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User Manual for the LMD Martian Atmospheric General Circulation

1. 3 6 Tracer transport and sources 37 Th rmosphere aie A es ae dk he medo wes Running the model a practice simulation 4 1 Obtaining the model 42 Installing the model 4 3 Compiling the model 4 4 Input files initial states and def files 45 Running the model sos 04 den pa RR s 4 6 Visualizing the output files 4 6 1 Using GrAds to visualize outputs 4 7 Resuming a simulation 4 8 Chansmulations sereo a he dex RE eek ee aed 4 9 Creating and modifying initial states 4 9 1 Using program newstart 4 9 2 Creating the initial start_archive nc file 4 9 3 Changing the horizontal or vertical grid resolution 10 Program organization and compilation script 5 1 Organization of the model source files 9 2 Programming ws ue ure RU Tb RR wn eG Bars 5 3 Model organization es aeh ha x RH d a 5 4 Compilngthemodel Input Output 6 1 NetCDFE format ocv Be ae S Sg pus 6 1 1 NetCDF file editor ncdump 6 1 2 Graphic visualization of the NetCDF files using GrAds 6 2 Input and parameter files 6 2 0 ume 8 sce an
2. Figure 2 4 Vertical grid description of the 11m or nlayer atmospheric layers in the programming code 11m is the variable used in the dynamical part and nlayer is used in the physical part Variables ap bp and aps bps indicate the hybrid levels at the interlayer levels and at middle of the layers respectively Pressure at the interlayer is Plev l ap l bp I x Ps and pressure in the middle of the layer is defined by Play l aps l bps l x Ps where Ps is surface pressure Sigma coordinates are merely a specific case of hybrid coordinates such that aps 0 and bps P Ps Note that for the hybrid coordinates bps 0 above 50 km leading to purely pressure levels The user can choose whether to run the model using hybrid coordinates or not by setting variable hybrid in run def to True or False 2 4 Variables used in the model 2 4 1 Dynamical variables The dynamical state variables are the atmospheric temperature surface pressure winds and tracer concentrations In practice the formulation selected to solve the equations in the dynamics is optimised using the following less natural variables potential temperature 0 teta in the code linked to temperature T by 0 T P Pref with R C note that is called kappa in the dynamical code and rcp in the physical code We take Pref 610 Pa on Mars surface pressure ps in the code mass the atmosphere mass in each grid box masse i
3. h2o_vap title Traceur h2o vap float masse Time altitude latitude longitude masse title C est quoi float ps Time latitude longitude ps title Pression au sol global attributes title Dynamic start file List of contents of a start fi nc file ncdump h startfi nc netcdf startfi dimensions index 100 physical points 738 subsurface layers 18 nlayer plus 1 19 number of advected fields 3 variables float controle index controle title Control parameters float soildepth subsurface layers Soildepth title Soil mid layer depth float longitude physical points longitude title Longitudes of physics grid float latitude physical points latitude title Latitudes of physics grid float area physical_points area title Mesh area float phisfi physical points phisfi title Geopotential at the surface float albedodat physical points albedodat title Albedo of bare ground float ZMEA physical points ZMEA title Relief mean relief float ZSTD physical points ZSTD title Relief standard deviation float ZSIG physical points ZSIG title Relief sigma parameter float ZGAM physical points ZGAM title Relief gamma parameter float ZTHE physical points ZTHE title Relief theta parameter float co2ice physical points CO2 ice title CO2 ice cover float inertiedat subsurface layers physical points i
4. 3 C m gt t 2 t 2 ucov D co2ice D C tsurf D j tsoil j C D eee 2 i m i co2ice J u P 1 tsurf m E E tsoil D Figure 6 2 Organization of NetCDF files Files start nc and startfi nc like all the NetCDF files of the GCM are constructed on the same model see NetCDF file composition figure 6 2 They contain a header with a control variable followed by a series of variables defining the physical and dynamical grids a series of non temporal variables that give information about surface conditions on the planet a time variable giving the values of the different instants at which the temporal variables are stored a single time value t 0 for start as it describes the dynamical initial 38 states and no time values for startfi as it describes only a physical state To visualize the contents of a start nc file using the ncdump command ncdump h start nc netcdf start dimensions index 100 rlonu 33 latitude 25 longitude 33 rlatv 24 altitude 18 interlayer 19 Time UNLIMITED 1 currently variables float controle index controle title Parametres de controle float rlonu rlonu rlonu title Longitudes des points U float rlatu latitude rlatu title Latitudes des points U float rlonv longitude rlonv title Longitudes des points V
5. Arvidson M Kahre F Seelos S Murchie and Savij rvi Wavelength dependence of dust aerosol single scattering albedo as observed by the Compact Reconnais sance Imaging Spectrometer Journal of Geophysical Research Planets 114 E13 0 2009 63
6. stats nc Simulation 2 callphys def run def callphys def Z2sig def run def i z2sig def Figure 4 1 Input output data 20 distrib local grads sample For example to visualize files diagfi nc and stats nc NetCDF files diagfi nc and stats nc can be accessed directly using GrAdS thanks to utility program gradsnc the user does not need to intervene To visualize the temperature in the 5th layer using file diagfi noc for example GrAdS session grads return return opens a landscape window ga sdfopen diagfi nc ga query file displays info about the open file including the name of the stored variables Shortcut q file ga set z 5 fixes the altitude to the 5th layer ga set t 1 fixes the time to the first stored value ga query dims indicates the fixed values for the 4 dimensions Shortcut q dims ga display temp displays the temperature card for the 5th layer and for the first time value stored Shortcut d T ga gt clear clears the display Shortcut c ga set gxout shaded nota contour plot but a shaded one ga display temp ga set gxout contour returns to contour mode to display the levels ga display temp superimposes the contours if the clear command is not used 4 7 Resuming a simulation At the end of a simulation the model generates restart files files restart nc and restartfi nc which contain the
7. 80 87 94 101 108 115 122 129 136 143 150 157 164 171 178 185 192 199 206 213 220 227 234 241 248 2554 262 269 276 283 290 297 304 311 318 325 332 339 346 3595 360 9040 4010 7780 5138 9666 0626 25527 4369 369 369 369 369 369 369 369 369 369 37 37 37 ou 37 37 37 37 37 34 37 37 Sd 37 37 37 37 37 37 37 37 oF 37 37 37 37 37 37 37 37 oF 37 37 37 Ou 34 37 EEE DB EE DB D NS BR DB BB GB GB GB GB GB GB GB GB GB GB GB BS BBB GE GB GB GB GPS GB BB BBB GB GB GB BR BA a4 37 367 374 381 388 395 437 437 437 437 437 6 2 5 Initialization files start and startfi DYNAMIQUE PHYSIQUE ex start ex startfi Ent te Ent te 1 controle tab cntrl 1_ controle tab cntrl 2 rlonu 2 hor coor 3 rlatu Informations 3 vert coor Informations 4 rlonv sur la 4 vert2 coor sur la grille grille Conditions de surface Conditions de surface 1_ phisinit 1_ phisfi 2 albedodat 4 zmea temps temps Valeur des instants auxquels Valeur des instants auxquels sont stock es les variables sont stock es les variables Stockage des variables temporelles Stockage des variables temporelles t 1 ien C ucov co2ice D C tsurf D C h C tsoil
8. H20 vapor volume mixing ratio total sta ndard deviation over the season E vmr h2ovapor sd units mol mol loat vmr h2oice Time altitude latitude longitude vmr_h2oice title H20 ice volume mixing ratio vmr_h2oice units mol mol i loat vmr h2oice sd Time altitude latitude longitude 47 vmr h20ice sd title 20 ice volume mixing ratio total standar d deviation over the season vmr h20ice sd units mol mol float mtot Time latitude longitude mtot title total mass of water vapor mtot units kg m2 float mtot sd Time latitude longitude mtot sd title total mass of water vapor total standard deviat ion over the season mtot sd units kg m2 float icetot Time latitude longitude icetot title total mass of water ice icetot units kg m2 float icetot sd Time latitude longitude icetot sd title total mass of water ice total standard deviat ion over the season icetot sd units kg m2 The structure of the file is simillar to the diagfi nc file except that as stated before the average of variables are given for 12 times of the day and that RMS standard deviation are also provided 48 Chapter 7 Zoomed simulations The LMD GCM can use a zoom to enhance the resolution locally In practice one can increase the latitudinal resolution on the one hand and the longitudinal resolution on the other hand 7 1 To define the zoomed area The zoom is de
9. start nc and startfi nc and output files restart nc and restartfi nc are stored using individual tracer names e g co2 for CO2 gas h2o_vap for water vapour h20_ice for water ice The first line of the traceur def file an ASCII file must contain the number of tracers to load and use this number should be the same as given to the t option of the makegocm script when the GCM was compiled followed by the tracer names one per line Note that if the corresponding tracers are not found in input files start nc and startfi nc then the tracer is initialized to zero Example of a traceur def file with water vapour and ice tracers 2 2 _1 h2o_vap 6 2 4 z2sig def The Z2sig def file contains the pseudo altitudes in km at which the user wants to set the vertical levels Note that levels should be unevenly spread with a higher resolution near the surface in order to capture the rapid variations of variables there It is recommended to use the altitude levels as set in the z2sig def file provided in the deft ank directory Example of z2sig def file this version for 50 layers between 0 and 400 km 10 00000 H atmospheric scale height km used as a reference only 0040 Typical pseudo altitude m for 1st layer z H log sigma 018 PS Pa an Sire Gee LE GAGew Iud Mayer ecc 0400 1000 228200 460400 907000 73630 Fo Q QO Oc 36 3 1 5 49 8 9 13 18 25 31 38 45 D 295 66 T3
10. to run the GCM run def callphys def util A set of programs useful for post processing GCM outputs makegcm Script that should be used to compile the GCM as well as related utilities newstart start2archive testphysld create make Executable used to create the makefil This command is run automatically by makegcm see below 5 1 Organization of the model source files The model source files are stored in various sub directories in directory libf These sub directories correspond to the different parts of the model 25 grid mainly made up of dimensions h file which contains the parameters that define the model grid i e the number of points in longitude IIM latitude JJM and altitude LLM as well as the number of tracers NQMX dyn3d contains the dynamical subroutines bibio contains some generic subroutines not specifically related to physics or dynamics but used by either or both phymars contains the Martian physics routines filtrez contains the longitudinal filter sources applied in the upper latitudes where the Courant Friedrich Levy stability criterion is violated aeronomars contains the Martian chemistry and thermosphere routines 5 2 Programming The model is written in Fortran 77 and Fortran 90 e The program sources are written in file F or file F90 files The extension F is the standard extension for fixed form Fortran and the extension F90 is for free
11. 50 24 666 290 135 750 530 279 783 55 27 043 295 138 275 535 282 965 60 29 407 300 140 821 540 286 130 65 31 758 305 143 388 545 289 277 70 34 096 310 145 975 550 292 406 75 36 423 315 148 585 555 295 515 80 38 739 320 151 217 560 298 604 85 41 046 325 153 872 565 301 671 90 43 343 330 156 550 570 304 715 95 45 631 335 159 251 575 307 737 100 47 912 340 161 977 580 310 735 105 50 186 345 164 727 585 313 709 110 52 453 350 167 502 590 316 658 115 54 714 355 170 301 595 319 583 120 56 970 360 173 126 600 322 483 125 59 222 365 175 975 605 325 358 130 61 471 370 178 850 610 328 207 5 371 99 180 Autumn equinox N 135 63 716 375 181 750 615 331 032 140 65 959 380 184 675 620 333 831 145 68 201 385 187 624 625 336 606 150 70 442 390 190 598 630 339 356 155 72 683 395 193 596 635 342 082 160 74 925 400 196 618 640 344 783 165 77 168 405 199 662 645 347 461 170 79 413 410 202 729 650 350 116 175 81 661 415 205 818 655 352 748 180 83 912 420 208 927 660 355 357 185 86 167 425 212 056 665 357 945 669 0 Spring equinox N 190 88 427 430 215 203 670 0 512 193 47 90 Summer solstice N 195 90 693 435 218 368 675 3 057 200 92 965 440 221 549 680 5 583 205 95 245 445 224 746 685 8 089 210 97 532 450 227 955 690 10 577 215 99 827 455 231 177 695 13 046 220 102 131 460 234 409 700 15 498 225 104 446 465 237 650 705 17 933 230 106 770 470 240 89
