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// ------------------------------------------------------------------------
//
// SPDX-License-Identifier: LGPL-2.1-or-later
// Copyright (C) 1999 - 2025 by the deal.II authors
//
// This file is part of the deal.II library.
//
// Part of the source code is dual licensed under Apache-2.0 WITH
// LLVM-exception OR LGPL-2.1-or-later. Detailed license information
// governing the source code and code contributions can be found in
// LICENSE.md and CONTRIBUTING.md at the top level directory of deal.II.
//
// ------------------------------------------------------------------------
#include <deal.II/base/data_out_base.h>
#include <deal.II/base/memory_consumption.h>
#include <deal.II/base/mpi.h>
#include <deal.II/base/mpi_large_count.h>
#include <deal.II/base/parameter_handler.h>
#include <deal.II/base/thread_management.h>
#include <deal.II/base/utilities.h>
#include <deal.II/numerics/data_component_interpretation.h>
#include <algorithm>
#include <cmath>
#include <cstdint>
#include <cstring>
#include <ctime>
#include <fstream>
#include <future>
#include <iomanip>
#include <limits>
#include <memory>
#include <numeric>
#include <set>
#include <sstream>
#include <vector>
#ifdef DEAL_II_WITH_ZLIB
# include <zlib.h>
#endif
#ifdef DEAL_II_WITH_HDF5
# include <hdf5.h>
#endif
#include <boost/iostreams/copy.hpp>
#include <boost/iostreams/device/back_inserter.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#ifdef DEAL_II_WITH_ZLIB
# include <boost/iostreams/filter/zlib.hpp>
#endif
DEAL_II_NAMESPACE_OPEN
#ifndef DOXYGEN
// we need the following exception from a global function, so can't declare it
// in the usual way inside a class
namespace
{
DeclException2(ExcUnexpectedInput,
std::string,
std::string,
<< "Unexpected input: expected line\n <" << arg1
<< ">\nbut got\n <" << arg2 << ">");
# ifdef DEAL_II_WITH_ZLIB
constexpr bool deal_ii_with_zlib = true;
# else
constexpr bool deal_ii_with_zlib = false;
# endif
# ifdef DEAL_II_WITH_ZLIB
/**
* Convert between the CompressionLevel enum (used inside VtkFlags
* for example) and the preprocessor constant defined by zlib.
*/
int
get_zlib_compression_level(const DataOutBase::CompressionLevel level)
{
switch (level)
{
case (DataOutBase::CompressionLevel::no_compression):
return Z_NO_COMPRESSION;
case (DataOutBase::CompressionLevel::best_speed):
return Z_BEST_SPEED;
case (DataOutBase::CompressionLevel::best_compression):
return Z_BEST_COMPRESSION;
case (DataOutBase::CompressionLevel::default_compression):
return Z_DEFAULT_COMPRESSION;
default:
DEAL_II_NOT_IMPLEMENTED();
return Z_NO_COMPRESSION;
}
}
# ifdef DEAL_II_WITH_MPI
/**
* Convert between the CompressionLevel enum and the preprocessor
* constant defined by boost::iostreams::zlib.
*/
int
get_boost_zlib_compression_level(const DataOutBase::CompressionLevel level)
{
switch (level)
{
case (DataOutBase::CompressionLevel::no_compression):
return boost::iostreams::zlib::no_compression;
case (DataOutBase::CompressionLevel::best_speed):
return boost::iostreams::zlib::best_speed;
case (DataOutBase::CompressionLevel::best_compression):
return boost::iostreams::zlib::best_compression;
case (DataOutBase::CompressionLevel::default_compression):
return boost::iostreams::zlib::default_compression;
default:
DEAL_II_NOT_IMPLEMENTED();
return boost::iostreams::zlib::no_compression;
}
}
# endif
# endif
/**
* Do a zlib compression followed by a base64 encoding of the given data. The
* result is then returned as a string object.
*/
template <typename T>
std::string
compress_array(const std::vector<T> &data,
const DataOutBase::CompressionLevel compression_level)
{
# ifdef DEAL_II_WITH_ZLIB
if (data.size() != 0)
{
const std::size_t uncompressed_size = (data.size() * sizeof(T));
// While zlib's compress2 uses unsigned long (which is 64bits
// on Linux), the vtu compression header stores the block size
// as an std::uint32_t (see below). While we could implement
// writing several smaller blocks, we haven't done that. Let's
// trigger an error for the user instead:
AssertThrow(uncompressed_size <=
std::numeric_limits<std::uint32_t>::max(),
ExcNotImplemented());
// allocate a buffer for compressing data and do so
auto compressed_data_length = compressBound(uncompressed_size);
AssertThrow(compressed_data_length <=
std::numeric_limits<std::uint32_t>::max(),
ExcNotImplemented());
std::vector<unsigned char> compressed_data(compressed_data_length);
int err = compress2(&compressed_data[0],
&compressed_data_length,
reinterpret_cast<const Bytef *>(data.data()),
uncompressed_size,
get_zlib_compression_level(compression_level));
(void)err;
Assert(err == Z_OK, ExcInternalError());
// Discard the unnecessary bytes
compressed_data.resize(compressed_data_length);
// now encode the compression header
const std::uint32_t compression_header[4] = {
1, /* number of blocks */
static_cast<std::uint32_t>(uncompressed_size), /* size of block */
static_cast<std::uint32_t>(
uncompressed_size), /* size of last block */
static_cast<std::uint32_t>(
compressed_data_length)}; /* list of compressed sizes of blocks */
const auto *const header_start =
reinterpret_cast<const unsigned char *>(&compression_header[0]);
return (Utilities::encode_base64(
{header_start, header_start + 4 * sizeof(std::uint32_t)}) +
Utilities::encode_base64(compressed_data));
}
else
return {};
# else
(void)data;
(void)compression_level;
Assert(false,
ExcMessage("This function can only be called if cmake found "
"a working libz installation."));
return {};
# endif
}
/**
* Convert an array of data objects into a string that will form part of
* what we then output as data into VTU objects.
*
* If libz was found during configuration, this function compresses and
* encodes the entire data block. Otherwise, it simply writes it element by
* element.
*/
template <typename T>
std::string
vtu_stringize_array(const std::vector<T> &data,
const DataOutBase::CompressionLevel compression_level,
const int precision)
{
if (deal_ii_with_zlib &&
(compression_level != DataOutBase::CompressionLevel::plain_text))
{
// compress the data we have in memory
return compress_array(data, compression_level);
}
else
{
std::ostringstream stream;
stream.precision(precision);
for (const T &el : data)
stream << el << ' ';
return stream.str();
}
}
/**
* The header in binary format that the parallel intermediate files
* start with.
*
* @note We are using std::uint64_t for all variables for simplicity below,
* so that we don't have to worry about packing/data member alignment
* by the compiler.
*/
struct ParallelIntermediateHeader
{
std::uint64_t magic;
std::uint64_t version;
std::uint64_t compression;
std::uint64_t dimension;
std::uint64_t space_dimension;
std::uint64_t n_ranks;
std::uint64_t n_patches;
};
} // namespace
#endif
// some declarations of functions and locally used classes
namespace DataOutBase
{
#ifndef DOXYGEN
namespace
{
/**
* Class holding the data of one cell of a patch in two space dimensions for
* output. It is the projection of a cell in three-dimensional space (two
* coordinates, one height value) to the direction of sight.
*/
class SvgCell
{
public:
// Center of the cell (three-dimensional)
Point<3> center;
/**
* Vector of vertices of this cell (three-dimensional)
*/
Point<3> vertices[4];
/**
* Depth into the picture, which is defined as the distance from an
* observer at an the origin in direction of the line of sight.
*/
float depth;
/**
* Vector of vertices of this cell (projected, two-dimensional).
*/
Point<2> projected_vertices[4];
// Center of the cell (projected, two-dimensional)
Point<2> projected_center;
/**
* Comparison operator for sorting.
*/
bool
operator<(const SvgCell &) const;
};
bool
SvgCell::operator<(const SvgCell &e) const
{
// note the "wrong" order in which we sort the elements
return depth > e.depth;
}
/**
* Class holding the data of one cell of a patch in two space dimensions for
* output. It is the projection of a cell in three-dimensional space (two
* coordinates, one height value) to the direction of sight.
*/
class EpsCell2d
{
public:
/**
* Vector of vertices of this cell.
*/
Point<2> vertices[4];
/**
* Data value from which the actual colors will be computed by the
* colorization function stated in the <tt>EpsFlags</tt> class.
*/
float color_value;
/**
* Depth into the picture, which is defined as the distance from an
* observer at an the origin in direction of the line of sight.
*/
float depth;
/**
* Comparison operator for sorting.
*/
bool
operator<(const EpsCell2d &) const;
};
bool
EpsCell2d::operator<(const EpsCell2d &e) const
{
// note the "wrong" order in which we sort the elements
return depth > e.depth;
}
/**
* This is a helper function that converts all of the data stored
* in the `patches` array into one global data table. That data
* table has as many rows as there are data sets in the patches,
* and as many columns as there data points at which to output
* data. In the end, each data set is then stored in one row of
* this table, rather than scattered throughout the various patches.
*
* This function is used by all those output formats that write
* data one data set at a time, rather than one cell at a time.
*/
template <int dim, int spacedim, typename Number = double>
std::unique_ptr<Table<2, Number>>
create_global_data_table(const std::vector<Patch<dim, spacedim>> &patches)
{
// If there is nothing to write, just return
if (patches.empty())
return std::make_unique<Table<2, Number>>();
// unlike in the main function, we don't have here the data_names field,
// so we initialize it with the number of data sets in the first patch.
// the equivalence of these two definitions is checked in the main
// function.
// we have to take care, however, whether the points are appended to the
// end of the patch.data table
const unsigned int n_data_sets = patches[0].points_are_available ?
(patches[0].data.n_rows() - spacedim) :
patches[0].data.n_rows();
const unsigned int n_data_points =
std::accumulate(patches.begin(),
patches.end(),
0U,
[](const unsigned int count,
const Patch<dim, spacedim> &patch) {
return count + patch.data.n_cols();
});
std::unique_ptr<Table<2, Number>> global_data_table =
std::make_unique<Table<2, Number>>(n_data_sets, n_data_points);
// loop over all patches
unsigned int next_value = 0;
for (const auto &patch : patches)
{
const unsigned int n_subdivisions = patch.n_subdivisions;
(void)n_subdivisions;
Assert((patch.data.n_rows() == n_data_sets &&
!patch.points_are_available) ||
(patch.data.n_rows() == n_data_sets + spacedim &&
patch.points_are_available),
ExcDimensionMismatch(patch.points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patch.data.n_rows()));
Assert(patch.reference_cell != ReferenceCells::get_hypercube<dim>() ||
(n_data_sets == 0) ||
(patch.data.n_cols() ==
Utilities::fixed_power<dim>(n_subdivisions + 1)),
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
for (unsigned int i = 0; i < patch.data.n_cols(); ++i, ++next_value)
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
(*global_data_table)[data_set][next_value] =
patch.data(data_set, i);
}
Assert(next_value == n_data_points, ExcInternalError());
return global_data_table;
}
} // namespace
#endif
DataOutFilter::DataOutFilter()
: flags(false, true)
, node_dim(numbers::invalid_unsigned_int)
, num_cells(0)
{}
DataOutFilter::DataOutFilter(const DataOutBase::DataOutFilterFlags &flags)
: flags(flags)
, node_dim(numbers::invalid_unsigned_int)
, num_cells(0)
{}
template <int dim>
void
DataOutFilter::write_point(const unsigned int index, const Point<dim> &p)
{
node_dim = dim;
Point<3> int_pt;
for (unsigned int d = 0; d < dim; ++d)
int_pt[d] = p[d];
const Map3DPoint::const_iterator it = existing_points.find(int_pt);
unsigned int internal_ind;
// If the point isn't in the set, or we're not filtering duplicate points,
// add it
if (it == existing_points.end() || !flags.filter_duplicate_vertices)
{
internal_ind = existing_points.size();
existing_points.insert(std::make_pair(int_pt, internal_ind));
}
else
{
internal_ind = it->second;
}
// Now add the index to the list of filtered points
filtered_points[index] = internal_ind;
}
void
DataOutFilter::internal_add_cell(const unsigned int cell_index,
const unsigned int pt_index)
{
filtered_cells[cell_index] = filtered_points[pt_index];
// (Re)-initialize counter at any first call to this method.
if (cell_index == 0)
num_cells = 1;
}
void
DataOutFilter::fill_node_data(std::vector<double> &node_data) const
{
node_data.resize(existing_points.size() * node_dim);
for (const auto &existing_point : existing_points)
{
for (unsigned int d = 0; d < node_dim; ++d)
node_data[node_dim * existing_point.second + d] =
existing_point.first[d];
}
}
void
DataOutFilter::fill_cell_data(const unsigned int local_node_offset,
std::vector<unsigned int> &cell_data) const
{
cell_data.resize(filtered_cells.size());
for (const auto &filtered_cell : filtered_cells)
{
cell_data[filtered_cell.first] =
filtered_cell.second + local_node_offset;
}
}
std::string
DataOutFilter::get_data_set_name(const unsigned int set_num) const
{
return data_set_names.at(set_num);
}
unsigned int
DataOutFilter::get_data_set_dim(const unsigned int set_num) const
{
return data_set_dims.at(set_num);
}
const double *
DataOutFilter::get_data_set(const unsigned int set_num) const
{
return data_sets[set_num].data();
}
unsigned int
DataOutFilter::n_nodes() const
{
return existing_points.size();
}
unsigned int
DataOutFilter::n_cells() const
{
return num_cells;
}
unsigned int
DataOutFilter::n_data_sets() const
{
return data_set_names.size();
}
void
DataOutFilter::flush_points()
{}
void
DataOutFilter::flush_cells()
{}
template <int dim>
void
DataOutFilter::write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets)
{
++num_cells;
const unsigned int base_entry =
index * GeometryInfo<dim>::vertices_per_cell;
switch (dim)
{
case 0:
{
internal_add_cell(base_entry + 0, start);
break;
}
case 1:
{
const unsigned int d1 = offsets[0];
internal_add_cell(base_entry + 0, start);
internal_add_cell(base_entry + 1, start + d1);
break;
}
case 2:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
internal_add_cell(base_entry + 0, start);
internal_add_cell(base_entry + 1, start + d1);
internal_add_cell(base_entry + 2, start + d2 + d1);
internal_add_cell(base_entry + 3, start + d2);
break;
}
case 3:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
const unsigned int d3 = offsets[2];
internal_add_cell(base_entry + 0, start);
internal_add_cell(base_entry + 1, start + d1);
internal_add_cell(base_entry + 2, start + d2 + d1);
internal_add_cell(base_entry + 3, start + d2);
internal_add_cell(base_entry + 4, start + d3);
internal_add_cell(base_entry + 5, start + d3 + d1);
internal_add_cell(base_entry + 6, start + d3 + d2 + d1);
internal_add_cell(base_entry + 7, start + d3 + d2);
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
}
void
DataOutFilter::write_cell_single(const unsigned int index,
const unsigned int start,
const unsigned int n_points,
const ReferenceCell &reference_cell)
{
++num_cells;
const unsigned int base_entry = index * n_points;
static const std::array<unsigned int, 5> table = {{0, 1, 3, 2, 4}};
for (unsigned int i = 0; i < n_points; ++i)
internal_add_cell(base_entry + i,
start + (reference_cell == ReferenceCells::Pyramid ?
table[i] :
i));
}
void
DataOutFilter::write_data_set(const std::string &name,
const unsigned int dimension,
const unsigned int set_num,
const Table<2, double> &data_vectors)
{
unsigned int new_dim;
// HDF5/XDMF output only supports 1d or 3d output, so force rearrangement if
// needed
if (flags.xdmf_hdf5_output && dimension != 1)
new_dim = 3;
else
new_dim = dimension;
// Record the data set name, dimension, and allocate space for it
data_set_names.push_back(name);
data_set_dims.push_back(new_dim);
data_sets.emplace_back(new_dim * existing_points.size());
// TODO: averaging, min/max, etc for merged vertices
for (unsigned int i = 0; i < filtered_points.size(); ++i)
{
const unsigned int r = filtered_points[i];
for (unsigned int d = 0; d < new_dim; ++d)
{
if (d < dimension)
data_sets.back()[r * new_dim + d] = data_vectors(set_num + d, i);
else
data_sets.back()[r * new_dim + d] = 0;
}
}
}
} // namespace DataOutBase
//----------------------------------------------------------------------//
// Auxiliary data
//----------------------------------------------------------------------//
namespace
{
const char *gmv_cell_type[4] = {"", "line 2", "quad 4", "hex 8"};
const char *ucd_cell_type[4] = {"pt", "line", "quad", "hex"};
const char *tecplot_cell_type[4] = {"", "lineseg", "quadrilateral", "brick"};
/**
* Return the tuple (vtk cell type, number of cells, number of nodes)
* for a patch.
*
* The logic used here is as follows:
* - If a cell is not subdivided or we don't use higher order cells,
* then we use linear cells
* - For hypercubes, we support subdividing cells into sub-cells,
* which are then treated as each being linear
* - For triangles and tetrahedra, we special-case the situation of
* n_subdivisions==2, in which case we treat the cell as a single
* quadratic cell (i.e., higher order)
*/
template <int dim, int spacedim>
std::array<unsigned int, 3>
extract_vtk_patch_info(const DataOutBase::Patch<dim, spacedim> &patch,
const bool write_higher_order_cells)
{
std::array<unsigned int, 3> vtk_cell_id = {
{/* cell type, tbd: */ numbers::invalid_unsigned_int,
/* # of cells, default: just one cell */ 1,
/* # of nodes, default: as many nodes as vertices */
patch.reference_cell.n_vertices()}};
if (write_higher_order_cells)
{
vtk_cell_id[0] = patch.reference_cell.vtk_lagrange_type();
vtk_cell_id[2] = patch.data.n_cols();
}
else if (patch.data.n_cols() == patch.reference_cell.n_vertices())
// One data set per vertex -> a linear cell
vtk_cell_id[0] = patch.reference_cell.vtk_linear_type();
else if (patch.reference_cell == ReferenceCells::Triangle &&
patch.data.n_cols() == 6)
{
Assert(patch.n_subdivisions == 2, ExcInternalError());
vtk_cell_id[0] = patch.reference_cell.vtk_quadratic_type();
vtk_cell_id[2] = patch.data.n_cols();
}
else if (patch.reference_cell == ReferenceCells::Tetrahedron &&
patch.data.n_cols() == 10)
{
Assert(patch.n_subdivisions == 2, ExcInternalError());
vtk_cell_id[0] = patch.reference_cell.vtk_quadratic_type();
vtk_cell_id[2] = patch.data.n_cols();
}
else if (patch.reference_cell.is_hyper_cube())
{
// For hypercubes, we support sub-divided linear cells
vtk_cell_id[0] = patch.reference_cell.vtk_linear_type();
vtk_cell_id[1] = Utilities::pow(patch.n_subdivisions, dim);
}
else if (patch.reference_cell.is_simplex())
{
vtk_cell_id[0] = patch.reference_cell.vtk_lagrange_type();
vtk_cell_id[2] = patch.data.n_cols();
}
else
{
DEAL_II_NOT_IMPLEMENTED();
}
return vtk_cell_id;
}
//----------------------------------------------------------------------//
// Auxiliary functions
//----------------------------------------------------------------------//
// For a given patch that corresponds to a hypercube cell, compute the
// location of a node interpolating the corner nodes linearly
// at the point lattice_location/n_subdivisions where lattice_location
// is a dim-dimensional integer vector. If the points are
// saved in the patch.data member, return the saved point instead.
template <int dim, int spacedim>
inline Point<spacedim>
get_equispaced_location(
const DataOutBase::Patch<dim, spacedim> &patch,
const std::initializer_list<unsigned int> &lattice_location,
const unsigned int n_subdivisions)
{
// This function only makes sense when called on hypercube cells
Assert(patch.reference_cell.is_hyper_cube(), ExcInternalError());
Assert(lattice_location.size() == dim, ExcInternalError());
const unsigned int xstep = (dim > 0 ? *(lattice_location.begin() + 0) : 0);
const unsigned int ystep = (dim > 1 ? *(lattice_location.begin() + 1) : 0);
const unsigned int zstep = (dim > 2 ? *(lattice_location.begin() + 2) : 0);
// If the patch stores the locations of nodes (rather than of only the
// vertices), then obtain the location by direct lookup.
if (patch.points_are_available)
{
Assert(n_subdivisions == patch.n_subdivisions, ExcNotImplemented());
unsigned int point_no = 0;
switch (dim)
{
case 3:
AssertIndexRange(zstep, n_subdivisions + 1);
point_no += (n_subdivisions + 1) * (n_subdivisions + 1) * zstep;
DEAL_II_FALLTHROUGH;
case 2:
AssertIndexRange(ystep, n_subdivisions + 1);
point_no += (n_subdivisions + 1) * ystep;
DEAL_II_FALLTHROUGH;
case 1:
AssertIndexRange(xstep, n_subdivisions + 1);
point_no += xstep;
DEAL_II_FALLTHROUGH;
case 0:
// break here for dim<=3
break;
default:
DEAL_II_NOT_IMPLEMENTED();
}
Point<spacedim> node;
for (unsigned int d = 0; d < spacedim; ++d)
node[d] = patch.data(patch.data.size(0) - spacedim + d, point_no);
return node;
}
else
// The patch does not store node locations, so we have to interpolate
// between its vertices:
{
if constexpr (dim == 0)
return patch.vertices[0];
else
{
// perform a dim-linear interpolation
const double stepsize = 1. / n_subdivisions;
const double xfrac = xstep * stepsize;
Point<spacedim> node =
(patch.vertices[1] * xfrac) + (patch.vertices[0] * (1 - xfrac));
if (dim > 1)
{
const double yfrac = ystep * stepsize;
node *= 1 - yfrac;
node += ((patch.vertices[3] * xfrac) +
(patch.vertices[2] * (1 - xfrac))) *
yfrac;
if (dim > 2)
{
const double zfrac = zstep * stepsize;
node *= (1 - zfrac);
node += (((patch.vertices[5] * xfrac) +
(patch.vertices[4] * (1 - xfrac))) *
(1 - yfrac) +
((patch.vertices[7] * xfrac) +
(patch.vertices[6] * (1 - xfrac))) *
yfrac) *
zfrac;
}
}
return node;
}
}
}
// For a given patch, compute the nodes for arbitrary (non-hypercube) cells.
// If the points are saved in the patch.data member, return the saved point
// instead.
template <int dim, int spacedim>
inline Point<spacedim>
get_node_location(const DataOutBase::Patch<dim, spacedim> &patch,
const unsigned int node_index)
{
// Due to a historical accident, we are using a different indexing
// for pyramids in this file than we do where we create patches.
// So translate if necessary.
unsigned int point_no_actual = node_index;
if (patch.reference_cell == ReferenceCells::Pyramid)
{
AssertDimension(patch.n_subdivisions, 1);
static const std::array<unsigned int, 5> table = {{0, 1, 3, 2, 4}};
point_no_actual = table[node_index];
}
// If the patch stores the locations of nodes (rather than of only the
// vertices), then obtain the location by direct lookup.
if (patch.points_are_available)
{
Point<spacedim> node;
for (unsigned int d = 0; d < spacedim; ++d)
node[d] =
patch.data(patch.data.size(0) - spacedim + d, point_no_actual);
return node;
}
else
// The patch does not store node locations, so we have to interpolate
// between its vertices. This isn't currently implemented for anything
// other than one subdivision, but would go here.
//
// For n_subdivisions==1, the locations are simply those of vertices, so
// get the information from there.
{
AssertDimension(patch.n_subdivisions, 1);
return patch.vertices[point_no_actual];
}
}
/**
* Count the number of nodes and cells referenced by the given
* argument, and return these numbers (in order nodes, then cells)
* as a tuple.
*/
template <int dim, int spacedim>
std::tuple<unsigned int, unsigned int>
count_nodes_and_cells(
const std::vector<DataOutBase::Patch<dim, spacedim>> &patches)
{
unsigned int n_nodes = 0;
unsigned int n_cells = 0;
for (const auto &patch : patches)
{
Assert(patch.reference_cell != ReferenceCells::Invalid,
ExcMessage(
"The reference cell for this patch is set to 'Invalid', "
"but that is clearly not a valid choice. Did you forget "
"to set the reference cell for the patch?"));
if (patch.reference_cell.is_hyper_cube())
{
n_nodes += Utilities::fixed_power<dim>(patch.n_subdivisions + 1);
n_cells += Utilities::fixed_power<dim>(patch.n_subdivisions);
}
else
{
Assert(patch.n_subdivisions == 1, ExcNotImplemented());
n_nodes += patch.reference_cell.n_vertices();
n_cells += 1;
}
}
return std::make_tuple(n_nodes, n_cells);
}
/**
* Count the number of nodes and cells referenced by the given
* argument, and return these numbers (in order nodes, then cells, then cells
* plus points) as a tuple.
*/
template <int dim, int spacedim>
std::tuple<unsigned int, unsigned int, unsigned int>
count_nodes_and_cells_and_points(
const std::vector<DataOutBase::Patch<dim, spacedim>> &patches,
const bool write_higher_order_cells)
{
unsigned int n_nodes = 0;
unsigned int n_cells = 0;
unsigned int n_points_and_n_cells = 0;
for (const auto &patch : patches)
{
if (patch.reference_cell.is_hyper_cube())
{
n_nodes += Utilities::fixed_power<dim>(patch.n_subdivisions + 1);
if (write_higher_order_cells)
{
// Write all of these nodes as a single higher-order cell. So
// add one to the number of cells, and update the number of
// points appropriately.
n_cells += 1;
n_points_and_n_cells +=
1 + Utilities::fixed_power<dim>(patch.n_subdivisions + 1);
}
else
{
// Write all of these nodes as a collection of d-linear
// cells. Add the number of sub-cells to the total number of
// cells, and then add one for each cell plus the number of
// vertices per cell for each subcell to the number of points.
const unsigned int n_subcells =
Utilities::fixed_power<dim>(patch.n_subdivisions);
n_cells += n_subcells;
n_points_and_n_cells +=
n_subcells * (1 + GeometryInfo<dim>::vertices_per_cell);
}
}
else
{
n_nodes += patch.data.n_cols();
n_cells += 1;
n_points_and_n_cells += patch.data.n_cols() + 1;
}
}
return std::make_tuple(n_nodes, n_cells, n_points_and_n_cells);
}
/**
* Class describing common functionality between different output streams.
*
* @ingroup output
*/
template <typename FlagsType>
class StreamBase
{
public:
/*
* Constructor. Stores a reference to the output stream for immediate use.
*/
StreamBase(std::ostream &stream, const FlagsType &flags)
: selected_component(numbers::invalid_unsigned_int)
, stream(stream)
, flags(flags)
{}
/**
* Output operator for points. All inheriting classes should implement this
* function.
*/
template <int dim>
void
write_point(const unsigned int, const Point<dim> &)
{
Assert(false,
ExcMessage("The derived class you are using needs to "
"reimplement this function if you want to call "
"it."));
}
/**
* Do whatever is necessary to terminate the list of points. The default
* implementation does nothing; derived classes that do not require any
* action do not need to reimplement this.
*/
void
flush_points()
{}
/**
* Write dim-dimensional cell with first vertex at number start and further
* vertices offset by the specified values. Values not needed are ignored.
* All inheriting classes should implement this function.
*/
template <int dim>
void
write_cell(const unsigned int /*index*/,
const unsigned int /*start*/,
std::array<unsigned int, dim> & /*offsets*/)
{
Assert(false,
ExcMessage("The derived class you are using needs to "
"reimplement this function if you want to call "
"it."));
}
/**
* Write dim-dimensional @p index cell with @p n_point vertices and first
* vertex at number @p start.
*
* @note All inheriting classes should implement this function.
*/
void
write_cell_single(const unsigned int index,
const unsigned int start,
const unsigned int n_points,
const ReferenceCell &reference_cell)
{
(void)index;
(void)start;
(void)n_points;
(void)reference_cell;
Assert(false,
ExcMessage("The derived class you are using needs to "
"reimplement this function if you want to call "
"it."));
}
/**
* Do whatever is necessary to terminate the list of cells. This function is
* usually only reimplemented if deal.II is compiled with zlib. The default
* implementation does nothing; derived classes that do not require any
* action do not need to reimplement this.
*/
void
flush_cells()
{}
/**
* Forwarding of an output stream. This function is usually only
* reimplemented if inheriting classes use zlib.
*/
template <typename T>
std::ostream &
operator<<(const T &t)
{
stream << t;
return stream;
}
/**
* Since the GMV and Tecplot formats read the x, y and z coordinates in
* separate fields, we enable write() to output only a single selected
* component at once and do this dim times for the whole set of nodes. This
* integer can be used to select the component written.
*/
unsigned int selected_component;
protected:
/**
* The ostream to use. Since the life span of these objects is small, we use
* a very simple storage technique.
*/
std::ostream &stream;
/**
* The flags controlling the output.
*/
const FlagsType flags;
};
/**
* Class for writing basic entities in @ref SoftwareOpenDX format, depending on the flags.
*/
class DXStream : public StreamBase<DataOutBase::DXFlags>
{
public:
DXStream(std::ostream &stream, const DataOutBase::DXFlags &flags);
template <int dim>
void
write_point(const unsigned int index, const Point<dim> &);
/**
* The order of vertices for these cells in different dimensions is
* <ol>
* <li> [0,1]
* <li> [0,2,1,3]
* <li> [0,4,2,6,1,5,3,7]
* </ol>
*/
template <int dim>
void
write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets);
/**
* Write a complete set of data for a single node.
*
* The index given as first argument indicates the number of a data set, as
* some output formats require this number to be printed.
*/
template <typename data>
void
write_dataset(const unsigned int index, const std::vector<data> &values);
};
/**
* Class for writing basic entities in @ref SoftwareGMV format, depending on the flags.
*/
class GmvStream : public StreamBase<DataOutBase::GmvFlags>
{
public:
GmvStream(std::ostream &stream, const DataOutBase::GmvFlags &flags);
template <int dim>
void
write_point(const unsigned int index, const Point<dim> &);
/**
* The order of vertices for these cells in different dimensions is
* <ol>
* <li> [0,1]
* <li> [0,1,3,2]
* <li> [0,1,3,2,4,5,7,6]
* </ol>
*/
template <int dim>
void
write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets);
};
/**
* Class for writing basic entities in @ref SoftwareTecplot format, depending on the flags.
*/
class TecplotStream : public StreamBase<DataOutBase::TecplotFlags>
{
public:
TecplotStream(std::ostream &stream, const DataOutBase::TecplotFlags &flags);
template <int dim>
void
write_point(const unsigned int index, const Point<dim> &);
/**
* The order of vertices for these cells in different dimensions is
* <ol>
* <li> [0,1]
* <li> [0,1,3,2]
* <li> [0,1,3,2,4,5,7,6]
* </ol>
*/
template <int dim>
void
write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets);
};
/**
* Class for writing basic entities in UCD format for @ref SoftwareAVS, depending on the flags.
*/
class UcdStream : public StreamBase<DataOutBase::UcdFlags>
{
public:
UcdStream(std::ostream &stream, const DataOutBase::UcdFlags &flags);
template <int dim>
void
write_point(const unsigned int index, const Point<dim> &);
/**
* The additional offset 1 is added inside this function.
*
* The order of vertices for these cells in different dimensions is
* <ol>
* <li> [0,1]
* <li> [0,1,3,2]
* <li> [0,1,5,4,2,3,7,6]
* </ol>
*/
template <int dim>
void
write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets);
/**
* Write a complete set of data for a single node.
*
* The index given as first argument indicates the number of a data set, as
* some output formats require this number to be printed.
