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update from taifun

This commit is contained in:
Michael Stumpf (ifhcluster) 2019-11-04 14:33:57 +01:00
parent f85c839a8b
commit 0490050e24
7 changed files with 153 additions and 66 deletions
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44
matlab/read_grid_ucf.m
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@ -1,6 +1,5 @@
function [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,...
nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,nxp,nyp,nzp] = read_grid_ucf(file,varargin)
% [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp] = read_grid_ucf(file,varargin)
function [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,xs,ys,zs] = read_grid_ucf(file,varargin)
% [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,xs,ys,zs] = read_grid_ucf(file,varargin)
% Reads staggered grid from ucf file.
% Input
% file file to be read
@ -11,7 +10,8 @@ function [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,...
% xu,yu,zu velocity grid u
% xv,yv,zv velocity grid v
% xw,yw,zw velocity grid w
% xp,yp,zp pressure grid / scalar grid
% xp,yp,zp pressure grid
% xs,ys,zs scalar grid
% Parse optional input arguments
par = inputParser;
@ -19,10 +19,6 @@ function [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,...
addParamValue(par,'debug',0,@isnumeric);
addParamValue(par,'tarmode',0,@isnumeric); % deprecated
parse(par,varargin{:});
% Define sets to be read
sets = {'u','v','w','p'};
nset = numel(sets);
% Open UCF file and read
obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
@ -35,6 +31,15 @@ function [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,...
otherwise
error('Input file type not supported: %s',class(file));
end
% Define sets to be read
isDualMesh=(obj.UCFVersion>=2);
if isDualMesh
sets = {'u','v','w','p','s'};
else
sets = {'u','v','w','p'};
end
nset = numel(sets);
% Read raw data
x = cell(1,nset);
@ -59,31 +64,30 @@ function [xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,...
xu = x{iset};
yu = y{iset};
zu = z{iset};
nxu = nx{iset};
nyu = ny{iset};
nzu = nz{iset};
iset = find(strcmp(sets,'v'));
xv = x{iset};
yv = y{iset};
zv = z{iset};
nxv = nx{iset};
nyv = ny{iset};
nzv = nz{iset};
iset = find(strcmp(sets,'w'));
xw = x{iset};
yw = y{iset};
zw = z{iset};
nxw = nx{iset};
nyw = ny{iset};
nzw = nz{iset};
iset = find(strcmp(sets,'p'));
xp = x{iset};
yp = y{iset};
zp = z{iset};
nxp = nx{iset};
nyp = ny{iset};
nzp = nz{iset};
if isDualMesh
iset = find(strcmp(sets,'s'));
xs = x{iset};
ys = y{iset};
zs = z{iset};
else
xs = xp;
ys = yp;
zs = zp;
end
end

11
matlab/read_particles_ucf.m
View File

@ -11,7 +11,8 @@ function [pp,col,stime] = read_particles_ucf(file,varargin)
% 'cell' cell array with dim(1,nt) and plain arrays with dim(ncol,np) inside
% ? verbosity verbose output? (default: no)
% ? debug debug output? (default: no)
% ? tarmode read from tar-file? (default: 0)
% ? tarmode read from tar-file? (default: 0)
% ? append read an append file? Only matters for tar archives (default: 0)
% Output
% pp particle data in specified format
% col container map 'char'->'double' which maps quantity names to column index
@ -24,9 +25,11 @@ function [pp,col,stime] = read_particles_ucf(file,varargin)
addParamValue(par,'verbosity',0,@isnumeric);
addParamValue(par,'debug',0,@isnumeric);
addParamValue(par,'tarmode',0,@isnumeric); % deprecated (automatically checked now)
addParamValue(par,'append',0,@isnumeric);
parse(par,varargin{:});
istep = par.Results.step;
mlformat = par.Results.format;
isappend = par.Results.append;
% Open file
obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
@ -34,7 +37,11 @@ function [pp,col,stime] = read_particles_ucf(file,varargin)
case 'char'
obj.open(file);
case {'ustar','ucfmulti'}
ptr = file.pointer('particles.bin');
if isappend
ptr = file.pointer('append_particles.bin');
else
ptr = file.pointer('particles.bin');
end
obj.opentar(ptr);
otherwise
error('Input file type not supported: %s',class(file));

