TREX/trexio
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Merge branch 'master' into permutations

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Anthony Scemama 2024-03-13 15:28:58 +01:00
commit 5ed85a0a49
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45
.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: ${{ github.event.pull_request.head.sha }}
@ -31,15 +31,25 @@ jobs:
COMMIT_MSG=$(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: check versions
run: |
grep AC_INIT configure.ac | tr -d '[]' | awk -F, '{ print $2 }' > configure_v
grep -w VERSION CMakeLists.txt | grep -v 'cmake_minimum_required' | awk '{ print $2 }' > cmake_v
grep version python/pytrexio/_version.py | tr -d '"' | awk '{ print $3 }' > python_v
grep version rust/trexio/Cargo.toml | grep -v features | tr -d '"' | awk '{ print $3 }' > rust_v
grep version ocaml/trexio/dune-project | tr -d '()' | awk '{ print $2 }' > ocaml_v
diff configure_v cmake_v
diff configure_v python_v
diff configure_v rust_v
diff configure_v ocaml_v
- name: install dependencies
run: |
@ -84,7 +94,7 @@ jobs:
if: >-
contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
github.event_name == 'release'
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
with:
name: pytrexio-source
path: ./trexio-*.tar.gz
@ -114,29 +124,38 @@ jobs:
run: make maintainer-clean
trexio_macos:
runs-on: macos-11
name: x86 MacOS 11
name: x86 MacOS 12
runs-on: macos-12
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
- name: install dependencies
run: |
brew install emacs
brew install hdf5
brew install automake
brew --prefix hdf5
- name: configure with autotools
run: |
./autogen.sh
./configure FC=gfortran-10 --enable-silent-rules
./configure FC=gfortran-12 --enable-silent-rules
- name: compile TREXIO
run: make -j 2
run: make -j3
- name: check TREXIO
run: make check
run: make -j3 check
- name: compile Python API
run: |
export H5_CFLAGS="-I$(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()

101
.github/workflows/build-wheels.yml vendored
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@ -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: ${{ github.event.pull_request.head.sha }}
@ -42,14 +42,14 @@ jobs:
runs-on: ubuntu-20.04
strategy:
matrix:
manylinux_tag: [2010_x86_64, 2014_x86_64, 2_24_x86_64]
manylinux_tag: [2014_x86_64, 2_24_x86_64]
steps:
- name: Checkout the branch
uses: actions/checkout@v2
uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v1
uses: actions/setup-python@v4
with:
python-version: '3.9'
@ -94,102 +94,18 @@ jobs:
name: pytrexio-manylinux-${{ matrix.manylinux_tag }}
path: ./python/wheelhouse/*.whl
build_macos_wheels:
name: Build MacOS wheels for different versions of CPython
needs: get_commit_message
if: >-
contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
(github.repository == 'TREX-CoE/trexio' && startsWith(github.ref, 'refs/tags/v'))
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [macos-10.15]
python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
# 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
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
run: python --version
- 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
- name: Print the PYTREXIO_VERSION
run: echo ${{ env.PYTREXIO_VERSION }}
- name: Download the Python API distribution tarball
uses: dawidd6/action-download-artifact@v2
with:
workflow: actions.yml
workflow_conclusion: success
name: pytrexio-source
path: python
- name: Extract the Python distribution
run: gzip -cd trexio-${{ env.PYTREXIO_VERSION }}.tar.gz | tar xvf -
working-directory: python
- name: Install Python dependencies
run: pip install --upgrade pip setuptools build delocate pytest
- name: Build wheel for a given version of CPython
run: |
mkdir wheelhouse/
cd trexio-${{ env.PYTREXIO_VERSION }}/
python -m build --wheel --outdir=./
delocate-wheel trexio-*.whl
mv trexio-*.whl ../wheelhouse/
working-directory: python
# Some issues with Python 3.10 wheels on MacOS-11
- name: Install the wheel
run: python -m pip install wheelhouse/trexio-*.whl
working-directory: python
- name: Test the wheel
run: pytest -v test_api.py
working-directory: python/test
- name: Upload produced wheels as artifacts
uses: actions/upload-artifact@v2
with:
name: pytrexio-${{ matrix.os }}
path: ./python/wheelhouse/*.whl
publish_wheels:
name: Publish all wheels on PyPI
needs: [build_linux_wheels, build_macos_wheels]
needs: [build_linux_wheels]
runs-on: ubuntu-20.04
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'
@ -215,8 +131,7 @@ jobs:
run: |
ls -R
mv pytrexio-manylinux-*/trexio-*.whl ./
mv pytrexio-macos-*/trexio-*.whl ./
rm -rf -- pytrexio-manylinux-*/ pytrexio-macos-*/
rm -rf -- pytrexio-manylinux-*/
ls -sh -w 1
working-directory: dist

28
CITATION.cff Normal file
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@ -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

15
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 2.5.0
DESCRIPTION "TREX I/O library"
LANGUAGES C Fortran
)
@ -15,8 +15,9 @@ set(CMAKE_C_STANDARD_REQUIRED ON)
# Optional configure for developer mode to generate source code from org-mode files.
option(TREXIO_DEVEL "TREXIO developer mode (for code generation)." OFF)
option(TREXIO_TESTS "Whether to perform tests for TREXIO" ON)
if(EXISTS "${CMAKE_SOURCE_DIR}/.devel")
if(EXISTS "${PROJECT_SOURCE_DIR}/.devel")
set(TREXIO_DEVEL ON)
find_package(Python3 REQUIRED)
if(Python3_FOUND)
@ -48,8 +49,8 @@ if(EXISTS "${CMAKE_SOURCE_DIR}/.devel")
set(TREXIO_USER_NAME $ENV{USER})
# replace placeholders in the templace config.h.in file to produce config.h
# config.h is needed to insert TREXIO_PACKAGE_VERSION and TREXIO_GIT_HASH into trexio.h
configure_file(${CMAKE_SOURCE_DIR}/include/cmake_config.h.in
${CMAKE_SOURCE_DIR}/include/config.h
configure_file(${PROJECT_SOURCE_DIR}/include/cmake_config.h.in
${PROJECT_SOURCE_DIR}/include/config.h
@ONLY)
endif()
@ -60,5 +61,7 @@ include_directories(include)
add_subdirectory(src)
# Add subdirectory with unit tests.
enable_testing()
add_subdirectory(tests)
if(TREXIO_TESTS)
enable_testing()
add_subdirectory(tests)
endif()

18
ChangeLog
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@ -1,9 +1,24 @@
CHANGES
=======
2.5
---
- Added index permutations in integrals
2.4
---
- Added state/energy
- Made state/id an index instead of an int
- Added JSON configuration data as a C variable in trexio.h
- Added JSON configuration file in tar.gz release
- Added Rust interface
2.3
---
- Removed dependency to hdf5_hl
- Fixed Fortran interface on 32-bit (e.g. i386) architectures
- Changed the structure of the state group
- Sparse data type is patched to work with different dimensions
@ -19,14 +34,11 @@ CHANGES
- Added OCaml binding
- Added spin and energy in MOs
- Added CSF group
- Added index permutations
- Added phase change in determinant list to bitstring conversion
- Added Jastrow group
- Added Amplitude group
- Added Cholesky-decomposed two-electron integrals
- Added Cholesky-decomposed RDMs for Gammcor
- Added `trexio_flush` functionality
- Added `trexio_cp`
- Optional compilation `--without-fortran`
2.2

87
Makefile.am
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@ -34,10 +34,9 @@
ACLOCAL_AMFLAGS = -I m4
CLEANFILES = trexio.mod
BUILT_SOURCES = trex.json
if HAVE_FORTRAN
BUILT_SOURCES = trexio.mod
else
BUILT_SOURCES =
BUILT_SOURCES += trexio.mod
endif
EXTRA_DIST = .git_hash
@ -77,22 +76,73 @@ 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)
# Include CMake-related files in the distribution.
EXTRA_DIST += CMakeLists.txt \
trex.json \
src/CMakeLists.txt \
tests/CMakeLists.txt \
tests/test_macros.h \
cmake/cmake_uninstall.cmake.in \
cmake/FindTREXIO.cmake
# =============== TESTS =============== #
TEST_FILES = \
tests/delete_group.c \
tests/delete_group_hdf5.c \
tests/delete_group_text.c \
tests/io_all.c \
tests/io_determinant.c \
tests/io_determinant_hdf5.c \
tests/io_determinant_text.c \
tests/io_dset_float.c \
tests/io_dset_float_hdf5.c \
tests/io_dset_float_text.c \
tests/io_dset_int.c \
tests/io_dset_int_hdf5.c \
tests/io_dset_int_text.c \
tests/io_dset_sparse.c \
tests/io_dset_sparse_hdf5.c \
tests/io_dset_sparse_text.c \
tests/io_dset_str.c \
tests/io_dset_str_hdf5.c \
tests/io_dset_str_text.c \
tests/io_jastrow.c \
tests/io_jastrow_hdf5.c \
tests/io_jastrow_text.c \
tests/io_num.c \
tests/io_num_hdf5.c \
tests/io_num_text.c \
tests/io_safe_dset_float.c \
tests/io_safe_dset_float_hdf5.c \
tests/io_safe_dset_float_text.c \
tests/io_str.c \
tests/io_str_hdf5.c \
tests/io_str_text.c \
tests/open.c \
tests/open_hdf5.c \
tests/open_text.c \
tests/overwrite_all.c \
tests/overwrite_all_hdf5.c \
tests/overwrite_all_text.c \
tests/pre_close.c \
tests/template_hdf5.c \
tests/template_text.c \
tests/test_f.f90 \
tests/test_macros.h \
tests/trexio_f.f90
EXTRA_DIST += $(TEST_FILES)
TESTS_C = \
tests/open_text \
tests/io_num_text \
@ -160,11 +210,13 @@ 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,
@ -217,6 +269,8 @@ src/trexio.c: $(trexio_h)
$(trexio_h): $(ORG_FILES) $(GENERATOR_FILES)
cd $(srcdir)/tools && ./build_trexio.sh
trex.json: $(trexio_h)
$(htmlizer): $(ORG_FILES) $(srcdir)/src/README.org
touch $(htmlizer)
cd $(srcdir)/tools && ./build_doc.sh
@ -257,10 +311,18 @@ pytrexio_i = $(srcdir)/src/pytrexio.i
numpy_i = $(srcdir)/src/numpy.i
if HAVE_HDF5
python-test: $(TEST_PY)
python3 -m pytest -v --all $(TEST_PY)
$(RM) -r -- __pycache__
$(RM) -f -- test_file_py.h5 unsafe_test_file_py.h5
$(RM) -rf -- test_file_py.dir unsafe_test_file_py.dir
else
python-test: $(TEST_PY)
python3 -m pytest -v $(TEST_PY)
$(RM) -r -- __pycache__
$(RM) -f -- test_file_py.h5 unsafe_test_file_py.h5
$(RM) -r -- __pycache__
$(RM) -rf -- test_file_py.dir unsafe_test_file_py.dir
endif
python-install: $(pytrexio_py) $(setup_py) $(setup_cfg)
cd python && \
@ -270,11 +332,15 @@ python-sdist: $(pytrexio_py) $(setup_py) $(setup_cfg)
cd python && \
python3 -m build --sdist
if HAVE_HDF5
$(pytrexio_py): $(pytrexio_c)
cd tools && ./prepare_python.sh
else
$(pytrexio_py): $(pytrexio_c)
cd tools && ./prepare_python.sh --without-hdf5
endif
# Build Python module and C wrapper code for TREXIO using SWIG
# [?] swig -python -threads pytrexio.i ----> Add thread support for all the interface
$(pytrexio_c): $(ORG_FILES) $(GENERATOR_FILES) $(trexio_h) $(pytrexio_i) $(numpy_i)
@if [[ $(SWIG).x != ".x" ]] ; then \
cp $(trexio_h) src/ ; \
@ -303,7 +369,7 @@ DEB_FILES = \
helpers-debian/libtrexio0.install \
helpers-debian/libtrexio-dev.install \
helpers-debian/source \
helpers-debian/README.source
helpers-debian/README.source
debian_from_dist: $(DEB_FILES) $(SOURCES) $(trexio_h)
cp ../trexio-$(PACKAGE_VERSION).tar.gz ../libtrexio_$(PACKAGE_VERSION).orig.tar.gz
@ -313,6 +379,9 @@ debian_from_dist: $(DEB_FILES) $(SOURCES) $(trexio_h)
CLEANFILES += $(pytrexio_c) \
$(pytrexio_py) \
$(trexio_py) \
$(srcdir)/src/trexio.py \
$(srcdir)/src/pytrexio.py \
$(srcdir)/src/trexio.h \
python/src/*.c \
python/src/*.h

334
README.md
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@ -1,68 +1,50 @@
# TREXIO
<img src="https://trex-coe.eu/sites/default/files/styles/responsive_no_crop/public/2022-01/TREXIO%20Code.png" width=200>
[![build](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml/badge.svg)](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml)
![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)
TREX library for efficient I/O.
TREXIO is an open-source file format and library developed for the storage and
manipulation of data produced by quantum chemistry calculations. It is designed
with the goal of providing a reliable and efficient method of storing and
exchanging wave function parameters and matrix elements. The library consists
of a front-end implemented in the C programming language and two different
back-ends: a text back-end and a binary back-end utilizing the HDF5 library
which enables fast read and write operations. It is compatible with a variety
of platforms and has interfaces for the Fortran, Python, OCaml and Rust
programming languages.
* [TREXIO](#trexio)
* [Installation](#installation)
* [Installation using a package manager](#installation-using-a-package-manager)
* [Debian/Ubuntu](#debianubuntu)
* [Conda](#conda)
* [Spack](#spack)
* [Guix](#guix)
* [Installation from source](#installation-from-source)
* [Minimal requirements (for users):](#minimal-requirements-for-users)
* [Recommended: Installation from the release tarball](#recommended-installation-from-the-release-tarball)
* [Compilation without the HDF5 library](#compilation-without-the-hdf5-library)
* [For TREXIO developers: from the GitHub repo clone](#for-trexio-developers-from-the-github-repo-clone)
* [Using CMake instead of Autotools](#using-cmake-instead-of-autotools)
* [Using TREXIO](#using-trexio)
* [Naming convention](#naming-convention)
* [Tutorial](#tutorial)
* [Documentation](#documentation)
* [Linking to your program](#linking-to-your-program)
* [Distributing TREXIO with your code](#distributing-trexio-with-your-code)
* [APIs for other languages](#apis-for-other-languages)
* [Python](#python)
* [Rust](#rust)
* [OCaml](#ocaml)
* [Citation](#citation)
* [Miscellaneous](#miscellaneous)
## Minimal requirements (for users):
- Autotools (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2) or CMake (>= 3.16)
- C compiler (gcc/icc/clang)
- Fortran compiler (gfortran/ifort)
- HDF5 library (>= 1.8) [optional, recommended for high performance]
## Installation procedure from the tarball (for users):
1. Download the `trexio-<version>.tar.gz` file
2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
3. `cd trexio-<version>`
4. `./configure`
5. `make`
6. `make check`
7. `sudo make install`
**Note: on systems with no `sudo` access, one can replace `./configure` with `./configure prefix=${PWD}/build` in order to execute `make install/uninstall` commands without `sudo` privileges.**
**Note: when linking against an MPI-enabled HDF5 library one usually has to specify the MPI wrapper for the C compiler by adding, e.g., `CC=mpicc` to the `./configure` command.**
## Additional requirements (for developers):
- python3 (>= 3.6)
- Emacs (>= 26.0)
- SWIG (>= 4.0) [required for the Python API]
## Installation procedure from the GitHub repo clone (for developers):
1. `git clone https://github.com/TREX-CoE/trexio.git`
2. `cd trexio`
3. `./autogen.sh`
4. `./configure`
5. `make`
6. `make check`
7. `sudo make install`
## Installation procedure for CMake users (from the tarball or GitHub repo clone):
The aforementioned instructions rely on [Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html) build system.
[CMake](https://cmake.org) users can achieve the same with the following steps (an example of out-of-source build):
1. `cmake -S. -Bbuild`
2. `cd build`
3. `make`
4. `ctest` (or `make test`)
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.**
**Note: when linking against an MPI-enabled HDF5 library one usually has to specify the MPI wrapper for the C compiler by adding, e.g., `-DCMAKE_C_COMPILER=mpicc` to the `cmake` command.**
## Installation procedure for conda users
## Installation
### Installation using a package manager
#### Conda
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/trexio/badges/version.svg)](https://anaconda.org/conda-forge/trexio)
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/trexio/badges/platforms.svg)](https://anaconda.org/conda-forge/trexio)
@ -71,28 +53,13 @@ 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).
Note that both parallel (see `mpi_openmpi` prefix) and serial (`nompi`) variants are provided.
## Installation procedure for Guix users
The official releases of TREXIO `>=2.0.0` can be installed using the
[GNU Guix](https://guix.gnu.org) functional package manager.
The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
Schema file contains the manifest specification for the `trexio` package.
It can be installed within the selected `$GUIX_PROFILE` as follows:
```
guix package \
--profile=$GUIX_PROFILE \
--cores=<n_cores> \
--install-from-file=trexio.scm
```
## Installation procedure for Spack users
#### Spack
The official releases `>=2.0.0` and the development version of TREXIO can be installed using the
[Spack](https://spack.io/) package manager.
@ -101,10 +68,71 @@ 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
```
## Compilation without the HDF5 library
#### Guix
The official releases of TREXIO `>=2.0.0` can be installed using the
[GNU Guix](https://guix.gnu.org) functional package manager.
The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
Schema file contains the manifest specification for the `trexio` package.
It can be installed as follows:
```
guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
```
#### Debian/Ubuntu
The official release of TREXIO `2.2.0` is available as a Debian (`.deb`) package thanks to the [Debichem Team](https://wiki.debian.org/Debichem).
The source code is hosted [here](https://salsa.debian.org/debichem-team/libtrexio) and
the pre-built binary files are available via the [Debian package registry](https://packages.debian.org/bookworm/libtrexio-dev).
TREXIO is also available on [Ubuntu 23.04 (Lunar Lobster)](https://packages.ubuntu.com/lunar/libtrexio-dev) and newer and can be installed as follows:
```
sudo apt-get update && sudo apt-get install libtrexio-dev
```
### Installation from source
#### Minimal requirements (for users):
- Autotools (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2) or CMake (>= 3.16)
- C compiler (gcc/icc/clang)
- Fortran compiler (gfortran/ifort)
- HDF5 library (>= 1.8) [optional, recommended for high performance]
#### Recommended: Installation from the release tarball
1. Download the `trexio-<version>.tar.gz` file from the GitHub release page
2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
3. `cd trexio-<version>`
4. `./configure`
5. ```make -j 4 ```
6. ```make -j 4 check```
7. `sudo make install`
In environments where `sudo` access is unavailable, a common workaround for
executing `make install/uninstall` commands without requiring superuser
privileges involves a modification to the `./configure` command.
This modification typically includes specifying an installation prefix within
the user's home directory to circumvent the need for system-wide installation
permissions. For instance, `./configure prefix=$HOME/.local` can be employed,
where `$HOME/.local` is often recommended for user-space software installations.
However, this is merely a suggestion, and users are free to choose any suitable
directory as their installation prefix, depending on their specific
requirements and system configurations.
Regarding the integration with an MPI (Message Passing Interface) enabled HDF5
library, it's typical to specify the MPI compiler wrapper for the C compiler.
This is done by appending a directive like `CC=mpicc` to the `./configure`
command. However, as TREXIO does not utilize MPI features, it is advisable to
link against a non-MPI (serial) version of the HDF5 library for the sake of
simplicity.
#### Compilation without the HDF5 library
By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).
This search can be disabled if HDF5 is not present/installable on the user machine.
@ -113,31 +141,41 @@ To build TREXIO without HDF5 back end, append `--without-hdf5` option to `config
- `./configure --without-hdf5`
- `cmake -S. -Bbuild -DENABLE_HDF5=OFF`
## Linking to your program
#### For TREXIO developers: from the GitHub repo clone
The `make install` command takes care of installing the TREXIO shared library on the user machine.
Once installed, add `-ltrexio` to the list of compiler options.
Additional requirements:
In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
In order to link the program against TREXIO, the search paths can be modified as follows:
- Python3 (>= 3.6)
- Emacs (>= 26.0)
- SWIG (>= 4.0) [required for the Python API]
`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
**Note:** The source code is auto-generated from the Emacs org-mode (`.org`) files following the literate programming approach. This is why the `src` directory is initially empty.
(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
1. `git clone https://github.com/TREX-CoE/trexio.git`
2. `cd trexio`
3. `./autogen.sh`
4. `./configure`
5. ```make -j 4```
6. ```make -j 4 check```
7. `sudo make install`
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)
module to find and link TREXIO library automatically.
#### Using CMake instead of Autotools
In Fortran applications, make sure that the `trexio_f.f90` module file is included in the source tree.
You might have to manually copy it into your program source directory.
The `trexio_f.f90` module file can be found in the `include/` directory of the TREXIO source code distribution.
The aforementioned instructions rely on [Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html) build system.
[CMake](https://cmake.org) users can achieve the same with the following steps (an example of out-of-source build):
**Note:** there is no need to include `trexio.h` header file during compilation of Fortran programs.
Only the installed library and the Fortran module file are required.
1. `cmake -S. -Bbuild`
2. `cd build`
3. ```make -j 4```
4. ```ctest -j 4```
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.
## Naming convention
**Note**: when linking against an MPI-enabled HDF5 library one usually has to specify the MPI wrapper for the C compiler by adding, e.g., `-DCMAKE_C_COMPILER=mpicc` to the `cmake` command.
## Using TREXIO
### Naming convention
The primary TREXIO API is composed of the following functions:
@ -156,7 +194,58 @@ There is no naming conflict when, for example, `num` variable exists both in the
These quantities can be accessed using the corresponding `trexio_[has|read|write]_nucleus_num` and `trexio_[has|read|write]_mo_num`, respectively.
## Python API
### Tutorial
TREXIO tutorials in Jupyter notebook format can be found in the
[corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials)
or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).
For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)
### Documentation
[Documentation generated from TREXIO org-mode files.](https://trex-coe.github.io/trexio/)
### Linking to your program
The `make install` command takes care of installing the TREXIO shared library on the user machine.
After installation, append `-ltrexio` to the list of compiler (`$LIBS`) options.
In some cases (e.g. when using custom installation prefix during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LD_LIBRARY_PATH`.
In order to link the program against TREXIO, the search path can be modified as follows:
`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib`
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)
module to find and link TREXIO library automatically.
In Fortran applications, make sure that the `trexio_f.f90` module file is included in the source tree.
You might have to manually copy it into your program source directory.
The `trexio_f.f90` module file can be found in the `include/` directory of the TREXIO source code distribution.
**Note:** there is no need to include `trexio.h` header file during compilation of Fortran programs.
Only the installed library and the Fortran module file are required.
### Distributing TREXIO with your code
The TREXIO software is distributed under the 3-clause BSD license, renowned for
its permissiveness. Consequently, it is entirely acceptable for you to
provide the TREXIO release tarball in conjunction with your own code.
Should you opt to include TREXIO with your software, it is recommended to
distribute the release tarball, instead of the content of the git repository.
The release tarballs contain pre-generated source files. This not only
accelerates the compilation process but also significantly reduces dependency
requirements.
## APIs for other languages
### Python
[![PyPI version](https://badge.fury.io/py/trexio.svg)](https://badge.fury.io/py/trexio)
@ -170,8 +259,7 @@ In order to install the Python API with the latest changes, follow the developer
make python-install
```
**Note: this implies that both HDF5 and SWIG are installed and available.
At the moment, it is not possible to configure the Python API without HDF5 library.**
**Note: this implies that SWIG is installed and available.**
We rely on the `pytest` package for unit testing. It can be installed via `pip install pytest`. To test the installation, run
@ -182,24 +270,62 @@ make python-test
We highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.
## Tutorial
### Rust
TREXIO tutorials in Jupyter notebook format can be found in the
[corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials)
or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).
The Rust API is available on Crates.io, so you can simply run
```
cargo add trexio
```
to your Rust project.
For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)
If you prefer to install the Rust API provided with this repository:
```
cargo add --path /path/to/trexio/rust/trexio
```
### OCaml
## Documentation
The TREXIO OCaml API is available in OPAM:
```
opam install trexio
```
[Documentation generated from TREXIO org-mode files.](https://trex-coe.github.io/trexio/)
If you prefer to install it from this repository,
```
cd ocaml/trexio
make
opam install .
```
## 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.

