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Add standard transect sections

Also adds a script that was originally used to create the sections (for provenance) and a driver script for merging the features together into a region group based on their common tag.
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@xylar
xylar authored Oct 6, 2017
2 parents dc4acae + c0fb04b commit dcbb2b9
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31 changes: 31 additions & 0 deletions driver_scripts/setup_ocean_standard_transport_sections.py
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#!/usr/bin/env python

"""
This script creates region groups for the standard set of transport sections,
all of which have the "standard_transport_sections" tag.
Author: Xylar Asay-Davis
"""

import os
import os.path
import subprocess

tag = 'standard_transport_sections'
fileName = 'standard_transport_sections.geojson'
groupName = 'StandardTransportSectionsRegionsGroup'

if os.path.exists(fileName):
os.remove(fileName)


subprocess.check_call(['./merge_features.py',
'-d', 'ocean/transect',
'-t', tag,
'-o', fileName])

subprocess.check_call(['./set_group_name.py',
'-f', fileName,
'-g', groupName])

# vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python
280 changes: 280 additions & 0 deletions feature_creation_scripts/transport_transects/transport_sections.m
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%function transport_sections

% Specify data files, coordinates and text, then call functions
% to find edge sections, load data, and compute transport through
% each section.
%
% This script produces new netcdf files in the subdirectory
% netcdf_files which can then be merged with grid.nc or restart.nc
% files to collect transport data in MPAS-Ocean
%
% To merge the new *_section_edge_data.nc with an existing grid or
% restart file, use:
% ncks -A -v sectionEdgeIndex,sectionEdgeSign,nEdgesInSection,\
% sectionText,sectionAbbreviation,sectionCoord \
% your_file_section_edge_data.nc your_restart_file.nc
%
% Mark Petersen, MPAS-Ocean Team, LANL, March 2014

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Specify data files
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% all plots are placed in the f directory. Comment out if not needed.
unix('mkdir -p f netcdf_files docs text_files');

% The text string [wd '/' sim(i).dir '/' sim(i).netcdf_file ] is the file path,
% where wd is the working directory and dir is the run directory.

wd = '/var/tmp/mpeterse/runs/';
dir='m91';
abc = 'klmnop';

for letter=1:length(abc)

% These files only need to contain a small number of variables.
% You may need to reduce the file size before copying to a local
% machine using:
% ncks -v avgNormalVelocity,avgNormalTransportVelocity,nAverage,latVertex,lonVertex,verticesOnEdge,edgesOnVertex,refLayerThickness,dvEdge \
% file_in.nc file_out.nc

clear sim
for j=1:3
sim(j).dir=[dir abc(letter)];
sim(j).netcdf_file = ['output.00' num2str_fixed0(16+j,'%g',2) '-02-01_00.00.00.nc_transport_vars.nc'];
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Specify section coordinates and text
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% sectionText a cell array with text describing each section
sectionText = {
'Drake Passage, S Ocean -56 to -63 lat, 68W lon, section A21, 140+/- 6 Sv in Ganachaud_Wunsch00n and Ganachaud99thesis',...
'Tasmania-Ant, S Ocean -44 to -66 lat, 140E lon, section P12, 157+/-10 Sv in Ganachaud_Wunsch00n and Ganachaud99thesis',...
'Africa-Ant, S Ocean -31.3to -70 lat, 30E lon, section I6, Sv in Ganachaud99thesis ',...
'Antilles Inflow, Carib. -18.4+/-4.7Sv in Johns_ea02dsr '...
'Mona Passage, Caribbian -2.6+/-1.2Sv in Johns_ea02dsr '...
'Windward Passage, Carib -7.0 Sv in Nelepo_ea76sr, Roemmich81jgr '...
'Florida-Cuba, Caribbian 31.5+/-1.5Sv in Johns_ea02dsr, 32.3+/-3.2Sv Larsen92rslpt'...
'Florida-Bahamas, Carib. 27 lat, -80 to -78.8lon, 31.5+/-1.5Sv in Johns_ea02dsr, 32.3+/-3.2Sv Larsen92rslpt'...
'Indonesian Throughflow, -9 to -18 lat, 116E lon, section J89, -16+/- 5 Sv in Ganachaud_Wunsch00n and Ganachaud99thesis',...
'Agulhas -70+/-20 Sv in Bryden_Beal01dsr ',...
'Mozambique Channel, -25 lat, 35 to 44E lon, section I4 , -14+/- 6 Sv in Ganachaud_Wunsch00n and Ganachaud99thesis',...
'Bering Strait, Arctic 0.83+/-0.66Sv in Roach_ea95jgr '...
};
%'Lancaster Sound, Arctic 0.67+/-0.3Sv in Maltrud_McLean05om '...
%'Fram Strait, Arctic -4.2+/-2.3Sv in Fahrbach_ea01pr '...
%'Robeson Channel, Arctic -0.75+/-0.2Sv in Maltrud_McLean05om '...

