Merge branch 'master' into sts

.travis.yml

@@ -1,52 +1,62 @@
 # .travis.yml
-# Defines build matrix and regression tests for Travis CI.com
+# Defines build matrix and regression tests for Travis CI
 language: cpp
 branches:
   only:
   - master
   - dust
   - mhd4_3D
-# Default build matrix is 4x Ubuntu builds:
+# Default build matrix is 4x Ubuntu builds (inherit the default stage name "test"):
 os:
   - linux
 dist: trusty
 sudo: false # use faster container-based build
 addons:
   apt:
+    sources:
+      - llvm-toolchain-trusty-5.0
     packages:
       - "python3"
       - "python3-pip"
+      - "clang-5.0"  # Ubuntu 14.04 ships wit Clang 3.5.0 as of 2018-10-29
 # OpenMPI and MPICH implementations:
 env:
   matrix:
-  - MPI_CHOICE=mpich
-  - MPI_CHOICE=openmpi
+    - MPI_CHOICE=mpich
+    - MPI_CHOICE=openmpi
 compiler:
   - g++
   - clang++
 # Define Ubuntu build caches (cache ignored inside "include:" matrix)
 cache:
   pip: true # Caching NumPy for regression test script
-  directories:
+  directories: # TODO(felker): sync "version_str=" lines in install scripts with cache dir names
     # For caching Linux source directories:
-    - openmpi-3.0.2 # released 6/1/18
-    - mpich-3.2.1 # stable maintenance release from 11/10/17
+    - openmpi-3.0.2
+    - mpich-3.2.1
     # Caching Linux install directories:
     - openmpi
     - mpich
     - fftw
-    - fftw-3.3.7 # stable release as of 11/8/17
+    - fftw-3.3.8
     - hdf5
-    - hdf5-1.10.1 # released on 2017-04-27
+    - hdf5-1.10.4
 
-# Explicitly includilng the 2x macOS jobs in build matrix
+# Explicitly includilng the 2x macOS jobs in build matrix (inherit the default stage name "test")
 # Must specify complete build details, or the jobs will inherit
 # the first value in the above arrays. Could encapsulate in script
+# --------------
+# History of Travis CI default osx_image (date = when used in this file)
+# (2018-10-30) xcode9.4 on macOS 10.13 High Sierra
+# (2018-04-11) xcode8.3 on macOS 10.12 Sierra
+# TODO(felker): improve syncing of osx "softwareupdate" cmd xcode version argument in
+# tst/ci/travis/ install_mpich.sh, install_openmpi.sh (workaround for Homebrew GCC)
 matrix:
   include:
     - os: osx
-      osx_image: xcode9.3 # macOS 10.13 High Sierra
+      osx_image: xcode9.4
       compiler: clang++
+      addons:
       env:
         - MPI_CHOICE=mpich
       # Override Linux cache mapping
@@ -67,8 +77,9 @@ matrix:
           - hdf5
           - "/usr/local/Cellar/hdf5/"
     - os: osx
-      osx_image: xcode8.3 # macOS 10.12 Sierra. Default as of 4/11/18
+      osx_image: xcode9.4
       compiler: clang++
+      addons:
       env:
         - MPI_CHOICE=openmpi
         - TMPDIR=/tmp
@@ -93,12 +104,23 @@ matrix:
     - stage: python linter
       before_install: skip
       install: skip
+      addons:
+        apt:
+          packages:
+            - "python3"
+            - "python3-pip"
+      env:
+      compiler:
       script: python3 -m flake8 --exclude=cpplint.py,openmpi-* && echo "Finished linting Python files with flake8"
     # Test Google C++ Style Guide adherence for .cpp, .hpp files:
     - stage: c++ linter
       before_install: skip
       install: skip
       before_script: skip
+      addons:
+      env:
+      compiler:
+      # "python" must point to Py2 distro, otherwise cpplint.py will silently quit while checking 1st file
       script: cd tst/style/ && ./cpplint_athena.sh
 
