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Polyphemus 1.0 User's Guide - Cerea

1. 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 GLCF 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 36 CHAPTER 3 PREPROCESSING 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 latlong 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 1latlong 1km landcover bsq lies LUC_in Name of t
2. 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 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 109 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
3. 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 117 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 gives 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_meteo1 shows the puff at t 0s t 3s and t 8s for the fir
4. meteo main configuration file secondary configuration file date meteo main configuration file date meteo date Arguments main configuration file optional main configuration file Default meteo cfg secondary configuration file optional secondary configuration file date date in format YYYYMMDD Program meteo takes from one to three arguments Below are three possible calls Further details about specific programs are provided in chapter 3 18 CHAPTER 2 USING POLYPHEMUS meteo 20010422 meteo meteo cfg 20010422 meteo general cfg meteo cfg 20010422 The first line is equivalent to meteo meteo cfg 20010422 The third line involves two configuration files The program meteo 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 meteo general cfg meteo cfg 20010422 with the two configuration files general cfg and meteo cfg is the advocated line The con figuration 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
5. 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 or 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 110 APPENDIX A POLYPHEMUS EULERIAN TEST CASE A 6 2 Using IPython For details see Section 7 1 2 Remember
6. 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 data Data description Path to the configuration file that describes input data Horizontal diffusion Horizontal diffusion coefficient in m s 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 TestCase 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 t
7. volume_emission_aerosol Entries Fields Filename Date min Delta _t Fields Filename Fields Filename file Date min Delta _t Fields Filename Date min Delta _t Nz Fields Filename Comments If initial conditions are activated With_initial_condition_aerosol If boundary conditions are activated With_boundary_condition_aerosol If deposition is activated With deposition aerosol and de position velocities are not computed Compute deposition aerosol set to no Path to the file which defines the point emissions If point emissions are activated With_point_emissions_aerosol If surface emissions are activated With_surface_emission_aerosol If volume emissions are activated With_volume_emission_aerosol Nz is the number of levels in which pollutants are 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 PARO2 PALK1 PNA PSO4 POLE1 PAPI1 PNH4 PNO3 PAPI2 PLIM1 PHCL 5 8 Polair3DChemistryAssimConc PARO1 PLIM2 PPOA PH20 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 5 9 CASTORTRANSPORT assimilation 89 Polair3DChemistryAssimConc is configured with three configuration files polair3d cfg
8. 8 9 10 11 12 13 14 15 16 17 1 1 0 1 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 1 01 0 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 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 gm 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 SUN 3 6 EMISSIONS Delta_t Rates Terpenes Terpenes_ratios 53 biogenic Time step in hours
9. Minimum value of Kz in PBLH for cloudy conditions in ms Minimum value of Kz above PBLH in ms Maximum value for Kz in ms Among output files one may find e the altitude in meters e the air density AirDensity bin e the pressure in Pa Pressure bin e the temperature and temperature at 2 m in K Temperature bin and Temperature_2m bin e the meridional wind zonal wind convective velocity and wind module at 10 m MeridionalWind bin ZonalWind bin ConvectiveVelocity bin and WindModule_10m bin in ms 1 3 5 DEPOSITION VELOCITIES 47 e the boundary layer height in m PBLH bin e the vertical diffusion coefficients using Troen and Mahrt parameterization Kz bin in el Ine B e the specific humidity in kgkg SpecificHumidity bin e the surface relative humidity SurfaceRelativeHumidity bin e the liquid water content in kgkg LiquidWaterContent bin e the cloud attenuation coefficients Attenuation bin e the soil moisture SoilMoisture bin e the aerodynamic resistance AerodynamicResistance bin e the friction velocity in ms FrictionModule bin 3 5 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 com
10. solar radiation 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 xj Lis the land category and it must contain proportions in 0 1 of each land category in every grid cell Index of sea in land categories recall that indices start at 0 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 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 where output meteorological files are stored Directory where the vertical diffusion using Troen and Mahrt pa rameterization is stored output of Kz_TM ECMWF t_ min First hour stored in every ECMWF 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 ymin 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 in
11. CHAPTER 3 PREPROCESSING 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 similar sections situation at the end of the file Species data file it contains several sections but not all are needed for the preprocessing The needed sections are species Contains the list of all species scavenging Contains the list of the species for which scavenging occurs The scavenging coefficient of the others is set to 0 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 s71 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 scave
12. MODULES cp x y 2 where A is the s x s filiation matrix and C x y z co x y z with c x y z the Co x Y z concentration of species 7 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 0 0 1 0 0 8 0 1 0 05 0 1 0 1 0 6 0 1 0 15 0 0 1 0 7 The matrix for aerosol species is very similar to the one for gaseous species Chapter 7 Postprocessing 7 1 Visualizing Results 7 1 1 Configuration File disp cfg Once you have checked that your binary files seem to be all right see Section 2 5 6 you may want to visualize the results The first step to do that using Matplotlibt is to create a configuration file usually named disp cfg which contains the following information input Nt Number of time steps for which the concentrations are saved Nx Space steps in the x direction Ny Space steps in the y direction Nz Number of vertical layers on which concentrations are saved file Binary file containing the results to be visualized relative or ab solute path Here is an example of such a configuration file input Nt 121 x_min 10 0 Delta_x
13. 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 Component 10 meter V Component SURFACE ALBEDO SURFACE MOISTURE AVAILABILITY BIBIANA 2 4 USEFUL TOOLS 25 SFEM 2 27 2 CA fraction SURFACE EMISSIVITY AT 9 um SFZO 2 27 2 CA cm SURFACE ROUGHNESS LENGTH THERIN 2 27 2 CA 100 cal cm 2 K 1 s71 2 SURFACE THERMAL INERTIA SFHC 2 27 2 CA J m 3 K 1 SOIL HEAT CAPACITY SCFX 1 27 CA fraction SNOW COVER EFFECT SIGMAH 1 25 H S sigma VERTICAL COORDINATE Total number of time steps read in the file 97 For each variable is provided its name its number of dimensions its length along dimension 1 if applicable its length along dimension 2 if applicable r its length along dimension 3 if applicable 4 its length along dimension 4 if applicable 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 its dimensions ordering its unit or DIMENSIONLESS a short description 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 ca
14. 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 115 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 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 simula
15. 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 2 5 SETTING UP A SIMULATION 29 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 e North South surface stress accumulated 181 e Evaporation accumulated 182 e Low cloud cover 186 e Medium cloud cover 187 e High cloud cover 188 e Skin temperature 235 e Forecast albedo 243 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 scav
16. for 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 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 class
17. 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 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 and Species 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 described in Section 5 3 The only data that may differ are the paths to the input files 5 4 2 Source Description pu
18. the deposition velocity is constant for one 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 are given the temperature in Celsius degrees the wind angle in degrees the wind speed in ms the inversion height in m and the stability class which is given by a letter between a and f based on the Pasquill stability classes These five data must always be provided the inversion height is set to 0 if not known and they are written in the output file which will be the meteorological data file of the main program Other meteorological data might be needed depending on the chosen parameterization 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 mm h 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 62
19. 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 y min Origin of the subdomain along y 4 7 OBSERVATION MANAGERS 73 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 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 7 1 GroundObservationManager The GroundObservationManager 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 interpolate
20. 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 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 108 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
