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[Getfem-commits] r5417 - in /trunk/getfem: contrib/opt_assembly/ interfa
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From: |
Yves . Renard |
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Subject: |
[Getfem-commits] r5417 - in /trunk/getfem: contrib/opt_assembly/ interface/src/ interface/tests/matlab/ src/ src/getfem/ src/gmm/ tests/ |
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Date: |
Fri, 14 Oct 2016 07:37:51 -0000 |
Author: renard
Date: Fri Oct 14 09:37:49 2016
New Revision: 5417
URL: http://svn.gna.org/viewcvs/getfem?rev=5417&view=rev
Log:
transfer Cuthill Mc Kee ordering in mesh::optimize_structure. The dof numbering
is modified
Modified:
trunk/getfem/contrib/opt_assembly/opt_assembly.cc
trunk/getfem/interface/src/gf_mesh.cc
trunk/getfem/interface/src/gf_mesh_set.cc
trunk/getfem/interface/tests/matlab/check_mesh_fem.m
trunk/getfem/interface/tests/matlab/demo_laplacian.m
trunk/getfem/src/getfem/bgeot_mesh_structure.h
trunk/getfem/src/getfem/getfem_mesh.h
trunk/getfem/src/getfem_mesh.cc
trunk/getfem/src/getfem_mesh_fem.cc
trunk/getfem/src/getfem_regular_meshes.cc
trunk/getfem/src/gmm/gmm_vector.h
trunk/getfem/tests/test_assembly.cc
trunk/getfem/tests/test_mesh.cc
Modified: trunk/getfem/contrib/opt_assembly/opt_assembly.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/contrib/opt_assembly/opt_assembly.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/contrib/opt_assembly/opt_assembly.cc (original)
+++ trunk/getfem/contrib/opt_assembly/opt_assembly.cc Fri Oct 14 09:37:49 2016
@@ -433,35 +433,35 @@
// - Instructions execution except for assembly ones
// new | old | sto | asse | exec | J | Ins |
test_new_assembly(2, 400, 1); // ndofu = 321602 ndofp = 160801 ndofchi = 1201
- // Mass (scalar) : 0.36 | 0.61 | 0.07 | 0.10 | 0.20 | 0.06 | 0.06 |
- // Mass (vector) : 0.46 | 0.82 | 0.12 | 0.22 | 0.15 | 0.05 | 0.09 |
- // Laplacian : 0.26 | 0.83 | 0.05 | 0.07 | 0.14 | 0.06 | 0.05 |
- // Homogeneous elas : 0.46 | 1.88 | 0.14 | 0.22 | 0.13 | 0.05 | 0.11 |
- // Non-homogeneous elast: 0.57 | 2.26 | 0.14 | 0.22 | 0.13 | 0.05 | 0.21 |
+ // Mass (scalar) : 0.34 | 0.61 | 0.05 | 0.08 | 0.20 | 0.06 | 0.06 |
+ // Mass (vector) : 0.43 | 0.82 | 0.10 | 0.20 | 0.14 | 0.05 | 0.09 |
+ // Laplacian : 0.23 | 0.83 | 0.02 | 0.04 | 0.14 | 0.06 | 0.05 |
+ // Homogeneous elas : 0.43 | 1.88 | 0.11 | 0.19 | 0.13 | 0.05 | 0.11 |
+ // Non-homogeneous elast: 0.53 | 2.26 | 0.10 | 0.18 | 0.13 | 0.05 | 0.21 |
test_new_assembly(3, 36, 1); // ndofu = 151959 ndofp = 50653 ndofchi = 6553
- // Mass (scalar) : 0.44 | 0.77 | 0.08 | 0.12 | 0.24 | 0.11 | 0.08 |
- // Mass (vector) : 0.94 | 1.57 | 0.18 | 0.39 | 0.20 | 0.11 | 0.35 |
