boutproject · ZedThree · Jul 7, 2021 · Feb 28, 2020 · Feb 28, 2020 · Feb 28, 2020
diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
@@ -48,7 +48,7 @@ jobs:
         with:
           build_dir: build
           apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
-          clang_tidy_checks: '-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg'
+          clang_tidy_checks: '-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*'
           # Googletest triggers a _lot_ of clang-tidy warnings, so ignore all
           # the unit tests until they're fixed or ignored upstream
           exclude: "tests/unit/*cxx"
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -78,6 +78,19 @@ jobs:
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
 
+          - name: "CMake, shared, Ubuntu 20.04, 3D metrics"
+            os: ubuntu-20.04
+            cmake_options: "-DBUILD_SHARED_LIBS=ON
+                            -DBOUT_ENABLE_METRIC_3D=ON
+                            -DBOUT_ENABLE_OPENMP=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_HDF5=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_ENABLE_PYTHON=OFF
+                            -DSUNDIALS_ROOT=/home/runner/local"
+            omp_num_threads: 2
+
           - name: "Coverage"
             os: ubuntu-18.04
             configure_options: "--enable-shared

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -46,6 +46,19 @@
 - `PhysicsModel` expects the options `datadir` and `dump_format` to
   have been set; this is only a problem if you don't call
   `BoutInitialise`. [\#2062](https://github.com/boutproject/BOUT-dev/pull/2062)
+- `dz` is now a `Field2D`, and `Coordinates::zlength()` also returns a
+  `Field2D`. In most cases, wrapping these in a call to `getUniform`
+  in order to get a `BoutReal` will do the correct thing. If checks
+  are enabled, `getUniform` will throw an exception if its argument is
+  not uniform (that is, that all values are identical).
+  [\#2025](https://github.com/boutproject/BOUT-dev/pull/2025)
+- The parallel boundaries `BNDRY_PAR_FWD` and `BNDRY_PAR_BKWD` have
+  been expanded to distinguish between the inner and outer boundaries
+  in x; the enums have been replaced with `BNDRY_PAR_*_XIN`, and
+  `BNDRY_PAR_*_XOUT` for both `FWD` and
+  `BKWD`. [\#2025](https://github.com/boutproject/BOUT-dev/pull/2025)
+- Support for reading/writing HDF5 files has been removed ahead of completely
+  refactoring the I/O
 - Support for reading/writing HDF5 files has been removed ahead of
   completely refactoring the I/O
   systems. [\#2208](https://github.com/boutproject/BOUT-dev/pull/2208)

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -552,6 +552,14 @@ endif()
 message(STATUS "Enable OpenMP: ${BOUT_ENABLE_OPENMP}")
 set(BOUT_USE_OPENMP ${BOUT_ENABLE_OPENMP})
 
+option(BOUT_ENABLE_METRIC_3D "Enable 3D metric support" OFF)
+if(BOUT_ENABLE_METRIC_3D)
+  set(BOUT_METRIC_TYPE "3D")
+else()
+  set(BOUT_METRIC_TYPE "2D")
+endif()
+set(BOUT_USE_METRIC_3D ${BOUT_ENABLE_METRIC_3D})
+
 # Optional dependencies
 
 option(BOUT_USE_PVODE "Enable support for bundled PVODE" ON)
@@ -991,6 +999,7 @@ message("
    Field name tracking      : ${BOUT_USE_TRACK}
    Floating point exceptions: ${BOUT_USE_SIGFPE}
    Backtrace enabled        : ${BOUT_USE_BACKTRACE}
+   Metric type              : ${BOUT_METRIC_TYPE}
    Python API support       : ${BOUT_USE_PYTHON}
    Sanitizers enabled       : ${BOUT_USE_SANITIZERS}
 

diff --git a/autoconf_build_defines.hxx.in b/autoconf_build_defines.hxx.in
@@ -51,6 +51,9 @@
 /* Use libuuid for UUID generation */
 #undef BOUT_HAS_UUID_SYSTEM_GENERATOR
 
+/* Type of the metric fields */
+#undef BOUT_METRIC_TYPE
+
 /* OpenMP schedule */
 #undef BOUT_OPENMP_SCHEDULE
 