 # Recommended by Travis CI documentation to unset these for MPI builds to prevent conflicts

CHANGELOG.md

@@ -55,7 +55,7 @@ Feature branches to merge to `master`:
 - Improved readability of `TimeIntegratorTaskList`
 - Fixed spherical coordinates terms for non-ideal MHD
 - Fixed reflective symmetry preservation for hydrodynamic viscosity calculations
-- Eliminated small floating point errors when analyzing uniform grid results using included Python HDF5 reader
+- Eliminated small floating-point errors when analyzing uniform grid results using included Python HDF5 reader
 - Changed turbulence driving switches to avoid possible bug during initial cycle
 - Plugged MPI resource leaks in Multigrid
 
@@ -67,10 +67,10 @@ Feature branches to merge to `master`:
 - Viscosity terms break Rayleigh-Taylor symmetry [\#144](https://github.com/PrincetonUniversity/athena/issues/144)
 - SIMD vectorization disabled for Roe-type Riemann solvers [\#126](https://github.com/PrincetonUniversity/athena/issues/126)
 - Memory leak in jeans\_3d.py test MPI run [\#115](https://github.com/PrincetonUniversity/athena/issues/115)
-- athena\_read.py athdf\(\) results in small floating point errors [\#111](https://github.com/PrincetonUniversity/athena/issues/111)
+- athena\_read.py athdf\(\) results in small floating-point errors [\#111](https://github.com/PrincetonUniversity/athena/issues/111)
 - Remove unused GravityBoundaryFunction\_\[\] array from Mesh class [\#149](https://github.com/PrincetonUniversity/athena/pull/149) ([felker](https://github.com/felker))
 - Cleanup minor issues before v1.1.1 release; fix viscosity asymmetry  [\#147](https://github.com/PrincetonUniversity/athena/pull/147) ([felker](https://github.com/felker))
-- Return exact floating point values when reading HDF5 coordinates [\#145](https://github.com/PrincetonUniversity/athena/pull/145) ([c-white](https://github.com/c-white))
+- Return exact floating-point values when reading HDF5 coordinates [\#145](https://github.com/PrincetonUniversity/athena/pull/145) ([c-white](https://github.com/c-white))
 - Fixed spherical coordinates for non-ideal MHD [\#142](https://github.com/PrincetonUniversity/athena/pull/142) ([tomidakn](https://github.com/tomidakn))
 - Added interactive spherical plotting: [\#139](https://github.com/PrincetonUniversity/athena/pull/139) ([c-white](https://github.com/c-white))
 - Use \#pragma omp declare simd for functions called in SIMD loops [\#138](https://github.com/PrincetonUniversity/athena/pull/138) ([felker](https://github.com/felker))
@@ -117,7 +117,7 @@ Feature branches to merge to `master`:
 - Characteristic variable reconstruction (PLM and PPM)  with `time/xorder=2c` or `3c` runtime option
 - Redesign of time-integrator to support high-order schemes
 - Turbulence driving
-- Double precision floating point HDF5 output
+- Double precision floating-point HDF5 output
 - Software development tools (mostly) exclusive to private repository:
   - Continuous integration (Jenkins and Travis CI)
   - C++ style checker
@@ -142,9 +142,9 @@ Feature branches to merge to `master`:
 - Conflicting restart and input parameters for writing output [\#62](https://github.com/PrincetonUniversity/athena/issues/62)
 - Add double precision option for HDF5 output [\#28](https://github.com/PrincetonUniversity/athena/issues/28)
 - Improve vectorization for loops in PPM [\#121](https://github.com/PrincetonUniversity/athena/pull/121) ([beiwang2003](https://github.com/beiwang2003))
-- Improve symmetry-preservation of HLLD floating point operations [\#120](https://github.com/PrincetonUniversity/athena/pull/120) ([felker](https://github.com/felker))
+- Improve symmetry-preservation of HLLD floating-point operations [\#120](https://github.com/PrincetonUniversity/athena/pull/120) ([felker](https://github.com/felker))
 - Fix restarted simulation calculation of next\_time for writing outputs [\#116](https://github.com/PrincetonUniversity/athena/pull/116) ([felker](https://github.com/felker))
-- Support double precision floating point HDF5 output [\#108](https://github.com/PrincetonUniversity/athena/pull/108) ([felker](https://github.com/felker))
+- Support double precision floating-point HDF5 output [\#108](https://github.com/PrincetonUniversity/athena/pull/108) ([felker](https://github.com/felker))
 - Add templates for Issue and PR; creating draft of CONTRIBUTING.md [\#93](https://github.com/PrincetonUniversity/athena/pull/93) ([felker](https://github.com/felker))
 - Make athdf a class which will delay reading until data is requested [\#84](https://github.com/PrincetonUniversity/athena/pull/84) ([msbc](https://github.com/msbc))
 - Improve TimeIntegratorTaskList performance [\#80](https://github.com/PrincetonUniversity/athena/pull/80) ([felker](https://github.com/felker))
@@ -210,7 +210,7 @@ Feature branches to merge to `master`:
 - Add Bash wrapper to join\_vtk++ for many MeshBlocks, output steps [\#91](https://github.com/PrincetonUniversity/athena/pull/91) ([felker](https://github.com/felker))
 - Add CODEOWNERS file to new .github/ root dir [\#90](https://github.com/PrincetonUniversity/athena/pull/90) ([felker](https://github.com/felker))
 - Add ShearingBox component   [\#89](https://github.com/PrincetonUniversity/athena/pull/89) ([jmshi](https://github.com/jmshi))
-- Improve floating point precision consistency throughout code [\#82](https://github.com/PrincetonUniversity/athena/pull/82) ([felker](https://github.com/felker))
+- Improve floating-point precision consistency throughout code [\#82](https://github.com/PrincetonUniversity/athena/pull/82) ([felker](https://github.com/felker))
 - Add primitive variable flooring functions to the EquationOfState class  [\#81](https://github.com/PrincetonUniversity/athena/pull/81) ([felker](https://github.com/felker))
 - Add MG and FFT convergence regression tests based on 3D linear Jeans instability [\#75](https://github.com/PrincetonUniversity/athena/pull/75) ([alwinm](https://github.com/alwinm))
 - Add cylindrical and spherical polar coordinates limiter terms to PPM [\#69](https://github.com/PrincetonUniversity/athena/pull/69) ([felker](https://github.com/felker))