9
cmake/FindTREXIO.cmake
View File

@ -11,6 +11,7 @@
# $ export TREXIO_DIR=<custom_path>
# to indicate the prefix used during the TREXIO installation
# (typically `./configure prefix=<custom_path> ..` or `cmake -DCMAKE_INSTALL_DIR=<custom_path> ..`)
# Alternatively, TREXIO_DIR can be provided in a CMake cache.
# This file should be located WITHIN your project source tree.
# (e.g. in cmake/FindTREXIO.cmake)
@ -45,9 +46,13 @@ set(TREXIO_SEARCH_PATHS
/opt
)
if (NOT TREXIO_DIR)
set(TREXIO_DIR $ENV{TREXIO_DIR})
endif()
find_path(TREXIO_INCLUDE_DIR
NAMES trexio.h
HINTS $ENV{TREXIO_DIR}
HINTS "${TREXIO_DIR}"
PATH_SUFFIXES include/trexio include
PATHS ${TREXIO_SEARCH_PATHS}
)
@ -57,7 +62,7 @@ find_path(TREXIO_INCLUDE_DIR
# suffix (e.g. .so on Unix or .dylib on MacOS) in NAMES. CMake takes care of that.
find_library(TREXIO_LIBRARY
NAMES trexio
HINTS $ENV{TREXIO_DIR}
HINTS "${TREXIO_DIR}"
PATH_SUFFIXES lib64 lib
PATHS ${TREXIO_SEARCH_PATHS}
)

206
configure.ac
View File

@ -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],[2.5.0],[https://github.com/TREX-CoE/trexio/issues])
AC_CONFIG_SRCDIR([Makefile.in])
AC_CONFIG_HEADERS([include/config.h])
@ -41,6 +41,25 @@ AC_SUBST([UNAME])
## Checks for programs
## -------------------
# Fortran API [default: --with-fortran], do not disable in the dev mode
AC_PROG_FC
AC_ARG_WITH(fortran, [AS_HELP_STRING([--without-fortran],[do not test and install the Fortran API])], ok=$withval, ok=yes)
AS_IF([test "$ok" = "yes"],[
AC_FC_FREEFORM
AC_FC_SRCEXT([f90])
AC_PROG_FC_C_O
AC_FC_LIBRARY_LDFLAGS
# Specific options required with some compilers
AS_CASE([$FC],
[*gfortran*], [FCFLAGS="$FCFLAGS -fPIC"],
[*flang*], [FCFLAGS="$FCFLAGS -fPIC"],
[*ifort*], [FCFLAGS="$FCFLAGS -fPIC"],
[])
])
AM_CONDITIONAL([HAVE_FORTRAN],[test "$ok" = "yes"])
AC_LANG(C)
AC_PROG_CC
@ -52,51 +71,18 @@ AC_PROG_CC_C_O
AM_PROG_CC_C_O
# Fortran API [default: --with-fortran], do not disable in the dev mode
AC_ARG_WITH(fortran, [AS_HELP_STRING([--without-fortran],[do not test and install the Fortran API])], ok=$withval, ok=yes)
if test "$ok" = "yes"; then
AC_PROG_FC
AC_FC_FREEFORM
AC_FC_SRCEXT([f90])
AC_PROG_FC_C_O
AC_FC_LIBRARY_LDFLAGS
fi
AM_CONDITIONAL([HAVE_FORTRAN],[test "$ok" = "yes"])
# pkg-config
PKG_PROG_PKG_CONFIG()
PKG_CFLAGS=""
PKG_LIBS=""
AC_PROG_INSTALL
AC_PROG_LN_S
AC_PROG_GREP
# Specific options required with some compilers
case $FC in
*gfortran*)
FCFLAGS="$FCFLAGS -fPIC"
;;
*flang*)
FCFLAGS="$FCFLAGS -fPIC"
;;
*ifort*)
FCFLAGS="$FCFLAGS -fPIC"
;;
esac
case $CC in
*gcc*)
CFLAGS="$CFLAGS -fPIC"
;;
*clang*)
CFLAGS="$CFLAGS -fPIC"
;;
*icc*)
CFLAGS="$CFLAGS -fPIC"
;;
esac
AS_CASE([$CC],
[*gcc*], [CFLAGS="$CFLAGS -fPIC"],
[*clang*], [CFLAGS="$CFLAGS -fPIC"],
[*icc*], [CFLAGS="$CFLAGS -fPIC"],
[])
# Check if `cp -r -n` works, otherwise use `cp -r`
AC_CHECK_PROGS(CP_PROG, [cp])
@ -109,7 +95,7 @@ AC_RUN_IFELSE(
execl("/bin/sh", "sh", "-c", "mkdir tmpdir1 && \
touch tmpdir1/test_file && \
$CP_PROG -r -n tmpdir1 tmpdir2 && \
exec ls tmpdir2/test_file", NULL);
exec ls tmpdir2/test_file > /dev/null", NULL);
])],
[ rm -rf tmpdir1 tmpdir2
CP_COMMAND="\"$CP_PROG\", \"-r\", \"-n\""
@ -135,64 +121,108 @@ AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd
### HDF5
### ----
# Configure with HDF5 (default: --with-hdf5 using pkg-config) [optional]:
# ./configure [--with-hdf5 or --with-hdf5=yes]
# Configure with user-provided path to HDF5:
# ./configure --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial
# Configure without HDF5:
# ./configure --without-hdf5 [or --with-hdf5=no]
PKG_HDF5=""
AX_LIB_HDF5()
HDF5_LIBS=""
HDF5_LDFLAGS=""
HDF5_CFLAGS=""
HDF5_CPPFLAGS=""
AC_ARG_WITH([hdf5],
AS_HELP_STRING([--with-hdf5=PATH], [Path to HDF5 library and headers]), [
with_hdf5="$withval"], [with_hdf5="yes"])
if test "x${with_hdf5}" = xno; then
AC_MSG_WARN([
------------------------------------------
Configuring with the HDF5 library is
recommended to build efficient TREXIO.
------------------------------------------])
else
AC_CHECK_LIB([hdf5_hl],[main],[],[AC_MSG_ERROR(
-----------------------------------
Error: hdf5_hl library is required
-----------------------------------
)],[])ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
AS_IF([test "x$with_hdf5" == "xno"], [],
[test "x$with_hdf5" != "xyes"], [
HDF5_LIBS="-lhdf5"
HDF5_PATH="$with_hdf5"
HDF5_LDFLAGS="-L$HDF5_PATH/lib"
HDF5_CPPFLAGS="-I$HDF5_PATH/include"
AC_DEFINE([HAVE_HDF5], 1, [Define to 1 if HDF5 is available]) ],
[
PKG_CHECK_EXISTS([hdf5], [
PKG_CHECK_MODULES([HDF5], [hdf5 >= 1.8])
PKG_HDF5="hdf5"
],
[ AC_PATH_PROG([H5CC],[h5cc],[not_found])
AS_IF([test "$H5CC" != "not_found"], [
HDF5_LIBS="-lhdf5"
AC_REQUIRE([AC_PROG_SED])
AC_REQUIRE([AC_PROG_AWK])
AC_REQUIRE([AC_PROG_GREP])
# Look for "HDF5 Version: X.Y.Z"
HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
| $AWK '{print $[]3}')
fi
# A ideal situation would be where everything we needed was
# in the AM_* variables. However most systems are not like this
# and seem to have the values in the non-AM variables.
#
# We try the following to find the flags:
# (1) Look for "NAME:" tags
# (2) Look for "H5_NAME:" tags
# (3) Look for "AM_NAME:" tags
#
HDF5_tmp_flags=$(eval $H5CC -showconfig \
| $GREP 'FLAGS\|Extra libraries:' \
| $AWK -F: '{printf("%s "), $[]2}' )
CFLAGS="${HDF5_CFLAGS} ${CFLAGS}"
dnl Find the installation directory and append include/
HDF5_tmp_inst=$(eval $H5CC -showconfig \
| $GREP 'Installation point:' \
| $AWK '{print $[]NF}' )
dnl Add this to the CPPFLAGS
HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
HDF5_SHOW=$(eval $H5CC -show)
dnl Now sort the flags out based upon their prefixes
for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
case "$arg" in
-I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_CPPFLAGS="$HDF5_CPPFLAGS $arg"
;;
-L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LDFLAGS="$HDF5_LDFLAGS $arg"
;;
-l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LIBS="$HDF5_LIBS $arg"
;;
esac
done
])
])
AC_DEFINE([HAVE_HDF5], 1, [Define to 1 if HDF5 is available])
])
AM_CONDITIONAL([HAVE_HDF5],[test "x$with_hdf5" != "xno"])
AC_SUBST([PKG_HDF5])
AC_SUBST([HDF5_LDFLAGS])
AC_SUBST([HDF5_LIBS])
AC_SUBST([HDF5_CFLAGS])
AC_SUBST([HDF5_CPPFLAGS])
CPPFLAGS="${HDF5_CPPFLAGS} ${CPPFLAGS}"
CFLAGS="${HDF5_CFLAGS} ${CFLAGS}"
LDFLAGS="${HDF5_LDFLAGS} ${LDFLAGS}"
LIBS="${HDF5_LIBS} ${LIBS}"
# Check if HDF5 is available with pkg-config.
PKG_CHECK_MODULES([HDF5], [hdf5 >= 1.8], [
PKG_HDF5="hdf5"
],[
PKG_HDF5=""
])
PKG_CFLAGS="${HDF5_CFLAGS}"
PKG_LIBS="${HDF5_LIBS}"
AC_SUBST([PKG_HDF5])
AC_SUBST([PKG_CFLAGS])
AC_SUBST([PKG_LIBS])
AM_CONDITIONAL([HAVE_HDF5],[test "$with_hdf5" = "yes"])
AS_IF([test "x$with_hdf5" != "xno"], [
OLD_LIBS=$LIBS
AC_CHECK_LIB([hdf5], [H5Fcreate], [], [
AC_MSG_ERROR([-lhdf5 fails, use ./configure --with-hdf5=...]) ])
AC_CHECK_HEADER([hdf5.h], [], [
AC_MSG_ERROR([hdf5.h not found, use ./configure --with-hdf5=...]) ])
LIBS=$OLD_LIBS
])
# The block below should only execute if the ax_lib_hdf5.m4 macro failed to find HDF5.
# It is only needed to manually build Python API because setup.py depends on HDF5.
if test "$HDF5_LDFLAGS" = "" || "$HDF5_CFLAGS" = ""; then
HDF5_LDFLAGS="${PKG_LIBS}"
HDF5_CFLAGS="${PKG_CFLAGS}"
AC_SUBST([HDF5_CFLAGS])
AC_SUBST([HDF5_LDFLAGS])
fi
#if test x"$HDF5_LDFLAGS" = "x" || x"$HDF5_CFLAGS" = "x"; then
# AC_SUBST([HDF5_CFLAGS])
# AC_SUBST([HDF5_LDFLAGS])
#fi
# Checks for typedefs, structures, and compiler characteristics.
AC_TYPE_INT32_T
@ -286,7 +316,7 @@ AC_CONFIG_FILES([Makefile
pkgconfig/trexio.pc])
AC_OUTPUT
echo \
AS_ECHO([ \
"-------------------------------------------------
${PACKAGE_NAME} Version ${PACKAGE_VERSION} ${GIT_HASH} ${TREXIO_DEVEL}
@ -309,4 +339,4 @@ where the optional <target> is:
all - build C library and Fortran binding
check - run unit tests
install - install the library
--------------------------------------------------"
--------------------------------------------------"])

276
examples.org → docs/examples.org
View File

@ -1,8 +1,146 @@
#+TITLE: Examples
#+STARTUP: latexpreview
#+SETUPFILE: docs/theme.setup
#+SETUPFILE: ./theme.setup
* Writing nuclear coordinates
Here is a demonstration of how to use TREXIO to write the nuclear
coordinates of a water molecule to a file. It shows the basic steps
involved in opening a file, writing the data, and closing the file,
as well as the necessary TREXIO functions to perform these actions.
** C
#+begin_src c
#include <stdio.h>
#include <trexio.h>
int main() {
int num = 3; // Number of atoms
double coord[][3] = {
// xyz coordinates in atomic units
0. , 0. , -0.24962655,
0. , 2.70519714, 1.85136466,
0. , -2.70519714, 1.85136466 };
trexio_exit_code rc;
// Open the TREXIO file
trexio_t* f = trexio_open("water.trexio", 'w', TREXIO_HDF5, &rc);
if (rc != TREXIO_SUCCESS) {
fprintf(stderr, "Error: %s\n", trexio_string_of_error(rc));
return -1;
}
// Write the number of nuclei
rc = trexio_write_nucleus_num (f, num);
if (rc != TREXIO_SUCCESS) {
fprintf(stderr, "Error: %s\n", trexio_string_of_error(rc));
return -1;
}
// Write the nuclear coordinates
rc = trexio_write_nucleus_coord (f, &coord[0][0]);
if (rc != TREXIO_SUCCESS) {
fprintf(stderr, "Error: %s\n", trexio_string_of_error(rc));
return -1;
}
// Close the TREXIO file
rc = trexio_close(f);
if (rc != TREXIO_SUCCESS) {
fprintf(stderr, "Error: %s\n", trexio_string_of_error(rc));
return -1;
}
return 0;
}
#+end_src
** Python
This code uses the TREXIO Python binding to create a new TREXIO file named
=water.trexio=, and write the nuclear coordinates of a water molecule.
The ~coord~ variable is a list of three lists, each containing the x, y,
and z coordinates of the water molecule's nuclei.
The ~with~ statement is used to ensure the file is properly closed after
the write is complete.
The ~trexio.write_nucleus_num~ function is used to write the number of
nuclei in the system.
The ~trexio.write_nucleus_coord~ function is used to write the nuclear
coordinates of the system.
#+begin_src python
import trexio
coord = [ # xyz coordinates in atomic units
[0. , 0., -0.24962655],
[0. , 2.70519714, 1.85136466],
[0. , -2.70519714, 1.85136466]
]
# The Python API calls can raise `trexio.Error`
# exceptions to be handled via try/except clauses
# in the user application
with trexio.File("water.trexio", 'w',
back_end=trexio.TREXIO_HDF5) as f:
trexio.write_nucleus_num(f, len(coord))
trexio.write_nucleus_coord(f, coord)
#+end_src
** Fortran
#+begin_src f90
program trexio_water
use trexio
integer, parameter :: num=3 ! Number of nuclei
double precision :: coord(3,3) ! Array of atom coordinates
integer(trexio_t) :: f ! The TREXIO file handle
integer(trexio_exit_code) :: rc ! TREXIO return code
character*(128) :: err_msg ! String holding the error message
coord(:,:) = reshape( (/ 0.d0 , 0.d0 , -0.24962655d0, &
0.d0 , 2.70519714d0, 1.85136466d0, &
0.d0 , -2.70519714d0, 1.85136466d0 /), &
shape(coord) )
! Open the TREXIO file
f = trexio_open ('water.trexio', 'w', TREXIO_HDF5, rc)
if (rc /= TREXIO_SUCCESS) then
call trexio_string_of_error(rc, err_msg)
print *, 'Error: '//trim(err_msg)
call exit(-1)
end if
! Write the number of nuclei
rc = trexio_write_nucleus_num (f, num)
if (rc /= TREXIO_SUCCESS) then
call trexio_string_of_error(rc, err_msg)
print *, 'Error: '//trim(err_msg)
call exit(-1)
end if
! Write the nuclear coordinates
rc = trexio_write_nucleus_coord (f, coord)
if (rc /= TREXIO_SUCCESS) then
call trexio_string_of_error(rc, err_msg)
print *, 'Error: '//trim(err_msg)
call exit(-1)
end if
! Close the TREXIO file
rc = trexio_close(f)
if (rc /= TREXIO_SUCCESS) then
call trexio_string_of_error(rc, err_msg)
print *, 'Error: '//trim(err_msg)
call exit(-1)
end if
end program
#+end_src
* Accessing sparse quantities (integrals)
** Fortran
@ -62,7 +200,7 @@ program print_energy
#+begin_src f90
call getarg(1, filename)
f = trexio_open (filename, 'r', TREXIO_HDF5, rc)
f = trexio_open (filename, 'r', TREXIO_AUTO, rc)
if (rc /= TREXIO_SUCCESS) then
call trexio_string_of_error(rc, err_msg)
print *, 'Error opening TREXIO file: '//trim(err_msg)
@ -272,9 +410,141 @@ program print_energy
end program
#+end_src
** Python
:PROPERTIES:
:header-args: :tangle print_energy.py
:END:
#+begin_src python
import sys
import trexio
import numpy as np
BUFSIZE = 100000
#+end_src
This program computes the energy as:
\[
E = E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle k l | i j
\rangle\; \textrm{ with } \; 0 < i,j,k,l \le n
\]
One needs to read from the TREXIO file:
- $n$ :: The number of molecular orbitals
- $E_{\text{NN}}$ :: The nuclear repulsion energy
- $\gamma_{ij}$ :: The one-body reduced density matrix
- $\langle j |h| i \rangle$ :: The one-electron Hamiltonian integrals
- $\Gamma_{ijkl}$ :: The two-body reduced density matrix
- $\langle k l | i j \rangle$ :: The electron repulsion integrals
*** Obtain the name of the TREXIO file from the command line, and open it for reading
#+begin_src python
filename = sys.argv[1]
f = trexio.File(filename, 'r', trexio.TREXIO_AUTO)
#+end_src
*** Read the nuclear repulsion energy
#+begin_src python
E_nn = trexio.read_nucleus_repulsion(f)
#+end_src
*** Read the number of molecular orbitals
#+begin_src python
n = trexio.read_mo_num(f)
#+end_src
*** Read one-electron quantities
#+begin_src python
if not trexio.has_mo_1e_int_core_hamiltonian(f):
print("No core hamiltonian in file")
sys.exit(-1)
h0 = trexio.read_mo_1e_int_core_hamiltonian(f)
if not trexio.has_rdm_1e(f):
print("No 1e RDM in file")
sys.exit(-1)
D = trexio.read_rdm_1e(f)
#+end_src
*** Read two-electron quantities
**** Electron repulsion integrals
#+begin_src python
if not trexio.has_mo_2e_int_eri(f):
print("No electron repulsion integrals in file")
sys.exit(-1)
size_max = trexio.read_mo_2e_int_eri_size(f)
offset = 0
icount = BUFSIZE
feof = False
W = np.zeros( (n,n,n,n) )
while not feof:
buffer_index, buffer_values, icount, feof = trexio.read_mo_2e_int_eri(f, offset, icount)
for m in range(icount):
i, j, k, l = buffer_index[m]
W[i,j,k,l] = buffer_values[m]
W[k,j,i,l] = buffer_values[m]
W[i,l,k,j] = buffer_values[m]
W[k,l,i,j] = buffer_values[m]
W[j,i,l,k] = buffer_values[m]
W[j,k,l,i] = buffer_values[m]
W[l,i,j,k] = buffer_values[m]
W[l,k,j,i] = buffer_values[m]
#+end_src
**** Reduced density matrix
#+begin_src python
if not trexio.has_rdm_2e(f):
print("No two-body density matrix in file")
offset = 0
icount = BUFSIZE
feof = False
G = np.zeros( (n,n,n,n) )
while not feof:
buffer_index, buffer_values, icount, feof = trexio.read_rdm_2e(f, offset, icount)
for m in range(icount):
i, j, k, l = buffer_index[m]
G[i,j,k,l] = buffer_values[m]
#+end_src
*** Compute the energy
When the orbitals are real, we can use
\begin{eqnarray*}
E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle k l | i j
\rangle \\
&=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle i | h | j \rangle\,
+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle i j | k l
\rangle \\
\end{eqnarray*}
#+begin_src python
G = np.reshape(G, (n*n, n*n) )
W = np.reshape(W, (n*n, n*n) )
E = E_nn
E += 0.5*sum( [ np.dot(G[:,l], W[:,l]) for l in range(n*n) ] )
E += sum( [ np.dot(D[:,l], h0[:,l]) for l in range(n) ] )
print (f"Energy: {E}")
#+end_src
* Reading determinants
** Fortran
:PROPERTIES:
:header-args: :tangle print_dets.f90

60
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@ -0,0 +1,60 @@
#+TITLE: Motivation
#+STARTUP: latexpreview
#+SETUPFILE: ./theme.setup
#+BEGIN_EXPORT html
</td>
<td>
<img src="trexio_logo.png" alt="TREXIO logo"
align="left" width="200" vspace="20" hspace="20" />
</td></tr>
</table>
#+END_EXPORT
Quantum chemistry relies on quantum mechanics to explain and predict
the properties and behaviors of atoms, molecules, and materials.
Although density functional theory (DFT) is one of the most widely
used approaches thanks to its excellent ratio between computational
cost and accuracy, another important tool is wave function theory
(WFT), which describes the behavior of a quantum system in terms of
its wave function.
In order to perform WFT calculations, it is necessary to manipulate a
large number of parameters, such as the expansion coefficients of the
wave function and the matrix elements of the Hamiltonian operator.
These parameters can be numerous and difficult to handle, making it
important to have a robust and efficient method for storing and
accessing them.
Reproducible research remains a challenging topic, despite recent
advances such as the introduction of the FAIR (findable, accessible,
interoperable, reusable) data principles. A key
aspect of reproducibility is software interoperability, which refers
to the ability of different programs to work together and exchange
information, allowing different systems to communicate and exchange
data in order to function as a cohesive whole.
Interoperable software is prevalent nowadays and is a key component of
the Unix philosophy. In Unix shells, the most
straightforward application of software interoperability is made
through the use of the /pipe/ operator, where the output of a
program is the input of another program.
Similarly, shell scripts are created through the composition of
smaller programs, exchanging data through files or pipes.
A major challenge of reproducible research is the unified input/output
(I/O) of data within a particular research domain. The Unix
philosophy recommends the use of text files because they are
architecture-independent, readable in any language, and can be read as
a stream, which is useful for making programs communicate over a
network.
However, storing data in a text format can result in larger file sizes
and conversion from ASCII to binary format can be computationally
expensive for large data sets. To address this concern,
domain-specific binary formats have been developed, such as the Joint
Photographic Experts Group (JPEG) format for digital images
and the Moving Picture Experts Group (MPEG) format for videos.
These binary formats are utilized through a standardized application
programming interface (API).
In the field of wave function theory such a standard format and API is
still lacking, and the purpose of the TREXIO library is to fill this gap.

