Homec4science
Diffusion akantu (features/changes-to-address-joss-review) Browse

rAKA/src/fe_engine/element_class_tmpl.hh
51dda7e0bc1dfeatures/changes-to…

Last Change
Raw File

element_class_tmpl.hh
View Options

/**
* @file element_class_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 29 2017
*
* @brief Implementation of the inline templated function of the element class
* descriptions
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "gauss_integration_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_TMPL_HH_
#define AKANTU_ELEMENT_CLASS_TMPL_HH_
namespace akantu {
template <ElementType element_type, ElementKind element_kind>
inline constexpr auto
ElementClass<element_type, element_kind>::getFacetTypes() {
return VectorProxy<const ElementType>(
element_class_extra_geom_property::facet_type.data(),
geometrical_element::getNbFacetTypes());
}
/* -------------------------------------------------------------------------- */
/* GeometricalElement */
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline constexpr auto
GeometricalElement<geometrical_type,
shape>::getFacetLocalConnectivityPerElement(UInt t) {
int pos = 0;
for (UInt i = 0; i < t; ++i) {
pos += geometrical_property::nb_facets[i] *
geometrical_property::nb_nodes_per_facet[i];
}
return MatrixProxy<const UInt>(
geometrical_property::facet_connectivity_vect.data() + pos,
geometrical_property::nb_facets[t],
geometrical_property::nb_nodes_per_facet[t]);
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement() {
UInt total_nb_facets = 0;
for (UInt n = 0; n < geometrical_property::nb_facet_types; ++n) {
total_nb_facets += geometrical_property::nb_facets[n];
}
return total_nb_facets;
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement(UInt t) {
return geometrical_property::nb_facets[t];
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
template <class vector_type>
inline bool GeometricalElement<geometrical_type, shape>::contains(
const vector_type & coords) {
return GeometricalShapeContains<shape>::contains(coords);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_point>::contains(const vector_type & coords) {
return (coords(0) < std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_square>::contains(const vector_type & coords) {
bool in = true;
for (UInt i = 0; i < coords.size() && in; ++i) {
in &= ((coords(i) >= -(1. + std::numeric_limits<Real>::epsilon())) &&
(coords(i) <= (1. + std::numeric_limits<Real>::epsilon())));
}
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_triangle>::contains(const vector_type & coords) {
bool in = true;
Real sum = 0;
for (UInt i = 0; (i < coords.size()) && in; ++i) {
in &= ((coords(i) >= -(Math::getTolerance())) &&
(coords(i) <= (1. + Math::getTolerance())));
sum += coords(i);
}
if (in) {
return (in && (sum <= (1. + Math::getTolerance())));
}
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_prism>::contains(const vector_type & coords) {
bool in = ((coords(0) >= -1.) && (coords(0) <= 1.)); // x in segment [-1, 1]
// y and z in triangle
in &= ((coords(1) >= 0) && (coords(1) <= 1.));
in &= ((coords(2) >= 0) && (coords(2) <= 1.));
Real sum = coords(1) + coords(2);
return (in && (sum <= 1));
}
/* -------------------------------------------------------------------------- */
/* InterpolationElement */
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeShapes(
const Matrix<Real> & natural_coord, Matrix<Real> & N) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(N(p));
Vector<Real> ncoord_p(natural_coord(p));
computeShapes(ncoord_p, Np);
}
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeDNDS(
const Matrix<Real> & natural_coord, Tensor3<Real> & dnds) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> dnds_p(dnds(p));
Vector<Real> ncoord_p(natural_coord(p));
computeDNDS(ncoord_p, dnds_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on a point a field for which values are given on the
* node of the element using the shape functions at this interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Vector<Real> & shapes,
Vector<Real> & interpolated) {
Matrix<Real> interpm(interpolated.storage(), nodal_values.rows(), 1);
Matrix<Real> shapesm(
shapes.storage(),
InterpolationProperty<interpolation_type>::nb_nodes_per_element, 1);