36
matlab/read_procgrid_ucf.m
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@ -2,12 +2,12 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
ibegv,iendv,jbegv,jendv,kbegv,kendv,...
ibegw,iendw,jbegw,jendw,kbegw,kendw,...
ibegp,iendp,jbegp,jendp,kbegp,kendp,...
nxprocs,nyprocs,nzprocs] = read_procgrid_ucf(file,varargin)
ibegs,iends,jbegs,jends,kbegs,kends] = read_procgrid_ucf(file,varargin)
% [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
% ibegv,iendv,jbegv,jendv,kbegv,kendv,...
% ibegw,iendw,jbegw,jendw,kbegw,kendw,...
% ibegp,iendp,jbegp,jendp,kbegp,kendp,...
% nxprocs,nyprocs,nzprocs] = read_procgrid_ucf(file,varargin)
% ibegs,iends,jbegs,jends,kbegs,kends] = read_procgrid_ucf(file,varargin)
% Reads processor grids.
% Input
% file file name (if tar-mode: ustar handle)
@ -18,7 +18,7 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
% ibegv,iendv,jbegv,jendv,kbegv,kendv processor grid v
% ibegw,iendw,jbegw,jendw,kbegw,kendw processor grid w
% ibegp,iendp,jbegp,jendp,kbegp,kendp processor grid p
% nxprocs,nyprocs,nzprocs number of processors
% ibegs,iends,jbegs,jends,kbegs,kends processor grid s
% Parse optional input arguments
par = inputParser;
@ -27,10 +27,6 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
addParamValue(par,'tarmode',0,@isnumeric);
parse(par,varargin{:});
% Define sets to be read
sets = {'u','v','w','p'};
nset = numel(sets);
% Open file
obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
switch class(file)
@ -43,6 +39,15 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
error('Input file type not supported: %s',class(file));
end
% Define sets to be read
isDualMesh=(obj.UCFVersion>=2);
if isDualMesh
sets = {'u','v','w','p','s'};
else
sets = {'u','v','w','p'};
end
nset = numel(sets);
% Read raw data
ibeg = cell(1,nset);
iend = cell(1,nset);
@ -99,4 +104,21 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
jendp = cast(jend{iset},'double');
kbegp = cast(kbeg{iset},'double');
kendp = cast(kend{iset},'double');
if isDualMesh
iset = find(strcmp(sets,'s'));
ibegs = cast(ibeg{iset},'double');
iends = cast(iend{iset},'double');
jbegs = cast(jbeg{iset},'double');
jends = cast(jend{iset},'double');
kbegs = cast(kbeg{iset},'double');
kends = cast(kend{iset},'double');
else
ibegs = ibegp;
iends = iendp;
jbegs = jbegp;
jends = jendp;
kbegs = kbegp;
kends = kendp;
end
end

8
matlab/read_scal_complete_ucf.m
View File

@ -62,7 +62,7 @@ function [s] = read_scal_complete_ucf(file,varargin)
% Reassign content from loop and create global arrays
s = zeros(nx,ny,nz,nscal,class(q{1}));
for iscal=1:nscal
s(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1,iscal) = q{iset};
s(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1,iscal) = q{iscal};
end
% Close the first file
@ -113,7 +113,7 @@ function [s] = read_scal_complete_ucf(file,varargin)
% Reassign content from loop and create global arrays
for iscal=1:nscal
s(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1,iscal) = q{iset};
s(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1,iscal) = q{iscal};
end
% Close file
@ -123,9 +123,9 @@ function [s] = read_scal_complete_ucf(file,varargin)
ifile = ifile+1;
switch class(file)
case 'char'
fname = sprintf('scal.%05d',ifile);
case {'ustar','ucfmulti'}
fname = sprintf('%s/%s.%05d',fdir,fbase,ifile);
case {'ustar','ucfmulti'}
fname = sprintf('scal.%05d',ifile);
end
end
end

