Merge pull request #136 from mir-group/develop

Phoebe 1.0 merge to master

.github/workflows/buildandtest.yml

@@ -0,0 +1,105 @@
+name: Build and Test
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        omp: [OFF, ON]
+        mpi: [OFF, ON]
+    name: "(OpenMP, MPI) ="
+    runs-on: ubuntu-20.04
+    env:
+      BUILD_DIR: build_${{ matrix.omp }}_${{ matrix.mpi }}
+      OMP_NUM_THREADS: 4
+    steps:
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt install -y libopenblas-dev liblapack-dev libhdf5-dev libhdf5-openmpi-dev libscalapack-openmpi-dev python3-pip -o Acquire::Retries=3 --fix-missing
+          pip3 install numpy
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          submodules: true
+      - name: Configure
+        run: |
+          mkdir ${BUILD_DIR}
+          cd ${BUILD_DIR}
+          cmake .. -DOMP_AVAIL=${{ matrix.omp }} -DKokkos_ENABLE_OPENMP=${{ matrix.omp }} -DMPI_AVAIL=${{ matrix.mpi }} -DHDF5_AVAIL=ON
+      - name: Build
+        run: |
+          cd ${BUILD_DIR}
+          make -j4
+          make -j4 runTests
+      - name: RunTests
+        run : |
+          cd ${BUILD_DIR}
+          ./runTests
+      - name: Download test data
+        run: |
+          wget github.com/mir-group/phoebe-data/archive/master.zip
+          unzip -j master.zip "phoebe-data-master/example/Silicon-ph/qe-phonons/*" -d "example/Silicon-ph/qe-phonons"
+          unzip -j master.zip "phoebe-data-master/example/Silicon-ph/qe-ph-anharmonic/*" -d "example/Silicon-ph/qe-ph-anharmonic"
+          unzip -j master.zip "phoebe-data-master/example/Silicon-el/qe-elph/*" -d "example/Silicon-el/qe-elph"
+          unzip 'example/Silicon-el/qe-elph/silicon.phoebe.*.dat.zip' -d example/Silicon-el/qe-elph/
+          cp example/Silicon-el/qe-elph/* example/Silicon-epa/qe-elph
+          mkdir example/Silicon-epa/qe-elph/out
+          unzip -j master.zip "phoebe-data-master/example/Silicon-epa/qe-elph/out/*" -d "example/Silicon-epa/qe-elph/out"
+      - name: Run epa example without MPI
+        working-directory: example/Silicon-epa
+        run: |
+          ../../${BUILD_DIR}/phoebe -in qeToPhoebeEPA.in
+          ../../${BUILD_DIR}/phoebe -in epaTransport.in
+          ../../${BUILD_DIR}/phoebe -in electronFourierBands.in
+          ../../${BUILD_DIR}/phoebe -in electronFourierDos.in
+          python3 reference/run_check.py
+      - name: Run epa example with MPI
+        working-directory: example/Silicon-epa
+        if: matrix.mpi == 'ON'
+        run: |
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in epaTransport.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronFourierBands.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronFourierDos.in
+          python3 reference/run_check.py
+      - name: Run ph example without MPI
+        working-directory: example/Silicon-ph
+        run: |
+          ../../${BUILD_DIR}/phoebe -in phononTransport.in
+          ../../${BUILD_DIR}/phoebe -in phononBands.in
+          ../../${BUILD_DIR}/phoebe -in phononDos.in
+          ../../${BUILD_DIR}/phoebe -in phononLifetimes.in
+          python3 reference/run_check.py
+      - name: Run ph example with MPI
+        working-directory: example/Silicon-ph
+        if: matrix.mpi == 'ON'
+        run: |
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononTransport.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononBands.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononDos.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in phononLifetimes.in
+          python3 reference/run_check.py
+      - name: Run el example without MPI
+        working-directory: example/Silicon-el
+        run: |
+          ../../${BUILD_DIR}/phoebe -in qeToPhoebeWannier.in
+          ../../${BUILD_DIR}/phoebe -in electronWannierTransport.in
+          ../../${BUILD_DIR}/phoebe -in electronWannierBands.in
+          ../../${BUILD_DIR}/phoebe -in electronWannierDos.in
+          ../../${BUILD_DIR}/phoebe -in electronLifetimes.in
+          python3 reference/run_check.py
+      - name: Run el example with MPI
+        working-directory: example/Silicon-el
+        if: matrix.mpi == 'ON'
+        run: |
+          # Note: don't run this as it runs out-of-memory on the VM
+          #mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in qeToPhoebeWannier.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronWannierTransport.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronWannierBands.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronWannierDos.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -in electronLifetimes.in
+          python3 reference/run_check.py
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -ps 2 -in electronWannierTransport.in
+          mpirun -np 4 --oversubscribe ../../${BUILD_DIR}/phoebe -ps 2 -in electronLifetimes.in
+          python3 reference/run_check.py
+

.gitignore

@@ -1,3 +1,9 @@
+# Build folders
+*build*/
+
+# Output files
+*.json
+
 # Prerequisites
 *.d
 
