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Merge pull request #3197 from akva2/move_to_comp_units

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Move to separate compilation units
This commit is contained in:
Bård Skaflestad
2021-04-30 16:50:54 +02:00
committed by GitHub
parent 7be6e5bbf1 cf06a322ec
commit aa1df1352f
8 changed files with 356 additions and 237 deletions
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3
CMakeLists_files.cmake
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@@ -23,8 +23,10 @@
# originally generated with the command:
# find opm -name '*.c*' -printf '\t%p\n' | sort
list (APPEND MAIN_SOURCE_FILES
opm/core/props/phaseUsageFromDeck.cpp
opm/core/props/satfunc/RelpermDiagnostics.cpp
opm/simulators/timestepping/SimulatorReport.cpp
opm/simulators/flow/countGlobalCells.cpp
opm/simulators/flow/KeywordValidation.cpp
opm/simulators/linalg/ExtractParallelGridInformationToISTL.cpp
opm/simulators/linalg/FlexibleSolver1.cpp
@@ -39,6 +41,7 @@ list (APPEND MAIN_SOURCE_FILES
opm/simulators/timestepping/gatherConvergenceReport.cpp
opm/simulators/utils/DeferredLogger.cpp
opm/simulators/utils/gatherDeferredLogger.cpp
opm/simulators/utils/ParallelFileMerger.cpp
opm/simulators/utils/ParallelRestart.cpp
opm/simulators/wells/GroupState.cpp
opm/simulators/wells/WGState.cpp

164
opm/core/props/phaseUsageFromDeck.cpp Normal file
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@@ -0,0 +1,164 @@
/*
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 <opm/core/props/phaseUsageFromDeck.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/parser/eclipse/Deck/Deck.hpp>
#include <opm/parser/eclipse/EclipseState/EclipseState.hpp>
#include <opm/parser/eclipse/EclipseState/Runspec.hpp>
namespace Opm
{
PhaseUsage phaseUsage(const Phases& phases)
{
PhaseUsage pu;
pu.phase_used.fill(0);
// Discover phase usage.
pu.phase_used[BlackoilPhases::Aqua] = phases.active(Phase::WATER);
pu.phase_used[BlackoilPhases::Liquid] = phases.active(Phase::OIL);
pu.phase_used[BlackoilPhases::Vapour] = phases.active(Phase::GAS);
pu.num_phases = 0;
int numActivePhases = 0;
for (int phaseIdx = 0; phaseIdx < BlackoilPhases::MaxNumPhases; ++phaseIdx) {
if (!pu.phase_used[phaseIdx]) {
pu.phase_pos[phaseIdx] = -1;
}
else {
pu.phase_pos[phaseIdx] = numActivePhases;
++ numActivePhases;
pu.num_phases = numActivePhases;
}
}
// We need oil systems, since we do not support the keywords needed for
// water-gas systems.
if (!pu.phase_used[BlackoilPhases::Liquid] && !(pu.num_phases == 1)) {
OPM_THROW(std::runtime_error, "Cannot handle cases with no OIL, i.e. water-gas systems.");
}
// Add solvent info
pu.has_solvent = phases.active(Phase::SOLVENT);
if (pu.has_solvent) {