- // Laplacian : 0.41 | 1.38 | 0.06 | 0.09 | 0.19 | 0.11 | 0.14 |
- // Homogeneous elas : 1.28 | 4.58 | 0.48 | 0.59 | 0.19 | 0.11 | 0.51 |
- // Non-homogeneous elast: 1.42 | 6.81 | 0.49 | 0.63 | 0.18 | 0.11 | 0.61 |
+ // Mass (scalar) : 0.42 | 0.77 | 0.06 | 0.10 | 0.24 | 0.11 | 0.08 |
+ // Mass (vector) : 0.92 | 1.54 | 0.17 | 0.38 | 0.19 | 0.11 | 0.35 |
+ // Laplacian : 0.39 | 1.38 | 0.04 | 0.07 | 0.19 | 0.11 | 0.14 |
+ // Homogeneous elas : 1.26 | 4.58 | 0.46 | 0.57 | 0.19 | 0.11 | 0.51 |
+ // Non-homogeneous elast: 1.38 | 6.73 | 0.45 | 0.59 | 0.18 | 0.11 | 0.61 |
test_new_assembly(2, 200, 2); // ndofu = 321602 ndofp = 160801 ndofchi = 1201
- // Mass (scalar) : 0.15 | 0.25 | 0.04 | 0.07 | 0.05 | 0.02 | 0.03 |
- // Mass (vector) : 0.34 | 0.45 | 0.07 | 0.15 | 0.05 | 0.02 | 0.14 |
+ // Mass (scalar) : 0.14 | 0.25 | 0.04 | 0.07 | 0.04 | 0.02 | 0.03 |
+ // Mass (vector) : 0.34 | 0.44 | 0.07 | 0.15 | 0.05 | 0.02 | 0.14 |
// Laplacian : 0.13 | 0.37 | 0.03 | 0.05 | 0.04 | 0.02 | 0.04 |
// Homogeneous elas : 0.37 | 1.28 | 0.13 | 0.19 | 0.04 | 0.01 | 0.14 |
- // Non-homogeneous elast: 0.45 | 2.40 | 0.13 | 0.18 | 0.04 | 0.01 | 0.23 |
+ // Non-homogeneous elast: 0.44 | 2.40 | 0.12 | 0.17 | 0.04 | 0.01 | 0.23 |
test_new_assembly(3, 18, 2); // ndofu = 151959 ndofp = 50653 ndofchi = 6553
- // Mass (scalar) : 0.23 | 0.30 | 0.10 | 0.15 | 0.04 | 0.02 | 0.04 |
+ // Mass (scalar) : 0.23 | 0.29 | 0.10 | 0.15 | 0.04 | 0.02 | 0.04 |
// Mass (vector) : 1.46 | 0.90 | 0.33 | 0.64 | 0.04 | 0.02 | 0.78 |
// Laplacian : 0.18 | 0.55 | 0.08 | 0.10 | 0.03 | 0.02 | 0.05 |
// Homogeneous elas : 2.37 | 3.47 | 1.20 | 1.37 | 0.03 | 0.02 | 0.97 |
- // Non-homogeneous elast: 2.45 | 9.25 | 1.20 | 1.37 | 0.03 | 0.02 | 1.05 |
+ // Non-homogeneous elast: 2.44 | 9.25 | 1.20 | 1.37 | 0.03 | 0.02 | 1.04 |
test_new_assembly(3, 9, 4); // ndofu = 151959 ndofp = 50653 ndofchi = 6553
- // Mass (scalar) : 0.75 | 0.38 | 0.25 | 0.39 | 0.01 | .005 | 0.35 |
- // Mass (vector) : 5.10 | 1.33 | 0.42 | 1.86 | 0.01 | .005 | 3.23 |
- // Laplacian : 0.61 | 0.79 | 0.25 | 0.34 | 0.01 | .005 | 0.26 |
- // Homogeneous elas : 10.8 | 5.52 | 2.40 | 3.29 | 0.01 | .005 | 7.50 |
- // Non-homogeneous elast: 11.0 | 48.0 | 2.35 | 3.19 | 0.01 | .005 | 7.80 |
+ // Mass (scalar) : 0.74 | 0.36 | 0.24 | 0.38 | 0.01 | .005 | 0.35 |
+ // Mass (vector) : 5.08 | 1.33 | 0.41 | 1.85 | 0.01 | .005 | 3.22 |
+ // Laplacian : 0.60 | 0.79 | 0.25 | 0.34 | 0.01 | .005 | 0.25 |
+ // Homogeneous elas : 10.7 | 5.47 | 2.40 | 3.29 | 0.01 | .005 | 7.40 |
+ // Non-homogeneous elast: 10.8 | 48.0 | 2.35 | 3.29 | 0.01 | .005 | 7.50 |
// Conclusions :
// - Desactivation of debug test has no sensible effect.