12. case 25 Mars Year 25 from TES assimilation ie a year with a global dust storm 26 Mars Year 26 from TES assimilation iaervar 24 Dust vertical distribution 0 old distrib Pollack90 1 top set by topdustref 2 Viking scenario 3 MGS scenario iddist 3 Dust top altitude km Matters only if iddist 1 topdustref 55 Physical Parameterizations RO call radiative transfer callrad true call NLTE radiative schemes matters only if callrad T callnite true call CO2 NIR absorption matters only if callrad T callnirco2 true call turbulent vertical diffusion calldifv true call convective adjustment calladj true call CO2 condensation callcond true call thermal conduction in the soil callsoil true call Lott s gravity wave subgrid topography scheme calllott true Radiative transfer options EE EEN ENT ND the rad transfer is computed every iradia physical timestep iradia 1 Output of the exchange coefficient mattrix for diagnostic only callg2d false Rayleigh scattering should be false for now rayleigh false Tracer dust water ice and or chemical species options used if tracer T DUST Transported dust if gt 0 use dustbin dust bins dustbin 0 DUST Radiatively active dust matters if dustbin gt 0 active false DUST use mass and number m
13. de stockage fichier histmoy en jour periodav 60 periode de la dissipation en pas idissip 1 choix de l operateur de dissipation star ou non star lstardis true avec ou sans coordonnee hybrides hybrid true nombre d iterations de l operateur de dissipation gradiv nitergdiv 1 nombre d iterations de l operateur de dissipation nxgradrot nitergrot 2 nombre d iterations de l operateur de dissipation divgrad niterh 2 temps de dissipation des plus petites long d ondes pour u v gradiv tetagdiv 3000 temps de dissipation des plus petites long d ondes pour u v nxgradrot tetagrot 9000 temps de dissipation des plus petites long d ondes pour h divgrad tetatemp 9000 coefficient pour gamdissip coefdis 0 choix du shema d integration temporelle Matsuno ou Matsuno leapfrog purmats false avec ou sans physique physic true periode de la physique en pas iphysiq 10 choix d une grille reguliere grireg true frequence en pas de l ecriture du fichier diagfi ecritphy 120 longitude en degres du centre du zoom clon 63 latitude en degres du centre du zoom clat 0 facteur de grossissement du zoom selon longitude grossismx 1 33 facteur de grossissement du zoom selon latitude grossismy l Fonction f y hyperbolique si true sinon sinusoidale fxyhypb false extension en longitude de la zone du zoom fraction de la zone totale dzoom
14. doubleq false DUST lifted by GCM surface winds lifting false DUST lifted by dust devils callddevil false DUST Scavenging by CO2 snowfall scavenging false DUST WATERICE Gravitationnal sedimentation sedimentation true WATERICE Radiatively active transported atmospheric water ice activice false WATER Compute water cycle water true WATER current permanent caps at both poles True IS RECOMMENDED with true North cap is a source of water and South pole is a cold trap caps true PHOTOCHEMISTRY include chemical species photochem true e You will need the up to date file jmars yyyymmdd e g jmars 20030707 which contains the photodissociation rates It should be in the datafile directory in which are stored datafiles used by the GCM the path to these files is set in file datafile h inthe phymars directory e Compilation 53 You need to compile with 15 tracers if you don t have dust dustbin 0 13 chemical species co2 co o o 1d 02 03 h h2 oh ho2 h202 n2 ar along with water ice h20_ice and water vapor h20 Compilation is done with the command lines makegcm d 64x48x25 t 15 p mars newstart makegcm d 64x48x25 t 15 p mars gcm Of course the traceur def file should contain the number and name of all the tracers e g 15 co2 co 1 o2 03 h h2 oh ho2 h202 n2 ar h20 ice h2o_vap Run Same as usual Jus
15. downloading precompiled binaries of the library Once the NetCDF library has been compiled or downloaded you should have access to the library 1ibnetcdf a itself the various files netcd inc netcdf mod to include in programs and basic NetCDF software nc dump and ncgen To ensure that during compilation the model can find the NetCDF library and in clude files you must declare environment variables NCDFLIB and NCDFINC again it is also possible to set these environment variables in the makegcm script as explained below NCDFLIB must contain the path to the directory containing the object library libnetcdf a and NCDFINC must contain the path to the directory con taining the include files net cdf inc If using Csh setenv NCDFINC wherever is netcdf include setenv NCDFLIB wherever is netcdf lib If using Bash export NCDFINC wherever is netcdf include export NCDFLIB wherever is netcdf lib Install software with which can load and display NetCDF files such as GrAdS or Ferret 17 For people working at LMD thanks to the excellent Laurent Fairhead Grads and Ferret are installed and ready to go Go to your LMDZ MARS and adapt makegcm script to fit your needs e Examples of makegcm scripts adapted for different compilers pgf90 95 gfortran and ifort are provided files makegcm makegocm g95 makegcm gfortran makegcm ifort copy or rename the relevant as makegcn in the same dire
16. form Fortran These files must be preprocessed by aC preprocessor such as cpp before compilation this behaviour is for most compilers implicitly obtained but using a capital F in the extention of the file names Constants are placed in COMMON declarations located in the common include files file h In general variables are passed from subroutine to subroutine as arguments and never as COMMON blocks In some parts of the code for historical reasons the following rule is sometimes used in the subroutine the variables ex name passed as an argument by the calling program are given the prefix p ex pname while the local variables are given the prefix z ex zname As a result several variables change their prefix and thus their name when passing from a calling subroutine to a called subroutine 5 3 Model organization Figure 5 1 describes the main subroutines called by physiq F 5 4 Compiling the model Technically the model is compiled using the Unix utility make The file makefile which describes the code dependencies and requirements is created automatically by the script create make gcm This utility script recreates the makefile file when necessary for example when a source file has been added or removed since the last compilation None of this is visible to the user To compile the model just run the command makegcm 26 1 Tnitialisation phyeta0 F surfini F iniorbit F initracer F solarlong
17. iq isotherm Temperatures isothermes et vents nuls co2ice 0 elimination des calottes polaires de CO2 ptot pression totale Program newstart e creates files restart nc and restartfi nc that you gen erally need to rename for instance rename them in startO nc and startfi0 nc if you want to use runO or run mcd starting with season 0 rename them start nc and startfi nc if you just want to perform one run with gcm e 4 9 2 Creating the initial start archive nc file Archive file start archive noc is created from files start nc and startfi nc by program start2archive Program start2archive compiles to the same grid resolution as the start nc and startfi nc grid resolution For example makegcm d 64x48x25 p mars start2archive Thenrun start2archive e You now have start archive nc file for one season that you can use with newstart If you want to gather other states obtained at other times of year rerun start2archive e with the start nc and startfi nc corresponding to these These additional initial states will automatically be added to the start archive nc file present in the directory 4 9 3 Changing the horizontal or vertical grid resolution To run at a different grid resolution than available initial conditions files one needs to use tools newstart and start2archive 23 For example to create initial states at grid resolution 32x24x25 from NetCDF files start and startfi at grid resolution 64x48x32 e Create file sta
18. to re interpolate data in order to yield values at the same given local time useful to mimic satellite observations or analyse day to day variations at given local time Input files may be of diagfi nc stats nc or concat nc type and the output file name is build from the input one to which _LT nc is appened e g if the input file is myfile nc then output file will be myfile LT nc B 4 zrecast With this program you can recast atmospheric i e 4D dimentional longitude latitude altitude time data from GCM outputs e g as given in diagfi nc concat nc and stats nc files onto either pressure or altitude above areoid vertical coordinates Since integrating the hydrostatic equation is required to recast the data the input file must contain surface pressure and atmospheric temperature as well as the ground geopotential If recasting data onto pressure coordinates then the output file name is given by the input file name to which P nc will be appened If recasting data onto altitude above areoid coordinates then a nc will be appened B 5 This program is designed to interpolate data in Solar Longitude Ls linear time coordinate usable with grads diagfi ncorconcat nc files 60 Islin also create a Islin ctl file that can be read directly by grads gt xdfopen 1sllin ctl to plot in Ls coordinate to avoid some problem with grads when grads think that the time interval is too small B 6 hrecast This program can interpol
19. 0 NOTE A script is available for performing annual runs with 12 seasons at 30 solar longitude as it is in the database script run_mcd also found in directory de tank This script functions with script run0 Just set the number of simulations to 1 in Then copy run def into run def ref and set nday to 9990 in this file To start from startN c edit the file run mcd and comment with a the N months already created and describe N in num run Then run 4 9 Creating and modifying initial states 4 9 4 Using program newstart Several model parameters for example the dust optical depth are stored in the initial states NetCDF files start nc and startfi nc To change these parameters or to generally change the model resolution use program newstart This program is also used to create an initial state In practice we usually reuse an old initial state and modify it using newstart Like the GCM program newstart must be compiled using the makegcm script to the required grid resolution For example makegcm d 64x48x25 p mars newstart Then run newstart e The program then gives you two options A partir de quoi souhaitez vous creer vos etats initiaux 0 d un fichier start archive 1 un fichier start e Option 1 allows you to read and modify the information needed to create a new initial state from the files start nc startfi nc e Option 0 allows you to read and modify the inform
20. 40 1993 F Lef vre J L Bertaux T Clancy T Encrenaz Fast F Forget S Lebonnois F Montmessin and S Perrier Heterogeneous chemistry in the atmosphere of Mars Nature 454 971 975 2008 F Lef vre S Lebonnois F Montmessin and F Forget Three dimensional modeling of ozone on Mars Journal of Geophysical Research Planets 109 E07004 2004 S R Lewis M Collins P L Read F Forget F Hourdin R Fournier C Hourdin O Talagrand and J P Huot A climate database for Mars J Geophys Res 104 24 177 24 194 1999 F Lott and M Miller A new sub grid scale orographic drag parametrization its formulation and testing J R Meteorol Soc 123 101 128 1997 J B Madeleine F Forget E Millour L Montabone and M J Wolff Revisiting the radiative impact of dust on Mars using the LMD Global Climate Model Journal of Geophysical Research Planets 116 11010 Nov 2011 F Montmessin F Forget P Rannou M Cabane and R M Haberle Origin and role of water ice clouds in the Martian water cycle as inferred from a general circulation model Journal of Geophysical Research Planets 109 E18 10004 2004 62 18 O B Toon C P McKay T P Ackerman and K Santhanam Rapid calculation of radiative heating rates and photodissociation rates in inhomogeneous multiple scattering atmospheres J Geophys Res 94 16 287 16 301 1989 19 M J Wolff M D Smith T Clancy
