 0 0 0000000 eee ee 126 A 3 1 Land Use Cover sare e e m ai e 126 A 3 2 Roughness ened Ba hoe a Be A A AR CO BA A 127 A 4 Computing Mete
21. Directory_attenuation Directory where the output of program attenuation is stored attenuation Type Parameterization to be used to compute cloud attenuation Put 1 to use RADM parameterization or put 2 to use ESQUIF parameteri zation clouds Min_height Minimum cloud basis height in m Just like in program meteo ECMWF data is read and interpolated Then the relative humidity and the critical relative humidity are computed respectively with ComputeRelativeHumidity and ComputeCriticalRelativeHumidity The cloud fraction is computed with ComputeCloudFraction For it the cloudiness and cloud height are diagnosed using ComputeCloudiness and ComputeCloudHeight Finally attenua tion coefficients are computed with ComputeAttenuation LWC RADM parameterization or ComputeAttenuation ESQUIF ESQUIF parameterization Output files are e the rain intensity Rain bin in mmh e the convective rain intensity ConvectiveRain bin in mmh e the 3D cloud attenuation coefficient in 0 2 e the cloud height in m 3 4 3 Program Kz Program Kz computes the vertical diffusion coefficients needed in almost all applications using Louis parameterization Louis 1979 It should be launched after attenuation 46 CHAPTER 3 PREPROCESSING The reference configuration files for Kz is Polyphemus preprocessing meteo meteo cfg together with Polyphemus preprocessing general cfg In addition to the domain definition and to the entries of
22. Kuhn M and Seefeld S 1997 A new mechanism for regional atmospheric chemistry modeling J Geophys Res 102 D22 25 847 25 879 Troen I and Mahrt L 1986 A simple model of the atmospheric boundary layer sensitivity to surface evaporation Boundary Layer Meteor 37 129 148 Vehkam ki H Kulmala M Napari I Lehtinen K E J Timmreck C Noppel M and Laaksonen A 2002 An improved parameterization for sulfuric acid water nucleation rates for tropospheric and stratospheric conditions J Geophys Res 107 D22 139 140 BIBLIOGRAPHY Wesely M L 1989 Parameterization of surface resistances to gaseous dry deposition in regional scale numerical models Atmos Env 23 1 293 1 304 Zhang L Brook J R and Vet R 2003 A revised parameterization for gaseous dry depo sition in air quality models Atmos Chem Phys 3 2 067 2 082 Zhang L Moran M D Makar P A Brook J R and Gong S 2002 Modelling gaseous dry deposition in AURAMS a unified regional air quality modelling system Atmos Env 36 537 060
23. Species Meteo and Diameters 94 50 Polair3D Transport Via a e a oe dee A Ra ap ee bs al ea 94 5 5 1 Main Configuration File polair3d cfg o o 94 5 5 2 Data Description polair3d data cfg o e 96 5 5 3 Vertical Levels and Species 2 2 e e 98 5 6 Polars DChemistry s ana a nd tp ee ee Os RS 99 5 6 1 Main Configuration File polair3d cfg o 100 5 6 2 Data Description polair3d data cfg o 100 5 6 3 Vertical Levels and Species 2 oaa 100 Dif Polair3DAerosol che bese wk db sew a ie Se ot eb ka 101 5 7 1 Main Configuration File polair3d cfg 101 CONTENTS 5 1 2 Data Description polair3d data cfg o 102 5 7 3 Vertical Levels and Species o e 102 5 8 Polair3DChemistryAssimUlonc 000002 eee ee 102 5 9 CastorTransport e o soaa hose ec a ee Po ee Ba a a a 103 5 9 1 Main Configuration File castor cfg 103 5 9 2 Data Description castor data cfg 104 5 9 3 Vertical Levels and Species o e e 104 5 10 CastorChemistid woe is et Bh e ds a de det di EO a h 105 5 10 1 Main Configuration File castor cfg 105 5 10 2 Data Description and Species e e 105 510 3 Chemistry Filesi aca ia ta pe BEE a a a s 105 Modules 107 6 1 Transport modules Ts a ia a a i B LR ea at a 107 GAs AdvectiOnDS13
24. Ve Ve Po Ns rtical_levels Path to the text file that stores the altitudes in m of input level interfaces hence Nz_in 1 values are read rtical distribution Path to the file with the input vertical distribution of emissions This file should contain one line per emission sector Each line contains the percentage of emissions at ground level first column and the percentage of emis sions in each vertical level Nz_in following columns lair vertical distribution Path to the output file where the output vertical distri bution of emissions should be stored The format is the same as in file Vertical distribution ectors Number of activity sectors 3 6 Pro 2 Anthropogenic Emissions EMEP emissions gram emissions processes an EMEP emission inventory and generates anthropogenic sur face and volume emissions needed by Polair3D First you must download Expert emissions inventories from http webdab emep int Download emissions for CO NH3 NNMVOC NOx SOx PM2 5 and PMcoarse and make sure to have a file for each species called CO dat NH3 dat NMVOC dat NOX dat SOX dat PM2 5 dat and PMcoarse dat Download files with the following options 3 6 EMISSIONS e for all countries 55 e for the year of your choice up to 2004 e for all activity sectors SNAP note that emissions for the eleventh EMEP sector are better estimated with program bio see Section 3 6 3 but that if they are included in
25. W DIRECTION 86 MAP PROJECTION 1 LAMBERT CONFORMAL 2 POLAR STEREOGRAPHIC 3 MERCATOR 1 IS COARSE DOMAIN EXPANDED 1 YES O NO O EXPANDED COARSE DOMAIN GRID DIMENSION IN I DIRECTION 76 EXPANDED COARSE DOMAIN GRID DIMENSION IN J DIRECTION 86 GRID OFFSET IN I DIR DUE TO COARSE GRID EXPANSION O GRID OFFSET IN J DIR DUE TO COARSE GRID EXPANSION O DOMAIN ID 1 MOTHER DOMAIN ID 1 2 4 USEFUL TOOLS 27 NEST LEVEL 0 COARSE MESH 0 DOMAIN GRID DIMENSION IN I DIRECTION 76 DOMAIN GRID DIMENSION IN J DIRECTION 86 I LOCATION IN THE MOTHER DOMAIN OF THE DOMAIN POINT 1 1 1 J LOCATION IN THE MOTHER DOMAIN OF THE DOMAIN POINT 1 1 1 DOMAIN GRID SIZE RATIO WITH RESPECT TO COARSE DOMAIN 1 1 REGRID Version 3 MM5 System Format Edition Number 2 REGRID Program Version Number 16 REGRID Program Minor Revision Number 1 COARSE DOMAIN GRID DISTANCE m 36000 COARSE DOMAIN CENTER LATITUDE degree 47 COARSE DOMAIN CENTER LONGITUDE degree 6 CONE FACTOR 0 715567 TRUE LATITUDE 1 degree 60 TRUE LATITUDE 2 degree 30 POLE POSITION IN DEGREE LATITUDE 90 APPROX EXPANSION m 360000 GRID DISTANCE m OF THIS DOMAIN 36000 I LOCATION IN THE COARSE DOMAIN OF THE DOMAIN POINT 1 1 1 J LOCATION IN THE COARSE DOMAIN OF THE DOMAIN POINT 1 1 1 I LOCATION IN THE COARSE DOMAIN OF THE DOMAIN POINT IX JX 76 J LOCATION IN THE COARSE DOMAIN OF THE DOMAIN POINT IX JX 86 TERRAIN DATA RESOLUTION in degre
26. for given species Is dry deposition taken into account Are point emissions provided Are emissions at ground provided Are volume emissions provided Which scavenging model is applied If none the scavenging is not taken into account Otherwise the following model is applied constant for constant scavenging coefficient belot for the Belot model of the form a pp where po is the rain intensity in mmh or microphysical for the scavenging model based on microphysi cal properties of species Are the dry deposition fluxes are collected in order to postprocess them if dry deposition is taken into account Are the wet deposition fluxes are collected in order to postprocess them if wet deposition is taken into account data Path to the configuration file that describes input data Horizontal diffusion coefficient in m s 96 CHAPTER 5 MODELS Isotropic_diffusion If activated horizontal diffusion is set equal to vertical diffusion output Configuration file Path to the configuration for the output saver 5 5 2 Data Description polair3d data cfg This configuration file describes input data files binary files It is divided into sections for deposition for meteorological fields etc A section roughly looks like this meteo Date_min 2004 08 09 Delta_t 10800 Fields MeridionalWind ZonalWind Temperature Pressure Rain CloudHeight Attenuation SpecificHumidity Filename u cergrene a ahmed dm TestC
27. for the calculation of the first decreasing ratio m End_index Index for the calculation of the last decreasing ratio n With_left_finite_difference_checking Checking left side finite difference results Display_sensitivity Display sensitivity results for the decreasing perturbation se quences Option With trajectory management Trajectory delta t Trajectory file are similar to those for 4DVar in Section 4 5 5 4 6 2 GradientDriver The objective function is chosen to be the norm of the difference between model simulations and synthetic observations This driver aims at the verification of the backward integration algorithm of adjoint model for gradient calculations Options Norm_perturbation_vector With_random_perturbation Decreasing root Start index End_index and With_left_finite_difference_checking in section adjoint have the same meanings as those in Section 4 6 1 Option Display_cost indicates whether the values of the objective function are displayed when perturbation decreases accordingly 4 6 3 Gradient4DVarDriver The objective function is chosen to be the observation discrepancy in the 4DVar objective function This driver aims at the verification of the adjoint code of observation operator All 80 CHAPTER 4 DRIVERS the options for this driver are same as those in Section 4 6 2 4 7 Output Savers 4 7 1 BaseOutputSaver The saver BaseOutputSaver is configured with a file that contains one or seve
28. from TestCase cd TestCase Polyphemus driver plume config plume cfg The output on screen will be Temperature Wind angle Wind velocity Stability Case 0 15 100 0 5 D Case 1 10 5 2 D Case 2 10 20 5 D Case 3 10 60 10 D Results are stored in results plume B 3 2 Puff with Aerosol Species The simulation uses puff_aer which is the program for puffs with aerosol species and the following data e Gaseous species Caesium Iodine e Aerosol species aerl aer2 e Sources 1 point source per species e Meteorological situations 4 situations rotating wind with an increasing speed 0 1m s 2m s 5m s et 10m s e Urban environment The simulation uses the following files e puff_aer cfg gives the simulation domain options and the paths to the other files 134 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE e gaussian levels dat gives the vertical levels e gaussian species_aer dat gives all meteorological data and data on scavenging and deposition It was created during preprocessing see Section B 1 e puff source_aer dat contains all the data on gaseous and aerosol sources e puff saver_aer cfg contains the options and paths to save the results Compile the program puff_aer cd Polyphemus driver make puff_aer Then execute it from TestCase cd TestCase Polyphemus driver puff_aer config puff_aer cfg Results are stored in results puff_aer B 3 3 Puff with Line Source The simulation
29. gaussian gaussian meteo_aer dat 2 preprocessing discretization to generate source files for line emission and gaussian deposition or gaussian deposition_aer to compute deposition velocities and scavenging coeffi cients without or with aerosol species respectively For more details see Section 3 9 2 5 SETTING UP A SIMULATION 33 3 compiling the right combination of model GaussianPlume GaussianPlume_aer GaussianPuff GaussianPuff_aer and driver PlumeDriver or PuffDriver 2 5 3 Mandatory Data in Preprocessing ECMWF Fields In ECMWF files it is recommended to have the following fields with their Grib codes e Volumetric soil water layer 1 39 e Volumetric soil water layer 2 40 e Volumetric soil water layer 3 41 e Volumetric soil water layer 4 42 e Temperature 3D 130 e U velocity 3D 131 e V velocity 3D 132 e Specific humidity 3D 133 e Snow depth 141 e Stratiform precipitation Large scale precipitation accumulated 142 e Convective precipitation accumulated 143 e Snowfall convective stratiform accumulated 144 e Surface sensible heat flux accumulated 146 e Surface latent heat flux accumulated 147 e Logarithm of surface pressure 152 e Boundary layer height 159 e Total cloud cover 164 e 2 meter temperature 167 e Surface solar radiation downwards accumulated 169 e Surface solar radiation accumulated 176 e East West surface stress accumulated 180
30. general Home u cergrene a ahmed dm Path_to_test_case lt Home gt TestCase 1 0 Path_to_polyphemus lt Home gt Polyphemus 1 0 Directory_raw_data lt Path_to_test_case gt raw_data Directory_computed_fields lt Path_to_test_case gt data Directory_ground_data lt Directory_computed_fields gt ground Programs lt Path_to_polyphemus gt preprocessing domain Date 20040809 t_min 0 0 Delta_t 1 0 Nt 24 x_min 10 0 Delta_x 0 5 Nx 65 y_min 40 5 Delta_y 0 5 Ny 33 Nz 5 Vertical_levels lt Programs gt levels dat Replace Home by the path to your home directory Path_to_test_case by the path to TestCase and Path _to_polyphemus by the path to Polyphemus Other paths needed for the simulation depend on these ones so modifying them should be sufficient The domain is defined for a simulation over Europe Make sure that the date is 20040809 date for which meteorological raw data is provided It is advised to put both TestCase and Polyphemus in your home directory as this is what will be used below A 3 Computing Ground Data Ground data are not necessary to perform the simulation but they are needed to compute the vertical diffusion using Troen and Mahrt parameterization If you wish to use Louis parameter ization this step is not necessary and you can go to Section A 4 A 3 1 Land Use Cover Compile and execute luc usgs from your Polyphemus directory cd Polyphemus preprocessing ground make luc usgs
31. introduced in Section 5 5 1 the following fields are read by Polair3DChemistry options With_chemistry Should chemistry occur With photolysis Should photolysis occur With_forced_concentrations If activated the concentrations of a few species are set to values read in files Source_splitting If activated source splitting is used within chemistry in tegration Advection and diffusion fluxes are included in the chemistry integration as sources This slightly in creases the memory requirements but is recommended for numerical stability 5 6 2 Data Description polair3d data cfg In addition to the configuration described in Section 5 5 2 a section photolysis _rates may be required if the chemical mechanism includes photolysis reactions Photolysis rates depend on days time angle latitude and altitude During the time integration they are linearly inter polated in all cells Section Entries Comments photolysis_rates Date_min Starting date of photolysis rates Delta_t Time step in days Ndays Number of steps Time_angle_min Starting time angle in hours Delta time angle Time angle step in hours Ntime angle Number of time angles Latitude_min First latitude in degrees Delta latitude Step along latitude in degrees Nlatitude Number of latitude steps Altitudes List of altitudes in meters at which photolysis rates are provided Fields Filename Photolysis reaction names and the paths to the files in which
32. is given in the main configuration file Temperature if With_air_density is set to yes or for microphysical scavenging model Pressure if With_air_density is set to yes or for micro physical scavenging model Polair3DChemistry The same as Polair3DTransport and SpecificHumidity Attenuation Polair3DChemistry AssimConc The same as Polair3DChemistry 2 5 SETTING UP A SIMULATION 35 Polair3DAerosol The same as Polair3DChemistry and LiquidWaterContent SnowHeight Gaussian Temperature Wind_angle Wind wind module Inversion_height Stability All data for Eulerian models are outputs of meteorological preprocessing programs e meteo Kz attenuation and Kz_TM if you use Troen Mahrt parameterization for ver tical diffusion for models of type Polair3D while using raw meteorological data from ECMWF e MM5 meteo and Kz_TM if you use Troen amp Mahrt parameterization for vertical diffusion for models of type Polair3D while using raw meteorological data from model MM5 e MM5 meteo castor and Kz_TM if you use Troen amp Mahrt parameterization for vertical diffusion for models of type Castor while using raw meteorological data from model MM5 2 5 5 Models Modules Compatibilities Models of type Polair3D require two transport modules one for advection and one for dif fusion while models of type Castor only require one transport m
33. meteo cfg and Polyphemus grid is described in general cfg For the sake of simplicity it is recommended to work with ECMWF files containing data for one day all Polyphemus programs work on a daily basis Program meteo should be called for each day preferably from Oh to 24h that is for each available ECMWFE file except the first one see below If ECMWF files are not provided on a daily basis it is recommended to contact the Polyphemus team at polyphemus cerea enpc fr In order to process the ECMWF file for a given day the ECMWF file for the previous day must be available Indeed ECMWF files contain data that is accumulated over several time steps like rain and values from previous steps including from the previous day must be subtracted to get the actual value of the field Here is the list of input data needed in ECMWF files with their Grib code surface temper ature 167 skin temperature 235 surface pressure 152 temperature 130 specific humidity 133 liquid water content 246 medium cloudiness 187 high cloudiness 188 meridional wind 132 zonal wind 131 zonal friction velocity 180 meridional friction velocity 181 solar radiation 169 boundary layer height 159 soil water content 39 sensible heat 146 evaporation 182 The list of output variables is pressure surface pressure temperature surface temperature skin temperature Richardson number surface Richardson number specific humidit
34. photolysis rates are stored 5 6 3 Vertical Levels and Species Section 5 5 3 is relevant for Polair3DChemistry and in particular the file giving the lev els is exactly the same As for species a section molecular weight lists the molecu lar weights in gmol of all species If photolysis reactions are involved the section photolysis_reaction_index is required This section provides all reaction names and their indices in the list of reactions Below is an example photolysis_reaction_index N02 0 0301D 1 0303P 2 HONO 3 HNO3 4 HNO4 5 NO3NO 6 NO3N02 7 H202 8 HCHOmol 9 HCHOrad 10 ALD 11 5 7 POLAIR3DAEROSOL 101 MHP 12 HOP 13 PAA 14 KETONE 15 GLYform 16 GLYmol 17 MGLY 18 UDC 19 ORGNIT 20 MACR 21 HKET 22 The previous section is quoted from Polyphemus driver species dat and is consistent with RACM as implemented in ChemistryRACM Section 6 2 1 5 7 Polair3DAerosol Polair3DAerosol is configured with three configuration files polair3d cfg polair3d data cfg and polair3d saver cfg and two data files levels dat and species dat The main con figuration file polair3d cfg provides the paths to the four other files A configuration for Polair3DAerosol is an extension of the configuration for Polair3DChemistry In this section the description is limited to Polair3DAerosol additional parameters See Sec tion 5 6 for the rest of the configuration 5 7 1 Main Configuration File polair3d cfg In addition to fields intr
35. physical fields Polair3D f Physics i Libraries with physical f parameterizations AtmoData Figure 1 1 Polyphemus flowchart preprocessing model computations postprocessing As a consequence Polyphemus code is organized with the following directories tree preprocessing bc boundary conditions Mozart 2 Gocart INCA bio biogenic emissions dep deposition velocities emissions pollutant emissions EMEP ground ground data land use cover roughness ic initial conditions Mozart 2 meteo meteorological data ECMWF and MM5 including cloud attenuation and vertical diffusion driver forward simulations data assimilation example a series of examples of configuration files for several applications observation observation managers for data assimilation ground observations and simulated observations optimization optimization algorithms output_saver modules to save the results of a simulation perturbation management of model perturbations Monte Carlo postprocessing comparisons to measurements water_plume liquid water diagnosis in a plume include Talos C library to manage configuration files used everywhere in Polyphemus dates and string processing SeldonData C library to perform data processing interpolations input output operations 1 2 REQUIREMENTS 11 AtmoData C and Fortran library for physical parameterizations and atmospheric dat
36. settling velocity calculated by the program Note that while some gaseous species might not be concerned by scavenging or deposition the loss processes are assumed to occur for all aerosol species Therefore there is no need of a section containing the species for which scavenging or deposition occur in the case of aerosol species as it is the case for gaseous species Here is an example of species file containing the sections dedicated to aerosol species laerosol_species aerl aer2 aer3 scavenging_constant_aer Scavenging coefficient for aerosol species Unit seconds 1 Depends on the diameter first value diameter index in file diameter dat Only one diameter per line 0 1 e 4 1 2 e 4 deposition_constant_aer Dry deposition velocity diffusive part of the species Unit m s Depends on the diameter 72 CHAPTER 3 PREPROCESSING Only one diameter per line 0 0 05e 2 1 0 5e 2 density_aer Particle density aerosol species kg m 3 Only one species per line aeri 1 88 aer2 1 aer3 4 93 Output File The output file is the same file as the one for gaussian deposition except that the scavenging coefficients and deposition velocities of aerosol species are also written One coefficient corresponds to a given species of a given diameter It is written as species name diameter index followed by the value of the corresponding scavenging coefficient or deposition vel
37. source to be discretized The line source is a continuous line made of segments Each segment is defined by two end points The data file contains three columns corresponding to the coordi nates X Y Z in meters of all end points It contains at least the coordinates of two points This is an example of data file defining a straight line emission between two points X m Y m Z m O O 30 66 CHAPTER 3 PREPROCESSING 20 O 30 The output data file contains a list of point sources All points have the same source data and their coordinates have been calculated by the program It is presented as a list of sections named source each section containing the coordinates and other data for one point source 3 9 2 Programs gaussian deposition and gaussian deposition aer The aim of these programs is to calculate the scavenging coefficient and the deposition velocity of the species The program gaussian deposition is used when all species are gaseous species and gaussian deposition_aer is used when some or all species are aerosol species The input data are meteorological data and species data and the output file is a file containing meteorological data and the scavenging coefficients and deposition velocities of all species This file can be used as input meteorological file for the programs plume and puff for gaseous species or plume aer and puff_aer in the case of aerosol species Program gaussian deposition Configuration File Th
38. the inventory they are ignored e in format Grid 50 km x 50 km Semicolon Separated e for one species at a time In addition to the domain definition Section 3 2 2 program emissions reads a configuration file such as emissions cfg Directory_surface_emissions Directory_volume_emissions Polair_vertical_distribution Input_directory Hourly_factors Weekdays_factors Monthly_factors Time_zones Nx_emep Ny_emep Ncountries Species Nsectors Urban _ratio Forest_ratio Other_ratio File x_min Delta_x Nx ymin paths Directory where the computed surface emissions are stored Directory where the computed volume emis sions are stored This should be different from Directory_surface_emissions since files for surface emissions and volume emissions have the same names species names EMEP File where the vertical distribution of emissions is stored This file should contain one line per emission sector Each line contains the percentage of emissions at ground level first column and the percentage of emissions in each vertical level Nz following columns Directory containing EMEP emissions inventory File defining hourly factors see below File defining weekdays factors see below File defining monthly factors see below File defining the time zone for various countries Number of cells along longitude integer in EMEP grid Number of cells along latitude integer in EMEP grid Maximu
39. the date for which you want to generate the initial conditions In addition to the domain definition Section 3 2 2 below is the information required in the configuration for ic see example ic cfg ic_input_domain Date_ic Date for which initial conditions are generated Nt Number of time steps in Mozart 2 files Delta _t Time step of Mozart 2 files in hours Nx Number of grid points along latitude in Mozart 2 files integer Ny Number of grid points along longitude in Mozart 2 files integer Nz Number of vertical levels in Mozart 2 files integer Database_ic Directory where the Mozart 2 files are available Mozart 2 file names are in form h00xx nc where xx is computed by the program according to the date Date_ic lic_files Species File providing correspondence between the name of species in Mozart 2 files and the name of species in simulation In this file the first column contains Mozart 2 species After each Mozart 2 species name the corresponding output species e g RACM species is put if any If Mozart 2 species gath ers two output species put the names of all output species followed by their proportion in Mozart 2 bulk species For instance the line C4H10 HC5 0 4 HC3 0 6 splits Mozart 2 species C4H10 into HC5 40 and HC8 60 Three ex amples are provided preprocessing bc species_v1 dat preprocessing bc species_v2 dat and preprocessing bc species_v3 dat Molecular_weight File providing
40. the entries for Kz_TM path LUC_file Path to the binary file that describes land use cover over the output grid described in section domain This file must be in format l y x lis the land category and it must contain proportions in 0 1 of each land category in every grid cell Sea_index Index of sea in land categories remember that indices start at 0 It is O for GLCF description and 15 for USGS description Roughness_file Path to the binary file that describes roughness heights in meters in output grid cells Its format is y x It is needed only if option Flux_diagnosed is activated Directory_meteo Directory where output meteorological files are stored File_Kz Name of the file where the vertical diffusion coefficients as com puted with the Louis parameterization are stored Directory Kz_TM Name of the directory where the vertical diffusion coefficients out put are stored the filename being Kz_TM Kz Min Lower threshold for vertical diffusion in m Max Higher threshold for vertical diffusion in m 231 291 3 4 METEOROLOGICAL FIELDS 47 Apply vert If set to no the lower threshold is applied only at the top of the first layer otherwise it is applied to all levels p Coefficient used in Troen and Mahrt parameterization see Troen and Mahrt 1986 C Coefficient used in Troen and Mahrt parameterization see Troen and Mahrt 1986 SBL Ratio between the surface layer and the atmospheri
41. the test case directory cd TestCase Polyphemus preprocessing emissions discretization config discretization cfg The output on screen will be Reading configuration file done Reading trajectory data done Length of the trajectory 48 0278 Number of points on the trajectory 26 Writing source data done The file puff source discretized dat has been created in the directory TestCase config It contains a series of puffs representing the discretized line source B 3 Simulations B 3 1 Plume This simulation uses the program plume which is the program for the Gaussian plume model It uses the following data e Gaseous species Caesium Iodine e Sources 2 point sources for Iodine one point source for Caesium e Meteorological situations 4 situations rotating wind with an increasing speed 0 1m s 2m s 5m s et 10m s e Urban environment B 3 SIMULATIONS 133 The simulation uses the following files e plume cfg gives the simulation domain the options and the paths to the other files e gaussian levels dat gives the vertical levels e gaussian species_aer dat gives all meteorological data and scavenging and deposition coefficients It was created during preprocessing see Section B 1 e plume source dat contains all the data on stationary sources e plume saver cfg contains the options and paths to save the results Compile the program plume cd Polyphemus driver make plume Then execute it