% sectionAbbreviation an 8-character title for each section
sectionAbbreviation = [...
'Drake Pa';...
'Tasm-Ant';...
'Afri-Ant';...
'Antilles';...
'Mona Pas';...
'Wind Pas';...
'FL-Cuba ';...
'FL-Baham';...
'Ind Thru';...
'Agulhas ';...
'Mozam Ch';...
'Bering ';...
];
% 'Lancastr';...
% 'Fram ';...
% 'Robeson ';...

% sectionCoord(nSections,4) endpoints of sections, with one section per row as
% [startlat startlon endlat endlon]
% Traverse from south to north, and from east to west.
% Then positive velocities are eastward and northward.
sectionCoord = [...
-64.5 -64 -55 -65.3;... % Drake
-67 140 -43.5 147 ;... % Tasm-Ant
-70.0 30 -31.3 30 ;... % Afri-Ant
10.7 -63.2 18.0 -65.9;... % Antilles
18.4 -67.2 18.4 -68.5;... % Mona Passage
19.8 -73.4 20.1 -74.3;... % Windward Passage
23.1 -81.0 25.15 -81.0;... % Florida-Cuba
26.52 -78.78 26.7 -80.1;... % Florida-Bahamas
-21 116.0 -8.8 116 ;... % Ind Thru
-32.4 32.0 -31.0 30.2;... % Agulhas
-25 44.0 -25.0 34 ;... % Mozam Ch
65.8 -167.7 66.1 -169.7;... % Bering St
];
% 73.7 -80.6 74.6 -81.0;... % Lancaster Sound- was not able to
% get this to connect for all resolutions
% 79.7 10.7 79.7 -17.7;... % Fram St - crosses 0 lon. This is not in code yet.
% 81.0 -63.5 82.0 -63.5;... % Robeson Ch - was not able to get this to connect

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Specify variables
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% var_name(nVars) a cell array with text for each variable to
% load or compute.
% var_conv_factor multiply each variable by this unit conversion.
% var_lims(nVars,3) contour line definition: min, max, interval

% Eulerian velocity from prognostic momentum equation
var_name = {'avgNormalVelocity'};
% total transport velocity
%var_name = {'avgNormalTransportVelocity'}

var_conv_factor = [1 1 1]; % No conversion here.

var_lims = [-10 10 2.5; -10 10 2.5; 0 20 2.5];

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Specify actions to be taken
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

find_edge_sections_flag = true ;
write_edge_sections_text_flag = false ;
write_edge_sections_netcdf_flag = false ;
plot_edge_sections_flag = true ;
compute_transport_flag = true ;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Begin main code. Normally this does not need to change.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%close all

% change the coordinate range to be 0 to 360.
sectionCoord(:,2) = mod(sectionCoord(:,2),360);
sectionCoord(:,4) = mod(sectionCoord(:,4),360);

for iSim = 1:length(sim)

fprintf(['**** simulation: ' sim(iSim).dir ' ' sim(iSim).netcdf_file '\n'])
unix(['mkdir -p docs/' sim(iSim).netcdf_file '_dir/f']);
fid_latex = fopen('temp.tex','w');
fprintf(fid_latex,['%% file created by plot_mpas_cross_sections, ' date '\n\n']);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Find edges that connect beginning and end points of section
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if find_edge_sections_flag
[sim(iSim).sectionEdgeIndex, sim(iSim).sectionEdgeSign, sim(iSim).nEdgesInSection, ...
sim(iSim).latSectionVertex,sim(iSim).lonSectionVertex, ...
sim(iSim).latVertexDeg,sim(iSim).lonVertexDeg] ...
= find_edge_sections(wd,sim(iSim).dir,sim(iSim).netcdf_file, ...
sectionText,sectionCoord);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Write section edge information to a netcdf file
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if write_edge_sections_text_flag
write_edge_sections_text...
(sim(iSim).dir, sim(iSim).sectionEdgeIndex, ...
sim(iSim).sectionEdgeSign, sim(iSim).nEdgesInSection, ...
sectionText,sectionAbbreviation,sectionCoord)
end