21. 9 are supported Note that your compiler may exclude a few versions Blas Lapack any recent version NewRan C library for generation of random numbers from version 2 0 NetCDF C library any version from series 3 x should work Numarray series 1 x is supported 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 10 CHAPTER 1 INTRODUCTION AND INSTALLATION 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 uses the class SimObservationManager with data assimilation drivers Table 1 1 Polyphemus requirements Blitz4 Blas Lapack NetCDF Numarray 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
22. Driver aa ee gie at Bee Gi oe aeons Le de tore we Pe eet a i 70 4 5 OptimallInterpolationDriver 200000000 eee eee 70 4 6 Output Savers se re cera kasha a a ae e eee ke ead a ee 70 4 6 1 BaseOutputSaver aoaaa ee 70 4 6 2 SaverUnitDomain and SaverUnitDomain_aer 71 4 6 3 SaverUnitSubdomain and SaverUnitSubdomain_aer 72 4 6 4 SaverUnitDomain_assimilation 0 e e 72 4 6 5 SaverUnitNesting and SaverUnitNesting_aer 72 4 7 Observation Managers 73 4 7 1 GroundObservationManager e 73 4 7 2 SimObservationManager 0 eee ee 73 CONTENTS 5 Models 51 GaussianPlume s at Yak sou 0 222 kee PRR EE eS ae aes 5 1 1 Configuration File plume cfg _ e e 5 1 2 Source Description plume source dat o o 5 1 3 Vertical Levels plume level dat o o 5 1 4 Species gaussian species dat o e 5 2 GaussianPlume re 5 2 1 Configuration File plume_aer C B 5 2 2 Source Description plume source_aer dat o o ooo 5 2 3 Vertical Levels plume level dat o 5 2 4 Species gaussian species aer dat o o 5 2 5 Diameters diameter dat e 5 3 Gaussian Puth eri a cee ee at Na AN 5 3 1 Configuration File puff cfg 0 00000 5 3 2 Puff Description puff dat 2 2 ee ee 5 3 3 V
23. 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 define 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 12 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 flexible 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 provi
24. Polair3DChemistry AssimConc X X CastorChemistry X 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 OptimalInterpolationDriver for data assimilation optimal interpolation to be asso ciated with Polair3DAssimConc model 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 Ni x Nz x Ny x Nz bytes where Ny and N are the space steps along x and y directions respectively N 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 32 CHAPTER 2 USING POLYPHEMUS Second you should check that the fields have reasonable values using the programs from direc
25. USING POLYPHEMUS 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 gaussian gaussian meteo_aer dat 2 preprocessing discretization to generate source files and gaussian deposition or gaussian deposition_aer to compute deposition velocities without or with aerosol species respectively For more details see Section 3 9 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
26. Use of Two Values of Decay Another option is that each species has two values of T 2 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 2 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 hal1f_life_time_aerosol Half lives in days put O for species without decay First value for day second for night 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 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 C l a y z AC x y z 98 CHAPTER 6
27. WATER MIXING RATIO RNW 3 76 86 25 C 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 C YXS K DAY ATMOSPHERIC RADIATION TENDENCY W 3 76 86 26 C YXW m s VERTICAL WIND COMPONENT PP 3 76 86 25 C YXS Pa PRESSURE PERTURBATION PSTARCRS 2 76 86 C YX Pa REFERENCE SURFACE PRESSURE MINUS PTOP GROUND T 2 76 86 C YX K GROUND TEMPERATURE RAIN CON 2 76 86 C YX cm ACCUMULATED CONVECTIVE PRECIPITATION RAIN NON 2 76 86 C YX cm ACCUMULATED NONCONVECTIVE PRECIPITATION TERRAIN 2 76 86 C YX m TERRAIN ELEVATION MAPFACCR 2 76 86 C YX DIMENSIONLESS MAP SCALE FACTOR 24 MAPFACDT CORIOLIS RES TEMP LATITCRS LONGICRS LAND USE TSEASFC PBL HGT REGIME SHFLUX LHFLUX UST SWDOWN LWDOWN SWOUT LWOUT SOIL SOIL SOIL SOIL SOIL SOIL SOIL SOIL SOIL SOIL SOIL SOIL W CANOPYM WEASD SNOWH SNOWCOVR ALB GRNFLX VEGFRC SEAICE SFCRNOFF UGDRNOFF T2 Q2 U10 V10 ALBD SLMO Sees SS BHAA A eU Ne AUNE PWN BK N N hee e e e e e e a e WN NNNNNNNNNNNNNNyNyyNyyNynyNnynNnynynnynynynyyny ny 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 76 27 27 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86
28. 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 20010422 t_min 0 0 Delta_t 3 0 Nt 9 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 introduced 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 2 3 RUNNING PROGRAMS 19 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 programs Programs and to the output results Directory_computed fields and Directory ground data and one chooses its simulation domain Other configuration files pr
29. 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 particle 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 3 9 PREPROCESSING FOR GAUSSIAN MODELS 65 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 1 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 a
30. emissions is required to compute anthropogenic emissions program emissions the vertical distribution can be generated by other means including by hand 50 CHAPTER 3 PREPROCESSING Nz Vertical levels Nz_in Vertical_levels Vertical distribution Polair_vertical distribution Nsectors domain Number of output vertical levels Path to the text file that stores the altitudes in m of output level interfaces hence Nz 1 values are read EMEP Number of input vertical levels Path to the text file that stores the altitudes in m of input level interfaces hence Nz_in 1 values are read 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 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 Number of activity sectors 3 6 2 Anthropogenic Emissions EMEP emissions Program 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 f
31. 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 SETTING UP A SIMULATION 31 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 module which deals with advection and diffusion This does not mean that a module could not be shared by both models although there is no common 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 X X Polair3DChemistry X X Polair3DAerosol X X Polair3DChemistry AssimConc X X Castor Transport X CastorChemistry X Table 2 3 Compatibility between models and chemistry modules Castor RACM RADM SIREAM Decay Polair3DChemistry X X X X Polair3DAerosol X X
32. 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 Entries Comments initial_condition Fields Filename If initial conditions are activated With_initial_condition boundary_condition Date_min If boundary conditions are activated Delta t Fields With boundary_condition Filename meteo Date min Deltat Required fields are MeridionalWind Fields Filename and ZonalWind if advection is activated VerticalDiffusion if diffusion is activated and Temperature and Pressure in case air density is taken into account deposition Date_min Delta_t If deposition is activated With_deposition Fields Filename point_emission file Path to the file which defines the point emis sions described below If point emissions are activated With point emissions 84 surface_emission Date_min Delta_t Fields Filename volume_emission Date_min Delta_t Nz Fields Filename scavenging Fields CHAPTER 5 MODELS If sur
33. is used to solve sulfate condensation Choices are equilibrium or dynamic Which redistribution method is used Which nucleation model is used Is aerosol density fixed in the module Which method is used to compute aerosol wet diameters 6 2 CHEMISTRY MODULES 95 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 Aerosol 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 Ex
34. o o a 39 34T Program Meteo som tir Al ele ar eee ea ae A ee de 39 3 4 2 Program attenuation e 40 AD Program KZ eck hea ho oa a a Ny oY 41 3AA Program KZeTM aa eh tov A Ae kav eo PE ben 42 3 4 5 Program MM5 meteo 2 02 ee eee ee ee ee 43 3 4 6 Program MMS meteo castor 0 0000 eee eee 45 3 0 Deposition Velocities i etr tose Sh kd A OE ee LP AS Red ae SE 47 3L POSTA dep ti is be ee a le oe Wa 47 3 5 2 Program dep emberson 00000000000 0004 49 3 07 Emissions og A A a RB a DA oe elec a 49 3 6 1 Mapping Two Vertical Distributions distribution 49 3 6 2 Anthropogenic Emissions EMEP emissions 50 3 6 3 Biogenic Emissions for Polair3D Models bio 52 3 6 4 Sea Salt Emissions sea salt 00002000008 53 37 ital Conditions ici ada BA ek Pe a eae ee ee hes BE 54 3 8 Boundary Conditions 54 3 8 1 Boundary Conditions for Gaseous Species DC 54 3 8 2 Boundary Conditions for Aerosol Species bc gocart 55 3 9 Preprocessing for Gaussian Models e o 59 3 9 1 Program discretizations rod das De ey WR Bow A eG 59 3 9 2 Programs gaussian deposition and gaussian depositionaer 60 4 Drivers 69 AL BaseDriver iia Bue Pelee ee a ee ae 69 4 2 PlumeDriv r escri ed eda Ee ae LR ee aa be 69 43 TPULDIVE mos hide de ee Bae ea eh yee eh RS ae Re od ae AS e Ped ee BE 69 AA Stationary
35. 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 Species Levels Error_covariance_model Background_error_variance Balgovind_scale background Model_error_variance Balgovind_scale_model Configuration_file state List of species included in model state vector List of vertical levels of model domain included in model state vector 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_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 for background error covariance The model grid 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 observation management Choose between observation cfg to use observations and observation sim cfg to use simulated
36. 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 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 5 1 GAUSSIANPLUME TT Altitude 0 5 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 m 2 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 preproc
