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Merge pull request #968 from atgeirr/add-vtk-writing

Browse Source 
Re-add vtk writing functionality
This commit is contained in:
Joakim Hove 2016-12-06 11:09:48 +01:00 committed by GitHub
commit 15108f3499
14 changed files with 389 additions and 26 deletions
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32
CMakeLists_files.cmake
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@ -48,7 +48,7 @@ list (APPEND MAIN_SOURCE_FILES
opm/autodiff/VFPProdProperties.cpp
opm/autodiff/VFPInjProperties.cpp
opm/autodiff/WellMultiSegment.cpp
opm/autodiff/MultisegmentWells.cpp
opm/autodiff/MultisegmentWells.cpp
opm/autodiff/BlackoilSolventState.cpp
opm/autodiff/MissingFeatures.cpp
opm/polymer/PolymerState.cpp
@ -66,7 +66,8 @@ list (APPEND MAIN_SOURCE_FILES
opm/polymer/fullyimplicit/PolymerPropsAd.cpp
opm/simulators/SimulatorCompressibleTwophase.cpp
opm/simulators/SimulatorIncompTwophase.cpp
opm/simulators/WellSwitchingLogger.cpp
opm/simulators/WellSwitchingLogger.cpp
opm/simulators/vtk/writeVtkData.cpp
)
@ -86,16 +87,16 @@ list (APPEND TEST_SOURCE_FILES
tests/test_vfpproperties.cpp
tests/test_singlecellsolves.cpp
tests/test_solventprops_ad.cpp
tests/test_multisegmentwells.cpp
# tests/test_thresholdpressure.cpp
tests/test_wellswitchlogger.cpp
tests/test_multisegmentwells.cpp
# tests/test_thresholdpressure.cpp
tests/test_wellswitchlogger.cpp
)
list (APPEND TEST_DATA_FILES
tests/fluid.data
tests/VFPPROD1
tests/VFPPROD2
tests/msw.data
tests/msw.data
)
@ -145,7 +146,7 @@ list (APPEND PUBLIC_HEADER_FILES
opm/autodiff/AutoDiffMatrix.hpp
opm/autodiff/AutoDiff.hpp
opm/autodiff/BackupRestore.hpp
opm/autodiff/BlackoilDetails.hpp
opm/autodiff/BlackoilDetails.hpp
opm/autodiff/BlackoilModel.hpp
opm/autodiff/BlackoilModelBase.hpp
opm/autodiff/BlackoilModelBase_impl.hpp
@ -158,7 +159,7 @@ list (APPEND PUBLIC_HEADER_FILES
opm/autodiff/Compat.hpp
opm/autodiff/CPRPreconditioner.hpp
opm/autodiff/createGlobalCellArray.hpp
opm/autodiff/DefaultBlackoilSolutionState.hpp
opm/autodiff/DefaultBlackoilSolutionState.hpp
opm/autodiff/BlackoilSequentialModel.hpp
opm/autodiff/BlackoilSolventModel.hpp
opm/autodiff/BlackoilSolventModel_impl.hpp
@ -179,7 +180,7 @@ list (APPEND PUBLIC_HEADER_FILES
opm/autodiff/GridInit.hpp
opm/autodiff/ImpesTPFAAD.hpp
opm/autodiff/ISTLSolver.hpp
opm/autodiff/IterationReport.hpp
opm/autodiff/IterationReport.hpp
opm/autodiff/moduleVersion.hpp
opm/autodiff/NewtonIterationBlackoilCPR.hpp
opm/autodiff/NewtonIterationBlackoilInterface.hpp
@ -194,16 +195,16 @@ list (APPEND PUBLIC_HEADER_FILES
opm/autodiff/ParallelRestrictedAdditiveSchwarz.hpp
opm/autodiff/RateConverter.hpp
opm/autodiff/RedistributeDataHandles.hpp
opm/autodiff/SimFIBODetails.hpp
opm/autodiff/SimFIBODetails.hpp
opm/autodiff/SimulatorBase.hpp
opm/autodiff/SimulatorBase_impl.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilEbos.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilEbos.hpp
opm/autodiff/SimulatorFullyImplicitBlackoil.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilSolvent.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilSolvent_impl.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilMultiSegment.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilMultiSegment_impl.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilOutputEbos.hpp
opm/autodiff/SimulatorFullyImplicitBlackoilOutputEbos.hpp
opm/autodiff/SimulatorIncompTwophaseAd.hpp
opm/autodiff/SimulatorSequentialBlackoil.hpp
opm/autodiff/TransportSolverTwophaseAd.hpp
@ -223,7 +224,7 @@ list (APPEND PUBLIC_HEADER_FILES
opm/autodiff/WellHelpers.hpp
opm/autodiff/StandardWells.hpp
opm/autodiff/StandardWells_impl.hpp
opm/autodiff/StandardWellsDense.hpp
opm/autodiff/StandardWellsDense.hpp
opm/autodiff/StandardWellsSolvent.hpp
opm/autodiff/StandardWellsSolvent_impl.hpp
opm/autodiff/MissingFeatures.hpp
@ -256,7 +257,8 @@ list (APPEND PUBLIC_HEADER_FILES
opm/simulators/ParallelFileMerger.hpp
opm/simulators/SimulatorCompressibleTwophase.hpp
opm/simulators/SimulatorIncompTwophase.hpp
opm/simulators/thresholdPressures.hpp
opm/simulators/WellSwitchingLogger.hpp
opm/simulators/thresholdPressures.hpp
opm/simulators/WellSwitchingLogger.hpp
opm/simulators/vtk/writeVtkData.hpp
)

