Noresm landsites

CONTRIBUTING.md

@@ -10,6 +10,9 @@ https://github.com/NorESMhub/INES_workshop_2020/blob/gh-pages/files/Torsvik_gitc
 # How to contribute
 We recommend that you open a new [discussion item](https://github.com/NorESMhub/NorESM/issues) if you have questions about code contribution, or an [issue](https://github.com/NorESMhub/NorESM/issues) to discuss specific changes or additions you want to include. This is done by selecting **New issue** in the top right corner of the issues page, and selecting one of the suggested issue types in the following menu. Through the issue discussion, you can work with the NorESM developers to implement the code changes in the correct repository and in the correct branch. 
 
+# Who can contribute
+Everybody with a github account can fork the repository, change a file and create a pull request, suggesting a change to the code or the documentation. The changes will, upon being merged by a member with write access, be visible to all. If you wish to have more access rights to any of the NorESMhub repositories, write to the NorESM team via email to noresm-ncc(at)met.no .
+
 ## Reporting bugs
 Please, ensure that the bug was not already reported by searching on https://github.com/NorESMhub/NorESM/issues
 

Externals.cfg

@@ -13,52 +13,98 @@ local_path = components/cice
 required = True
 
 [cime]
-local_path = cime
+tag = cime6.0.45
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.15
+local_path = cime
 required = True
 
 [cism]
-local_path = components/cism
+tag = cism2_1_69
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cism2_1_69
+local_path = components/cism
 externals = Externals_CISM.cfg
 required = True
 
 [clm]
-tag = ctsm5.1.dev090
+tag = ctsm5.1.dev108
 protocol = git
 repo_url = https://github.com/ESCOMP/CTSM.git
 local_path = components/clm
 externals = Externals_CLM.cfg
 required = True
 
+[mosart]
+tag = mosart1_0_45
+protocol = git
+repo_url = https://github.com/ESCOMP/MOSART
+local_path = components/mosart
+required = True
+
+[pop]
+tag = pop2_cesm2_1_rel_n01
+protocol = svn
+repo_url = https://svn-ccsm-models.cgd.ucar.edu/pop2/release_tags
+local_path = components/pop
+externals = Externals_POP.cfg
+required = False
+
+[blom]
+tag = v1.1.0
+protocol = git
+repo_url = https://github.com/NorESMhub/BLOM
+local_path = components/blom
+required = True
+
+[rtm]
+tag = rtm1_0_73
+protocol = git
+repo_url = https://github.com/ESCOMP/rtm
+local_path = components/rtm
+required = True
+
+[ww3]
+tag = ww3_cesm2_1_rel_01
+protocol = svn
+repo_url = https://svn-ccsm-models.cgd.ucar.edu/ww3/release_tags
+local_path = components/ww3
+required = False
+
+[norcpm]
+tag = cime5.6.10_cesm2_1_rel_06-Nor_v1.0.5
+protocol = git
+repo_url = [email protected]:NorESMhub/norcpm.git
+local_path = norcpm
+required = False
+
+[externals_description]
+schema_version = 1.0.0
+
 [cmeps]
-tag = cmeps0.13.47
+tag = cmeps0.13.71
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.41
+tag = cdeps0.12.63
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals = Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl7.0.12
+tag = cpl7.0.14
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.10
+tag = share1.0.12
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share
@@ -72,19 +118,12 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_6
+tag = pio2_5_7
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio
 required = True
 
-[mosart]
-local_path = components/mosart
-protocol = git
-repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_38
-required = True
-
 [mizuRoute]
 local_path = components/mizuRoute
 protocol = git
@@ -93,47 +132,8 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.15
+tag = ccs_config_cesm0.0.38
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
 required = True
-
-[pop]
-tag = pop2_cesm2_1_rel_n01
-protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/pop2/release_tags
-local_path = components/pop
-externals = Externals_POP.cfg
-required = False
-
-[blom]
-tag = v1.1.0
-protocol = git
-repo_url = https://github.com/NorESMhub/BLOM
-local_path = components/blom
-required = True
-
-[rtm]
-local_path = components/rtm
-protocol = git
-repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_73
-required = True
-
-[ww3]
-tag = ww3_cesm2_1_rel_01
-protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/ww3/release_tags
-local_path = components/ww3
-required = False
-
-[doc-builder]
-local_path = doc/doc-builder
-protocol = git
-repo_url = https://github.com/ESMCI/doc-builder
-tag = v1.0.5
-required = False
-
-[externals_description]
-schema_version = 1.0.0

doc/configurations/cmip6_compsets.rst

@@ -59,8 +59,8 @@ CMIP6 DECK Compsets
 
 For a detailed overview of case names, experiment setup, restart files etc. please see: 
 
