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43
Sheet7/E14/jacob_template/ascii_read_meshvector.m Normal file
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function [ xc, ia, v ] = ascii_read_meshvector( fname )
%
% Loads the 2D triangular mesh (coordinates, vertex connectivity)
% together with values on its vertices from an ASCII file.
% Matlab indexing is stored (starts with 1).
%
% The input file format is compatible
% with Mesh_2d_3_matlab:Write_ascii_matlab(..) in jacobi_oo_stl/geom.h
%
%
% IN: fname - filename
% OUT: xc - coordinates
% ia - mesh connectivity
% v - solution vector
DELIMETER = ' ';
fprintf('Read file %s\n',fname)
% Read mesh constants
nn = dlmread(fname,DELIMETER,[0 0 0 3]); %% row_1, col_1, row_2, col_2 in C indexing!!!
nnode = nn(1);
ndim = nn(2);
nelem = nn(3);
nvert = nn(4);
% Read coordinates
row_start = 0+1;
row_end = 0+nnode;
xc = dlmread(fname,DELIMETER,[row_start 0 row_end ndim-1]);
% Read connectivity
row_start = row_end+1;
row_end = row_end+nelem;
ia = dlmread(fname,DELIMETER,[row_start 0 row_end nvert-1]);
% Read solution
row_start = row_end+1;
row_end = row_end+nnode;
v = dlmread(fname,DELIMETER,[row_start 0 row_end 0]);
end

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Sheet7/E14/jacob_template/ascii_write_mesh.m Normal file
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function ascii_write_mesh( xc, ia, e, basename)
%
% Saves the 2D triangular mesh in the minimal way (only coordinates, vertex connectivity, minimal boundary edge info)
% in an ASCII file.
% Matlab indexing is stored (starts with 1).
%
% The output file format is compatible with Mesh_2d_3_matlab:Mesh_2d_3_matlab(std::string const &fname) in jacobi_oo_stl/geom.h
%
% IN:
% coordinates xc: [2][nnode]
% connectivity ia: [4][nelem] with t(4,:) are the subdomain numbers
% edges e: [7][nedges] boundary edges
% e([1,2],:) - start/end vertex of edge
% e([3,4],:) - start/end values
% e(5,:) - segment number
% e([6,7],:) - left/right subdomain
% basename: file name without extension
%
% Data have been generated via <https://de.mathworks.com/help/pde/ug/initmesh.html initmesh>.
%
fname = [basename, '.txt'];
nnode = int32(size(xc,2));
ndim = int32(size(xc,1));
nelem = int32(size(ia,2));
nvert_e = int32(3);
dlmwrite(fname,nnode,'delimiter','\t','precision',16) % number of nodes
dlmwrite(fname,ndim,'-append','delimiter','\t','precision',16) % space dimension
dlmwrite(fname,nelem,'-append','delimiter','\t','precision',16) % number of elements
dlmwrite(fname,nvert_e,'-append','delimiter','\t','precision',16) % number of vertices per element
%% dlmwrite(fname,xc(:),'-append','delimiter','\t','precision',16) % coordinates
dlmwrite(fname,xc([1,2],:).','-append','delimiter','\t','precision',16) % coordinates
%% no subdomain info transferred
tmp=int32(ia(1:3,:));
% dlmwrite(fname,tmp(:),'-append','delimiter','\t','precision',16) % connectivity in Matlab indexing
dlmwrite(fname,tmp(:,:).','-append','delimiter','\t','precision',16) % connectivity in Matlab indexing
%% store only start and end point of boundary edges,
nbedges = size(e,2);
dlmwrite(fname,nbedges,'-append','delimiter','\t','precision',16) % number boundary edges
tmp=int32(e(1:2,:));
% dlmwrite(fname,tmp(:),'-append','delimiter','\t','precision',16) % boundary edges in Matlab indexing
dlmwrite(fname,tmp(:,:).','-append','delimiter','\t','precision',16) % boundary edges in Matlab indexing
%% Add subdomain information to edges
tmp=int32(e(6:7,:));
dlmwrite(fname,tmp(:,:).','-append','delimiter','\t','precision',16) % subdomain information to edges
end

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Sheet7/E14/jacob_template/ascii_write_subdomains.m Normal file
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function ascii_write_subdomains( xc, ia, e, basename)
%
% Saves the 2D triangular mesh in the minimal way (only coordinates, vertex connectivity, minimal boundary edge info)
% in an ASCII file.
