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[Getfem-commits] (no subject)
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From: |
Tetsuo Koyama |
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Subject: |
[Getfem-commits] (no subject) |
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Date: |
Sun, 27 Dec 2020 06:11:42 -0500 (EST) |
branch: devel-tetsuo-fix-export-vtu
commit 2d3812300b9be7d0587dcac30d7feb73b187a126
Author: Tetsuo Koyama <tkoyama010@gmail.com>
AuthorDate: Sun Dec 27 20:02:44 2020 +0900
Fix empty response error of export vtu
---
...ty_finite_strain_linear_hardening_tension_3D.py | 4 +-
...strain_linear_hardening_tension_axisymmetric.py | 4 +-
...strain_linear_hardening_tension_plane_strain.py | 4 +-
interface/tests/python/check_export_vtu.py | 120 +++++++++++++++++----
src/getfem/getfem_export.h | 4 +-
src/getfem_export.cc | 44 ++++++--
6 files changed, 145 insertions(+), 35 deletions(-)
diff --git
a/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_3D.py
b/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_3D.py
index f041500..bd5eca9 100644
---
a/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_3D.py
+++
b/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_3D.py
@@ -128,7 +128,7 @@ if dH > 0:
pts[2,i] -= (z*dH)/(2*H) * (1 + np.cos(2.*np.pi*x/L))
mesh.set_pts(pts)
-mesh.export_to_vtk("%s/mesh.vtk" % resultspath)
+mesh.export_to_vtu("%s/mesh.vtu" % resultspath)
# FEM
mfN = gf.MeshFem(mesh, N)
@@ -238,7 +238,7 @@ with open("%s/tension_3D.dat" % resultspath, "w") as f1:
mfu, md.variable("u"), "Displacements",
mfout2, md.interpolation("dirmult", mfout2, XP_RG), "Nominal
reaction traction",
mfout2, md.local_projection(mim, "gamma", mfout2), "plastic
strain")
- mfout2.export_to_vtk("%s/tension_3D_%i.vtk" % (resultspath, step),
*output)
+ mfout2.export_to_vtu("%s/tension_3D_%i.vtu" % (resultspath, step),
*output)
md.set_variable("gamma0", md.interpolation("gamma", mimd1, -1))
md.set_variable("invCp0vec",
diff --git
a/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_axisymmetric.py
b/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_axisymmetric.py
index 8fc92ae..5ee76d8 100644
---
a/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_axisymmetric.py
+++
b/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_axisymmetric.py
@@ -119,7 +119,7 @@ if dH > 0:
pts[1,i] -= (y*dH)/(2*H) * (1 + np.cos(2.*np.pi*x/L))
mesh.set_pts(pts)
-mesh.export_to_vtk("%s/mesh.vtk" % resultspath)
+mesh.export_to_vtu("%s/mesh.vtu" % resultspath)
# FEM
mfN = gf.MeshFem(mesh, N)
@@ -227,7 +227,7 @@ with open("%s/tension_axisymmetric.dat" % resultspath, "w")
as f1:
mfu, md.variable("u"), "Displacements",
mfout2, md.interpolation("dirmult", mfout2, XP_RG), "Nominal
reaction traction",
mfout2, md.local_projection(mim, "gamma", mfout2), "plastic
strain")
- mfout2.export_to_vtk("%s/tension_axisymmetric_%i.vtk" % (resultspath,
step), *output)
+ mfout2.export_to_vtu("%s/tension_axisymmetric_%i.vtu" % (resultspath,
step), *output)
md.set_variable("gamma0", md.interpolation("gamma", mimd1, -1))
md.set_variable("invCp0vec",
diff --git
a/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_plane_strain.py
b/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_plane_strain.py
index 422efe1..af489fd 100644
---
a/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_plane_strain.py
+++
b/contrib/continuum_mechanics/plasticity_finite_strain_linear_hardening_tension_plane_strain.py
@@ -118,7 +118,7 @@ if dH > 0:
pts[1,i] -= (y*dH)/(2*H) * (1 + np.cos(2.*np.pi*x/L))
mesh.set_pts(pts)
-mesh.export_to_vtk("%s/mesh.vtk" % resultspath)
+mesh.export_to_vtu("%s/mesh.vtu" % resultspath)
# FEM
mfN = gf.MeshFem(mesh, N)
@@ -225,7 +225,7 @@ with open("%s/tension_plane_strain.dat" % resultspath, "w")
as f1:
mfu, md.variable("u"), "Displacements",
mfout2, md.interpolation("dirmult", mfout2, XP_RG), "Nominal
reaction traction",
mfout2, md.local_projection(mim, "gamma", mfout2), "plastic
strain")
- mfout2.export_to_vtk("%s/tension_plane_strain_%i.vtk" % (resultspath,
step), *output)
+ mfout2.export_to_vtu("%s/tension_plane_strain_%i.vtu" % (resultspath,
step), *output)
md.set_variable("gamma0", md.interpolation("gamma", mimd1, -1))
md.set_variable("invCp0vec",
diff --git a/interface/tests/python/check_export_vtu.py
b/interface/tests/python/check_export_vtu.py
index d6c45f9..0f20332 100644
--- a/interface/tests/python/check_export_vtu.py
+++ b/interface/tests/python/check_export_vtu.py
@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
# Python GetFEM interface
#
-# Copyright (C) 2004-2020 Yves Renard, Julien Pommier.