311
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@ -0,0 +1,311 @@
#+TITLE: The TREXIO library
#+STARTUP: latexpreview
#+SETUPFILE: ./theme.setup
* Format specification
#+BEGIN_EXPORT html
</td>
<td>
<img src="trex_specs.png" alt="TREX in a library"
align="right" width="300" vspace="20" hspace="20" />
</td></tr>
</table>
#+END_EXPORT
#
The TREXIO format is designed to store all the necessary information
to represent a wave function.
One notable feature of TREXIO is that it is self-contained, meaning
that all the parameters needed to recreate the wave function are
explicitly stored within the file, eliminating the need for external
databases. For example, instead of storing the name of a basis set
(such as cc-pVDZ), the actual basis set parameters used in the
calculation are stored.
** Organization of the data
The data in TREXIO are organized into *groups*, each containing
multiple *attributes* defined by their *type* and *dimensions*. Each
attribute within a group corresponds to a single scalar or array
variable in a code. In what follows, the notation
~<group>.<attribute>~ will be used to identify an attribute within a
group. For example, ~nucleus.charge~ refers to the
~charge~ attribute in the ~nucleus~ group. It is an array of type
~float~ with dimensions ~nucleus.num~, the attribute describing the
number of nuclei.
** Data types
So that TREXIO can be used in any language, we use a limited number
of data types. The main data types are ~int~ for integers,
~float~ for floating-point values, and ~str~ for
character strings. For complex numbers, their real and imaginary
parts are stored as ~float~. To minimize the risk of integer
overflow and accuracy loss, numerical data types are stored using
64-bit representations by default. However, in specific cases where
integers are bounded (such as orbital indices in four-index
integrals), the smallest possible representation is used to reduce the
file size. The API handles any necessary type conversions.
There are also two types derived from ~int~: ~dim~ and ~index~.
~dim~ is used for dimensioning variables, which are positive integers
used to specify the dimensions of an array. In the previous example,
~nucleus.num~ is a dimensioning variable that specifies the
dimensions of the ~nucleus.charge~ array. ~index~ is used for
integers that correspond to array indices, because some languages
(such as C or Python) use zero-based indexing, while others (such as
Fortran) use one-based indexing. For convenience, values of the
~index~ type are shifted by one when TREXIO is used in one-based
languages to be consistent with the semantics of the language.
You may also encounter some ~dim readonly~ variables. It means
that the value is automatically computed and written by the TREXIO
library, thus it is read-only and cannot be (over)written by the
user.
Arrays can be stored in either dense or sparse formats. If the
sparse format is selected, the data is stored in coordinate format.
For example, the element ~A(i,j,k,l)~ is stored as a quadruplet of
integers $(i,j,k,l)$ along with the corresponding value. Typically,
two-dimensional arrays are stored as dense arrays, while arrays with
higher dimensions are stored in sparse format.
For sparse data structures the data can be too large to fit in memory
and the data needs to be fetched using multiple function calls to
perform I/O on buffers. For more information on how to read/write
sparse data structures, see the [[./examples.html][examples]].
For the Configuration Interaction (CI) and Configuration State
Function (CSF) groups, the ~buffered~ data type is introduced, which
allows similar incremental I/O as for ~sparse~ data but without the
need to write indices of the sparse values.
For determinant lists (integer bit fields), the ~special~ attribute
is present in the type. This means that the source code is not
produced by the generator, but hand-written.
Some data may be complex. In that case, the real part should be stored
in the variable, and the imaginary part will be stored in the variable
with the same name suffixed by ~_im~.
* The TREXIO library
#+BEGIN_EXPORT html
</td>
<td>
<img src="trex_lib.png" alt="TREX in a library"
align="left" width="300" vspace="20" hspace="20" />
</td></tr>
</table>
#+END_EXPORT
The TREXIO library is written is the C language, and is licensed under
the open-source 3-clause BSD license to allow for use in all types of
quantum chemistry software, whether commercial or not.
The design of the library is divided into two main sections: the
front-end and the back-end. The front-end serves as the interface
between users and the library, while the back-end acts as the
interface between the library and the physical storage.
** The front-end
By using the TREXIO library, users can store and extract data in a
consistent and organized manner. The library provides a user-friendly
API, including functions for reading, writing, and checking for the
existence of data. The functions follow the pattern
~trexio_[has|read|write]_<group>_<attribute>~, where the
group and attribute specify the particular data being accessed. It
also includes an error handling mechanism, in which each function call
returns an exit code of type ~trexio_exit_code~, explaining
the type of error.
This can be used to catch exceptions and improve debugging in the
upstream user application.
To ensure the consistency of the data, the attributes can only be
written if all the other attributes on which they explicitly depend
have been written. For example, as the ~nucleus.coord~ array is
dimensioned by the number of nuclei ~nucleus.num~, the ~nucleus.coord~
attribute can only be written after ~nucleus.num~. However, the
library is not aware of non-explicit dependencies, such as the
relation between the electron repulsion integrals (ERIs) and MO
coefficients. A complete control of the consistency of the data is
therefore impossible, so the attributes were chosen to be by default
/immutable/. By only allowing data to be written only once, the
risk of modifying data in a way that creates inconsistencies is
reduced. For example, if the ERIs have already been written, it would
be inconsistent to later modify the MO coefficients. To allow for
flexibility, the library also allows for the use of an /unsafe/
mode, in which data can be overwritten. However, this mode carries
the risk of producing inconsistent files, and the ~metadata~ group's
~unsafe~ attribute is set to ~1~ to indicate that the file has
potentially been modified in a dangerous way. This attribute can be
manually reset to ~0~ if the user is confident that the modifications
made are safe.
** The back-end
At present, TREXIO supports two back-ends: one relying only on the
C standard library to produce plain text files (the so-called /text/
back-end), and one relying on the HDF5 library.
With the text back-end, the TREXIO "file" is a directory containing
multiple text files, one for each group. This back end is intended
to be used in development environments, as it gives access to the
user to the standard tools such as ~diff~ and ~grep~.
In addition, text files are better adapted than binary files for
version control systems such as Git, so this format can be also
used for storing reference data for unit tests.
HDF5 is a binary file format and library for storing and managing
large amounts of data in a hierarchical structure. It allows users
to manipulate data in a way similar to how files and directories
are manipulated within the file system. The HDF5 library provides
optimal performance through its memory mapping mechanism and
supports advanced features such as serial and parallel I/O,
chunking, and compression filters. However, HDF5 files are in
binary format, which requires additional tools such as ~h5dump~ to
view them in a human-readable format. It is widely used in
scientific and engineering applications, and is known for its high
performance and ability to handle large data sets efficiently.
The TREXIO HDF5 back-end is the recommended choice for production
environments, as it provides high I/O performance. Furthermore,
all data is stored in a single file, making it especially suitable
for parallel file systems like Lustre. These file systems are
optimized for large, sequential I/O operations and are not
well-suited for small, random I/O operations. When multiple small
files are used, the file system may become overwhelmed with
metadata operations like creating, deleting, or modifying files,
which can adversely affect performance.
In a benchmarking program designed to compare the two back-ends of
the library, the HDF5 back-end was found to be significantly faster
than the text back-end. The program wrote a wave function made up
of 100 million Slater determinants and measured the time taken to
write the Slater determinants and CI coefficients. The HDF5
back-end achieved a speed of $10.4\times10^6$ Slater determinants
per second and a data transfer rate of 406 MB/s, while the text
back-end had a speed of $1.1\times10^6$ determinants per second and
a transfer rate of 69 MB/s. These results were obtained on a DELL
960 GB mix-use solid-state drive (SSD). The HDF5 back-end was able
to achieve a performance level close to the peak performance of the
SSD, while the text back-end's performance was limited by the speed
of the CPU for performing binary to ASCII conversions.
In addition to the HDF5 and text back-ends, it is also possible to
introduce new back-ends to the library. For example, a back-end
could be created to support object storage systems, such as those
used in cloud-based applications or for archiving in open data
repositories.
** Supported languages
One of the main benefits of using C as the interface for a library is
that it is easy to use from other programming languages. Many
programming languages, such as Python or Julia, provide built-in
support for calling C functions, which means that it is relatively
straightforward to write a wrapper that allows a library written in C
to be called from another language.
In general, libraries with a C interface are the easiest to use from
other programming languages, because C is widely supported and has a
simple, stable application binary interface (ABI). Other languages,
such as Fortran and C++, may have more complex ABIs and may
require more work to interface with them.
TREXIO has been employed in codes developed in various programming
languages, including C, C++, Fortran, Python, OCaml, and Julia. While
Julia is designed to enable the use of C functions without the need
for additional manual interfacing, the TREXIO C header file was
automatically integrated into Julia programs using the
~CBindings.jl~ package.
In contrast, specific bindings have been provided for Fortran, Python,
and OCaml to simplify the user experience.
In particular, the binding for Fortran is not distributed as multiple
compiled Fortran module files (~.mod~), but instead as a single
Fortran source file (~.F90~). The distribution of the source file
instead of the compiled module has multiple benefits. It ensures that
the TREXIO module is always compiled with the same compiler as the
client code, avoiding the compatibility problem of ~.mod~ files
between different compiler versions and vendors. The single-file
model requires very little changes in the build system of the user's
codes, and it facilitates the search for the interface of a particular
function. In addition, advanced text editors can parse the TREXIO
interface to propose interactive auto-completion of the TREXIO
function names to the developers.
Finally, the Python module, partly generated with SWIG and fully
compatible with NumPy, allows Python users to interact with the
library in a more intuitive and user-friendly way. Using the Python
interface is likely the easiest way to begin using TREXIO and
understanding its features. In order to help users get started with
TREXIO and understand its functionality, tutorials in Jupyter
notebooks are available on GitHub
(https://github.com/TREX-CoE/trexio-tutorials), and can be executed
via the Binder platform.
** Source code generation and documentation
Source code generation is a valuable technique that can significantly
improve the efficiency and consistency of software development. By
using templates to generate code automatically, developers can avoid
manual coding and reduce the risk of errors or inconsistencies. This
approach is particularly useful when a large number of functions
follow similar patterns, as in the case of the TREXIO library, where
functions are named according to the pattern
~trexio_[has|read|write]_<group>_<attribute>~.
By generating these functions from the format specification using
templates, the developers can ensure that the resulting code follows a
consistent structure and is free from errors or inconsistencies.
The description of the format is written in a text file in the Org
format. Org is a structured plain text format, containing information
expressed in a lightweight markup language similar to the popular
Markdown language. While Org was introduced as a mode of the GNU
Emacs text editor, its basic functionalities have been implemented in
most text editors such as Vim, Atom or VS Code.
There are multiple benefits in using the Org format. The first
benefit is that the Org syntax is easy to learn and allows for the
insertion of equations in \LaTeX{} syntax. Additionally, Org files
can be easily converted to HyperText Markup Language (HTML) or
Portable Document Format (PDF) for generating documentation. The
second benefit is that GNU Emacs is a programmable text editor and
code blocks in Org files can be executed interactively, similar to
Jupyter notebooks. These code blocks can also manipulate data defined
in tables and this feature is used to automatically transform tables
describing groups and attributes in the documentation into a
JavaScript Object Notation (JSON) file.
This JSON file is then used by a Python script to generate the needed
functions in C language, as well as header files and some files
required for the Fortran, Python, and OCaml interfaces.
With this approach, contributions to the development of the TREXIO
library can be made simply by adding new tables to the Org file, which
can be submitted as /pull requests/ on the project's GitHub
repository (https://github.com/trex-coe/trexio). Overall, this
process allows for a more efficient and consistent development process
and enables contributions from a wider range of individuals,
regardless of their programming skills.
** Availability
The TREXIO library is designed to be portable and easy to install
on a wide range of systems. It follows the C99 standard to ensure
compatibility with older systems, and can be configured with either
the GNU Autotools or the CMake build systems. The only external
dependency is the HDF5 library, which is widely available on HPC
platforms and as packages on major Linux distributions. Note that
it is possible to disable the HDF5 back-end at configuration time,
allowing TREXIO to operate only with the text back-end and have
zero external dependencies. This can be useful for users who may
not be able to install HDF5 on certain systems.
TREXIO is distributed as a tarball containing the source code,
generated code, documentation, and Fortran interface. It is also
available as a binary ~.deb~ package for Debian-based Linux
distributions and as packages for Guix, Spack and Conda. The Python
module can be found in the PyPI repository, the OCaml binding is
available in the official OPAM repository, and the ~.deb~ packages
are available in Ubuntu 23.04.

4
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# -*- mode: org; -*-
#+HTML_LINK_HOME: index.html
#+OPTIONS: H:4 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t d:(HIDE)
#+OPTIONS: H:4 num:t toc:nil \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t d:(HIDE)
####### #+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+INFOJS_OPT: toc:t mouse:underline path:org-info.js
#+INFOJS_OPT: mouse:underline path:org-info.js
#+HTML_HEAD: <link rel="stylesheet" title="Standard" href="trexio.css" type="text/css" />
#+STARTUP: align nodlcheck hidestars oddeven lognotestate

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# ===========================================================================
# https://www.gnu.org/software/autoconf-archive/ax_lib_hdf5.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_LIB_HDF5([serial/parallel])
#
# DESCRIPTION
#
# This macro provides tests of the availability of HDF5 library.
#
# The optional macro argument should be either 'serial' or 'parallel'. The
# former only looks for serial HDF5 installations via h5cc. The latter
# only looks for parallel HDF5 installations via h5pcc. If the optional
# argument is omitted, serial installations will be preferred over
# parallel ones.
#
# The macro adds a --with-hdf5 option accepting one of three values:
#
# no - do not check for the HDF5 library.
# yes - do check for HDF5 library in standard locations.
# path - complete path to the HDF5 helper script h5cc or h5pcc.
#
# If HDF5 is successfully found, this macro calls
#
# AC_SUBST(HDF5_VERSION)
# AC_SUBST(HDF5_CC)
# AC_SUBST(HDF5_CFLAGS)
# AC_SUBST(HDF5_CPPFLAGS)
# AC_SUBST(HDF5_LDFLAGS)
# AC_SUBST(HDF5_LIBS)
# AC_SUBST(HDF5_FC)
# AC_SUBST(HDF5_FFLAGS)
# AC_SUBST(HDF5_FLIBS)
# AC_SUBST(HDF5_TYPE)
# AC_DEFINE(HAVE_HDF5)
#
# and sets with_hdf5="yes". Additionally, the macro sets
# with_hdf5_fortran="yes" if a matching Fortran wrapper script is found.
# Note that Autoconf's Fortran support is not used to perform this check.
# H5CC and H5FC will contain the appropriate serial or parallel HDF5
# wrapper script locations.
#
# If HDF5 is disabled or not found, this macros sets with_hdf5="no" and
# with_hdf5_fortran="no".
#
# Your configuration script can test $with_hdf to take any further
# actions. HDF5_{C,CPP,LD}FLAGS may be used when building with C or C++.
# HDF5_F{FLAGS,LIBS} should be used when building Fortran applications.
#
# To use the macro, one would code one of the following in "configure.ac"
# before AC_OUTPUT:
#
# 1) dnl Check for HDF5 support
# AX_LIB_HDF5()
#
# 2) dnl Check for serial HDF5 support
# AX_LIB_HDF5([serial])
#
# 3) dnl Check for parallel HDF5 support
# AX_LIB_HDF5([parallel])
#
# One could test $with_hdf5 for the outcome or display it as follows
#
# echo "HDF5 support: $with_hdf5"
#
# You could also for example, override the default CC in "configure.ac" to
# enforce compilation with the compiler that HDF5 uses:
#
# AX_LIB_HDF5([parallel])
# if test "$with_hdf5" = "yes"; then
# CC="$HDF5_CC"
# else
# AC_MSG_ERROR([Unable to find HDF5, we need parallel HDF5.])
# fi
#
# The HDF5_TYPE environment variable returns "parallel" or "serial",
# depending on which type of library is found.
#
# LICENSE
#
# Copyright (c) 2009 Timothy Brown <tbrown@freeshell.org>
# Copyright (c) 2010 Rhys Ulerich <rhys.ulerich@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 20
AC_DEFUN([AX_LIB_HDF5], [
AC_REQUIRE([AC_PROG_SED])
AC_REQUIRE([AC_PROG_AWK])
AC_REQUIRE([AC_PROG_GREP])
dnl Check first argument is one of the recognized values.
dnl Fail eagerly if is incorrect as this simplifies case statements below.
if test "m4_normalize(m4_default([$1],[]))" = "" ; then
: # Recognized value
elif test "m4_normalize(m4_default([$1],[]))" = "serial" ; then
: # Recognized value
elif test "m4_normalize(m4_default([$1],[]))" = "parallel"; then
: # Recognized value
else
AC_MSG_ERROR([
Unrecognized value for AX[]_LIB_HDF5 within configure.ac.
If supplied, argument 1 must be either 'serial' or 'parallel'.
])
fi
dnl Add a default --with-hdf5 configuration option.
AC_ARG_WITH([hdf5],
AS_HELP_STRING(
[--with-hdf5=[yes/no/PATH]],
m4_case(m4_normalize([$1]),
[serial], [location of h5cc for serial HDF5 configuration],
[parallel], [location of h5pcc for parallel HDF5 configuration],
[location of h5cc or h5pcc for HDF5 configuration])
),
[if test "$withval" = "no"; then
with_hdf5="no"
elif test "$withval" = "yes"; then
with_hdf5="yes"
else
with_hdf5="yes"
H5CC="$withval"
fi],
[with_hdf5="yes"]
)
dnl Set defaults to blank
HDF5_CC=""
HDF5_VERSION=""
HDF5_CFLAGS=""
HDF5_CPPFLAGS=""
HDF5_LDFLAGS=""
HDF5_LIBS=""
HDF5_FC=""
HDF5_FFLAGS=""
HDF5_FLIBS=""
HDF5_TYPE=""
dnl Try and find hdf5 compiler tools and options.
if test "$with_hdf5" = "yes"; then
if test -z "$H5CC"; then
dnl Check to see if H5CC is in the path.
AC_PATH_PROGS(
[H5CC],
m4_case(m4_normalize([$1]),
[serial], [h5cc],
[parallel], [h5pcc],
[h5cc h5pcc]),
[])
else
AC_MSG_CHECKING([Using provided HDF5 C wrapper])
AC_MSG_RESULT([$H5CC])
fi
AC_MSG_CHECKING([for HDF5 type])
AS_CASE([$H5CC],
[*h5pcc], [HDF5_TYPE=parallel],
[*h5cc], [HDF5_TYPE=serial],
[HDF5_TYPE=neither])
AC_MSG_RESULT([$HDF5_TYPE])
AC_MSG_CHECKING([for HDF5 libraries])
if test ! -f "$H5CC" || test ! -x "$H5CC"; then
AC_MSG_RESULT([no])
AC_MSG_WARN(m4_case(m4_normalize([$1]),
[serial], [
Unable to locate serial HDF5 compilation helper script 'h5cc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5cc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).
], [parallel],[
Unable to locate parallel HDF5 compilation helper script 'h5pcc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5pcc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).
], [
Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).
]))
with_hdf5="no"
with_hdf5_fortran="no"
else
dnl Get the h5cc output
HDF5_SHOW=$(eval $H5CC -show)
dnl Get the actual compiler used
HDF5_CC=$(eval $H5CC -show | head -n 1 | $AWK '{print $[]1}')
if test "$HDF5_CC" = "ccache"; then
HDF5_CC=$(eval $H5CC -show | head -n 1 | $AWK '{print $[]2}')
fi
dnl h5cc provides both AM_ and non-AM_ options
dnl depending on how it was compiled either one of
dnl these are empty. Lets roll them both into one.
dnl Look for "HDF5 Version: X.Y.Z"
HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
| $AWK '{print $[]3}')
dnl A ideal situation would be where everything we needed was
dnl in the AM_* variables. However most systems are not like this
dnl and seem to have the values in the non-AM variables.
dnl
dnl We try the following to find the flags:
dnl (1) Look for "NAME:" tags
dnl (2) Look for "H5_NAME:" tags
dnl (3) Look for "AM_NAME:" tags
dnl
HDF5_tmp_flags=$(eval $H5CC -showconfig \
| $GREP 'FLAGS\|Extra libraries:' \
| $AWK -F: '{printf("%s "), $[]2}' )
dnl Find the installation directory and append include/
HDF5_tmp_inst=$(eval $H5CC -showconfig \
| $GREP 'Installation point:' \
| $AWK '{print $[]NF}' )
dnl Add this to the CPPFLAGS
HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
dnl Now sort the flags out based upon their prefixes
for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
case "$arg" in
-I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_CPPFLAGS="$HDF5_CPPFLAGS $arg"
;;
-L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LDFLAGS="$HDF5_LDFLAGS $arg"
;;
-l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LIBS="$HDF5_LIBS $arg"
;;
esac
done
HDF5_LIBS="-lhdf5 $HDF5_LIBS"
AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
dnl See if we can compile
AC_LANG_PUSH([C])
ax_lib_hdf5_save_CC=$CC
ax_lib_hdf5_save_CPPFLAGS=$CPPFLAGS
ax_lib_hdf5_save_LIBS=$LIBS
ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
CC=$HDF5_CC
CPPFLAGS=$HDF5_CPPFLAGS
LIBS=$HDF5_LIBS
LDFLAGS=$HDF5_LDFLAGS
AC_CHECK_HEADER([hdf5.h], [ac_cv_hadf5_h=yes], [ac_cv_hadf5_h=no])
AC_CHECK_LIB([hdf5], [H5Fcreate], [ac_cv_libhdf5=yes],
[ac_cv_libhdf5=no])
if test "$ac_cv_hadf5_h" = "no" && test "$ac_cv_libhdf5" = "no" ; then
AC_MSG_WARN([Unable to compile HDF5 test program])
fi
dnl Look for HDF5's high level library
AC_CHECK_LIB([hdf5_hl], [main],[HDF5_LIBS="-lhdf5_hl $HDF5_LIBS"], [], [])
CC=$ax_lib_hdf5_save_CC
CPPFLAGS=$ax_lib_hdf5_save_CPPFLAGS
LIBS=$ax_lib_hdf5_save_LIBS
LDFLAGS=$ax_lib_hdf5_save_LDFLAGS
AC_LANG_POP([C])
AC_MSG_CHECKING([for matching HDF5 Fortran wrapper])
dnl Presume HDF5 Fortran wrapper is just a name variant from H5CC
H5FC=$(eval echo -n $H5CC | $SED -n 's/cc$/fc/p')
if test -x "$H5FC"; then
AC_MSG_RESULT([$H5FC])
with_hdf5_fortran="yes"
AC_SUBST([H5FC])
dnl Again, pry any remaining -Idir/-Ldir from compiler wrapper
for arg in `$H5FC -show`
do
case "$arg" in #(
-I*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
|| HDF5_FFLAGS="$HDF5_FFLAGS $arg"
;;#(
-L*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
|| HDF5_FFLAGS="$HDF5_FFLAGS $arg"
dnl HDF5 installs .mod files in with libraries,
dnl but some compilers need to find them with -I
echo $HDF5_FFLAGS | $GREP -e "-I${arg#-L}" >/dev/null \
|| HDF5_FFLAGS="$HDF5_FFLAGS -I${arg#-L}"
;;
esac
done
dnl Make Fortran link line by inserting Fortran libraries
for arg in $HDF5_LIBS
do
case "$arg" in #(
-lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5hl_fortran $arg"
;; #(
-lhdf5) HDF5_FLIBS="$HDF5_FLIBS -lhdf5_fortran $arg"
;; #(
*) HDF5_FLIBS="$HDF5_FLIBS $arg"
;;
esac
done
else
AC_MSG_RESULT([no])
with_hdf5_fortran="no"
fi
AC_SUBST([HDF5_VERSION])
AC_SUBST([HDF5_CC])
AC_SUBST([HDF5_CFLAGS])
AC_SUBST([HDF5_CPPFLAGS])
AC_SUBST([HDF5_LDFLAGS])
AC_SUBST([HDF5_LIBS])
AC_SUBST([HDF5_FC])
AC_SUBST([HDF5_FFLAGS])
AC_SUBST([HDF5_FLIBS])
AC_SUBST([HDF5_TYPE])
AC_DEFINE([HAVE_HDF5], [1], [Defined if you have HDF5 support])
fi
fi
])

9
ocaml/trexio/Makefile
View File

@ -4,6 +4,13 @@ default: sources
lib/trexio.ml: ../../trex.json read_json.py src/trexio.ml src/trexio.mli src/trexio_stubs.c
./read_json.py
sources: lib/trexio.ml
lib/trexio.h:
cp ../../include/trexio.h lib/
sources: lib/trexio.ml lib/trexio.h
clean:
rm lib/trexio.h lib/trexio.ml lib/trexio.mli lib/trexio_stubs.c
dune clean
.PHONY: sources default

33
ocaml/trexio/compile-lib.sh Executable file
View File

@ -0,0 +1,33 @@
#!/bin/sh
PREFIX=$1
TASK=$2
PKGCONFIG_COMMAND="pkg-config --libs --cflags trexio"
INSTALLED="no"
# Try with system defaults
if cc test.c >/dev/null 2>&1 ; then
exit
fi
# Try with pkg-config
if eval $PKGCONFIG_COMMAND >/dev/null 2>&1; then
exit
fi
# Compile C library
set -e
if test "$TASK" = "build" ; then
tar -zxf trexio-*.tar.gz
cd trexio-*
# ./configure --prefix=${PREFIX} --without-fortran --enable-static --disable-shared
./configure --prefix=${PWD}/.. --without-fortran --enable-static --disable-shared
make -j 4
make -j install
cd ../
elif test "$TASK" = "install" ; then
cd trexio-*
make install
rm -rf trexio-*/
fi

4
ocaml/trexio/dune-project
View File

@ -1,9 +1,9 @@
(lang dune 3.1)
(name trexio)
(version 2.3.0)
(version 2.5.0)
(generate_opam_files true)
(generate_opam_files false)
(source
(github trex-coe/trexio_ocaml))

