Merge branch 'main' into tMaker_field_interp

.github/workflows/build_test.yaml → .github/workflows/ci_build.yaml

@@ -9,16 +9,18 @@ on:
 
 jobs:
   build:
-    name: ${{ matrix.config.name }}
+    name: ${{ format('{0} ({1})', matrix.config.name, matrix.parallel) }}
     runs-on: ${{ matrix.config.os }}
     env:
       CC: ${{ matrix.config.cc }}
       CXX: ${{ matrix.config.cxx }}
       FC: ${{ matrix.config.fc }}
+      OMP_NUM_THREADS: 2
 
     strategy:
       fail-fast: false
       matrix:
+        parallel: ["openmp", "mpi_openmp"]
         config:
         - {
             name: "Ubuntu 20.04 GCC 10",
@@ -42,7 +44,8 @@ jobs:
           }
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout repo
+      uses: actions/checkout@v4
 
     - name: Install prerequisites
       run: ${{ matrix.config.pip }} install pytest numpy scipy h5py triangle
@@ -52,10 +55,10 @@ jobs:
       uses: actions/cache@v4
       with:
         path: libs
-        key: ${{ runner.os }}-build-${{ hashFiles('src/utilities/build_libs.py') }}
+        key: ${{ matrix.config.os }}-build-${{ matrix.parallel }}-${{ hashFiles('src/utilities/build_libs.py') }}
 
-    - if: ${{ steps.cache-ext-libs.outputs.cache-hit != 'true' }}
-      name: Create build dir
+    - name: Create build dir
+      if: ${{ steps.cache-ext-libs.outputs.cache-hit != 'true' }}
       run: mkdir libs
 
     - name: Check compilers
@@ -64,14 +67,25 @@ jobs:
         $CXX --version
         $FC --version
 
-    - name: Build external
+    - name: Build external (OpenMP)
+      if: ${{ matrix.parallel == 'openmp' }}
       shell: bash
       working-directory: libs
       run: >
         ${{ matrix.config.python }} ../src/utilities/build_libs.py --no_dl_progress --nthread=2 --ref_blas
         --build_umfpack=1 --build_arpack=1 --oft_build_tests=1
+    
+    - name: Build external (MPI+OpenMP)
+      if: ${{ matrix.parallel == 'mpi_openmp' }}
+      shell: bash
+      working-directory: libs
+      run: >
+        ${{ matrix.config.python }} ../src/utilities/build_libs.py --no_dl_progress --nthread=2 --ref_blas
+        --build_mpi=1 --build_umfpack=1 --build_superlu=1 --build_superlu_dist=1
+        --build_arpack=1 --oft_build_tests=1
 
-    - uses: actions/upload-artifact@v4
+    - name: Upload library failure log
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: Library failure log

.github/workflows/cov_build.yaml

@@ -0,0 +1,94 @@
+name: Open FUSION Toolkit code coverage build
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, reopened, synchronize]
+
+jobs:
+  build:
+    name: Code coverage
+    runs-on: ubuntu-22.04
+    env:
+      CC: gcc-13
+      CXX: g++-13
+      FC: gfortran-13
+      OMP_NUM_THREADS: 1
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v4
+
+    - name: Install prerequisites
+      run: |
+        sudo apt -y install lcov
+        pip3 install pytest numpy scipy h5py triangle
+
+    - name: Cache external libraries
+      id: cache-ext-libs
+      uses: actions/cache@v4
+      with:
+        path: libs
+        key: cov_build-${{ hashFiles('src/utilities/build_libs.py') }}
+
+    - name: Create build dir
+      if: ${{ steps.cache-ext-libs.outputs.cache-hit != 'true' }}
+      run: mkdir libs
+
+    - name: Check compilers
+      run: |
+        $CC --version
+        $CXX --version
+        $FC --version
+
+    - name: Build external
+      shell: bash
+      working-directory: libs
+      run: >
+        python3 ../src/utilities/build_libs.py --no_dl_progress --nthread=2
+        --ref_blas --build_mpi=1 --build_umfpack=1 --build_superlu=1 --build_superlu_dist=1
+        --build_arpack=1 --oft_build_tests=1 --oft_build_coverage
+
+    - name: Upload library failure log
+      uses: actions/upload-artifact@v4
+      if: failure()
+      with:
+        name: Library failure log
+        path: libs/build/build_error.log
+
+    - name: Remove external build directory
+      shell: bash
+      working-directory: libs
+      run: rm -rf build
+
+    - name: Configure OFT
+      shell: bash
+      working-directory: libs
+      run: bash config_cmake.sh
+
+    - name: Build OFT
+      shell: bash
+      working-directory: libs/build_release
+      run: make
+
+    - name: Test OFT
+      shell: bash
+      working-directory: libs/build_release
+      run: make test_cov
+
+    - name: Generate coverage report
+      shell: bash
+      working-directory: libs/build_release
+      run: |
+        lcov -c --directory . --output-file main_coverage.info --gcov-tool gcov-13
+        lcov --ignore-errors unused -r main_coverage.info -o cleaned_coverage.txt '/opt/*' '/usr/*'
+    
+    - name: Upload coverage report to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: libs/build_release/cleaned_coverage.txt
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: hansec/OpenFUSIONToolkit
+        verbose: true