// this is quite a hack: even though solvent is not considered as in
// MaxNumPhases and pu.num_phases because this would break a lot of
// assumptions in old code, it is nevertheless an index to be translated
// to. solvent and solvent are even larger hacks because not even this can be
// done for them.
pu.phase_pos[BlackoilPhases::Solvent] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Solvent] = -1;
// Add polymer info
pu.has_polymer = phases.active(Phase::POLYMER);
if (pu.has_polymer) {
// this is quite a hack: even though polymer is not considered as in
// MaxNumPhases and pu.num_phases because this would break a lot of
// assumptions in old code, it is nevertheless an index to be translated
// to. polymer and solvent are even larger hacks because not even this can be
// done for them.
pu.phase_pos[BlackoilPhases::Polymer] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Polymer] = -1;
// Add energy info
pu.has_energy = phases.active(Phase::ENERGY);
if (pu.has_energy) {
// this is quite a hack: even though energy is not considered as in
// MaxNumPhases and pu.num_phases because this would break a lot of
// assumptions in old code, it is nevertheless an index to be translated
// to. polymer and solvent are even larger hacks because not even this can be
// done for them.
pu.phase_pos[BlackoilPhases::Energy] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Energy] = -1;
// Add polymer molecular weight related
pu.has_polymermw = phases.active(Phase::POLYMW);
if (pu.has_polymermw) {
if (!pu.has_polymer) {
OPM_THROW(std::runtime_error, "pu.has_polymermw is true while pu.has_polymer is false");
}
pu.phase_pos[BlackoilPhases::PolymerMW] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::PolymerMW] = -1;
// Add foam info
pu.has_foam = phases.active(Phase::FOAM);
if (pu.has_foam) {
pu.phase_pos[BlackoilPhases::Foam] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Foam] = -1;
// Add brine info
pu.has_brine = phases.active(Phase::BRINE);
if (pu.has_brine) {
pu.phase_pos[BlackoilPhases::Brine] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Brine] = -1;
// Add zFraction info
pu.has_zFraction = phases.active(Phase::ZFRACTION);
if (pu.has_zFraction) {
pu.phase_pos[BlackoilPhases::ZFraction] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::ZFraction] = -1;
return pu;
}
PhaseUsage phaseUsageFromDeck(const Opm::EclipseState& eclipseState)
{
const auto& phases = eclipseState.runspec().phases();
return phaseUsage(phases);
}
/// Looks at presence of WATER, OIL and GAS keywords in deck
/// to determine active phases.
PhaseUsage phaseUsageFromDeck(const Opm::Deck& deck)
{
Runspec runspec( deck );
const auto& phases = runspec.phases();
return phaseUsage(phases);
}
}