37. 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 the entries for Kz_TM LUC_file Sea_index Roughness_file Directory_meteo File_Kz Directory_Kz_TM path 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 xj Lis the land category and it must contain proportions in 0 1 of each land category in every grid cell Index of sea in land categories remember that indices start at 0 Path to the binary file that describes roughness heights in meters in output grid cells Its format is y xz It is needed only if option Flux_diagnosed is activated Directory where output meteorological files are stored Name of the file where the vertical diffusion coefficients as com puted with the Louis parameterization are stored Name of the directory where the vertical dif
38. 0 CHAPTER 7 POSTPROCESSING 60 80 100 140 160 180 120 Figure 7 2 Concentration map obtained with the command contourf 7 2 Aerosol Postprocessing 7 2 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 input Number of size bins If yes the bin bounds are computed using a logarithmic 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 PMi9 PM25 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 o
39. 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 previous 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 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 bo
40. 0 5 Nx 67 y_min 35 Delta_y 0 5 Ny 46 Nz 8 file u cergrene a ahmed dm Polyphemus RC driver results 03 bin An easy way to do that is to copy the section domain of the configuration file used for the simulation in this file But the number of time steps and vertical layers might be different from those used for the simulation for it depends on what has been specified in the saver configuration file 7 1 2 Visualizing Results The quicker way to visualize the results is to use the interactive python interpreter IPython launched with the command ipython However you can also write your commands into a http matplotlib sourceforge net 99 100 CHAPTER 7 POSTPROCESSING python script that you will launch afterwards with the command python script py In any case you must first check that the program extract_configuration see Section 1 3 has been compiled before you follow the steps below First you need to make sure that Python will look in include atmopy for unknown modules Therefore to use it it is necessary to put it in the PYTHONPATH For example for bash users export PYTHONPATH usr lib python Using a Background Map In the case of continental simulations follow these steps to visualize your results with a back ground map corresponding to your simulation domain That is irrelevant in the case of regional or local simulations especially if you are using Cartesian coordinates instead of longitude
41. 00 to 23 Minutes and seconds range from 00 to 59 2 3 RUNNING PROGRAMS 17 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 II 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 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 a date Most pro grams provide help when launched without any input file Here is an example with the program meteo Polyphemus preprocessing meteo gt meteo Usage
42. 85 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 1 for instance scavenging_coefficient Scavenging is applied above the following threshold over rain mm h Scavenging _rain_threshold 1 Scavenging coefficient of the species s 1 NO2 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 scavenging coefficient will be used for all scavenged species e The belot model has the following expression a pp 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 molL atm and gas phase d
43. 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86 au aaa aaaQAaoaas aaaaa aa aaa an x4 x 010141N110N4N1N440101400Aa YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX YX CA CA CHAPTER 2 DIMENSIONLESS 1 s K DEGREES DEGREES category K m DIMENSIONLESS W m 2 W m 2 m s W m 2 W m 2 W m 2 W m 2 na A A m 3 m 3 m 3 m73 m 3 m 3 m 3 m 3 m 3 m 3 m 3 m 3 m 3 m 3 m 3 m 3 m mm m fraction fraction W m 2 fraction DIMENSIONLESS mm mm K kg kg 1 m s 1 m s 1 PERCENT fraction USING POLYPHEMUS MAP SCALE FACTOR CORIOLIS PARAMETER INFINITE RESERVOIR SLAB TEMPERATURE LATITUDE SOUTH NEGATIVE LONGITUDE WEST NEGATIVE LANDUSE CATEGORY SEA SURFACE TEMPERATURE PBL HEIGHT PBL REGIME SENSIBLE HEAT FLUX LATENT HEAT FLUX FRICTIONAL VELOCITY SURFACE DOWNWARD SHORTWAVE RADIATION SURFACE DOWNWARD LONGWAVE RADIATION TOP OUTGOING SHORTWAVE RADIATION TOP OUTGOING LONGWAVE RADIATION SOIL TEMPERATURE IN LAYER SOIL TEMPERATURE IN LAYER SOIL TEMPERATURE IN LAYER SOIL TEMPERATURE IN LAYER TOTAL SOIL MOIS IN LYR 1 TOTAL SOIL MOIS IN LYR 2 TOTAL SOIL MOIS IN LYR 3 TOTAL SOIL MOIS IN LYR 4 SOIL LQD WATER IN LYR 1 SOIL LQD WATER IN LYR 2 SOIL LQD WATER IN LYR 3 SOIL LQD WATER IN LYR 4 CANOPY MOISTUR E CONTENT WATER EQUIVALENT SNOW DEPTH
44. ARSE 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 2 4 USEFUL TOOLS 23 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 degree 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 4 Stag Ord Units Description U 3 76 86 25 D YXS m s U COMPONENT OF HORIZONTAL WIND V 3 T6 86 25 D YXS m s V COMPONENT OF HORIZONTAL WIND T 3 76 86 25 C YXS K TEMPERATURE Q 3 76 86 25 C YXS kg kg MIXING RATIO CLW 3 76 86 25 C YXS kg kg CLOUD
45. CM 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 93 94 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 Another step before using ChemistryyRACM_SIREAM is to modify slightly the file Polair3DChemistry cxx in models e 414 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
46. Delta_x Nx y min Delta y Ny Nz projection_type Horizontal _interpolation Dot_coordinates Relative _humidity_threshold Low_cloud_top_max Min_dry Min_wet Min_above_PBLH Max CHAPTER 3 PREPROCESSING 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 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 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 Minimum value of Kz in PBLH for dry conditions in ms
47. Here is a list of all types of saver units available at the moment Table 4 4 Types of saver domain domain_aer domain_assimilation nesting nesting _aer subdomain subdomain_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 4 6 2 SaverUnitDomain and Saver UnitDomain_aer The output saver SaverUnitDomain defines an output saver unit when Type is set to do main and requires additional parameters presented in the table below Levels Averaged Initial_concentration 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 Should concentrations be averaged over Interval_length If not instantaneous concentrations are saved Should initial concentrations be saved This option is only avail able if concentrations are not averaged 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 co
48. 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 Mhttp www enpc fr cerea polyphemus 105 106 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 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
49. 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 3 4 METEOROLOGICAL FIELDS 45 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 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 fi
50. Polyphemus 1 0 User s Guide CEREA ENPC EDF R amp D Meryem Ahmed de Biasi Vivien Mallet Irene Korsakissok Edouard Debry Lin Wu and Marilyne Tombette http www enpc fr cerea polyphemus polyphemus cerea enpc fr Contents 1 Introduction and Installation 1 1 1 2 1 3 Polyphemus Overview sa mii a BANE Wee Eee ee E Requirements sara eho ee Oe Oe aa ea GOS Ue ea Ge i Installationen ann dey oe eS Sem a oo Me ee Hass r yes eas ag tte nea ake atte Moms ee Meola aby Be 1 3 1 1 3 2 1 3 3 Mami instructions ll fn Bele BG EB ne BoM om Po ee ok AMO Vi A Soke patie Mss Bae eos ET oe A ING Wade ao a Tec a Ait er Noe eats dora Mint Ghats eae arog 2 Using Polyphemus 2k Remark orion Boe hae th Pee ap eae Se Se ee oe a ee he ee f3 22 Configuration Filesi sa Dai an gah a A e 22 1 Definitions 2 4 LA A A A a eek AA ee et th Re 2 22 Hlexibility 2 sa ee tba beg wee BEERS Se aa ge a 22 3 Comments io esaa a RA Re Oe AL a Ba pele Be 22A Markup sah Sts as eel Pay A A tan 4 22 5 NECIOS ii AA E BLP ae Ge ie oe et ee ee Bee BS 2 26 Multiple Files i cat A eg bat edo Me a hae eis 24 ate 220 Dates sea ac ee Seb a We Bre a ea RN 22 8 BOG Eans m 25 a cee ee BE Se sa EI ee ee od 2 3 Runmia Programs sk OAM eh Beh a ed E Ai ee Pe ks 8 4 23 1 Compiine PropraWs 05 yc Bt teed ee BEE o a Be eA dae Be Bed 2 3 2 Running a Program is miras e a a ee eh ee a 2 33 Sharing Configuration s ss rana ste 0 0202 eee e
51. 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 With_pH Scavenging model Lwc_cloud_threshold With_coagulation With_condensation With nucleation Fixed_aerosol_density With_cloud_chemistry With_in_cloud_scavenging With heterogeneous reactions With_kelvin_effect Dynamic_condensation_solver Fixed_cutting_ diameter Sulfate_computation Redistribution_method Nucleation model With_fixed_density Wet diameter estimation options Does the aerosol module returns cloud droplet pH Which below cloud scavenging model is used Liquid water content threshold for clouds Is coagulation taken into account Is condensation taken into account Is nucleation taken into account Fixed aerosol density in kg m used in the module Is cloud chemistry taken into account Is in cloud scavenging taken into account Are heterogeneous reactions taken into account Is Kelvin effect taken into account Which solver is used for dynamic condensation Fixed cutting diameter in um Which method
52. Running Preprocessing Programs Most preprocessing programs e accept one or two configuration files as arguments e process data day per day one call to a program processes a single day 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 meteorological 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 20010519 meteo general cfg meteo cfg 20010520 meteo general cfg meteo cfg 20010521 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 33 34 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 c
53. ace 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 123 124 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 36 537 960
54. aesium 6 36257e 05 Iodine 0 000212514 Deposition velocity of the species m s 64 CHAPTER 3 PREPROCESSING Deposition_velocity Caesium 0 0005 Iodine 0 005 Program gaussian deposition_aer The program gaussian deposition_aer works the same way as the program 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 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
