Merge branch 'master' into cppcheck

.github/workflows/actions.yml

@@ -20,7 +20,7 @@ jobs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
       - name: Checkout the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
         # Gets the correct commit message for pull request
         with:
           ref: ${{ github.event.pull_request.head.sha }}
@@ -31,15 +31,13 @@ jobs:
           COMMIT_MSG=$(git log --no-merges -1 --oneline)
           echo "::set-output name=message::$COMMIT_MSG"
 
-
   trexio_ubuntu:
-
-    runs-on: ubuntu-20.04
     name: x86 Ubuntu 20.04
+    runs-on: ubuntu-20.04
     needs: get_commit_message
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
       - name: install dependencies
         run: |
@@ -84,7 +82,7 @@ jobs:
         if: >-
           contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
           github.event_name == 'release'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
         with:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
@@ -114,12 +112,11 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-
-    runs-on: macos-11
     name: x86 MacOS 11
+    runs-on: macos-11
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
       - name: install dependencies
         run: |
@@ -133,10 +130,10 @@ jobs:
           ./configure FC=gfortran-10 --enable-silent-rules
 
       - name: compile TREXIO
-        run: make -j 2
+        run: make -j3
 
       - name: check TREXIO
-        run: make check
+        run: make -j3 check
 
       - name: Archive test log file
         if: failure()

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.3.0
+	VERSION 2.3.1
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

README.md

@@ -22,8 +22,8 @@ TREX library for efficient I/O.
 2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
 3. `cd trexio-<version>`
 4. `./configure`
-5. `make`
+5. ```make -j`getconf _NPROCESSORS_ONLN` ```
-6. `make check`
+6. ```make -j`getconf _NPROCESSORS_ONLN` check```
 7. `sudo make install`
 
 
@@ -45,8 +45,8 @@ TREX library for efficient I/O.
 2. `cd trexio`
 3. `./autogen.sh`
 4. `./configure`
-5. `make`
+5. ```make -j`getconf _NPROCESSORS_ONLN` ```
-6. `make check`
+6. ```make -j`getconf _NPROCESSORS_ONLN` check```
 7. `sudo make install`
 
 ## Installation procedure for CMake users (from the tarball or GitHub repo clone):
@@ -56,8 +56,8 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
 
 1. `cmake -S. -Bbuild`
 2. `cd build`
-3. `make`
+3. ```make -j`getconf _NPROCESSORS_ONLN` ```
-4. `ctest` (or `make test`)
+4. ```ctest -j`getconf _NPROCESSORS_ONLN` ```
 5. `sudo make install`
 
 **Note: on systems with no `sudo` access, one can add `-DCMAKE_INSTALL_PREFIX=build` as an argument to the `cmake` command so that `make install/uninstall` can be run without `sudo` privileges.**
@@ -73,7 +73,7 @@ The official releases of TREXIO `>2.0.0` are also available via the `conda-forge
 The pre-compiled stable binaries of `trexio` can be installed as follows:
 
 ```
-conda install trexio -c conda-forge
+conda install -c conda-forge trexio
 ```
 
 More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
@@ -88,7 +88,7 @@ Schema file contains the manifest specification for the `trexio` package.
 It can be installed as follows:
 
 ```
-guix package --cores=<n_cores> --install-from-file=trexio.scm
+guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
 ```
 
 ## Installation procedure for Spack users
@@ -100,7 +100,7 @@ file contains the Spack specifications required to build different variants of `
 It can be installed as follows
 
 ```
-spack install --jobs <n_cores> trexio
+spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
 ```
 
 ## Installation procedure for Debian/Ubuntu users
@@ -127,14 +127,14 @@ To build TREXIO without HDF5 back end, append `--without-hdf5` option to `config
 ## Linking to your program
 
 The `make install` command takes care of installing the TREXIO shared library on the user machine.
-Once installed, add `-ltrexio` to the list of compiler options.
+After installation, append `-ltrexio` to the list of compiler  (`$LIBS`) options.
 
-In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
+In some cases (e.g. when using custom installation prefix during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LD_LIBRARY_PATH`.
-In order to link the program against TREXIO, the search paths can be modified as follows:
+In order to link the program against TREXIO, the search path can be modified as follows:
 
-`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
+`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib`
 
-(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
+where the `<path_to_trexio>` has to be replaced by the prefix used during the installation.
 
