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added documentation

This commit is contained in:
Michael Stumpf (ifhcluster) 2019-03-26 12:23:53 +00:00
parent 82fefdc6ac
commit ed8a3835f0
3 changed files with 63 additions and 108 deletions
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96
matlab/generate_grid.m
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@ -1,8 +1,16 @@
function [nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,... function [nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
xu1,yu1,zu1,xv1,yv1,zv1,xw1,yw1,zw1,xp1,yp1,zp1,dx,dy,dz]=... xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,dx,dy,dz]=...
generate_grid(a,b,c,d,e,f,nxp,nyp,nzp,x_periodic,y_periodic,z_periodic) generate_grid(a,b,c,d,e,f,nxp,nyp,nzp,xperiodic,yperiodic,zperiodic)
% [nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
% xu,yu,zu,xv,yv,zv,xw,yw,zw,xp,yp,zp,dx,dy,dz]=...
% generate_grid(a,b,c,d,e,f,nxp,nyp,nzp,xperiodic,yperiodic,zperiodic)
% Generates a staggered grid.
% Input
% a,b,c,d,e,f domain bounds
% nxp,nyp,nzp number of points for pressure grid
% x/y/zperiodic domain periodicity
if x_periodic==1 if xperiodic==1
nxu=nxp; nxu=nxp;
nxv=nxp; nxv=nxp;
nxw=nxp; nxw=nxp;
@ -11,7 +19,7 @@ function [nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
nxv=nxp; nxv=nxp;
nxw=nxp; nxw=nxp;
end end
if y_periodic==1 if yperiodic==1
nyu=nyp; nyu=nyp;
nyv=nyp; nyv=nyp;
nyw=nyp; nyw=nyp;
@ -20,7 +28,7 @@ function [nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
nyv=nyp+1; nyv=nyp+1;
nyw=nyp; nyw=nyp;
end end
if z_periodic==1 if zperiodic==1
nzu=nzp; nzu=nzp;
nzv=nzp; nzv=nzp;
nzw=nzp; nzw=nzp;
@ -30,83 +38,83 @@ function [nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
nzw=nzp+1; nzw=nzp+1;
end end
%grid step: %grid step:
if x_periodic==1 if xperiodic==1
dx=(b-a)/(nxp); dx=(b-a)/(nxp);
else else
dx=(b-a)/(nxp-1); dx=(b-a)/(nxp-1);
end end
if y_periodic==1 if yperiodic==1
dy=(d-c)/(nyp); dy=(d-c)/(nyp);
else else
dy=(d-c)/(nyp-1); dy=(d-c)/(nyp-1);
end end
if z_periodic==1 if zperiodic==1
dz=(f-e)/(nzp); dz=(f-e)/(nzp);
else else
dz=(f-e)/(nzp-1); dz=(f-e)/(nzp-1);
end end
% %
if x_periodic==1 if xperiodic==1
xu1=a+((1:nxu)-1)*dx; xu=a+((1:nxu)-1)*dx;
else else
xu1=a+((1:nxu)-3/2)*dx; xu=a+((1:nxu)-3/2)*dx;
end end
if y_periodic==1 if yperiodic==1
yu1=c+((1:nyu)-1/2)*dy; yu=c+((1:nyu)-1/2)*dy;
else else
yu1=c+((1:nyu)-1)*dy; yu=c+((1:nyu)-1)*dy;
end end
if z_periodic==1 if zperiodic==1
zu1=e+((1:nzu)-1/2)*dz; zu=e+((1:nzu)-1/2)*dz;
else else
zu1=e+((1:nzu)-1)*dz; zu=e+((1:nzu)-1)*dz;
end end
% %
if x_periodic==1 if xperiodic==1
xv1=a+((1:nxv)-1/2)*dx; xv=a+((1:nxv)-1/2)*dx;
else else
xv1=a+((1:nxv)-1)*dx; xv=a+((1:nxv)-1)*dx;
end end
if y_periodic==1 if yperiodic==1
yv1=c+((1:nyv)-1)*dy; yv=c+((1:nyv)-1)*dy;
else else
yv1=c+((1:nyv)-3/2)*dy; yv=c+((1:nyv)-3/2)*dy;
end end
if z_periodic==1 if zperiodic==1
zv1=e+((1:nzv)-1/2)*dz; zv=e+((1:nzv)-1/2)*dz;
else else
zv1=e+((1:nzv)-1)*dz; zv=e+((1:nzv)-1)*dz;
end end
% %
if x_periodic==1 if xperiodic==1
xw1=a+((1:nxw)-1/2)*dx; xw=a+((1:nxw)-1/2)*dx;
else else
xw1=a+((1:nxw)-1)*dx; xw=a+((1:nxw)-1)*dx;
end end
if y_periodic==1 if yperiodic==1
yw1=c+((1:nyw)-1/2)*dy; yw=c+((1:nyw)-1/2)*dy;
else else
yw1=c+((1:nyw)-1)*dy; yw=c+((1:nyw)-1)*dy;
end end
if z_periodic==1 if zperiodic==1
zw1=e+((1:nzw)-1)*dz; zw=e+((1:nzw)-1)*dz;
else else
zw1=e+((1:nzw)-3/2)*dz; zw=e+((1:nzw)-3/2)*dz;
end end
% %
if x_periodic==1 if xperiodic==1
xp1=a+((1:nxp)-1/2)*dx; xp=a+((1:nxp)-1/2)*dx;
else else
xp1=a+((1:nxp)-1)*dx; xp=a+((1:nxp)-1)*dx;
end end
if y_periodic==1 if yperiodic==1
yp1=c+((1:nyp)-1/2)*dy; yp=c+((1:nyp)-1/2)*dy;
else else
yp1=c+((1:nyp)-1)*dy; yp=c+((1:nyp)-1)*dy;
end end
if z_periodic==1 if zperiodic==1
zp1=e+((1:nzp)-1/2)*dz; zp=e+((1:nzp)-1/2)*dz;
else else
zp1=e+((1:nzp)-1)*dz; zp=e+((1:nzp)-1)*dz;
end end
end end

