Merge branch 'master' into cppcheck

.github/workflows/actions.yml

@@ -112,8 +112,8 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-    name: x86 MacOS 11
+    name: x86 MacOS 12
-    runs-on: macos-11
+    runs-on: macos-12
 
     steps:
       - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
@@ -123,17 +123,27 @@ jobs:
           brew install emacs
           brew install hdf5
           brew install automake
+          brew --prefix hdf5
 
       - name: configure with autotools
         run: |
           ./autogen.sh
-          ./configure FC=gfortran-10 --enable-silent-rules
+          ./configure FC=gfortran-12 --enable-silent-rules
 
       - name: compile TREXIO
         run: make -j3
 
       - name: check TREXIO
         run: make -j3 check
+      
+      - name: compile Python API
+        run: |
+          export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
+          export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
+          make python-install
+      
+      - name: test Python API
+        run: make python-test
 
       - name: Archive test log file
         if: failure()

.github/workflows/build-wheels.yml

@@ -21,7 +21,7 @@ jobs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
       - name: Checkout the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         # Gets the correct commit message for pull request
         with:
           ref: ${{ github.event.pull_request.head.sha }}
@@ -42,14 +42,14 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        manylinux_tag: [2010_x86_64, 2014_x86_64, 2_24_x86_64]
+        manylinux_tag: [2014_x86_64, 2_24_x86_64]
 
     steps:
       - name: Checkout the branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: '3.9'
 
@@ -103,22 +103,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-10.15]
+        os: [macos-12]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-# TODO: normally, one could include macos-11 and the OS list above but the produced wheels receive an error upon installation:
+
-# ERROR: trexio-1.1.0-cp39-cp39-macosx_11_0_x86_64.whl is not a supported wheel on this platform.
-# This happens even with the MACOSX_DEPLOYMENT_TARGET trick. Perhaps it can be solved by configuring the build system
-# to produce the wheels for MacOS-11 from the very beginning
-        #exclude:
-        #  - os: macos-11
-    env:
-        H5_LDFLAGS: '-L/usr/local/Cellar/hdf5/1.12.1/lib'
-        H5_CFLAGS: '-I/usr/local/Cellar/hdf5/1.12.1/include'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -128,11 +120,6 @@ jobs:
       - name: Install HDF5
         run: brew install hdf5@1.12
 
-      # This step is needed to produce wheels with the correct platform tag for MacOS-11 (Big Sur)
-      #- name: Set MACOSX_DEPLOYMENT_TARGET environment variable
-      #  if: ${{ matrix.os == 'macos-11' }}
-      #  run: echo "MACOSX_DEPLOYMENT_TARGET=11.0" >> $GITHUB_ENV
-
       - name: Compute the PYTREXIO_VERSION environment variable
         run: echo "PYTREXIO_VERSION=$(grep __version__ python/pytrexio/_version.py | cut -d\  -f3 | tr -d '"')" >> $GITHUB_ENV
 
@@ -158,6 +145,8 @@ jobs:
         run: |
           mkdir wheelhouse/
           cd trexio-${{ env.PYTREXIO_VERSION }}/
+          export H5_CFLAGS="-I$(brew --prefix hdf5)/include"
+          export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"
           python -m build --wheel --outdir=./
           delocate-wheel trexio-*.whl
           mv trexio-*.whl ../wheelhouse/
@@ -186,10 +175,10 @@ jobs:
 
     steps:
       - name: Checkout the branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: '3.9'
 

CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Scemama"
+  given-names: "Anthony"
+  orcid: "https://orcid.org/0000-0003-4955-7136"
+- family-names: "Posenitskiy"
+  given-names: "Evgeny"
+  orcid: "https://orcid.org/0000-0002-1623-0594"
+title: "TREX I/O library "
+version: 2.3.1
+date-released: 2023-04-26
+url: "https://github.com/TREX-CoE/trexio"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Posenitskiy"
+    given-names: "Evgeny"
+  - family-names: "et al."
+    given-names: ""
+  doi: "10.1063/5.0148161"
+  journal: "The Journal of Chemical Physics"
+  month: 5
+  start: 174801 # First page number
+  title: "TREXIO: A file format and library for quantum chemistry"
+  issue: 17
+  volume: 158
+  year: 2023

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.3.1
+	VERSION 2.4.0
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

ChangeLog

@@ -1,6 +1,12 @@
 CHANGES
 =======
 
+2.4
+---
+
+- Added state/energy
+- Made state/id an index instead of an int
+
 2.3
 ---
 

Makefile.am

@@ -77,9 +77,11 @@ endif
 ORG_FILES = \
   src/templates_front/templator_front.org \
   src/templates_text/templator_text.org \
-  src/templates_hdf5/templator_hdf5.org \
   trex.org
 