+# Copyright (C) 2020-2020 Tetsuo Koyama.
#
# This file is a part of GetFEM
#
@@ -29,6 +29,7 @@
import getfem as gf
import numpy as np
import sys
+
try:
import pyvista as pv
except:
@@ -41,26 +42,105 @@ mesh = gf.Mesh("cartesian", [0.0, 1.0, 2.0])
pts = mesh.pts()[0]
-filenames = [
- "check_mesh_ascii.vtk",
- "check_mesh_binary.vtk",
- "check_mesh_ascii.vtu",
- "check_mesh_binary.vtu",
-]
+file_name = "check_mesh_ascii.vtk"
+mesh.export_to_vtk(file_name, "ascii")
+unstructured_grid = pv.read(file_name)
+expected = pts
+actual = unstructured_grid.points[:, 0]
+np.testing.assert_equal(expected, actual, "export of mesh pts is not correct.")
+expected = convex_connectivity
+actual = unstructured_grid.cell_connectivity
+np.testing.assert_equal(expected, actual, "export of mesh convex is not
correct.")
+
+file_name = "check_mesh_binary.vtk"
+mesh.export_to_vtk(file_name)
+unstructured_grid = pv.read(file_name)
+expected = pts
+actual = unstructured_grid.points[:, 0]
+np.testing.assert_equal(expected, actual, "export of mesh pts is not correct.")
+expected = convex_connectivity
+actual = unstructured_grid.cell_connectivity
+np.testing.assert_equal(expected, actual, "export of mesh convex is not
correct.")
+
+file_name = "check_mesh_ascii.vtu"
+mesh.export_to_vtu(file_name, "ascii")
+unstructured_grid = pv.read(file_name)
+expected = pts
+actual = unstructured_grid.points[:, 0]
+np.testing.assert_equal(expected, actual, "export of mesh pts is not correct.")
+expected = convex_connectivity
+actual = unstructured_grid.cell_connectivity
+np.testing.assert_equal(expected, actual, "export of mesh convex is not
correct.")
+
+file_name = "check_mesh_binary.vtu"
+mesh.export_to_vtu(file_name)
+unstructured_grid = pv.read(file_name)
+expected = pts
+actual = unstructured_grid.points[:, 0]
+np.testing.assert_equal(expected, actual, "export of mesh pts is not correct.")
+expected = convex_connectivity
+actual = unstructured_grid.cell_connectivity
+np.testing.assert_equal(expected, actual, "export of mesh convex is not
correct.")
+
+mfu = gf.MeshFem(mesh, 1)
+mfu.set_classical_fem(1)
+U1 = np.array([2.0, 1.0, 0.0])
+
+file_name = "check_meshfem_ascii.vtk"
+mfu.export_to_vtk(file_name, "ascii", U1, "U1")
+unstructured_grid = pv.read(file_name)
+expected = U1
+actual = unstructured_grid.point_arrays["U1"]
+np.testing.assert_equal(expected, actual, "export of U1 is not correct.")
+
+file_name = "check_meshfem_binary.vtk"
+mfu.export_to_vtk(file_name, U1, "U1")
+unstructured_grid = pv.read(file_name)
+expected = U1
+actual = unstructured_grid.point_arrays["U1"]
+np.testing.assert_equal(expected, actual, "export of U1 is not correct.")
