"This package allows the use of CGAL's geometry algorithms in Akantu. Note that it needs a version of CGAL $\\geq$ 4.5 and needs activation of boost's system component."
""
"CGAL checks with an assertion that the compilation flag \\shellcode{-frounding-math} is activated, which forbids the use of Valgrind on any code compilated with the package."
"This package enables the \\href{http://mumps.enseeiht.fr/}{MUMPS} parallel direct solver for sparce matrices."
"This is necessary to solve static or implicit problems."
""
"Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
""
"\\begin{command}"
" > sudo apt-get install libmumps-seq-dev # for sequential"
" > sudo apt-get install libmumps-dev # for parallel"
"\\end{command}"
""
"Under Mac OS X the installation requires the following steps:"
"\\begin{command}"
" > sudo port install mumps"
"\\end{command}"
""
"If you activate the advanced option AKANTU\\_USE\\_THIRD\\_PARTY\\_MUMPS the make system of akantu can automatically compile MUMPS. For this you will have to download MUMPS from \\url{http://mumps.enseeiht.fr/} or \\url{http://graal.ens-lyon.fr/MUMPS} and place it in \\shellcode{<akantu source>/third-party}"
"This package enable the use of the optimization alogorithm library \\href{http://ab-initio.mit.edu/wiki/index.php/NLopt}{NLopt}."
"Since there are no packaging for the common operating system by default \\akantu compiles it as a third-party project. This behavior can be modified with the option \\code{AKANTU\\_USE\\_THIRD\\_PARTY\\_NLOPT}."
""
"If the automated download fails please download \\href{http://ab-initio.mit.edu/nlopt/nlopt-${NLOPT_VERSION}.tar.gz}{nlopt-${NLOPT_VERSION}.tar.gz} and place it in \\shellcode{<akantu source>/third-party} download."
os<<"NLOPT_STOPVAL_REACHED: Optimization stopped because stopval (above) was reached."<<endl;
break;
case 3:
os<<"NLOPT_FTOL_REACHED: Optimization stopped because ftol_rel or ftol_abs (above) was reached."<<endl;
break;
case 4:
os<<"NLOPT_XTOL_REACHED: Optimization stopped because xtol_rel or xtol_abs (above) was reached."<<endl;
break;
case 5:
os<<"NLOPT_MAXEVAL_REACHED: Optimization stopped because maxeval (above) was reached."<<endl;
break;
case 6:
os<<"NLOPT_MAXTIME_REACHED: Optimization stopped because maxtime (above) was reached."<<endl;
break;
case -1:
os<<"NLOPT_FAILURE: Generic failure code."<<endl;
break;
case -2:
os<<"NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etc.)"<<endl;
break;
case -3:
os<<"NLOPT_OUT_OF_MEMORY: Ran out of memory."<<endl;
break;
case -4:
os<<"NLOPT_ROUNDOFF_LIMITED: Halted because roundoff errors limited progress. (In this case, the optimization still typically returns a useful result."<<endl;
break;
case -5:
os<<"NLOPT_FORCED_STOP: Halted because of a forced termination: the user called nlopt_force_stop(opt) on the optimizationâs nlopt_opt object opt from the userâs objective function or constraints."<<endl;
/// Generic (templated by the enum InterpolationType which specifies the order and the dimension of the interpolation) class handling the elemental interpolation
* 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$
* 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$
* 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$
/// Compute intersection points between the mesh primitives (segments) and a query (surface in 3D or a curve in 2D), double intersection points for the same primitives are not considered. A maximum intersection node per element is set : 2 in 2D and 4 in 3D
AKANTU_DEBUG_ERROR("This function is not implemented for spheres (It was to generic and has been replaced by computeMeshQueryIntersectionPoint");
}
/// Compute intersection points between the mesh primitives (segments) and a query (surface in 3D or a curve in 2D), double intersection points for the same primitives are not considered. A maximum is set to the number of intersection nodes per element: 2 in 2D and 4 in 3D
AKANTU_DEBUG_ASSERT(f < mesh.getNbFacetsPerElement(elem.type), "The element " << elem << " seems to have too many facets!! (" << f << " < " << mesh.getNbFacetsPerElement(elem.type) << ")");
AKANTU_DEBUG_ASSERT(tmp.getSize() == vect.getSize(), "Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(tmp.getSize() == vect.getSize(), "Something strange append some mater was created or disappeared in "<< vect.getID() << "("<< vect.getSize() <<"!=" << tmp.getSize() <<") ""!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.getSize(); ++i) {
inline Real GeneralizedTrapezoidal::getTemperatureCoefficient<GeneralizedTrapezoidal::_temperature_rate_corrector>(Real delta_t) {
return alpha * delta_t;
}
template<>
inline Real GeneralizedTrapezoidal::getTemperatureRateCoefficient<GeneralizedTrapezoidal::_temperature_rate_corrector>(__attribute__ ((unused)) Real delta_t) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" <<getID() << ") does not contain a vector " << vect_id << "(" << fvect_id << ") [" << e << "]");
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID() << ") does not contain a vector " << vect_id << "(" << fvect_id << ") [" << e << "]");
AKANTU_SILENT_EXCEPTION("The material " << name << "(" <<getID() << ") does not contain a vector " << vect_id << "(" << fvect_id << ") [" << e << "]");
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID() << ") does not contain a vector " << vect_id << "(" << fvect_id << ") [" << e << "]");
AKANTU_DEBUG_ASSERT(_spatial_dimension == spatial_dimension, "This assert was inserted because the current variable shadows a template parameter: cannot know which to use");
AKANTU_DEBUG_ERROR("The function \"computeCauchyStressPlaneStress\" can only be used in 2D Plane stress problems, which means that you made a mistake somewhere!! ");
/// access K(i, j). Works only for dofs on this processor!!!!
Real PETScMatrix::operator()(UInt i, UInt j) const{
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(this->dof_synchronizer->isLocalOrMasterDOF(i) && this->dof_synchronizer->isLocalOrMasterDOF(j), "Operator works only for dofs on this processor");
// if (!(nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]])) {
// rhs_rotated.storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = Ti_small_rhs(ni % nb_degree_of_freedom, 0);
// nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = true;
// }
// }
// else{
// if (!(nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]])) {
// rhs_rotated.storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = rhs.storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]];
// nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = true;
AKANTU_DEBUG_ASSERT(gather_scatter_scheme_initialized == true, "You should call initScatterGatherCommunicationScheme before trying to gather a Array !!");
AKANTU_DEBUG_ASSERT(gather_scatter_scheme_initialized == true, "You should call initScatterGatherCommunicationScheme before trying to scatter a Array !!");