17
ocaml/trexio/read_json.py
View File

@ -7,6 +7,21 @@ stubs_file= "trexio_stubs.c"
ml_file = "trexio.ml"
mli_file = ml_file+"i"
def check_version():
with open('trexio.opam','r') as f:
for line in f:
if line.startswith("version"):
ocaml_version = line.split(':')[1].strip()[1:-1]
break
with open('../../configure.ac','r') as f:
for line in f:
if line.startswith("AC_INIT"):
trexio_version = line.split(',')[1].strip()[1:-1]
break
if ocaml_version != trexio_version:
print(f"Inconsistent versions:\nTREXIO:{trexio_version}\nOCaml: {ocaml_version}\n")
raise
def write_stubs(data):
with open("src/"+stubs_file,'r') as f:
@ -643,10 +658,12 @@ def write_ml(data):
def main():
check_version()
with open(json_file,'r') as f:
data = json.load(f)
for group in data:
for element in data[group]:
print(f"{group}_{element}")
if data[group][element][0] == "str":
data[group][element][0] = "string"

49
ocaml/trexio/trexio.opam Normal file
View File

@ -0,0 +1,49 @@
# This file is generated by dune, edit dune-project instead
opam-version: "2.0"
version: "2.4.2"
synopsis: "Binding for the TREXIO Input/Output library"
description:
"TREXIO is a file format and library for storing wave functions and integrals for quantum chemistry."
maintainer: ["Anthony Scemama <scemama@irsamc.ups-tlse.fr>"]
authors: [
"Anthony Scemama <scemama@irsamc.ups-tlse.fr>"
"Evgeny Posenitskiy <posenitskiy@irsamc.ups-tlse.fr>"
]
license: "BSD-3-Clause"
tags: ["Quantum chemistry" "Library"]
homepage: "https://github.com/trex-coe/trexio_ocaml"
doc: "https://trex-coe.github.io/trexio/"
bug-reports: "https://github.com/trex-coe/trexio_ocaml/issues"
depends: [
"dune" {>= "3.1"}
"dune-configurator" {build}
"conf-pkg-config" {build}
"odoc" {with-doc}
]
depexts: [
["hdf5"] {os-distribution = "alpine"}
["epel-release" "hdf5-devel"] {os-distribution = "centos"}
["libhdf5-dev"] {os-distribution = "debian"}
["hdf5"] {os-distribution = "homebrew"}
["libhdf5-dev"] {os-distribution = "ubuntu"}
]
build: [
["dune" "subst"] {dev}
["./compile-lib.sh" "%{prefix}%" "build"]
[
"dune"
"build"
"-p"
name
"-j"
jobs
"@install"
"@runtest" {with-test}
"@doc" {with-doc}
]
]
install: [
["./compile-lib.sh" "%{prefix}%" "install"]
["dune" "install"]
]
dev-repo: "git+https://github.com/trex-coe/trexio_ocaml.git"

1
python/MANIFEST.in
View File

@ -4,6 +4,7 @@ include examples/notebooks/*
include examples/README.md
include requirements.txt tools/set_NUMPY_INCLUDEDIR.sh
include test/benzene_data.py
include test/conftest.py
exclude examples/LICENSE
exclude examples/requirements.txt

4
python/README.md
View File

@ -27,6 +27,10 @@ However, it is good practice to first check for updates of the build-system pack
**Note: we highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.**
For more details, see the corresponding part of the [Python documentation](https://docs.python.org/3/library/venv.html#creating-virtual-environments).
**Note: our build farm (GitHub Actions) does not support ARM64 architectures (including the Mac M1/M2 chips). Therefore, `pip install trexio` does not work on an ARM64-based machine. Thus, we recommend to install TREXIO from source on an ARM64-based machine. If one uses a Mac where HDF5 is installed with brew (i.e., `brew install hdf5`), a workaround is to execute the following 2 lines before doing `pip install trexio`:**
- `export H5_CFLAGS="-I$(brew --prefix hdf5)/include"`
- `export H5_LDFLAGS="-L$(brew --prefix hdf5)/lib"`
## Additional requirements (for installation from source)

4
python/build_manylinux_wheels.sh
View File

@ -89,7 +89,7 @@ function build_wheel_for_py()
# cleaning
rm -rf -- dist/ build/ trexio.egg-info/
rm -- test_file_py.h5 unsafe_test_file_py.h5
#rm -- test_file_py.h5 unsafe_test_file_py.h5
# deactivate the current environment
deactivate
@ -103,7 +103,7 @@ function build_wheel_for_py()
# build wheels for all versions of CPython in this container
for CPYVERSION in 36 37 38 39 310
for CPYVERSION in 37 38 39 310
do
build_wheel_for_py ${CPYVERSION}
done

40
python/install_pytrexio.sh
View File

@ -16,7 +16,45 @@ done
# check that both variables are set
if [[ -z ${H5_LDFLAGS_LOCAL} ]] || [[ -z ${H5_CFLAGS_LOCAL} ]]; then
if [[ -z ${H5_LDFLAGS} ]] || [[ -z ${H5_CFLAGS} ]]; then
echo "Paths to the HDF5 installation are not provided. pkgconfig will try to detect them."
# If pkg-config fails, try to locate hdf5 using h5cc
which h5cc &> /dev/null && HAS_H5CC=1
pkg-config --libs hdf5
if [[ $? -ne 0 && $HAS_H5CC == "1" ]] ; then
HDF5_tmp_flags=$(h5cc -showconfig \
| grep 'FLAGS\|Extra libraries:' \
| awk -F: '{printf("%s "), $2}' )
echo $HDF5_tmp_flags
# Find the installation directory and append include/
HDF5_tmp_inst=$(h5cc -showconfig \
| grep 'Installation point:' \
| awk '{print $NF}' )
echo $HDF5_tmp_inst
# Add this to the CPPFLAGS
HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
HDF5_SHOW=$(h5cc -show)
# Now sort the flags out based upon their prefixes
for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
case "$arg" in
-I*) echo $HDF5_CPPFLAGS | grep -e "$arg" 2>&1 >/dev/null \
|| HDF5_CPPFLAGS="$HDF5_CPPFLAGS $arg"
;;
-L*) echo $HDF5_LDFLAGS | grep -e "$arg" 2>&1 >/dev/null \
|| HDF5_LDFLAGS="$HDF5_LDFLAGS $arg"
;;
-l*) echo $HDF5_LIBS | grep -e "$arg" 2>&1 >/dev/null \
|| HDF5_LIBS="$HDF5_LIBS $arg"
;;
esac
done
export H5_LDFLAGS="$HDF5_LDFLAGS"
export H5_CFLAGS="$HDF5_CPPFLAGS"
else
echo "Paths to the HDF5 installation are not provided. pkgconfig will try to detect them."
fi
else
echo "Using exported H5_LDFLAGS and H5_CFLAGS environment variables."
fi

21
python/pyproject.toml
View File

@ -3,25 +3,6 @@ requires = [
"setuptools>=42",
"wheel",
"pkgconfig",
# Numpy requirements for different OS/architectures
# Copied from https://github.com/scipy/scipy/blob/master/pyproject.toml (which is also licensed under BSD)
"numpy==1.17.3; python_version=='3.6' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64' and platform_python_implementation != 'PyPy'",
"numpy==1.17.3; python_version=='3.7' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64' and platform_python_implementation != 'PyPy'",
"numpy==1.18.3; python_version=='3.8' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64' and platform_python_implementation != 'PyPy'",
"numpy==1.19.3; python_version=='3.9' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_python_implementation != 'PyPy'",
"numpy==1.21.4; python_version=='3.10' and platform_python_implementation != 'PyPy'",
# Aarch64(Python 3.9 requirements are the same as AMD64)
"numpy==1.19.2; python_version=='3.6' and platform_machine=='aarch64'",
"numpy==1.19.2; python_version=='3.7' and platform_machine=='aarch64'",
"numpy==1.19.2; python_version=='3.8' and platform_machine=='aarch64'",
# Darwin Arm64
"numpy>=1.20.0; python_version=='3.8' and platform_machine=='arm64' and platform_system=='Darwin'",
"numpy>=1.20.0; python_version=='3.9' and platform_machine=='arm64' and platform_system=='Darwin'",
# For Python versions which aren't yet officially supported,
# we specify an unpinned NumPy which allows source distributions
# to be used and allows wheels to be used as soon as they
# become available.
"numpy; python_version>='3.11'",
"numpy; python_version>='3.8' and platform_python_implementation=='PyPy'",
"oldest-supported-numpy"
]
build-backend = "setuptools.build_meta"

2
python/pytrexio/_version.py
View File

@ -1 +1 @@
__version__ = "1.3.0"
__version__ = "2.5.0"

2
python/requirements.txt
View File

@ -1,4 +1,4 @@
setuptools>=42
pkgconfig
numpy<1.23.0
numpy<1.27.0
numpy>=1.17.3

53
python/setup.py
View File

@ -40,7 +40,7 @@ if numpy_isUndefined and not do_sdist:
rootpath = os.path.dirname(os.path.abspath(__file__))
srcpath = os.path.join(rootpath, 'src')
c_files = ['trexio.c', 'trexio_hdf5.c', 'trexio_text.c', 'pytrexio_wrap.c']
c_files = ['trexio.c', 'trexio_text.c']
with open("README.md", "r") as fh:
@ -61,12 +61,15 @@ if not version_r:
# The block below is needed to derive additional flags related to the HDF5 library,
# which is required to build pytrexio extension module during the setup.py execution
h5_present = False
h5_ldflags_withl = os.environ.get("H5_LDFLAGS", None)
h5_cflags_withI = os.environ.get("H5_CFLAGS", None)
h5_ldflags_isUndefined = h5_ldflags_withl is None or h5_ldflags_withl==""
h5_cflags_isUndefined = h5_cflags_withI is None or h5_cflags_withI==""
h5_present = (not h5_ldflags_isUndefined) & (not h5_cflags_isUndefined)
if (h5_ldflags_isUndefined or h5_cflags_isUndefined) and not do_sdist:
try:
@ -76,31 +79,51 @@ if (h5_ldflags_isUndefined or h5_cflags_isUndefined) and not do_sdist:
try:
assert pk.exists('hdf5')
h5_present = True
except AssertionError:
raise Exception("pkg-config could not locate HDF5")
print("pkg-config could not locate HDF5; installing TREXIO with TEXT back-end only!")
h5_cflags_withI = pk.cflags('hdf5')
h5_ldflags_withl = pk.libs('hdf5')
if h5_present:
h5_cflags_withI = pk.cflags('hdf5')
h5_ldflags_withl = pk.libs('hdf5')
h5_cflags = h5_cflags_withI.replace("-I","").split(" ")[0] if not do_sdist else ""
h5_ldflags = h5_ldflags_withl.split(" ")[0] if not do_sdist else ""
if h5_present:
h5_cflags = h5_cflags_withI.replace("-I","").split(" ")[0] if not do_sdist else ""
h5_ldflags = h5_ldflags_withl.split(" ")[0] if not do_sdist else ""
c_files.append('trexio_hdf5.c')
# ============================ End of the HDF5 block ============================ #
# Define pytrexio extension module based on TREXIO source codes + SWIG-generated wrapper
pytrexio_module = Extension('pytrexio._pytrexio',
c_files.append('pytrexio_wrap.c')
compile_args = [
'-std=c99',
'-Wno-discarded-qualifiers',
'-Wno-unused-variable',
'-Wno-unused-but-set-variable'
]
# if config.h is present then we are building via Autotools
if os.path.isfile(os.path.join(srcpath, "config.h")):
compile_args.append('-DHAVE_CONFIG_H')
# explicit hack needed when building from sdist tarball
if h5_present:
compile_args.append('-DHAVE_HDF5')
# define C extension module
if h5_present:
pytrexio_module = Extension('pytrexio._pytrexio',
sources = [os.path.join(srcpath, code) for code in c_files],
include_dirs = [h5_cflags, srcpath, numpy_includedir],
libraries = ['hdf5', 'hdf5_hl'],
extra_compile_args = [
'-std=c99',
'-Wno-discarded-qualifiers',
'-Wno-unused-variable',
'-Wno-unused-but-set-variable'
],
libraries = ['hdf5' ],
extra_compile_args = compile_args,
extra_link_args = [h5_ldflags]
)
else:
pytrexio_module = Extension('pytrexio._pytrexio',
sources = [os.path.join(srcpath, code) for code in c_files],
include_dirs = [srcpath, numpy_includedir],
extra_compile_args = compile_args
)
setup(name = 'trexio',

17
python/test/conftest.py Normal file
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@ -0,0 +1,17 @@
# content of conftest.py
import pytest
def pytest_addoption(parser):
parser.addoption(
"--all", action="store_true", help="Run all back-ends"
)
def pytest_generate_tests(metafunc):
if "backend" in metafunc.fixturenames:
if metafunc.config.getoption("all"):
backends = ['hdf5', 'text']
else:
backends = ['text']
metafunc.parametrize("backend", backends)

113
python/test/test_api.py
View File

@ -6,19 +6,22 @@ import trexio
from benzene_data import *
FILENAME = 'test_file_py.h5'
BACK_END = trexio.TREXIO_HDF5
def clean():
def clean(back_end, filename):
"""Remove test files."""
import os
try:
os.remove(FILENAME)
os.remove('unsafe_' + FILENAME)
except FileNotFoundError:
pass
if back_end == trexio.TREXIO_HDF5:
import os
try:
os.remove(filename)
os.remove('unsafe_' + filename)
except FileNotFoundError:
pass
else:
import shutil
try:
shutil.rmtree(filename)
shutil.rmtree('unsafe_' + filename)
except FileNotFoundError:
pass
def test_info():
@ -29,7 +32,7 @@ def test_info():
def test_void():
"""Check raise of an error upon I/O on non-existing file."""
with pytest.raises(trexio.Error):
_ = trexio.File('void.file', 'r', BACK_END)
_ = trexio.File('void.file', 'r', trexio.TREXIO_TEXT)
def test_orbital_list():
@ -53,20 +56,30 @@ def test_bitfield_list():
class TestIO:
"""Unit tests for writing/reading different blocks of the TREXIO file."""
filename = FILENAME
back_end = BACK_END
mode = 'w'
test_file = None
clean()
@pytest.fixture(autouse=True)
def setup(self, backend):
self.mode = 'w'
self.test_file = None
if backend == 'hdf5':
self.back_end = trexio.TREXIO_HDF5
self.filename = 'test_file_py.h5'
elif backend == 'text':
self.back_end = trexio.TREXIO_TEXT
self.filename = 'test_file_py.dir'
else:
raise ValueError("Wrong TREXIO back-end supplied to pytest.")
def __del__(self):
if self.test_file:
if self.test_file.isOpen:
self.test_file.close()
def test_clean(self):
"""Clean existing files."""
clean(self.back_end, self.filename)
#def __del__(self):
# """Class destructor."""
# if self.test_file:
# if self.test_file.isOpen:
# self.test_file.close()
def open(self, filename=None, mode=None, back_end=None):
"""Create a TREXIO file and open it for writing."""
if not filename:
@ -107,12 +120,17 @@ class TestIO:
with pytest.raises(trexio.Error):
trexio.write_nucleus_num(self.test_file, nucleus_num * 2)
if self.test_file.isOpen:
self.test_file.close()
def test_num(self):
"""Write a number."""
self.open()
trexio.write_nucleus_num(self.test_file, nucleus_num)
assert trexio.has_nucleus_num(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_str(self):
@ -120,6 +138,8 @@ class TestIO:
self.open()
trexio.write_nucleus_point_group(self.test_file, point_group)
assert trexio.has_nucleus_point_group(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_array_str(self):
@ -129,6 +149,8 @@ class TestIO:
self.test_num()
trexio.write_nucleus_label(self.test_file, nucleus_label)
assert trexio.has_nucleus_label(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_array_1D(self):
@ -138,6 +160,8 @@ class TestIO:
self.test_num()
trexio.write_nucleus_charge(self.test_file, nucleus_charge)
assert trexio.has_nucleus_charge(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_array_2D(self):
@ -147,6 +171,8 @@ class TestIO:
self.test_num()
trexio.write_nucleus_coord(self.test_file, nucleus_coord)
assert trexio.has_nucleus_coord(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_indices(self):
@ -159,6 +185,8 @@ class TestIO:
# now write the indices
trexio.write_basis_nucleus_index(self.test_file, indices_np)
assert trexio.has_basis_nucleus_index(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_sparse(self):
@ -170,6 +198,8 @@ class TestIO:
offset = 0
trexio.write_ao_2e_int_eri(self.test_file, offset, num_integrals, indices, values)
assert trexio.has_ao_2e_int_eri(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_determinant(self):
@ -189,31 +219,39 @@ class TestIO:
assert trexio.has_determinant_coefficient(self.test_file)
# manually check the consistency between coefficient_size and number of determinants
assert trexio.read_determinant_coefficient_size(self.test_file) == trexio.read_determinant_num(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_delete_group(self):
"""Delete a group."""
self.open(filename='unsafe_' + self.filename, mode='u', back_end=self.back_end)
self.test_num()
self.test_array_1D()
self.test_array_2D()
trexio.write_nucleus_num(self.test_file, nucleus_num)
trexio.write_nucleus_charge(self.test_file, nucleus_charge)
trexio.flush(self.test_file)
assert trexio.has_nucleus_num(self.test_file)
assert trexio.has_nucleus_charge(self.test_file)
assert trexio.has_nucleus(self.test_file)
trexio.delete_nucleus(self.test_file)
assert not trexio.has_nucleus_num(self.test_file)
assert not trexio.has_nucleus_charge(self.test_file)
assert not trexio.has_nucleus_coord(self.test_file)
assert not trexio.has_nucleus(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_has_group(self):
"""Check existense of a group."""
self.open()
assert trexio.has_nucleus(self.test_file)
assert not trexio.has_rdm(self.test_file)
if self.test_file.isOpen:
self.test_file.close()
def test_context_manager(self):
@ -231,6 +269,8 @@ class TestIO:
self.open(mode='r')
num_r = trexio.read_nucleus_num(self.test_file)
assert num_r == nucleus_num
if self.test_file.isOpen:
self.test_file.close()
def test_read_array_1D(self):
@ -240,6 +280,8 @@ class TestIO:
assert charges_np_r.dtype is np.dtype(np.float64)
assert charges_np_r.size == nucleus_num
np.testing.assert_array_almost_equal(charges_np_r, np.array(nucleus_charge), decimal=8)
if self.test_file.isOpen:
self.test_file.close()
def test_read_array_2D(self):
@ -250,6 +292,8 @@ class TestIO:
assert coords_np.dtype is np.dtype(np.float64)
assert coords_np.size == nucleus_num * 3
np.testing.assert_array_almost_equal(coords_np, np.array(nucleus_coord).reshape(nucleus_num,3), decimal=8)
if self.test_file.isOpen:
self.test_file.close()
def test_read_errors(self):
@ -258,6 +302,8 @@ class TestIO:
# unsafe call to read_safe should fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM
with pytest.raises(trexio.Error):
_ = trexio.read_nucleus_charge(self.test_file, dim=nucleus_num/2)
if self.test_file.isOpen:
self.test_file.close()
def test_read_integers(self):
@ -276,7 +322,8 @@ class TestIO:
assert indices_np_64.dtype is np.dtype(np.int64)
assert indices_np_64.size == basis_shell_num
assert (indices_np_64 == np.array(nucleus_index)).all()
if self.test_file.isOpen:
self.test_file.close()
def test_sparse_read(self):
"""Read a sparse array."""
@ -300,7 +347,8 @@ class TestIO:
assert read_buf_size == (num_integrals - buf_size)
assert indices_sparse_np[0][0] == offset_file * 4
assert indices_sparse_np[read_buf_size-1][3] == (offset_file + read_buf_size) * 4 - 1
if self.test_file.isOpen:
self.test_file.close()
def test_determinant_read(self):
"""Read the CI determinants."""
@ -320,7 +368,8 @@ class TestIO:
#print(f'First complete read of determinant coefficients: {read_buf_size}')
assert not eof
assert read_buf_size == buf_size
if self.test_file.isOpen:
self.test_file.close()
def test_array_str_read(self):
"""Read an array of strings."""
@ -328,6 +377,8 @@ class TestIO:
labels_r = trexio.read_nucleus_label(self.test_file)
assert len(labels_r) == nucleus_num
assert labels_r == nucleus_label
if self.test_file.isOpen:
self.test_file.close()
def test_str_read(self):
@ -335,3 +386,5 @@ class TestIO:
self.open(mode='r')
point_group_r = trexio.read_nucleus_point_group(self.test_file)
assert point_group_r == point_group
if self.test_file.isOpen:
self.test_file.close()

5
rust/trexio/.gitignore vendored Normal file
View File

@ -0,0 +1,5 @@
Cargo.lock
src/generated.rs
target/
wrapper.h

26
rust/trexio/Cargo.toml Normal file
View File

@ -0,0 +1,26 @@
[package]
name = "trexio"
version = "2.5.0"
edition = "2021"
license = "BSD-3-Clause"
authors = ["Anthony Scemama <scemama@irsamc.ups-tlse.fr>", "Evgeny Posenitskiy"]
description = "TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements."
repository = "https://github.com/trex-coe/trexio"
keywords = ["quantum", "chemistry"]
readme = "README.md"
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
[build-dependencies]
bindgen = "0.65.1"
serde_json = "1.0"
serde = { version = "1.0", features = ["derive"] }
reqwest = { version = "0.11", features = ["blocking", "rustls-tls"] }
tar = "0.4"
flate2 = "1.0"
[lib]
doctest = false
[dependencies]
hdf5 = "0.8.1"

10
rust/trexio/Makefile Normal file
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@ -0,0 +1,10 @@
default: src/generated.rs
cargo build
cargo test
src/generated.rs: build.py
python3 build.py
test: default
- cargo test -- --show-output

42
rust/trexio/README.md Normal file
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@ -0,0 +1,42 @@
# TREXIO
<img src="https://trex-coe.eu/sites/default/files/styles/responsive_no_crop/public/2022-01/TREXIO%20Code.png" width=200>
TREXIO is an open-source file format and library developed for the storage and
manipulation of data produced by quantum chemistry calculations. It is designed
with the goal of providing a reliable and efficient method of storing and
exchanging wave function parameters and matrix elements.
This crate is the Rust binding for the TREXIO C library:
![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)
## Documentation
[TREXIO Documentation.](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)

