Merge branch 'release' of https://github.com/dylan-jayatilaka/tonto i…

…nto release

.ctags

@@ -3,7 +3,7 @@
 --regex-foo=/^   type ([A-Z][A-Z0-9_(){},]*)/\1/t,types/
 --regex-foo=/^   array type ([A-Z][A-Z0-9_(){},]*)/\1/v,array types/
 --regex-foo=/^   ([a-zA-Z][a-zA-Z0-9_]*[a-zA-Z0-9]) +:: +[A-Z][A-Z0-9_(){},]*\*?/\1/g,module variables/
---regex-foo=/^     ([a-zA-Z][a-zA-Z0-9_]*[a-zA-Z0-9]) +:: +[A-Z][A-Z0-9_(){},]*\*?/\1/a,attributes/
+--regex-foo=/^     ([a-zA-Z][a-zA-Z0-9_]*[a-zA-Z0-9]?) +:: +[A-Z][A-Z0-9_(){},]*\*?/\1/a,attributes/
 --regex-foo=/^   ([a-zA-Z][a-zA-Z0-9]|[a-df-zA-Z][a-mo-zA-Z0-9_][a-ce-z0-9]|[a-zA-Z][a-zA-Z0-9_]{2,}[a-zA-Z0-9])([(][^)"]*[)])?( *result *[(][^)]*[)])?( *$| *:::)/\1/r,routines/
 --regex-foo=/^   interface +([a-z][a-zA-Z0-9_]*[a-z0-9])/\1/i,interfaces/
 --foo-types=+mtvgai

.github/workflows/cmake.yml

@@ -0,0 +1,44 @@
+name: CMake
+
+on:
+  push:
+    branches:
+      - master
+      - release
+  pull_request:
+    branches:
+      - master
+      - release
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with: 
+        submodules: true
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+
+    - name: Build
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      # Execute tests defined by the CMake configuration.  
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest -C ${{env.BUILD_TYPE}} -L short
+

.gitignore

@@ -52,3 +52,12 @@ cscope.*
 # vim swap files
 .*.swp
 
+# Krita files & backups
+lg-movie.kra
+lg-movie.kra~
+*.bmp
+*.kra
+*.kra~
+*movie*
+*~
+

CMakeLists.txt

@@ -1,12 +1,14 @@
 # CMake
-cmake_minimum_required(VERSION 3.0.0)
+cmake_minimum_required(VERSION 3.6.0)
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 # Install where?
 set(CMAKE_INSTALL_PREFIX /usr/local CACHE PATH "Install prefix")
 
 # Allow arbitrary characters in test names
+if(CMAKE_VERSION VERSION_GREATER 3.19) 
 cmake_policy(SET CMP0110 NEW)
+endif()
 