55. al 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 92 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 numerical 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 ChemistryRA
56. alculated 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 aerl and the diameter of index 1 that is equal to 1 um and so on 68 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 solut
57. ality 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 notably 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 CHAPTER 1 INTRODUCTION AND INSTALLATION Polyphemus Database Data processing libraries AtmoData SeldonData Input data processing Files 5 Numerical Statistics integration AtmoPy Computes physical fields Polair3D Physics i Libraries with physical Z parameterizations a 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 bi
58. ata file reference line emission dat contains the coordinates of the line 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 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 g
59. ata 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 humidity 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 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 ECMWE 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 at
60. aussian deposition Configuration File The 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 3 9 PREPROCESSING FOR GAUSSIAN MODELS 61 With_comment Are comments written in the output file put yes or no Output 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 e constant
61. ber 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 px vs 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 82 CHAPTER 5 MODELS With_boundary_condition Are boundary conditions available for given species With deposition Is dry deposition taken into account With_point_emission Are point emissions provided With surface emission Are emissions at ground provided With_volume_emission Are volume emissions provided Scavenging model Which scavenging model is applied If none the scavenging is
62. culated given the line coordinates and the 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 60 CHAPTER 3 PREPROCESSING Source _velocity Source velocity in kmh 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 d
63. d 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 specified in general section Input_directory Directory where the observations are stored tude and altitude amp s in path names is replaced by species name 4 7 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 Simulation_option Specifies how observations are provided The current version deals only with observations at ground stations 74 Input_file Date min Delta_t Levels Initial_concentration CHAPTER 4 DRIVERS Files containing the observation data They usually are generated by certain reference run of Polair3D amp s in path names is replaced by species name Starting date for the simulation results in data files Time step in seconds for the simulation results in data files Levels for t
64. ded 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 xmin 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 J e line break 13 14 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 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 y_min 6 2 Delta_y 1 Ny 230 The order in which the fields are placed may or may not be important In most Polyphemus configu
65. ding to Louis parameterization 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 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 Put 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 2 1 Ss The program basically reads data in MM5 output file and interpolates it in time and space to Polyphemus grid
66. dules 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 ChemistryRACM 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 1 Information about Binary Files Two programs provided in Polyphemus utils are meant to provide inf
67. e 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 notably 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 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 ITI 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
68. e 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 39 3 4 Meteorological Fields 3 4 1 Program meteo Program Polyphemus preprocessing meteo meteo reads ECMWF Grib files and generates meteorological fields required by chemistry transport models Most fields are interpolated from ECMWF 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 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 Database_meteo LUC_file Sea_index Roughness_file Roughness_in Directory_meteo Directory_Kz_TM paths Directory in which ECMWF 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
69. eat EN ek Yoh ae en Nt ole SA ee 6 13 TransportPPM gt poacher wo pis Pekar a BOM OD Rae AA SG 6 2 Chemistry Modules opta A oe ee oe aaa e 6 2 1 ChemistryRACM 0 0 020 02 eee ee ee es 6 2 2 ChemistryRACM SIREAM 2 000200 0004 6 23 ChemisttvR ADM E ge A E A ii ds a 6 24 Chemistry Castor iso lse a aea rr e e ed 6 2 5 DECAY eale be a ee SU el gn A eR ee oe Bee eh es 75 75 75 76 TT TT 78 78 78 78 78 78 79 79 80 80 80 80 80 81 81 81 82 85 86 86 86 87 87 87 88 88 88 89 89 90 91 6 CONTENTS 7 Postprocessing 99 Ti Visualizing Results ocsi 224 44a 22 4 be a aa Dee 99 7 1 1 Configuration File disp cfg 0 0 00 0000 99 11 2 Visualizino Results dar ed Sea doe oS bees 23 99 7 2 Aerosol Postprocessing 2 ao a aT E E a AE e AE ae A aR 102 7 2 1 Configuration File o Baa e s e 102 1 2 2 Script anitsaerosol py ri ra AA a deeb a 103 7 2 3 Script graph_aerosol py e 103 A Polyphemus Eulerian Test Case 105 Asl Preparing the Testas i il a A a a SY 105 A 2 Modifying the General Configuration File 00 0 106 A 3 Computing Ground Data 0 000000 22 ee ee 106 AL Land Use Covet us ee a ee el a 106 AZ Roughness co yeahs ele Be eee ecko nce Roe ee ee ee Be oe Bs 107 A 4 Computing Meteorological Data o e e 107 A 5 Launching the Simulation 2 2 0 0 0 20000000002 ee eee 108 A 5 1 Mod
70. ecies 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 If 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 6 1 where Tijo is the species half life time in days and fo 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 Spi Sp2 Sp3 Sp4 aerosol_species Aeri Aer2 half_life Half lives in days put O for species without decay Sp1 300 Sp2 216 Sp3 0 Sp4 41 6 2 CHEMISTRY MODULES half_life_aerosol Half lives in days put O for species without decay Aer1 250 Aer2 120
71. ecies 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 velocity 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 3 9 PREPROCESSING FOR GAUSSIAN MODELS 67 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 gas1 0 0001 gas2 0 0001 Deposition velocity of the gaseous species m s Deposition_velocity gas1 0 0005 gas2 0 005 Scavenging coefficient of the aerosol species s 1 Scavenging _coefficient_aer aer1 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 aeri 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 c
72. ee es 2 3 4 Notes about Models 0 0 02 0002 eee ee ee 2A Useful Tools cea Gal a a ede Bes ote Pe 2 4 1 Information about Binary Files 0 200 4 2 4 2 Differences between Two Binary Files ZAS MMS Files o has es eee Cites Str ae E y 2AA SCriptiGal dates muls esdi eee Gods ein la ok Ga we lee les E i 2 5 Setting Up a Simulation 2 5 1 Suggested Directory Tree o eee eee 25 2 Roadmaps 3 205 2 Ada de eleva a a A ee a 2 5 3 Mandatory Data in Preprocessing 2 02 0004 2 5 4 Mandatory Data for Models 0 2 2 22 22 0004 2 5 5 Models Modules Compatibilities o 2 5 6 Checking Results e 2 5 7 Important Notice e o oNN 10 10 11 11 4 CONTENTS 3 Preprocessing 33 3a Remark o ose soma a a a a a o 33 32 lntrodtichion i aa eege A Be A RAE A ek a BE 33 3 2 1 Running Preprocessing Programs a 33 3 2 2 Configuration i e so a On ee eo ER ae a R AE ee de 34 32 3 Data Files rig casn 24h 2a P Go Se a a a D 35 3 31 Ground Datas sers Ak eee eee ta A A Oe he at ok he ON aod 35 3 3 1 Land Use Cover GLCF luc glcf o o 35 3 3 2 Land Use Cover USGS luc usgs 36 3 3 3 Conversions luc convert 02 0000 eee eee ee 37 3 3 4 Roughness roughness 2 0 0 E a a ee g a h 38 3 4 Meteorological Fields
73. enging In the table Gaussian represents any Gaussian model GaussianPlume GaussianPuff GaussianPlume_aer or GaussianPuff_aer as they all need the same data 30 CHAPTER 2 USING POLYPHEMUS Table 2 1 Mandatory data for each models Model Data necessary CastorTransport Temperature Pressure Altitude AirDensity Meridional Wind ZonalWind Vertical Diffusion CastorChemistry The same as Castor Transport and Specific Humidity Liquid WaterContent Attenuation Polair3DTransport MeridionalWind for advection ZonalWind for advection VerticalDiffusion for diffusion Horizontal diffusion if Isotropic_diffusion is set to no this value 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 Polair3DAerosol The same as Polair3DChemistry and Liquid WaterContent 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 amp Mahrt parameterization for ver tical diffusion
74. eorological data refers to this date The date must be in a format described in Section 2 2 7 tmin Hours at which the simulation is starting Delta_t Time step in hour of output meteorological data processed by Polyphemus Nt Number integer of meteorological steps per day 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 Number of vertical levels integer Vertical levels Path to the file that defines vertical levels interfaces in m 3 2 3 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 Loop on time t Loop on z Loop on y Loop on x Let this storage be symbolized by t z y x 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 x or t z y
75. er 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 distribution 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 x 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 LUC_file File where the land use cover data are stored e g computed using Directory_roughness Roughness_out Roughness data file luc glcf or luc usgs Directory where the output file will be stored Output file name data 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 th