729
rust/trexio/build.rs Normal file
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@ -0,0 +1,729 @@
extern crate reqwest;
extern crate tar;
extern crate flate2;
const WRAPPER_H: &str = "wrapper.h";
const GENERATED_RS: &str = "generated.rs";
use std::env;
use std::path::PathBuf;
use std::collections::HashMap;
use std::fs::File;
use std::io::{self, BufRead, BufReader, Write};
use serde_json::Value;
use flate2::read::GzDecoder;
use tar::Archive;
fn download_trexio() -> PathBuf {
let version = env::var("CARGO_PKG_VERSION").unwrap();
println!("Version : {}", version);
let out_path = PathBuf::from(env::var("OUT_DIR").unwrap());
let trexio_url = format!("https://github.com/TREX-CoE/trexio/releases/download/v{version}/trexio-{version}.tar.gz");
// Download the .tar.gz archive
let tar_gz = out_path.join("trexio.tar.gz");
let trexio_dir= out_path.join("trexio_dir");
let mut resp = reqwest::blocking::get(trexio_url).expect("Failed to download the archive");
let mut out = File::create(tar_gz.clone()).expect("Failed to create archive file");
std::io::copy(&mut resp, &mut out).expect("Failed to copy content");
// Unpack the .tar.gz archive
let tar_gz = File::open(tar_gz).unwrap();
let tar = GzDecoder::new(tar_gz);
let mut archive = Archive::new(tar);
archive.unpack(trexio_dir.clone()).expect("Failed to unpack");
// Assume that the archive extracts to a directory named 'trexio-0.1.0'
trexio_dir.join(format!("trexio-{}", version))
}
fn install_trexio(trexio_dir: &PathBuf) -> PathBuf {
println!("{}", trexio_dir.display());
let out_path = PathBuf::from(env::var("OUT_DIR").unwrap());
let install_path = out_path.join("trexio_install");
// Run configure script
let configure_status = std::process::Command::new("./configure")
.arg(format!("--prefix={}",install_path.display()))
.arg("--without-fortran")
.current_dir(&trexio_dir)
.status()
.unwrap();
assert!(configure_status.success());
// Run make
let make_status = std::process::Command::new("make")
.arg("install")
.current_dir(&trexio_dir)
.status()
.unwrap();
assert!(make_status.success());
install_path
}
/// This function reads from `trexio.h`, extracts the exit codes and backends, and writes them to `wrapper.h`.
fn make_interface(trexio_h: &PathBuf) -> io::Result<()> {
let mut err = HashMap::new();
let mut be = HashMap::new();
let trexio_file = File::open(trexio_h)?;
let trexio_reader = BufReader::new(trexio_file);
for line in trexio_reader.lines() {
let line = line?;
let buf = line.trim_start();
if buf.starts_with("#define TREXIO_") && buf.contains("(trexio_exit_code)") {
let buf2 = buf.replace(")", "");
let buf2 = buf2.replace("(", "");
let buf2: Vec<&str> = buf2.split_whitespace().collect();
err.insert(buf2[1].to_string(), buf2[3].trim().parse::<i32>().unwrap());
}
if buf.starts_with("#define TREXIO_") && buf.contains("(back_end_t)") {
let buf2 = buf.replace(")", "");
let buf2 = buf2.replace("(", "");
let buf2: Vec<&str> = buf2.split_whitespace().collect();
be.insert(buf2[1].to_string(), buf2[3].trim().parse::<i32>().unwrap());
}
}
let out_path = PathBuf::from(env::var("OUT_DIR").unwrap());
let wrapper_h = out_path.join(WRAPPER_H);
let mut wrapper_file = File::create(wrapper_h)?;
write!(&mut wrapper_file, "#include <trexio.h>\n")?;
for (k, v) in &err {
write!(&mut wrapper_file, "#undef {}\n", k)?;
write!(&mut wrapper_file, "const trexio_exit_code {} = {};\n", k, v)?;
}
for (k, v) in &be {
write!(&mut wrapper_file, "#undef {}\n", k)?;
write!(&mut wrapper_file, "const back_end_t {} = {};\n", k, v)?;
}
write!(&mut wrapper_file, "#undef TREXIO_AUTO\n")?;
write!(&mut wrapper_file, "const back_end_t TREXIO_AUTO = TREXIO_INVALID_BACK_END;\n")?;
Ok(())
}
/// Type conversions for Rust API
fn convert_r(typ: &str) -> String {
match typ {
"int" => "i64",
"int special" => "usize",
"float" | "float sparse" | "float buffered" => "f64",
"dim" | "dim readonly" | "index" => "usize",
"str" => "str",
_ => panic!("Unknown type to convert: {}", typ)
}.to_string()
}
/// Type conversion to call C functions
fn convert_c(typ: &str) -> String {
match typ {
"int" | "int special" | "dim" | "dim readonly" | "index" => "i64",
"float" | "float sparse" | "float buffered" => "f64",
"str" => "str",
_ => panic!("Unknown type to convert: {}", typ)
}.to_string()
}
/// Generate has-functions for checking the existence of groups and elements in a TREXIO file.
///
/// # Parameters
/// * `data` - The JSON-like data containing the groups and elements.
///
/// # Returns
/// A `Vec<String>` containing the generated Rust code as strings.
fn make_has_functions(data: &Value) -> Vec<String> {
let mut r = Vec::new();
if let Value::Object(groups) = data {
for (group, elements) in groups.iter() {
let group_l = group.to_lowercase();
let has_group_func = format!(
"/// Checks if the group `{group}` exists in the file.
/// # Parameters
///
/// None
///
/// # Returns
///
/// * `Result<bool, ExitCode>` - Returns `Ok(true)` if the element exists in the file,
/// otherwise returns `Ok(false)`. An error during the execution results in `Err(ExitCode)`.
pub fn has_{group_l}(&self) -> Result<bool, ExitCode> {{
let rc = unsafe {{ c::trexio_has_{group}(self.ptr) }};
match rc {{
c::TREXIO_SUCCESS => Ok(true),
c::TREXIO_HAS_NOT => Ok(false),
x => Err(ExitCode::from(x)),
}}
}}");
r.push(has_group_func);
if let Value::Object(elements_map) = elements {
for (element, _types_value) in elements_map.iter() {
let element_l = element.to_lowercase();
let has_element_func = format!(
"/// Checks if the element `{element}` of the group `{group}` exists in the file.
///
/// # Parameters
///
/// None
///
/// # Returns
///
/// * `Result<bool, ExitCode>` - Returns `Ok(true)` if the element exists in the file,
/// otherwise returns `Ok(false)`. An error during the execution results in `Err(ExitCode)`.
pub fn has_{group_l}_{element_l}(&self) -> Result<bool, ExitCode> {{
let rc = unsafe {{ c::trexio_has_{group}_{element}(self.ptr) }};
match rc {{
c::TREXIO_SUCCESS => Ok(true),
c::TREXIO_HAS_NOT => Ok(false),
x => Err(ExitCode::from(x)),
}}
}}");
r.push(has_element_func);
}
}
}
}
r
}
fn make_scalar_functions(data: &serde_json::Value) -> Vec<String> {
let mut r: Vec<String> = Vec::new();
for group in data.as_object().unwrap().keys() {
let group_l = group.to_lowercase();
for (element, attributes) in data[group].as_object().unwrap() {
let typ = attributes[0].as_str().unwrap();
let type_c = convert_c(typ);
let type_r = convert_r(typ);
let element_l = element.to_lowercase();
if attributes[1].as_array().unwrap().is_empty() {
match typ {
"int" | "float" | "dim" | "index" => {
let s = format!(r#"
/// Reads the scalar element `{element}` from the group `{group}` in the file.
///
/// # Parameters
///
/// None
///
/// # Returns
///
/// * `Result<{type_r}, ExitCode>` - Returns the scalar element as a `{type_r}` upon successful
/// operation. If the operation fails, it returns `Err(ExitCode)`.
pub fn read_{group_l}_{element_l}(&self) -> Result<{type_r}, ExitCode> {{
let mut data_c: {type_c} = 0{type_c};
let (rc, data) = unsafe {{
let rc = c::trexio_read_{group}_{element}_64(self.ptr, &mut data_c);
(rc, data_c.try_into().expect("try_into failed in read_{group_l}_{element_l}"))
}};
rc_return(data, rc)
}}
/// Writes the scalar element `{element}` into the group `{group}` in the file.
///
/// # Parameters
///
/// * `data: {type_r}` - A `{type_r}` scalar element that will be written into `{element}` in the group `{group}`.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` upon successful operation, otherwise returns `Err(ExitCode)`.
pub fn write_{group_l}_{element_l}(&self, data: {type_r}) -> Result<(), ExitCode> {{
let data: {type_c} = data.try_into().expect("try_into failed in write_{group_l}_{element_l}");
let rc = unsafe {{ c::trexio_write_{group}_{element}_64(self.ptr, data) }};
rc_return((), rc)
}}
"#);
r.push(s);
},
"str" => {
let s = format!(r#"
/// Reads the string attribute `{element}` contained in the group `{group}`.
/// # Parameters
///
/// * `capacity: usize` - The maximum buffer size allocated for the string to be read.
///
/// # Returns
///
/// * `Result<String, ExitCode>` - Returns the attribute as a `String` upon successful operation.
/// If the operation fails, it returns `Err(ExitCode)`.
pub fn read_{group_l}_{element_l}(&self, capacity: usize) -> Result<String, ExitCode> {{
let data_c = CString::new(vec![ b' ' ; capacity]).expect("CString::new failed");
let (rc, data) = unsafe {{
let data_c = data_c.into_raw() as *mut c_char;
let rc = c::trexio_read_{group}_{element}(self.ptr, data_c, capacity.try_into().expect("try_into failed in read_{group_l}_{element_l}"));
(rc, CString::from_raw(data_c))
}};
let result : String = CString::into_string(data).expect("into_string failed in read_{group_l}_{element_l}");
rc_return(result, rc)
}}
/// Writes the string attribute `{element}` into the group `{group}`.
///
/// # Parameters
///
/// * `data: &str` - The string attribute that will be written into the `{element}` field in the `{group}` group.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` upon successful operation.
/// If the operation fails, it returns `Err(ExitCode)`.
pub fn write_{group_l}_{element_l}(&self, data: &str) -> Result<(), ExitCode> {{
let size : i32 = data.len().try_into().expect("try_into failed in write_{group_l}_{element_l}");
let data = string_to_c(data);
let data = data.as_ptr() as *const c_char;
let rc = unsafe {{ c::trexio_write_{group}_{element}(self.ptr, data, size) }};
rc_return((), rc)
}}
"#);
r.push(s);
},
"dim readonly" => {
let s = format!(r#"
/// Reads the dimensioning variable `{element}` from the group `{group}`.
///
/// # Parameters
///
/// None.
///
/// # Returns
///
/// * `Result<{type_r}, ExitCode>` - Returns the dimensioning variable `{element}` of type `{type_r}`
/// upon successful operation. If the operation fails, it returns `Err(ExitCode)`.
pub fn read_{group_l}_{element_l}(&self) -> Result<{type_r}, ExitCode> {{
let mut data_c: {type_c} = 0{type_c};
let (rc, data) = unsafe {{
let rc = c::trexio_read_{group}_{element}_64(self.ptr, &mut data_c);
(rc, data_c.try_into().expect("try_into failed in read_{group_l}_{element_l}"))
}};
rc_return(data, rc)
}}
"#);
r.push(s);
},
_ => {}
}
}
}
}
r
}
fn make_array_functions(data: &serde_json::Value) -> Vec<String> {
let mut r: Vec<String> = Vec::new();
for group in data.as_object().unwrap().keys() {
let group_l = group.to_lowercase();
for (element, attributes) in data[group].as_object().unwrap() {
let typ = attributes[0].as_str().unwrap();
let type_c = convert_c(typ);
let type_r = convert_r(typ);
let element_l = element.to_lowercase();
let dimensions = attributes[1].as_array().unwrap();
let dimensions: Vec<&str> = dimensions.iter().map(|x| x.as_str().unwrap()).collect();
let dimensions_str = format!("{:?}", dimensions).replace("\"","");
if ! dimensions.is_empty() {
match typ {
"int" | "float" | "dim" | "index" => {
r.push(format!(r#"
/// Reads the `{element}` array from the group `{group}` in the file.
///
/// # Dimensions
///
/// The array is of dimension `{dimensions_str}`.
///
/// # Returns
///
/// * `Result<Vec<{type_r}>, ExitCode>` - Returns a flattened one-dimensional vector that contains
/// the elements of the `{element}` array. If the operation is unsuccessful, it returns `Err(ExitCode)`.
///
///"#));
if dimensions.len() > 1 {
r.push(format!(r#"
/// # Example
///
/// To reshape the one-dimensional vector back into a two-dimensional array, you can use the [`chunks`] method:
///
/// ```text
/// let one_d_array = trexio_file.read_{}_{}()?;"#, group_l, element_l));
if let Some(dim) = dimensions.first() {
if dim.contains('.') {
let parts: Vec<&str> = dim.split('.').collect();
r.push(format!("/// let {}_{} = trexio_file.read_{}_{}()?;", parts[0], parts[1], parts[0], parts[1]));
r.push(format!("/// let two_d_array: Vec<_> = one_d_array.chunks({}_{}).collect();", parts[0], parts[1]));
} else {
r.push(format!("/// let two_d_array: Vec<_> = one_d_array.chunks({}).collect();", dim));
}
}
r.push(String::from("/// ```"));
r.push(String::from("///\n/// [`chunks`]: slice::chunks"));
}
r.push(format!(r#"pub fn read_{}_{}(&self) -> Result<Vec<{}>, ExitCode> {{
let mut size = 1;"#, group_l, element_l, type_r));
for dim in &dimensions {
if dim.contains('.') {
let parts: Vec<&str> = dim.split('.').collect();
r.push(format!(" size *= self.read_{}_{}()?;", parts[0], parts[1]));
} else {
r.push(format!(" size *= {};", dim));
}
}
r.push(format!(r#" let mut data: Vec<{type_r}> = Vec::with_capacity(size);
let rc = unsafe {{
let data_c = data.as_mut_ptr() as *mut {type_c};
let rc = c::trexio_read_safe_{group}_{element}_64(self.ptr, data_c, size.try_into().expect("try_into failed in read_{group}_{element} (size)"));
data.set_len(size);
rc
}};
rc_return(data, rc)
}}"#));
r.push(format!(r#"
/// Writes the `{element}` array into the group `{group}` in the file.
///
/// # Parameters
///
/// * `data: &[{type_r}]` - A one-dimensional vector that contains the elements of the `{element}` array
/// to be written into the file. The vector should be flattened from a two-dimensional array with
/// dimensions `{dimensions_str}`.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` if the operation is successful,
/// otherwise returns `Err(ExitCode)`.""", """\
pub fn write_{group_l}_{element_l}(&self, data: &[{type_r}]) -> Result<(), ExitCode> {{
let size: i64 = data.len().try_into().expect("try_into failed in write_{group_l}_{element_l}");
let data = data.as_ptr() as *const {type_c};
let rc = unsafe {{ c::trexio_write_safe_{group}_{element}_64(self.ptr, data, size) }};
rc_return((), rc)
}}
"#));
}
,
"str" => {
r.push(format!(r#"
/// Reads the `{element}` array from the group `{group}` in the file.
///
/// # Dimensions
///
/// The array is of dimension `{dimensions_str}`.
///
/// # Returns
///
/// * `Result<Vec<{type_r}>, ExitCode>` - Returns a flattened one-dimensional vector that contains
/// the elements of the `{element}` array. If the operation is unsuccessful, it returns `Err(ExitCode)`.
///
/// "#));
if dimensions.len() > 1 {
r.push(format!(r#"/// # Example
///
/// To reshape the one-dimensional vector back into a two-dimensional array, you can use the [`chunks`] method:
///
/// ```text
/// let one_d_array = trexio_file.read_{}_{}()?;"#, group_l, element_l));
if let Some(dim) = dimensions.first() {
if dim.contains('.') {
let parts: Vec<&str> = dim.split('.').collect();
r.push(format!("/// let {}_{} = trexio_file.read_{}_{}()?;", parts[0], parts[1], parts[0], parts[1]));
r.push(format!("/// let two_d_array: Vec<_> = one_d_array.chunks({}_{}).collect();", parts[0], parts[1]));
} else {
r.push(format!("/// let two_d_array: Vec<_> = one_d_array.chunks({}).collect();", dim));
}
}
r.push(String::from("/// ```"));
r.push(String::from("///\n/// [`chunks`]: slice::chunks"));
}
r.push(format!(r#"pub fn read_{}_{}(&self, capacity: usize) -> Result<Vec<String>, ExitCode> {{
let mut size = 1;"#, group_l, element_l));
for dim in &dimensions {
if dim.contains('.') {
let parts: Vec<&str> = dim.split('.').collect();
r.push(format!(" size *= self.read_{}_{}()?;", parts[0], parts[1]));
} else {
r.push(format!(" size *= {};", dim));
}
}
r.push(format!(r#" // Allocate an array of *mut i8 pointers (initialized to null)
let mut dset_out: Vec<*mut i8> = vec![std::ptr::null_mut(); size];
// Allocate C-style strings and populate dset_out
for item in dset_out.iter_mut().take(size) {{
let c_str: *mut i8 = unsafe {{ std::alloc::alloc_zeroed(std::alloc::Layout::array::<i8>(capacity).unwrap()) as *mut i8 }};
if c_str.is_null() {{
return Err(ExitCode::AllocationFailed);
}}
*item = c_str;
}}
let rc = unsafe {{
c::trexio_read_{group}_{element}(self.ptr, dset_out.as_mut_ptr(), capacity.try_into().expect("try_into failed in read_{group}_{element} (capacity)") )
}};
// Convert the populated C strings to Rust Strings
let mut rust_strings = Vec::new();
for &c_str in &dset_out {{
let rust_str = unsafe {{
std::ffi::CStr::from_ptr(c_str)
.to_string_lossy()
.into_owned()
}};
rust_strings.push(rust_str);
}}
// Clean up allocated C strings
for &c_str in &dset_out {{
unsafe {{ std::alloc::dealloc(c_str as *mut u8, std::alloc::Layout::array::<i8>(capacity).unwrap()) }};
}}
rc_return(rust_strings, rc)
}}
/// Writes the `{element}` array into the group `{group}` in the file.
///
/// # Parameters
///
/// * `data: &[{type_r}]` - A one-dimensional vector that contains the elements of the `{element}` array
/// to be written into the file. The vector should be flattened from a two-dimensional array with
/// dimensions `{dimensions_str}`.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` if the operation is successful,
/// otherwise returns `Err(ExitCode)`.
pub fn write_{group_l}_{element_l}(&self, data: &[&str]) -> Result<(), ExitCode> {{
let mut size = 0;
// Find longest string
for s in data {{
let l = s.len();
size = if l>size {{l}} else {{size}};
}}
size += 1;
let data_c : Vec<CString> = data.iter().map(|&x| string_to_c(x)).collect::<Vec<_>>();
let data_c : Vec<*const c_char> = data_c.iter().map(|x| x.as_ptr() as *const c_char).collect::<Vec<_>>();
let size : i32 = size.try_into().expect("try_into failed in write_{group}_{element} (size)");
let data_c = data_c.as_ptr() as *mut *const c_char;
let rc = unsafe {{ c::trexio_write_{group}_{element}(self.ptr, data_c, size) }};
rc_return((), rc)
}}
"#));
},
"float sparse" => {
let size = dimensions.len();
let typ = [ "(", (vec![ "usize" ; size ]).join(", ").as_str(),", f64)"].join("");
r.push(format!(r#"
/// Reads a buffer of {element} from group {group}.
///
/// # Parameters
///
/// * `offset: usize` - The starting point in the array from which data will be read.
/// * `buffer_size: usize` - The size of the buffer in which read data will be stored.
///
/// # Returns
///
/// * `Result<Vec<{typ}>, ExitCode>` - Returns a vector of tuples containing
/// the indices and the value of the element. The vector has a length of at most `buffer_size`.
///
/// # Notes
///
/// The reading process is a buffered operation, meaning that only a segment of the full array
/// is read into the memory.
pub fn read_{group_l}_{element_l}(&self, offset: usize, buffer_size:usize) -> Result<Vec<{typ}>, ExitCode> {{
let mut idx = Vec::<i32>::with_capacity({size}*buffer_size);
let mut val = Vec::<f64>::with_capacity(buffer_size);
let idx_ptr = idx.as_ptr() as *mut i32;
let val_ptr = val.as_ptr() as *mut f64;
let offset: i64 = offset.try_into().expect("try_into failed in read_{group}_{element} (offset)");
let mut buffer_size_read: i64 = buffer_size.try_into().expect("try_into failed in read_{group}_{element} (buffer_size)");
let rc = unsafe {{ c::trexio_read_safe_{group}_{element}(self.ptr,
offset, &mut buffer_size_read, idx_ptr, buffer_size_read, val_ptr, buffer_size_read)
}};
let rc = match ExitCode::from(rc) {{
ExitCode::End => ExitCode::to_c(&ExitCode::Success),
_ => rc
}};
let buffer_size_read: usize = buffer_size_read.try_into().expect("try_into failed in read_{group}_{element} (buffer_size)");
unsafe {{ idx.set_len({size}*buffer_size_read) }};
unsafe {{ val.set_len(buffer_size_read) }};
let idx: Vec::<&[i32]> = idx.chunks({size}).collect();
let mut result = Vec::<{typ}>::with_capacity(buffer_size);
for (i, v) in zip(idx, val) {{
result.push( ("#));
let mut x = Vec::new();
for k in 0..size {
x.push(format!("i[{k}].try_into().unwrap()"))
};
x.push("v));\n }\n rc_return(result, rc)\n}".to_string());
r.push(x.join(", "));
r.push(format!(r#"/// Writes a buffer of {element} from group {group}.
///
/// # Parameters
///
/// * `offset: usize` - The starting point in the array at which data will be written.
/// * `data: &[{typ}]` - A slice of tuples containing the indices and the value of the element.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` if the writing operation is successful,
/// otherwise returns `Err(ExitCode)`.
///
/// # Notes
///
/// The writing process is a buffered operation, meaning that only a segment of the full array
/// is written into the file.
pub fn write_{group_l}_{element_l}(&self, offset: usize, data: &[{typ}]) -> Result<(), ExitCode> {{
let mut idx = Vec::<i32>::with_capacity({size}*data.len());
let mut val = Vec::<f64>::with_capacity(data.len());
for d in data {{ "#));
let mut x = Vec::new();
for k in 0..size {
x.push(format!(" idx.push(d.{k}.try_into().unwrap());"))
};
r.push(x.join("\n"));
r.push(format!(r#"
val.push(d.{size});
}}
let size_max: i64 = data.len().try_into().expect("try_into failed in write_{group}_{element} (size_max)");
let buffer_size = size_max;
let idx_ptr = idx.as_ptr() as *const i32;
let val_ptr = val.as_ptr() as *const f64;
let offset: i64 = offset.try_into().expect("try_into failed in write_{group}_{element} (offset)");
let rc = unsafe {{ c::trexio_write_safe_{group}_{element}(self.ptr,
offset, buffer_size, idx_ptr, size_max, val_ptr, size_max) }};
rc_return((), rc)
}}"#));
},
_ => {}
}
}
}
}
r
}
/// Reads the JSON file, processes its contents, and generates Rust functions according to the specifications in the JSON data.
fn make_functions(json_path: &PathBuf) -> std::io::Result<()> {
let file = File::open(json_path).unwrap();
let data: Value = serde_json::from_reader(file).unwrap();
let mut r: Vec<String> = vec![
String::from("
use std::ffi::CString;
use std::iter::zip;
/// This implementation block includes additional functions automatically generated from tables.
/// For more details, refer to [TREXIO tables documentation](https://trex-coe.github.io/trexio/trex.html).
impl File {
#![allow(clippy::unnecessary_cast)]
#![allow(clippy::useless_conversion)]
#![allow(clippy::type_complexity)]
"),
];
r.append(&mut make_has_functions(&data));
r.append(&mut make_scalar_functions(&data));
r.append(&mut make_array_functions(&data));
r.push(String::from("}"));
let out_path = PathBuf::from(env::var("OUT_DIR").unwrap());
let generated_rs = out_path.join(GENERATED_RS);
let mut f = File::create(&generated_rs)?;
f.write_all(r.join("\n").as_bytes())?;
Ok(())
}
fn main() {
let source_path = download_trexio();
println!("source path: {}", source_path.display());
let install_path = install_trexio(&source_path);
println!("install path: {}", install_path.display());
// Tell cargo to look for shared libraries in the specified directory
println!("cargo:rustc-link-search={}/lib", install_path.display());
// Tell cargo to tell rustc to link the system trexio shared library.
println!("cargo:rustc-link-lib=trexio");
let out_path = PathBuf::from(env::var("OUT_DIR").unwrap());
let trexio_h = install_path.join("include").join("trexio.h");
println!("trexio.h: {}", trexio_h.display());
make_interface(&trexio_h).unwrap();
// The bindgen::Builder is the main entry point
// to bindgen, and lets you build up options for
// the resulting bindings.
let wrapper_h = out_path.join(WRAPPER_H);
println!("wrapper.h: {}", wrapper_h.display());
let bindings = bindgen::Builder::default()
// The input header we would like to generate
// bindings for.
.header(wrapper_h.to_str().unwrap())
// Tell cargo to invalidate the built crate whenever any of the
// included header files changed.
.parse_callbacks(Box::new(bindgen::CargoCallbacks))
// Finish the builder and generate the bindings.
.generate()
// Unwrap the Result and panic on failure.
.expect("Unable to generate bindings");
// Write the bindings to the $OUT_DIR/bindings.rs file.
let bindings_path = out_path.join("bindings.rs");
println!("bindings.rs: {}", bindings_path.display());
bindings
.write_to_file(&bindings_path)
.expect("Couldn't write bindings!");
let json_path = source_path.join("trex.json");
println!("json path: {}", json_path.display());
make_functions(&json_path).unwrap();
}

35
rust/trexio/src/back_end.rs Normal file
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@ -0,0 +1,35 @@
use crate::c;
#[derive(Debug, PartialEq)]
pub enum BackEnd {
/// The TREXIO "file" is a directory with text files for each group.
/// A fallback when HDF5 is not available.
Text,
/// Should be used for production. The TREXIO file is a single HDF5 file.
Hdf5,
/// Automatic discovery of the appropriate backend
Auto,
}
impl BackEnd {
/// Creation from a C value
pub fn from(b: c::back_end_t) -> Self {
match b {
c::TREXIO_TEXT => Self::Text,
c::TREXIO_HDF5 => Self::Hdf5,
c::TREXIO_AUTO => Self::Auto,
_ => panic!("Invalid backend"),
}
}
/// Conversion to a C value
pub fn to_c(self) -> c::back_end_t {
match self {
Self::Text => c::TREXIO_TEXT,
Self::Hdf5 => c::TREXIO_HDF5,
Self::Auto => c::TREXIO_AUTO,
}
}
}

