Merge remote-tracking branch 'upstream/master' into ert

Conflicts:
	Makefile.am
	opm/core/grid/cpgpreprocess/preprocess.h
	tests/Makefile.am

This brings ert branch up-to-date with current Github master branch.

examples/Makefile.am

@@ -3,12 +3,24 @@ ERT_INCLUDE_PATH = $(ERT_ROOT)/include
 
 AM_CPPFLAGS =					\
 -I$(top_srcdir)					\
-$(OPM_BOOST_CPPFLAGS)				\
--I$(ERT_INCLUDE_PATH)
+-I$(ERT_INCLUDE_PATH)				\
+$(OPM_BOOST_CPPFLAGS)
 
 # All targets link to the library
 LDADD =						\
-$(top_builddir)/lib/libopmcore.la		\
+$(top_builddir)/lib/libopmcore.la
+
+# Convenience definition for targets that use Boost.Filesystem directly.
+# While libopmcore depends on (and references) Boost.Filesystem (through
+# the $(BOOST_FILESYSTEM_LIB) macro) this indirect dependency is not
+# sufficient to satisfy the requirements of targets that use the indirect
+# libraries directly.
+#
+# Additional details at
+#   https://fedoraproject.org/wiki/UnderstandingDSOLinkChange
+#
+LINK_BOOST_FILESYSTEM =				\
+$(OPM_BOOST_LDFLAGS)				\
 $(BOOST_FILESYSTEM_LIB)				\
 $(BOOST_SYSTEM_LIB)
 
@@ -18,6 +30,7 @@ $(BOOST_SYSTEM_LIB)
 # Please keep the list sorted.
 
 noinst_PROGRAMS =				\
+compute_tof					\
 refine_wells					\
 scaneclipsedeck					\
 sim_2p_comp_reorder				\
@@ -32,10 +45,19 @@ wells_example
 #
 # Please maintain sort order from "noinst_PROGRAMS".
 
+compute_tof_SOURCES           = compute_tof.cpp
+compute_tof_LDADD             = $(LDADD) $(LINK_BOOST_FILESYSTEM)
 refine_wells_SOURCES          = refine_wells.cpp
+
 sim_2p_comp_reorder_SOURCES   = sim_2p_comp_reorder.cpp
+sim_2p_comp_reorder_LDADD     = $(LDADD) $(LINK_BOOST_FILESYSTEM)
+
 sim_2p_incomp_reorder_SOURCES = sim_2p_incomp_reorder.cpp
+sim_2p_incomp_reorder_LDADD   = $(LDADD) $(LINK_BOOST_FILESYSTEM)
+
 sim_wateroil_SOURCES          = sim_wateroil.cpp
+sim_wateroil_LDADD            = $(LDADD) $(LINK_BOOST_FILESYSTEM)
+
 wells_example_SOURCES         = wells_example.cpp
 
 # ----------------------------------------------------------------------
@@ -47,5 +69,6 @@ noinst_PROGRAMS += spu_2p
 spu_2p_SOURCES   = spu_2p.cpp
 spu_2p_LDADD     =				\
 $(LDADD)					\
+$(LINK_BOOST_FILESYSTEM)			\
 $(LAPACK_LIBS) $(BLAS_LIBS) $(LIBS)
 endif