1
opm/autodiff/SimulatorBase.hpp
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@ -40,7 +40,6 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/simulator/AdaptiveSimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/miscUtilitiesBlackoil.hpp>

2
opm/autodiff/SimulatorFullyImplicitBlackoilOutput.cpp
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@ -28,7 +28,7 @@
#include <opm/core/simulator/BlackoilState.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/autodiff/Compat.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/parser/eclipse/Units/Units.hpp>

2
opm/autodiff/SimulatorFullyImplicitBlackoilOutputEbos.cpp
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@ -27,7 +27,7 @@
#include <opm/core/simulator/BlackoilState.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/autodiff/Compat.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/parser/eclipse/Units/Units.hpp>

1
opm/autodiff/SimulatorFullyImplicitBlackoilSolvent.hpp
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@ -44,7 +44,6 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
//#include <opm/core/simulator/AdaptiveSimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/miscUtilitiesBlackoil.hpp>

2
opm/autodiff/SimulatorIncompTwophaseAd.cpp
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@ -38,7 +38,7 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/wells/WellsManager.hpp>

2
opm/polymer/SimulatorCompressiblePolymer.cpp
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@ -35,7 +35,7 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/miscUtilitiesBlackoil.hpp>

2
opm/polymer/SimulatorPolymer.cpp
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@ -38,7 +38,7 @@
#include <opm/core/utility/StopWatch.hpp>
#include <opm/autodiff/Compat.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/wells/WellsManager.hpp>

1
opm/polymer/fullyimplicit/SimulatorFullyImplicitBlackoilPolymer.hpp
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@ -45,7 +45,6 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
//#include <opm/core/simulator/AdaptiveSimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/miscUtilitiesBlackoil.hpp>

1
opm/polymer/fullyimplicit/SimulatorFullyImplicitCompressiblePolymer.hpp
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@ -39,7 +39,6 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/output/eclipse/EclipseWriter.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/miscUtilitiesBlackoil.hpp>

2
opm/simulators/SimulatorCompressibleTwophase.cpp
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@ -35,7 +35,7 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/miscUtilitiesBlackoil.hpp>

2
opm/simulators/SimulatorIncompTwophase.cpp
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@ -36,7 +36,7 @@
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/utility/DataMap.hpp>
#include <opm/core/utility/StopWatch.hpp>
#include <opm/output/vtk/writeVtkData.hpp>
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/Event.hpp>