@@ -33,4 +39,41 @@
 *phoebe
 
 #IDE files
-.project
+.project
+.pydevproject
+
+#MacOS specific files
+.DS_Store
+
+.Makefile.swp
+
+#CMake stuff:
+*CMakeCache.txt
+*CMakeFiles
+*cmake_install.cmake
+CMakeDoxy*
+Makefile
+CMakeLists.txt.orig
+CTestTestfile.cmake
+
+eigen_dep-prefix/
+epa_test/
+example/Silicon/log
+googletest/
+pugixml_dep-prefix/
+runTests*_include.cmake
+scalapack_dep-prefix/
+spglib_dep-prefix/
+runTests[1]_include.cmake
+
+runTests
+tags
+*.plist
+
+# Clion IDE
+.idea
+
+*zip
+
+# built by cmake for version number
+src/main.h

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "lib/kokkos"]
+	path = lib/kokkos
+	url = https://github.com/kokkos/kokkos.git

CITATION.cff

@@ -0,0 +1,30 @@
+# YAML 1.2
+---
+authors: 
+  -
+    affiliation: "Harvard University"
+    family-names: Cepellotti
+    given-names: Andrea
+  -
+    affiliation: "Harvard University"
+    family-names: Coulter
+    given-names: Jennifer
+  -
+    affiliation: "Harvard University"
+    family-names: Johansson
+    given-names: Anders
+  -
+    affiliation: "Harvard University"
+    family-names: Fedorova
+    given-names: Natalya
+  -
+    affiliation: "Harvard University"
+    family-names: Kozinsky
+    given-names: Boris
+cff-version: "1.1.0"
+license: "MIT License"
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/mir-group/phoebe"
+title: "Phoebe: a collection of Phonon and Electron Boltzmann Equation solvers"
+version: "1.0"
+...

