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ReadStag3D_LeaV.m
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function [varargout] = ReadStag3D_Lea(directory, fname_input, fname_number,Type)% Reads a STAG3D output file and transforms it into a MATLAB file
%
% Tested for 3D cartesian
%
%
% Syntax:
% For scalar fields:
%
% [X_3D, Y_3D, Z_3D, DATA_3D] = ReadStag3D(fname_input, fname_number, {'viscosity','temperature'});
%
% For vector fields:
%
% [X_3D, Y_3D, Z_3D, VX_3D, VY_3D, VZ_3D, P_3D] = ReadStag3D(fname_input, fname_number, {'viscosity','temperature'});
%
%
% Boris Kaus
%
% Modifications by Paul Tackley August 2010:
% - extra fields: topography, topography self-grav, crustal
% thickness, age, strain rate, geoid
% - unimplemented 2Dfield stuff deleted: 3D routine works for 2D fields
% - velocities & p now read into 4D arrays: yy split is done on output
% - correction to the storage order of v* and p
% - checks magic whether #components matches nval
% - compatibility with magic=9 storing extra x & y points for vectors
% - added missing scaling factor read for vectors
%
%
% Adapted by Lea Bello and Marie Bocher to be used in Error_Temp (for forecasting time calculation)
%
start_dir = pwd;
cd(directory);
FileFormat = 'n'; % native - default
%FileFormat = 'l'; % Little Endian
%FileFormat = 'b'; % Big Endian
if fname_number<10000
number_string = num2str(10000+fname_number);
number_string(1)='0';
else
number_string = num2str(10000+fname_number);
end
switch Type
case 'velocity'
fname = [fname_input,'_vp',number_string];
scalardata = false;
case 'residue'
fname = [fname_input,'_rs',number_string];
scalardata = false;
case 'temperature'
fname = [fname_input,'_t',number_string];
scalardata = true;
case 'viscosity'
fname = [fname_input,'_eta',number_string];
scalardata = true;
case 'composition'
fname = [fname_input,'_comp',number_string];
scalardata = true;
case 'cont root'
fname = [fname_input,'_c',number_string];
scalardata = true;
case 'cont crust'
fname = [fname_input,'_cc',number_string];
scalardata = true;
case 'cont belt'
fname = [fname_input,'_ccc',number_string];
scalardata = true;
case 'cont suture'
fname = [fname_input,'_cccc',number_string];
scalardata = true;
case 'cont plot'
fname = [fname_input,'_cpl',number_string];
scalardata = true;
case 'continent'
fname = [fname_input,'_nrc',number_string];
scalardata = true;
case 'melt fraction'
fname = [fname_input,'_f',number_string];
scalardata = true;
case 'topography'
fname = [fname_input,'_cs',number_string];
scalardata = true;
case 'topography self-grav'
fname = [fname_input,'_csg',number_string];
scalardata = true;
case 'crustal thickness'
fname = [fname_input,'_cr',number_string];
scalardata = true;
case 'age'
fname = [fname_input,'_age',number_string];
scalardata = true;
case 'strain rate'
fname = [fname_input,'_ed',number_string];
scalardata = true;
case 'geoid'
fname = [fname_input,'_g',number_string];
scalardata = true;
case 'stress'
fname = [fname_input,'_str',number_string];
scalardata = true;
case 'damage'
fname = [fname_input,'_d',number_string];
scalardata = true;
case 'heat flux'
fname = [fname_input,'_hf',number_string];
scalardata = true;
otherwise
error('Unknown property')
end
if ~exist(fname)
% The file does not exist and we should stop processing data
cd(start_dir);
for i=1:10
varargout{i} = -999;
end
return
end
if scalardata
nval = 1; % temperature has only one value