76. er 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 As for ECMWF files Kz_TM can be used afterwards The configuration file MM5 meteo cfg contains several options paths Database _MM5 meteo 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 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 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 44 Directory_meteo Directory_attenuation File_Kz t_min Delta_t Nt x_min Delta_x Nx ymin Delta_y Ny Nz projection_type Prev_accumulated_rain Type Min height Min Max Apply_vert CHAPTER 3 PREPROCESSING Directory where output meteorological files are stored Directory where the output of program attenuation is stored Name of the file where the vertical diffusion coefficients computed accor
77. erent 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 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 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 28 CHAPTER 2
78. erosol species e for a non stationary simulation at local scale with a Gaussian model GaussianPuff or GaussianPuff_aer if there are aerosol species 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 module 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 20 CHAPTER 2 USING POLYPHEMUS BaseDriver lt real ClassModel BaseQutputSaver 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 mo
79. ertical Levels and Species 0 02 0000 eee eee es 54 GaussianPuff aer avoir ee be Se ee ee 5 4 1 Configuration File puff_aer cfg 5 4 2 Source Description puff_aer dat o e 5 4 3 Vertical Levels Species and Diameters 55 Polair38D Transport moi a AN lt et et pe Oe 5 5 1 Main Configuration File polairBd C 8 5 5 2 Data Description polair3d data cfg 5 5 3 Vertical Levels and Species 2 2 2 02 0000 ee ee eee 56 Polair3D Chemistry 3 2 ek baie tS ib a Pas Poa oe do Be is a 5 6 1 Main Configuration File polair3d cfg 0 0 5 6 2 Data Description polair3d data cfg 5 6 3 Vertical Levels and Species 0 02 0002 ee ee ees 5 7 Polair3DAerosol mice ck ne ee ee a 5 7 1 Main Configuration File polair3d cfg 00 5 1 2 Data Description polair3d data cfg 5 7 3 Vertical Levels and Species e o 5 8 Polair3DChemistryAssimClonc 0 a 5 9 CastorTransport gt avi eea Sd eee aa a a es 5 9 1 Main Configuration File castor cfg o o 5 9 2 Data Description castor data cfg 5 9 3 Vertical Levels and Species 2 2 0 0 0 000 ee ee ee ee 6 Modules 6 1 Transport modules 2 2 2 20 00 0 E a a a ee 6 1 1 AdvectionDST3 a 4 pa e eo Rae be el ea eee em aca D 6 12 Diffusion ROs2 i Yak
80. es 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 6 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 of the lower left cell 79 76 Delta_y Ny Nz Vertical levels Land_category Time Species With_plume_rise With_radioactive_decay With_biological_decay With_scavenging With_dry_deposition 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 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 plume rise taken
81. es 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 54 CHAPTER 3 PREPROCESSING 3 7 Initial Conditions ic Climatological concentrations from Mozart 2 Horowitz et al 2003 Home page at http gctm acd ucar edu mozart index shtml 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 https cdp ucar edu In addition to the domain definition Section 3 2 2 below is the information required in the configuration for ic see example ic cfg Date_ic Nt Delta t Nx Ny Nz Database_ic Species Molecular_weight Directory_ic ic_input_domain Date for which initial conditions are generated Number of time steps in Mozart 2 files Time step of Mozart 2 files in hours Number of grid points along latitude in Mozart 2 files integer Number of grid points along longitude in Mozart 2 files integer Number of vertical levels in Mozart 2 files integer 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 File providing correspondence betwee
82. es 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 according 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 52 CHAPTER 3 PREPROCESSING 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 2 1 1 640 1 520 FEB MAR APR MAY JUN JUL 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 2 1 1 0159 TUE WED Thu FRI SAT 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
83. essing 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 biological_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 Half life of the species Unit days 0 coresponds to non radioactive species Caesium 1 1e4 Iodine 8 04 biol 0 78 CHAPTER 5 MODELS biological_decay Half life of the species Unit seconds First value day second value night O 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 2 GaussianPlume aer It is the Gaussian
84. face 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 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 ending 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 Date_end source Abscissa Ordinate Altitude 2001 04 22_00 05 2001 04 22_00 07 10 3 48 80 Species S02 Type puff Quantity 1 Date 2001 04 22 00 05 5 5 POLAIREDTRANSPORT
85. ff_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 5 POLAIR3DTRANSPORT 81 5 4 3 Vertical Levels Species and Diameters Vertical level file has been described in Section 5 1 and diameter files is the same as in Sec tion 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 Date_min Delta_t Nt xmin Delta_x Nx ymin Delta y Ny Nz Vertical_levels Cartesian Species With_advection With_diffusion With_air_density With_initial_condition 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 x in degrees longitude or in meters for Carte sian coordinates Num
86. fusion coefficients out put are stored the filename being Kz_TM kz Min Lower threshold for vertical diffusion in m s7 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 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 atmospheric boundary layer 0 1 in Troen and Mahrt 1986 Ric Critical Richardson number used to estimate the atmospheric Fluxes_diagnosed 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 3 4 METEOROLOGICAL FIELDS 43 diagnosis this option is more robust and it is recommended boundary layer BL_diag 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 TM_stable 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
87. he 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 xmin 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 the input file Nc Number of land use categories The output land cover file is in format c y x where c stands for land use category To launch luc g1cf 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 url 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 01le 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 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 htt
88. he 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 2 2 5 Sections Fields and values may be protected inside sections Assume that two domains are defined one 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 16 CHAPTER 2 USING POLYPHEMUS 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 lin
89. he 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 5 5 POLAIR3DTRANSPORT 83 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 to specify all chemical species involved in the process e g deposition Date_min 2001 01 02 Delta_t 10800 Fields 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 u cergrene A mallet 2001 data dep 2005 01 19 ALD modified bin CO 0 002 Notice that CO is not associated with a path but with a numerical value This
90. he simulated data in files Flag that indicates whether initial concentrations are included in data file 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 effect 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 fil
91. ides all reaction names and their indices in the list of reactions Below is an example photolysis_reaction_index NO2 0 0301D 1 0303P 2 HONO 3 HNO3 4 HNO4 5 NO3NO 6 NO3N02 7 H202 8 HCHOmol 9 HCHOrad 10 ALD 11 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 Polair3D Chemistry 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 introduced in Section 5 6 1 the following fields are read by Polair3DChemistry domain Bin_bounds The bounds of the diameter classes for aerosol species Note that the classes are the same for each aerosol species options With_initial_condition aerosol Are initial conditions provided for given aerosol species If not initial concentrations are set to zero With_boundary_condition_aerosol Are boundary condition
92. ies 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 generate 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 3 6 EMISSIONS 49 to Zhang categories 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 paths Altitude File where altitude is stored SurfaceTemperature File where surface temperature is stored SurfaceRelativeHumidity File where surface relative humidity is stored FrictionVelocity File where the friction velocit
93. iffusivities 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 86 CHAPTER 5 MODELS 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 5 6 1 Main Configuration File polair3d cfg In addition to fields introduced in Section 5 5 1 the following fields are read by Polair3DChemistry options Should chemistry occur Should photolysis occur With_chemistry With_photolysis With_forced_concentrations Source_splitting If activated the concentrations of a few species are set to values read in files If activated source splitting is used within chemistry in tegration Advection and diffusion fluxes are included in the chemistry integration as source
94. ifying the Configuration File 0 0 108 A 5 2 Modifying the Data File o e e 108 A 5 3 Modifying Saver File 200000002 eee eee 109 A oil SIMULACION ardor a at Bee ees tae 109 A60 Visualizing Results a rrinin ps a e e 109 A 6 1 Modifying Configuration File o e 109 A62 Use IBAMOS A Pe A ea les A 110 B Polyphemus Gaussian Test Case 113 Bl Preprocessing ette A ds A os 113 B2 Discretization a a A A A a E 114 B3 Simulations Rai A O al ee 114 B32 li Pi a a A ekg da ya 114 B 3 2 Puff with Aerosol Species o 115 B 3 3 Puff with Line Source e 116 B 4 Result Visualization o oas x sa soaa ee 117 B 4 1 Gaussian Plume 0 0 0 00 02 eee ee ee ee 117 B 4 2 Gaussian Puff with Aerosol Species 2 2 0004 117 B 4 3 Gaussian Puff with Line Source 0 0 0 0 0000004 118 Chapter 1 Introduction and Installation 1 1 Polyphemus Overview Polyphemus is an air quality modeling system built to manage several scales local regional and continental 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 qu
