Added batch templated

src/CMORlight/control_cmor.ini

@@ -1 +1 @@
-control_cmor_FPS1999.ini
+control_cmor_FPS1999_batch.ini

src/CMORlight/control_cmor_FPS1995_batch.ini

@@ -0,0 +1,324 @@
+#
+# configuration file to control the processing
+#
+# Lists must be comma-separated without spaces
+#
+# 2016,2017 DKRZ, Hans Ramthun, ETHZ Matthias Göbel
+# 2020      MET Norway, Andreas Dobler
+#
+################################################################################################
+[settings]
+#tag used as extension for the simulation specific settings (e.g. settings_CCLM) lower down
+simulation=HCLIM
+
+
+# path settings
+#change DataPath and BasePath; the other paths can be left as they are
+
+#base path for DirIn, DirOut, DirWork and DirDerotated; leave this empty if you want to specify absolute paths below
+DataPath=/home/sm_anddo/CORDEX-FPS/HCLIM2CMOR_clean/data
+
+#base path for DirConfig and DirLog; leave this empty if you want to specify absolute paths below
+BasePath=/home/sm_anddo/CORDEX-FPS/HCLIM2CMOR_clean
+
+#Paths relative to BasePath
+#where the parameter table, the coordinates file and the vertices file are located
+DirConfig=src/CMORlight/Config
+#for logging
+DirLog=logs/cmorlight
+
+#Paths relative to Dataath:
+#Input directory for processing
+DirIn=work/input_CMORlight/FcpECE1995/
+#Output directory
+DirOut=OUT
+#directory for temporary files
+DirWork=temp_batch
+#where the derotated
+DirDerotated=work/output_derotated
+
+#######################################################################################################################################################################################
+#
+# IMPORTANT NOTE
+# The following list of global attributes
+# - contain the mandatory attributes necessary according to the CORDEX standard (see latest document on "CORDEX Arcive Desgin", March 2013
+# - additional optional attributes "invented" by Hans-Juergen Panitz
+#
+# This control_ini file cannot be used together with that CCLM2CMOR tool version, which has been built to follow the CLM-Community suggestions
+# for extended directory- and filenmae structures and extended list of global attributes for CMORization of data from a double-nest simulation
+#
+# By the way, the latest official version is that, which gives the possibilty to consider an additional sub-daily frequency, an implementation by Marie-Estelle
+# This is important because the user has to take this into account in his CSV table (input from $DirConfig - see above); this table now must have 30 columns
+#
+#  H.-J. Panitz, September 2020
+#
+########################################################################################################################################################################################
+
+#HJP March 2019 Begin
+#Global attributes that should be taken from this .ini file
+#----------------------------------------------------------
+# "global_attr_list" must not be empty.
+#
+# Mandatory attributes are:
+# project_id,driving_model_id,experiment_id,driving_experiment_name,driving_model_ensemble_member,CORDEX_domain,institute_id,model_id,rcm_version_id,contact
+#
+# All other attributes are optional.
+# Entries for listed attributes are defined in section 'settings' below; each attribute set in "global_attr_list" needs an entry/"value", otherwise the tool will stop.
+#
+# The attributes set in "global_attr_list" appear in the global attributes of the final file
+# The sequence of appearance in the file is determined by the sequence of their setting in this list
+
+global_attr_list=Conventions,conventionsURL,title,project_id,CORDEX_domain,driving_model_id,driving_experiment_name,experiment_id,driving_experiment,driving_model_ensemble_member,experiment,model_id,institute_id,institution,rcm_version_id,contact,nesting_levels,comment_nesting,comment,source,references
+#
+#HJP March 2019 End
+
+#global attributes that should be taken from .nc files if present; will overwrite settings from global_attr_list!