% Matlab indexing is stored (starts with 1).
%
% The output file format is compatible with Mesh_2d_3_matlab:Mesh_2d_3_matlab(std::string const &fname) in jacobi_oo_stl/geom.h
%
% IN:
% coordinates xc: [2][nnode]
% connectivity ia: [4][nelem] with t(4,:) are the subdomain numbers
% edges e: [7][nedges] boundary edges
% e([1,2],:) - start/end vertex of edge
% e([3,4],:) - start/end values
% e(5,:) - segment number
% e([6,7],:) - left/right subdomain
% basename: file name without extension
%
% Data have been generated via <https://de.mathworks.com/help/pde/ug/initmesh.html initmesh>.
%
fname = [basename, '_sd.txt'];
nnode = int32(size(xc,2));
ndim = int32(size(xc,1));
nelem = int32(size(ia,2))
nvert_e = int32(3);
% dlmwrite(fname,nnode,'delimiter','\t','precision',16) % number of nodes
% dlmwrite(fname,ndim,'-append','delimiter','\t','precision',16) % space dimension
% dlmwrite(fname,nelem,'-append','delimiter','\t','precision',16) % number of elements
dlmwrite(fname,nelem,'delimiter','\t','precision',16) % number of elements
% dlmwrite(fname,nvert_e,'-append','delimiter','\t','precision',16) % number of vertices per element
% % dlmwrite(fname,xc(:),'-append','delimiter','\t','precision',16) % coordinates
% dlmwrite(fname,xc([1,2],:).','-append','delimiter','\t','precision',16) % coordinates
% subdomain info
tmp=int32(ia(4,:));
% % dlmwrite(fname,tmp(:),'-append','delimiter','\t','precision',16) % connectivity in Matlab indexing
% dlmwrite(fname,tmp(:,:).','-append','delimiter','\t','precision',16) % connectivity in Matlab indexing
dlmwrite(fname,tmp(:,:).','-append','delimiter','\t') % connectivity in Matlab indexing
% % store only start and end point of boundary edges,
% nbedges = size(e,2);
% dlmwrite(fname,nbedges,'-append','delimiter','\t','precision',16) % number boundary edges
% tmp=int32(e(1:2,:));
% % dlmwrite(fname,tmp(:),'-append','delimiter','\t','precision',16) % boundary edges in Matlab indexing
% dlmwrite(fname,tmp(:,:).','-append','delimiter','\t','precision',16) % boundary edges in Matlab indexing
end

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Sheet7/E14/jacob_template/cuthill_mckee_ordering.cpp Normal file
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//=======================================================================
// Copyright 1997, 1998, 1999, 2000 University of Notre Dame.
// Authors: Andrew Lumsdaine, Lie-Quan Lee, Jeremy G. Siek
//
// This file is part of the Boost Graph Library
//
// You should have received a copy of the License Agreement for the
// Boost Graph Library along with the software; see the file LICENSE.
// If not, contact Office of Research, University of Notre Dame, Notre
// Dame, IN 46556.
//
// Permission to modify the code and to distribute modified code is
// granted, provided the text of this NOTICE is retained, a notice that
// the code was modified is included with the above COPYRIGHT NOTICE and
// with the COPYRIGHT NOTICE in the LICENSE file, and that the LICENSE
// file is distributed with the modified code.
//
// LICENSOR MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED.