examples/compute_tof.cpp

@@ -0,0 +1,254 @@
+/*
+  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/>.
+*/
+
+
+
+#if HAVE_CONFIG_H
+#include "config.h"
+#endif // HAVE_CONFIG_H
+
+#include <opm/core/pressure/FlowBCManager.hpp>
+
+#include <opm/core/grid.h>
+#include <opm/core/GridManager.hpp>
+#include <opm/core/newwells.h>
+#include <opm/core/wells/WellsManager.hpp>
+#include <opm/core/utility/ErrorMacros.hpp>
+#include <opm/core/utility/initState.hpp>
+#include <opm/core/utility/StopWatch.hpp>
+#include <opm/core/utility/miscUtilities.hpp>
+#include <opm/core/utility/parameters/ParameterGroup.hpp>
+
+#include <opm/core/fluid/IncompPropertiesBasic.hpp>
+#include <opm/core/fluid/IncompPropertiesFromDeck.hpp>
+
+#include <opm/core/linalg/LinearSolverFactory.hpp>
+
+#include <opm/core/simulator/TwophaseState.hpp>
+#include <opm/core/simulator/WellState.hpp>
+#include <opm/core/pressure/IncompTpfa.hpp>
+#include <opm/core/transport/reorder/TransportModelTracerTof.hpp>
+#include <opm/core/transport/reorder/TransportModelTracerTofDiscGal.hpp>
+
+#include <boost/scoped_ptr.hpp>
+#include <boost/filesystem.hpp>
+
+#include <algorithm>
+#include <iostream>
+#include <vector>
+#include <numeric>
+
+
+namespace
+{
+    void warnIfUnusedParams(const Opm::parameter::ParameterGroup& param)
+    {
+        if (param.anyUnused()) {
+            std::cout << "--------------------   Unused parameters:   --------------------\n";
+            param.displayUsage();
+            std::cout << "----------------------------------------------------------------" << std::endl;
+        }
+    }
+} // anon namespace
+
+
+
+// ----------------- Main program -----------------
+int
+main(int argc, char** argv)
+{
+    using namespace Opm;
+
+    std::cout << "\n================    Test program for incompressible tof computations     ===============\n\n";
+    parameter::ParameterGroup param(argc, argv, false);
+    std::cout << "---------------    Reading parameters     ---------------" << std::endl;
+
+    // If we have a "deck_filename", grid and props will be read from that.
+    bool use_deck = param.has("deck_filename");
+    boost::scoped_ptr<EclipseGridParser> deck;
+    boost::scoped_ptr<GridManager> grid;
+    boost::scoped_ptr<IncompPropertiesInterface> props;
+    boost::scoped_ptr<Opm::WellsManager> wells;
+    TwophaseState state;
+    // bool check_well_controls = false;
+    // int max_well_control_iterations = 0;
+    double gravity[3] = { 0.0 };
+    if (use_deck) {
+        std::string deck_filename = param.get<std::string>("deck_filename");
+        deck.reset(new EclipseGridParser(deck_filename));
+        // Grid init
+        grid.reset(new GridManager(*deck));
+        // Rock and fluid init
+        props.reset(new IncompPropertiesFromDeck(*deck, *grid->c_grid()));
+        // Wells init.
+        wells.reset(new Opm::WellsManager(*deck, *grid->c_grid(), props->permeability()));
+        // Gravity.
+        gravity[2] = deck->hasField("NOGRAV") ? 0.0 : unit::gravity;
+        // Init state variables (saturation and pressure).
+        if (param.has("init_saturation")) {
+            initStateBasic(*grid->c_grid(), *props, param, gravity[2], state);
+        } else {
+            initStateFromDeck(*grid->c_grid(), *props, *deck, gravity[2], state);
+        }
+    } else {
+        // Grid init.
+        const int nx = param.getDefault("nx", 100);
+        const int ny = param.getDefault("ny", 100);
+        const int nz = param.getDefault("nz", 1);
+        const double dx = param.getDefault("dx", 1.0);
+        const double dy = param.getDefault("dy", 1.0);
+        const double dz = param.getDefault("dz", 1.0);
+        grid.reset(new GridManager(nx, ny, nz, dx, dy, dz));
+        // Rock and fluid init.
+        props.reset(new IncompPropertiesBasic(param, grid->c_grid()->dimensions, grid->c_grid()->number_of_cells));
+        // Wells init.
+        wells.reset(new Opm::WellsManager());
+        // Gravity.
+        gravity[2] = param.getDefault("gravity", 0.0);
+        // Init state variables (saturation and pressure).
+        initStateBasic(*grid->c_grid(), *props, param, gravity[2], state);
+    }
+
+    // Warn if gravity but no density difference.
+    bool use_gravity = (gravity[0] != 0.0 || gravity[1] != 0.0 || gravity[2] != 0.0);
+    if (use_gravity) {
+        if (props->density()[0] == props->density()[1]) {
+            std::cout << "**** Warning: nonzero gravity, but zero density difference." << std::endl;
+        }
+    }
+    const double *grav = use_gravity ? &gravity[0] : 0;
+
+    // Initialising src
+    std::vector<double> porevol;