*/
template <typename data>
void
write_dataset(const unsigned int index, const std::vector<data> &values);
};
/**
* Class for writing basic entities in @ref SoftwareVTK format, depending on the flags.
*/
class VtkStream : public StreamBase<DataOutBase::VtkFlags>
{
public:
VtkStream(std::ostream &stream, const DataOutBase::VtkFlags &flags);
template <int dim>
void
write_point(const unsigned int index, const Point<dim> &);
/**
* The order of vertices for these cells in different dimensions is
* <ol>
* <li> [0,1]
* <li> []
* <li> []
* </ol>
*/
template <int dim>
void
write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets);
/**
* Print vertices [start, start+n_points[
*/
void
write_cell_single(const unsigned int index,
const unsigned int start,
const unsigned int n_points,
const ReferenceCell &reference_cell);
/**
* Write a high-order cell type, i.e., a Lagrange cell
* in the VTK terminology.
* The connectivity order of the points is given in the
* @p connectivity array, which are offset
* by the global index @p start.
*/
template <int dim>
void
write_high_order_cell(const unsigned int start,
const std::vector<unsigned> &connectivity);
};
//----------------------------------------------------------------------//
DXStream::DXStream(std::ostream &out, const DataOutBase::DXFlags &f)
: StreamBase<DataOutBase::DXFlags>(out, f)
{}
template <int dim>
void
DXStream::write_point(const unsigned int, const Point<dim> &p)
{
if (flags.coordinates_binary)
{
float data[dim];
for (unsigned int d = 0; d < dim; ++d)
data[d] = p[d];
stream.write(reinterpret_cast<const char *>(data), dim * sizeof(*data));
}
else
{
for (unsigned int d = 0; d < dim; ++d)
stream << p[d] << '\t';
stream << '\n';
}
}
// Separate these out to avoid an internal compiler error with intel 17
namespace DataOutBaseImplementation
{
/**
* Set up the node numbers for a given cell being written to an output
* stream.
*/
std::array<unsigned int, GeometryInfo<0>::vertices_per_cell>
set_node_numbers(const unsigned int /*start*/,
const std::array<unsigned int, 0> & /*d1*/)
{
DEAL_II_ASSERT_UNREACHABLE();
return {};
}
std::array<unsigned int, GeometryInfo<1>::vertices_per_cell>
set_node_numbers(const unsigned int start,
const std::array<unsigned int, 1> &offsets)
{
std::array<unsigned int, GeometryInfo<1>::vertices_per_cell> nodes;
nodes[0] = start;
nodes[1] = start + offsets[0];
return nodes;
}
std::array<unsigned int, GeometryInfo<2>::vertices_per_cell>
set_node_numbers(const unsigned int start,
const std::array<unsigned int, 2> &offsets)
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
std::array<unsigned int, GeometryInfo<2>::vertices_per_cell> nodes;
nodes[0] = start;
nodes[1] = start + d1;
nodes[2] = start + d2;
nodes[3] = start + d2 + d1;
return nodes;
}
std::array<unsigned int, GeometryInfo<3>::vertices_per_cell>
set_node_numbers(const unsigned int start,
const std::array<unsigned int, 3> &offsets)
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
const unsigned int d3 = offsets[2];
std::array<unsigned int, GeometryInfo<3>::vertices_per_cell> nodes;
nodes[0] = start;
nodes[1] = start + d1;
nodes[2] = start + d2;
nodes[3] = start + d2 + d1;
nodes[4] = start + d3;
nodes[5] = start + d3 + d1;
nodes[6] = start + d3 + d2;
nodes[7] = start + d3 + d2 + d1;
return nodes;
}
} // namespace DataOutBaseImplementation
template <int dim>
void
DXStream::write_cell(const unsigned int,
const unsigned int start,
const std::array<unsigned int, dim> &offsets)
{
const auto nodes =
DataOutBaseImplementation::set_node_numbers(start, offsets);
if (flags.int_binary)
{
std::array<unsigned int, GeometryInfo<dim>::vertices_per_cell> temp;
for (unsigned int i = 0; i < nodes.size(); ++i)
temp[i] = nodes[GeometryInfo<dim>::dx_to_deal[i]];
stream.write(reinterpret_cast<const char *>(temp.data()),
temp.size() * sizeof(temp[0]));
}
else
{
for (unsigned int i = 0; i < nodes.size() - 1; ++i)
stream << nodes[GeometryInfo<dim>::dx_to_deal[i]] << '\t';
stream << nodes[GeometryInfo<dim>::dx_to_deal[nodes.size() - 1]]
<< '\n';
}
}
template <typename data>
inline void
DXStream::write_dataset(const unsigned int, const std::vector<data> &values)
{
if (flags.data_binary)
{
stream.write(reinterpret_cast<const char *>(values.data()),
values.size() * sizeof(data));
}
else
{
for (unsigned int i = 0; i < values.size(); ++i)
stream << '\t' << values[i];
stream << '\n';
}
}
//----------------------------------------------------------------------//
GmvStream::GmvStream(std::ostream &out, const DataOutBase::GmvFlags &f)
: StreamBase<DataOutBase::GmvFlags>(out, f)
{}
template <int dim>
void
GmvStream::write_point(const unsigned int, const Point<dim> &p)
{
Assert(selected_component != numbers::invalid_unsigned_int,
ExcNotInitialized());
stream << p[selected_component] << ' ';
}
template <int dim>
void
GmvStream::write_cell(const unsigned int,
const unsigned int s,
const std::array<unsigned int, dim> &offsets)
{
// Vertices are numbered starting with one.
const unsigned int start = s + 1;
stream << gmv_cell_type[dim] << '\n';
switch (dim)
{
case 0:
{
stream << start;
break;
}
case 1:
{
const unsigned int d1 = offsets[0];
stream << start;
stream << '\t' << start + d1;
break;
}
case 2:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
stream << start;
stream << '\t' << start + d1;
stream << '\t' << start + d2 + d1 << '\t' << start + d2;
break;
}
case 3:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
const unsigned int d3 = offsets[2];
stream << start;
stream << '\t' << start + d1;
stream << '\t' << start + d2 + d1 << '\t' << start + d2;
stream << '\t' << start + d3 << '\t' << start + d3 + d1 << '\t'
<< start + d3 + d2 + d1 << '\t' << start + d3 + d2;
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
stream << '\n';
}
TecplotStream::TecplotStream(std::ostream &out,
const DataOutBase::TecplotFlags &f)
: StreamBase<DataOutBase::TecplotFlags>(out, f)
{}
template <int dim>
void
TecplotStream::write_point(const unsigned int, const Point<dim> &p)
{
Assert(selected_component != numbers::invalid_unsigned_int,
ExcNotInitialized());
stream << p[selected_component] << '\n';
}
template <int dim>
void
TecplotStream::write_cell(const unsigned int,
const unsigned int s,
const std::array<unsigned int, dim> &offsets)
{
const unsigned int start = s + 1;
switch (dim)
{
case 0:
{
stream << start;
break;
}
case 1:
{
const unsigned int d1 = offsets[0];
stream << start;
stream << '\t' << start + d1;
break;
}
case 2:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
stream << start;
stream << '\t' << start + d1;
stream << '\t' << start + d2 + d1 << '\t' << start + d2;
break;
}
case 3:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
const unsigned int d3 = offsets[2];
stream << start;
stream << '\t' << start + d1;
stream << '\t' << start + d2 + d1 << '\t' << start + d2;
stream << '\t' << start + d3 << '\t' << start + d3 + d1 << '\t'
<< start + d3 + d2 + d1 << '\t' << start + d3 + d2;
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
stream << '\n';
}
UcdStream::UcdStream(std::ostream &out, const DataOutBase::UcdFlags &f)
: StreamBase<DataOutBase::UcdFlags>(out, f)
{}
template <int dim>
void
UcdStream::write_point(const unsigned int index, const Point<dim> &p)
{
stream << index + 1 << " ";
// write out coordinates
for (unsigned int i = 0; i < dim; ++i)
stream << p[i] << ' ';
// fill with zeroes
for (unsigned int i = dim; i < 3; ++i)
stream << "0 ";
stream << '\n';
}
template <int dim>
void
UcdStream::write_cell(const unsigned int index,
const unsigned int start,
const std::array<unsigned int, dim> &offsets)
{
const auto nodes =
DataOutBaseImplementation::set_node_numbers(start, offsets);
// Write out all cells and remember that all indices must be shifted by one.
stream << index + 1 << "\t0 " << ucd_cell_type[dim];
for (unsigned int i = 0; i < nodes.size(); ++i)
stream << '\t' << nodes[GeometryInfo<dim>::ucd_to_deal[i]] + 1;
stream << '\n';
}
template <typename data>
inline void
UcdStream::write_dataset(const unsigned int index,
const std::vector<data> &values)
{
stream << index + 1;
for (unsigned int i = 0; i < values.size(); ++i)
stream << '\t' << values[i];
stream << '\n';
}
//----------------------------------------------------------------------//
VtkStream::VtkStream(std::ostream &out, const DataOutBase::VtkFlags &f)
: StreamBase<DataOutBase::VtkFlags>(out, f)
{}
template <int dim>
void
VtkStream::write_point(const unsigned int, const Point<dim> &p)
{
// write out coordinates
stream << p;
// fill with zeroes
for (unsigned int i = dim; i < 3; ++i)
stream << " 0";
stream << '\n';
}
template <int dim>
void
VtkStream::write_cell(const unsigned int,
const unsigned int start,
const std::array<unsigned int, dim> &offsets)
{
stream << GeometryInfo<dim>::vertices_per_cell << '\t';
switch (dim)
{
case 0:
{
stream << start;
break;
}
case 1:
{
const unsigned int d1 = offsets[0];
stream << start;
stream << '\t' << start + d1;
break;
}
case 2:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
stream << start;
stream << '\t' << start + d1;
stream << '\t' << start + d2 + d1 << '\t' << start + d2;
break;
}
case 3:
{
const unsigned int d1 = offsets[0];
const unsigned int d2 = offsets[1];
const unsigned int d3 = offsets[2];
stream << start;
stream << '\t' << start + d1;
stream << '\t' << start + d2 + d1 << '\t' << start + d2;
stream << '\t' << start + d3 << '\t' << start + d3 + d1 << '\t'
<< start + d3 + d2 + d1 << '\t' << start + d3 + d2;
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
stream << '\n';
}
void
VtkStream::write_cell_single(const unsigned int index,
const unsigned int start,
const unsigned int n_points,
const ReferenceCell &reference_cell)
{
(void)index;
static const std::array<unsigned int, 5> table = {{0, 1, 3, 2, 4}};
stream << '\t' << n_points;
for (unsigned int i = 0; i < n_points; ++i)
stream << '\t'
<< start +
(reference_cell == ReferenceCells::Pyramid ? table[i] : i);
stream << '\n';
}
template <int dim>
void
VtkStream::write_high_order_cell(const unsigned int start,
const std::vector<unsigned> &connectivity)
{
stream << connectivity.size();
for (const auto &c : connectivity)
stream << '\t' << start + c;
stream << '\n';
}
} // namespace
namespace DataOutBase
{
const unsigned int Deal_II_IntermediateFlags::format_version = 4;
template <int dim, int spacedim>
const unsigned int Patch<dim, spacedim>::space_dim;
template <int dim, int spacedim>
const unsigned int Patch<dim, spacedim>::no_neighbor;
template <int dim, int spacedim>
Patch<dim, spacedim>::Patch()
: patch_index(no_neighbor)
, n_subdivisions(1)
, points_are_available(false)
, reference_cell(ReferenceCells::Invalid)
// all the other data has a constructor of its own, except for the "neighbors"
// field, which we set to invalid values.
{
for (const unsigned int i : GeometryInfo<dim>::face_indices())
neighbors[i] = no_neighbor;
AssertIndexRange(dim, spacedim + 1);
Assert(spacedim <= 3, ExcNotImplemented());
}
template <int dim, int spacedim>
bool
Patch<dim, spacedim>::operator==(const Patch &patch) const
{
if (reference_cell != patch.reference_cell)
return false;
// TODO: make tolerance relative
const double epsilon = 3e-16;
for (const unsigned int i : GeometryInfo<dim>::vertex_indices())
if (vertices[i].distance(patch.vertices[i]) > epsilon)
return false;
for (const unsigned int i : GeometryInfo<dim>::face_indices())
if (neighbors[i] != patch.neighbors[i])
return false;
if (patch_index != patch.patch_index)
return false;
if (n_subdivisions != patch.n_subdivisions)
return false;
if (points_are_available != patch.points_are_available)
return false;
if (data.n_rows() != patch.data.n_rows())
return false;
if (data.n_cols() != patch.data.n_cols())
return false;
for (unsigned int i = 0; i < data.n_rows(); ++i)
for (unsigned int j = 0; j < data.n_cols(); ++j)
if (data[i][j] != patch.data[i][j])
return false;
return true;
}
template <int dim, int spacedim>
std::size_t
Patch<dim, spacedim>::memory_consumption() const
{
return (sizeof(vertices) / sizeof(vertices[0]) *
MemoryConsumption::memory_consumption(vertices[0]) +
sizeof(neighbors) / sizeof(neighbors[0]) *
MemoryConsumption::memory_consumption(neighbors[0]) +
MemoryConsumption::memory_consumption(patch_index) +
MemoryConsumption::memory_consumption(n_subdivisions) +
MemoryConsumption::memory_consumption(data) +
MemoryConsumption::memory_consumption(points_are_available) +
sizeof(reference_cell));
}
template <int dim, int spacedim>
void
Patch<dim, spacedim>::swap(Patch<dim, spacedim> &other_patch) noexcept
{
std::swap(vertices, other_patch.vertices);
std::swap(neighbors, other_patch.neighbors);
std::swap(patch_index, other_patch.patch_index);
std::swap(n_subdivisions, other_patch.n_subdivisions);
data.swap(other_patch.data);
std::swap(points_are_available, other_patch.points_are_available);
std::swap(reference_cell, other_patch.reference_cell);
}
template <int spacedim>
const unsigned int Patch<0, spacedim>::space_dim;
template <int spacedim>
const unsigned int Patch<0, spacedim>::no_neighbor;
template <int spacedim>
unsigned int Patch<0, spacedim>::neighbors[1] = {
Patch<0, spacedim>::no_neighbor};
template <int spacedim>
const unsigned int Patch<0, spacedim>::n_subdivisions = 1;
template <int spacedim>
const ReferenceCell Patch<0, spacedim>::reference_cell =
ReferenceCells::Vertex;
template <int spacedim>
Patch<0, spacedim>::Patch()
: patch_index(no_neighbor)
, points_are_available(false)
{
Assert(spacedim <= 3, ExcNotImplemented());
}
template <int spacedim>
bool
Patch<0, spacedim>::operator==(const Patch &patch) const
{
const unsigned int dim = 0;
// TODO: make tolerance relative
const double epsilon = 3e-16;
for (const unsigned int i : GeometryInfo<dim>::vertex_indices())
if (vertices[i].distance(patch.vertices[i]) > epsilon)
return false;
if (patch_index != patch.patch_index)
return false;
if (points_are_available != patch.points_are_available)
return false;
if (data.n_rows() != patch.data.n_rows())
return false;
if (data.n_cols() != patch.data.n_cols())
return false;
for (unsigned int i = 0; i < data.n_rows(); ++i)
for (unsigned int j = 0; j < data.n_cols(); ++j)
if (data[i][j] != patch.data[i][j])
return false;
return true;
}
template <int spacedim>
std::size_t
Patch<0, spacedim>::memory_consumption() const
{
return (sizeof(vertices) / sizeof(vertices[0]) *
MemoryConsumption::memory_consumption(vertices[0]) +
MemoryConsumption::memory_consumption(data) +
MemoryConsumption::memory_consumption(points_are_available));
}
template <int spacedim>
void
Patch<0, spacedim>::swap(Patch<0, spacedim> &other_patch) noexcept
{
std::swap(vertices, other_patch.vertices);
std::swap(patch_index, other_patch.patch_index);
data.swap(other_patch.data);
std::swap(points_are_available, other_patch.points_are_available);
}
UcdFlags::UcdFlags(const bool write_preamble)
: write_preamble(write_preamble)
{}
GnuplotFlags::GnuplotFlags()
{
space_dimension_labels.emplace_back("x");
space_dimension_labels.emplace_back("y");
space_dimension_labels.emplace_back("z");
}
GnuplotFlags::GnuplotFlags(const std::vector<std::string> &labels)
: space_dimension_labels(labels)
{}
std::size_t
GnuplotFlags::memory_consumption() const
{
return MemoryConsumption::memory_consumption(space_dimension_labels);
}
PovrayFlags::PovrayFlags(const bool smooth,
const bool bicubic_patch,
const bool external_data)
: smooth(smooth)
, bicubic_patch(bicubic_patch)
, external_data(external_data)
{}
DataOutFilterFlags::DataOutFilterFlags(const bool filter_duplicate_vertices,
const bool xdmf_hdf5_output)
: filter_duplicate_vertices(filter_duplicate_vertices)
, xdmf_hdf5_output(xdmf_hdf5_output)
{}
void
DataOutFilterFlags::declare_parameters(ParameterHandler &prm)
{
prm.declare_entry(
"Filter duplicate vertices",
"false",
Patterns::Bool(),
"Whether to remove duplicate vertex values. deal.II duplicates "
"vertices once for each adjacent cell so that it can output "
"discontinuous quantities for which there may be more than one "
"value for each vertex position. Setting this flag to "
"'true' will merge all of these values by selecting a "
"random one and outputting this as 'the' value for the vertex. "
"As long as the data to be output corresponds to continuous "
"fields, merging vertices has no effect. On the other hand, "
"if the data to be output corresponds to discontinuous fields "
"(either because you are using a discontinuous finite element, "
"or because you are using a DataPostprocessor that yields "
"discontinuous data, or because the data to be output has been "
"produced by entirely different means), then the data in the "
"output file no longer faithfully represents the underlying data "
"because the discontinuous field has been replaced by a "
"continuous one. Note also that the filtering can not occur "
"on processor boundaries. Thus, a filtered discontinuous field "
"looks like a continuous field inside of a subdomain, "
"but like a discontinuous field at the subdomain boundary."
"\n\n"
"In any case, filtering results in drastically smaller output "
"files (smaller by about a factor of 2^dim).");
prm.declare_entry(
"XDMF HDF5 output",
"false",
Patterns::Bool(),
"Whether the data will be used in an XDMF/HDF5 combination.");
}
void
DataOutFilterFlags::parse_parameters(const ParameterHandler &prm)
{
filter_duplicate_vertices = prm.get_bool("Filter duplicate vertices");
xdmf_hdf5_output = prm.get_bool("XDMF HDF5 output");
}
DXFlags::DXFlags(const bool write_neighbors,
const bool int_binary,
const bool coordinates_binary,
const bool data_binary)
: write_neighbors(write_neighbors)
, int_binary(int_binary)
, coordinates_binary(coordinates_binary)
, data_binary(data_binary)
, data_double(false)
{}
void
DXFlags::declare_parameters(ParameterHandler &prm)
{
prm.declare_entry("Write neighbors",
"true",
Patterns::Bool(),
"A boolean field indicating whether neighborship "
"information between cells is to be written to the "
"OpenDX output file");
prm.declare_entry("Integer format",
"ascii",
Patterns::Selection("ascii|32|64"),
"Output format of integer numbers, which is "
"either a text representation (ascii) or binary integer "
"values of 32 or 64 bits length");
prm.declare_entry("Coordinates format",
"ascii",
Patterns::Selection("ascii|32|64"),
"Output format of vertex coordinates, which is "
"either a text representation (ascii) or binary "
"floating point values of 32 or 64 bits length");
prm.declare_entry("Data format",
"ascii",
Patterns::Selection("ascii|32|64"),
"Output format of data values, which is "
"either a text representation (ascii) or binary "
"floating point values of 32 or 64 bits length");
}
void
DXFlags::parse_parameters(const ParameterHandler &prm)
{
write_neighbors = prm.get_bool("Write neighbors");
// TODO:[GK] Read the new parameters
}
void
UcdFlags::declare_parameters(ParameterHandler &prm)
{
prm.declare_entry("Write preamble",
"true",
Patterns::Bool(),
"A flag indicating whether a comment should be "
"written to the beginning of the output file "
"indicating date and time of creation as well "
"as the creating program");
}
void
UcdFlags::parse_parameters(const ParameterHandler &prm)
{
write_preamble = prm.get_bool("Write preamble");
}
SvgFlags::SvgFlags(const unsigned int height_vector,
const int azimuth_angle,
const int polar_angle,
const unsigned int line_thickness,
const bool margin,
const bool draw_colorbar)
: height(4000)
, width(0)
, height_vector(height_vector)
, azimuth_angle(azimuth_angle)
, polar_angle(polar_angle)
, line_thickness(line_thickness)
, margin(margin)
, draw_colorbar(draw_colorbar)
{}
void
PovrayFlags::declare_parameters(ParameterHandler &prm)
{
prm.declare_entry("Use smooth triangles",
"false",
Patterns::Bool(),
"A flag indicating whether POVRAY should use smoothed "
"triangles instead of the usual ones");
prm.declare_entry("Use bicubic patches",
"false",
Patterns::Bool(),
"Whether POVRAY should use bicubic patches");
prm.declare_entry("Include external file",
"true",
Patterns::Bool(),
"Whether camera and lighting information should "
"be put into an external file \"data.inc\" or into "
"the POVRAY input file");
}
void
PovrayFlags::parse_parameters(const ParameterHandler &prm)
{
smooth = prm.get_bool("Use smooth triangles");
bicubic_patch = prm.get_bool("Use bicubic patches");
external_data = prm.get_bool("Include external file");
}
EpsFlags::EpsFlags(const unsigned int height_vector,
const unsigned int color_vector,
const SizeType size_type,
const unsigned int size,
const double line_width,
const double azimut_angle,
const double turn_angle,
const double z_scaling,
const bool draw_mesh,
const bool draw_cells,
const bool shade_cells,
const ColorFunction color_function)
: height_vector(height_vector)
, color_vector(color_vector)
, size_type(size_type)
, size(size)
, line_width(line_width)
, azimut_angle(azimut_angle)
, turn_angle(turn_angle)
, z_scaling(z_scaling)
, draw_mesh(draw_mesh)
, draw_cells(draw_cells)
, shade_cells(shade_cells)
, color_function(color_function)
{}
EpsFlags::RgbValues
EpsFlags::default_color_function(const double x,
const double xmin,
const double xmax)
{
RgbValues rgb_values = {0, 0, 0};
// A difficult color scale:
// xmin = black [1]
// 3/4*xmin+1/4*xmax = blue [2]
// 1/2*xmin+1/2*xmax = green (3)
// 1/4*xmin+3/4*xmax = red (4)
// xmax = white (5)
// Makes the following color functions:
//
// red green blue
// __
// / /\ / /\ /
// ____/ __/ \/ / \__/
// { 0 [1] - (3)
// r = { ( 4*x-2*xmin+2*xmax)/(xmax-xmin) (3) - (4)
// { 1 (4) - (5)
//
// { 0 [1] - [2]
// g = { ( 4*x-3*xmin- xmax)/(xmax-xmin) [2] - (3)
// { (-4*x+ xmin+3*xmax)/(xmax-xmin) (3) - (4)
// { ( 4*x- xmin-3*xmax)/(xmax-xmin) (4) - (5)
//
// { ( 4*x-4*xmin )/(xmax-xmin) [1] - [2]
// b = { (-4*x+2*xmin+2*xmax)/(xmax-xmin) [2] - (3)
// { 0 (3) - (4)
// { ( 4*x- xmin-3*xmax)/(xmax-xmin) (4) - (5)
double sum = xmax + xmin;
double sum13 = xmin + 3 * xmax;
double sum22 = 2 * xmin + 2 * xmax;
double sum31 = 3 * xmin + xmax;
double dif = xmax - xmin;
double rezdif = 1.0 / dif;
int where;
if (x < (sum31) / 4)
where = 0;
else if (x < (sum22) / 4)
where = 1;
else if (x < (sum13) / 4)
where = 2;
else
where = 3;
if (dif != 0)
{
switch (where)
{
case 0:
rgb_values.red = 0;
rgb_values.green = 0;
rgb_values.blue = (x - xmin) * 4. * rezdif;
break;
case 1:
rgb_values.red = 0;
rgb_values.green = (4 * x - 3 * xmin - xmax) * rezdif;
rgb_values.blue = (sum22 - 4. * x) * rezdif;
break;
case 2:
rgb_values.red = (4 * x - 2 * sum) * rezdif;
rgb_values.green = (xmin + 3 * xmax - 4 * x) * rezdif;
rgb_values.blue = 0;
break;
case 3:
rgb_values.red = 1;
rgb_values.green = (4 * x - xmin - 3 * xmax) * rezdif;
rgb_values.blue = (4. * x - sum13) * rezdif;
break;
default:
break;
}
}
else // White
rgb_values.red = rgb_values.green = rgb_values.blue = 1;
return rgb_values;
}
EpsFlags::RgbValues
EpsFlags::grey_scale_color_function(const double x,
const double xmin,
const double xmax)
{
EpsFlags::RgbValues rgb_values;
rgb_values.red = rgb_values.blue = rgb_values.green =
(x - xmin) / (xmax - xmin);
return rgb_values;
}
EpsFlags::RgbValues
EpsFlags::reverse_grey_scale_color_function(const double x,
const double xmin,
const double xmax)
{
EpsFlags::RgbValues rgb_values;
rgb_values.red = rgb_values.blue = rgb_values.green =
1 - (x - xmin) / (xmax - xmin);
return rgb_values;
}
void
EpsFlags::declare_parameters(ParameterHandler &prm)
{
prm.declare_entry("Index of vector for height",
"0",
Patterns::Integer(),
"Number of the input vector that is to be used to "
"generate height information");
prm.declare_entry("Index of vector for color",
"0",
Patterns::Integer(),
"Number of the input vector that is to be used to "
"generate color information");
prm.declare_entry("Scale to width or height",
"width",
Patterns::Selection("width|height"),
"Whether width or height should be scaled to match "
"the given size");
prm.declare_entry("Size (width or height) in eps units",
"300",
Patterns::Integer(),
"The size (width or height) to which the eps output "
"file is to be scaled");
prm.declare_entry("Line widths in eps units",
"0.5",
Patterns::Double(),
"The width in which the postscript renderer is to "
"plot lines");
prm.declare_entry("Azimut angle",
"60",
Patterns::Double(0, 180),
"Angle of the viewing position against the vertical "
"axis");
prm.declare_entry("Turn angle",
"30",
Patterns::Double(0, 360),
"Angle of the viewing direction against the y-axis");
prm.declare_entry("Scaling for z-axis",
"1",
Patterns::Double(),
"Scaling for the z-direction relative to the scaling "
"used in x- and y-directions");
prm.declare_entry("Draw mesh lines",
"true",
Patterns::Bool(),
"Whether the mesh lines, or only the surface should be "
"drawn");
prm.declare_entry("Fill interior of cells",
"true",
Patterns::Bool(),
"Whether only the mesh lines, or also the interior of "
"cells should be plotted. If this flag is false, then "
"one can see through the mesh");
prm.declare_entry("Color shading of interior of cells",
"true",
Patterns::Bool(),
"Whether the interior of cells shall be shaded");
prm.declare_entry("Color function",
"default",
Patterns::Selection(
"default|grey scale|reverse grey scale"),
"Name of a color function used to colorize mesh lines "
"and/or cell interiors");
}
void
EpsFlags::parse_parameters(const ParameterHandler &prm)
{
height_vector = prm.get_integer("Index of vector for height");
color_vector = prm.get_integer("Index of vector for color");
if (prm.get("Scale to width or height") == "width")
size_type = width;
else
size_type = height;
size = prm.get_integer("Size (width or height) in eps units");
line_width = prm.get_double("Line widths in eps units");
azimut_angle = prm.get_double("Azimut angle");
turn_angle = prm.get_double("Turn angle");
z_scaling = prm.get_double("Scaling for z-axis");
draw_mesh = prm.get_bool("Draw mesh lines");
draw_cells = prm.get_bool("Fill interior of cells");
shade_cells = prm.get_bool("Color shading of interior of cells");
if (prm.get("Color function") == "default")
color_function = &default_color_function;
else if (prm.get("Color function") == "grey scale")
color_function = &grey_scale_color_function;
else if (prm.get("Color function") == "reverse grey scale")
color_function = &reverse_grey_scale_color_function;
else
// we shouldn't get here, since the parameter object should already have
// checked that the given value is valid
DEAL_II_ASSERT_UNREACHABLE();
}
Hdf5Flags::Hdf5Flags(const CompressionLevel compression_level)
: compression_level(compression_level)
{}
TecplotFlags::TecplotFlags(const char *zone_name, const double solution_time)
: zone_name(zone_name)
, solution_time(solution_time)
{}
std::size_t
TecplotFlags::memory_consumption() const
{
return sizeof(*this) + MemoryConsumption::memory_consumption(zone_name);
}
VtkFlags::VtkFlags(const double time,
const unsigned int cycle,
const bool print_date_and_time,
const CompressionLevel compression_level,
const bool write_higher_order_cells,
const std::map<std::string, std::string> &physical_units)
: time(time)
, cycle(cycle)
, print_date_and_time(print_date_and_time)
, compression_level(compression_level)
, write_higher_order_cells(write_higher_order_cells)
, physical_units(physical_units)
{}
OutputFormat
parse_output_format(const std::string &format_name)
{
if (format_name == "none")
return none;
if (format_name == "dx")
return dx;
if (format_name == "ucd")
return ucd;
if (format_name == "gnuplot")
return gnuplot;
if (format_name == "povray")
return povray;
if (format_name == "eps")
return eps;
if (format_name == "gmv")
return gmv;
if (format_name == "tecplot")
return tecplot;
if (format_name == "vtk")
return vtk;
if (format_name == "vtu")
return vtu;
if (format_name == "deal.II intermediate")
return deal_II_intermediate;
if (format_name == "hdf5")
return hdf5;
AssertThrow(false,
ExcMessage("The given file format name is not recognized: <" +
format_name + ">"));
// return something invalid
return OutputFormat(-1);
}
std::string
get_output_format_names()
{
return "none|dx|ucd|gnuplot|povray|eps|gmv|tecplot|vtk|vtu|hdf5|svg|deal.II intermediate";
}
std::string
default_suffix(const OutputFormat output_format)
{
switch (output_format)
{
case none:
return "";
case dx:
return ".dx";
case ucd:
return ".inp";
case gnuplot:
return ".gnuplot";
case povray:
return ".pov";
case eps:
return ".eps";
case gmv:
return ".gmv";
case tecplot:
return ".dat";
case vtk:
return ".vtk";
case vtu:
return ".vtu";
case deal_II_intermediate:
return ".d2";
case hdf5:
return ".h5";
case svg:
return ".svg";
default:
DEAL_II_NOT_IMPLEMENTED();
return "";
}
}
//----------------------------------------------------------------------//
/**
* Obtain the positions of all nodes referenced in the patches given as
* argument.