95. inal 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 578390 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 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 i
96. 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 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 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 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
97. ion 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 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 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 s71 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 42 CHAPTER 3 PREPROCESSING Simple corrections are also performed to take into account convective conditions The output is a 3D time dependent field format t z y x 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
98. ion 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 gaseous 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 69 70 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 OptimalIn
99. ion 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 MMS SYSTEM FORMAT EDITION NUMBER 1 TERRAIN PROGRAM VERSION NUMBER 6 TERRAIN PROGRAM MINOR REVISION NUMBER O COARSE DOMAIN GRID DIMENSION IN I N S DIRECTION 76 COARSE DOMAIN GRID DIMENSION IN J E W DIRECTION 86 MAP PROJECTION 1 LAMBERT CONFORMAL 2 POLAR STEREOGRAPHIC 3 MERCATOR 1 IS COARSE DOMAIN EXPANDED 1 YES 0 NO O EXPANDED COARSE DOMAIN GRID DIMENSION IN 1 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 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 CO
100. 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 Are boundary conditions provided Is deposition taken into account Are volume emissions taken into account data Path to the configuration file that describes input data 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 Entries Comments initial_condition Fields Filename If initial conditions are activated With initial condition and not inter polated Interpolated_initial_condition set to no boundary_condition Fields Filename If boundary conditions are activated With_boundary_condition meteo Date_min Delta_t Required fields are Temperature Pressure Fields Filename Altitude AirDensity MeridionalWind ZonalWind and VerticalDiffusion deposition Date_min Delta_t If deposition is activated With_deposition Fields Filename volume_emission Date_min Delta_t Nz If volume emissions are activated Fields Filename With volume emission Nz is the num ber of levels in which pollutants are emitted 5 9 CASTORTRANSPORT 91 5 9 3 Vertical Levels and Species A file containing vertic
101. latitude 1 The first step is to import the modules that are needed import atmopy from atmopy display import 2 Then import the data from the configuration file m d getmd disp cfg In that step you have created an array named d but you can name it otherwise which contains your results It is a 4D array of shape N x Nz xX Ny x Ng given in the configuration file You can access a concentration at time t level z point x y with the command d t Zz y x You can also verify its shape with the command d shape 3 Display the concentration map at time step t and vertical level z disp m d t z Figure 7 1 gives an example of output figure with the command disp m d t z The simulation domain corresponds to Europe so that is the background map You can afterwards save the figures in any format you wish png eps If you want to display results for several species you do not have to create the background map each time because you will use the same for all species In that case for all species but the first create only a data with function getd This is similar to what is shown below Without a Background Map The following steps allow you to visualize your results without a background map This is especially required in the case of local simulations so the example given here has been made with Gaussian models 1 The first step is to import the modules that are needed import atmopy fro
102. life times of both gaseous and aerosol species 5 2 5 Diameters diameter dat See Section 3 9 2 5 3 GAUSSIANPUFF 5 3 GaussianPuff 79 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 6 5 3 1 Configuration File puff cfg Show_date Date min Delta_t Nt x min Delta_x Nx 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 Nchamberlain Configuration_file display Irrelevant Provide any Boolean domain Irrelevant Provide any date see Section 2 2 7 Time step of the simulation in seconds Number of time steps integer Abscissa in meter of the center of the lower left cell Step length along x in m Number of cells along x integer Ordinate in meter of the center of the l
103. ll 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 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 s71 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 Only one species per line must be provided This section is needed in order to calculate the g
104. m atmopy display import 7 1 VISUALIZING RESULTS 101 10 5 0 5 10 15 20 Figure 7 1 Concentration map obtained with the command disp 160000 140000 120000 100000 8000001 6000001 400000 2000001 2 Then import the data from the configuration file d getd disp cfg In that step you have created an array named d but you can name it otherwise which contains your results It is a 4D array of shape N x N x Ny x Nz given in the configuration file You can access a concentration at time t level z point x y with the command d t z y x You can also verify its shape with the command d shape 3 Display the concentration at time step t and vertical level z contourf d t z 4 Add a colorbar You can specify the type of notation you want in the colorbar e colorbar 4n mf to have numbers in decimal format with n significant figures before the dot and m significant figures after e colorbar n me to have numbers in scientific notation with n significant figures before the dot and m significant figures after Figure 7 2 gives an example of concentration map Note that In that case the information necessary is only N Nz Ny and Nz and the filename You don t need to use a configuration file to give these parameters you can also modify the call to function getd d getd filename 03 bin Nt 24 Nz 1 Ny 19 Nx 13 102 180 0 0 20 4
105. mputation 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 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
106. n be used TestCase raw_data MM5 gt get_info_MM5 MM5 2004 08 09 GROUND T Min Max Mean Std 271 911 327 747 294 112 dev 6 46779 TestCase raw_data MM5 gt get_info_MM5 MM5 2004 08 09 ALB Min Max Mean Std 0 0738 0 8 0 122658 dev 0 0501975 26 CHAPTER 2 USING POLYPHEMUS 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 launched 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 OZ CPU Oavgtext 0avgdata Omaxresident k Oinputs 0outputs Omajor 176minor pagefaults Oswaps nice time echo Current date 20060721 Current date 20060721 0 O0user 0 00system 0 00 00elapsed 0 CPU Oavgtext 0avgdata Omaxresident k Oinput
107. n 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 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 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 follows xx 40 pa ae 2 and where Ng is the number of days since the beginning of the year 0 for first January 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 In addition to the domain definition Section 3 2 2 below is the information required in the configuration for bc see example bc cfg 3 8 BOUNDARY CONDITIONS 55 Nt Delta t Nx Ny Nz Directory bc Species Molecular
108. ncentrations 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 72 CHAPTER 4 DRIVERS 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 6 3 SaverUnitSubdomain and SaverUnitSubdomain 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 for these saver units are Initial _concentration 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 concentra
109. nd 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 kg kg 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 paths Database_MM5_meteo 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 Roughness_file Path to the binary file that describes roughness heights in meters per month in output grid cells Hybrid_coefficients File containing the parameters alpha and beta used to compute the pressure at various levels and the altitudes 46 Directory_meteo t_min Delta_t Nt x_min
110. ng 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 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 Rc be saved This may take a lot of storage space put no if you do not work on the deposition parameteriza tions 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 entr
111. nging 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 deposition 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 3 9 PREPROCESSING FOR GAUSSIAN MODELS 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 Iodine 0 5e 2 63 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 C
112. o 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 output_saver modules to save the results of a simulation 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 AtmoData C library of physical parameterizations atmopy AtmoPy is a Python library for statistical analysis and visualization 1 2 REQUIREMENTS 9 common some functions used to parse and manage the arguments of preprocessing programs 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 some useful tools Polyphemus is an open source software distributed under the GNU Gene
113. observations 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 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 90 Delta_x Nx y min Delta_y Ny Nz Vertical levels Species With_transport With_initial_condition Interpolated_initial condition With_boundary_condition With_deposition With_volume_emission Data_description CHAPTER 5 MODELS Step length along x in degrees longitude or in meters for Cartesian 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 Cartesian coordinates Number of cells along y integer Number of vertical levels integer Path to the file that defines vertical levels interfaces This field is read but