README.md

@@ -1,7 +1,8 @@
 Open Flexible Unstructured Simulation Infrastructure with Open Numerics (FUSION) Toolkit (OFT)
 =====================================
 
-![CI status](https://github.com/hansec/OpenFUSIONToolkit/actions/workflows/build_test.yaml/badge.svg?branch=main)
+![CI status](https://github.com/hansec/OpenFUSIONToolkit/actions/workflows/ci_build.yaml/badge.svg?branch=main)
+[![codecov](https://codecov.io/gh/hansec/OpenFUSIONToolkit/graph/badge.svg?token=GG282HKNAO)](https://codecov.io/gh/hansec/OpenFUSIONToolkit)
 [![DOI](https://zenodo.org/badge/710415041.svg)](https://zenodo.org/doi/10.5281/zenodo.10306801)
 
 The Open FUSION Toolkit (OFT) is a suite of modeling tools, and their underlying finite element

codecov.yml

@@ -0,0 +1,16 @@
+coverage:
+  # Set ranges for status displays
+  range: 50..80
+  round: down
+  precision: 1
+  # Make check informational only (not blocking/failing)
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+# GitHub specific settings
+github_checks:
+  annotations: false # Disable code annotations

src/CMakeLists.txt

@@ -17,6 +17,7 @@ option(OFT_BUILD_DOCS "Build documentation?" OFF)
 option(OFT_DOCS_ONLY "Build documentation only?" OFF)
 option(OFT_PACKAGE_BUILD "Perform a destributable package?" OFF)
 option(OFT_PACKAGE_NIGHTLY "Perform a nightly build and include git hash in package filename?" ON)
+option(OFT_COVERAGE "Build with code coverage information?" OFF)
 
 # Internal variables
 set(OFT_SHARED_LIBS CACHE INTERNAL "package_shared_libs")
@@ -91,12 +92,20 @@ if ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Intel")
     set( EXT_LIBS "-lstdc++" )
   endif()
 elseif("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
-  set( CMAKE_C_FLAGS_DEBUG "-g -O0" )
+  if(OFT_COVERAGE)
+    set( CMAKE_C_FLAGS_DEBUG "-Og --coverage -fprofile-update=atomic -g -Wuninitialized" ) # -fprofile-arcs -ftest-coverage
+    set( CMAKE_C_FLAGS_RELEASE "-Og --coverage -fprofile-update=atomic -g" ) # -fprofile-arcs -ftest-coverage
+    set(CMAKE_C_OUTPUT_EXTENSION_REPLACE ON)
+    set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE ON)
+    set(CMAKE_Fortran_OUTPUT_EXTENSION_REPLACE ON)
+  else()
+    set( CMAKE_C_FLAGS_DEBUG "-g -O0 -Wuninitialized" )
+    set( CMAKE_C_FLAGS_RELEASE "-O2" )
+  endif()
   set( CMAKE_CXX_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} )
-  set( CMAKE_Fortran_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} )
-  set( CMAKE_C_FLAGS_RELEASE "-O2" )
   set( CMAKE_CXX_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} )
-  set( CMAKE_Fortran_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} )
+  set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -Werror=line-truncation -Wconversion" )
+  set( CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -Werror=line-truncation -Wconversion" )
   if(NOT OFT_PACKAGE_BUILD)
     set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fcheck=all" )
   endif()