*/
template <int dim, int spacedim>
std::vector<Point<spacedim>>
get_node_positions(const std::vector<Patch<dim, spacedim>> &patches)
{
Assert(dim <= 3, ExcNotImplemented());
static const std::array<unsigned int, 5> table = {{0, 1, 3, 2, 4}};
std::vector<Point<spacedim>> node_positions;
for (const auto &patch : patches)
{
// special treatment of non-hypercube cells
if (patch.reference_cell != ReferenceCells::get_hypercube<dim>())
{
for (unsigned int point_no = 0; point_no < patch.data.n_cols();
++point_no)
node_positions.emplace_back(get_node_location(
patch,
(patch.reference_cell == ReferenceCells::Pyramid ?
table[point_no] :
point_no)));
}
else
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n = n_subdivisions + 1;
switch (dim)
{
case 0:
node_positions.emplace_back(
get_equispaced_location(patch, {}, n_subdivisions));
break;
case 1:
for (unsigned int i1 = 0; i1 < n; ++i1)
node_positions.emplace_back(
get_equispaced_location(patch, {i1}, n_subdivisions));
break;
case 2:
for (unsigned int i2 = 0; i2 < n; ++i2)
for (unsigned int i1 = 0; i1 < n; ++i1)
node_positions.emplace_back(get_equispaced_location(
patch, {i1, i2}, n_subdivisions));
break;
case 3:
for (unsigned int i3 = 0; i3 < n; ++i3)
for (unsigned int i2 = 0; i2 < n; ++i2)
for (unsigned int i1 = 0; i1 < n; ++i1)
node_positions.emplace_back(get_equispaced_location(
patch, {i1, i2, i3}, n_subdivisions));
break;
default:
DEAL_II_ASSERT_UNREACHABLE();
}
}
}
return node_positions;
}
template <int dim, int spacedim, typename StreamType>
void
write_nodes(const std::vector<Patch<dim, spacedim>> &patches, StreamType &out)
{
// Obtain the node locations, and then output them via the given stream
// object
const std::vector<Point<spacedim>> node_positions =
get_node_positions(patches);
int count = 0;
for (const auto &node : node_positions)
out.write_point(count++, node);
out.flush_points();
}
template <int dim, int spacedim, typename StreamType>
void
write_cells(const std::vector<Patch<dim, spacedim>> &patches, StreamType &out)
{
Assert(dim <= 3, ExcNotImplemented());
unsigned int count = 0;
unsigned int first_vertex_of_patch = 0;
for (const auto &patch : patches)
{
// special treatment of simplices since they are not subdivided
if (patch.reference_cell != ReferenceCells::get_hypercube<dim>())
{
out.write_cell_single(count++,
first_vertex_of_patch,
patch.data.n_cols(),
patch.reference_cell);
first_vertex_of_patch += patch.data.n_cols();
}
else // hypercube cell
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n = n_subdivisions + 1;
switch (dim)
{
case 0:
{
const unsigned int offset = first_vertex_of_patch;
out.template write_cell<0>(count++, offset, {});
break;
}
case 1:
{
constexpr unsigned int d1 = 1;
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const unsigned int offset =
first_vertex_of_patch + i1 * d1;
out.template write_cell<1>(count++, offset, {{d1}});
}
break;
}
case 2:
{
constexpr unsigned int d1 = 1;
const unsigned int d2 = n;
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const unsigned int offset =
first_vertex_of_patch + i2 * d2 + i1 * d1;
out.template write_cell<2>(count++,
offset,
{{d1, d2}});
}
break;
}
case 3:
{
constexpr unsigned int d1 = 1;
const unsigned int d2 = n;
const unsigned int d3 = n * n;
for (unsigned int i3 = 0; i3 < n_subdivisions; ++i3)
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const unsigned int offset = first_vertex_of_patch +
i3 * d3 + i2 * d2 +
i1 * d1;
out.template write_cell<3>(count++,
offset,
{{d1, d2, d3}});
}
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
// Update the number of the first vertex of this patch
first_vertex_of_patch +=
Utilities::fixed_power<dim>(n_subdivisions + 1);
}
}
out.flush_cells();
}
template <int dim, int spacedim, typename StreamType>
void
write_high_order_cells(const std::vector<Patch<dim, spacedim>> &patches,
StreamType &out,
const bool legacy_format)
{
unsigned int first_vertex_of_patch = 0;
// Array to hold all the node numbers of a cell
std::vector<unsigned> connectivity;
for (const auto &patch : patches)
{
if (patch.reference_cell != ReferenceCells::get_hypercube<dim>())
{
connectivity.resize(patch.data.n_cols());
for (unsigned int i = 0; i < patch.data.n_cols(); ++i)
connectivity[i] = i;
out.template write_high_order_cell<dim>(first_vertex_of_patch,
connectivity);
first_vertex_of_patch += patch.data.n_cols();
}
else
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n = n_subdivisions + 1;
connectivity.resize(Utilities::fixed_power<dim>(n));
switch (dim)
{
case 0:
{
Assert(false,
ExcMessage("Point-like cells should not be possible "
"when writing higher-order cells."));
break;
}
case 1:
{
for (unsigned int i1 = 0; i1 < n_subdivisions + 1; ++i1)
{
const unsigned int local_index = i1;
const unsigned int connectivity_index =
patch.reference_cell
.template vtk_lexicographic_to_node_index<1>(
{{i1}}, {{n_subdivisions}}, legacy_format);
connectivity[connectivity_index] = local_index;
}
break;
}
case 2:
{
for (unsigned int i2 = 0; i2 < n_subdivisions + 1; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions + 1; ++i1)
{
const unsigned int local_index = i2 * n + i1;
const unsigned int connectivity_index =
patch.reference_cell
.template vtk_lexicographic_to_node_index<2>(
{{i1, i2}},
{{n_subdivisions, n_subdivisions}},
legacy_format);
connectivity[connectivity_index] = local_index;
}
break;
}
case 3:
{
for (unsigned int i3 = 0; i3 < n_subdivisions + 1; ++i3)
for (unsigned int i2 = 0; i2 < n_subdivisions + 1; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions + 1; ++i1)
{
const unsigned int local_index =
i3 * n * n + i2 * n + i1;
const unsigned int connectivity_index =
patch.reference_cell
.template vtk_lexicographic_to_node_index<3>(
{{i1, i2, i3}},
{{n_subdivisions,
n_subdivisions,
n_subdivisions}},
legacy_format);
connectivity[connectivity_index] = local_index;
}
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
// Having so set up the 'connectivity' data structure,
// output it:
out.template write_high_order_cell<dim>(first_vertex_of_patch,
connectivity);
// Finally update the number of the first vertex of this patch
first_vertex_of_patch += Utilities::fixed_power<dim>(n);
}
}
out.flush_cells();
}
template <int dim, int spacedim, typename StreamType>
void
write_data(const std::vector<Patch<dim, spacedim>> &patches,
unsigned int n_data_sets,
const bool double_precision,
StreamType &out)
{
Assert(dim <= 3, ExcNotImplemented());
unsigned int count = 0;
for (const auto &patch : patches)
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n = n_subdivisions + 1;
// Length of loops in all dimensions
Assert((patch.data.n_rows() == n_data_sets &&
!patch.points_are_available) ||
(patch.data.n_rows() == n_data_sets + spacedim &&
patch.points_are_available),
ExcDimensionMismatch(patch.points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patch.data.n_rows()));
Assert(patch.data.n_cols() == Utilities::fixed_power<dim>(n),
ExcInvalidDatasetSize(patch.data.n_cols(), n));
std::vector<float> floats(n_data_sets);
std::vector<double> doubles(n_data_sets);
// Data is already in lexicographic ordering
for (unsigned int i = 0; i < Utilities::fixed_power<dim>(n);
++i, ++count)
if (double_precision)
{
for (unsigned int data_set = 0; data_set < n_data_sets;
++data_set)
doubles[data_set] = patch.data(data_set, i);
out.write_dataset(count, doubles);
}
else
{
for (unsigned int data_set = 0; data_set < n_data_sets;
++data_set)
floats[data_set] = patch.data(data_set, i);
out.write_dataset(count, floats);
}
}
}
namespace
{
/**
* This function projects a three-dimensional point (Point<3> point)
* onto a two-dimensional image plane, specified by the position of
* the camera viewing system (Point<3> camera_position), camera
* direction (Point<3> camera_position), camera horizontal (Point<3>
* camera_horizontal, necessary for the correct alignment of the
* later images), and the focus of the camera (float camera_focus).
*/
Point<2>
svg_project_point(Point<3> point,
Point<3> camera_position,
Point<3> camera_direction,
Point<3> camera_horizontal,
float camera_focus)
{
Point<3> camera_vertical;
camera_vertical[0] = camera_horizontal[1] * camera_direction[2] -
camera_horizontal[2] * camera_direction[1];
camera_vertical[1] = camera_horizontal[2] * camera_direction[0] -
camera_horizontal[0] * camera_direction[2];
camera_vertical[2] = camera_horizontal[0] * camera_direction[1] -
camera_horizontal[1] * camera_direction[0];
float phi;
phi = camera_focus;
phi /= (point[0] - camera_position[0]) * camera_direction[0] +
(point[1] - camera_position[1]) * camera_direction[1] +
(point[2] - camera_position[2]) * camera_direction[2];
Point<3> projection;
projection[0] =
camera_position[0] + phi * (point[0] - camera_position[0]);
projection[1] =
camera_position[1] + phi * (point[1] - camera_position[1]);
projection[2] =
camera_position[2] + phi * (point[2] - camera_position[2]);
Point<2> projection_decomposition;
projection_decomposition[0] = (projection[0] - camera_position[0] -
camera_focus * camera_direction[0]) *
camera_horizontal[0];
projection_decomposition[0] += (projection[1] - camera_position[1] -
camera_focus * camera_direction[1]) *
camera_horizontal[1];
projection_decomposition[0] += (projection[2] - camera_position[2] -
camera_focus * camera_direction[2]) *
camera_horizontal[2];
projection_decomposition[1] = (projection[0] - camera_position[0] -
camera_focus * camera_direction[0]) *
camera_vertical[0];
projection_decomposition[1] += (projection[1] - camera_position[1] -
camera_focus * camera_direction[1]) *
camera_vertical[1];
projection_decomposition[1] += (projection[2] - camera_position[2] -
camera_focus * camera_direction[2]) *
camera_vertical[2];
return projection_decomposition;
}
/**
* Function to compute the gradient parameters for a triangle with given
* values for the vertices.
*/
Point<6>
svg_get_gradient_parameters(Point<3> points[])
{
Point<3> v_min, v_max, v_inter;
// Use the Bubblesort algorithm to sort the points with respect to the
// third coordinate
for (int i = 0; i < 2; ++i)
{
for (int j = 0; j < 2 - i; ++j)
{
if (points[j][2] > points[j + 1][2])
{
Point<3> temp = points[j];
points[j] = points[j + 1];
points[j + 1] = temp;
}
}
}
// save the related three-dimensional vectors v_min, v_inter, and v_max
v_min = points[0];
v_inter = points[1];
v_max = points[2];
Point<2> A[2];
Point<2> b, gradient;
// determine the plane offset c
A[0][0] = v_max[0] - v_min[0];
A[0][1] = v_inter[0] - v_min[0];
A[1][0] = v_max[1] - v_min[1];
A[1][1] = v_inter[1] - v_min[1];
b[0] = -v_min[0];
b[1] = -v_min[1];
double x, sum;
bool col_change = false;
if (A[0][0] == 0)
{
col_change = true;
A[0][0] = A[0][1];
A[0][1] = 0;
double temp = A[1][0];
A[1][0] = A[1][1];
A[1][1] = temp;
}
for (unsigned int k = 0; k < 1; ++k)
{
for (unsigned int i = k + 1; i < 2; ++i)
{
x = A[i][k] / A[k][k];
for (unsigned int j = k + 1; j < 2; ++j)
A[i][j] = A[i][j] - A[k][j] * x;
b[i] = b[i] - b[k] * x;
}
}
b[1] = b[1] / A[1][1];
for (int i = 0; i >= 0; i--)
{
sum = b[i];
for (unsigned int j = i + 1; j < 2; ++j)
sum = sum - A[i][j] * b[j];
b[i] = sum / A[i][i];
}
if (col_change)
{
double temp = b[0];
b[0] = b[1];
b[1] = temp;
}
double c = b[0] * (v_max[2] - v_min[2]) + b[1] * (v_inter[2] - v_min[2]) +
v_min[2];
// Determine the first entry of the gradient (phi, cf. documentation)
A[0][0] = v_max[0] - v_min[0];
A[0][1] = v_inter[0] - v_min[0];
A[1][0] = v_max[1] - v_min[1];
A[1][1] = v_inter[1] - v_min[1];
b[0] = 1.0 - v_min[0];
b[1] = -v_min[1];
col_change = false;
if (A[0][0] == 0)
{
col_change = true;
A[0][0] = A[0][1];
A[0][1] = 0;
double temp = A[1][0];
A[1][0] = A[1][1];
A[1][1] = temp;
}
for (unsigned int k = 0; k < 1; ++k)
{
for (unsigned int i = k + 1; i < 2; ++i)
{
x = A[i][k] / A[k][k];
for (unsigned int j = k + 1; j < 2; ++j)
A[i][j] = A[i][j] - A[k][j] * x;
b[i] = b[i] - b[k] * x;
}
}
b[1] = b[1] / A[1][1];
for (int i = 0; i >= 0; i--)
{
sum = b[i];
for (unsigned int j = i + 1; j < 2; ++j)
sum = sum - A[i][j] * b[j];
b[i] = sum / A[i][i];
}
if (col_change)
{
double temp = b[0];
b[0] = b[1];
b[1] = temp;
}
gradient[0] = b[0] * (v_max[2] - v_min[2]) +
b[1] * (v_inter[2] - v_min[2]) - c + v_min[2];
// determine the second entry of the gradient
A[0][0] = v_max[0] - v_min[0];
A[0][1] = v_inter[0] - v_min[0];
A[1][0] = v_max[1] - v_min[1];
A[1][1] = v_inter[1] - v_min[1];
b[0] = -v_min[0];
b[1] = 1.0 - v_min[1];
col_change = false;
if (A[0][0] == 0)
{
col_change = true;
A[0][0] = A[0][1];
A[0][1] = 0;
double temp = A[1][0];
A[1][0] = A[1][1];
A[1][1] = temp;
}
for (unsigned int k = 0; k < 1; ++k)
{
for (unsigned int i = k + 1; i < 2; ++i)
{
x = A[i][k] / A[k][k];
for (unsigned int j = k + 1; j < 2; ++j)
A[i][j] = A[i][j] - A[k][j] * x;
b[i] = b[i] - b[k] * x;
}
}
b[1] = b[1] / A[1][1];
for (int i = 0; i >= 0; i--)
{
sum = b[i];
for (unsigned int j = i + 1; j < 2; ++j)
sum = sum - A[i][j] * b[j];
b[i] = sum / A[i][i];
}
if (col_change)
{
double temp = b[0];
b[0] = b[1];
b[1] = temp;
}
gradient[1] = b[0] * (v_max[2] - v_min[2]) +
b[1] * (v_inter[2] - v_min[2]) - c + v_min[2];
// normalize the gradient
gradient /= gradient.norm();
const double lambda = -gradient[0] * (v_min[0] - v_max[0]) -
gradient[1] * (v_min[1] - v_max[1]);
Point<6> gradient_parameters;
gradient_parameters[0] = v_min[0];
gradient_parameters[1] = v_min[1];
gradient_parameters[2] = v_min[0] + lambda * gradient[0];
gradient_parameters[3] = v_min[1] + lambda * gradient[1];
gradient_parameters[4] = v_min[2];
gradient_parameters[5] = v_max[2];
return gradient_parameters;
}
} // namespace
template <int dim, int spacedim>
void
write_ucd(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const UcdFlags &flags,
std::ostream &out)
{
// Note that while in theory dim==0 should be implemented, this is not
// tested, therefore currently not allowed.
AssertThrow(dim > 0, ExcNotImplemented());
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
const unsigned int n_data_sets = data_names.size();
UcdStream ucd_out(out, flags);
// first count the number of cells and cells for later use
unsigned int n_nodes;
unsigned int n_cells;
std::tie(n_nodes, n_cells) = count_nodes_and_cells(patches);
//---------------------
// preamble
if (flags.write_preamble)
{
out
<< "# This file was generated by the deal.II library." << '\n'
<< "# Date = " << Utilities::System::get_date() << '\n'
<< "# Time = " << Utilities::System::get_time() << '\n'
<< "#" << '\n'
<< "# For a description of the UCD format see the AVS Developer's guide."
<< '\n'
<< "#" << '\n';
}
// start with ucd data
out << n_nodes << ' ' << n_cells << ' ' << n_data_sets << ' ' << 0
<< ' ' // no cell data at present
<< 0 // no model data
<< '\n';
write_nodes(patches, ucd_out);
out << '\n';
write_cells(patches, ucd_out);
out << '\n';
//---------------------------
// now write data
if (n_data_sets != 0)
{
out << n_data_sets << " "; // number of vectors
for (unsigned int i = 0; i < n_data_sets; ++i)
out << 1 << ' '; // number of components;
// only 1 supported presently
out << '\n';
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
out << data_names[data_set]
<< ",dimensionless" // no units supported at present
<< '\n';
write_data(patches, n_data_sets, true, ucd_out);
}
// make sure everything now gets to disk
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
template <int dim, int spacedim>
void
write_dx(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const DXFlags &flags,
std::ostream &out)
{
// Point output is currently not implemented.
AssertThrow(dim > 0, ExcNotImplemented());
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
// Stream with special features for dx output
DXStream dx_out(out, flags);
// Variable counting the offset of binary data.
unsigned int offset = 0;
const unsigned int n_data_sets = data_names.size();
// first count the number of cells and cells for later use
unsigned int n_nodes;
unsigned int n_cells;
std::tie(n_nodes, n_cells) = count_nodes_and_cells(patches);
// start with vertices order is lexicographical, x varying fastest
out << "object \"vertices\" class array type float rank 1 shape "
<< spacedim << " items " << n_nodes;
if (flags.coordinates_binary)
{
out << " lsb ieee data 0" << '\n';
offset += n_nodes * spacedim * sizeof(float);
}
else
{
out << " data follows" << '\n';
write_nodes(patches, dx_out);
}
//-----------------------------
// first write the coordinates of all vertices
//---------------------------------------
// write cells
out << "object \"cells\" class array type int rank 1 shape "
<< GeometryInfo<dim>::vertices_per_cell << " items " << n_cells;
if (flags.int_binary)
{
out << " lsb binary data " << offset << '\n';
offset += n_cells * sizeof(int);
}
else
{
out << " data follows" << '\n';
write_cells(patches, dx_out);
out << '\n';
}
out << "attribute \"element type\" string \"";
if constexpr (dim == 1)
out << "lines";
else if constexpr (dim == 2)
out << "quads";
else if constexpr (dim == 3)
out << "cubes";
out << "\"" << '\n' << "attribute \"ref\" string \"positions\"" << '\n';
// TODO:[GK] Patches must be of same size!
//---------------------------
// write neighbor information
if (flags.write_neighbors)
{
out << "object \"neighbors\" class array type int rank 1 shape "
<< GeometryInfo<dim>::faces_per_cell << " items " << n_cells
<< " data follows";
for (const auto &patch : patches)
{
const unsigned int n = patch.n_subdivisions;
const unsigned int n1 = (dim > 0) ? n : 1;
const unsigned int n2 = (dim > 1) ? n : 1;
const unsigned int n3 = (dim > 2) ? n : 1;
const unsigned int x_minus = (dim > 0) ? 0 : 0;
const unsigned int x_plus = (dim > 0) ? 1 : 0;
const unsigned int y_minus = (dim > 1) ? 2 : 0;
const unsigned int y_plus = (dim > 1) ? 3 : 0;
const unsigned int z_minus = (dim > 2) ? 4 : 0;
const unsigned int z_plus = (dim > 2) ? 5 : 0;
unsigned int cells_per_patch = Utilities::fixed_power<dim>(n);
unsigned int dx = 1;
unsigned int dy = n;
unsigned int dz = n * n;
const unsigned int patch_start =
patch.patch_index * cells_per_patch;
for (unsigned int i3 = 0; i3 < n3; ++i3)
for (unsigned int i2 = 0; i2 < n2; ++i2)
for (unsigned int i1 = 0; i1 < n1; ++i1)
{
const unsigned int nx = i1 * dx;
const unsigned int ny = i2 * dy;
const unsigned int nz = i3 * dz;
// There are no neighbors for dim==0. Note that this case is
// caught by the AssertThrow at the beginning of this
// function anyway. This condition avoids compiler warnings.
if (dim < 1)
continue;
out << '\n';
// Direction -x Last cell in row of other patch
if (i1 == 0)
{
const unsigned int nn = patch.neighbors[x_minus];
out << '\t';
if (nn != patch.no_neighbor)
out
<< (nn * cells_per_patch + ny + nz + dx * (n - 1));
else
out << "-1";
}
else
{
out << '\t' << patch_start + nx - dx + ny + nz;
}
// Direction +x First cell in row of other patch
if (i1 == n - 1)
{
const unsigned int nn = patch.neighbors[x_plus];
out << '\t';
if (nn != patch.no_neighbor)
out << (nn * cells_per_patch + ny + nz);
else
out << "-1";
}
else
{
out << '\t' << patch_start + nx + dx + ny + nz;
}
if (dim < 2)
continue;
// Direction -y
if (i2 == 0)
{
const unsigned int nn = patch.neighbors[y_minus];
out << '\t';
if (nn != patch.no_neighbor)
out
<< (nn * cells_per_patch + nx + nz + dy * (n - 1));
else
out << "-1";
}
else
{
out << '\t' << patch_start + nx + ny - dy + nz;
}
// Direction +y
if (i2 == n - 1)
{
const unsigned int nn = patch.neighbors[y_plus];
out << '\t';
if (nn != patch.no_neighbor)
out << (nn * cells_per_patch + nx + nz);
else
out << "-1";
}
else
{
out << '\t' << patch_start + nx + ny + dy + nz;
}
if (dim < 3)
continue;
// Direction -z
if (i3 == 0)
{
const unsigned int nn = patch.neighbors[z_minus];
out << '\t';
if (nn != patch.no_neighbor)
out
<< (nn * cells_per_patch + nx + ny + dz * (n - 1));
else
out << "-1";
}
else
{
out << '\t' << patch_start + nx + ny + nz - dz;
}
// Direction +z
if (i3 == n - 1)
{
const unsigned int nn = patch.neighbors[z_plus];
out << '\t';
if (nn != patch.no_neighbor)
out << (nn * cells_per_patch + nx + ny);
else
out << "-1";
}
else
{
out << '\t' << patch_start + nx + ny + nz + dz;
}
}
out << '\n';
}
}
//---------------------------
// now write data
if (n_data_sets != 0)
{
out << "object \"data\" class array type float rank 1 shape "
<< n_data_sets << " items " << n_nodes;
if (flags.data_binary)
{
out << " lsb ieee data " << offset << '\n';
offset += n_data_sets * n_nodes *
((flags.data_double) ? sizeof(double) : sizeof(float));
}
else
{
out << " data follows" << '\n';
write_data(patches, n_data_sets, flags.data_double, dx_out);
}
// loop over all patches
out << "attribute \"dep\" string \"positions\"" << '\n';
}
else
{
out << "object \"data\" class constantarray type float rank 0 items "
<< n_nodes << " data follows" << '\n'
<< '0' << '\n';
}
// no model data
out << "object \"deal data\" class field" << '\n'
<< "component \"positions\" value \"vertices\"" << '\n'
<< "component \"connections\" value \"cells\"" << '\n'
<< "component \"data\" value \"data\"" << '\n';
if (flags.write_neighbors)
out << "component \"neighbors\" value \"neighbors\"" << '\n';
{
out << "attribute \"created\" string \"" << Utilities::System::get_date()
<< ' ' << Utilities::System::get_time() << '"' << '\n';
}
out << "end" << '\n';
// Write all binary data now
if (flags.coordinates_binary)
write_nodes(patches, dx_out);
if (flags.int_binary)
write_cells(patches, dx_out);
if (flags.data_binary)
write_data(patches, n_data_sets, flags.data_double, dx_out);
// make sure everything now gets to disk
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
template <int dim, int spacedim>
void
write_gnuplot(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const GnuplotFlags &flags,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most
// of the times, people just forget to call build_patches when there
// are no patches, so a warning is in order. that said, the
// assertion is disabled if we support MPI since then it can
// happen that on the coarsest mesh, a processor simply has no
// cells it actually owns, and in that case it is legit if there
// are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
const unsigned int n_data_sets = data_names.size();
// write preamble
{
out << "# This file was generated by the deal.II library." << '\n'
<< "# Date = " << Utilities::System::get_date() << '\n'
<< "# Time = " << Utilities::System::get_time() << '\n'
<< "#" << '\n'
<< "# For a description of the GNUPLOT format see the GNUPLOT manual."
<< '\n'
<< "#" << '\n'
<< "# ";
AssertThrow(spacedim <= flags.space_dimension_labels.size(),
GnuplotFlags::ExcNotEnoughSpaceDimensionLabels());
for (unsigned int spacedim_n = 0; spacedim_n < spacedim; ++spacedim_n)
{
out << '<' << flags.space_dimension_labels.at(spacedim_n) << "> ";
}
for (const auto &data_name : data_names)
out << '<' << data_name << "> ";
out << '\n';
}
// loop over all patches
for (const auto &patch : patches)
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n_points_per_direction = n_subdivisions + 1;
Assert((patch.data.n_rows() == n_data_sets &&
!patch.points_are_available) ||
(patch.data.n_rows() == n_data_sets + spacedim &&
patch.points_are_available),
ExcDimensionMismatch(patch.points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patch.data.n_rows()));
auto output_point_data =
[&out, &patch, n_data_sets](const unsigned int point_index) mutable {
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
out << patch.data(data_set, point_index) << ' ';
};
switch (dim)
{
case 0:
{
Assert(patch.reference_cell == ReferenceCells::Vertex,
ExcInternalError());
Assert(patch.data.n_cols() == 1,
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
// compute coordinates for this patch point
out << get_equispaced_location(patch, {}, n_subdivisions)
<< ' ';
output_point_data(0);
out << '\n';
out << '\n';
break;
}
case 1:
{
Assert(patch.reference_cell == ReferenceCells::Line,
ExcInternalError());
Assert(patch.data.n_cols() ==
Utilities::fixed_power<dim>(n_points_per_direction),
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
for (unsigned int i1 = 0; i1 < n_points_per_direction; ++i1)
{
// compute coordinates for this patch point
out << get_equispaced_location(patch, {i1}, n_subdivisions)
<< ' ';
output_point_data(i1);
out << '\n';
}
// end of patch
out << '\n';
out << '\n';
break;
}
case 2:
{
if (patch.reference_cell == ReferenceCells::Quadrilateral)
{
Assert(patch.data.n_cols() == Utilities::fixed_power<dim>(
n_points_per_direction),
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
for (unsigned int i2 = 0; i2 < n_points_per_direction; ++i2)
{
for (unsigned int i1 = 0; i1 < n_points_per_direction;
++i1)
{
// compute coordinates for this patch point
out << get_equispaced_location(patch,
{i1, i2},
n_subdivisions)
<< ' ';
output_point_data(i1 + i2 * n_points_per_direction);
out << '\n';
}
// end of row in patch
out << '\n';
}
}
else if (patch.reference_cell == ReferenceCells::Triangle)
{
Assert(n_subdivisions == 1, ExcNotImplemented());
Assert(patch.data.n_cols() == 3, ExcInternalError());
// Gnuplot can only plot surfaces if each facet of the
// surface is a bilinear patch, or a subdivided bilinear
// patch with equally many points along each row of the
// subdivision. This is what the code above for
// quadrilaterals does. We emulate this by repeating the
// third point of a triangle twice so that there are two
// points for that row as well -- i.e., we write a 2x2
// bilinear patch where two of the points are collapsed onto
// one vertex.
//
// This also matches the example here:
// https://stackoverflow.com/questions/42784369/drawing-triangular-mesh-using-gnuplot
out << get_node_location(patch, 0) << ' ';
output_point_data(0);
out << '\n';
out << get_node_location(patch, 1) << ' ';
output_point_data(1);
out << '\n';
out << '\n'; // end of one row of points
out << get_node_location(patch, 2) << ' ';
output_point_data(2);
out << '\n';
out << get_node_location(patch, 2) << ' ';
output_point_data(2);
out << '\n';
out << '\n'; // end of the second row of points
out << '\n'; // end of the entire patch
}
else
// There aren't any other reference cells in 2d than the
// quadrilateral and the triangle. So whatever we got here
// can't be any good
DEAL_II_ASSERT_UNREACHABLE();
// end of patch
out << '\n';
break;
}
case 3:
{
if (patch.reference_cell == ReferenceCells::Hexahedron)
{
Assert(patch.data.n_cols() == Utilities::fixed_power<dim>(
n_points_per_direction),
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
// for all grid points: draw lines into all positive
// coordinate directions if there is another grid point
// there
for (unsigned int i3 = 0; i3 < n_points_per_direction; ++i3)
for (unsigned int i2 = 0; i2 < n_points_per_direction;
++i2)
for (unsigned int i1 = 0; i1 < n_points_per_direction;
++i1)
{
// compute coordinates for this patch point
const Point<spacedim> this_point =
get_equispaced_location(patch,
{i1, i2, i3},
n_subdivisions);
// line into positive x-direction if possible
if (i1 < n_subdivisions)
{
// write point here and its data
out << this_point << ' ';
output_point_data(i1 +
i2 * n_points_per_direction +
i3 * n_points_per_direction *
n_points_per_direction);
out << '\n';
// write point there and its data
out << get_equispaced_location(patch,
{i1 + 1, i2, i3},
n_subdivisions)
<< ' ';
output_point_data((i1 + 1) +
i2 * n_points_per_direction +
i3 * n_points_per_direction *
n_points_per_direction);
out << '\n';
// end of line
out << '\n' << '\n';
}
// line into positive y-direction if possible
if (i2 < n_subdivisions)
{
// write point here and its data
out << this_point << ' ';
output_point_data(i1 +
i2 * n_points_per_direction +
i3 * n_points_per_direction *
n_points_per_direction);
out << '\n';
// write point there and its data
out << get_equispaced_location(patch,
{i1, i2 + 1, i3},
n_subdivisions)
<< ' ';
output_point_data(
i1 + (i2 + 1) * n_points_per_direction +
i3 * n_points_per_direction *
n_points_per_direction);
out << '\n';
// end of line
out << '\n' << '\n';
}
// line into positive z-direction if possible
if (i3 < n_subdivisions)
{
// write point here and its data
out << this_point << ' ';
output_point_data(i1 +
i2 * n_points_per_direction +
i3 * n_points_per_direction *
n_points_per_direction);
out << '\n';
// write point there and its data
out << get_equispaced_location(patch,
{i1, i2, i3 + 1},
n_subdivisions)
<< ' ';
output_point_data(
i1 + i2 * n_points_per_direction +
(i3 + 1) * n_points_per_direction *
n_points_per_direction);
out << '\n';
// end of line
out << '\n' << '\n';
}
}
}
else if (patch.reference_cell == ReferenceCells::Tetrahedron)
{
Assert(n_subdivisions == 1, ExcNotImplemented());
// Draw the tetrahedron as a collection of two lines.
for (const unsigned int v : {0, 1, 2, 0, 3, 2})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of first line
for (const unsigned int v : {3, 1})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of second line
}
else if (patch.reference_cell == ReferenceCells::Pyramid)
{
Assert(n_subdivisions == 1, ExcNotImplemented());
// Draw the pyramid as a collection of two lines.
for (const unsigned int v : {0, 1, 3, 2, 0, 4, 1})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of first line
for (const unsigned int v : {2, 4, 3})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of second line
}
else if (patch.reference_cell == ReferenceCells::Wedge)
{
Assert(n_subdivisions == 1, ExcNotImplemented());
// Draw the wedge as a collection of three
// lines. The first one wraps around the base,
// goes up to the top, and wraps around that. The
// second and third are just individual lines
// going from base to top.
for (const unsigned int v : {0, 1, 2, 0, 3, 4, 5, 3})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of first line
for (const unsigned int v : {1, 4})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of second line
for (const unsigned int v : {2, 5})
{
out << get_node_location(patch, v) << ' ';
output_point_data(v);
out << '\n';
}
out << '\n'; // end of second line
}
else
// No other reference cells are currently implemented
DEAL_II_NOT_IMPLEMENTED();
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
}
// make sure everything now gets to disk
out.flush();
AssertThrow(out.fail() == false, ExcIO());
}
namespace
{
template <int dim, int spacedim>
void
do_write_povray(const std::vector<Patch<dim, spacedim>> &,
const std::vector<std::string> &,
const PovrayFlags &,
std::ostream &)
{
Assert(false,
ExcMessage("Writing files in POVRAY format is only supported "
"for two-dimensional meshes."));
}
void
do_write_povray(const std::vector<Patch<2, 2>> &patches,
const std::vector<std::string> &data_names,
const PovrayFlags &flags,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most
// of the times, people just forget to call build_patches when there
// are no patches, so a warning is in order. that said, the
// assertion is disabled if we support MPI since then it can
// happen that on the coarsest mesh, a processor simply has no cells it
// actually owns, and in that case it is legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
constexpr int dim = 2;
(void)dim;
constexpr int spacedim = 2;
const unsigned int n_data_sets = data_names.size();
(void)n_data_sets;
// write preamble
{
out
<< "/* This file was generated by the deal.II library." << '\n'
<< " Date = " << Utilities::System::get_date() << '\n'
<< " Time = " << Utilities::System::get_time() << '\n'
<< '\n'
<< " For a description of the POVRAY format see the POVRAY manual."