+if HAVE_HDF5
+ORG_FILES += src/templates_hdf5/templator_hdf5.org
+endif
 
 src_libtrexio_la_SOURCES = $(trexio_h) $(SOURCES)
 
@@ -160,11 +162,13 @@ EXTRA_DIST += $(trexio_scm)
 
 HTML_TANGLED = docs/index.html            \
                docs/examples.html         \
-               docs/templator_hdf5.html   \
                docs/trex.html             \
                docs/README.html           \
                docs/templator_front.html  \
                docs/templator_text.html
+if HAVE_HDF5
+HTML_TANGLED += docs/templator_hdf5.html
+endif
 
 htmldir = $(docdir)
 # This $(htmlizer) file and the corresponding target rule allow to avoid circular dependency,

README.md

@@ -208,9 +208,34 @@ For example, the tutorial covering TREXIO basics using benzene molecule as an ex
 [Documentation generated from TREXIO org-mode files.](https://trex-coe.github.io/trexio/)
 
 
+## Citation
+
+The journal article reference describing TREXIO can be cited as follows:
+
+```
+@article{10.1063/5.0148161,
+    author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Michał and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josué and Filippi, Claudia and Nakano, Kosuke and Kohulák, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and Ríos, Pablo López and Alavi, Ali and Scemama, Anthony},
+    title = "{TREXIO: A file format and library for quantum chemistry}",
+    journal = {The Journal of Chemical Physics},
+    volume = {158},
+    number = {17},
+    year = {2023},
+    month = {05},
+    issn = {0021-9606},
+    doi = {10.1063/5.0148161},
+    url = {https://doi.org/10.1063/5.0148161},
+    note = {174801},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0148161/17355866/174801\_1\_5.0148161.pdf},
+}
+```
+
+Journal paper: [![doi](https://img.shields.io/badge/doi-10.1063/5.0148161-5077AB.svg)](https://doi.org/10.1063/5.0148161)
+
+ArXiv paper: [![arXiv](https://img.shields.io/badge/arXiv-2302.14793-b31b1b.svg)](https://arxiv.org/abs/2302.14793)
+
 ### Miscellaneous
 
-Note: The code should be compliant with the C99
+The code should be compliant with the C99
 [CERT C coding standard](https://resources.sei.cmu.edu/downloads/secure-coding/assets/sei-cert-c-coding-standard-2016-v01.pdf).
 This can be checked with the `cppcheck` tool.
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.3.1],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])
@@ -130,8 +130,7 @@ AC_ARG_WITH([hdf5],
   AS_HELP_STRING([--with-hdf5=PATH], [Path to HDF5 library and headers]), [
   with_hdf5="$withval"], [with_hdf5="yes"])
 
-AS_IF([test "x$with_hdf5" == "xno"], [
+AS_IF([test "x$with_hdf5" == "xno"], [], 
-           AC_DEFINE([HAVE_HDF5], 0, [Define to 1 if HDF5 is available]) ],
       [test "x$with_hdf5" != "xyes"], [
            HDF5_LIBS="-lhdf5"
            HDF5_PATH="$with_hdf5"

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "1.3.2"
+__version__ = "2.4.0"

python/requirements.txt

@@ -1,4 +1,4 @@
 setuptools>=42
 pkgconfig
-numpy<1.23.0
+numpy<1.24.0
 numpy>=1.17.3

src/templates_front/templator_front.org

@@ -1732,6 +1732,12 @@ def _cp(source: str, destination: str):
     and write it as ~state_id~ attribute.
  ~trexio_get_state~ returns current state of the ~trexio_t~ file handle.
 
+    **Warning:** The ~trexio_set_state~ and ~trexio_get_state~ functions still
+    use the old convention where the ground state was state ~0~. From version 2.4.0,
+    the ~state_id~ variable has changed to ~index~ type, so using the more recent
+ ~trexio_write_state_id~ and ~trexio_read_state_id~ will give different results
+    in Fortran.
+
     input parameters:
  ~file~  -- TREXIO file handle.
  ~state~ -- ~int32_t~ ID of a state (0 for ground state).
@@ -2132,24 +2138,35 @@ trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* cons
   if (num  == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
 
+  trexio_exit_code rc = TREXIO_GROUP_READ_ERROR;
+    
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_read_$group_num$(file, num);
+    rc = trexio_text_read_$group_num$(file, num);
+    break;
 
   case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-    return trexio_hdf5_read_$group_num$(file, num);
+    rc = trexio_hdf5_read_$group_num$(file, num);
 #else
-    return TREXIO_BACK_END_MISSING;
+    rc = TREXIO_BACK_END_MISSING;
 #endif
+    break;
 /*
   case TREXIO_JSON:
-    return trexio_json_read_$group_num$(file, num);
+    rc = trexio_json_read_$group_num$(file, num);
+    break;
 ,*/
   }
 