208
rust/trexio/src/bitfield.rs Normal file
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@ -0,0 +1,208 @@
#[derive(Debug, PartialEq)]
pub struct Bitfield {
data: Vec<i64>,
}
use crate::c;
use crate::ExitCode;
impl Bitfield {
/// Creates a new bitfield , using a number of i64 elements consistent
/// with the number of MOs in the TREXIO file.
pub fn from(n_int: usize, orb_list: &[usize]) -> (Self, f64) {
let orb_list: Vec<i32> = orb_list.iter().map(|&x| x as i32).collect();
let occ_num = orb_list
.len()
.try_into()
.expect("try_into failed in Bitfield::from");
let orb_list_ptr: *const i32 = orb_list.as_ptr();
let n_int32: i32 = n_int.try_into().expect("try_into failed in Bitfield::from");
let mut b = vec![0i64; n_int];
let bit_list = b.as_mut_ptr() as *mut c::bitfield_t;
std::mem::forget(b);
let rc = unsafe { c::trexio_to_bitfield_list(orb_list_ptr, occ_num, bit_list, n_int32) };
let data = unsafe { Vec::from_raw_parts(bit_list, n_int, n_int) };
let result = Bitfield { data };
match ExitCode::from(rc) {
ExitCode::Success => (result, 1.0),
ExitCode::PhaseChange => (result, -1.0),
x => panic!("TREXIO Error {}", x),
}
}
pub fn from_vec(v: &[i64]) -> Bitfield {
Bitfield { data: v.to_vec() }
}
pub fn from_alpha_beta(alpha: &Bitfield, beta: &Bitfield) -> Bitfield {
if alpha.data.len() != beta.data.len() {
panic!("alpha and beta parts have different lengths");
};
let mut data = alpha.data.clone();
data.extend_from_slice(&beta.data);
Bitfield { data }
}
/// Returns the alpha part
pub fn alpha(&self) -> Bitfield {
let n_int = self.data.len() / 2;
Bitfield {
data: (self.data[0..n_int]).to_vec(),
}
}
/// Returns the beta part
pub fn beta(&self) -> Bitfield {
let n_int = self.data.len() / 2;
Bitfield {
data: (self.data[n_int..2 * n_int]).to_vec(),
}
}
/// Converts to a format usable in the C library
pub fn as_ptr(&self) -> *const c::bitfield_t {
let len = self.data.len();
let result = &self.data[0..len];
result.as_ptr() as *const c::bitfield_t
}
/// Converts to a format usable in the C library
pub fn as_mut_ptr(&mut self) -> *mut c::bitfield_t {
let len = self.data.len();
let result = &mut self.data[0..len];
result.as_mut_ptr() as *mut c::bitfield_t
}
/// Converts the bitfield into a list of orbital indices (0-based)
pub fn to_orbital_list(&self) -> Vec<usize> {
let n_int: i32 = self
.data
.len()
.try_into()
.expect("try_into failed in to_orbital_list");
let d1 = self.as_ptr();
let cap = self.data.len() * 64;
let mut list = vec![0i32; cap];
let list_c: *mut i32 = list.as_mut_ptr();
std::mem::forget(list);
let mut occ_num: i32 = 0;
let rc = unsafe { c::trexio_to_orbital_list(n_int, d1, list_c, &mut occ_num) };
match ExitCode::from(rc) {
ExitCode::Success => (),
x => panic!("TREXIO Error {}", x),
};
let occ_num = occ_num as usize;
let list = unsafe { Vec::from_raw_parts(list_c, occ_num, cap) };
let mut result: Vec<usize> = Vec::with_capacity(occ_num);
for i in list.iter() {
result.push(*i as usize);
}
result
}
/// Converts the bitfield into a vector
pub fn as_vec(&self) -> &[i64] {
&self.data
}
/// Converts the determinant into a list of orbital indices (0-based)
pub fn to_orbital_list_up_dn(&self) -> (Vec<usize>, Vec<usize>) {
let n_int: i32 = (self.data.len() / 2)
.try_into()
.expect("try_into failed in to_orbital_list");
let d1 = self.as_ptr();
let cap = self.data.len() / 2 * 64;
let mut b = vec![0i32; cap];
let list_up_c: *mut i32 = b.as_mut_ptr();
std::mem::forget(b);
let mut b = vec![0i32; cap];
let list_dn_c: *mut i32 = b.as_mut_ptr();
std::mem::forget(b);
let mut occ_num_up: i32 = 0;
let mut occ_num_dn: i32 = 0;
let rc = unsafe {
c::trexio_to_orbital_list_up_dn(
n_int,
d1,
list_up_c,
list_dn_c,
&mut occ_num_up,
&mut occ_num_dn,
)
};
match ExitCode::from(rc) {
ExitCode::Success => (),
x => panic!("TREXIO Error {}", x),
};
let occ_num_up = occ_num_up as usize;
let occ_num_dn = occ_num_dn as usize;
let list_up = unsafe { Vec::from_raw_parts(list_up_c, occ_num_up, cap) };
let list_dn = unsafe { Vec::from_raw_parts(list_dn_c, occ_num_dn, cap) };
let mut result_up: Vec<usize> = Vec::with_capacity(occ_num_up);
for i in list_up.iter() {
result_up.push(*i as usize);
}
let mut result_dn: Vec<usize> = Vec::with_capacity(occ_num_dn);
for i in list_dn.iter() {
result_dn.push(*i as usize);
}
(result_up, result_dn)
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn creation_from_list() {
let list0 = vec![0, 1, 2, 3, 4];
let list1 = vec![0, 1, 2, 4, 3];
let list2 = vec![0, 1, 4, 2, 3];
let (alpha0, phase0) = Bitfield::from(2, &list0);
let list = alpha0.to_orbital_list();
assert_eq!(list, list0);
let (alpha1, phase1) = Bitfield::from(2, &list1);
let list = alpha1.to_orbital_list();
assert_eq!(list, list0);
assert_eq!(phase1, -phase0);
let (alpha2, phase2) = Bitfield::from(2, &list2);
let list = alpha2.to_orbital_list();
assert_eq!(list, list0);
assert_eq!(phase2, phase0);
}
#[test]
fn creation_alpha_beta() {
let (alpha, _) = Bitfield::from(2, &[0, 1, 2, 3, 4]);
let (beta, _) = Bitfield::from(2, &[0, 1, 2, 4, 5]);
let det = Bitfield::from_alpha_beta(&alpha, &beta);
let list = det.to_orbital_list();
assert_eq!(list, [0, 1, 2, 3, 4, 128, 129, 130, 132, 133]);
assert_eq!(det.alpha(), alpha);
assert_eq!(det.beta(), beta);
}
#[test]
#[should_panic]
fn creation_alpha_beta_with_different_nint() {
let (alpha, _) = Bitfield::from(1, &[0, 1, 2, 3, 4]);
let (beta, _) = Bitfield::from(2, &[0, 1, 2, 4, 5]);
let _ = Bitfield::from_alpha_beta(&alpha, &beta);
}
}

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#![allow(non_upper_case_globals)]
#![allow(non_camel_case_types)]
#![allow(non_snake_case)]
#![allow(dead_code)]
include!(concat!(env!("OUT_DIR"), "/bindings.rs"));

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use crate::c;
#[derive(Debug, PartialEq)]
pub enum ExitCode {
/// Unknown failure
Failure,
/// Everything went fine
Success,
/// Invalid argument
InvalidArg(usize),
/// End of file
End,
/// Read-only file
ReadOnly,
/// Error returned by Errno
Errno,
/// Invalid ID
InvalidId,
/// Allocation failed
AllocationFailed,
/// Element absent
HasNot,
/// Invalid (negative or 0) dimension
InvalidNum,
/// Attribute already exists
AttrAlreadyExists,
/// Dataset already exists
DsetAlreadyExists,
/// Error opening file
OpenError,
/// Error locking file
LockError,
/// Error unlocking file
UnlockError,
/// Invalid file
FileError,
/// Error reading group
GroupReadError,
/// Error writing group
GroupWriteError,
/// Error reading element
ElemReadError,
/// Error writing element
ElemWriteError,
/// Access to memory beyond allocated
UnsafeArrayDim,
/// Attribute does not exist in the file
AttrMissing,
/// Dataset does not exist in the file
DsetMissing,
/// Requested back end is disabled
BackEndMissing,
/// Invalid max_str_len
InvalidStrLen,
/// Possible integer overflow
IntSizeOverflow,
/// Unsafe operation in safe mode
SafeMode,
/// Inconsistent number of electrons
InvalidElectronNum,
/// Inconsistent number of determinants
InvalidDeterminantNum,
/// Inconsistent state of the file
InvalidState,
/// Failed to parse package_version
VersionParsingIssue,
/// The function succeeded with a change of sign
PhaseChange,
}
impl ExitCode {
/// Creation from a C value
pub fn from(rc: c::trexio_exit_code) -> Self {
match rc {
c::TREXIO_FAILURE => Self::Failure,
c::TREXIO_SUCCESS => Self::Success,
c::TREXIO_INVALID_ARG_1 => Self::InvalidArg(1),
c::TREXIO_INVALID_ARG_2 => Self::InvalidArg(2),
c::TREXIO_INVALID_ARG_3 => Self::InvalidArg(3),
c::TREXIO_INVALID_ARG_4 => Self::InvalidArg(4),
c::TREXIO_INVALID_ARG_5 => Self::InvalidArg(5),
c::TREXIO_END => Self::End,
c::TREXIO_READONLY => Self::ReadOnly,
c::TREXIO_ERRNO => Self::Errno,
c::TREXIO_INVALID_ID => Self::InvalidId,
c::TREXIO_ALLOCATION_FAILED => Self::AllocationFailed,
c::TREXIO_HAS_NOT => Self::HasNot,
c::TREXIO_INVALID_NUM => Self::InvalidNum,
c::TREXIO_ATTR_ALREADY_EXISTS => Self::AttrAlreadyExists,
c::TREXIO_DSET_ALREADY_EXISTS => Self::DsetAlreadyExists,
c::TREXIO_OPEN_ERROR => Self::OpenError,
c::TREXIO_LOCK_ERROR => Self::LockError,
c::TREXIO_UNLOCK_ERROR => Self::UnlockError,
c::TREXIO_FILE_ERROR => Self::FileError,
c::TREXIO_GROUP_READ_ERROR => Self::GroupReadError,
c::TREXIO_GROUP_WRITE_ERROR => Self::GroupWriteError,
c::TREXIO_ELEM_READ_ERROR => Self::ElemReadError,
c::TREXIO_ELEM_WRITE_ERROR => Self::ElemWriteError,
c::TREXIO_UNSAFE_ARRAY_DIM => Self::UnsafeArrayDim,
c::TREXIO_ATTR_MISSING => Self::AttrMissing,
c::TREXIO_DSET_MISSING => Self::DsetMissing,
c::TREXIO_BACK_END_MISSING => Self::BackEndMissing,
c::TREXIO_INVALID_ARG_6 => Self::InvalidArg(6),
c::TREXIO_INVALID_ARG_7 => Self::InvalidArg(7),
c::TREXIO_INVALID_ARG_8 => Self::InvalidArg(8),
c::TREXIO_INVALID_STR_LEN => Self::InvalidStrLen,
c::TREXIO_INT_SIZE_OVERFLOW => Self::IntSizeOverflow,
c::TREXIO_SAFE_MODE => Self::SafeMode,
c::TREXIO_INVALID_ELECTRON_NUM => Self::InvalidElectronNum,
c::TREXIO_INVALID_DETERMINANT_NUM => Self::InvalidDeterminantNum,
c::TREXIO_INVALID_STATE => Self::InvalidState,
c::TREXIO_VERSION_PARSING_ISSUE => Self::VersionParsingIssue,
c::TREXIO_PHASE_CHANGE => Self::PhaseChange,
_ => panic!("Unknown exit code"),
}
}
/// Conversion to a C value
pub fn to_c(&self) -> c::trexio_exit_code {
match self {
Self::Failure => c::TREXIO_FAILURE,
Self::Success => c::TREXIO_SUCCESS,
Self::InvalidArg(1) => c::TREXIO_INVALID_ARG_1,
Self::InvalidArg(2) => c::TREXIO_INVALID_ARG_2,
Self::InvalidArg(3) => c::TREXIO_INVALID_ARG_3,
Self::InvalidArg(4) => c::TREXIO_INVALID_ARG_4,
Self::InvalidArg(5) => c::TREXIO_INVALID_ARG_5,
Self::End => c::TREXIO_END,
Self::ReadOnly => c::TREXIO_READONLY,
Self::Errno => c::TREXIO_ERRNO,
Self::InvalidId => c::TREXIO_INVALID_ID,
Self::AllocationFailed => c::TREXIO_ALLOCATION_FAILED,
Self::HasNot => c::TREXIO_HAS_NOT,
Self::InvalidNum => c::TREXIO_INVALID_NUM,
Self::AttrAlreadyExists => c::TREXIO_ATTR_ALREADY_EXISTS,
Self::DsetAlreadyExists => c::TREXIO_DSET_ALREADY_EXISTS,
Self::OpenError => c::TREXIO_OPEN_ERROR,
Self::LockError => c::TREXIO_LOCK_ERROR,
Self::UnlockError => c::TREXIO_UNLOCK_ERROR,
Self::FileError => c::TREXIO_FILE_ERROR,
Self::GroupReadError => c::TREXIO_GROUP_READ_ERROR,
Self::GroupWriteError => c::TREXIO_GROUP_WRITE_ERROR,
Self::ElemReadError => c::TREXIO_ELEM_READ_ERROR,
Self::ElemWriteError => c::TREXIO_ELEM_WRITE_ERROR,
Self::UnsafeArrayDim => c::TREXIO_UNSAFE_ARRAY_DIM,
Self::AttrMissing => c::TREXIO_ATTR_MISSING,
Self::DsetMissing => c::TREXIO_DSET_MISSING,
Self::BackEndMissing => c::TREXIO_BACK_END_MISSING,
Self::InvalidArg(6) => c::TREXIO_INVALID_ARG_6,
Self::InvalidArg(7) => c::TREXIO_INVALID_ARG_7,
Self::InvalidArg(8) => c::TREXIO_INVALID_ARG_8,
Self::InvalidStrLen => c::TREXIO_INVALID_STR_LEN,
Self::IntSizeOverflow => c::TREXIO_INT_SIZE_OVERFLOW,
Self::SafeMode => c::TREXIO_SAFE_MODE,
Self::InvalidElectronNum => c::TREXIO_INVALID_ELECTRON_NUM,
Self::InvalidDeterminantNum => c::TREXIO_INVALID_DETERMINANT_NUM,
Self::InvalidState => c::TREXIO_INVALID_STATE,
Self::VersionParsingIssue => c::TREXIO_VERSION_PARSING_ISSUE,
Self::PhaseChange => c::TREXIO_PHASE_CHANGE,
_ => panic!("Unknown exit code"),
}
}
pub fn to_str(&self) -> Result<&'static str, Utf8Error> {
let c_error = self.to_c();
let c_buf: *const c_char = unsafe { c::trexio_string_of_error(c_error) };
let c_str: &CStr = unsafe { CStr::from_ptr(c_buf) };
c_str.to_str()
}
}
use std::error::Error;
use std::ffi::c_char;
use std::ffi::CStr;
use std::fmt;
use std::str::Utf8Error;
impl fmt::Display for ExitCode {
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
write!(f, "{}", self.to_str().unwrap())
}
}
impl Error for ExitCode {
fn description(&self) -> &str {
self.to_str().unwrap()
}
}

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//! TREXIO is an open-source file format and library developed for the storage and manipulation of
//! data produced by quantum chemistry calculations. It was designed with the goal of providing a
//! reliable and efficient method of storing and exchanging wave function parameters and matrix
//! elements.
//!
//! For comprehensive documentation, consult: [TREXIO Documentation](https://trex-coe.github.io/trexio/)
//!
//! The C library source code is available on GitHub: [TREXIO GitHub Repository](https://github.com/trex-coe/trexio)
//!
use ::std::os::raw::c_char;
mod c;
/// Enumeration representing the various error codes that might be returned by function calls.
/// These error codes are mapped to those defined in the original C TREXIO library.
pub mod exit_code;
pub use exit_code::ExitCode;
use exit_code::ExitCode::InvalidArg;
/// Enum representing the different backends that TREXIO can employ for data storage.
pub mod back_end;
pub use back_end::BackEnd;
/// Structure representing bit fields. Mainly utilized for encapsulating determinant descriptions.
pub mod bitfield;
pub use bitfield::Bitfield;
/// A constant string representing the package version of the linked C TREXIO library.
pub const PACKAGE_VERSION: &str =
unsafe { std::str::from_utf8_unchecked(c::TREXIO_PACKAGE_VERSION) };
/// Utility function to convert Rust results into TREXIO exit codes.
fn rc_return<T>(result: T, rc: c::trexio_exit_code) -> Result<T, ExitCode> {
let rc = ExitCode::from(rc);
match rc {
ExitCode::Success => Ok(result),
x => Err(x),
}
}
/// Utility function to convert Rust string to C-compatible string.
fn string_to_c(s: &str) -> std::ffi::CString {
std::ffi::CString::new(s).unwrap()
}
/// Function to print out diagnostic information about the linked C TREXIO library.
pub fn info() -> Result<(), ExitCode> {
let rc = unsafe { c::trexio_info() };
rc_return((), rc)
}
/// Type representing a TREXIO file. Wraps a pointer to the underlying C structure.
pub struct File {
ptr: *mut c::trexio_t,
}
impl File {
/// Opens a TREXIO file. Returns a `File` instance that can be used for subsequent I/O operations.
///
/// # Parameters
/// - `file_name`: The path to the TREXIO file.
/// - `mode`: Specifies the file access mode. `'r'` for read-only, `'w'` for safe write (write
/// if the data doesn't exist), `'u'` for unsafe write (update existing data).
/// - `back_end`: Specifies the backend used for data storage.
///
/// # Returns
/// - `Result<File, ExitCode>`: `File` instance or an error code.
pub fn open(file_name: &str, mode: char, back_end: BackEnd) -> Result<File, ExitCode> {
let file_name_c = string_to_c(file_name);
let file_name_c = file_name_c.as_ptr() as *const c_char;
let mode = mode as c_char;
let back_end = back_end.to_c();
let rc: *mut c::trexio_exit_code = &mut c::TREXIO_SUCCESS.clone();
let result = unsafe { c::trexio_open(file_name_c, mode, back_end, rc) };
let rc = unsafe { *rc };
rc_return(File { ptr: result }, rc)
}
/// Closes the current TREXIO file and releases associated resources.
///
/// # Returns
/// - `Result<(), ExitCode>`: An error code in case of failure.
pub fn close(self) -> Result<(), ExitCode> {
let rc = unsafe { c::trexio_close(self.ptr) };
rc_return((), rc)
}
/// Inquires if a file with the specified name exists.
///
/// # Parameters
///
/// * `file_name: &str` - The name of the file to inquire about.
///
/// # Returns
///
/// * `Result<bool, ExitCode>` - Returns `Ok(true)` if the file exists,
/// `Ok(false)` otherwise. Returns `Err(ExitCode)` if an error occurs
/// during the operation.
pub fn inquire(file_name: &str) -> Result<bool, ExitCode> {
let file_name_c = string_to_c(file_name);
let file_name_c = file_name_c.as_ptr() as *const c_char;
let rc = unsafe { c::trexio_inquire(file_name_c) };
match ExitCode::from(rc) {
ExitCode::Failure => Ok(false),
ExitCode::Success => Ok(true),
x => Err(x),
}
}
/// Retrieves the ID of the electronic state stored in the file.
///
/// # Parameters
///
/// None
///
/// # Returns
///
/// * `Result<usize, ExitCode>` - Returns the ID as `Ok(usize)` if the operation is successful,
/// otherwise returns `Err(ExitCode)`.
pub fn get_state(&self) -> Result<usize, ExitCode> {
let mut num = 0i32;
let rc = unsafe { c::trexio_get_state(self.ptr, &mut num) };
let result: usize = num.try_into().expect("try_into failed in get_state");
rc_return(result, rc)
}
/// Sets the ID of the electronic state to be stored in the file.
///
/// # Parameters
///
/// * `num: usize` - The ID of the electronic state.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` if the operation is successful,
/// otherwise returns `Err(ExitCode)`.
pub fn set_state(&self, num: usize) -> Result<(), ExitCode> {
let num: i32 = num.try_into().expect("try_into failed in set_state");
let rc = unsafe { c::trexio_set_state(self.ptr, num) };
rc_return((), rc)
}
/// Retrieves the number of `i64` required to store a determinant as a bit-field.
/// This corresponds to \(\frac{\text{mo\_num}}{64}+1\).
///
/// # Parameters
///
/// None
///
/// # Returns
///
/// * `Result<usize, ExitCode>` - Returns the number of `i64` as `Ok(usize)` if the operation is successful,
/// otherwise returns `Err(ExitCode)`.
pub fn get_int64_num(&self) -> Result<usize, ExitCode> {
let mut num = 0i32;
let rc = unsafe { c::trexio_get_int64_num(self.ptr, &mut num) };
let num: usize = num.try_into().expect("try_into failed in get_int64_num");
rc_return(num, rc)
}
/// Writes a vector of determinants, represented as [Bitfield] objects.
///
/// # Parameters
///
/// * `offset: usize` - The number of determinants to skip in the file before writing.
/// * `determinants: &[Bitfield]` - The array of determinants to write.
///
/// # Returns
///
/// * `Result<(), ExitCode>` - Returns `Ok(())` if the operation is successful,
/// otherwise returns `Err(ExitCode)`.
pub fn write_determinant_list(
&self,
offset: usize,
determinants: &[Bitfield],
) -> Result<(), ExitCode> {
let n_int = self.get_int64_num()?;
match determinants.len() {
0 => return Ok(()),
_ => {
if determinants[0].as_vec().len() != 2 * n_int {
return Err(InvalidArg(3));
}
}
};
let offset: i64 = offset
.try_into()
.expect("try_into failed in write_determinant_list");
let buffer_size: i64 = determinants
.len()
.try_into()
.expect("try_into failed in write_determinant_list");
let mut one_d_array: Vec<i64> = Vec::with_capacity(determinants.len() * n_int);
for det in determinants {
for i in det.as_vec() {
one_d_array.push(*i);
}
}
let dset: *const i64 = one_d_array.as_ptr();
let rc = unsafe { c::trexio_write_determinant_list(self.ptr, offset, buffer_size, dset) };
rc_return((), rc)
}
/// Reads a vector of determinants, represented as [Bitfield] objects.
///
/// # Parameters
///
/// * `offset: usize` - The number of determinants to skip in the file before reading.
/// * `buffer_size: usize` - The number of determinants to read.
///
/// # Returns
///
/// * `Result<Vec<Bitfield>, ExitCode>` - Returns the read determinants as `Ok(Vec<Bitfield>)`
/// if the operation is successful, otherwise returns `Err(ExitCode)`.
pub fn read_determinant_list(
&self,
offset: usize,
buffer_size: usize,
) -> Result<Vec<Bitfield>, ExitCode> {
let n_int = self.get_int64_num()?;
let mut one_d_array: Vec<i64> = Vec::with_capacity(buffer_size * 2 * n_int);
let one_d_array_ptr = one_d_array.as_ptr() as *mut i64;
let rc = unsafe {
let offset: i64 = offset
.try_into()
.expect("try_into failed in read_determinant_list (offset)");
let mut buffer_size_read: i64 = buffer_size
.try_into()
.expect("try_into failed in read_determinant_list (buffer_size)");
let rc = c::trexio_read_determinant_list(
self.ptr,
offset,
&mut buffer_size_read,
one_d_array_ptr,
);
let buffer_size_read: usize = buffer_size_read
.try_into()
.expect("try_into failed in read_determinant_list (buffer_size)");
one_d_array.set_len(n_int * 2usize * buffer_size_read);
match ExitCode::from(rc) {
ExitCode::End => ExitCode::to_c(&ExitCode::Success),
ExitCode::Success => {
assert_eq!(buffer_size_read, buffer_size);
rc
}
_ => rc,
}
};
let result: Vec<Bitfield> = one_d_array
.chunks(2 * n_int)
.collect::<Vec<_>>()
.iter()
.map(|x| (Bitfield::from_vec(x)))
.collect::<Vec<_>>();
rc_return(result, rc)
}
}
include!(concat!(env!("OUT_DIR"), "/generated.rs"));