Modified: trunk/getfem/interface/src/gf_mesh.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/interface/src/gf_mesh.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/interface/src/gf_mesh.cc (original)
+++ trunk/getfem/interface/src/gf_mesh.cc Fri Oct 14 09:37:49 2016
@@ -190,7 +190,7 @@
}
pmesh->add_convex_by_points(pgt, pts.begin());
}
- pmesh->optimize_structure();
+ pmesh->optimize_structure(false);
}
getfem::base_small_vector diff(N);
Modified: trunk/getfem/interface/src/gf_mesh_set.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/interface/src/gf_mesh_set.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/interface/src/gf_mesh_set.cc (original)
+++ trunk/getfem/interface/src/gf_mesh_set.cc Fri Oct 14 09:37:49 2016
@@ -372,7 +372,7 @@
);
- /address@hidden ('optimize structure')
+ /address@hidden ('optimize structure'[, @int with_renumbering])
Reset point and convex numbering.
After optimisation, the points (resp. convexes) will
@@ -381,8 +381,10 @@
(resp. MESH:GET('max cvid'))address@hidden to
``MESH:GET('max pid')-1`` (resp. ``MESH:GET('max cvid')-1``)address@hidden/
sub_command
- ("optimize structure", 0, 0, 0, 0,
- pmesh->optimize_structure();
+ ("optimize structure", 0, 1, 0, 0,
+ bool with_renumbering = true;
+ if (in.remaining()) with_renumbering = (in.pop().to_integer(0,1) != 0);
+ pmesh->optimize_structure(with_renumbering);
);
Modified: trunk/getfem/interface/tests/matlab/check_mesh_fem.m
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/interface/tests/matlab/check_mesh_fem.m?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/interface/tests/matlab/check_mesh_fem.m (original)
+++ trunk/getfem/interface/tests/matlab/check_mesh_fem.m Fri Oct 14
09:37:49 2016
@@ -167,11 +167,11 @@
gf_mesh_fem_get(mf,'nbdof') % should be 99 or 100 (element 0 and 1 are not
really neigbhor but can be viewed as such)
d=gf_mesh_fem_get(mf,'basic dof from cv',[1 5])
- gfassert(['d==[1 2 3 4 5 6 38 41 43 44 45 46 47 48 49 50 51 52 53 54 55 56
57 58]']);
+ gfassert(['d==[1 2 3 4 5 6 29 32 34 35 36 37 38 39 40 41 42 43 44 45 46 47
48 49]']);
d=gf_mesh_fem_get(mf,'basic dof from cv',[1 5;1 2])
- gfassert('d==[3 5 6 38 41 43 46 48 51 53 56 58]');
+ gfassert('d==[3 5 6 29 32 34 37 39 42 44 47 49]');
d=gf_mesh_fem_get(mf,'basic dof from cvid',5)
- gfassert('d==[38 44 45 46 47 48 41 49 50 51 52 53 43 54 55 56 57 58]');
+ gfassert('d==[29 35 36 37 38 39 32 40 41 42 43 44 34 45 46 47 48 49]');
s2=gf_mesh_get(mf,'char');
gfassert('length(s2)>500');
@@ -227,9 +227,9 @@
gf_mesh_set(m, 'boundary', 7, [3 4; 3 2]);
cl=[1:5 7 8];
asserterr('gf_mesh_fem_get(mf_u, ''non conformal basic dof'')');
- d=gf_mesh_fem_get(mf_u, 'non conformal basic dof',cl);
+ d=gf_mesh_fem_get(mf_u, 'non conformal basic dof',cl)