139
opm/core/props/phaseUsageFromDeck.hpp
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@@ -22,148 +22,23 @@
#define OPM_PHASEUSAGEFROMDECK_HEADER_INCLUDED
#include <opm/core/props/BlackoilPhases.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/parser/eclipse/Deck/Deck.hpp>
#include <opm/parser/eclipse/EclipseState/EclipseState.hpp>
#include <opm/parser/eclipse/EclipseState/Runspec.hpp>
namespace Opm
{
class Deck;
class EclipseState;
class Phases;
/// Determine the active phases
inline PhaseUsage phaseUsage(const Phases& phases) {
PhaseUsage pu;
pu.phase_used.fill(0);
// Discover phase usage.
pu.phase_used[BlackoilPhases::Aqua] = phases.active(Phase::WATER);
pu.phase_used[BlackoilPhases::Liquid] = phases.active(Phase::OIL);
pu.phase_used[BlackoilPhases::Vapour] = phases.active(Phase::GAS);
pu.num_phases = 0;
int numActivePhases = 0;
for (int phaseIdx = 0; phaseIdx < BlackoilPhases::MaxNumPhases; ++phaseIdx) {
if (!pu.phase_used[phaseIdx]) {
pu.phase_pos[phaseIdx] = -1;
}
else {
pu.phase_pos[phaseIdx] = numActivePhases;
++ numActivePhases;
pu.num_phases = numActivePhases;
}
}
// We need oil systems, since we do not support the keywords needed for
// water-gas systems.
if (!pu.phase_used[BlackoilPhases::Liquid] && !(pu.num_phases == 1)) {
OPM_THROW(std::runtime_error, "Cannot handle cases with no OIL, i.e. water-gas systems.");
}
// Add solvent info
pu.has_solvent = phases.active(Phase::SOLVENT);
if (pu.has_solvent) {
// this is quite a hack: even though solvent is not considered as in
// MaxNumPhases and pu.num_phases because this would break a lot of
// assumptions in old code, it is nevertheless an index to be translated
// to. solvent and solvent are even larger hacks because not even this can be
// done for them.
pu.phase_pos[BlackoilPhases::Solvent] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Solvent] = -1;
// Add polymer info
pu.has_polymer = phases.active(Phase::POLYMER);
if (pu.has_polymer) {
// this is quite a hack: even though polymer is not considered as in
// MaxNumPhases and pu.num_phases because this would break a lot of
// assumptions in old code, it is nevertheless an index to be translated
// to. polymer and solvent are even larger hacks because not even this can be
// done for them.
pu.phase_pos[BlackoilPhases::Polymer] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Polymer] = -1;
// Add energy info
pu.has_energy = phases.active(Phase::ENERGY);
if (pu.has_energy) {
// this is quite a hack: even though energy is not considered as in
// MaxNumPhases and pu.num_phases because this would break a lot of
// assumptions in old code, it is nevertheless an index to be translated
// to. polymer and solvent are even larger hacks because not even this can be
// done for them.
pu.phase_pos[BlackoilPhases::Energy] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Energy] = -1;
// Add polymer molecular weight related
pu.has_polymermw = phases.active(Phase::POLYMW);
if (pu.has_polymermw) {
if (!pu.has_polymer) {
OPM_THROW(std::runtime_error, "pu.has_polymermw is true while pu.has_polymer is false");
}
pu.phase_pos[BlackoilPhases::PolymerMW] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::PolymerMW] = -1;
// Add foam info
pu.has_foam = phases.active(Phase::FOAM);
if (pu.has_foam) {
pu.phase_pos[BlackoilPhases::Foam] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Foam] = -1;
// Add brine info
pu.has_brine = phases.active(Phase::BRINE);
if (pu.has_brine) {
pu.phase_pos[BlackoilPhases::Brine] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::Brine] = -1;
// Add zFraction info
pu.has_zFraction = phases.active(Phase::ZFRACTION);
if (pu.has_zFraction) {
pu.phase_pos[BlackoilPhases::ZFraction] = numActivePhases;
++ numActivePhases;
}
else
pu.phase_pos[BlackoilPhases::ZFraction] = -1;
return pu;
}
PhaseUsage phaseUsage(const Phases& phases);
/// Looks at presence of WATER, OIL and GAS keywords in state object
/// to determine active phases.
inline PhaseUsage phaseUsageFromDeck(const Opm::EclipseState& eclipseState)
{
const auto& phases = eclipseState.runspec().phases();
return phaseUsage(phases);
}
PhaseUsage phaseUsageFromDeck(const Opm::EclipseState& eclipseState);
/// Looks at presence of WATER, OIL and GAS keywords in deck
/// to determine active phases.
inline PhaseUsage phaseUsageFromDeck(const Opm::Deck& deck)
{
Runspec runspec( deck );
const auto& phases = runspec.phases();
return phaseUsage(phases);
}
PhaseUsage phaseUsageFromDeck(const Opm::Deck& deck);
}
#endif // OPM_PHASEUSAGEFROMDECK_HEADER_INCLUDED