-  return TREXIO_FAILURE;
+  if (rc != TREXIO_SUCCESS) return rc;
+
+ /* Handle index type */
+  if ($is_index$) {
+    ,*num += ($group_num_dtype_double$) 1;
+  }
+  return rc;
 }
      #+end_src
 
@@ -2161,20 +2178,26 @@ trexio_write_$group_num$_64 (trexio_t* const file, const $group_num_dtype_double
   //if (num <= 0L) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
   if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
+ /* Handle index type */
+  $group_num_dtype_double$ num_write = num;
+  if ($is_index$) {
+    num_write -= ($group_num_dtype_double$) 1;
+  }
+
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_write_$group_num$(file, num);
+    return trexio_text_write_$group_num$(file, num_write);
 
   case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-    return trexio_hdf5_write_$group_num$(file, num);
+    return trexio_hdf5_write_$group_num$(file, num_write);
 #else
     return TREXIO_BACK_END_MISSING;
 #endif
 /*
   case TREXIO_JSON:
-    return trexio_json_write_$group_num$(file, num);
+    return trexio_json_write_$group_num$(file, num_write);
 ,*/
   }
 
@@ -2219,6 +2242,12 @@ trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* cons
   if (rc != TREXIO_SUCCESS) return rc;
 
   ,*num = ($group_num_dtype_single$) num_64;
+
+ /* Handle index type */
+  if ($is_index$) {
+    ,*num += ($group_num_dtype_single$) 1;
+  }
+
   return TREXIO_SUCCESS;
 }
      #+end_src
@@ -2232,20 +2261,26 @@ trexio_write_$group_num$_32 (trexio_t* const file, const $group_num_dtype_single
   //if (num <= 0) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
   if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
+ /* Handle index type */
+  $group_num_dtype_single$ num_write = num;
+  if ($is_index$) {
+    num_write -= ($group_num_dtype_single$) 1;
+  }
+
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num);
+    return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num_write);
 
   case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-    return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num);
+    return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num_write);
 #else
     return TREXIO_BACK_END_MISSING;
 #endif
 /*
   case TREXIO_JSON:
-    return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num);
+    return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num_write);
     break;
 ,*/
   }

tests/io_dset_int.c

@@ -13,6 +13,7 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
   // parameters to be written
   int num = 12;
   int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
+  int state_id = 2;
 
 /*================= START OF TEST ==================*/
 
@@ -28,6 +29,10 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
   rc = trexio_write_basis_nucleus_index(file, nucl_index);
   assert (rc == TREXIO_SUCCESS);
 
+  // write index attribute in a file
+  rc = trexio_write_state_id(file, state_id);
+  assert (rc == TREXIO_SUCCESS);
+
   // close current session
   rc = trexio_close(file);
   assert (rc == TREXIO_SUCCESS);
@@ -85,8 +90,9 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
   trexio_exit_code rc;
 
   // parameters to be read
-  int num;
+  int num = 0;
-  int* nucl_index;
+  int* nucl_index = NULL;
+  int state_id = 0;
 
 /*================= START OF TEST ==================*/
 
@@ -99,6 +105,11 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
   assert (rc == TREXIO_SUCCESS);
   assert (num == 12);
 
+  // read index attribute from the file
+  rc = trexio_read_state_id(file, &state_id);
+  assert (rc == TREXIO_SUCCESS);
+  assert (state_id == 2);
+
   // read numerical dataset from the file
   nucl_index = (int*) calloc(num, sizeof(int));
   rc = trexio_read_basis_nucleus_index(file, nucl_index);

tests/io_dset_int_hdf5.c

@@ -2,4 +2,3 @@
 #define TREXIO_FILE_PREFIX "io_dset_int"
 #include "test_macros.h"
 #include "io_dset_int.c"
-

tests/test_f.f90

@@ -85,6 +85,7 @@ subroutine test_write(file_name, back_end)
 
   integer :: i, j, n_buffers = 5
   integer(8) :: buf_size_sparse, buf_size_det, offset
+  integer   :: state_id
 
   buf_size_sparse = 100/n_buffers
   buf_size_det    = 50/n_buffers
@@ -107,6 +108,7 @@ subroutine test_write(file_name, back_end)
 