+
+file_name = "check_meshfem_ascii.vtu"
+mfu.export_to_vtu(file_name, "ascii", U1, "U1")
+unstructured_grid = pv.read(file_name)
+expected = U1
+actual = unstructured_grid.point_arrays["U1"]
+np.testing.assert_equal(expected, actual, "export of U1 is not correct.")
+
+file_name = "check_meshfem_binary.vtu"
+mfu.export_to_vtu(file_name, U1, "U1")
+unstructured_grid = pv.read(file_name)
+expected = U1
+actual = unstructured_grid.point_arrays["U1"]
+np.testing.assert_equal(expected, actual, "export of U1 is not correct.")
+
+sl = gf.Slice(("boundary",), mesh, 1)
+U2 = np.array([3.0, 2.0, 1.0, 0.0])
-mesh.export_to_vtk(filenames[0], "ascii")
-mesh.export_to_vtk(filenames[1])
-mesh.export_to_vtu(filenames[2], "ascii")
-mesh.export_to_vtu(filenames[3])
+file_name = "check_slice_ascii.vtk"
+sl.export_to_vtk(file_name, "ascii", U2, "U2")
+unstructured_grid = pv.read(file_name)
+expected = U2
+actual = unstructured_grid.point_arrays["U2"]
+np.testing.assert_equal(expected, actual, "export of U2 is not correct.")
-for filename in filenames:
- print(filename)
- unstructured_grid = pv.read(filename)
+file_name = "check_slice_binary.vtk"
+sl.export_to_vtk(file_name, U2, "U2")
+unstructured_grid = pv.read(file_name)
+expected = U2
+actual = unstructured_grid.point_arrays["U2"]
+np.testing.assert_equal(expected, actual, "export of U2 is not correct.")
- expected = pts
- actual = unstructured_grid.points[:, 0]
- np.testing.assert_equal(expected, actual, "export of mesh pts is not
correct.")
+file_name = "check_slice_ascii.vtu"
+sl.export_to_vtu(file_name, "ascii", U2, "U2")
+unstructured_grid = pv.read(file_name)
+expected = U2
+actual = unstructured_grid.point_arrays["U2"]
+np.testing.assert_equal(expected, actual, "export of U2 is not correct.")
- expected = convex_connectivity
- actual = unstructured_grid.cell_connectivity
- np.testing.assert_equal(expected, actual, "export of mesh convex is not
correct.")
+file_name = "check_slice_binary.vtu"
+sl.export_to_vtu(file_name, U2, "U2")
+unstructured_grid = pv.read(file_name)
+expected = U2
+actual = unstructured_grid.point_arrays["U2"]
+np.testing.assert_equal(expected, actual, "export of U2 is not correct.")
diff --git a/src/getfem/getfem_export.h b/src/getfem/getfem_export.h
index d54c0e5..5d03795 100644
--- a/src/getfem/getfem_export.h
+++ b/src/getfem/getfem_export.h
@@ -255,6 +255,7 @@ namespace getfem {
"inconsistency in the size of the dataset: "
<< gmm::vect_size(U) << " != " << nb_val << "*" << Q);
if (vtk) write_separ();
+ if (!vtk && !ascii) write_val(float(gmm::vect_size(U)));
if (Q == 1) {
if (vtk)
os << "SCALARS " << remove_spaces(name) << " float 1\n"
@@ -288,8 +289,9 @@ namespace getfem {
} else
GMM_ASSERT1(false, std::string(vtk ? "vtk" : "vtu")
+ " does not accept vectors of dimension > 3");
+ write_vals();
if (vtk) write_separ();
- if (!vtk) os << (ascii ? "" : "\n") << "</DataArray>\n";
+ if (!vtk) os << "\n" << "</DataArray>\n";
}
diff --git a/src/getfem_export.cc b/src/getfem_export.cc
index 0d3fe84..ab331de 100644
--- a/src/getfem_export.cc
+++ b/src/getfem_export.cc
@@ -448,6 +448,7 @@ namespace getfem
os << "<DataArray type=\"Float32\" Name=\"Points\" ";
os << "NumberOfComponents=\"3\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
+ if (!ascii) write_val(int(sizeof(float)*psl->nb_points()*3));
}
/*
points are not merge, vtk is mostly fine with that (except for
@@ -473,6 +474,16 @@ namespace getfem