42. to specify all chemical species involved in the process e g 5 5 POLAIR3DTRANSPORT deposition Date_min 2001 01 02 Delta_t 10800 Fields 97 03 NO N02 H202 HCHO PAN HONO S02 HNO3 OP1 PAA ORA1 Filename u cergrene A mallet 2001 data dep 2005 01 19 amp f bin ALD CO 0 002 u cergrene A mallet 2001 data dep 2005 01 19 ALD modified bin Notice that CO is not associated with a path but with a numerical value This is a feature a binary file may be replaced with a numerical value In this case the field in the example CO deposition velocity is set to a constant value in every cell and at every time step This works with any field including meteorological fields section meteo This feature is often used to set constant boundary conditions In polair3d data cfg several sections are required Several sections have to be included only if given options are activated In the following table all possible sections are listed with their entries Section initial_condition boundary_condition meteo deposition point_emission surface_emission volume_emission scavenging Entries Fields Filename Date min Delta_t Fields Filename Date min Delta_t Fields Filename Date min Delta_t Fields Filename file Date_min Delta_t Fields Filename Date min Delta_t Nz Fields Filename Fields Comments If initial conditions are activated With initial conditi
43. uses puff which is the program for puffs with gaseous species only and the following data e Gaseous species Iodine e Source 1 line source e Meteorological situations 4 situations rotating wind with an increasing speed 0 1m s 2m s 5m s et 10m s e Urban environment The simulation uses the following files e puff cfg gives the simulation domain options and the paths to the other files e gaussian levels dat gives the vertical levels e gaussian species_aer dat gives all meteorological data and scavenging and deposition coefficients It was created during preprocessing see Section 3 e puff source discretized dat gives data on the discretized source It has been created using program discretization see Section B 2 e puff saver cfg gives the options and paths to save the results Compile the program puff cd Polyphemus driver make puff Then execute it from TestCase cd TestCase Polyphemus driver puff config puff cfg Results are stored in results puff_line B 4 RESULT VISUALIZATION 135 B 4 Result Visualization B 4 1 Gaussian Plume Python scripts are provided to display easily and quickly the results of a simulation For the plume simulation just launch cd TestCase python results plume display_plume py It creates 5 figures in results plume e plume_gas_max gives the repartition of the maximum of concentration of Iodine for all meteorological situations e plume gas meteol g
44. value of WindModule_10m Species between which terpene emissions are distributed Ratio of the terpene emissions for each of the above species 3 6 5 Sea Salt Emissions sea salt Program sea_salt computes the emissions of sea salt aerosols Its options and parameters are given in sea_salt cfg Surface_wind_module_file Directory_sea_salt Threshold_radius Delta_t File Nb_luc Sea_index Section_computed Diameter min Diameter max Nsections File_sections paths Binary where the wind module at surface is stored Directory where sea salt emissions are stored sea_salt Radius above which Monahan parameterization is used in um Time step for sea salt emissions computation LUC File containing land use cover Number of land categories Index of sea in land categories recall that indices start at 0 PM Should diameter classes bounds be computed Otherwise they are read in File_sections Minimum diameter if diameter classes bounds are com puted Maximum diameter if diameter classes bounds are com puted Number of diameter classes File containing the diameter classes bounds if they are not computed 3 7 Initial Conditions ic Climatological concentrations from Mozart 2 Horowitz et al 2003 are used to generate initial concentrations for photochemistry simulation with Polair3D Program ic has been tested with Mozart 2 output files downloaded on NCAR data portal at http cdp ucar edu
45. 0 0 500500 0 424750 0 352000 0 283750 0 222750 0 172150 0 132200 0 100050 0 0730000 0 0449750 0 029000 0 00950000 e 1996 1997 26 vertical sigma layers centered at 0 993935 0 971300 0 929925 0 875060 0 812500 0 745000 0 674500 0 604500 0 536500 0 471500 0 410000 0 352500 0 301500 0 257977 0 220273 0 187044 0 157881 0 132807 0 111722 0 0940350 0 0792325 0 0668725 0 0565740 0 0447940 0 0288250 0 00997900 e 2000 2002 30 vertical sigma layers centered at 0 998547 0 994147 0 986350 0 974300 0 956950 0 933150 0 901750 0 861500 0 811000 0 750600 0 682900 0 610850 0 537050 0 463900 0 393650 0 328275 0 269500 0 218295 0 174820 0 138840 0 109790 0 0866900 0 0684150 0 0539800 0 0425750 0 0335700 0 0239900 0 0136775 0 00501750 0 00053000 3 8 BOUNDARY CONDITIONS 63 Gocart files processing Gocart files are handled by bc gocart program which takes 4 arguments bc gocart general cfg bc gocart CC cfg 200101 CC STD tv15 g day 200101 where e general cfg is the general configuration file e bc gocart CC cfg is the configuration file for CC Gocart species e 200101 CC STD tv15 g day is the Gocart file e 200101 is the date of Gocart file this file corresponds to daily carbonaceous values during month of January 2001 The gocart configuration file bc gocart CC cfg provides all necessary informations to read Gocart fields and how to translate them into polair3d species pat
46. 2 y Under IPython print is useless just type 2 y gt gt gt y 7 print y y Combined commands with semicolon y 7 gt gt gt a 1 5 3 a is a list gt gt gt print al0 O is the first index gt gt gt a range 10 print a 0 1 2 3 4 5 6 7 8 9 gt gt gt for i in range 3 print i i Il Ne oO In Python blocks are delimited by the indentation For instance without the prompt gt gt gt y 0 x 0 for i in 2 5 15 First loop 116 CHAPTER 7 POSTPROCESSING for j in 1 3 9 Nested loop x i j Inside the inner loop y x Outside the inner loop but still inside the outer loop print y Outside the loops the loops are closed Arrays NumPy gt gt gt from numpy import Loads NumPy gt gt gt a arange 6 dtype d d means double floating point precision gt gt gt print a 0 1 2 3 4 5 gt gt gt a zeros 2 3 dtype d 2D array gt gt gt print a shape 2 3 gt gt gt ali 2 5 gt gt gt al0 10 Fills the first line gt gt gt al1 0 2 1 From column O to column 1 2 is excluded gt gt gt print a 10 10 10 1 1 5 gt gt gt print a sum a max a min a mean al 0 sum 33 0 10 0 1 0 5 5 9 0 gt gt gt print 2 al 1 2 Calculation without the first column E 18 18 4 8 Matplotlib gt gt gt from numpy import gt
47. 3 1 Compiling Programs Along with all programs are provided makefiles in the same directory Edit these makefiles to change the compiler Main variables are the C compiler CC the Fortran compiler F77 the linker LINK and maybe the libraries LIBS and the include paths INCPATH 2 3 2 Running a Program Most programs require one or two input configuration files and sometimes one or two dates beginning and end dates see Section 3 2 3 Most programs provide help when launched without any input file Here is an example with the program bio Further details about specific programs are provided in chapter 3 22 CHAPTER 2 USING POLYPHEMUS Polyphemus preprocessing bio gt bio Usage bio main configuration file secondary config file first date second date time int bio main configuration file fisrt date second date time interval bio main configuration file secondary config file first date bio first date second date time interval bio first date Arguments main configuration file optional main configuration file Default bio cfg secondary configuration file optional secondary configuration file Default first date beginning date in any valid format second date end date in any valid format time interval optional Interval in format NdMh or Nd Mh where N is the number of days Program bio takes from one to four arguments Below are four possible calls bio 2001 04 22
48. 5 0 470 5 535 1 1 5 470 8 535 4 2 5 470 8 535 4 4 5 470 8 535 4 7 5 470 8 535 4 10 5 470 8 535 4 13 5 470 8 535 4 17 5 470 8 535 4 Point_file lt Results gt point txt Note that coordinates are entered in meters first z then y then x or just y then x In the previous example every point for which only two coordinates are entered is saved at 1 5 meters above ground For one point one wished to save concentrations at different heights above ground so heights have been explicitly written When dealing with aerosol species one just has to put indices_list_aer or coordinates list aer instead of indices_list or coordinates_list respectively 4 7 8 SaverUnitWetDeposition and SaverUnitDryDeposition The output savers SaverUnitWetDeposition and SaverUnitDryDeposition define output saver units when Type is set to wet_deposition or dry_deposition and both require additional parameters presented in the table below save Averaged Should concentrations be averaged over Interval_length If not instantaneous concentrations are saved Initial_concentration Should initial concentrations be saved This option is only avail able if concentrations are not averaged If Species is set to all the deposition fluxes will be saved for all scavenged or dry deposited species 4 7 9 SaverUnitWetDeposition_aer and SaverUnitDry Deposition aer The output savers SaverUnitWetDeposition_aer and SaverUnitDryDeposition_aer d
49. 5 1 and contain the half life times of both gaseous and aerosol species 5 2 5 Diameters diameter dat See Section 3 9 2 5 2 6 Meteorological data gaussian meteo dat See Section 5 1 5 5 3 GaussianPuff Model GaussianPuff is the Gaussian puff model for gaseous species only The associated pro gram to be run is puff and it is configured with one configuration file puff cfg and four data files puff dat puff level dat gaussian meteo dat and gaussian species dat The configuration file provides the paths to the four other files Basically given a series of instan taneous puffs emitted at different times it calculates the concentration of each species along a specified grid There are several output files one for each species that are binary files same as in the Gaussian plume model and fully described in Section 4 7 5 3 1 Configuration File puff cfg display Show_date Irrelevant Provide any Boolean domain Date_min Irrelevant Provide any date see Section 2 2 7 Delta_t Time step of the simulation in seconds Nt Number of time steps integer x min Abscissa in meter of the center of the lower left cell Delta x Step length along x in m Nx Number of cells along x integer 5 3 GAUSSIANPUFF ymin Delta_y Ny Nz Vertical_levels Land_category Time Species With_radioactive_decay With_biological_decay With_scavenging With_dry_deposition File_meteo File_puff Deposition_model
50. 86 Cc YX cm ACCUMULATED CONVECTIVE PRECIPITATION RAIN NON 2 76 86 Cc YX cm ACCUMULATED NONCONVECTIVE PRECIPITATION TERRAIN 2 76 86 Cc YX m TERRAIN ELEVATION MAPFACCR 2 76 86 Cc YX DIMENSIONLESS MAP SCALE FACTOR MAPFACDT 2 76 86 D YX DIMENSIONLESS MAP SCALE FACTOR CORIOLIS 2 76 86 D YX 1 s CORIOLIS PARAMETER RES TEMP 2 76 86 C YX K INFINITE RESERVOIR SLAB TEMPERATURE LATITCRS 2 76 86 0 YX DEGREES LATITUDE SOUTH NEGATIVE LONGICRS 2 76 86 Cc YX DEGREES LONGITUDE WEST NEGATIVE LAND USE 2 76 86 C YX category LANDUSE CATEGORY TSEASFC 2 76 86 C YX K SEA SURFACE TEMPERATURE PBL HGT 2 76 86 C YX m PBL HEIGHT REGIME 2 76 86 Cc YX DIMENSIONLESS PBL REGIME SHFLUX 2 76 86 C YX W m 2 SENSIBLE HEAT FLUX LHFLUX 2 76 86 Cc YX W m 2 LATENT HEAT FLUX UST 2 76 86 C YX m s FRICTIONAL VELOCITY SWDOWN 2 76 86 Cc YX W m 2 SURFACE DOWNWARD SHORTWAVE RADIATION LWDOWN 2 76 86 Cc YX W m 2 SURFACE DOWNWARD LONGWAVE RADIATION SWOUT 2 76 86 C YX W m 2 TOP OUTGOING SHORTWAVE RADIATION LWOUT 2 76 86 Cc YX W m 2 TOP OUTGOING LONGWAVE RADIATION SOIL T 2 76 86 Cc YX K SOIL TEMPERATURE IN LAYER 1 SOIL T2 2 76 86 Cc YX K SOIL TEMPERATURE IN LAYER 2 SOIL T3 2 76 86 C YX K SOIL TEMPERATURE IN LAYER 3 SOIL T4 2 76 86 C YX K SOIL TEMPERATURE IN LAYER 4 SOIL M1 2 76 86 C YX m 3 m 3 TOTAL SOIL MOIS IN LYR 1 4 SOIL M2 2 76 86 Cc YX m 3 m 3 TOTAL SOIL MOIS IN LYR 2 4 SOILM3 2 76 86 Cc YX m3 m73 TOTAL SOIL MOIS IN LYR 3 4 SOIL M4 2 76 86 C Y
51. 916 gsfc nasa gov People Chin gocartinfo html 62 CHAPTER 3 PREPROCESSING e imx total number of longitudinal grid 144 jmx total number of latitudinal grid 91 Imx total number of vertical layers version dependent e nmx total number of species 4 or 5 see species list above e ntl yyyymmdd after 2000 year month day e g 20010201 or yymmdd before 2000 e g 970101 e nt2 hhmmss hour minute second e g 120000 e nn tracer number see species list above e Q 3 dimensional concentration of tracer nn nstep total time step e g in 200101 nstep 4 31 for 4 times day nstep 31 for daily average files and nstep 1 for monthly average files Important e If you plan to read Gocart data on your own do not forget to translate files from big endian to little endian if necessary e The conventions and format of Gocart files may change in the future Fields resolution The horizontal resolution of Gocart fields is 2 degree latitude x 2 5 degree longitude except at the poles where latitudinal resolution is 1 degree In other words the longitude interval is 180 2 5 177 5 144 cells and the latitude one is 89 5 88 2 8889 5 91 cells The vertical resolution is given as a given number of vertical sigma levels The number of vertical levels depends of the year e 1980 1995 20 sigma layers centered at 0 993936 0 971300 0 929925 0 874137 0 807833 0 734480 0 657114 0 57839
52. CHAPTER 2 USING POLYPHEMUS Here is an example with get_diff float Polyphemus driver results gt utils get_diff_float 03 bin 03 other bin File 0 File 1 Minima 0 0145559 0 0181665 Maxima 136 795 175 123 Means 71 578 65 4088 Standard dev 26 958 28 643 Difference Minimum 57 324 Maximum 66 9219 Mean 6 16919 Standard dev 14 4999 Correlation between files 0 and 1 0 865696 2 4 3 MM5 Files It can be useful to get information from MM5 file in particular to modify the configuration file MM5 meteo cfg see Section 3 4 5 To do so two programs are provided e MM5_var list gives a list of all variables stored in a MM5 file It also gives miscellaneous information about the file Information provided can be needed in preprocessing step program MM5 meteo Section 3 4 5 number of space steps time step and projection type e get_info_MM5 gives the minimum maximum mean and standard deviation of a variable stored in a MM5 file use program MM5_var_list to know what variables are stored in the file For instance the output of MM5_var_list for the file MM5 2004 08 09 used in the Eulerian test case see Section A is Metadata 999 means unknown OUTPUT FROM PROGRAM MM5 V3 11 TERRAIN VERSION 3 MM5 SYSTEM FORMAT EDITION NUMBER 1 TERRAIN PROGRAM VERSION NUMBER 6 TERRAIN PROGRAM MINOR REVISION NUMBER O COARSE DOMAIN GRID DIMENSION IN 1 N S DIRECTION 76 COARSE DOMAIN GRID DIMENSION IN J E
53. Directory where the output files are stored Species Number of species for which data are provided 54 CHAPTER 3 PREPROCESSING The program must be launched with dep emberson general cfg dep emberson cfg 20040809 3 6 Emissions Emissions are generated on the basis of land data anthropogenic emissions and meteorological fields biogenic emissions The programs must be launched after meteorological and ground preprocessing For Gaussian models a preprocessing step may also be required in case line emissions are included see Section 3 9 1 3 6 1 Mapping Two Vertical Distributions distribution Program distribution may be used to define the distribution of emissions along the vertical It reads the vertical distribution of emissions in some input grid and maps this distribution on an output vertical grid Thus it generates a file with the vertical distribution of emissions in the output grid It is based on AtmoData function ComputeVerticalDistribution Running this program is not compulsory Even if the vertical distribution of emissions is required to compute anthropogenic emissions program emissions the vertical distribution can be generated by other means including by hand domain Nz Number of output vertical levels Vertical_levels Path to the text file that stores the altitudes in m of output level interfaces hence Nz 1 values are read EMEP Nz_in Number of input vertical levels
54. F luc glcf In order to prepare land use cover from GLCF one should use program luc glcf It is rec ommended to download the global land use cover file at 1 km resolution provided in latitude longitude coordinates At the time this documentation is written the file is available at ftp ftp glcf umiacs umd edu glcf Global_Land_Cover Global gl latlong 1km landcover gl latlong 1km landcover bsq gz single line no white space you may use wget to download it or copy and paste the URL in your favorite browser You need to uncompress this file e g gunzip gl latlong 1km landcover bsq gz Finally you have to fill the configuration file luc glcf cfg Note that the default values in section GLCF are for file gl 1atlong 1km landcover bsq no need to change them if you downloaded this recommended file paths Database_luc glcf Directory where the raw data from GLCF can be found directory where gl latlong 1km landcover bsq lies LUC_in Name of the file containing raw data i e gl latlong 1km landcover bsq or its new name if you re named it Directory _luc glcf Output directory LUC_out Output filename The default filename LUC glcf bin is recom mended for clarity GLCF Step Space step in degrees in GLCF input file x_min Minimum longitude in the input file degrees ymin Minimum latitude in the input file degrees Nx Number of cells along longitude in the input file Ny Number of cells along latitude in t
55. G Vertical_levels Database_MM5_meteo Roughness_file Directory_meteo t_min Delta_t Nt x_min Delta_x Nx ymin Delta_y Ny Nz projection_type Horizontal_interpolation Dot_coordinates Relative_humidity_threshold Low_cloud_top_max domain File containing the parameters alpha and beta used to compute the pressure at various levels and the alti tudes Note that for most preprocessing programs this field designates file preprocessing levels dat but not for this specific application for which you can use file preprocessing meteo hybrid_coefficients dat paths Directory in which MM5 input files may be found If amp D appears in the file name it is replaced by YYYY MM DD where YYYY is the year MM the month and DD the day Path to the binary file that describes roughness heights in meters per month in output grid cells Note that this file is not the output of program roughness Directory where output meteorological files are stored MM5 First hour stored in every MM5 file Time step in hour of data stored in every MM5 file Number of time steps stored in every MM5 file Index in MM5 coordinates of the center of the lower left cell in MM5 grid This is most likely 0 5 Index MM5 coordinates increase along longitude of MM5 grid This is most likely 1 Number of cells or dot points along longitude integer in MMB grid Index in MM5 coordinates of the center of the lower left cell in MM5 grid T
56. IAN MODELS 71 3 Species file it is the same as described before but the sections described for gaussian deposition concern only gaseous species All data concerning aerosol species are added in the following sections e aerosol_species Contains the list of all aerosol species e scavenging constant_aer This section is needed when the type of parameteri zation chosen for the scavenging for aerosol species is constant In that case the scavenging coefficient is assumed to be constant for one particle diameter So the section contains the index of one diameter followed by the corresponding value of the scavenging coefficient in s Only one diameter per line must be provided e deposition_constant_aer This section is needed when the type of parameteriza tion chosen for the deposition of aerosol species is constant It contains the index of a diameter followed by the value of its deposition velocity in ms Only one diameter per line must be provided e density_aer It contains the density of the aerosol species That is the name of each aerosol species followed by the corresponding density in kgm gt Only one species per line must be provided This section is needed in order to calculate the gravitational settling velocity of a particle The calculated deposition velocity of one species of a given diameter is therefore a combination of the diffusive part given in the section deposition_constant_aer and the gravitational
57. It cannot be more If you want to load all available steps put 0 Nt will be deduced from the file size and other dimensions Nx Ny and Nz If you do so please check the number of steps that are actually read by AtmoPy if the number of steps is surprising check Nx Ny and Nz in your configuration file x min Abscissa longitude of the center of the lower left cell It is primarily used to load a background map in figures Delta_x Space step along x longitude It is primarily used to load a background map in figures Nx Number of cells along z ymin Ordinate latitude of the center of the lower left cell It is primarily used to load a background map in figures Delta_y Space step along y latitude It is primarily used to load a background map in figures Ny Number of cells along y Nz Number of vertical layers file Path to the binary file containing the data Here is an example of such a configuration file where the data to be read is in results 03 bin e g ozone at ground level in Nt x_m y_m Nz fil put 121 in 10 0 Delta_x 0 5 Nx 67 in 35 Delta_y 0 5 Ny 46 1 e results 03 bin Note that general cfg polair3d cfg contain similar entries You may simply copy and paste these entries The number of time steps and vertical layers might be different For instance polair3d cfg contains the number of model layers not necessary the number of levels in t he target file P
58. Needed for sqrt see below gt gt gt print sqrt d d_ref d d_ref mean Elementwise multiplication 22 6488311576 gt gt gt print d 10 25 d_ref 10 25 min Selected time steps 78 5329427719 gt gt gt print d 0 23 34 d_ref 0 23 34 max Selected cell in the middle of the domain 1 01527786255 Python Commands Visualization Using AtmoPy gt gt gt from atmopy import Loads AtmoPy gt gt gt from atmopy display import Loads AtmoPy submodule display gt gt gt from pylab import Matplotlib is needed for figure and plot gt gt gt d getd disp cfg d is a 4D array gt gt gt m getm disp cfg Loads the background map an empty figure should pop up gt gt gt disp m d 2 0 Displays data at the third time step and first level gt gt gt disp m d 2 1 Next vertical level gt gt gt figure Another figure gt gt gt disp m d 0 0 vmin 0 vmax 200 Data range for the color bar gt gt gt dispcf m d 10 0 With contours gt gt gt dispcf m d 10 0 V 10 With ten contours gt gt gt dispcf m d 10 0 V O 50 100 150 200 Sets the contours gt gt gt disp m d 10 0 interpolation nearest No interpolation 7 1 GRAPHICAL OUTPUT 119 Figure 7 1 shows the result of dispcf with 25 contours Without disp or dispcf in case there is no background map e g at small scale gt gt gt conto
59. Polyphemus 1 1a User s Guide CEREA ENPC EDF R amp D Meryem Ahmed de Biasi Vivien Mallet Ir ne Korsakissok Edouard Debry Lin Wu http www enpc fr cerea polyphemus polyphemus cerea enpc fr Contents 1 Introduction and Installation 9 1 1 Polyphemus Overview E2 Requirements sai a IA A eee A 11 137 Installation it de a ed ae A de BE SA a 12 13 1 Main instructions gana ee le si la bg ts a iia ES ad 12 1 32 AGMOPY on cot a ee ee ol le ee Bs a ee lS 13 dd NEWLAND case Bek ak ee Ele ok BA Shak ek ee A 13 1 34 Fortran Subro tin s paria fb s Po ee hy Ae ae ee es 14 2 Using Polyphemus 17 Za Remark Tr a pele ee ee ce at ap aS Ni cage a OS eesti end A ae ee aga 17 2 2 Configuration Pileggi o a ee Soke a He Be oe Bd 17 22 1 Definitions s ge aes A RAG Ro Pee ae 17 2 22 Flexibility zoo a a ae a a e a OE ee a 17 LD Comments A oa ee 19 22A Markups 23 ac a ety ete ei be oR a Mae a E ee A D 19 2210 HSCCHONS 3 as thas te had oy Bode ra ake a eee a Hod es Bee a 20 2 2 6 Multiple Files 2 263 4 aa ale Se a las See es 20 224 Dates 0 bose fees Lhe as Soe A eee Ee aA 21 2 28 t Booleans iiaee o Boe a ks Re Gy A Boa PP ede ES 21 2 3 Running Programs gos cece als Ms a bead ek Sea alpen AA de 21 2 3 0 Compiling Programs 62 4 8 Seca peak kao a ee ee Bad ace ay 21 2 3 2 Runninga Program oea amon ior e a a de ae a 21 2 33 Sharing Configuration 22 2 3 4 Notes about Models s
60. RACM SIREAM also needs Fortran routines but a specific makefile is provided for simulations using this module If you are not confident with your own changes have a look at the examples it is likely that you find a close combination there In case you try an unusual combination you may contact polyphemus cerea enpc fr The directory named driver example provides examples of configuration and data files to use with the programs These examples should be launched in directory driver Their outputs will then be stored in driver results so make sure that this directory exists before you start the simulation indeed Polyphemus programs do not create directories before saving results 2 4 Useful Tools A few useful tools are provided in directory Polyphemus utils Here is a brief explanation of their aim and their use 2 4 USEFUL TOOLS 25 2 4 1 Information about Binary Files Two programs provided in Polyphemus utils are meant to provide information about the content of binary files It is highly recommended to use these programs to check the output files of preprocessing programs and drivers models e g in Section 2 5 6 These two programs perform the same thing but on binary files with different floating pre cision e get_info float gives the minimum maximum and mean of a binary file in single precision e get_info_double gives the minimum maximum and mean of a binary file in double pre cision It is assumed that the binary fi
61. SaverUnitPoint and Saver UnitPoint_aer The saver units SaverUnitPoint and SaverUnitPoint_aer are used to save concentrations at a list of given points There are two possible types indices_list saves concentrations at given indices in the simulation grid provided in the main configuration file in section domain and coordinates_list saves concentrations at given cartesian coordinates and is available for Gaussian models only In case the saver is of type coordinates_list the simulation grid is still 4 7 OUTPUT SAVERS 83 read but is not used as concentrations are computed directly at each point of interest The list of points where concentrations are to be saved has to be specified in the section save of the saver configuration file It has to be written just after the line containing the field Output_file The list begins with the field Indices in case the saver type is indices list and Coordinates if the type is coordinates_list In both cases the list must end with a line containing the field Point_file which is used to specify a file name where the list of all points where concentrations are saved is to be written during the simulation This looks like Type indices_list Levels 0 2 Output_file lt Results gt amp f bin Indices 0 0 5 15 20 25 30 30 Point_file lt Results gt point txt One line corresponds to one point There can be either two or three indices In case there are two indices on the line the first
62. Should concentrations be averaged over Interval_length If not Initial_concentration Should initial concentrations be saved This option is only avail For aerosol species the saver should be SaverUnitDomain_aer and the Type domain_aer The section save is very similar to the one for gaseous species except that you have to specify for which diameters the concentrations are saved Hence the list of species to be saved looks like this Species aer1_10 aer 1_ 2 aer2_ 0 1 In that case the species named aerl is to be saved for the diameter of indices 0 and 2 and aer2 for the diameters of indices 0 and 1 In Output_file amp f will be replaced by the species name and amp n by the bin index You can use any symbol which is not a delimiter or even nothing to separate the species name from the bin index even though amp f_ amp n bin is the advised form If Species is set to all the concentrations will be saved for all aerosol species and for all diameters 4 7 3 SaverUnitSubdomain and Saver UnitSubdomain_aer These saver units allow the user to save concentrations only over an horizontal subdomain for example if they perform a simulation over the whole of Europe but only want the concentrations over one country or region Their Type is subdomain and subdomain _aer respectively The user must provide between which indices for x and y they want to save concentrations The specific parameters fo