@@ -60,6 +63,9 @@
 /* Enable color logs option */
 #undef BOUT_USE_COLOR
 
+/* Is the metric field 3D */
+#undef BOUT_USE_METRIC_3D
+
 /* Enable MsgStack for traces */
 #undef BOUT_USE_MSGSTACK
 

diff --git a/bin/bout-config.in b/bin/bout-config.in
@@ -44,6 +44,8 @@ has_fftw="@BOUT_HAS_FFTW@"
 
 petsc_has_sundials="@PETSC_HAS_SUNDIALS@"
 
+metric_type="@BOUT_METRIC_TYPE@"
+
 usage()
 {
     cat <<EOF
@@ -79,6 +81,8 @@ Available values for OPTION include:
   --has-nls     Natural Language Support
 
   --petsc-has-sundials 
+
+  --metric-type
 EOF
 
     exit $1
@@ -116,6 +120,7 @@ all()
         echo
         echo "  --petsc-has-sundials -> $petsc_has_sundials"
         echo
+        echo "  --metric-type -> $metric_type"        
 }
 
 if test $# -eq 0; then
@@ -233,6 +238,9 @@ while test $# -gt 0; do
 	    echo $has_nls
 	    ;;
 
+    --metric-type)
+	    echo $metric_type
+	    ;;
 
     --petsc-version)
         # TODO: Remove in next release

diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in
@@ -10,6 +10,7 @@ set(BOUT_USE_BACKTRACE @BOUT_USE_BACKTRACE@)
 set(BOUT_USE_OPENMP @BOUT_USE_OPENMP@)
 set(BOUT_HAS_OUTPUT_DEBUG @BOUT_HAS_OUTPUT_DEBUG@)
 set(BOUT_CHECK_LEVEL @BOUT_CHECK_LEVEL@)
+set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@)
 
 set(BOUT_HAS_PVODE @BOUT_HAS_PVODE@)
 set(BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@)

diff --git a/cmake_build_defines.hxx.in b/cmake_build_defines.hxx.in
@@ -26,6 +26,8 @@
 #cmakedefine01 BOUT_USE_SIGFPE
 #cmakedefine01 BOUT_USE_SIGNAL
 #cmakedefine01 BOUT_USE_TRACK
+#cmakedefine BOUT_METRIC_TYPE @BOUT_METRIC_TYPE@
+#cmakedefine01 BOUT_USE_METRIC_3D
 #cmakedefine01 BOUT_USE_MSGSTACK
 
 // CMake build does not support legacy interface

diff --git a/configure b/configure
@@ -629,6 +629,7 @@ PETSC_ARCH
 PETSC_DIR
 PETSC_MAKE_INCLUDE
 PETSC_HAS_SUNDIALS
+BOUT_METRIC_TYPE
 BOUT_USE_MSGSTACK
 BOUT_USE_TRACK
 BOUT_USE_SIGNAL
@@ -827,6 +828,7 @@ enable_static
 enable_openmp
 with_openmp_schedule
 enable_pvode_openmp
+enable_metric_3d
 with_gcov
 enable_code_coverage
 enable_nls
@@ -1487,6 +1489,7 @@ Optional Features:
   --enable-static         Enable building bout++ into an static library
   --enable-openmp         Enable building with OpenMP support
   --enable-pvode-openmp   Enable building PVODE with OpenMP support
+  --enable-metric-3d      Use Field3D to store coordinates metric data
   --disable-openmp        do not use OpenMP
   --enable-code-coverage  Whether to enable code coverage support
   --disable-nls           do not use Native Language Support
@@ -2588,6 +2591,13 @@ else
   enable_pvode_openmp=no
 fi
 
+# Check whether --enable-metric_3d was given.
+if test "${enable_metric_3d+set}" = set; then :
+  enableval=$enable_metric_3d;
+else
+  enable_metric_3d=no
+fi
+
 
 
 