318
opm/simulators/vtk/writeVtkData.cpp Normal file
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@ -0,0 +1,318 @@
/*
Copyright 2012 SINTEF ICT, Applied Mathematics.
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
#include "config.h"
#include <opm/simulators/vtk/writeVtkData.hpp>
#include <opm/common/OpmLog/OpmLog.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/core/grid.h>
#include <set>
#include <cmath>
#include <algorithm>
#include <iostream>
#include <iterator>
#include <vector>
namespace Opm
{
void writeVtkData(const std::array<int, 3>& dims,
const std::array<double, 3>& cell_size,
const std::map< std::string, const std::vector< double >* >& data,
std::ostream& os)
{
// Dimension is hardcoded in the prototype and the next two lines,
// but the rest is flexible (allows dimension == 2 or 3).
int dimension = 3;
int num_cells = dims[0]*dims[1]*dims[2];
assert(dimension == 2 || dimension == 3);
assert(num_cells == dims[0]*dims[1]* (dimension == 2 ? 1 : dims[2]));
os << "# vtk DataFile Version 2.0\n";
os << "Structured Grid\n \n";
os << "ASCII \n";
os << "DATASET STRUCTURED_POINTS\n";
os << "DIMENSIONS "
<< dims[0] + 1 << " "
<< dims[1] + 1 << " ";
if (dimension == 3) {
os << dims[2] + 1;
} else {
os << 1;
}
os << "\n";
os << "ORIGIN " << 0.0 << " " << 0.0 << " " << 0.0 << "\n";
os << "SPACING " << cell_size[0] << " " << cell_size[1];
if (dimension == 3) {
os << " " << cell_size[2];
} else {
os << " " << 0.0;
}
os << "\n";
os << "\nCELL_DATA " << num_cells << '\n';
for (auto dit = data.begin(); dit != data.end(); ++dit) {
std::string name = dit->first;
os << "SCALARS " << name << " float" << '\n';
os << "LOOKUP_TABLE " << name << "_table " << '\n';
const std::vector<double>& field = *(dit->second);
// We always print only the first data item for every
// cell, using 'stride'.
// This is a hack to get water saturation nicely.
// \TODO: Extend to properly printing vector data.
const int stride = field.size()/num_cells;
const int num_per_line = 5;
for (int c = 0; c < num_cells; ++c) {
os << field[stride*c] << ' ';
if (c % num_per_line == num_per_line - 1
|| c == num_cells - 1) {
os << '\n';
}
}
}
}
typedef std::map<std::string, std::string> PMap;
struct Tag
{
Tag(const std::string& tag, const PMap& props, std::ostream& os)
: name_(tag), os_(os)
{
indent(os);
os << "<" << tag;
for (PMap::const_iterator it = props.begin(); it != props.end(); ++it) {
os << " " << it->first << "=\"" << it->second << "\"";
}
os << ">\n";
++indent_;
}
Tag(const std::string& tag, std::ostream& os)
: name_(tag), os_(os)
{
indent(os);
os << "<" << tag << ">\n";
++indent_;
}
~Tag()
{
--indent_;
indent(os_);
os_ << "</" << name_ << ">\n";
}
static void indent(std::ostream& os)
{
for (int i = 0; i < indent_; ++i) {
os << " ";
}
}
private:
static int indent_;
std::string name_;
std::ostream& os_;
};
int Tag::indent_ = 0;
void writeVtkData(const UnstructuredGrid& grid,
const std::map< std::string, const std::vector< double >* >& data,
std::ostream& os)
{
if (grid.dimensions != 3) {
OPM_THROW(std::runtime_error, "Vtk output for 3d grids only");
}
os.precision(12);
os << "<?xml version=\"1.0\"?>\n";
PMap pm;
pm["type"] = "UnstructuredGrid";
Tag vtkfiletag("VTKFile", pm, os);
Tag ugtag("UnstructuredGrid", os);
int num_pts = grid.number_of_nodes;
int num_cells = grid.number_of_cells;
pm.clear();
pm["NumberOfPoints"] = std::to_string(num_pts);
pm["NumberOfCells"] = std::to_string(num_cells);
Tag piecetag("Piece", pm, os);
{
Tag pointstag("Points", os);
pm.clear();
pm["type"] = "Float64";
pm["Name"] = "Coordinates";
pm["NumberOfComponents"] = "3";
pm["format"] = "ascii";
Tag datag("DataArray", pm, os);
for (int i = 0; i < num_pts; ++i) {
Tag::indent(os);
os << grid.node_coordinates[3*i + 0] << ' '
<< grid.node_coordinates[3*i + 1] << ' '
<< grid.node_coordinates[3*i + 2] << '\n';
}
}
{
Tag cellstag("Cells", os);
pm.clear();
pm["type"] = "Int32";
pm["NumberOfComponents"] = "1";
pm["format"] = "ascii";
std::vector<int> cell_numpts;
