example updates & fix in HDF5 plot and mesh handling

matlab/PlotHDF5FieldData.m

@@ -25,7 +25,10 @@ mesh = ReadHDF5Mesh(file);
 fields = ReadHDF5FieldData(file);
 
 if (mesh.type==0)
-    [X Y Z] = meshgrid(double(mesh.lines{1}),double(mesh.lines{2}),double(mesh.lines{3}));
+    % matlab is building a meshgrid incorrect, adressing it like X(y,x,z)
+    % ??it's not a bug, it's a feature??
+    % check if this workaround is correct  (TL)
+    [X Y Z] = meshgrid(mesh.lines{2},mesh.lines{1},mesh.lines{3});
 else
     disp(['PlotHDF5FieldData:: Error: unknown mesh type ' num2str(mesh.type)]);
 end
@@ -34,13 +37,13 @@ max_amp = 0;
 
 if (component>0)
     for n=1:numel(fields.values)
-        Field{n} = double(fields.values{n}(:,:,:,component));
+        Field{n} = fields.values{n}(:,:,:,component);
     end
 else 
     for n=1:numel(fields.values)
-        fx = double(fields.values{n}(:,:,:,1));
+        fx = fields.values{n}(:,:,:,1);
-        fy = double(fields.values{n}(:,:,:,2));
+        fy = fields.values{n}(:,:,:,2);
-        fz = double(fields.values{n}(:,:,:,3));
+        fz = fields.values{n}(:,:,:,3);
         Field{n} = sqrt(fx.^2 + fy.^2 + fz.^2);
     end        
 end

matlab/ReadHDF5Mesh.m

@@ -22,7 +22,7 @@ end
 
 hdf_mesh.names = names;
 for n=1:numel(names)
-    hdf_mesh.lines{n} = hdf5read(file,names{n});
+    hdf_mesh.lines{n} = double(hdf5read(file,names{n}));
 end
 
 if (strcmp(names{1},'/mesh/rho'))

matlab/examples/Circ_Waveguide.m

@@ -33,16 +33,19 @@ openEMS_opts = '';
 % openEMS_opts = [openEMS_opts ' --disable-dumps'];
 % openEMS_opts = [openEMS_opts ' --debug-material'];
 % openEMS_opts = [openEMS_opts ' --debug-operator'];
-% openEMS_opts = [openEMS_opts ' --engine=multithreaded'];
+openEMS_opts = [openEMS_opts ' --engine=sse-compressed'];
 
 Sim_Path = 'tmp';
 Sim_CSX = 'Circ_WG.xml';
 
+if (exist(Sim_Path,'dir'))
+    rmdir(Sim_Path,'s');
+end
 mkdir(Sim_Path);
 
 %% setup FDTD parameter & excitation function %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 FDTD = InitFDTD(1000,1e-6,'OverSampling',5);
-T = 1/f0;
+T = 4*1/f0;
 FDTD = SetCustomExcite(FDTD,f0,[ '(1-exp(-1*(t/' num2str(T) ')^2) ) * sin(2*pi*' num2str(f0) '*t)' ]);
 BC = [1 1 1 1 1 1] * 0;
 FDTD = SetBoundaryCond(FDTD,BC);
@@ -85,23 +88,13 @@ CSX = SetExcitationWeight(CSX, 'excite', weight );
 CSX = AddCylinder(CSX,'excite', 5 ,[0 0 -0.1],[0 0 0.1],rad);
  
 %% define dump boxes... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-CSX = AddDump(CSX,'Et','SubSampling','2,2,4','FileType',1,'DumpMode',2);
+CSX = AddDump(CSX,'Et','SubSampling','2,2,2','FileType',1,'DumpMode',2);
 start = [mesh.x(1) , mesh.y(1) , mesh.z(1)];
 stop = [mesh.x(end) , mesh.y(end) , mesh.z(end)];
 CSX = AddBox(CSX,'Et',0 , start,stop);
 