114. onfiguration 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 format YYYYMMDD 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 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 20010102 t min 0 0 Delta_t 3 0 Nt 9 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 3 3 GROUND DATA 35 domain Date The date at which the simulation of the chemistry transport model is starting It is also the date at which meteorological data processed by Polyphemus output from programs meteo or MM5 meteo starts As a consequence any program that needs to read this met
115. or 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 e for all countries e for the year of your choice up to 2004 e for all activity sectors SNAP or even better without the eleventh EMEP sector whose emissions are better estimated with program bio Section 3 6 3 e in format Grid 50 km x 50 km Semicolon Separated e for one species 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 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 3 6 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 y min Delta y Ny N Aggregation Speciation directory Deposition_factor_NH3 51 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 fir
116. ormat c y x where c stands for land use category To launch luc usgs just type 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 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 Database_luc convert File_ in Directory_luc convert paths Directory where the input file input land use categories is located Input file name in Database luc convert Directory where the output file output land use categories should be stored 38 File_out Nc_in Nc_out CHAPTER 3 PREPROCESSING Output file name in Directory_luc convert dimensions Number of land categories in the input format Numb
117. ormation 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 file 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 2 4 USEFUL TOOLS 21 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 ge
118. ovide 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 model 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 a simulation with chemistry for gaseous species Polair3DChemistry or CastorChemistry e for a simulation with aerosol species Polair3DAerosol e for a simulation 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 a
119. ower 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 80 CHAPTER 5 MODELS 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 the model will stick to it 3 the abscissa of the point of emission
120. p glcf umiacs umd edu index shtml 3 3 GROUND DATA 37 Database_luc usgs LUC_in_ea LUC_in_af Directory_luc usgs LUC_out Step lon_ origin ea lat_origin ea lon_origin_af lat_origin af lon_upper_left_ea lat_upper_left_ea lon_upper_left_af lat_upper_left_af Nx_ea Nx_af Ny_ea Ny_af Nc Sea_index paths Directory where the raw data from USGS can be found Input file containing raw data for Eurasia Input file containing raw data for Africa Output directory Output file name The default filename LUC usgs bin is recom mended for clarity USGS Space step in meters Longitude of the center of lower right cell for Eurasia Latitude of the center of the lower right cell for Eurasia Longitude of the center of the lower right cell for Africa Latitude of the center of the lower right cell for Eurasia Longitude of the center of the upper left cell for Eurasia Latitude of the center of the upper left cell for Eurasia Longitude of the center of the upper left cell for Africa Latitude of the center of the upper left cell for Africa Number of cells along longitude in the input file for Eurasia Number of cells along longitude in the input file for Africa Number of cells along latitude in the input file for Eurasia Number of cells along latitude in the input file for Africa Number of land categories Index of the sea in land categories Remember that indices start at 0 The output land cover file is in f
121. plicit 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 the 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 ae
122. 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 6 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 5 1 and contain the half
123. putes 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 paths SurfaceTemperature File where surface temperature is stored SurfaceRichardson File where surface Richardson number is stored SolarRadiation File where solar radiation is stored WindModule File where wind module is stored PAR File where photosynthetically active radiation is stored PARdiff File where the diffuse part of the photosynthetically active radia tion is stored PARdir File where the direct beam part of photosynthetically active radi ation is stored SpecificHumidity File where 3D specific humidity is stored SurfacePressure File where surface pressure is stored FrictionVelocity File where friction velocity is stored CanopyWetness File where canopy wetness is stored Rain File where rain is stored RoughnessHeight File where roughness height is stored Type Configuration file that describes land use cover see below for de tails about this file 48 Data Directory_dep Ns CellRoughness Ra Rb Re Save_resistance CHAPTER 3 PREPROCESSING 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 Zha
124. ral 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 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 Corresponding Fortran compilers are acceptable GNU G77 3 2 3 3 and 3 4 GNU GFOR TRAN 4 0 and 4 1 and Intel Fortran compilers IFC 7 1 and IFORT 8 0 Note for GCC users Please note that Fortran 77 compiler has changed between version 3 x and version 4 x of GCC and that those two versions are not compatible In particular if you choose to use GFORTRAN make sure to use the corresponding C compiler and not an older version Python supported versions are 2 3 and 2 4 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
125. ration files the order does not matter Then x_min 12 5 Delta_x 0 5 Nx 100 y_min 6 2 Delta_y 1 Ny 230 is the same as y_min 6 2 Delta_y 1 Ny 230 Nx 100 x_min 12 5 Delta_x 0 5 gt Recommandation Use equal sign between a field and its value if the value is a number 1 and use semi colon if the value is a string Example x_min 12 5 Output_directory home user path 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 CONFIGURATION FILES 15 2 2 4 Markups In order to avoid duplications in a configuration 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 T
126. ravitational 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 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 66 CHAPTER 3 PREPROCESSING 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 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 sp
127. rosol 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_density option 6 2 3 ChemistryRADM Module ChemistryRADM is quite similar to ChemistryRACM RACM has actually been derived from RADM 96 CHAPTER 6 MODULES 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 6 2 5 Decay This chemistry module is used for sp
128. rosol 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 104 CHAPTER 7 POSTPROCESSING Appendix A Polyphemus Eulerian Test Case The test case is available on Polyphemus site 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 that 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
129. s 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 photolysis rates Date min Delta_t Ndays Time_angle_min Delta_time_angle Ntime_angle Latitude min Delta_latitude Nlatitude Altitudes Fields Filename Comments Starting date of photolysis rates Time step in days Number of steps Starting time angle in hours Time angle step in hours Number of time angles First latitude in degrees Step along latitude in degrees Number of latitude steps List of altitudes in meters at which photolysis rates are provided Photolysis reaction names and the paths to the files in which photolysis rates are stored 5 7 POLAIR3DAEROSOL 87 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 prov
130. s 0outputs Omajor 177minor pagefaults Oswaps nice time echo Current date 20060722 Current date 20060722 0 O0user 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 The whole Polyphemus directory should not be modified except maybe makefiles Copy 2 5 SETTING UP A SIMULATION 27 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 E results reference new_emissions T 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 diff
131. s available for given aerosol species With_pH Does the aerosol module returns cloud droplet pH Lwc_cloud_threshold Liquid water content threshold above which a cloud is diagnosed in the cell Fixed_aerosol_density Fixed aerosol density in kg m used in the model With_deposition aerosol Compute_deposition_aerosol 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 88 With_point_emission_aerosol With surface emission aerosol With_volume_emission_aerosol With_scavenging aerosol CHAPTER 5 MODELS 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 The bin bounds are presented as follow Bin_bounds diameter of the particle classes in micrometers 0 0 0 111 525 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 initial_condition aerosol boundary_condition_aerosol deposition_velocity_aerosol point_emission_aerosol surface_emission_aerosol
132. s shown in Section 3 7 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 Boundary 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 hnttp code916 gsfc nasa gov People Chin gocartinfo html 56 CHAPTER 3 PREPROCESSING 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 SU sulfur Total 4 1 DMS 2 SO2 3 SO4 4 MSA CC BC 0C Total 4 1 hydrophobic BC 2 hydrophobic OC 3 hydrophilic BC 4 hydrophilic OC 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
133. s 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 paths Temperature Meteorological file of temperature Directory_bc Directory where output will be written bc_input_domain 58 CHAPTER 3 PREPROCESSING 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
134. 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 luc usgs TestCase config luc usgs cfg TestCase config general cfg The output on screen will be A 4 COMPUTING METEOROLOGICAL DATA 107 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
