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Implement Geometry class #3

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merged 4 commits into from
Sep 23, 2020
Merged

Implement Geometry class #3

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7db3024
ctest passed for Geometry class
loganchen39 Sep 21, 2020
8444628
Modified test CMakeLists.txt
loganchen39 Sep 22, 2020
e4ca6e8
Travis's suggested changes completed by Ligang
loganchen39 Sep 23, 2020
9b4ada2
Travis's suggested changes completed by Ligang
loganchen39 Sep 23, 2020
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49 changes: 33 additions & 16 deletions src/oisst/Geometry/Geometry.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -9,42 +9,59 @@

#include "eckit/config/Configuration.h"

#include "atlas/grid.h"

#include "oops/util/abor1_cpp.h"

namespace oisst {

// ----------------------------------------------------------------------------

Geometry::Geometry(const eckit::Configuration & conf,
const eckit::mpi::Comm & comm)
: comm_(comm) {
util::abor1_cpp("Geometry::Geometry() needs to be implemented.",
__FILE__, __LINE__);
Geometry::Geometry(const eckit::Configuration & conf, const eckit::mpi::Comm & comm) : comm_(comm) {
//util::abor1_cpp("Geometry::Geometry() needs to be implemented.", __FILE__, __LINE__);

atlas::RegularLonLatGrid atlasRllGrid("Slat360x180");
atlasFunctionSpace_.reset(new atlas::functionspace::StructuredColumns(atlasRllGrid,
atlas::option::halo(0)));

atlasFieldSet_.reset(new atlas::FieldSet());
}

// ----------------------------------------------------------------------------

Geometry::Geometry(const Geometry & other)
: comm_(other.comm_) {
util::abor1_cpp("Geometry::Geometry() needs to be implemented.",
__FILE__, __LINE__);
Geometry::Geometry(const Geometry & other) : comm_(other.comm_) {
//util::abor1_cpp("Geometry::Geometry() needs to be implemented.", __FILE__, __LINE__);

atlasFunctionSpace_.reset(new atlas::functionspace::StructuredColumns(other.atlasFunctionSpace_->grid(),
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I'm not sure if all this is needed in the copy constructor here, it might work if the unique pointers were changed to shared pointers, and you just copy the pointers instead. Doesn't really matter at this point though, we can worry about that later when it's time to optimize the code

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Yes let's worry about it later, right now what I (and Jim) want is to get an initial result first. Later on we will optimize the code as I get more familiar with JEDI and ATLAS etc.

atlas::option::halo(0)));

atlasFieldSet_.reset(new atlas::FieldSet());
for (int ifield = 0; ifield < other.atlasFieldSet_->size(); ifield++) {
atlas::Field atlasField = other.atlasFieldSet_->field(ifield);
atlasFieldSet_->add(atlasField);
}
}

// ----------------------------------------------------------------------------

Geometry::~Geometry() {
util::abor1_cpp("Geometry::~Geometry() needs to be implemented.",
__FILE__, __LINE__);
//util::abor1_cpp("Geometry::~Geometry() needs to be implemented.", __FILE__, __LINE__);


}

// ----------------------------------------------------------------------------

void Geometry::print(std::ostream & os) const {
util::abor1_cpp("Geometry::print() needs to be implemented.",
__FILE__, __LINE__);
os << "Geometry: "
<< "(TODO, print diagnostic info about the geometry here)"
<< std::endl;
//util::abor1_cpp("Geometry::print() needs to be implemented.", __FILE__, __LINE__);
os << "Geometry: " << "(TODO, print diagnostic info about the geometry here)" << std::endl;

int nx, ny;
//double dx, dy;
ny = int(atlasFunctionSpace()->grid().ny());
nx = int(((atlas::RegularLonLatGrid&)(atlasFunctionSpace()->grid())).nx());

os << "Geometry: nx = " << nx << ", ny = " << ny << std::endl;
}

// ----------------------------------------------------------------------------
Expand Down
23 changes: 16 additions & 7 deletions src/oisst/Geometry/Geometry.h
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,12 @@
#include <ostream>
#include <string>