// By way of example, but not limitation, Licensor MAKES NO
// REPRESENTATIONS OR WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY
// PARTICULAR PURPOSE OR THAT THE USE OF THE LICENSED SOFTWARE COMPONENTS
// OR DOCUMENTATION WILL NOT INFRINGE ANY PATENTS, COPYRIGHTS, TRADEMARKS
// OR OTHER RIGHTS.
// Modyfied 2019 by Gundolf Haase, University of Graz
//=======================================================================
#include "cuthill_mckee_ordering.h"
#include <boost/config.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/graph/bandwidth.hpp>
#include <boost/graph/cuthill_mckee_ordering.hpp>
#include <boost/graph/properties.hpp>
#include <iostream>
#include <vector>
/*
Sample Output
original bandwidth: 8
Reverse Cuthill-McKee ordering starting at: 6
8 3 0 9 2 5 1 4 7 6
bandwidth: 4
Reverse Cuthill-McKee ordering starting at: 0
9 1 4 6 7 2 8 5 3 0
bandwidth: 4
Reverse Cuthill-McKee ordering:
0 8 5 7 3 6 4 2 1 9
bandwidth: 4
*/
/*
int main(int, char *[])
{
using namespace boost;
using namespace std;
typedef adjacency_list<vecS, vecS, undirectedS,
property<vertex_color_t, default_color_type,
property<vertex_degree_t, int> > > Graph;
typedef graph_traits<Graph>::vertex_descriptor Vertex;
typedef graph_traits<Graph>::vertices_size_type size_type;
typedef std::pair<std::size_t, std::size_t> Pair;
Pair edges[14] = { Pair(0, 3), //a-d
Pair(0, 5), //a-f
Pair(1, 2), //b-c
Pair(1, 4), //b-e
Pair(1, 6), //b-g
Pair(1, 9), //b-j
Pair(2, 3), //c-d
Pair(2, 4), //c-e
Pair(3, 5), //d-f
Pair(3, 8), //d-i
Pair(4, 6), //e-g
Pair(5, 6), //f-g
Pair(5, 7), //f-h
Pair(6, 7)
}; //g-h
Graph G(10);
for (int i = 0; i < 14; ++i)
add_edge(edges[i].first, edges[i].second, G);
graph_traits<Graph>::vertex_iterator ui, ui_end;
property_map<Graph, vertex_degree_t>::type deg = get(vertex_degree, G);
for (boost::tie(ui, ui_end) = vertices(G); ui != ui_end; ++ui)
deg[*ui] = degree(*ui, G);
property_map<Graph, vertex_index_t>::type
index_map = get(vertex_index, G);
std::cout << "original bandwidth: " << bandwidth(G) << std::endl;
std::vector<Vertex> inv_perm(num_vertices(G));
std::vector<size_type> perm(num_vertices(G));
{
Vertex s = vertex(6, G);
//reverse cuthill_mckee_ordering
cuthill_mckee_ordering(G, s, inv_perm.rbegin(), get(vertex_color, G),
get(vertex_degree, G));
cout << "Reverse Cuthill-McKee ordering starting at: " << s << endl;
cout << " ";
for (std::vector<Vertex>::const_iterator i = inv_perm.begin();
i != inv_perm.end(); ++i)
cout << index_map[*i] << " ";
cout << endl;
for (size_type c = 0; c != inv_perm.size(); ++c)
perm[index_map[inv_perm[c]]] = c;
std::cout << " bandwidth: "
<< bandwidth(G, make_iterator_property_map(&perm[0], index_map, perm[0]))
<< std::endl;
}
{
Vertex s = vertex(0, G);
//reverse cuthill_mckee_ordering
cuthill_mckee_ordering(G, s, inv_perm.rbegin(), get(vertex_color, G),
get(vertex_degree, G));
cout << "Reverse Cuthill-McKee ordering starting at: " << s << endl;
cout << " ";
for (std::vector<Vertex>::const_iterator i = inv_perm.begin();
i != inv_perm.end(); ++i)