21. 8 710 20 351 235 109 107 475 244 151 715 22 755 240 111 455 480 247 408 720 25 143 59 Appendix B Utilities A few post processing tools which handle GCM outputs files diagfi nc and stats nc are available in the LMDZ MARS util subdirectory This directory contains the sources codes along with a README exec file which explains what the various programs are for and how to compile them B 1 concatnc This program concatenates consecutive output files diagfi nc or even stats nc files for a selection of variable in order to obtain one single big file The time dimension of the output can be sols or Ls note that in that latter case Ls values won t be evenly distributed and software like Grads may not be able to use and plot the data To obtain an evenly sampled Ls timescale you can use the 1s1in e program described below The output file created by conctanc e is concat nc B 2 Islin This program is designed to interpolate data given in irregular Solar Longitude Ls into an evenly sampled linear time coordinate usable with Grads Input Netcdf files may be diagfi nc or concat nc files and the resulting output file is 1s1in nc Islin also create a 1slin ct1 file that can be read directly by grads gt xdfopen lslin ct1 to plot in Ls coordinate to avoid some problem with grads when Grads think that the time interval is too small B 3 localtime The localtime e program is designed
22. Erud em C SU Sa S te er 25 25 26 26 30 30 31 31 32 34 36 38 44 44 44 45 49 49 49 50 51 53 Chapter 1 Introduction This document is a user manual for the General Circulation Model of the Martian atmo sphere developed by the Laboratoire de M t orologie Dynamique of the CNRS in Paris in collaboration with the Atmospheric and Oceanic Planetary Physics sub department in Oxford It corresponds to the version of the model available since November 2002 that includes the new dynamic code Imdz3 3 and the input and output data in NetCDF format The physical part has been available since June 2001 including the NLTE radiative transfer code valid at up to 120 km tracer transport the water cycle with water vapour and ice the double mode dust transport model and with optional photochemistry and extension in the thermosphere up to 250km A more general scientific description of the model without tracers can be found in Forget et al 1999 Chapter 2 of this document to be read before any of the others describes the main features of the model The model is divided into two relatively independent parts 1 The hydrodynamic code that is shared by all atmospheres Earth Mars etc that integrates the fluid mechanics equations in time and on the globe and 2 a set of Martian physical pa rameterizations including for example the radiative transfer calculation in the atmosphere and the turbulence mix in
23. F 1 5 Calculation of mean mass and cp R and thermal conduction coeff concentration F Calculation of the radiative tendencies radiative transfer longwave and shortwave for CO2 and dust dustopacity F and callradite F 8 Gravity wave and subgrid scale topography drag calldrag noro F 10 Vertical diffusion turbulent mixing N vidfc F 12 Convective adjustment convadj F physiq F 14 Condensation and sublimation of carbon dioxide newcondens F 7 TRACERS 6a water and water ice watercloud F 6b call for photochemistry when tracers are chemical species callchim F 6c other scheme for tracer dust transport lifting sedimentation dustdevil F callsedim F 6d updates CO2 pressure variations surface budget 19 Thermosphere thermosphere F 85 Surface and sub surface temperature calculations soil F 9 Wnting output files startfi histfi if it s time physdem4 F saving statistics if callstats true wstats F dumping eof if calleofdump true eofdump F output any needed variables in diagfi writediagfi F Figure 5 1 Organigram of subroutine function physiq F 27 with adequate options e g makegcm d 62x48x32 p mars gom as discussed below and described in section 4 3 The makegcm command compiles the model gem and related utilities newstart start2archive testphys1d A detailed description of how to use it and of the various parameters that can be supplied is giv
24. MD model As the best introduction to the model is surely to run a simulation here we explain how to go about it All you will need are files and scripts necessary to build the GCM all are in the LMDZ MARS directory which you will download as explained in the next sections as well as some initial states to initiate simulations and if not working on the LMD machines some extra datafiles for external forcings topography dust scenarios radiative properties of dust and water ice etc Once you have followed the example given below you can then go on to change the control parameters and the initial states as you wish A more detailed description of the model s organization as well as associated inputs and outputs are given in sections 5 and 6 4 1 Obtaining the model The LMD model project is developped using subversion svn the free software versioning and a revision control system To obtain download the latest version of the model simply go to the directory where you want to install the model and use the relevant svn command svn checkout http svn lmd jussieu fr Planeto trunk LMDZ MARS which will output a LMDZ MARS directory the contents of this directory are described in chapter 5 If you are not on the LMD machines you will also need to download the set of files available online at http www lmd jussieu fr forget datagcm datafile preserve the file names and subdirectory structure This directory contains input files t
25. Mars Climate Model Martian Years 24 29 available online at http www mars lmd jussieu fr WP2011 wp12 1 1 pdf Thermal IR radiation lwmain e Numerical method et al 1989 e Optical properties of dust Madeleine et al 2011 Solar radiation swmain e Numerical method Toon et al 1989 e Optical properties of dust see the discussion in Madeleine et al 2011 which quotes properties from Wolff et al 2009 3 3 Subgrid atmospheric dynamical processes 3 3 1 Turbulent diffusion in the upper layer vdifc e Implicit numerical scheme in the vertical see the thesis of Laurent Li LMD Uni versit Paris 7 1990 Appendix C2 e Calculation of the turbulent diffusion coefficients Forget et al 1999 e fluxes in the near surface layer Colaitis et al 2012 techni cal note WP13 1 3d of ESA contract Ref ESA 11369 95 NL JG SC New Mars Climate Model d New convection and boundary layer schemes and their impact on Mars meteorology available online at http www mars lmd jussieu fr WP2011 wp13 1 3d pdf 13 3 3 2 Convection convadj e For some details on the convective adjustement see Hourdin et al 1993 e The thermals mass flux scheme is described in Colaitis et al 2012 technical note WP13 1 3d of ESA contract Ref ESA 11369 95 NL JG SC New Mars Climate Model d New convection and boundary layer schemes and their impact on Mars meteorology available online at http www m
26. User Manual for the LMD Martian Atmospheric General Circulation Model Ehouarn MILLOUR Francois FORGET Contributors to earlier versions Karine Dassas Christophe HOURDIN Fr d ric HOURDIN and Yann WANHERDRICK initial version translated by Gwen Davis LMD January 26 2012 Contents Introduction Main features of the model 2 1 Basicpnnciples s 425 5 us Le BAG meu AA 2 20 Dynamical Physical separation 2 3 Grids BOXES ios ud ale ted dub edly he a ge Rei beets 233 1 Horizontal strids bk ee 2 3 2 Vertical gnds ans Sou duane dente hon ee BALA RAUS 2 4 Variables used in the model 24 1 Dynamical variables 2 4 2 Physical variables 24 3 Tracers o Reuse Dus EL ce Me et aa Sape ov te The physical parameterizations of the Martian model some references 3 1 General soe Exon rA Rez ese RME nt Brie AE node S 3 25 Radiative transfer zs 250 een ind ee made a 3 2 1 gas absorption emission 3 3 Subgrid atmospheric dynamical processes 3 3 1 Turbulent diffusion the upper layer 3 3 2 Convection nw LE DA d ie na 3 3 3 Effects of subgrid orography and gravity waves 3 4 Surface thermal conduction 3 5 Condensation
27. Zonal East West wind total standard deviation ov er the season u sd units m s 1 loat v Time altitude latitude longitude vititle Meridional North South wind viunits m s 1 float v_sd Time altitude latitude longitude tion over Hh v Sd title Meridional North South wind total standard devia the season v Sd units m s 1 loat w Time altitude latitude longitude w title Vertical down up wind w units m s 1 float w sd Time altitude latitude longitude w Sd title Vertical down up wind total standard deviation o ver the season Hh j w Sd units m s 1 loat rho Time altitude latitude longitude rho title Atmospheric density rho units none loat rho sd Time altitude latitude longitude rho sd title Atmospheric density total standard deviation ove r the season Hh fi rho_sd units none loat q2 Time altitude latitude longitude q2 title Boundary layer eddy kinetic energy q2 units m2 s 2 loat q2_sd Time altitude latitude longitude q2_sd title Boundary layer eddy kinetic energy total standard deviation over the season 3 fi q2 sd units m2 s 2 loat vmr h2ovapor Time altitude latitude longitude vmr_h2ovapor title H2O vapor volume mixing ratio vmr h2ovapor units mol mol loat vmr h2ovapor sd Time altitude latitude longitude vmr h2ovapor sd title
28. ab 1 27 tauvis tab cntr1 28 0 tab cntr1 29 0 tab cntrl1 30 0 Soil properties tab 1 35 volcapa so x time e number of nodes on physics grid number of atmospheric layers initial day initiale time of day f dynamics and physics dius of Mars m 3397200 tation rate rad s 1 avity m s 2 3 72 lar mass of the atmosphere g mol 1 43 49 r cp 70 256793 kappa dans dynamique ngth of a sol s 788775 ime step in the physics r physics length of year sols min Sun Mars distance Mkm 7206 66 max SUn Mars distance Mkm 7249 22 date of perihelion sols since N spring Obliquity of the planet deg 723 98 7668 6 surface roughness m 0 01 mixing length 100 minimal energy 1 e 8 and ground emissivity Albedo of northern cap Albedo of southern cap Emissivity of northern cap Emissivity of southern cap 70 95 Emissivity of martian soil 7 95 mean scat radius of CO2 snow north mean scat radius of CO2 snow south time scale for snow metamorphism north time scale for snow metamorphism south 70 5 70 25 70 95 mean visible optical depth il volumetric heat capacity 43 6 3 Output files 6 3 1 NetCDF restart files restart nc and restartfi nc These files are of the exact same format as start startfi nc 6 3 2 NetCDF file diagfi nc NetCDF file diagfi nc stores the instantaneous physical variables throughout the sim ulati
29. alindo F Forget M A L pez Valverde and M Angelats i Coll A Ground to Exosphere Martian General Circulation Model 2 The Atmosphere During Perihelion Conditions Thermospheric Polar Warming Journal of Geophysical Research Planets 114 E13 E08004 2009 F Gonz lez Galindo F Forget M A L pez Valverde M Angelats i Coll and E Millour A Ground to Exosphere Martian General Circulation Model 1 Seasonal Diurnal and Solar Cycle Variation of Thermo spheric Temperatures Journal of Geophysical Research Planets 114 E13 4001 2009 F Gonz lez Galindo M A L pez Valverde M Angelats i Coll and F Forget Extension of a Martian general circulation model to thermospheric altitudes UV heating and photochemical models Journal of Geophysical Research Planets 110 E9 9008 2005 C Hourdin J L Dufresnes R Fournier and F Hourdin Net exchange reformulation of radiative transfer in the CO2 15 band on mars Article in preparation 2000 Hourdin A new representation of the CO2 15 jm band for a Martian general circulation model J Geo phys Res 97 E11 18 319 18 335 1992 F Hourdin and A Armengaud Test of a hierarchy of finite volume schemes for transport of trace species in an atmospheric general circulation model Mon Wea Rev 127 822 837 1999 F Hourdin P Le Van F Forget and O Talagrand Meteorological variability and the annual surface pressure cycle on Mars J Atmos Sci 50 3625 36
30. ars lmd jussieu fr WP2011 wp13 1 3d pdf 3 3 3 Effects of subgrid orography and gravity waves calldrag noro drag noro See Forget et al 1999 and Lott and Miller 1997 3 4 Surface thermal conduction soil The numerical scheme is described in section 2 of technical note WP11 1 of ESA contract Ref ESA 11369 95 NL JG SC Improvement of the high latitude processes in the Mars Global Climate Model available online at http www mars lmd jussieu fr WP2008 Polar processes pdf 3 5 Condensation In Forget et al 1998 article published in Icarus Numerical method for calculating the condensation and sublimation levels at the surface and in the atmosphere newcondens explained in the appendix Description of the numerical scheme for calculating the evolution of snow emissivity co2snow explained in section 4 1 Noncondensable gaz treatment see Forget et al 2008 available online at http www lpi usra edu meetings modeling2008 pdf 9106 pdf Inclusion of sub surface water ice table thermal effect varying albedo of polar caps and tuning of the CO2 cycle are descibed in technical note WP13 1 3e of ESA contract Ref ESA 11369 95 NL JG SC New Mars Global Climate Model e Improved CO2 cycle and seasonal pressure variations available online at http www mars lmd jussieu fr WP2011 wp13 1 3e pdf 3 6 Tracer transport and sources e Van Leer transport scheme used in the dynamical part 1 a
