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Diffusion FENNECS: Finite Element Non-Neutral Electron Cloud Simulator (master) Browse

fennecs/matlab/savegeomtoh5.m
b121cf310431master

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savegeomtoh5.m
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function savegeomtoh5(filename,splines,dist_extent,overwrite)
% saves the geometry to be used with Fennecs
% splines is a structure array containing each individual boundary
% Overwrite defines if the .h5 file must be overwritten
% dist_extent is the distance in m on which the geometric weight goes from 0 to 1
% dist_extent can also be set in the job input file
% To look how to define each spline read the function
if nargin<4
overwrite=false;
end
group='/geometry_spl/';
try
fid=H5F.create(filename);
H5F.flush(fid,'H5F_SCOPE_LOCAL')
catch
if overwrite
delete(filename);
fid=H5F.create(filename);
H5F.flush(fid,'H5F_SCOPE_LOCAL')
else
error('cFile "%s" already exists\n',filename) ;
end
end
nbsplines=length(splines);
gid=H5G.create(fid,group,64);
h5writeatt(filename,group,'nbsplines',nbsplines); % total number of spline curves
h5writeatt(filename,group,'dist_extent',dist_extent);
if iscell(splines)
splines=cell2mat(splines);
end
for i=1:nbsplines
grp=sprintf('/geometry_spl/%2.2d',i);
gid=H5G.create(fid,grp,64);
h5writeatt(filename,grp,'Dirichlet_val',splines(i).Dval); % value of the electic potential in V at the boundary surface
h5writeatt(filename,grp,'order',splines(i).order); % order of the spline used to define the boundary
h5writeatt(filename,grp,'dim',splines(i).dim); % dimension of the spline curve
% epsge and epsce have no clear effect default values can be used
if isfield(splines(i),'epsge')
h5writeatt(filename,grp,'epsge',splines(i).epsge); % geometric presicion used by SISL for calculating distance to curve
else
h5writeatt(filename,grp,'epsge',1e-6); % geometric presicion used by SISL for calculating distance to curve
end
if isfield(splines(i),'epsce')
h5writeatt(filename,grp,'epsce',splines(i).epsce); % geometric presicion used by SISL for calculating distance to curve
else
h5writeatt(filename,grp,'epsce',1e-6); % geometric presicion used by SISL for calculating distance to curve
end
h5writeatt(filename,grp,'name',splines(i).name); % name of the boundary for readability of h5(not used in fennecs)
if isfield(splines(i),'type')
% boundary condition type (0 dirichlet fixed value)
% 1 Dirichlet with value depending on position
% 2 Natural
h5writeatt(filename,grp,'type',splines(i).type);
else
h5writeatt(filename,grp,'type',0);
end
if isfield(splines(i),'periodic')
% periodicity of the curve 1 closed periodic 0 open
h5writeatt(filename,grp,'periodic',splines(i).periodic);
else
h5writeatt(filename,grp,'periodic',0);
end
points=splines(i).points;
if size(splines(i).points,2)>splines(i).dim
points=points';
end
h5create(filename,[grp,'/pos'],size(points));
h5write(filename,[grp,'/pos'],points); % control points defining the curve
end
H5F.close(fid);
end
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