   ! parameters to be written
   nucleus_num = 12
+  state_id = 2
   charge = (/ 6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.  /)
   coord  = reshape( (/ 0.00000000d0,  1.39250319d0 ,  0.00000000d0 , &
                       -1.20594314d0,  0.69625160d0 ,  0.00000000d0 , &
@@ -182,6 +184,9 @@ subroutine test_write(file_name, back_end)
   rc = trexio_write_basis_nucleus_index(trex_file, basis_nucleus_index)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX')
 
+  rc = trexio_write_state_id(trex_file, state_id)
+  call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX TYPE')
+
   ! write ao_num which will be used to determine the optimal size of int indices
   if (trexio_has_ao_num(trex_file) == TREXIO_HAS_NOT) then
     rc = trexio_write_ao_num(trex_file, ao_num)
@@ -302,6 +307,7 @@ subroutine test_read(file_name, back_end)
   integer*8 :: offset_det_data_read = 5
   integer*8 :: determinant_num
   integer   :: int_num
+  integer   :: state_id
 
   ! orbital lists
   integer*4 :: orb_list_up(150)
@@ -312,6 +318,7 @@ subroutine test_read(file_name, back_end)
 
   num = 12
   basis_shell_num = 24
+  state_id = 0
 
   index_sparse_ao_2e_int_eri = 0
   value_sparse_ao_2e_int_eri = 0.0d0
@@ -379,6 +386,15 @@ subroutine test_read(file_name, back_end)
     call exit(-1)
   endif
 
+  rc = trexio_read_state_id(trex_file, state_id)
+  call trexio_assert(rc, TREXIO_SUCCESS)
+  if (state_id == 2) then
+    write(*,*) 'SUCCESS READ INDEX TYPE'
+  else
+    print *, 'FAILURE INDEX TYPE CHECK'
+    call exit(-1)
+  endif
+
 
   rc = trexio_read_nucleus_point_group(trex_file, sym_str, 10)
   call trexio_assert(rc, TREXIO_SUCCESS)

tools/generator_tools.py

@@ -611,8 +611,13 @@ def get_detailed_num_dict (configuration: dict) -> dict:
                     tmp_dict.update(get_dtype_dict(v2[0], 'num'))
                     if v2[0] in ['int', 'dim', 'dim readonly']:
                         tmp_dict['trex_json_int_type'] = v2[0]
+                        tmp_dict['is_index'] = 'false'
+                    elif v2[0] in ['index']:
+                        tmp_dict['trex_json_int_type'] = v2[0]
+                        tmp_dict['is_index'] = 'file->one_based'
                     else:
                         tmp_dict['trex_json_int_type'] = ''
+                        tmp_dict['is_index'] = 'false'
 
                     num_dict[tmp_num] = tmp_dict
 

trex.org

@@ -190,13 +190,14 @@
    The ~id~ and ~current_label~ attributes need to be specified for each file.
 
    #+NAME: state
-   | Variable        | Type  | Dimensions    | Description                                                                                 |
+   | Variable        | Type    | Dimensions    | Description                                                                                 |
-   |-----------------+-------+---------------+---------------------------------------------------------------------------------------------|
+   |-----------------+---------+---------------+---------------------------------------------------------------------------------------------|
-   | ~num~           | ~dim~ |               | Number of states (including the ground state)                                               |
+   | ~num~           | ~dim~   |               | Number of states (including the ground state)                                               |
-   | ~id~            | ~int~ |               | Index of the current state (0 is ground state)                                              |
+   | ~id~            | ~index~ |               | Index of the current state (0 is ground state)                                              |
-   | ~current_label~ | ~str~ |               | Label of the current state                                                                  |
+   | ~energy~        | ~float~ |               | Energy of the current state                                                                 |
-   | ~label~         | ~str~ | ~(state.num)~ | Labels of all states                                                                        |
+   | ~current_label~ | ~str~   |               | Label of the current state                                                                  |
-   | ~file_name~     | ~str~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
+   | ~label~         | ~str~   | ~(state.num)~ | Labels of all states                                                                        |
+   | ~file_name~     | ~str~   | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
 
    #+CALL: json(data=state, title="state")
 
@@ -204,11 +205,12 @@
    :results:
    #+begin_src python :tangle trex.json
        "state": {
-                     "num" : [ "dim", []              ]
+                     "num" : [ "dim"  , []              ]
-         ,            "id" : [ "int", []              ]
+         ,            "id" : [ "index", []              ]
-         , "current_label" : [ "str", []              ]
+         ,        "energy" : [ "float", []              ]
-         ,         "label" : [ "str", [ "state.num" ] ]
+         , "current_label" : [ "str"  , []              ]
-         ,     "file_name" : [ "str", [ "state.num" ] ]
+         ,         "label" : [ "str"  , [ "state.num" ] ]
+         ,     "file_name" : [ "str"  , [ "state.num" ] ]
        } ,
    #+end_src
    :end: