void ExodusII_IO::write_global_data (const std::vector<Number> & soln,
const std::vector<std::string> & names)
{
if(MeshOutput<MeshBase>::mesh().processor_id())
return;
if (!exio_helper->opened_for_writing)
libmesh_error_msg("ERROR, ExodusII file must be initialized before outputting global variables.");
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
std::vector<std::string> complex_names = exio_helper->get_complex_names(names);
exio_helper->initialize_global_variables(complex_names);
unsigned int num_values = soln.size();
unsigned int num_vars = names.size();
unsigned int num_elems = num_values / num_vars;
// This will contain the real and imaginary parts and the magnitude
// of the values in soln
std::vector<Real> complex_soln(3*num_values);
for (unsigned i=0; i<num_vars; ++i)
{
for (unsigned int j=0; j<num_elems; ++j)
{
Number value = soln[i*num_vars + j];
complex_soln[3*i*num_elems + j] = value.real();
}
for (unsigned int j=0; j<num_elems; ++j)
{
Number value = soln[i*num_vars + j];
complex_soln[3*i*num_elems + num_elems +j] = value.imag();
}
for (unsigned int j=0; j<num_elems; ++j)
{
Number value = soln[i*num_vars + j];
complex_soln[3*i*num_elems + 2*num_elems + j] = std::abs(value);
}
}
exio_helper->write_global_values(complex_soln, _timestep);
#else
exio_helper->initialize_global_variables(names);
exio_helper->write_global_values(soln, _timestep);
#endif
}
void LinearElasticityWithContact::move_mesh (MeshBase & input_mesh,
const NumericVector<Number> & input_solution)
{
// Maintain a set of node ids that we've encountered.
LIBMESH_BEST_UNORDERED_SET<dof_id_type> encountered_node_ids;
// Localize input_solution so that we have the data to move all
// elements (not just elements local to this processor).
UniquePtr< NumericVector<Number> > localized_input_solution =
NumericVector<Number>::build(input_solution.comm());
localized_input_solution->init (input_solution.size(), false, SERIAL);
input_solution.localize(*localized_input_solution);
MeshBase::const_element_iterator el = input_mesh.active_elements_begin();
const MeshBase::const_element_iterator end_el = input_mesh.active_elements_end();
for ( ; el != end_el; ++el)
{
Elem * elem = *el;
Elem * orig_elem = _sys.get_mesh().elem_ptr(elem->id());
for (unsigned int node_id=0; node_id<elem->n_nodes(); node_id++)
{
Node & node = elem->node_ref(node_id);
if (encountered_node_ids.find(node.id()) != encountered_node_ids.end())
continue;
encountered_node_ids.insert(node.id());
std::vector<std::string> uvw_names(3);
uvw_names[0] = "u";
uvw_names[1] = "v";
uvw_names[2] = "w";
{
const Point master_point = elem->master_point(node_id);
Point uvw;
for (unsigned int index=0; index<uvw_names.size(); index++)
{
const unsigned int var = _sys.variable_number(uvw_names[index]);
const FEType & fe_type = _sys.get_dof_map().variable_type(var);
FEComputeData data (_sys.get_equation_systems(), master_point);
FEInterface::compute_data(elem->dim(),
fe_type,
elem,
data);
std::vector<dof_id_type> dof_indices_var;
_sys.get_dof_map().dof_indices (orig_elem, dof_indices_var, var);
for (unsigned int i=0; i<dof_indices_var.size(); i++)
{
Number value = (*localized_input_solution)(dof_indices_var[i]) * data.shape[i];
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
// We explicitly store the real part in uvw
uvw(index) += value.real();
#else
uvw(index) += value;
#endif
}
}
// Update the node's location
node += uvw;
}
}
}
}
void ExodusII_IO::write_element_data (const EquationSystems & es)
{
// Be sure the file has been opened for writing!
if (MeshOutput<MeshBase>::mesh().processor_id() == 0 && !exio_helper->opened_for_writing)
libmesh_error_msg("ERROR, ExodusII file must be initialized before outputting element variables.");
// This function currently only works on SerialMeshes. We rely on
// having a reference to a non-const MeshBase object from our
// MeshInput parent class to construct a MeshSerializer object,
// similar to what is done in ExodusII_IO::write(). Note that
// calling ExodusII_IO::write_timestep() followed by
// ExodusII_IO::write_element_data() when the underlying Mesh is a
// ParallelMesh will result in an unnecessary additional
// serialization/re-parallelization step.
MeshSerializer serialize(MeshInput<MeshBase>::mesh(), !MeshOutput<MeshBase>::_is_parallel_format);
// To be (possibly) filled with a filtered list of variable names to output.
std::vector<std::string> names;
// If _output_variables is populated, only output the monomials which are
// also in the _output_variables vector.
if (_output_variables.size() > 0)
{
std::vector<std::string> monomials;
const FEType type(CONSTANT, MONOMIAL);
// Create a list of monomial variable names
es.build_variable_names(monomials, &type);
// Filter that list against the _output_variables list. Note: if names is still empty after
// all this filtering, all the monomial variables will be gathered
std::vector<std::string>::iterator it = monomials.begin();
for (; it!=monomials.end(); ++it)
if (std::find(_output_variables.begin(), _output_variables.end(), *it) != _output_variables.end())
names.push_back(*it);
}
// If we pass in a list of names to "get_solution" it'll filter the variables coming back
std::vector<Number> soln;
es.get_solution(soln, names);
if(soln.empty()) // If there is nothing to write just return
return;
// The data must ultimately be written block by block. This means that this data
// must be sorted appropriately.
if(MeshOutput<MeshBase>::mesh().processor_id())
return;
const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
std::vector<std::string> complex_names = exio_helper->get_complex_names(names);
exio_helper->initialize_element_variables(complex_names);
unsigned int num_values = soln.size();
unsigned int num_vars = names.size();
unsigned int num_elems = num_values / num_vars;
// This will contain the real and imaginary parts and the magnitude
// of the values in soln
std::vector<Real> complex_soln(3*num_values);
for (unsigned i=0; i<num_vars; ++i)
{
for (unsigned int j=0; j<num_elems; ++j)
{
Number value = soln[i*num_vars + j];
complex_soln[3*i*num_elems + j] = value.real();
}
for (unsigned int j=0; j<num_elems; ++j)
{
Number value = soln[i*num_vars + j];
complex_soln[3*i*num_elems + num_elems +j] = value.imag();
}
for (unsigned int j=0; j<num_elems; ++j)
{
Number value = soln[i*num_vars + j];
complex_soln[3*i*num_elems + 2*num_elems + j] = std::abs(value);
}
}
exio_helper->write_element_values(mesh, complex_soln, _timestep);
#else
exio_helper->initialize_element_variables(names);
exio_helper->write_element_values(mesh, soln, _timestep);
#endif
}