 If your project relies on CMake build system, feel free to use the
 [FindTREXIO.cmake](https://github.com/TREX-CoE/trexio/blob/master/cmake/FindTREXIO.cmake)

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.3.0],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.3.1],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "1.3.0"
+__version__ = "1.3.1"

src/CMakeLists.txt

@@ -66,7 +66,7 @@ option(ENABLE_HDF5 "Enable HDF5 support" ON)
 
 if(ENABLE_HDF5)
   # Try to detect HDF5 installation using built-in FindHDF5.cmake macro.
-  find_package(HDF5 REQUIRED COMPONENTS C HL)
+  find_package(HDF5 REQUIRED COMPONENTS C)
 
   if(HDF5_FOUND)
     message(STATUS "HDF5 version     :: ${HDF5_VERSION}")
@@ -87,9 +87,7 @@ if(ENABLE_HDF5)
   # - include directories with HDF5 header files
   target_include_directories(trexio PRIVATE ${HDF5_C_INCLUDE_DIRS})
   # - link to HDF5 C libraries
-  target_link_libraries(trexio PRIVATE
+  target_link_libraries(trexio PRIVATE ${HDF5_C_LIBRARIES})
-         ${HDF5_C_HL_LIBRARIES}
-         ${HDF5_C_LIBRARIES})
 endif()
 
 # Private headers have to be listed as sources, otherwise they are installed

src/templates_front/templator_front.org

@@ -3327,7 +3327,7 @@ trexio_read_$group_dset$(trexio_t* const file,
 
   /* To be set by generator : number of unique dimensions
      (e.g. 1 for ERI in AO basis because only ao_num is present in the list of dimensions) */
-  const uint32_t unique_rank = $group_dset_unique_rank$;
+#define unique_rank $group_dset_unique_rank$
   int64_t unique_dims[$group_dset_unique_rank$];
 
   // Below part is populated by the generator when unique_rank > 1
@@ -3335,11 +3335,12 @@ trexio_read_$group_dset$(trexio_t* const file,
 
  /* Find the maximal value along all dimensions to define the compression technique in the back end */
   int64_t max_dim = unique_dims[0];
-  if (unique_rank != 1) {
+#if (unique_rank != 1) 
-    for (uint32_t i = 1; i < unique_rank; i++) {
+  for (uint32_t i = 1; i < unique_rank; i++) {
-      if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
+    if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
-    }
   }
+#endif
+#undef unique_rank
 
   // introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
   int64_t eof_read_size = 0L;
@@ -3459,7 +3460,7 @@ trexio_write_$group_dset$(trexio_t* const file,
 
   /* To be set by generator : number of unique dimensions
      (e.g. 1 for ERI in AO basis because only ao_num is present in the list of dimensions) */
-  const uint32_t unique_rank = $group_dset_unique_rank$;
+#define unique_rank $group_dset_unique_rank$
   int64_t unique_dims[$group_dset_unique_rank$];
 
   // Below part is populated by the generator when unique_rank > 1
@@ -3467,11 +3468,12 @@ trexio_write_$group_dset$(trexio_t* const file,
 
  /* Find the maximal value along all dimensions to define the compression technique in the back end */
   int64_t max_dim = unique_dims[0];
-  if (unique_rank != 1) {
+#if (unique_rank != 1) 
-    for (uint32_t i = 1; i < unique_rank; i++) {
+  for (uint32_t i = 1; i < unique_rank; i++) {
-      if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
+    if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
-    }
   }
+#endif
+#undef unique_rank
 
   // shift indices to be zero-based if Fortran API is used
   if (file->one_based) {
@@ -5619,19 +5621,15 @@ trexio_exit_code trexio_to_bitfield_list (const int32_t* orb_list,
       bit_list[j] = (bitfield_t) 0;
   }
 
-  uint32_t i;
-  uint32_t k;
-  uint32_t iorb;
-  bitfield_t mask;
   uint32_t nswaps = 0;
 
   for (int32_t pos = 0 ; pos < occupied_num ; pos++) {
-    iorb = ((uint32_t) (orb_list[pos] + 1)) - TREXIO_ORBITAL_SHIFT;
+    const uint32_t iorb = ((uint32_t) (orb_list[pos] + 1)) - TREXIO_ORBITAL_SHIFT;
 
     // Set the bit of to one
-    i = (uint32_t) (iorb >> TREXIO_NORB_PER_INT_SHIFT);
+    const uint32_t i = (uint32_t) (iorb >> TREXIO_NORB_PER_INT_SHIFT);
-    k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
+    const uint32_t k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
-    mask = ((bitfield_t) 1) << k;
+    bitfield_t mask = ((bitfield_t) 1) << k;
     bit_list[i] |= mask;
 
     // Check for phase changes
@@ -5662,21 +5660,16 @@ trexio_exit_code trexio_to_orbital_list(const int32_t N_int,
   if (list == NULL) return TREXIO_INVALID_ARG_3;
   if (occupied_num == NULL) return TREXIO_INVALID_ARG_4;
 