%gf_plot_mesh(mf_u, 'dof', 'on');
- gfassert('d==[11 12 13 14 15 16 21 22]');
+ gfassert('d==[19 20 21 22 23 24 29 30]');
f=gf_mesh_fem_get(mf2, 'fem');
f5=gf_mesh_fem_get(mf2, 'fem',5);
@@ -319,7 +319,7 @@
gfassert('ncv < maxcvid');
- gf_mesh_set(m,'optimize structure');
+ gf_mesh_set(m,'optimize structure', false);
maxpid=gf_mesh_get(m,'max pid');
maxcvid=gf_mesh_get(m,'max cvid');
Modified: trunk/getfem/interface/tests/matlab/demo_laplacian.m
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/interface/tests/matlab/demo_laplacian.m?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/interface/tests/matlab/demo_laplacian.m (original)
+++ trunk/getfem/interface/tests/matlab/demo_laplacian.m Fri Oct 14
09:37:49 2016
@@ -36,6 +36,7 @@
else
m=gf_mesh('import','structured',sprintf('GT="GT_PK(2,1)";SIZES=[1,1];NOISED=0;NSUBDIV=[%d,%d];',
NX, NX));
end
+gf_mesh_set(m, 'optimize structure')
% Create a mesh_fem of for a field of dimension 1 (i.e. a scalar field)
mf = gf_mesh_fem(m,1);
@@ -55,7 +56,8 @@
GAMMAD=1;
gf_mesh_set(m, 'region', GAMMAD, border);
if (draw)
- gf_plot_mesh(m, 'regions', [GAMMAD]); % the boundary edges appear in red
+ figure(1);
+ gf_plot_mesh(m, 'regions', [GAMMAD], 'convexes', 'on'); % the boundary edges
appear in red
pause(1);
end
@@ -89,6 +91,7 @@
U = gf_model_get(md, 'variable', 'u');
if (draw)
+ figure(2);
subplot(2,1,1); gf_plot(mf,U,'mesh','off');
colorbar; title('computed solution');
Modified: trunk/getfem/src/getfem/bgeot_mesh_structure.h
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/src/getfem/bgeot_mesh_structure.h?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/src/getfem/bgeot_mesh_structure.h (original)
+++ trunk/getfem/src/getfem/bgeot_mesh_structure.h Fri Oct 14 09:37:49 2016
@@ -253,7 +253,7 @@
/** Return the cuthill_mc_kee ordering on the convexes */
void APIDECL cuthill_mckee_on_convexes(const bgeot::mesh_structure &ms,
- std::vector<size_type> &cmk);
+ std::vector<size_type> &cmk);
template<class ITER>
bool mesh_structure::is_convex_having_points(size_type ic,
Modified: trunk/getfem/src/getfem/getfem_mesh.h
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/src/getfem/getfem_mesh.h?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/src/getfem/getfem_mesh.h (original)
+++ trunk/getfem/src/getfem/getfem_mesh.h Fri Oct 14 09:37:49 2016
@@ -443,7 +443,7 @@
void sup_convex_from_regions(size_type cv);
/** Pack the mesh : renumber convexes and nodes such that there
is no holes in their numbering. Do NOT do the Cuthill-McKee. */
- void optimize_structure();
+ void optimize_structure(bool with_renumbering = true);
/// Return the list of convex IDs for a Cuthill-McKee ordering
const std::vector<size_type> &cuthill_mckee_ordering() const;
/// Erase the mesh.