interpm.mul<false, false>(nodal_values, shapesm);
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on several points a field for which values are given on the
* node of the element using the shape functions at the interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated values of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Matrix<Real> & shapes,
Matrix<Real> & interpolated) {
UInt nb_points = shapes.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(shapes(p));
Vector<Real> interpolated_p(interpolated(p));
interpolate(nodal_values, Np, interpolated_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate the field on a point given in natural coordinates the field which
* values are given on the node of the element
*
* @param natural_coords natural coordinates of point where to interpolate \xi
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::interpolateOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated) {
Vector<Real> shapes(
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeShapes(natural_coords, shapes);
interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
/// @f$ gradient_{ij} = \frac{\partial f_j}{\partial s_i} = \sum_k
/// \frac{\partial N_k}{\partial s_i}f_{j n_k} @f$
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::gradientOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & f,
Matrix<Real> & gradient) {
Matrix<Real> dnds(
InterpolationProperty<interpolation_type>::natural_space_dimension,
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeDNDS(natural_coords, dnds);
gradient.mul<false, true>(f, dnds);
}
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J) {
UInt nb_points = dnds.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> J_p(J(p));
Matrix<Real> dnds_p(dnds(p));
computeJMat(dnds_p, node_coords, J_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J) {
/// @f$ J = dxds = dnds * x @f$
J.mul<false, true>(dnds, node_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
UInt nb_points = natural_coords.cols();
Matrix<Real> dnds(interpolation_property::natural_space_dimension,
interpolation_property::nb_nodes_per_element);
Matrix<Real> J(natural_coords.rows(), node_coords.rows());
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> ncoord_p(natural_coords(p));
interpolation_element::computeDNDS(ncoord_p, dnds);
computeJMat(dnds, node_coords, J);
computeJacobian(J, jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
computeJacobian(J(p), jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeJacobian(const Matrix<Real> & J,
Real & jacobians) {
if (J.rows() == J.cols()) {
jacobians = Math::det<element_property::spatial_dimension>(J.storage());
} else {
interpolation_element::computeSpecialJacobian(J, jacobians);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p(shape_deriv(p));
computeShapeDerivatives(J(p), dnds(p), shape_deriv_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv) {
Matrix<Real> inv_J(J.rows(), J.cols());
Math::inv<element_property::spatial_dimension>(J.storage(), inv_J.storage());
shape_deriv.mul<false, false>(inv_J, dnds);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeNormalsOnNaturalCoordinates(
const Matrix<Real> & coord, Matrix<Real> & f, Matrix<Real> & normals) {
UInt dimension = normals.rows();
UInt nb_points = coord.cols();
AKANTU_DEBUG_ASSERT((dimension - 1) ==
interpolation_property::natural_space_dimension,
"cannot extract a normal because of dimension mismatch "
<< dimension - 1 << " "
<< interpolation_property::natural_space_dimension);
Matrix<Real> J(dimension, interpolation_property::natural_space_dimension);
for (UInt p = 0; p < nb_points; ++p) {
interpolation_element::gradientOnNaturalCoordinates(coord(p), f, J);
if (dimension == 2) {
Math::normal2(J.storage(), normals(p).storage());
}
if (dimension == 3) {
Math::normal3(J(0).storage(), J(1).storage(), normals(p).storage());
}
}
}
/* ------------------------------------------------------------------------- */
/**
* In the non linear cases we need to iterate to find the natural coordinates
*@f$\xi@f$
* provided real coordinates @f$x@f$.
*
* We want to solve: @f$ x- \phi(\xi) = 0@f$ with @f$\phi(\xi) = \sum_I N_I(\xi)
*x_I@f$
* the mapping function which uses the nodal coordinates @f$x_I@f$.