63. Species name Species_name Iodine Source rate mass s Rate 56 5 Source velocity m s Velocity 10 1 Source temperature Celsius degrees Temperature 60 Source section m2 Section 5 725 In this example only one section is provided but other sources may be added simply by adding the corresponding sections at the end of the file One species may have several sources The source file can contain a list of point sources provided by the user or a discretized line source In that case it corresponds to the output file of the discretization preprocessing program discretization 5 1 3 Vertical Levels plume level dat Vertical levels are defined in a single data file They are defined by their interfaces This means that the file contains Nz 1 heights where Nz is the number of levels specified in the main configuration file The concentrations are computed at layers mid points 5 1 4 Species gaussian species dat Species are listed in the section species of a data file the same as the species data file used in the preprocessing program gaussian deposition see Section 3 9 2 When radioactive or biological decay is taken into account a section containing the half life times of the species has to be provided The section radioactive_decay contains the list of all species followed by their half life time in days put 0 in the case of non radioactive species Provide only one species per line The section biologic
64. X m3 m73 TOTAL SOIL MOIS IN LYR 4 4 SOIL Wi 2 76 86 Cc YX m 3 m 3 SOIL LQD WATER IN LYR 1 4 SOIL W2 2 76 86 Cc YX m 3 m73 SOIL LQD WATER IN LYR 2 4 2 4 USEFUL TOOLS SOIL W3 2 76 86 C YX m 3 m73 SOILW 4 2 76 86 C YX m 3 m 3 CANOPYM 2 76 86 C YX m WEASD 2 76 86 C YX mm SNOWH 2 76 86 C YX m SNOWCOVR 2 76 86 C YX fraction ALB 2 76 86 C YX fraction GRNFLX 2 76 86 Cc YX W m 2 VEGFRC 2 76 86 C YX fraction SEAICE 2 76 86 C YX DIMENSIONLESS SFCRNOFF 2 76 86 Cc YX mm UGDRNOFF 2 76 86 C YX mm T2 2 76 86 C YX K Q2 2 76 86 C YX kg kg 1 U10 2 76 86 Cc YX m st 1 V10 2 76 86 C YX m s 1 ALBD 2 27 2 CA PERCENT SLMO 2 27 2 CA fraction SFEM 2 27 2 CA fraction SFZO 2 27 2 CA cm THERIN 2 27 2 CA 100 cal cm 2 K 1 s71 2 SFHC 2 27 2 CA J m 3 K7 1 SCFX 1 27 CA fraction SIGMAH 1 25 H S sigma Total number of time steps read in the file 97 For each variable is provided e its name e its number of dimensions e its length along dimension 1 if applicable e its length along dimension 2 if applicable e its length along dimension 3 if applicable e its length along dimension 4 if applicable 29 SOIL LQD WATER IN LYR 3 4 SOIL LQD WATER IN LYR 4 4 CANOPY MOISTUR E CONTENT WATER EQUIVALENT SNOW DEPTH PHYSICAL SNOW DEPTH FRACTIONAL SNOW COVER ALBEDO GROUND HEAT FLUX VEGETATION COVERAGE SEA ICE FLAG SURFACE RUNOFF UNDERGROUND RUNOFF 2 meter Temperature 2 meter Mixing Ratio 10 meter U Co
65. _constant the corresponding error covari ance matrix is a diagonal matrix of which the diagonal elements are error variances Error variance for background concentrations The unit for the option value is ug m Balgovind scale background Balgovind scale for background error covariance The model grid Model_error_variance Balgovind_scale_model interval is chosen to be the unit for option values Error variance for model simulations in ug m Balgovind scale for model error covariance The model grid inter val is chosen to be the unit for option values The data file is the same as in Section 5 6 2 the species and levels files are the same as those presented in Section 5 6 3 5 9 CastorTransport 5 9 1 Main Configuration File castor cfg Model CastorTransport is based on IPSL model Chimere Its option are provided in a config uration file Date_min Delta_t Nt x_min Delta_x Nx ymin Delta_y Ny Nz domain Starting date in any legal format see Section 2 2 7 The date can therefore include seconds Time step in seconds Number of iterations of the simulation integer Abscissa of the center of the lower left cell Provide a longitude in degrees or in case Cartesian coordinates are chosen an abscissa in meters Step length along z in degrees longitude or in meters for Cartesian coordinates Number of cells along x integer Ordinate of the center of the lower left cell Provid
66. _mode The expected rank number column number of the square root mode matrix of forecast error covariance matrix Number_model_mode The number of the columns of the square root of model error co variance matrix to be added to the mode matrix 78 CHAPTER 4 DRIVERS Number_observation_mode The number of the columns of the square root of observation error covariance matrix to be added to the analyzed mode matrix Propagation_option The option for the forecast of the columns of mode matrix Only finite difference is supported Finite_difference_perturbation Perturbation coefficient for mode forecast using finite difference method set to 1 Model perturbations are employed to generate the columns of the square root of model error covariance matrix see PerturbationManager configurations in Section 4 9 4 5 5 FourDimVarDriver It is the driver dedicated to data assimilation applications using four dimensional variational as similation algorithm 4D Var The assimilation period is from time step 0 to Nt_assimilation 1 The optimal model state at initial time step is obtained by minimizing an objective function which is the background departure plus discrepancy between model simulations and observations during the assimilation period The model is supposed to be perfect thus no model error terms are considered The gradient of the objective function is calculated efficiently using adjoint model of the underlying model The algo
67. a processing atmopy AtmoPy is a Python library for statistical analysis and visualization common functions used to parse and manage the arguments of preprocessing pro grams models chemistry transport models to be used by the drivers modules common a base module from which transport and chemistry modules derive transport numerical schemes for advection and diffusion chemistry chemical mechanisms utils useful tools mostly to get information on binary files Polyphemus is an open source software distributed under the GNU General Public License It is available at http www enpc fr cerea polyphemus Polyphemus development and sup port team can be contacted at polyphemus cerea enpc fr 1 2 Requirements Polyphemus is designed to run under Unix or Linux based systems It should be able to run under Windows AtmoPy has been tested under Windows and the Eulerian model Polair3D has been compiled with Microsoft Visual Studio NET 2003 There is no obvious reason why other parts of Polyphemus should not work under Windows Polyphemus is based on three computer languages C Fortran 77 and Python There are also a very few lines of C Supported C compilers are GNU GCC G 3 2 3 3 3 4 4 0 and 4 1 GNU GCC 2 x series is too old to compile Polyphemus Intel C compiler ICC versions 7 1 and 8 0 should work Any other decent C compiler compliant with the standard should compile Polyphemus If not please report to pol
68. air3DChemistry cxx in models e 1414 and 415 comment out if this gt option_process with_chemistry Chemistry_ Init this e 1601 comment out Chemistry_ Forward this And finally compile the file polair3d siream cpp using the makefile makefile siream provided A specific makefile has been provided because ChemistryRACM_SIREAM redefines some Fortran routines defined by ChemistryRACM ChemistryRACM_SIREAM This chemistry module is used for gas and aerosol species for general purposes as air quality modeling and risk assessment The gas chemistry is solved with the RACM Stockwell et al 1997 mechanism and the aerosol dynamics by the SIREAM model Debry et al 2006 When a cloud is diagnosed in one cell of the domain then instantaneous aerosol activation is assumed and the SIREAM model is replaced by the VSRM cloud chemistry model Fahey and Pandis 2003 The number of aerosol bins is directly inferred from the number of bounds provided by the Bin_bounds option in main configuration file polair3d cfg Further options are required in this configuration file options With_pH Does the aerosol module returns cloud droplet pH Scavenging model Which below cloud scavenging model is used Lwc_cloud_threshold Liquid water content threshold for clouds With_coagulation Is coagulation taken into account With condensation Is condensation taken into account With nucleation Is nucleation taken into account Fixed aerosol dens
69. al scales many pollutants from non reactive species to particulate matter several chemistry transport models a bunch of advanced methods in data assimilation and ensemble forecasting model integration Further details are available in Mallet V Qu lo D and Sportisse B 2005 Software architecture of an ideal modeling plat form in air quality A first step Polyphemus Technical Report 11 CEREA Polyphemus is made of data processing abilities available in libraries a library for physical parameterizations library AtmoData programs to compute input data to chemistry transport models chemistry transport models drivers that is object oriented codes responsible for driving models in order to perform for instance simulations and data assimilation programs to analyze and display output concentrations primarily based on the library AtmoPy Its flowchart is shown in Figure 1 1 in which three steps may be identified 1 preprocess ing interpolations physical parameterizations 2 model computations possibly with data assimilation or any other method implemented in a driver 3 postprocessing comparisons to measurements statistics visualization 10 CHAPTER 1 INTRODUCTION AND INSTALLATION Polyphemus Database Data processing libraries AtmoData SeldonData Input data processing Files Numerical Statistics integration AtmoPy Computes
70. al_decay contains two values following each species name the first corresponding to its half life time in s during daytime and the second to the value during nighttime put 0 in the case of non biological species Here is an example species List of the species Caesium Iodine biol radioactive_decay 90 CHAPTER 5 MODELS Half life of the species Unit days 0 coresponds to non radioactive species Caesium 1 1e4 Iodine 8 04 biol 0 biological_decay Half life of the species Unit seconds First value day second value night 0 corresponds to non radioactive species Caesium 0 0 Iodine 0 0 biol 1000 500 In that case we have two radioactive species Caesium and Iodine and one biological species biol If scavenging is taken into account sections scavenging and scavenging constant must be added The section scavenging contains the name of all species for which scavenging occur and scavenging constant their constants in s71 5 1 5 Meteorological data file gaussian meteo dat This file contains basic meteorological information needed to run Gaussian models In case there are scavenging and deposition it is the output file of preprocessing program gaussian deposition described in section 3 9 2 Information that are always needed are e Temperature C e Wind angle from x axis e Wind speed ms e Inversion height m These information are prov
71. and the Gaussian test case respectively B 1 Preprocessing Prior to use Gaussian models you need to compute scavenging coefficients and deposition ve locities for the various species This is achieved by using gaussian deposition _aer First compile it cd Polyphemus preprocessing dep make gaussian deposition_aer Then run it from the test case directory cd TestCase Polyphemus preprocessing dep gaussian deposition_aer config gaussian deposition_aer cfg The output on screen will be Reading configuration file done Reading meteorological data done 131 132 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE Reading species done Reading diameter done Computation of the scavenging coefficients done Computation of the deposition velocities done Writing data done The file gaussian meteo_aer dat has been created in the directory TestCase config It will be used for all simulations Note that if your simulation only involves gaseous species you can use the preprocessing program gaussian deposition Here we use gaussian deposition_aer because its output can be used for simulations with or without aerosol species B 2 Discretization This step is only necessary for the simulation with a line source Its aim is to discretize this source into a series of puffs To do so compile the preprocessing program discretization cd Polyphemus preprocessing emissions make discretization Then run it from
72. another set of land use categories This means for example summing up the contributions of sparsely vegetated and bare ground tundra USGS categories 19 and 22 to estimate the proportion of barren land in Wesely description category 8 An input category may also be split into several output categories In practice one may want to convert in Wesely or Zhang land use cover using luc convert In particular it is necessary to convert land data from USGS or GLCF to Zhang categories before computing deposition velocities with program dep see Section 3 5 1 In addition to the domain definition Section 3 2 2 below is the information required in the configuration file or configuration files for luc convert paths Database_luc convert Directory where the input file input land use categories is located File_in Input file name in Database_luc convert Directory _luc convert Directory where the output file output land use categories should be stored File_out Output file name in Directory_luc convert dimensions Nc_in Number of land categories in the input format Nc_out Number of land categories in the output format coefficients Correspondence matrix between input land categories and output land categories Each line corresponds to an input category Each line contains the index of the category or any number this first column is not read and the distribution of the input category in all output categories columns The distr
73. ap and AtmoPy Please refer to Sections 1 2 and 1 3 for system wide installation notes Below are installation notes for the user IPython and Matplotlib Matplotlib is a Python 2D plotting library which produces high quality figures On its website http matplotlib sourceforge net you may find help for all Matplotlib commands You may also find many useful examples Sections Screenshots and Examples zip a complete tutorial a useful FAQ an interesting cookbook wiki and other resources We highly rec ommend the use of Matplotlib actually imported through module pylab see below together with IPython enhanced Python shell http ipython scipy org to benefit from a powerful interactive mode Once IPython NumPy and Matplotlib installed launch IPython with command ipython IPython needs to be launched once to complete its user installation You should get the prompt In 1 If you are aware of Python you can execute Python commands from this prompt Now try to import Matplotlib In 1 from pylab import If no error occurs your installation is mostly complete Quit Python ctr1 d and RET Now edit Matplotlib configuration file Under Linux or Unix it is located in matplotlib matplotlibrc Under Windows it is in C Documents and Settings yourname matplotlib You should find the entries numerix and interactive Edit them if necessary warning it is case sensi tive so that you have nume
74. ase 1 0 data meteo amp f bin VerticalDiffusion u cergrene a ahmed dm TestCase 1 0 data meteo Kz_TM bin It is assumed that all binary files start at the same date and this date is Date min see dates formats in Section 2 2 7 The time step is Delta_t in seconds Then a list of fields is provided after Fields These are fields that the model needs and their names are determined by the model Below all fields required by the model depending on its options are listed A generic path full file name is then provided entry Filename In this path the shortcut amp f refers to a field name In the previous example the full path to the temperature is u cergrene a ahmed dm TestCase 1 0 data Temperature bin In the specific case of boundary conditions the shortcut amp c is replaced by x y and z If a few fields are not stored in a file with a generic path their specific paths can be provided after the entry Filename This is the case for VerticalDiffusion in the previous example Note that 1 entries Fields Filename and additional paths must be at the end of the section and in this order 2 at least one element possibly not a required field must be provided to Fields and at least one element possibly not a path to Filename for instance Fields Filename means no generic path but Fields Illegal one element required Filename Illegal one element required In most sections Fields is used
75. ationManager o 85 4 8 2 SimObservationManager 1 2 2 0 000 eee ee ee ee 85 4 9 Perturbation Manager 86 5 Models 87 Del GatissianP lume arii y nak he ee ee et oR ee hg Bt a oe as eee ds 87 5 1 1 Configuration File plume cfg 87 5 1 2 Source Description plume source dat o 88 5 1 3 Vertical Levels plume level dat o o 89 5 1 4 Species gaussian species dat o 89 5 1 5 Meteorological data file gaussian meteo dat 90 5 2 GaussianPlime a r s o s soa ekoe a a aa a 91 5 2 1 Configuration File plume aer C 8 92 5 2 2 Source Description plume source_aer dat o o 92 5 2 3 Vertical Levels plume level dat o o 92 5 2 4 Species gaussian species aer dat o o o 92 5 2 5 Diameters diameter dat eee eee ne 92 5 2 6 Meteorological data gaussian meteo dat o o 92 5 3 Gaussian Putt sorg a A A ee ol Ra en al ai 92 5 3 1 Configuration File puff cfg 000 92 5 3 2 Puff Description pull dat e 93 5 3 3 Vertical Levels Species and Meteorological data 94 5A Gaussian Paithaer ies cs a te a At ea A et a 94 5 4 1 Configuration File puff_aer cfg 94 5 4 2 Source Description puff_aer dat e 94 5 4 3 Vertical Levels
76. background state It involves with observation managements described in Section 4 8 and storage man agements of forecast and analysis results see for instance Section 4 7 4 The background error covariance matrix can be either diagonal or generated by Balgovind correlation functions see Section 5 8 4 5 3 EnkKFDriver It is the driver dedicated to data assimilation applications using ensemble Kalman filter algo rithm It consists of two steps forecast and analysis It differs from optimal interpolation in that the background error covariance is flow dependent and approximated by an ensemble of perturbed model forecast The algorithm parameters are set in section EnKF EnKF Number_ensemble The number of samples in the ensemble With_observation_perturbation ensemble With_positivity_requirement If positivity of the assimilated species concentrations is required If observations are perturbed for consistent statistics for analyzed The generation of the ensemble is detailed in PerturbationManager configurations see Sec tion 4 9 4 5 4 RRSQRTDriver It is the driver dedicated to data assimilation applications using reduced rank square root Kalman filter algorithm RRSQRT It consists of two steps forecast and analysis The back ground error covariance is flow dependent and approximated by an explicit low rank represen tation The algorithm parameters are set in section RRSQRT RRSQRT Number_analysis
77. base BDQA Pioneer Directory where observations are stored output Name of the station for which concentrations and observations are displayed 7 2 POSTPROCESSING FOR GASEOUS SPECIES 121 t_range concentrations paired daily_basis y range scatter meas_style sim_style select_station measure cutoff ratio output Dates for which concentrations and observations are displayed What kind of concentrations are displayed hourly daily or peak concentrations Should peak concentrations be paired in time In case daily concentrations are chosen are observations provided on a daily basis If two numbers are provided they define the axis range along y and along x for scatter plots If only one number is provided the axis ranges are automatically set Is there a scatter plot See the configuration file for the various options Style for the display of measurements Style for the display of simulated data Which stations are involved in statistical measures Either set to single for a single station defined in station all for all stations or a couple Field Value for all stations for which Field is equal to Value Statistical measures to be applied to data see configuration file for all measures available All observations below cutoff are discarded All stations for which the ratio between the number of available observations and the total number of time steps is below ratio are discarded For ins
78. btained using Python and AtmoPy unit is ug m You can create other data if you like to visualize concentrations for other species In that case the map has already been created and less information is needed to create the data In particular it is not necessary to provide a file disp cfg d2 getd filename NO bin Nt 22 Nz 1 Ny 33 Nx 65 disp m d2 7 0 Appendix B Polyphemus Gaussian Test Case This document explains how to proceed to perform simulations using the test case for Gaussian models provided with Polyphemus When the archive TestCase 1 0 Gaussian tar bz2 is extracted a directory TestCase 1 0 Gaussian is created It is referred to below as TestCase tar xjvf TestCase 1 0 Gaussian tar bz2 The subdirectory config holds all configuration files necessary and the subdirectory results is meant to store the results of simulations It is divided in three subdirectories one for each pos sible simulation puff_line for the Gaussian puff model and a gaseous line source puff _aer for the puff model with point sources of gaseous and aerosol species and plume for the Gaussian plume model with gaseous species only In each of those subdirectory a python program which allows to visualize some results easily can be found To launch the test cases you do not need to modify the configuration files You just have to make sure to replace Polyphemus and TestCase by your path to the last version of Polyphemus
79. c Situation 3 4 0e 01 3 5e 01 3 0e 01 2 5e 01 2 0e 01 1 5e 01 1 0e 01 5 0e 02 0 0e 00 2 5e 01 2 0e 01 1 5e 01 1 0e 01 5 0e 02 0 08 00 POLYPHEMUS GAUSSIAN TEST CASE 0 0e 00 80 100 120 140 160 180 b Situation 2 2 5e 01 2 0e 01 1 5e 01 1 0e 01 5 0e 02 80 100 120 140 160 180 SOROD d Situation 4 Figure B 1 Plume for the various meteorological situations B 4 3 Gaussian Puff with Line Source Launch the python script to display the results cd TestCase python results puff_line display_puff py This create 4 figures in results puff_line e linepuff meteol gives the concentration for the first meteorological situation e linepuff meteo2 gives the concentration for the second meteorological situation e linepuff meteo3 gives the concentration for the third meteorological situation e linepuff meteo4 gives the concentration for the fourth meteorological situation Concentrations are given for lodine at t 4s middle of the simulation Figure B 3 shows what is displayed B 4 RESULT VISUALIZATION 137 2 0e 21 asl 12e 19 sl 1 0e 19 SOL sal 15e 21 8 0e 20 15 st 1 0e 21 6 0e 20 10F 10 4 0e 20 5 0e 22 st 5 2 0e 20 o 10 20 30 20 50 0 0e 00 o 10 20 0 0e 00 a Situation 1 Concentration at t Os t 3s and b Situation 2 Concentration at t Os t 3s and t 8s t 8s 1 2e 22 25 1 0e 02 1 0e 22
80. c boundary layer 0 1 in Troen and Mahrt 1986 Ric Critical Richardson number used to estimate the atmospheric Fluxes diagnosed BL_diag TM_stable boundary layer height in case BL_diag is set to 2 Should the friction module the evaporation and the sensible heat be diagnosed If not they are read in input data which is recom mended What kind of diagnosis is used to estimate the boundary layer height Put 1 to use Troen and Mahrt diagnosis Troen and Mahrt 1986 put 2 to rely on a critical Richardson number and put 3 to use ECMWF or MM5 boundary layer height so there is no diagnosis this option is more robust and it is recommended The vertical diffusion as computed by Troen and Mahrt parame terization is applied only within the boundary layer It is possible to further restrict its application if TM_stable is set to no the parameterization is not applied in stable conditions In this case the Troen and Mahrt parameterization is only applied in unstable boundary layer Several meteorological fields are computed with ComputePotentialTemperature ComputeSaturationHumidity and ComputeSurfaceHumidity diag If fluxes are not di agnosed the Monin Obukhov length is computed with ComputeLMO Then the boundary layer height may be diagnosed with ComputePBLH_TM Troen Mahrt parameterization or ComputePBLH Richardson critical Richardson number Finally the vertical diffusion coefficients are computed with C
81. cies in Mozart 2 files and the name of species in simulation In this file the first column contains Mozart 2 species After each Mozart 2 species name the corresponding output species e g RACM species is put if any If Mozart 2 species gath ers two output species put the names of all output species followed by their proportion in Mozart 2 bulk species For instance the line C4H10 HC5 0 4 HC8 0 6 splits Mozart 2 species C4H10 into HC5 40 and HC8 60 Three ex amples are provided preprocessing bc species_v1 dat preprocessing bc species_v2 dat and preprocessing bc species_v3 dat File providing the molecular weights of output species Program bc processes an entire Mozart 2 output file If this file contains concentrations for 10 days the program generates boundary conditions for 10 days The program must be launched with bc bc cfg general cfg net libre adjoint mallet mozart h0067 nc The last argument is the path to the Mozart 2 file You have to select the file to use according to date as what is shown in Section 3 7 3 8 BOUNDARY CONDITIONS 61 The results are stored as amp f_ amp c bin where amp f is replaced by the name of the species and amp c by the direction associated with the boundary condition x y or z For example the concentrations in 03_x bin are interpolated at both ends of the domain along x for all grid points along y and z 3 8 2 Boundary Conditions for Aerosol Species bc gocart Boun
82. cloudiness and cloud height are diagnosed using ComputeCloudiness and ComputeCloudHeight Finally attenua tion coefficients are computed with ComputeAttenuation_LWC RADM parameterization or ComputeAttenuation ESQUIF ESQUIF parameterization The vertical diffusion coefficients are computed with ComputeLouiskz Louis 1979 Finally photosynthetically active radiation are estimated based on solar radiation and zenith angle ZenithAngle Among output files one may find e the pressure and the surface pressure in Pa e the temperature the surface temperature and the skin temperature in K e the meridional and zonal winds MeridionalWind bin and ZonalWind bin in ms e the Richardson number and the surface Richardson number e the boundary layer height in m e the vertical diffusion coefficients time dependent 3D field defined on layer interfaces on the vertical Kz_Louis bin in m s e the specific humidity in kgkg e the liquid water content in kgkg e the cloud attenuation coefficients 3D field Attenuation bin in 0 2 e the solar radiation intensity SolarRadiation bin in Wm e the rain intensity Rain bin in mmh e the convective rain intensity ConvectiveRain bin in mmh e the cloud height in m 3 4 6 Program MM5 meteo castor Program MM5 meteo castor processes MM5 data and generates meteorological fields required by chemistry transport model Castor 50 CHAPTER 3 PREPROCESSIN
