CESM 1.0.5 near past initial conditions user guide
Contents
1. owa1vq uniAur xB sz 0 9 4 pec sz 60 dew pue O iva uniAw 9ALxB Figure 7 Various steps to compute the coupler mapping files described in section 3 2 Source Nan Rosembloom yep ns R EG ejepjunsyuu 100 ou uni ur uiuo Jou odoj 5 1001 1530 ou uiug unsure uuo y eyepoey p 0808 M oie ou 31vq uniAur ou31vqunaAur yd ou31vq uniAur yemuey uu yd ppe 10quBieu ym 0 0 0 JOS pue pg NS32 sjulod Mau 14 JO Se qeJ8A s9AJeu ppy jou uequn psy azea OJ8Z 0 Sjuiod ueqin jeS m 9u 31 vq unikur syu ou31vq uniAur yd ou 31vq unaAur 6 jisyuu o 626090 4 6 syw 9u 0 9060 098 01 esnpue ou gcyr0S0 ewue 00808 M oo ou umiAw eung CMCC Research Papers2. Figure 8 Various steps to compute the land surface dataset files described in section 4 Source Nan Rosembloom pyew ins oua CESM 1 0 5 near past initial conditions user guide prescribing ice sheets topo bnd topo ice myrun 10min nc Gridfile fv 0 9x1 25 nc Landmask landm coslat nc Make ross true definesurf mod landm coslat ncl topo myrun remap 09x25 mod DATE nc cam buildnml csh topo bnd Figure 9 Various steps to compute the atmospheric topography described in section 5 Source Nan Rosembloom O Centro Euro Mediterraneo sui Cambiamenti Climatici 2014 Visit www cmcc it for information on our activities and publications The Euro Mediteranean Centre on Climate Change is a Ltd Company with its registered office and administration in Lecce and local units in Bologna Venice Capua Sassari Viterbo Benevento and Milan Ccmcc The society doesn t pursue profitable ends and aims to realize and manage the Centre its promotion and Centro Euro Mediterraneo research coordination and different scientific and applied activities in the field of climate change study sul Cambiamenti Climatici Centro Euro Mediterraneo sui Cambiamenti Climatici CO
3. termines if the user will compute a surface dataset for dynamical vegetation use or for steady state conditions The corresponding file to compute dynamic vegetation is called pftdyn hist simyr1850 2005 txt and contains the name of the raw vegetation files for each year from 1850 to 2005 included In this guide we compute steady state vegetation conditions A crucial aspect of this file is its format since the mksurfdata Fortran code reads it with a specific format statement A125 1x 14 users home ans021 BC surface bc surf ncl mksrf pft mis6 harvest nn 111021 nc 1850 BE SURE when modifying the absolute path of this file that the format is respected After some modifications in the Makefile the user must compile the package following those options in the Makefile SMP TRUE then to compile gt gmake SMP TRUI j 64 It is critical to follow those recommendations to run the executable in a reasonable time Without those optimisations the run could last for hours and or days The executable is optimised and can be submitted to a queue On the CMCC supercomputing platform the batch script is mksurfdata run bin csh f SVN Id SVN SURLS BSUB n 64 BSUB R span ptile 64 BSUB q poe medium BSUB a poe BSUB o poe stdout J BSUB e poe stderr J BSUB J maprunoff BSUB W 2 00 setenv LID date y m d H M S setenv OMP NUM THREADS 64 cd fis01 cgd cseg csm mapping mak
4. Flow chart showing the various steps of the procedure described in the user guide Source Nan Rosembloom Various steps to compute the coupler mapping files described in section 3 2 Source Nan Rosembloom Various steps to compute the land surface dataset files described in section 4 Source Nan Rosembloom Various steps to compute the atmospheric topography described in section 5 Source Nan Rosembloom Centro Euro Mediterraneo sui Cambiamenti Climatici O1 CMCC Research Papers Legend USER INPUT Paleo tools land ocn mask 1deg nc CESM1 0 tools topo ice 10min nc Required if using CLM restart files with new landcover change kmt ncl Step1 gt or gt KMT myrun kmtEd mk remap csh Step2 gt mk runoff remap csh I coupler mapping E T 5 a genrunoff 7 2 gencdoman Ind domain myrun 2 fracdata myResolution Step 4 mkgriddata 1 fracdata 10min myrun BEDS convert mksrf F90 mksrf myrun files t paleo mkraw csh o Step 6 mksurfdata surface dataset myr
5. 0 0 0 0 9 GIN Sea 0 0 0 0 0 0 9 GIN Sea 0 0 0 0 0 0 10 Arctic Ocean 0 0 0 0 0 0 10 Arctic Ocean 0 0 0 0 0 0 11 Hudson Bay 61 0 2950 0 0 11 Black Sea 40 0 25 0 3 0e15 12 Baltic Sea 560 8 0 3 0e15 12 Caspian Sea 820 72 0 3 0e15 13 Black Sea 40 0 25 0 3 0e15 14 Caspian Sea 70 0 65 0 3 0e15 The second feature that may change due to the new land sea mask is the location of the overflows areas In POP the location of the overflows for present day bathymetry are prescribed in an initial input file that the user may find in CESM 1 0 5 models ocn pop2 input templates gx1 v6 overflow In this file there are several regions where overflows occur due to ocean bathymetry as for example the Denmark Strait the Faroe Bank Channel the Ross Sea and the Weddell Sea Typically for a glaciation case only the overflow located in the Denmark Strait is preserved 2 2 Coupler mapping files The mapping files contain informations weights etc used by the coupler to interpolate the fields from ocean grid onto the atmospheric grid and vice versa The runoff to ocean map is also part of this process since to be computed it uses one of the ocean mapping file generated The script that computes the four mapping files is the shell script mk remap gx1v6 csh This script needs the SCRIP software which handles the interpolation of the various grids See Software requirements To perform the interpolation between ocean and
6. Mediterraneo sui Cambiamenti Climatici NO CMCC Research Papers Line 951 se j jc min 1 tmp gt old version se j jc min 1 0d0 tmp new version fixed bug Finally to correct the gradual land fraction the user has to edit the script fix landm coslat ncl to correct the areas where some new land have been added or removed in the new topography for example the Bering Strait To execute gt fix landm coslat ncl The final output is the new topography file that will be directly red by the CESM 1 0 5 during the initialisation of the run The initialisation is performed from whatever cami file the default CAM initial condition file The atmosphere will quickly adjust to the new topography CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Setting the namelists B case In this final section are indicated the namelists fields where the user has to prescribed the new initial conditions files computed along the entire procedure First of all the user has to indicate to the CESM 1 0 5 where are located the new files Since all the default input files for the CESM 1 0 5 runs are located in csm inputdata used to put them there as well because it limits the changes introduced into the namelists Once the B case directory is created the first script to be modified is env conf xml Then the case is configured and the user may edit the namelists located in USER_case Buildco
7. atmosphere mk remap gx1v6 csh needs the original ocean and atmosphere grid files and the new ocean KMT file generated at the previous step All the input and output files are reported in Table 4 BE AWARE mk remap gx1v6 csh has to be executed two times This is because two of the mapping files are computed using a conservative interpolation method while the two others are generated using a bilinear interpolation method In the script one of the two methods is commented and the user has to comment them successively to get the four mapping files CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Table 4 New coupler mapping runoff and domain files Numerical tool Scripts Inputs Outputs shell SCRIP mk remap gx1v6 csh Input kmt gx1v6 user ieeei4 fv0 9x1 25 070727 nc CAM grid at 0 9x1 25 res horiz grid 20010402 ieeer8 POP present day horizontal grid Output _ atm user aave nc map atm to ocn user aave nc map ocn to atm user bilin nc map atm to ocn user bilin nc 9x1v6 user nc new ocean grid only used for runoff map Fortran 90 gen runoff build calypso csh runoff calypso run Input gx1v6 user nc rdirc 05 061026 Output map r05_to_gx1v6_user nc Fortran 90 gen_domain one time for conservative interpolation scrip_ina scrip_in I scripdir scrip one time for bilinear interpolation scrip inb scrip in I scripdir scrip Inp