*
* To that end we use the Newton method and the following series:
*
* @f$ \frac{\partial \phi(x_k)}{\partial \xi} \left( \xi_{k+1} - \xi_k \right)
*= x - \phi(x_k)@f$
*
* When we consider elements embedded in a dimension higher than them (2D
*triangle in a 3D space for example)
* @f$ J = \frac{\partial \phi(\xi_k)}{\partial \xi}@f$ is of dimension
*@f$dim_{space} \times dim_{elem}@f$ which
* is not invertible in most cases. Rather we can solve the problem:
*
* @f$ J^T J \left( \xi_{k+1} - \xi_k \right) = J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that
*
* @f$ d\xi = \xi_{k+1} - \xi_k = (J^T J)^{-1} J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that if the series converges we have:
*
* @f$ 0 = J^T \left( \phi(\xi_\infty) - x \right) @f$
*
* And we see that this is ill-posed only if @f$ J^T x = 0@f$ which means that
*the vector provided
* is normal to any tangent which means it is outside of the element itself.
*
* @param real_coords: the real coordinates the natural coordinates are sought
*for
* @param node_coords: the coordinates of the nodes forming the element
* @param natural_coords: output->the sought natural coordinates
* @param spatial_dimension: spatial dimension of the problem
*
**/
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Vector<Real> & real_coords, const Matrix<Real> & node_coords,
Vector<Real> & natural_coords, Real tolerance) {
UInt spatial_dimension = real_coords.size();
UInt dimension = natural_coords.size();
// matrix copy of the real_coords
Matrix<Real> mreal_coords(real_coords.storage(), spatial_dimension, 1);
// initial guess
// Matrix<Real> natural_guess(natural_coords.storage(), dimension, 1);
natural_coords.zero();
// real space coordinates provided by initial guess
Matrix<Real> physical_guess(dimension, 1);
// objective function f = real_coords - physical_guess
Matrix<Real> f(dimension, 1);
// dnds computed on the natural_guess
// Matrix<Real> dnds(interpolation_element::nb_nodes_per_element,
// spatial_dimension);
// J Jacobian matrix computed on the natural_guess
Matrix<Real> J(spatial_dimension, dimension);
// G = J^t * J
Matrix<Real> G(spatial_dimension, spatial_dimension);
// Ginv = G^{-1}
Matrix<Real> Ginv(spatial_dimension, spatial_dimension);
// J = Ginv * J^t
Matrix<Real> F(spatial_dimension, dimension);
// dxi = \xi_{k+1} - \xi in the iterative process
Matrix<Real> dxi(spatial_dimension, 1);
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
// do interpolation
auto update_f = [&f, &physical_guess, &natural_coords, &node_coords,
&mreal_coords, dimension]() {
Vector<Real> physical_guess_v(physical_guess.storage(), dimension);
interpolation_element::interpolateOnNaturalCoordinates(
natural_coords, node_coords, physical_guess_v);
// compute initial objective function value f = real_coords - physical_guess
f = mreal_coords;
f -= physical_guess;
// compute initial error
auto error = f.norm<L_2>();
return error;
};
auto inverse_map_error = update_f();
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
while (tolerance < inverse_map_error) {
// compute J^t
interpolation_element::gradientOnNaturalCoordinates(natural_coords,
node_coords, J);
// compute G
G.mul<true, false>(J, J);
// inverse G
Ginv.inverse(G);
// compute F
F.mul<false, true>(Ginv, J);
// compute increment
dxi.mul<false, false>(F, f);
// update our guess
natural_coords += Vector<Real>(dxi(0));
inverse_map_error = update_f();
}
// memcpy(natural_coords.storage(), natural_guess.storage(), sizeof(Real) *
// natural_coords.size());
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Matrix<Real> & real_coords, const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords, Real tolerance) {
UInt nb_points = real_coords.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> X(real_coords(p));
Vector<Real> ncoord_p(natural_coords(p));
inverseMap(X, node_coords, ncoord_p, tolerance);
}
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_CLASS_TMPL_HH_ */
c4science · Help