Makefile.in

@@ -26,8 +26,8 @@ SRC_FILES := $(wildcard src/*.cpp) \
 	     $(wildcard src/bvals/*.cpp) \
 	     $(wildcard src/coordinates/*.cpp) \
 	     src/eos/$(EOS_FILE) \
-	     $(wildcard src/fft/*.cpp) \
 	     src/eos/eos_high_order.cpp \
+	     $(wildcard src/fft/*.cpp) \
 	     $(wildcard src/field/*.cpp) \
 	     $(wildcard src/field/field_diffusion/*.cpp) \
 	     $(wildcard src/gravity/*.cpp) \

configure.py

@@ -28,7 +28,8 @@
 #   --fftw_path=path  path to FFTW libraries (requires the FFTW library)
 #   --grav=xxx        use xxx as the self-gravity solver
 #   --cxx=xxx         use xxx as the C++ compiler
-#   --ccmd=name       use name as the command to call the C++ compiler
+#   --ccmd=name       use name as the command to call the (non-MPI) C++ compiler
+#   --mpiccmd=name    use name as the command to call the MPI C++ compiler
 #   --cflag=string    append string whenever invoking compiler/linker
 #   --include=path    use -Ipath when compiling
 #   --lib=path        use -Lpath when linking
@@ -207,7 +208,12 @@
 # --ccmd=[name] argument
 parser.add_argument('--ccmd',
                     default=None,
-                    help='override for command to use to call C++ compiler')
+                    help='override for command to use to call (non-MPI) C++ compiler')
+
+# --mpiccmd=[name] argument
+parser.add_argument('--mpiccmd',
+                    default=None,
+                    help='override for command to use to call MPI C++ compiler')
 
 # --cflag=[string] argument
 parser.add_argument('--cflag',
@@ -461,7 +467,6 @@
 else:
     definitions['SINGLE_PRECISION_ENABLED'] = '0'
 
-
 # -debug argument
 if args['debug']:
     definitions['DEBUG'] = 'DEBUG'
@@ -478,6 +483,10 @@
 else:
     definitions['DEBUG'] = 'NOT_DEBUG'
 
