Resources for CESM1.2 Paleosimulations
Esther Brady
Bette Otto-Bliesner
National Center for Atmospheric Research
- Getting Started
- Introduction
- Before you begin
- Deep Time vs Quaternary paleoclimate
- FlowChart for creating a paleoclimate simulation
- Should I use CCSM3 or CESM1.2
- How do I take the CESM Tutorial (Recommended)
- Getting help: CESM on-line Paleoclimate community forum
- Download paleoclimate resources
- What input files do I need?
- Ocean
- Modifying the ocean grid for Deep Time paleo simulations
- How do I design/create a new ocean grid
- How do I build a new ocean grid
- How do I change the region mask and the region IDs
- Modifying the ocean grid for Near Modern paleo simulations
- What POP2 namelist settings should I use for Deep Time (user_nl_pop2)
- How do I turn off the modern overflow regions
- Changing timesteps in the ocean (See also dt_count in the user_nl_pop section)
- Coupler mapping
- River runoff
- What files will I need for the RTM runoff model
- How do I map river runoff on the land model (rdirc)
- Do I need to modify rdirc for a near-Modern glacial run
- How do I create ROF2OCN_RMAPNAME
- How do I create ROF2OCN_FMAPNAME
- Atmospheric model (CAM4/CAM5)
- How do I change topography in a Near Modern simulation
- How do I change topography in a Deep Time simulation
- How do I change the atmospheric timestep to improve stability
- Atmosphere (aerosols, dust, volcanic)
- Landuse/landcover (CLM4.0)
- How do I create vegetation for a Deep Time simulation in CLM4.0
- How do I create a 'vegetation.nc' file for Deep Time
- How do I create a new surface dataset
- Can I run the land model from arbitrary initial conditions
- How can I restart from a previous run if I have changed the land/sea mask
- How do I initialize CN in a paleo run
- How do I turn on CNDV
- Land ice
- How can I use a restart file from a previous run if I have changed the land/sea mask
- Sea ice
- Run time issues
A brief note to users ...
The Community Earth System Model (CESM1) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CESM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Please see the brief overview of the notable model improvements in the current version of CESM1.
The CESM and its component models have been invaluable tools for the national and international
research communities. These models have been used by researchers worldwide, starting with the
first version CSM1, to explore problems of both greenhouse and icehouse past climates. They have
been shown to be adaptable for both deep-time paleoclimate applications, when the continental
configurations were much different from present, to the more near-term past climates of the
glacial-interglacial cycles of the last million years. Over 60 research articles using versions
of CESM for studying past climates have been published by the community. Low-resolution versions
of CESM1 have been developed and supported to allow paleoclimate researchers to integrate the
model for thousands and even tens of thousands of years. This document outlines the procedures
for setting up paleoclimate simulations with CESM1, released in 2010. The science of the
paleoclimate simulation still rests on the researcher. Choices will need to be made on the
appropriate conditions (i.e., land-ocean configuration, topography and bathymetry, ice sheets,
vegetation) for the specific paleoclimate research topic being explored. Additional information
on the component models and options that may need to be set can be found in the technical notes of
these models. We thank all those who have contributed their time and expertise for maintaining
the paleoclimate versions of CESM1.
Introduction
This document describes procedures developed at NCAR for creating paleoclimate simulations using the NCAR CESM1.2 series model in the fully coupled (all active components) configuration. We do not describe the creation of the forcing files used in Data Model components or in stand-alone component model runs. Note that this documentation does not discuss CLM4.5 or later land model versions. We provide tools and examples of the processes we have used to create paleoclimate simulations using the computing resources at the National Center for Atmospheric Research (NCAR). However, since the CESM model evolves continuously, this document is to be used as a guide; researchers are ultimately responsible for modifying the processes to accommodate their time period of interest as well as adapting the tools we provide to the model version they are using and the computer resources they have available. All tools discussed in this FAQ were developed to run on the computing platforms at the National Center for Atmospheric Research (NCAR) and are unsupported on all other platforms. We provide limited user support for the current version of tools on NWSC computers. Outside researchers may need to modify these procedures to accommodate earlier versions of the CESM1 model, or for the computer resources available on their home machines. Finally, the information we provide is intended to supplement the detailed usage information for each CESM1.2 series component model that can be found in the CESM1 User's Guide and a general familiarity by the user of CESM1 terminology and concepts is assumed.
