22.cleanup_and_mpi.patch

diff --git a/.travis.yml b/.travis.yml
index 07d9d899..1c8337f3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,9 +3,7 @@
 language: cpp
 branches:
   only:
-  - master
-  - dust
-  - mhd4_3D
+  - snap-mods
 # Default build matrix is 4x Ubuntu builds (inherit the default stage name "test"):
 os:
   - linux
diff --git a/bench/CMakeLists.txt b/bench/CMakeLists.txt
index d3f498ef..5c64ee66 100644
--- a/bench/CMakeLists.txt
+++ b/bench/CMakeLists.txt
@@ -8,25 +8,27 @@ string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
 add_executable(shock_tube.${buildl} main.cpp shock_tube.cpp dummy.cpp)
 
 set_target_properties(shock_tube.${buildl}
-	PROPERTIES
-	RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
-	COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
-	)
+  PROPERTIES
+  RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
+  COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
+  )
 
 target_link_libraries(shock_tube.${buildl}
-    ${ATHENAPP_LIBRARY_${buildu}}
-	)
+  ${ATHENAPP_LIBRARY_${buildu}}
+  ${MPI_CXX_LIBRARIES}
+  )
 
 target_include_directories(shock_tube.${buildl}
-	PRIVATE
-    ${ATHENAPP_INCLUDE_DIR}
-	)
+  PRIVATE
+  ${ATHENAPP_INCLUDE_DIR}
+  ${MPI_CXX_INCLUDE_PATH}
+  )
 
 # copy input files to build directory
 file(GLOB infiles athinput.*)
 foreach(infile ${infiles})
-	get_filename_component(name ${infile} NAME)
-	configure_file(${infile}
-		${CMAKE_BINARY_DIR}/bin/${name} COPYONLY
-		)
+  get_filename_component(name ${infile} NAME)
+  configure_file(${infile}
+    ${CMAKE_BINARY_DIR}/bin/${name} COPYONLY
+    )
 endforeach()
diff --git a/cmake/parameters.cmake b/cmake/parameters.cmake
index 6fc32363..869befaa 100644
--- a/cmake/parameters.cmake
+++ b/cmake/parameters.cmake
@@ -67,6 +67,10 @@ SET_IF_EMPTY(FFT_OPTION "NO_FFT")
 # MPI parallelization (MPI_PARALLEL or NOT_MPI_PARALLEL)
 SET_IF_EMPTY(MPI_OPTION "NOT_MPI_PARALLEL")
 
+IF(MPI_OPTION STREQUAL "MPI_PARALLEL")
+  find_package(MPI REQUIRED)
+endif()
+
 # OpenMP parallelization (OPENMP_PARALLEL or NOT_OPENMP_PARALLEL)
 SET_IF_EMPTY(OPENMP_OPTION "NOT_OPENMP_PARALLEL")
 
@@ -111,8 +115,8 @@ SET_IF_EMPTY(NUMBER_GHOST_CELLS 2)
 math(EXPR NHYDRO_VARIABLES "5 + ${NVAPOR}")
 math(EXPR NWAVE_VALUE "5 + ${NVAPOR}")
 
-SET_IF_EMPTY(NCLOUDS 0)
-SET_IF_EMPTY(NTRACER 0)
+SET_IF_EMPTY(NCLOUD 0)
 SET_IF_EMPTY(NCHEMISTRY 0)
+SET_IF_EMPTY(NTRACER 0)
 
-math(EXPR NUMBER_PASSIVE_SCALARS "${NCLOUDS} + ${NTRACER} + ${NCHEMISTRY}")
+math(EXPR NUMBER_PASSIVE_SCALARS "${NCLOUD} + ${NCHEMISTRY} + ${NTRACER}")
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ecdb67f3..d155490f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -28,8 +28,6 @@ set(EOS_FILE ${EOS_FILE}.cpp)
 set(RSOLVER_FILE ${RSOLVER_FILE}.cpp)
 set(PROBLEM_FILE ${PROBLEM_FILE}.cpp)
 
-message(STATUS ${RSOLVER_DIR}${RSOLVER_FILE})
-
 # source files are defined in Makefile.in
 file(GLOB src_files
     *.cpp
@@ -71,24 +69,6 @@ file(GLOB src_files
 # remove main file
 list(FILTER src_files EXCLUDE REGEX ".*/src/main\\.cpp$")
 
-# user mod calcualte_fluxes
-if (EXISTS "${CMAKE_SOURCE_DIR}/athena_mod/hydro/calculate_fluxes.cpp")
-    message(STATUS "Found calculate_fluxes.cpp in ${CMAKE_SOURCE_DIR}/athena_mod/hydro/calculate_fluxes.cpp")
-    list(FILTER src_files EXCLUDE REGEX ".*/src/hydro/calculate_fluxes\\.cpp$")
-endif()
-
-# user mod new_blockdt
-if (EXISTS "${CMAKE_SOURCE_DIR}/athena_mod/hydro/new_blockdt.cpp")
-    message(STATUS "Found new_blockdt.cpp in ${CMAKE_SOURCE_DIR}/athena_mod/hydro/new_blockdt.cpp")
-    list(FILTER src_files EXCLUDE REGEX ".*/src/hydro/new_blockdt\\.cpp$")
-endif()
-
-# user mod outputs delegates
-if (EXISTS "${CMAKE_SOURCE_DIR}/athena_mod/outputs/outputs.cpp")
-    message(STATUS "Found outputs.cpp in ${CMAKE_SOURCE_DIR}/athena_mod/outputs/outputs.cpp")
-    list(FILTER src_files EXCLUDE REGEX ".*/src/outputs/outputs\\.cpp$")
-endif()
-
 string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
 string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
 
diff --git a/src/mesh/mesh.hpp b/src/mesh/mesh.hpp
index 01ff45d5..4144da63 100644
--- a/src/mesh/mesh.hpp
+++ b/src/mesh/mesh.hpp
@@ -143,9 +143,6 @@ class MeshBlock {
   void UserWorkInLoop();                          // called in TimeIntegratorTaskList
 
   // opaque pointer
-  class IndexMap;
-  std::shared_ptr<IndexMap> pindex;
-
   class Impl;
   std::shared_ptr<Impl> pimpl;
 
diff --git a/src/reconstruct/interpolation.hpp b/src/reconstruct/interpolation.hpp
index 6162a7c1..5b503fdc 100644
--- a/src/reconstruct/interpolation.hpp
+++ b/src/reconstruct/interpolation.hpp
@@ -5,21 +5,9 @@
 
 // Athena++
 #include "../defs.hpp"
-//#include "../math/core.h"
 
 #define sqr(x) ( (x)*(x) )
 
-/* 2-nd order plm for non-uniform grid
-template<typename T>
-inline T interp_plm(T phim1, T phi, T phip1, Real dxl, Real dx) {
-  Real dwl = phi - phim1;
-  Real dwr = phip1 - phi;
-  Real dw2 = dwl*dwr;
-  Real dwm = 2.0*dw2/(dwl + dwr);
-  if (dw2 <= 0.0) dwm = 0.0;
-  return phi - dxl/dx*dwm;
-}*/
-
 // limiter
 template<typename T>
 inline T minmod(T a, T b) {