Atlantis BGM Files

Author

Gorton, Bec (Environment, Hobart)

Background

The bgm file defines the polygons that create the map for the Atlantis model. A full documentation of this file is coming and various support programs exist to help draw this box. The single most important rule is that

Box 0 MUST be a BOUNDARY box (i.e. sit outside the active model domain).
Box 1 MUST be a dynamic or (INTERNAL) box (i.e. be a dynamic box in the model).

Generating

You can use the bgmeriser to generate your bgm file for you from a shapefile.

File Structure

The .bgm file defines the geography used in the Atlantis model to define the bathymetry of the model system, but also used by DIVE for display of the model. The model is cast in x-y terms (rather than latitude-longitude), using an equal area projection.
The area in the bgm file is in the units of the bgm file, so if the bgm file is in x-y co-ord then the area is in m^2.

The structure of the bgm file is as follows

box model geometry comment

# number of boxes in horizontal plane
nbox nb

number of faces dynamic in horizontal plane

nface nf

Maximum bottom depth (m) if botz > this reset botz

# to be this as far as model is concerned
maxwcbotz -20

vertices of polygon defining the boundary of the dynamic model spaces, polygons outside this are treated as boundary boxes

bnd_vert 4846663.054 2672181.026
bnd_vert 4846577.624 2671694.641
bnd_vert 4846769.65 2671316.256
bnd_vert 4846620.269 2670658.417
bnd_vert 4846647.232 2670053.268
bnd_vert 4846896.231 2669701.554
bnd_vert 4846895.551 2668853.126
bnd_vert 4846480.926 2668328.515
bnd_vert 4846068.874 2668006.796
bnd_vert 4846040.837 2667847.55

Data for box number 0

box0.label box0
box0.inside 4850502.794 2660539.214 // midpoint of polygon
box0.nconn 1 // number of neighbouring dynamic boxes
box0.iface 0 // face numbers connecting box with dynamic neighbouring boxes
box0.ibox 1 // box-id numbers of dynamic neighbouring boxes
box0.botz -7.58 // depth of the box
box0.area 4.96E+05 // area of the box
box0.vertmix 0.000001 // vertical mixing scalar for the polygon
box0.horizmix 1 // horizontal transport scalar for the polygon
box0.vert 4850016.494 2660989.963 // vertices of polygon
box0.vert 4850411.21 2660812.231
box0.vert 4851009.235 2660650.395
box0.vert 4850843.256 2660162.581
box0.vert 4850087.844 2660321.401
box0.vert 4850016.494 2660989.963

AND SO ON FOR nb BOXES

Data for face number 0

face0.p1 4850016.494 2660989.963 // one endpoint of face
face0.p2 4850087.844 2660321.401 // other endpoint of face
face0.length 672.3586014 // length of face
face0.cs -0.106119971 0.994353333 // cosine and sine of this vs (0,0)
face0.lr 0 1 // box to left and right of face standing at p1 looking at p2

AND SO ON FOR nf faces

Projections

The Atlantis BGM files now take a projection string that can be used by DIVE (the netcdf visualisation tool) to project the box locations. The projection string is also used by Atlantis to calculate the number of daylight hours when lim_sum_hours is turned on in the biology input file.

Format

Atlantis expects the format to be in PROJ4 format. These look like:

projection proj=aea lat_1=-18 lat_2=-36 lat_0=0 lon_0=134 x_0=3000000 y_0=6000000 ellps=GRS80 towgs84=0,0,0,0,0,0,0 units=m no_defs

The parameters should be space seperated - there should not be a ‘+’ between the strings (ignore this in the examples below)

To find the projection of your BGM file the Spatial Reference List is a good place to look.

Here are some more examples from Mike.

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Mikes notes for BGMEditor PROJ4 implementation
ESRI WKT implementation
PROJ4 equivalent
EPSG where available

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Convert to decimal degrees
-f ‘%.8f’

proj -I -f ‘%.8f’ +proj=lcc +lat_1=17.5 +lat_2=29.5 +lat_0=0 +lon_0=-102.0 +x_0=2000000.0 +y_0=0 +ellps=clrk66 +datum=NAD27 +units=m +no_defs goc2_testproj.txt

