DART namelists are @@ -68,40 +70,50 @@ Character strings that contain a '/' must be enclosed in quotes to prevent them from prematurely terminating the namelist.

MODULES USED

PUBLIC INTERFACES

- A note about documentation style. - Optional arguments are enclosed in brackets + A note about documentation style. + Optional arguments are enclosed in brackets [like this].

- call subroutine1(arg1, [, arg2]) @@ Diff output truncated at 40000 characters. @@ From nancy at ucar.edu Tue Oct 8 16:40:01 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Tue, 08 Oct 2013 16:40:01 -0600 Subject: [Dart-dev] [6500] DART/trunk/doc/html/boilerplate/Makefile: make a simple makefile for these programs. Message-ID: Revision: 6500 Author: nancy Date: 2013-10-08 16:40:00 -0600 (Tue, 08 Oct 2013) Log Message: ----------- make a simple makefile for these programs. Added Paths: ----------- DART/trunk/doc/html/boilerplate/Makefile -------------- next part -------------- Added: DART/trunk/doc/html/boilerplate/Makefile =================================================================== --- DART/trunk/doc/html/boilerplate/Makefile (rev 0) +++ DART/trunk/doc/html/boilerplate/Makefile 2013-10-08 22:40:00 UTC (rev 6500) @@ -0,0 +1,25 @@ + +include ../../../mkmf/mkmf.template + +ALL = html_namelist html_function html_subroutine html_type html_functoc + +default: $(ALL) + +html_namelist : html_namelist.f90 + $(FC) $(FFLAGS) $< -o $@ + +html_function: html_function.f90 + $(FC) $(FFLAGS) $< -o $@ + +html_subroutine: html_subroutine.f90 + $(FC) $(FFLAGS) $< -o $@ + +html_type: html_type.f90 + $(FC) $(FFLAGS) $< -o $@ + +html_functoc: html_functoc.f90 + $(FC) $(FFLAGS) $< -o $@ + + +clean: + rm -f $(ALL) fort.22 Property changes on: DART/trunk/doc/html/boilerplate/Makefile ___________________________________________________________________ Added: svn:mime-type + text/plain Added: svn:keywords + Date Rev Author HeadURL Id Added: svn:eol-style + native From nancy at ucar.edu Wed Oct 9 14:42:12 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 14:42:12 -0600 Subject: [Dart-dev] [6502] DART/trunk/models/CESM/shell_scripts: make all the time tests in the assimilate scripts be a positive Message-ID: Revision: 6502 Author: nancy Date: 2013-10-09 14:42:12 -0600 (Wed, 09 Oct 2013) Log Message: ----------- make all the time tests in the assimilate scripts be a positive test, and return in the else clause instead of a negative test. add a perfect_model script which is modeled on the assimilate script. it calls 3 perfect_model scripts which are to be written. Modified Paths: -------------- DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh DART/trunk/models/CESM/shell_scripts/clm_assimilate.csh DART/trunk/models/CESM/shell_scripts/pop_assimilate.csh Added Paths: ----------- DART/trunk/models/CESM/shell_scripts/perfect_model.csh -------------- next part -------------- Modified: DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh 2013-10-09 20:29:18 UTC (rev 6501) +++ DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh 2013-10-09 20:42:12 UTC (rev 6502) @@ -9,9 +9,10 @@ # This block is an attempt to localize all the machine-specific # changes to this script such that the same script can be used # on multiple platforms. This will help us maintain the script. +# Search below for TIMECHECK to see what times this script will +# assimilate. echo "`date` -- BEGIN CAM_ASSIMILATE" -echo "custom version assimilates at 0,6,12,18Z" set nonomatch # suppress "rm" warnings if wildcard does not match anything @@ -82,12 +83,13 @@ # If not, return before assimilating. #------------------------------------------------------------------------- -if ( $ATM_HOUR != 0 && $ATM_HOUR != 6 && $ATM_HOUR != 12 && $ATM_HOUR != 18) then +## TIMECHECK: +if ( $ATM_HOUR == 0 || $ATM_HOUR == 6 || $ATM_HOUR == 12 || $ATM_HOUR == 18) then + echo "Hour is $ATM_HOUR so we are assimilating the atmosphere" +else echo "Hour is not 0,6,12 or 18Z so we are skipping the atmosphere assimilation" echo "`date` -- END CAM_ASSIMILATE" exit 0 -else - echo "Hour is $ATM_HOUR so we are assimilating the atmosphere" endif #------------------------------------------------------------------------- Modified: DART/trunk/models/CESM/shell_scripts/clm_assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/clm_assimilate.csh 2013-10-09 20:29:18 UTC (rev 6501) +++ DART/trunk/models/CESM/shell_scripts/clm_assimilate.csh 2013-10-09 20:42:12 UTC (rev 6502) @@ -9,9 +9,10 @@ # This block is an attempt to localize all the machine-specific # changes to this script such that the same script can be used # on multiple platforms. This will help us maintain the script. +# Search below for TIMECHECK to see what times this script will +# assimilate. echo "`date` -- BEGIN CLM_ASSIMILATE" -echo "this version assimilates only when hour is 0Z" set nonomatch # suppress "rm" warnings if wildcard does not match anything @@ -82,21 +83,21 @@ # If not, return before assimilating. #------------------------------------------------------------------------- -if ( $LND_HOUR != 0 && $LND_HOUR != 6 && $LND_HOUR != 12 && $LND_HOUR != 18) then +## TIMECHECK: +if ( $LND_HOUR == 0 || $LND_HOUR == 6 || $LND_HOUR == 12 || $LND_HOUR == 18 ) then + echo "Hour is $LND_HOUR so we are assimilating the land" +else echo "Hour is not 0,6,12 or 18Z so we are skipping the land assimilation" echo "`date` -- END CLM_ASSIMILATE" exit 0 -else - echo "Hour is $LND_HOUR so we are assimilating the land" endif -# if you want to only assimilate at 0Z each day, substitute the -# following two lines for the longer test above. we have flux tower -# observations which need to be assimilated every 6 hours; if you -# aren't going to assimilate them and are only assimilating some obs type -# that is only available once a day, you can change to this test instead. -#if ( $LND_HOUR != 0 ) then -# echo "Hour is not 0Z so we are skipping the land assimilation" +# we have flux tower observations which can be assimilated every 6 hours, +# but if you want to only assimilate at 0Z each day, change the LND_HOUR +# check to this one: +# if ( $LND_HOUR == 0 ) then +# and the message in the else clause to this: +# echo "Hour is not 0Z so we are skipping the land assimilation" #------------------------------------------------------------------------- # Create temporary working directory for the assimilation and go there Added: DART/trunk/models/CESM/shell_scripts/perfect_model.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/perfect_model.csh (rev 0) +++ DART/trunk/models/CESM/shell_scripts/perfect_model.csh 2013-10-09 20:42:12 UTC (rev 6502) @@ -0,0 +1,30 @@ +#!