else
nval = 4; % assumed that we have a velocity-pressure file
end
fid = fopen(fname,'r',FileFormat); % Open File
%==========================================================================
% READ HEADER
%==========================================================================
magic = fread(fid,1,'int32'); % Version
if (magic<100 && nval>1) || (magic>300 && nval==1) % check #components
error('wrong number of components in field')
end
magic = mod(magic,100);
if magic>=9 && nval==4
xyp = 1; % extra ghost point in x & y direction
else
xyp = 0;
end
nxtot = fread(fid,1,'int32'); % nx total
nytot = fread(fid,1,'int32'); % ny total
nztot = fread(fid,1,'int32'); % nz total
nblocks = fread(fid,1,'int32'); % # of blocks, 2 for yinyang
Aspect = fread(fid,2,'single'); % Aspect ratio
nnx = fread(fid,1,'int32'); % Number of parallel subdomains
nny = fread(fid,1,'int32'); % in the x,y,z and b directions
nnz = fread(fid,1,'int32'); %
nnb = fread(fid,1,'int32'); %
nz2 = nztot*2 + 1;
zg = fread(fid,nz2,'single'); % z-coordinates
% compute nx, ny, nz and nb PER CPU
nx = nxtot/nnx;
ny = nytot/nny;
nz = nztot/nnz;
nb = nblocks/nnb;
npi = (nx+xyp)*(ny+xyp)*nz*nb*nval; % the number of values per 'read' block
rcmb = fread(fid,1,'single');
istep = fread(fid,1,'int32');
time = fread(fid,1,'single');
erupta_total= fread(fid,1,'single');
botT_val = fread(fid,1,'single');
x = fread(fid,nxtot,'single'); % x-coordinates
y = fread(fid,nytot,'single'); % y-coordinates
z = fread(fid,nztot,'single'); % z-coordinates
% read the parallel blocks
if scalardata
DATA_3D = zeros(nxtot,nytot,nztot);
else
scalefac= fread(fid,1,'single'); % scale factor
VX_3D = zeros(nxtot,nytot,nztot); % Vx
VY_3D = zeros(nxtot,nytot,nztot); % Vy
VZ_3D = zeros(nxtot,nytot,nztot); % Vz
P_3D = zeros(nxtot,nytot,nztot); % Pressure
end
for ibc=1:nnb % loop over parallel subdomains
for izc =1:nnz
for iyc =1:nny
for ixc =1:nnx
data_CPU = fread(fid,npi,'single'); % read the data for this CPU
% Create a 3D matrix from these data
if scalardata
data_CPU_3D = reshape(data_CPU, [nx ny nz nb]) ;
else
data_CPU_3D = reshape(data_CPU*scalefac, [nval nx+xyp ny+xyp nz nb]);
end
% Add local 3D matrix to global matrix
if scalardata
% Scalar data
DATA_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz),(ibc-1)*nb + (1:nb)) = data_CPU_3D;
else
% velocity-pressure data
VX_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(1,1:nx,1:ny,:,:));
VY_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(2,1:nx,1:ny,:,:));
VZ_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(3,1:nx,1:ny,:,:));
P_3D( (ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(4,1:nx,1:ny,:,:));
RX_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(1,1:nx,1:ny,:,:));
RY_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(2,1:nx,1:ny,:,:));
RZ_3D((ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(3,1:nx,1:ny,:,:));
RP_3D( (ixc-1)*nx + (1:nx), (iyc-1)*ny + (1:ny), (izc-1)*nz + (1:nz), (ibc-1)*nb + (1:nb)) = squeeze(data_CPU_3D(4,1:nx,1:ny,:,:));
end
end
end
end
end
fclose(fid); % close file
[Y_3D, X_3D, Z_3D] = meshgrid(y,x,z);
% Transform coordinates for Yin & Yang grids
RYin = Z_3D+rcmb;
ThYin = pi/4-X_3D;
PhiYin = Y_3D-3*pi/4;
XYin=RYin.*cos(ThYin).*cos(PhiYin);
YYin=RYin.*cos(ThYin).*sin(PhiYin);
ZYin = RYin.*sin(ThYin);
XYang=-XYin;
YYang=ZYin;
ZYang=YYin;
RedFlagYin=zeros(size(XYin));
RedFlagYang=zeros(size(XYang));
for kray=1:nztot