83. configuration files done Memory allocation for grids done Memory allocation for output data fields done Conversion from sigma levels to heights done Converting from latlon to MM5 indices done Applying transformation to read fields done Computing pressure done Computing surface pressure done Interpolations done Computing Richardson number done Computing attenuation 128 APPENDIX A POLYPHEMUS EULERIAN TEST CASE Computing relative humidity and critical relative humidity done Computing cloud profile done Computing attenuation done Linear interpolations Attenuation SpecificHumidity Liquid Water content CloudHeight SurfaceTemperature SkinTemperature SoilWater SensibleHeat Evaporation SolarRadiation Rain FrictionModule BoundaryHeight done Computing Kz done Computing PAR done Writing data done If you want to compute vertical diffusion using Troen and Mahrt parameterization compile and execute Kz_TM make Kz_TM Kz_TM TestCase config MM5 meteo cfg TestCase config general cfg 20040809 The output on screen will be Reading configuration files done Memory allocation for data fields done Extracting fields done Computing Kz done Writing output files done A 5 Launching the Simulation A 5 1 Modifying the Configuration File You should check and modify polair3d cfg if necessary You have to check
84. cording to the type of land urban forests and other categories For instance in an EMEP cell emissions are distributed so that the ratio between total urban emissions and total emissions is Urban_ratio on top of the sum of Urban_ratio Forest_ratio and Other_ratio Temporal Factors EMEP emissions are provided as annual values They are multiplied by temporal factors to estimate their time evolution as function of month week day and hour in all emission sectors and in all countries Here are examples on how these factors should be provided e monthly _factors dat gives the factors for each country index CC each activity sector SNAPsector and each month Formate CC SNAPsector JAN FEB MAR APR MAY JUN JUL 2 1 1 640 1 520 1 236 1 137 0 798 0 459 0 393 e weekdays_factors dat gives the factors for each country index CC each activity sector SNAPsector and each day of the week Formate CC SNAPsector MON TUE WED Thu FRI SAT 2 1 1 0159 1 0348 1 0399 1 0299 1 0298 0 9651 0 8846 e hourly factors dat gives the factor for each activity sector SNAPsector and each hour 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 1 1 01 0 1 01 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 01 0 1 01 0 In addition to these factors a file called time_zones dat is necessary It gives the various countries in EMEP inventories and their time zone offset to GMT Please note that the list of countries in the inventories may vary without warnings If
85. dary conditions for aerosol species are obtained using Gocart model thanks to the program bc gocart Gocart format and conventions Gocart model usually provides files with the following naming convention file name signification yyyymm XX vs g 6 hourly concentrations in gm yyyymm XX vs g day daily averaged concentrations in gm yyyymm XX vs g avg monthly averaged concentrations in gm where yyyymm is the year and month e g 200103 XX is the Gocart species which can be either SU sulfur CC carbonaceous DU dust SS sea salt and vs is the version e g STD tv12 Gocart species may have further speciations e SU sulfur Total 4 1 DMS 2 502 3 SO4 4 MSA e CC BC 0C Total 4 1 hydrophobic BC 2 hydrophobic OC 3 hydrophilic BC 4 hydrophilic OC e DU dust Total 5 1 Re 0 1 1 2 Re 1 1 8 3 Re 1 8 3 4 Re 3 6 5 Re 6 10 um The first group 0 1 1 um contains the following subgroups 0 10 0 18 um fraction 0 01053 0 18 0 30 um fraction 0 08421 0 30 0 60 um fraction 0 25263 0 60 1 00 um fraction 0 65263 e SS sea salt Total 4 1 Re 0 1 0 5 2 Re 0 5 1 5 3 Re 1 5 5 4 Re 5 10 um The data format of Gocart files is direct access binary 32 bits big endian As an example here is how they should be read in Fortran 77 language dimension Q imx jmx 1mx do k 1 nstep do n 1 nmx read unit nt1 nt2 nn Q end do enddo where http code
86. ding dates of the emissions with format as described in Section 2 2 7 The puff emission is described with entries Quantity and Date It may look like this source Abscissa 5 2 Ordinate 48 5 Altitude 10 Species NO Type continuous Rate 1 Date_beg 2001 04 22_00 05 Date_end 2001 04 22_00 07 source Abscissa 10 3 Ordinate 48 Altitude 80 Species S02 Type puff Quantity 1 Date 2001 04 22_00 05 5 5 3 Vertical Levels and Species Vertical levels are defined in a single data file They are defined by their interfaces This means that the file contains Nz 1 heights where Nz is the number of levels specified in the main configuration file The concentrations are computed at layers mid points Species are listed in the section species of a configuration file In addition some scav enging models needs extra data e The constant model requires a section scavenging coefficient which contains a threshold of rain to apply scavenging in mmh and the name of the species with its associated scavenging coefficient in s for instance 5 6 POLAIR3DCHEMISTRY 99 scavenging coefficient Scavenging is applied above the following threshold over rain mm h Scavenging _rain_threshold 1 Scavenging coefficient of the species s 1 N02 1 e 4 S02 1 e 4 Notice that if the previous lines are replaced by Scavenging coefficient of the species s 1 all 1 e 4 the same scaveng
87. e 0 0833333 LANDUSE DATA RESOLUTION in degree 0 0833333 MM5 Version 3 MM5 System Format Edition Number 1 MM5 Program Version Number 6 MM5 Program Minor Revision Number 1 FOUR DIGIT YEAR OF START TIME 2004 INTEGER MONTH OF START TIME 8 DAY OF THE MONTH OF THE START TIME 9 HOUR OF THE START TIME O MINUTES OF THE START TIME O SECONDS OF THE START TIME O TEN THOUSANDTHS OF A SECOND OF THE START TIME O MKX NUMBER OF LAYERS IN MM5 OUTPUT 25 TIMAX SIMULATION END TIME MINUTES 5760 TISTEP COARSE DOMAIN TIME STEP IN SECONDS 100 TAPFRQ TIME INTERVAL MINUTES THAT DATA WERE SAVED FOR GRIN 60 Outputs Name Dim 1 2 3 44 Stag Ord Units Description U 3 76 86 25 D YXS m s U COMPONENT OF HORIZONTAL WIND V 3 76 86 25 D YXS m s V COMPONENT OF HORIZONTAL WIND T 3 76 86 25 C YXS K TEMPERATURE 28 CHAPTER 2 USING POLYPHEMUS Q 3 76 86 25 C YXS kg kg MIXING RATIO CLW 3 76 86 25 C YXS kg kg CLOUD WATER MIXING RATIO RNW 3 76 86 25 Cc YXS kg kg RAIN WATER MIXING RATIO ICE 3 76 86 25 C YXS kg kg CLOUD ICE MIXING RATIO SNOW 3 76 86 25 C YXS kg kg SNOW MIXING RATIO GRAUPEL 3 76 86 25 C YXS kg kg GRAUPEL MIXING RATIO RAD TEND 3 76 86 25 Cc YXS K DAY ATMOSPHERIC RADIATION TENDENCY W 3 76 86 26 C YXW m s VERTICAL WIND COMPONENT PP 3 76 86 25 Cc YXS Pa PRESSURE PERTURBATION PSTARCRS 2 76 86 C YX Pa REFERENCE SURFACE PRESSURE MINUS PTOP GROUND T 2 76 86 Cc YX K GROUND TEMPERATURE RAIN CON 2 76
88. e a latitude in degrees or in case Cartesian coordinates are chosen an ordinate in meters Step length along y in degrees latitude or in meters for Cartesian coordinates Number of cells along y integer Number of vertical levels integer 104 Vertical_levels Species With_transport With_initial_condition Interpolated_initial_condition With_boundary_condition With_deposition With_volume_emission Data_description Path to the file that defines vertical levels interfaces This field is read but is not used Path to the file that defines involved species and their chemical properties options Is transport taken into account Are initial conditions used If set to yes initial conditions are interpolated from boundary conditions otherwise they are read in binary files data Path to the configuration file that describes input data Are boundary conditions provided Is deposition taken into account Are volume emissions taken into account CHAPTER 5 MODELS 5 9 2 Data Description castor data cfg The data description is very similar to that of Polair3DTransport see Section 5 5 1 except that the data can be different Section initial condition boundary_condition meteo deposition volume_emission Entries Fields Filename Fields Filename Date_min Delta_t Fields Filename Date min Delta_t Fields Filename Date min Delta_t Nz Fields
89. e configuration files These configuration files define simulation domains input and output paths options etc Configurations files are text files preferably with extension cfg They primarily contain fields that is entries associated with values provided by the user In a configuration file a line usually reads field value A practical example is a discretization definition x_min 12 5 Delta_x 0 5 Nx 100 The fields x_min Delta_x and Nx are associated with proper values specified by the user The characters put between a field and its value are delimiters In the previous example the delimiters are blank spaces and equal signs Delimiters are discarded characters They may be put anywhere in a configuration file but they are always ignored Their aims are to delimit words i e fields and values and to make the configuration file clearer 2 2 2 Flexibility The fields and values can be introduced in many ways First many delimiters are supported e blank space e tabulation e line break 17 18 CHAPTER 2 USING POLYPHEMUS e equal sign e colon e semicolon e coma and e vertical bar For example x_min 12 5 Delta_x 0 5 Nx 100 is equivalent to x_min 12 5 Delta_x 0 5 Nx 100 Recall that delimiters can only be used to delimit words and are discarded otherwise It means that a field or a value cannot contain a delimiter The fact that the colon is a delimiter may ra
90. e diameters Concerning the deposition velocity the type can be chosen between e none the deposition velocity is set to 0 for all species e constant the diffusive part of the deposition velocity is constant for one given diameter and entered in the species file The gravitational settling velocity is calculated for each particle given the density and the diameter provided in the species file and the pressure and temperature provided in the meteorological data file Input Files 1 Meteorological data file it is the same as the one for gaussian deposition If the pa rameterization type for the deposition velocity calculation is constant the pressure must be provided in Pa 2 Diameter file it contains the list of particle diameters in um The first number is the diameter of index 0 the second of index 1 and so on This is an example of diameter file Diameter micrometer diameter 0 1 iL The diameter of index 0 corresponds to the value 0 1 um the diameter of index 1 to the value 1 um and so on When referring to a given diameter in the other data files one has to give the corresponding index Note that there is only one diameter file for all aerosol species Therefore all particulate species are assumed to have the same diameter distribution The diameter file can also be the main configuration file In that case the section diameter is simply added to the main configuration file 3 9 PREPROCESSING FOR GAUSS
91. e emitted 5 7 3 Vertical Levels and Species Section 5 6 3 is relevant for Polair3DAerosol In addition there is at least a section added in the file species dat aerosol_species PMD PBC PNA PS04 PNH4 PNO3 PHCL PARO1 PARO2 PALKi POLE1 PAPI1 PAPI2 PLIM1 PLIM2 PPOA PH20 5 8 Polair3DChemistry AssimConc Polair3DChemistryAssimConc is dedicated for a state space formulation of the underlying dy namical model The stochastic modeling is implemented for diverse applications such as data assimilation Polair3DChemistryAssimConc is configured with three configuration files polair3d cfg polair3d data cfg and polair3d saver cfg and two data files levels dat and species dat The four files other than the main configuration file polair3d cfg are the same as those for Polair3DChemistry The main configuration file is an extension of that of Polair3DChemistry The additional parameters are 5 9 CASTORTRANSPORT 103 Species Levels Error_covariance_model Background_error_variance state List of species included in model state vector All species must be on the same line List of vertical levels of model domain included in model state vector All levels must be on the same line data_assimilation Stochastic model for model and background error covariance With option set to Balgovind the corresponding error covariance matrix is calculated using Balgovind correlation function with option set to diagonal
92. e end of condensation Two methods are possible number conserving or interpolation The former conserves the relationship between mass and number concentration in each bin the latter relaxes this relationship Available nucleation models are either binary nucleation H SO H O Vehkam ki et al 2002 or ternary nucleation H SO H O NH Arstila et al 1999 In the aerosol module the aerosol density can be either fixed or recomputed at run time according to option With_fixed_density If set to yes the aerosol density will always be equal to the fixed aerosol density mentioned above if set to no the module will recompute one density for each aerosol bins according to their chemical compositions given by the thermodynamic model Two parameterizations are available to compute wet diameters depending on the option Wet_diameter_estimation If set to Isorropia the aerosol liquid water content computed by the thermodynamic model for instance ISORROPIA is used If set to Gerber a simpler but faster method the Gerber formula is used Note that when Gerber option is used the aerosol density is fixed for all aerosol processes except condensation even if option With_fixed_density is set to no In other words if run time computation of density is chosen it will only affect condensation Indeed when using the Gerber formula for fastness purpose there is little interest in recomputing density Then the fixed density is that specified with Fixed_aerosol_de
93. e how as ahad ta el Ga Oo ee aS 75 43 PUEDEVE ce elec ed ae ae Ho al A ee a A A ee A Be Ga a a 75 4 4 StationaryDriver 4 2 acres a A a Sl a me ae a a 76 4 5 Data Assimilation Drivers 0000 0 2 ee 76 4 5 1 Assimilation Driver ix so gos oe Ba ke oe Rs oe ed ee 76 4 5 2 OptimallInterpolationDriver 2 2 2 2004 77 45 37 ENKEDIVE 60 000 efi Gara oe A hoe Ba Pe A 77 4 54 IRRSORWDriver o ria bend ee eee Hela ho Be Oe Bode ek BS 77 do RourbimVarDriver ute il eh pe BO ae Se ee a 78 4 6 Drivers for the verification of adjoint coding 200 78 46 17 Adjoint Driver se 2 6 ra te ek OR A Map ec on Pek oor has 79 CONTENTS 5 ASG Gradient Driver o ia ie A ace te CR Ae a e ee i 79 4 6 3 Gradient4DVarDriver e 79 Ah COI DUI AVERSA a AE Rel Ai E Qt da lee dd 80 Al Base QUiputOaveT ss serpii a la a e A pa le a 80 4 7 2 SaverUnitDomain and SaverUnitDomain_aer 81 4 7 3 SaverUnitSubdomain and SaverUnitSubdomain_aer 81 4 7 4 SaverUnitDomain_assimilation e e o 82 4 7 5 SaverUnitDomain_prediction e o 82 4 7 6 SaverUnitNesting and SaverUnitNesting_aer 82 4 7 7 SaverUnitPoint and SaverUnitPoint_aer 82 4 7 8 SaverUnitWetDeposition and SaverUnitDryDeposition 84 4 7 9 SaverUnitWetDeposition_aer and SaverUnitDryDeposition_aer 84 4 8 Observation Managers 85 4 8 1 GroundObserv
94. e model will stick to it 3 the abscissa of the point of emission m 4 the ordinate of the point of emission m 5 the height of the point of emission m and 6 the species that is emitted source Source coordinates meters Abscissa 0 Ordinate 5 Altitude 25 Species name Species_name Iodine Release time seconds Release_time 0 Total mass released mass Quantity 1 94 CHAPTER 5 MODELS One species may have several puffs The puff file can contain a list of puffs provided by the user or a discretized line source or trajectory In that case it corresponds to the output file of the discretization preprocessing program discretization 5 3 3 Vertical Levels Species and Meteorological data They are exactly the same file as those described in Section 5 1 5 4 GaussianPuff_aer It is the Gaussian puff model for aerosol species It can be run when there are aerosol species only or both aerosol and gaseous species It takes the same input files as the Gaussian puff model except that they contain in addition some sections dedicated to aerosol species It takes in addition another input file that describes the diameters of particles file diameter dat already described in the Section 3 9 2 The output files are binary files one for each gaseous species and one for each couple species diameter 5 4 1 Configuration File puff_aer cfg It is exactly the same file as the configuration file de
95. e number of points to discretize the line or the source velocity in the case of a moving source for puff sources only The program discretization is launched with one configuration file The reference config uration file is discretization cfg It contains the following information trajectory Trajectory file Path to the data file that contains the line coordinates Np Number of points to calculate on the discretized trajectory Used only when the source is continuous or when it is not moving Delta_t Time step to calculate the discretized trajectory in the case of a moving source source Source_type Source type puff or continuous Species name Name of the species emitted by the source only one species for one line source plume source Rate Source rate in mass per second of the line source Velocity Velocity of the gas or aerosol emitted by the source in ms Temperature Temperature of the gas or aerosol emitted by the source Celsius degrees Section Section of the source in m puff source Quantity Total mass released on the line source mass unit Source_velocity Source velocity in km h 0 for non mobile sources tinit Release time for the first trajectory point in s output With_comment Are comments written Source_file Path to the data file where the list of sources will be written The associated data file reference line emission dat contains the coordinates of the line
96. e program gaussian deposition is launched with one configuration file and two input files The configuration file contains the path to the two input files and to the output file The reference configuration file is gaussian deposition cfg It contains the following information data Species Path to the data file that contains the species data Meteo Path to the data file that contains the meteorological data scavenging Type Parameterization to be used to calculate the scavenging coeffi cients deposition Type Parameterization to be used to calculate the deposition velocities output With_comment Are comments written in the output file put yes or no Dutput_file Path to the file where the output data are written The parameterization type for the scavenging coefficient can be chosen between e none the scavenging coefficient is set to 0 for all species e constant the scavenging coefficient is constant for one given species and entered in the species file e belot the scavenging coefficient is calculated with a Belot parameterization In that case the input data are a rainfall rate given in the meteorological data file and coefficients a and b given for each species in the species file Concerning the deposition velocity the type can be chosen between e none the deposition velocity is set to 0 for all species 3 9 PREPROCESSING FOR GAUSSIAN MODELS 67 e constant the deposition velocity is constant for o
97. e use_namespace define name spaces Compile the library here with GNU C compiler make f nr_gnu mak libnewran a This should create include newran libnewran a To complete the installation you have to create a directory where the seed values are stored for instance mkdir newran cp fm txt lgm txt lgm_mix txt mother txt mt19937 txt multwc txt wh txt newran Recall the path to your seed directory since this is an entry of a configuration file driver example assimilation perturbation cfg Mhttp www scons org 14 CHAPTER 1 INTRODUCTION AND INSTALLATION 1 3 4 Fortran Subroutines A difficulty with Fortran subroutines is that some compilers append a trailing underscore at the end of routine s name when it contains an underscore whereas other compilers append two underscores In order to include the Fortran 77 routines a test is performed on the compiler used It works for the supported compilers see Section 1 2 but if you use another compiler you might need to complete the tests As for now tests are performed in e include AtmoData Aerosol hxx e include AtmoData Meteorology hxx e include models Polair3DTransport hxx e include models Polair3DAerosol hxx e include modules transport DiffusionROS2 hxx and e preprocessing dep gaussian deposition aer cpp Here is an example of test in file include AtmoData Meteorology hxx Fortran functions if defined __GNUG__ amp amp __GNUG__ lt 4 amp amp d
98. ed and may be referred by other configuration files such as meteo cfg Actually most configuration files meteo cfg luc usgs cfg emissions cfg etc pro vided in Polyphemus along with the programs are examples that refer to the markups defined in general cfg Essentially three markups are defined in general cfg e Directory_computed fields where output results i e fields computed by preprocessing programs are stored e Directory_ground data where ground data land use cover roughness is stored e Programs path to Polyphemus preprocessing directory Polyphemus configuration files are written so that mainly changes in general cfg should be needed to perform a reference simulation In general cfg one changes the paths markups to the preprocessing programs Programs and to the output results Directory_computed fields and Directory_ground_data and one chooses its simulation domain Other configuration files provide paths to input data meteorological files emissions data etc and fine options 2 3 4 Notes about Models To launch a simulation you have to compile and execute a C program which differs from preprocessing programs After preprocessing steps the simulation is made of a driver on top of the model itself a model and its modules if any See Section 1 1 for a short description of the flowchart The program of the simulation looks like driver polair3d cpp it is a short C code that declares the driver the mode
99. efine output saver units when Type is set to wet_deposition_aer or dry_deposition_aer The sec tion save is very similar to the one for gaseous species except that you have to specify for 4 8 OBSERVATION MANAGERS 85 which diameters the deposition fluxes are saved Hence the list of species to be saved looks like this Species aer1_10 aer 1_ 2 aer2_ 0 1 In that case the species named aerl is to be saved for the diameter of indices 0 and 2 and aer2 for the diameters of indices 0 and 1 In Output_file amp f will be replaced by the species name and amp n by the bin index You can use any symbol which is not a delimiter or even nothing to separate the species name from the bin index even though amp f_ amp n bin is the advised form If Species is set to all the deposition fluxes will be saved for all aerosol species and for all scavenged or dry deposited diameters 4 8 Observation Managers The observation managers deal with available observational data at different locations and dates These managers are designed to prepare for applications related to observation treatments especially for data assimilation The observation operator are implemented for the mapping from observation space into model space For a given date these managers retrieve observation data values and the corresponding statistical information e g observational error covariances 4 8 1 GroundObservationManager The GroundOb
100. efined __INTEL_COMPILER define _compute_relative_humidity compute_relative_humidity__ ttelse define _compute_relative_humidity compute_relative_humidity_ endif extern C void _compute_relative_humidity double double double double If the test fails you will have an error message during compilation saying that compute_relative_humidity _ is undefined in that case modify the test as Fortran functions define _compute_relative_humidity compute_relative_humidity_ extern C void _compute_relative_humidity double double double double 3 If the error message says that compute_relative_humidity_ is undefined modify the test as Fortran functions define _compute_relative_humidity compute_relative_humidity__ extern C 1 3 INSTALLATION 15 void _compute_relative_humidity double double double double Warn Polyphemus development team polyphemus cerea enpc fr in case the test fails You are advised against deleting lines if you have to modify the code such as shown previously but to comment them by adding two slashes Commented line 16 CHAPTER 1 INTRODUCTION AND INSTALLATION Chapter 2 Using Polyphemus 2 1 Remark In configurations files in output logs and so on indices start at 0 as in C and Python not at 1 as in Fortran 2 2 Configuration Files 2 2 1 Definitions All Polyphemus programs rely on flexibl
101. emble Kalman filter RRSQRTDriver reduced rank square root filter FourDimVarDriver 4D Var to be associated with Polair3DAssimConc model e Drivers for the verification of adjoint coding in variational assimilation AdjointDriver GradientDriver Gradient4DVarDriver 2 5 6 Checking Results It is highly recommended to check the fields generated by Polyphemus programs meteorological fields deposition velocities output concentrations First you can check the size of the binary files The results are saved as floating point numbers with single precision This means that most results file must be of size 4 x N x Nz x Ny x Nz bytes where Nz and Ny are the space steps along x and y directions respectively Nz is the number of vertical levels of the field and N is the number of time steps Note that N is not the number of time steps of the simulation but the number of time steps for which concentrations are saved Second you should check that the fields have reasonable values using the programs from direc tory utils mainly get_info float see Section 2 4 1 The command line to use get _info float is get_info_float results 03 bin And the output looks like Minimum 0 0563521 Maximum 169 219 Mean 91 3722 2 5 7 Important Notice As for now under Linux Talos cannot read text files with Windows end of lines In particular if you send a configuration file through FTP or transfer it on a USB flash disk chances are the coding
102. emus output from programs meteo or MM5 meteo starts As a consequence any program that needs to read this meteorological data refers to this date The date must be in a format described in Section 2 2 7 Number of vertical levels integer 3 2 3 Dates Many preprocessing programs require a starting and end date In that case the starting date must always be provided in command line but there are three possibilities for the end date 1 provide an end date in any valid format see Section 2 2 7 e g MM5 meteo general cfg MM5 meteo cfg 2004 08 09_12 00 00 2004 08 11_06 00 00 provide a duration in format NdMh for a duration of N days and M hours Alternatively you can put a duration of Mh for M hours or Nd for N days Valid duration can be for instance 3d5h or 5d or 14h E g MM5 meteo general cfg MM5 meteo cfg 2004 08 09_12 00 00 1d12h provide no end date nor duration In that case a duration of one day is used E g MM5 meteo general cfg MM5 meteo cfg 2004 08 09_12 00 00 Please note that in all three cases the end date is excluded The advantage of it is that if for whatever reason you want to use the preprocessing program several times in a row you can use the end date as the starting date for the next time Then the number of iterations is computed from the interval between the starting and end dates and from the time step you provided in the general configuration file The first date g
103. enerate a land use description with these categories referred as Zhang categories The recommended program to generate this file is luc convert which is described in Section 3 3 3 You should use this program to convert GLCF or USGS land cover to Zhang categories Please note that the program dep chooses which land use file to use according to the month of the beginning date only Therefore if you need deposition velocities for a date range during which the season changes make sure to launch different simulations for the different seasons The program may be launched this way dep general cfg dep cfg 20040809 3 5 2 Program dep emberson The program dep emberson is used to compute deposition velocities for Castor model using Emberson parameterization Altitude SurfaceTemperature SurfaceRelativeHumidity FrictionVelocity Attenuation AerodynamicResistance LUC_file Ne Nveg Land_data Species_data Directory_dep Ns paths File where altitude is stored File where surface temperature is stored File where surface relative humidity is stored File where the friction velocity is stored File where the attenuation is stored File where the aerodynamic resistance is stored File containing the land use cover Number of land use cover categories Number of vegetation classes File containing land data in Chimere format File containing the data for species molecular weight Henry con stant reactivity