-- NorESM2-MM: https://noresmhub.github.io/noresm-exp/noresm2_deck/noresm2_mm_deck.html 
-- NorESM2-LM: https://noresmhub.github.io/noresm-exp/noresm2_deck/noresm2_lm_deck.html
+- NorESM2-MM: https://noresmhub.github.io/noresm-exp/content/noresm2_deck/noresm2_mm_deck.html
+- NorESM2-LM: https://noresmhub.github.io/noresm-exp/content/noresm2_deck/noresm2_lm_deck.html
 
 CMIP6 Scenario compsets (only frc2 compsets):
 ^^^^^
@@ -70,13 +70,13 @@ CMIP6 Scenario compsets (only frc2 compsets):
 - **ssp370** : NSSP370frc2
 - **ssp585** : NSSP585frc2
 
-An overview of NorESM2 CMIP6 SSP experiments details, case names, restart files can be found here: https://noresmhub.github.io/noresm-exp/NSSPs/noresm2_mm_nssp.html 
+An overview of NorESM2 CMIP6 SSP experiments details, case names, restart files can be found here: https://noresmhub.github.io/noresm-exp/content/NSSPs/noresm2_mm_nssp.html 
 
 CMIP6 AMIP and fixed SST compsets
 ^^^^^
 - **amip** : NFHISTnorpddmsbc
 
-Detailed information on NorESM2-LM AMIP simulation can be accessed here: https://noresmhub.github.io/noresm-exp/noresm2_deck/noresm2_lm_amip.html
+Detailed information on NorESM2-LM AMIP simulation can be accessed here: https://noresmhub.github.io/noresm-exp/content/noresm2_deck/noresm2_lm_amip.html
 
 Useful compsets for calculating aerosol ERF:
 
@@ -177,8 +177,8 @@ and the long name for ``N1850frc2`` is ::
 
 Overview of piControl case names, detailed setup (machine settings, node settings etc.), raw output and restart files: 
 
-- NorESM2-LM: https://noresmhub.github.io/noresm-exp/noresm2_deck/noresm2_lm_piC.html
-- NorESM2-MM: https://noresmhub.github.io/noresm-exp/noresm2_deck/noresm2_mm_piC.html
+- NorESM2-LM: https://noresmhub.github.io/noresm-exp/content/noresm2_deck/noresm2_lm_piC.html
+- NorESM2-MM: https://noresmhub.github.io/noresm-exp/content/noresm2_deck/noresm2_mm_piC.html
 
 Historical
 ^^^^^^
@@ -250,8 +250,8 @@ and for ``NHISTfrc2`` is ::
 
 Overview of historical case names, members, detailed setup (machine settings, node settings etc.), raw output and restart files: 
 
-- NorESM2-LM: https://noresmhub.github.io/noresm-exp/noresm2_hist/noresm2_lm_hist.html
-- NorESM2-MM: https://noresmhub.github.io/noresm-exp/noresm2_hist/noresm2_hist.html
+- NorESM2-LM: https://noresmhub.github.io/noresm-exp/content/noresm2_hist/noresm2_lm_hist.html
+- NorESM2-MM: https://noresmhub.github.io/noresm-exp/content/noresm2_hist/noresm2_hist.html
 
 SSP5-8.5
 ^^^^^
@@ -325,5 +325,5 @@ and for ``NSSP585frc2`` is ::
 
 Overview of scenario experiment case names, members, detailed setup (machine settings, node settings etc.), raw output and restart files: 
 
-- NorESM2-LM and NorESM2-MM: https://noresmhub.github.io/noresm-exp/NSSPs/noresm2_mm_nssp.html
+- NorESM2-LM and NorESM2-MM: https://noresmhub.github.io/noresm-exp/content/NSSPs/noresm2_mm_nssp.html
 

doc/configurations/configurations.rst

@@ -7,7 +7,7 @@ Running NorESM2
  :maxdepth: 2
  :numbered:
 
- newbie-guide.rst
+ newbie_guide.rst
  experiments.rst
  experiment_environment.rst
  cmip6_compsets.rst

doc/configurations/experiment_environment.rst

@@ -293,8 +293,9 @@ Note that BLOM uses a different syntax than the rest. In user_nl_blom::
 
  set BDMC2 = .15
  set NIWGF = .5
+ set SRF_ANO3 = 0, 2, 2
 
-you need to include **set** before the name of the variable and it does not matter what namelist group the variable belong.
+you need to include **set** before the name of the variable and it does not matter what namelist group the variable belong. Input entries in user_nl_blom are case-insensitive (for model developers: variable names defined in the BLOM ``buildnml`` file should be capitalized to allow replacement values from user_nl_blom).
 
 
 Input data

doc/configurations/experiments.rst

@@ -69,6 +69,18 @@ For an overview of common compsets used for NorESM2 CMIP6 experiments, please se
 
 For an overview of the compsets provided for CESM2, please see: http://www.cesm.ucar.edu/models/cesm2/config/compsets.html.
 
+Emission-driven compsets
+''''''''''''''''''''''''
+NorESM2 can be run in emission-driven mode for interactive carbon-cycle studies. Currently, this configuration is only supported for the LM-resolution. In order to run NorESM2-LM in emission-driven mode, the biogeochemical physics ``[_BGC]%pys`` is set to ``%BPRPDMS`` (instead of ``%BDRDDMS``)
+
+There exists some predefined-emission driven compsets which usually ends with **esm** :
+
+* **N1850esm**: Emission driven coupled configuration for NorESM for pre-industrial (1850) conditions
+* **NHISTesm**: Emission driven historical configuration from 1850 to year 2014 
+* **NSSP585esm**: Emission driven SSP5-8.5 scenario configuration from 2015 to year 2100
+* **NSSP534esm**: Emission driven SSP5-3.4 scenario configuration from 2015 to year 2100
+
+With the exception of preindustrial control, running in CO2 emission-driven mode requires time-varying spatial CO2 emissions boundary condition files. 
 
 Creating your own compset
 '''''''''''''''''''''''''

doc/configurations/newbie-guide.rst → doc/configurations/newbie_guide.rst

@@ -6,9 +6,9 @@ Newbies guide
 This guide provides basic instructions on how set up and run a standard NorESM case by executing 4 steps:
 
  - create a new case (the **create_newcase** script)
- - configure case (the **case_setup** script)
- - build case (the **case_build** script)
- - submit case (the **case_submit** script). 
+ - configure case (the **case.setup** script)
+ - build case (the **case.build** script)
+ - submit case (the **case.submit** script). 
 
 It is assumed that you have sucsessfully downloaded the model (see :ref:`download_code`), which means you have a copy of the model on your computer in a folder with a name of your choice. For simplicity we call this folder ``<noresm-base>`` in this guide.
 
@@ -24,7 +24,7 @@ The **create_newcase** script is an executable python script located in:
 The script for creating a new case takes several command line arguments as input to know how to configure your case.
 Some of the most important arguments are as follows:
 
- - ``--case`` defines a casename of your choice and creates a folder by that name. The argument respects absolute and relative paths (e.g. ``--case ../../cases/<casename>``).
+ - ``--case`` defines a casename of your choice and creates a folder by that name. The argument respects absolute and relative paths (e.g. ``--case ~/NorESM/cases/<casename>``). It is good parctice to make a case folder named ``cases`` where your NorESM cases are stored, e.g. ``mkdir NorESM/cases/`` in your home directory
 
  - ``--mach`` defines the machine you will run the model on. The model NorESM2 has been configured to be run on a set of different machines (see list at :ref:`platforms`). If you are running the model on a machine not listed you will need to configure the model beyond this newbie guide. 
 