8. landice_MIS6_10min tinfile1 140 5 srcCode author _ In this example NCL was used to generate this new topographic file but any kind of tool can be used to do it Centro Euro Mediterraneo sui Cambiamenti Climatici GO N Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers 2 Ocean and coupler initial conditions files This part is dedicated to the computation of the initial conditions for POP ocean and CPL coupler The whole procedure is described bellow and illustrated by the flow chart in Figure 4 In this section seven files are generated a new land sea mask a region mask distribution of the various oceanic basins and marginal seas Figure 3 the coupler mapping files x4 handle the interpolation from to the oceanic grid to from the atmospheric grid a new runoff to ocean map to handle the interpolation from land to ocean the land and oceanic domains land sea masks used to create surface conditions The execution time of the all the scripts used in this section is detailed in Table 9 2 1 Ocean topography and region mask First of all the initial pre processed topography at 10 min resolution has to be interpolated at 1 x1 Similarly to the previous section the script must be created by the user The new topography interpolated at 1 should contain the same variables than in the original
9. most recent version of this runoff tool The namelist runoff map gx1 nml has to be set up properly as following amp input nml gridtype rtm file roff rdirc 05 061026 file ocn gxiv6 user nc file gx1v6 nc file smooth smoother gx1v6 nc file new map_r05_to_gx1v6_user nc title runoffmap r05 gt gx v6 full ice coverage in NH eFold 1000000 0 rMax 300000 0 The runoff is then computed executing the batch script runoff calypso run The computation time is larger than 5 min that is why it is recommended to avoid running interactively gt bsub runoff run 2 3 Domain and fraction files The penultimate step of this section is the computation of the land and oceanic domain files using the gen domain package provided with the Paleo Toolkit and located in atmindfrac First edit the namelist gen domain nm with the new mapping files The user may also edit the Makefile to specify the NetCDF library and the Fortran compiler To compile and execute the package do gt make AIX csh gt gen_domain aix lt gen domain nml gt gen domain out Finally the land fraction file both at the run resolution here fv 0 9x1 25 and at 10 min resolution can be created Those files are generated through the mkgriddata package CESM 1 0 5 mod els Ind clm tools The package produces three files containing land fraction topography and a new grid file The two l
10. the B case for 5 days only The default configuration of env run xml is already set up for a 5 day run At the end of this run the user gets a CLM restart file clm r new paleo which is used to interpolate the original CLM initial conditions file b40 1850 track1 1deg 006 clm2 r 0863 01 01 00000 nc The interpolation is performed using the interpinic package located in the CESM 1 0 5 repository CESM 1 0 5 models Ind clm tools interpinic The user will have to edit the Makefile to change the path of the NetCDF libraries and will have to compile the routines To execute interpinic gt interpinic i b40 1850 trackl 1deg 006 c1m2 r 0863 01 01 00000 nc 0 clm r new paleo The file clm r new paleo will be then overwritten with the variables contained b40 1850 track1 1deg 006 clm2 r 0863 01 01 00000 nc that is why we recommend to re name it for example b40 1850 track1 1deg 006 clm2 r 0863 01 01 00000 interp paleo nc Production run Finally the user can run the final paleo experiment by CESM 1 0 5 near past initial conditions user guide prescribing ice sheets 1 recreate or reuse the B case directory 2 set the namelists and scripts XML as in Section 3 point at the new interpolated CLM file in the finidat field of the CLM namelist 4 compile and run the case Useful links related to CESM 1 0 5 paleoclimate modelling During the entire procedure and for the first paleo runs found the following Wiki pages very useful for
11. 0000000000 000000000000000000 seq frac check atm init ofrac min max 0 00000000000000000 0 00000000000000000 seq_frac_check atm init ifrac min max 0 00000000000000000 0 00000000000000000 seq_frac_check atm init lfrin min max 1 000000000000000000 000000000000000000 seq frac check atm init sum min max 1 000000000000000000 000000000000000000 atm init sum ncnt maxerr 0 0 00000000000000000 seq mct drv Model initialization complete NOTA BENE when everything get successful the user is in total state of happiness and can eventually enjoy and party most of the problems are solved Florence Colleoni CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Before Starting First of all to change the initial conditions it is important to understand what are the steps of the procedure and why the user must strictly follows the order of the various steps It is important to understand that the procedure starts with the computation of ocean and coupler initials conditions on which most of the surface datasets are based The user can have an overview of the whole procedure in Figure 4 The entire procedure begins with the computation of ocean new bathymetry and basins distribution In POP the World Ocean is divided in 10 basins and 4 marginal seas Figure 3 Southern Ocean Pacific Ocean Indian Ocean Atlantic Ocean Arctic Ocean Persian Gulf Mediterranean La
12. CCSM4 version For CESM 1 0 5 the user has to consider the CCSMA tar file which corresponds to the fully coupled configuration B1850 using 5 presents large improvements about the chemistry of atmosphere which are not of direct interest in our case Therefore simulations performed using the early versions of CESM with CAM4 are similar to simulations performed with the last release of CCSM4 However some of the packages from CCSM3 may also be useful In the directory ccsm4 extra pub 2012mar16 nr the scripts are ordered such as atmindfrac scripts for steps and steps 4 cam 0015 for deep past CAM stand alone run docn mk docn domain ncl cn nitdep for cases using Carbon Nitrogene pools convert mksrf scripts for step 5 mapping scripts for step 2 nd for deep past mksurfdata empty package located under CESM1 0 5 models Ind clm tools modify kmt scripts for step 1 Centro Euro Mediterraneo sui Cambiamenti Climatici CO Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers paleo ccsm4 aerosol to prescribe a different aerosol distribution for paleo time period not used in this procedure but could be included if the user needs to prescribe a new aerosol distribution paleo mkraw for deep past for near past use convert mksrf scripts rtm for deep past only For near past use the tool gen runoff located in the Paleo