Modified: trunk/getfem/src/getfem_mesh.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/src/getfem_mesh.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/src/getfem_mesh.cc (original)
+++ trunk/getfem/src/getfem_mesh.cc Fri Oct 14 09:37:49 2016
@@ -217,10 +217,9 @@
}
#endif
- void mesh::optimize_structure() {
+ void mesh::optimize_structure(bool with_renumbering) {
pts.resort();
- size_type i, j;
- j = nb_convex();
+ size_type i, j = nb_convex(), nbc = j;
for (i = 0; i < j; i++)
if (!convex_tab.index_valid(i))
swap_convex(i, convex_tab.ind_last());
@@ -231,14 +230,20 @@
while (i < j && j != ST_NIL && !(pts.index()[j])) --j;
if (i < j && j != ST_NIL ) swap_points(i, j);
}
- }
-
- const std::vector<size_type> &mesh::cuthill_mckee_ordering() const {
- if (!cuthill_mckee_uptodate) {
- bgeot::cuthill_mckee_on_convexes(*this, cmk_order);
- cuthill_mckee_uptodate = true;
- }
- return cmk_order;
+ if (with_renumbering) { // Could be optimized no using only swap_convex
+ std::vector<size_type> cmk, iord(nbc), iordinv(nbc);
+ for (i = 0; i < nbc; ++i) iord[i] = iordinv[i] = i;
+
+ bgeot::cuthill_mckee_on_convexes(*this, cmk);
+ for (i = 0; i < nbc; ++i) {
+ j = iordinv[cmk[i]];
+ if (i != j) {
+ swap_convex(i, j);
+ std::swap(iord[i], iord[j]);
+ std::swap(iordinv[iord[i]], iordinv[iord[j]]);
+ }
+ }
+ }
}
void mesh::translation(const base_small_vector &V)
Modified: trunk/getfem/src/getfem_mesh_fem.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/src/getfem_mesh_fem.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/src/getfem_mesh_fem.cc (original)
+++ trunk/getfem/src/getfem_mesh_fem.cc Fri Oct 14 09:37:49 2016
@@ -307,7 +307,15 @@
if (first_pf && first_pf->is_on_real_element()) is_uniform_ = false;
// Gives the Cuthill McKee ordering to iterate on elements
- const std::vector<size_type> &cmk = linked_mesh().cuthill_mckee_ordering();
+ // const std::vector<size_type> &cmk =
linked_mesh().cuthill_mckee_ordering();
+
+
+ // std::vector<size_type> cmk;
+ // for (dal::bv_visitor cv(linked_mesh().convex_index()); !cv.finished();
++cv)
+ // cmk.push_back(cv);
+
+
+
// Dof counter
size_type nbdof = 0;
@@ -334,7 +342,9 @@
bgeot::pgeometric_trans pgt_old = 0;
bgeot::pgeotrans_precomp pgp = 0;
- for (size_type cv : cmk) {
+ // for (size_type cv : cmk) {
+ for (dal::bv_visitor cv(linked_mesh().convex_index());
+ !cv.finished(); ++cv) {
if (fe_convex.is_in(cv)) {
gmm::copy(linked_mesh().points_of_convex(cv)[0], bmin);
gmm::copy(bmin, bmax);
@@ -350,8 +360,10 @@
}
dal::bit_vector cv_done;
-
- for (size_type cv : cmk) { // Loop on elements
+
+ //for (size_type cv : cmk) {
+ for (dal::bv_visitor cv(linked_mesh().convex_index());
+ !cv.finished(); ++cv) { // Loop on elements
if (!fe_convex.is_in(cv)) continue;
pfem pf = fem_of_element(cv);
if (pf != first_pf) is_uniform_ = false;
Modified: trunk/getfem/src/getfem_regular_meshes.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/src/getfem_regular_meshes.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/src/getfem_regular_meshes.cc (original)
+++ trunk/getfem/src/getfem_regular_meshes.cc Fri Oct 14 09:37:49 2016