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D: PROJCS[“North_America_Albers_Equal_Area_Conic”,GEOGCS[“GCS_North_American_1983”,DATUM[“D_North_American_1983”,SPHEROID[“GRS_1980”,6378137.0,298.257222101]],PRIMEM[“Greenwich”,0.0],UNIT[“Degree”,0.0174532925199433]],PROJECTION[“Albers”],PARAMETER[“False_Easting”,700000.0],PARAMETER[“False_Northing”,0.0],PARAMETER[“Central_Meridian”,-117.0],PARAMETER[“Standard_Parallel_1”,43.0],PARAMETER[“Standard_Parallel_2”,48.0],PARAMETER[“Latitude_Of_Origin”,41.0],UNIT[“Meter”,1.0]]

Chesapeake

D: PROJCS[“NAD_1983_UTM_Zone_18N”,GEOGCS[“GCS_North_American_1983”,DATUM[“D_North_American_1983”,SPHEROID[“GRS_1980”,6378137.0,298.257222101]],PRIMEM[“Greenwich”,0.0],UNIT[“Degree”,0.0174532925199433]],PROJECTION[“Transverse_Mercator”],PARAMETER[“False_Easting”,500000.0],PARAMETER[“False_Northing”,0.0],PARAMETER[“Central_Meridian”,-75.0],PARAMETER[“Scale_Factor”,0.9996],PARAMETER[“Latitude_Of_Origin”,0.0],UNIT[“Meter”,1.0]]

EPSG:26918http://spatialreference.org/ref/epsg/26918/esriwkt/
PROJCS[“NAD_1983_UTM_Zone_18N”,GEOGCS[“GCS_North_American_1983”,DATUM[“D_North_American_1983”,SPHEROID[“GRS_1980”,6378137,298.257222101]],PRIMEM[“Greenwich”,0],UNIT[“Degree”,0.017453292519943295]],PROJECTION[“Transverse_Mercator”],PARAMETER[“latitude_of_origin”,0],PARAMETER[“central_meridian”,-75],PARAMETER[“scale_factor”,0.9996],PARAMETER[“false_easting”,500000],PARAMETER[“false_northing”,0],UNIT[“Meter”,1]]

PROJ4
+proj=utm +zone=18 +ellps=GRS80 +datum=NAD83 +units=m +no_defs

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GOC

D: PROJCS[“GoC”,GEOGCS[“GCS_North_American_1927”,DATUM[“D_North_American_1927”,SPHEROID[“Clarke_1866”,6378206.4,294.9786982]],PRIMEM[“Greenwich”,0.0],UNIT[“Degree”,0.0174532925199433]],PROJECTION[“Lambert_Conformal_Conic”],PARAMETER[“False_Easting”,2000000.0],PARAMETER[“False_Northing”,0.0],PARAMETER[“Central_Meridian”,-102.0],PARAMETER[“Standard_Parallel_1”,17.5],PARAMETER[“Standard_Parallel_2”,29.5],PARAMETER[“Scale_Factor”,1.0],PARAMETER[“Latitude_Of_Origin”,0.0],UNIT[“Meter”,1.0]]

+proj=lcc +lat_1=17.5 +lat_2=29.5 +lat_0=0 +lon_0=-102.0 +x_0=2000000.0 +y_0=0 +ellps=clrk66 +datum=NAD27 +units=m +no_defs

+to_meter=0.3048006096012192

Nearest:
PROJCS[“NAD27 / California zone VII”,GEOGCS[“GCS_North_American_1927”,DATUM[“D_North_American_1927”,SPHEROID[“Clarke_1866”,6378206.4,294.9786982138982]],PRIMEM[“Greenwich”,0],UNIT[“Degree”,0.017453292519943295]],PROJECTION[“Lambert_Conformal_Conic”],PARAMETER[“standard_parallel_1”,34.41666666666666],PARAMETER[“standard_parallel_2”,33.86666666666667],PARAMETER[“latitude_of_origin”,34.13333333333333],PARAMETER[“central_meridian”,-118.3333333333333],PARAMETER[“false_easting”,4186692.58],PARAMETER[“false_northing”,4160926.74],UNIT[“Foot_US”,0.30480060960121924]]

http://spatialreference.org/ref/epsg/26799/

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ECCAL

D: ESRI:102008

PROJCS[“North_America_Albers_Equal_Area_Conic”,GEOGCS[“GCS_North_American_1983”,DATUM[“D_North_American_1983”,SPHEROID[“GRS_1980”,6378137.0,298.257222101]],PRIMEM[“Greenwich”,0.0],UNIT[“Degree”,0.0174532925199433]],PROJECTION[“Albers”],PARAMETER[“False_Easting”,700000.0],PARAMETER[“False_Northing”,0.0],PARAMETER[“Central_Meridian”,-117.0],PARAMETER[“Standard_Parallel_1”,43.0],PARAMETER[“Standard_Parallel_2”,48.0],PARAMETER[“Latitude_Of_Origin”,41.0],UNIT[“Meter”,1.0]]