Before you begin
One of the goals of the Paleoclimate Working Group is to allow the community to address scientific questions about past climates in Earth history using the CESM model. To that end we include useful tools that are designed to modify the forcing and input files for paleoclimate applications. If you are considering a Paleoclimate project using the CESM model you may find it useful to explore the questions listed below before you begin. We also strongly recommend that you complete the exercises in the CESM tutorial, and run a short pre-industrial simulation of the CESM model before you start configuring your paleoclimate simulation. We ask that users submit questions to the CESM Discussion Forum so that other users may contribute to, or benefit from, the discussion. Browse the Paleoclimate Section of the CESM Bulletin Board for related community discussion.
Question 1: What scientific question do you plan to investigate with the CESM?- The current release of the CESM may not resolve all the necessary processes nor have adequate resolution critical for your climate study. It is up to the project scientist to decide on initial and forcing conditions as well as the appropriate topography, bathymetry and vegetation/landcover files for the time period of interest.
- The boundary conditions and forcing files included as part of the CESM release pertain to modern time periods: pre-industrial, present day and future scenarios. Configuring the CESM for past time periods requires that the investigator specify forcings and boundary conditions for the geologic time period of configuration, the investigator may also need to provide, for example, bathymetry, atmospheric aerosols, etc. The Paleo User Resources site provides tools and guidance for modifying forcing and boundary conditions.
- It may be useful to know whether others have used the current version of CESM to simulate your time period in case they would be willing to share their model setup. Posting a query on the CESM forums web page is an efficient way to look for collaborative opportunities. In addition, we encourage you to attend one of our Paleoclimate Working Group meetings to share your interest and results and hear about our activities and plans. This is also a great way to link up with other investigators who may be working on similar projects.
- Your research may allow a reduced model configuration. For example, you may be able to implement active land and atmosphere component models driven by prescribed SST and sea ice distributions. This may be a good place to start if you have limited computational time and storage allocation. 
- A slab ocean model (SOM) is also available. The SOM is much faster and computationally more cost-effective than running the fully-coupled model with an active full-depth ocean component, which takes a few thousand model years to spin up to a quasi-equilibrium. See the CESM User's Guide for details on potential CESM configurations.
- Running an "out-of-the-box" (OTB) pre-industrial CESM simulation and completing the CESM Tutorial are prerequisites for configuring a paleoclimate simulation.
- Follow the CESM Tutorial to become familiar with running the CESM model and changing the model forcing parameters. Refer to the CESM User's Guide for the model version you plan to use to find more detailed information.
- Do you have allocated computer time and storage on the NCAR-Wyoming Supercomputers?
- Running the CESM at any resolution or configuration is computationally expensive and produces large amounts (Giga- to Tera- bytes) of output. This means you will need supercomputer access and storage space to carry out your simulations.
- Information on access to the Yellowstone computer resources at the NCAR-Wyoming Supercomputing Center (NWSC) can be found here: http://www2.cisl.ucar.edu/docs/allocations. Refer to the CESM User's Guide for information on porting the CESM model to other computers.
- This documentation describes tools and procedures for creating paleoclimate simulations using the NCAR CESM1 model. Using the CESM1 model for paleoclimate modeling requires complex, multi-step modifications to the input and forcing files used by the model, particularly for Deep Time simulations where continental configurations have changed. These tools are developed on the computing resources at the National Center for Atmospheric Research (NCAR) and we strive to keep pace with the current version of the CESM1 model. Researchers may need to modify these procedures to accommodate the version of the CESM1 model they are using, or for the computer resources available on their home machines. To gain more understanding about the CESM1 component models and input files, see the CESM1 documentation http://www2.cesm.ucar.edu/.