<< '\n'
<< "*/ " << '\n';
// include files
out << "#include \"colors.inc\" " << '\n'
<< "#include \"textures.inc\" " << '\n';
// use external include file for textures, camera and light
if (flags.external_data)
out << "#include \"data.inc\" " << '\n';
else // all definitions in data file
{
// camera
out << '\n'
<< '\n'
<< "camera {" << '\n'
<< " location <1,4,-7>" << '\n'
<< " look_at <0,0,0>" << '\n'
<< " angle 30" << '\n'
<< "}" << '\n';
// light
out << '\n'
<< "light_source {" << '\n'
<< " <1,4,-7>" << '\n'
<< " color Grey" << '\n'
<< "}" << '\n';
out << '\n'
<< "light_source {" << '\n'
<< " <0,20,0>" << '\n'
<< " color White" << '\n'
<< "}" << '\n';
}
}
// max. and min. height of solution
Assert(patches.size() > 0, ExcNoPatches());
double hmin = patches[0].data(0, 0);
double hmax = patches[0].data(0, 0);
for (const auto &patch : patches)
{
const unsigned int n_subdivisions = patch.n_subdivisions;
Assert((patch.data.n_rows() == n_data_sets &&
!patch.points_are_available) ||
(patch.data.n_rows() == n_data_sets + spacedim &&
patch.points_are_available),
ExcDimensionMismatch(patch.points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patch.data.n_rows()));
Assert(patch.data.n_cols() ==
Utilities::fixed_power<dim>(n_subdivisions + 1),
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
for (unsigned int i = 0; i < n_subdivisions + 1; ++i)
for (unsigned int j = 0; j < n_subdivisions + 1; ++j)
{
const int dl = i * (n_subdivisions + 1) + j;
if (patch.data(0, dl) < hmin)
hmin = patch.data(0, dl);
if (patch.data(0, dl) > hmax)
hmax = patch.data(0, dl);
}
}
out << "#declare HMIN=" << hmin << ";" << '\n'
<< "#declare HMAX=" << hmax << ";" << '\n'
<< '\n';
if (!flags.external_data)
{
// texture with scaled niveau lines 10 lines in the surface
out << "#declare Tex=texture{" << '\n'
<< " pigment {" << '\n'
<< " gradient y" << '\n'
<< " scale y*(HMAX-HMIN)*" << 0.1 << '\n'
<< " color_map {" << '\n'
<< " [0.00 color Light_Purple] " << '\n'
<< " [0.95 color Light_Purple] " << '\n'
<< " [1.00 color White] " << '\n'
<< "} } }" << '\n'
<< '\n';
}
if (!flags.bicubic_patch)
{
// start of mesh header
out << '\n' << "mesh {" << '\n';
}
// loop over all patches
for (const auto &patch : patches)
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n = n_subdivisions + 1;
const unsigned int d1 = 1;
const unsigned int d2 = n;
Assert((patch.data.n_rows() == n_data_sets &&
!patch.points_are_available) ||
(patch.data.n_rows() == n_data_sets + spacedim &&
patch.points_are_available),
ExcDimensionMismatch(patch.points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patch.data.n_rows()));
Assert(patch.data.n_cols() == Utilities::fixed_power<dim>(n),
ExcInvalidDatasetSize(patch.data.n_cols(),
n_subdivisions + 1));
std::vector<Point<spacedim>> ver(n * n);
for (unsigned int i2 = 0; i2 < n; ++i2)
for (unsigned int i1 = 0; i1 < n; ++i1)
{
// compute coordinates for this patch point, storing in ver
ver[i1 * d1 + i2 * d2] =
get_equispaced_location(patch, {i1, i2}, n_subdivisions);
}
if (!flags.bicubic_patch)
{
// approximate normal vectors in patch
std::vector<Point<3>> nrml;
// only if smooth triangles are used
if (flags.smooth)
{
nrml.resize(n * n);
// These are difference quotients of the surface
// mapping. We take them symmetric inside the
// patch and one-sided at the edges
Point<3> h1, h2;
// Now compute normals in every point
for (unsigned int i = 0; i < n; ++i)
for (unsigned int j = 0; j < n; ++j)
{
const unsigned int il = (i == 0) ? i : (i - 1);
const unsigned int ir =
(i == n_subdivisions) ? i : (i + 1);
const unsigned int jl = (j == 0) ? j : (j - 1);
const unsigned int jr =
(j == n_subdivisions) ? j : (j + 1);
h1[0] =
ver[ir * d1 + j * d2][0] - ver[il * d1 + j * d2][0];
h1[1] = patch.data(0, ir * d1 + j * d2) -
patch.data(0, il * d1 + j * d2);
h1[2] =
ver[ir * d1 + j * d2][1] - ver[il * d1 + j * d2][1];
h2[0] =
ver[i * d1 + jr * d2][0] - ver[i * d1 + jl * d2][0];
h2[1] = patch.data(0, i * d1 + jr * d2) -
patch.data(0, i * d1 + jl * d2);
h2[2] =
ver[i * d1 + jr * d2][1] - ver[i * d1 + jl * d2][1];
nrml[i * d1 + j * d2][0] =
h1[1] * h2[2] - h1[2] * h2[1];
nrml[i * d1 + j * d2][1] =
h1[2] * h2[0] - h1[0] * h2[2];
nrml[i * d1 + j * d2][2] =
h1[0] * h2[1] - h1[1] * h2[0];
// normalize Vector
double norm = std::hypot(nrml[i * d1 + j * d2][0],
nrml[i * d1 + j * d2][1],
nrml[i * d1 + j * d2][2]);
if (nrml[i * d1 + j * d2][1] < 0)
norm *= -1.;
for (unsigned int k = 0; k < 3; ++k)
nrml[i * d1 + j * d2][k] /= norm;
}
}
// setting up triangles
for (unsigned int i = 0; i < n_subdivisions; ++i)
for (unsigned int j = 0; j < n_subdivisions; ++j)
{
// down/left vertex of triangle
const int dl = i * d1 + j * d2;
if (flags.smooth)
{
// writing smooth_triangles
// down/right triangle
out << "smooth_triangle {" << '\n'
<< "\t<" << ver[dl][0] << "," << patch.data(0, dl)
<< "," << ver[dl][1] << ">, <" << nrml[dl][0]
<< ", " << nrml[dl][1] << ", " << nrml[dl][2]
<< ">," << '\n';
out << " \t<" << ver[dl + d1][0] << ","
<< patch.data(0, dl + d1) << "," << ver[dl + d1][1]
<< ">, <" << nrml[dl + d1][0] << ", "
<< nrml[dl + d1][1] << ", " << nrml[dl + d1][2]
<< ">," << '\n';
out << "\t<" << ver[dl + d1 + d2][0] << ","
<< patch.data(0, dl + d1 + d2) << ","
<< ver[dl + d1 + d2][1] << ">, <"
<< nrml[dl + d1 + d2][0] << ", "
<< nrml[dl + d1 + d2][1] << ", "
<< nrml[dl + d1 + d2][2] << ">}" << '\n';
// upper/left triangle
out << "smooth_triangle {" << '\n'
<< "\t<" << ver[dl][0] << "," << patch.data(0, dl)
<< "," << ver[dl][1] << ">, <" << nrml[dl][0]
<< ", " << nrml[dl][1] << ", " << nrml[dl][2]
<< ">," << '\n';
out << "\t<" << ver[dl + d1 + d2][0] << ","
<< patch.data(0, dl + d1 + d2) << ","
<< ver[dl + d1 + d2][1] << ">, <"
<< nrml[dl + d1 + d2][0] << ", "
<< nrml[dl + d1 + d2][1] << ", "
<< nrml[dl + d1 + d2][2] << ">," << '\n';
out << "\t<" << ver[dl + d2][0] << ","
<< patch.data(0, dl + d2) << "," << ver[dl + d2][1]
<< ">, <" << nrml[dl + d2][0] << ", "
<< nrml[dl + d2][1] << ", " << nrml[dl + d2][2]
<< ">}" << '\n';
}
else
{
// writing standard triangles down/right triangle
out << "triangle {" << '\n'
<< "\t<" << ver[dl][0] << "," << patch.data(0, dl)
<< "," << ver[dl][1] << ">," << '\n';
out << "\t<" << ver[dl + d1][0] << ","
<< patch.data(0, dl + d1) << "," << ver[dl + d1][1]
<< ">," << '\n';
out << "\t<" << ver[dl + d1 + d2][0] << ","
<< patch.data(0, dl + d1 + d2) << ","
<< ver[dl + d1 + d2][1] << ">}" << '\n';
// upper/left triangle
out << "triangle {" << '\n'
<< "\t<" << ver[dl][0] << "," << patch.data(0, dl)
<< "," << ver[dl][1] << ">," << '\n';
out << "\t<" << ver[dl + d1 + d2][0] << ","
<< patch.data(0, dl + d1 + d2) << ","
<< ver[dl + d1 + d2][1] << ">," << '\n';
out << "\t<" << ver[dl + d2][0] << ","
<< patch.data(0, dl + d2) << "," << ver[dl + d2][1]
<< ">}" << '\n';
}
}
}
else
{
// writing bicubic_patch
Assert(n_subdivisions == 3,
ExcDimensionMismatch(n_subdivisions, 3));
out << '\n'
<< "bicubic_patch {" << '\n'
<< " type 0" << '\n'
<< " flatness 0" << '\n'
<< " u_steps 0" << '\n'
<< " v_steps 0" << '\n';
for (int i = 0; i < 16; ++i)
{
out << "\t<" << ver[i][0] << "," << patch.data(0, i) << ","
<< ver[i][1] << ">";
if (i != 15)
out << ",";
out << '\n';
}
out << " texture {Tex}" << '\n' << "}" << '\n';
}
}
if (!flags.bicubic_patch)
{
// the end of the mesh
out << " texture {Tex}" << '\n' << "}" << '\n' << '\n';
}
// make sure everything now gets to disk
out.flush();
AssertThrow(out.fail() == false, ExcIO());
}
} // namespace
template <int dim, int spacedim>
void
write_povray(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const PovrayFlags &flags,
std::ostream &out)
{
do_write_povray(patches, data_names, flags, out);
}
template <int dim, int spacedim>
void
write_eps(
const std::vector<Patch<dim, spacedim>> & /*patches*/,
const std::vector<std::string> & /*data_names*/,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const EpsFlags & /*flags*/,
std::ostream & /*out*/)
{
// not implemented, see the documentation of the function
AssertThrow(dim == 2, ExcNotImplemented());
}
template <int spacedim>
void
write_eps(
const std::vector<Patch<2, spacedim>> &patches,
const std::vector<std::string> & /*data_names*/,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const EpsFlags &flags,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
// set up an array of cells to be written later. this array holds the cells
// of all the patches as projected to the plane perpendicular to the line of
// sight.
//
// note that they are kept sorted by the set, where we chose the value of
// the center point of the cell along the line of sight as value for sorting
std::multiset<EpsCell2d> cells;
// two variables in which we will store the minimum and maximum values of
// the field to be used for colorization
float min_color_value = std::numeric_limits<float>::max();
float max_color_value = std::numeric_limits<float>::min();
// Array for z-coordinates of points. The elevation determined by a function
// if spacedim=2 or the z-coordinate of the grid point if spacedim=3
double heights[4] = {0, 0, 0, 0};
// compute the cells for output and enter them into the set above note that
// since dim==2, we have exactly four vertices per patch and per cell
for (const auto &patch : patches)
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n = n_subdivisions + 1;
const unsigned int d1 = 1;
const unsigned int d2 = n;
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
Point<spacedim> points[4];
points[0] =
get_equispaced_location(patch, {i1, i2}, n_subdivisions);
points[1] =
get_equispaced_location(patch, {i1 + 1, i2}, n_subdivisions);
points[2] =
get_equispaced_location(patch, {i1, i2 + 1}, n_subdivisions);
points[3] = get_equispaced_location(patch,
{i1 + 1, i2 + 1},
n_subdivisions);
switch (spacedim)
{
case 2:
Assert((flags.height_vector < patch.data.n_rows()) ||
patch.data.n_rows() == 0,
ExcIndexRange(flags.height_vector,
0,
patch.data.n_rows()));
heights[0] =
patch.data.n_rows() != 0 ?
patch.data(flags.height_vector, i1 * d1 + i2 * d2) *
flags.z_scaling :
0;
heights[1] = patch.data.n_rows() != 0 ?
patch.data(flags.height_vector,
(i1 + 1) * d1 + i2 * d2) *
flags.z_scaling :
0;
heights[2] = patch.data.n_rows() != 0 ?
patch.data(flags.height_vector,
i1 * d1 + (i2 + 1) * d2) *
flags.z_scaling :
0;
heights[3] = patch.data.n_rows() != 0 ?
patch.data(flags.height_vector,
(i1 + 1) * d1 + (i2 + 1) * d2) *
flags.z_scaling :
0;
break;
case 3:
// Copy z-coordinates into the height vector
for (unsigned int i = 0; i < 4; ++i)
heights[i] = points[i][2];
break;
default:
DEAL_II_NOT_IMPLEMENTED();
}
// now compute the projection of the bilinear cell given by the
// four vertices and their heights and write them to a proper cell
// object. note that we only need the first two components of the
// projected position for output, but we need the value along the
// line of sight for sorting the cells for back-to- front-output
//
// this computation was first written by Stefan Nauber. please
// no-one ask me why it works that way (or may be not), especially
// not about the angles and the sign of the height field, I don't
// know it.
EpsCell2d eps_cell;
const double pi = numbers::PI;
const double cx =
-std::cos(pi - flags.azimut_angle * 2 * pi / 360.),
cz = -std::cos(flags.turn_angle * 2 * pi / 360.),
sx =
std::sin(pi - flags.azimut_angle * 2 * pi / 360.),
sz = std::sin(flags.turn_angle * 2 * pi / 360.);
for (unsigned int vertex = 0; vertex < 4; ++vertex)
{
const double x = points[vertex][0], y = points[vertex][1],
z = -heights[vertex];
eps_cell.vertices[vertex][0] = -cz * x + sz * y;
eps_cell.vertices[vertex][1] =
-cx * sz * x - cx * cz * y - sx * z;
// ( 1 0 0 )
// D1 = ( 0 cx -sx )
// ( 0 sx cx )
// ( cy 0 sy )
// Dy = ( 0 1 0 )
// (-sy 0 cy )
// ( cz -sz 0 )
// Dz = ( sz cz 0 )
// ( 0 0 1 )
// ( cz -sz 0 )( 1 0 0 )(x) (
// cz*x-sz*(cx*y-sx*z)+0*(sx*y+cx*z) )
// Dxz = ( sz cz 0 )( 0 cx -sx )(y) = (
// sz*x+cz*(cx*y-sx*z)+0*(sx*y+cx*z) )
// ( 0 0 1 )( 0 sx cx )(z) ( 0*x+
// *(cx*y-sx*z)+1*(sx*y+cx*z) )
}
// compute coordinates of center of cell
const Point<spacedim> center_point =
(points[0] + points[1] + points[2] + points[3]) / 4;
const double center_height =
-(heights[0] + heights[1] + heights[2] + heights[3]) / 4;
// compute the depth into the picture
eps_cell.depth = -sx * sz * center_point[0] -
sx * cz * center_point[1] + cx * center_height;
if (flags.draw_cells && flags.shade_cells)
{
Assert((flags.color_vector < patch.data.n_rows()) ||
patch.data.n_rows() == 0,
ExcIndexRange(flags.color_vector,
0,
patch.data.n_rows()));
const double color_values[4] = {
patch.data.n_rows() != 0 ?
patch.data(flags.color_vector, i1 * d1 + i2 * d2) :
1,
patch.data.n_rows() != 0 ?
patch.data(flags.color_vector, (i1 + 1) * d1 + i2 * d2) :
1,
patch.data.n_rows() != 0 ?
patch.data(flags.color_vector, i1 * d1 + (i2 + 1) * d2) :
1,
patch.data.n_rows() != 0 ?
patch.data(flags.color_vector,
(i1 + 1) * d1 + (i2 + 1) * d2) :
1};
// set color value to average of the value at the vertices
eps_cell.color_value = (color_values[0] + color_values[1] +
color_values[3] + color_values[2]) /
4;
// update bounds of color field
min_color_value =
std::min(min_color_value, eps_cell.color_value);
max_color_value =
std::max(max_color_value, eps_cell.color_value);
}
// finally add this cell
cells.insert(eps_cell);
}
}
// find out minimum and maximum x and y coordinates to compute offsets and
// scaling factors
double x_min = cells.begin()->vertices[0][0];
double x_max = x_min;
double y_min = cells.begin()->vertices[0][1];
double y_max = y_min;
for (const auto &cell : cells)
for (const auto &vertex : cell.vertices)
{
x_min = std::min(x_min, vertex[0]);
x_max = std::max(x_max, vertex[0]);
y_min = std::min(y_min, vertex[1]);
y_max = std::max(y_max, vertex[1]);
}
// scale in x-direction such that in the output 0 <= x <= 300. don't scale
// in y-direction to preserve the shape of the triangulation
const double scale =
(flags.size /
(flags.size_type == EpsFlags::width ? x_max - x_min : y_min - y_max));
const Point<2> offset(x_min, y_min);
// now write preamble
{
out << "%!PS-Adobe-2.0 EPSF-1.2" << '\n'
<< "%%Title: deal.II Output" << '\n'
<< "%%Creator: the deal.II library" << '\n'
<< "%%Creation Date: " << Utilities::System::get_date() << " - "
<< Utilities::System::get_time() << '\n'
<< "%%BoundingBox: "
// lower left corner
<< "0 0 "
// upper right corner
<< static_cast<unsigned int>((x_max - x_min) * scale + 0.5) << ' '
<< static_cast<unsigned int>((y_max - y_min) * scale + 0.5) << '\n';
// define some abbreviations to keep the output small:
// m=move turtle to
// l=define a line
// s=set rgb color
// sg=set gray value
// lx=close the line and plot the line
// lf=close the line and fill the interior
out << "/m {moveto} bind def" << '\n'
<< "/l {lineto} bind def" << '\n'
<< "/s {setrgbcolor} bind def" << '\n'
<< "/sg {setgray} bind def" << '\n'
<< "/lx {lineto closepath stroke} bind def" << '\n'
<< "/lf {lineto closepath fill} bind def" << '\n';
out << "%%EndProlog" << '\n' << '\n';
// set fine lines
out << flags.line_width << " setlinewidth" << '\n';
}
// check if min and max values for the color are actually different. If
// that is not the case (such things happen, for example, in the very first
// time step of a time dependent problem, if the initial values are zero),
// all values are equal, and then we can draw everything in an arbitrary
// color. Thus, change one of the two values arbitrarily
if (max_color_value == min_color_value)
max_color_value = min_color_value + 1;
// now we've got all the information we need. write the cells. note: due to
// the ordering, we traverse the list of cells back-to-front
for (const auto &cell : cells)
{
if (flags.draw_cells)
{
if (flags.shade_cells)
{
const EpsFlags::RgbValues rgb_values =
(*flags.color_function)(cell.color_value,
min_color_value,
max_color_value);
// write out color
if (rgb_values.is_grey())
out << rgb_values.red << " sg ";
else
out << rgb_values.red << ' ' << rgb_values.green << ' '
<< rgb_values.blue << " s ";
}
else
out << "1 sg ";
out << (cell.vertices[0] - offset) * scale << " m "
<< (cell.vertices[1] - offset) * scale << " l "
<< (cell.vertices[3] - offset) * scale << " l "
<< (cell.vertices[2] - offset) * scale << " lf" << '\n';
}
if (flags.draw_mesh)
out << "0 sg " // draw lines in black
<< (cell.vertices[0] - offset) * scale << " m "
<< (cell.vertices[1] - offset) * scale << " l "
<< (cell.vertices[3] - offset) * scale << " l "
<< (cell.vertices[2] - offset) * scale << " lx" << '\n';
}
out << "showpage" << '\n';
out.flush();
AssertThrow(out.fail() == false, ExcIO());
}
template <int dim, int spacedim>
void
write_gmv(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const GmvFlags &flags,
std::ostream &out)
{
// The gmv format does not support cells that only consist of a single
// point. It does support the output of point data using the keyword
// 'tracers' instead of 'nodes' and 'cells', but this output format is
// currently not implemented.
AssertThrow(dim > 0, ExcNotImplemented());
Assert(dim <= 3, ExcNotImplemented());
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
GmvStream gmv_out(out, flags);
const unsigned int n_data_sets = data_names.size();
// check against # of data sets in first patch. checks against all other
// patches are made in write_gmv_reorder_data_vectors
Assert((patches[0].data.n_rows() == n_data_sets &&
!patches[0].points_are_available) ||
(patches[0].data.n_rows() == n_data_sets + spacedim &&
patches[0].points_are_available),
ExcDimensionMismatch(patches[0].points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patches[0].data.n_rows()));
//---------------------
// preamble
out << "gmvinput ascii" << '\n' << '\n';
// first count the number of cells and cells for later use
unsigned int n_nodes;
unsigned int n_cells;
std::tie(n_nodes, n_cells) = count_nodes_and_cells(patches);
// For the format we write here, we need to write all node values relating
// to one variable at a time. We could in principle do this by looping
// over all patches and extracting the values corresponding to the one
// variable we're dealing with right now, and then start the process over
// for the next variable with another loop over all patches.
//
// An easier way is to create a global table that for each variable
// lists all values. This copying of data vectors can be done in the
// background while we're already working on vertices and cells,
// so do this on a separate task and when wanting to write out the
// data, we wait for that task to finish.
Threads::Task<std::unique_ptr<Table<2, double>>>
create_global_data_table_task = Threads::new_task(
[&patches]() { return create_global_data_table(patches); });
//-----------------------------
// first make up a list of used vertices along with their coordinates
//
// note that we have to print 3 dimensions
out << "nodes " << n_nodes << '\n';
for (unsigned int d = 0; d < spacedim; ++d)
{
gmv_out.selected_component = d;
write_nodes(patches, gmv_out);
out << '\n';
}
gmv_out.selected_component = numbers::invalid_unsigned_int;
for (unsigned int d = spacedim; d < 3; ++d)
{
for (unsigned int i = 0; i < n_nodes; ++i)
out << "0 ";
out << '\n';
}
//-------------------------------
// now for the cells. note that vertices are counted from 1 onwards
out << "cells " << n_cells << '\n';
write_cells(patches, gmv_out);
//-------------------------------------
// data output.
out << "variable" << '\n';
// Wait for the reordering to be done and retrieve the reordered data:
const Table<2, double> data_vectors =
std::move(*create_global_data_table_task.return_value());
// then write data. the '1' means: node data (as opposed to cell data, which
// we do not support explicitly here)
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
{
out << data_names[data_set] << " 1" << '\n';
std::copy(data_vectors[data_set].begin(),
data_vectors[data_set].end(),
std::ostream_iterator<double>(out, " "));
out << '\n' << '\n';
}
// end of variable section
out << "endvars" << '\n';
// end of output
out << "endgmv" << '\n';
// make sure everything now gets to disk
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
template <int dim, int spacedim>
void
write_tecplot(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const TecplotFlags &flags,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
// The FEBLOCK or FEPOINT formats of tecplot only allows full elements (e.g.
// triangles), not single points. Other tecplot format allow point output,
// but they are currently not implemented.
AssertThrow(dim > 0, ExcNotImplemented());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
TecplotStream tecplot_out(out, flags);
const unsigned int n_data_sets = data_names.size();
// check against # of data sets in first patch. checks against all other
// patches are made in write_gmv_reorder_data_vectors
Assert((patches[0].data.n_rows() == n_data_sets &&
!patches[0].points_are_available) ||
(patches[0].data.n_rows() == n_data_sets + spacedim &&
patches[0].points_are_available),
ExcDimensionMismatch(patches[0].points_are_available ?
(n_data_sets + spacedim) :
n_data_sets,
patches[0].data.n_rows()));
// first count the number of cells and cells for later use
unsigned int n_nodes;
unsigned int n_cells;
std::tie(n_nodes, n_cells) = count_nodes_and_cells(patches);
//---------
// preamble
{
out
<< "# This file was generated by the deal.II library." << '\n'
<< "# Date = " << Utilities::System::get_date() << '\n'
<< "# Time = " << Utilities::System::get_time() << '\n'
<< "#" << '\n'
<< "# For a description of the Tecplot format see the Tecplot documentation."
<< '\n'
<< "#" << '\n';
out << "Variables=";
switch (spacedim)
{
case 1:
out << "\"x\"";
break;
case 2:
out << "\"x\", \"y\"";
break;
case 3:
out << "\"x\", \"y\", \"z\"";
break;
default:
DEAL_II_NOT_IMPLEMENTED();
}
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
out << ", \"" << data_names[data_set] << "\"";
out << '\n';
out << "zone ";
if (flags.zone_name)
out << "t=\"" << flags.zone_name << "\" ";
if (flags.solution_time >= 0.0)
out << "strandid=1, solutiontime=" << flags.solution_time << ", ";
out << "f=feblock, n=" << n_nodes << ", e=" << n_cells
<< ", et=" << tecplot_cell_type[dim] << '\n';
}
// For the format we write here, we need to write all node values relating
// to one variable at a time. We could in principle do this by looping
// over all patches and extracting the values corresponding to the one
// variable we're dealing with right now, and then start the process over
// for the next variable with another loop over all patches.
//
// An easier way is to create a global table that for each variable
// lists all values. This copying of data vectors can be done in the
// background while we're already working on vertices and cells,
// so do this on a separate task and when wanting to write out the
// data, we wait for that task to finish.
Threads::Task<std::unique_ptr<Table<2, double>>>
create_global_data_table_task = Threads::new_task(
[&patches]() { return create_global_data_table(patches); });
//-----------------------------
// first make up a list of used vertices along with their coordinates
for (unsigned int d = 0; d < spacedim; ++d)
{
tecplot_out.selected_component = d;
write_nodes(patches, tecplot_out);
out << '\n';
}
//-------------------------------------
// data output.
//
// Wait for the reordering to be done and retrieve the reordered data:
const Table<2, double> data_vectors =
std::move(*create_global_data_table_task.return_value());
// then write data.
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
{
std::copy(data_vectors[data_set].begin(),
data_vectors[data_set].end(),
std::ostream_iterator<double>(out, "\n"));
out << '\n';
}
write_cells(patches, tecplot_out);
// make sure everything now gets to disk
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
template <int dim, int spacedim>
void
write_vtk(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
const VtkFlags &flags,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
VtkStream vtk_out(out, flags);
const unsigned int n_data_sets = data_names.size();
// check against # of data sets in first patch.
if (patches[0].points_are_available)
{
AssertDimension(n_data_sets + spacedim, patches[0].data.n_rows());
}
else
{
AssertDimension(n_data_sets, patches[0].data.n_rows());
}
//---------------------
// preamble
{
out << "# vtk DataFile Version 3.0" << '\n'
<< "#This file was generated by the deal.II library";
if (flags.print_date_and_time)
{
out << " on " << Utilities::System::get_date() << " at "
<< Utilities::System::get_time();
}
else
out << '.';
out << '\n' << "ASCII" << '\n';
// now output the data header
out << "DATASET UNSTRUCTURED_GRID\n" << '\n';
}
// if desired, output time and cycle of the simulation, following the
// instructions at
// http://www.visitusers.org/index.php?title=Time_and_Cycle_in_VTK_files
{
const unsigned int n_metadata =
((flags.cycle != std::numeric_limits<unsigned int>::min() ? 1 : 0) +
(flags.time != std::numeric_limits<double>::min() ? 1 : 0));
if (n_metadata > 0)
{
out << "FIELD FieldData " << n_metadata << '\n';
if (flags.cycle != std::numeric_limits<unsigned int>::min())
{
out << "CYCLE 1 1 int\n" << flags.cycle << '\n';
}
if (flags.time != std::numeric_limits<double>::min())
{
out << "TIME 1 1 double\n" << flags.time << '\n';
}
}
}
// first count the number of cells and cells for later use
unsigned int n_nodes;
unsigned int n_cells;
unsigned int n_points_and_n_cells;
std::tie(n_nodes, n_cells, n_points_and_n_cells) =
count_nodes_and_cells_and_points(patches, flags.write_higher_order_cells);
// For the format we write here, we need to write all node values relating
// to one variable at a time. We could in principle do this by looping
// over all patches and extracting the values corresponding to the one
// variable we're dealing with right now, and then start the process over
// for the next variable with another loop over all patches.
//
// An easier way is to create a global table that for each variable
// lists all values. This copying of data vectors can be done in the
// background while we're already working on vertices and cells,
// so do this on a separate task and when wanting to write out the
// data, we wait for that task to finish.
Threads::Task<std::unique_ptr<Table<2, double>>>
create_global_data_table_task = Threads::new_task(
[&patches]() { return create_global_data_table(patches); });
//-----------------------------
// first make up a list of used vertices along with their coordinates
//
// note that we have to print d=1..3 dimensions
out << "POINTS " << n_nodes << " double" << '\n';
write_nodes(patches, vtk_out);
out << '\n';
//-------------------------------
// now for the cells
out << "CELLS " << n_cells << ' ' << n_points_and_n_cells << '\n';
if (flags.write_higher_order_cells)
write_high_order_cells(patches, vtk_out, /* legacy_format = */ true);
else
write_cells(patches, vtk_out);
out << '\n';
// next output the types of the cells. since all cells are the same, this is
// simple
out << "CELL_TYPES " << n_cells << '\n';
// need to distinguish between linear cells, simplex cells (linear or
// quadratic), and high order cells
for (const auto &patch : patches)
{
const auto vtk_cell_id =
extract_vtk_patch_info(patch, flags.write_higher_order_cells);
for (unsigned int i = 0; i < vtk_cell_id[1]; ++i)
out << ' ' << vtk_cell_id[0];
}
out << '\n';
//-------------------------------------
// data output.