/bin/csh +# +# DART software - Copyright 2004 - 2013 UCAR. This open source software is +# provided by UCAR, "as is", without charge, subject to all terms of use at +# http://www.image.ucar.edu/DAReS/DART/DART_download +# +# DART $Id$ + +# This block is an attempt to localize all the machine-specific +# changes to this script such that the same script can be used +# on multiple platforms. This will help us maintain the script. + +echo "`date` -- BEGIN CESM PERFECT MODEL" + +${CASEROOT}/cam_perfect_model.csh +if ( $status != 0 ) exit $status +${CASEROOT}/pop_perfect_model.csh +if ( $status != 0 ) exit $status +${CASEROOT}/clm_perfect_model.csh +if ( $status != 0 ) exit $status + +echo "`date` -- END CESM PERFECT MODEL" + +exit 0 + +# +# $URL$ +# $Revision$ +# $Date$ + Property changes on: DART/trunk/models/CESM/shell_scripts/perfect_model.csh ___________________________________________________________________ Added: svn:executable + * Added: svn:mime-type + text/plain Added: svn:keywords + Date Rev Author HeadURL Id Added: svn:eol-style + native Modified: DART/trunk/models/CESM/shell_scripts/pop_assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/pop_assimilate.csh 2013-10-09 20:29:18 UTC (rev 6501) +++ DART/trunk/models/CESM/shell_scripts/pop_assimilate.csh 2013-10-09 20:42:12 UTC (rev 6502) @@ -9,9 +9,10 @@ # This block is an attempt to localize all the machine-specific # changes to this script such that the same script can be used # on multiple platforms. This will help us maintain the script. +# Search below for TIMECHECK to see what times this script will +# assimilate. echo "`date` -- BEGIN POP_ASSIMILATE" -echo "this version assimilates only when hour is 0Z" set nonomatch # suppress "rm" warnings if wildcard does not match anything @@ -84,8 +85,15 @@ # restart configuration for pop (data_assim or rest). #------------------------------------------------------------------------- +## TIMECHECK: ${REMOVE} ${CASEROOT}/user_nl_pop2_*back -if ( $OCN_HOUR != 0 ) then +if ( $OCN_HOUR == 0 ) then + echo "Hour is $OCN_HOUR so we are assimilating the ocean" + foreach nml ( ${CASEROOT}/user_nl_pop2_* ) + ${MOVE} $nml ${nml}.back + sed -e "s/'rest'/'data_assim'/" ${nml}.back >! $nml + end +else echo "Hour is not 0Z so we are skipping the ocean assimilation" foreach nml ( ${CASEROOT}/user_nl_pop2_* ) ${MOVE} $nml ${nml}.back @@ -93,12 +101,6 @@ end echo "`date` -- END POP_ASSIMILATE" exit 0 -else - echo "Hour is $OCN_HOUR so we are assimilating the ocean" - foreach nml ( ${CASEROOT}/user_nl_pop2_* ) - ${MOVE} $nml ${nml}.back - sed -e "s/'rest'/'data_assim'/" ${nml}.back >! $nml - end endif #------------------------------------------------------------------------- From nancy at ucar.edu Wed Oct 9 15:08:32 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 15:08:32 -0600 Subject: [Dart-dev] [6503] DART/trunk/models/CESM/shell_scripts: minor tweek to cam_assimilate to be consistent with Message-ID: Revision: 6503 Author: nancy Date: 2013-10-09 15:08:31 -0600 (Wed, 09 Oct 2013) Log Message: ----------- minor tweek to cam_assimilate to be consistent with how we generally form instance numbers. also add tim's script which must be called when we stop CESM but aren't doing a cam assimilation. Modified Paths: -------------- DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh Added Paths: ----------- DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh -------------- next part -------------- Modified: DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh 2013-10-09 20:42:12 UTC (rev 6502) +++ DART/trunk/models/CESM/shell_scripts/cam_assimilate.csh 2013-10-09 21:08:31 UTC (rev 6503) @@ -512,11 +512,11 @@ set member = 1 while ( ${member} <= ${ensemble_size} ) - set n4 = `printf %04d $member` + set inst_string = `printf _%04d $member` - set ATM_INITIAL_FILENAME = `printf ${MYCASE}.cam_%04d.i.${ATM_DATE_EXT}.nc ${member}` + set ATM_INITIAL_FILENAME = ${MYCASE}.cam${inst_string}.i.${ATM_DATE_EXT}.nc - ${LINK} ${ATM_INITIAL_FILENAME} cam_initial_${n4}.nc || exit -9 + ${LINK} ${ATM_INITIAL_FILENAME} cam_initial${inst_string}.nc || exit -9 @ member++ Added: DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh (rev 0) +++ DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh 2013-10-09 21:08:31 UTC (rev 6503) @@ -0,0 +1,71 @@ +#!/bin/csh +# +# DART software - Copyright 2004 - 2013 UCAR. This open source software is +# provided by UCAR, "as is", without charge, subject to all terms of use at +# http://www.image.ucar.edu/DAReS/DART/DART_download +# +# DART $Id$ + +# This block is an attempt to localize all the machine-specific +# changes to this script such that the same script can be used +# on multiple platforms. This will help us maintain the script. + +echo "`date` -- BEGIN CAM_NO_ASSIMILATE" + +# The FORCE options are not optional. +# The VERBOSE options are useful for debugging though +# some systems don't like the -v option to any of the following +switch ("`hostname`") + case be*: + # NCAR "bluefire" + set LINK = '/usr/local/bin/ln -fvs' + breaksw + + default: + set LINK = 'ln -fvs' + breaksw +endsw + +set ensemble_size = ${NINST_ATM} + +#------------------------------------------------------------------------- +# Determine time of model state ... from file name of first member +# of the form "./${CASE}.cam_${ensemble_member}.i.2000-01-06-00000.nc" +#------------------------------------------------------------------------- + +set FILE = `head -n 1 rpointer.atm_0001` +set FILE = $FILE:t +set FILE = $FILE:r +set MYCASE = `echo $FILE | sed -e "s#\..*##"` +set ATM_DATE_EXT = `echo $FILE:e` + +#========================================================================= +# As implemented, the input filenames are static in the CESM namelists. +# We must link the new uniquely-named files to static names so that when +# the short-term archiver 'restores' the CESM files, the links are right. +#========================================================================= + +cd ${RUNDIR} + +set member = 1 +while ( ${member} <= ${ensemble_size} ) + + set inst_string = `printf _%04d $member` + + set ATM_INITIAL_FILENAME = ${MYCASE}.cam${inst_string}.i.${ATM_DATE_EXT}.nc + + ${LINK} ${ATM_INITIAL_FILENAME} cam_initial${inst_string}.nc || exit -9 + + @ member++ + +end + +echo "`date` -- END CAM_NO_ASSIMILATE" + +exit 0 + +# +# $URL$ +# $Revision$ +# $Date$ + Property changes on: DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh ___________________________________________________________________ Added: svn:executable + * Added: svn:mime-type + text/plain Added: svn:keywords + Date Rev Author HeadURL Id Added: svn:eol-style + native From nancy at ucar.edu Wed Oct 9 15:10:49 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 15:10:49 -0600 Subject: [Dart-dev] [6504] DART/trunk/models/CESM/shell_scripts/assimilate.csh: add note that if you are skipping the CAM assimilation for any Message-ID: Revision: 6504 Author: nancy Date: 2013-10-09 15:10:49 -0600 (Wed, 09 Oct 2013) Log Message: ----------- add note that if you are skipping the CAM assimilation for any reason, you still have to call a script to link the right initial files for each ensemble member. Modified Paths: -------------- DART/trunk/models/CESM/shell_scripts/assimilate.csh -------------- next part -------------- Modified: DART/trunk/models/CESM/shell_scripts/assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/assimilate.csh 2013-10-09 21:08:31 UTC (rev 6503) +++ DART/trunk/models/CESM/shell_scripts/assimilate.csh 2013-10-09 21:10:49 UTC (rev 6504) @@ -10,6 +10,11 @@ # changes to this script such that the same script can be used # on multiple platforms. This will help us maintain the script. +# if you are skipping the POP or CLM assimilations you can simply +# comment out the calls to the xxx_assimilate.csh scripts. however +# if you are skipping the CAM assimilation you must replace the +# call below with a call to ${CASEROOT}/cam_no_assimilate.csh + echo "`date` -- BEGIN CESM ASSIMILATE" ${CASEROOT}/cam_assimilate.csh From nancy at ucar.edu Wed Oct 9 15:20:06 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 15:20:06 -0600 Subject: [Dart-dev] [6505] DART/trunk/models/cam/shell_scripts/assimilate.csh: this script no longer needs the DARTDIR for anything; Message-ID: Revision: 6505 Author: nancy Date: 2013-10-09 15:20:06 -0600 (Wed, 09 Oct 2013) Log Message: ----------- this script no longer needs the DARTDIR for anything; the sampling error correction file is copied over to the CASEROOT dir by the CESM_DART_config script and that was the final reference to the dart source code tree. Modified Paths: -------------- DART/trunk/models/cam/shell_scripts/assimilate.csh -------------- next part -------------- Modified: DART/trunk/models/cam/shell_scripts/assimilate.csh =================================================================== --- DART/trunk/models/cam/shell_scripts/assimilate.csh 2013-10-09 21:10:49 UTC (rev 6504) +++ DART/trunk/models/cam/shell_scripts/assimilate.csh 2013-10-09 21:20:06 UTC (rev 6505) @@ -26,7 +26,6 @@ set REMOVE = '/usr/local/bin/rm -fr' set BASEOBSDIR = /glade/proj3/image/Observations/ACARS - set DARTDIR = ${HOME}/svn/DART/trunk set LAUNCHCMD = mpirun.lsf breaksw @@ -38,7 +37,6 @@ set REMOVE = 'rm -fr' set BASEOBSDIR = /glade/p/image/Observations/ACARS - set DARTDIR = ${HOME}/svn/DART/trunk set LAUNCHCMD = mpirun.lsf breaksw @@ -50,7 +48,6 @@ set REMOVE = 'rm -fr' set BASEOBSDIR = /scratch/scratchdirs/nscollin/ACARS - set DARTDIR = ${HOME}/trunk set LAUNCHCMD = "aprun -n $NTASKS" breaksw endsw @@ -142,7 +139,7 @@ set SECSTRING = `echo $MYSTRING[2] | tr '[:upper:]' '[:lower:]'` if ( $SECSTRING == true ) then - set SAMP_ERR_FILE = ${DARTDIR}/system_simulation/final_full_precomputed_tables/final_full.${ensemble_size} + set SAMP_ERR_FILE = ${CASEROOT}/final_full.${ensemble_size} if ( -e ${SAMP_ERR_FILE} ) then ${COPY} ${SAMP_ERR_FILE} . else From nancy at ucar.edu Wed Oct 9 16:18:51 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 16:18:51 -0600 Subject: [Dart-dev] [6506] DART/trunk/models/CESM/shell_scripts: first stab at perfect model scripts when running the fully coupled Message-ID: Revision: 6506 Author: nancy Date: 2013-10-09 16:18:50 -0600 (Wed, 09 Oct 2013) Log Message: ----------- first stab at perfect model scripts when running the fully coupled CESM model. untested as of yet. Added Paths: ----------- DART/trunk/models/CESM/shell_scripts/cam_perfect_model.csh DART/trunk/models/CESM/shell_scripts/clm_perfect_model.csh DART/trunk/models/CESM/shell_scripts/pop_perfect_model.csh -------------- next part -------------- Added: DART/trunk/models/CESM/shell_scripts/cam_perfect_model.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/cam_perfect_model.csh (rev 0) +++ DART/trunk/models/CESM/shell_scripts/cam_perfect_model.csh 2013-10-09 22:18:50 UTC (rev 6506) @@ -0,0 +1,256 @@ +#!/bin/csh +# +# DART software - Copyright 2004 - 2013 UCAR. This open source software is +# provided by UCAR, "as is", without charge, subject to all terms of use at +# http://www.image.ucar.edu/DAReS/DART/DART_download +# +# DART $Id$ + +# This block is an attempt to localize all the machine-specific +# changes to this script such that the same script can be used +# on multiple platforms. This will help us maintain the script. +# Search below for TIMECHECK to see what times this script will +# run. + +echo "`date` -- BEGIN GENERATE CAM TRUE STATE" + +set nonomatch # suppress "rm" warnings if wildcard does not match anything + +# The FORCE options are not optional. +# The VERBOSE options are useful for debugging though +# some systems don't like the -v option to any of the following +switch ("`hostname`") + case be*: + # NCAR "bluefire" + set MOVE = '/usr/local/bin/mv -fv' + set COPY = '/usr/local/bin/cp -fv --preserve=timestamps' + set LINK = '/usr/local/bin/ln -fvs' + set REMOVE = '/usr/local/bin/rm -fr' + + set BASEOBSDIR = /glade/proj3/image/Observations/ACARS + breaksw + + case ys*: + # NCAR "yellowstone" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /glade/p/image/Observations/ACARS + breaksw + + default: + # NERSC "hopper" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /scratch/scratchdirs/nscollin/ACARS + breaksw +endsw + +#------------------------------------------------------------------------- +# Determine time of model state ... from file name of first member +# of the form "./${CASE}.cam_${ensemble_member}.i.2000-01-06-00000.nc" +# +# Piping stuff through 'bc' strips off any preceeding zeros. +#------------------------------------------------------------------------- + +set FILE = `head -n 1 rpointer.atm_0001` +set FILE = $FILE:t +set FILE = $FILE:r +set ATM_DATE_EXT = `echo $FILE:e` +set ATM_DATE = `echo $FILE:e | sed -e "s#-# #g"` +set ATM_YEAR = `echo $ATM_DATE[1] | bc` +set ATM_MONTH = `echo $ATM_DATE[2] | bc` +set ATM_DAY = `echo $ATM_DATE[3] | bc` +set ATM_SECONDS = `echo $ATM_DATE[4] | bc` +set ATM_HOUR = `echo $ATM_DATE[4] / 3600 | bc` + +echo "valid time of model is $ATM_YEAR $ATM_MONTH $ATM_DAY $ATM_SECONDS (seconds)" +echo "valid time of model is $ATM_YEAR $ATM_MONTH $ATM_DAY $ATM_HOUR (hours)" + +#------------------------------------------------------------------------- +# Determine if current time is a perfect model time. +# If not, return before doing anything. +#------------------------------------------------------------------------- + +## TIMECHECK: +if ( $ATM_HOUR == 0 || $ATM_HOUR == 6 || $ATM_HOUR == 12 || $ATM_HOUR == 18) then + echo "Hour is $ATM_HOUR so we are generating perfect obs for the atmosphere" +else + echo "Hour is not 0,6,12 or 18Z so we are skipping generating perfect obs for the atmosphere" + echo "`date` -- END CAM_ASSIMILATE" + exit 0 +endif + +#------------------------------------------------------------------------- +# Create temporary working directory for the perfect model and go there +#------------------------------------------------------------------------- + +set temp_dir = pmo_cam +echo "temp_dir is $temp_dir" + +if ( -d $temp_dir ) then + ${REMOVE} $temp_dir/* +else + mkdir -p $temp_dir +endif +cd $temp_dir + +#----------------------------------------------------------------------------- +# Get observation sequence file ... or die right away. +# The observation file names have a