33
matlab/read_statistics_channel_ucf.m
View File

@ -1,10 +1,29 @@
function [tbeg,tend,nstat,um,uu,vv,ww,uv,uub,uvb,varargout] = read_statistics_channel_ucf(file,varargin)
% [tbeg,tend,nstat,um,uu,vv,ww,uv,uub,uvb,varargout] = read_statistics_channel_ucf(file,varargin)
% Reads statistics file for channel data in UCF format.
% Input
% file file name (if tar-mode: ustar handle)
% ? verbosity verbose output? (default: no)
% ? debug debug output? (default: no)
% ? pure read an statistics_pure file? Only matters for tar archives (default: 0)
% Output
% tbeg time at beginning of sampling
% tend time at end of sampling
% nstat number of samples
% um mean streamwise velocity
% uu,vv,ww <u'u'>, <v'v'>, <w'w'>
% uv <u'v'>
% uub <uu>
% uvb <uv>
% ? fxp,fyp,fzp particle force in Eulerian frame
% Parse optional input arguments
par = inputParser;
addParamValue(par,'verbosity',0,@isnumeric);
addParamValue(par,'debug',0,@isnumeric);
addParamValue(par,'pure',0,@isnumeric);
parse(par,varargin{:});
ispure = par.Results.pure;
% Define sets to be read
sets = {'um','uu','vv','ww','uv','uub','uvb'};
@ -12,7 +31,19 @@ function [tbeg,tend,nstat,um,uu,vv,ww,uv,uub,uvb,varargout] = read_statistics_ch
% Open UCF file and read
obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
obj.open(file);
switch class(file)
case 'char'
obj.open(file);
case {'ustar','ucfmulti'}
if ispure
ptr = file.pointer('statistics_pure.bin');
else
ptr = file.pointer('statistics.bin');
end
obj.opentar(ptr);
otherwise
error('Input file type not supported: %s',class(file));
end
tend = obj.getSimulationTime();
% Read first dataset

32
matlab/write_uvwp_complete_ucf.m
View File

@ -62,35 +62,35 @@ function [] = write_uvwp_complete_ucf(file,...
ighost = 0;
% Write u
nxul = size(u,1)-2*ighost;
nyul = size(u,2)-2*ighost;
nzul = size(u,3)-2*ighost;
params = int64([ighost,ibu,jbu,kbu,nxul,nyul,nzul,nxu,nyu,nzu]);
data = u(ibu:ieu,jbu:jeu,kbu:keu);
nxul = size(data,1)-2*ighost;
nyul = size(data,2)-2*ighost;
nzul = size(data,3)-2*ighost;
params = int64([ighost,ibu,jbu,kbu,nxul,nyul,nzul,nxu,nyu,nzu]);
obj.appendSet(data,params);
% Write v
nxvl = size(v,1)-2*ighost;
nyvl = size(v,2)-2*ighost;
nzvl = size(v,3)-2*ighost;
params = int64([ighost,ibv,jbv,kbv,nxvl,nyvl,nzvl,nxv,nyv,nzv]);
data = v(ibv:iev,jbv:jev,kbv:kev);
nxvl = size(data,1)-2*ighost;
nyvl = size(data,2)-2*ighost;
nzvl = size(data,3)-2*ighost;
params = int64([ighost,ibv,jbv,kbv,nxvl,nyvl,nzvl,nxv,nyv,nzv]);
obj.appendSet(data,params);
% Write w
nxwl = size(w,1)-2*ighost;
nywl = size(w,2)-2*ighost;
nzwl = size(w,3)-2*ighost;
params = int64([ighost,ibw,jbw,kbw,nxwl,nywl,nzwl,nxw,nyw,nzw]);
data = w(ibw:iew,jbw:jew,kbw:kew);
nxwl = size(data,1)-2*ighost;
nywl = size(data,2)-2*ighost;
nzwl = size(data,3)-2*ighost;
params = int64([ighost,ibw,jbw,kbw,nxwl,nywl,nzwl,nxw,nyw,nzw]);
obj.appendSet(data,params);
% Write p
nxpl = size(p,1)-2*ighost;
nypl = size(p,2)-2*ighost;
nzpl = size(p,3)-2*ighost;
params = int64([ighost,ibp,jbp,kbp,nxpl,nypl,nzpl,nxp,nyp,nzp]);
data = p(ibp:iep,jbp:jep,kbp:kep);
nxpl = size(data,1)-2*ighost;
nypl = size(data,2)-2*ighost;
nzpl = size(data,3)-2*ighost;
params = int64([ighost,ibp,jbp,kbp,nxpl,nypl,nzpl,nxp,nyp,nzp]);
obj.appendSet(data,params);
% Close chunk file

