MITgcm_contrib/gmaze_pv/compute_density.m

%
% [RHO] = compute_density(SNAPSHOT)
%
% For a time snapshot, this program computes the 
% 3D density from potential temperature and salinity fields.
% THETA and SALTanom are supposed to be defined on the same 
% domain and grid. 
% SALTanom is by default a salinity anomaly vs 35PSU.
% If not, (is absolute value) set the global variable is_SALTanom to 0
% 
%
% Files names are:
% INPUT:
% ./netcdf-files/<SNAPSHOT>/<netcdf_THETA>.<netcdf_domain>.<netcdf_suff>
% ./netcdf-files/<SNAPSHOT>/<netcdf_SALTanom>.<netcdf_domain>.<netcdf_suff>
% OUPUT:
% ./netcdf-files/<SNAPSHOT>/RHO.<netcdf_domain>.<netcdf_suff>
% 
% 06/21/2006
% gmaze@mit.edu
%

  
function varargout = compute_density(snapshot)


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Setup
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global sla netcdf_THETA netcdf_SALTanom netcdf_domain netcdf_suff
global is_SALTanom
pv_checkpath


%% THETA and SALTanom files name:
filTHETA = strcat(netcdf_THETA   ,'.',netcdf_domain);
filSALTa = strcat(netcdf_SALTanom,'.',netcdf_domain);

%% Path and extension to find them:
pathname = strcat('netcdf-files',sla,snapshot);
%pathname = '.';
ext      = strcat('.',netcdf_suff);

%% Load netcdf files:
ferfile = strcat(pathname,sla,filTHETA,ext);
ncTHETA = netcdf(ferfile,'nowrite');
THETAvariables = var(ncTHETA);

ferfile = strcat(pathname,sla,filSALTa,ext);
ncSALTa = netcdf(ferfile,'nowrite');
SALTavariables = var(ncSALTa);

%% Gridding:
% Don't care about the grid here !
% SALTanom and THETA are normaly defined on the same grid
% So we compute rho on it.

%% Flags:
global toshow % Turn to 1 to follow the computing process


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Now we compute the density
%% The routine used is densjmd95.m
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Axis (usual netcdf files):
if toshow,disp('Dim');end
[lon lat dpt] = coordfromnc(ncTHETA);
nx = length(lon);
ny = length(lat);
nz = length(dpt);

% Pre-allocate:
if toshow,disp('Pre-allocate');end
RHO = zeros(nz,ny,nx);

global is_SALTanom
if exist('is_SALTanom')
  if is_SALTanom == 1
    bS = 35;
  else
    bS = 0;
  end
end

% Then compute density RHO:
for iz = 1 : nz
  if toshow,disp(strcat('Compute density at level:',num2str(iz),'/',num2str(nz)));end
  
  S = SALTavariables{4}(iz,:,:) + bS; % Move the anom to an absolute field
  T = THETAvariables{4}(iz,:,:);
  P = (0.09998*9.81*dpt(iz))*ones(ny,nx);
  RHO(iz,:,:) = densjmd95(S,T,P);
  
end %for iz


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Record output:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% General informations: 
netfil     = strcat('RHO','.',netcdf_domain,'.',netcdf_suff);
units      = 'kg/m^3';
ncid       = 'RHO';
longname   = 'Density';
uniquename = 'density';

% Open output file:
nc = netcdf(strcat(pathname,sla,netfil),'clobber');

