Merge pull request #116 from fastalgorithms/docs

Docs

Author: mrachh

chunkie/+chnk/+helm2d/transmission_helper.m

@@ -84,7 +84,9 @@
     ncurve = length(chnkrs);
     sources = cell(1,ncurve);
     charges = cell(1,ncurve);
-    exposed_curves = ones(1,ncurve);
+    
+    exposed_curves = (cs(1,:)==1) -(cs(2,:)==1);
+
     for i=1:ncurve
         sources{i} = zeros(2,1);
         charges{i} = 0 + 1j*0;

chunkie/@chunker/merge.m

@@ -28,7 +28,7 @@
 w = chnkrs(1).wstor;
 chnkrout = chunker(pref,t,w);
 
-for i = 1:length(chnkrs)
+for i = 1:numel(chnkrs)
   chnkrtemp = chnkrs(i);
   assert(chnkrtemp.dim == chnkrout.dim && chnkrtemp.k == chnkrout.k,...
       'chunkers to merge must be in same dimension and same order');

chunkie/@chunkgraph/chunkgraph.m

@@ -58,6 +58,11 @@
 %   obj = refine(obj,varargin) - refine the curve
 %   wts = weights(obj) - scaled integration weights on curve
 %   rn = normals(obj) - recompute normal vectors
+%   flag = flagnear(obj,pts) - find points close to the chunkgraph
+%   flag = flagnear_rectangle(obj,pts) - find points close to chunkgraph
+%           using bounding rectangles
+%   flag = flagnear_rectangle_grid(obj,x,y) - find points defined via 
+%      a meshgrid of points that are close to the chunkgraph
 %   obj = obj.move(r0,r1,trotat,scale) - translate, rotate, etc
 %   rmin = min(obj) - minimum of coordinate values
 %   rmax = max(obj) - maximum of coordinate values
@@ -70,9 +75,8 @@
 %   kappa = signed_curvature(obj) - get signed curvature along curve
 %   obj = makedatarows(obj,nrows) - add nrows rows to the data storage.
 %   rflag = datares(obj,opts) - check if data in data rows is resolved
-%
-%   To add:
-%     flagnear
+%   edge_reg = find_regions_of_edges(obj) - determine regions on either 
+%                side of each edge
 %
 % Syntax:
 %
@@ -418,6 +422,7 @@
         obj = makedatarows(obj, nrows)
         scatter(obj, varargin)
         rres = datares(obj, opts)
+        edge_regs = find_edge_regions(obj)
 
 
     end

chunkie/@chunkgraph/find_edge_regions.m

@@ -0,0 +1,28 @@
+function edge_regs = find_edge_regions(obj)
+%FIND_EDGE_REGIONS find regions on either side of the edges
+% in a chunkgraph.
+%
+% Syntax: edge_regs = find_edge_regions(obj)
+%
+% Input:
+%   obj - chunkgraph object describing curve
+%   
+% Output:
+%   edge_regs - (2,nedge) array where nedges
+%     is the number of edges in the chunkgraph. 
+%     edge_reg(1,i) is index of the region in which the 
+%     normal to edge i is pointing and edge_reg(2,i)
+%     is the index corresponding to the negative of
+%     the normal.
+%
+% author: Tristan Goodwill
+
+
+    edge_regs = zeros(2,size(obj.edgesendverts,2));
+    nreg = length(obj.regions);
+    for i = 1:nreg
+        id_edge = obj.regions{i}{1};
+        edge_regs(1,id_edge(id_edge>0)) = i;
+        edge_regs(2,-id_edge(id_edge<0)) = i;
+    end
+end

chunkie/@kernel/elast2d.m

@@ -30,6 +30,8 @@
 %
 % See also CHNK.ELAST2D.KERN
 
+% author : Dan Fortunato, Travis Askham, Manas Rachh
+
 if ( nargin < 1 )
     error('Missing elasticity kernel type.');
 end

chunkie/@kernel/helm2d.m

@@ -20,6 +20,8 @@
 %   COEFS(2)*KERNEL.HELM2D('sp', ZK).
 % See also CHNK.HELM2D.KERN.
 
+% author: Dan Fortunato
+  
 if ( nargin < 1 )
     error('Missing Helmholtz kernel type.');
 end

chunkie/@kernel/kernel.m

@@ -48,6 +48,15 @@
 %        single source and target, respectively. For scalar kernels,
 %        opdims = [1 1].
 %
+%      - K.sing: a string/character array specifying the singularity  
+%        strength of the kernel for sources and targets which are on
+%        the same curve. Currently recognized singularities are considered
+%        as part of a hierarchy
+%        - 'smooth' a smooth integral kernel
+%        - 'log' sum of above type kernel and phi(s)log(s-t)
+%        - 'pv' sum of above type kernels and phi(s)/(s-t)
+%        - 'hs' sum of above type kernels and phi(s)/(s-t)^2
+%
 %      - K.fmm: A function handle which calls the FMM for the corresponding
 %        kernel. K.fmm(eps, s, t, sigma) evaluates the kernel with density
 %        sigma from sources s to targets t with accuracy eps.

chunkie/@kernel/stok2d.m

@@ -55,6 +55,8 @@
 
 % See also CHNK.STOK2D.KERN.
 
+% author: Dan Fortunato  
+
 if ( nargin < 1 )
     error('Missing Stokes kernel type.');
 end

chunkie/demo/demo_Neumann_combined.m

@@ -18,7 +18,7 @@
 rado = 5;
 for i = 1:narms
     verts(:,2*i-1) = radi*[real(rots(i));imag(rots(i))];
-    verts(:,2*i  ) = rado*[real(rots(i));imag(rots(i))];
+    verts(:,2*i) = rado*[real(rots(i));imag(rots(i))];
 end
 nverts = size(verts,2);
 edge2verts = [1:nverts;circshift(1:nverts,-1)];
@@ -28,27 +28,18 @@
 frq = 5;
 
 % define curve for each edge
-fchnks = {};
+fchnks = cell(2*narms,1);
 for i = 1:narms
     % odd edges are straight
     fchnks{2*i-1} = [];
     % even edges are curved
-    fchnks{2*i  } = @(t) sinearc(t,amp,frq);
+    fchnks{2*i} = @(t) sinearc(t,amp,frq);
 end
 
 cparams = [];
 cparams.maxchunklen = min(4.0/zk,.5);
 [cgrph] = chunkgraph(verts,edge2verts,fchnks,cparams);
 
-
-% plot
-figure(1);clf
-plot(cgrph)
-% hold on
-% quiver(cgrph)
-% hold off
-axis equal
-
 %% Define system
 
 % define kernels
@@ -74,6 +65,8 @@
    c3*Sik  Z        Z        ;
    c3*Sikp Z        Z        ];
 K = kernel(K);
+
+
 Keval = c1*kernel([Sk 1i*alpha*Dk Z]);
 
 npts = cgrph.npt;
@@ -132,6 +125,8 @@
 plot(cgrph,'k')
 axis equal
 title('$u^{\textrm{tot}}$','Interpreter','latex','FontSize',12)
+% END DEMO NEUMANN COMBINED
+saveas(figure(2),"demo_neumann_combined_plot.png")
 
 
 function [r,d,d2] = sinearc(t,amp,frq)