cout << index_map[*i] << " ";
cout << endl;
for (size_type c = 0; c != inv_perm.size(); ++c)
perm[index_map[inv_perm[c]]] = c;
std::cout << " bandwidth: "
<< bandwidth(G, make_iterator_property_map(&perm[0], index_map, perm[0]))
<< std::endl;
}
{
//reverse cuthill_mckee_ordering
cuthill_mckee_ordering(G, inv_perm.rbegin(), get(vertex_color, G),
make_degree_map(G));
cout << "Reverse Cuthill-McKee ordering:" << endl;
cout << " ";
for (std::vector<Vertex>::const_iterator i = inv_perm.begin();
i != inv_perm.end(); ++i)
cout << index_map[*i] << " ";
cout << endl;
for (size_type c = 0; c != inv_perm.size(); ++c)
perm[index_map[inv_perm[c]]] = c;
std::cout << " bandwidth: "
<< bandwidth(G, make_iterator_property_map(&perm[0], index_map, perm[0]))
<< std::endl;
}
return 0;
}
*/
// ------------- Modifications by Gundolf Haase
// std::vector<int> _edges; //!< edges of mesh (vertices ordered ascending)
using namespace boost;
using namespace std;
typedef adjacency_list<vecS, vecS, undirectedS,
property<vertex_color_t, default_color_type,
property<vertex_degree_t, int> > > Graph;
typedef graph_traits<Graph>::vertex_descriptor Vertex;
typedef graph_traits<Graph>::vertices_size_type size_type;
typedef std::pair<std::size_t, std::size_t> Pair;
vector<int> cuthill_mckee_reordering(vector<int> const &_edges)
{
size_t const nnodes = *max_element(cbegin(_edges), cend(_edges)) + 1;
cout << "NNODES = " << nnodes << endl;
//size_t const nedges = _edges.size()/2;
Graph G(nnodes);
for (size_t i = 0; i < _edges.size(); i+=2)
add_edge(_edges[i], _edges[i+1], G);
graph_traits<Graph>::vertex_iterator ui, ui_end;
property_map<Graph, vertex_degree_t>::type deg = get(vertex_degree, G);
for (boost::tie(ui, ui_end) = vertices(G); ui != ui_end; ++ui)
deg[*ui] = degree(*ui, G);
property_map<Graph, vertex_index_t>::type
index_map = get(vertex_index, G);
std::cout << "original bandwidth: " << bandwidth(G) << std::endl;
std::vector<Vertex> inv_perm(num_vertices(G));
//std::vector<size_type> perm(num_vertices(G));
std::vector<int> perm(num_vertices(G));
{
Vertex s = vertex(nnodes/2, G);
//reverse cuthill_mckee_ordering
cuthill_mckee_ordering(G, s, inv_perm.rbegin(), get(vertex_color, G),
get(vertex_degree, G));
//cout << "Reverse Cuthill-McKee ordering starting at: " << s << endl;
//cout << " ";
//for (std::vector<Vertex>::const_iterator i = inv_perm.begin(); i != inv_perm.end(); ++i)
//cout << index_map[*i] << " ";
//cout << endl;
for (size_type c = 0; c != inv_perm.size(); ++c)
perm[index_map[inv_perm[c]]] = c;
std::cout << "improved bandwidth: "
<< bandwidth(G, make_iterator_property_map(&perm[0], index_map, perm[0]))
<< std::endl;
}
assert(perm.size()==nnodes);
return perm;
}
// ------------- end Modifications

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Sheet7/E14/jacob_template/cuthill_mckee_ordering.h Normal file
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#ifndef CUTHILL_MCKEE_ORDERING
#define CUTHILL_MCKEE_ORDERING
#include <vector>
std::vector<int> cuthill_mckee_reordering(std::vector<int> const &_edges);
#endif