50
opm/simulators/flow/countGlobalCells.cpp Normal file
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@@ -0,0 +1,50 @@
/*
Copyright 2013, 2015 SINTEF ICT, Applied Mathematics.
Copyright 2014, 2015 Dr. Blatt - HPC-Simulation-Software & Services
Copyright 2014, 2015 Statoil ASA.
Copyright 2015 NTNU
Copyright 2015 IRIS AS
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 "countGlobalCells.hpp"
#include <cassert>
namespace Opm {
namespace detail {
std::vector<int> buildAllCells(const int nc) {
std::vector<int> all_cells(nc);
std::iota(all_cells.begin(), all_cells.end(), 0);
return all_cells;
}
double getGravity(const double* g, const int dim) {
double grav = 0.0;
if (g) {
// Guard against gravity in anything but last dimension.
for (int dd = 0; dd < dim - 1; ++dd) {
assert(g[dd] == 0.0);
}
grav = g[dim - 1];
}
return grav;
}
} // namespace detail
} // namespace Opm

33
opm/simulators/flow/countGlobalCells.hpp
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@@ -21,28 +21,24 @@
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef OPM_BLACKOILDETAILS_HEADER_INCLUDED
#define OPM_BLACKOILDETAILS_HEADER_INCLUDED
#ifndef OPM_COUNTGLOBALCELLS_HEADER_INCLUDED
#define OPM_COUNTGLOBALCELLS_HEADER_INCLUDED
#include <opm/simulators/linalg/ParallelIstlInformation.hpp>
#include <opm/core/props/BlackoilPhases.hpp>
#include <dune/grid/common/gridview.hh>
#include <boost/range/iterator_range.hpp>
#include <any>
#include <vector>
namespace Opm {
namespace detail {
inline
std::vector<int>
buildAllCells(const int nc)
{
std::vector<int> all_cells(nc);
for (int c = 0; c < nc; ++c) { all_cells[c] = c; }
return all_cells;
}
std::vector<int> buildAllCells(const int nc);
@@ -80,18 +76,7 @@ namespace detail {
inline
double getGravity(const double* g, const int dim) {
double grav = 0.0;
if (g) {
// Guard against gravity in anything but last dimension.
for (int dd = 0; dd < dim - 1; ++dd) {
assert(g[dd] == 0.0);
}
grav = g[dim - 1];
}
return grav;
}
double getGravity(const double* g, const int dim);
/// \brief Compute the Euclidian norm of a vector

113
opm/simulators/utils/ParallelFileMerger.cpp Normal file
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@@ -0,0 +1,113 @@
/*
Copyright 2016 Dr. Blatt - HPC-Simulation-Software & Services
Copyright 2016 STATOIL AS.
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 <opm/simulators/utils/ParallelFileMerger.hpp>
#include <iostream>
namespace Opm
{
namespace detail
{
ParallelFileMerger::ParallelFileMerger(const fs::path& output_dir,
const std::string& deckname,
bool show_fallout)
: debugFileRegex_(deckname+"\\.\\d+\\.DBG"),
logFileRegex_(deckname+"\\.\\d+\\.PRT"),
fileWarningRegex_(deckname+"\\.(\\d+)\\.[^.]+"),
show_fallout_(show_fallout)
{
if ( show_fallout_ )
{
auto debugPath = output_dir;
debugPath /= (deckname + ".DBG");
debugStream_.reset(new std::ofstream(debugPath,
std::ofstream::app));
auto logPath = output_dir;
logPath /= ( deckname + ".PRT");
logStream_.reset(new std::ofstream(logPath,
std::ofstream::app));
}
}
void ParallelFileMerger::operator()(const fs::path& file)
{
std::smatch matches;
std::string filename = file.filename().native();
if ( std::regex_match(filename, matches, fileWarningRegex_) )
{
std::string rank = std::regex_replace(filename, fileWarningRegex_, "\\1");
if( std::regex_match(filename, logFileRegex_) )
{
if ( show_fallout_ ){
appendFile(*logStream_, file, rank);
}else{
fs::remove(file);
}
}
else
{
if (std::regex_match(filename, debugFileRegex_) )
{
if ( show_fallout_ ){
appendFile(*debugStream_, file, rank);
}else{
fs::remove(file);
}
}
else
{
if ( show_fallout_ ){
std::cerr << "WARNING: Unrecognized file with name "
<< filename
<< " that might stem from a parallel run."
<< std::endl;
}
}
}
}
}
void ParallelFileMerger::appendFile(std::ofstream& of, const fs::path& file, const std::string& rank)
{
if( fs::file_size(file) )
{
std::cerr << "WARNING: There has been logging to file "
<< file.string() <<" by process "
<< rank << std::endl;
std::ifstream in(file);
of<<std::endl<< std::endl;
of<<"=======================================================";
of<<std::endl<<std::endl;
of << " Output written by rank " << rank << " to file " << file.string();
of << ":" << std::endl << std::endl;
of << in.rdbuf() << std::endl << std::endl;
of << "======================== end output =====================";
of << std::endl;
in.close();
}
fs::remove(file);
}
} // end namespace detail
} // end namespace Opm