14
matlab/generate_procgrid.m
View File

@ -4,9 +4,17 @@ function [ibegu,iendu,jbegu,jendu,kbegu,kendu,...
ibegp,iendp,jbegp,jendp,kbegp,kendp]=generate_procgrid(... ibegp,iendp,jbegp,jendp,kbegp,kendp]=generate_procgrid(...
nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,... nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
nxp,nyp,nzp,nxprocs,nyprocs,nzprocs) nxp,nyp,nzp,nxprocs,nyprocs,nzprocs)
% %[ibegu,iendu,jbegu,jendu,kbegu,kendu,...
% determine the 3d decomposition (pointers) of fields for u,v,w,p % ibegv,iendv,jbegv,jendv,kbegv,kendv,...
% % ibegw,iendw,jbegw,jendw,kbegw,kendw,...
% ibegp,iendp,jbegp,jendp,kbegp,kendp]=generate_procgrid(...
% nxu,nyu,nzu,nxv,nyv,nzv,nxw,nyw,nzw,...
% nxp,nyp,nzp,nxprocs,nyprocs,nzprocs)
% Generates a processore grid for a given grid.
% Input
% nxu,nyu,nzu,... staggered grids
% nxprocs,... number of processors
chi='_'; chi='_';
% U: % U:
[ibegu,iendu]=mpe_decomp1d(nxu,nxprocs,chi); [ibegu,iendu]=mpe_decomp1d(nxu,nxprocs,chi);

61
matlab/read_field_complete_ucfmf.m
View File

@ -1,61 +0,0 @@
function [q,x,y,z] = read_field_complete_ucfmf(fdir,iseq,field,varargin)
% [q,x,y,z] = read_field_complete_ucfmf(fdir,iseq,field,varargin)
% Reads a specific field from all processor chunks (multi-file tar version)
% Input
% fdir directory with files
% iseq sequence index
% field field to be read
% {'u','v','w','p','s1','s2',...}
% ? step index of step to be read (default: 1)
% ? verbosity verbose output? (default: 0)
% ? debug debug output? (default: 0)
% Output
% q complete field
% x,y,z corresponding grid
% Parse optional input arguments
par = inputParser;
addParamValue(par,'step',1,@isnumeric);
addParamValue(par,'verbosity',0,@isnumeric);
addParamValue(par,'debug',0,@isnumeric);
parse(par,varargin{:});
istep = par.Results.step;
% Parse field
if ischar(field)
switch field(1)
case 'u'; ifield=1; fbase='uvwp'; cmesh='u';
case 'v'; ifield=2; fbase='uvwp'; cmesh='v';
case 'w'; ifield=3; fbase='uvwp'; cmesh='w';
case 'p'; ifield=4; fbase='uvwp'; cmesh='p';
case 's'; ifield=str2double(field(2:end)); fbase='scal'; cmesh='p';
otherwise; error('Invalid field: %s',field);
end
% Read parameters
fparam = sprintf('%s/parameters_%04d.asc',fdir,iseq);
params = read_parameters_ucf(fparam,'tarmode',0);
% Construct an array with final mesh size
nx = params.mesh.(sprintf('nx%s',cmesh));
ny = params.mesh.(sprintf('ny%s',cmesh));
nz = params.mesh.(sprintf('nz%s',cmesh));
q = zeros(nx,ny,nz);
% Read grid
fgrid = sprintf('%s/grid_%04d.bin',fdir,iseq);
[x.u,y.u,z.u,x.v,y.v,z.v,x.w,y.w,z.w,x.p,y.p,z.p] = read_grid_ucf(fgrid,'tarmode',0);
x = x.(cmesh);
y = y.(cmesh);
z = z.(cmesh);
% Get number of processors
nprocs = params.parallel.nprocs;
% Now read chunk by chunk
for iproc=0:nprocs-1
fq = sprintf('%s/%s_%04d.%05d',fdir,fbase,iseq,iproc);
[data,ib,jb,kb,nxl,nyl,nzl] = read_field_chunk_ucf(fq,ifield,'tarmode',0,'ghost',0,'step',istep);
q(ib:ib+nxl-1,jb:jb+nyl-1,kb:kb+nzl-1) = data;
end
end