-  bitfield_t  tmp;
+  int32_t k = 0;
-  int32_t     shift;
+  int32_t shift = TREXIO_ORBITAL_SHIFT;
-  int32_t     k;
-  int32_t     pos;
-
-  k = 0;
-  shift = TREXIO_ORBITAL_SHIFT;
 
   for (int32_t i=0 ; i<N_int ; i++)
   {
-      tmp = d1[i];
+      bitfield_t tmp = d1[i];
 
       while (tmp != (bitfield_t) 0)
       {
-          pos = trailz(tmp);
+          const int32_t pos = trailz(tmp);
           if (pos < 0) return TREXIO_FAILURE;
 
           list[k] = ( (int32_t) pos) + shift - 1;

src/templates_text/templator_text.org

@@ -145,10 +145,10 @@ trexio_text_inquire (const char* file_name)
   if (file_exists) {
 
     bool is_a_directory = false;
-#ifdef S_IFDIR
+#if defined(S_IFDIR)
     is_a_directory = st.st_mode & S_IFDIR;
-#elif S_ISDIR
+#elif defined(S_ISDIR)
-    is_a_directory = S_ISDIR(s.st_mode);
+    is_a_directory = S_ISDIR(st.st_mode);
 #else
     printf("Some important macros are missing for directory handling.\n");
     return TREXIO_FAILURE;
@@ -162,6 +162,29 @@ trexio_text_inquire (const char* file_name)
 }
     #+end_src
 
+On non-POSIX file systems, the function ~mkdtemp~ might is not defined.
+In that case, we define an alternate one, which is not as safe as the original one.
+
+    #+begin_src c :tangle basic_text.c
+#if defined _POSIX_C_SOURCE && (_POSIX_C_SOURCE - 0) >= 200809L
+#else
+
+char* mkdtemp(char* template) {
+    char* dir = NULL;
+    dir = tmpnam(dir);
+    if (dir == NULL) return NULL;
+
+    if (mkdir(dir, S_IRWXU | S_IRWXG | S_IRWXO) != 0) {
+        return NULL;
+    }
+
+    strcpy(template, dir);
+    return template;
+}
+
+#endif
+    #+end_src
+
     #+begin_src c :tangle basic_text.c
 trexio_exit_code
 trexio_text_init (trexio_t* const file)

tools/trexio.scm

@@ -60,8 +60,22 @@
 		"1n9n1gbk5hgvg73am991xrv7ap002rz719a3nvh8m8ff9x10qd76"
                 ))))))
 
+(define-public trexio-2.3
+  (package/inherit trexio-2.0
+    (version "2.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/TREX-CoE/trexio/releases/download/v" version
+				  "/trexio-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+		;; the hash below is produced by guix download <url>
+		"183wljg1avsia2pf2wb59s2i2qw6y19qfw164ffy1g024b6362ii"
+                ))))))
+
 (define-public trexio
   ;; Default version of TREXIO.
-  trexio-2.2)
+  trexio-2.3)
 
 trexio

trex.org

@@ -386,20 +386,22 @@ prim_factor =
    \[
    V_A^{\text{ECP}} =
    V_{A \ell_{\max}+1} +
-   \sum_{\ell=0}^{\ell_{\max}} V_{A \ell}
+   \sum_{\ell=0}^{\ell_{\max}}
-   \sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle  \langle Y_{\ell m} |
+   \delta V_{A \ell}\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
    \]
 
-   The first term in the equation above is sometimes attributed to the local channel,
+   The first term in this equation is attributed to the local channel, while
-   while the remaining terms correspond to the non-local channel projections.
+   the remaining terms correspond to non-local channel projections.  $\ell_{\max}$
-
+   refers to the maximum angular momentum in the non-local component of the ECP.
-   All the functions $V_{A\ell}$ are parameterized as:
+   The functions \(\delta V_{A \ell}\) and \(V_{A \ell_{\max}+1}\) are parameterized as:
-   \[
+   \begin{eqnarray}
-   V_{A \ell}(\mathbf{r}) =
+      \delta V_{A \ell}(\mathbf{r}) &=&
-   \sum_{q=1}^{N_{q \ell}}
+      \sum_{q=1}^{N_{q \ell}}
-   \beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
+      \beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
-   e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 }
+      e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 } \nonumber\\
-   \].
+      V_{A \ell_{\max}+1}(\mathbf{r}) &=& -\frac{Z_\text{eff}}{|\mathbf{r}-\mathbf{R}_{A}|}+\delta V_{A \ell_{\max}+1}(\mathbf{r})
+   \end{eqnarray}
+   where $Z_\text{eff}$ is the effective nuclear charge of the center.
 
    See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info.