% Define axis:
nc('X') = nx;
nc('Y') = ny;
nc('Z') = nz;

nc{'X'} = 'X';
nc{'Y'} = 'Y';
nc{'Z'} = 'Z';

nc{'X'}            = ncfloat('X');
nc{'X'}.uniquename = ncchar('X');
nc{'X'}.long_name  = ncchar('longitude');
nc{'X'}.gridtype   = nclong(0);
nc{'X'}.units      = ncchar('degrees_east');
nc{'X'}(:)         = lon;

nc{'Y'}            = ncfloat('Y'); 
nc{'Y'}.uniquename = ncchar('Y');
nc{'Y'}.long_name  = ncchar('latitude');
nc{'Y'}.gridtype   = nclong(0);
nc{'Y'}.units      = ncchar('degrees_north');
nc{'Y'}(:)         = lat;
 
nc{'Z'}            = ncfloat('Z');
nc{'Z'}.uniquename = ncchar('Z');
nc{'Z'}.long_name  = ncchar('depth');
nc{'Z'}.gridtype   = nclong(0);
nc{'Z'}.units      = ncchar('m');
nc{'Z'}(:)         = dpt;

% And main field:
nc{ncid}               = ncfloat('Z', 'Y', 'X'); 
nc{ncid}.units         = ncchar(units);
nc{ncid}.missing_value = ncfloat(NaN);
nc{ncid}.FillValue_    = ncfloat(NaN);
nc{ncid}.longname      = ncchar(longname);
nc{ncid}.uniquename    = ncchar(uniquename);
nc{ncid}(:,:,:)        = RHO;


% Close files:
close(ncTHETA);
close(ncSALTa);
close(nc);