104. eposition velocity in ms Only one species per line must be provided All species listed in the section deposition must be present the others will be ignored A species file might look like this species Caesium Iodine scavenging Iodine Caesium deposition Caesium Iodine scavenging constant Caesium 1 e 4 Iodine 1 e 4 scavenging_belot Caesium 2 8e 05 0 51 Iodine 7e 05 0 69 deposition_constant Caesium 0 05e 2 3 9 PREPROCESSING FOR GAUSSIAN MODELS 69 Iodine 0 5e 2 Output File The output data file contains as many sections as there are meteorological situ ations Each section situation contains the temperature wind angle wind speed inversion height and stability class that are provided In addition it contains the list of all species followed by their scavenging coefficient and the list of all species followed by their deposition velocity It looks like this situation Temperature Celsius degrees Temperature 10 Wind angle degrees Wind_angle 30 Wind speed m s Wind 3 Inversion height m Inversion_height 1000 Stability class Stability D Scavenging coefficient of the species s 1 Scavenging coefficient Caesium 6 36257e 05 Iodine 0 000212514 Deposition velocity of the species m s Deposition_velocity Caesium 0 0005 Iodine 0 005 Program gaussian deposition_aer The program gaussian deposition_aer works the same way as the program
105. erl and the diameter of index 1 that is equal to 1 um and so on 74 CHAPTER 3 PREPROCESSING Chapter 4 Drivers 4 1 BaseDriver BaseDriver is configured with a file which contains the displaying options for the simulation display Show_iterations If activated each iteration is displayed on screen Show_date If activated the starting date of each iteration is displayed on screen in format YYYY MM DD HH II notations from Sec tion 2 2 7 4 2 PlumeDriver It is the driver dedicated to the Gaussian plume model The associated configuration file is the same as the one for the BaseDriver and it is usually part of the model configuration file described in Section 5 1 The associated input data file describes the meteorological data ref erence gaussian meteo dat for gaseous species and gaussian meteo aer dat for aerosol and or gaseous species The meteorological data file contains the meteorological data that are needed It can be the output file of the preprocessing program gaussian deposition The meteorological data file describes one or several meteorological situations For each situ ation the driver calls the model to calculate the concentrations that is the stationary solution for the given meteorological situation It is associated with two models the GaussianPlume model for gaseous species only described in Section 5 1 and the GaussianPlume_aer model which is the same model for aerosol and or gaseo
106. f the lower left cell 87 88 Delta_y Ny Nz Vertical_levels Land_category Time Species With_plume_rise With_radioactive_decay With_biological_decay With_scavenging With_dry_deposition Sigma_parameterization File_meteo File source Deposition_model Nchamberlain Configuration_file CHAPTER 5 MODELS Step length along y in m Number of cells along y integer Number of vertical levels integer Path to the file that defines vertical levels heights Land category choose between rural and urban Relevant only when standard deviations are computed with Briggs parameteri zation Choose whether it is nighttime night or daytime day Rel evant only when there is biological decay or when Doury sigma parameterization is used Path to the file that defines involved species gaussian Is plume rise taken into account Is radioactive decay taken into account Is biological decay taken into account Is scavenging taken into account Is dry deposition taken into account Parameterization used to compute standard deviations Briggs for Briggs parameterization Doury for Doury parameterization and similarity_theory for a parameterization based on similarity theory Path to the file containing the meteorological data Path to the file that describes the sources deposition Model used to take dry deposition into account Chamberlain for Chamberlain model Overcamp for Overcamp model Numbe
107. ground 2 preprocessing of meteorological fields preprocessing meteo 3 other preprocessing steps if relevant deposition velocities emissions 4 compiling the right combination of model module s and driver see Sections 2 5 5 and 2 3 4 Passive tracer Below is a possible sequence of programs to be launched to perform a basic passive simulation preprocessing ground luc glcf preprocessing ground roughness preprocessing meteo MM5 meteo preprocessing meteo Kz_TM driver polair3d transport Program polair3d transport is not provided with Polyphemus It should be built with Polyphemus components BaseDriver driver Polair3DTransport model AdvectionDST3 module DiffusionROS2 module See Section 2 3 4 for details Photochemistry Below is a possible sequence of programs to be launched to perform a pho tochemistry simulation preprocessing ground luc glcf preprocessing ground roughness preprocessing meteo MM5 meteo preprocessing meteo Kz_TM preprocessing emissions emissions preprocessing bio bio preprocessing dep dep preprocessing ic ic preprocessing bc bc driver polair3d Roadmaps with Gaussian Models In short the main steps to set up a Gaussian simulation are 1 generation of meteorological data no program is available to do it but as only little information is required this should be quite easy Examples of meteo rological files are provided in driver example gaussian gaussian meteo dat and driver example
108. he input file Nc Number of land use categories Y In case the file has been moved try to find it from http glcf umiacs umd edu data landcover or even from GLCF homepage http glcf umiacs umd edu index shtml 3 3 GROUND DATA 41 The output land cover file is in format c y xj where c stands for land use category Program luc glcf does not require any date as an input in command line To launch luc glcf just type luc glcf general cfg luc glcf cfg 3 3 2 Land Use Cover USGS luc usgs For a simulation over Europe program luc usgs requires two files found at http edcsns17 cr usgs gov glcc e USGS Land Use Land Cover Scheme for Eurasia in Lambert Azimuthal Equal Area Projec tion optimized for Europe available at http edcftp cr usgs gov pub data glcc ea lamberte eausgs2_Ole img gz in compressed format e USGS Land Use Land Cover Scheme for Africa in Lambert Azimuthal Equal Area Projec tion available at http edcftp cr usgs gov pub data glcc af lambert afusgs2 01 img gz in compressed format The configuration file luc usgs cfg requires paths Database luc usgs Directory where the raw data from USGS can be found LUC_in_ea Input file containing raw data for Eurasia eausgs2 Ole img LUC_in af Input file containing raw data for Africa afusgs2 0l img Directory_luc usgs Output directory LUC_out Output file name The default filename LUC usgs bin is recom mended for clarity USGS
109. his is most likely 0 5 Index MM5 coordinates increase along latitude of MM5 grid This is most likely 1 Number of cells or dot points along latitude integer in MMB grid Number of vertical layers integer in MM5 grid Type of projection 1 corresponds to Lambert conformal conic 2 to Mercator and 3 to stereographic Type of horizontal interpolation used MM5 corresponds to MM5 coordinates and latlon to latitude longitude coordinates File containing coordinates of dot points Used if Horizontal_interpolation is set to latlon meteo Minimum relative humidity above which cloud are formed Low clouds maximum height in m Kz 3 5 DEPOSITION VELOCITIES 51 Min_dry Minimum value of Kz in PBLH for dry conditions in ms Min_wet Minimum value of Kz in PBLH for cloudy conditions in ms Min_above_PBLH Minimum value of Kz above PBLH in ms Max Maximum value for Kz in ms Among output files one may find 3 9 the altitude in meters the air density AirDensity bin the pressure in Pa Pressure bin the temperature and temperature at 2 m in K Temperature bin and Temperature 2m bin the meridional wind zonal wind convective velocity and wind module at 10 m MeridionalWind bin ZonalWind bin ConvectiveVelocity bin and WindModule_10m bin in mst the boundary layer height in m PBLH bin the vertical diffusion coefficients using Troen and Mahrt parameterization Kz bin in
110. hs Temperature Meteorological file of temperature Directory _be Directory where output will be written bc_input domain x_min Minimum longitude in Gocart resolution y min Minimum latitude in Gocart resolution Delta_x Gocart longitude resolution Delta y Gocart latitude resolution Nx Number of grid cells in the longitude Gocart axe Ny Number of grid cells in the latitude Gocart axe Nz Number of Gocart vertical layers Sigma levels File where are written the center of Gocart sigma levels Scale height Scale height in meter Surface pressure Surface pressure in atm Top pressure Pressure at top of Gocart level in atm There are two more sections in configuration file The first one is input_species Each non blank line of this section corresponds to one speciation of Gocart species e g CC is sub divided in CC 1 CC 2 CC 3 CC 4 The range after the delimiter is the aerosol size range in SIum to which this sub species apply Most of the time this is the whole aerosol size range of polair3d model e g 0 1 10 0 but in the case of dust DU each sub species may correspond to a precise part of the polair3d aerosol size range see configuration file bc gocart DU cfg for an illustration The second section is output_species Each non blank line of this section corresponds to one aerosol species of polair3d model The columns after delimiter correspond to the Gocart sub species Therefore the number of line in pre
111. ht Aer1 250 350 Aer2 120 180 Decay tests whether it is day or night and chooses the value of half life time to use Use of a Filiation Matrix The last solution is that a single matrix called filiation matrix is specified for all gaseous species and one for all aerosol species which takes into account both decay and the fact that a species can react to form other species As a result the evo 112 CHAPTER 6 MODULES lution of the concentration due to chemistry only is described in equation 6 2 In that case With time dependence is set to no and With filiation matrix to yes O x y z AC eyz 6 2 co x y 2 where A is the s x s filiation matrix and C x y z CPE y z with c x y z the Cet x Y z concentration of species at time step n in point of coordinate x y z and s the number of species involved The parameters are specified as follows in species dat species Spl Sp2 Sp3 Sp4 aerosol_species Aer1 Aer2 filiation_matrix File example decay matrix dat filiation_matrix_aerosol File example decay matrix_aer dat The s x s filiation matrix is specified in file matrix dat as below 0 7 0 05 O 0 1 0 0 8 0 1 0 05 0 1 0 1 0 6 0 1 0 15 O 0 1 0 7 The matrix for aerosol species is very similar to the one for gaseous species Chapter 7 Postprocessing 7 1 Graphical Output 7 1 1 Installation and Python Modules In Polyphemus we advocate the use of Matplotlib with NumPy Basem
112. ibution is a set of numbers in 0 1 whose sum should be 1 Several configuration files are provided to convert GLCF or USGS categories to We sely or Zhang categories glcf_to_wesely cfg glcf_to_zhang cfg usgs_to_wesely cfg and usgs_to_zhang cfg The output land cover file is in format c y xj where c stands for land use category The conversion can be launched with luc convert general cfg usgs_to_wesely cfg 3 3 4 Roughness roughness After land use cover has been computed roughness data can be estimated using program roughness domain Nx Number of grid points along longitude Ny Number of grid points along latitude paths 3 4 METEOROLOGICAL FIELDS 43 LUC_file File where the land use cover data are stored e g computed using luc glcf or luc usgs Directory_roughness Directory where the output file will be stored Roughness out Output file name data Roughness_data_file Path to the file giving the roughness of land categories This file should be a text file with three columns the land category in dex starting at 0 the roughness height in m and the cate gory name Two examples are provided roughness glcf dat and roughness usgs dat The program may be launched with roughness general cfg roughness cfg Section domain is in general cfg and the other sections are read in roughness cfg 3 4 Meteorological Fields 3 4 1 Program meteo Program Polyphemus preprocess
113. ided inside a section situation and the meteorological data file contains as many sections are there are situations If the inversion height is set to 0 it is not taken into account Otherwise reflections on the inversion layer are performed This value can be set equal to the boundary layer height if known during day and to 0 during night It can also be set to 0 all the time if no other value is known situation Temperature Celsius degrees Temperature 15 Wind angle degrees Wind_angle 100 Wind speed m s 5 2 GAUSSIANPLUME_AER 91 Wind 0 5 Inversion height m Inversion_height 1000 In case the Briggs parameterization for standard deviation is used a stability class between A very unstable and F very stable has to be provided Stability class Stability A In case the standard deviations are computed with similarity theory a lot more information have to be provided e Boundary layer height m e Friction velocity ms e Convective velocity ms e Monin Obukhov length m e Coriolis parameter s If not known the Coriolis parameter can be set to 1074871 situation Boundary layer height m Boundary_height 500 0 Friction velocity m s Friction_velocity 0 37 Convective velocity m s Convective_velocity 0 81 Monin Obukhov Length m LMO 120 0 Coriolis parameter s Coriolis 1 4e 04 5 2 GaussianPlume aer It is the Gaussia
114. imilar sections situation at the end of the file 2 Species data file it contains several sections but not all are needed for the preprocessing The needed sections are e species Contains the list of all species e scavenging Contains the list of the species for which scavenging occurs The scavenging coefficient of the others is set to 0 68 CHAPTER 3 PREPROCESSING deposition Contains the list of the species for which deposition occurs The deposition velocity of the others is set to 0 scavenging constant This section is needed when the type of parameterization chosen for the scavenging is constant It contains the name of a species followed by the value of its scavenging coefficient in s Only one species per line must be provided All species listed in the section scavenging must be present the order is not important the others will be ignored scavenging belot This section is needed when the type of parameterization cho sen for the scavenging is belot It contains the name of a species followed by two values corresponding to the coefficients a and b respectively in the Belot parameteri zation Only one species per line must be provided All species listed in the section scavenging must be present the others will be ignored deposition_constant This section is needed when the type of parameterization chosen for the deposition is constant It contains the name of a species followed by the value of its d
115. ing coefficient will be used for all scavenged species e The belot model has the following expression a po where coefficients a and b have to be provided for every species in a section belot for instance belot Coefficients a and b for the Belot parameterization a p_0 b where po is the rain intensity mm h species a b all 1 e 05 0 8 e In case the microphysical model is used Henry constants in mol L atm and gas phase diffusivities in cm s should be provided Henry constants are listed in section henry for instance henry Henry constant mol L atm 03 1 e 2 NO 2 e 3 N02 1 e 2 H202 1 e5 HCHO 6 e3 ALD 15 PAN 3 6 HONO 1 e5 S02 1 e5 HNO3 1 e14 OP1 2 4e2 PAA 5 4e2 ORA1 4 e6 CO 1 e3 N205 1 e14 Gas phase diffusivities are provided in the same way in section diffusivity 5 6 Polair3DChemistry Model Polair3DChemistry is configured with three configuration files polair3d cfg polair3d data cfg and polair3d saver cfg and two data files levels dat and species dat The main configuration file polair3d cfg provides the paths to the four other files A configuration for Polair3DChemistry is an extension of the configuration for Po lair3DTransport In this section the description is limited to Polair3DChemistry additional configuration See Section 5 5 for the rest of the configuration 100 CHAPTER 5 MODELS 5 6 1 Main Configuration File polair3d cfg In addition to fields
116. ing meteo meteo reads ECMWF Grib files and generates meteorological fields required by chemistry transport models Most fields are interpolated from ECMWFE grid to a regular grid latitude longitude in the horizontal altitudes in meters in the vertical It is assumed that ECMWF input data are stored in daily Grib files That is why this program as well as attenuation and Kz only processes data daily and requires only one date as an input in command line Note that meteo needs as input data the land use cover which can be built using programs in preprocessing ground The reference configuration files for meteo is Polyphemus preprocessing meteo meteo cfg together with Polyphemus preprocessing general cfg In addition to the domain definition below are options of meteo paths Database_meteo Directory in which ECMWEF input files may be found It is as sumed that ECMWF file names are in format ECMWF YYYYMMDD where YYYY is the year MM the month and DD the day If program meteo is launched for a day D ECMWF data files for days D 1 and D must be available Data for day D 1 are needed to process cumulated data e g solar radiation Roughness_in Path to the binary file that describes roughness heights in meters in ECMWF grid cells Its format is y x It is needed only if option Richardson with_roughness is activated Directory_meteo Directory where output meteorological files are stored ECMWF Date Date at which the meteorological fi
117. ion file Polyphemus features a markup management A markup is denoted with surrounding lt and gt e g lt path gt A markup is automatically replaced with its value whenever it is found Its value should be provided somewhere in the configuration file with a proper field for instance lt path gt refers to the field path Here is a complete example Root home user Input_directory lt Root gt input Output_directory lt Root gt output means Input_directory home user input Output_directory home user output The markup can be used before its value is defined Input_directory lt Root gt input Output_directory lt Root gt output Root home user After calls to lt Root gt This is legal Any field may be used as a markup The user may define any new markup that is a new field Moreover several markup substitutions can be performed in a single value and nested markups are properly handled Home home user Root lt Home gt Polyphemus work Number 7 Input_directory lt Root gt input lt Number gt is accepted and means Input_directory home user Polyphemus work input 7 Notice that markups may also replace numbers and may be based on preexisting fields x_min 12 5 Delta_x 0 5 Nx 100 y_min lt x_min gt Delta_y 1 Ny lt Nx gt 20 CHAPTER 2 USING POLYPHEMUS 2 2 5 Sections Fields and values may be protected inside sections Assume that two domains are defined o
118. is put in a common configuration file called general cfg An example of such a file is Polyphemus preprocessing general cfg whose content is quoted below general Home u cergrene 0 bordas Directory_computed_fields lt Home gt B data Directory_ground_data lt Directory_computed_fields gt ground Programs lt Home gt codes Polyphemus HEAD domain Date 2001 01 02 Delta_t 3 0 x_min 10 0 Delta_x 0 5 Nx 65 y_min 40 5 Delta_y 0 5 Ny 33 Nz 5 Vertical_levels lt Programs gt levels dat Entries in section general are markups provided for convenience See Section 2 3 3 for further explanations The section domain contains the domain in space and time description domain 3 2 INTRODUCTION 39 Date The date at which the simulation of the chemistry transport model is Delta _t Time step in hour of output meteorological data processed by Polyphemus x_min Abscissa of the center of the lower left cell It is usually in longitude de grees Delta_x Step length along x usually in degrees longitude Nx Number of cells along x integer y min Ordinate of the center of the lower left cell It is usually in latitude degrees Delta y Step length along y usually in degrees latitude Ny Number of cells along y integer Nz Vertical levels Path to the file that defines vertical levels interfaces in m starting It is also the date at which meteorological data processed by Polyph
119. ise a problem under Windows where drives are called C D In the current version of Polyphemus full paths that is with the drive name should not be used under Windows If you need a workaround please contact the Polyphemus teams at polyphemus cerea enpc fr Fields and values go by pair but they can be placed anywhere In particular several fields may be put on a single line x_min 12 5 Delta_x 0 5 Nx 100 6 2 Delta_y 1 Ny 230 y_min The order in which the fields are placed may or may not be important In most Polyphemus configuration files the order does not matter Then x_min 12 5 Delta_x 0 5 Nx 100 6 2 Delta_y 1 Ny 230 y_min is the same as y_min 6 2 Delta_y 1 Ny 230 Nx 100 x_min 12 5 Delta_x 0 5 Recommandation Use equal sign between a field and its value if the value is a number 9 and use semi colon if the value is a string Example x_min 12 5 Output_directory home user path 2 2 CONFIGURATION FILES 19 2 2 3 Comments Comment lines may be added They start with or with Path where results are written Output_directory home user path They may also be put at the end of a line Output_directory home user path Path where results are written Recommandation Prefer for comments so as to be consistent with Polyphemus default configuration files 2 2 4 Markups In order to avoid duplications in a configurat
120. it happens the code should raise an error and tell you what country code in time_zones dat is unknown SUN 3 6 EMISSIONS 57 3 6 3 Biogenic Emissions for Polair3D Models bio Program bio computes biogenic emissions on the basis of meteorological fields and land use cover In addition to the domain definition Section 3 2 2 below is the information required in the configuration for bio see example bio cfg SurfaceTemperature PAR LUC_file Land_data Directory_bio Delta_t Rates Terpenes Terpenes_ratios paths Binary file where the surface temperature is stored Binary file where the photosynthetically active radiation is stored Binary file where the land use cover is stored Data file giving emission factors for isoprene terpenes and NO for all land categories defined in LUC_file In this file each line which is not empty or does not start with provides data for one land use category for such a line the first 55 characters are discarded you may put the category number and description for convenience Then four columns are read with the biomass density g m and the emission factors for isoprene terpenes and NO in this order Two examples are provided with land_data_glcf dat and land_data_usgs dat to be used in combination with land use cover generated by luc glcf or luc usgs respectively Directory where output biogenic emissions are stored biogenic Time step in hours f
121. itional options relevant for the chosen output saver Here is a list of all types of saver units available at the moment Table 4 12 Types of saver domain domain_aer domain_assimilation nesting nesting _aer subdomain subdomain_aer wet_deposition dry_deposition wet_deposition_aer dry_deposition_aer To save entire vertical layers The same as domain but for aerosol species The same as domain but for data assimilation applications To perform nested simulations The same as nesting but for aerosol species To save concentrations only for an horizontal subdomain The same as subdomain but for aerosol species To save entire wet deposition fluxes To save entire dry deposition fluxes The same as wet_deposition but for aerosol species The same as dry_deposition but for aerosol species 4 7 OUTPUT SAVERS 81 4 7 2 SaverUnitDomain and SaverUnitDomain_aer The output saver SaverUnitDomain defines an output saver unit when Type is set to domain or domain_ensemble and requires additional parameters presented in the table below save while concentration are saved in the middle of each levels instantaneous concentrations are saved able if concentrations are not averaged Levels A list of integers that determines the vertical layers to be saved Note that 0 is the first layer Remember that the heights you specified in the file levels dat are those of the level interfaces Averaged
122. ity Fixed aerosol density in kg m used in the module With_cloud_ chemistry Is cloud chemistry taken into account With_in_cloud_scavenging Is in cloud scavenging taken into account With_heterogeneous_reactions Are heterogeneous reactions taken into account With _kelvin_effect Is Kelvin effect taken into account Dynamic_condensation_solver Which solver is used for dynamic condensation Fixed_cutting diameter Fixed cutting diameter in um Sulfate_computation Which method is used to solve sulfate condensation Choices are equilibrium or dynamic 6 2 CHEMISTRY MODULES 109 Redistribution_method Which redistribution method is used Nucleation_model Which nucleation model is used With fixed_density Is aerosol density fixed in the module Wet_diameter_estimation Which method is used to compute aerosol wet diameters The liquid water content threshold is the amount of liquid water in the air above which a cloud is diagnosed in the cell This chemistry module returns the cloud droplet pH this means that With_pH can be set to yes and that microphysical pH scavenging model can be used Otherwise choosing the microphysical pH scavenging model may result in crash or errors Note that options With_pH Lwc_cloud threshold and Fixed aerosol density are used by both model and module That is to say the fixed aerosol density is the same in the model as in the module The fixed cutting diameter has to be given as an aerosol diameter in um Aer
123. iven in command line is the date at which the preprocessing starts this time It might differ from the date given in general cfg if the preprocessing program is launched several times in a row for example because the meteorological data file does not cover the whole time span of the simulation 3 2 4 Data Files Polyphemus reads ECMWF Grib files MM5 files NetCDF files for Mozart 2 text files and binary files All files generated by Polyphemus are text files or binary files Unless specified otherwise all binary files store single precision floating point numbers They do not contain any header Each binary file only stores the values of a single field Four dimensional fields are stored this way 40 CHAPTER 3 PREPROCESSING Loop on time t Loop on z Loop on y Loop on x Let this storage be symbolized by t z y Dimensions t z y and x always appear in this order For instance three dimensional fields may be stored in formats z y x or t y x t z a or t z y 3 3 Ground Data Computing ground data is the first step of a preprocessing as they are necessary to pro cess meteorological fields All programs related to ground data generation are available in Polyphemus preprocessing ground The first step should be program luc usgs or luc glcf depending on what raw data you have Land use data may come from the US Geological Survey USGS or from the Global Land Cover Facility GLCF 3 3 1 Land Use Cover GLC
124. ives the concentration for the first meteorological situation e plume_gas_meteo2 gives the concentration for the second meteorological situation e plume_gas_meteo3 gives the concentration for the third meteorological situation e plume_gas_meteo4 gives the concentration for the fourth meteorological situation Figure B 1 shows the result of display_plume py Note that you can replace Iodine bin with Caesium bin in results plume disp cfg to display the results for Caesium B 4 2 Gaussian Puff with Aerosol Species Launch the python script to display the results cd TestCase python results puff_aer display_puff py This creates 4 figures in results puff_aer e puff_aer_meteol shows the puff at t Os t 3s and t 8s for the first meteorological situation e puff aer meteo2 shows the puff at t 0s t 3s and t 8s for the second meteorological situation e puff_aer_meteo3 shows the puff at t 0s t 3s and t 8s for the third meteorological situation e puff_aer_meteo4 shows the puff at t 0s t 3s and t 8s for the fourth meteorological situation Figure B 2 shows what is displayed It shows how the puff evolves in time By default the species displayed is the first aerosol species and the first diameter class aer1_0 Just modify the file results puff_aer disp_puff cfg to display other species or diameters 136 APPENDIX B 80 100 120 140 160 180 a Situation 1 80 100 120 140 160 180