+global_attr_file=
+
+#list of variables to process if not specified in terminal
+varlist=
+
+#Supported output resolution : 1hr, 3hr, 6hr, day, mon, sem, fx
+#The desired output resolutions can be chosen by the option "-r". However, the "governing" setting comes from the CSV-table
+reslist=1hr,3hr,6hr,day,mon,sem,fx
+
+#list of variables to exclude from processing
+var_skip_list=
+
+#Subdirectory to put chunked files into, if not specified: chunks are placed in same folder as input files for chunking
+chunk_into=
+
+#name of the level type in the variables table if the variable is on pressure levels
+PModelType=PressureLevel
+#name of the level type in the variables table if the variable is on model levels
+MModelType=ModelLevel
+#HJP Mar 2010 Begin
+#name of the level type in the variables table if the variable is on Z levels
+ZModelType=ZLevel
+#HJP Mar 2010 End
+
+# type of cdo netcdf format
+cdo_nctype=nc4c
+
+#dimensions that should no be copied to output files
+varlist_reject=pressure,height_2m,height_10m,height_toa,soil1,soil1_bnds,height,plev,nb2,bnds,time_bnds
+
+#attributes that should no be copied to output files
+attrlist_reject=par,lvt,lev,tri
+
+#time units of output; for CORDEX: days since 1949-12-01 00:00:00 or equivalent
+units=days since 1994-12-01T00:00:00Z
+
+#time units of input if the units attribute is not correct
+alt_units=days since 1995-01-01T00:00:00Z
+
+
+
+################################################################################################
+[boolean]
+#if True: add /driving_model_id/driving_experiment_name (as defined below or given in function call) to the DirIn path
+extend_DirIn=False
+
+#Add version (default: current date; other values can be set in command line) to output path to not overwrite previously processed data
+add_version_to_outpath=False
+
+# compression of netcdf file: requested by CORDEX
+nc_compress=True
+
+# add vertices from extra file
+add_vertices=False
+
+# use different units for input data than written in units attribute (from entry 'alt_units' (in this file))
+use_alt_units=False
+################################################################################################
+[float]
+#value to set as missing value in output; should be 1.e+20
+missing_value=1.e+20
+
+################################################################################################
+[index]
+#column numbers in the variables table
+INDEX_RCM_NAME = 0
+INDEX_RCM_NAME_ORG = 1
+INDEX_VAR = 2
+INDEX_VAR_ROTATE = 4
+INDEX_MODEL_LEVEL = 5
+INDEX_CONVERT_FACTOR = 6
+#MED>> create column 7 for hourly information
+INDEX_VAR_CM_ASU = 7
+#MED<<
+INDEX_VAR_CM_SUB = 8
+INDEX_VAR_CM_DAY = 9
+INDEX_VAR_CM_MON = 10
+INDEX_VAR_CM_SEM = 11
+INDEX_VAL_LEV_MAX = 12
+INDEX_SOIL_LEV_CNT = 12
+INDEX_VAL_PLEV = 12
+INDEX_VAL_HEIGHT = 12
+INDEX_VAL_LEV = 12
+INDEX_UNIT = 13
+#MED>> create columns 14 and 15 for hourly frequency and aggregation method
+INDEX_FRE_ASU = 14
+#MED<<
+INDEX_FRE_SUB = 15
+INDEX_FRE_AGG = 16
+INDEX_FRE_DAY = 17
+INDEX_FRE_MON = 19
+INDEX_FRE_SEM = 21
+INDEX_FX=23
+INDEX_VAR_LONG_NAME = 24
+#HJP March 2019 Begin
+#Create index name for column 25 of CSV-table where one can include some explaining comment for a variable.
+#This explanation will be included in the output files as variables's attribute "comment".
+INDEX_VAR_COMMENT = 25
+#HJP March 2019 End
+INDEX_VAR_STD_NAME = 26
+INDEX_UP_DOWN = 27
+INDEX_REALM = 28
+INDEX_CM_AREA = 29
+
+
+################################################################################################
+[integer]
+
+# number of years in chunks for daily,monthly and seasonal resolution; the default values (5,10 and 10) are recommended
+#AGG_DAY must be 5 or less:
+AGG_DAY = 5
+#AGG_MON and AGG_SEM must be 10 or less
+AGG_MON = 10
+AGG_SEM = 10
+
+################################################################################################
+
+#simulation specific settings
+[settings_HCLIM]
+
+# file with lon/lat [and perhaps vertices]
+coordinates_file=coordinates_HCLIM_ALP3.nc
+
+# file with vertices [and perhaps lon/lat]
+vertices_file=
+
+#variables table
+vartable=FPS_Convection_HCLIM_variables_4_CMOR.csv
+
+#list of constant varibles
+var_list_fixed=orog,sftlf
+
+#######################
+# global attributes HCLIM
+#######################
+
+# define the attributes set in  "global_attr_list" (see above)
+# please note: ALL elements set in the "global_attr_list" must get a definition here; otherwise the CMOR-Tool will stop with an error message
+
+#mandatory attributes:
+#====================
+# Note that some mandatory global attributes are automatically generated by the CMOR tool: creation_date, frequency, product
+
+project_id=CORDEX-FPSCONV
+
+#driving model id: gcm_institute id + '-' + gcm_model_id; usually from http://cordex.dmi.dk/joomla/images/CORDEX/GCMModelName.txt
+driving_model_id=ICHEC-EC-EARTH
+
+#experiment_id: evaluation, historical, rcp85
+experiment_id=historical 
+
+#driving_experiment_name: evaluation or the experiment_id of the used CMIP experiment
+driving_experiment_name=historical
+
+#ensemble member of the driving CMIP experiment; r1i1p1 for evaluation runs
+driving_model_ensemble_member=r12i1p1
+
+#domain name as provided by CORDEX
+CORDEX_domain=ALP-3
+
+#institute id: usually from this list
+institute_id=HCLIMcom
+
+#rcm_model_id: rcm_institute_id + '-' + rcm_model_acronym; usually from http://cordex.dmi.dk/joomla/images/CORDEX/RCMModelName.txt
+model_id=HCLIMcom-HCLIM38-AROME
+
+#contact: email address
+contact[email protected]
+
+#rcm_version_id: identifies reruns with perturbed parameters or smaller RCM release upgrades;...
+#...differences between different rcm_version_id should be explained in the comments attribute or referred to in the source attribute
+rcm_version_id=fpsconv-x2yn2-v1
+
+# rcm_nesting_information within "rcm_version_id": 
+#  the contents of the mandatory attribute can be chosen freely.
+#  here, we give an example for data from the Convections FPS, therefore the additionsl prefix "fpsconv"
+#  The whole structure is according to agreements within the FPSC Community
+#
+#  Element describing the number of nesting levels (n)
+#  and possible differences between simulation setups for different nesting levels which cannot be indicated otherwise (x2)
+#  if such setup differences exist, this calls for extra flags, which is designated by a letter(s), being y,z,j or k
+#  The reason for the extra flags associated with x2 is due to the possibility that a model team may
+#  run more than one simulation with differences between nesting levels. In this case, without an extra
+#  flag, the filenames would be the same and this is not permitted.
+#
+#  v signifies the version of the simulation. This can be changed in the event of a rerun with an
+#  updated version of either the intermediate model or the cprcm
+#
+#  THE SPECIAL CASE OF DIRECT DOWNSCALING (1-nest approach) TO CP SCALES N.B.!
+#   Use x0n1-v1. The nesting flag is self-explanatory while the x0 is maybe redundant but signifies
+#   that the downscaling is direct from a GCM or Reanalysis product with no intermediate step.
+#
+#   SUMMARY OF NESTING INFORMATION
+#   One nest:                                                   use x0n1-v1
+#   Two nest, no differences in simulation setups of both runs: use x1n2-v1
+#   Two nest, differences between setups:                       use x2yn2-v1
+#   Two nest, additional differences between setups:            use x2yzn2-v1
+#
+
+
+#recommended but not mandatory  attributes:
+#======================
+# Note that some recommended global attributes are automatically generated by the CMOR tool: tracking_id
+
+driving_experiment=ICHEC-EC-EARTH, historical, r12i1p1  
+
+experiment=Historical scenario run with forcing from the downscaled ICHEC-EC-EARTH_r12i1p1 first nesting run
+
+#Conventions: used version of CF conventions
+Conventions=CF-1.4
+
+
+#optional attributes:
+#===================
+title=HCLIMcom-HCLIM38-AROME model output prepared for CORDEX FPS Convection
+
+institution=The HARMONIE Climate Modelling Community (HCLIM-Com)
+
+#nesting_levels: indicates the number of nests applied for the current simulation
+#nesting_levels=1: only one nest; corresponds to a direct downscaling approach
+#nesting_levels=2: 2 nest-approach; current simulation (= 2nd nest) is foreced by results of a first nest
+nesting_levels=2
+#
+comment_nesting=This data was produced by a two step nesting approach; The differences between the two steps (CPRCM 3km/RCM 12km) are the following. Dynamics: non-hydrostatic/hydrostatic. Physics package: AROME/ALADIN. Sub grid scale orography parameterisation: None/Z01D. Turbulence scheme: HARATU/CBR. Boundary condition update: 3-hourly/6-hourly
+
+comment=This simulation was performed by the Danish Meteorological Institute in collaboration with the HCLIM-Community
+
+#further optional global attributes
+#============================================================================
+conventionsURL=http://www.cfconventions.org
+
+source=HARMONIE Climate Modelling Community (HCLIM-Com)
+
+references=https://www.hirlam.org/trac/wiki/HarmonieClimate
+
+
+table_id=
+modeling_realm=
+initialization_method=
+physics_version=
+parent_id=
+
+#calendar: to specify calendar attribute of time variable IF NOT present or not correct in input files
+#calendar=360_day
+
+
+[settings_WRF]
+
+####