% Output:
output = struct('RHO',RHO,'dpt',dpt,'lat',lat,'lon',lon);
switch nargout
 case 1
  varargout(1) = {output};
end
1	gmaze	1.1	%
2	gmaze	1.4	% [RHO] = compute_density(SNAPSHOT)
3	gmaze	1.1	%
4			% For a time snapshot, this program computes the
5	gmaze	1.3	% 3D density from potential temperature and salinity fields.
6	gmaze	1.1	% THETA and SALTanom are supposed to be defined on the same
7	gmaze	1.3	% domain and grid.
8			% SALTanom is by default a salinity anomaly vs 35PSU.
9			% If not, (is absolute value) set the global variable is_SALTanom to 0
10			%
11	gmaze	1.1	%
12	gmaze	1.2	% Files names are:
13			% INPUT:
14			% ./netcdf-files/<SNAPSHOT>/<netcdf_THETA>.<netcdf_domain>.<netcdf_suff>
15			% ./netcdf-files/<SNAPSHOT>/<netcdf_SALTanom>.<netcdf_domain>.<netcdf_suff>
16			% OUPUT:
17			% ./netcdf-files/<SNAPSHOT>/RHO.<netcdf_domain>.<netcdf_suff>
18			%
19	gmaze	1.1	% 06/21/2006
20			% gmaze@mit.edu
21			%
22
23
24	gmaze	1.4	function varargout = compute_density(snapshot)
25	gmaze	1.1
26
27			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
28			%% Setup
29			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
30			global sla netcdf_THETA netcdf_SALTanom netcdf_domain netcdf_suff
31	gmaze	1.3	global is_SALTanom
32	gmaze	1.1	pv_checkpath
33
34
35			%% THETA and SALTanom files name:
36			filTHETA = strcat(netcdf_THETA ,'.',netcdf_domain);
37			filSALTa = strcat(netcdf_SALTanom,'.',netcdf_domain);
38
39			%% Path and extension to find them:
40			pathname = strcat('netcdf-files',sla,snapshot);
41	gmaze	1.5	%pathname = '.';
42	gmaze	1.1	ext = strcat('.',netcdf_suff);
43
44			%% Load netcdf files:
45			ferfile = strcat(pathname,sla,filTHETA,ext);
46			ncTHETA = netcdf(ferfile,'nowrite');
47			THETAvariables = var(ncTHETA);
48
49			ferfile = strcat(pathname,sla,filSALTa,ext);
50			ncSALTa = netcdf(ferfile,'nowrite');
51			SALTavariables = var(ncSALTa);
52
53			%% Gridding:
54			% Don't care about the grid here !
55			% SALTanom and THETA are normaly defined on the same grid
56			% So we compute rho on it.
57
58			%% Flags:
59			global toshow % Turn to 1 to follow the computing process
60
61
62			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
63			%% Now we compute the density
64			%% The routine used is densjmd95.m
65			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
66
67			% Axis (usual netcdf files):
68			if toshow,disp('Dim');end
69			[lon lat dpt] = coordfromnc(ncTHETA);
70			nx = length(lon);
71			ny = length(lat);
72			nz = length(dpt);
73
74			% Pre-allocate:
75			if toshow,disp('Pre-allocate');end
76			RHO = zeros(nz,ny,nx);
77
78	gmaze	1.3	global is_SALTanom
79			if exist('is_SALTanom')
80			if is_SALTanom == 1
81			bS = 35;
82			else
83			bS = 0;
84			end
85			end
86
87	gmaze	1.1	% Then compute density RHO:
88			for iz = 1 : nz
89			if toshow,disp(strcat('Compute density at level:',num2str(iz),'/',num2str(nz)));end
90
91	gmaze	1.3	S = SALTavariables{4}(iz,:,:) + bS; % Move the anom to an absolute field
92	gmaze	1.1	T = THETAvariables{4}(iz,:,:);
93			P = (0.099989.81dpt(iz))*ones(ny,nx);
94			RHO(iz,:,:) = densjmd95(S,T,P);
95
96			end %for iz
97
98
99
100
101			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
102			%% Record output:
103			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
104
105			% General informations:
106			netfil = strcat('RHO','.',netcdf_domain,'.',netcdf_suff);
107			units = 'kg/m^3';
108			ncid = 'RHO';
109			longname = 'Density';
110			uniquename = 'density';
111
112			% Open output file:
113			nc = netcdf(strcat(pathname,sla,netfil),'clobber');
114
115			% Define axis:
116			nc('X') = nx;
117			nc('Y') = ny;
118			nc('Z') = nz;
119
120			nc{'X'} = 'X';
121			nc{'Y'} = 'Y';
122			nc{'Z'} = 'Z';
123
124			nc{'X'} = ncfloat('X');
125			nc{'X'}.uniquename = ncchar('X');
126			nc{'X'}.long_name = ncchar('longitude');
127			nc{'X'}.gridtype = nclong(0);
128			nc{'X'}.units = ncchar('degrees_east');
129			nc{'X'}(:) = lon;
130
131			nc{'Y'} = ncfloat('Y');
132			nc{'Y'}.uniquename = ncchar('Y');
133			nc{'Y'}.long_name = ncchar('latitude');
134			nc{'Y'}.gridtype = nclong(0);
135			nc{'Y'}.units = ncchar('degrees_north');
136			nc{'Y'}(:) = lat;
137
138			nc{'Z'} = ncfloat('Z');
139			nc{'Z'}.uniquename = ncchar('Z');
140			nc{'Z'}.long_name = ncchar('depth');
141			nc{'Z'}.gridtype = nclong(0);
142			nc{'Z'}.units = ncchar('m');
143			nc{'Z'}(:) = dpt;
144
145			% And main field:
146			nc{ncid} = ncfloat('Z', 'Y', 'X');
147			nc{ncid}.units = ncchar(units);
148			nc{ncid}.missing_value = ncfloat(NaN);
149			nc{ncid}.FillValue_ = ncfloat(NaN);
150			nc{ncid}.longname = ncchar(longname);
151			nc{ncid}.uniquename = ncchar(uniquename);
152			nc{ncid}(:,:,:) = RHO;
153
154
155	gmaze	1.3
156			% Close files:
157			close(ncTHETA);
158			close(ncSALTa);
159			close(nc);
160
161
162			% Output:
163	gmaze	1.4	output = struct('RHO',RHO,'dpt',dpt,'lat',lat,'lon',lon);
164	gmaze	1.3	switch nargout
165			case 1
166	gmaze	1.4	varargout(1) = {output};
167	gmaze	1.3	end