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use trexio::back_end::BackEnd;
use trexio::bitfield::Bitfield;
fn write(file_name: &str, back_end: BackEnd) -> Result<(), trexio::ExitCode> {
// Prepare data to be written
let nucleus_num = 12;
let state_id = 2;
let charge = vec![6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.0f64];
let coord = vec![
[0.00000000f64, 1.39250319, 0.00],
[-1.20594314, 0.69625160, 0.00],
[-1.20594314, -0.69625160, 0.00],
[0.00000000, -1.39250319, 0.00],
[1.20594314, -0.69625160, 0.00],
[1.20594314, 0.69625160, 0.00],
[-2.14171677, 1.23652075, 0.00],
[-2.14171677, -1.23652075, 0.00],
[0.00000000, -2.47304151, 0.00],
[2.14171677, -1.23652075, 0.00],
[2.14171677, 1.23652075, 0.00],
[0.00000000, 2.47304151, 0.00],
];
let flat_coord = coord.into_iter().flatten().collect::<Vec<f64>>();
let mo_num = 150;
let ao_num = 1000;
let basis_shell_num = 24;
let basis_nucleus_index: Vec<usize> = (0..24).collect();
let label = vec![
"C", "Na", "C", "C 66", "C", "C", "H 99", "Ru", "H", "H", "H", "H",
];
let sym_str = "B3U with some comments";
println!("Write {}", file_name);
assert!(!trexio::File::inquire(file_name)?);
let trex_file = trexio::File::open(file_name, 'w', back_end)?;
assert!(!trex_file.has_nucleus()?);
assert!(!trex_file.has_nucleus_num()?);
assert!(!trex_file.has_nucleus_charge()?);
assert!(!trex_file.has_ao_2e_int()?);
assert!(!trex_file.has_ao_2e_int_eri()?);
assert!(!trex_file.has_determinant_list()?);
trex_file.write_nucleus_num(nucleus_num)?;
trex_file.write_nucleus_charge(&charge)?;
trex_file.write_nucleus_point_group(sym_str)?;
trex_file.write_nucleus_coord(&flat_coord)?;
trex_file.write_nucleus_label(&label)?;
trex_file.write_basis_shell_num(basis_shell_num)?;
trex_file.write_basis_nucleus_index(&basis_nucleus_index)?;
trex_file.write_state_id(state_id)?;
if !trex_file.has_ao_num()? {
trex_file.write_ao_num(ao_num)?;
}
if !trex_file.has_mo_num()? {
trex_file.write_mo_num(mo_num)?;
}
let mut energy = Vec::with_capacity(mo_num);
for i in 0..mo_num {
let e: f64 = i as f64 - 100.0f64;
energy.push(e);
}
trex_file.write_mo_energy(&energy)?;
let mut spin = vec![0; mo_num];
for i in mo_num / 2..mo_num {
spin[i] = 1;
}
trex_file.write_mo_spin(&spin)?;
// Integrals
let nmax = 100;
let mut ao_2e_int_eri = Vec::<(usize, usize, usize, usize, f64)>::with_capacity(nmax);
let n_buffers = 5;
let bufsize = nmax / n_buffers;
for i in 0..100 {
// Quadruplet of indices + value
let data = (4 * i, 4 * i + 1, 4 * i + 2, 4 * i + 3, 3.14 + (i as f64));
ao_2e_int_eri.push(data);
}
let mut offset = 0;
for _ in 0..n_buffers {
trex_file.write_ao_2e_int_eri(offset, &ao_2e_int_eri[offset..offset + bufsize])?;
offset += bufsize;
}
// Determinants
let det_num = 50;
let mut det_list = Vec::with_capacity(det_num);
for i in 0..det_num {
let mut d = [0i64; 6];
for j in 0..6 {
d[j] = 6 * (i as i64) + (j as i64);
}
det_list.push(Bitfield::from_vec(&d));
}
let n_buffers = 5;
let bufsize = 50 / n_buffers;
let mut offset = 0;
for _ in 0..n_buffers {
trex_file.write_determinant_list(offset, &det_list[offset..offset + bufsize])?;
offset += bufsize;
}
trex_file.close()
}
fn read(file_name: &str, back_end: BackEnd) -> Result<(), trexio::ExitCode> {
println!("Read {}", file_name);
assert!(trexio::File::inquire(file_name)?);
let trex_file = trexio::File::open(file_name, 'r', back_end)?;
assert!(trex_file.has_nucleus()?);
assert!(trex_file.has_nucleus_num()?);
assert!(trex_file.has_nucleus_charge()?);
assert!(trex_file.has_ao_2e_int()?);
assert!(trex_file.has_ao_2e_int_eri()?);
assert!(trex_file.has_determinant_list()?);
let nucleus_num = trex_file.read_nucleus_num()?;
assert_eq!(nucleus_num, 12);
let sym_str = trex_file.read_nucleus_point_group(64)?;
assert_eq!(sym_str, "B3U with some comments");
let charge = trex_file.read_nucleus_charge()?;
assert_eq!(
charge,
vec![6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.0f64]
);
let coord = trex_file.read_nucleus_coord()?;
assert_eq!(
coord,
vec![
0.00000000f64,
1.39250319,
0.00,
-1.20594314,
0.69625160,
0.00,
-1.20594314,
-0.69625160,
0.00,
0.00000000,
-1.39250319,
0.00,
1.20594314,
-0.69625160,
0.00,
1.20594314,
0.69625160,
0.00,
-2.14171677,
1.23652075,
0.00,
-2.14171677,
-1.23652075,
0.00,
0.00000000,
-2.47304151,
0.00,
2.14171677,
-1.23652075,
0.00,
2.14171677,
1.23652075,
0.00,
0.00000000,
2.47304151,
0.00
]
);
let label = trex_file.read_nucleus_label(6)?;
assert_eq!(
label,
vec!["C", "Na", "C", "C 66", "C", "C", "H 99", "Ru", "H", "H", "H", "H"]
);
let basis_shell_num = trex_file.read_basis_shell_num()?;
assert_eq!(basis_shell_num, 24);
let basis_nucleus_index = trex_file.read_basis_nucleus_index()?;
let ref_val: Vec<usize> = (0..24).collect();
assert_eq!(basis_nucleus_index, ref_val);
let state_id = trex_file.read_state_id()?;
assert_eq!(state_id, 2);
let ao_num = trex_file.read_ao_num()?;
assert_eq!(ao_num, 1000);
let mo_num = trex_file.read_mo_num()?;
assert_eq!(mo_num, 150);
let mut energy_ref = Vec::with_capacity(mo_num);
for i in 0..mo_num {
let e: f64 = i as f64 - 100.0f64;
energy_ref.push(e);
}
let energy = trex_file.read_mo_energy()?;
assert_eq!(energy, energy_ref);
let mut spin_ref = vec![0; mo_num];
for i in mo_num / 2..mo_num {
spin_ref[i] = 1;
}
let spin = trex_file.read_mo_spin()?;
assert_eq!(spin, spin_ref);
// Integrals
let nmax = 100;
let mut ao_2e_int_eri_ref = Vec::<(usize, usize, usize, usize, f64)>::with_capacity(nmax);
let n_buffers = 8;
let bufsize = nmax / n_buffers + 10;
for i in 0..100 {
// Quadruplet of indices + value
let data = (4 * i, 4 * i + 1, 4 * i + 2, 4 * i + 3, 3.14 + (i as f64));
ao_2e_int_eri_ref.push(data);
}
let mut offset = 0;
let mut ao_2e_int_eri = Vec::<(usize, usize, usize, usize, f64)>::with_capacity(nmax);
for _ in 0..n_buffers {
let buffer = trex_file.read_ao_2e_int_eri(offset, bufsize)?;
offset += buffer.len();
ao_2e_int_eri.extend(buffer);
}
assert_eq!(ao_2e_int_eri_ref, ao_2e_int_eri);
// Determinants
let det_num = trex_file.read_determinant_num()?;
assert_eq!(det_num, 50);
let mut det_list_ref = Vec::with_capacity(det_num);
for i in 0..det_num {
let mut d = [0i64; 6];
for j in 0..6 {
d[j] = 6 * (i as i64) + (j as i64);
}
det_list_ref.push(Bitfield::from_vec(&d));
}
let n_buffers = 8;
let bufsize = det_num / n_buffers + 20;
let mut offset = 0;
let mut det_list: Vec<Bitfield> = Vec::with_capacity(det_num);
for _ in 0..n_buffers {
let buffer = trex_file.read_determinant_list(offset, bufsize)?;
offset += buffer.len();
det_list.extend(buffer);
}
assert_eq!(det_list_ref, det_list);
trex_file.close()
}
#[test]
pub fn info() {
let _ = trexio::info();
}
use std::fs;
#[test]
pub fn text_backend() {
let _ = write("tmp/test_write.dir", trexio::BackEnd::Text).unwrap();
let _ = read("tmp/test_write.dir", trexio::BackEnd::Text).unwrap();
fs::remove_dir_all("tmp/test_write.dir").unwrap()
}
#[test]
pub fn hdf5_backend() {
let _ = write("tmp/test_write.hdf5", trexio::BackEnd::Hdf5).unwrap();
let _ = read("tmp/test_write.hdf5", trexio::BackEnd::Hdf5).unwrap();
fs::remove_file("tmp/test_write.hdf5").unwrap()
}

1
rust/trexio/tmp/.gitignore vendored Normal file
View File

@ -0,0 +1 @@
*

18
src/CMakeLists.txt
View File

@ -19,7 +19,7 @@ set(TREXIO_SOURCES
${CMAKE_CURRENT_SOURCE_DIR}/trexio.c
${CMAKE_CURRENT_SOURCE_DIR}/trexio_text.c
)
set(TREXIO_PUBLIC_HEADERS ${CMAKE_SOURCE_DIR}/include/trexio.h)
set(TREXIO_PUBLIC_HEADERS ${PROJECT_SOURCE_DIR}/include/trexio.h)
set(TREXIO_PRIVATE_HEADERS
${CMAKE_CURRENT_SOURCE_DIR}/trexio_s.h
${CMAKE_CURRENT_SOURCE_DIR}/trexio_private.h
@ -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
@ -103,7 +101,7 @@ include(FortranCInterface)
FortranCInterface_VERIFY()
# Fortran module
set(TREXIO_MOD_FILE ${CMAKE_SOURCE_DIR}/include/trexio_f.f90)
set(TREXIO_MOD_FILE ${PROJECT_SOURCE_DIR}/include/trexio_f.f90)
# Export to parent scope so tests directory picks this up.
set(TREXIO_MOD_FILE ${TREXIO_MOD_FILE} PARENT_SCOPE)
# Add TREXIO Fortran module as a library.
@ -117,7 +115,7 @@ if(TREXIO_DEVEL)
set(ORG_FILES
templates_front/templator_front.org
templates_text/templator_text.org
${CMAKE_SOURCE_DIR}/trex.org
${PROJECT_SOURCE_DIR}/trex.org
)
if(ENABLE_HDF5)
list(APPEND ORG_FILES templates_hdf5/templator_hdf5.org)
@ -129,8 +127,8 @@ if(TREXIO_DEVEL)
${TREXIO_PRIVATE_HEADERS}
${TREXIO_MOD_FILE}
COMMAND ./build_trexio.sh
DEPENDS ${ORG_FILES} ${CMAKE_SOURCE_DIR}/include/config.h
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/tools
DEPENDS ${ORG_FILES} ${PROJECT_SOURCE_DIR}/include/config.h
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/tools
COMMENT "Generating TREXIO source code from org-mode files."
VERBATIM)
@ -158,7 +156,7 @@ install(FILES ${TREXIO_MOD_FILE} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
# https://gitlab.kitware.com/cmake/community/wikis/FAQ#can-i-do-make-uninstall-with-cmake
if(NOT TARGET uninstall)
configure_file(
"${CMAKE_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
"${PROJECT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
"${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
IMMEDIATE @ONLY)

59
src/README.org
View File

@ -2,34 +2,75 @@
#+PROPERTY: comments org
#+SETUPFILE: ../docs/theme.setup
--------------------------------
#+BEGIN_EXPORT html
<script async src="https://cse.google.com/cse.js?cx=a67f8ab65a66f97f2"></script>
<div class="gcse-search"></div>
#+END_EXPORT
--------------------------------
------------------
TREXIO is an open-source file format and library developed for the storage and
manipulation of data produced by quantum chemistry calculations. It was
designed with the goal of providing a reliable and efficient method of storing
and exchanging wave function parameters and matrix elements.
- [[./tutorial_benzene.html][Tutorial]]
The library consists of a front-end implemented in the C programming language
and two different back-ends: a text back-end and a binary back-end utilizing
the HDF5 library enabling fast read and write speeds. It is compatible with a
variety of platforms and has interfaces for Fortran, Python, and OCaml.
If you use TREXIO, please cite this article published in the [[https://doi.org/10.1063/5.0148161][Journal of Chemical Physics]]:
#+begin_src latex
@article{trexio_2023,
author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Micha{\l} and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josu{\'{e}} and Filippi, Claudia and Nakano, Kosuke and Kohul{\'{a}}k, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and R{\'{\i}}os, Pablo L{\'{o}}pez and Alavi, Ali and Scemama, Anthony},
title = {{TREXIO: A file format and library for quantum chemistry}},
journal = {J. Chem. Phys.},
volume = {158},
number = {17},
year = {2023},
month = may,
issn = {0021-9606},
publisher = {AIP Publishing},
doi = {10.1063/5.0148161}
}
#+end_src
If you don't have access to the journal, you can access the manuscript on
[[https://doi.org/10.48550/arXiv.2302.14793][arXiv:2302.14793]].
--------------------------------
#+BEGIN_EXPORT html
<table style="width:100%">
<tr><td style="width:50%">
#+END_EXPORT
- [[./intro.html][Motivation]]
- [[./lib.html][The TREXIO library]]
- [[./trex.html][Data stored with TREXIO]]
- [[./examples.html][How-to guide]]
- [[./tutorial_benzene.html][Tutorial]]
- [[./examples.html][Examples]]
- [[./templator_front.html][Front end API]]
- [[./templator_hdf5.html][HDF5 back end]]
- [[./templator_text.html][TEXT back end]]
#+BEGIN_EXPORT html
</td>
<td>
<img src="trexio.png" alt="T-Rex talking about chemistry"
align="right" width="300"/>
</td></tr>
</table>
#+END_EXPORT
--------------------------------
The TREXIO library defines a standard format for storing wave functions,
together with an C-compatible API such that it can be easily used in any
programming language.
The source code of the library is available at
https://github.com/trex-coe/trexio
and bug reports should be submitted at
https://github.com/trex-coe/trexio/issues.
The TREXIO library is licensed under the open-source 3-clause BSD license.
------------------
[[https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg]] [[https://trex-coe.eu][TREX: Targeting Real Chemical Accuracy at the Exascale]] project has received funding from the European Union’s Horizon 2020 - Research and Innovation program - under grant agreement no. 952165. The content of this document does not represent the opinion of the European Union, and the European Union is not responsible for any use that might be made of such content.

22
src/pytrexio.i
View File

@ -34,14 +34,14 @@
num variable is modified by address
*/
/* Return num variables as part of the output tuple */
%apply int *OUTPUT { int32_t* const num};
%apply int *OUTPUT { int64_t* const num};
%apply int *OUTPUT { int32_t* const num_up};
%apply int *OUTPUT { int32_t* const num_dn};
%apply int *OUTPUT { int64_t* const num_up};
%apply int *OUTPUT { int64_t* const num_dn};
%apply int32_t *OUTPUT { int32_t* const num};
%apply int64_t *OUTPUT { int64_t* const num};
%apply int32_t *OUTPUT { int32_t* const num_up};
%apply int32_t *OUTPUT { int32_t* const num_dn};
%apply int64_t *OUTPUT { int64_t* const num_up};
%apply int64_t *OUTPUT { int64_t* const num_dn};
%apply float *OUTPUT { float* const num};
%apply float *OUTPUT { double* const num};
%apply double *OUTPUT { double* const num};
/* Return TREXIO exit code from trexio_open as part of the output tuple */
%apply int *OUTPUT { trexio_exit_code* const rc_open};
/* Return number of sparse data points stored in the file as part of the output tuple */
@ -108,6 +108,14 @@ import_array();
/* For some reasons SWIG does not apply the proper bitfield_t typemap, so one has to manually specify int64_t* ARGOUT_ARRAY1 below */
%apply (int64_t* ARGOUT_ARRAY1, int32_t DIM1) {(bitfield_t* const bit_list, const int32_t N_int)};
/* NAO functions */
%apply double *OUTPUT { double* const log_r_out, double* const amplitude};
%apply (double *ARGOUT_ARRAY1, int DIM1) {(double* const amplitudes, int amplitude_cnt)};
%apply (double* IN_ARRAY1, int DIM1) {(double* grid_r, int n_grid_r),
(double* interpolator, int n_interp), (double* nucleus_coords, int n_nuc_co), (double* normalization, int n_norm)};
%apply (int64_t* IN_ARRAY1, int DIM1) {(int64_t* grid_start, int n_grid_st),
(int64_t* grid_size, int n_grid_si), (int64_t* nucleus_index, int n_nuc_id)};
/* This tells SWIG to treat char ** dset_in pattern as a special case
Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.
by converting input list of strings from Python into char ** of C

783
src/templates_front/templator_front.org
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File diff suppressed because it is too large Load Diff

1
src/templates_hdf5/build.sh
View File

@ -18,4 +18,5 @@ cat hrw_determinant_hdf5.h >> trexio_hdf5.h
cat *_determinant_hdf5.c >> trexio_hdf5.c
cat helpers_hdf5.c >> trexio_hdf5.c
cat suffix_hdf5.c >> trexio_hdf5.c
cat suffix_hdf5.h >> trexio_hdf5.h

138
src/templates_hdf5/templator_hdf5.org
View File

@ -38,15 +38,23 @@
#include <assert.h>
#include <sys/stat.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#
#ifdef HAVE_HDF5
#include "hdf5.h"
#include "hdf5_hl.h"
#+end_src
#+begin_src c :tangle prefix_hdf5.c :noweb yes
<<header>>
#include "trexio_hdf5.h"
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#
#ifdef HAVE_HDF5
#+end_src
* Template for HDF5 definitions
@ -380,18 +388,21 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
}
FREE(ddims);
/* Read dataset */
herr_t status = H5Dread(dset_id,
H5T_$GROUP_DSET_H5_DTYPE$,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Sclose(dspace_id);
H5Dclose(dset_id);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
herr_t status = H5LTread_dataset(f->$group$_group,
$GROUP_DSET$_NAME,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
if (status < 0) return TREXIO_FAILURE;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_dset_data_hdf5.c
@ -411,7 +422,8 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
Consider using HDF5-native h5repack utility after deleting/overwriting big datasets.
,*/
if (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == 'u') {
if ((trexio_hdf5_has_$group_dset$(file) == TREXIO_SUCCESS) && (file->mode == 'u')) {
herr_t status_del = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (status_del < 0) return TREXIO_FAILURE;
}
@ -454,14 +466,13 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
@ -495,7 +506,8 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
hid_t index_dtype;
void* index_p = NULL;
const void* index_p = NULL;
void* index_p_non_const = NULL;
uint64_t size_ranked = (uint64_t) size * $group_dset_rank$;
/* Determine the optimal type for storing indices depending on the size_max (usually mo_num or ao_num) */
if (size_max < UINT8_MAX) {
@ -505,6 +517,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
index[i] = (uint8_t) index_sparse[i];
}
index_p = index;
index_p_non_const = index;
index_dtype = H5T_NATIVE_UINT8;
} else if (size_max < UINT16_MAX) {
uint16_t* index = CALLOC(size_ranked, uint16_t);
@ -513,9 +526,10 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
index[i] = (uint16_t) index_sparse[i];
}
index_p = index;
index_p_non_const = index;
index_dtype = H5T_NATIVE_UINT16;
} else {
index_p = (int32_t*) index_sparse;
index_p = index_sparse;
index_dtype = H5T_NATIVE_INT32;
}
@ -534,12 +548,12 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
trexio_exit_code rc_write = TREXIO_FAILURE;
/* NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! */
if ( H5LTfind_dataset(f->$group$_group, dset_index_name) != 1 ) {
if (trexio_hdf5_has_$group_dset$(file) == TREXIO_HAS_NOT) {
/* If the file does not exist -> create it and write */
/* Create chunked dataset with index_dtype datatype and write indices into it */
rc_write = trexio_hdf5_create_write_dset_sparse(f->$group$_group, dset_index_name, index_dtype, chunk_i_dims, index_p);
if (index_p != index_sparse) FREE(index_p);
if (index_p != index_sparse) FREE(index_p_non_const);
if (rc_write != TREXIO_SUCCESS) return rc_write;
/* Create chunked dataset with value_dtype datatype and write values into it */
@ -553,7 +567,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
/* Create chunked dataset with index_dtype datatype and write indices into it */
rc_write = trexio_hdf5_open_write_dset_sparse(f->$group$_group, dset_index_name, index_dtype, chunk_i_dims, offset_i, index_p);
if (index_p != index_sparse) FREE(index_p);
if (index_p != index_sparse) FREE(index_p_non_const);
if (rc_write != TREXIO_SUCCESS) return rc_write;
/* Create chunked dataset with value_dtype datatype and write values into it */
@ -657,14 +671,13 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME "_values");
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, $GROUP_DSET$_NAME "_values", H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
@ -693,7 +706,7 @@ trexio_exit_code trexio_hdf5_read_$group_dset$(trexio_t* const file,
if (eof_read_size == NULL) return TREXIO_INVALID_ARG_5;
if (dset == NULL) return TREXIO_INVALID_ARG_6;
const char dset_name[256] = "$group_dset$";
const char* dset_name = "$group_dset$";
const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
@ -717,7 +730,7 @@ trexio_exit_code trexio_hdf5_write_$group_dset$(trexio_t* const file,
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (dset == NULL) return TREXIO_INVALID_ARG_5;
const char dset_name[256] = "$group_dset$";
const char* dset_name = "$group_dset$";
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
@ -728,7 +741,7 @@ trexio_exit_code trexio_hdf5_write_$group_dset$(trexio_t* const file,
trexio_exit_code rc_write = TREXIO_FAILURE;
/* NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! */
if ( H5LTfind_dataset(f->$group$_group, dset_name) != 1 ) {
if (trexio_hdf5_has_$group_dset$(file) == TREXIO_HAS_NOT) {
/* If the file does not exist -> create it and write */
/* Create chunked dataset with dtype datatype and write indices into it */
@ -755,7 +768,7 @@ trexio_hdf5_read_$group_dset$_size (trexio_t* const file, int64_t* const size_ma
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (size_max == NULL) return TREXIO_INVALID_ARG_2;
const char dset_name[256] = "$group_dset$";
const char* dset_name = "$group_dset$";
const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
@ -791,16 +804,15 @@ trexio_exit_code trexio_hdf5_has_$group_dset$(trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
const char dset_name[256] = "$group_dset$";
const char* dset_name = "$group_dset$";
herr_t status = H5LTfind_dataset(f->$group$_group, dset_name);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, dset_name, H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
#+end_src
@ -936,7 +948,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const char** $group_dset$,
Consider using HDF5-provided h5repack utility after deleting/overwriting big datasets.
,*/
if (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == 'u') {
if ( (trexio_hdf5_has_$group_dset$(file) == TREXIO_SUCCESS) && (file->mode == 'u') ) {
herr_t status_del = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (status_del < 0) return TREXIO_FAILURE;
}
@ -991,14 +1003,13 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
@ -1231,7 +1242,7 @@ trexio_exit_code trexio_hdf5_write_determinant_list(trexio_t* const file,
trexio_exit_code rc_write = TREXIO_FAILURE;
/* NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! */
if ( H5LTfind_dataset(f->determinant_group, dset_det_name) != 1 ) {
if ( trexio_hdf5_has_determinant_list(file) == TREXIO_HAS_NOT ) {
/* If the file does not exist -> create it and write */
/* Create chunked dataset with det_dtype datatype and write indices into it */
@ -1260,14 +1271,13 @@ trexio_exit_code trexio_hdf5_has_determinant_list(trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->determinant_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->determinant_group, "determinant_list");
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->determinant_group, "determinant_list", H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
#+end_src
@ -1467,8 +1477,6 @@ trexio_hdf5_open_read_dset_sparse (const hid_t group_id,
uint16_t* index = CALLOC(size_ranked, uint16_t);
if (index == NULL) return TREXIO_ALLOCATION_FAILED;
index_p = index;
} else {
index_p = data_sparse;
}
}
@ -1476,7 +1484,7 @@ trexio_hdf5_open_read_dset_sparse (const hid_t group_id,
if (status < 0) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
if (index_p != data_sparse) FREE(index_p);
if (index_p != NULL) FREE(index_p);
return TREXIO_INVALID_ID;
}
@ -1484,15 +1492,22 @@ trexio_hdf5_open_read_dset_sparse (const hid_t group_id,
if (memspace_id < 0) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
if (index_p != data_sparse) FREE(index_p);
if (index_p != NULL) FREE(index_p);
return TREXIO_INVALID_ID;
}
if (is_index == 1) {
status = H5Dread(dset_id,
dtype,
memspace_id, fspace_id, H5P_DEFAULT,
index_p);
if (index_p != NULL) {
status = H5Dread(dset_id,
dtype,
memspace_id, fspace_id, H5P_DEFAULT,
index_p);
} else {
status = H5Dread(dset_id,
dtype,
memspace_id, fspace_id, H5P_DEFAULT,
data_sparse);
}
} else {
status = H5Dread(dset_id,
dtype,
@ -1504,7 +1519,7 @@ trexio_hdf5_open_read_dset_sparse (const hid_t group_id,
H5Sclose(memspace_id);
H5Dclose(dset_id);
if (status < 0) {
if (index_p != data_sparse) FREE(index_p);
if (index_p != NULL) FREE(index_p);
return TREXIO_FAILURE;
}
@ -1537,5 +1552,10 @@ trexio_exit_code trexio_hdf5_create_write_dset_sparse (const hid_t group_id, con
trexio_exit_code trexio_hdf5_open_write_dset_sparse (const hid_t group_id, const char* dset_name, const hid_t dtype_id, const hsize_t* chunk_dims, const hsize_t* offset_file, const void* data_sparse);
trexio_exit_code trexio_hdf5_open_read_dset_sparse (const hid_t group_id, const char* dset_name, const uint32_t dset_rank, const hsize_t* offset_file, hsize_t* const size_read, int64_t* const eof_read_size, const int is_index, void* const data_sparse);
#endif
#endif
#+end_src
#+begin_src c :tangle suffix_hdf5.c :noweb yes
#endif
#+end_src