135. st 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 Maximum 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 Step length in degrees along latitude of LUC grid Number of cells along latitude integer in LUC grid Species Number of emitted species Aggregation matrix file relations of the emitted species to the real chemical species 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 Part of emitted NH which is deposited right away The program emissions reads EMEP emissions inventory multipli
136. st 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 118 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE 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 119 a Situation 1 b Situation 2 180 160 140 120 100 80 60 40 20 c Situation 3 d Situation 4 Figure B 1 Plume for the
137. 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 _1ine 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 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 113 114 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE Reading species done Reading diameter done Computation of the scavenging coefficients done Co
138. t 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 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 22 CHAPTER 2 USING POLYPHEMUS 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 deviat
139. t 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 BaseOutputSaver 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 Chemical species to be saved If it is set to all concentrations for all species are saved 4 6 OUTPUT SAVERS Date_beg Date_end Interval length Type Output_file 71 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 4 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 additional options relevant for the chosen output saver
140. tar gz tar jxvf Polyphemus tar bz2 Polyphemus programs must be compiled by the user when needed Makefiles are provided so that program compilation should be easy For instance one may compile the program meteo cpp in this way cd Polyphemus preprocessing meteo make meteo Then the program meteo is compiled and can be run Launch make 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 http www scons org 1 3 INSTALLATION 11 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 wuw 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
141. teger in ECMWF grid 40 CHAPTER 3 PREPROCESSING 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 t_min plus Accumulated_index times Delta_t 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 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 ECMWF 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 ECMWE 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 d
142. tenuation 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 3 4 METEOROLOGICAL FIELDS Al 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 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 parameterizat
143. terpolationDriver It is the driver dedicated to data assimilation applications using optimal interpolation algo rithm The associated configuration file is an extension of that of BaseDriver and it is usually part of the model configuration file exemplified in Section 5 8 It has an additional section observation management similar to what can be seen below observation_management For configuration file choose between observation cfg and observation sim cfg Configuration_file example assimilation observation cfg The value of Configuration file can be set to observation cfg if you use GroundObservationManager see Section 4 7 1 and to observation sim cfg if you use SimObservationManager see Section 4 7 2 The optimal interpolation algorithm estimates model state status by minimizing the error variance of the estimation called analysis in data assimilation terminology It searches for a linear combination between background state model simulations and the background depar tures The background departures are defined as the discrepancies between observations and background state It involves with observation managements described in Section 4 7 and storage managements of forecast and analysis results see for instance Section 4 6 4 4 6 Output Savers 4 6 1 BaseOutputSaver The saver BaseQutputSaver is configured with a file that contains one or several sections save Each section is associated with one element of a lis
144. that the directory atmopy should be in your PYTHONPATH Launch IPython and then type in command line comments starting with have been added to explain the meaning of each line dispc 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 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 A 6 VISUALIZING RESULTS Figure A 1 Figure obtained using Python and AtmoPy unit is ug m 111 180 160 40 20 112 APPENDIX A POLYPHEMUS EULERIAN TEST CASE 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 bz2is 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
145. the parameterization is not applied in stable conditions In this case the Troen and Mahrt parameterization is only applied in unstable 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 amp Mahrt parameterization or ComputePBLH_Richardson critical Richardson number Finally the vertical diffusion coefficients are computed with ComputeTM_Kz The main output is a 3D time dependent field format t z y xj 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 LMQ 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 cov
146. tion domain options and the paths to the other files 116 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 uses puff which is the program for puffs with gaseous species only and the following data e Gaseous species lodine 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
147. tion 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 Borjesson 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 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 surf
148. tions be averaged over Interval_length If not instantaneous concentrations are saved Should initial concentrations be saved This option is only avail able if concentrations are not averaged i_min Minimum latitude index of the subdomain i_max Maximum latitude index of the subdomain j min Minimum longitude index of the subdomain j max Maximum longitude index of the subdomain 4 6 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 assimilation results Date_file The full path name of the file that stores the date sequences of the 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 6 5 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
149. 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 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
150. 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 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 0 end do enddo where imx total number of longitudinal grid 144 jmx total number of latitudinal grid 91 Imx total number of vertical layers version dependent nmx total number of species 4 or 5 see species list above ntl yyyymmdd after 2000 year month day e g 20010201 or yymmdd before 2000 e g 970101 nt2 hhmmss hour minute second e g 120000 nn tracer number see species list above 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 3 8 BOUNDARY CONDITIONS 57 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 latitud
151. undary 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 3 9 PREPROCESSING FOR GAUSSIAN MODELS 59 The file given in Temperature field of configuration file bc gocart 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 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 cal
152. various meteorological situations 120 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE 25 25 20 20 15 15 10 10 a Situation 1 Concentration at t 0s t 3s and b Situation 2 Concentration at t 0s t 3s and t 8s t 8s 25 20 15 10 10 c Situation 3 Concentration at t 0s t 0 5s and d Situation 4 Concentration at t 0s t 0 5s and t 2 58 t 2 58 Figure B 2 Evolution of the puff for the various meteorological situations B 4 RESULT VISUALIZATION 121 25 20 ry N a Situation 1 b Situation 2 c Situation 3 d Situation 4 Figure B 3 Concentration at t 4s for the various meteorological situations 122 APPENDIX B POLYPHEMUS GAUSSIAN TEST CASE 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 model 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 simula
153. ver the domain defined by i_range and j_range 7 2 AEROSOL POSTPROCESSING 103 i_range First and last indices in x direction for the considered domain j range First and last indices in y direction for the considered domain log plot If yes the mass and number distributions will be displayed with a log scale for diameters directory_list 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 2 2 Script init_aerosol py The outputs of the model for aerosols will be several files lt species gt _ lt number 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 PM 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 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 2 3 Script graph_ae
154. weight bc input domain Number of time steps in Mozart 2 files Time step of Mozart 2 files in hours Number of grid points along latitude in Mozart 2 files integer Number of grid points along longitude in Mozart 2 files integer Number of vertical levels in Mozart 2 files integer bc files Directory where the output boundary conditions must be stored 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 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 i
155. y is stored Attenuation File where the attenuation is stored AerodynamicResistance File where the aerodynamic resistance is stored LUC_file File containing the land use cover Nc Number of land use cover categories Nveg Number of vegetation classes Land _data File containing land data in Chimere format Species data File containing the data for species molecular weight Henry con stant reactivity Directory dep Directory where the output files are stored Species Ns Number of species for which data are provided 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

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