time that matches the stopping time of CAM. +#----------------------------------------------------------------------------- + +set YYYYMM = `printf %04d%02d ${ATM_YEAR} ${ATM_MONTH}` +set OBSFNAME = `printf obs_seq%04d%02d%02d%02d ${ATM_YEAR} ${ATM_MONTH} ${ATM_DAY} ${ATM_HOUR}` +set OBS_FILE = ${BASEOBSDIR}/${YYYYMM}_6H/${OBSFNAME} + +if ( -e ${OBS_FILE} ) then + ${LINK} ${OBS_FILE} obs_seq.in +else + echo "ERROR ... no observation file $OBS_FILE" + echo "ERROR ... no observation file $OBS_FILE" + exit -1 +endif + +#========================================================================= +# Block 1: Populate a run-time directory with the input needed to run DART. +#========================================================================= + +echo "`date` -- BEGIN COPY BLOCK" + +if ( -e ${CASEROOT}/cam_input.nml ) then + ${COPY} ${CASEROOT}/cam_input.nml input.nml +else + echo "ERROR ... DART required file ${CASEROOT}/cam_input.nml not found ... ERROR" + echo "ERROR ... DART required file ${CASEROOT}/cam_input.nml not found ... ERROR" + exit -2 +endif + +echo "`date` -- END COPY BLOCK" + +#========================================================================= +# Block 2: Convert 1 CAM restart file to DART initial conditions file. +# At the end of the block, we have DART initial condition file perfect_ics +# that came from pointer file ../rpointer.atm_0001 +# +# REQUIRED DART namelist settings: +# &perfect_model_obs_nml: restart_in_file_name = 'perfect_ics' +# &cam_to_dart_nml: cam_to_dart_output_file = 'dart_ics' +#========================================================================= + +echo "`date` -- BEGIN CAM-TO-DART" + +set member = 1 + + set MYTEMPDIR = member_${member} + mkdir -p $MYTEMPDIR + cd $MYTEMPDIR + + # Turns out the .h0. files are timestamped with the START of the + # run, which is *not* ATM_DATE_EXT ... I just link to a whatever + # is convenient (since the info is static). + # make sure there are no old output logs hanging around + $REMOVE output.${member}.cam_to_dart + + set ATM_INITIAL_FILENAME = "../../${CASE}.cam.i.${ATM_DATE_EXT}.nc" + set ATM_HISTORY_FILENAME = `ls -1t ../../${CASE}.cam*.h0.* | head -n 1` + set DART_IC_FILENAME = `printf filter_ics.%04d ${member}` + set DART_RESTART_FILE = `printf filter_restart.%04d ${member}` + + sed -e "s#dart_ics#../${DART_IC_FILENAME}#" \ + -e "s#dart_restart#../${DART_RESTART_FILE}#" < ../input.nml >! input.nml + + ${LINK} $ATM_INITIAL_FILENAME caminput.nc + ${LINK} $ATM_HISTORY_FILENAME cam_phis.nc + + ${EXEROOT}/cam_to_dart >! output.${member}.cam_to_dart + + if ($status != 0) then + echo "ERROR ... DART died in 'cam_to_dart' ... ERROR" + echo "ERROR ... DART died in 'cam_to_dart' ... ERROR" + exit -6 +endif + +echo "`date` -- END CAM-TO-DART" + +#========================================================================= +# Block 3: Advance the model and harvest the synthetic observations. +# Will result in a single file : 'perfect_restart' which we don't need +# for a perfect model experiment with CESM. +# +# DART namelist settings required: +# &perfect_model_obs_nml: async = 0, +# &perfect_model_obs_nml: adv_ens_command = "./no_model_advance.csh", +# &perfect_model_obs_nml: restart_in_file_name = 'perfect_ics' +# &perfect_model_obs_nml: restart_out_file_name = 'perfect_restart' +# &perfect_model_obs_nml: obs_sequence_in_name = 'obs_seq.in' +# &perfect_model_obs_nml: obs_sequence_out_name = 'obs_seq.out' +# &perfect_model_obs_nml: init_time_days = -1, +# &perfect_model_obs_nml: init_time_seconds = -1, +# &perfect_model_obs_nml: first_obs_days = -1, +# &perfect_model_obs_nml: first_obs_seconds = -1, +# &perfect_model_obs_nml: last_obs_days = -1, +# &perfect_model_obs_nml: last_obs_seconds = -1, +# +#========================================================================= + +# CAM:static_init_model() always needs a caminput.nc and a cam_phis.nc +# for geometry information, etc. + +set ATM_INITIAL_FILENAME = ../${CASE}.cam.i.${ATM_DATE_EXT}.nc +set ATM_HISTORY_FILENAME = `ls -1t ../${CASE}.cam*.h0.* | head -n 1` + +${LINK} $ATM_INITIAL_FILENAME caminput.nc +${LINK} $ATM_HISTORY_FILENAME cam_phis.nc + +echo "`date` -- BEGIN CAM PERFECT_MODEL_OBS" +${LAUNCHCMD} ${EXEROOT}/perfect_model_obs_cam || exit -7 +echo "`date` -- END CAM PERFECT_MODEL_OBS" + +${MOVE} Prior_Diag.nc ../cam_Prior_Diag.${ATM_DATE_EXT}.nc +${MOVE} Posterior_Diag.nc ../cam_Posterior_Diag.${ATM_DATE_EXT}.nc +${MOVE} obs_seq.final ../cam_obs_seq.${ATM_DATE_EXT}.final +${MOVE} dart_log.out ../cam_dart_log.${ATM_DATE_EXT}.out + +#========================================================================= +# Block 4: Update the cam restart file +#========================================================================= + +# not needed ... perfect_model_obs does not update the model state. + +#========================================================================= +# Block 5: Link the next cam file to the static name needed here. +#========================================================================= + +cd ${RUNDIR} + + set ATM_INITIAL_FILENAME = ${CASE}.cam.i.${ATM_DATE_EXT}.nc + + ${LINK} ${ATM_INITIAL_FILENAME} cam_initial.nc || exit -9 + +end + +#------------------------------------------------------------------------- +# Cleanup +# we (DART) do not need these files, and CESM does not need them either +# to continue a run. if we remove them here they do not get moved to +# the short-term archiver. +#------------------------------------------------------------------------- + +# ${REMOVE} ${RUNDIR}/*.rh0.* +# ${REMOVE} ${RUNDIR}/*.rs1.* + +echo "`date` -- END GENERATE CAM TRUE STATE" + +exit 0 + +# +# $URL$ +# $Revision$ +# $Date$ + Property changes on: DART/trunk/models/CESM/shell_scripts/cam_perfect_model.csh ___________________________________________________________________ Added: svn:executable + * Added: svn:mime-type + text/plain Added: svn:keywords + Date Rev Author HeadURL Id Added: svn:eol-style + native Added: DART/trunk/models/CESM/shell_scripts/clm_perfect_model.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/clm_perfect_model.csh (rev 0) +++ DART/trunk/models/CESM/shell_scripts/clm_perfect_model.csh 2013-10-09 22:18:50 UTC (rev 6506) @@ -0,0 +1,290 @@ +#!