125. ke in order to compile all programs in a given directory In directory driver you may use scons instead of make if you are familiar with SCons 1 3 2 AtmoPy A special step is required with the Python library AtmoPy This library makes calls to a C program in order to parse configuration files Follow the steps below to have AtmoPy fully installed cd Polyphemus include atmopy talos g I Talos o extract_configuration extract_configuration cpp You may replace g with any supported compiler see Section 1 2 1 33 Newran The library Newran is required with Kalman algorithms RRSQRT and ensemble to generate random numbers It should be installed in include newran Download Newran from http www robertnz net download html or type Newran in search engine At the time these lines are written Newran 3 0 beta is available at http www robertnz net ftp newran03 tar gz The following commands work with Newran 3 0 beta released 22 April 2006 there may be slight changes with other versions Create directory include newran expand Newran in it mkdir Polyphemus include newran cd Polyphemus include newran wget http www robertnz net ftp newran03 tar gz tar zxvf newran03 tar gz If all is fine you should have a file called include newran newran h Next you have to edit include newran include h and uncomment the line define use_namespace define name spaces That is remove the first two slashes defin
126. l J Geophys Res 108 D22 Horowitz L W Walters S Mauzerall D L Emmons L K Rasch P J Granier C Tie X Lamarque J F Schultz M G Tyndall G S Orlando J J and Brasseur G P 2003 A global simulation of tropospheric ozone and related tracers description and evaluation of MOZART version 2 J Geophys Res 108 D24 Louis J F 1979 A parametric model of vertical eddy fluxes in the atmosphere Boundary Layer Meteor 17 187 202 Mallet V Qu lo D and Sportisse B 2005 Software architecture of an ideal modeling platform in air quality A first step Polyphemus Technical Report 11 CEREA Nenes A Pandis S N and Pilinis C 1998 ISORROPIA A new thermodynamic equilibrium model for multiphase multicomponent inorganic aerosols Aquat Geoch 4 1 123 152 Njomgang H Mallet V and Musson Genon L 2005 AtmoData scientific documentation Technical Report 10 CEREA Rosenbrock H H 1963 Some general implicit processes for the numerical solution of differ ential equations Computer J 5 329 330 Simpson D Winiwarter W B rjesson G Cinderby S Ferreiro A Guenther A Hewitt C N Janson R Khalil M A K Owen S Pierce T E Puxbaum H Shearer M Skiba U Steinbrecher R Tarras n L and quist M G 1999 Inventorying emissions from nature in Europe J Geophys Res 104 D7 8 113 8 152 Stockwell W R Kirchner F
127. l simulations observations and statistics information aiming at and validated by a better pre diction Data assimilation methods can roughly be catalogued into variational and sequential ones For the former the variational principle applies The objective can be defined by the dis crepancy between model simulation and a block of observations usually combined with a priori background knowledge This can be theorized and solved efficiently by optimal control theory FourDimVarDriver The sequential methods make use of observations instantaneously This is a filtering process and filter theory linear or nonlinear applies OptimalInterpolationDriver EnKFDriver and RRSQRTDriver A typical data assimilation system consists of three components model physics data observation and assimilation algorithm The data assimilation drivers organize model and data to perform assimilations The associated configuration file is an extension of that of the model configuration file exemplified in Section 5 8 For data part it has an additional section observation management observation management Configuration_file Path to the file containing the configuration of the ob servation management In the distribution directory driver example assimilation choose between observa tion cfg to use observations and observation sim cfg to use simulated observations The value of Configuration file can be set to observation cfg if you use
128. l and the modules You may have to modify this program in case you change the model the driver or a module In that case duplicate driver polair3d cpp or another example and modify it according to the notes below Actually it is likely that the model driver combination is already in use in one of the examples have a look in driver cpp First determine which model you need depending on your simulation target e for a passive simulation Polair3DTransport or CastorTransport e for asimulation with chemistry for gaseous species Polair3DChemistry or CastorChemistry e for a simulation with aerosol species Polair3DAerosol e for asimulation with gaseous species and data assimilation Polair3DChemistryAssimConc e for a simulation at local scale using an Eulerian model one of Polair3D models with driver StationaryDriver e for a simulation with a plume Gaussian model GaussianPlume or GaussianPlume aer if there are aerosol species e for a non stationary simulation at local scale with a Gaussian model GaussianPuff or GaussianPuff_aer if there are aerosol species 24 CHAPTER 2 USING POLYPHEMUS To set the model just modify the definition of ClassModel typedef MyModel lt Argument s gt ClassModel For instance typedef Polair3DAerosol lt real AdvectionDST3 lt real gt DiffusionROS2 lt real gt Decay lt real gt gt ClassModel If you change a model you may also change the modules a model may need less modules or no mod
129. le begins It is referred as amp D which is the date given in command line because it is supposed that ECMWF Grib files store data daily 44 CHAPTER 3 PREPROCESSING tmin First hour stored in the Grib file Delta_t Time step in hour of data stored in every ECMWF file Nt Number of time steps stored in every ECMWF file x min Longitude in degrees of the center of the lower left cell in ECMWF grid Delta x Step length in degrees along longitude of ECMWF grid Nx Number of cells along longitude integer in ECMWF grid y min Latitude in degrees of the center of the lower left cell in ECMWF grid Delta y Step length in degrees along latitude of ECMWF grid Ny Number of cells along latitude integer in ECMWF grid Nz Number of vertical layers integer in ECMWF grid meteo Richardson with roughness Should the surface Richardson number be computed taking into account roughness height accumulated_data Accumulated_time For data storing values cumulated in time e g solar radiation length number of time steps over which data is cumulated Accumulated_index Start index of the first complete cycle of cumulated data Data is then cumulated from tmin plus Accumulated_index times Delta_t To launch the program just type meteo general cfg meteo cfg 2001 04 22 The program basically reads data in the ECMWF Grib file and interpolates it in time and space to Polyphemus grid ECMWF data is described in
130. le to be analyzed by get_info float or get info double contains only floating point numbers No extra data such as headers should be in the file Out put binary files from preprocessing programs and from drivers models satisfy this condition and can be properly read by get_info_float or get_info_double Note that Polyphemus programs usually generate single precision files it is very likely that one only uses get_info float Using get_info_ float or get_info double is straightforward get_info_float Temperature bin Minimum 257 621 Maximum 300 882 Mean 282 262 get_info_float Temperature bin Pressure bin File Temperature bin Minimum 257 621 Maximum 300 882 Mean 282 262 File Pressure bin Minimum 56369 2 Maximum 102496 Mean 87544 1 2 4 2 Differences between Two Binary Files There are two different types of programs to compute statistics about the differences between two files e get diff precision where precision is float or double They return statistics about the difference between two files As for get_info_precision the files should only contain floating point numbers e get_partial_diff_precision where precision is float or double They return statis tics about the difference between two files If these two files have the same size get_partial diff precision does the same as get_diff_precision If the files do not have the same size only the first values as much as possible are compared 26
131. m number of countries covered by the inventory Names of inventory species Number of activity sectors Emission ratio for urban areas see below Emission ratio for forest see below Emission ratio for other areas see below LUC Path to land use cover file Longitude in degrees of the center of the lower left cell in LUC grid Step length in degrees along longitude of LUC grid Number of cells along longitude integer in LUC grid Latitude in degrees of the center of the lower left cell in LUC grid 56 CHAPTER 3 PREPROCESSING Delta y Step length in degrees along latitude of LUC grid Ny Number of cells along latitude integer in LUC grid Species N Number of emitted species Aggregation Aggregation matrix file relations of the emitted species to the real chemical species Speciation directory Directory in which for each inventory species XXX a file XXX dat contains the speciation to real chemical species as function of the emission sector columns Deposition factor NH3 Part of emitted NH which is deposited right away The program emissions reads EMEP emissions inventory multiplies them by temporal factors and interpolates them on Polair3D grids EMEP emissions are read with AtmoData function ReadEmep The spatial interpolation is performed with EmepToLatLon Urban forest and other ratios Ratios Urban_ratio Forest_ratio and Other_ratio enable to distribute emissions of an EMEP cell ac
132. merical solver for transport used in Castor model It uses piecewise parabolic method PPM for advection but can also use an upwind scheme for some species In the species file associated with castor there are two sections species and ppm_species For all species in species but not in ppm_species an upwind scheme will be used 6 2 Chemistry Modules 6 2 1 ChemistryRACM Module ChemistryRACM is the most common photochemical module used with Polair3D It implements RACM Stockwell et al 1997 and uses a second order Rosenbrock method for time integration Computations are performed by Fortran routines automatically generated by the chemical preprocessor SPACK and a C program is used as a frame to launch all these calculations It only deals with gaseous species and manages 72 species 237 reactions including 23 pho tolysis reactions 107 108 CHAPTER 6 MODULES 6 2 2 ChemistryRACM SIREAM Remark Before using this module please read the file README SIREAM provided in driver To use this module sources for ISORROPIA Nenes et al 1998 are necessary You can obtain them from its home page http nenes eas gatech edu ISORROPIA After you ob tained and extracted the files you have to rename ISOCOM FOR as isocom f ISOFWD FOR as isofwd f ISOREV FOR as isorev f and ISRPIA INC as isrpia inc and to put them in direc tory include isorropia Another step before using ChemistryRACM SIREAM is to modify slightly the file Pol
133. meteo cfg introduced in Section 3 4 1 and 3 4 2 below are options for Kz paths File Kz Name of the file where the vertical diffusion coefficients output are stored kz Min Lower threshold for vertical diffusion in m s Max Higher threshold for vertical diffusion in m s Apply_vert If set to no the lower threshold is applied only at the top of the first layer otherwise it is applied to all levels This programs mainly computes the vertical diffusion coefficients with a call to ComputeLouiskz Simple corrections are also performed to take into account convective conditions The output is a 3D time dependent field format t z y of vertical diffusion coefficients in m s Along the vertical the coefficients are defined on the interfaces So the size of the field for each day is Nt x Nz 1 x Nyx Nz It is stored in the path given by entry File Kz 3 4 4 Program Kz_TM Program Kz_TM overwrites in the boundary layer height the vertical diffusion coefficients computed with Louis parameterization with coefficients computed according to Troen amp Mahrt parameterization Troen and Mahrt 1986 It should be launched either after Kz or after MM5 meteo The reference configuration files for Kz_TM is Polyphemus preprocessing meteo meteo cfg or Polyphemus preprocessing meteo MM5 meteo cfg together with Polyphemus preprocessing general cfg In addition to the domain definition in general cfg below are
134. mission Scavenging_model Collect_dry_flux Collect_wet_flux Data_description Horizontal_diffusion 95 Abscissa of the center of the lower left cell Provide a longitude in degrees or in case Cartesian coordinates are chosen an abscissa in meters Step length along x in degrees longitude or in meters for Carte sian coordinates Number of cells along x integer Ordinate of the center of the lower left cell Provide a latitude in degrees or in case Cartesian coordinates are chosen an ordinate in meters Step length along y in degrees latitude or in meters for Carte sian coordinates Number of cells along y integer Number of vertical levels integer Path to the file that defines vertical levels interfaces If activated coordinates are Cartesian and in meters Otherwise coordinates are latitudes and longitudes in degrees Path to the file that defines involved species and their chemical properties options Are species advected Are species diffused If activated vertical wind is diagnosed from div pV 0 where p is the air density and V the wind and the diffusion term is div pK ve where c is the concentration and K is the diffusion matrix If this option is not activated it is assumed that p is constant and therefore disappears from the previous equations Are initial conditions provided for given species If not initial concentrations are set to zero Are boundary conditions available
135. mponent 10 meter V Component SURFACE ALBEDO SURFACE MOISTURE AVAILABILITY SURFACE EMISSIVITY AT 9 um SURFACE ROUGHNESS LENGTH SURFACE THERMAL INERTIA SOIL HEAT CAPACITY SNOW COVER EFFECT VERTICAL COORDINATE e the position at which the variable is given Stag dot points D corner of the grid squares or cross points C center of the grid squares e its dimensions ordering e its unit or DIMENSIONLESS e a short description 30 CHAPTER 2 USING POLYPHEMUS Then you can use the program get_info_MM5 to have statistical data about one of the variables only Note that some variables have a blank space in their name so in that case you need to put the name between quotes to use get_info_MM5 If the name has no blank spaces quotes are not necessary but can be used TestCase raw_data MM5 gt get_info_MM5 MM5 2004 08 09 GROUND T Min 271 911 Max 327 747 Mean 294 112 Std dev 6 46779 TestCase raw_data MM5 gt get_info_MM5 MM5 2004 08 09 ALB Min 0 0738 Max 0 8 Mean 0 122658 Std dev 0 0501975 2 4 4 Script call_dates The script call_dates allows to call a program in particular for preprocessing over several consecutive days Launch it without arguments to get help Polyphemus utils gt call_dates Script call_dates calls a program over a range of dates Usage call_dates program arguments first date second date number of days Arguments program program to be lau
136. n plume model for aerosol species The corresponding program is plume_aer It can be run when there are aerosol species only or both aerosol and gaseous species It takes the same input files as the Gaussian plume model except that they contain in addition some sections dedicated to aerosol species It takes in addition another input file that describes the diameters of particles file diameter dat already described in Section 3 9 2 The output files are binary files one for each gaseous species and one for each couple aerosol species diameter The way results are saved is described in an additional configuration file reference plume saver_aer cfg described in Section 4 7 92 CHAPTER 5 MODELS 5 2 1 Configuration File plume_aer cfg It is exactly the same file as the configuration file described in Section 5 1 The only data that may differ are the paths to the input files 5 2 2 Source Description plume source_aer dat It is the same file as the source file for gaseous species except that obviously some or all emitted species will be particulate species The corresponding sections are named aerosol _source 5 2 3 Vertical Levels plume level dat It is the same file as in Section 5 1 5 2 4 Species gaussian species aer dat The section species lists the gaseous species and the section aerosol_species lists the aerosol species In the case of radioactive or biological decay the sections are the same as described in Section
137. nched over the range of dates arguments arguments Any occurence of D is replaced with the date otherwise the date is assumed to be the last argument first date first date of the range of dates second date number of days last date of the range of dates or number of days of this range Below is an example Polyphemus utils gt call_dates echo Current date 20060720 20060722 nice time echo Current date 20060720 Current date 20060720 0 00user 0 00system 0 00 00elapsed O CPU Oavgtext 0avgdata Omaxresident k Oinputs 0outputs Omajor 176minor pagefaults Oswaps nice time echo Current date 20060721 Current date 20060721 0 00user 0 00system 0 00 00elapsed O CPU Oavgtext 0avgdata Omaxresident k 2 5 SETTING UP A SIMULATION 31 Oinputs 0outputs Omajor 177minor pagefaults Oswaps nice time echo Current date 20060722 Current date 20060722 0 00user 0 00system 0 00 00elapsed 200 CPU Oavgtext 0avgdata Omaxresident k Oinputs 0outputs Omajor 177minor pagefaults Oswaps For each day the command that is launched is shown note that nice time has been prepended and its output is displayed below 2 5 Setting Up a Simulation This section is a quick overview of how a simulation should be set up It is not meant to and cannot replace the chapters about preprocessing models modules 2 5 1 Suggested Directory Tree It is advocated not to modify Polyphemus code including the configuration files provided with it
138. ne for input data and another for output data Instead of x_min_in 12 5 Delta_x_in 0 5 Nx_in 100 x_min_out 35 8 Delta_x_out 0 3 Nx_out 400 one may prefer input x_min 12 5 Delta_x 0 5 Nx 100 output x_min 35 8 Delta_x 0 3 Nx 400 Conflicts are avoided and the syntax is clear This is why most Polyphemus configuration files have sections Sections are enclosed by square brackets and Markups are not bound to any section Recommandation Put two blank lines before each section and one blank line after blank line blank line input blank line x_min 12 5 Delta_x 0 5 Nx 100 output x_min 12 5 Delta_x 0 5 Nx 100 2 2 6 Multiple Files Several Polyphemus programs accept two configuration files as input Providing two config uration files is then equivalent to providing a single configuration file that would contain all the lines of both files This is useful to let several programs share a same configuration base For instance the simulation domain whose description is needed by most programs is usually defined in a configuration file that is provided to every program in addition to a file dedicated to the specific configuration of the program For instance emissions general cfg emissions cfg 20010506 launches the program emissions with two configuration files as input 1 the configuration file general cfg shared with other programs and no
139. ne given species and is given in the species file Input Files There are two input data files for this program the meteorological data file ref erence meteo dat and the species file reference species dat 1 Meteorological data file it contains as many sections as there are meteorological situations For each situation meteorological data temperature wind are given as described in section 5 1 5 They will be written unchanged in the output file which will be the me teorological data file of the main program Other meteorological data might be needed depending on the chosen parameterization to compute scavenging coefficients and deposi tion velocities Currently the only parameterization that needs other information is the Belot parameterization If the type belot is chosen for the calculation of the scavenging coefficient a rainfall rate must be provided in mmh If the chosen type is constant or none the rainfall rate or other information can be provided but will be ignored by the program So the meteorological data file finally looks like this situation Temperature Celsius degrees Temperature 10 Wind angle degrees Wind_angle 30 Wind speed m s Wind 3 0 Inversion height m Inversion_height 1000 Stability class Stability D Rainfall rate mm hr Rainfall_rate 1 In this example there is only one meteorological situation described Others can be added simply by adding s
140. nsity option 110 CHAPTER 6 MODULES 6 2 3 ChemistryRADM Module ChemistryRADM is quite similar to ChemistryRACM RACM has actually been derived from RADM RADM manages 61 species 157 reactions involving those species and 21 photolysis reactions 6 2 4 ChemistryCastor Module ChemistryCastor is the default chemical module for Castor It involves 44 species and 118 reactions It is based on several data files which must be provided Reaction_file Stoichiometry_file Photolysis_file and Rate file See Section 5 10 3 for more details about these files 6 2 5 Decay This chemistry module is used for species gaseous or particulate which have a radioactive or biological decay that is to say a natural decrease in their concentrations over time This decay requires two more options in the configuration file polair3d cfg options With_time_dependence If set to yes the value of the half life time for each species depend on the time of the day see below With _filiation matrix Tf set to yes decay and filiation are represented by a matrix see below Note that With_time_dependence and With_filiation matrix cannot be both set to yes at the same time Use of One Value of Decay The first possibility is that each species has a half life time which is given in species dat In that case With_time dependence and With filiation matrix are both set to no The variation of concentration due to decay only is described in equation
141. o load it In the distribution AtmoPy is in directory Polyphemus include atmopy When you load AtmoPy under Python from atmopy import in a program or in IPython Python searches for the directory atmopy in the local directory that is atmopy If atmopy is not in the current directory Python searches for atmopy in all paths of PYTHONPATH under Linux and Unix Hence you have two options 1 copy directory atmopy from Polyphemus include into the current directory or create a symbolic link to it ln s path to Polyphemus include atmopy or 2 update PYTHONPATH so that it includes the path to atmopy e g in Bash export PYTHONPATH PYTHONPATH path to Polyphemus include atmopy which you may put in bashrc If Matplotlib and Basemap are properly installed then AtmoPy should work A test function is provided with AtmoPy to check gt gt gt from atmopy import gt gt gt atmopy_test If you get Figure 7 1 AtmoPy is properly installed 7 1 GRAPHICAL OUTPUT 115 Figure 7 1 Output of function atmopy test If you get this figure AtmoPy is properly installed 7 1 2 A Very Short Introduction to Python and Matplotlib In this section several examples are meant to introduce to Python and Matplotlib The following commands are sometimes given with comments after character You can execute them under IPython if you wish Base and Lists gt gt gt x 5 gt gt gt y 2 xt 7 gt gt gt print
142. ocity The following example corresponds to a case with two gaseous species named gas1 and gas2 and three aerosol species named aerl aer2 and aer3 The diameter file is the same as displayed before that is contains two diameters The output file looks like this situation Temperature Celsius degrees Temperature 10 Pressure Pa Pressure 101325 Wind angle degrees Wind_angle 30 Wind speed m s Wind 3 Inversion height m Inversion_height 1000 Stability class Stability D Scavenging coefficient of the gaseous species s 1 Scavenging coefficient gasi 0 0001 gas2 0 0001 Deposition velocity of the gaseous species m s Deposition_velocity 3 9 PREPROCESSING FOR GAUSSIAN MODELS 73 gas1 0 0005 gas2 0 005 Scavenging coefficient of the aerosol species s 1 Scavenging coefficient_aer aeri 0 5 95238e 05 aerl 1 5 95238e 05 aer2 0 5 95238e 05 aer2 1 5 95238e 05 aer3 0 5 95238e 05 aer3 1 5 95238e 05 Deposition velocity of the aerosol species m s Deposition_velocity_aer aer1 O 2 11708 aer1 1 6 69479 aer2 0 1 54404 aer2 1 4 88268 aer3 0 3 42833 aer3 1 10 8413 The value following aerl 0 corresponds to the calculated coefficient for the species aer1 and the diameter of index 0 that is in the case of our diameter file the diameter equal to 0 1 um The value following aer1 1 corresponds to the coefficient for the species a
143. oduced in Section 5 6 1 the following fields are read by Polair3DAerosol Bin_bounds With_initial_condition_aerosol With_boundary_condition_aerosol With pH Lwc_cloud_threshold Fixed_aerosol_density With_deposition_aerosol Compute_deposition_aerosol With_point_emission_aerosol With_surface_emission_aerosol With_volume_emission_aerosol With_scavenging aerosol Collect_dry_flux_aerosol Collect_wet_flux_aerosol domain The bounds of the diameter classes for aerosol species Note that the classes are the same for each aerosol species options Are initial conditions provided for given aerosol species If not initial concentrations are set to zero Are boundary conditions available for given aerosol species Does the aerosol module returns cloud droplet pH Liquid water content threshold above which a cloud is diagnosed in the cell Fixed aerosol density in kgm Is dry deposition taken into account for aerosol species If set to yes deposition velocities for aerosol species are computed with land data otherwise they are read in files Only needed if dry deposition is taken into account Are point emissions provided for aerosol species Are emissions at ground provided for aerosol species Are volume emissions provided for aerosol species Is there scavenging for aerosol species Are the dry deposition fluxes are collected in order to postprocess them if dry deposition is taken into account Are the wet deposition fl
144. odule which deals with advection and diffusion This does models although there is no common not mean that a module could not be shared by both module in current Polyphemus version Table 2 2 and Table 2 3 present a summary of the compatibility between models and modules Note that Gaussian models are not included in these tables because they don t need any module Table 2 2 Compatibility between models and transport modules AdvectionDST3 DiffusionROS2 TransportPPM Polair3DTransport Polair3DChemistry Polair3DAerosol Polair3DChemistry AssimConc CastorTransport CastorChemistry X X X X X X X X Table 2 3 Compatibility between models and chemistry modules Castor RACM RADM SIREAM Decay Polair3DChemistry Polair3DAerosol Polair3DChemistry AssimConc CastorChemistry X X X X X X 36 CHAPTER 2 USING POLYPHEMUS In Table 2 3 module names are shortened to be displayed on one line Castor is actually ChemistryCastor RACM is ChemistryRACM RADM is ChemistryRADM SIREAM is ChemistryRACM SIREAM As for drivers BaseDriver is the simplest and the most used of them The other drivers available are e StationaryDriver for local scale Eulerian simulations e PlumeDriver for Gaussian plume model with or without aerosol species e PuffDriver for Gaussian puff model with or without aerosol species e Data assimilation drivers OptimalInterpolationDriver optimal interpolation EnKFDriver ens