+    computePorevolume(*grid->c_grid(), props->porosity(), porevol);
+    int num_cells = grid->c_grid()->number_of_cells;
+    std::vector<double> src(num_cells, 0.0);
+    if (use_deck) {
+        // Do nothing, wells will be the driving force, not source terms.
+    } else {
+        const double tot_porevol_init = std::accumulate(porevol.begin(), porevol.end(), 0.0);
+        const double default_injection = use_gravity ? 0.0 : 0.1;
+        const double flow_per_sec = param.getDefault<double>("injected_porevolumes_per_day", default_injection)
+            *tot_porevol_init/unit::day;
+        src[0] = flow_per_sec;
+        src[num_cells - 1] = -flow_per_sec;
+    }
+
+    // Boundary conditions.
+    FlowBCManager bcs;
+    if (param.getDefault("use_pside", false)) {
+        int pside = param.get<int>("pside");
+        double pside_pressure = param.get<double>("pside_pressure");
+        bcs.pressureSide(*grid->c_grid(), FlowBCManager::Side(pside), pside_pressure);
+    }
+
+    // Linear solver.
+    LinearSolverFactory linsolver(param);
+
+    // Pressure solver.
+    Opm::IncompTpfa psolver(*grid->c_grid(), *props, 0, linsolver,
+                            0.0, 0.0, 0,
+                            grav, wells->c_wells(), src, bcs.c_bcs());
+
+    // Choice of tof solver.
+    bool use_dg = param.getDefault("use_dg", false);
+    int dg_degree = -1;
+    if (use_dg) {
+        dg_degree = param.getDefault("dg_degree", 0);
+    }
+
+    // Write parameters used for later reference.
+    bool output = param.getDefault("output", true);
+    std::ofstream epoch_os;
+    std::string output_dir;
+    if (output) {
+        output_dir =
+            param.getDefault("output_dir", std::string("output"));
+        boost::filesystem::path fpath(output_dir);
+        try {
+            create_directories(fpath);
+        }
+        catch (...) {
+            THROW("Creating directories failed: " << fpath);
+        }
+        std::string filename = output_dir + "/epoch_timing.param";
+        epoch_os.open(filename.c_str(), std::fstream::trunc | std::fstream::out);
+        // open file to clean it. The file is appended to in SimulatorTwophase
+        filename = output_dir + "/step_timing.param";
+        std::fstream step_os(filename.c_str(), std::fstream::trunc | std::fstream::out);
+        step_os.close();
+        param.writeParam(output_dir + "/simulation.param");
+    }
+
+    // Init wells.
+    Opm::WellState well_state;
+    well_state.init(wells->c_wells(), state);
+
+    // Main solvers.
+    Opm::time::StopWatch pressure_timer;
+    double ptime = 0.0;
+    Opm::time::StopWatch transport_timer;
+    double ttime = 0.0;
+    Opm::time::StopWatch total_timer;
+    total_timer.start();
+    std::cout << "\n\n================    Starting main solvers     ===============" << std::endl;
+
+    // Solve pressure.
+    pressure_timer.start();
+    psolver.solve(1.0, state, well_state);
+    pressure_timer.stop();
+    double pt = pressure_timer.secsSinceStart();
+    std::cout << "Pressure solver took:  " << pt << " seconds." << std::endl;
+    ptime += pt;
+
+    // Process transport sources (to include bdy terms and well flows).
+    std::vector<double> transport_src;
+    Opm::computeTransportSource(*grid->c_grid(), src, state.faceflux(), 1.0,
+                                wells->c_wells(), well_state.perfRates(), transport_src);
+
+    // Solve time-of-flight.
+    std::vector<double> tof;
+    if (use_dg) {
+        Opm::TransportModelTracerTofDiscGal tofsolver(*grid->c_grid());
+        transport_timer.start();
+        tofsolver.solveTof(&state.faceflux()[0], &porevol[0], &transport_src[0], dg_degree, tof);
+        transport_timer.stop();
+    } else {
+        Opm::TransportModelTracerTof tofsolver(*grid->c_grid());
+        transport_timer.start();
+        tofsolver.solveTof(&state.faceflux()[0], &porevol[0], &transport_src[0], tof);
+        transport_timer.stop();
+    }
+    double tt = transport_timer.secsSinceStart();
+    std::cout << "Transport solver took: " << tt << " seconds." << std::endl;
+    ttime += tt;
+    total_timer.stop();
+
+    // Output.
+    if (output) {
+        std::string tof_filename = output_dir + "/tof.txt";
+        std::ofstream tof_stream(tof_filename.c_str());
+        std::copy(tof.begin(), tof.end(), std::ostream_iterator<double>(tof_stream, "\n"));
+    }
+
+    std::cout << "\n\n================    End of simulation     ===============\n"
+              << "Total time taken: " << total_timer.secsSinceStart()
+              << "\n  Pressure time:  " << ptime
+              << "\n  Transport time: " << ttime << std::endl;
+}