31. ate GCM output on any horizontal grid regular lat lon as long as it cover all the planet Useful to compare runs obtained at different horizontal resolutions B 7 expandstartfi This program takes a physics start file start fi nc and recasts it on the corresponding lonxlat grid so its contents may easily be displayed using Grads Ferret etc B 8 extract This program extracts ie interpolates pointwise values of an atmospheric variable from a zrecast ed diagfi file works if altitude is geometrical height or a pressure vertical coordinates 61 Bibliography 6 10 11 12 13 14 15 16 17 M Angelats i Coll Forget M A L pez Valverde and Gonz lez Galindo The first Mars thermospheric general circulation model The Martian atmosphere from the ground to 240 km Geophys Res Lett 32 4201 2005 J L Dufresne R Fournier C Hourdin and F Hourdin Net Exchange Reformulation of Radiative Transfer in the CO2 15 um Band on Mars Journal of Atmospheric Sciences 62 3303 3319 2005 F Forget F Hourdin R Fournier C Hourdin O Talagrand M Collins S R Lewis P L Read and J P Huot Improved general circulation models of the Martian atmosphere from the surface to above 80 km J Geophys Res 104 24 155 24 176 1999 Forget F Hourdin and Talagrand CO2 snow fall on Mars Simulation with a general circulation model Icarus 131 302 316 1998 F Gonz lez G
32. ation needed to cre ate a new initial state from file start archive nc whatever the start archive nc grid resolution is If you use tracers make sure that they are taken into account in your start files either start or start archive Then answer to the various questions in the scroll menu These questions allow you to modify the initial state for the following parameters 22 First set of questions Modifications of variables in tab_cntrl day_ini Jour initial 0 a Ls 0 20 surface roughness m emin_turb energie minimale lmixmin longueur de melange emissiv Emissivite du sol martien emisice Emissivite des calottes albedice Albedo des calotte iceradius mean scat radius of CO2 snow dtemisice time scale for snow metamorphism tauvis profondeur optique visible moyenne obliquit planet obliquity deg peri day perihelion date sol since Ls 0 periheli min sun mars dist Mkm aphelie max sun mars dist Mkm Second set of questions flat no topography aquaplanet bilball albedo inertie thermique uniforme coldspole sous sol froid et haut albedo au pole sud q 0 traceurs a zero ini traceurs initialises pour la chimie ini q H20 idem sauf le dernier traceur H20 ini q iceH20 idem sauf ice et H20 watercapn H20 ice sur la calotte permanente nord watercaps H20 ice sur la calotte permanente sud wetstart start with a wet atmosphere igset give a specific value to tracer
33. ations variables and attribute values The values of the non coordinate variable data are not displayed at the output ncdump h diagfi nc Shows only the informative header of the file which is the declaration of the dimensions variables and attributes but not the values of these variables The output is identical to that in option c except for the fact that the coordinated variable values are not included ncdump v varl varn diagfi nc The output includes the specific variable values as well as all the dimensions variables and attributes More that one variable can be specified in the list following this option The list must be a simple argument for the command and must not contain any spaces If no variable is specified the command displays all the values of the variables in the file by default 30 90N 150 60N 30N 170 mone 170 170 180 3 30S 60S 90S 180 120W 60W 0 60E 120E 180 Figure 6 1 Example of temperature data at a given time using GrADS visualization 6 1 2 Graphic visualization of the NetCDF files using GrAds GrAdS The Grid Analysis and Display System is a graphic software developed by Brian Doty at the Center for Ocean Land Atmosphere COLA One of its functions is to enable data stored in NetCDF format to be visualized directly In figure 6 1 for example we can see the GrADS visualization of the temperature data at a give
34. brid sigma at interlayers bp units float soildepth subsurface layers Soildepth long name Soil mid layer depth soildepth units m soildepth positive down 44 float cu latitude rlonu cu title Conversion coefficients cov lt gt natural float cv rlatv longitude cv title Conversion coefficients cov lt gt natural float aire latitude longitude aire title Mesh area float phisinit latitude longitude phisinit title Geopotential at the surface float emis Time latitude longitude emis title Surface emissivity emis units w m 1 float tsurf Time latitude longitude tsurf title Surface temperature tsurf units K float ps Time latitude longitude ps title surface pressure ps units Pa float co2ice Time latitude longitude co2ice title co2 ice thickness co2ice units kg m 2 float mtot Time latitude longitude mtot title total mass of water vapor mtot units kg m2 float icetot Time latitude longitude icetot title total mass of water ice icetot units kg m2 float tauTES Time latitude longitude tauTES title tau abs 825 cm 1 tauTES units float 20 ice s Time latitude longitude h20 ice s title surface h2o ice h20 ice s units kg m 2 The structure of the file is thus as follows the dimensions variable time containing the time of the timestep stored in the file in Martian
35. cle with the LMD GCM e In callphys def set tracer to true tracer true Use the same op tions as below for the Tracer part the rest does not change compared to the basic callphys def The important parameters are water true to use water vapor and ice tracers and sedimentation true to allow sedimentation of water ice clouds Tracer dust water ice and or chemical species options used if tracer T o n a DUST Transported dust if gt 0 use dustbin dust bins dustbin 0 DUST Radiatively active dust matters if dustbin gt 0 active false DUST use mass and number mixing ratios to predict dust size must also have dustbin 1 doubleq false DUST lifted by GCM surface winds lifting false DUST lifted by dust devils callddevil false DUST Scavenging by CO2 snowfall scavenging false DUST WATERICE Gravitationnal sedimentation sedimentation true WATERICE Radiatively active transported atmospheric water ice activice false WATER Compute water cycle water true WATER current permanent caps at both poles True IS RECOMMENDED with true North cap is a source of water and South pole is a cold trap caps true e Compilation You need to compile with at least 2 tracers If you don t have dust dustbin 0 or other chemical species photochem F compilation is done with the command lines makegcm d 64x48x25 t 2 p mars new
36. ctory e As mentionned above you may edit the script to hard code values of LMDGCM LIBOGCM NCDFINC and NCDFLIB instead of relying on the use of environ ment variables see the commented out examples in the scripts at lignes 20 30 Note that since the makegocm is a Csh script Csh syntax must be used there Finally make sure that you have access to all the executables needed for building and using the model and remember to set environment variables to the correct corre sponding pathes note that if you do not want to have to redefine these every session you should put the definitions in the corresponding cshrc or bashrc files UNIX function imake a Fortran compiler ncdump grads or ferret 4 5 Compiling the model Example 1 Compiling the Martian model at grid resolution 64x48x25 for example type in compliance with the manual for the makegcm function given in section 5 4 makegcm d 64x48x25 p mars You can find executable gem e the compiled model in the directory where you ran the makegcm command Example 2 Compiling the Martian model with 3 tracers e g CO2 water vapour and ice to simulate the water cycle makegcm d 64x48x25 t 2 p mars gcm Example 3 Compiling the the Martian model with your choice of compiler options e g to check for array overflow useful for debugging warning the model is then much slower makegcm d 64x48x25 p mars O C gcm Note that the makegocm scrip
37. d dimensions h which contains the 3 dimensions of the horizontal grid im jm lm plus the number of tracers passively advected by the dynamics ntrac in 4 PARAMETER FORTRAN format with a new file SLMDGCM libf grid dimension dimensions im jm lm tntrac If the file does not exist already it is created by the script SLMDGCM libf grid dimension makdim 28 s nscat Number of radiatively active scatterers p PHYS Selects the set of physical parameterizations you want to compile the model with The model is then compiled using the physical parameterization sources in directory S LMDGCM libf phyPHYS g grille Selects the grid type This option overwrites file SLMDGCM libf grid fxyprim h with file SLMDGCM libf grid fxy grille h the grid can take the following values 1 reg the regular grid 2 sin to obtain equidistant points in terms of sin latitude 3 new to zoom into a part of the globe O compilation options set of fortran compilation options to use include path Used if the subroutines contain include files ccp that are located in directories that are not referenced by default adjnt Compiles the adjoint model to the dynamical code olddyn To compile GCM with old dynamics filtre filter To select the longitudinal filter in the polar regions filter corresponds to the name of a directory located in SLMDGCM libf The standard filter for the model is filtrez which can be used for a regular grid and f
38. days since the beginning of the run variable control containing many parameters as described above from rhonu to phisinit a list of data describing the geometrical coordinates of the data file plus the surface topography finally all the 2D or 3D data stored in the run 6 3 3 Stats files As an option stats must be set to true in callphys def the model can accumulate any variable from any subroutine of the physics by calling subroutine wstat This save is performed at regular intervals 12 times a day An average of the daily evolutions over the whole run is calculated for example for a 10 day run the averages of the variable values at ORTU 2hTU 4hTU 24hTU are calculated along with RMS standard deviations of the variables This ouput is given in file stats nc Illustrative example of the contents of a stats nc file using ncdump ncdump h stats nc netcdf stats dimensions 45 latitude 49 longitude 65 al 11 ltitude 25 Impl 26 Time UNLIMITED 12 currently variables 1 e season f loat Time Time Time title Time Time units days since 0000 00 0 00 00 00 loat latitude latitude latitude title latitude latitude units degrees north loat longitude longitude longitude title East longitude longitude units degrees east loat altitude altitude altitude long name altitude altitude units km altitude positiv
39. described in section 5 4 makegcm d 25 p mars testphysld You can find executable testphys1d e the compiled model in the directory from which you ran the makegcm command 10 2 1 D runs and input files The 1 D model does not use an initial state file the simulation must be long enough to obtain a balanced state Thus to generate a simulation simply type testphysld e The following example files are available in the deftank directory copy them into your working directory first callphys def controls the options in the physics just like for the 3D GCM Z2sig def controls the vertical discretization no change needed in general func tions as with the 3D GCM traceur def controls the tracer names this file may not be present as long as you run without tracers option tracer false incallphys def run def controls the 1 D run parameters and initializations this is actally file run def 1d the deftank directory which must be renamed run def to be read by the program The last file is different from the 3D GCM s run def input file as it contains options specific to the 1 D model as shown in the example below Time integration parameters Initial date in martian sols 0 at Ls 0 day0 0 Initial local time in hours between 0 and 24 time 0 Number of time steps per sol day_step 48 Number of sols to run ndt 100 Physical parameters Surface pressure Pa ps
