For Baltic Sea Biogeochemical Analysis and Forecasting ...cmems-resources.cls.fr/documents/PUM/CMEMS-BAL-PUM-003-007.pdf · For Baltic Sea Biogeochemical Analysis and Forecasting

For Baltic Sea Biogeochemical Analysis and Forecasting Product

BALTICSEA_ANALYSIS_FORECAST_BIO_003_007

Issue: 1.9

Contributors: V. Huess

CMEMS version scope : Version 4.0

Approval Date by the CMEMS products team : 5 March 2018

PUM for Baltic Sea Biogeochemical Analysis and

Forecasting Product


Ref: CMEMS-BAL-PUM-003-007

Date : January 2018

Issue : 1.9

© EU Copernicus Marine Service – Public Page 2/ 18

CHANGE RECORD

Issue Date § Description of Change Author Validated By

1.0

January 2013

All

New product:

MYO-BAL-PUM-003-007 superseding old product (MYO-BAL-PUM-003-002)

V. Huess V. Huess

1.1 February 2013

Minor changes V.Huess V.Huess

1.2 March 2013 Minor corrections V. Huess V. Huess

1.3 January 2014

Update for the V4 upgrade V. Huess V. Huess

L. Crosnier

1.4 December 2014

Update for the V5 upgrade V. Huess L. Crosnier

1.5 May

2015

all Change format to fit CMEMS graphical rules

L. Crosnier

1.6 January

2016

All Update for the CMEMS V2.0 upgrade

V. Huess

1.7 January 2017

All Update for the CMEMS V3.0 upgrade

V. Huess

1.8 March 2017 All Design Update for the CMEMS V3.0 upgrade

C. Derval, MO

V. Huess

1.9 January 2018

All Updated for the CMEMS V4.0/March 2018 system upgrade

V. Huess CMEMS products team


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Table of contents

I INTRODUCTION ......................................................................................................................................... 5

I.1 Summary ...................................................................................................................................................... 5

I.2 History of changes ....................................................................................................................................... 5

II DESCRIPTION OF THE PRODUCT SPECIFICATION .......................................................................... 8

II.1 General Information .................................................................................................................................. 8

II.2 Details of datasets ...................................................................................................................................... 9

II.3 Production System Description .............................................................................................................. 10

II.3.1 Summary of the operational model setups ...................................................................................... 11

II.4 Processing information ............................................................................................................................ 13

II.4.1 Update Time .................................................................................................................................... 13

II.4.2 Temporal extend of analysis and forecast stored on delivery mechanism....................................... 14

III HOW TO DOWNLOAD A PRODUCT .................................................................................................. 15

III.1 Download a product through the CMEMS Web Portal ..................................................................... 15

IV NOMENCLATURE OF FILES .................................................................................................................. 16

IV.1 Nomenclature of files when downloaded through the CMEMS Web Portal Subsetter Service ...... 16

IV.2 Nomenclature of files when downloaded through the CMEMS Web Portal FTP Service .............. 16

V FILE FORMAT ........................................................................................................................................... 18

V.1 Netcdf ........................................................................................................................................................ 18

V.2 Reading software...................................................................................................................................... 18


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GLOSSARY AND ABBREVIATIONS

MFC Monitoring and Forecasting Centre

BAL Baltic

NetCDF Network Common Data Form

CF Climate Forecast (convention for NetCDF)

PC Production Center

PU Production Unit

ftp Protocol to download files

OpenDAP Open-Source Project for a Network Data Access Protocol. Protocol to download subset of data from a n-dimensional gridded dataset (ie: 4 dimensions: lon-lat,depth,time)

Subsetter CMEMS service tool to download a NetCDF file of a selected geographical box using values of longitude an latitude, and time range

Directgetfile CMEMS service tool (FTP like) to download a NetCDF file


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I INTRODUCTION

I.1 Summary

This guide describes the data product BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 from the Copernicus Marine Environment Monitoring Service’s (CMEMS) Baltic Monitoring and Forecasting Centre (BAL MFC), what data services are available to access them, and how to use the files and services.

