mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-25 06:31:43 +02:00
Merge branch 'master' into cppcheck
This commit is contained in:
commit
3a4691e667
19
.github/workflows/actions.yml
vendored
19
.github/workflows/actions.yml
vendored
@ -20,7 +20,7 @@ jobs:
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message: ${{ steps.commit_message.outputs.message }}
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steps:
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- name: Checkout the repo
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uses: actions/checkout@v2
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uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
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# Gets the correct commit message for pull request
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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@ -31,15 +31,13 @@ jobs:
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COMMIT_MSG=$(git log --no-merges -1 --oneline)
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echo "::set-output name=message::$COMMIT_MSG"
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trexio_ubuntu:
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runs-on: ubuntu-20.04
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name: x86 Ubuntu 20.04
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runs-on: ubuntu-20.04
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needs: get_commit_message
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
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- name: install dependencies
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run: |
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@ -84,7 +82,7 @@ jobs:
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if: >-
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contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
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github.event_name == 'release'
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
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with:
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name: pytrexio-source
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path: ./trexio-*.tar.gz
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@ -114,12 +112,11 @@ jobs:
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run: make maintainer-clean
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trexio_macos:
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runs-on: macos-11
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name: x86 MacOS 11
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runs-on: macos-11
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
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- name: install dependencies
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run: |
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@ -133,10 +130,10 @@ jobs:
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./configure FC=gfortran-10 --enable-silent-rules
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- name: compile TREXIO
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run: make -j 2
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run: make -j3
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- name: check TREXIO
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run: make check
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run: make -j3 check
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- name: Archive test log file
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if: failure()
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@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
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# Initialize the CMake project.
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project(Trexio
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VERSION 2.3.0
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VERSION 2.3.1
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DESCRIPTION "TREX I/O library"
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LANGUAGES C Fortran
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)
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28
README.md
28
README.md
@ -22,8 +22,8 @@ TREX library for efficient I/O.
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2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
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3. `cd trexio-<version>`
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4. `./configure`
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5. `make`
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6. `make check`
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5. ```make -j`getconf _NPROCESSORS_ONLN` ```
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6. ```make -j`getconf _NPROCESSORS_ONLN` check```
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7. `sudo make install`
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@ -45,8 +45,8 @@ TREX library for efficient I/O.
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2. `cd trexio`
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3. `./autogen.sh`
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4. `./configure`
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5. `make`
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6. `make check`
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5. ```make -j`getconf _NPROCESSORS_ONLN` ```
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6. ```make -j`getconf _NPROCESSORS_ONLN` check```
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7. `sudo make install`
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## Installation procedure for CMake users (from the tarball or GitHub repo clone):
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@ -56,8 +56,8 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
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1. `cmake -S. -Bbuild`
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2. `cd build`
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3. `make`
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4. `ctest` (or `make test`)
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3. ```make -j`getconf _NPROCESSORS_ONLN` ```
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4. ```ctest -j`getconf _NPROCESSORS_ONLN` ```
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5. `sudo make install`
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**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.**
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@ -73,7 +73,7 @@ The official releases of TREXIO `>2.0.0` are also available via the `conda-forge
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The pre-compiled stable binaries of `trexio` can be installed as follows:
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```
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conda install trexio -c conda-forge
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conda install -c conda-forge trexio
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```
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More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
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@ -88,7 +88,7 @@ Schema file contains the manifest specification for the `trexio` package.
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It can be installed as follows:
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```
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guix package --cores=<n_cores> --install-from-file=trexio.scm
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guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
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```
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## Installation procedure for Spack users
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@ -100,7 +100,7 @@ file contains the Spack specifications required to build different variants of `
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It can be installed as follows
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```
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spack install --jobs <n_cores> trexio
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spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
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```
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## Installation procedure for Debian/Ubuntu users
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@ -127,14 +127,14 @@ To build TREXIO without HDF5 back end, append `--without-hdf5` option to `config
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## Linking to your program
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The `make install` command takes care of installing the TREXIO shared library on the user machine.
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Once installed, add `-ltrexio` to the list of compiler options.
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After installation, append `-ltrexio` to the list of compiler (`$LIBS`) options.
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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 `$LIBRARY_PATH`.
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In order to link the program against TREXIO, the search paths can be modified as follows:
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In some cases (e.g. when using custom installation prefix during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LD_LIBRARY_PATH`.
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In order to link the program against TREXIO, the search path can be modified as follows:
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`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
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`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib`
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(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
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where the `<path_to_trexio>` has to be replaced by the prefix used during the installation.
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If your project relies on CMake build system, feel free to use the
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[FindTREXIO.cmake](https://github.com/TREX-CoE/trexio/blob/master/cmake/FindTREXIO.cmake)
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@ -2,7 +2,7 @@
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# Process this file with autoconf to produce a configure script.
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AC_PREREQ([2.69])
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AC_INIT([trexio],[2.3.0],[https://github.com/TREX-CoE/trexio/issues])
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AC_INIT([trexio],[2.3.1],[https://github.com/TREX-CoE/trexio/issues])
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AC_CONFIG_SRCDIR([Makefile.in])
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AC_CONFIG_HEADERS([include/config.h])
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@ -1 +1 @@
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__version__ = "1.3.0"
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__version__ = "1.3.1"
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@ -66,7 +66,7 @@ option(ENABLE_HDF5 "Enable HDF5 support" ON)
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if(ENABLE_HDF5)
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# Try to detect HDF5 installation using built-in FindHDF5.cmake macro.