+proj=aea +lat_1=43 +lat_2=48 +lat_0=41 +lon_0=-117 +x_0=700000 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs

http://spatialreference.org/ref/esri/102008/esriwkt/
Different parameters to above
PROJCS[“North_America_Albers_Equal_Area_Conic”,GEOGCS[“GCS_North_American_1983”,DATUM[“D_North_American_1983”,SPHEROID[“GRS_1980”,6378137,298.257222101]],PRIMEM[“Greenwich”,0],UNIT[“Degree”,0.017453292519943295]],PROJECTION[“Albers”],PARAMETER[“False_Easting”,0],PARAMETER[“False_Northing”,0],PARAMETER[“central_meridian”,-96],PARAMETER[“Standard_Parallel_1”,20],PARAMETER[“Standard_Parallel_2”,60],PARAMETER[“latitude_of_origin”,40],UNIT[“Meter”,1]]

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Clarence, VicMPA, AMS

Mikes Albers_3 projection
PROJCS[“Albers_3”,GEOGCS[“GCS_GDA_1994”,DATUM[“D_GDA_1994”,SPHEROID[“GRS_1980”,6378137.0,298.257222101]],PRIMEM[“Greenwich”,0.0],UNIT[“Degree”,0.0174532925199433]],PROJECTION[“Albers”],PARAMETER[“False_Easting”,3000000.0],PARAMETER[“False_Northing”,6000000.0],PARAMETER[“Central_Meridian”,134.0],PARAMETER[“Standard_Parallel_1”,-36.0],PARAMETER[“Standard_Parallel_2”,-18.0],PARAMETER[“Latitude_Of_Origin”,0.0],UNIT[“Meter”,1.0]]

+proj=aea +lat_1=-18 +lat_2=-36 +lat_0=0 +lon_0=134 +x_0=3000000.0 +y_0=6000000.0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs

Closest - No false easting or northing, and different +lon_0
GDA94 / Australian Albers
ESPG:3577
+proj=aea +lat_1=-18 +lat_2=-36 +lat_0=0 +lon_0=132 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
PROJCS[“Australia Albers Equal Area (134)”,GEOGCS[“GDA94”,DATUM[“D_GDA_1994”,SPHEROID[“GRS_1980”,6378137,298.257222101]],PRIMEM[“Greenwich”,0],UNIT[“Degree”,0.017453292519943295]],PROJECTION[“Albers”],PARAMETER[“standard_parallel_1”,-18],PARAMETER[“standard_parallel_2”,-36],PARAMETER[“latitude_of_origin”,0],PARAMETER[“central_meridian”,134],PARAMETER[“false_easting”,0],PARAMETER[“false_northing”,0],UNIT[“Meter”,1]]

NSW

The albers_3 projection without the false eastings and northings.

Storm Bay, Port Phillip Bay (PPB)

BGM Projection String:
projection proj=utm zone=55 south ellps=GRS80 towgs84=0,0,0,0,0,0,0 units=m no_defs

ArcMap:

Projected coordinate system name: GDA_1994_MGA_Zone_55
Geographic coordinate system name: GCS_GDA_1994

Reference: http://spatialreference.org/ref/epsg/28355/

TasCERF

BGM projection string:

proj=laea +lat_0=-41.1 +lon_0=146.5 +x_0=0 +y_0=0 +ellps=WGS84
++datum=WGS84 +units=m +no_defs

ESRI WKT String is
GEOGCS[“GCS_WGS_1984”,DATUM[“D_WGS_1984”,SPHEROID“WGS_1984”,6378137.0,298.257223563],PRIMEM“Greenwich”,0.0,UNIT“Degree”,0.0174532925199433],PROJECTION“Lambert_Azimuthal_Equal_Area”,PARAMETER“False_Easting”,0.0,PARAMETER“False_Northing”,0.0,PARAMETER“Central_Meridian”,146.5,PARAMETER“Latitude_Of_Origin”,-41.1,UNIT“Meter”,1.0]

Norway

Useful links:

http://qgis.spatialthoughts.com/2012/01/importing-spreadsheets-or-csv-files-to.html