The product BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 is CMEMS’s operational biogeochemical product for the Baltic Sea and contains model calculations for the biogeochemical condition in the Baltic Sea. Data are served with 6th hourly resolution for the parameters: chlorophyll-a,dissolved oxygen, nitrate, phosphate and ammonium at up to 25 vertical levels. Further the Secchi Depth and the bottom value of dissolved oxygen are provided at each grid point.

A new forecast for the next 5 days (120 hours) is produced twice per day and updated in the CMEMS Catalogue at 10 AM and 10 PM. Model hindcast data are available 2 years back in time in the online CMEMS Catalogue.

The product BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 is based on simulations with the BALMFC-ERGOM version of the bio-geo-chemical model ERGOM original developed at IOW, Germany. The BALMFC-ERGOM version is further developed at DMI and BSH.

The BALMFC-ERGOM model is run online coupled with the HBM ocean model code (HIROMB-BOOS-Model).

See the Quality Document CMEMS-BAL-QUID-003-007 for more information on the products’ quality.

I.2 History of changes

On March 22 2018 (V4) the following changes occurred:

The HBM-ERGOM coupled ocean-biogeochemical model code was upgraded by these improvements:

o The thermodymic routine has been re-tuned, i.e. a modified near surface heat conduction, a modified insolation and heat absorption in the surface layer as well as a modified heat release through openings in sea ice, has been introduced. This new thermodynamic routine should improve especially the description of sea ice during


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growing and melting season. In addition some changes in the model description of sea surface temperature are expected.

o A new light modul was implemented following the implementation of (Neumann, Siegel et al. 2015). Therefore a new state variable was added to ERGOM, the labile dissolved organic nitrogen. The new light routine allows a better representation of the attenuation coefficient kpar and the calculation of Secchi Depth. The influence of coloured dissolved organic matter (CDOM) on kpar and the Secchi Depth is set in relation to salinity in this approach.

o Chlorophyll is calculated diagnostically following the attempt of Doron, Brasseur et al.(

2013). It uses a variable “Chl to N ratio” and the actual light to calculate the chlorophyll at a given time.

o The Secchi Depth is now calculated from the model and added as a product.

o Ammonium is added as a product.

For the data product these changes have been included:

o The forecast product will from the March 2018 upgrade consists of a 5 days forecast (120 hours) produced by forcing the model system HBM-ERGOM with DMI-HARMONIE weather forcing for the first 2.5 days and with forcing data from ECMWF for the next 2.5 days.

o These dataset are now available:

“Hourly dataset” serves data each 6th hour.

“Daily mean dataset” serves 24 hourly averaged means.

“Monthly mean dataset” serves calendar monthly means.

o The products will be served in netcdf4 format.

On April 19 2017 (V3) the following changes occurred:

The HBM-ERGOM coupled ocean-biogeochemical code was upgraded by these improvements: o The description of the atmospheric deposition has been upgraded o N/P ratio has been upgraded. o Sea ice module has been improved by including fast ice. o Turbulence scheme has been further developed and improved o Technical performance of the code has been improved.

See the Quality Document CMEMS-BAL-QUID-003-007 for more information.


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Further the dataset names have been slightly renamed.


Daily mean values are provided for all variables in addition to the hourly instantaneous values. The daily means are calculated in post-process mode by a simple mean of the 24 time steps available for each calendar day.


o Temporal coverage available online is increased from [3 months ago; ongoing] up to [2 years ago; ongoing]

o The ERGOM code is improved :

Possibility to turn off the eco-model calculation in river areas is activated


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II DESCRIPTION OF THE PRODUCT SPECIFICATION

II.1 General Information

Product Specification BALTIC_ANALYSIS_FORECAST_BIO_003_007

Geographical coverage 9°E 30°E ; 53°N 66°N

Variables Chlorophyll a Nitrate Phosphate Ammonium Dissolved oxygen Bottom Dissolved oxygen Secchi Depth (only available in the hourly dataset)

Analysis Yes

Forecast Yes: 120 hours forecasts

Available time series The latest 2 years of model forecasts are available on-line via the CMEMS webportal.