-% CSX = AddDump(CSX,'Ht','SubSampling','2,2,4','DumpType',1,'FileType',1,'DumpMode',2);
+CSX = AddDump(CSX,'Ht','SubSampling','2,2,2','DumpType',1,'FileType',1,'DumpMode',2);
-% CSX = AddBox(CSX,'Ht',0,start,stop);
+CSX = AddBox(CSX,'Ht',0,start,stop);
-
-% CSX = AddDump(CSX,'Excite_');
-% start = [mesh.x(1) , mesh.y(1) , 0];
-% stop = [mesh.x(end) , mesh.y(end) ,0];
-% CSX = AddBox(CSX,'Excite_',0 , start,stop);
-% 
-% CSX = AddDump(CSX,'Exy');
-% start = [mesh.x(1) , mesh.y(1) , length/2];
-% stop = [mesh.x(end) , mesh.y(end) , length/2];
-% CSX = AddBox(CSX,'Exy',0 , start,stop);
 
 %% define voltage calc boxes %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %voltage calc
@@ -124,6 +117,7 @@ UI = ReadUI('ut1','tmp/');
 plot(UI.TD{1}.t,UI.TD{1}.val);
 grid on;
 
+figure
 % plotting
 if exist('tmp/Et.h5','file')
     PlotArgs.slice = {mesh.x(round(end/2)) mesh.y(round(end/2)) mesh.z(round(end/2))};

matlab/examples/Circ_Waveguide_CylinderCoords.m

@@ -34,7 +34,6 @@ openEMS_opts = '';
 % openEMS_opts = [openEMS_opts ' --disable-dumps'];
 % openEMS_opts = [openEMS_opts ' --debug-material'];
 % openEMS_opts = [openEMS_opts ' --debug-operator'];
-% openEMS_opts = [openEMS_opts ' --engine=multithreaded'];
 
 if (do_Half_Waveguide)
     Sim_Path = 'tmp_half_CWG_CC';
@@ -43,6 +42,9 @@ else
 end
 Sim_CSX = 'Circ_WG_CC.xml';
 
+if (exist(Sim_Path,'dir'))
+    rmdir(Sim_Path,'s');
+end
 mkdir(Sim_Path);
 
 %% setup FDTD parameter & excitation function %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -88,18 +90,19 @@ stop(3)=0.5;
 CSX = AddBox(CSX,'excite', 5 ,start,stop);
  
 %% define dump boxes... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-CSX = AddDump(CSX,'Et','FileType',1,'DumpMode',0,'SubSampling','1,1,5');
+CSX = AddDump(CSX,'Et','FileType',1,'DumpMode',0,'SubSampling','2,2,5');
 start = [mesh.x(1) , mesh.y(1)-y_delta , 0];
 stop = [mesh.x(end) , mesh.y(end)+y_delta , length];
 CSX = AddBox(CSX,'Et',0 , start,stop);
 
-CSX = AddDump(CSX,'Ht','FileType',1,'DumpType',1,'DumpMode',0,'SubSampling','1,1,5');
+CSX = AddDump(CSX,'Ht','FileType',1,'DumpType',1,'DumpMode',0,'SubSampling','2,2,5');
 CSX = AddBox(CSX,'Ht',0 , start,stop);
 
-CSX = AddDump(CSX,'Et_rz_','FileType',0,'DumpMode',2,'SubSampling','1,1,5');
+% % dumpt r-z-plane to vtk-file
-start = [mesh.x(1) , 0 , 0];
+% CSX = AddDump(CSX,'Et_rz_','FileType',0,'DumpMode',2,'SubSampling','1,1,5');
-stop = [mesh.x(end) , 0 , length];
+% start = [mesh.x(1) , 0 , 0];
-CSX = AddBox(CSX,'Et_rz_',0 , start,stop);
+% stop = [mesh.x(end) , 0 , length];
+% CSX = AddBox(CSX,'Et_rz_',0 , start,stop);
 
 %% define voltage calc boxes %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 CSX = AddProbe(CSX,'ut_exc',0);

matlab/examples/Coax.m

@@ -20,18 +20,24 @@ epsR = 1;
 
 %% define openEMS options %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 openEMS_opts = '';
-openEMS_opts = [openEMS_opts ' --disable-dumps'];
 % openEMS_opts = [openEMS_opts ' --debug-material'];
+% openEMS_opts = [openEMS_opts ' --debug-operator'];
+
+% openEMS_opts = [openEMS_opts ' --disable-dumps --engine=fastest'];
+openEMS_opts = [openEMS_opts ' --engine=sse-compressed'];
 
 Sim_Path = 'tmp';
 Sim_CSX = 'coax.xml';
 
+if (exist(Sim_Path,'dir'))
+    rmdir(Sim_Path,'s');
+end
 mkdir(Sim_Path);
 
