Fortuna 2.5 Single Column Model
This page describes the steps and modifications necessary to build and run the Single Column Model (SCM) under Fortuna 2.5 on discover. It assumes that you have successfully run the model as described in Fortuna 2.5 Quick Start.
Back to GEOS-5 Documentation for Fortuna 2.5
Checking Out and Updating GEOS-5 for SCM
The Fortuna model tag Fortuna-2_5 has all code necessary to run the single column model with any of the cases below. The executable of the Single Column Model is identical to the global model; the only differences are the environment and settings with which it runs.
Setting Up and Running Existing SCM Experiments
The setup script for the SCM experiments is /discover/nobackup/aeichman/scm/setup/getSCMdataf2.4.sh . You do not have to run the gcm_setup script as you do to set up a global run. The SCM environment and setup scripts have been changed for Fortuna 2.4 and older versions will not work for the current model tag.
At the time of this writing there are twenty experiments to choose from:
- ARM Southern Great Plains site (http://www.arm.gov/sites/sgp), July 1997
- KWAJEX (http://www.atmos.washington.edu/kwajex/)
- ARM-SCSMEX (http://www.cawcr.gov.au/bmrc/wefor/research/scsmex.htm)
- ARM-TWP (http://acrf-campaign.arm.gov/twpice/)
- TRMM-LBA (http://radarmet.atmos.colostate.edu/lba_trmm/)
- Five experiments with about the same times and locations as the five above, but forced with MERRA data
- TOGA COARE (http://www.atmos.washington.edu/togacoare/summaries.html)
- Six CGILS cases (http://atmgcm.msrc.sunysb.edu/cfmip_figs/Case_specification.html)
- NAMECORE (forced with MERRA data) (http://www.eol.ucar.edu/projects/name/)
- NAMEAZNM (forced with MERRA data) (http://www.eol.ucar.edu/projects/name/)
- NAMMA (forced with MERRA data) (http://namma.msfc.nasa.gov/)
Create your own directory and copy to it the script getSCMdataf2.5.sh, then modify and uncomment the first executable line, which assigns ESMADIR to your local Fortuna 2.5 build that you are using for the SCM (you may already have this set as an environment variable). Uncomment one of the lines that assign the variable CASEDIR to choose the experiment to run. Then run the script. It will copy all of the necessary resource, forcing and data files to the working directory. Each experiment requires its own directory. If you modify the resource files (e.g., HISTORY.rc) you may want to copy the setup directory to your own area and modify it and the setup script accordingly so that you don't clobber your modifications.
Then you can just run the model executable from the command line in the directory you created. You will have to load the proper modules by sourcing src/g5_modules. Although it runs with a single processor, on discover you should run it from an interactive job on a compute node (as opposed to the discover front end). This can be done by running qsub -I ijob, where ijob is the job script that sets up the environment (examples are in ~aeichman or ~amolod). Once the job starts it starts an interactive shell on the job node, from which you can run the GEOS-5 executable. Since all of the necessary configuration files are copied to the experiment directory, it requires none of the extra environmental infrastructure needed for a global experiment that the run script gcm_run.j creates.
Creating Driving Datasets from MERRA
Given the resource and other files that come with a complete SCM configuration (either from an existing case or created with the procedure below), a driving data file for the same location and time span can be generated using MERRA output. The current scheme for MERRA data includes the analysis increments in the advection terms that were left out in previous versions.
Obtaining MERRA Data
MERRA output files are located under /archive on NCCS discover and can be time consuming to obtain. For this purpose a set of scripts have been created to make the task easier. To use them, create a subdirectory and copy the contents of /discover/nobackup/aeichman/scm/util/get-merra to it. You should have the following:
getter.j MERRAobsys.rc README watcher.j
To use the scripts, modify the line in getter.j starting setenv PATH ${PATH}: ... to point to the directory
src/Linux/bin in your local Fortuna 2.2 build, which
contains the necessary utilities. These use perl
libraries, which might require additions to your environment. (Assume at first that they don't.) To specify the range of MERRA data to obtain, modify the variables
BEGIN_date and END_date (both in the format YYYYMMDD). You may need
to modify your group name in the PBS environment variables as well.