Model data older than 2 years are available on request to the CMEMS Service Desk: [email protected]

Temporal resolution Hourly instantaneous values. Daily mean values. Monthly mean values.

Target delivery time New Forecast: twice daily at 10 am and pm UTC.

Delivery mechanism CMEMS Information System (Subsetter and FTP)

Horizontal resolution App. 1 nautical miles:

Delta Longitude: 1’40’’ or 0.028 degrees Delta Latitude: 1’ or 0.017 degrees

Number of vertical levels Up to 25 levels. Levels [m]: 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 300, 400

Format Netcdf & CF1.0

Table 1: BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 Product Specification

http://www.myocean.eu/web/21-contact-us.php


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II.2 Details of datasets

BALTIC_ANALYSIS_FORECAST_BIO_003_007

dat

aset

-bal

-anal

ysi

s-fo

reca

st-b

io-h

ourl

y

dat

aset

-bal

-anal

ysi

s-fo

reca

st-b

io-d

aily

mea

ns

dat

aset

-bal

-anal

ysi

s-fo

reca

st-b

io-m

onth

lym

eans

dataset-bal-analysis-forecast-bio-hourly contains: 6th hourly instantaneous values dataset-bal-analysis-forecast-bio-dailymeans contains: daily mean values (25 hours average) dataset-bal-analysis-forecast-bio-monthlymeans: contains monthly mean values Variables name in the NetCDF file and Unit Long_name Standard_name

no3 [mmol /m3] Nitrate_Concentration mole_concentration_of_nitrate_in_sea_water

po4 [mmol /m3] Phosphate_Concentration mole_concentration_of_phosphate_in_sea_water

nh4 [mmol /m3] Ammonium_Concentration mole_concentration_of_ammonium _in_sea_water

chl [mg /m3] Chlorophyll_a_Concentration mass_concentration_of_chlorophyll_a_in_sea_water

o2 [mmol/m3] Dissolved_Oxygen_Concentration mole_concentration_of_dissolved_molecular_oxygen_in_sea_water

o2b [mmol /m3] Sea floor Dissolved_Oxygen_Concentration mole_concentration_of_dissolved_molecular_oxygen_in_sea_water

zsd [m] Secchi_depth secchi_depth_of_sea_water zsd is N/A in the daily and monthly means dataset.

Table 2 list of the datasets (column 1) and variable names and unit (column2) for the BALTIC_ANALYSIS_FORECAST_PHY_003_007 product


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II.3 Production System Description

The product BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 is based on simulations with the BAL MFC-ERGOM version of the bio-geo-chemical model ERGOM original developed at IOW, Germany. The BAL MFC -ERGOM version is further developed at DMI and BSH and is run online coupled with the HBM ocean model code (HIROMB-BOOS-Model).

For details on the ERGOM biogeochemical module please see (Neumann, 2000; Neuman, 2002).

For details on the HBM ocean code please see (Berg, 2012; Berg and Poulsen, 2012; Poulsen and Berg, 2012; Poulsen and Berg, 2013). For information on the quality of the HBM results see CMEMS-BAL-QUID-003-006; and for the BAL MFC ERGOM results see CMEMS-BAL-QUID-003-007. Both available via the CMEMS on-line Catalogue

The production of the forecast product for the bio-chemical conditions in the Baltic Sea is performed at DMI (the Danish Meteorological Institute), Denmark


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II.3.1 Summary of the operational model setups

Domain

Resolution and grid

Geographic coverage

North Sea – Baltic Sea : 53°N - 66°N, 9°E - 30°E

The horizontal grid step is regular in latitude and longitude and is of approximately 1 nautical miles (lat: 0.017 degrees; lon: 0.028 degrees) for. The grid is a staggered Arakawa C-grid (see figure 1). The dataset of the scalar variables (all the biogeochemical variables) are centred in the T point of the grid; at the grid cell node.