src/base/oft_base.F90

@@ -922,20 +922,43 @@ END SUBROUTINE orient_listn_inv
 !! @warning This function requires `x` be sorted lowest to highest.
 !! @note This function performs an interval search each time it is called.
 !!
-!! @returns \f$ F(xx) \f$
+!! @returns \f$ F(xx) \f$ (-1.E99 if outside domain and `extrap=0`)
 !------------------------------------------------------------------------------
-PURE FUNCTION linterp(x,y,n,xx) result(yy)
+FUNCTION linterp(x,y,n,xx,extrap) result(yy)
 REAL(r8), INTENT(in) :: x(n) !< Paramaterizing array \f$ x_i \f$ [n]
 REAL(r8), INTENT(in) :: y(n) !< Function values \f$ F(x_i) \f$ [n]
-REAL(r8), INTENT(in) :: xx !< Length of function parameterization
-INTEGER(i4), INTENT(in) :: n !< Location to perform interpolation
+REAL(r8), INTENT(in) :: xx !< Location to perform interpolation
+INTEGER(i4), INTENT(in) :: n !< Length of function parameterization
+INTEGER(i4), OPTIONAL, INTENT(in) :: extrap !< Extrapolation mode (0: none, 1: constant, 2: linear)
 INTEGER(i4) :: i
 REAL(r8) :: yy
 yy=-1.d99
 DO i=2,n
   IF(x(i-1)<=xx.AND.x(i)>=xx)EXIT
 END DO
-IF(i<=n)yy=(y(i)-y(i-1))*(xx-x(i-1))/(x(i)-x(i-1)) + y(i-1)
+IF(i<=n)THEN
+  yy=(y(i)-y(i-1))*(xx-x(i-1))/(x(i)-x(i-1)) + y(i-1)
+ELSE
+  IF(PRESENT(extrap))THEN
+    SELECT CASE(extrap)
+    CASE(0)
+    CASE(1)
+      IF(xx<x(1))THEN
+        yy=y(1)
+      ELSE IF(xx>x(n))THEN
+        yy=y(n)
+      END IF
+    CASE(2)
+      IF(xx<x(1))THEN
+        yy=(y(2)-y(1))*(xx-x(1))/(x(2)-x(1)) + y(1)
+      ELSE IF(xx>x(n))THEN
+        yy=(y(n)-y(n-1))*(xx-x(n-1))/(x(n)-x(n-1)) + y(n-1)
+      END IF
+    CASE DEFAULT
+      CALL oft_abort("Invalid extrapolation type","linterp",__FILE__)
+    END SELECT
+  END IF
+END IF
 END FUNCTION linterp
 !---------------------------------------------------------------------------
 !> Reset the stack