40. e up loat aps altitude aps title hybrid pressure at midlayers aps units loat bps altitude bps title hybrid sigma at midlayers bps units loat ps Time latitude longitude ps title Surface pressure ps units Pa loat ps sd Time latitude longitude ps sd title Surface pressure total standard deviation over th ps sd units Pa loat tsurf Time latitude longitude tsurf title Surface temperature tsurf units K loat tsurf sd Time latitude longitude tsurf sd title Surface temperature total standard deviation o ver the season Ti 3 he season fi 1 tsurf sd units K loat co2ice Time latitude longitude co2ice title CO2 ice cover co2ice units kg m 2 loat co2ice sd Time latitude longitude 2 sd title CO2 ice cover total standard deviation over t co2ice sd units kg m 2 loat fluxsurf lw Time latitude longitude fluxsurf lw title Thermal IR radiative flux to surface fluxsurf lw units W m 2 loat fluxsurf lw sd Time latitude longitude fluxsurf lw sd title Thermal IR radiative flux to surface tot al standard deviation over the season T 3 andard deviation over the season E fluxsurf lw sd units W m 2 loat fluxsurf sw Time latitude longitude fluxsurf sw title Solar radiative flux to surface fluxsurf sw units W m 2 loat fluxsurf sw sd Tim
41. e latitude longitude fluxsurf sw sd title Solar radiative flux to surface total st fluxsurf sw sd units W m 2 loat fluxtop lw Time latitude longitude fluxtop lw title Thermal IR radiative flux to space fluxtop_lw units W m 2 1 loat fluxtop lw sd Time latitude longitude fluxtop lw sd title Thermal IR radiative flux to space total standard deviation over the season fluxtop sd units W m 2 46 loat fluxtop_sw Time latitude longitude fluxtop_sw title Solar radiative flux to space fluxtop_sw units W m 2 float fluxtop_sw_sd Time latitude longitude fluxtop_sw_sd title Solar radiative flux to space total stand ard deviation over the season fluxtop sw sd units W m 2 loat dod Time latitude longitude dod title Dust optical depth dod units float dod sd Time latitude longitude dod sd title Dust optical depth total standard deviation over the season dod sd units loat temp Time altitude latitude longitude temp title Atmospheric temperature temp units K float temp sd Time altitude latitude longitude temp sd title Atmospheric temperature total standard deviatio n over the season temp sd units K loat u Time altitude latitude longitude u title Zonal East West wind u units m s 1 float u sd Time altitude latitude longitude u sd title
42. e subgrid scale topography For the dynamics physinit for the initial state of surface geopotential Remark variables phisfi and physinit contain the same information surface geopotential but phisfi gives the geopotential values on the physical grid while physinit give the values on the dynamical grid Physical and dynamical state variables To save disk space the initialization files store the variables used by the model rather than the natural variables For the dynamics ucov and vcov the covariant winds These variables are linked to the natural winds by ucov cu uandvcov cv v teta the potential temperature or more precisely the potential enthalpy linked to temperature T by 0 P the tracers ps surface pressure masse the atmosphere mass in each grid box 41 Vectorial variables ucov and vcov are stored on staggered grids u and v respectively in the dynamics see section 2 2 Scalar variables h q tracers ps masse are stored on the scalar grid of the dynamical part For the physics co2ice surface dry ice tsurf surface temperature tsoil temperatures at different layers under the surface emis surface emissivity q2 wind variance or more precisely the square root of the turbulent kinetic energy the surface tracer budget kg m All these variables are stored on the physical grid see section 2 2 The con
43. en in the help manual below which will also be given by the makegcm h command Note that before compiling the GCM with makegcm you should have set the environment variable LIBOGCM to a path where intermediate objects and libraries will be generated If using Csh setenv LIBOGCM where you want objects to go libo If using Bash export LIBOGCM where you want objects to go libo Help manual for the makegcm script makegcm Options prog The makegcm script 1 compiles a series of subroutines located in the S LMDGCM libf sub directories The objects are then stored in the libraries in LIBOGCM 2 then makegcm compiles program prog f located by default in SLMDGCM libf dyn3d and makes the link with the libraries Environment Variables LMDGCM and S LIBOGCM must be set as environment variables or directly in the makegcm file The makegcm command is used to control the different versions of the model in parallel compiled using the compilation options and the various dimensions without having to recompile the whole model The FORTRAN libraries are stored in directory S LIBOGCM OPTIONS The following options can either be defined by default by editing the makegcm script or in interactive mode d imxjmxlm where im jm and lm are the number of longitudes latitudes and vertical layers respectively t ntrac Selects the number of tracers present in the model Options d and t overwrite file SLMDGCM libf gri
44. es which may have several modes chemical species which depict the chemical composition of the atmosphere water vapor and water ice particles 10 In the code all tracers are stored in one three dimensional array q the third index of which corresponds to each individual tracer In input and output files startfi nc see Section 4 tracers are stored seperately using their individual names Load ing specific tracers requires that the approriate tracer names are set in the traceur def file see Section 6 2 3 and specific computations for given tracers e g computing the water cycle chemistry in the upper atmosphere is controled by setting coresponding options in the callphys def file see Section 6 2 2 11 Chapter 3 The physical parameterizations of the Martian model some references 3 1 General The Martian General Circulation Model uses a large number of physical parameterizations based on various scientific theories and some generated using specific numerical methods A list of these parameterizations is given below along with the most appro priate references for each one Most of these documents can be consulted at http www mars lmd jussieu fr mars publi html General references A document attempts to give a complete scientific description of the current version of the GCM a version without tracers e Forget et al 1999 article published in the JGR 3 2 Radiative transfer T
45. fferent variables listed below that control or describe the Martian meteorology and climate at different points of a 3D grid see below that covers the entire atmosphere From an initial state the model calculates the evolution of these variables timestep by timestep e At instant t we know variable X temperature for example at one point in the atmosphere e We calculate the evolution the tendencies 25 5 etc arising from each physical phenomenon calculated by a parameterization of each of these phe nomenon for example heating due to absorption of solar radiation e At the next time step t dt we can calculate X 5 from X and 5 This is the integration of the variables in time For example X 5 X t 2x 1 X The main task of the model is to calculate these tendencies arising from the t different parameterized phenomenon 2 2 Dynamical Physical separation In practice the 3D model operates in two parts one dynamical part containing the numerical solution of the general equations for at mospheric circulation This part including the programming is common to the Earth and Martian model and in general for all atmospheres of the terrestrial type a second physical part that is specific to the planet in question and which calculates the forced circulation and the climate details at each point The calculations for the dynamical part are made on a 3D grid with hori
46. final state of the model As shown in figure 4 1 these files which are of the same format as the start files can later be used as initial states for a new simulation The restart files just need to be renamed mv restart nc start nc mv restartfi nc startfi nc and running a simulation with these will in fact resume the simulation from where the previous run ended 4 8 Chain simulations In practice we recommend running a chain of simulations lasting several days or longer or hundreds of days at low resolution To do this a script named is available in LMDZ MARS deftank which should be used as follows e Set the length of each simulation in run def i e set the value of nday 21 e Set the maximum number of simulations at the beginning of the run0 script i e set the value of nummax e Copy start files start nc startfi nc over and rename them start0 nc startfi0 nc e Run script runO runO runs a series of simulations that generate the indexed output files e g start1 startfil diagfil etc including files 1run1 lrun2 etc containing the redi rection of the display and the information about the run NOTE to restart a series of simulations after a first series for example starting from start5 and startfi5 just write the index of the initial files e g 5 in the file named num run If num run exists the model will start from the index written in num run If not it will start from start0 and startfi
47. fined in run def Here are the variables that you want to set e East longitude in degrees of zoom center clon e latitude in degrees of zoom center clat e zooming factors along longitude grossismx Typically 1 5 2 or even 3 see be low e zooming factors along latitude grossismy Typically 1 5 2 or even 3 see below e fxyhypb must be set to T for a zoom whereas it must be F otherwise e extention in longitude of zoomed area dzoomx This is the total longitudinal exten sion of the zoomed region degree It is recommended that grossismx x dzoomx 200 e extention in latitude of the zoomed region dzoomy This is the total latitudinal extension of the zoomed region degree It is recommended that grossismy x dzoomy 100 e stiffness of the zoom along longitudes taux 2 is for a smooth transition in longi tude more means sharper transition e stiffness of the zoom along latitudes taux 2 is for a smooth transition in latitude more means sharper transition 7 2 Making a zoomed initial state One must start from an initial state archive start archive noc obtained from a previ ous simulation see section 4 9 Then compile and run newstart e using the run def file designed for the zoom After running newstart e The zoomed grid may be visualized using grads for instance Here is a grads script that can be used to map the grid above a topography map 49 set mpdraw off set grid off sdfopen restart nc set g
48. float rlatv rlatv rlatv title Latitudes des points V float ap interlayer ap title Coef A hybrid pressure levels float bp interlayer bp title Coef B hybrid sigma levels float aps altitude aps title Coef AS hybrid pressure at midlayers float bps altitude bps title Coef BS hybrid sigma at midlayers float presnivs altitude float latitude latitude latitude units degrees north latitude long name North latitude float longitude longitude longitude long name East longitude longitude units degrees east float altitude altitude altitude long name pseudo alt altitude units km altitude positive up float cu latitude rlonu cu title Coefficient de passage pour U float cv rlatv longitude cv title Coefficient de passage pour V float aire latitude longitude aire title Aires de chaque maille float phisinit latitude longitude phisinit title Geopotentiel au sol float Time Time Time title Temps de simulation Time units days since 1 01 01 00700300 gt float ucov Time altitude latitude rlonu ucov title Vitesse U float vcov Time altitude rlatv longitude vcov title Vitesse V float teta Time altitude latitude longitude teta title Temperature float h2o_ice Time altitude latitude longitude h20 ice title Traceur h20 ice float h2o_vap Time altitude latitude longitude 39