+# --ccmd=[name] argument
+if args['ccmd'] is not None:
+    definitions['COMPILER_COMMAND'] = makefile_options['COMPILER_COMMAND'] = args['ccmd']
+
 # -mpi argument
 if args['mpi']:
     definitions['MPI_OPTION'] = 'MPI_PARALLEL'
@@ -489,6 +498,9 @@
         makefile_options['COMPILER_FLAGS'] += ' -h mpi1'
     if args['cxx'] == 'bgxl':
         definitions['COMPILER_COMMAND'] = makefile_options['COMPILER_COMMAND'] = 'mpixlcxx'  # noqa
+    # --mpiccmd=[name] argument
+    if args['mpiccmd'] is not None:
+        definitions['COMPILER_COMMAND'] = makefile_options['COMPILER_COMMAND'] = args['mpiccmd'] # noqa
 else:
     definitions['MPI_OPTION'] = 'NOT_MPI_PARALLEL'
 
@@ -577,10 +589,6 @@
 else:
     definitions['H5_DOUBLE_PRECISION_ENABLED'] = '0'
 
-# --ccmd=[name] argument
-if args['ccmd'] is not None:
-    definitions['COMPILER_COMMAND'] = makefile_options['COMPILER_COMMAND'] = args['ccmd']
-
 # --cflag=[string] argument
 if args['cflag'] is not None:
     makefile_options['COMPILER_FLAGS'] += ' '+args['cflag']

src/defs.hpp.in

@@ -54,7 +54,7 @@
 // enable GR frame transformations? default=0 (false)
 #define FRAME_TRANSFORMATIONS @FRAME_TRANSFORMATIONS@
 
-// floating point single precision option
+// floating-point single precision option
 #define SINGLE_PRECISION_ENABLED @SINGLE_PRECISION_ENABLED@
 
 // MPI parallelization (MPI_PARALLEL or NOT_MPI_PARALLEL)
@@ -66,7 +66,7 @@
 // HDF5 output (HDF5OUTPUT or NO_HDF5OUTPUT)
 #define @HDF5_OPTION@
 
-// HDF5 floating point ouptut precision option
+// HDF5 floating-point ouptut precision option
 #define H5_DOUBLE_PRECISION_ENABLED @H5_DOUBLE_PRECISION_ENABLED@
 
 // compiler options

src/hydro/rsolvers/mhd/hlld.cpp

@@ -74,7 +74,7 @@ void Hydro::RiemannSolver(const int kl, const int ku, const int jl, const int ju
 
     // Compute L/R states for selected conserved variables
     Real bxsq = bxi*bxi;
-    // (KGF): group transverse vector components for floating point associativity symmetry
+    // (KGF): group transverse vector components for floating-point associativity symmetry
     Real pbl = 0.5*(bxsq + (SQR(wli[IBY]) + SQR(wli[IBZ])));  // magnetic pressure (l/r)
     Real pbr = 0.5*(bxsq + (SQR(wri[IBY]) + SQR(wri[IBZ])));
     Real kel = 0.5*wli[IDN]*(SQR(wli[IVX]) + (SQR(wli[IVY]) + SQR(wli[IVZ])));
@@ -141,7 +141,7 @@ void Hydro::RiemannSolver(const int kl, const int ku, const int jl, const int ju
     Real sdr = spd[4] - wri[IVX];
 
     // S_M: eqn (38) of Miyoshi & Kusano
-    // (KGF): group ptl, ptr terms for floating point associativity symmetry
+    // (KGF): group ptl, ptr terms for floating-point associativity symmetry
     spd[2] = (sdr*ur.mx - sdl*ul.mx + (ptl - ptr))/(sdr*ur.d - sdl*ul.d);
 
     Real sdml   = spd[0] - spd[2];  // S_i-S_M (i=L or R)
@@ -190,10 +190,10 @@ void Hydro::RiemannSolver(const int kl, const int ku, const int jl, const int ju
       ulst.bz = ul.bz * tmp;
     }
     // v_i* dot B_i*
-    // (KGF): group transverse momenta terms for floating point associativity symmetry
+    // (KGF): group transverse momenta terms for floating-point associativity symmetry
     Real vbstl = (ulst.mx*bxi+(ulst.my*ulst.by+ulst.mz*ulst.bz))*ulst_d_inv;
     // eqn (48) of M&K
-    // (KGF): group transverse by, bz terms for floating point associativity symmetry
+    // (KGF): group transverse by, bz terms for floating-point associativity symmetry
     ulst.e = (sdl*ul.e - ptl*wli[IVX] + ptst*spd[2] +
               bxi*(wli[IVX]*bxi + (wli[IVY]*ul.by + wli[IVZ]*ul.bz) - vbstl))*sdml_inv;
 