13. Ccmocc Centro Euro Mediterraneo sui Cambiamenti Climatici Research Papers Issue RP0221 May 2014 Application and Numerical Scenarios By Florence Colleoni Centro Euro Mediterraneo sui i Cambiamenti Climatici Bologna Italy flocolleoni gmail com Nan Rosenbloom National Center for Atmospheric Research USA nanr ucar edu We acknowledge Bette Otto Bliesner for its scientific support on CESM We gratefully acknowledge the support of Italian Ministry of Education University and Research and Ministry for Environment Land and Sea through the project GEMINA CESM 1 0 5 near past initial conditions user guide prescribing ice sheets SUMMARY The Community Earth System Model developed and maintained by NCAR is the first completely open source Earth System Model In this document will refer to CESM 1 0 5 which corresponds to the last official release of CESM 1 0 the more recent version is now CESM 1 2 CESM 1 0 5 includes atmosphere land ocean sea ice and a partially coupled ice sheet model Several grid resolutions have been developed for each component of CEMS and for present day Earth s topography bathymetry One of the major advantage of this model is that the procedure to run it is straightforward in its present day configuration However the CESM is not flexible when changes in the topography and bathymetry have to be introduced in order to simulate near and deep past climates To implement a different land se
14. Toolkit for CCSWM3 This tool aims at providing a new file of river flow directions used by the RTM model coupled to CLM However for near past simulations using almost present day topography the user may use the default CESM rdir05 nc already prescribed in the namelist But the user will have to produce the runoff mapping file using the gen runoff tool to account for the new land sea mask if needed In alternative a more recent version of this tool runoff to ocn is available CESM 1 1 and more recent versions under CESM 1 1 mapping gen mapping files The user may also find it in this CESM forum post In the directory ccsm3 setup tools 110319 NR 120316 the user can find atm scripts for step 7 The only tool that will be used form this directory is the definesurf tool There are two versions present in the directory definesurf svn100709 is the most recent version of this tool accounting for the changes between CCSM3 and CESM1 0 The other version definsurf paleo quaternary contains a directory landmcoslat in which the user can find the script fix landm coslat ncl used at step 7 cpl the user can find the gen runoff package which is used to compute the runoff mapping files needed by the coupler For each step of this guide the scripts the input and output files are listed in the different Tables and the settings and execution are extensively detailed All the scripts ported on CMCC supercomputing platforms were initia
15. a mask as well as different surface conditions such as vegetation cover ice sheets etc each component of CESM requires substantial changes in its initial conditions files which require an advanced knowledge of the model structure In order to make those kind of changes accessible to new users the following document aims at detailing a relatively simple procedure to modify the initial conditions files for the coupled atmosphere land ocean sea ice configuration of the CESM 1 0 5 B compset This procedure was developed at NCAR and is based on the script released by the Paleo working Group This procedure has been successfully tested on CMCC IBM supercomputing facilities In this user guide the procedure is applied to a glaciation case i e when large ice sheets covered the Northern Hemisphere repeatedly in the past and when sea level drop of about 120 meters This procedure is by far non automatic and requires substantial manual work at each stage described in the document Finally following this procedure does not provide any guarantees that the simulations will be successful Table of Contents liu RT E C ___ 1 The Community Earth System 2 Modelling near past climates Balbie eser n nex PERE RECS de eee eae UE ons 1 Software requirements 2NCAR sPaleo Toolkit 3 Building a
16. allowable difference for lat 0 100000000000000 11 domain check grid mct the domain size is 48 domain check grid mct maximum difference for lon 0 568434188608080E 13 domain check grid mct maximum allowable difference for lon 0 100000000000000 11 domain check grid mct the domain size is 48 domain check grid mct maximum difference for area 0 476528601300874E 09 domain check grid mct maximum allowable difference for area 0 900000000000000E 06 domain check mct checking fractions in domains domain check mct maximum difference for ofrac sum 0 00000000000000 domain check mct maximum difference for ifrac sum 0 00000000000000 domain check mct maximum allowable difference for frac sum 0 100000000000000E 01 domain check mct maximum allowable tolerance for valid frac 0 100000000000000E 01 domain check mct domain check mct min max ascale 0 00000000000000 1 00000000000004 atmdom a domain check mct domain check mct min max ascale 0 999999999999841 1 00000000000004 lnddom 1 domain areafactinit mct min max mdl2drv 0 999718744540964 1 00061729371141 areafact a domain areafactinit mct min max drv2mdl 0 999383087105043 1 00028133458592 areafact a domain areafactinit mct min max mdl2drv 0 979340530542676 1 01536195556158 areafact i domain areafactinit mct min max drv2mdl 0 984870463702687 1 02109528689257 areafact i seq mct drv Initializing fractions map atm2ocn mct callingl npfix C
17. and initial conditions In this section the final CLM initial surface data file will be computed at 0 5 resolution For that reason the initial 10 min topography will be interpolated at 0 5 resolution However to create the final CLM initial surface data file an additional topographic file at 10 min resolution including some bedrock informations has to be created The flow chart in Appendix I Figure 8 illustrates the various steps of this section 3 1 Pre processing topography For steps 4 2 to 4 3 the initial pre processed topography at 10 min resolution used in step 2 has to be interpolated at 0 5 x0 5 As for the interpolation at 1 the user has to create its own script to interpolate the 10 min topography The coordinates have to match those of the default mkglacier nc file for example Be sure that the following variables are computed in the indicated ranges ICE 0 100 LANDFRACT 0 1 LANDMASK 0 1 For step 3 4 the user also needs an additional topographic file at 10 min resolution which contains a variable named TOPO_BEDROCK This is done using the script create mksrf topo ncl provided in the Paleo Toolkit in convert mksr This script also needs the original present day CESM mk srf topo 10min nc file downloaded from the NCAR repositories Table 5 To execute the script the user has to point to the topo files and gt ncl create mksrf topo ncl NOTE the bedrock topography corresponds to an ice free topogr
18. aphy Those informations are available for present day e g ETOPO2 and ETOPO1 but for example in the compset of glaciations if the user only knows about the surface elevation and the landice distribution but does not have any information about the ice thickness the bedrock topography cannot be retrieved However this information is only necessary in the compset of running a dynamical ice sheets model which requires both ice thickness and bedrock topography as input fields Since no ice sheet model has been implemented yet in CESM 1 0 5 at the time of this user guide the bedrock topography is not necessary to run the simulations Consequently TOPO_BEDROCK is set equal to TOPO_ICE in create mksrf topo ncl 3 2 Adding glaciers to the list of PFTs The ice sheets distribution is extracted from the 0 5 resolution topography interpolated at the previous step and transformed into a PFT type and landunit file CLM initial conditions file considers 15 PFTs by default Figure 5 As the user can note the type glaciers is not included into this CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Table 5 Pre processing topography for surface dataset Numerical tool Scripts Inputs Outputs User based User based Input topo_user_10min nc Output topo user 05deg nc NCL create mksrf topo ncl Input topo user 10min nc mksrf topo 10min c080912 nc Output mksrf topo 10min user nc Fortran mkgriddata packa