What are the differences between Deep Time and Quaternary paleoclimate simulations.
Throughout this document we differentiate between the procedures required to create (1) near-modern (e.g., Quaternary, Pliocene) or (2) Deep-Time (pre-Quaternary/Pliocene) model simulations. In near-modern simulations, the continents are in their present-day positions, and the land/sea masks do not require significant modification. Quaternary modelers are often able to use existing forcing files to simulate past climate. By contrast, deep-time simulations require drastic modifications to the land/sea mask, and the modeler is responsible for providing the orographic/bathymetric maps for their geologic period of interest.
Flow Chart
- Create a new ocean KMT file to reflect changes to land/sea mask.
- Create SCRIPgrid file
- NCL code
- mk_SCRIPTgrid.csh
Coupler mapping ESMF tools - gen_cesm_maps.sh
- gen_domain.sh
Modify topography Create a new initialization (topo_bnd) file for CAM. - definesurf
river runoff Create a runoff file - rdirc
- runoff_map
- create_ESMP_map.sh
Modify landcover Create a new surface dataset for CLM4.0 - Create new 0.5o resolution raw ‘mksrf’ datafiles
- Create SCRIPgrid mapping file (Required if land/sea mask has changed)
- Map SCRIPgrid mapping file to CLM land grid. (Required if land/sea mask has changed)
- Create surface dataset.
- mkmapgrids
- mkmapdata
- mksurfdata_map
Restart CLM with modified restart file - run 5 day case with new land/sea mask, setting finidat=" "
- interpinic old.clm.r into new.clm.r
- interpinic
- Create a new ocean grid file
- Create a new ocean KMT file
- Create SCRIPgrid file
- Carefully check grid and KMT files (use NCL to visualize the SCRIP mapping file)
- ns_dipole.f90 (pole placement)
- paleotopo.f90 (embed KMT into grid)
- grid_bin2nc.f90 (convert to viewable netCDF file)
- mk_SCRIPTgrid.csh (uses myConvertPOPT to create SCRIP file)
- NCL code to visualize grid
- gen_cesm_maps.sh
- gen_domain.sh
- definesurf
- Create new 0.5o resolution raw ‘mksrf’ datafiles
- Create SCRIPgrid mapping file (Required if land/sea mask has changed)
- Map SCRIPgrid mapping file to CLM land grid. (Required if land/sea mask has changed)
- Create surface dataset.
- paleo_mkraw
- mkmapgrid
- mkmapdat
- mksurfdata_map
- run 5 day case with new land/sea mask, setting finidat=" "
- interpinic old.clm.r into new.clm.r
- interpinic
Near Modern Modifications | ||
---|---|---|
Procedure | Tools | |
Modify land/sea mask |
|
|
Deep Time Modifications | ||
---|---|---|
Procedure | Tools | |
Create paleo ocean grid with embedded continents |
| |
Coupler mapping | ESMF tools |
|
Modify topography | Create a new initialization (topo_bnd) file for CAM. |
|
Modify landcover | Create a new surface dataset for CLM4.0
| |
Restart CLM with modified restart file |
CCSM3 vs CESM1.2
The Community Climate System Model, version 3 (CCSM3) is a legacy version of the Community Earth System Model (CESM). Support for CCSM3 and all previous versions of CCSM have expired. The tools described in the CCSM3 documentation were developed to work on NCAR platforms that have since been retired and therefore these tools are no longer actively maintained. Furthermore, using the CCSM3 model is no longer supported on NCAR machines.
- Download the NCAR Technote for discussion on using the CCSM3 model for Paleoclimate.
- Download an Overview presentation that describes key differences between CESM1 and CCSM3 for paleo climate modellers.