Then qsub watcher.j (not getter.j). It will submit the getter.j
script while submitting a version of itself to monitor the "getter"
job. getter.j uses the acquire utility to smoothly transfer files from /archive to the current directory. If the getter job ends without finishing -- most likely
because the allotted walltime ran out -- then the watcher job will
repeat the process, until all the data in the specified range are
copied to the current directory. For data sets of a month or so this may take a few hours, but the scripts should run without intervention. If something interrupts this process, the same scripts may be started again, and acquire will be intelligent enough figure out where it needs to pick up. Keep in mind that response time of the /archive filesystem can vary considerably (on the scale of hours to days, depending on downtime).
For more details, see README.
Some Discussion About How to Use and Configure SCM
The following section contains excerpts from emails from users along with replies that might answer questions that can come up.
The VERTICAL_ADVECTION Flag
From ARM_97JUL, I do see there is a flag "VERTICAL_ADVECTION" in AGCM.rc. I am trying to turn it off by setting it to "0". Is it the right way to use observed vertical advection?
yes sir, that is the way to turn it off. but turning it off is what gives 50 deg temp biases. there is a code change that i am testing today or tomorrow that greg walker tried and said made a big difference. we are suspecting that the T vertical advection term in the obs dataset is missing the adiabatic expansion term (ie, that it is dT/dp and not the total vert tend). so we will try to use the vertical advection of s term (it is already divided by Cp i think). in that case the idea would be to go into the reader.F90 term and (greg walker did this) do something like:
add the line:
TMP(13,:,:) = TMP(13,:,:)/3600.0
near where we do other stuff like this. and then: instead of:
T_V_ADV(i,k) = -dv(7,K,I)
put in something like:
if (filename.eq."arm_97jul.dat") then
T_V_ADV(i,k) = -dv(13,K,I) ! Vertical_s_Advec/cp (K/s)
else
T_V_ADV(i,k) = -dv(7,K,I) ! Vertical_T_Advec (K/s) [is omega*alpha included?]
endif
got it? the idea is to use the vertical advection of s term for arm 97 july case for now (its possible that there are other cases that we have to do this also, but until we know that we want to try it for arm 97 july only).
so - if you want to turn off the calculation of vertical advection you set VERTICAL_ADVECTION to 0 in the AGCM.rc (or leave it out - 0 is the default). and then i would HIGHLY recommend doing what i suggest here.
CGILS Experiments
It will be great if we can have some cases to study low clouds such as off coasts of California and Peru. Joao and I are interested to use SCM for the low clouds study.
just to let you both know that there is a new set of cases that we can now do with the scm, but they may not make their way into the 'official' set of cases. they are the CGILS cases. this is the set of CFMIP-GCSS simulations at three points on the transect from the calif coast to the mid pacific (stratus, strato cu, cu). the CGILS project includes a set of 3 or 4 LES simulations of the same 3 spots. the SCM forcing is idealized and the simulation is perpetual july 15 with no diurnal cycle (code changes needed for this to the model will not be in 'official' code releases - that's why these experiments won't be ones that are on the 'list'), but the set-up is great for testing pbl schemes and the interaction with the shallow and deep convection in marine boundary layers. i have done the simulations with our fortuna-2_0 code and i've also done a suite of sensitivity experiments and am continuing to do more. if you'd like the code mods for these runs i can provide them.
Parameters for progno_cloud
The following is a list of parameters for progno_cloud that can be in the AGCM.rc configuration file.