19. atter are not further used by the procedure neither during the run time To use CESM 1 0 5 near past initial conditions user guide prescribing ice sheets the package the user has to set up the namelist and compile the package Some modifications of the NetCDF library path and compiler name in the Makefile are necessary The mkgriddata has to be run two times 10 min resolution uses the topographic file at 10 min resolution The fraction file produced at 10 min will be used in the next section to compute the land surface conditions fv 0 9x1 25 or other resolution uses the land domain file domain Ind fv09 1 25 gx1v6 nc from previous step The fraction file produced at run resolution will be prescribed in the CLM namelist Compile the package and then execute it gt mkgriddata lt mkgriddata namelist gt mkgriddata out BE AWARE that the mkgriddata package produces coordinates that sometimes do not completely match with the coordinates of the surfdata nc file To avoid this problem the user has to insert the default CLM grid file in the namelist The routines will force the land fraction to be calculated on the CLM grid Some instructions are detailed in the README file included into the mkgridata package This is not necessary when generating the land fraction at 10 min resolution Centro Euro Mediterraneo sui Cambiamenti Climatici CO Centro Euro Mediterraneo sui Cambiamenti Climatici NO CMCC Research Papers 3 L
20. brador Sea Hudson Bay GIN Sea Red Sea Baltic Sea Black Sea Caspian Sea Changes in sea level sometimes imply a reorganization of the World Ocean basins and occasionally some marginal Seas or small peripheral basins may be removed by the procedure Figure 3 Distribution of ocean basins and marginal seas within POP for present day topography Once the ocean land sea mask and basins have been created it is then possible to compute the coupler mapping files The mapping files contain the interpolation weights needed to interpolate from POP to CAM and vice versa In this step a mapping file to interpolate the runoff from land to ocean is also computed The next step is to compute the CLM surface conditions which account for the newly created land sea mask and the new ice sheets and vegetation distribution The final step is to compute the initial conditions for CAM which accounts for changes in surface topography and land sea mask Centro Euro Mediterraneo sui Cambiamenti Climatici e Centro Euro Mediterraneo sui Cambiamenti Climatici E CMCC Research Papers USER INPUT Legend land ocn mask Ideg nc topo ice Omin nc Scripts or packages Outputs KMT_new region_basins Ocean to atmosphere mapping files Runoff to ocean mapping files ocn domain amp Ind domain mksrf files surface_dataset n topography P Y step clm r new pale
21. ce it will be used to create the 5 days CLM restart file accouting for the new land sea mask and needed to run a proper case using the new initial conditions see section 7 and Figure 4 step 7 Centro Euro Mediterraneo sui Cambiamenti Climatici NO Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers Creating initial conditions files 1 Pre processing the topography Using a very clean topography from the beginning is particularly important for the rest of the procedure especially for the ocean and for the coupler For that reason the user should spend as much time as necessary to obtain a satisfying initial topography What does it mean It means removing all the small islands that might create problems during the various interpolation steps required during the entire procedure described in this guide Indeed the initial topography file should be at 10 min horizontal resolution During the various steps this file will be interpolated at 0 5 at 1 and finally at the CESM 1 0 5 case resolution e g f09 g16 T31_gx3v7 see the CESM 1 0 user guide for more details on the supported resolutions Table 1 Pre processing initial topography script and associated files Numerical tool Scripts Inputs Outputs User based User based Input USGS gtopo30 10min nc Relief user 10min nc topography at 10min res landice user nc ice mask Output topo user 10min nc htopo ice landfract lan
22. ciation case The Baltic Sea as well as the Hudson Bay have been removed and filled with land The basins no longer exist in the new ocean bathymetry file and as a consequence the user has to modify the list and re assign values to the Black Sea and the Caspian Sea Note that a negative value is indicative of a marginal sea Those modifications are necessary because the POP ocean model checks for the total number of ocean basins prescribed the gx1v6 region ids and takes the absolute value of the maximum number written in this file In our case this number is abs 12 12 for Centro Euro Mediterraneo sui Cambiamenti Climatici O1 Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers present day it would be abs 14 14 Those changes have to be done before building the compset Present day gx1v6 region ids file provided in CESM 1 0 5 left Erw dm of gx1v6 region ids file provided by users right 1 Southern Ocean 0 0 0 0 0 0 1 Southern Ocean 0 0 0 0 0 0 2 Pacific Ocean 0 0 0 0 0 0 2 Pacific Ocean 0 0 0 0 0 0 3 Indian Ocean 0 0 0 0 0 0 3 Indian Ocean 0 0 0 0 0 0 4 Persian Gulf 22 0 60 0 0 0 4 Persian Gulf 220 60 0 0 0 5 Red Sea 14 0 47 0 3 0e15 5 Sea 14 0 47 0 3 0e15 6 Atlantic Ocean 0 0 0 0 0 0 6 Atlantic Ocean 0 0 0 0 0 0 7 Mediterranean Sea 36 0 3540 0 0 7 Mediterranean Sea 36 0 3540 0 0 8 Labrador Sea 0 0 0 0 0 0 8 Labrador Sea 0 0
23. d ocean basins decomposition require a large amount of work both to create the initial files and to modify some specific default files into the model itself which are set up with present day characteristics Near past the ocean bathymetry is kept at its modern state only some of the oceanic basins CESM 1 0 5 near past initial conditions user guide prescribing ice sheets are removed from the default modern decomposition due to sea level drops The land sea mask and surface topography are modified depending on whether or not the user introduces some ice sheets or topographic features The concept is to add some slight differences relative to present day global topography in order to reduce the number of changes introduced in the model This also limits the inconsistencies between the various components of the CESM In this user guide we focus on how to generate the initial conditions for near past climates and in particular how to change sea level and prescribe ice sheets over North America and Eurasia in the CESM 1 0 5 fully coupled configuration B case Those changes implicate substantial modifications at all levels for all components Beside the model itself is particularly sensitive to inconsistencies between the land sea mask of the various component In CESM some of the components are decomposed on the same grid atmosphere CAM and land CLM share the same grid ocean POP and sea ice CICE share the same grid Once the
24. diterraneo sui Cambiamenti Climatici CMCC Research Papers Table 6 New PFTs distribution adding glaciers to the landcover Numerical tool Scripts Inputs Outputs NCL convert mksrf F90 Input topo_user_05deg nc mksrf topo 10min c080912 nc Output mksrf_glacier_user nc mksrf_pft_user nc mksrf_landwat_user nc NCL add_harvest ncl Input mksrf_pft_user nc mksrf_landuse_rc1850_c090630 nc Output mksrf_pft_user_harvest nc NCL nn_fill ncl Input mksrf_glacier_user 111021 nc mksrf_lanwat_user 111021 nc mksrf_pft_user harvest 111021 nc mksrf soitex 10level c010119 nc mksrf organic 10level 0 5deg 081112 nc mksrf_fmax 070406 nc mksrf soilcol_global_c090324 nc mksrf_lai_global_c090506 nc Output mksrf_glacier_user nn nc mksrf_lanwat_user nn nc mksrf_pft_user harvest nn nc mksrf_soitex 1 Olevel_user nn nc mksrf_organic 10level 0 5deg_user nn nc mksrf_fmax_user nn nc mksrf_soilcol_user nn nc mksrf_lai_global_user nn nc NCL create_urban ncl Input mksrf urban 3den 0 5x0 5 simyr2000 c090223 v1 nc mksrf pft mis6 harvest nn 111021 nc Output mksrf urban user nc CESM 1 0 5 near past initial conditions user guide prescribing ice sheets 0 cp convert_mksrf template convert mksrf template myrun 1 edit convert mksrf template myrun and then to compile and execute gt convert_mksrf template myrun convert mksrf F90 gt gmake gt convert mksrf 3 3 Finalising the new PFTs distributio
25. dsmask variance Most of the scripts that will be used in the following steps are based on default present day CESM 1 0 5 initial conditions files to which the differences provided by the user new input conditions are added To create the initial topography file the user must create his own script The purpose of this step is to add the topographic difference between the topography provided by the user and present day topography on top of the CESM USGS present day 10 min topography file The input and output files are reported in Table 1 The new topographic file should contain the following variables htopo already in USGS topo file Changes in topography have to be added on this variable Jandfract already in USGS topo file Changes in land sea mask have to be added on this variable Make sure that the values range between 0 1 variance already in USGS topo file This variable does not have to be modified The user may copy and paste the USGS variance variable in his own topographic file ice ice sheets and glaciers mask provided by the user This variable may equals 100 where ice sheets are present and 0 elsewhere This also includes Greenland and Antarctica CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Jandmask this variable is a simple land sea mask with 1 for land and 0 for ocean WARNING the longitudes and latitudes have to be equals to USGS topo file The user must therefore interpola
26. e SDIN LOC ROOT ocn pop gx3v7 grid region mask user ieeei4 set topography filename DIN LOC ROOT ocn pop gx3v7 grid kmt gxi1v6 user ieeei4 5 6 CICE namelist cice buildnml csh Since CICE shares the same grid with POP the bathymetry has to be consistent amp grid nml kmt file LOC ROOT ocn pop gx3v7 grid kmt gx1v6 user ieeei4 Centro Euro Mediterraneo sui Cambiamenti Climatici Centro Euro Mediterraneo sui Cambiamenti Climatici OO NO CMCC Research Papers GENERATING THE NEW INITIAL CLM INITIAL CONDITIONS RESTART FILE THE 5 DAYS CESM 1 0 5 RUN When running on a new platform outside of NCAR it might be necessary to regenerate the initial boundary conditions file for CLM This is due to some differences in the allocation of the processors and memory during the compilation of the model This part corresponds step 8 and step 9 on Figure 4 showing the whole procedure in Appendix I To do so the user has to configure all the namelists as shown in section 6 except for the CLM namelist in which the original option pointing at the initial boundary conditions file is modified amp clm_inparm finidat SUSER_REPOSITORY b40 1850 track1 1ldeg 006 clm2 r 0863 01 01 00000 nc into amp clm_inparm finidat This will allow the model make a cold restart i e create a new restart file containing the CLM initial conditions adapted to the platform After this modification the user can run
27. ectral and finite volume grids resolutions have been developed for each component The model has been calibrated for present day Earth s topography bathymetry and extensively validated against present day climate observations One of the major advantage of this model is that it is straightforward to run in its present day configuration Community Earth System Model 0 KH T Me IS Parallel Ocean Program Climatological Slab Ocean Data Model DOCN Figure 1 CESM 1 0 5 architecture See CESM 1 0 5 webpage for more details The CESM 1 0 5 has been successfully tested for paleoclimate simulations however its climate components are not flexible to simulate near or deep past climates requiring different topographies and or batymetries relative to present day To use a continental distribution or a sea level departing from present day ones each component of CESM needs substantial changes in its initial conditions which requires an advanced knowledge of the model The procedure is not simple but has been however tested successfully by NCAR Paleo Working Group for various time periods Last Glaciation Centro Euro Mediterraneo sui Cambiamenti Climatici CO e Centro Euro Mediterraneo sui Cambiamenti Climatici E CMCC Research Papers and deglaciation Pliocene Miocene Permian Cretaceous etc In order to make those kind of changes more accessible to new users the following document aims at describing this procedure t
28. emaps r05 your working dir Centro Euro Mediterraneo sui Cambiamenti Climatici O1 Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers Computing CLM initial conditions file Numerical tool Scripts Inputs Outputs Fortran NetCDF mksurfdata package Input griddata 0 9x1 25 070212 nc mksrf soitex 10level c010119 nc mksrf_vocef c060502 nc fracdata_1080x2160 nc mksrf_glacier_user nn 111021 nc mksrf_lanwat_user nn 111021 nc mksrf_urban_mis6 111021 nc mksrf_organic 10level 0 5deg_user nn 111021 nc mksrf_fmax_user nn 111021 nc mksrf_pft_user harvest nn 111021 nc mksrf_soilcol_user nn 111021 nc mksrf_lai_global_user nn 111021 nc mksrf topo 10min use 111021 nc pftdyn hist simyr1850 txt Output surfdata pftdyn 0192x0288 user nc surfdata_0192x0288_user nc CLM namelist set SRCDIR users home ans021 BC surface_bc mksurfdata echo time echo tail start computing surface dataset date SSRCDIR mksurfdata lt mksurfdata namelist amp mksurfdat out finished computing surface dataset 200 out LID date CESM 1 0 5 near past initial conditions user guide prescribing ice sheets 4 Atmosphere initial conditions The last CESM 1 0 5 component for which the user has to create new initial conditions is CAM The procedure uses the definesurf package Paleo Toolkit for CCSMS definesurf svn100709 This package is based on a pre existing master T42 file landm c
29. entro Euro Mediterraneo sui Cambiamenti Climatici O1 CMCC Research Papers Centro Euro Mediterraneo sui Cambiamenti Climatic Seq frac check seq mct drv seq mct drv Setting fractions Initializing atm ocn flux component Calling map lnd2atm mct Calling map ocn2atm mct for mapping o2x ox to o2x ax Calling map ocn2atm mct for mapping xao ox to xao ax Calling map ice2atm mct for mapping i2x ix to i2x ax Calling mrg x2a run mct Calling atm init mct seq mct drv seq mct drv seq mct drv seq mct drv seq mct drv seq mct drv seq frac check lnd init afrac min max 1 000000000000000000 000000000000000000 seq frac check lnd init lfrac min max 1 000000000000000000 000000000000000000 seq frac check lnd init lfrin min max 1 000000000000000000 000000000000000000 seq frac check ice init afrac min max 0 00000000000000000 1 00000000000000622 seq frac check ice init ofrac min max 0 00000000000000000 000000000000000000 seq frac check ice init ifrac min max 0 00000000000000000 0 00000000000000000 seq frac check ocn init afrac min max 0 00000000000000000 1 00000000000000622 seq frac check ocn init ofrac min max 0 00000000000000000 000000000000000000 seq frac check ocn init ifrac min max 0 00000000000000000 0 00000000000000000 seq frac check atm init afrac min max 1 000000000000000000 000000000000000000 seq frac check atm init lfrac min max 1 00000000