CMakeLists.txt

@@ -0,0 +1,196 @@
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE "Release" CACHE
+      STRING "Choose the type of build." FORCE)
+endif(NOT CMAKE_BUILD_TYPE)
+
+if(Kokkos_ENABLE_CUDA)
+    set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "don't touch")
+    set(CMAKE_CXX_COMPILER ${CMAKE_CURRENT_SOURCE_DIR}/lib/kokkos/bin/nvcc_wrapper)
+endif()
+
+cmake_minimum_required(VERSION 3.16)
+set(CMAKE_CXX_STANDARD 14)
+
+project(Phoebe LANGUAGES C CXX Fortran VERSION 1.0)
+
+configure_file(src/main.h.in ../src/main.h)
+
+## load custom cmake find_package
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+
+if(CMAKE_CXX_COMPILER_ID MATCHES GNU)
+    SET(GCC_COVERAGE_COMPILE_FLAGS "-Wall -Wextra -ggdb -fno-omit-frame-pointer -Wno-deprecated-copy -Wno-ignored-attributes")
+    add_definitions(${GCC_COVERAGE_COMPILE_FLAGS})
+    add_compile_options(-Wno-error=parentheses)
+endif()
+
+############ OPTIONS ################
+# these can be toggled in a build script by
+# supplying arguments to cmake like cmake -DHDF5_AVAIL=OFF ../
+option(MPI_AVAIL "Build with MPI wrappers" ON)
+option(OMP_AVAIL "Build with OMP" ON)
+option(HDF5_AVAIL "Build with HDF5" ON)
+option(HDF5_SERIAL "Force build to accomodate serial only HDF5, but still use MPI" OFF)
+option(BUILD_DOC "Build documentation" ON)
+
+############### SOURCE ###############
+
+FILE(GLOB_RECURSE SOURCE_FILES src src/*.cpp)
+list(REMOVE_ITEM SOURCE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/src/main.cpp)
+
+message(${CMAKE_CURRENT_SOURCE_DIR})
+message(${SOURCE_FILES})
+
+FILE(GLOB TEST_SOURCES test/*.cpp test/interaction3ph/*.cpp)
+
+include_directories(src src/algebra src/apps src/bands src/bte src/constants src/harmonic src/interaction src/mpi src/observable src/parser src/points)
+
+include(lib/CMakeLists.txt)
+include(GoogleTest)
+
+add_executable(phoebe src/main.cpp ${SOURCE_FILES})
+add_executable(runTests ${TEST_SOURCES} ${SOURCE_FILES})
+set_target_properties(runTests PROPERTIES EXCLUDE_FROM_ALL TRUE)
+
+# dependencies
+add_dependencies(phoebe spglib_dep pugixml_dep eigen_dep)
+add_dependencies(runTests spglib_dep pugixml_dep eigen_dep)
+
+target_link_libraries(phoebe symspg pugixml kokkos nlohmann_json::nlohmann_json)
+enable_testing()
+target_link_libraries(runTests symspg pugixml gtest_main kokkos nlohmann_json::nlohmann_json)
+
+gtest_discover_tests(
+    runTests
+    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+)
+
+################ PARALLEL ####################
+# build with MPI and scalapack
+if (MPI_AVAIL)
+  find_package(MPI REQUIRED)
+  target_link_libraries(phoebe MPI::MPI_CXX)
+  target_link_libraries(runTests MPI::MPI_CXX)
+  add_definitions("-DMPI_AVAIL") # this sets turns on ifdefs for mpi in the cpp
+
+  find_library(SCALAPACK_LIB NAMES scalapack scalapack-openmpi mkl_scalapack_lp64 PATHS ENV LD_LIBRARY_PATH)
+  if(${SCALAPACK_LIB} MATCHES NOTFOUND)
+      ExternalProject_Add(scalapack_dep
+          BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/scalapack_build
+          SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/scalapack_src
+          GIT_REPOSITORY https://github.com/Reference-ScaLAPACK/scalapack.git
+          INSTALL_COMMAND ""
+          UPDATE_COMMAND ""
+          CMAKE_ARGS
+              -DCMAKE_BUILD_TYPE=Release
+              -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+              -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+              -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+          )
+      set(SCALAPACK_LIB scalapack)
+      message(WARNING "No SCALAPACK library found in CMAKE_LIBRARY_PATH, building our own.")
+      add_dependencies(phoebe scalapack_dep)
+  else()
+      if(${SCALAPACK_LIB} MATCHES mkl)
+          if("${MPI_CXX_LIBRARIES}" MATCHES openmpi)
+              find_library(BLACS_LIB NAMES mkl_blacs_openmpi_lp64 PATHS ENV LD_LIBRARY_PATH)
+          elseif("${MPI_CXX_LIBRARIES}" MATCHES intel)
+              find_library(BLACS_LIB NAMES mkl_blacs_intelmpi_lp64 PATHS ENV LD_LIBRARY_PATH)
+          else()
+              message(FATAL_ERROR "Confused by MPI library when looking for BLACS.")
+          endif()
+          if(${BLACS_LIB} MATCHES NOTFOUND)
+              message(FATAL_ERROR "Found Intel SCALAPACK but not BLACS")
+          endif()
+          message(STATUS "Found BLACS: ${BLACS_LIB}")
+      endif()
+      message(STATUS "Found SCALAPACK: ${SCALAPACK_LIB}")
+  endif()
+
+  find_package(BLAS REQUIRED)
+  find_package(LAPACK REQUIRED)
+  include_directories(${BLAS_INCLUDE_DIR})
+  include_directories(${LAPACK_INCLUDE_DIR})
+  ## Very important to link scalapack before blas and lapack
+  target_link_libraries(phoebe ${SCALAPACK_LIB} ${BLACS_LIB} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
+  target_link_libraries(runTests ${SCALAPACK_LIB} ${BLACS_LIB} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
+
+else()
+  set(HDF5_SERIAL ON)
+
+  ## even for the serial version, we require lapack
+  find_package(BLAS REQUIRED)
+  find_package(LAPACK REQUIRED)
+  include_directories(${BLAS_INCLUDE_DIR})
+  include_directories(${LAPACK_INCLUDE_DIR})
+  target_link_libraries(phoebe ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
+  target_link_libraries(runTests ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} -lgfortran)
+
+endif()
+
+# build with openMP
+if(OMP_AVAIL)
+  find_package(OpenMP)
+  target_link_libraries(phoebe OpenMP::OpenMP_CXX)
+  target_link_libraries(runTests OpenMP::OpenMP_CXX)
+  add_definitions("-DOMP_AVAIL")
+endif()
+
+# build with HDF5
+if(HDF5_AVAIL)
+  if(HDF5_SERIAL)
+    add_definitions("-DHDF5_SERIAL")
+  else()
+    set(HDF5_PREFER_PARALLEL TRUE)
+  endif()
+  add_dependencies(phoebe highfive_dep)
+  add_dependencies(runTests highfive_dep)
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(phoebe ${HDF5_LIBRARIES})
+  target_link_libraries(runTests ${HDF5_LIBRARIES})
+  include_directories(${HDF5_INCLUDE_DIRS})
+  add_definitions("-DHDF5_AVAIL")
+endif()
+
+############# DOCS ############
+
+find_package(Doxygen)
+find_package(Sphinx)
+
+IF (BUILD_DOC)
+    IF (NOT DOXYGEN_FOUND)
+        message("Doxygen need to be installed to generate the doxygen documentation")
+    else()
+        # set input and output files
+        set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/doc/doxygen/Doxyfile)
+        set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/doc/doxygen/Doxyfile.out)
+
+        # request to configure the file
+        configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+        message("Doxygen configured")
+
+        # note the option ALL which allows to build the docs together with the application
+        add_custom_target(
+            docDevel
+            COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_IN}
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/../doc/doxygen
+            COMMENT "Generating API documentation with Doxygen"
+            VERBATIM)
+
+	IF (NOT SPHINX_FOUND)
+	  message("Documentation needs also sphinx")
+	else()
+	  add_custom_target(
+	    doc
+	    COMMAND make html
+	    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/../doc/sphinx
+	    COMMENT "Building user documentation with Sphinx"
+	    VERBATIM)
+	  add_dependencies(doc docDevel)
+	endif()
+
+    ENDIF()
+endif()
+
+
+