// Wait for the reordering to be done and retrieve the reordered data:
const Table<2, double> data_vectors =
std::move(*create_global_data_table_task.return_value());
// then write data. the 'POINT_DATA' means: node data (as opposed to cell
// data, which we do not support explicitly here). all following data sets
// are point data
out << "POINT_DATA " << n_nodes << '\n';
// when writing, first write out all vector data, then handle the scalar
// data sets that have been left over
std::vector<bool> data_set_written(n_data_sets, false);
for (const auto &nonscalar_data_range : nonscalar_data_ranges)
{
AssertThrow(std::get<3>(nonscalar_data_range) !=
DataComponentInterpretation::component_is_part_of_tensor,
ExcMessage(
"The VTK writer does not currently support outputting "
"tensor data. Use the VTU writer instead."));
AssertThrow(std::get<1>(nonscalar_data_range) >=
std::get<0>(nonscalar_data_range),
ExcLowerRange(std::get<1>(nonscalar_data_range),
std::get<0>(nonscalar_data_range)));
AssertThrow(std::get<1>(nonscalar_data_range) < n_data_sets,
ExcIndexRange(std::get<1>(nonscalar_data_range),
0,
n_data_sets));
AssertThrow(std::get<1>(nonscalar_data_range) + 1 -
std::get<0>(nonscalar_data_range) <=
3,
ExcMessage(
"Can't declare a vector with more than 3 components "
"in VTK"));
// mark these components as already written:
for (unsigned int i = std::get<0>(nonscalar_data_range);
i <= std::get<1>(nonscalar_data_range);
++i)
data_set_written[i] = true;
// write the header. concatenate all the component names with double
// underscores unless a vector name has been specified
out << "VECTORS ";
if (!std::get<2>(nonscalar_data_range).empty())
out << std::get<2>(nonscalar_data_range);
else
{
for (unsigned int i = std::get<0>(nonscalar_data_range);
i < std::get<1>(nonscalar_data_range);
++i)
out << data_names[i] << "__";
out << data_names[std::get<1>(nonscalar_data_range)];
}
out << " double" << '\n';
// now write data. pad all vectors to have three components
for (unsigned int n = 0; n < n_nodes; ++n)
{
switch (std::get<1>(nonscalar_data_range) -
std::get<0>(nonscalar_data_range))
{
case 0:
out << data_vectors(std::get<0>(nonscalar_data_range), n)
<< " 0 0" << '\n';
break;
case 1:
out << data_vectors(std::get<0>(nonscalar_data_range), n)
<< ' '
<< data_vectors(std::get<0>(nonscalar_data_range) + 1, n)
<< " 0" << '\n';
break;
case 2:
out << data_vectors(std::get<0>(nonscalar_data_range), n)
<< ' '
<< data_vectors(std::get<0>(nonscalar_data_range) + 1, n)
<< ' '
<< data_vectors(std::get<0>(nonscalar_data_range) + 2, n)
<< '\n';
break;
default:
// VTK doesn't support anything else than vectors with 1, 2,
// or 3 components
DEAL_II_ASSERT_UNREACHABLE();
}
}
}
// now do the left over scalar data sets
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
if (data_set_written[data_set] == false)
{
out << "SCALARS " << data_names[data_set] << " double 1" << '\n'
<< "LOOKUP_TABLE default" << '\n';
std::copy(data_vectors[data_set].begin(),
data_vectors[data_set].end(),
std::ostream_iterator<double>(out, " "));
out << '\n';
}
// make sure everything now gets to disk
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
void
write_vtu_header(std::ostream &out, const VtkFlags &flags)
{
AssertThrow(out.fail() == false, ExcIO());
out << "<?xml version=\"1.0\" ?> \n";
out << "<!-- \n";
out << "# vtk DataFile Version 3.0" << '\n'
<< "#This file was generated by the deal.II library";
if (flags.print_date_and_time)
{
out << " on " << Utilities::System::get_time() << " at "
<< Utilities::System::get_date();
}
else
out << '.';
out << "\n-->\n";
if (flags.write_higher_order_cells)
out << "<VTKFile type=\"UnstructuredGrid\" version=\"2.2\"";
else
out << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\"";
if (deal_ii_with_zlib &&
(flags.compression_level != CompressionLevel::plain_text))
out << " compressor=\"vtkZLibDataCompressor\"";
#ifdef DEAL_II_WORDS_BIGENDIAN
out << " byte_order=\"BigEndian\"";
#else
out << " byte_order=\"LittleEndian\"";
#endif
out << ">";
out << '\n';
out << "<UnstructuredGrid>";
out << '\n';
}
void
write_vtu_footer(std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
out << " </UnstructuredGrid>\n";
out << "</VTKFile>\n";
}
template <int dim, int spacedim>
void
write_vtu(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
const VtkFlags &flags,
std::ostream &out)
{
write_vtu_header(out, flags);
write_vtu_main(patches, data_names, nonscalar_data_ranges, flags, out);
write_vtu_footer(out);
out << std::flush;
}
template <int dim, int spacedim>
void
write_vtu_main(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
const VtkFlags &flags,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
// If the user provided physical units, make sure that they don't contain
// quote characters as this would make the VTU file invalid XML and
// probably lead to all sorts of difficult error messages. Other than that,
// trust the user that whatever they provide makes sense somehow.
for (const auto &unit : flags.physical_units)
{
(void)unit;
Assert(
unit.second.find('\"') == std::string::npos,
ExcMessage(
"A physical unit you provided, <" + unit.second +
">, contained a quotation mark character. This is not allowed."));
}
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the
// times, people just forget to call build_patches when there are no
// patches, so a warning is in order. that said, the assertion is disabled
// if we support MPI since then it can happen that on the coarsest mesh, a
// processor simply has no cells it actually owns, and in that case it is
// legit if there are no patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
{
// we still need to output a valid vtu file, because other CPUs might
// output data. This is the minimal file that is accepted by paraview
// and visit. if we remove the field definitions, visit is complaining.
out << "<Piece NumberOfPoints=\"0\" NumberOfCells=\"0\" >\n"
<< "<Cells>\n"
<< "<DataArray type=\"UInt8\" Name=\"types\"></DataArray>\n"
<< "</Cells>\n"
<< " <PointData Scalars=\"scalars\">\n";
std::vector<bool> data_set_written(data_names.size(), false);
for (const auto &nonscalar_data_range : nonscalar_data_ranges)
{
// mark these components as already written:
for (unsigned int i = std::get<0>(nonscalar_data_range);
i <= std::get<1>(nonscalar_data_range);
++i)
data_set_written[i] = true;
// write the header. concatenate all the component names with double
// underscores unless a vector name has been specified
out << " <DataArray type=\"Float32\" Name=\"";
if (!std::get<2>(nonscalar_data_range).empty())
out << std::get<2>(nonscalar_data_range);
else
{
for (unsigned int i = std::get<0>(nonscalar_data_range);
i < std::get<1>(nonscalar_data_range);
++i)
out << data_names[i] << "__";
out << data_names[std::get<1>(nonscalar_data_range)];
}
out << "\" NumberOfComponents=\"3\"></DataArray>\n";
}
for (unsigned int data_set = 0; data_set < data_names.size();
++data_set)
if (data_set_written[data_set] == false)
{
out << " <DataArray type=\"Float32\" Name=\""
<< data_names[data_set] << "\"></DataArray>\n";
}
out << " </PointData>\n";
out << "</Piece>\n";
out << std::flush;
return;
}
#endif
// first up: metadata
//
// if desired, output time and cycle of the simulation, following the
// instructions at
// http://www.visitusers.org/index.php?title=Time_and_Cycle_in_VTK_files
{
const unsigned int n_metadata =
((flags.cycle != std::numeric_limits<unsigned int>::min() ? 1 : 0) +
(flags.time != std::numeric_limits<double>::min() ? 1 : 0));
if (n_metadata > 0)
out << "<FieldData>\n";
if (flags.cycle != std::numeric_limits<unsigned int>::min())
{
out
<< "<DataArray type=\"Float32\" Name=\"CYCLE\" NumberOfTuples=\"1\" format=\"ascii\">"
<< flags.cycle << "</DataArray>\n";
}
if (flags.time != std::numeric_limits<double>::min())
{
out
<< "<DataArray type=\"Float32\" Name=\"TIME\" NumberOfTuples=\"1\" format=\"ascii\">"
<< flags.time << "</DataArray>\n";
}
if (n_metadata > 0)
out << "</FieldData>\n";
}
const unsigned int n_data_sets = data_names.size();
// check against # of data sets in first patch. checks against all other
// patches are made in write_gmv_reorder_data_vectors
if (patches[0].points_are_available)
{
AssertDimension(n_data_sets + spacedim, patches[0].data.n_rows());
}
else
{
AssertDimension(n_data_sets, patches[0].data.n_rows());
}
const char *ascii_or_binary =
(deal_ii_with_zlib &&
(flags.compression_level != CompressionLevel::plain_text)) ?
"binary" :
"ascii";
// first count the number of cells and cells for later use
unsigned int n_nodes;
unsigned int n_cells;
std::tie(n_nodes, n_cells, std::ignore) =
count_nodes_and_cells_and_points(patches, flags.write_higher_order_cells);
// -----------------
// In the following, let us first set up a number of lambda functions that
// will be used in building the different parts of the VTU file. We will
// later call them in turn on different tasks.
// first make up a list of used vertices along with their coordinates
const auto stringize_vertex_information = [&patches,
&flags,
output_precision =
out.precision(),
ascii_or_binary]() {
std::ostringstream o;
o << " <Points>\n";
o << " <DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\""
<< ascii_or_binary << "\">\n";
const std::vector<Point<spacedim>> node_positions =
get_node_positions(patches);
// VTK/VTU always wants to see three coordinates, even if we are
// in 1d or 2d. So pad node positions with zeros as appropriate.
std::vector<float> node_coordinates_3d;
node_coordinates_3d.reserve(node_positions.size() * 3);
for (const auto &node_position : node_positions)
{
for (unsigned int d = 0; d < 3; ++d)
if (d < spacedim)
node_coordinates_3d.emplace_back(node_position[d]);
else
node_coordinates_3d.emplace_back(0.0f);
}
o << vtu_stringize_array(node_coordinates_3d,
flags.compression_level,
output_precision)
<< '\n';
o << " </DataArray>\n";
o << " </Points>\n\n";
return o.str();
};
//-------------------------------
// Now for the cells. The first part of this is how vertices
// build cells.
const auto stringize_cell_to_vertex_information = [&patches,
&flags,
ascii_or_binary,
output_precision =
out.precision()]() {
std::ostringstream o;
o << " <Cells>\n";
o << " <DataArray type=\"Int32\" Name=\"connectivity\" format=\""
<< ascii_or_binary << "\">\n";
std::vector<std::int32_t> cells;
Assert(dim <= 3, ExcNotImplemented());
unsigned int first_vertex_of_patch = 0;
for (const auto &patch : patches)
{
// First treat a slight oddball case: For triangles and tetrahedra,
// the case with n_subdivisions==2 is treated as if the cell was
// output as a single, quadratic, cell rather than as one would
// expect as 4 sub-cells (for triangles; and the corresponding
// number of sub-cells for tetrahedra). This is courtesy of some
// special-casing in the function extract_vtk_patch_info().
if ((dim >= 2) &&
(patch.reference_cell == ReferenceCells::get_simplex<dim>()) &&
(patch.n_subdivisions == 2))
{
const unsigned int n_points = patch.data.n_cols();
Assert((dim == 2 && n_points == 6) ||
(dim == 3 && n_points == 10),
ExcInternalError());
if (deal_ii_with_zlib &&
(flags.compression_level !=
DataOutBase::CompressionLevel::plain_text))
{
for (unsigned int i = 0; i < n_points; ++i)
cells.push_back(first_vertex_of_patch + i);
}
else
{
for (unsigned int i = 0; i < n_points; ++i)
o << '\t' << first_vertex_of_patch + i;
o << '\n';
}
first_vertex_of_patch += n_points;
}
// Then treat all of the other non-hypercube cases since they can
// currently not be subdivided (into sub-cells, or into higher-order
// cells):
else if (patch.reference_cell != ReferenceCells::get_hypercube<dim>())
{
Assert(patch.n_subdivisions == 1, ExcNotImplemented());
const unsigned int n_points = patch.data.n_cols();
if (deal_ii_with_zlib &&
(flags.compression_level !=
DataOutBase::CompressionLevel::plain_text))
{
for (unsigned int i = 0; i < n_points; ++i)
cells.push_back(
first_vertex_of_patch +
patch.reference_cell.vtk_vertex_to_deal_vertex(i));
}
else
{
for (unsigned int i = 0; i < n_points; ++i)
o << '\t'
<< (first_vertex_of_patch +
patch.reference_cell.vtk_vertex_to_deal_vertex(i));
o << '\n';
}
first_vertex_of_patch += n_points;
}
else // a hypercube cell
{
const unsigned int n_subdivisions = patch.n_subdivisions;
const unsigned int n_points_per_direction = n_subdivisions + 1;
std::vector<unsigned> local_vertex_order;
// Output the current state of the local_vertex_order array,
// then clear it:
const auto flush_current_cell = [&flags,
&o,
&cells,
first_vertex_of_patch,
&local_vertex_order]() {
if (deal_ii_with_zlib &&
(flags.compression_level !=
DataOutBase::CompressionLevel::plain_text))
{
for (const auto &c : local_vertex_order)
cells.push_back(first_vertex_of_patch + c);
}
else
{
for (const auto &c : local_vertex_order)
o << '\t' << first_vertex_of_patch + c;
o << '\n';
}
local_vertex_order.clear();
};
if (flags.write_higher_order_cells == false)
{
local_vertex_order.reserve(Utilities::fixed_power<dim>(2));
switch (dim)
{
case 0:
{
local_vertex_order.emplace_back(0);
flush_current_cell();
break;
}
case 1:
{
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const unsigned int starting_offset = i1;
local_vertex_order.emplace_back(starting_offset);
local_vertex_order.emplace_back(starting_offset +
1);
flush_current_cell();
}
break;
}
case 2:
{
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const unsigned int starting_offset =
i2 * n_points_per_direction + i1;
local_vertex_order.emplace_back(
starting_offset);
local_vertex_order.emplace_back(
starting_offset + 1);
local_vertex_order.emplace_back(
starting_offset + n_points_per_direction + 1);
local_vertex_order.emplace_back(
starting_offset + n_points_per_direction);
flush_current_cell();
}
break;
}
case 3:
{
for (unsigned int i3 = 0; i3 < n_subdivisions; ++i3)
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions;
++i1)
{
const unsigned int starting_offset =
i3 * n_points_per_direction *
n_points_per_direction +
i2 * n_points_per_direction + i1;
local_vertex_order.emplace_back(
starting_offset);
local_vertex_order.emplace_back(
starting_offset + 1);
local_vertex_order.emplace_back(
starting_offset + n_points_per_direction +
1);
local_vertex_order.emplace_back(
starting_offset + n_points_per_direction);
local_vertex_order.emplace_back(
starting_offset + n_points_per_direction *
n_points_per_direction);
local_vertex_order.emplace_back(
starting_offset +
n_points_per_direction *
n_points_per_direction +
1);
local_vertex_order.emplace_back(
starting_offset +
n_points_per_direction *
n_points_per_direction +
n_points_per_direction + 1);
local_vertex_order.emplace_back(
starting_offset +
n_points_per_direction *
n_points_per_direction +
n_points_per_direction);
flush_current_cell();
}
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
}
else // use higher-order output
{
local_vertex_order.resize(
Utilities::fixed_power<dim>(n_points_per_direction));
switch (dim)
{
case 0:
{
Assert(false,
ExcMessage(
"Point-like cells should not be possible "
"when writing higher-order cells."));
break;
}
case 1:
{
for (unsigned int i1 = 0; i1 < n_subdivisions + 1;
++i1)
{
const unsigned int local_index = i1;
const unsigned int connectivity_index =
patch.reference_cell
.template vtk_lexicographic_to_node_index<1>(
{{i1}},
{{n_subdivisions}},
/* use VTU, not VTK: */ false);
local_vertex_order[connectivity_index] =
local_index;
}
flush_current_cell();
break;
}
case 2:
{
for (unsigned int i2 = 0; i2 < n_subdivisions + 1;
++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions + 1;
++i1)
{
const unsigned int local_index =
i2 * n_points_per_direction + i1;
const unsigned int connectivity_index =
patch.reference_cell
.template vtk_lexicographic_to_node_index<
2>({{i1, i2}},
{{n_subdivisions, n_subdivisions}},
/* use VTU, not VTK: */ false);
local_vertex_order[connectivity_index] =
local_index;
}
flush_current_cell();
break;
}
case 3:
{
for (unsigned int i3 = 0; i3 < n_subdivisions + 1;
++i3)
for (unsigned int i2 = 0; i2 < n_subdivisions + 1;
++i2)
for (unsigned int i1 = 0; i1 < n_subdivisions + 1;
++i1)
{
const unsigned int local_index =
i3 * n_points_per_direction *
n_points_per_direction +
i2 * n_points_per_direction + i1;
const unsigned int connectivity_index =
patch.reference_cell
.template vtk_lexicographic_to_node_index<
3>({{i1, i2, i3}},
{{n_subdivisions,
n_subdivisions,
n_subdivisions}},
/* use VTU, not VTK: */ false);
local_vertex_order[connectivity_index] =
local_index;
}
flush_current_cell();
break;
}
default:
DEAL_II_NOT_IMPLEMENTED();
}
}
// Finally update the number of the first vertex of this
// patch
first_vertex_of_patch +=
Utilities::fixed_power<dim>(patch.n_subdivisions + 1);
}
}
// Flush the 'cells' object we created herein.
if (deal_ii_with_zlib && (flags.compression_level !=
DataOutBase::CompressionLevel::plain_text))
{
o << vtu_stringize_array(cells,
flags.compression_level,
output_precision)
<< '\n';
}
o << " </DataArray>\n";
return o.str();
};
//-------------------------------
// The second part of cell information is the offsets in
// the array built by the previous lambda function that indicate
// individual cells.
//
// Note that this separates XML VTU format from the VTK format; the latter
// puts the number of nodes per cell in front of the connectivity list for
// each cell, whereas the VTU format uses one large list of vertex indices
// and a separate array of offsets.
//
// The third piece to cell information is that we need to
// output the types of the cells.
//
// The following function does both of these pieces.
const auto stringize_cell_offset_and_type_information =
[&patches,
&flags,
ascii_or_binary,
n_cells,
output_precision = out.precision()]() {
std::ostringstream o;
o << " <DataArray type=\"Int32\" Name=\"offsets\" format=\""
<< ascii_or_binary << "\">\n";
std::vector<std::int32_t> offsets;
offsets.reserve(n_cells);
// std::uint8_t might be an alias to unsigned char which is then not
// printed as ascii integers
std::vector<unsigned int> cell_types;
cell_types.reserve(n_cells);
unsigned int first_vertex_of_patch = 0;
for (const auto &patch : patches)
{
const auto vtk_cell_id =
extract_vtk_patch_info(patch, flags.write_higher_order_cells);
for (unsigned int i = 0; i < vtk_cell_id[1]; ++i)
{
cell_types.push_back(vtk_cell_id[0]);
first_vertex_of_patch += vtk_cell_id[2];
offsets.push_back(first_vertex_of_patch);
}
}
o << vtu_stringize_array(offsets,
flags.compression_level,
output_precision);
o << '\n';
o << " </DataArray>\n";
o << " <DataArray type=\"UInt8\" Name=\"types\" format=\""
<< ascii_or_binary << "\">\n";
if (deal_ii_with_zlib &&
(flags.compression_level != CompressionLevel::plain_text))
{
std::vector<std::uint8_t> cell_types_uint8_t(cell_types.size());
for (unsigned int i = 0; i < cell_types.size(); ++i)
cell_types_uint8_t[i] = static_cast<std::uint8_t>(cell_types[i]);
o << vtu_stringize_array(cell_types_uint8_t,
flags.compression_level,
output_precision);
}
else
{
o << vtu_stringize_array(cell_types,
flags.compression_level,
output_precision);
}
o << '\n';
o << " </DataArray>\n";
o << " </Cells>\n";
return o.str();
};
//-------------------------------------
// data output.
const auto stringize_nonscalar_data_range =
[&flags,
&data_names,
ascii_or_binary,
n_data_sets,
n_nodes,
output_precision = out.precision()](const Table<2, float> &data_vectors,
const auto &range) {
std::ostringstream o;
const auto first_component = std::get<0>(range);
const auto last_component = std::get<1>(range);
const auto &name = std::get<2>(range);
const bool is_tensor =
(std::get<3>(range) ==
DataComponentInterpretation::component_is_part_of_tensor);
const unsigned int n_components = (is_tensor ? 9 : 3);
AssertThrow(last_component >= first_component,
ExcLowerRange(last_component, first_component));
AssertThrow(last_component < n_data_sets,
ExcIndexRange(last_component, 0, n_data_sets));
if (is_tensor)
{
AssertThrow((last_component + 1 - first_component <= 9),
ExcMessage(
"Can't declare a tensor with more than 9 components "
"in VTK/VTU format."));
}
else
{
AssertThrow((last_component + 1 - first_component <= 3),
ExcMessage(
"Can't declare a vector with more than 3 components "
"in VTK/VTU format."));
}
// write the header. concatenate all the component names with double
// underscores unless a vector name has been specified
o << " <DataArray type=\"Float32\" Name=\"";
if (!name.empty())
o << name;
else
{
for (unsigned int i = first_component; i < last_component; ++i)
o << data_names[i] << "__";
o << data_names[last_component];
}
o << "\" NumberOfComponents=\"" << n_components << "\" format=\""
<< ascii_or_binary << "\"";
// If present, also list the physical units for this quantity. Look
// this up for either the name of the whole vector/tensor, or if that
// isn't listed, via its first component.
if (!name.empty())
{
if (flags.physical_units.find(name) != flags.physical_units.end())
o << " units=\"" << flags.physical_units.at(name) << "\"";
}
else
{
if (flags.physical_units.find(data_names[first_component]) !=
flags.physical_units.end())
o << " units=\""
<< flags.physical_units.at(data_names[first_component]) << "\"";
}
o << ">\n";
// now write data. pad all vectors to have three components
std::vector<float> data;
data.reserve(n_nodes * n_components);
for (unsigned int n = 0; n < n_nodes; ++n)
{
if (!is_tensor)
{
switch (last_component - first_component)
{
case 0:
data.push_back(data_vectors(first_component, n));
data.push_back(0);
data.push_back(0);
break;
case 1:
data.push_back(data_vectors(first_component, n));
data.push_back(data_vectors(first_component + 1, n));
data.push_back(0);
break;
case 2:
data.push_back(data_vectors(first_component, n));
data.push_back(data_vectors(first_component + 1, n));
data.push_back(data_vectors(first_component + 2, n));
break;
default:
// Anything else is not yet implemented
DEAL_II_ASSERT_UNREACHABLE();
}
}
else
{
Tensor<2, 3> vtk_data;
vtk_data = 0.;
const unsigned int size = last_component - first_component + 1;
if (size == 1)
// 1d, 1 element
{
vtk_data[0][0] = data_vectors(first_component, n);
}
else if (size == 4)
// 2d, 4 elements
{
for (unsigned int c = 0; c < size; ++c)
{
const auto ind =
Tensor<2, 2>::unrolled_to_component_indices(c);
vtk_data[ind[0]][ind[1]] =
data_vectors(first_component + c, n);
}
}
else if (size == 9)
// 3d 9 elements
{
for (unsigned int c = 0; c < size; ++c)
{
const auto ind =
Tensor<2, 3>::unrolled_to_component_indices(c);
vtk_data[ind[0]][ind[1]] =
data_vectors(first_component + c, n);
}
}
else
{
DEAL_II_ASSERT_UNREACHABLE();
}
// now put the tensor into data
// note we pad with zeros because VTK format always wants to
// see a 3x3 tensor, regardless of dimension
for (unsigned int i = 0; i < 3; ++i)
for (unsigned int j = 0; j < 3; ++j)
data.push_back(vtk_data[i][j]);
}
} // loop over nodes
o << vtu_stringize_array(data,
flags.compression_level,
output_precision);
o << '\n';
o << " </DataArray>\n";
return o.str();
};
const auto stringize_scalar_data_set =
[&flags,
&data_names,
ascii_or_binary,
output_precision = out.precision()](const Table<2, float> &data_vectors,
const unsigned int data_set) {
std::ostringstream o;
o << " <DataArray type=\"Float32\" Name=\"" << data_names[data_set]
<< "\" format=\"" << ascii_or_binary << "\"";
// If present, also list the physical units for this quantity.
if (flags.physical_units.find(data_names[data_set]) !=
flags.physical_units.end())
o << " units=\"" << flags.physical_units.at(data_names[data_set])
<< "\"";
o << ">\n";
const std::vector<float> data(data_vectors[data_set].begin(),
data_vectors[data_set].end());
o << vtu_stringize_array(data,
flags.compression_level,
output_precision);
o << '\n';
o << " </DataArray>\n";
return o.str();
};
// For the format we write here, we need to write all node values relating
// to one variable at a time. We could in principle do this by looping
// over all patches and extracting the values corresponding to the one
// variable we're dealing with right now, and then start the process over
// for the next variable with another loop over all patches.
//
// An easier way is to create a global table that for each variable
// lists all values. This copying of data vectors can be done in the
// background while we're already working on vertices and cells,
// so do this on a separate task and when wanting to write out the
// data, we wait for that task to finish.
Threads::Task<std::unique_ptr<Table<2, float>>>
create_global_data_table_task = Threads::new_task([&patches]() {
return create_global_data_table<dim, spacedim, float>(patches);
});
// -----------------------------
// Now finally get around to actually doing anything. Let's start with
// running the first three tasks generating the vertex and cell information:
Threads::TaskGroup<std::string> mesh_tasks;
mesh_tasks += Threads::new_task(stringize_vertex_information);
mesh_tasks += Threads::new_task(stringize_cell_to_vertex_information);
mesh_tasks += Threads::new_task(stringize_cell_offset_and_type_information);
// For what follows, we have to have the reordered data available. So wait
// for that task to conclude and get the resulting data table:
const Table<2, float> data_vectors =
std::move(*create_global_data_table_task.return_value());
// Then create the strings for the actual values of the solution vectors,
// again on separate tasks:
Threads::TaskGroup<std::string> data_tasks;
// When writing, first write out all vector and tensor data
std::vector<bool> data_set_handled(n_data_sets, false);
for (const auto &range : nonscalar_data_ranges)
{
// Mark these components as already handled:
const auto first_component = std::get<0>(range);
const auto last_component = std::get<1>(range);
for (unsigned int i = first_component; i <= last_component; ++i)
data_set_handled[i] = true;
data_tasks += Threads::new_task([&, range]() {
return stringize_nonscalar_data_range(data_vectors, range);
});
}
// Now do the left over scalar data sets
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
if (data_set_handled[data_set] == false)
{
data_tasks += Threads::new_task([&, data_set]() {
return stringize_scalar_data_set(data_vectors, data_set);
});
}
// Alright, all tasks are now running. Wait for their conclusion and output
// all of the data they have produced:
out << "<Piece NumberOfPoints=\"" << n_nodes << "\" NumberOfCells=\""
<< n_cells << "\" >\n";
for (const auto &s : mesh_tasks.return_values())
out << s;
out << " <PointData Scalars=\"scalars\">\n";
for (const auto &s : data_tasks.return_values())
out << s;
out << " </PointData>\n";
out << " </Piece>\n";
// make sure everything now gets to disk
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
void
write_pvtu_record(
std::ostream &out,
const std::vector<std::string> &piece_names,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
const VtkFlags &flags)
{
AssertThrow(out.fail() == false, ExcIO());
// If the user provided physical units, make sure that they don't contain
// quote characters as this would make the VTU file invalid XML and
// probably lead to all sorts of difficult error messages. Other than that,
// trust the user that whatever they provide makes sense somehow.
for (const auto &unit : flags.physical_units)
{
(void)unit;
Assert(
unit.second.find('\"') == std::string::npos,
ExcMessage(
"A physical unit you provided, <" + unit.second +
">, contained a quotation mark character. This is not allowed."));
}
const unsigned int n_data_sets = data_names.size();
out << "<?xml version=\"1.0\"?>\n";
out << "<!--\n";
out << "#This file was generated by the deal.II library"
<< " on " << Utilities::System::get_date() << " at "
<< Utilities::System::get_time() << "\n-->\n";
out
<< "<VTKFile type=\"PUnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";
out << " <PUnstructuredGrid GhostLevel=\"0\">\n";
out << " <PPointData Scalars=\"scalars\">\n";
// We need to output in the same order as the write_vtu function does:
std::vector<bool> data_set_written(n_data_sets, false);
for (const auto &nonscalar_data_range : nonscalar_data_ranges)
{
const auto first_component = std::get<0>(nonscalar_data_range);
const auto last_component = std::get<1>(nonscalar_data_range);
const bool is_tensor =
(std::get<3>(nonscalar_data_range) ==
DataComponentInterpretation::component_is_part_of_tensor);
const unsigned int n_components = (is_tensor ? 9 : 3);
AssertThrow(last_component >= first_component,
ExcLowerRange(last_component, first_component));
AssertThrow(last_component < n_data_sets,
ExcIndexRange(last_component, 0, n_data_sets));
if (is_tensor)
{
AssertThrow((last_component + 1 - first_component <= 9),
ExcMessage(
"Can't declare a tensor with more than 9 components "
"in VTK"));
}
else
{
Assert((last_component + 1 - first_component <= 3),
ExcMessage(
"Can't declare a vector with more than 3 components "
"in VTK"));
}
// mark these components as already written:
for (unsigned int i = std::get<0>(nonscalar_data_range);
i <= std::get<1>(nonscalar_data_range);
++i)
data_set_written[i] = true;
// write the header. concatenate all the component names with double
// underscores unless a vector name has been specified
out << " <PDataArray type=\"Float32\" Name=\"";
const std::string &name = std::get<2>(nonscalar_data_range);
if (!name.empty())
out << name;
else
{
for (unsigned int i = std::get<0>(nonscalar_data_range);
i < std::get<1>(nonscalar_data_range);
++i)
out << data_names[i] << "__";
out << data_names[std::get<1>(nonscalar_data_range)];
}
out << "\" NumberOfComponents=\"" << n_components
<< "\" format=\"ascii\"";
// If present, also list the physical units for this quantity. Look this
// up for either the name of the whole vector/tensor, or if that isn't
// listed, via its first component.