@@ -6045,6 +6055,20 @@ fi
 
 fi
 
+if test "x$enable_metric_3d" != "xno"; then :
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Using Field3D to store coordinates data, this is experimental." >&5
+$as_echo "$as_me: WARNING: Using Field3D to store coordinates data, this is experimental." >&2;}
+  BOUT_METRIC_TYPE="3D"
+
+else
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: Using Field2D to store coordinates data" >&5
+$as_echo "$as_me: Using Field2D to store coordinates data" >&6;}
+  BOUT_METRIC_TYPE="2D"
+
+fi
+
 #############################################################
 # Build into shared object (pic)
 #############################################################
@@ -15759,6 +15783,18 @@ fi
 
 
 
+cat >>confdefs.h <<_ACEOF
+#define BOUT_METRIC_TYPE $BOUT_METRIC_TYPE
+_ACEOF
+
+BOUT_METRIC_3D=$(test $BOUT_METRIC_TYPE != 3D ; echo $?)
+
+cat >>confdefs.h <<_ACEOF
+#define BOUT_USE_METRIC_3D $BOUT_METRIC_3D
+_ACEOF
+
+
+
 
 
 
@@ -17299,6 +17335,8 @@ $as_echo "$as_me:   Enable FP exceptions    : $BOUT_USE_SIGFPE" >&6;}
 $as_echo "$as_me:   Enable signal handlers  : $BOUT_USE_SIGNAL" >&6;}
 { $as_echo "$as_me:${as_lineno-$LINENO}:   Enable field names      : $BOUT_USE_TRACK" >&5
 $as_echo "$as_me:   Enable field names      : $BOUT_USE_TRACK" >&6;}
+{ $as_echo "$as_me:${as_lineno-$LINENO}:   Metric type             : $BOUT_METRIC_TYPE" >&5
+$as_echo "$as_me:   Metric type             : $BOUT_METRIC_TYPE" >&6;}
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: " >&5
 $as_echo "$as_me: " >&6;}

diff --git a/configure.ac b/configure.ac
@@ -97,6 +97,8 @@ AC_ARG_WITH(openmp_schedule,[AS_HELP_STRING([--with-openmp-schedule=static/dynam
         [Set OpenMP schedule (default: static)])],,[with_openmp_schedule=static])
 AC_ARG_ENABLE(pvode_openmp, [AS_HELP_STRING([--enable-pvode-openmp],
         [Enable building PVODE with OpenMP support])],,[enable_pvode_openmp=no])
+AC_ARG_ENABLE(metric_3d, [AS_HELP_STRING([--enable-metric-3d],
+        [Use Field3D to store coordinates metric data])],,[enable_metric_3d=no])
 
 AC_ARG_VAR(EXTRA_INCS,[Extra compile flags])
 AC_ARG_VAR(EXTRA_LIBS,[Extra linking flags])
@@ -423,6 +425,14 @@ AS_IF([test "x$enable_backtrace" = "xyes" || test "x$enable_backtrace" = "xmaybe
   ])
 ])
 
+AS_IF([test "x$enable_metric_3d" != "xno"], [
+  AC_MSG_WARN([Using Field3D to store coordinates data, this is experimental.])
+  BOUT_METRIC_TYPE="3D"
+], [
+  AC_MSG_NOTICE([Using Field2D to store coordinates data])
+  BOUT_METRIC_TYPE="2D"
+])
+
 #############################################################
 # Build into shared object (pic)
 #############################################################
@@ -1372,6 +1382,10 @@ BOUT_DEFINE_SUBST(BOUT_USE_SIGFPE, [Enable floating point exceptions])
 BOUT_DEFINE_SUBST(BOUT_USE_SIGNAL, [Enable signal handlers])
 BOUT_DEFINE_SUBST(BOUT_USE_TRACK, [Enable field name tracking])
 BOUT_DEFINE_SUBST(BOUT_USE_MSGSTACK, [Enable MsgStack for traces])
+AC_DEFINE_UNQUOTED([BOUT_METRIC_TYPE], $BOUT_METRIC_TYPE, [Type of the metric fields])
+BOUT_METRIC_3D=$(test $BOUT_METRIC_TYPE != 3D ; echo $?)
+AC_DEFINE_UNQUOTED([BOUT_USE_METRIC_3D], $BOUT_METRIC_3D, [Is the metric field 3D])
+AC_SUBST(BOUT_METRIC_TYPE)
 