@@ -41,32 +41,32 @@ To investigate the full list of arguments, enter the *<noresm_base>/cime/scripts
 To create a new case, enter the scripts directory and run the **create_newcase** scripts:
 ::
  cd <noresm_base>/cime/scripts/
- ./create_newcase --case ../../cases/$CASENAME --mach $MACHINE --res f19_tn14 --compset $COMPSET
+ ./create_newcase --case <casepath>/<casename> --mach <machine> --res f19_tn14 --compset <compset>
 
-You have now created the case folder *<noresm_base>/cases/$CASENAME*! Go to the case folder to start configuring your experiment.
+You have now created the case folder *<casepath>/<casename>*! Go to the case folder to start configuring your experiment.
 
 More advanced examples
 ++++++++++++++++++++++
-The following example creates the case *test1910_1* on the machine Fram:
+The following example creates the case *N1850_f19_tn14_test01* on the machine Fram:
 ::
 
- ./create_newcase --case ../../cases/test1910_1 --compset N1850 --res f19_tn14 --machine fram --project snic2019-1-2 --user-mods-dir cmip6_noresm_DECK 
+ ./create_newcase --case ~/NorESM/cases/N1850_f19_tn14_test01 --compset N1850 --res f19_tn14 --machine fram --project snic2019-1-2 --user-mods-dir cmip6_noresm_DECK 
 
-Here we use the *N1850* compset, which configures the case as a 1850 pre-industrial control simulation. The argument ``--project`` should correspond to the id of the project used in the batch system accounting on Fram. The argument ``--user-mods-dir`` provides the path to a folder containing files that will further configure your case (like user namelists, shell scripts with xmlchange commands or SourceMods). The default location for this folder is under *<noresm_base>/cime_config/usermods_dirs/*.
+Here we store the case with the casename *N1850_f19_tn14_test01* in a subdirectory ``NorESM/cases/`` in the home directory on fram. We use the *N1850* compset, which configures the case as a 1850 pre-industrial control simulation. The argument ``--project`` should correspond to the id of the project used in the batch system accounting on Fram. The argument ``--user-mods-dir`` provides the path to a folder containing files that will further configure your case (like user namelists, shell scripts with xmlchange commands or SourceMods). The default location for this folder is under *<noresm_base>/cime_config/usermods_dirs/*.
 
-The following example creates a case (also called *test1910_1*), but on the machine Tetralith:
+The following example creates a case (also called *N1850_f19_tn14_test01*), but on the machine Tetralith:
 ::
 
- ./create_newcase --case ../../cases/test1910_1 --walltime 24:00:00 --compset N1850 --res f19_tn14 --machine tetralith --project snic2019-1-2 --output-root /proj/bolinc/users/${USER}/NorESM2/noresm2_out
+ ./create_newcase --case ~/NorESM/cases/N1850_f19_tn14_test01 --walltime 24:00:00 --compset N1850 --res f19_tn14 --machine tetralith --project snic2019-1-2 --output-root /proj/bolinc/users/${USER}/NorESM2/noresm2_out
 
 Note that here we use the argument ``--output-root``, which is only required if the *noresm_run_dir* (the running directory of the mode) differs from default running directory *<path_to_run_dir>/noresm/*. 
 
 Configure the case
 ---------------------
-The case folder *<noresm_base>/cases/$CASENAME/* is where you configure your case by changing enviroment files (such as the *<noresm_base>/cases/$CASENAME/env_run.xml* file; see :ref:`experiment_environments`), changing the user namelists for the different model components (files named ``user_nl_$COMP`` where $COMP is a model component such as ``cam``), or even add your own code changes to ``SourceMods/src.$COMP/``. But for now we stick to the standard out-of-the-box set up and configure the case as follows:
+The case folder *<casepath>/<casename>/* is where you configure your case by changing enviroment files (such as the *<casepath>/<casename>/env_run.xml* file; see :ref:`experiment_environments`), changing the user namelists for the different model components (files named ``user_nl_<component>`` where <component> is a model component such as ``cam``), or even add your own code changes to ``SourceMods/src.<component>/``. But for now we stick to the standard out-of-the-box set up and configure the case as follows:
 ::
 
- cd <noresm_base>/cases/$CASENAME
+ cd <casepath>/<casename>
  ./case.setup