145. omputeTM Kz The main output is a 3D time dependent field format t z y 2 of vertical diffusion co efficients in m s Along the vertical the coefficients are defined on the interfaces So the size of the field for each day is Nt x Nz 1 x Ny x Na It is stored in Kz_TM bin in the directory given by entry Directory Kz_TM The surface relative humidity is saved in SurfaceRelativeHumidity bin Depending on the options additional fields may be saved such as the Monin Obukhov length in file LMO bin 3 4 5 Program MM5 meteo Program Polyphemus preprocessing meteo MM5 meteo processes MM5 data and generates meteorological fields required by chemistry transport models Most fields are interpolated from MM5 grid to a regular grid latitude longitude in the horizontal altitudes in meters in the vertical Note that MM5 meteo needs as input data the land use cover which can be built using programs in preprocessing ground Note for ECMWF users program MM5 meteo is equivalent to what is performed by meteo attenuation and Kz successively Similarly to ECMWF files Kz_TM can be used afterwards 48 CHAPTER 3 PREPROCESSING Program MM5 meteo can be launched as follows MM5 meteo general cfg MM5 meteo cfg 2004 08 09_09 00 00 MM5 meteo general cfg MM5 meteo cfg 2004 08 09_09 00 00 2004 08 10_09 00 00 MM5 meteo general cfg MM5 meteo cfg 2004 08 09_09 00 00 1d The configuration file MM5 meteo cfg contains several options
146. on If boundary conditions are activated With boundary condition Required fields are MeridionalWind and ZonalWind if advection is activated VerticalDiffusion if diffusion is activated and Temperature and Pressure in case air density is taken into account If deposition is activated With deposition Path to the file which defines the point emis sions described below If point emissions are activated With point emissions If surface emissions are activated With surface emission If volume emissions are activated With_volume_emission Nz is the num ber of levels in which pollutants are emitted If the scavenging model is not set to none Scavenging model The file for point emissions have to contain a section source for each point emissions with the following features e its location Abscissa and Ordinate are given in degrees or in meters in case Cartesian coordinates are chosen and Altitude is the vertical height in meters Notice that the 98 CHAPTER 5 MODELS emission is released in the cell containing the location of the point emission e the emitted species is filled after Species Only one species is possible for each section source e the type Type may be continuous or puff for instantaneous release The continuous emission is described with entries Rate which corresponds to the quantity averaged on the duration of the release Date_beg and Date_end which are the beginning and en
147. one corresponds to index along y the second one to the index along x and concentrations are saved at this point for each vertical level specified in the field Levels In the previous example the file lt Results gt point txt will be created during the simulation and look like tz y x 0 0 0 2 0 0 0o 5 15 2 5 15 0 20 25 2 20 25 0 30 30 2 30 30 In case there are three indices on a line concentrations are saved only at the specified point no matter what the field Levels contains The first value on the line corresponds to index along z the second to index along y and the third to index along x Note that lines containing two or three values can be entered in any order The output binary file containing concentrations will simply follow the order given in the file lt Results gt point txt for each time step It means that the resulting binary file will be of size Ny x Npoint where N is the number of time steps to be saved and Npoint is the number of points where concentrations are saved To save coordinates instead of indices one simply has to change the type to coordinates _list to add the field Levels_coordinates to specified values of z where concentrations are to be 84 CHAPTER 4 DRIVERS saved and to write the field Coordinates instead of Indices The field Levels is still read but not used Here is an example Levels 0 Levels_coordinates 1 5 Output_file lt Results gt amp f bin Coordinates 470 0 535 0 470 7 53
148. or the output biogenic emissions For simulations with Polair3D anthropogenic emissions and biogenic emissions must have the same time step that is usually one hour Should emission rates be saved These rates are not needed by chemistry transport models Names of the species included in terpenes emissions For RACM Stockwell et al 1997 put API and LIM Distribution of terpenes emissions among species entry Terpenes Biogenic emissions are computed according to Simpson et al 1999 Meteorological data is first interpolated in time so that its time step is Delta_t section biogenic Emission rates are then computed using AtmoData function ComputeBiogenicRates and emissions using ComputeBiogenicEmissions 3 6 4 Biogenic Emissions for Castor Models bio castor Program bio castor is slightly different from bio in particular regarding the data provided SurfaceTemperature WindModule_10m paths Binary file where the surface temperature is stored Binary file where the wind module at 10 m is stored 58 Attenuation SoilMoisture ConvectiveVelocity Land_data Directory_bio Minimum_wind_velocity Terpenes Terpenes_ratios CHAPTER 3 PREPROCESSING Binary file where attenuation data are stored Binary file where the moisture of the ground is stored Binary file where the convective velocity is stored Land data in Chimere format Directory where output biogenic emissions are stored biogenic Minimum
149. orological Data 0 20020000022 eee 127 A 5 Launching the Simulation 0 0 0 0 00000002 e eee eee 128 A 5 1 Modifying the Configuration File 128 A 5 2 Modifying the Data File 0 o e e 128 A 5 3 Modifying Saver File 2 2 0 0 02 0 0000002 eee eee 129 CONTENTS 7 A DA SS 4s cee eed eh Re eet aes Mee Sei ee Bes eA ee 2 129 A 6 Visualizing Results ee 129 A 6 1 Modifying Configuration File o e o 129 AO62 Using IPython lt 2 iv kee or Sle wes ek ede seb Bee amp ee s 130 B Polyphemus Gaussian Test Case 131 B L Preprocessin seird Bn es She AA Ge SS A ee a A 131 B 2 Discretization it a Sek eA a SS Bee a Boe a a 132 B 3 Sinmilations as 2 4 a abate kde ae a ee A A ede 132 Bisel SPM o beg dee ede E elas ein Ae okay he BG Ge ps else i 132 B 3 2 Puff with Aerosol Species 2 2 ee 133 B 3 3 Puff with Line Source os ee eee king aop wR Se See ee a 134 BA Result Visualization 2 peana oh 4 gente eee yan il Be ee a a 135 BAJ Gaussian Plume noade nane hoe eo he GOR toe ee ls ew ee a 135 B 4 2 Gaussian Puff with Aerosol Species 135 B 4 3 Gaussian Puff with Line Source 0 0 0 0 0 00 0 00084 136 CONTENTS Chapter 1 Introduction and Installation 1 1 Polyphemus Overview Polyphemus is an air quality modeling system built to manage several scales local regional and continent
150. orological data over one day To generate data from day 2001 05 19 to day 2001 05 21 one should launch meteo general cfg meteo cfg 2001 05 19 meteo general cfg meteo cfg 2001 05 20 meteo general cfg meteo cfg 2001 05 21 Another option is to use the script call_dates see Section 2 4 4 In that case to generate data from day 2005 05 19 to day 2005 05 21 one should launch meteo gt utils call_dates meteo general cfg meteo cfg 20050519 20050521 or meteo gt utils call_dates meteo general cfg meteo cfg 20050519 3 37 38 CHAPTER 3 PREPROCESSING Remember that the results are appended at the end of the output files if they already exist If you decide to recompute your fields from the first day you have to first remove old output binary files In order to know what are the arguments of a program you may launch it without arguments For instance emissions gt emissions Usage emissions main configuration file secondary configuration file date emissions main configuration file date emissions date Arguments main configuration file optional main configuration file Default emissions cfg secondary configuration file optional secondary configuration file date date in any valid format 3 2 2 Configuration Almost all programs require the description of the domain over which computations should be performed Since this configuration is shared by many programs it
151. osol bins below that diameter are assumed at equilibrium and those above that diameter are not considered at equilibrium The criteria is the comparison between the fixed cutting diameter and the bin bounds The aerosol bin whose bounds are surrounding the fixed cutting diameter is included in the equilibrium bins Dynamic condensation is intended for aerosol bins which are not at equilibrium and therefore time resolved mass transfer has to be computed for them The solver for dynamic condensation may be set to either etr or ros2 or ebi The etr solver is an Explicit Trapezoidal Rule second order algorithm the ros2 solver is the Rosenbrock implicit second order scheme Rosenbrock 1963 and ebi is an Euler Backward Iterative scheme Each of these solvers usually needs some numerical parameters these are gathered in the Fortran include file paraero inc Option With_kelvin_effect only affects dynamic bins Among aerosol species sulfate condensation may have a different treatment If Sulfate_computation is set to equilibrium then its treatment is equivalent to other species for both equilibrium and dynamic bins But if it is set to dynamic then sulfate condensation is time resolved for all bins using an analytic solution of mass transfer equations This method is implemented in the sulfdyn f Fortran routine As dynamic condensation is solved with a Lagrangian scheme a redistribution process over the fixed aerosol size grid has to be performed at th
152. perturbation coefficient and VJ is the gradient calculated by adjoint model lt gt denotes inner product With a 0 the ratio p is supposed to approach to 1 with high precision then becomes unstable due to round off errors In practice a D i m m 1 n where D is the decreasing factor typical values are 2 and 10 m is the integer for largest perturbation typical value is 0 and n is the integer for smallest perturbation 4 6 1 AdjointDriver The objective function is chosen to be the model output of a given grid point in model domain with respect to initial model status The corresponding gradient can therefore be interpreted as the sensitivity This driver aims at the verification of adjoint code obtained by automatic differentiation of underlying model code using Odyss e version 1 7 The following options in section adjoint provide flexible control of the verification ladjoint Point_species_name Species name of the selected point in model domain for sensitivity calculation Point_nx x index of the selected point for sensitivity calculation Point _ny y index of the selected point for sensitivity calculation Point_nz z index of the selected point for sensitivity calculation Norm_perturbation vector Norm of the initial perturbation vector With_random perturbation With random directions for the perturbation Decreasing root Decreasing factor of the sequence of perturbation vectors D Start_index Index
153. r concentrations averaged over Interval length by setting Averaged to no or yes respectively A 5 4 Simulation Compile the driver cd Polyphemus driver make polair3d Launch the simulation from TestCase cd TestCase Polyphemus driver polair3d config polair3d cfg A 6 Visualizing Results A 6 1 Modifying Configuration File Modify results disp cfg if necessary in particular if you have modified polair3d saver cfg input Number of time steps for which concentrations are saved Nt 22 Domain description for x and y x_min 10 0 Delta_x 0 5 Nx 65 y_min 40 5 Delta_y 0 5 Ny 33 Number of levels for which concentration are saved Nz 1 file 03 bin 130 APPENDIX A POLYPHEMUS EULERIAN TEST CASE A 6 2 Using Python For details see Section 7 1 3 Remember that the directory atmopy should be in your PYTHONPATH Launch Python and then type in command line comments starting with have been added to explain the meaning of each line dispcf m d 7 0 Display the data for the 8th time step and the first vertical level remember that indices start at 0 from atmopy display import Import to the interactive session all functions from the module display of atmopy m getm disp cfg Create the map d getd disp cfg Create a data with the results The image obtained is Figure A 1 180 160 40 20 Figure A 1 Figure o
154. r of points to calculate the Chamberlain integral integer Relevant only when dry deposition with Chamberlain model is taken into account output Path to the configuration for the output saver Note The Chamberlain integral for the calculation of dry deposition is discretized and approx imated as a sum The integer that is provided corresponds to the number of terms of the sum in the plume model In the puff model it is incremented at each time step so as to have a number of points consistent with the range of the integral that is not to have too many points to discretize an integral whose range is very small 5 1 2 Source Description plume source dat Sources are described in a single configuration file containing as many sections as there are sources Each section named source is associated with a new source Each section contains the following information 1 the emission rate in mass per seconds the mass unit does not matter the model will stick to it 2 the velocity of emitted pollutants ms 3 the temperature of pollutants when emitted C 4 the section area in m of the source most likely a stack 5 the abscissa of the source m 6 the ordinate of the source m 7 the 5 1 GAUSSIANPLUME 89 height of the source m and 8 the species that is emitted A typical source file looks like this source Source coordinates meters Abscissa 100 Ordinate 100 Altitude 0 5
155. r these saver units are save Levels A list of integers that determines the vertical layers to be saved Note that 0 is the first layer Remember that the heights you specified in the file levels dat are those of the level interfaces while concentration are saved in the middle of each levels Averaged Should concentrations be averaged over Interval_length If not instantaneous concentrations are saved Initial_concentration Should initial concentrations be saved This option is only avail able if concentrations are not averaged imin Minimum latitude index of the subdomain imax Maximum latitude index of the subdomain jonin Minimum longitude index of the subdomain j_ max Maximum longitude index of the subdomain 82 CHAPTER 4 DRIVERS 4 7 4 SaverUnitDomain_assimilation The output saver SaverUnitDomain_assimilation defines an output saver unit similar to SaverUnitDomain except that it requires additional parameters presented in the table below save Date file The full path name of the file that stores the date sequences of the assimilation results The group attribute of the output saver SaverUnitDomain_assimilation is set to analy sis whereas the group attributes of other saver units are set to forecast by default Its Type is domain_assimilation 4 7 5 SaverUnitDomain_prediction The output saver SaverUnitDomain prediction defines an output saver unit similar to SaverUni
156. ral sections save Each section is associated with one element of a list of output saver units managed by BaseOutputSaver According to the value of Type in every section different saver units are called Note however that a group attribute can be set in BaseQutputSaver the default being all and the other choices being forecast and analysis and that only savers with the same group are called Some parameters must be provided for any kind of savers Species Date_beg Date_end Interval_length Type Output_file save Chemical species to be saved If it is set to all concentrations for all species are saved The date from which the concentrations are saved If concen trations are averaged the first step at which concentrations are actually saved if not Date_beg but Date_beg plus the number of steps over which concentrations are averaged If the value 1 is supplied Date_beg is set at the start of the simulation The last date at which concentrations may be saved If the value 1 is supplied Date_end is set at the end of the simulation The number of steps between saves The type of saver see Table 4 12 for details The full path of output files in which amp f will be replaced by the name of the chemical species Note that the directory in which the files are written must exist before the simulation is started Note that Species Date_beg Date_end Interval_length must appear before Type After Type put add
157. ribed in Section 5 9 2 is that more meteorological fields are necessary see Section 2 5 4 Species The species file is exactly the same as the one presented in Section 5 9 3 5 10 3 Chemistry Files When model CastorChemistry is used four files are necessary to describe the chemistry e Reaction file which gives the reactions between the species managed in the format 2 CO OH 2 H02 C02 The first column gives n the number of species reacting the n following columns give the name of the species reacting the following columns are the number and names of the species resulting from the reaction e Stoichiometry file e Photolysis_file e Rates_file 106 CHAPTER 5 MODELS Chapter 6 Modules 6 1 Transport modules 6 1 1 AdvectionDST3 Module AdvectionDST3 is the transport module associated to advection for Polair3D It is based on a third order direct space time scheme with a Koren Sweby flux limiter The data needed are the wind components and boundary conditions if they are available Please note that Courant Friedrichs Lewy CFL condition is not verified and that the user should choose the mesh dimensions and the time step of simulations very carefully 6 1 2 DiffusionROS2 Module DiffusionROS2 is the transport module associated to diffusion for Polair3D It is based on a second order Rosenbrock method Fortran routines are used to perform all numerical computations 6 1 3 TransportPPM Module TransportPPM is the nu
158. rithm parameters are set in section 4DVar 4DVar Display_precision Display precision for optimization results Jb_file Name of the file that saves background departure during optimiza tion Jo_file Name of the file that saves observation discrepancy during opti mization Gradient_norm_file Name of the file that saves gradient norms during optimization With trajectory management If the trajectory of model integration is saved to disk for adjoint integration Trajectory_delta_t Trajectory time step in seconds Trajectory file Name of the file that saves model trajectory The parameters for numerical optimization algorithm are set in section optimizer optimizer Type Type of optimization solver only BFGS is supported Maximal_iteration The number of the maximal iteration for numerical optimization Display_iterations If the optimization results during iteration are displayed 4 6 Drivers for the verification of adjoint coding The three drivers AdjointDriver GradientDriver Gradient4DVarDriver are dedicated to the verifications of adjoint model The gradient of a given objective function calculated by adjoint model is compared with the gradient calculated by finite difference The following ratio is checked _ J e ah I x a Ved h 4 6 DRIVERS FOR THE VERIFICATION OF ADJOINT CODING 79 where J is the objective function x is the control variable h is the perturbation direction a is the
159. rix numpy numpy Numeric or numarray interactive True see http matplotlib sourceforge net interactive html You may change the backend depending on what is installed on your computer Polyphemus development team mostly uses the backend TkAgg but other interactive backends are fine If you have any question about the backends consult Matplotlib website Now we test the installation Launch Python and 113 114 CHAPTER 7 POSTPROCESSING In 1 from pylab import In 2 plot 5 8 On screen you should get a new window a figure with a line first diagonal from 0 5 to 1 8 And the prompt should still be available In 3 Make another plot In 3 plot 6 71 You should get a new line in green probably The prompt should still be there In 4 Basemap Basemap extends Matplotlib so that one may display fields with a map in the background World map Europe map You can test your Basemap installation with gt gt gt from pylab import gt gt gt from matplotlib toolkits basemap import Basemap gt gt gt m Basemap projection cyl gt gt gt m drawcountries gt gt gt m drawcoastlines gt gt gt draw This should show a World map Other examples are available on Matplotlib website AtmoPy Recall that extract _configuration cpp must be compiled in atmopy talos see Section 1 3 Then make sure that Python will be able to find the AtmoPy directory in order t
160. s a toolkit available on Matplotlib website http matplotlib sourceforge net but usually not included in Matplotlib package SciPy any recent version All of them are open source software Requirements are shown in Table 1 1 NewRan is not included in Table 1 1 because it is only needed if one performs data assimi lation Table 1 1 Polyphemus requirements Blitz Blas Lapack NetCDF NumPy Matplotlib SciPy driver X X include atmopy X X X preprocessing bc bio dep emissions ground ic meteo postprocessing X X X water_plume X PS PS PS PS PS PS PS 1 3 Installation 1 3 1 Main instructions As soon as libraries and compilers are available Polyphemus is almost installed First extract Polyphemus sources to a given directory Polyphemus is usually distributed in a tar tgz tar gz or tar bz2 file These files are extracted with one of these commands tar xvf Polyphemus tar tar zxvf Polyphemus tgz tar zxvf Polyphemus tar gz tar jxvf Polyphemus tar bz2 Polyphemus programs must be compiled by the user when needed Makefiles called makefile are provided so that program compilation should be easy Depending on your compilers and maybe the paths to the libraries you might need to slightly modify the makefiles Then one may compile the program meteo cpp in this way cd Polyphemus preprocessing meteo make meteo 1 3 INSTALLATION 13 Then the program meteo is compiled and can be run Launch ma
161. scribed in Section 5 3 The only data that may differ are the paths to the input files 5 4 2 Source Description puff_aer dat It is the same file as the puff file for gaseous species described in Section 5 3 except that obviously some or all emitted species will be particulate species The corresponding sections are named aerosol_source 5 4 3 Vertical Levels Species Meteo and Diameters Vertical level file and gaussian meteo file have been described in Section 5 1 and diameter files is the same as in Section 3 9 2 Species file is the same file as described for the plume model for aerosol species Section 5 2 4 5 5 Polair3DTransport The model Polair3DTransport is configured with three configuration files polair3d cfg polair3d data cfg and polair3d saver cfg and two data files levels dat and species dat The main configuration file polair3d cfg provides the paths to the four other files 5 5 1 Main Configuration File polair3d cfg domain Date_min Starting date in any legal format see Section 2 2 7 The date can therefore include seconds Delta_t Time step in seconds Nt Number of iterations of the simulation integer 5 5 POLAIR3DTRANSPORT x min Delta_x Nx ymin Delta y Ny Nz Vertical_levels Cartesian Species With_advection With_diffusion With_air_density With_initial_condition With_boundary_condition With_deposition With_point_emission With_surface_emission With_volume_e
162. servationManager is dedicated to ground observation managements general Species Name of observed species The current version deals with only one observed species Error_variance Error variance for the observed species With_spatial_interpolation Should observations be interpolated at adjacent model grid points With_perturbation Should the observation be perturbed Perturbation_scale If With_perturbation is set to yes gives the amplitude of the perturbation stations Nstations Total number of stations Stations_file File containing station information code name latitude longi tude and altitude amp s in path names is replaced by species name specified in general section Input_directory Directory where the observations are stored 4 8 2 SimObservationManager The SimObservationManager is dedicated to synthetic observation managements Library NewRan is needed for random number generations Note that NewRan is not included in the distribution and it is the user s duty to install NewRan The associated configuration file is an extension of that of GroundObservationManager The additional sections are mainly for data specifications of the binary data files simulation manager 86 CHAPTER 4 DRIVERS Simulation_option Specifies how observations are provided The current version deals only with observations at ground stations Input_file Files containing the observation data They usually are generated
163. sir r a ee eon cae e e ee e sk 23 274 Useful To ls 2 0 40h phere a ane eee RG a el a ace ed a 24 2 4 1 Information about Binary Files 0 25 2 4 2 Differences between Two Binary Files 25 23403 a MM5 Biles acto oc A A A AA A Be 26 24 4 Seript call dates Ud Sec aa eae we ee 30 2 5 Setting Up a Simulation o aa pu suce d aa 0 0 0202 a aa a eee 31 2 5 1 Suggested Directory Tree aoaaa a 31 20 2 Roadmaps ses i eheee gr pet a a uE AA aaa aae a E e Bee E i ae 32 2 5 3 Mandatory Data in Preprocessing ooo 02005 33 2 5 4 Mandatory Data for Models aoaaa a 34 2 5 5 Models Modules Compatibilities o oo aaa a 35 2 5 6 Checking Results a a G A ee 36 2 5 7 Important Notice ee 36 4 CONTENTS 3 Preprocessing 37 Sal Remark iia She done Veet o BS BATS A ae a 37 32 Introductions A ok ee fe do ah Bate ey aa 37 3 2 1 Running Preprocessing Programs a 37 3 2 2 Configuration me lr a ee ee eee BR Aap es De Pee ew a a 38 3 294 Dates e ok 8st A ba SE a Pepe a 39 32d Data Eiles o te hn A ae a el ed le AAA ad 39 3 30 Ground Data r g sae as de a ee ee Se ee Eo Set a ee as 40 3 3 1 Land Use Cover GLCF luc glcf o 40 3 3 2 Land Use Cover USGS luc usgs 20004 41 3 3 3 Conversions luc convert sacosa o 42 3 3 4 Roughness roughness 2 0 00 0 R S ah K ee ee 42 3 4 Meteorological Fields 2
164. synthetically active radiation is stored File where the diffuse part of the photosynthetically active radia tion is stored File where the direct beam part of photosynthetically active radi ation is stored File where 3D specific humidity is stored File where surface pressure is stored File where friction velocity is stored File where canopy wetness is stored File where rain is stored File where roughness height is stored Configuration file that describes land use cover see below for de tails about this file File containing the data for species This file should contain the species name the molecular weight gmol Henry con stant diffusivity reactivity alpha Zhang et al 2003 beta Zhang et al 2003 Rm An example for RADM RACM is available in preprocessing dep input species data txt Directory where the output files are stored Species Number of species for which data are pro vided This should be the number of columns in preprocessing dep input species data txt Options If this option is set to yes the roughness height used in calculations only depends on the model cell and not on the land use category In this case it uses the data file whose path is given in entry RoughnessHeight section paths If the options is set to no recommended the roughness height depends on the land use category see entry Type Parameterization used to compute the aerodynamic resistance You can choose between fh
165. system will be Windows and Talos won t be able to read the configuration In that case to solve the problem if needed simply open the file with emacs If in the mode line line at the bottom of the buffer appears DOS the coding system is incorrect To modify it type C X lt Ret gt f lt Ret gt Actually the last lt Ret gt sets the coding system to its default value which is UNIX encoding http www gnu org software emacs Chapter 3 Preprocessing This chapter introduces all preprocessing programs It details the input files data files and configuration files of every program and it describes their output files In Section 3 2 config urations and features shared by almost all programs are explained 3 1 Remark In the descriptions of preprocessing programs there are references to functions like ComputePressure ComputeAttenuation LWC etc These functions are part of AtmoData and are described in AtmoData scientific documentation Njomgang et al 2005 3 2 Introduction 3 2 1 Running Preprocessing Programs Most preprocessing programs e accept one or two configuration files as arguments e process data daily unless specified otherwise see Section 3 2 3 e append their results at the end of binary files if they already exist or create them Note that they cannot create the directory so you have to make sure it exists before launching a preprocessing program For instance program meteo processes mete