30. ge Input NetCDF topo user 10min nc domain Ind fv09 1 25 gx1v6 user nc Output fracdata 10min nc griddata 10min nc not used topodata 10min nc not used fracdata fv09 1 25 nc CLM namelist griddata_fv09_1 25 nc not used topodata_fv09_1 25 nc not used default distribution Consequently this step aims at introducing the 16th PFT in the new initial boundary conditions file All the scripts and input output files are reported in Table 6 Three files are created the land ice distribution the glaciers PFT type and the new landuse distribution The Fortran 90 routine is called convert mksrf F90 and uses three default present day files from CESM 1 0 5 containing the present day glaciers mask the present day landunit distribution and present day landuse map in our case the default distribution corresponds to that of pre industrial Indeed in CLM a type of landunit is attributed to each pixel Figure 5 In total there are five declared landunits Urban Lake Wetland Glacier and Vegetated The Vegetated type is further divided into PFTs To add some ice sheets over the ground the user has to declare how much of each pixel will be Glacier and or vegetated This is exactly what convert mksrf F90 does The routine is based on a template routine in which the user has to point to the default CESM 1 0 5 files listed in Table 6 To edit the script Centro Euro Mediterraneo sui Cambiamenti Climatici Centro Euro Me
31. ion Source from http www CESM 1 0 2 ucar edu models clm surface heterogeneity html To create new surface initial conditions a special package mksurfdata has been released and is located in the CESM 1 0 5 directory CESM 1 0 5 models land clm tools This package combines all the files created in the previous steps into a unique file that will be given as input to CLM First of all the user has to set up the namelist mksurfdata namelist according to the input files listed in Table 7 amp clmexp mksrf fgrid csm inputdata lnd clm2 griddata griddata 0 9x1 25 070212 nc mksrf fsoitex mksrf soitex 101evel c010119 nc mksrf forganic mksrf organic 10level 0 5deg mksrf flanwat mksrf lanwat mis6 nn 111021 nc mksrf fmax mksrf fmax mis6 nn 111021 nc mksrf fglacier mksrf glacier mis6 nn 111021 nc mksrf furban mksrf urban mis6 111021 nc mksrf fvegtyp kerf pft mis6 harvest nn 111021 nc mksrf fsoicol mestt soilsol mise nn lil021 nc mksrf flai mksrf lai global mis6 nn 111021 nc mksrf ftopo mksrf topo 10min mis6 111021 nc mksrf ffrac fracdata 1080x2160 nc mksrf fvocef mksrf vocef c060502 nc mksrf firrig pa mksrf fdynuse pftdyn hist simyr1850 txt CESM 1 0 5 near past initial conditions user guide prescribing ice sheets outnc double true In this package one of the input files pftdyn hist simyr1850 txt is particularly important and de
32. lly developed by Nan Rosembloom and Christina Shield NCAR In all the tables of this document the files generated from the scripts or provided by the user are distinguished from the original raw grid files or others directly coming from CESM 1 0 5 by using the following color code blue default CESM 1 0 5 present day raw data files red user provided files orange files computed during the procedure 3 Building a new CESM 1 0 5 B ca Most of the scripts that will be used in this procedure introduce changes based on default present day CESM 1 0 initial conditions files that the user can get building the CESM default case and for which new boundary conditions will be created In this manual the procedure is described for case atm Ind ocn sic CESM 1 0 5 near past initial conditions user guide prescribing ice sheets using pre industrial period files 81850 compset finite volume 0 9x1 25 atmospheric resolution and displaced pole 1 ocean resolution 09 g16 see the CESM 1 0 user guide for more details on the supported resolutions The instructions to build the case are provided in the CESM 1 0 User Guide This process will automatically download all the files required by all the components of the B1850 compset to run with the default configurations already implemented in CESM 1 0 Once the user has built the case he can proceed with the steps described in the forthcoming sections Do not clean up the case directory sin
33. n After creating the new glaciers PFT type the user has to add those modifications to the landunits and the PFTs of pre industrial or present day pre existing default distribution First the crop areas are modified and substituted by the new PFT Glacier computed at the previous step This step is done using the script add harvest ncl provided in the Paleo Toolkit and located in convert mksrf This script that uses the new distribution mksrf pft user nc created at the previous step Due to the new distribution of the glaciers and harvest PFTs some of the pixels could have remained empty To fill them the user has to execute the script nn fill nc which corresponds to a near neighbor algorithm filling the empty pixels by using their nearest PFTs and soil properties and computes all the soil properties This step uses all the default CESM 1 0 5 soil properties files as for example the vertical distribution of organic matter the soil texture the LAI etc Those files are listed in Table 6 This script is not provided in the Paleo Toolkit and has to be required to Nan Rosembloom In alternative the user may use any kind of tool to do this step Finally since for the near past and deep past simulations there are no urban areas the user has to remove the urban landunit see Figure 5 and substitute it by vegetated areas to allow CLM to recreate some consistent hydrological conditions during the run This final step is performed by
34. new CESM 1 05 Creating initial conditions filles lt a sassa llle 1 Pre processing the topography 2 Ocean and coupler initial conditions files 3 Land initial conditions ee R x eese 4 Atmosphere initial conditions Setting the namelists B case Generating the new initial CLM initial conditions restart file the 5 days CESM 1 0 5 run aine Useful links related to CESM 1 0 5 paleoclimate modelling Appendix 0 Execution time of the scripts used in this user guide Appendix Flow charts summarizing the procedure described in this user guide 32 CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Introduction 1 The Community Earth System Model The Community Earth System Model CESM is an Earth System Model composed of an AGCM an OGCM POP a land model CLM a sea ice model CICE and a dynamical ice sheets model CISM The CESM 1 0 5 is developed jointly by NCAR and LANL POP CICE CISM and is maintained by NCAR The code and its documentation are available on the CESM 1 0 5 website http www cesm ucar edu models cesm1 0 The CESM 1 0 5 fully coupled compset B compset includes atmosphere CAM land CLM ocean POP sea ice CICE which are managed by the coupler Figure 1 Several sp
35. nf see CESM 1 0 user guide 5 1 Coupler mapping files env conf xml The user has to substitute the default mapping files by the ones computed in section 3 2 lt atm to ocn flux mapping file for fluxes char gt entry id MAP A2OF FILE value map fv09 1 25 to gxlv6 user aave da nc gt atm to ocn state mapping file for states char gt entry id MAP 205 FILE value map fv09 1 25 to gxlv6 user bilin da nc gt lt to atm mapping file for fluxes char gt entry id MAP O2AF FILE value map gxl1v6 to fv09 1 25 user aave da nc gt lt 1 to atm mapping file for states char gt entry id MAP O2AS FILE value map gxl1v6 to fv09 1 25 user aave da nc gt runoff 5 degree to ocn mapping file char gt entry id MAP R20 FILE R05 value map r05 to gxl1v6 user nc gt Once the mapping files have been pointed by the user configure the case gt configure case 5 2 Orbital parameters env run xml To set up the orbital forcing the epoch of the simulation is specified in time A D 1950 time For example for the penultimate glaciation that occurred 140 kyrs BP the time will be gt vi env rum xml ORBITAL MODE fixed year ORBITAL YEAR 138050 Centro Euro Mediterraneo sui Cambiamenti Climatici CO Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers For past