 %% setup FDTD parameter & excitation function %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 FDTD = InitFDTD(5e5,1e-5);
 FDTD = SetGaussExcite(FDTD,f0,f0);
-BC = [1 1 1 1 1 1] * 0;
+BC = [0 0 0 0 0 0]; %electric walls only
 FDTD = SetBoundaryCond(FDTD,BC);
 
 %% setup CSXCAD geometry & mesh %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

matlab/examples/Coax_CylinderCoords.m

@@ -29,6 +29,9 @@ openEMS_opts = [openEMS_opts ' --disable-dumps'];
 Sim_Path = 'tmp';
 Sim_CSX = 'coax.xml';
 
+if (exist(Sim_Path,'dir'))
+    rmdir(Sim_Path,'s');
+end
 mkdir(Sim_Path);
 
 %% setup FDTD parameter & excitation function %%%%%%%%%%%%%%%%%%%%%%%%%%%%%

matlab/examples/Coax_partial_CylinderCoords.m

@@ -1,128 +0,0 @@
-close all
-clear
-clc
-
-EPS0 = 8.85418781762e-12;
-MUE0 = 1.256637062e-6;
-C0 = 1/sqrt(EPS0*MUE0);
-Z0 = sqrt(MUE0/EPS0);
-
-f0 = 0.5e9;
-epsR = 3.6;
-
-abs_length = 250;
-length = 6000;
-port_dist = 1500;
-rad_i  = 100;
-rad_a = 230;
-partial = 0.25;
-max_mesh = 10;
-max_alpha = max_mesh;
-N_alpha = ceil(rad_a * 2*pi * partial / max_alpha);
-mesh_res = [max_mesh 2*pi*partial/N_alpha max_mesh];
-
-openEMS_opts = '';
-openEMS_opts = [openEMS_opts ' --disable-dumps'];
-% openEMS_opts = [openEMS_opts ' --debug-material'];
-
-Sim_Path = 'tmp';
-Sim_CSX = 'coax.xml';
-
-mkdir(Sim_Path);
-
-%setup FDTD parameter
-FDTD = InitCylindricalFDTD(1e5,1e-5);
-FDTD = SetGaussExcite(FDTD,f0,f0);
-BC = [0 0 1 1 0 0];
-FDTD = SetBoundaryCond(FDTD,BC);
-
-%setup CSXCAD geometry
-CSX = InitCSX();
-mesh.x = rad_i : mesh_res(1) : rad_a;
-mesh.y = -pi*partial-mesh_res(2)/2 : mesh_res(2) : pi*partial+mesh_res(2)/2;
-mesh.z = 0 : mesh_res(3) : length;
-CSX = DefineRectGrid(CSX, 1e-3,mesh);
-
-%%%fake pml
-finalKappa = 0.3/abs_length^4;
-finalSigma = finalKappa*MUE0/EPS0/epsR;
-CSX = AddMaterial(CSX,'pml');
-CSX = SetMaterialProperty(CSX,'pml','Kappa',finalKappa,'Epsilon',epsR);
-CSX = SetMaterialProperty(CSX,'pml','Sigma',finalSigma);
-CSX = SetMaterialWeight(CSX,'pml','Kappa',['pow(abs(z)-' num2str(length-abs_length) ',4)']);
-CSX = SetMaterialWeight(CSX,'pml','Sigma',['pow(abs(z)-' num2str(length-abs_length) ',4)']);
-
-start = [rad_i mesh.y(1) length-abs_length];
-stop = [rad_a mesh.y(end) length];
-CSX = AddBox(CSX,'pml',0 ,start,stop);
-
-
-CSX = AddMaterial(CSX,'fill');
-CSX = SetMaterialProperty(CSX,'fill','Epsilon',epsR);
-start = [mesh.x(1) mesh.y(1) 0];
-stop = [mesh.x(end) mesh.y(end) length];
-CSX = AddBox(CSX,'fill',0 ,start,stop);
-
-
-start = [rad_i mesh.y(1) 0];
-stop = [rad_a mesh.y(end) 0];
-
-CSX = AddExcitation(CSX,'excite',0,[1 0 0]);
-weight{1} = '1/rho';
-weight{2} = 0;
-weight{3} = 0;
-CSX = SetExcitationWeight(CSX, 'excite', weight );
-CSX = AddBox(CSX,'excite',0 ,start,stop);
- 
-%dump
-CSX = AddDump(CSX,'Et_','DumpMode',2);
-start = [mesh.x(1) , 0 , mesh.z(1)];
-stop = [mesh.x(end) , 0 , mesh.z(end)];
-CSX = AddBox(CSX,'Et_',0 , start,stop);
-
-CSX = AddDump(CSX,'Ht_','DumpType',1,'DumpMode',2);
-CSX = AddBox(CSX,'Ht_',0,start,stop);
-
-% voltage calc (take a voltage average to be at the same spot as the
-% current calculation)
-CSX = AddProbe(CSX,'ut1_1',0);
-start = [ rad_i 0 port_dist ];stop = [ rad_a 0 port_dist ];
-CSX = AddBox(CSX,'ut1_1', 0 ,start,stop);
-CSX = AddProbe(CSX,'ut1_2',0);
-start = [ rad_i 0 port_dist+mesh_res(3) ];stop = [ rad_a 0 port_dist+mesh_res(3) ];
-CSX = AddBox(CSX,'ut1_2', 0 ,start,stop);
-
-% current calc
-CSX = AddProbe(CSX,'it1',1);
-mid = 0.5*(rad_i+rad_a);
-start = [ 0 mesh.y(1) port_dist ];stop = [ mid mesh.y(end) port_dist ];
-CSX = AddBox(CSX,'it1', 0 ,start,stop);
-
-%Write openEMS compatoble xml-file
-WriteOpenEMS([Sim_Path '/' Sim_CSX],FDTD,CSX);
-
-%cd to working dir and run openEMS
-savePath = pwd();
-cd(Sim_Path); %cd to working dir
-args = [Sim_CSX ' ' openEMS_opts];
-invoke_openEMS(args)
-cd(savePath);
-
-UI = ReadUI({'ut1_1','ut1_2','it1'},'tmp/');
-u_f = (UI.FD{1}.val + UI.FD{2}.val)/2;          %averaging voltages to fit current
-i_f = UI.FD{3}.val / partial;
-
-delta_t = UI.TD{3}.t(1) - UI.TD{1}.t(1);        % half time-step (s) 
-i_f2 = i_f .* exp(-1i*2*pi*UI.FD{1}.f*delta_t); % compensate half time-step advance of H-field
-
-ZL = Z0/2/pi/sqrt(epsR)*log(rad_a/rad_i); %analytic line-impedance of a coax
-plot(UI.FD{1}.f,ZL*ones(size(u_f)),'g');
-hold on;
-grid on;
-Z = u_f./i_f2;
-plot(UI.FD{1}.f,real(Z),'Linewidth',2);
-plot(UI.FD{1}.f,imag(Z),'r','Linewidth',2);
-xlim([0 2*f0]);
-legend('Z_L','\Re\{Z\}','\Im\{Z\}','Location','Best');
-
-