 # Tonto version info and build date
 string(TIMESTAMP VERSION_MAJOR "%y")
@@ -177,6 +179,8 @@ set(FOO_SRC
     ${FOO_DIR}/vec{evec{evec{intrinsic}}}.foo
     ${FOO_DIR}/vec{evec{evec{int}}}.foo
     ${FOO_DIR}/vec{evec{evec{real}}}.foo
+    ${FOO_DIR}/mat{evec{int}}.foo
+    ${FOO_DIR}/mat{evec{real}}.foo
     ${FOO_DIR}/map{vec{key},vec{val}}.foo
     ${FOO_DIR}/map{int,int}.foo
     ${FOO_DIR}/map{key,val}.foo
@@ -190,7 +194,9 @@ set(FOO_SRC
     ${FOO_DIR}/atom.foo
     ${FOO_DIR}/basis.foo
     ${FOO_DIR}/becke_grid.foo
+#   ${FOO_DIR}/breakdown_data.foo
     ${FOO_DIR}/buffer.foo
+    ${FOO_DIR}/output_style.foo
     ${FOO_DIR}/textfile.foo
     ${FOO_DIR}/datafile.foo
     ${FOO_DIR}/json.foo
@@ -202,9 +208,11 @@ set(FOO_SRC
     ${FOO_DIR}/colour_function.foo
     ${FOO_DIR}/coppensbasis.foo
     ${FOO_DIR}/coppensorbital.foo
-    ${FOO_DIR}/debug.foo
     ${FOO_DIR}/dft_functional.foo
-    ${FOO_DIR}/diffraction_data.foo
+    ${FOO_DIR}/diffraction_data.inq.foo
+    ${FOO_DIR}/diffraction_data.set.foo
+    ${FOO_DIR}/diffraction_data.read.foo
+    ${FOO_DIR}/diffraction_data.put.foo
     ${FOO_DIR}/diis.foo
     ${FOO_DIR}/rys.foo
     ${FOO_DIR}/rms_indices.foo
@@ -241,7 +249,8 @@ set(FOO_SRC
     ${FOO_DIR}/spacegroup.foo
     ${FOO_DIR}/reflection.foo
     ${FOO_DIR}/crystal.foo
-    ${FOO_DIR}/spherical.foo
+    ${FOO_DIR}/crystal23.foo
+    ${FOO_DIR}/spherical_harmonic.foo
     ${FOO_DIR}/table_column.foo
     ${FOO_DIR}/t_tensor.foo
     ${FOO_DIR}/atom_group.foo
@@ -266,21 +275,25 @@ set(FOO_SRC
     ${FOO_DIR}/opvector.foo
     ${FOO_DIR}/mo_localiser.foo
     ${FOO_DIR}/pair_energy.foo
+    ${FOO_DIR}/molecule.inq.foo
+    ${FOO_DIR}/molecule.set.foo
+    ${FOO_DIR}/molecule.read.foo
+    ${FOO_DIR}/molecule.put.foo
     ${FOO_DIR}/molecule.base.foo
-    ${FOO_DIR}/molecule.ce.foo
-    ${FOO_DIR}/molecule.cp.foo
-    ${FOO_DIR}/molecule.nomo.foo
-    ${FOO_DIR}/molecule.fock.foo
+#   ${FOO_DIR}/molecule.rel.foo ! for now
     ${FOO_DIR}/molecule.grid.foo
+    ${FOO_DIR}/molecule.xtal.foo
+    ${FOO_DIR}/molecule.ce.foo
     ${FOO_DIR}/molecule.ints.foo
-    ${FOO_DIR}/molecule.main.foo
-    ${FOO_DIR}/molecule.misc.foo
-    ${FOO_DIR}/molecule.plot.foo
-    ${FOO_DIR}/molecule.prop.foo
-    ${FOO_DIR}/molecule.rel.foo
+    ${FOO_DIR}/molecule.fock.foo
+#   ${FOO_DIR}/molecule.nomo.foo ! for now
     ${FOO_DIR}/molecule.scf.foo
-    ${FOO_DIR}/molecule.tad.foo
-    ${FOO_DIR}/molecule.xtal.foo
+    ${FOO_DIR}/molecule.prop.foo
+    ${FOO_DIR}/molecule.plot.foo
+    ${FOO_DIR}/molecule.cp.foo
+    ${FOO_DIR}/molecule.har.foo
+    ${FOO_DIR}/molecule.misc.foo
+    ${FOO_DIR}/molecule.main.foo
 )
 