166. t 1 to use RADM parameterization or put 2 to use ESQUIF parameteri zation clouds Minimum cloud basis height in m Kz Lower threshold for vertical diffusion in m Higher threshold for vertical diffusion in m s If set to no the lower threshold is applied only at the top of the first layer otherwise it is applied to all levels Z 1 Sve 3 4 METEOROLOGICAL FIELDS 49 The program basically reads data in MM5 output file and interpolates it in time and space to Polyphemus grid MM5 file is described in MM5 meteo cfg and Polyphemus grid is described in general cfg Note that each time a field is loaded by MM5 meteo all time steps are loaded in memory Note that the fields are released from memory when unused but you may still need a lot of memory for big MM5 output files The program first computes the altitude of MM5 layers and converts the Polyphe mus grid coordinates latitude longitude to MM5 grid coordinates Lambert Mercator or stereographic for interpolations Interpolations on the horizontal are performed in MM5 grid for efficiency The pressure is computed based on MM5 fields The winds are ro tated this gives meridional and zonal winds The Richardson number is then computed ComputeRichardson The relative humidity and the critical relative humidity are computed respectively with ComputeRelativeHumidity and ComputeCriticalRelativeHumidity The cloud fraction is computed with ComputeCloudFraction For it the
167. t CC cfg must respectively start and end exactly at dates 2001 04 15 and 2001 06 15 The python script bc gocart py provides an easy way to compute boundary conditions without worrying about how many times to launch bc gocart In the last example one should simply launch bc gocart py general cfg 04 06 where 04 and 06 respectively stands for the first and last month to treat Pay attention that some paths must be supplied inside this script paths of Gocart configuration and data files for it to work Remarks Gocart does not provide any boundary conditions for nitrate and ammonia you have to com pute them on your own Nevertheless a quick way to compute boundary conditions for ammonia is to apply electroneutrality to already computed aerosol boundary conditions from Gocart or whatever else in fact This can be done by bc nh4 program which takes two arguments bc nh4 general cfg bc nh4 cfg The electroneutrality equation is set in configuration file bc nh4 cfg 3 9 PREPROCESSING FOR GAUSSIAN MODELS 65 3 9 Preprocessing for Gaussian Models 3 9 1 Program discretization The aim of this program is to discretize a line emission in the case of a continuous source plume source or an instantaneous one puff source It reads a line source given by two points or more and gives in return the discretized source The output data is a list of point sources whose coordinates have been calculated given the line coordinates and th
168. t of a continuous plume or instantaneous puff source of pollutant As for now Castor models only deal with gaseous species while the other models deal with gaseous or aerosol species 5 1 GaussianPlume Model GaussianPlume is the Gaussian plume model for gaseous species only The associated pro gram to be run is plume and it is configured with one configuration file plume cfg and four data files plume source dat plume level dat gaussian meteo dat and gaussian species dat The configuration file provides the paths to the four other files Basically given a series of con tinuous point sources it calculates the concentration of each species along a specified grid There are several output files one for each species that are binary files The way results are saved is described in an additional configuration file which corresponds to the file described in Section 4 7 reference plume saver cfg In these configuration files there are entries that are not relevant for the Gaussian model but that must be provided anyway In descriptions of configuration files below they are described as irrelevant 5 1 1 Configuration File plume cfg domain Date_min Irrelevant Provide a date Delta_t Irrelevant Provide any number Nt Irrelevant Provide an integer x_min Abscissa in meter of the center of the lower left cell Delta_x Step length along x in m Nx Number of cells along x integer ymin Ordinate in meter of the center o
169. t you should have Polyphemus installed and working in order to use the test case A 1 Preparing the Test Case The first step is to extract the archive TestCase tar bz2 tar xjvf TestCase tar bz2 The directory TestCase that will be created is divided in four subdirectories e data which contains all precomputed data e raw_data which contains all data used for preprocessing After preprocessing the results are stored in data to be used directly during the simulation e config where configuration files are provided e results where the results of the simulation are stored In addition a file version is included to indicate for which version of Polyphemus the test case is designed and which versions of the libraries are needed MM5 2004 08 09 should be extracted and then placed in raw_data tar xjvf MM5 2004 08 09 tar bz2 mv MM5 2004 08 09 TestCase raw_data MM5 Now you have all data necessary to perform preprocessing for the ground and for meteorological data All other data emissions deposition velocities are provided and ready to use nttp www enpc fr cerea polyphemus 125 126 APPENDIX A POLYPHEMUS EULERIAN TEST CASE A 2 Modifying the General Configuration File The file general cfg is used by all preprocessing programs and as such must be the first file you modify when performing preprocessing Make sure to modify and use the file provided in the directory TestCase config Here is a copy of this file
170. tDomain The group attribute of the output saver SaverUnitDomain prediction is set to prediction Its Type is domain prediction It works in a similar way to SaverUnitDomain_assimilation except that it is designed for the storage of model predic tions starting from analyzed model state at the end of the assimilation period 4 7 6 SaverUnitNesting and SaverUnitNesting_aer The saver units SaverUnitNesting and SaverUnitNesting aer are used to perform nested simulations That means that the results of a first simulation on a large domain are interpolated and saved at the boundary of a subdomain and are then used as boundary conditions for a second simulation on the subdomain If the saver unit is of Type nesting or nesting_aer the additional parameters needed in the section save are presented in the table below save x_min Origin of the subdomain along zx Delta x Step along x for the subdomain Nx Number of points along x for the subdomain ymin Origin of the subdomain along y Delta_y Step along y for the subdomain Ny Number of points along y for the subdomain levels File giving the interfaces of the layers for the subdomain Nz Number of layers in the subdomain In Output_file amp f and amp n are replaced as for SaverUnitDomain or SaverUnitDomain_aer and amp c is replaced by the direction along which the boundary conditions were interpolated that means that amp c is replaced by x y or z 4 7 7
171. tably defining the domain description 2 a specific configuration file emissions cfg that includes options for emission generation Markups defined in one configuration file can be used in the other file Note however that each section must be defined in one file only 2 3 RUNNING PROGRAMS 21 2 2 7 Dates Date formats are YYYY Year YYYY MM With the month YYYY MM DD With the day YYYY MM DD_HH With the hour YYYY MM DD_HH IT With the minute YYYY MM DD_HH II SS With the second Months range from 01 to 12 Days range from 01 to 31 Hours range from 00 to 23 Minutes and seconds range from 00 to 59 If the month is not specified format YYYY then the month is set to 01 January If the day is not specified formats YYYY and YYYY MM it is set to 01 first day of the month If the hour the minute or the second is not specified it is set to zero 00 Hyphens and underscores may be replaced with any character that is neither a delimiter see Section 2 2 2 nor a cipher They can also be removed Examples 19960413 1996 04 13_20h30 1996 04 1302030 Recommandation Use hyphens around the month and around minutes Use an underscore between the day and the hour YYYY MM DD_HH 11 SS 2 2 8 Booleans Booleans are supported in configuration files and can be specified in any of the following ways true t yes y false f no n This is case unsensitive e g True or NO are valid 2 3 Running Programs 2
172. tance if ratio is set to 0 3 stations with over 70 of missing observations are discarded Type of the output summary statistics for all stations or results written in a file file list List of files used if multiple file is set to yes legend List of the legends associated to the files in file 1ist in the same order 7 2 2 Script evaluation py Script evaluation py is meant to assess the performances of a chemistry transport model CTM Results of the CTM are compared to measurements at stations and statistics on the differences are computed The output of the script is presented on screen or can be saved in a file 7 2 3 Script disp py This script written in Python allows to display concentrations and observations at the sta tion station with regard to the time Measurements are displayed with the style defined in meas_style and simulation results with sim_style 122 CHAPTER 7 POSTPROCESSING 7 3 Aerosol Postprocessing 7 3 1 Configuration File The configuration file simulation_aerosol cfg is the same as simulation cfg described pre viously where aerosol parameters are added Nbins computed Dmin Dmax file_bounds bin index shift primary inorganics organics primary_names inorganics_names output_species with_organics graph_type graphs_at_station i_range j range log_plot directory_list input Number of size bins If yes the bin bounds are computed using a logari
173. the molecular weights of output species Directory_ic Directory where the output initial conditions must be stored The name of the Mozart 2 files must be in the form h00xx nc where xx is computed as 60 CHAPTER 3 PREPROCESSING shown in Equation 3 1 3 1 Na 6 va 40 int a 10 with Na the number of days since the beginning of the year 0 for first January and int x represents the integral part of x In case your Mozart 2 files do not satisfy this format this may happen if Mozart files are updated on the NCAR data portal you may modify the code or contact Polyphemus team at polyphemus cerea enpc fr 3 8 Boundary Conditions 3 8 1 Boundary Conditions for Gaseous Species bc Boundary condition for gaseous species are generated using Mozart 2 files See Section 3 7 on how to get those files In addition to the domain definition Section 3 2 2 below is the information required in the configuration for bc see example bec cfg bc_input_domain Nt Number of time steps in Mozart 2 files Delta_t Time step of Mozart 2 files in hours Nx Number of grid points along latitude in Mozart 2 files integer Ny Number of grid points along longitude in Mozart 2 files integer Nz Number of vertical levels in Mozart 2 files integer bc_files Directory_bc Species Molecular weight Directory where the output boundary conditions must be stored File providing correspondence between the name of spe
174. the paths in particular check that the data and saver files are config polair3d data cfg and config polair3d saver cfg and to make sure that the date for the simulation is 20040809 date for which the meteorological data have been computed A 5 2 Modifying the Data File Check config polair3d data cfg If you decided to use Louis parameterization for vertical diffusion modify the file associated to VerticalDiffusion in the section meteo A 6 VISUALIZING RESULTS 129 As before check the paths and dates In particular if the dates in any section except for photolysis see below are not right you can have an error message ERROR An input output operation failed in FormatBinary lt T gt Read ifstreamg FileStream Array lt TA N gt amp A Unable to read 42900 byte s The input stream is empty Indeed input data can be computed for several days so the program will discard the data for the days between Date _min in a section of polair3d data and Date _min for the simulation Here as the data has been computed for one day only it would be as if the data files were empty hence this error Remark In the case of photolysis data are provided for a whole year and Date_min must be 2004 01 01_12 A 5 3 Modifying Saver File The file polair3d saver cfg should be ready to use You can modify the species to save you are advised against saving concentrations for all species You can choose to save instantaneous concentrations o
175. thmic law If no they are given in a file If bin bounds are computed the minimum and the maximum di ameters If bin bounds are given in a file the name of the file Number of the first bin typically 0 or 1 Names of the primary species in the model Names of the inorganic species in the model Names of the organic species in the model Real names of the primary species to be displayed Real names of the inorganic species to be displayed Aggregated data in output PMjo PMa2 5 total mass for each chemical component total mass and number in each bin If yes total masses will take into account organic species Graphs that will be displayed when launching graph aerosol py chemical composition mass and number distribution time series If yes the graphs will be displayed for the simulation at a given station If no graphs will be an average over the domain defined by i range and j_range First and last indices in x direction for the considered domain First and last indices in y direction for the considered domain If yes the mass and number distributions will be displayed with a log scale for diameters List of directories where outputs are the aggregated data will be written in a file in the same directory as the output The file simulation_aerosol cfg is used by scripts init_aerosol py and graph_aerosol py 7 3 2 Script init_aerosol py The outputs of the model for aerosols will be several files lt species gt _ lt n
176. ule at all remove them is necessary The modules are all template arguments of the model AdvectionDST3 lt real gt DiffusionROS2 lt real gt and Decay lt real gt in the previous example except for real that should not be changed The order in which the modules are provided matters it is always advection diffusion and chemistry or transport single module and chemistry See Section 2 5 5 for the modules you can use with the model you chose Then in your main C program declare the right driver You may replace BaseDriver with a new driver at this line in driver polair3d cpp BaseDriver lt real ClassModel BaseOutputSaver lt real ClassModel gt gt Driver argv 1 Finally make sure to include all models modules drivers and output savers you use at the beginning of the file statements include cxx The makefile may need changes too if the module uses Fortran functions In particular chemistry modules ChemistryRADM and ChemistryRACM need Fortran routines make sure that they are included in SRC77 e for ChemistryRACM LU_decompose f LU solve f angzen edf f chem f dratedc f fexchem f jacdchemdc f kinetic f rates f roschem f and solvlin f in directory include modules chemistry ChemistryRACM e for ChemistryRADM LU_decompose f LU_solve f angzen edf f chem f fex chem f jacdchemdc f kinetic f roschem f and solvlin f in directory include modules chemistry ChemistryRADM Chemistry module Chemistry
177. umber gt bin where lt species gt is an aerosol chemical component in aerosol_species see Section 5 5 3 and lt number gt is the index of the size bin But often measurements are aggregated data e PMjo and PM2 5 are the mass of aerosol with a diameter smaller than 10 um and 2 5 um respectively e Total mass of one chemical component One can also be interested by the number of particles in each size bin granulometry or by the mass distribution along the size bins This will be done by the script graph_aerosol py but before you have to launch init_aerosol py by the command 7 3 AEROSOL POSTPROCESSING 123 python init_aerosol py simulation_aerosol cfg Then you can launch disp py and evaluation py with species such as PM10 PM2 5 PNA total mass for sodium etc 7 3 3 Script graph_aerosol py You can launch graph_aerosol py by the command python graph_aerosol py simulation_aerosol cfg Then each desired graphs specified in graph type section of the configuration file will be displayed in a different window 124 CHAPTER 7 POSTPROCESSING Appendix A Polyphemus Eulerian Test Case The test case is available on Polyphemus sitet In order to use the test case you should download e The meteorological data file MM5 2004 08 09 tar bz2 The file is not included in the test case so that it can be used for various applications and has not to be downloaded each time e The archive TestCase tar bz2 Note tha
178. urf d 10 0 gt gt gt colorbar Fig 0 0 20 40 60 80 100 120 140 160 180 Figure 7 2 Concentration map obtained with the command contourf In addition functions stat spatial distribution and stat time evolution may be very useful gt gt gt d getd disp cfg gt gt gt print d shape 48 1 46 67 gt gt gt d_max stat spatial_distribution d max Takes time maxima gt gt gt print d_max shape 1 46 67 In every cell function stat spatial_distribution takes the maximum concentration over the time If you want to display the time averages gt gt gt dispcf m stat spatial_distribution d mean 0 Function stat time_evolution computes the time evolution of a spatial indicator For instance gt gt gt d_min stat time_evolution d min Spatial minimum as function of time gt gt gt print d_min shape 48 gt gt gt plot d_min label Spatial minimum gt gt gt plot stat time_evolution d max label Spatial maximum 120 To Get Further Help CHAPTER 7 POSTPROCESSING In IPython command line you can get help this way gt gt gt help plot gt gt gt help stat time_evolution In addition all AtmoPy functions are described in a reference documentation generated with epydoc See AtmoPy web page http www enpc fr cerea polyphemus atmopy html Other online resources 1 http diveintopython org learning Python most useful chapters
179. us species see Section 5 2 4 3 PuffDriver It is the driver dedicated to the Gaussian puff model The associated configuration file is the same as the one for the BaseDriver and it is usually part of the model configuration file described in Section 5 3 The associated input data file describes the meteorological data It is the same file as for the plume model For each meteorological situation the driver calculates the concentrations that depend on time That is for a given situation it makes a loop on time and calls the model at each time step to calculate the current concentrations It is associated with two models the GaussianPuff model for gaseous species only described in Section 5 3 and the GaussianPuff_aer model which is the same model for aerosol and or gaseous species see Section 5 4 75 76 CHAPTER 4 DRIVERS 4 4 StationaryDriver This driver as the Gaussian drivers presented before is used to perform a simulation at local scale the only difference being that in that case an Eulerian model is used An additional section stationary is necessary in the configuration file stationary Nt Number of stationary steps Delta t Time step between stationary steps 4 5 Data Assimilation Drivers 4 5 1 AssimilationDriver It is the base driver from which all data assimilation drivers are derived Data assimilation is the concept and methods that estimate model state from diverse available sources e g mode
180. uxes are collected in order to postprocess them if wet deposition is taken into account 3 used in the model The bin bounds are presented as follow Bin_bounds 102 CHAPTER 5 MODELS diameter of the particle classes in micrometers 0 00 111 525 Note that these values are the bounds of the various diameter classes and that therefore there is one more value than there are classes 5 7 2 Data Description polair3d data cfg In addition to the sections described in Section 5 6 2 some parameters may be necessary Section Entries Comments initial condition aerosol Fields Filename If initial conditions are activated With_initial_condition_aerosol boundary condition aerosol Date min Deltat If boundary conditions are activated Fields Filename With_boundary_condition_aerosol deposition velocity aerosol Fields Filename If deposition is activated With_deposition_aerosol and de position velocities are not computed Compute_deposition_aerosol set to no point_emission_aerosol file Path to the file which defines the point emissions If point emissions are activated With_point_emissions_aerosol surface_emission_aerosol Date min Delta t If surface emissions are activated Fields Filename With_surface_emission_aerosol volume emission aerosol Date min Deltat If volume emissions are activated Nz Fields With_volume_emission_aerosol Nz Filename is the number of levels in which pollutants ar
181. viation Observation maximum_spread Every random number for observation perturbations cannot exceed the mean plus or minus Observation_maximum_spread times the standard deviation For fields listed in section AdditionalField eg Attenuation and VerticalDiffusionCoefficient the perturbations do not depend on species For each additional field or each species of species dependent fields the perturbation is performed according to lognormal LN or normal N law with given standard derivation The probability distribution types are listed in the PDF column and the standard derivations are listed in the Parameter column Sometimes there are two additional columns for species dependent fields indicating correlated species and correlation coefficient The correlation coefficients can only be set to 1 Chapter 5 Models There are three major types of models Gaussian models see Section 5 1 5 2 5 3 and 5 4 Polair models see Section 5 5 5 6 and 5 7 and Castor models see Section 5 9 All variants of a model have the same principles but can deal with various applications and phenomena Polair models were the first implemented in Polyphemus They allow as well as Castor models to compute the advection and diffusion of pollutants at a large scale and can integrate various additional phenomena such as photochemical chemistry or deposition Gaussian mod els have been added to perform simulation at a local scale of the effec
182. vious section must equal the number of column after delimiter The numbers in these columns are the fraction between 0 0 1 0 of given Gocart sub species that will contribute to given model species As an example in bc gocart CC cfg the first line PBC 1 O 1 O 64 CHAPTER 3 PREPROCESSING means that sub species CC 1 and CC 3 will fall into PBC Polair3D species and nowhere else In the same way the following line PPOA O 0 4 O 0 4 means that PPOA species is composed of 40 of CC 2 and 40 of CC 4 Important The Gocart files are proceeded month by month e The beginning date of computation is the one provided in general cfg if the beginning month is equal to the Gocart month beginning of Gocart month otherwise e The end date of computation is provided by the length of file Temperature If this length exceeds the Gocart month the end date is set to end of Gocart month e If some boundary files already exist the program bc gocart will not overwrite them but append its result to each For example if you want to compute boundary conditions between 15th of April to 15th of June 2001 you would launch bc gocart three times bc gocart general cfg bc gocart CC cfg 200104 CC STD tv15 g day 200104 bc gocart general cfg bc gocart CC cfg 200105 CC STD tv15 g day 200105 bc gocart general cfg bc gocart CC cfg 200106 CC STD tv15 g day 200106 The file given in Temperature field of configuration file bc gocar
183. y liquid wa ter content solar radiation photosynthetically active radiations direct beam diffuse and total zonal wind meridional wind wind module wind friction module boundary layer height soil 3 4 METEOROLOGICAL FIELDS 45 water content evaporation sensible heat and first level wind module Inside meteo ECMWF variables are read and decumulated in time if necessary Pres sures at ECMWF levels are computed with ComputePressure and altitudes are computed with ComputeInterfHeight and ComputeMiddleHeight Richardson number is then estimated with ComputeRichardson All input fields are then interpolated on the vertical Finally photosynthet ically active radiation are estimated based on solar radiation and zenith angle ZenithAngle To get the complete set of input meteorological data for a transport model one should then launch attenuation Kz and maybe Kz_TM 3 4 2 Program attenuation Program Polyphemus preprocessing attenuation should be launched after program meteo It computes cloud attenuation for photolysis rates It also computes cloud related data such as cloud height Even for passive simulations this program should be launched The reference configuration files for attenuation is Polyphemus preprocessing meteo meteo cfg together with Polyphemus preprocessing general cfg In addition to the domain definition and to the entries of meteo cfg introduced in Section 3 4 1 below are options for attenuation paths
184. yphemus cerea enpc fr Corresponding Fortran compilers are acceptable GNU G77 3 2 3 3 and 3 4 GNU GFortran 4 0 and 4 1 take care GFortran is rather slow according to our tests and Intel Fortran compilers IFC 7 1 and IFORT 8 0 Note for GCC users Please note that the Fortran compiler has changed between versions 3 x and versions 4 x of GCC If you use G 4 x please use GFortran to compile Polyphemus Fortran programs unless you know what you are doing Similarly if you use G 3 x please use G77 Python version 2 3 and higher are supported With regard to software requirements below is a list of possible requirements depending on the programs to be run the C library Blitz http www oonumerics org blitz versions 0 6 0 7 0 8 and 0 9 are supported Note that your compiler may exclude a few versions Blas Lapack compiled libraries any recent version NewRan C library for generation of random numbers from version 2 0 NetCDF compiled libraries and headers C library any version from series 3 x should work 12 CHAPTER 1 INTRODUCTION AND INSTALLATION NumPy any recent version Make sure that your versions of NumPy and Matplotlib see below are compatible Matplotlib any recent version and corresponding pylab version usually pylab is included in Matplotlib package It is recommended to install the corresponding version of Basemap in order to benefit from AtmoPy map visualizations Basemap i
185. ython Commands Loading and Processing Data In IPython AtmoPy first reads the configuration file disp cfg gt gt gt from atmopy import Loads AtmoPy 118 CHAPTER 7 POSTPROCESSING gt gt gt from atmopy display import Loads AtmoPy submodule display gt gt gt d getd disp cfg d is a 4D array You may overwrite the entries in disp cfg gt gt gt d getd disp cfg filename results NO bin Loads another file without editing disp cfg gt gt gt d getd disp cfg Nt 0 Overwrites Nt gt gt gt d getd disp cfg filename results NO bin Nt 0 gt gt gt d getd disp cfg filename results NO bin Nt 0 Nz 2 The array d has four dimensions Nt xNzxNyxNx Hence d 10 0 2 9 refers to data at the time step 10 11t time step since indices start at 0 in the first level in horizontal cell with indices 2 along y and 9 along x Another example is d 15 0 which is a 2D array dimensions y x of data at 16 time step and in the first layer A few examples show the way data can be manipulated gt gt gt d getd disp cfg filename results 03 bin gt gt gt d_ref getd disp cfg filename results 03 reference bin gt gt gt print d shape Same as d_ref shape Nt 48 Nz 1 Ny 46 Nx 67 48 1 46 67 gt gt gt print d mean 78 5597571528 gt gt gt print abs d d_ref mean 16 99608674 gt gt gt from numpy import

Polyphemus 1.1α User's Guide

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Polyphemus 1.1α User's Guide