/bin/csh +# +# DART software - Copyright 2004 - 2013 UCAR. This open source software is +# provided by UCAR, "as is", without charge, subject to all terms of use at +# http://www.image.ucar.edu/DAReS/DART/DART_download +# +# DART $Id$ + +# This block is an attempt to localize all the machine-specific +# changes to this script such that the same script can be used +# on multiple platforms. This will help us maintain the script. + +echo "`date` -- BEGIN GENERATE CLM TRUE STATE" + +set nonomatch # suppress "rm" warnings if wildcard does not match anything + +# The FORCE options are not optional. +# The VERBOSE options are useful for debugging though +# some systems don't like the -v option to any of the following +switch ("`hostname`") + case be*: + # NCAR "bluefire" + set MOVE = '/usr/local/bin/mv -fv' + set COPY = '/usr/local/bin/cp -fv --preserve=timestamps' + set LINK = '/usr/local/bin/ln -fvs' + set REMOVE = '/usr/local/bin/rm -fr' + + set BASEOBSDIR = /glade/proj3/image/Observations/FluxTower + breaksw + + case ys*: + # NCAR "yellowstone" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /glade/p/image/Observations/land + breaksw + + case lone*: + # UT lonestar + set MOVE = '/bin/mv -fv' + set COPY = '/bin/cp -fv --preserve=timestamps' + set LINK = '/bin/ln -fvs' + set REMOVE = '/bin/rm -fr' + + set BASEOBSDIR = ${WORK}/DART/observations/snow/work/obs_seqs + breaksw + + case la*: + # LBNL "lawrencium" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /your/observation/directory/here + breaksw + + default: + # NERSC "hopper" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /scratch/scratchdirs/nscollin/ACARS + breaksw +endsw + +#------------------------------------------------------------------------- +# Determine time of model state ... from file name of first member +# of the form "./${CASE}.clm2.r.2000-01-06-00000.nc" +# +# Piping stuff through 'bc' strips off any preceeding zeros. +#------------------------------------------------------------------------- + +set FILE = `head -n 1 rpointer.lnd` +set FILE = $FILE:r +set LND_DATE_EXT = `echo $FILE:e` +set LND_DATE = `echo $FILE:e | sed -e "s#-# #g"` +set LND_YEAR = `echo $LND_DATE[1] | bc` +set LND_MONTH = `echo $LND_DATE[2] | bc` +set LND_DAY = `echo $LND_DATE[3] | bc` +set LND_SECONDS = `echo $LND_DATE[4] | bc` +set LND_HOUR = `echo $LND_DATE[4] / 3600 | bc` + +echo "valid time of model is $LND_YEAR $LND_MONTH $LND_DAY $LND_SECONDS (seconds)" +echo "valid time of model is $LND_YEAR $LND_MONTH $LND_DAY $LND_HOUR (hours)" + +#------------------------------------------------------------------------- +# Determine if current time is an perfect model time. +# If not, return before doing anything. +#------------------------------------------------------------------------- + +## TIMECHECK: +if ( $LND_HOUR == 0 || $LND_HOUR == 6 || $LND_HOUR == 12 || $LND_HOUR == 18 ) then + echo "Hour is $LND_HOUR so we are generating perfect obs for the land" +else + echo "Hour is not 0,6,12 or 18Z so we are skipping generating perfect obs for the land" + echo "`date` -- END GENERATE TRUE STATE" + exit 0 +endif + +# we have flux tower observations which can be processed every 6 hours, +# but if you want to only processed at 0Z each day, change the LND_HOUR +# check to this one: +# if ( $LND_HOUR == 0 ) then +# and the message in the else clause to this: +# echo "Hour is not 0Z so we are skipping generating perfect obs for the land" + +#------------------------------------------------------------------------- +# Create temporary working directory for the perfect model and go there +#------------------------------------------------------------------------- + +set temp_dir = pmo_clm +echo "temp_dir is $temp_dir" + +if ( -d $temp_dir ) then + ${REMOVE} $temp_dir/* +else + mkdir -p $temp_dir +endif +cd $temp_dir + +#----------------------------------------------------------------------------- +# Get observation sequence file ... or die right away. +# The observation file names have a time that matches the stopping time of CLM. +# +# The CLM observations are stowed in two sets of directories. +# If you are stopping every 24 hours or more, the obs are in directories like YYYYMM. +# In all other situations the observations come from directories like YYYYMM_6H. +# The only ugly part here is if the first advance and subsequent advances are +# not the same length. The observations _may_ come from different directories. +# +# The contents of the file must match the history file contents if one is using +# the obs_def_tower_mod or could be the 'traditional' +/- 12Z ... or both. +# Since the history file contains the previous days' history ... so must the obs file. +#----------------------------------------------------------------------------- + +if ($STOP_N >= 24) then + set OBSDIR = `printf %04d%02d ${LND_YEAR} ${LND_MONTH}` +else + set OBSDIR = `printf %04d%02d_6H ${LND_YEAR} ${LND_MONTH}` +endif + +set OBS_FILE = ${BASEOBSDIR}/${OBSDIR}/obs_seq.${LND_DATE_EXT} + +if ( -e ${OBS_FILE} ) then + ${COPY} ${OBS_FILE} obs_seq.in +else + echo "ERROR ... no observation file $OBS_FILE" + echo "ERROR ... no observation file $OBS_FILE" + exit -1 +endif + +#========================================================================= +# Block 1: Populate a run-time directory with the input needed to run DART. +#========================================================================= + +echo "`date` -- BEGIN COPY BLOCK" + +if ( -e ${CASEROOT}/clm_input.nml ) then + ${COPY} ${CASEROOT}/clm_input.nml input.nml +else + echo "ERROR ... DART required file ${CASEROOT}/clm_input.nml not found ... ERROR" + echo "ERROR ... DART required file ${CASEROOT}/clm_input.nml not found ... ERROR" + exit -2 +endif + +echo "`date` -- END COPY BLOCK" + +#========================================================================= +# Block 2: convert 1 clm restart file to a DART initial conditions file. +# At the end of the block, we have a DART restart file perfect_ics +# that came from the pointer file ../rpointer.lnd_0001 +# +# DART namelist settings appropriate/required: +# &perfect_model_obs_nml: restart_in_file_name = 'perfect_ics' +# &clm_to_dart_nml: clm_to_dart_output_file = 'dart_ics' +#========================================================================= + +echo "`date` -- BEGIN CLM-TO-DART" + +set member = 1 + + set MYTEMPDIR = member_${member} + mkdir -p $MYTEMPDIR + cd $MYTEMPDIR + + # make sure there are no old output logs hanging around + $REMOVE output.${member}.clm_to_dart + + set LND_RESTART_FILENAME = ${CASE}.clm2.r.${LND_DATE_EXT}.nc + set LND_HISTORY_FILENAME = ${CASE}.clm2.h0.${LND_DATE_EXT}.nc + set OBS1_HISTORY_FILENAME = ${CASE}.clm2.h1.${LND_DATE_EXT}.nc + set OBS2_HISTORY_FILENAME = ${CASE}.clm2_0001.h1.${LND_DATE_EXT}.nc + set DART_IC_FILENAME = perfect_ics + + sed -e "s/dart_ics/..\/${DART_IC_FILENAME}/" < ../input.nml >! input.nml + + ${LINK} ../../$LND_RESTART_FILENAME clm_restart.nc + ${LINK} ../../$LND_HISTORY_FILENAME clm_history.nc + + if (-e $OBS1_HISTORY_FILENAME) then + ${LINK} ../../$OBS1_HISTORY_FILENAME $OBS2_HISTORY_FILENAME + endif + + # patch the CLM restart files to ensure they have the proper + # _FillValue and missing_value attributes. +# ncatted -O -a _FillValue,frac_sno,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a missing_value,frac_sno,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a _FillValue,DZSNO,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a missing_value,DZSNO,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a _FillValue,H2OSOI_LIQ,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a missing_value,H2OSOI_LIQ,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a _FillValue,H2OSOI_ICE,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a missing_value,H2OSOI_ICE,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a _FillValue,T_SOISNO,o,d,1.0e+36 clm_restart.nc +# ncatted -O -a missing_value,T_SOISNO,o,d,1.0e+36 clm_restart.nc + + ${EXEROOT}/clm_to_dart >! output.