if (!name.empty())
{
if (flags.physical_units.find(name) != flags.physical_units.end())
out << " units=\"" << flags.physical_units.at(name) << "\"";
}
else
{
if (flags.physical_units.find(
data_names[std::get<1>(nonscalar_data_range)]) !=
flags.physical_units.end())
out << " units=\""
<< flags.physical_units.at(
data_names[std::get<1>(nonscalar_data_range)])
<< "\"";
}
out << "/>\n";
}
// Now for the scalar fields
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
if (data_set_written[data_set] == false)
{
out << " <PDataArray type=\"Float32\" Name=\""
<< data_names[data_set] << "\" format=\"ascii\"";
if (flags.physical_units.find(data_names[data_set]) !=
flags.physical_units.end())
out << " units=\"" << flags.physical_units.at(data_names[data_set])
<< "\"";
out << "/>\n";
}
out << " </PPointData>\n";
out << " <PPoints>\n";
out << " <PDataArray type=\"Float32\" NumberOfComponents=\"3\"/>\n";
out << " </PPoints>\n";
for (const auto &piece_name : piece_names)
out << " <Piece Source=\"" << piece_name << "\"/>\n";
out << " </PUnstructuredGrid>\n";
out << "</VTKFile>\n";
out.flush();
// assert the stream is still ok
AssertThrow(out.fail() == false, ExcIO());
}
void
write_pvd_record(
std::ostream &out,
const std::vector<std::pair<double, std::string>> ×_and_names)
{
AssertThrow(out.fail() == false, ExcIO());
out << "<?xml version=\"1.0\"?>\n";
out << "<!--\n";
out << "#This file was generated by the deal.II library"
<< " on " << Utilities::System::get_date() << " at "
<< Utilities::System::get_time() << "\n-->\n";
out
<< "<VTKFile type=\"Collection\" version=\"0.1\" ByteOrder=\"LittleEndian\">\n";
out << " <Collection>\n";
std::streamsize ss = out.precision();
out.precision(12);
for (const auto &time_and_name : times_and_names)
out << " <DataSet timestep=\"" << time_and_name.first
<< "\" group=\"\" part=\"0\" file=\"" << time_and_name.second
<< "\"/>\n";
out << " </Collection>\n";
out << "</VTKFile>\n";
out.flush();
out.precision(ss);
AssertThrow(out.fail() == false, ExcIO());
}
void
write_visit_record(std::ostream &out,
const std::vector<std::string> &piece_names)
{
out << "!NBLOCKS " << piece_names.size() << '\n';
for (const auto &piece_name : piece_names)
out << piece_name << '\n';
out << std::flush;
}
void
write_visit_record(std::ostream &out,
const std::vector<std::vector<std::string>> &piece_names)
{
AssertThrow(out.fail() == false, ExcIO());
if (piece_names.empty())
return;
const double nblocks = piece_names[0].size();
Assert(nblocks > 0,
ExcMessage("piece_names should be a vector of nonempty vectors."));
out << "!NBLOCKS " << nblocks << '\n';
for (const auto &domain : piece_names)
{
Assert(domain.size() == nblocks,
ExcMessage(
"piece_names should be a vector of equal sized vectors."));
for (const auto &subdomain : domain)
out << subdomain << '\n';
}
out << std::flush;
}
void
write_visit_record(
std::ostream &out,
const std::vector<std::pair<double, std::vector<std::string>>>
×_and_piece_names)
{
AssertThrow(out.fail() == false, ExcIO());
if (times_and_piece_names.empty())
return;
const double nblocks = times_and_piece_names[0].second.size();
Assert(
nblocks > 0,
ExcMessage(
"time_and_piece_names should contain nonempty vectors of filenames for every timestep."));
for (const auto &domain : times_and_piece_names)
out << "!TIME " << domain.first << '\n';
out << "!NBLOCKS " << nblocks << '\n';
for (const auto &domain : times_and_piece_names)
{
Assert(domain.second.size() == nblocks,
ExcMessage(
"piece_names should be a vector of equal sized vectors."));
for (const auto &subdomain : domain.second)
out << subdomain << '\n';
}
out << std::flush;
}
template <int dim, int spacedim>
void
write_svg(
const std::vector<Patch<dim, spacedim>> &,
const std::vector<std::string> &,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>> &,
const SvgFlags &,
std::ostream &)
{
DEAL_II_NOT_IMPLEMENTED();
}
template <int spacedim>
void
write_svg(
const std::vector<Patch<2, spacedim>> &patches,
const std::vector<std::string> & /*data_names*/,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
& /*nonscalar_data_ranges*/,
const SvgFlags &flags,
std::ostream &out)
{
const unsigned int height = flags.height;
unsigned int width = flags.width;
// margin around the plotted area
unsigned int margin_in_percent = 0;
if (flags.margin)
margin_in_percent = 5;
// determine the bounding box in the model space
double x_dimension, y_dimension, z_dimension;
const auto &first_patch = patches[0];
unsigned int n_subdivisions = first_patch.n_subdivisions;
unsigned int n = n_subdivisions + 1;
const unsigned int d1 = 1;
const unsigned int d2 = n;
Point<spacedim> projected_point;
std::array<Point<spacedim>, 4> projected_points;
Point<2> projection_decomposition;
std::array<Point<2>, 4> projection_decompositions;
projected_point =
get_equispaced_location(first_patch, {0, 0}, n_subdivisions);
if (first_patch.data.n_rows() != 0)
{
AssertIndexRange(flags.height_vector, first_patch.data.n_rows());
}
double x_min = projected_point[0];
double x_max = x_min;
double y_min = projected_point[1];
double y_max = y_min;
double z_min = first_patch.data.n_rows() != 0 ?
first_patch.data(flags.height_vector, 0) :
0;
double z_max = z_min;
// iterate over the patches
for (const auto &patch : patches)
{
n_subdivisions = patch.n_subdivisions;
n = n_subdivisions + 1;
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
{
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
projected_points[0] =
get_equispaced_location(patch, {i1, i2}, n_subdivisions);
projected_points[1] =
get_equispaced_location(patch, {i1 + 1, i2}, n_subdivisions);
projected_points[2] =
get_equispaced_location(patch, {i1, i2 + 1}, n_subdivisions);
projected_points[3] = get_equispaced_location(patch,
{i1 + 1, i2 + 1},
n_subdivisions);
x_min = std::min(x_min, projected_points[0][0]);
x_min = std::min(x_min, projected_points[1][0]);
x_min = std::min(x_min, projected_points[2][0]);
x_min = std::min(x_min, projected_points[3][0]);
x_max = std::max(x_max, projected_points[0][0]);
x_max = std::max(x_max, projected_points[1][0]);
x_max = std::max(x_max, projected_points[2][0]);
x_max = std::max(x_max, projected_points[3][0]);
y_min = std::min(y_min, projected_points[0][1]);
y_min = std::min(y_min, projected_points[1][1]);
y_min = std::min(y_min, projected_points[2][1]);
y_min = std::min(y_min, projected_points[3][1]);
y_max = std::max(y_max, projected_points[0][1]);
y_max = std::max(y_max, projected_points[1][1]);
y_max = std::max(y_max, projected_points[2][1]);
y_max = std::max(y_max, projected_points[3][1]);
Assert((flags.height_vector < patch.data.n_rows()) ||
patch.data.n_rows() == 0,
ExcIndexRange(flags.height_vector,
0,
patch.data.n_rows()));
z_min = std::min<double>(z_min,
patch.data(flags.height_vector,
i1 * d1 + i2 * d2));
z_min = std::min<double>(z_min,
patch.data(flags.height_vector,
(i1 + 1) * d1 + i2 * d2));
z_min = std::min<double>(z_min,
patch.data(flags.height_vector,
i1 * d1 + (i2 + 1) * d2));
z_min =
std::min<double>(z_min,
patch.data(flags.height_vector,
(i1 + 1) * d1 + (i2 + 1) * d2));
z_max = std::max<double>(z_max,
patch.data(flags.height_vector,
i1 * d1 + i2 * d2));
z_max = std::max<double>(z_max,
patch.data(flags.height_vector,
(i1 + 1) * d1 + i2 * d2));
z_max = std::max<double>(z_max,
patch.data(flags.height_vector,
i1 * d1 + (i2 + 1) * d2));
z_max =
std::max<double>(z_max,
patch.data(flags.height_vector,
(i1 + 1) * d1 + (i2 + 1) * d2));
}
}
}
x_dimension = x_max - x_min;
y_dimension = y_max - y_min;
z_dimension = z_max - z_min;
// set initial camera position
Point<3> camera_position;
Point<3> camera_direction;
Point<3> camera_horizontal;
float camera_focus = 0;
// translate camera from the origin to the initial position
camera_position[0] = 0.;
camera_position[1] = 0.;
camera_position[2] = z_min + 2. * z_dimension;
camera_direction[0] = 0.;
camera_direction[1] = 0.;
camera_direction[2] = -1.;
camera_horizontal[0] = 1.;
camera_horizontal[1] = 0.;
camera_horizontal[2] = 0.;
camera_focus = .5 * z_dimension;
Point<3> camera_position_temp;
Point<3> camera_direction_temp;
Point<3> camera_horizontal_temp;
const float angle_factor = 3.14159265f / 180.f;
// (I) rotate the camera to the chosen polar angle
camera_position_temp[1] =
std::cos(angle_factor * flags.polar_angle) * camera_position[1] -
std::sin(angle_factor * flags.polar_angle) * camera_position[2];
camera_position_temp[2] =
std::sin(angle_factor * flags.polar_angle) * camera_position[1] +
std::cos(angle_factor * flags.polar_angle) * camera_position[2];
camera_direction_temp[1] =
std::cos(angle_factor * flags.polar_angle) * camera_direction[1] -
std::sin(angle_factor * flags.polar_angle) * camera_direction[2];
camera_direction_temp[2] =
std::sin(angle_factor * flags.polar_angle) * camera_direction[1] +
std::cos(angle_factor * flags.polar_angle) * camera_direction[2];
camera_horizontal_temp[1] =
std::cos(angle_factor * flags.polar_angle) * camera_horizontal[1] -
std::sin(angle_factor * flags.polar_angle) * camera_horizontal[2];
camera_horizontal_temp[2] =
std::sin(angle_factor * flags.polar_angle) * camera_horizontal[1] +
std::cos(angle_factor * flags.polar_angle) * camera_horizontal[2];
camera_position[1] = camera_position_temp[1];
camera_position[2] = camera_position_temp[2];
camera_direction[1] = camera_direction_temp[1];
camera_direction[2] = camera_direction_temp[2];
camera_horizontal[1] = camera_horizontal_temp[1];
camera_horizontal[2] = camera_horizontal_temp[2];
// (II) rotate the camera to the chosen azimuth angle
camera_position_temp[0] =
std::cos(angle_factor * flags.azimuth_angle) * camera_position[0] -
std::sin(angle_factor * flags.azimuth_angle) * camera_position[1];
camera_position_temp[1] =
std::sin(angle_factor * flags.azimuth_angle) * camera_position[0] +
std::cos(angle_factor * flags.azimuth_angle) * camera_position[1];
camera_direction_temp[0] =
std::cos(angle_factor * flags.azimuth_angle) * camera_direction[0] -
std::sin(angle_factor * flags.azimuth_angle) * camera_direction[1];
camera_direction_temp[1] =
std::sin(angle_factor * flags.azimuth_angle) * camera_direction[0] +
std::cos(angle_factor * flags.azimuth_angle) * camera_direction[1];
camera_horizontal_temp[0] =
std::cos(angle_factor * flags.azimuth_angle) * camera_horizontal[0] -
std::sin(angle_factor * flags.azimuth_angle) * camera_horizontal[1];
camera_horizontal_temp[1] =
std::sin(angle_factor * flags.azimuth_angle) * camera_horizontal[0] +
std::cos(angle_factor * flags.azimuth_angle) * camera_horizontal[1];
camera_position[0] = camera_position_temp[0];
camera_position[1] = camera_position_temp[1];
camera_direction[0] = camera_direction_temp[0];
camera_direction[1] = camera_direction_temp[1];
camera_horizontal[0] = camera_horizontal_temp[0];
camera_horizontal[1] = camera_horizontal_temp[1];
// (III) translate the camera
camera_position[0] = x_min + .5 * x_dimension;
camera_position[1] = y_min + .5 * y_dimension;
camera_position[0] += (z_min + 2. * z_dimension) *
std::sin(angle_factor * flags.polar_angle) *
std::sin(angle_factor * flags.azimuth_angle);
camera_position[1] -= (z_min + 2. * z_dimension) *
std::sin(angle_factor * flags.polar_angle) *
std::cos(angle_factor * flags.azimuth_angle);
// determine the bounding box on the projection plane
double x_min_perspective, y_min_perspective;
double x_max_perspective, y_max_perspective;
double x_dimension_perspective, y_dimension_perspective;
n_subdivisions = first_patch.n_subdivisions;
n = n_subdivisions + 1;
Point<3> point;
projected_point =
get_equispaced_location(first_patch, {0, 0}, n_subdivisions);
if (first_patch.data.n_rows() != 0)
{
AssertIndexRange(flags.height_vector, first_patch.data.n_rows());
}
point[0] = projected_point[0];
point[1] = projected_point[1];
point[2] = first_patch.data.n_rows() != 0 ?
first_patch.data(flags.height_vector, 0) :
0;
projection_decomposition = svg_project_point(point,
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
x_min_perspective = projection_decomposition[0];
x_max_perspective = projection_decomposition[0];
y_min_perspective = projection_decomposition[1];
y_max_perspective = projection_decomposition[1];
// iterate over the patches
for (const auto &patch : patches)
{
n_subdivisions = patch.n_subdivisions;
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
{
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const std::array<Point<spacedim>, 4> projected_vertices{
{get_equispaced_location(patch, {i1, i2}, n_subdivisions),
get_equispaced_location(patch, {i1 + 1, i2}, n_subdivisions),
get_equispaced_location(patch, {i1, i2 + 1}, n_subdivisions),
get_equispaced_location(patch,
{i1 + 1, i2 + 1},
n_subdivisions)}};
Assert((flags.height_vector < patch.data.n_rows()) ||
patch.data.n_rows() == 0,
ExcIndexRange(flags.height_vector,
0,
patch.data.n_rows()));
const std::array<Point<3>, 4> vertices = {
{Point<3>{projected_vertices[0][0],
projected_vertices[0][1],
patch.data.n_rows() != 0 ?
patch.data(0, i1 * d1 + i2 * d2) :
0},
Point<3>{projected_vertices[1][0],
projected_vertices[1][1],
patch.data.n_rows() != 0 ?
patch.data(0, (i1 + 1) * d1 + i2 * d2) :
0},
Point<3>{projected_vertices[2][0],
projected_vertices[2][1],
patch.data.n_rows() != 0 ?
patch.data(0, i1 * d1 + (i2 + 1) * d2) :
0},
Point<3>{projected_vertices[3][0],
projected_vertices[3][1],
patch.data.n_rows() != 0 ?
patch.data(0, (i1 + 1) * d1 + (i2 + 1) * d2) :
0}}};
projection_decompositions = {
{svg_project_point(vertices[0],
camera_position,
camera_direction,
camera_horizontal,
camera_focus),
svg_project_point(vertices[1],
camera_position,
camera_direction,
camera_horizontal,
camera_focus),
svg_project_point(vertices[2],
camera_position,
camera_direction,
camera_horizontal,
camera_focus),
svg_project_point(vertices[3],
camera_position,
camera_direction,
camera_horizontal,
camera_focus)}};
x_min_perspective =
std::min(x_min_perspective,
static_cast<double>(
projection_decompositions[0][0]));
x_min_perspective =
std::min(x_min_perspective,
static_cast<double>(
projection_decompositions[1][0]));
x_min_perspective =
std::min(x_min_perspective,
static_cast<double>(
projection_decompositions[2][0]));
x_min_perspective =
std::min(x_min_perspective,
static_cast<double>(
projection_decompositions[3][0]));
x_max_perspective =
std::max(x_max_perspective,
static_cast<double>(
projection_decompositions[0][0]));
x_max_perspective =
std::max(x_max_perspective,
static_cast<double>(
projection_decompositions[1][0]));
x_max_perspective =
std::max(x_max_perspective,
static_cast<double>(
projection_decompositions[2][0]));
x_max_perspective =
std::max(x_max_perspective,
static_cast<double>(
projection_decompositions[3][0]));
y_min_perspective =
std::min(y_min_perspective,
static_cast<double>(
projection_decompositions[0][1]));
y_min_perspective =
std::min(y_min_perspective,
static_cast<double>(
projection_decompositions[1][1]));
y_min_perspective =
std::min(y_min_perspective,
static_cast<double>(
projection_decompositions[2][1]));
y_min_perspective =
std::min(y_min_perspective,
static_cast<double>(
projection_decompositions[3][1]));
y_max_perspective =
std::max(y_max_perspective,
static_cast<double>(
projection_decompositions[0][1]));
y_max_perspective =
std::max(y_max_perspective,
static_cast<double>(
projection_decompositions[1][1]));
y_max_perspective =
std::max(y_max_perspective,
static_cast<double>(
projection_decompositions[2][1]));
y_max_perspective =
std::max(y_max_perspective,
static_cast<double>(
projection_decompositions[3][1]));
}
}
}
x_dimension_perspective = x_max_perspective - x_min_perspective;
y_dimension_perspective = y_max_perspective - y_min_perspective;
std::multiset<SvgCell> cells;
// iterate over the patches
for (const auto &patch : patches)
{
n_subdivisions = patch.n_subdivisions;
for (unsigned int i2 = 0; i2 < n_subdivisions; ++i2)
{
for (unsigned int i1 = 0; i1 < n_subdivisions; ++i1)
{
const std::array<Point<spacedim>, 4> projected_vertices = {
{get_equispaced_location(patch, {i1, i2}, n_subdivisions),
get_equispaced_location(patch, {i1 + 1, i2}, n_subdivisions),
get_equispaced_location(patch, {i1, i2 + 1}, n_subdivisions),
get_equispaced_location(patch,
{i1 + 1, i2 + 1},
n_subdivisions)}};
Assert((flags.height_vector < patch.data.n_rows()) ||
patch.data.n_rows() == 0,
ExcIndexRange(flags.height_vector,
0,
patch.data.n_rows()));
SvgCell cell;
cell.vertices[0][0] = projected_vertices[0][0];
cell.vertices[0][1] = projected_vertices[0][1];
cell.vertices[0][2] = patch.data.n_rows() != 0 ?
patch.data(0, i1 * d1 + i2 * d2) :
0;
cell.vertices[1][0] = projected_vertices[1][0];
cell.vertices[1][1] = projected_vertices[1][1];
cell.vertices[1][2] = patch.data.n_rows() != 0 ?
patch.data(0, (i1 + 1) * d1 + i2 * d2) :
0;
cell.vertices[2][0] = projected_vertices[2][0];
cell.vertices[2][1] = projected_vertices[2][1];
cell.vertices[2][2] = patch.data.n_rows() != 0 ?
patch.data(0, i1 * d1 + (i2 + 1) * d2) :
0;
cell.vertices[3][0] = projected_vertices[3][0];
cell.vertices[3][1] = projected_vertices[3][1];
cell.vertices[3][2] =
patch.data.n_rows() != 0 ?
patch.data(0, (i1 + 1) * d1 + (i2 + 1) * d2) :
0;
cell.projected_vertices[0] =
svg_project_point(cell.vertices[0],
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
cell.projected_vertices[1] =
svg_project_point(cell.vertices[1],
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
cell.projected_vertices[2] =
svg_project_point(cell.vertices[2],
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
cell.projected_vertices[3] =
svg_project_point(cell.vertices[3],
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
cell.center = .25 * (cell.vertices[0] + cell.vertices[1] +
cell.vertices[2] + cell.vertices[3]);
cell.projected_center = svg_project_point(cell.center,
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
cell.depth = cell.center.distance(camera_position);
cells.insert(cell);
}
}
}
// write the svg file
if (width == 0)
width = static_cast<unsigned int>(
.5 + height * (x_dimension_perspective / y_dimension_perspective));
unsigned int additional_width = 0;
if (flags.draw_colorbar)
additional_width = static_cast<unsigned int>(
.5 + height * .3); // additional width for colorbar
// basic svg header and background rectangle
out << "<svg width=\"" << width + additional_width << "\" height=\""
<< height << "\" xmlns=\"http://www.w3.org/2000/svg\" version=\"1.1\">"
<< '\n'
<< " <rect width=\"" << width + additional_width << "\" height=\""
<< height << "\" style=\"fill:white\"/>" << '\n'
<< '\n';
unsigned int triangle_counter = 0;
// write the cells in the correct order
for (const auto &cell : cells)
{
Point<3> points3d_triangle[3];
for (unsigned int triangle_index = 0; triangle_index < 4;
triangle_index++)
{
switch (triangle_index)
{
case 0:
points3d_triangle[0] = cell.vertices[0],
points3d_triangle[1] = cell.vertices[1],
points3d_triangle[2] = cell.center;
break;
case 1:
points3d_triangle[0] = cell.vertices[1],
points3d_triangle[1] = cell.vertices[3],
points3d_triangle[2] = cell.center;
break;
case 2:
points3d_triangle[0] = cell.vertices[3],
points3d_triangle[1] = cell.vertices[2],
points3d_triangle[2] = cell.center;
break;
case 3:
points3d_triangle[0] = cell.vertices[2],
points3d_triangle[1] = cell.vertices[0],
points3d_triangle[2] = cell.center;
break;
default:
break;
}
Point<6> gradient_param =
svg_get_gradient_parameters(points3d_triangle);
double start_h =
.667 - ((gradient_param[4] - z_min) / z_dimension) * .667;
double stop_h =
.667 - ((gradient_param[5] - z_min) / z_dimension) * .667;
unsigned int start_r = 0;
unsigned int start_g = 0;
unsigned int start_b = 0;
unsigned int stop_r = 0;
unsigned int stop_g = 0;
unsigned int stop_b = 0;
unsigned int start_i = static_cast<unsigned int>(start_h * 6.);
unsigned int stop_i = static_cast<unsigned int>(stop_h * 6.);
double start_f = start_h * 6. - start_i;
double start_q = 1. - start_f;
double stop_f = stop_h * 6. - stop_i;
double stop_q = 1. - stop_f;
switch (start_i % 6)
{
case 0:
start_r = 255,
start_g = static_cast<unsigned int>(.5 + 255. * start_f);
break;
case 1:
start_r = static_cast<unsigned int>(.5 + 255. * start_q),
start_g = 255;
break;
case 2:
start_g = 255,
start_b = static_cast<unsigned int>(.5 + 255. * start_f);
break;
case 3:
start_g = static_cast<unsigned int>(.5 + 255. * start_q),
start_b = 255;
break;
case 4:
start_r = static_cast<unsigned int>(.5 + 255. * start_f),
start_b = 255;
break;
case 5:
start_r = 255,
start_b = static_cast<unsigned int>(.5 + 255. * start_q);
break;
default:
break;
}
switch (stop_i % 6)
{
case 0:
stop_r = 255,
stop_g = static_cast<unsigned int>(.5 + 255. * stop_f);
break;
case 1:
stop_r = static_cast<unsigned int>(.5 + 255. * stop_q),
stop_g = 255;
break;
case 2:
stop_g = 255,
stop_b = static_cast<unsigned int>(.5 + 255. * stop_f);
break;
case 3:
stop_g = static_cast<unsigned int>(.5 + 255. * stop_q),
stop_b = 255;
break;
case 4:
stop_r = static_cast<unsigned int>(.5 + 255. * stop_f),
stop_b = 255;
break;
case 5:
stop_r = 255,
stop_b = static_cast<unsigned int>(.5 + 255. * stop_q);
break;
default:
break;
}
Point<3> gradient_start_point_3d, gradient_stop_point_3d;
gradient_start_point_3d[0] = gradient_param[0];
gradient_start_point_3d[1] = gradient_param[1];
gradient_start_point_3d[2] = gradient_param[4];
gradient_stop_point_3d[0] = gradient_param[2];
gradient_stop_point_3d[1] = gradient_param[3];
gradient_stop_point_3d[2] = gradient_param[5];
Point<2> gradient_start_point =
svg_project_point(gradient_start_point_3d,
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
Point<2> gradient_stop_point =
svg_project_point(gradient_stop_point_3d,
camera_position,
camera_direction,
camera_horizontal,
camera_focus);
// define linear gradient
out << " <linearGradient id=\"" << triangle_counter
<< "\" gradientUnits=\"userSpaceOnUse\" "
<< "x1=\""
<< static_cast<unsigned int>(
.5 +
((gradient_start_point[0] - x_min_perspective) /
x_dimension_perspective) *
(width - (width / 100.) * 2. * margin_in_percent) +
((width / 100.) * margin_in_percent))
<< "\" "
<< "y1=\""
<< static_cast<unsigned int>(
.5 + height - (height / 100.) * margin_in_percent -
((gradient_start_point[1] - y_min_perspective) /
y_dimension_perspective) *
(height - (height / 100.) * 2. * margin_in_percent))
<< "\" "
<< "x2=\""
<< static_cast<unsigned int>(
.5 +
((gradient_stop_point[0] - x_min_perspective) /
x_dimension_perspective) *
(width - (width / 100.) * 2. * margin_in_percent) +
((width / 100.) * margin_in_percent))
<< "\" "
<< "y2=\""
<< static_cast<unsigned int>(
.5 + height - (height / 100.) * margin_in_percent -
((gradient_stop_point[1] - y_min_perspective) /
y_dimension_perspective) *
(height - (height / 100.) * 2. * margin_in_percent))
<< "\""
<< ">" << '\n'
<< " <stop offset=\"0\" style=\"stop-color:rgb(" << start_r
<< "," << start_g << "," << start_b << ")\"/>" << '\n'
<< " <stop offset=\"1\" style=\"stop-color:rgb(" << stop_r
<< "," << stop_g << "," << stop_b << ")\"/>" << '\n'
<< " </linearGradient>" << '\n';
// draw current triangle
double x1 = 0, y1 = 0, x2 = 0, y2 = 0;
double x3 = cell.projected_center[0];
double y3 = cell.projected_center[1];
switch (triangle_index)
{
case 0:
x1 = cell.projected_vertices[0][0],
y1 = cell.projected_vertices[0][1],
x2 = cell.projected_vertices[1][0],
y2 = cell.projected_vertices[1][1];
break;
case 1:
x1 = cell.projected_vertices[1][0],
y1 = cell.projected_vertices[1][1],
x2 = cell.projected_vertices[3][0],
y2 = cell.projected_vertices[3][1];
break;
case 2:
x1 = cell.projected_vertices[3][0],
y1 = cell.projected_vertices[3][1],
x2 = cell.projected_vertices[2][0],
y2 = cell.projected_vertices[2][1];
break;
case 3:
x1 = cell.projected_vertices[2][0],
y1 = cell.projected_vertices[2][1],
x2 = cell.projected_vertices[0][0],
y2 = cell.projected_vertices[0][1];
break;
default:
break;
}
out << " <path d=\"M "
<< static_cast<unsigned int>(
.5 +
((x1 - x_min_perspective) / x_dimension_perspective) *
(width - (width / 100.) * 2. * margin_in_percent) +
((width / 100.) * margin_in_percent))
<< ' '
<< static_cast<unsigned int>(
.5 + height - (height / 100.) * margin_in_percent -
((y1 - y_min_perspective) / y_dimension_perspective) *
(height - (height / 100.) * 2. * margin_in_percent))
<< " L "
<< static_cast<unsigned int>(
.5 +
((x2 - x_min_perspective) / x_dimension_perspective) *
(width - (width / 100.) * 2. * margin_in_percent) +
((width / 100.) * margin_in_percent))
<< ' '
<< static_cast<unsigned int>(
.5 + height - (height / 100.) * margin_in_percent -
((y2 - y_min_perspective) / y_dimension_perspective) *
(height - (height / 100.) * 2. * margin_in_percent))
<< " L "
<< static_cast<unsigned int>(
.5 +
((x3 - x_min_perspective) / x_dimension_perspective) *
(width - (width / 100.) * 2. * margin_in_percent) +
((width / 100.) * margin_in_percent))
<< ' '
<< static_cast<unsigned int>(
.5 + height - (height / 100.) * margin_in_percent -
((y3 - y_min_perspective) / y_dimension_perspective) *
(height - (height / 100.) * 2. * margin_in_percent))
<< " L "
<< static_cast<unsigned int>(
.5 +
((x1 - x_min_perspective) / x_dimension_perspective) *
(width - (width / 100.) * 2. * margin_in_percent) +
((width / 100.) * margin_in_percent))
<< ' '
<< static_cast<unsigned int>(
.5 + height - (height / 100.) * margin_in_percent -
((y1 - y_min_perspective) / y_dimension_perspective) *
(height - (height / 100.) * 2. * margin_in_percent))
<< "\" style=\"stroke:black; fill:url(#" << triangle_counter
<< "); stroke-width:" << flags.line_thickness << "\"/>" << '\n';
++triangle_counter;
}
}
// draw the colorbar
if (flags.draw_colorbar)
{
out << '\n' << " <!-- colorbar -->" << '\n';
unsigned int element_height = static_cast<unsigned int>(
((height / 100.) * (71. - 2. * margin_in_percent)) / 4);
unsigned int element_width =
static_cast<unsigned int>(.5 + (height / 100.) * 2.5);
additional_width = 0;
if (!flags.margin)
additional_width =
static_cast<unsigned int>(.5 + (height / 100.) * 2.5);
for (unsigned int index = 0; index < 4; ++index)
{
double start_h = .667 - ((index + 1) / 4.) * .667;
double stop_h = .667 - (index / 4.) * .667;
unsigned int start_r = 0;
unsigned int start_g = 0;
unsigned int start_b = 0;
unsigned int stop_r = 0;
unsigned int stop_g = 0;
unsigned int stop_b = 0;
unsigned int start_i = static_cast<unsigned int>(start_h * 6.);
unsigned int stop_i = static_cast<unsigned int>(stop_h * 6.);
double start_f = start_h * 6. - start_i;
double start_q = 1. - start_f;
double stop_f = stop_h * 6. - stop_i;
double stop_q = 1. - stop_f;
switch (start_i % 6)
{
case 0:
start_r = 255,
start_g = static_cast<unsigned int>(.5 + 255. * start_f);
break;
case 1:
start_r = static_cast<unsigned int>(.5 + 255. * start_q),
start_g = 255;
break;
case 2:
start_g = 255,
start_b = static_cast<unsigned int>(.5 + 255. * start_f);
break;
case 3:
start_g = static_cast<unsigned int>(.5 + 255. * start_q),
start_b = 255;
break;
case 4:
start_r = static_cast<unsigned int>(.5 + 255. * start_f),
start_b = 255;
break;
case 5:
start_r = 255,
start_b = static_cast<unsigned int>(.5 + 255. * start_q);
break;
default:
break;
}
switch (stop_i % 6)
{
case 0:
stop_r = 255,
stop_g = static_cast<unsigned int>(.5 + 255. * stop_f);
break;
case 1:
stop_r = static_cast<unsigned int>(.5 + 255. * stop_q),
stop_g = 255;
break;
case 2:
stop_g = 255,
stop_b = static_cast<unsigned int>(.5 + 255. * stop_f);
break;
case 3:
stop_g = static_cast<unsigned int>(.5 + 255. * stop_q),
stop_b = 255;
break;
case 4:
stop_r = static_cast<unsigned int>(.5 + 255. * stop_f),
stop_b = 255;
break;
case 5:
stop_r = 255,
stop_b = static_cast<unsigned int>(.5 + 255. * stop_q);
break;
default:
break;
}
// define gradient
out << " <linearGradient id=\"colorbar_" << index
<< "\" gradientUnits=\"userSpaceOnUse\" "
<< "x1=\"" << width + additional_width << "\" "
<< "y1=\""
<< static_cast<unsigned int>(.5 + (height / 100.) *
(margin_in_percent + 29)) +
(3 - index) * element_height
<< "\" "
<< "x2=\"" << width + additional_width << "\" "
<< "y2=\""
<< static_cast<unsigned int>(.5 + (height / 100.) *
(margin_in_percent + 29)) +
(4 - index) * element_height
<< "\""
<< ">" << '\n'
<< " <stop offset=\"0\" style=\"stop-color:rgb(" << start_r
<< "," << start_g << "," << start_b << ")\"/>" << '\n'
<< " <stop offset=\"1\" style=\"stop-color:rgb(" << stop_r
<< "," << stop_g << "," << stop_b << ")\"/>" << '\n'
<< " </linearGradient>" << '\n';
// draw box corresponding to the gradient above
out
<< " <rect"
<< " x=\"" << width + additional_width << "\" y=\""
<< static_cast<unsigned int>(.5 + (height / 100.) *
(margin_in_percent + 29)) +
(3 - index) * element_height
<< "\" width=\"" << element_width << "\" height=\""
<< element_height
<< "\" style=\"stroke:black; stroke-width:2; fill:url(#colorbar_"
<< index << ")\"/>" << '\n';
}
for (unsigned int index = 0; index < 5; ++index)
{
out
<< " <text x=\""
<< width + additional_width +
static_cast<unsigned int>(1.5 * element_width)
<< "\" y=\""
<< static_cast<unsigned int>(
.5 + (height / 100.) * (margin_in_percent + 29) +
(4. - index) * element_height + 30.)
<< "\""
<< " style=\"text-anchor:start; font-size:80; font-family:Helvetica";
if (index == 0 || index == 4)
out << "; font-weight:bold";
out << "\">"
<< static_cast<float>(
(static_cast<int>((z_min + index * (z_dimension / 4.)) *
10000)) /
10000.);
if (index == 4)
out << " max";
if (index == 0)
out << " min";
out << "</text>" << '\n';
}
}
// finalize the svg file
out << '\n' << "</svg>";
out.flush();
}
template <int dim, int spacedim>
void
write_deal_II_intermediate(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
const Deal_II_IntermediateFlags & /*flags*/,
std::ostream &out)
{
AssertThrow(out.fail() == false, ExcIO());
// first write tokens indicating the template parameters. we need this in
// here because we may want to read in data again even if we don't know in
// advance the template parameters:
out << dim << ' ' << spacedim << '\n';
// then write a header
out << "[deal.II intermediate format graphics data]" << '\n'
<< "[written by " << DEAL_II_PACKAGE_NAME << " "
<< DEAL_II_PACKAGE_VERSION << "]" << '\n'
<< "[Version: " << Deal_II_IntermediateFlags::format_version << "]"
<< '\n';
out << data_names.size() << '\n';
for (const auto &data_name : data_names)
out << data_name << '\n';
out << patches.size() << '\n';
for (unsigned int i = 0; i < patches.size(); ++i)
out << patches[i] << '\n';
out << nonscalar_data_ranges.size() << '\n';
for (const auto &nonscalar_data_range : nonscalar_data_ranges)
out << std::get<0>(nonscalar_data_range) << ' '
<< std::get<1>(nonscalar_data_range) << '\n'
<< std::get<2>(nonscalar_data_range) << '\n';
out << '\n';
// make sure everything now gets to disk
out.flush();
}
template <int dim, int spacedim>
void
write_deal_II_intermediate_in_parallel(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
const Deal_II_IntermediateFlags &flags,
const std::string &filename,
const MPI_Comm comm,
const CompressionLevel compression)
{
#ifndef DEAL_II_WITH_MPI
(void)patches;
(void)data_names;
(void)nonscalar_data_ranges;
(void)flags;
(void)filename;
(void)comm;
(void)compression;
AssertThrow(false,
ExcMessage("This functionality requires MPI to be enabled."));
#else
// We write a simple format based on the text format of
// write_deal_II_intermediate() on each MPI rank. The text format
// is quite verbose and we should probably change this to a more
// efficient binary representation at some point. The file layout
// is as follows:
//
// 1. A binary header with layout struct
// ParallelIntermediateHeaderType.
// 2. A list of uint64_t with one value per rank denoting the
// compressed size of the chunks of the next step.
// 3. The (potentially compressed) chunks as generated by
// write_deal_II_intermediate() on each MPI rank.
// First generate my data by writing (optionally compressed) data into
// my_buffer:
std::vector<char> my_buffer;
{
boost::iostreams::filtering_ostream f;
AssertThrow(compression != CompressionLevel::plain_text,
ExcNotImplemented());
if (compression != CompressionLevel::no_compression)
# ifdef DEAL_II_WITH_ZLIB
f.push(boost::iostreams::zlib_compressor(
get_boost_zlib_compression_level(compression)));
# else
AssertThrow(
false,
ExcMessage(
"Compression requires deal.II to be configured with ZLIB support."));
# endif
boost::iostreams::back_insert_device<std::vector<char>> inserter(
my_buffer);
f.push(inserter);
write_deal_II_intermediate<dim, spacedim>(
patches, data_names, nonscalar_data_ranges, flags, f);
}
const std::uint64_t my_size = my_buffer.size();
const unsigned int my_rank = Utilities::MPI::this_mpi_process(comm);
const std::uint64_t n_ranks = Utilities::MPI::n_mpi_processes(comm);
const std::uint64_t n_patches = Utilities::MPI::sum(patches.size(), comm);
const ParallelIntermediateHeader header{
0x00dea111,
Deal_II_IntermediateFlags::format_version,
static_cast<std::uint64_t>(compression),
dim,
spacedim,
n_ranks,
n_patches};
// Rank 0 also collects and writes the size of the data from each
// rank in bytes. The static_cast for the destination buffer looks
// useless, but without it clang-tidy will complain about a wrong
// MPI type.
std::vector<std::uint64_t> chunk_sizes(n_ranks);
int ierr = MPI_Gather(&my_size,
1,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
static_cast<std::uint64_t *>(chunk_sizes.data()),
1,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
0,
comm);
AssertThrowMPI(ierr);
MPI_Info info;
ierr = MPI_Info_create(&info);
AssertThrowMPI(ierr);
MPI_File fh;
ierr = MPI_File_open(
comm, filename.c_str(), MPI_MODE_CREATE | MPI_MODE_WRONLY, info, &fh);
AssertThrow(ierr == MPI_SUCCESS, ExcFileNotOpen(filename));
ierr = MPI_Info_free(&info);
AssertThrowMPI(ierr);
// Delete the file contents:
ierr = MPI_File_set_size(fh, 0);
AssertThrowMPI(ierr);
// This barrier is necessary, because otherwise others might already write
// while one core is still setting the size to zero.
ierr = MPI_Barrier(comm);
AssertThrowMPI(ierr);
// Write the two parts of the header on rank 0:
if (my_rank == 0)
{
ierr = Utilities::MPI::LargeCount::File_write_at_c(
fh, 0, &header, sizeof(header), MPI_CHAR, MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
ierr = Utilities::MPI::LargeCount::File_write_at_c(
fh,
/* offset = */ sizeof(header),
chunk_sizes.data(),
chunk_sizes.size(),
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}
// Write the main part on each rank:
{
std::uint64_t prefix_sum = 0;
ierr = MPI_Exscan(&my_size,
&prefix_sum,
1,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
MPI_SUM,
comm);
AssertThrowMPI(ierr);
// Locate specific offset for each processor.
const MPI_Offset offset = static_cast<MPI_Offset>(sizeof(header)) +
n_ranks * sizeof(std::uint64_t) + prefix_sum;
ierr = Utilities::MPI::LargeCount::File_write_at_all_c(
fh, offset, my_buffer.data(), my_size, MPI_CHAR, MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}
// Make sure we sync to disk. As written in the standard,
// MPI_File_close() actually already implies a sync but there seems
// to be a bug on at least one configuration (running with multiple
// nodes using OpenMPI 4.1) that requires it. Without this call, the
// footer is sometimes missing.
ierr = MPI_File_sync(fh);
AssertThrowMPI(ierr);
ierr = MPI_File_close(&fh);
AssertThrowMPI(ierr);
#endif
}
std::pair<unsigned int, unsigned int>
determine_intermediate_format_dimensions(std::istream &input)
{
AssertThrow(input.fail() == false, ExcIO());
unsigned int dim, spacedim;
input >> dim >> spacedim;
return std::make_pair(dim, spacedim);
}
} // namespace DataOutBase
/* --------------------------- class DataOutInterface ---------------------- */
template <int dim, int spacedim>
DataOutInterface<dim, spacedim>::DataOutInterface()
: default_subdivisions(1)
, default_fmt(DataOutBase::default_format)
{}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_dx(std::ostream &out) const
{
DataOutBase::write_dx(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
dx_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_ucd(std::ostream &out) const
{
DataOutBase::write_ucd(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
ucd_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_gnuplot(std::ostream &out) const
{
DataOutBase::write_gnuplot(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
gnuplot_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_povray(std::ostream &out) const
{
DataOutBase::write_povray(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
povray_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_eps(std::ostream &out) const
{
DataOutBase::write_eps(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
eps_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_gmv(std::ostream &out) const
{
DataOutBase::write_gmv(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
gmv_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_tecplot(std::ostream &out) const
{
DataOutBase::write_tecplot(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
tecplot_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_vtk(std::ostream &out) const
{
DataOutBase::write_vtk(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
vtk_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_vtu(std::ostream &out) const
{
DataOutBase::write_vtu(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
vtk_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_svg(std::ostream &out) const
{
DataOutBase::write_svg(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
svg_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_vtu_in_parallel(
const std::string &filename,
const MPI_Comm comm) const
{
#ifndef DEAL_II_WITH_MPI
// without MPI fall back to the normal way to write a vtu file:
(void)comm;
std::ofstream f(filename);
AssertThrow(f, ExcFileNotOpen(filename));
write_vtu(f);
#else
const unsigned int myrank = Utilities::MPI::this_mpi_process(comm);
const unsigned int n_ranks = Utilities::MPI::n_mpi_processes(comm);
MPI_Info info;
int ierr = MPI_Info_create(&info);
AssertThrowMPI(ierr);
MPI_File fh;
ierr = MPI_File_open(
comm, filename.c_str(), MPI_MODE_CREATE | MPI_MODE_WRONLY, info, &fh);
AssertThrow(ierr == MPI_SUCCESS, ExcFileNotOpen(filename));
ierr = MPI_File_set_size(fh, 0); // delete the file contents
AssertThrowMPI(ierr);
// this barrier is necessary, because otherwise others might already write
// while one core is still setting the size to zero.
ierr = MPI_Barrier(comm);
AssertThrowMPI(ierr);
ierr = MPI_Info_free(&info);
AssertThrowMPI(ierr);
// Define header size so we can broadcast later.
unsigned int header_size;
std::uint64_t footer_offset;
// write header
if (myrank == 0)
{
std::stringstream ss;
DataOutBase::write_vtu_header(ss, vtk_flags);
header_size = ss.str().size();
// Write the header on rank 0 at the start of a file, i.e., offset 0.
ierr = Utilities::MPI::LargeCount::File_write_at_c(
fh, 0, ss.str().c_str(), header_size, MPI_CHAR, MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}
ierr = MPI_Bcast(&header_size, 1, MPI_UNSIGNED, 0, comm);
AssertThrowMPI(ierr);
{
const auto &patches = get_patches();
const types::global_dof_index my_n_patches = patches.size();
const types::global_dof_index global_n_patches =
Utilities::MPI::sum(my_n_patches, comm);
// Do not write pieces with 0 cells as this will crash paraview if this is
// the first piece written. But if nobody has any pieces to write (file is
// empty), let processor 0 write their empty data, otherwise the vtk file is
// invalid.
std::stringstream ss;
if (my_n_patches > 0 || (global_n_patches == 0 && myrank == 0))
DataOutBase::write_vtu_main(patches,
get_dataset_names(),
get_nonscalar_data_ranges(),
vtk_flags,
ss);
// Use prefix sum to find specific offset to write at.
const std::uint64_t size_on_proc = ss.str().size();
std::uint64_t prefix_sum = 0;
ierr = MPI_Exscan(&size_on_proc,
&prefix_sum,
1,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
MPI_SUM,
comm);
AssertThrowMPI(ierr);
// Locate specific offset for each processor.
const MPI_Offset offset = static_cast<MPI_Offset>(header_size) + prefix_sum;
ierr = Utilities::MPI::LargeCount::File_write_at_all_c(fh,
offset,
ss.str().c_str(),
ss.str().size(),
MPI_CHAR,
MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
if (myrank == n_ranks - 1)
{
// Locating Footer with offset on last rank.
footer_offset = size_on_proc + offset;
std::stringstream ss;
DataOutBase::write_vtu_footer(ss);
const unsigned int footer_size = ss.str().size();
// Writing footer:
ierr = Utilities::MPI::LargeCount::File_write_at_c(fh,
footer_offset,
ss.str().c_str(),
footer_size,
MPI_CHAR,
MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}
}
// Make sure we sync to disk. As written in the standard,
// MPI_File_close() actually already implies a sync but there seems
// to be a bug on at least one configuration (running with multiple
// nodes using OpenMPI 4.1) that requires it. Without this call, the
// footer is sometimes missing.
ierr = MPI_File_sync(fh);
AssertThrowMPI(ierr);
ierr = MPI_File_close(&fh);
AssertThrowMPI(ierr);
#endif
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_pvtu_record(
std::ostream &out,
const std::vector<std::string> &piece_names) const
{
DataOutBase::write_pvtu_record(out,
piece_names,
get_dataset_names(),
get_nonscalar_data_ranges(),
vtk_flags);
}
template <int dim, int spacedim>
std::string
DataOutInterface<dim, spacedim>::write_vtu_with_pvtu_record(
const std::string &directory,
const std::string &filename_without_extension,
const unsigned int counter,
const MPI_Comm mpi_communicator,
const unsigned int n_digits_for_counter,
const unsigned int n_groups) const
{
const unsigned int rank = Utilities::MPI::this_mpi_process(mpi_communicator);
const unsigned int n_ranks =
Utilities::MPI::n_mpi_processes(mpi_communicator);
const unsigned int n_files_written =
(n_groups == 0 || n_groups > n_ranks) ? n_ranks : n_groups;
Assert(n_files_written >= 1, ExcInternalError());
// the "-1" is needed since we use C++ style counting starting with 0, so
// writing 10 files means the filename runs from 0 to 9
const unsigned int n_digits =
Utilities::needed_digits(std::max(0, int(n_files_written) - 1));
const unsigned int color = rank % n_files_written;
const std::string filename =
directory + filename_without_extension + "_" +
Utilities::int_to_string(counter, n_digits_for_counter) + "." +
Utilities::int_to_string(color, n_digits) + ".vtu";
if (n_groups == 0 || n_groups > n_ranks)
{
// every processor writes one file
std::ofstream output(filename);
AssertThrow(output, ExcFileNotOpen(filename));
this->write_vtu(output);
}
else if (n_groups == 1)
{
// write only a single data file in parallel
this->write_vtu_in_parallel(filename, mpi_communicator);
}
else
{
#ifdef DEAL_II_WITH_MPI
// write n_groups data files
MPI_Comm comm_group;
int ierr = MPI_Comm_split(mpi_communicator, color, rank, &comm_group);
AssertThrowMPI(ierr);
this->write_vtu_in_parallel(filename, comm_group);
Utilities::MPI::free_communicator(comm_group);
#else
AssertThrow(false, ExcMessage("Logical error. Should not arrive here."));
#endif
}
// write pvtu record
const std::string pvtu_filename =
filename_without_extension + "_" +
Utilities::int_to_string(counter, n_digits_for_counter) + ".pvtu";
if (rank == 0)
{
std::vector<std::string> filename_vector;
for (unsigned int i = 0; i < n_files_written; ++i)
{
const std::string filename =
filename_without_extension + "_" +
Utilities::int_to_string(counter, n_digits_for_counter) + "." +
Utilities::int_to_string(i, n_digits) + ".vtu";
filename_vector.emplace_back(filename);
}
std::ofstream pvtu_output(directory + pvtu_filename);
this->write_pvtu_record(pvtu_output, filename_vector);
}
return pvtu_filename;
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_deal_II_intermediate(
std::ostream &out) const
{
DataOutBase::write_deal_II_intermediate(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
deal_II_intermediate_flags,
out);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_deal_II_intermediate_in_parallel(
const std::string &filename,
const MPI_Comm comm,
const DataOutBase::CompressionLevel compression) const
{
DataOutBase::write_deal_II_intermediate_in_parallel(
get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
deal_II_intermediate_flags,
filename,
comm,
compression);
}
template <int dim, int spacedim>
XDMFEntry
DataOutInterface<dim, spacedim>::create_xdmf_entry(
const DataOutBase::DataOutFilter &data_filter,
const std::string &h5_filename,
const double cur_time,
const MPI_Comm comm) const
{
return create_xdmf_entry(
data_filter, h5_filename, h5_filename, cur_time, comm);
}
template <int dim, int spacedim>
XDMFEntry
DataOutInterface<dim, spacedim>::create_xdmf_entry(
const DataOutBase::DataOutFilter &data_filter,
const std::string &h5_mesh_filename,
const std::string &h5_solution_filename,
const double cur_time,
const MPI_Comm comm) const
{
AssertThrow(spacedim == 2 || spacedim == 3,
ExcMessage("XDMF only supports 2 or 3 space dimensions."));
#ifndef DEAL_II_WITH_HDF5
// throw an exception, but first make sure the compiler does not warn about
// the now unused function arguments
(void)data_filter;
(void)h5_mesh_filename;
(void)h5_solution_filename;
(void)cur_time;
(void)comm;
AssertThrow(false, ExcMessage("XDMF support requires HDF5 to be turned on."));
return {};
#else
std::uint64_t local_node_cell_count[2], global_node_cell_count[2];
local_node_cell_count[0] = data_filter.n_nodes();
local_node_cell_count[1] = data_filter.n_cells();
const int myrank = Utilities::MPI::this_mpi_process(comm);
// And compute the global total
int ierr = MPI_Allreduce(local_node_cell_count,
global_node_cell_count,
2,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
MPI_SUM,
comm);
AssertThrowMPI(ierr);
// The implementation is a bit complicated because we are supposed to return
// the correct data on rank 0 and an empty object on all other ranks but all
// information (for example the attributes) are only available on ranks that
// have any cells.
// We will identify the smallest rank that has data and then communicate
// from this rank to rank 0 (if they are different ranks).
const bool have_data = (data_filter.n_nodes() > 0);
MPI_Comm split_comm;
{
const int key = myrank;
const int color = (have_data ? 1 : 0);
const int ierr = MPI_Comm_split(comm, color, key, &split_comm);
AssertThrowMPI(ierr);
}
const bool am_i_first_rank_with_data =
have_data && (Utilities::MPI::this_mpi_process(split_comm) == 0);
ierr = MPI_Comm_free(&split_comm);
AssertThrowMPI(ierr);
const int tag = 47381;
// Output the XDMF file only on the root process of all ranks with data:
if (am_i_first_rank_with_data)
{
const auto &patches = get_patches();
Assert(patches.size() > 0, DataOutBase::ExcNoPatches());
// We currently don't support writing mixed meshes:
if constexpr (running_in_debug_mode())
{
for (const auto &patch : patches)
Assert(patch.reference_cell == patches[0].reference_cell,
ExcNotImplemented());
}
XDMFEntry entry(h5_mesh_filename,
h5_solution_filename,
cur_time,
global_node_cell_count[0],
global_node_cell_count[1],
dim,
spacedim,
patches[0].reference_cell);
const unsigned int n_data_sets = data_filter.n_data_sets();
// The vector names generated here must match those generated in
// the HDF5 file
for (unsigned int i = 0; i < n_data_sets; ++i)
{
entry.add_attribute(data_filter.get_data_set_name(i),
data_filter.get_data_set_dim(i));
}
if (myrank != 0)
{
// send to rank 0
const std::vector<char> buffer = Utilities::pack(entry, false);
ierr = MPI_Send(buffer.data(), buffer.size(), MPI_BYTE, 0, tag, comm);
AssertThrowMPI(ierr);
return {};
}
return entry;
}
if (myrank == 0 && !am_i_first_rank_with_data)
{
// receive the XDMF data on rank 0 if we don't have it...
MPI_Status status;
int ierr = MPI_Probe(MPI_ANY_SOURCE, tag, comm, &status);
AssertThrowMPI(ierr);
int len;
ierr = MPI_Get_count(&status, MPI_BYTE, &len);
AssertThrowMPI(ierr);
std::vector<char> buffer(len);
ierr = MPI_Recv(buffer.data(),
len,
MPI_BYTE,
status.MPI_SOURCE,
tag,
comm,
MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
return Utilities::unpack<XDMFEntry>(buffer, false);
}
// default case for any other rank is to return an empty object
return {};
#endif
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_xdmf_file(
const std::vector<XDMFEntry> &entries,
const std::string &filename,
const MPI_Comm comm) const
{
#ifdef DEAL_II_WITH_MPI
const int myrank = Utilities::MPI::this_mpi_process(comm);
#else
(void)comm;
const int myrank = 0;
#endif
// Only rank 0 process writes the XDMF file
if (myrank == 0)
{
std::ofstream xdmf_file(filename);
xdmf_file << "<?xml version=\"1.0\" ?>\n";
xdmf_file << "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []>\n";
xdmf_file << "<Xdmf Version=\"2.0\">\n";
xdmf_file << " <Domain>\n";
xdmf_file
<< " <Grid Name=\"CellTime\" GridType=\"Collection\" CollectionType=\"Temporal\">\n";
for (const auto &entry : entries)
{
xdmf_file << entry.get_xdmf_content(3);
}
xdmf_file << " </Grid>\n";
xdmf_file << " </Domain>\n";
xdmf_file << "</Xdmf>\n";
xdmf_file.close();
}
}
/*
* Write the data in this DataOutInterface to a DataOutFilter object. Filtering
* is performed based on the DataOutFilter flags.
*/
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_filtered_data(
DataOutBase::DataOutFilter &filtered_data) const
{
DataOutBase::write_filtered_data(get_patches(),
get_dataset_names(),
get_nonscalar_data_ranges(),
filtered_data);
}
namespace
{
#ifdef DEAL_II_WITH_HDF5
/**
* Helper function to actually perform the HDF5 output.
*/
template <int dim, int spacedim>
void
do_write_hdf5(const std::vector<DataOutBase::Patch<dim, spacedim>> &patches,
const DataOutBase::DataOutFilter &data_filter,
const DataOutBase::Hdf5Flags &flags,
const bool write_mesh_file,
const std::string &mesh_filename,
const std::string &solution_filename,
const MPI_Comm comm)
{
hid_t h5_mesh_file_id = -1, h5_solution_file_id, file_plist_id, plist_id;
hid_t node_dataspace, node_dataset, node_file_dataspace,
node_memory_dataspace, node_dataset_id;
hid_t cell_dataspace, cell_dataset, cell_file_dataspace,
cell_memory_dataspace;
hid_t pt_data_dataspace, pt_data_dataset, pt_data_file_dataspace,
pt_data_memory_dataspace;
herr_t status;
std::uint64_t local_node_cell_count[2];
hsize_t count[2], offset[2], node_ds_dim[2], cell_ds_dim[2];
std::vector<double> node_data_vec;
std::vector<unsigned int> cell_data_vec;
local_node_cell_count[0] = data_filter.n_nodes();
local_node_cell_count[1] = data_filter.n_cells();
// Create file access properties
file_plist_id = H5Pcreate(H5P_FILE_ACCESS);
AssertThrow(file_plist_id != -1, ExcIO());
// If MPI is enabled *and* HDF5 is parallel, we can do parallel output
# ifdef DEAL_II_WITH_MPI
# ifdef H5_HAVE_PARALLEL
// Set the access to use the specified MPI_Comm object
status = H5Pset_fapl_mpio(file_plist_id, comm, MPI_INFO_NULL);
AssertThrow(status >= 0, ExcIO());
# endif
# endif
// if zlib support is disabled flags are unused
# ifndef DEAL_II_WITH_ZLIB
(void)flags;
# endif
// Compute the global total number of nodes/cells and determine the offset
// of the data for this process
std::uint64_t global_node_cell_count[2] = {0, 0};
std::uint64_t global_node_cell_offsets[2] = {0, 0};
# ifdef DEAL_II_WITH_MPI
int ierr =
MPI_Allreduce(local_node_cell_count,
global_node_cell_count,
2,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
MPI_SUM,
comm);
AssertThrowMPI(ierr);
ierr = MPI_Exscan(local_node_cell_count,
global_node_cell_offsets,
2,
Utilities::MPI::mpi_type_id_for_type<std::uint64_t>,
MPI_SUM,
comm);
AssertThrowMPI(ierr);
# else
global_node_cell_count[0] = local_node_cell_count[0];
global_node_cell_count[1] = local_node_cell_count[1];
global_node_cell_offsets[0] = global_node_cell_offsets[1] = 0;
# endif
// Create the property list for a collective write
plist_id = H5Pcreate(H5P_DATASET_XFER);
AssertThrow(plist_id >= 0, ExcIO());
# ifdef DEAL_II_WITH_MPI
# ifdef H5_HAVE_PARALLEL
status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
AssertThrow(status >= 0, ExcIO());
# endif
# endif
if (write_mesh_file)
{
// Overwrite any existing files (change this to an option?)
h5_mesh_file_id = H5Fcreate(mesh_filename.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
file_plist_id);
AssertThrow(h5_mesh_file_id >= 0, ExcIO());
// Create the dataspace for the nodes and cells. HDF5 only supports 2-
// or 3-dimensional coordinates
node_ds_dim[0] = global_node_cell_count[0];
node_ds_dim[1] = (spacedim < 2) ? 2 : spacedim;
node_dataspace = H5Screate_simple(2, node_ds_dim, nullptr);
AssertThrow(node_dataspace >= 0, ExcIO());
cell_ds_dim[0] = global_node_cell_count[1];
cell_ds_dim[1] = patches[0].reference_cell.n_vertices();
cell_dataspace = H5Screate_simple(2, cell_ds_dim, nullptr);
AssertThrow(cell_dataspace >= 0, ExcIO());
// Create the dataset for the nodes and cells
# if H5Gcreate_vers == 1
node_dataset = H5Dcreate(h5_mesh_file_id,
"nodes",
H5T_NATIVE_DOUBLE,
node_dataspace,
H5P_DEFAULT);
# else
node_dataset_id = H5Pcreate(H5P_DATASET_CREATE);
# ifdef DEAL_II_WITH_ZLIB
H5Pset_deflate(node_dataset_id,
get_zlib_compression_level(flags.compression_level));
H5Pset_chunk(node_dataset_id, 2, node_ds_dim);
# endif
node_dataset = H5Dcreate(h5_mesh_file_id,
"nodes",
H5T_NATIVE_DOUBLE,
node_dataspace,
H5P_DEFAULT,
node_dataset_id,
H5P_DEFAULT);
H5Pclose(node_dataset_id);
# endif
AssertThrow(node_dataset >= 0, ExcIO());
# if H5Gcreate_vers == 1
cell_dataset = H5Dcreate(h5_mesh_file_id,
"cells",
H5T_NATIVE_UINT,
cell_dataspace,
H5P_DEFAULT);
# else
node_dataset_id = H5Pcreate(H5P_DATASET_CREATE);
# ifdef DEAL_II_WITH_ZLIB
H5Pset_deflate(node_dataset_id,
get_zlib_compression_level(flags.compression_level));
H5Pset_chunk(node_dataset_id, 2, cell_ds_dim);
# endif
cell_dataset = H5Dcreate(h5_mesh_file_id,
"cells",
H5T_NATIVE_UINT,
cell_dataspace,
H5P_DEFAULT,
node_dataset_id,
H5P_DEFAULT);
H5Pclose(node_dataset_id);
# endif
AssertThrow(cell_dataset >= 0, ExcIO());
// Close the node and cell dataspaces since we're done with them
status = H5Sclose(node_dataspace);
AssertThrow(status >= 0, ExcIO());
status = H5Sclose(cell_dataspace);
AssertThrow(status >= 0, ExcIO());
// Create the data subset we'll use to read from memory. HDF5 only
// supports 2- or 3-dimensional coordinates
count[0] = local_node_cell_count[0];
count[1] = (spacedim < 2) ? 2 : spacedim;
offset[0] = global_node_cell_offsets[0];
offset[1] = 0;
node_memory_dataspace = H5Screate_simple(2, count, nullptr);
AssertThrow(node_memory_dataspace >= 0, ExcIO());
// Select the hyperslab in the file
node_file_dataspace = H5Dget_space(node_dataset);
AssertThrow(node_file_dataspace >= 0, ExcIO());
status = H5Sselect_hyperslab(
node_file_dataspace, H5S_SELECT_SET, offset, nullptr, count, nullptr);
AssertThrow(status >= 0, ExcIO());
// And repeat for cells
count[0] = local_node_cell_count[1];
count[1] = patches[0].reference_cell.n_vertices();
offset[0] = global_node_cell_offsets[1];
offset[1] = 0;
cell_memory_dataspace = H5Screate_simple(2, count, nullptr);
AssertThrow(cell_memory_dataspace >= 0, ExcIO());
cell_file_dataspace = H5Dget_space(cell_dataset);
AssertThrow(cell_file_dataspace >= 0, ExcIO());
status = H5Sselect_hyperslab(
cell_file_dataspace, H5S_SELECT_SET, offset, nullptr, count, nullptr);
AssertThrow(status >= 0, ExcIO());
// And finally, write the node data
data_filter.fill_node_data(node_data_vec);
status = H5Dwrite(node_dataset,
H5T_NATIVE_DOUBLE,
node_memory_dataspace,
node_file_dataspace,
plist_id,
node_data_vec.data());
AssertThrow(status >= 0, ExcIO());
node_data_vec.clear();
// And the cell data
data_filter.fill_cell_data(global_node_cell_offsets[0], cell_data_vec);
status = H5Dwrite(cell_dataset,
H5T_NATIVE_UINT,
cell_memory_dataspace,
cell_file_dataspace,
plist_id,
cell_data_vec.data());
AssertThrow(status >= 0, ExcIO());
cell_data_vec.clear();
// Close the file dataspaces
status = H5Sclose(node_file_dataspace);
AssertThrow(status >= 0, ExcIO());
status = H5Sclose(cell_file_dataspace);
AssertThrow(status >= 0, ExcIO());
// Close the memory dataspaces
status = H5Sclose(node_memory_dataspace);
AssertThrow(status >= 0, ExcIO());
status = H5Sclose(cell_memory_dataspace);
AssertThrow(status >= 0, ExcIO());
// Close the datasets
status = H5Dclose(node_dataset);
AssertThrow(status >= 0, ExcIO());
status = H5Dclose(cell_dataset);
AssertThrow(status >= 0, ExcIO());
// If the filenames are different, we need to close the mesh file
if (mesh_filename != solution_filename)
{
status = H5Fclose(h5_mesh_file_id);
AssertThrow(status >= 0, ExcIO());
}
}
// If the filenames are identical, continue with the same file
if (mesh_filename == solution_filename && write_mesh_file)
{
h5_solution_file_id = h5_mesh_file_id;
}
else
{
// Otherwise we need to open a new file
h5_solution_file_id = H5Fcreate(solution_filename.c_str(),
H5F_ACC_TRUNC,
H5P_DEFAULT,
file_plist_id);
AssertThrow(h5_solution_file_id >= 0, ExcIO());
}
// when writing, first write out all vector data, then handle the scalar
// data sets that have been left over
unsigned int i;
std::string vector_name;
for (i = 0; i < data_filter.n_data_sets(); ++i)
{
// Allocate space for the point data
// Must be either 1d or 3d
const unsigned int pt_data_vector_dim = data_filter.get_data_set_dim(i);
vector_name = data_filter.get_data_set_name(i);
// Create the dataspace for the point data
node_ds_dim[0] = global_node_cell_count[0];
node_ds_dim[1] = pt_data_vector_dim;
pt_data_dataspace = H5Screate_simple(2, node_ds_dim, nullptr);
AssertThrow(pt_data_dataspace >= 0, ExcIO());
# if H5Gcreate_vers == 1
pt_data_dataset = H5Dcreate(h5_solution_file_id,
vector_name.c_str(),
H5T_NATIVE_DOUBLE,
pt_data_dataspace,
H5P_DEFAULT);
# else
node_dataset_id = H5Pcreate(H5P_DATASET_CREATE);
# ifdef DEAL_II_WITH_ZLIB
H5Pset_deflate(node_dataset_id,
get_zlib_compression_level(flags.compression_level));
H5Pset_chunk(node_dataset_id, 2, node_ds_dim);
# endif
pt_data_dataset = H5Dcreate(h5_solution_file_id,
vector_name.c_str(),
H5T_NATIVE_DOUBLE,
pt_data_dataspace,
H5P_DEFAULT,
node_dataset_id,
H5P_DEFAULT);
H5Pclose(node_dataset_id);
# endif
AssertThrow(pt_data_dataset >= 0, ExcIO());
// Create the data subset we'll use to read from memory
count[0] = local_node_cell_count[0];
count[1] = pt_data_vector_dim;
offset[0] = global_node_cell_offsets[0];
offset[1] = 0;
pt_data_memory_dataspace = H5Screate_simple(2, count, nullptr);
AssertThrow(pt_data_memory_dataspace >= 0, ExcIO());
// Select the hyperslab in the file
pt_data_file_dataspace = H5Dget_space(pt_data_dataset);
AssertThrow(pt_data_file_dataspace >= 0, ExcIO());
status = H5Sselect_hyperslab(pt_data_file_dataspace,
H5S_SELECT_SET,
offset,
nullptr,
count,
nullptr);
AssertThrow(status >= 0, ExcIO());
// And finally, write the data
status = H5Dwrite(pt_data_dataset,
H5T_NATIVE_DOUBLE,
pt_data_memory_dataspace,
pt_data_file_dataspace,
plist_id,
data_filter.get_data_set(i));
AssertThrow(status >= 0, ExcIO());
// Close the dataspaces
status = H5Sclose(pt_data_dataspace);
AssertThrow(status >= 0, ExcIO());
status = H5Sclose(pt_data_memory_dataspace);
AssertThrow(status >= 0, ExcIO());
status = H5Sclose(pt_data_file_dataspace);
AssertThrow(status >= 0, ExcIO());
// Close the dataset
status = H5Dclose(pt_data_dataset);
AssertThrow(status >= 0, ExcIO());
}
// Close the file property list
status = H5Pclose(file_plist_id);
AssertThrow(status >= 0, ExcIO());
// Close the parallel access
status = H5Pclose(plist_id);
AssertThrow(status >= 0, ExcIO());
// Close the file
status = H5Fclose(h5_solution_file_id);
AssertThrow(status >= 0, ExcIO());
}
#endif
} // namespace
template <int dim, int spacedim>
void
DataOutBase::write_filtered_data(
const std::vector<Patch<dim, spacedim>> &patches,
const std::vector<std::string> &data_names,
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
&nonscalar_data_ranges,
DataOutBase::DataOutFilter &filtered_data)
{
const unsigned int n_data_sets = data_names.size();
#ifndef DEAL_II_WITH_MPI
// verify that there are indeed patches to be written out. most of the times,
// people just forget to call build_patches when there are no patches, so a
// warning is in order. that said, the assertion is disabled if we support MPI
// since then it can happen that on the coarsest mesh, a processor simply has
// no cells it actually owns, and in that case it is legit if there are no
// patches
Assert(patches.size() > 0, ExcNoPatches());
#else
if (patches.empty())
return;
#endif
unsigned int n_nodes;
std::tie(n_nodes, std::ignore) = count_nodes_and_cells(patches);
// For the format we write here, we need to write all node values relating
// to one variable at a time. We could in principle do this by looping
// over all patches and extracting the values corresponding to the one
// variable we're dealing with right now, and then start the process over
// for the next variable with another loop over all patches.