49. ghtforward and flexible values given to parameters must be given as parameter value Any blank line or line beginning with symbol is a comment and instruction lines may be written in any order Moreover not specifying a parameter value set e g deleting it or commenting it out means you want the GCM to use a default built in value Additionally one may use a specific keyword INCLUDEDEF to specify another text file in which to also read values of parameters e g INCLUDEDEF callphys def Here are some details about some of the parameters which may be set in run def e day step the number of dynamical steps per day to use for the time integration This needs to be large enough for the model to remain stable this is related to the CFL sta bility criterion which essentially depends on the horizontal resolution of the model On Mars in theory the GCM can run with day step 480 using the 64 48 grid but model stability improves when this number is higher day st ep 960 is recom mended when using the 64x48 grid According to the CFL criterion day_step should vary in proportion with the resolution for example day_step 480 using the 32x24 horizontal resolution Note that day step must also be divisible by iperiod e tetagdiv tetagrot tetatemp control the dissipation intensity It is better to limit the dissipation intensity tetagdiv tetagrot tetatemp should not be too low However the model diverges if tetagd
50. he radiative transfer parameterizations are used to calculate the heating and cooling ratios in the atmosphere and the radiative flux at the surface 3 2 4 gas absorption emission Thermal IR radiation lwmain e New numerical method solution for the radiative transfer equation Dufresne et al 2005 Model validation and inclusion of the Doppler effect but using an old numerical formulation Hourdin 1992 article e At high altitudes parameterization of the thermal radiative transfer n1tecool when the local thermodynamic balance is no longer valid e g within 0 1 Pa Lopez Valverde et al 2001 Report for the ESA available on the web as CO2 non LTE cooling rate at 15 um and its parameterization for the Mars atmosphere 12 Absorption of near infrared radiation nirco2abs e Forget et al 1999 3 2 2 Absorption emission and diffusion by dust Dust spatial distribution aeropacity e The method for semi interactive dust vertical distribution is detailed in Madeleine et al 2011 Vertical distribution and description of MGS and Viking scenarios in the ESA re port Mars Climate Database V3 0 Detailed Design Document by Lewis et al 2001 available on the web e For the MY24 MY26 scenarios the dust distributions were derived from observations made by TES data is used See technical note WP12 2 1 of ESA contract Ref ESA 11369 95 NL JG SC New dust scenarios for the
51. hen counting from the north pole N B In the Fortran program the following variables are used iim IM Lipl IM 1 jjm JM jjpl1 JM 1 at the same place Similarly the extreme j 1 and j JM 1 nodes on the dynamical grid respectively corresponding to North and South poles are duplicated IM 1 times In contrast the physical grid does not contain redundant points only one value for each pole and no extra point along longitudes as shown in figure 2 2 In practice computa tions relative to the physics are made for a series of ngrid atmospheric columns where NGRID IMx JM 1 2 2 3 2 Vertical grids hybrid coordinates set to false hybrid coordinates set to true 25 layers 25 layers cA zs A T 1 0 z H log palayer pref km H log p layer pref km z Figure 2 3 Sketch illustrating the difference between hybrid and non hybrid coordinates The GCM was initially programmed using sigma coordinates p ps atmospheric pressure over surface pressure ratio which had the advantage of using a constant domain c 1 at the surface and o 0 at the top of the atmosphere whatever the underlying topography However it is obvious that these coordinates significantly disturb the strato spheric dynamical representation as the topography is propagated to the top of the model by the coordinate system This problem can elegantly be sol
52. hese two nodes are actualy located e grille scalaire de la dynamique Exemple IM 6 JM 4 grille physique 1 IM IM 1 1 2 3 4 5 6 j 1 2 3 JIM 4 JM 1 5 1 e e e u u u u u u u vL vL vL vL vL vL vL 2 3 4 SS 6 7 e e e u u u u u u u vL vL vL vL vL vL vL 8 9 I I 1 1 T e T I T fel T g T e u vL vL vL vL vL vL vL 1 1 1 17 1 1 ii cmd NEL s WE vi vi vi vL vL rlatv 2 rlatu 5 e T e e TE d lt a boite grille scalaire rlonv M 1 IM 1 rlonu Tj 1 1M 1 e H e rlatu 1 JM 1 u i 1 j u i j rlatv 1 JM v i j Figure 2 2 Dynamical and physical grids for a 6 x 7 horizontal resolution In the dynam ics but not in the physics winds u and v are on specific staggered grids Other dynamical variables are on the dynamical scalar grid The physics uses the same scalar grid for all the variables except that nodes are indexed in a single vector containing NGRID 2 JM 1 xIM points w
53. iv tetagrot tetatemp are too high especially if there is a lot of dust in the atmosphere Example used with nitergdiv 1 and nitergrot niterh 2 using the 32x24 grid tetagdiv 6000 s tetagrot tetatemp 30000 s using the 64x48 grid tetagdiv 3000 s tetagrot tetatemp 9000 s e idissip is the time step used for the dissipation dissipation is computed and added every idissip dynamical time step If idissip is too short the model waste time in these calculations But if idissip is too long the dissipation will not be parametrized correctly and the model will be more likely to diverge A check must be made so that idissip tetagdivxdaystep 88775 same rule for tetagrot and tetatemp This is tested automatically during the run e iphysiq is the time step used for the physics physical tendencies are computed every iphysig dynamical time step In practice we usually set the physical time step to be of the order of half an hour We thus generally set iphysiq day_step 48 Example of run def file a i a ee OP Pru PD in ae ep ee TS Parametres de controle du run ET EE da ER eae E EDEN T See EA Nombre de jours d integration nday 9999 nombre de pas par jour multiple de iperiod ici pour dt 1 min 32 day_step 480 periode pour le pas Matsuno en pas iperiod 5 periode de sortie des variables de controle en pas iconser 120 periode d ecriture du fichier histoire en jour iecri 100 periode
54. ixing ratios to predict dust size must also have dustbin 1 doubleq false DUST lifted by GCM surface winds lifting false DUST lifted by dust devils callddevil false DUST Scavenging by CO2 snowfall scavenging false DUST WATERICE Gravitationnal sedimentation sedimentation false WATERICE Radiatively active transported atmospheric water ice activice false WATER Compute water cycle water false WATER current permanent caps at both poles True IS RECOMMENDED with true North cap is a source of water and South pole is a cold trap 35 caps true PHOTOCHEMISTRY include chemical species photochem false Thermospheric options relevant if tracer T PP Ee SNE ata oe T call thermosphere callthermos false WATER included without cycle only if water false thermoswater false call thermal conduction only if callthermos true callconduct false call EUV heating only if callthermos true calleuv false call molecular viscosity only if callthermos true callmolvis false call molecular diffusion only if callthermos true callmoldiff false call thermospheric photochemistry only if callthermos true thermochem false date for solar flux calculation 1985 lt date lt 2002 Solar min 1996 4 ave 1993 4 max 1990 6 solarcondate 1993 4 6 2 3 traceur def Tracers in input
55. les at the following timesteps subroutine integrd F 3 Every iphysig dynamical timestep a call to the interface subroutine calfis F with the physical model physiq F that calculates the evolution of some of the purely physical variables e g surface temperature t surf and returns the tenden cies 9x arising from the physical part 4 Integration of the physical variables subroutine addfi F 5 Similarly calculation and integration of tendencies due to the horizontal dissipation and the sponge layer is done every idissip dynamical time step Remark The physical part can be run separately for a 1 D calculation for a single column using program testphysid F 2 3 Grid boxes Examples of typical grid values are 64x48x25 64x48x32 or 32x24x25 in longitudexlati tudexaltitude For Mars radius 3400 km a 64x48 horizontal grid corresponds to grid boxes of the order of 330x220 kilometers near the equator 2 3 1 Horizontal grids Dynamics and physics use different grids Figure 2 2 shows the correspondance and in dexing of the physical and dynamical grids as well as the different locations of variables on these grids To identify the coordinates of a variable at one grid point up down right or left we use coordinates rlonu rlatu rlonv rlatv longitudes and latitudes in radians On the dynamical grid values at i 1 are the same as at i IM 1 as the latter node is a redundant point due to the periodicity in longitude t
56. ming factor along longitude tab 1 22 grossismy zooming factor along latitude tab cntrl 24 dzoomx extention in longitude of zoom tab 1 25 dzoomy extention in latitude of zoom tab cntrl 27 taux stiffness factor of zoom in longitude tab cntr1 28 tauy stiffness factor of zoom in latitude The controle array in the header of a physical NetCDF file startfi nc 42 c Informations on the physics grid tab cntrl 1 float ngridmx tab cntrl 2 float nlayerm tab cntrl 3 day ini int tab cntrl 4 time int tim c Informations about Mars used by tab cntrl 5 rad ra tab cntrl 6 omeg ro tab cntrl 7 g gr tab 1 8 mugaz Mo tab cntrl1 9 rcp tab cntrl1 10 daysec le tab cntrl 11 phystep t tab cntrl1 12 0 tab cntr1 13 0 c Informations about Mars only fo tab cntrl 14 tab cntrl 15 periheli tab cntrl 16 aphelie l tab cntrl 17 peri_day tab_cntrl 18 obliquit c Boundary layer and turbulence tab cntrl 19 z0 tab cntr1 20 lmixmin tab 1 21 emin_turb c Optical properties of polar caps tab cntr1 22 albedice 1 tab cntr1 23 albedice 2 tab 1 24 emisice 1 tab cntrl 25 tab_cntrl1 26 tab cntrl 31 tab enteri 32 tab cntrl 33 tab cntrl 34 emisice 2 emissiv iceradius 1 iceradius 2 dtemisice 1 dtemisice 2 c dust aerosol properties t
57. n moment However unlike NetCDF GrADS only recognizes files where all the variables are stored on the same horizontal grid These variables can be in 1 2 3 or 4 dimensions X Y Z and t GrADS can also be obtained on the WWW http grads iges org grads 6 2 Input and parameter files The 3D version of the GCM requires the input of two initialization files in NetCDF format start nc contains the initial states of the dynamical variables startfi nc contains the initial states of the physical variables Note that collections of initial states can be retreived at http www lmd jussieu fr forget datagcm Starts Extracting start nc and startfi nc from these archived requires using program newstart as described in section 4 9 To run the GCM also requires the four following parameter files ascii text files run def the parameters of the dynamical part of the program and the temporal integration of the model callphys def the parameters for calling the physical part traceur def the names of the tracer to use Z2sig def the vertical distribution of the atmospheric layers Examples of these parameter files can be found in the LMDZ MARS deftank directory 3l 6 2 1 run def A typical run def file is given as an example below The choice of variables to be set is simple e g nday number of modeled days to run while the others do not need to be changed for normal use The format of the run def file is quite strai
58. n the code the covariant meridional and zonal winds ucov and vcov These variables are linked to the natural winds by ucov cu uandvcov cv v where cu and cv are constants that only depend on the latitude mixing ratio of tracers in the atmosphere typically expressed in kg kg array q in the code ucov and vcov vectorial variables are stored on scalari grids u and v respec tively in the dynamics see section 2 2 teta q ps masse scalar variables are stored on the scalar grid of the dynamics 2 4 2 Physical variables In the physics the state variables of the dynamics are transmitted via an interface that interpolates the winds on the scalar grid that corresponds to the physical grid and trans forms the dynamical variables into more natural variables Thus we have winds u and v 1 5 1 temperature T pressure at the middle of the layers play Pa and at interlayers plev Pa tracers q etc kg kg on the same grid Furthermore the physics also handle the evolution of the purely physical state variables co2ice CO ice on the surface tsurf surface temperature K tsoil temperature at different layers under the surface K emis surface emissivity q2 wind variance or more precisely the square root of the turbulent kinetic energy qsurf tracer on the surface kg m 2 4 3 Tracers The model may include different types of tracers dust particl