matlab/examples/Helix.m

@@ -18,11 +18,13 @@ f_excite = 300e6;
 
 %% define openEMS options %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 openEMS_opts = '';
-% openEMS_opts = [openEMS_opts ' --disable-dumps'];
+% openEMS_opts = [openEMS_opts ' --debug-material'];
-openEMS_opts = [openEMS_opts ' --debug-material'];
+% openEMS_opts = [openEMS_opts ' --debug-boxes'];
-openEMS_opts = [openEMS_opts ' --debug-boxes'];
 % openEMS_opts = [openEMS_opts ' --debug-operator'];
 
+% openEMS_opts = [openEMS_opts ' --disable-dumps --engine=fastest'];
+openEMS_opts = [openEMS_opts ' --engine=sse-compressed'];
+
 Sim_Path = 'tmp';
 Sim_CSX = 'helix.xml';
 

matlab/examples/PlaneWave.m

@@ -14,15 +14,16 @@ MUE0 = 1.256637062e-6;
 
 %% define openEMS options %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 openEMS_opts = '';
-openEMS_opts = [openEMS_opts ' --disable-dumps'];
+% openEMS_opts = [openEMS_opts ' --disable-dumps'];
 % openEMS_opts = [openEMS_opts ' --debug-material'];
-openEMS_opts = [openEMS_opts ' --engine=multithreaded'];
+openEMS_opts = [openEMS_opts ' --engine=fastest'];
-% openEMS_opts = [openEMS_opts ' --engine=sse'];
-openEMS_opts = [openEMS_opts ' --engine=sse-compressed'];
 