@@ -218,10 +218,10 @@ void Hydro::RiemannSolver(const int kl, const int ku, const int jl, const int ju
       urst.bz = ur.bz * tmp;
     }
     // v_i* dot B_i*
-    // (KGF): group transverse momenta terms for floating point associativity symmetry
+    // (KGF): group transverse momenta terms for floating-point associativity symmetry
     Real vbstr = (urst.mx*bxi+(urst.my*urst.by+urst.mz*urst.bz))*urst_d_inv;
     // eqn (48) of M&K
-    // (KGF): group transverse by, bz terms for floating point associativity symmetry
+    // (KGF): group transverse by, bz terms for floating-point associativity symmetry
     urst.e = (sdr*ur.e - ptr*wri[IVX] + ptst*spd[2] +
               bxi*(wri[IVX]*bxi + (wri[IVY]*ur.by + wri[IVZ]*ur.bz) - vbstr))*sdmr_inv;
     // ul** and ur** - if Bx is near zero, same as *-states

src/inputs/hdf5_reader.cpp

@@ -26,7 +26,7 @@
   #include <mpi.h>  // MPI_COMM_WORLD, MPI_INFO_NULL
 #endif
 
-// Determine floating point precision (in memory, not file)
+// Determine floating-point precision (in memory, not file)
 #if SINGLE_PRECISION_ENABLED
   #define H5T_REAL H5T_NATIVE_FLOAT
 #else

src/mesh/mesh.cpp

@@ -1350,7 +1350,9 @@ void Mesh::Initialize(int res_flag, ParameterInput *pin) {
 
     // begin fourth-order correction of midpoint initial condition:
     // --------------------------
-    bool correct_ic = pmb->precon->correct_ic;
+
+    // correct IC on all MeshBlocks or none; switch cannot be toggled independently
+    bool correct_ic = pmb_array[0]->precon->correct_ic;
     if (correct_ic == true) {
 #pragma omp for private(pmb, phydro, pfield, pbval)
       for (int i=0; i<nmb; ++i) {

src/reconstruct/reconstruction.cpp

@@ -143,6 +143,16 @@ Reconstruction::Reconstruction(MeshBlock *pmb, ParameterInput *pin) {
           << "Reconfigure with Cartesian coordinates " << std::endl;
       throw std::runtime_error(msg.str().c_str());
     }
+
+    if (SHEARING_BOX) {
+      std::stringstream msg;
+      msg << "### FATAL ERROR in Reconstruction constructor" << std::endl
+          << "Selected time/xorder=" << input_recon << " flux calculations"
+          << "currently does not support shearing box boundary conditions " << std::endl;
+      throw std::runtime_error(msg.str().c_str());
+      return;
+    }
+
     // check for necessary number of ghost zones for PPM w/ fourth-order flux corrections
     int req_nghost = 4;
     // until new algorithm for face-averaged Field->bf to cell-averaged Hydro->bcc

src/utils/ran2.cpp

@@ -21,7 +21,7 @@
 // shuffle and added safeguards.  Returns a uniform random deviate between 0.0 and 1.0
 // (exclusive of the endpoint values).  Call with idum = a negative integer to
 // initialize; thereafter, do not alter idum between successive deviates in a sequence.
-// RNMX should appriximate the largest floating point value that is less than 1.
+// RNMX should appriximate the largest floating-point value that is less than 1.
 
 #define IMR1 2147483563
 #define IMR2 2147483399

src/utils/show_config.cpp

@@ -57,9 +57,9 @@ void ShowConfig(void) {
     std::cout<<"  General Relativity:         OFF " << std::endl;
   }
   if (SINGLE_PRECISION_ENABLED) {
-    std::cout<<"  Floating point precision:   single" << std::endl;
+    std::cout<<"  Floating-point precision:   single" << std::endl;
   } else {
-    std::cout<<"  Floating point precision:   double" << std::endl;
+    std::cout<<"  Floating-point precision:   double" << std::endl;
   }
   std::cout<<"  Number of ghost cells:      " << NGHOST << std::endl;
 #ifdef MPI_PARALLEL