59. nd vlsplt in the dynamical part Hourdin and Armengaud 1999 Transport by turbulent diffusion in vdifc convection in convad j sedi mentation sedim dust lifting by winds dustlift see note Preliminary design of dust lifting and transport in the Model ESA contract Work Package 4 1998 available on the web Dust transport by the Mass mixing ratio Number mixing ratio method for grain size evolution see article by Madeleine et al 2011 14 3 7 Watercycle see Montmessin et al 2004 and technical note WP13 1 3c of ESA contract Ref ESA 11369 95 NL JG SC New Mars Climate Model Inclusion of cloud microphysics dust scav enging and improvement of the water cycle available online at http www mars lmd jussieu fr WP2011 wp13 1 3c pdf Radiative effect of clouds see technical note WP13 1 3b of ESA contract Ref ESA 11369 95 NL JG SC New Mars Climate Model b Radiative ef fects of water ice clouds and impact on temperatures available online at http www mars lmd jussieu fr WP2011 wp13 1 3b pdf Chemistry see Lef vre et al 2004 and Lef vre et al 2008 Thermosphere A general description of the model is given in Gonz lez Galindo et al 2009 Details on photochemistry and EUV radiative transfer can be found in Angelats i Coll et al 2005 and Gonz lez Galindo et al 2005 15 Chapter 4 Running the model a practice simulation This chapter is meant for first time users of the L
60. nertiedat title Soil thermal inertia float tsurf physical points tsurf title Surface temperature float tsoil subsurface layers physical points tsoil title Soil temperature float emis physical points emis title Surface emissivity float 42 1 1 1 physical points q2 title pbl wind variance float h20 ice physical points h20 ice title tracer on surface global attributes title Physics start file 40 Physical and dynamical headers There are two types of headers one for the physical headers and one for the dynamical headers The headers always begin with a control variable described below that is allocated differently in the physical and dynamical parts The other variables in the header concern the physical and dynamical grids They are the following the horizontal coordinates rlonu rlatu rlonv rlatv for the dynamical part lati long for the physical part the coefficients for passing from the physical grid to the dynamical grid cu cv only in the dynamical header and finally the grid box areas aire for the dynamical part area for the physical part Surface conditions The surface conditions are mostly given in the physical NetCDF files by variables phisfi for the initial state of surface geopotential albedodat for the bare ground albedo inertiedat for the surface thermal inertia zmea zstd zsig zgam and zthe for th
61. on at regular intervals set by the value of parameter ecritphy in parameter file run def note that ecritphy should be a multiple of iphysigq as well as a divisor of day step Any variable from any sub routine of the physics can be stored by calling subroutine writediagfi Illustrative example of the contents of a diagfi nc file using ncdump ncdump h diagfi nc netcdf diagfi dimensions Time UNLIMITED 12 currently index 100 rlonu 65 latitude 49 longitude 65 rlatv 48 interlayer 26 altitude 25 subsurface layers 18 variables float Time Time Time long name Time Time units days since 0000 00 0 00 00 00 float controle index controle title Control parameters float rlonu rlonu rlonu title Longitudes at u nodes float latitude latitude latitude units degrees north latitude long name North latitude float longitude longitude longitude long name East longitude longitude units degrees east float altitude altitude altitude long name pseudo alt altitude units km altitude positive up float rlatv rlatv rlatv title Latitudes at v nodes float aps altitude aps title hybrid pressure at midlayers aps units Pa float bps altitude bps title hybrid sigma at midlayers bps units float ap interlayer ap title hybrid pressure at interlayers ap units Pa float bp interlayer bp title hy
62. opography dust scenarios radiative properties of scatteres etc which the GCM needs to run Where you put your local datafile directory or whatever name you choose for this directory is not critical as that location can be specified at runtime see sections 4 5 and 6 2 2 To run the model you will also need some initial condition files that can be downloaded from http www lmd jussieu fr forget datagcm Starts see section 4 4 4 2 Installing the model Set some environment variables needed for the compilation of the model it is also pos 16 sible to set the environment variables in the makegcm script as explained below LMDGCM Path to the directory where you have put the model full path If using Csh setenv LMDGCM where you put the model LMDZ MARS If using Bash export LMDGCM where you put the model LMDZ MARS LIBOGCM Path to the directory 1ibo for example where intermediate objects will be stored during the compilation of the model with the makegom script if that directory does not exist then makegcm will create it If using Csh setenv LIBOGCM where you want objects to go libo If using Bash export LIBOGCM where you want objects to go libo Install NetCDF and set environment variables NCDFINC and NCDFLIB The latest version of the NetCDF package is available on the web at the following address http www unidata ucar edu software netcdf along with instructions for building or
63. or a grid with longitudinal zoom link Ldirl lfilel Ldir2 lfile2 Adds a link to FORTRAN libraries libfilel a libfile2 a located in directories dirl dir2 respectively If dirn is a directory with an automatic path usr lib for example there is no need to specify Ldirn 29 Chapter 6 Input Output 6 1 NetCDF format GCM input output data are written in NetCDF format Network Common Data Form NetCDF is an interface used to store and access geophysical data and a library that pro vides an implementation of this interface The NetCDF library also defines a machine independent format for representing scientific data Together the interface library and format support the creation access and sharing of scientific data NetCDF was developed at the Unidata Program Center in Boulder Colorado The freely available source can be obtained from the Unidata website http www unidata ucar edu software netcdf A data set in NetCDF format is a single file as it is self descriptive 6 1 1 NetCDF file editor ncdump The editor is included in the NetCDF library By default it generates an ASCII representa tion as standard output from the NetCDF file specified at the input Main commands for ncdump ncdump diagfi nc dump contents of NetCDF file diagfi nc to standard output i e the screen ncdump c diagfi nc Displays the coordinate variable values variables which are also dimensions as well as the declar
64. r or even not given at all in which case default values are used by the program 56 10 3 Output data During the entire 1D simulation you can obtain output data for any variable from any physical subroutine by using subroutine writegld This subroutine creates file gld nc that can be read by GRADS This subroutine is typically called at the end of subroutine physiq Example of a call to subroutine writeg1d requesting temperature output ngrid horizontal point nlayer layers variable pt called in units CALL writegld ngrid nlayer pt T K 57 Appendix A GCM Martian Calendar For Mars dates and seasons are expressed in Solar Longitude Lg in degrees or in radians counting from the northern hemisphere spring equinox In the GCM time is counted in Martian solar days or sols 1 sols 88775 s from the northern spring equinox The following table gives the correspondence between sols and Ls calculated for the GCM using one Martian year 669 sols exactly 58 sol Ls sol Ls sol Ls 0 360 000 Spring equinox N 240 111 455 480 247 408 5 2 550 245 113 816 485 250 666 10 5 080 250 116 190 490 253 925 15 7 590 255 118 578 495 257 182 20 10 081 260 120 981 500 260 435 25 12 554 265 123 400 505 263 683 30 15 009 270 125 835 510 266 924 514 76 270 Winter solstice N 35 17 447 275 128 287 515 270 156 40 19 869 280 130 756 520 273 377 45 22 275 285 133 243 525 276 587
65. rectory simply execute the pro gram to run a simulation gcm e You might also want to keep all messages and diagnotics written to standard output i e the screen You should then redirect the standard output and error to some file e g gcm out If using Csh gcm e gt gcm out If using Bash gcm e gt gocm out 2 gt amp 1 4 6 Visualizing the output files As the model runs it generates output files diagfi nc and stats nc files The former contains instantaneous values of various fields and the later statistics over the whole run of some variables 4 6 1 Using GrAds to visualize outputs If you have never used the graphic software GrAds we strongly recommend spending half an hour to familiarize yourself with it by following the demonstration provided for that purpose The demo is fast and easy to follow and you will learn the basic commands To do this read file Note that if you ar not running on LMD machines you ll have to modify or add in file cal lphys def the line datadir path to datafile Where path to datafile is the full path to the directory which contains the set of files downloaded from http www lmd jussieu fr forget datagcm datafile 19 Creation of the initial state start_archive nc surface nc run def callphys def Z2sig def V starte startfi nc Simulation 1 V restarLnc restartfi nc jJ
66. rt_archive nc with start2archive e compiled at grid resolu tion 64x48 x25 using old file z2sig def used previously e Create files newstart nc and newstartfi nc with newstart e compiled at grid resolution 32x24 x25 using new file z2sig def If you want to create starts files with tarcers for 50 layers using a start archive nc obtained for 32 layers do not forget to use the ini q op tion in newstart in order to correctly initialize tracers value for layer 33 to layer 50 You just have to answer yes to the question on thermosphere initialization if you want to initialize the thermosphere part only 1233 to 1 50 and no if you want to initialize tracers for all layers 120 to 1250 24 Chapter 5 Program organization and compilation script All the elements of the LMD model are in the LMDZ MARS directory and subdirecto ries As explained in Section 4 this directory may be associated with environment variable LMDGCM If using Csh setenv LMDGCM where you put the model LMDZ MARS If using Bash export LMDGCM where you put the model LMDZ MARS An alternative to using anvironment variables is to set the LMDGCM variable in the makegem script Here is a brief description of the LMDZ MARS directory contents libf All the model FORTRAN Sources F or F90 and include files h organised in sub directories physics phymars dynamics dyn3d filters filtrez deftank A collection of examples of parameter files required
67. ses Ra use Ue RU eR a Shs 6 222 Callphysidefiy c So Paik lee ed Bae MEAS Ge ae 6 233 s rn hehe Des eo EU nt HUS Ee SOS ES 6 2 4 2251008 ele RE Ee mac up we fi 6 2 5 Initialization files start and startfi 6 3 Output s see ga er du v Oe oe Ba ee a 6 3 1 NetCDF restart files restart nc and restartfi nc 6 3 2 NetCDF file diagfinc 63 33 Stats eS me Re uns ee ay as eei Zoomed simulations 7 1 To define the zoomed area 7 2 7 3 Running a zoomed simulation and stability issue Water Cycle Simulation Photochemical Module 1D version of the Mars model 10 1 Compilations s Sider Se ge UR nerf dee Sige A 10 2 1 D runs and input files 10 3 Output dat s suom g ERE MR Lens GCM Martian Calendar Utilities Beals concatbic oc 6 2 cA eis e ek i erae den unie dans uk B 2 IS cia eue IRURE ete Uere I IT Bede localtmet er mE eU ue d udin Bid Ziecast s 4 8 uoo ce tae e eee dore USERS B 15 eu ay BE ola he APR RUNS SERM an a B 6 recast Red ber Ode ee RE e e e RR RR DE So ny raa Bie expandstartfi s utor art oe ce e d IRURE Wu ae me se B8 extract END S eet
68. start makegcm d 64x48x25 t 2 p mars gcm Of course you will also need an appropriate traceur def file indicating you will use tracers h2o_vap and h2o ice if you only run with 2 tracers then the contents of the traceeur def file should be 51 2 h20_ice h20_vap Note that the order in which tracers are set in the tracer def file is not important e Run Same as usual Just make sure that your start files contains the initial states for water with an initial state for water vapor and water ice particles 52 Chapter 9 Photochemical Module The LMD GCM now includes a photochemical module which allows to compute the at mospheric composition e 14 chemical species are included CO background gas CO O OC D O2 O4 H Ho OH H209 No Ar inert and H30 e In callphys def set tracer to true tracer true Use the same op tions as shown below for the tracer part of callphys def You need to set photochem true and to include the water cycle water true sedimentation true see Chapter 8 because composition is extremely de pendent on the water vapor abundance Tracer dust water ice and or chemical species options used if tracer T PRE EEE EEE EEE DUST Transported dust if gt 0 use dustbin dust bins dustbin 0 DUST Radiatively active dust matters if dustbin gt 0 active false DUST use mass and number mixing ratios to predict dust size must also have dustbin 1