 Sim_Path = 'tmp';
 Sim_CSX = 'plane_wave.xml';
 
+if (exist(Sim_Path,'dir'))
+    rmdir(Sim_Path,'s');
+end
 mkdir(Sim_Path);
 
 %% setup FDTD parameter & excitation function %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -63,7 +64,7 @@ start = [mesh.x(1) , mesh.y(1) , mesh.z(1)];
 stop = [mesh.x(end) , mesh.y(end) , mesh.z(end)];
 CSX = AddBox(CSX,'Et',0 , start,stop);
 
-CSX = AddDump(CSX,'Ht','DumpType',1,'FileType',1,'SubSampling','4,4,1');
+CSX = AddDump(CSX,'Ht','DumpType',1,'FileType',1,'SubSampling','4,4,1','DumpMode',2);
 CSX = AddBox(CSX,'Ht',0,start,stop);
 
 %% Write openEMS compatoble xml-file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -72,6 +73,7 @@ WriteOpenEMS([Sim_Path '/' Sim_CSX],FDTD,CSX);
 %% cd to working dir and run openEMS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 savePath = pwd();
 cd(Sim_Path); %cd to working dir
+
 args = [Sim_CSX ' ' openEMS_opts];
 invoke_openEMS(args);
 cd(savePath);
@@ -79,7 +81,7 @@ cd(savePath);
 %% do the plots %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 PlotArgs.slice = {mesh.x(round(end/2)) mesh.y(round(end/2)) mesh.z(round(end/2))};
 PlotArgs.pauseTime=0.01;
-PlotArgs.component=2;
+PlotArgs.component=1;
 PlotArgs.Limit = 'auto';
 
-PlotHDF5FieldData('tmp/Et.h5',PlotArgs)
+PlotHDF5FieldData('tmp/Ht.h5',PlotArgs)

matlab/examples/Rect_Waveguide.m

@@ -34,11 +34,14 @@ func_Ey = [num2str(m/a/unit) '*sin(' num2str(m*pi/a) '*x)*cos('  num2str(n*pi/b)
 openEMS_opts = '';
 % openEMS_opts = [openEMS_opts ' --disable-dumps'];
 % openEMS_opts = [openEMS_opts ' --debug-material'];
-% openEMS_opts = [openEMS_opts ' --engine=multithreaded'];
+openEMS_opts = [openEMS_opts ' --engine=sse-compressed'];
 
 Sim_Path = 'tmp';
 Sim_CSX = 'rect_wg.xml';
 
+if (exist(Sim_Path,'dir'))
+    rmdir(Sim_Path,'s');
+end
 mkdir(Sim_Path);
 
 %% setup FDTD parameter & excitation function %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -51,7 +54,7 @@ FDTD = SetBoundaryCond(FDTD,BC);
 CSX = InitCSX();
 mesh.x = 0 : mesh_res(1) : width;
 mesh.y = 0 : mesh_res(2) : height;
-mesh.z = -length: mesh_res(3) : length;
+mesh.z = 0 : mesh_res(3) : length;
 CSX = DefineRectGrid(CSX, unit,mesh);
 
 %% fake pml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -80,12 +83,12 @@ CSX = SetExcitationWeight(CSX,'excite',weight);
 CSX = AddBox(CSX,'excite',0 ,start,stop);
  
 %% define dump boxes... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-CSX = AddDump(CSX,'Et','FileType',1);
+CSX = AddDump(CSX,'Et','FileType',1,'SubSampling','4,4,4');
-start = [mesh.x(1) , height/2 , mesh.z(1)];
+start = [mesh.x(1) , mesh.y(1) , mesh.z(1)];
-stop = [mesh.x(end) , height/2 , mesh.z(end)];
+stop = [mesh.x(end) ,  mesh.y(end) , mesh.z(end)];
 CSX = AddBox(CSX,'Et',0 , start,stop);
 
-CSX = AddDump(CSX,'Ht','DumpType',1,'FileType',1);
+CSX = AddDump(CSX,'Ht','DumpType',1,'FileType',1,'SubSampling','4,4,4');
 CSX = AddBox(CSX,'Ht',0,start,stop);
 
 %% Write openEMS compatoble xml-file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%