 AC_SUBST(PETSC_HAS_SUNDIALS)
 AC_SUBST(PETSC_MAKE_INCLUDE)
@@ -1420,6 +1434,7 @@ AC_MSG_NOTICE([  Enable OpenMP           : $BOUT_USE_OPENMP])
 AC_MSG_NOTICE([  Enable FP exceptions    : $BOUT_USE_SIGFPE])
 AC_MSG_NOTICE([  Enable signal handlers  : $BOUT_USE_SIGNAL])
 AC_MSG_NOTICE([  Enable field names      : $BOUT_USE_TRACK])
+AC_MSG_NOTICE([  Metric type             : $BOUT_METRIC_TYPE])
 
 AC_MSG_NOTICE([])
 AC_MSG_NOTICE([-------------------------------])

diff --git a/examples/conducting-wall-mode/cwm.cxx b/examples/conducting-wall-mode/cwm.cxx
@@ -305,8 +305,8 @@ class CWM : public PhysicsModel {
         for (int jz = 0; jz < mesh->LocalNz; jz++) {
 
           var(xrup.ind, jy, jz) = var(xrup.ind, jy - 1, jz)
-                                  + coord->dy(xrup.ind, jy)
-                                        * sqrt(coord->g_22(xrup.ind, jy))
+                                  + coord->dy(xrup.ind, jy, jz)
+                                        * sqrt(coord->g_22(xrup.ind, jy, jz))
                                         * value(xrup.ind, jy, jz);
         }
       }
@@ -322,8 +322,8 @@ class CWM : public PhysicsModel {
         for (int jz = 0; jz < mesh->LocalNz; jz++) {
 
           var(xrdn.ind, jy, jz) = var(xrdn.ind, jy + 1, jz)
-                                  - coord->dy(xrdn.ind, jy)
-                                        * sqrt(coord->g_22(xrdn.ind, jy))
+                                  - coord->dy(xrdn.ind, jy, jz)
+                                        * sqrt(coord->g_22(xrdn.ind, jy, jz))
                                         * value(xrdn.ind, jy, jz);
         }
       }

diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
@@ -26,9 +26,11 @@ class ELMpb : public PhysicsModel {
   // 2D inital profiles
   Field2D J0, P0;         // Current and pressure
   Vector2D b0xcv;         // Curvature term
-  Field2D beta, gradparB; // Used for Vpar terms
+  Field2D beta;           // Used for Vpar terms
+  Coordinates::FieldMetric gradparB;
   Field2D phi0;           // When diamagnetic terms used
-  Field2D U0, Psixy, x;   // 0th vorticity of equilibrium flow,
+  Field2D Psixy, x;
+  Coordinates::FieldMetric U0; // 0th vorticity of equilibrium flow,
   // radial flux coordinate, normalized radial flux coordinate
 
   bool constn0;
@@ -659,8 +661,9 @@ class ELMpb : public PhysicsModel {
               for (int jy = 0; jy < mesh->LocalNy; jy++) {
                 for (int jz = 0; jz < mesh->LocalNz; jz++) {
 
-                  BoutReal angle = rmp_m * pol_angle(jx, jy)
-                                   + rmp_n * ((BoutReal)jz) * mesh->getCoordinates()->dz;
+                  BoutReal angle =
+                      rmp_m * pol_angle(jx, jy)
+                      + rmp_n * ((BoutReal)jz) * mesh->getCoordinates()->dz(jx, jy, jz);
                   rmp_Psi0(jx, jy, jz) =
                       (((BoutReal)(jx - 4)) / ((BoutReal)(mesh->LocalNx - 5)))
                       * rmp_factor * cos(angle);

diff --git a/examples/gyro-gem/gem.cxx b/examples/gyro-gem/gem.cxx
@@ -58,7 +58,7 @@ class GEM : public PhysicsModel {
 
   Vector3D B0vec; // Equilibrium B field vector
   Field2D logB;   // For curvature
-  Field2D Grad_par_logB; // Grad_par(log(B))
+  Coordinates::FieldMetric Grad_par_logB; // Grad_par(log(B))
 
   Field2D Ni0, Ne0; // Gyro-center densities
   Field2D Ti0, Te0; // Starting isotropic temperatures