69. t also has a debug option which includes a collection of adequate debugging options To use it simply add the debug option makegcm d 64x48x25 p mars debug gcm 18 4 4 Input files initial states and def files In directory LMDZ MARS deftank you will find some examples of run parameter files def files which the model needs at runtime The four files the model requires they must be in the same directory as the executable e are run def described in section 6 2 callphys def see section 6 2 2 callphys def z2sig def and traceur def The example def files given in the deft ank directory are for various configurations e g model resolution copy and eventually rename these files to match the generic names to the directory where you will run the model Copy initial condition files start nc and startfi nc described in section 6 2 to the same directory You can extract such files from start archive banks of initial states ie files which contain collections of initial states from stndard scenarios and which can thus be used to check if the model is installed correctly stored on the LMD website at http www lmd jussieu fr forget datagcm Starts See section 4 9 for a description of how to proceed to extract start files from start archives 4 5 Running the model Once you have the program gcm e input files start nc startfi nc and parameter files run def callphys def traceur def z2sig def in the same di
70. t make sure that your start files contains the correct num ber of tracers If you need to initialize the composition you can run newstart and use the options ini_q the 15 tracers are initialized including water ice and vapor ini q h2o the 13 chemical species are initialized water ice is put to zero and water vapor is kept untouched ini q iceh2o the 13 chemical species are initialized water ice and vapor are kept untouched The initialization is done with the files atmosfera LMD may dat and atmosfera min dat which should also be found in the datafile directory Outputs The outputs can be done from the aeronomars calchim F routine for the 14 chemical species The variables put in the diagfi ncand stats nc files are labeled where name is the name of the chemical species e g co2 n_name local density in molecule cm 3 dimensional field c name integrated column density in molecule cm 2 dimensional field 54 Chapter 10 1D version of the Mars model The physical part of the model can be used to generate realistic 1 D simulations one at mosphere column In practice the simulation is controlled from a main program called testphysld F which after initialization then calls the master subroutine of the physics physiq F described in the preceeding chapters 10 1 Compilation For example to compile the Martian model in 1 D with 25 layers type in compliance with the makegcm function manual
71. the upper layer It is followed by a list of references for anyone requiring a detailed description of the physics and the numerical formulation of the parameterizations of the Martian physical part Chapter 3 For your first contact with the model chapter 4 guides the user through a practice simulation choosing the initial states and parameters and visualizing the output files The document then describes the programming code for the model including a user computer manual for compiling and running the model Chapter 5 Chapter 6 describes the input output data of the model The input files are the files needed to initialize the model state of the atmosphere at the initial time 0 as well as a dataset of boundary conditions and the output files are time series i e records of the atmospheric flow evolution as simulated by the model the diagfi files the stats files the daily averages etc Some means to edit or visualize these files editor ncdump and the graphics software grads are also described Chapter 8 explains how to run a simulation including the water cycle Chapter 9 illus trates how to run the model with the photochemical module Finally chapter 10 will help you to use a 1 dimensional version of the model which may be a simplier tool for some analysis work Chapter 2 Main features of the model 2 1 Basic principles The General Circulation Model GCM calculates the temporal evolution of the di
72. trol array Both physical and dynamical headers of the GCM NetCDF files start with a controle vari able This variable is an array of 100 reals the vector called tab cnt r1 in the program which contains the program control parameters Parameters differ between the physical and dynamical sections and examples of both are listed below The contents of table tab cntrl can also be checked with the command ncdump ff v controle The control array in the header of a dynamical NetCDF file start tab cntrl 1 FLOAT iim number of nodes along longitude tab 1 2 FLOAT jjm number of nodes along latitude tab cntrl 3 FLOAT llm number of atmospheric layers tab cntrl 4 FLOAT idayref initial day tab cntrl 5 rad radius of the planet tab cntrl 6 rotation of the planet rad s tab cntrl 7 g gravity m s2 3 72 for Mars tab 1 8 cpp tab cntrl 9 kappa r cp tab 1 10 daysec lenght of a sol s 788775 tab cntrl 11 dtvr dynamical time step s tab cntrl 12 etotO total energy tab 1 13 ptotO total pressure tab cntrl 14 ztotO0 total enstrophy tab cntrl 15 stotO0 total enthalpy tab cntrl 16 angO total angular momentum tab cntrl 17 pa tab cntrl1 18 preff reference pressure Pa tab cntrl 19 clon longitude of center of zoom tab cntrl 20 clat latitude of center of zoom tab cntrl 21 grossismx zoo
73. urf 610 Reference dust opacity at 700 Pa in the visible true tau tauref psurf 700 tauvis 0 2 latitude in degrees latitude 0 Albedo of bare ground albedo 0 2 Soil thermal inertia SI inertia 400 zonal eastward component of the geostrophic wind m s u 10 meridional northward component of the geostrophic wind m s v 0 Initial CO2 ice on the surface kg m 2 co2ice 0 hybrid vertical coordinate true for hybrid and false for sigma levels hybrid true Initial atmospheric temperature profile Type of initial temperature profile ichoice 1 Constant Temperature T tref ichoice 2 Savidjari profile as Seiff but with dT dz cte ichoice 3 Lindner polar profile ichoice 4 inversion ichoice 5 Seiff standard profile based on Viking entry ichoice 6 constant T gaussian perturbation levels ichoice 7 constant T gaussian perturbation km ichoice 8 Read in an ascii file profile ichoice 5 Reference temperature tref K tref 200 Add a perturbation to profile if isin 1 isin 0 peak of gaussian perturbation for ichoice 6 or 7 pic 26 522 width of the gaussian perturbation for ichoice 6 or 7 largeur 10 height of the gaussian perturbation for ichoice 6 or 7 hauteur 30 some definitions for the physics in file callphys def INCLUDEDEF callphys def Note that just as for the 3 D GCM run def file input parameters may be given in any orde
74. ved by using a hybrid sigma P sima pressure hybrid coordinate which is equivalent to using o coordinates near the surface and gradualy shifting to purely pressure p coordinates with increasing altitude Figure 2 3 illustrates the importance of using these hybrid coordinates compared to simple o coordinates The distribution of the vertical layers is irregular to enable greater precision at ground level In general we use 25 levels to describe the atmosphere to a height of 80 km 32 levels for simulations up to 120 km or 50 levels to rise up to thermosphere The first layer describes the first few meters above the ground whereas the upper layers span several kilometers Figure 2 4 describes the vertical grid representation and associated variables DYNAMICS coordinates ap bp ap 11 1 0 bp aps 11m bps 1 ap llm bp llm aps llm 1 bps 1 lilm 1 bp 11 aps 2 bps 2 ap 2 bp 2 aps 1 bps 1 ap 1 1 bp 1 0 m 1m 1 0 iuj lm 1 1 KKKKKKKKKKKKKKKKKKKKKKKKKKKK 1 KKKKKKKKKKKKKKKKKKKKKKKKKKKK lm 1 layer 1 CkCk ck kck ck k ck ck k ck ck ck k ck ck kk ck k kk kkkk 2 KKKKKKKKKKKKKKKKKKKKKKKKKKKK jn tut frs 1 KKK KKK e x x SUL EAC KK KK KKK KKK PHYSICS pressures 1 1 0 layer layer layer 1 layer 1 ONO gto tg lt D D 5 5 9
75. x 0 extension en latitude de la zone du zoom fraction de la zone totale dzoomy 0 raideur du zoom en X taux 2 raideur du zoom en Y tauy 2 Fonction f y avec y Sin latit si TRUE Sinon y latit ysinus false Avec sponge layer callsponge true Sponge mode0O u v 0 model u umoy v 0 mode2 u umoy v vmoy mode_sponge 2 Sponge hauteur de sponge km hsponge 90 Sponge tetasponge secondes tetasponge 50000 some definitions for the physics in file callphys def INCLUDEDEF callphys def 6 2 2 callphys def The callphys def file along the same format as the run def file contains parame ter value sets for the physics Example of callphys def file General options Run with or without tracer transport tracer false Diurnal cycle if diurnal False diurnal averaged solar heating diurnal true Seasonal cycle if season False Ls stays constant to value set in start season true write some more output on the screen lwrite false Save statistics in file stats nc stats true Save EOF profiles in file profiles for Climate Database calleofdump false 34 Dust scenario Used if the dust is prescribed i e if tracer F or active F 1 Dust opt deph read in startfi 2 Viking scenario 3 MGS scenario 4 Mars Year 24 from TES assimilation same as 24 for now 24 Mars Year 24 from TES assimilation ie MCD reference
76. xout grid set digsiz 0 set lon 180 180 d ps close 1 replace the path to surface nc in the following line sdfopen u forget WWW datagcm datafile surface nc set lon 180 180 set gxout contour set clab off set cint 3 d zMOL 7 3 Running a zoomed simulation and stability issue e dynamical timestep Because of their higher resolution zoomed simulation requires a higher timestep Therefore in run def the number of dynamical timestep per day day step must be increased by more than grossismx or grossismy twice that if necessary However you can keep the same physical timestep 48 sol and thus increase iphysiq accordingly iphysiq day step 48 e It has been found that when zooming in longitude on must set ngroup 1 in dyn3d groupeun F Otherwise the run is less stable e The very first initial state made with newstart e can be noisy and dynamically unstable It may be necessary to strongly increase the intensity of the dissipation and increase day step in run def for 1 to 3 sols and then use less strict values e If the run remains very unstable and requires too much dissipation or a too small timestep a good tip to help stabilize the model is to decrease the vertical extension of your run and the number of layer one generally zoom to study near surface process so 20 to 22 layers and a vertical extension up to 60 or 80 km is usually enough 50 Chapter 8 Water Cycle Simulation In order to simulate the water cy
77. zontal ex changes between the grid boxes whereas the physical part can be seen as a juxtaposition of atmosphere columns that do not interact with each other see diagram 2 1 The dynamical and physical parts deal with variables of different natures and operate on grids that are differently constructed The temporal integration of the variables is based on different numerical schemes simple such as the one above for the physical part and more complicated the Matsuno Leapfrog scheme for the dynamical part The timesteps are also different The physical timestep is iphysiq times longer than the dynamical Dynamics Physics Dynamical tendencies a 2 ql x y z T z T z 910 910 Tendencies due to radiative transfer condensation subgrid dynamics Physical fields Figure 2 1 Physical dynamical interface timestep as the solution of the dynamic equations requires a shorter timestep than the forced calculation for the physical part In practice the main program that handles the whole model gcm F is located in the dynamical part When the temporal evolution is being calculated at each timestep the program calls the following 1 Call to the subroutine that handles the total tendency calculation 925 arising from t the dynamical part caldyn F 2 Integration of these dynamical tendencies to calculate the evolution of the variab

User Manual for the LMD Martian Atmospheric General Circulation

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