36. o introduce large changes in the land sea mask and surface conditions in a the coupled atmosphere land ocean sea ice configuration of the CESM 1 0 5 B case The user may note that this procedure is by far non automatic and requires substantial manual work at each stages Finally following this procedure does not provide any guarantees that the simulations will be successful 2 Modelling near past climates Simulating past climates implicates various changes in the Earth s topography Fifty million years ago Myrs the continental distribution highly differed from present day one and the modern configuration emerged about 10 Myrs ago Near past climate refers more or less to the last 10 Myrs during which only sea level and surface elevation changed as a result of the alternation of glacial interglacial cycles Figure 2 On the contrary Deep past climate refers to periods older than 10 Myrs more specifically when the continental distribution was totally different than the modern one T 100 W 0 100 Figure 2 Last Glacial Maximum topography from ICE 5G reconstruction LGM Peltier 2004 White areas correspond to LGM distribution of ice sheets and glaciers Note that LGM sea level is lower by about 130 m relative to present day one Creating initial conditions for Near Past or Deep Past has different implications Deep past changes in the surface topography land cover but also of the ocean bathymetry an
37. o map i c 2 clm r CESM standard pa mapped to a bue clm r new paleo map Production run CESM e Figure 4 Flow chart of the steps described in this user guide after Nan Rosembloom and Christina Shields s flow chart see Appendix II Orange boxes or blue boxes correspond to tools located in the main directory of the CESM while brown boxes correspond to the script developed and released in NCAR s Paleo toolkit CESM 1 0 5 near past initial conditions user guide prescribing ice sheets 1 Software requirements Fortran 90 NetCDF Fortran libraries NCAR Command Language download at http www ncl ucar edu Ncview Spherical Coordinates Remapping and Interpolation Package SCRIP needed to create mapping files for CESM 1 0 and earlier versions of CCSM Download the package and docu mentation on LANL SCRIP page 2 NCAR s Paleo Toolkit In 2012 NCAR Paleo Working Group released a Paleo Toolkit containing all the necessary scripts to modify the initial conditions as described in this user guide The Paleo Toolkit is available for download here https Awww2 cesm ucar edu working groups pwg documentation cesm1 paleo toolkit Furthermore the Paleo Working Group wiki page contains a lots of informations to properly set up the paleoclimate simulations and some of the scripts of the Paleo Toolkit This toolkit contains two tar files one dedicated to the old version of CCSM3 and one dedicated to
38. oslat nc containing the present day topography land fractions to the coastlines on the atmospheric grid on which the user wants to in terpolate his new topography here fv 0 9x1 25 nc and the topography at 10 min resolution obtained from section 2 To keep consistent with the gradual land fraction the script fix landm coslat ncl Paleo Toolkit for CCSM83 in definsurf paleo quaternary landmcoslat further modifies the new topography interpolated on the final atmospheric grid All those files are reported in Table 8 and the procedure is described in Appendix Figure 9 To execute the package first the user may compile it and then gt definesurf t topo mis6 lO0min nc g fv 0 9x1 25 nc l landm coslat nc newtopo nc Table 8 Creating CAM initial conditions Numerical tool Scripts Inputs Outputs Fortran definesurf package Input NetCDF fv_0 9x1 25 nc landm coslat nc topo user 10min nc Output topo user 0 9x1 25 remap nc NCL fix landm coslat ncl Input topo user 0 9x1 25 remap nc Output _ 0 9 1 25 remap mod nc BUGS A syntax bug was fixed in the routine map2f f90 This bug might have been corrected in the latest version of the code The user may contact NCAR directly to get a more recent version Line 926 SC j jc min 1 tmp gt old version SC j jc min 1 0d0 tmp gt new version fixed bug Centro Euro Mediterraneo sui Cambiamenti Climatici Centro Euro
39. te his own topography and land ice mask to USGS topography grid Check also that the coordinates are written in the same order than in USGS file The user file should look like the following netcdf topo mis6 10min 111021 dimensions lat 1080 lon 2160 variables float htopo lat lon FillValue 1 e 34f htopo units meter htopo long_name 10 min elevation from USGS 30 sec dataset double lat lat lat units cell center locations lat long_name latitude double lon lon lon units cell center locations lon long_name longitude float ice lat lon ice missing value 1 e 34f ice FillValue 1 e 34f ice long name landice ice history From landlandice MIS6 10min ice lonFlip longitude coordinate variable has been reordered via lonFlip float landfract lat lon landfract FillVal 1 e 34f landfract ong name RELIEF D Relief_140_aveclacs_casp0 GX RELIEF D Relief GY RELIEF D Relief landfract missing value 1 34 landfract lonFlip longitude coordinate variable has been reordered via lonFlip landfract _FillValue 1 e 34f landfract units meter int landmask lat lon landmask longname landmask _FillValue 9999 float variance lat lon variance long_name variance of 30 sec elevations variance units meter 2 global attributes sinfile3 USGS gtopo30 10min c050419 nc tinfile2
40. the script create urban ncl which uses the modern urban areas distribution and the combined new PFTs distribution including the harvest areas crop computed at the first step of this section IMPORTANT in the script create_urban ncl the user have to set pct_urban 0 As for nn fill ncl create urban ncl is not provided along with the Paleo Toolkit 3 4 Creating CLM initial conditions file Centro Euro Mediterraneo sui Cambiamenti Climatici Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers The files obtained in the previous steps 4 1 to 4 3 are combined together to create the new surface dataset that will constitute the input file to initialize CLM The path to those files will be set in the namelists before compiling and running the B case see section 6 Landunit c 0 Bare Glacier Wetland Vegetated Lake Urban Tree Columns 1 Needleleaf Evergreen Temperate 2 Needleleaf Evergreen Boreal Soil 3 Needleleaf Deciduous Boreal Typel 4 Broadleaf Evergreen Tropical 5 Broadleaf Evergreen Temperate 6 Broadleaf Deciduous Tropical 7 Broadleaf Deciduous Temperate 8 Broadleaf Deciduous Boreal Herbaceous Understorey 9 Broadleaf Evergreen Shrub Temperate 10 Broadleaf Deciduous Shrub Temperate 11 Broadleaf Deciduous Shrub Boreal 12 C3 Arctic Grass 13 C3 non Arctic Grass 14 C4 Grass 15 Crop PFTs Figure 5 CLM landcover pixel decomposit
41. the various crashes of the components of CESM 1 0 5 Paleo Documentation the user can find some further documentation and advices when configuring the run for paleo times The Paleo working group have created a wiki page which accessible to anybody The following websites are dedicated to paleo datasets and ice sheet configurations used to create paleo topographies PMIP3 Paleoclimate Models Intercomparison Phase 3 CE 5G W R Peltier Last glacial deglaciation 21k Ok ice sheets reconstructions Peltier 2004 Ice Cores Gateway to get the lastest GHGs records available for various parts of the world Centro Euro Mediterraneo sui Cambiamenti Climatici CO e Centro Euro Mediterraneo sui Cambiamenti Climatici OO E CMCC Research Papers Appendix 0 Execution time of the scripts used in this user guide Table 9 Computational time estimates on CALYPSO IBM power 6 platform Scripts Execution time change kmt ncl lt 5b mk remap gx1v6 csh lt 5min gen domain aix 5min runoff run lt 20 min mkgridata lt 5min create mksrf topo nc lt 5 convert mksrf lt 5 harvest ncl lt 5min nn fill ncl 5 min create_urban ncl lt 5 mksurfdata 20 min several hours definesurf lt 5 fix landm coslat ncl lt 5 CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Appendix I Flow charts summarizing the procedure described in this user guide
42. time the value is negative 5 3 CAM namelist cam buildnml csh To initialise the atmospheric component the user needs to set the new topography from section 5 The user may also changes the values of the GHGs according to the epoch considered Here the values are taken from and ice cores records retrieved from EPICA Dome C East Antarctica and corresponds to 140 kyrs BP amp cam inparm bnd topo SDIN LOC ROOT atm cam topo topo mis6 0 9x1 25 remap user mod nc amp chem surfvals nl ch4vmr 791 6e 9 co2vmr 284 7e 6 fllvmr 12 48e 12 fl2vmr 0 0 n2ovmr 275 68e 9 5 4 CLM namelist clm buildnml csh The user has to change the value of in agreement with that set up in CAM namelist above Since in this example we are modelling a past glaciation the option hac is switched off we removed the urban landunits from the surface dataset in section 4 3 amp clm inparm co2_ppmv 284 7 fatmlndfrc SDIN LOC ROOT lnd clm2 griddata fracdata 0 9x1 25 gxl1v6 user nc fsurdat SDIN LOC ROOT l1nd clm2 surfdata surfdata 192x288 user nc urban hac OFF 5 5 POP namelist pop2 buildnml csh As for CAM namelist the user has to indicate the new bathymetry and ocean basins distribution computed in section 3 1 identify all gxlv6 datasets residing in DIN LOC ROOT ocn pop CESM 1 0 5 near past initial conditions user guide prescribing ice sheets set regionmask filenam
43. un Step7 definesurf bnd topo myrun ene re d Step 8 5 day CESM clm r new paleo map Y Step 9 interpinic clm r spun up state mapped to new paleo map y Step 10 Production CESM Figure 6 Various steps of the procedure described in the user guide Source Nan Rosembloom N pyew INS aaSN LON bu ggzoxz6 L0 eyeppub opujune uso juupinq ur xccl 8 ou 31 vq uniAu 4 6 0 ejepoey CESM 1 0 5 near past initial conditions user guide prescribing ice sheets ou 31vqd 00 400019 xB oj dew GOOLOL lLzd LxB 901 dewyouns ep Gz 60 dew Buiddeju 919 soge 015 1 00435 VO soge dew jes Aue __ 3 ou31vq ep unsAw Sz 60 dew ou31VGq ep umAw Gz 604 dew ou31VvQ ep SZ 604 or cz y 6044 0y uniAur dew Buiddeyy szoroson _ still a 9u 2 040 SZ 1X6 0N 8199912070100 zuou m unsAw x6 A dewar ou3 Ivq uniKui
44. user has compiled the CESM and submit the job the coupler checks that the land sea masks computed for CAM and CLM matches the one computed for POP and CICE If this first stage is successful the user can hope that the new initial conditions are fine Bellow the end of the coupler log file is shown as an example seq mct drv Performing domain checking domain check mct checking ocn ice domains domain check grid mct the domain size is 40 domain check grid mct maximum difference for mask 0 00000000000000 domain check grid mct maximum allowable difference for mask 0 100000000000000E 01 domain check grid mct the domain size is 40 domain check grid mct maximum difference for lat 0 568434188608080E 13 domain check grid mct maximum allowable difference for lat 0 100000000000000 01 domain check grid mct the domain size is 40 domain check grid mct maximum difference for lon 0 568434188608080E 13 domain check grid mct maximum allowable difference for lon 0 100000000000000 01 domain check grid mct the domain size is 40 domain check grid mct maximum difference for area 0 130104260698261E 17 domain check grid mct maximum allowable difference for area 0 100000000000000E 00 domain check mct checking atm land domains domain check grid mct the domain size is 48 domain check grid mct maximum difference for lat 0 142108547152020E 13 domain check grid mct maximum
45. user provided topography at 10 min htopo landfract landmask variance ice WARNING be sure that the following variables are computed in the indicated ranges ICE 0 100 LANDFRACT 0 1 LANDMASK 0 1 This new topography is used to generate the new land sea mask and the ocean region mask Figure 3 This step is based on the CESM present day bathymetry KMT file located in csm inputdata ocn pop2 grid the present day land sea mask and region mask are binary files ieee4 The script change kmt ncl from the Paleo Toolkit is able to open those files and modify the areas where the new topography is different from present day POP is particularly sensitive to new continental points inserted in the new topography That is why for practical issue when sim ulating near past climates in the script present day bathymetry is preserved over the unchanged areas To generate the new KMT and region mask the user has to point to the new topography 1x1 nc file As reported in Table 2 change kmt nc also needs the original present day bathymetry regions and horizontal grid files provided directly for the resolution of interest in the csm inputdata ocn pop2 grid directory CESM 1 0 5 near past initial conditions user guide prescribing ice sheets Execute the script gt ncl change kmt ncl The execution time of the scripts is detailed in Table 9 Table 2 New ocean bathymetry and region mask files Numerical tool Scripts Inp
46. ut map ocn to atm aave nc Output domain ocn gx1 v6 user nc domain Ind fv09 1 25 gx1v6 user nc Do not forget to set the path for the SCRIP executable in mk remap gx1v6 csh To check the consistency of the mapping files the user may use scrip test executable and namelists which are designed to produce readable NetCDF outputs from the mapping files generated NOTES AND ADVICE producing the mapping files for the coupler is not an easy task and the user should pay attention to it since if it fails for some reasons and for only one pixel the model will not be able to run with the new conditions Then given the structure of this procedure the user may Centro Euro Mediterraneo sui Cambiamenti Climatici e Centro Euro Mediterraneo sui Cambiamenti Climatici CMCC Research Papers have to start again from almost the beginning of the procedure see all the flow charts in Figure 4 Once the mapping files have been generated the user may compute the runoff mapping file This file is generated at 0 5 horizontal resolution and is based on the new ocean grid file computed at the previous step Table 4 The runoff package gen runof has to be compiled first using the script build machine csh In alternative the user can download the new package runoff ocn available in the latest version of CESM 1 2 and similar to the gen runoff package See NCAR s Paleo Toolkit section The user can thus follow the instructions below using the
47. uts Outputs User provided User provided Input topo user 10min nc Output new topo _user_1x1 nc NCL change_kmt ncl Input new topo user 1x1 nc topography at 1 res topography 20090204 ieeei4 POP present day topo region mask 20090205 ieeei4 POP present day ocean basins horiz grid 20010402 ieeer8 POP present day horizontal grid Output kmt_gx1v6_user ieeei4 region_mask_gx1v6_user ieeei4 USER kmt nc file to check for disturbing pixels A NetCDF file USER kmt nc containing the main variables modified by change kmt ncl is also created to help the user to check whether the new land sea mask and region mask are correct It is important to check the number of basins contained in the new oceanic region mask In deed when changing the ocean bathymetry changes occur in the region mask since some basins may disappear In the present day region mask file each basin and marginal sea is assigned a value between 1 to 14 You can find the present day configuration in the main directory of the CESM 1 0 5 model CESM 1 0 5 models ocn pop2 input_templates gx1v6_region_ids The original gx1v6 region ids file provided in the CESM 1 0 5 for present day is shown in Table 3 If the topo provided by the user induces modifications in the present day basins distribution no Baltic Sea no Hudson Bay for example the previous values assigned to the basins have to be re assigned An example is given in Table 3 illustrating our gla
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