55
matlab/write_uvwp_newmesh_ucf.m
View File

@ -75,28 +75,51 @@ function [] = write_uvwp_newmesh_ucf(file,...
obj = ucf('verbosity',par.Results.verbosity,'debug',par.Results.debug);
obj.create(fname,'type','field','rank',[iproc,ixproc,iyproc,izproc],'endian',par.Results.endian);
obj.appendStep(time);
ighost = 0;
% Interpolate to refined chunk and write
tmp = giu({xun(ibu:ieu),yun(jbu:jeu),zun(kbu:keu)});
if any(isnan(tmp))
warning('NaN detected: u, proc #%d, %d occurences',iproc,sum(isnan(tmp(:))));
data = giu({xun(ibu:ieu),yun(jbu:jeu),zun(kbu:keu)});
if any(isnan(data))
warning('NaN detected: u, proc #%d, %d occurences',iproc,sum(isnan(data(:))));
end
obj.appendField(tmp,0,ibu,jbu,kbu,nxu,nyu,nzu);
tmp = giv({xvn(ibv:iev),yvn(jbv:jev),zvn(kbv:kev)});
if any(isnan(tmp))
warning('NaN detected: v, proc #%d, %d occurences',iproc,sum(isnan(tmp(:))));
nxul = size(data,1)-2*ighost;
nyul = size(data,2)-2*ighost;
nzul = size(data,3)-2*ighost;
params = int64([ighost,ibu,jbu,kbu,nxul,nyul,nzul,nxu,nyu,nzu]);
obj.appendSet(data,params);
% v
data = giv({xvn(ibv:iev),yvn(jbv:jev),zvn(kbv:kev)});
if any(isnan(data))
warning('NaN detected: v, proc #%d, %d occurences',iproc,sum(isnan(data(:))));
end
obj.appendField(tmp,0,ibv,jbv,kbv,nxv,nyv,nzv);
tmp = giw({xwn(ibw:iew),ywn(jbw:jew),zwn(kbw:kew)});
if any(isnan(tmp))
warning('NaN detected: w, proc #%d, %d occurences',iproc,sum(isnan(tmp(:))));
nxvl = size(data,1)-2*ighost;
nyvl = size(data,2)-2*ighost;
nzvl = size(data,3)-2*ighost;
params = int64([ighost,ibv,jbv,kbv,nxvl,nyvl,nzvl,nxv,nyv,nzv]);
obj.appendSet(data,params);
% w
data = giw({xwn(ibw:iew),ywn(jbw:jew),zwn(kbw:kew)});
if any(isnan(data))
warning('NaN detected: w, proc #%d, %d occurences',iproc,sum(isnan(data(:))));
end
obj.appendField(tmp,0,ibw,jbw,kbw,nxw,nyw,nzw);
tmp = gip({xpn(ibp:iep),ypn(jbp:jep),zpn(kbp:kep)});
if any(isnan(tmp))
warning('NaN detected: p, proc #%d, %d occurences',iproc,sum(isnan(tmp(:))));
nxwl = size(data,1)-2*ighost;
nywl = size(data,2)-2*ighost;
nzwl = size(data,3)-2*ighost;
params = int64([ighost,ibw,jbw,kbw,nxwl,nywl,nzwl,nxw,nyw,nzw]);
obj.appendSet(data,params);
% p
data = gip({xpn(ibp:iep),ypn(jbp:jep),zpn(kbp:kep)});
if any(isnan(data))
warning('NaN detected: p, proc #%d, %d occurences',iproc,sum(isnan(data(:))));
end
obj.appendField(tmp,0,ibp,jbp,kbp,nxp,nyp,nzp);
nxpl = size(data,1)-2*ighost;
nypl = size(data,2)-2*ighost;
nzpl = size(data,3)-2*ighost;
params = int64([ighost,ibp,jbp,kbp,nxpl,nypl,nzpl,nxp,nyp,nzp]);
obj.appendSet(data,params);
obj.close();
end