 # Fortran source files used by run_molecule/run_har
@@ -291,6 +304,7 @@ set(FORTRAN_SRC
     ${CMAKE_CURRENT_BINARY_DIR}/basis.F90
     ${CMAKE_CURRENT_BINARY_DIR}/becke_grid.F90
     ${CMAKE_CURRENT_BINARY_DIR}/bin.F90
+#   ${CMAKE_CURRENT_BINARY_DIR}/breakdown_data.F90
     ${CMAKE_CURRENT_BINARY_DIR}/buffer.F90
     ${CMAKE_CURRENT_BINARY_DIR}/capping_square.F90
     ${CMAKE_CURRENT_BINARY_DIR}/cif.F90
@@ -302,9 +316,13 @@ set(FORTRAN_SRC
     ${CMAKE_CURRENT_BINARY_DIR}/coppensorbital.F90
     ${CMAKE_CURRENT_BINARY_DIR}/cpx.F90
     ${CMAKE_CURRENT_BINARY_DIR}/crystal.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/crystal23.F90
     ${CMAKE_CURRENT_BINARY_DIR}/datafile.F90
     ${CMAKE_CURRENT_BINARY_DIR}/dft_functional.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/diffraction_data.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/diffraction_data.inq.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/diffraction_data.set.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/diffraction_data.read.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/diffraction_data.put.F90
     ${CMAKE_CURRENT_BINARY_DIR}/diis.F90
     ${CMAKE_CURRENT_BINARY_DIR}/file.F90
     ${CMAKE_CURRENT_BINARY_DIR}/gaussian.F90
@@ -333,26 +351,33 @@ set(FORTRAN_SRC
     ${CMAKE_CURRENT_BINARY_DIR}/mat_cpx.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mat_int.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mat_real.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/mat_evec_int.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/mat_evec_real.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mat_rms2_indices.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mat_rms_indices.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mat_shell1pair.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mat_str.F90
     ${CMAKE_CURRENT_BINARY_DIR}/mo_localiser.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.inq.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.set.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.read.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.put.F90
     ${CMAKE_CURRENT_BINARY_DIR}/molecule.base.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.ce.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.cp.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.nomo.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.fock.F90
+ #  ${CMAKE_CURRENT_BINARY_DIR}/molecule.rel.F90
     ${CMAKE_CURRENT_BINARY_DIR}/molecule.grid.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.xtal.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.ce.F90
     ${CMAKE_CURRENT_BINARY_DIR}/molecule.ints.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.main.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.misc.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.plot.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.prop.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.rel.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.fock.F90
+ #  ${CMAKE_CURRENT_BINARY_DIR}/molecule.nomo.F90
     ${CMAKE_CURRENT_BINARY_DIR}/molecule.scf.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.tad.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/molecule.xtal.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.prop.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.plot.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.cp.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.har.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.misc.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/molecule.main.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/output_style.F90
     ${CMAKE_CURRENT_BINARY_DIR}/opmatrix.F90
     ${CMAKE_CURRENT_BINARY_DIR}/opvector.F90
     ${CMAKE_CURRENT_BINARY_DIR}/plot_grid.F90
@@ -375,7 +400,7 @@ set(FORTRAN_SRC
     ${CMAKE_CURRENT_BINARY_DIR}/slaterbasis.F90
     ${CMAKE_CURRENT_BINARY_DIR}/slatershell.F90
     ${CMAKE_CURRENT_BINARY_DIR}/spacegroup.F90
-    ${CMAKE_CURRENT_BINARY_DIR}/spherical.F90
+    ${CMAKE_CURRENT_BINARY_DIR}/spherical_harmonic.F90
     ${CMAKE_CURRENT_BINARY_DIR}/str.F90
     ${CMAKE_CURRENT_BINARY_DIR}/system.F90
     ${CMAKE_CURRENT_BINARY_DIR}/table_column.F90
@@ -441,6 +466,7 @@ set(RUN_SRC
     ${RUNFILE_DIR}/run_rgbi.foo
     ${RUNFILE_DIR}/run_least_squares.foo
     ${RUNFILE_DIR}/run_mpi_test.foo
+    ${RUNFILE_DIR}/run_textfile.foo
     ${RUNFILE_DIR}/run_vec{str}.foo
 )
 
@@ -510,6 +536,7 @@ add_executable(run_real          EXCLUDE_FROM_ALL ${CMAKE_CURRENT_BINARY_DIR}/ru
 add_executable(run_rgbi          ${CMAKE_CURRENT_BINARY_DIR}/run_rgbi.F90)
 add_executable(run_vec_str       EXCLUDE_FROM_ALL ${CMAKE_CURRENT_BINARY_DIR}/run_vec_str.F90)
 add_executable(run_least_squares EXCLUDE_FROM_ALL ${CMAKE_CURRENT_BINARY_DIR}/run_least_squares.F90)
+add_executable(run_textfile      EXCLUDE_FROM_ALL ${CMAKE_CURRENT_BINARY_DIR}/run_textfile.F90)
 add_executable(run_mpi_test      ${CMAKE_CURRENT_BINARY_DIR}/run_mpi_test.F90)
 
 # Link exectables
@@ -535,6 +562,7 @@ target_link_libraries(run_rgbi          tonto ${LAPACK_LIBRARIES} ${MPI_LIBRARIE
 target_link_libraries(run_vec_str       tonto ${LAPACK_LIBRARIES} ${MPI_LIBRARIES})
 target_link_libraries(run_least_squares tonto ${LAPACK_LIBRARIES} ${MPI_LIBRARIES})
 target_link_libraries(run_mpi_test      tonto ${LAPACK_LIBRARIES} ${MPI_LIBRARIES})
+target_link_libraries(run_textfile      tonto ${LAPACK_LIBRARIES} ${MPI_LIBRARIES})
 target_link_libraries(run_shell2        tonto ${LAPACK_LIBRARIES} ${MPI_LIBRARIES})