${member}.clm_to_dart + + if ($status != 0) then + echo "ERROR ... DART died in 'clm_to_dart' ... ERROR" + echo "ERROR ... DART died in 'clm_to_dart' ... ERROR" + exit -3 + endif + + cd .. + +echo "`date` -- END CLM-TO-DART" + +#========================================================================= +# Block 3: Advance the model and harvest the synthetic observations. +# Will result in a single file : 'perfect_restart' which we don't need +# for a perfect model experiment with CESM. +# +# DART namelist settings required: +# &perfect_model_obs_nml: async = 0, +# &perfect_model_obs_nml: adv_ens_command = "./no_model_advance.csh", +# &perfect_model_obs_nml: restart_in_file_name = 'perfect_ics' +# &perfect_model_obs_nml: restart_out_file_name = 'perfect_restart' +# &perfect_model_obs_nml: obs_sequence_in_name = 'obs_seq.in' +# &perfect_model_obs_nml: obs_sequence_out_name = 'obs_seq.out' +# &perfect_model_obs_nml: init_time_days = -1, +# &perfect_model_obs_nml: init_time_seconds = -1, +# &perfect_model_obs_nml: first_obs_days = -1, +# &perfect_model_obs_nml: first_obs_seconds = -1, +# &perfect_model_obs_nml: last_obs_days = -1, +# &perfect_model_obs_nml: last_obs_seconds = -1, +# +#========================================================================= + +# clm always needs a clm_restart.nc, clm_history.nc for geometry information, etc. + +set LND_RESTART_FILENAME = ${CASE}.clm2.r.${LND_DATE_EXT}.nc +set LND_HISTORY_FILENAME = ${CASE}.clm2.h0.${LND_DATE_EXT}.nc + +${LINK} ../$LND_RESTART_FILENAME clm_restart.nc +${LINK} ../$LND_HISTORY_FILENAME clm_history.nc + +echo "`date` -- BEGIN CLM PERFECT_MODEL_OBS" +${EXEROOT}/perfect_model_obs_clm || exit -4 +echo "`date` -- END CLM PERFECT_MODEL_OBS" + +${MOVE} True_State.nc ../clm_True_State.${LND_DATE_EXT}.nc +${MOVE} obs_seq.out ../clm_obs_seq.${LND_DATE_EXT}.out +${MOVE} dart_log.out ../clm_dart_log.${LND_DATE_EXT}.out + +#========================================================================= +# Block 4: Update the clm restart files. +#========================================================================= + +# not needed ... perfect_model_obs does not update the model state. + +#------------------------------------------------------------------------- +# Cleanup +#------------------------------------------------------------------------- + +echo "`date` -- END GENERATE CLM TRUE STATE" + +exit 0 + +# +# $URL$ +# $Revision$ +# $Date$ + Property changes on: DART/trunk/models/CESM/shell_scripts/clm_perfect_model.csh ___________________________________________________________________ Added: svn:executable + * Added: svn:mime-type + text/plain Added: svn:keywords + Date Rev Author HeadURL Id Added: svn:eol-style + native Copied: DART/trunk/models/CESM/shell_scripts/pop_perfect_model.csh (from rev 6501, DART/trunk/models/CESM/shell_scripts/run_perfect_model_obs.csh) =================================================================== --- DART/trunk/models/CESM/shell_scripts/pop_perfect_model.csh (rev 0) +++ DART/trunk/models/CESM/shell_scripts/pop_perfect_model.csh 2013-10-09 22:18:50 UTC (rev 6506) @@ -0,0 +1,237 @@ +#!/bin/csh +# +# DART software - Copyright 2004 - 2013 UCAR. This open source software is +# provided by UCAR, "as is", without charge, subject to all terms of use at +# http://www.image.ucar.edu/DAReS/DART/DART_download +# +# DART $Id$ + +# This block is an attempt to localize all the machine-specific +# changes to this script such that the same script can be used +# on multiple platforms. This will help us maintain the script. +# Search below for TIMECHECK to see what times this script will +# evaluate obs. + +echo "`date` -- BEGIN GENERATE POP TRUE STATE" + +set nonomatch # suppress "rm" warnings if wildcard does not match anything + +# The FORCE options are not optional. +# The VERBOSE options are useful for debugging though +# some systems don't like the -v option to any of the following +switch ("`hostname`") + case be*: + # NCAR "bluefire" + set MOVE = '/usr/local/bin/mv -fv' + set COPY = '/usr/local/bin/cp -fv --preserve=timestamps' + set LINK = '/usr/local/bin/ln -fvs' + set REMOVE = '/usr/local/bin/rm -fr' + + set BASEOBSDIR = /glade/proj3/image/Observations/WOD09 + breaksw + + case ys*: + # NCAR "yellowstone" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /glade/p/image/Observations/WOD09 + breaksw + + default: + # NERSC "hopper" + set MOVE = 'mv -fv' + set COPY = 'cp -fv --preserve=timestamps' + set LINK = 'ln -fvs' + set REMOVE = 'rm -fr' + + set BASEOBSDIR = /scratch/scratchdirs/nscollin/ACARS + breaksw +endsw + +#------------------------------------------------------------------------- +# Determine time of model state ... from file name of first member +# of the form "./${CASE}.pop.r.2000-01-06-00000.nc" +# +# Piping stuff through 'bc' strips off any preceeding zeros. +#------------------------------------------------------------------------- + +set FILE = `head -n 1 rpointer.ocn.restart` +set FILE = $FILE:t +set FILE = $FILE:r +set OCN_DATE_EXT = `echo $FILE:e` +set OCN_DATE = `echo $FILE:e | sed -e "s#-# #g"` +set OCN_YEAR = `echo $OCN_DATE[1] | bc` +set OCN_MONTH = `echo $OCN_DATE[2] | bc` +set OCN_DAY = `echo $OCN_DATE[3] | bc` +set OCN_SECONDS = `echo $OCN_DATE[4] | bc` +set OCN_HOUR = `echo $OCN_DATE[4] / 3600 | bc` + +echo "valid time of model is $OCN_YEAR $OCN_MONTH $OCN_DAY $OCN_SECONDS (seconds)" +echo "valid time of model is $OCN_YEAR $OCN_MONTH $OCN_DAY $OCN_HOUR (hours)" + +#------------------------------------------------------------------------- +# Determine if current time is 0Z - if so, generate perfect obs. +# If not, return before doing anything. +#------------------------------------------------------------------------- + +## TIMECHECK: +if ( $OCN_HOUR == 0 ) then + echo "Hour is $OCN_HOUR so we are generating perfect obs for the ocean" +else + echo "Hour is not 0Z so we are skipping generating perfect obs for the ocean" + echo "`date` -- END GENERATE TRUE STATE" + exit 0 +endif + +#------------------------------------------------------------------------- +# Create temporary working directory for the perfect model and go there +#------------------------------------------------------------------------- + +set temp_dir = pmo_pop +echo "temp_dir is $temp_dir" + +if ( -d $temp_dir ) then + ${REMOVE} $temp_dir/* +else + mkdir -p $temp_dir +endif +cd $temp_dir + +#----------------------------------------------------------------------------- +# Get observation sequence file ... or die right away. +# The observation file names have a time that matches the stopping time of POP. +#----------------------------------------------------------------------------- + +set YYYYMM = `printf %04d%02d ${OCN_YEAR} ${OCN_MONTH}` +set OBSFNAME = `printf obs_seq.0Z.