VARIABLE GRID LON MIN LON MAX LAT MIN LAT MAX XPOINT

All scalar variables (see text)

T 9.0417˚E 30.31945˚E 53.025˚N 65.89˚N 767

Table 3: Description of the staggered grid and spatial coverage for each variable

Bathymetry GEBCO at 1-minute resolution

Figure 1: The staggered Arakawa C-grid used by BAL-MFC numerical models.


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Vertical levels 25 levels [m]: 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 300, 400.

The model native computational grid has a higher resolution (Maximum number of model depth levels: 122)

Model Version Production units Period of validation

HBM-ERGOM V4

DMI

01.10.2013–30.09.2015

Assimilation scheme

N/A

Assimilated observations

N/A

Initial conditions (spin-up process)

The model started at January 1st 2013 with an initial field from an earlier set up.

Surface forcing

Boundary forcing

The DMI calibration set up uses meteorological data from the DMI-HIRLAM SKA with a horizontal resolution of 3 km.

The forecast production is produced with forcing from the DMI-HARMONIE 2.5 km system for the first 2.5 days, and the available ECMWF forcing for the next 2.5 days.

Interpolated ICES data for DIN, DIP, silicate and oxygen. Zoo- and phytoplankton data are based on ICES observations of chlorophyll-a (chlorophyll to plankton biomass).

River run-off

Data from the operational hydrological model HBV of SMHI (Bergström, 1976 and Bergström, 1992).

HBM-ERGOM coupling

The biogeochemical model is coupled to the physical through an operator splitting scheme where first advection and diffusion of the tracers are calculated in HBM and thereafter ERGOM calculates the biogeochemical sinks and sources. The biogeochemical processes are updated at every advection timestep in HBM, i.e. 50 seconds.

For more details see http://cmems-resources.cls.fr/documents/QUID/CMEMS-BAL-QUID-003-007.pdf

http://cmems-resources.cls.fr/documents/QUID/CMEMS-BAL-QUID-003-007.pdf


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II.4 Processing information

II.4.1 Update Time

The BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 product is updated twice daily at 10 am and 10 pm. The production and update is like this:

The ocean model including the bio-geo-chemical module is run twice per day for the 00Z and 12Z analyses following this schedule:

The ocean model run starts when the weather model forecast for the 00Z analysis or 12Z analysis has finalized. First a 12 hours hindcast for the ocean is re-calculated with the best available weather analysis fields covering the 12 hours before the analysis time. This is followed by a 120 hours forecast calculation for the ocean with the new calculated weather forecast as forcing fields.

These ocean model data are after calculation processed onto the CMEMS BAL product grid and the products are updated as indicated in the figure above:

1 file containing the 12 hours best estimate for the hindcast period: these data substitutes the first 12 hours of the previous analysis forecast.

10 files containing the latest available 60 hours forecast, ie each file contains 12 hours of data.

The Baltic bio-geo-chemical data are updated at the CMEMS server at 10 UTC and 22 UTC at the latest for the 00 UTC and 12 UTC analysis, respectively.

Example of a product update: for the analysis valid at 00Z April 15th 2017 the biogeochemical-ocean model run will start at 03 AM UTC and the results will be updated into the CMEMS Catalogue at 10 AM UTC with these 6 new netcdf files:

- The 12 hours hindcast (best estimate) BAL-HBM_BIO-2017041412.nc This is a re-calculation of the previous forecast; and by that replaces the results in the file with the same name produced at the previous analysis from April 14th 12Z.

- The new 60 hours forecast covering the period April 15th 0Z – April 17th 12Z in these 10 files:


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BAL-HBM_BIO-2017041500.nc BAL-HBM_BIO-2017041512.nc BAL-HBM_BIO-2017041600.nc BAL-HBM_BIO-2017041612.nc BAL-HBM_BIO-2017041700.nc BAL-HBM_BIO-2017041712.nc BAL-HBM_BIO-2017041800.nc BAL-HBM_BIO-2017041812.nc BAL-HBM_BIO-2017041900.nc BAL-HBM_BIO-2017041912.nc

II.4.2 Temporal extend of analysis and forecast stored on delivery mechanism

BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 product’s temporal coverage is:

In the CMEMS online system data from the latest 2 years (running window) are available via these 3 download interfaces: Subsetter, ftp and DirectGetFile.