if write_edge_sections_netcdf_flag
write_edge_sections_netcdf...
(sim(iSim).dir, sim(iSim).sectionEdgeIndex, ...
sim(iSim).sectionEdgeSign, sim(iSim).nEdgesInSection, ...
sectionText,sectionAbbreviation,sectionCoord)
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Plot edge section locations on world map
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if plot_edge_sections_flag
sub_plot_edge_sections(sim(iSim).dir,sectionCoord, ...
sim(iSim).latSectionVertex,sim(iSim).lonSectionVertex, ...
sim(iSim).latVertexDeg,sim(iSim).lonVertexDeg, ...
sim(iSim).sectionEdgeIndex, sim(iSim).nEdgesInSection,...
fid_latex);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Load large variables from netcdf file
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if compute_transport_flag
[sim(iSim).sectionData] = load_large_variables_edge ...
(wd,sim(iSim).dir,sim(iSim).netcdf_file, var_name,var_conv_factor, ...
sim(iSim).sectionEdgeIndex, sim(iSim).nEdgesInSection);
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Compute transport through each section
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if compute_transport_flag
sim(iSim).tr_total = compute_transport ...
(wd,sim(iSim).dir,sim(iSim).netcdf_file, ...
sim(iSim).sectionEdgeIndex, sim(iSim).sectionEdgeSign, sim(iSim).nEdgesInSection, ...
sim(iSim).sectionData,sectionText,sectionAbbreviation);

if iSim==1
tr_total = sim(iSim).tr_total';
else
tr_total = [tr_total; sim(iSim).tr_total'];
end

end

fclose(fid_latex);

end % iSim

% tr_total
mean_transport = mean(tr_total,1);
%fprintf(['mean over time, ' sim(1).dir ' \n' ])
fprintf('%10.2f',mean_transport)
fprintf([' mean, ' sim(1).dir ' \n'])

var_transport = var(tr_total,1);
%fprintf(['variance over time, ' sim(1).dir ' \n' ])
fprintf('%10.2f',var_transport)
fprintf([' var, ' sim(1).dir ' \n'])

std_transport = std(tr_total,1);
%fprintf(['stdev over time, ' sim(1).dir ' \n' ])
fprintf('%10.2f',std_transport)
fprintf([' std, ' sim(1).dir ' \n'])

min_transport = min(tr_total,[],1);
%fprintf(['minimum over time, ' sim(1).dir ' \n' ])
fprintf('%10.2f',min_transport)
fprintf([' min, ' sim(1).dir ' \n'])

max_transport = max(tr_total,[],1);
%fprintf(['maximum over time, ' sim(1).dir ' \n' ])
fprintf('%10.2f',max_transport)
fprintf([' max, ' sim(1).dir ' \n'])

filename = ['data/' sim(1).dir '_' char(var_name) '_small_data_file.mat']
clear sim
save(filename)

end % letter
30 changes: 30 additions & 0 deletions ocean/transect/Africa-Ant/transect.geojson
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{
"type": "FeatureCollection",
"features": [
{
"type": "Feature",
"properties": {
"name": "Africa-Ant",
"tags": "standard_transport_sections",
"object": "transect",
"component": "ocean",
"author": "Mark Petersen, Xylar Asay-Davis",
"depth": "6000.0",
"note": "S Ocean, -31.3to -70 lat, 30E lon, section I6, Sv in Ganachaud99thesis"
},
"geometry": {
"type": "LineString",
"coordinates": [
[
30.000000,
-70.000000
],
[
30.000000,
-31.300000
]
]
}
}
]
}
30 changes: 30 additions & 0 deletions ocean/transect/Agulhas/transect.geojson
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{
"type": "FeatureCollection",
"features": [
{
"type": "Feature",
"properties": {
"name": "Agulhas",
"tags": "standard_transport_sections",
"object": "transect",
"component": "ocean",
"author": "Mark Petersen, Xylar Asay-Davis",
"depth": "6000.0",
"note": "-70+/-20 Sv in Bryden_Beal01dsr"
},
"geometry": {
"type": "LineString",
"coordinates": [
[
32.000000,
-32.400000
],
[
30.200000,
-31.000000
]
]
}
}
]
}
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