%04d%02d%02d ${OCN_YEAR} ${OCN_MONTH} ${OCN_DAY}` +set OBS_FILE = ${BASEOBSDIR}/${YYYYMM}/${OBSFNAME} + +if ( -e ${OBS_FILE} ) then + ${COPY} ${OBS_FILE} obs_seq.in +else + echo "ERROR ... no observation file $OBS_FILE" + echo "ERROR ... no observation file $OBS_FILE" + exit -1 +endif + +#========================================================================= +# Block 1: Populate a run-time directory with the input needed to run DART. +#========================================================================= + +echo "`date` -- BEGIN COPY BLOCK" + +if ( -e ${CASEROOT}/input.nml ) then + ${COPY} ${CASEROOT}/input.nml . +else + echo "ERROR ... DART required file ${CASEROOT}/input.nml not found ... ERROR" + echo "ERROR ... DART required file ${CASEROOT}/input.nml not found ... ERROR" + exit -2 +endif + +echo "`date` -- END COPY BLOCK" + +# Eat the cookie regardless +${REMOVE} ../pop_inflation_cookie + +#========================================================================= +# Block 2: convert 1 pop restart file to a DART initial conditions file. +# At the end of the block, we have a DART restart file perfect_ics +# that came from the pointer file ../rpointer.ocn.restart +# +# DART namelist settings appropriate/required: +# &perfect_model_obs_nml: restart_in_file_name = 'perfect_ics' +# &pop_to_dart_nml: pop_to_dart_output_file = 'dart_ics' +#========================================================================= + +echo "`date` -- BEGIN POP-TO-DART" + +set member = 1 + + set MYTEMPDIR = member_${member} + mkdir -p $MYTEMPDIR + cd $MYTEMPDIR + + # make sure there are no old output logs hanging around + $REMOVE output.${member}.pop_to_dart + + set OCN_RESTART_FILENAME = ${CASE}.pop.r.${OCN_DATE_EXT}.nc + set OCN_NML_FILENAME = pop2_in + set DART_IC_FILENAME = perfect_ics + set DART_RESTART_FILE = perfect_restart + + sed -e "s#dart_ics#../${DART_IC_FILENAME}#" \ + -e "s#dart_restart#../${DART_RESTART_FILE}#" < ../input.nml >! input.nml + + ${LINK} ../../$OCN_RESTART_FILENAME pop.r.nc + ${LINK} ../../$OCN_NML_FILENAME pop_in + + ${EXEROOT}/pop_to_dart >! output.${member}.pop_to_dart + + if ($status != 0) then + echo "ERROR ... DART died in 'pop_to_dart' ... ERROR" + echo "ERROR ... DART died in 'pop_to_dart' ... ERROR" + exit -3 + endif + + cd .. + +echo "`date` -- END POP-TO-DART" + +#========================================================================= +# Block 3: Advance the model and harvest the synthetic observations. +# Will result in a single file : 'perfect_restart' which we don't need +# for a perfect model experiment with CESM. +# +# DART namelist settings required: +# &perfect_model_obs_nml: async = 0, +# &perfect_model_obs_nml: adv_ens_command = "./no_model_advance.csh", +# &perfect_model_obs_nml: restart_in_file_name = 'perfect_ics' +# &perfect_model_obs_nml: restart_out_file_name = 'perfect_restart' +# &perfect_model_obs_nml: obs_sequence_in_name = 'obs_seq.in' +# &perfect_model_obs_nml: obs_sequence_out_name = 'obs_seq.out' +# &perfect_model_obs_nml: init_time_days = -1, +# &perfect_model_obs_nml: init_time_seconds = -1, +# &perfect_model_obs_nml: first_obs_days = -1, +# &perfect_model_obs_nml: first_obs_seconds = -1, +# &perfect_model_obs_nml: last_obs_days = -1, +# &perfect_model_obs_nml: last_obs_seconds = -1, +# +#========================================================================= + +# POP always needs a pop_in and a pop.r.nc to start. + +set OCN_RESTART_FILENAME = ${CASE}.pop.r.${OCN_DATE_EXT}.nc + +${LINK} ../$OCN_RESTART_FILENAME pop.r.nc +${LINK} ../pop2_in pop_in + +echo "`date` -- BEGIN PERFECT_MODEL_OBS" +${EXEROOT}/perfect_model_obs || exit -4 +echo "`date` -- END PERFECT_MODEL_OBS" + +${MOVE} True_State.nc ../pop_True_State.${OCN_DATE_EXT}.nc +${MOVE} obs_seq.out ../pop_obs_seq.${OCN_DATE_EXT}.out +${MOVE} dart_log.out ../pop_dart_log.${OCN_DATE_EXT}.out + +#========================================================================= +# Block 4: Update the pop restart files. +#========================================================================= + +# not needed ... perfect_model_obs does not update the model state. + +#------------------------------------------------------------------------- +# Cleanup +#------------------------------------------------------------------------- + +echo "`date` -- END GENERATE POP TRUE STATE" + +exit 0 + +# +# $URL$ +# $Revision$ +# $Date$ + From nancy at ucar.edu Wed Oct 9 16:31:00 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 16:31:00 -0600 Subject: [Dart-dev] [6507] DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh: no need for a separate MYCASE since we're called from Message-ID: Revision: 6507 Author: nancy Date: 2013-10-09 16:31:00 -0600 (Wed, 09 Oct 2013) Log Message: ----------- no need for a separate MYCASE since we're called from the CESM scripts which already define CASE for is. Modified Paths: -------------- DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh -------------- next part -------------- Modified: DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh =================================================================== --- DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh 2013-10-09 22:18:50 UTC (rev 6506) +++ DART/trunk/models/CESM/shell_scripts/cam_no_assimilate.csh 2013-10-09 22:31:00 UTC (rev 6507) @@ -36,7 +36,6 @@ set FILE = `head -n 1 rpointer.atm_0001` set FILE = $FILE:t set FILE = $FILE:r -set MYCASE = `echo $FILE | sed -e "s#\..*##"` set ATM_DATE_EXT = `echo $FILE:e` #========================================================================= @@ -52,7 +51,7 @@ set inst_string = `printf _%04d $member` - set ATM_INITIAL_FILENAME = ${MYCASE}.cam${inst_string}.i.${ATM_DATE_EXT}.nc + set ATM_INITIAL_FILENAME = ${CASE}.cam${inst_string}.i.${ATM_DATE_EXT}.nc ${LINK} ${ATM_INITIAL_FILENAME} cam_initial${inst_string}.nc || exit -9 From nancy at ucar.edu Wed Oct 9 16:37:21 2013 From: nancy at ucar.edu (nancy at ucar.edu) Date: Wed, 09 Oct 2013 16:37:21 -0600 Subject: [Dart-dev] [6508] DART/trunk/ensemble_manager/ensemble_manager_mod.html: change
to
to make html checker happy. Message-ID: Revision: 6508 Author: nancy Date: 2013-10-09 16:37:21 -0600 (Wed, 09 Oct 2013) Log Message: ----------- change
to
to make html checker happy. ditto with adding a 'summary' tag to all s. also removed unneeded s to make the routine argument tables more legible. doesn't seem to affect the resulting output in any way. Modified Paths: -------------- DART/trunk/ensemble_manager/ensemble_manager_mod.html -------------- next part -------------- Modified: DART/trunk/ensemble_manager/ensemble_manager_mod.html =================================================================== --- DART/trunk/ensemble_manager/ensemble_manager_mod.html 2013-10-09 22:31:00 UTC (rev 6507) +++ DART/trunk/ensemble_manager/ensemble_manager_mod.html 2013-10-09 22:37:21 UTC (rev 6508) @@ -11,7 +11,7 @@

