Merge branch 'master' into v4.3.0-rc

CHANGELOG.md

@@ -291,6 +291,20 @@
 - Add support for enum class [\#1328](https://github.com/boutproject/BOUT-dev/pull/1328) ([dschwoerer](https://github.com/dschwoerer))
 - Remove deprecated routines [\#1326](https://github.com/boutproject/BOUT-dev/pull/1326) ([d7919](https://github.com/d7919))
 
+## [v4.2.3](https://github.com/boutproject/BOUT-dev/tree/v4.2.3) (2019-10-23)
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.2.2...v4.2.3)
+
+**Merged pull requests:**
+
+- Add counters to Timers to avoid double-counting sections [\#1817](https://github.com/boutproject/BOUT-dev/pull/1817) ([ZedThree](https://github.com/ZedThree))
+- Bugfix: cyclic parallel derivative inversion done in wrong space [\#1807](https://github.com/boutproject/BOUT-dev/pull/1807) ([ZedThree](https://github.com/ZedThree))
+- Add instructions for Ubuntu 16.04 [\#1690](https://github.com/boutproject/BOUT-dev/pull/1690) ([dschwoerer](https://github.com/dschwoerer))
+- Allow relative paths to be followed when making [\#1670](https://github.com/boutproject/BOUT-dev/pull/1670) ([johnomotani](https://github.com/johnomotani))
+- Update examples/staggered\_grid for v4.2 [\#1645](https://github.com/boutproject/BOUT-dev/pull/1645) ([johnomotani](https://github.com/johnomotani))
+- Add EXTRA\_LIBS to LIBS when searching for libraries [\#1632](https://github.com/boutproject/BOUT-dev/pull/1632) ([ZedThree](https://github.com/ZedThree))
+- Recent fixes/improvements for Travis into master [\#1627](https://github.com/boutproject/BOUT-dev/pull/1627) ([ZedThree](https://github.com/ZedThree))
+- Bug in calculation of ShiftAngle \(qloop\) [\#1626](https://github.com/boutproject/BOUT-dev/pull/1626) ([bendudson](https://github.com/bendudson))
+
 ## [v4.2.2](https://github.com/boutproject/BOUT-dev/tree/v4.2.2) (2019-02-27)
 
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.2.1...v4.2.2)

examples/staggered_grid/data/BOUT.inp

@@ -6,6 +6,8 @@ MZ = 1
 
 grid = "test-staggered.nc"
 
+[mesh]
+
 StaggerGrids = true
 
 [mesh:ddy]

examples/staggered_grid/test_staggered.cxx

@@ -8,10 +8,15 @@
 #include <derivs.hxx>
 
 Field3D n, v;
+CELL_LOC maybe_ylow{CELL_CENTRE};
 
 int physics_init(bool UNUSED(restart)) {
+
+  if (mesh->StaggerGrids) {
+    maybe_ylow = CELL_YLOW;
+  }
 
-  v.setLocation(CELL_YLOW); // Staggered relative to n
+  v.setLocation(maybe_ylow); // Staggered relative to n
 
   SOLVE_FOR(n, v);
 
@@ -24,7 +29,7 @@ int physics_run(BoutReal UNUSED(time)) {
   //ddt(n) = -Div_par_flux(v, n, CELL_CENTRE);
   ddt(n) = -n*Grad_par(v, CELL_CENTRE) - Vpar_Grad_par(v, n, CELL_CENTRE);
 
-  ddt(v) = -Grad_par(n, CELL_YLOW);
+  ddt(v) = -Grad_par(n, maybe_ylow);
 
   // Have to manually apply the lower Y boundary region, using a width of 3
   for( RangeIterator rlow = mesh->iterateBndryLowerY(); !rlow.isDone(); rlow++)

make.config.in

@@ -310,8 +310,8 @@ endif
 # -MT  add a target to the generated dependency
 # Ignore failure, in case some compiler does not support this
 %.o: $(BOUT_CONFIG_FILE) %.cxx
-	@echo "  Compiling " $(@F:.o=.cxx)
-	@$(CXX) $(BOUT_INCLUDE) $(BOUT_FLAGS) -c $(@F:.o=.cxx) -o $@
+	@echo "  Compiling " $(@:.o=.cxx)
+	@$(CXX) $(BOUT_INCLUDE) $(BOUT_FLAGS) -c $(@:.o=.cxx) -o $@
 ifeq ("$(TARGET)","libfast")
 	test "$@" = "bout++.o" || touch $(BOUT_TOP)/lib/.last.o.file
 endif

manual/sphinx/user_docs/installing.rst

@@ -167,6 +167,9 @@ MPICH2 and the needed libraries by running::
     $ sudo apt-get install mpich2 libmpich2-dev
     $ sudo apt-get install libfftw3-dev libnetcdf-dev libnetcdf-cxx-legacy-dev
 
+On Ubuntu 16.04::
+
+    $ sudo apt-get libmpich-dev libfftw3-dev libnetcdf-dev libnetcdf-cxx-legacy-dev
 
 On Ubuntu 18.04::