minYYang=min(min(YYang(:,:,kray)));
maxYYang=max(max(YYang(:,:,kray)));
YinDel=XYin(:,:,kray)<=0&YYin(:,:,kray)<=maxYYang&YYin(:,:,kray)>=minYYang;
RedFlagYin(:,:,kray)=YinDel;
YangDel=XYang(:,:,kray)>=0&ZYang(:,:,kray)<=max(max(ZYin(:,:,kray)))&ZYang(:,:,kray)>=min(min(ZYin(:,:,kray)));
RedFlagYang(:,:,kray)=YangDel;
end
% erase overlapping points
RedFlag=[RedFlagYin RedFlagYang];
RYinYang=[RYin RYin];
CoordX=[XYin XYang];
CoordY=[YYin YYang];
CoordZ=[ZYin ZYang];
%% volume
VolYin=zeros(nxtot,nytot,nztot);
Vol=zeros(nxtot,2*nytot,nztot);
for i=1:nxtot
for k=1:nztot
dz(k)= zg(2*k+1)-zg(2*k-1);
VolYin(i,:,k)= dz(k) .* sin(pi/4+X_3D(i,:,k)).*(pi/(2*nxtot))^2 .* (rcmb+zg(2*k)).^2;
end
end
Vol=[VolYin VolYin]; %same evolution of the volume on yin and yang, decrasing with colatitude=pi/4+X_3D(i,:,k)
%Vol=Vol(~logical(RedFlag));
%% prepare output data
varargout{1} = Vol; % old version: varargout{1} = nblocks;
varargout{2} =CoordX; % ThYin;
varargout{3} =CoordY; %PhiYin;
varargout{4} =CoordZ; %CoordZ;
if nblocks==1
% no ying-yang
switch Type
case 'velocity'
varargout{5} = VX_3D;
varargout{6} = VY_3D;
varargout{7} = VZ_3D;
varargout{8} = P_3D;
varargout{9} = time;
varargout{10}= rcmb;
otherwise
varargout{5} = DATA_3D;
varargout{6} = time;
varargout{7} = rcmb;
end
else
% ying-yang grid
switch Type
case 'velocity'
varargout{5} = VX_3D(:,:,:,1);
varargout{6} = VY_3D(:,:,:,1);
varargout{7} = VZ_3D(:,:,:,1);
varargout{8} = RedFlag; %previous version: P_3D (:,:,:,1);
varargout{9} = VX_3D(:,:,:,2);
varargout{10} = VY_3D(:,:,:,2);
varargout{11} = VZ_3D(:,:,:,2);
varargout{12} = CoordZ(:,:,:); %previous version: P_3D (:,:,:,2);
varargout{13} = time;
varargout{14} = rcmb;
varargout{15} = z;
%% calcul of vsurf
RedFlagsurf=[RedFlagYin(:,:,size(RedFlagYin,3)) RedFlagYang(:,:,size(RedFlagYang,3))];
VXsurf = [VX_3D(:,:,size(VX_3D,3),1) VX_3D(:,:,size(VX_3D,3),2)];
VYsurf = [VY_3D(:,:,size(VY_3D,3),1) VY_3D(:,:,size(VY_3D,3),2)];
VZsurf = [VZ_3D(:,:,size(VZ_3D,3),1) VZ_3D(:,:,size(VZ_3D,3),2)];
vsurf_tot=(VXsurf.^2 + VYsurf.^2);
vsurf_tot_real=vsurf_tot(~logical(RedFlagsurf));
%bottom velocity
%RedFlagbot=[RedFlagYin(:,:,1) RedFlagYang(:,:,1)];
%VXsurf = [VX_3D(:,:,1,1) VX_3D(:,:,1,2)];
%VYsurf = [VY_3D(:,:,1,1) VY_3D(:,:,1,2)];
%vsurf_tot=(VXsurf.^2 + VYsurf.^2);
%vsurf_tot_real=vsurf_tot(~logical(RedFlagbot));
varargout{16} = mean(mean(vsurf_tot_real)).^(1/2);
% calcul of v
VX = [VX_3D(:,:,:,1) VX_3D(:,:,:,2)];
VY = [VY_3D(:,:,:,1) VY_3D(:,:,:,2)];
VZ = [VZ_3D(:,:,:,1) VZ_3D(:,:,:,2)];
v_tot=(VX.^2 + VY.^2 + VZ.^2);
varargout{17} = v_tot; %CAUTION: v_tot=velocity*Volume of cell
varargout{18} = VXsurf;
varargout{19} = VYsurf;
varargout{20} = RedFlagsurf;
case 'residue'
varargout{5} = RX_3D(:,:,:,1);
varargout{6} = RY_3D(:,:,:,1);
varargout{7} = RZ_3D(:,:,:,1);
varargout{8} = RP_3D (:,:,:,1);
varargout{9} = RX_3D(:,:,:,2);
varargout{10} = RY_3D(:,:,:,2);
varargout{11} = RZ_3D(:,:,:,2);
varargout{12} = RP_3D (:,:,:,2);
varargout{13} = time;
varargout{14} = zg;
otherwise
varargout{5} = DATA_3D(:,:,:,1);
varargout{6} = DATA_3D(:,:,:,2);
DATA_tot = [DATA_3D(:,:,:,1) DATA_3D(:,:,:,2)];
varargout{7} = DATA_tot(~logical(RedFlag));
varargout{8} = RedFlag;
varargout{9} = XYin;
varargout{10} = YYin;
varargout{11} = ZYin;
varargout{12} = CoordZ(:,:,:); %previous version: P_3D (:,:,:,2);
varargout{13} = time;
varargout{14} = rcmb;
varargout{15} = z;
end
end
cd(start_dir);