os << "<Cells>\n";
os << "<DataArray type=\"Int32\" Name=\"connectivity\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
+ if (!ascii) {
+ int size = 0;
+ for (size_type ic=0; ic < psl->nb_convex(); ++ic) {
+ const getfem::mesh_slicer::cs_simplexes_ct& s = psl->simplexes(ic);
+ for (const auto &val : s)
+ for (size_type j=0; j < val.dim()+1; ++j)
+ size += int(sizeof(int));
+ }
+ write_val(size);
+ }
}
for (size_type ic=0; ic < psl->nb_convex(); ++ic) {
const getfem::mesh_slicer::cs_simplexes_ct& s = psl->simplexes(ic);
@@ -494,6 +505,15 @@ namespace getfem
os << (ascii ? "" : "\n") << "</DataArray>\n";
os << "<DataArray type=\"Int32\" Name=\"offsets\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
+ if (!ascii) {
+ int size = 0;
+ for (size_type ic=0; ic < psl->nb_convex(); ++ic) {
+ const getfem::mesh_slicer::cs_simplexes_ct& s = psl->simplexes(ic);
+ for (const auto &val : s)
+ size += int(sizeof(int));
+ }
+ write_val(size);
+ }
}
int cnt = 0;
for (size_type ic=0; ic < psl->nb_convex(); ++ic) {
@@ -514,6 +534,15 @@ namespace getfem
os << (ascii ? "" : "\n") << "</DataArray>\n";
os << "<DataArray type=\"Int32\" Name=\"types\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
+ if (!ascii) {
+ int size = 0;
+ for (size_type ic=0; ic < psl->nb_convex(); ++ic) {
+ const getfem::mesh_slicer::cs_simplexes_ct& s = psl->simplexes(ic);
+ for (size_type i=0; i < s.size(); ++i)
+ size += int(sizeof(int));
+ }
+ write_val(size);
+ }
for (size_type ic=0; ic < psl->nb_convex(); ++ic) {
const getfem::mesh_slicer::cs_simplexes_ct& s = psl->simplexes(ic);
for (size_type i=0; i < s.size(); ++i) {
@@ -521,7 +550,7 @@ namespace getfem
}
}
write_vals();
- os << (ascii ? "" : "\n") << "</DataArray>\n";
+ os << "\n" << "</DataArray>\n";
os << "</Cells>\n";
}
state = STRUCTURE_WRITTEN;
@@ -542,11 +571,10 @@ namespace getfem
os << "<DataArray type=\"Float32\" Name=\"Points\" ";
os << "NumberOfComponents=\"3\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
+ if (!ascii) write_val(int(sizeof(float)*pmf_dof_used.card()*3));
}
std::vector<int> dofmap(pmf->nb_dof());
int cnt = 0;
- int size = int(sizeof(float)*pmf_dof_used.card()*3);
- if (!vtk && !ascii) write_val(size);
for (dal::bv_visitor d(pmf_dof_used); !d.finished(); ++d) {
dofmap[d] = cnt++;
base_node P = pmf->point_of_basic_dof(d);
@@ -568,8 +596,8 @@ namespace getfem
os << "<Cells>\n";
os << "<DataArray type=\"Int32\" Name=\"connectivity\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
- if (!vtk && !ascii) {
- size = 0;
+ if (!ascii) {
+ int size = 0;
for (dal::bv_visitor cv(pmf->convex_index()); !cv.finished(); ++cv) {
const std::vector<unsigned> &dmap =
select_vtk_dof_mapping(pmf_mapping_type[cv]);
size += int(sizeof(int)*dmap.size());
@@ -594,8 +622,8 @@ namespace getfem
os << (ascii ? "" : "\n") << "</DataArray>\n";
os << "<DataArray type=\"Int32\" Name=\"offsets\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
- if (!vtk && !ascii) {
- size = 0;
+ if (!ascii) {
+ int size = 0;
for (dal::bv_visitor cv(pmf->convex_index()); !cv.finished(); ++cv)
size += int(sizeof(int));
write_val(size);
@@ -611,7 +639,7 @@ namespace getfem
os << "<DataArray type=\"Int32\" Name=\"types\" ";
os << (ascii ? "format=\"ascii\">\n" : "format=\"binary\">\n");
if (!ascii) {
- size = 0;
+ int size = 0;
for (dal::bv_visitor cv(pmf->convex_index()); !cv.finished(); ++cv)
size += int(sizeof(int));
write_val(size);