src/bin/thincurr_td.F90

@@ -303,7 +303,7 @@ SUBROUTINE run_td_sim(self,dt,nsteps,vec,direct,nplot,sensors)
 t=0.d0
 IF(ntimes_curr>0)THEN
   DO j=1,self%n_icoils
-    icoil_curr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t)
+    icoil_curr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t,1)
   END DO
 END IF
 !---Save sensor data for t=0
@@ -373,32 +373,32 @@ SUBROUTINE run_td_sim(self,dt,nsteps,vec,direct,nplot,sensors)
     IF(ntimes_curr>0)THEN
       DO j=1,self%n_icoils
         ! Start of step
-        icoil_dcurr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt/4.d0)
-        icoil_dcurr(j)=icoil_dcurr(j)-linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t-dt/4.d0)
+        icoil_dcurr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt/4.d0,1)
+        icoil_dcurr(j)=icoil_dcurr(j)-linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t-dt/4.d0,1)
         ! End of step
-        icoil_dcurr(j)=icoil_dcurr(j)+linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*5.d0/4.d0)
-        icoil_dcurr(j)=icoil_dcurr(j)-linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*3.d0/4.d0)
+        icoil_dcurr(j)=icoil_dcurr(j)+linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*5.d0/4.d0,1)
+        icoil_dcurr(j)=icoil_dcurr(j)-linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*3.d0/4.d0,1)
       END DO
     END IF
     IF(ntimes_volt>0)THEN
       DO j=1,self%n_vcoils
         ! Start of step
-        pcoil_volt(j)=linterp(volt_waveform(:,1),volt_waveform(:,j+1),ntimes_volt,t)/2.d0
-        pcoil_volt(j)=pcoil_volt(j)+linterp(volt_waveform(:,1),volt_waveform(:,j+1),ntimes_volt,t+dt)/2.d0
+        pcoil_volt(j)=linterp(volt_waveform(:,1),volt_waveform(:,j+1),ntimes_volt,t,1)/2.d0
+        pcoil_volt(j)=pcoil_volt(j)+linterp(volt_waveform(:,1),volt_waveform(:,j+1),ntimes_volt,t+dt,1)/2.d0
       END DO
     END IF
   ELSE
     CALL Lmat%apply(u,g)
     IF(ntimes_curr>0)THEN
       DO j=1,self%n_icoils
-        icoil_dcurr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*5.d0/4.d0)
-        icoil_dcurr(j)=icoil_dcurr(j)-linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*3.d0/4.d0)
+        icoil_dcurr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*5.d0/4.d0,1)
+        icoil_dcurr(j)=icoil_dcurr(j)-linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t+dt*3.d0/4.d0,1)
       END DO
       icoil_dcurr=icoil_dcurr*2.d0
     END IF
     IF(ntimes_volt>0)THEN
       DO j=1,self%n_vcoils
-        pcoil_volt(j)=linterp(volt_waveform(:,1),volt_waveform(:,j+1),ntimes_volt,t+dt)
+        pcoil_volt(j)=linterp(volt_waveform(:,1),volt_waveform(:,j+1),ntimes_volt,t+dt,1)
       END DO
     END IF
   END IF
@@ -425,7 +425,7 @@ SUBROUTINE run_td_sim(self,dt,nsteps,vec,direct,nplot,sensors)
   CALL u%get_local(vals)
   IF(ntimes_curr>0)THEN
     DO j=1,self%n_icoils
-      icoil_curr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t)
+      icoil_curr(j)=linterp(curr_waveform(:,1),curr_waveform(:,j+1),ntimes_curr,t,1)
     END DO
   END IF
   IF(sensors%nfloops>0)THEN
@@ -531,7 +531,7 @@ SUBROUTINE plot_td_sim(self,dt,nsteps,nplot,sensors)
 t=0.d0
 IF(ntimes_curr>0)THEN
   DO j=1,self%n_icoils
-    coil_vec(j)=linterp(coil_waveform(:,1),coil_waveform(:,j+1),ntimes_curr,t)
+    coil_vec(j)=linterp(coil_waveform(:,1),coil_waveform(:,j+1),ntimes_curr,t,1)
   END DO
 END IF
 !
@@ -600,7 +600,7 @@ SUBROUTINE plot_td_sim(self,dt,nsteps,nplot,sensors)
   IF(MOD(i,nplot)==0)THEN
     IF(ntimes_curr>0)THEN
       DO j=1,self%n_icoils
-        coil_vec(j)=linterp(coil_waveform(:,1),coil_waveform(:,j+1),ntimes_curr,t)
+        coil_vec(j)=linterp(coil_waveform(:,1),coil_waveform(:,j+1),ntimes_curr,t,1)
       END DO
     END IF
     !

src/docs/thincurr_example2.md

@@ -67,8 +67,7 @@ ToDo: Describe current potential "holes"
 
 **Coil current waveform file** (`curr.drive`)
 \verbatim
-2 4
--1.0  1.E3
+2 3
 0.0   1.E3
 1.E-4 0.0
 1.0   0.0

src/docs/website/index.html

@@ -72,7 +72,7 @@ <h4>How To Cite</h4>
             <li><strong>MUG:</strong>
                 <ul class="no_bullet">
                     <li>C. Hansen et al., <em>Phys. Plasmas</em> <strong>22</strong>, 042505 (2015) <a href="http://dx.doi.org/10.1063/1.4917476">[DOI]</a></li>
-                    <li>C. Hansen et al., <em>PhD Thesis: U. Washington</em> (2014) <a href="http://hdl.handle.net/1773/25420">[URI]</a></li>
+                    <li>C. Hansen, <em>PhD Thesis: U. Washington</em> (2014) <a href="http://hdl.handle.net/1773/25420">[URI]</a></li>
                 </ul>
             </li>
             <li><strong>Marklin:</strong>