90
opm/simulators/utils/ParallelFileMerger.hpp
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@@ -21,11 +21,13 @@
#ifndef OPM_PARALLELFILEMERGER_HEADER_INCLUDED
#define OPM_PARALLELFILEMERGER_HEADER_INCLUDED
#include <fstream>
#include <memory>
#include <iostream>
#include <regex>
#include <string>
#include <opm/common/utility/FileSystem.hpp>
#include <regex>
namespace Opm
{
@@ -45,93 +47,19 @@ class ParallelFileMerger
public:
/// \brief Constructor
/// \param output_dir The output directory to use for reading/Writing.
/// \param deckanme The name of the deck.
/// \param deckname The name of the deck.
ParallelFileMerger(const fs::path& output_dir,
const std::string& deckname,
bool show_fallout = false)
: debugFileRegex_(deckname+"\\.\\d+\\.DBG"),
logFileRegex_(deckname+"\\.\\d+\\.PRT"),
fileWarningRegex_(deckname+"\\.(\\d+)\\.[^.]+"),
show_fallout_(show_fallout)
{
if ( show_fallout_ )
{
auto debugPath = output_dir;
debugPath /= (deckname + ".DBG");
debugStream_.reset(new std::ofstream(debugPath,
std::ofstream::app));
auto logPath = output_dir;
logPath /= ( deckname + ".PRT");
logStream_.reset(new std::ofstream(logPath,
std::ofstream::app));
}
}
bool show_fallout = false);
void operator()(const fs::path& file)
{
std::smatch matches;
std::string filename = file.filename().native();
void operator()(const fs::path& file);
if ( std::regex_match(filename, matches, fileWarningRegex_) )
{
std::string rank = std::regex_replace(filename, fileWarningRegex_, "\\1");
if( std::regex_match(filename, logFileRegex_) )
{
if ( show_fallout_ ){
appendFile(*logStream_, file, rank);
}else{
fs::remove(file);
}
}
else
{
if (std::regex_match(filename, debugFileRegex_) )
{
if ( show_fallout_ ){
appendFile(*debugStream_, file, rank);
}else{
fs::remove(file);
}
}
else
{
if ( show_fallout_ ){
std::cerr << "WARNING: Unrecognized file with name "
<< filename
<< " that might stem from a parallel run."
<< std::endl;
}
}
}
}
}
private:
/// \brief Append contents of a file to a stream
/// \brief of The output stream to use.
/// \brief file The file whose content to append.
/// \brief rank The rank that wrote the file.
void appendFile(std::ofstream& of, const fs::path& file, const std::string& rank)
{
if( fs::file_size(file) )
{
std::cerr << "WARNING: There has been logging to file "
<< file.string() <<" by process "
<< rank << std::endl;
std::ifstream in(file);
of<<std::endl<< std::endl;
of<<"=======================================================";
of<<std::endl<<std::endl;
of << " Output written by rank " << rank << " to file " << file.string();
of << ":" << std::endl << std::endl;
of << in.rdbuf() << std::endl << std::endl;
of << "======================== end output =====================";
of << std::endl;
in.close();
}
fs::remove(file);
}
void appendFile(std::ofstream& of, const fs::path& file, const std::string& rank);
/// \brief Regex to capture *.DBG
std::regex debugFileRegex_;
@@ -147,5 +75,5 @@ private:
bool show_fallout_;
};
} // end namespace detail
} // end namespace OPM
} // end namespace Opm
#endif // end header guard

1
tests/test_wellstatefullyimplicitblackoil.cpp
View File

@@ -27,6 +27,7 @@
#include <boost/test/unit_test.hpp>
#include <opm/parser/eclipse/Deck/Deck.hpp>
#include <opm/parser/eclipse/Parser/Parser.hpp>
#include <opm/parser/eclipse/Parser/ParseContext.hpp>
#include <opm/parser/eclipse/EclipseState/Schedule/Schedule.hpp>