TREX/trexio
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Merge branch 'master' into cppcheck

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This commit is contained in:
Anthony Scemama 2023-05-02 09:44:12 +02:00
commit 3a4691e667
10 changed files with 102 additions and 75 deletions
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19
.github/workflows/actions.yml vendored
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@ -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()

2
CMakeLists.txt
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@ -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
)

28
README.md
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@ -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`
6. `make check`
5. ```make -j`getconf _NPROCESSORS_ONLN` ```
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`
6. `make check`
5. ```make -j`getconf _NPROCESSORS_ONLN` ```
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`
4. `ctest` (or `make test`)
3. ```make -j`getconf _NPROCESSORS_ONLN` ```
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 order to link the program against TREXIO, the search paths can be modified as follows:
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 `$LD_LIBRARY_PATH`.
In order to link the program against TREXIO, the search path can be modified as follows:
`export LIBRARY_PATH=$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)

2
configure.ac
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@ -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])

2
python/pytrexio/_version.py
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@ -1 +1 @@
__version__ = "1.3.0"
__version__ = "1.3.1"

6
src/CMakeLists.txt
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@ -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
${HDF5_C_HL_LIBRARIES}
${HDF5_C_LIBRARIES})
target_link_libraries(trexio PRIVATE ${HDF5_C_LIBRARIES})
endif()
# Private headers have to be listed as sources, otherwise they are installed

47
src/templates_front/templator_front.org
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@ -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) {
for (uint32_t i = 1; i < unique_rank; i++) {
if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
}
#if (unique_rank != 1)
for (uint32_t i = 1; i < unique_rank; 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) {
for (uint32_t i = 1; i < unique_rank; i++) {
if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
}
#if (unique_rank != 1)
for (uint32_t i = 1; i < unique_rank; 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);
k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
mask = ((bitfield_t) 1) << k;
const uint32_t i = (uint32_t) (iorb >> TREXIO_NORB_PER_INT_SHIFT);
const uint32_t k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
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 shift;
int32_t k;
int32_t pos;
k = 0;
shift = TREXIO_ORBITAL_SHIFT;
int32_t k = 0;
int32_t 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;

29
src/templates_text/templator_text.org
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@ -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
is_a_directory = S_ISDIR(s.st_mode);
#elif defined(S_ISDIR)
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)

16
tools/trexio.scm
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@ -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

26
trex.org
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@ -386,20 +386,22 @@ prim_factor =
\[
V_A^{\text{ECP}} =
V_{A \ell_{\max}+1} +
\sum_{\ell=0}^{\ell_{\max}} V_{A \ell}
\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
\sum_{\ell=0}^{\ell_{\max}}
\delta V_{A \ell}\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
\]
The first term in the equation above is sometimes attributed to the local channel,
while the remaining terms correspond to the non-local channel projections.
All the functions $V_{A\ell}$ are parameterized as:
\[
V_{A \ell}(\mathbf{r}) =
\sum_{q=1}^{N_{q \ell}}
\beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 }
\].
The first term in this equation is attributed to the local channel, while
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.
The functions \(\delta V_{A \ell}\) and \(V_{A \ell_{\max}+1}\) are parameterized as:
\begin{eqnarray}
\delta V_{A \ell}(\mathbf{r}) &=&
\sum_{q=1}^{N_{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 } \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.