//
// An easier way is to create a global table that for each variable
// lists all values. This copying of data vectors can be done in the
// background while we're already working on vertices and cells,
// so do this on a separate task and when wanting to write out the
// data, we wait for that task to finish.
Threads::Task<std::unique_ptr<Table<2, double>>>
create_global_data_table_task = Threads::new_task(
[&patches]() { return create_global_data_table(patches); });
// Write the nodes/cells to the DataOutFilter object.
write_nodes(patches, filtered_data);
write_cells(patches, filtered_data);
// Wait for the reordering to be done and retrieve the reordered data:
const Table<2, double> data_vectors =
std::move(*create_global_data_table_task.return_value());
// when writing, first write out all vector data, then handle the scalar data
// sets that have been left over
unsigned int i, n_th_vector, data_set, pt_data_vector_dim;
std::string vector_name;
for (n_th_vector = 0, data_set = 0; data_set < n_data_sets;)
{
// Advance n_th_vector to at least the current data set we are on
while (n_th_vector < nonscalar_data_ranges.size() &&
std::get<0>(nonscalar_data_ranges[n_th_vector]) < data_set)
++n_th_vector;
// Determine the dimension of this data
if (n_th_vector < nonscalar_data_ranges.size() &&
std::get<0>(nonscalar_data_ranges[n_th_vector]) == data_set)
{
// Multiple dimensions
pt_data_vector_dim = std::get<1>(nonscalar_data_ranges[n_th_vector]) -
std::get<0>(nonscalar_data_ranges[n_th_vector]) +
1;
// Ensure the dimensionality of the data is correct
AssertThrow(
std::get<1>(nonscalar_data_ranges[n_th_vector]) >=
std::get<0>(nonscalar_data_ranges[n_th_vector]),
ExcLowerRange(std::get<1>(nonscalar_data_ranges[n_th_vector]),
std::get<0>(nonscalar_data_ranges[n_th_vector])));
AssertThrow(
std::get<1>(nonscalar_data_ranges[n_th_vector]) < n_data_sets,
ExcIndexRange(std::get<1>(nonscalar_data_ranges[n_th_vector]),
0,
n_data_sets));
// Determine the vector name. Concatenate all the component names with
// double underscores unless a vector name has been specified
if (!std::get<2>(nonscalar_data_ranges[n_th_vector]).empty())
{
vector_name = std::get<2>(nonscalar_data_ranges[n_th_vector]);
}
else
{
vector_name = "";
for (i = std::get<0>(nonscalar_data_ranges[n_th_vector]);
i < std::get<1>(nonscalar_data_ranges[n_th_vector]);
++i)
vector_name += data_names[i] + "__";
vector_name +=
data_names[std::get<1>(nonscalar_data_ranges[n_th_vector])];
}
}
else
{
// One dimension
pt_data_vector_dim = 1;
vector_name = data_names[data_set];
}
// Write data to the filter object
filtered_data.write_data_set(vector_name,
pt_data_vector_dim,
data_set,
data_vectors);
// Advance the current data set
data_set += pt_data_vector_dim;
}
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_hdf5_parallel(
const DataOutBase::DataOutFilter &data_filter,
const std::string &filename,
const MPI_Comm comm) const
{
DataOutBase::write_hdf5_parallel(
get_patches(), data_filter, hdf5_flags, filename, comm);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_hdf5_parallel(
const DataOutBase::DataOutFilter &data_filter,
const bool write_mesh_file,
const std::string &mesh_filename,
const std::string &solution_filename,
const MPI_Comm comm) const
{
DataOutBase::write_hdf5_parallel(get_patches(),
data_filter,
hdf5_flags,
write_mesh_file,
mesh_filename,
solution_filename,
comm);
}
template <int dim, int spacedim>
void
DataOutBase::write_hdf5_parallel(
const std::vector<Patch<dim, spacedim>> &patches,
const DataOutBase::DataOutFilter &data_filter,
const DataOutBase::Hdf5Flags &flags,
const std::string &filename,
const MPI_Comm comm)
{
write_hdf5_parallel(
patches, data_filter, flags, true, filename, filename, comm);
}
template <int dim, int spacedim>
void
DataOutBase::write_hdf5_parallel(
const std::vector<Patch<dim, spacedim>> &patches,
const DataOutBase::DataOutFilter &data_filter,
const DataOutBase::Hdf5Flags &flags,
const bool write_mesh_file,
const std::string &mesh_filename,
const std::string &solution_filename,
const MPI_Comm comm)
{
AssertThrow(
spacedim >= 2,
ExcMessage(
"DataOutBase was asked to write HDF5 output for a space dimension of 1. "
"HDF5 only supports datasets that live in 2 or 3 dimensions."));
#ifndef DEAL_II_WITH_HDF5
// throw an exception, but first make sure the compiler does not warn about
// the now unused function arguments
(void)patches;
(void)data_filter;
(void)flags;
(void)write_mesh_file;
(void)mesh_filename;
(void)solution_filename;
(void)comm;
AssertThrow(false, ExcNeedsHDF5());
#else
const unsigned int n_ranks = Utilities::MPI::n_mpi_processes(comm);
(void)n_ranks;
// If HDF5 is not parallel and we're using multiple processes, abort:
# ifndef H5_HAVE_PARALLEL
AssertThrow(
n_ranks <= 1,
ExcMessage(
"Serial HDF5 output on multiple processes is not yet supported."));
# endif
// Verify that there are indeed patches to be written out. most of
// the times, people just forget to call build_patches when there
// are no patches, so a warning is in order. That said, the
// assertion is disabled if we run with more than one MPI rank,
// since then it can happen that, on coarse meshes, a processor
// simply has no cells it actually owns, and in that case it is
// legit if there are no patches.
Assert((patches.size() > 0) || (n_ranks > 1), ExcNoPatches());
// The HDF5 routines perform a bunch of collective calls that expect all
// ranks to participate. One ranks without any patches we are missing
// critical information, so rather than broadcasting that information, just
// create a new communicator that only contains ranks with cells and
// use that to perform the write operations:
const bool have_patches = (patches.size() > 0);
MPI_Comm split_comm;
{
const int key = Utilities::MPI::this_mpi_process(comm);
const int color = (have_patches ? 1 : 0);
const int ierr = MPI_Comm_split(comm, color, key, &split_comm);
AssertThrowMPI(ierr);
}
if (have_patches)
{
do_write_hdf5<dim, spacedim>(patches,
data_filter,
flags,
write_mesh_file,
mesh_filename,
solution_filename,
split_comm);
}
const int ierr = MPI_Comm_free(&split_comm);
AssertThrowMPI(ierr);
#endif
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write(
std::ostream &out,
const DataOutBase::OutputFormat output_format_) const
{
DataOutBase::OutputFormat output_format = output_format_;
if (output_format == DataOutBase::default_format)
output_format = default_fmt;
switch (output_format)
{
case DataOutBase::none:
break;
case DataOutBase::dx:
write_dx(out);
break;
case DataOutBase::ucd:
write_ucd(out);
break;
case DataOutBase::gnuplot:
write_gnuplot(out);
break;
case DataOutBase::povray:
write_povray(out);
break;
case DataOutBase::eps:
write_eps(out);
break;
case DataOutBase::gmv:
write_gmv(out);
break;
case DataOutBase::tecplot:
write_tecplot(out);
break;
case DataOutBase::vtk:
write_vtk(out);
break;
case DataOutBase::vtu:
write_vtu(out);
break;
case DataOutBase::svg:
write_svg(out);
break;
case DataOutBase::deal_II_intermediate:
write_deal_II_intermediate(out);
break;
default:
DEAL_II_NOT_IMPLEMENTED();
}
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::set_default_format(
const DataOutBase::OutputFormat fmt)
{
Assert(fmt != DataOutBase::default_format, ExcNotImplemented());
default_fmt = fmt;
}
template <int dim, int spacedim>
template <typename FlagType>
void
DataOutInterface<dim, spacedim>::set_flags(const FlagType &flags)
{
if constexpr (std::is_same_v<FlagType, DataOutBase::DXFlags>)
dx_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::UcdFlags>)
ucd_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::PovrayFlags>)
povray_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::EpsFlags>)
eps_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::GmvFlags>)
gmv_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::Hdf5Flags>)
hdf5_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::TecplotFlags>)
tecplot_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::VtkFlags>)
vtk_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::SvgFlags>)
svg_flags = flags;
else if constexpr (std::is_same_v<FlagType, DataOutBase::GnuplotFlags>)
gnuplot_flags = flags;
else if constexpr (std::is_same_v<FlagType,
DataOutBase::Deal_II_IntermediateFlags>)
deal_II_intermediate_flags = flags;
else
DEAL_II_NOT_IMPLEMENTED();
}
template <int dim, int spacedim>
std::string
DataOutInterface<dim, spacedim>::default_suffix(
const DataOutBase::OutputFormat output_format) const
{
if (output_format == DataOutBase::default_format)
return DataOutBase::default_suffix(default_fmt);
else
return DataOutBase::default_suffix(output_format);
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::declare_parameters(ParameterHandler &prm)
{
prm.declare_entry("Output format",
"gnuplot",
Patterns::Selection(DataOutBase::get_output_format_names()),
"A name for the output format to be used");
prm.declare_entry("Subdivisions",
"1",
Patterns::Integer(),
"Number of subdivisions of each mesh cell");
prm.enter_subsection("DX output parameters");
DataOutBase::DXFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("UCD output parameters");
DataOutBase::UcdFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Gnuplot output parameters");
DataOutBase::GnuplotFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Povray output parameters");
DataOutBase::PovrayFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Eps output parameters");
DataOutBase::EpsFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Gmv output parameters");
DataOutBase::GmvFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("HDF5 output parameters");
DataOutBase::Hdf5Flags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Tecplot output parameters");
DataOutBase::TecplotFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Vtk output parameters");
DataOutBase::VtkFlags::declare_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("deal.II intermediate output parameters");
DataOutBase::Deal_II_IntermediateFlags::declare_parameters(prm);
prm.leave_subsection();
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::parse_parameters(ParameterHandler &prm)
{
const std::string &output_name = prm.get("Output format");
default_fmt = DataOutBase::parse_output_format(output_name);
default_subdivisions = prm.get_integer("Subdivisions");
prm.enter_subsection("DX output parameters");
dx_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("UCD output parameters");
ucd_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Gnuplot output parameters");
gnuplot_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Povray output parameters");
povray_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Eps output parameters");
eps_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Gmv output parameters");
gmv_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("HDF5 output parameters");
hdf5_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Tecplot output parameters");
tecplot_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("Vtk output parameters");
vtk_flags.parse_parameters(prm);
prm.leave_subsection();
prm.enter_subsection("deal.II intermediate output parameters");
deal_II_intermediate_flags.parse_parameters(prm);
prm.leave_subsection();
}
template <int dim, int spacedim>
std::size_t
DataOutInterface<dim, spacedim>::memory_consumption() const
{
return (sizeof(default_fmt) +
MemoryConsumption::memory_consumption(dx_flags) +
MemoryConsumption::memory_consumption(ucd_flags) +
MemoryConsumption::memory_consumption(gnuplot_flags) +
MemoryConsumption::memory_consumption(povray_flags) +
MemoryConsumption::memory_consumption(eps_flags) +
MemoryConsumption::memory_consumption(gmv_flags) +
MemoryConsumption::memory_consumption(hdf5_flags) +
MemoryConsumption::memory_consumption(tecplot_flags) +
MemoryConsumption::memory_consumption(vtk_flags) +
MemoryConsumption::memory_consumption(svg_flags) +
MemoryConsumption::memory_consumption(deal_II_intermediate_flags));
}
template <int dim, int spacedim>
std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
DataOutInterface<dim, spacedim>::get_nonscalar_data_ranges() const
{
return std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>();
}
template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::validate_dataset_names() const
{
if constexpr (running_in_debug_mode())
{
{
// Check that names for datasets are only used once. This is somewhat
// complicated, because vector ranges might have a name or not.
std::set<std::string> all_names;
const std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
ranges = this->get_nonscalar_data_ranges();
const std::vector<std::string> data_names = this->get_dataset_names();
const unsigned int n_data_sets = data_names.size();
std::vector<bool> data_set_written(n_data_sets, false);
for (const auto &range : ranges)
{
const std::string &name = std::get<2>(range);
if (!name.empty())
{
Assert(all_names.find(name) == all_names.end(),
ExcMessage(
"Error: names of fields in DataOut need to be unique, "
"but '" +
name + "' is used more than once."));
all_names.insert(name);
for (unsigned int i = std::get<0>(range);
i <= std::get<1>(range);
++i)
data_set_written[i] = true;
}
}
for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set)
if (data_set_written[data_set] == false)
{
const std::string &name = data_names[data_set];
Assert(all_names.find(name) == all_names.end(),
ExcMessage(
"Error: names of fields in DataOut need to be unique, "
"but '" +
name + "' is used more than once."));
all_names.insert(name);
}
}
}
}
// ---------------------------------------------- DataOutReader ----------
template <int dim, int spacedim>
void
DataOutReader<dim, spacedim>::read(std::istream &in)
{
AssertThrow(in.fail() == false, ExcIO());
// first empty previous content
{
std::vector<typename dealii::DataOutBase::Patch<dim, spacedim>> tmp;
tmp.swap(patches);
}
{
std::vector<std::string> tmp;
tmp.swap(dataset_names);
}
{
std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
tmp;
tmp.swap(nonscalar_data_ranges);
}
// then check that we have the correct header of this file. both the first and
// second real lines have to match, as well as the dimension information
// written before that and the Version information written in the third line
{
std::pair<unsigned int, unsigned int> dimension_info =
DataOutBase::determine_intermediate_format_dimensions(in);
AssertThrow((dimension_info.first == dim) &&
(dimension_info.second == spacedim),
ExcIncompatibleDimensions(
dimension_info.first, dim, dimension_info.second, spacedim));
// read to the end of the line
std::string tmp;
getline(in, tmp);
}
{
std::string header;
getline(in, header);
std::ostringstream s;
s << "[deal.II intermediate format graphics data]";
Assert(header == s.str(), ExcUnexpectedInput(s.str(), header));
}
{
std::string header;
getline(in, header);
std::ostringstream s;
s << "[written by " << DEAL_II_PACKAGE_NAME << " "
<< DEAL_II_PACKAGE_VERSION << "]";
Assert(header == s.str(), ExcUnexpectedInput(s.str(), header));
}
{
std::string header;
getline(in, header);
std::ostringstream s;
s << "[Version: "
<< dealii::DataOutBase::Deal_II_IntermediateFlags::format_version << "]";
Assert(header == s.str(),
ExcMessage(
"Invalid or incompatible file format. Intermediate format "
"files can only be read by the same deal.II version as they "
"are written by."));
}
// then read the rest of the data
unsigned int n_datasets;
in >> n_datasets;
dataset_names.resize(n_datasets);
for (unsigned int i = 0; i < n_datasets; ++i)
in >> dataset_names[i];
unsigned int n_patches;
in >> n_patches;
patches.resize(n_patches);
for (unsigned int i = 0; i < n_patches; ++i)
in >> patches[i];
unsigned int n_nonscalar_data_ranges;
in >> n_nonscalar_data_ranges;
nonscalar_data_ranges.resize(n_nonscalar_data_ranges);
for (unsigned int i = 0; i < n_nonscalar_data_ranges; ++i)
{
in >> std::get<0>(nonscalar_data_ranges[i]) >>
std::get<1>(nonscalar_data_ranges[i]);
// read in the name of that vector range. because it is on a separate
// line, we first need to read to the end of the previous line (nothing
// should be there any more after we've read the previous two integers)
// and then read the entire next line for the name
std::string name;
getline(in, name);
getline(in, name);
std::get<2>(nonscalar_data_ranges[i]) = name;
}
AssertThrow(in.fail() == false, ExcIO());
}
template <int dim, int spacedim>
void
DataOutReader<dim, spacedim>::read_whole_parallel_file(std::istream &in)
{
AssertThrow(in.fail() == false, ExcIO());
ParallelIntermediateHeader header;
in.read(reinterpret_cast<char *>(&header), sizeof(header));
AssertThrow(
header.magic == 0x00dea111,
ExcMessage(
"Invalid header of parallel deal.II intermediate format encountered."));
AssertThrow(
header.version == DataOutBase::Deal_II_IntermediateFlags::format_version,
ExcMessage(
"Incorrect header version of parallel deal.II intermediate format."));
std::vector<std::uint64_t> chunk_sizes(header.n_ranks);
in.read(reinterpret_cast<char *>(chunk_sizes.data()),
header.n_ranks * sizeof(std::uint64_t));
for (unsigned int n = 0; n < header.n_ranks; ++n)
{
// First read the compressed data into temp_buffer and then
// decompress and put into datastream
std::vector<char> temp_buffer(chunk_sizes[n]);
in.read(temp_buffer.data(), chunk_sizes[n]);
AssertThrow(static_cast<DataOutBase::CompressionLevel>(
header.compression) !=
DataOutBase::CompressionLevel::plain_text,
ExcNotImplemented());
boost::iostreams::filtering_istreambuf f;
if (static_cast<DataOutBase::CompressionLevel>(header.compression) !=
DataOutBase::CompressionLevel::no_compression)
#ifdef DEAL_II_WITH_ZLIB
f.push(boost::iostreams::zlib_decompressor());
#else
AssertThrow(
false,
ExcMessage(
"Decompression requires deal.II to be configured with ZLIB support."));
#endif
boost::iostreams::basic_array_source<char> source(temp_buffer.data(),
temp_buffer.size());
f.push(source);
std::stringstream datastream;
boost::iostreams::copy(f, datastream);
// Now we can load the data and merge this chunk into *this
if (n == 0)
{
read(datastream);
}
else
{
DataOutReader<dim, spacedim> temp_reader;
temp_reader.read(datastream);
merge(temp_reader);
}
}
}
template <int dim, int spacedim>
void
DataOutReader<dim, spacedim>::merge(const DataOutReader<dim, spacedim> &source)
{
using Patch = typename dealii::DataOutBase::Patch<dim, spacedim>;
const std::vector<Patch> &source_patches = source.get_patches();
Assert(patches.size() != 0, DataOutBase::ExcNoPatches());
Assert(source_patches.size() != 0, DataOutBase::ExcNoPatches());
// check equality of component names
Assert(get_dataset_names() == source.get_dataset_names(),
ExcIncompatibleDatasetNames());
// check equality of the vector data specifications
Assert(get_nonscalar_data_ranges().size() ==
source.get_nonscalar_data_ranges().size(),
ExcMessage("Both sources need to declare the same components "
"as vectors."));
for (unsigned int i = 0; i < get_nonscalar_data_ranges().size(); ++i)
{
Assert(std::get<0>(get_nonscalar_data_ranges()[i]) ==
std::get<0>(source.get_nonscalar_data_ranges()[i]),
ExcMessage("Both sources need to declare the same components "
"as vectors."));
Assert(std::get<1>(get_nonscalar_data_ranges()[i]) ==
std::get<1>(source.get_nonscalar_data_ranges()[i]),
ExcMessage("Both sources need to declare the same components "
"as vectors."));
Assert(std::get<2>(get_nonscalar_data_ranges()[i]) ==
std::get<2>(source.get_nonscalar_data_ranges()[i]),
ExcMessage("Both sources need to declare the same components "
"as vectors."));
}
// make sure patches are compatible
Assert(patches[0].n_subdivisions == source_patches[0].n_subdivisions,
ExcIncompatiblePatchLists());
Assert(patches[0].data.n_rows() == source_patches[0].data.n_rows(),
ExcIncompatiblePatchLists());
Assert(patches[0].data.n_cols() == source_patches[0].data.n_cols(),
ExcIncompatiblePatchLists());
// merge patches. store old number of elements, since we need to adjust patch
// numbers, etc afterwards
const unsigned int old_n_patches = patches.size();
patches.insert(patches.end(), source_patches.begin(), source_patches.end());
// adjust patch numbers
for (unsigned int i = old_n_patches; i < patches.size(); ++i)
patches[i].patch_index += old_n_patches;
// adjust patch neighbors
for (unsigned int i = old_n_patches; i < patches.size(); ++i)
for (const unsigned int n : GeometryInfo<dim>::face_indices())
if (patches[i].neighbors[n] !=
dealii::DataOutBase::Patch<dim, spacedim>::no_neighbor)
patches[i].neighbors[n] += old_n_patches;
}
template <int dim, int spacedim>
const std::vector<typename dealii::DataOutBase::Patch<dim, spacedim>> &
DataOutReader<dim, spacedim>::get_patches() const
{
return patches;
}
template <int dim, int spacedim>
std::vector<std::string>
DataOutReader<dim, spacedim>::get_dataset_names() const
{
return dataset_names;
}
template <int dim, int spacedim>
std::vector<
std::tuple<unsigned int,
unsigned int,
std::string,
DataComponentInterpretation::DataComponentInterpretation>>
DataOutReader<dim, spacedim>::get_nonscalar_data_ranges() const
{
return nonscalar_data_ranges;
}
// ---------------------------------------------- XDMFEntry ----------
XDMFEntry::XDMFEntry()
: valid(false)
, h5_sol_filename("")
, h5_mesh_filename("")
, entry_time(0.0)
, num_nodes(numbers::invalid_unsigned_int)
, num_cells(numbers::invalid_unsigned_int)
, dimension(numbers::invalid_unsigned_int)
, space_dimension(numbers::invalid_unsigned_int)
, cell_type()
{}
XDMFEntry::XDMFEntry(const std::string &filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const ReferenceCell &cell_type)
: XDMFEntry(filename, filename, time, nodes, cells, dim, dim, cell_type)
{}
XDMFEntry::XDMFEntry(const std::string &mesh_filename,
const std::string &solution_filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const ReferenceCell &cell_type)
: XDMFEntry(mesh_filename,
solution_filename,
time,
nodes,
cells,
dim,
dim,
cell_type)
{}
namespace
{
/**
* Deprecated XDMFEntry constructors do not fill the cell_type, so we use this
* little helper to convert it to the appropriate hex cell.
*/
ReferenceCell
cell_type_hex_if_invalid(const ReferenceCell &cell_type,
const unsigned int dimension)
{
if (cell_type == ReferenceCells::Invalid)
{
switch (dimension)
{
case 0:
return ReferenceCells::get_hypercube<0>();
case 1:
return ReferenceCells::get_hypercube<1>();
case 2:
return ReferenceCells::get_hypercube<2>();
case 3:
return ReferenceCells::get_hypercube<3>();
default:
AssertThrow(false, ExcMessage("Invalid dimension"));
}
}
else
return cell_type;
}
} // namespace
XDMFEntry::XDMFEntry(const std::string &mesh_filename,
const std::string &solution_filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const unsigned int spacedim,
const ReferenceCell &cell_type_)
: valid(true)
, h5_sol_filename(solution_filename)
, h5_mesh_filename(mesh_filename)
, entry_time(time)
, num_nodes(nodes)
, num_cells(cells)
, dimension(dim)
, space_dimension(spacedim)
, cell_type(cell_type_hex_if_invalid(cell_type_, dim))
{}
void
XDMFEntry::add_attribute(const std::string &attr_name,
const unsigned int dimension)
{
attribute_dims[attr_name] = dimension;
}
namespace
{
/**
* Small function to create indentation for XML file.
*/
std::string
indent(const unsigned int indent_level)
{
std::string res = "";
for (unsigned int i = 0; i < indent_level; ++i)
res += " ";
return res;
}
} // namespace
std::string
XDMFEntry::get_xdmf_content(const unsigned int indent_level) const
{
if (!valid)
return "";
std::stringstream ss;
ss.precision(12);
ss << indent(indent_level + 0)
<< "<Grid Name=\"mesh\" GridType=\"Uniform\">\n";
ss << indent(indent_level + 1) << "<Time Value=\"" << entry_time << "\"/>\n";
ss << indent(indent_level + 1) << "<Geometry GeometryType=\""
<< (space_dimension <= 2 ? "XY" : "XYZ") << "\">\n";
ss << indent(indent_level + 2) << "<DataItem Dimensions=\"" << num_nodes
<< " " << (space_dimension <= 2 ? 2 : space_dimension)
<< "\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n";
ss << indent(indent_level + 3) << h5_mesh_filename << ":/nodes\n";
ss << indent(indent_level + 2) << "</DataItem>\n";
ss << indent(indent_level + 1) << "</Geometry>\n";
// If we have cells defined, use the topology corresponding to the dimension
if (num_cells > 0)
{
ss << indent(indent_level + 1) << "<Topology TopologyType=\"";
if (dimension == 0)
{
ss << "Polyvertex";
}
else if (dimension == 1)
{
ss << "Polyline";
}
else if (dimension == 2)
{
Assert(cell_type == ReferenceCells::Quadrilateral ||
cell_type == ReferenceCells::Triangle,
ExcNotImplemented());
if (cell_type == ReferenceCells::Quadrilateral)
{
ss << "Quadrilateral";
}
else // if (cell_type == ReferenceCells::Triangle)
{
ss << "Triangle";
}
}
else if (dimension == 3)
{
Assert(cell_type == ReferenceCells::Hexahedron ||
cell_type == ReferenceCells::Tetrahedron,
ExcNotImplemented());
if (cell_type == ReferenceCells::Hexahedron)
{
ss << "Hexahedron";
}
else // if (reference_cell == ReferenceCells::Tetrahedron)
{
ss << "Tetrahedron";
}
}
ss << "\" NumberOfElements=\"" << num_cells;
if (dimension == 0)
ss << "\" NodesPerElement=\"1\">\n";
else if (dimension == 1)
ss << "\" NodesPerElement=\"2\">\n";
else
// no "NodesPerElement" for dimension 2 and higher
ss << "\">\n";
ss << indent(indent_level + 2) << "<DataItem Dimensions=\"" << num_cells
<< " " << cell_type.n_vertices()
<< "\" NumberType=\"UInt\" Format=\"HDF\">\n";
ss << indent(indent_level + 3) << h5_mesh_filename << ":/cells\n";
ss << indent(indent_level + 2) << "</DataItem>\n";
ss << indent(indent_level + 1) << "</Topology>\n";
}
// Otherwise, we assume the points are isolated in space and use a Polyvertex
// topology
else
{
ss << indent(indent_level + 1)
<< "<Topology TopologyType=\"Polyvertex\" NumberOfElements=\""
<< num_nodes << "\">\n";
ss << indent(indent_level + 1) << "</Topology>\n";
}
for (const auto &attribute_dim : attribute_dims)
{
ss << indent(indent_level + 1) << "<Attribute Name=\""
<< attribute_dim.first << "\" AttributeType=\""
<< (attribute_dim.second > 1 ? "Vector" : "Scalar")
<< "\" Center=\"Node\">\n";
// Vectors must have 3 elements even for 2d models
ss << indent(indent_level + 2) << "<DataItem Dimensions=\"" << num_nodes
<< " " << (attribute_dim.second > 1 ? 3 : 1)
<< "\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n";
ss << indent(indent_level + 3) << h5_sol_filename << ":/"
<< attribute_dim.first << '\n';
ss << indent(indent_level + 2) << "</DataItem>\n";
ss << indent(indent_level + 1) << "</Attribute>\n";
}
ss << indent(indent_level + 0) << "</Grid>\n";
return ss.str();
}
namespace DataOutBase
{
template <int dim, int spacedim>
std::ostream &
operator<<(std::ostream &out, const Patch<dim, spacedim> &patch)
{
// write a header line
out << "[deal.II intermediate Patch<" << dim << ',' << spacedim << ">]"
<< '\n';
// First export what kind of reference cell we are looking at:
out << patch.reference_cell << '\n';
// then write all the data that is in this patch
for (const unsigned int i : patch.reference_cell.vertex_indices())
out << patch.vertices[i] << ' ';
out << '\n';
for (const unsigned int i : patch.reference_cell.face_indices())
out << patch.neighbors[i] << ' ';
out << '\n';
out << patch.patch_index << ' ' << patch.n_subdivisions << '\n';
out << patch.points_are_available << '\n';
out << patch.data.n_rows() << ' ' << patch.data.n_cols() << '\n';
for (unsigned int i = 0; i < patch.data.n_rows(); ++i)
for (unsigned int j = 0; j < patch.data.n_cols(); ++j)
out << patch.data[i][j] << ' ';
out << '\n';
out << '\n';
return out;
}
template <int dim, int spacedim>
std::istream &
operator>>(std::istream &in, Patch<dim, spacedim> &patch)
{
AssertThrow(in.fail() == false, ExcIO());
// read a header line and compare it to what we usually write. skip all
// lines that contain only blanks at the start
{
std::string header;
do
{
getline(in, header);
while ((header.size() != 0) && (header.back() == ' '))
header.erase(header.size() - 1);
}
while ((header.empty()) && in);
std::ostringstream s;
s << "[deal.II intermediate Patch<" << dim << ',' << spacedim << ">]";
Assert(header == s.str(), ExcUnexpectedInput(s.str(), header));
}
// First import what kind of reference cell we are looking at:
if constexpr (dim > 0)
in >> patch.reference_cell;
// then read all the data that is in this patch
for (const unsigned int i : patch.reference_cell.vertex_indices())
in >> patch.vertices[i];
for (const unsigned int i : patch.reference_cell.face_indices())
in >> patch.neighbors[i];
in >> patch.patch_index;
// If dim>1, we also need to set the number of subdivisions, whereas
// in dim==1, this is a const variable equal to one that can't be changed.
unsigned int n_subdivisions;
in >> n_subdivisions;
if constexpr (dim > 1)
patch.n_subdivisions = n_subdivisions;
in >> patch.points_are_available;
unsigned int n_rows, n_cols;
in >> n_rows >> n_cols;
patch.data.reinit(n_rows, n_cols);
for (unsigned int i = 0; i < patch.data.n_rows(); ++i)
for (unsigned int j = 0; j < patch.data.n_cols(); ++j)
in >> patch.data[i][j];
AssertThrow(in.fail() == false, ExcIO());
return in;
}
} // namespace DataOutBase
// explicit instantiations
#include "base/data_out_base.inst"
DEAL_II_NAMESPACE_CLOSE
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