cell_numpts.reserve(num_cells);
{
pm["Name"] = "connectivity";
Tag t("DataArray", pm, os);
int hf = 0;
for (int c = 0; c < num_cells; ++c) {
std::set<int> cell_pts;
for (; hf < grid.cell_facepos[c+1]; ++hf) {
int f = grid.cell_faces[hf];
const int* fnbeg = grid.face_nodes + grid.face_nodepos[f];
const int* fnend = grid.face_nodes + grid.face_nodepos[f+1];
cell_pts.insert(fnbeg, fnend);
}
cell_numpts.push_back(cell_pts.size());
Tag::indent(os);
std::copy(cell_pts.begin(), cell_pts.end(),
std::ostream_iterator<int>(os, " "));
os << '\n';
}
}
{
pm["Name"] = "offsets";
Tag t("DataArray", pm, os);
int offset = 0;
const int num_per_line = 10;
for (int c = 0; c < num_cells; ++c) {
if (c % num_per_line == 0) {
Tag::indent(os);
}
offset += cell_numpts[c];
os << offset << ' ';
if (c % num_per_line == num_per_line - 1
|| c == num_cells - 1) {
os << '\n';
}
}
}
std::vector<int> cell_foffsets;
cell_foffsets.reserve(num_cells);
{
pm["Name"] = "faces";
Tag t("DataArray", pm, os);
const int* fp = grid.cell_facepos;
int offset = 0;
for (int c = 0; c < num_cells; ++c) {
Tag::indent(os);
os << fp[c+1] - fp[c] << '\n';
++offset;
for (int hf = fp[c]; hf < fp[c+1]; ++hf) {
int f = grid.cell_faces[hf];
const int* np = grid.face_nodepos;
int f_num_pts = np[f+1] - np[f];
Tag::indent(os);
os << f_num_pts << ' ';
++offset;
std::copy(grid.face_nodes + np[f],
grid.face_nodes + np[f+1],
std::ostream_iterator<int>(os, " "));
os << '\n';
offset += f_num_pts;
}
cell_foffsets.push_back(offset);
}
}
{
pm["Name"] = "faceoffsets";
Tag t("DataArray", pm, os);
const int num_per_line = 10;
for (int c = 0; c < num_cells; ++c) {
if (c % num_per_line == 0) {
Tag::indent(os);
}
os << cell_foffsets[c] << ' ';
if (c % num_per_line == num_per_line - 1
|| c == num_cells - 1) {
os << '\n';
}
}
}
{
pm["type"] = "UInt8";
pm["Name"] = "types";
Tag t("DataArray", pm, os);
const int num_per_line = 10;
for (int c = 0; c < num_cells; ++c) {
if (c % num_per_line == 0) {
Tag::indent(os);
}
os << "42 ";
if (c % num_per_line == num_per_line - 1
|| c == num_cells - 1) {
os << '\n';
}
}
}
}
{
pm.clear();
if (data.find("saturation") != data.end()) {
pm["Scalars"] = "saturation";
} else if (data.find("pressure") != data.end()) {
pm["Scalars"] = "pressure";
}
Tag celldatatag("CellData", pm, os);
pm.clear();
pm["NumberOfComponents"] = "1";
pm["format"] = "ascii";
pm["type"] = "Float64";
for (auto dit = data.begin(); dit != data.end(); ++dit) {
pm["Name"] = dit->first;
const std::vector<double>& field = *(dit->second);
const int num_comps = field.size()/grid.number_of_cells;
pm["NumberOfComponents"] = std::to_string(num_comps);
Tag ptag("DataArray", pm, os);
const int num_per_line = num_comps == 1 ? 5 : num_comps;
for (int item = 0; item < num_cells*num_comps; ++item) {
if (item % num_per_line == 0) {
Tag::indent(os);
}
double value = field[item];
if (std::fabs(value) < std::numeric_limits<double>::min()) {
// Avoiding denormal numbers to work around
// bug in Paraview.
value = 0.0;
}
os << value << ' ';
if (item % num_per_line == num_per_line - 1
|| item == num_cells - 1) {
os << '\n';
}
}
}
}
}
} // namespace Opm

47
opm/simulators/vtk/writeVtkData.hpp Normal file
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@ -0,0 +1,47 @@
/*
Copyright 2012 SINTEF ICT, Applied Mathematics.
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef OPM_WRITEVTKDATA_HEADER_INCLUDED
#define OPM_WRITEVTKDATA_HEADER_INCLUDED
#include <string>
#include <map>
#include <vector>
#include <array>
#include <iosfwd>
struct UnstructuredGrid;
namespace Opm
{
/// Vtk output for cartesian grids.
void writeVtkData(const std::array<int, 3>& dims,
const std::array<double, 3>& cell_size,
const std::map< std::string, const std::vector< double >* >& data,
std::ostream& os);
/// Vtk output for general grids.
void writeVtkData(const UnstructuredGrid& ,
const std::map< std::string, const std::vector< double >* >& data,
std::ostream& os);
} // namespace Opm
#endif // OPM_WRITEVTKDATA_HEADER_INCLUDED