@@ -234,7 +234,7 @@
/* apply a continuous deformation + some noise */
if (noised) noise_unit_mesh(m, nsubdiv, pgt);
- m.optimize_structure();
+ m.optimize_structure(false);
}
Modified: trunk/getfem/src/gmm/gmm_vector.h
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/src/gmm/gmm_vector.h?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/src/gmm/gmm_vector.h (original)
+++ trunk/getfem/src/gmm/gmm_vector.h Fri Oct 14 09:37:49 2016
@@ -1058,12 +1058,12 @@
iterator it = std::lower_bound(this->begin(), this->end(), ev);
if (it != this->end() && it->c == c) it->e = e;
else {
- size_type ind = it - this->begin();
- if (this->nb_stored() - ind > 1100)
+ size_type ind = it - this->begin(), nb = this->nb_stored();
+ if (nb - ind > 1100)
GMM_WARNING2("Inefficient addition of element in rsvector with "
<< this->nb_stored() - ind << " non-zero entries");
- base_type_::resize(this->nb_stored()+1, ev);
- if (ind != this->nb_stored() - 1) {
+ base_type_::resize(nb+1, ev);
+ if (ind != nb) {
it = this->begin() + ind;
iterator ite = this->end(); --ite; iterator itee = ite;
for (; ite != it; --ite) { --itee; *ite = *itee; }
@@ -1085,12 +1085,12 @@
iterator it = std::lower_bound(this->begin(), this->end(), ev);
if (it != this->end() && it->c == c) it->e += e;
else {
- size_type ind = it - this->begin();
- if (this->nb_stored() - ind > 1100)
+ size_type ind = it - this->begin(), nb = this->nb_stored();
+ if (nb - ind > 1100)
GMM_WARNING2("Inefficient addition of element in rsvector with "
<< this->nb_stored() - ind << " non-zero entries");
- base_type_::resize(this->nb_stored()+1, ev);
- if (ind != this->nb_stored() - 1) {
+ base_type_::resize(nb+1, ev);
+ if (ind != nb) {
it = this->begin() + ind;
iterator ite = this->end(); --ite; iterator itee = ite;
for (; ite != it; --ite) { --itee; *ite = *itee; }
Modified: trunk/getfem/tests/test_assembly.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/tests/test_assembly.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/tests/test_assembly.cc (original)
+++ trunk/getfem/tests/test_assembly.cc Fri Oct 14 09:37:49 2016
@@ -908,6 +908,7 @@
((std::string("GT_PK(") + Ns + ",1)").c_str());
std::vector<size_type> nsubdiv(N, NX);
getfem::regular_unit_mesh(m, nsubdiv, pgt);
+ m.optimize_structure();
const size_type NEUMANN_BOUNDARY_NUM = 1;
const size_type DIRICHLET_BOUNDARY_NUM = 2;
Modified: trunk/getfem/tests/test_mesh.cc
URL:
http://svn.gna.org/viewcvs/getfem/trunk/getfem/tests/test_mesh.cc?rev=5417&r1=5416&r2=5417&view=diff
==============================================================================
--- trunk/getfem/tests/test_mesh.cc (original)
+++ trunk/getfem/tests/test_mesh.cc Fri Oct 14 09:37:49 2016
@@ -198,7 +198,7 @@
m.sup_convex(0);
m.sup_convex(1);
assert(!m.region(3).is_in(0));
- m.optimize_structure();
+ m.optimize_structure(false);
m.write_to_file("test_mesh.mesh");
getfem::mesh m2; m2.read_from_file("test_mesh.mesh");
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- [Getfem-commits] r5417 - in /trunk/getfem: contrib/opt_assembly/ interface/src/ interface/tests/matlab/ src/ src/getfem/ src/gmm/ tests/,
Yves . Renard <=