Older data are archived in the Production Unit, and will be made accessible on request. Please contact the CMEMS Service Desk [email protected]

http://www.myocean.eu/web/21-contact-us.php


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III HOW TO DOWNLOAD A PRODUCT

Before download of a product you first need to register. Please register through CMEMS web page by following link 'Register now' (http://marine.copernicus.eu/services-portfolio/register-now/) or see the online tutorial at http://marine.copernicus.eu/tutorials/how-to-register-to-copernicus-marine-service-update-september-2015/

III.1 Download a product through the CMEMS Web Portal

Once registered, the tutorial:

http://marine.copernicus.eu/web/95-online-tutorials.php?item=1949

will guide you on How to download a product .

http://marine.copernicus.eu/services-portfolio/register-now/


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IV NOMENCLATURE OF FILES

IV.1 Nomenclature of files when downloaded through the CMEMS Web Portal Subsetter Service

BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 files nomenclature when downloaded through the CMEMS Web Portal Subsetter is based on product dataset name and a numerical reference related to the request date.

The scheme is: datasetname-nnnnnnnnnnnnn.nc

where :

datasetname is a character string:

“dataset-bal-analysis-forecast-bio-hourly”

“dataset-bal-analysis-forecast-bio-dailymeans”

“dataset-bal-analysis-forecast-bio-monthlymeans”

nnnnnnnnnnnnn: 13 digit integer corresponding to the current time (download time) in milliseconds

since January 1, 1970 midnight UTC.

.nc: standard NetCDF filename extension.

IV.2 Nomenclature of files when downloaded through the CMEMS Web Portal FTP Service

BALTICSEA_ANALYSIS_FORECAST_BIO_003_007 file nomenclature when downloaded through the CMEMS Web Portal FTP service is based on the original file names behind the products. The files are in NetCDF and are named:

For the hourly instantaneous values: BAL-HBM_BIO-“analysistime”.nc Each file contains 2 hours of data. “Analysistime” indicate the first timestamp in the file.

For the daily mean values:


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BAL-HBM_BIO-DailyMeans-“ccyymmdd”.nc Each file contains 1 timestamp for the calendar day.

For the monthly mean values: BAL-HBM_BIO-MonthlyMeans-“ccyymm”.nc Each file contains 1 timestamp for the calendar month.


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V FILE FORMAT

V.1 Netcdf

The products are stored using the NetCDF format.

NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data. The netCDF software was developed at the Unidata Program Center in Boulder, Colorado. The netCDF libraries define a machine-independent format for representing scientific data.

Please see Unidata netCDF pages for more information, and to retrieve netCDF software package.

NetCDF data is:

* Self-Describing. A netCDF file includes information about the data it contains.

* Architecture-independent. A netCDF file is represented in a form that can be accessed by computers with different ways of storing integers, characters, and floating-point numbers.

* Direct-access. A small subset of a large dataset may be accessed efficiently, without first reading through all the preceding data.

* Appendable. Data can be appended to a netCDF dataset along one dimension without copying the dataset or redefining its structure. The structure of a netCDF dataset can be changed, though this sometimes causes the dataset to be copied.

* Sharable. One writer and multiple readers may simultaneously access the same netCDF file.

V.2 Reading software

NetCDF data can be browsed and used through a number of software, like:

ncBrowse: http://www.epic.noaa.gov/java/ncBrowse/,

NetCDF Operator (NCO): http://nco.sourceforge.net/

IDL, Matlab, GMT…

Documents

For Baltic Sea Biogeochemical Analysis and Forecasting ...cmems-resources.cls.fr/documents/PUM/CMEMS-BAL-PUM-003-007.pdf · For Baltic Sea Biogeochemical Analysis and Forecasting