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find_package(HDF5 REQUIRED COMPONENTS C HL)
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find_package(HDF5 REQUIRED COMPONENTS C)
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if(HDF5_FOUND)
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message(STATUS "HDF5 version :: ${HDF5_VERSION}")
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@ -87,9 +87,7 @@ if(ENABLE_HDF5)
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# - include directories with HDF5 header files
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target_include_directories(trexio PRIVATE ${HDF5_C_INCLUDE_DIRS})
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# - link to HDF5 C libraries
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target_link_libraries(trexio PRIVATE
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${HDF5_C_HL_LIBRARIES}
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${HDF5_C_LIBRARIES})
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target_link_libraries(trexio PRIVATE ${HDF5_C_LIBRARIES})
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endif()
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# Private headers have to be listed as sources, otherwise they are installed
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@ -3327,7 +3327,7 @@ trexio_read_$group_dset$(trexio_t* const file,
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/* To be set by generator : number of unique dimensions
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(e.g. 1 for ERI in AO basis because only ao_num is present in the list of dimensions) */
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const uint32_t unique_rank = $group_dset_unique_rank$;
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#define unique_rank $group_dset_unique_rank$
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int64_t unique_dims[$group_dset_unique_rank$];
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// Below part is populated by the generator when unique_rank > 1
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@ -3335,11 +3335,12 @@ trexio_read_$group_dset$(trexio_t* const file,
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/* Find the maximal value along all dimensions to define the compression technique in the back end */
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int64_t max_dim = unique_dims[0];
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if (unique_rank != 1) {
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#if (unique_rank != 1)
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for (uint32_t i = 1; i < unique_rank; i++) {
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if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
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}
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}
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#endif
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#undef unique_rank
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// introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
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int64_t eof_read_size = 0L;
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@ -3459,7 +3460,7 @@ trexio_write_$group_dset$(trexio_t* const file,
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/* To be set by generator : number of unique dimensions
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(e.g. 1 for ERI in AO basis because only ao_num is present in the list of dimensions) */
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const uint32_t unique_rank = $group_dset_unique_rank$;
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#define unique_rank $group_dset_unique_rank$
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int64_t unique_dims[$group_dset_unique_rank$];
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// Below part is populated by the generator when unique_rank > 1
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@ -3467,11 +3468,12 @@ trexio_write_$group_dset$(trexio_t* const file,
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/* Find the maximal value along all dimensions to define the compression technique in the back end */
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int64_t max_dim = unique_dims[0];
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if (unique_rank != 1) {
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#if (unique_rank != 1)
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for (uint32_t i = 1; i < unique_rank; i++) {
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if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
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}
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}
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#endif
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#undef unique_rank
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// shift indices to be zero-based if Fortran API is used
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if (file->one_based) {
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@ -5619,19 +5621,15 @@ trexio_exit_code trexio_to_bitfield_list (const int32_t* orb_list,
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bit_list[j] = (bitfield_t) 0;
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}
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uint32_t i;
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uint32_t k;
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uint32_t iorb;
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bitfield_t mask;
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uint32_t nswaps = 0;
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for (int32_t pos = 0 ; pos < occupied_num ; pos++) {
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iorb = ((uint32_t) (orb_list[pos] + 1)) - TREXIO_ORBITAL_SHIFT;
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const uint32_t iorb = ((uint32_t) (orb_list[pos] + 1)) - TREXIO_ORBITAL_SHIFT;
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// Set the bit of to one
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i = (uint32_t) (iorb >> TREXIO_NORB_PER_INT_SHIFT);
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k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
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mask = ((bitfield_t) 1) << k;
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const uint32_t i = (uint32_t) (iorb >> TREXIO_NORB_PER_INT_SHIFT);
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const uint32_t k = (uint32_t) (iorb & (TREXIO_NORB_PER_INT - 1) );
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bitfield_t mask = ((bitfield_t) 1) << k;
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bit_list[i] |= mask;
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// Check for phase changes
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@ -5662,21 +5660,16 @@ trexio_exit_code trexio_to_orbital_list(const int32_t N_int,
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if (list == NULL) return TREXIO_INVALID_ARG_3;
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if (occupied_num == NULL) return TREXIO_INVALID_ARG_4;
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bitfield_t tmp;
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int32_t shift;
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int32_t k;
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int32_t pos;
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k = 0;
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shift = TREXIO_ORBITAL_SHIFT;
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int32_t k = 0;
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int32_t shift = TREXIO_ORBITAL_SHIFT;
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for (int32_t i=0 ; i<N_int ; i++)
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{
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tmp = d1[i];
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bitfield_t tmp = d1[i];
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while (tmp != (bitfield_t) 0)
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{
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pos = trailz(tmp);
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const int32_t pos = trailz(tmp);
|
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if (pos < 0) return TREXIO_FAILURE;
|
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|
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list[k] = ( (int32_t) pos) + shift - 1;
|
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|
@ -145,10 +145,10 @@ trexio_text_inquire (const char* file_name)
|
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if (file_exists) {
|
||||
|
||||
bool is_a_directory = false;
|
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#ifdef S_IFDIR
|
||||
#if defined(S_IFDIR)
|
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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
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printf("Some important macros are missing for directory handling.\n");
|
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return TREXIO_FAILURE;
|
||||
@ -162,6 +162,29 @@ trexio_text_inquire (const char* file_name)
|
||||
}
|
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#+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)
|
||||
|
@ -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
|
||||
|
22
trex.org
22
trex.org
@ -386,20 +386,22 @@ prim_factor =
|
||||
\[
|
||||
V_A^{\text{ECP}} =
|
||||
V_{A \ell_{\max}+1} +
|
||||
\sum_{\ell=0}^{\ell_{\max}} V_{A \ell}
|
||||
\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
|
||||
\sum_{\ell=0}^{\ell_{\max}}
|
||||
\delta V_{A \ell}\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
|
||||
\]
|
||||
|
||||
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}) =
|
||||
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 }
|
||||
\].
|
||||
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.
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user