Slot Name (AGCM.rc) default var. name description
---- -------------- ------- --------- ------------
1 'CNV_BETA:', 10.0 CNV_BETA Divide convective rain by cnv_beta for Marsh-Palm
drop size, number, velocity - used for evap of rain
2 'ANV_BETA:', 4.0 ANV_BETA Divide anvil rain rate by anv_beta
3 'LS_BETA:', 4.0 LS_BETA Divide Large Scale rain by ls_beta
4 'RH_CRIT:', 1.0 RH00 Upper limit on critical relative humidity for evap/condense
5 'AUTOC_LS:', 2.0e-3 C_00 Multiplication factor (+unit conversion) for autoconversion
rate (autoconvert exp(-rate * dt) )
6 'QC_CRIT_LS:', 8.0e-4 LWCRIT Scale autoconversion (impact ~ 1 - exp(-1/lwcrit)**2 )
7 'ACCRETION:', 2.0 C_ACC Scale factor for accretion of cloud water by rain/snow
8 'BASE_REVAP_FAC:', 1.0 C_EV Scale factor for rain/snow re-evap (re-evap ~ 1 - exp(- c_ev) )
9 'VOL_TO_FRAC:', -1.0 CLDVOL2FRC Not used
10 'SUPERSAT:', 0.0 RHSUP_ICE Not used
11 'SHEAR_EVAP_FAC:', 1.3 SHR_EVAP_FAC Not used
12 'MIN_ALLOW_CCW:', 1.0e-9 MIN_CLD_WATER Not used
13 'CCW_EVAP_EFF:', 3.3e-4 CLD_EVP_EFF Scale for evap of cloud water/(subl of ice) (+unit conv)
14 'NSUB_AUTOCONV:', 20. NSMAX Not used
15 'LS_SUND_INTER:', 4.8 LS_SDQV2 Factor to control how fast LS ice autonv drops at cold temps
16 'LS_SUND_COLD:', 4.8 LS_SDQV3 Factor to control how fast LS ice autonv drops at coldest temps
17 'LS_SUND_TEMP1:', 230. LS_SDQVT1 Temp at which to start decrease in LS ice autoconv ramping
18 'ANV_SUND_INTER:', 1.0 ANV_SDQV2 Factor to control how fast anvil ice autonv drops at cold temps
19 'ANV_SUND_COLD:', 1.0 ANV_SDQV3 Factor to control how fast anvil ice autonv drops at coldest temps
20 'ANV_SUND_TEMP1:', 230. ANV_SDQVT1 Temp at which to start decrease in anvil ice autoconv ramping
21 'ANV_TO_LS_TIME:', 14400. ANV_TO_LS Not used
22 'NCCN_WARM:', 50. N_WARM Not used
23 'NCCN_ICE:', 0.01 N_ICE Not used
24 'NCCN_ANVIL:', 0.1 N_ANVIL Not used
25 'NCCN_PBL:', 200. N_PBL Not used
26 'DISABLE_RAD:', 0. DISABLE_RAD Flag (=1) to disable radiative interaction with cloud/rain
27 'ICE_SETTLE:', 0. Not used
28 'ANV_ICEFALL:', 0.5 ANV_ICEFALL_C Scale for fall rate of anvil ice (used to scale ice autoconv)
29 'LS_ICEFALL:', 0.5 LS_ICEFALL_C Scale for fall rate of LS ice (used to scale ice autoconv)
30 'REVAP_OFF_P:', 2000. REVAP_OFF_P Max pressure at which to do precip re-evap (mb)
31 'CNV_ENVF:', 0.8 CNVENVFC Scale factor for convective rain/snow re-evap
(re-evap ~ 1 - exp(- envfrac) ) - fraction of re-evap in
environment as opposed to in the cloud
32 'WRHODEP:', 0.5 WRHODEP Control rate of dec/incr of ice fall speed with high/low press
33 'ICE_RAMP:', -40.0 T_ICE_ALL = ICE_RAMP + MAPL_TICE - Temp at which all cloud/precip is ice
(fraction=1, use L of ice)
34 'CNV_ICEPARAM:', 1.0 CNVICEPARAM Control on how much new conv precip is ice
(1=> use ice fraction, 0=> all liquid)
35 'CNV_ICEFRPWR:', 4.0 ICEFRPWR = CNV_ICEFRPWR + .001 -- Scale ice fraction (liquid/ice
partition for consensation/evap/melting&freezing)
Fraction = Fraction ** icefrpowr
36 'CNV_DDRF:', 0.0 CNVDDRFC Fraction of re-evap of conv precip to reserve for re-evap
lower in atm (in a "downdraft")
37 'ANV_DDRF:', 0.0 ANVDDRFC Fraction of re-evap of conv precip to reserve for re-evap
lower in atm (in a "downdraft")
38 'LS_DDRF:', 0.0 LSDDRFC Fraction of re-evap of conv precip to reserve for re-evap
lower in atm (in a "downdraft")
39 'AUTOC_ANV:', 1.0e-3 Not used
40 'QC_CRIT_ANV:', 8.0e-4 Not used
41 'TANHRHCRIT:', 1. tanhrhcrit Flag to use tanh vertical profile for Rh crit for condens/evap
42 'MINRHCRIT:', 0.8 minrhcrit Min Rh in tanh profile
43 'MAXRHCRIT:', 1.0 maxrhcrit Max Rh in tanh profile