#include "eckit/mpi/Comm.h"
#include <memory>

#include "atlas/functionspace.h"
#include "atlas/field.h"

#include "eckit/mpi/Comm.h"
#include "oops/util/ObjectCounter.h"
#include "oops/util/Printable.h"

Expand All @@ -27,11 +31,9 @@ namespace oisst {
// ----------------------------------------------------------------------------

namespace oisst {

// Geometry class
class Geometry : public util::Printable,
private util::ObjectCounter<Geometry> {
public:
class Geometry : public util::Printable, private util::ObjectCounter<Geometry> {
public:
static const std::string classname() {return "oisst::Geometry";}

// constructors and destructor
Expand All @@ -46,10 +48,17 @@ namespace oisst {
// TODO(template_impl) GeometryIterator begin() const;
// TODO(template_impl) GeometryIterator end() const;

private:
void print(std::ostream &) const;
// atlas::FunctionSpace* atlasFunctionSpace() const { return atlasFunctionSpace_.get(); }
atlas::functionspace::StructuredColumns* atlasFunctionSpace() const { return atlasFunctionSpace_.get(); }
atlas::FieldSet* atlasFieldSet() const { return atlasFieldSet_.get(); }

private:
void print(std::ostream &) const;
const eckit::mpi::Comm & comm_;


std::unique_ptr<atlas::functionspace::StructuredColumns> atlasFunctionSpace_;
std::unique_ptr<atlas::FieldSet> atlasFieldSet_;
};
} // namespace oisst

Expand Down
10 changes: 5 additions & 5 deletions test/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,11 @@ endforeach()
# TODO: uncomment all of these tests as the appropriate interfaces are implemented
#================================================================================

# ecbuild_add_test(
# TARGET test_oisst_geometry
# SOURCES executables/TestGeometry.cc
# ARGS testinput/geometry.yml
# LIBS oisst )
ecbuild_add_test(
TARGET test_oisst_geometry
SOURCES executables/TestGeometry.cc
ARGS testinput/geometry.yml
LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_state
Expand Down
80 changes: 80 additions & 0 deletions test/CMakeLists.txt_org
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Original file line number Diff line number Diff line change
@@ -0,0 +1,80 @@
list( APPEND oisst_test_input
testinput/geometry.yml
testinput/errorcovariance.yml
testinput/getvalues.yml
testinput/lineargetvalues.yml
testinput/linearmodel.yml
testinput/increment.yml
testinput/model.yml
testinput/modelaux.yml
testinput/state.yml
)


# link the input files for the tests
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/testinput)
foreach(FILENAME ${oisst_test_input})
execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink
${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}
${CMAKE_CURRENT_BINARY_DIR}/${FILENAME} )
endforeach()


#================================================================================
# Tests of class interfaces
# TODO: uncomment all of these tests as the appropriate interfaces are implemented
#================================================================================

# ecbuild_add_test(
# TARGET test_oisst_geometry
# SOURCES executables/TestGeometry.cc
# ARGS testinput/geometry.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_state
# SOURCES executables/TestState.cc
# ARGS testinput/state.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_increment
# SOURCES executables/TestIncrement.cc
# ARGS testinput/increment.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_modelauxcontrol
# SOURCES executables/TestModelAuxControl.cc
# ARGS testinput/modelaux.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_getvalues
# SOURCES executables/TestGetValues.cc
# ARGS testinput/getvalues.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_lineargetvalues
# SOURCES executables/TestLinearGetValues.cc
# ARGS testinput/lineargetvalues.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_errorcovariance
# SOURCES executables/TestErrorCovariance.cc
# ARGS testinput/errorcovariance.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_modelauxcovariance
# SOURCES executables/TestModelAuxCovariance.cc
# ARGS testinput/modelaux.yml
# LIBS oisst )

# ecbuild_add_test(
# TARGET test_oisst_modelauxincrement
# SOURCES executables/TestModelAuxIncrement.cc
# ARGS testinput/modelaux.yml
# LIBS oisst )