- Browse the CESM on-line forum for related community discussion.
- For more information on currently supported versions of the model see the CESM documentation: http://www2.cesm.ucar.edu/models.
What input files do I need
Deep time model users need to provide gridded input files that define the surface topography, ocean bathymetry, land/sea mask, and vegetation/landuse categories for their period of scientific interest.
Topography + Bathymetry format » topobathy.nc
The topobathy.nc netCDF file should contain topography and bathymetry on a regular latitude/longitude grid (e.g.,
2°x2°). Positive values represent height above sea level and negative values represent ocean bathymetry. The
topobathy.nc will define your land/ocean mask, your bathymetry (KMT), and your orography (expressed as PHIS; where PHIS = orography * 9.82m/s2).
- Coordinate variables: lat(lat), lon(lon)
- longitude: 0 to 360°
- latitude: -90 to 90°
netCDF format
Vegetation/Landuse » vegetation.nc
The vegetation.nc netCDF file should contain land use (i.e., vegetation) on a regular latitude/longitude grid (e.g.,
2°x2°).
- Coordinate variables: lat(lat), lon(lon)
- longitude: 0 to 360°
- latitude: -90 to 90°
netCDF format
CLM PLANT FUNCTION TYPE (PFT)
For most deep time paleo simulations, we assign LSM (Land Surface Model)
land-use types for each grid point and then convert these LSM types to CLM
(Community Land Model) surface information using the tool
paleo_mkraw_cesm1.csh. Because CLM requires a complicated array of surface
information for each grid cell, whereas LSM uses a simple integer value to
represent land-use at each grid point, assigning an LSM integer value and
using the paleo_mkraw_cesm1.csh tool to convert to LSM types to CLM format
provides a simple method to create surface data information for deep time.
Modelers may first need to construct LSM land cover maps from biome maps using the LSM definitions and CLM PFT definitions used in paleo_mkraw_cesm1.csh
LSM land-use types are used in paleo_mkraw_cesm1.csh because LSM was the predecessor to CLM3 and used in CSM1.4. If this does not suite your needs, you will need to modify paleo_mkraw.csh to convert from your preferred land-use type structure to CLM surface data information.
PFT | Description |
0 | bare |
1 | needleleaf evergreen temperate tree |
2 | needleleaf evergreen boreal tree |
3 | needleleaf deciduous boreal tree |
4 | broadleaf evergreen tropical tree |
5 | broadleaf evergreen temperate tree |
6 | broadleaf deciduous tropical tree |
7 | broadleaf deciduous temperate tree |
8 | broadleaf deciduous boreal tree |
9 | broadleaf evergreen temperate shrub |
10 | broadleaf deciduous temperate shrub |
11 | broadleaf deciduous boreal shrub |
12 | arctic c3 grass |
13 | cool c3 grass |
14 | warm c4 grass |
15 | crop 1 |
16 | crop 2 |
No Vegetation | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
0 | ocean | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 | land ice | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | desert | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Forest3 | cool needleleaf evergreen tree | 4 | cool needleleaf deciduous tree | 5 | cool broadleaf deciduous tree | 6 | cool mixed forest | 7 | warm needleleaf evergreen tree | 8 | warm broadleaf deciduous tree | 9 | warm mixed forest | 10 | tropical broadleaf evergreen forest | 11 | tropical broadleaf deciduous tree | Interrupted Woods | 12 | savanna | 13 | evergreen forest tundra | 14 | deciduous forest tundra | 15 | cool forest crop | 16 | warm forest crop | Non-woods | 17 | cool grassland | 18 | warm grassland | 19 | tundra | 20 | evergreen shrub land | 21 | deciduous shrub land | 22 | semi-desert | 23 | cool irrigated crop | 24 | cool crop | 25 | warm irrigated crop | 26 | warm crop | Wetland | 27 | forest wetland | 28 | non-forest wetland | |