MODULE ensemble_manager_mod

@@ -225,7 +225,7 @@

Routine	Message	Comment
xxxx
Revision:	$Revision$
Source:	$URL$
Change Date:	$Date$
Change history:	try "svn log" or "svn diff"
Change history:	try "svn log" or "svn diff"

Item	Type	Description
' // trim(arg_name(i)) // '	' // trim(arg_type(i)) // '	' // trim(c1) // '
' // trim(arg_name(i)) // '	' // trim(arg_type(i)) // '	' // trim(c1) // '

Component	Description
' // trim(item_name(i)) // '	' // trim(c1) // '

filename	purpose
input.nml

Routine	Message	Comment
comp_cov_factor
Revision:	$Revision$
Source:	$URL$
Change Date:	$Date$
Change history:	try "svn log" or "svn diff"
Change history:	try "svn log" or "svn diff"

Contents	Type	Description
ens_size	integer [default: 0]	The number of "i" and "j" rows processed each time the - modular physics is called.
spin_up_steps	integer	the month
num_steps	real(r8)	the day-of-month
output_start	real(r4)	the hour-of-day
ens_spin_up_steps	real(r4)	the minute
obs_freq,	real(r4)	the second
cov_inflate	real(r8)	uniformly monotonic time
mean_inflate	character(len=80)	the type of calendar being used
restart	integer	the type of calendar being used
add_on	integer	the type of calendar being used
noise_amp	integer	the type of calendar being used
name	type	(often multi-line) description +

Component	Description
Component	Description
x	is the nondimensional distance [0,1]
x	is the nondimensional distance [0,1]

Component	Description
year	the (non-negative) year
month	the month
day	the day-of-month
hour	the hour-of-day
minute	the minute
second	the second
umt	uniformly monotonic time
calendar	the type of calendar being used

filename	purpose
inputfile1	to read some input
input.nml
dart_log.nml [default name]	the record of all the namelists actually USED - contains the default values

var	Weighting factor.
z_in	Location of target.
target_kind	Generic kind of target.
localization_override
localization_override	Controls localization type if present. Same values as for namelist control.

var1	is the number of spark plugs in a '67 Cuda.
var2	is used for both input and output. Upon input, this contains the furlongs per weekday for every vertical level. Upon exit, we now have the number of - spotted gobies per square hectare at that level.
var3
var3	The leftmost dimension pertains to the number of feet in an orange-footed brush fowl, indiginous to Australia. The next dimension is the number of - feathers on said fowl, naturally.
global	is really, REALLY useful in certain situations.
global	is really, REALLY useful in certain situations.

var1	the first time you changed your oil.
var2
var2	miles between every oil change you've ever done. Don't lie.
var3
var3	the distances you've ridden. Each row corresponds to the hour-of-day, each column is a different day-of-the-week.
bob
bob	mean time between failures. in msec.
var
yyroutine2	number of gray hairs as a function of time. in kilohairs.

' // trim(arg_name(i)) // & - '	' // trim(c1) // '
' // trim(arg_name(i)) // & + '	Function return value. ' // trim(c1) // '	' // trim(c1) // '

ens_handle	Handle of ensemble.
start_copy
start_copy	Global index of first of continguous set of copies to be read.
end_copy
end_copy	Global index of last of contiguous set of copies to be read, copies(start_copy:end_copy).
start_from_restart
start_from_restart	If true, read all copies from file. If false, read one copy and perturb to get required number.
file_name
file_name	Name of file from which to read.
init_time
init_time	If present, set time of all copies read to this value.
force_single_file
force_single_file	If present and true, force the read to be from a single file which contains all copies.

ERROR CODES and CONDITIONS

FUTURE PLANS

PRIVATE COMPONENTS

Terms of Use

Description

NAMELIST

Discussion

Description

PROGRM OR MODULE name_of_thing

NAMELIST

MODULES USED

PUBLIC INTERFACES

MODULE ensemble_manager_mod

Overview

One-shot execution

Installation of the NCEP BUFR decoding program

Installation of the NCEP PREPBUFR decoding program

The decoding program: src/prepbufr.f

The blocking program blk_ublk/cwordsh

The blocking program blk_ublk/cword.x

Getting the NCEP Reanalysis BUFR format data from NCAR MSS.

Getting the NCEP Reanalysis PREPBUFR format data from NCAR HPSS.

Running the NCEP BUFR decoding program

Running the NCEP PREPBUFR decoding program

FILES

REFERENCES

ERROR CODES and CONDITIONS

KNOWN BUGS

FUTURE PLANS

PUBLIC INTERFACES

FILES

ERROR CODES and CONDITIONS

MODULE xxxxxxx

PROGRM OR MODULE name_of_thing

NAMELIST

OTHER MODULES USED

PUBLIC INTERFACES

FILES

REFERENCES

use ' // trim(module_name), ', only :	'//trim(item_name)//'
	'//trim(item_name)//'

ens_handle	Handle for the ensemble being initialized
num_copies

receiving_pe	This process ends up with the requested copy of the state vector.
ens_handle
ens_handle	Handle for ensemble.
copy
copy	The global index of the copy of the state vector that is to be retrieved.
vars
vars	One dimensional array in which the requested copy of the state vector is returned. Data is only returned in vars on the receiving PE; vars on all other PEs is unset.
mtime
mtime	If present returns the time of the requested copy.

sending_pe	This process sends the copy of the state vector.
ens_handle
ens_handle	Handle for ensemble.
copy
copy	The global index of the copy of the state vector that is to be sent.
vars
vars	One dimensional array in which the requested copy of the state vector is located. Only the data in vars on the sending PE is processed; vars on all other PEs is ignored.
mtime
mtime	If present send the time of the copy.

ens_handle	Handle for ensemble.
indx
indx	The local index of the copy of the state vector that is to be set.
mtime
mtime	The time to set for this copy.

var	Returns the number of copies stored by this process when storing all variables for a subset of copies.
ens_handle
ens_handle	Handle for an ensemble.

var	Returns the number of vars stored by this process when storing all copies of a subset of variables.
ens_handle
ens_handle	Handle for an ensemble.

ens_handle	Handle for an ensemble.
copies
copies	List of all copies stored by this process when storing subset of copies of all variables.

copy_number	Global index of a copy from an ensemble.
owner	Process Element (PE) that stores this copy when each has all variables of a subset of copies.
owners_index
owners_index	Local storage index for this copy on the owning process.

var_number	Global index of a variable in the vector from an ensemble.
owner	Process Element (PE) that stores this variable when each has all copies of subset of variables.
owners_index
owners_index	Local storage index for this variable on the owning process.

use xxxxxxx, only :	yyypubtype1
	yyyroutine1

ens_handle	The handle of the ensemble being transposed.
label
label	A character string label. If present, a timestamp with this label is printed at the start and end of the transpose.

var	Returns the largest number of copies any an individual PE when var complete.
num_copies
num_copies	Total number of copies in the ensemble.

var	Returns the largest number of vars any an individual PE when copy complete.
num_copies
num_copies	Total number of vars in an ensemble vector.

num_vars
pe
pe
var_list(:)
var_list(:)
pes_num_vars
pes_num_vars

num_copies
pe
pe
copy_list(:)
copy_list(:)
pes_num_copies
pes_num_copies

msg	character string to prepend to the time info
sync
sync	if present and true, execute an MPI_Barrier() to sync all MPI tasks before printing the time. this means the time will be the value of the slowest of the tasks to reach this point.
alltasks
alltasks	if present and true, have all tasks print out a timestamp. the default is for just task 0 to print. the usual combination is either sync=true and alltasks=false, or sync=false and alltasks=true. @@ -1909,12 +1911,12 @@

ens_handle	The derived type to print information about.
force
force	If the debug namelist item is false, set this to true to enable printing.
label
label	Optional string label to print to provide context for the output.