33
src/templates_text/templator_text.org
View File

@ -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 +162,33 @@ 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 /* Since glibc 2.19: */ _DEFAULT_SOURCE \
|| /* Glibc 2.19 and earlier: */ _BSD_SOURCE \
|| /* Since glibc 2.10: */ _POSIX_C_SOURCE >= 200809L
/* mkdtemp is defined */
#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)

85
tests/delete_group.c Normal file
View File

@ -0,0 +1,85 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
static int test_write_delete_group (const char* file_name, const back_end_t backend) {
/* Try to write a dimensioning attribute (num variable) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical dataset in a file
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
// write numerical attribute ao_cartesian as 0
rc = trexio_write_ao_cartesian(file, 0);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// open file in 'unsafe' mode
file = trexio_open(file_name, 'u', backend, &rc);
assert (file != NULL);
// delete a previously written group
rc = trexio_delete_nucleus(file);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_delete_group (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

93
tests/delete_group_hdf5.c
View File

@ -1,89 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_del.h5"
#define RM_COMMAND "rm -f -- " TREXIO_FILE
static int test_write_delete_group (const char* file_name, const back_end_t backend) {
/* Try to write a dimensioning attribute (num variable) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical dataset in a file
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
// write numerical attribute ao_cartesian as 0
rc = trexio_write_ao_cartesian(file, 0);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// open file in 'unsafe' mode
file = trexio_open(file_name, 'u', backend, &rc);
assert (file != NULL);
// delete a previously written group
rc = trexio_delete_nucleus(file);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_delete_group (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "delete_group"
#include "test_macros.h"
#include "delete_group.c"

93
tests/delete_group_text.c
View File

@ -1,89 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_del.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_delete_group (const char* file_name, const back_end_t backend) {
/* Try to write a dimensioning attribute (num variable) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical dataset in a file
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
// write numerical attribute ao_cartesian as 0
rc = trexio_write_ao_cartesian(file, 0);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// open file in 'unsafe' mode
file = trexio_open(file_name, 'u', backend, &rc);
assert (file != NULL);
// delete a previously written group
rc = trexio_delete_nucleus(file);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_delete_group (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "delete_group"
#include "test_macros.h"
#include "delete_group.c"

322
tests/io_determinant.c Normal file
View File

@ -0,0 +1,322 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define SIZE 100
#define N_CHUNKS 5
#define STATE_TEST 2
static int test_write_determinant (const char* file_name, const back_end_t backend, const int64_t offset, const int mo_num) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// parameters to be written
int64_t* det_list;
double* det_coef;
// write mo_num which will be used to determine the optimal size of int indices
if (trexio_has_mo_num(file) == TREXIO_HAS_NOT) {
rc = trexio_write_mo_num(file, mo_num);
assert(rc == TREXIO_SUCCESS);
}
// get the number of int64 bit fields per determinant
int int_num;
rc = trexio_get_int64_num(file, &int_num);
assert(rc == TREXIO_SUCCESS);
assert(int_num == (mo_num-1)/64 + 1);
// allocate memory and fill with values to be written
det_list = (int64_t*) calloc(2 * int_num * SIZE, sizeof(int64_t));
det_coef = (double*) calloc(SIZE, sizeof(double));
int64_t size_list = TREXIO_NORB_PER_INT * int_num;
const int32_t orb_list_up[4] = {0,1,2,3};
const int32_t orb_list_dn[3] = {0,1,2};
for(int i=0; i<SIZE; i++){
rc = trexio_to_bitfield_list (orb_list_up, 4, &(det_list[2*int_num*i]), int_num);
rc = trexio_to_bitfield_list (orb_list_dn, 3, &(det_list[2*int_num*i+int_num]), int_num);
det_coef[i] = 3.14 + (double) i;
}
// write dataset chunks of sparse data in the file (including FAKE statements)
uint64_t chunk_size = (uint64_t) SIZE/N_CHUNKS;
uint64_t offset_f = 0UL;
uint64_t offset_d = 0UL;
if (offset != 0L) offset_f += offset;
// write the state_id of a given file: 0 is ground state
if (trexio_has_state_id(file) == TREXIO_HAS_NOT) {
rc = trexio_write_state_id(file, STATE_TEST);
assert(rc == TREXIO_SUCCESS);
}
// write n_chunks times using write_sparse
for(int i=0; i<N_CHUNKS; ++i){
rc = trexio_write_determinant_list(file, offset_f, chunk_size, &det_list[2*int_num*offset_d]);
assert(rc == TREXIO_SUCCESS);
rc = trexio_write_determinant_coefficient(file, offset_f, chunk_size, &det_coef[offset_d]);
assert(rc == TREXIO_SUCCESS);
offset_d += chunk_size;
offset_f += chunk_size;
}
// manually check the consistency of the determinant_num and coefficient_size after writing
int64_t coeff_size = 0L;
int64_t determinant_num = 0L;
rc = trexio_read_determinant_num_64(file, &determinant_num);
assert(rc == TREXIO_SUCCESS);
rc = trexio_read_determinant_coefficient_size(file, &coeff_size);
assert(rc == TREXIO_SUCCESS);
assert(determinant_num == coeff_size);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the allocated memeory
free(det_list);
free(det_coef);
printf("write determinants OK\n");
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_determinant(const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// now check that previously written determinant_list exists
rc = trexio_has_determinant_list(file);
assert(rc==TREXIO_SUCCESS);
rc = trexio_has_state_id(file);
assert(rc==TREXIO_SUCCESS);
// now check that previously written determinant_coefficient exists
rc = trexio_has_determinant_coefficient(file);
assert(rc==TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
printf("has_determinant OK\n");
return 0;
}
static int test_read_determinant (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// compute how many integer bit fields is needed per determinant (for a given spin)
int64_t mo_num;
rc = trexio_read_mo_num_64(file, &mo_num);
assert (rc == TREXIO_SUCCESS);
int int_num;
rc = trexio_get_int64_num(file, &int_num);
assert (rc == TREXIO_SUCCESS);
assert (int_num == (mo_num - 1)/64 + 1);
// define arrays to read into
int64_t* det_list_read;
double* det_coef_read;
double check_diff;
uint64_t size_r = 40L;
det_list_read = (int64_t*) calloc(2*int_num*size_r,sizeof(int64_t));
det_coef_read = (double*) calloc(size_r,sizeof(double));
// specify the read parameters, here:
// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
int64_t chunk_read = 10L;
int64_t offset_file_read = 40L;
int offset_data_read = 5;
int64_t read_size_check;
read_size_check = chunk_read;
if (offset != 0L) offset_file_read += offset;
// read one chunk using the aforementioned parameters
printf("int_num: %d\n", int_num);
rc = trexio_read_determinant_list(file, offset_file_read, &chunk_read, &det_list_read[2*int_num*offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
assert(det_list_read[2*int_num*offset_data_read] == 15);
assert(det_list_read[2*int_num*offset_data_read+int_num] == 7);
rc = trexio_read_determinant_coefficient(file, offset_file_read, &chunk_read, &det_coef_read[offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
check_diff = det_coef_read[0] - 0.;
assert(check_diff*check_diff < 1e-14);
check_diff = det_coef_read[offset_data_read] - (3.14 + (double) (offset_file_read-offset));
//printf("%lf %lf\n", check_diff, det_coef_read[offset_data_read]);
assert(check_diff*check_diff < 1e-14);
int32_t state_id = 666;
rc = trexio_read_state_id(file, &state_id);
assert(rc == TREXIO_SUCCESS);
assert(state_id == STATE_TEST);
// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
offset_file_read = 97L;
offset_data_read = 1;
int64_t eof_read_size_check = SIZE - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
if (offset != 0L) offset_file_read += offset;
chunk_read = read_size_check;
// read one chunk that will reach EOF and return TREXIO_END code
rc = trexio_read_determinant_list(file, offset_file_read, &chunk_read, &det_list_read[2*int_num*offset_data_read]);
/*
printf("%s\n", trexio_string_of_error(rc));
for (int i=0; i<size_r; i++) {
printf("%lld %lld\n", det_list_read[6*i], det_list_read[6*i+5]);
}
*/
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
chunk_read = read_size_check;
rc = trexio_read_determinant_coefficient(file, offset_file_read, &chunk_read, &det_coef_read[offset_data_read]);
/*
printf("%s\n", trexio_string_of_error(rc));
for (int i=0; i<size_r; i++) {
printf("%lf\n", det_coef_read[i]);
}
*/
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
check_diff= det_coef_read[size_r-1] - 0.;
//printf("%lf %lf\n", check_diff, det_coef_read[size_r-1]);
assert(check_diff*check_diff < 1e-14);
// check the value of determinant_num
int32_t det_num = 0;
int32_t size_check = SIZE;
if (offset != 0L) size_check += offset;
rc = trexio_read_determinant_num(file, &det_num);
assert(rc == TREXIO_SUCCESS);
assert(det_num == size_check);
// check conversion of determinants into orbital lists
int64_t size_list = TREXIO_NORB_PER_INT * int_num;
int32_t* orb_list_up = (int32_t*) calloc(size_list, sizeof(int32_t));
int32_t* orb_list_dn = (int32_t*) calloc(size_list, sizeof(int32_t));
int32_t occ_num_up, occ_num_dn;
rc = trexio_read_determinant_list(file, 0L, &chunk_read, &det_list_read[0L]);
assert (rc == TREXIO_SUCCESS);
rc = trexio_to_orbital_list_up_dn (int_num, &det_list_read[0], orb_list_up, orb_list_dn, &occ_num_up, &occ_num_dn);
assert (rc == TREXIO_SUCCESS);
assert (occ_num_up == 4);
assert (occ_num_dn == 3);
// DEBUG printing
for (int i=0; i<occ_num_up; i++) {
assert(orb_list_up[i] == i);
}
for (int i=0; i<occ_num_dn; i++) {
assert(orb_list_dn[i] == i);
}
// check conversion of one orbital list into the bitfield determinant representation
int64_t* det_list_check = (int64_t*) calloc(int_num, sizeof(int64_t));
rc = trexio_to_bitfield_list (orb_list_up, occ_num_up, det_list_check, int_num);
assert (rc == TREXIO_SUCCESS);
for (int i=0; i<int_num; i++) {
assert (det_list_check[i] == det_list_read[2*int_num*5+i]);
}
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the memory
free(det_list_read);
free(det_coef_read);
free(det_list_check);
free(orb_list_up);
free(orb_list_dn);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int mo_nums[5] = {10, 20, 40, 100, 300};
for (int i=0 ; i<5 ; ++i) {
int rc = system(RM_COMMAND);
assert (rc == 0);
// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
printf("mo_num = %d\n", mo_nums[i]);
test_write_determinant (TREXIO_FILE, TEST_BACKEND, 0L, mo_nums[i]);
test_has_determinant (TREXIO_FILE, TEST_BACKEND);
test_read_determinant (TREXIO_FILE, TEST_BACKEND, 0L);
// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_determinant (TREXIO_FILE, TEST_BACKEND, (int64_t) SIZE, mo_nums[i]);
test_read_determinant (TREXIO_FILE, TEST_BACKEND, (int64_t) SIZE);
rc = system(RM_COMMAND);
assert (rc == 0);
}
return 0;
}

329
tests/io_determinant_hdf5.c
View File

@ -1,326 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_determinant"
#include "test_macros.h"
#include "io_determinant.c"
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_determinant.h5"
#define RM_COMMAND "rm -f -- " TREXIO_FILE
#define SIZE 100
#define N_CHUNKS 5
#define STATE_TEST 2
#define MO_NUM 150
static int test_write_determinant (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// parameters to be written
int64_t* det_list;
double* det_coef;
int mo_num = MO_NUM;
// write mo_num which will be used to determine the optimal size of int indices
if (trexio_has_mo_num(file) == TREXIO_HAS_NOT) {
rc = trexio_write_mo_num(file, mo_num);
assert(rc == TREXIO_SUCCESS);
}
// get the number of int64 bit fields per determinant
int int_num;
rc = trexio_get_int64_num(file, &int_num);
assert(rc == TREXIO_SUCCESS);
assert(int_num == (MO_NUM-1)/64 + 1);
// allocate memory and fill with values to be written
det_list = (int64_t*) calloc(2 * int_num * SIZE, sizeof(int64_t));
det_coef = (double*) calloc(SIZE, sizeof(double));
for(int i=0; i<SIZE; i++){
det_list[6*i] = 6*i;
det_list[6*i+1] = 6*i+1;
det_list[6*i+2] = 6*i+2;
det_list[6*i+3] = 6*i+3;
det_list[6*i+4] = 6*i+4;
det_list[6*i+5] = 6*i+5;
det_coef[i] = 3.14 + (double) i;
}
// write dataset chunks of sparse data in the file (including FAKE statements)
uint64_t chunk_size = (uint64_t) SIZE/N_CHUNKS;
uint64_t offset_f = 0UL;
uint64_t offset_d = 0UL;
if (offset != 0L) offset_f += offset;
// write the state_id of a given file: 0 is ground state
if (trexio_has_state_id(file) == TREXIO_HAS_NOT) {
rc = trexio_write_state_id(file, STATE_TEST);
assert(rc == TREXIO_SUCCESS);
}
// write n_chunks times using write_sparse
for(int i=0; i<N_CHUNKS; ++i){
rc = trexio_write_determinant_list(file, offset_f, chunk_size, &det_list[2*int_num*offset_d]);
assert(rc == TREXIO_SUCCESS);
rc = trexio_write_determinant_coefficient(file, offset_f, chunk_size, &det_coef[offset_d]);
assert(rc == TREXIO_SUCCESS);
offset_d += chunk_size;
offset_f += chunk_size;
}
// manually check the consistency of the determinant_num and coefficient_size after writing
int64_t coeff_size = 0L;
int64_t determinant_num = 0L;
rc = trexio_read_determinant_num_64(file, &determinant_num);
assert(rc == TREXIO_SUCCESS);
rc = trexio_read_determinant_coefficient_size(file, &coeff_size);
assert(rc == TREXIO_SUCCESS);
assert(determinant_num == coeff_size);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the allocated memeory
free(det_list);
free(det_coef);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_determinant(const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// now check that previously written determinant_list exists
rc = trexio_has_determinant_list(file);
assert(rc==TREXIO_SUCCESS);
rc = trexio_has_state_id(file);
assert(rc==TREXIO_SUCCESS);
// now check that previously written determinant_coefficient exists
rc = trexio_has_determinant_coefficient(file);
assert(rc==TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_determinant (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// compute how many integer bit fields is needed per determinant (for a given spin)
int64_t mo_num;
rc = trexio_read_mo_num_64(file, &mo_num);
assert (rc == TREXIO_SUCCESS);
assert (mo_num == MO_NUM);
int int_num;
rc = trexio_get_int64_num(file, &int_num);
assert (rc == TREXIO_SUCCESS);
assert (int_num == (MO_NUM - 1)/64 + 1);
// define arrays to read into
int64_t* det_list_read;
double* det_coef_read;
double check_diff;
uint64_t size_r = 40L;
det_list_read = (int64_t*) calloc(2*int_num*size_r,sizeof(int64_t));
det_coef_read = (double*) calloc(size_r,sizeof(double));
// specify the read parameters, here:
// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
int64_t chunk_read = 10L;
int64_t offset_file_read = 40L;
int offset_data_read = 5;
int64_t read_size_check;
read_size_check = chunk_read;
if (offset != 0L) offset_file_read += offset;
// read one chunk using the aforementioned parameters
rc = trexio_read_determinant_list(file, offset_file_read, &chunk_read, &det_list_read[2*int_num*offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
assert(det_list_read[0] == 0);
assert(det_list_read[2*int_num*offset_data_read] == 2 * int_num * (int64_t) (offset_file_read-offset));
rc = trexio_read_determinant_coefficient(file, offset_file_read, &chunk_read, &det_coef_read[offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
check_diff = det_coef_read[0] - 0.;
assert(check_diff*check_diff < 1e-14);
check_diff = det_coef_read[offset_data_read] - (3.14 + (double) (offset_file_read-offset));
//printf("%lf %lf\n", check_diff, det_coef_read[offset_data_read]);
assert(check_diff*check_diff < 1e-14);
int32_t state_id = 666;
rc = trexio_read_state_id(file, &state_id);
assert(rc == TREXIO_SUCCESS);
assert(state_id == STATE_TEST);
// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
offset_file_read = 97L;
offset_data_read = 1;
int64_t eof_read_size_check = SIZE - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
if (offset != 0L) offset_file_read += offset;
chunk_read = read_size_check;
// read one chunk that will reach EOF and return TREXIO_END code
rc = trexio_read_determinant_list(file, offset_file_read, &chunk_read, &det_list_read[2*int_num*offset_data_read]);
/*
printf("%s\n", trexio_string_of_error(rc));
for (int i=0; i<size_r; i++) {
printf("%lld %lld\n", det_list_read[6*i], det_list_read[6*i+5]);
}
*/
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
assert(det_list_read[2*int_num*size_r-1] == 0);
assert(det_list_read[2*int_num*offset_data_read] == 2 * int_num * (int64_t) (offset_file_read-offset));
chunk_read = read_size_check;
rc = trexio_read_determinant_coefficient(file, offset_file_read, &chunk_read, &det_coef_read[offset_data_read]);
/*
printf("%s\n", trexio_string_of_error(rc));
for (int i=0; i<size_r; i++) {
printf("%lf\n", det_coef_read[i]);
}
*/
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
check_diff= det_coef_read[size_r-1] - 0.;
//printf("%lf %lf\n", check_diff, det_coef_read[size_r-1]);
assert(check_diff*check_diff < 1e-14);
// check the value of determinant_num
int32_t det_num = 0;
int32_t size_check = SIZE;
if (offset != 0L) size_check += offset;
rc = trexio_read_determinant_num(file, &det_num);
assert(rc == TREXIO_SUCCESS);
assert(det_num == size_check);
// check conversion of determinants into orbital lists
int64_t size_list = TREXIO_NORB_PER_INT * int_num;
int32_t* orb_list_up = (int32_t*) calloc(size_list, sizeof(int32_t));
int32_t* orb_list_dn = (int32_t*) calloc(size_list, sizeof(int32_t));
int32_t occ_num_up, occ_num_dn;
rc = trexio_to_orbital_list_up_dn (int_num, &det_list_read[2*int_num*5], orb_list_up, orb_list_dn, &occ_num_up, &occ_num_dn);
assert (rc == TREXIO_SUCCESS);
assert (occ_num_up == 14);
assert (occ_num_dn == 17);
/* // DEBUG printing
printf("occ_num_up : %d ; occ_num_dn : %d \n", occ_num_up, occ_num_dn);
for (int i=0; i<occ_num_up; i++) {
printf("%d ", orb_list_up[i]);
}
printf("| ");
for (int i=0; i<occ_num_dn; i++) {
printf("%d ", orb_list_dn[i]);
}
printf("\n");
*/
// check conversion of one orbital list into the bitfield determinant representation
int64_t* det_list_check = (int64_t*) calloc(int_num, sizeof(int64_t));
rc = trexio_to_bitfield_list (orb_list_up, occ_num_up, det_list_check, int_num);
assert (rc == TREXIO_SUCCESS);
for (int i=0; i<int_num; i++) {
assert (det_list_check[i] == det_list_read[2*int_num*5+i]);
}
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the memory
free(det_list_read);
free(det_coef_read);
free(det_list_check);
free(orb_list_up);
free(orb_list_dn);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_determinant (TREXIO_FILE, TEST_BACKEND, 0);
test_has_determinant (TREXIO_FILE, TEST_BACKEND);
test_read_determinant (TREXIO_FILE, TEST_BACKEND, 0);
// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_determinant (TREXIO_FILE, TEST_BACKEND, SIZE);
test_read_determinant (TREXIO_FILE, TEST_BACKEND, SIZE);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

329
tests/io_determinant_text.c
View File

@ -1,326 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_determinant"
#include "test_macros.h"
#include "io_determinant.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_determinant.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
#define SIZE 100
#define N_CHUNKS 5
#define STATE_TEST 2
#define MO_NUM 150
static int test_write_determinant (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// parameters to be written
int64_t* det_list;
double* det_coef;
int mo_num = MO_NUM;
// write mo_num which will be used to determine the optimal size of int indices
if (trexio_has_mo_num(file) == TREXIO_HAS_NOT) {
rc = trexio_write_mo_num(file, mo_num);
assert(rc == TREXIO_SUCCESS);
}
// get the number of int64 bit fields per determinant
int int_num;
rc = trexio_get_int64_num(file, &int_num);
assert(rc == TREXIO_SUCCESS);
assert(int_num == (MO_NUM-1)/64 + 1);
// allocate memory and fill with values to be written
det_list = (int64_t*) calloc(2 * int_num * SIZE, sizeof(int64_t));
det_coef = (double*) calloc(SIZE, sizeof(double));
for(int i=0; i<SIZE; i++){
det_list[6*i] = 6*i;
det_list[6*i+1] = 6*i+1;
det_list[6*i+2] = 6*i+2;
det_list[6*i+3] = 6*i+3;
det_list[6*i+4] = 6*i+4;
det_list[6*i+5] = 6*i+5;
det_coef[i] = 3.14 + (double) i;
}
// write dataset chunks of sparse data in the file (including FAKE statements)
uint64_t chunk_size = (uint64_t) SIZE/N_CHUNKS;
uint64_t offset_f = 0UL;
uint64_t offset_d = 0UL;
if (offset != 0L) offset_f += offset;
// write the state_id of a given file: 0 is ground state
if (trexio_has_state_id(file) == TREXIO_HAS_NOT) {
rc = trexio_write_state_id(file, STATE_TEST);
assert(rc == TREXIO_SUCCESS);
}
// write n_chunks times using write_sparse
for(int i=0; i<N_CHUNKS; ++i){
rc = trexio_write_determinant_list(file, offset_f, chunk_size, &det_list[2*int_num*offset_d]);
assert(rc == TREXIO_SUCCESS);
rc = trexio_write_determinant_coefficient(file, offset_f, chunk_size, &det_coef[offset_d]);
assert(rc == TREXIO_SUCCESS);
offset_d += chunk_size;
offset_f += chunk_size;
}
// manually check the consistency of the determinant_num and coefficient_size after writing
int64_t coeff_size = 0L;
int64_t determinant_num = 0L;
rc = trexio_read_determinant_num_64(file, &determinant_num);
assert(rc == TREXIO_SUCCESS);
rc = trexio_read_determinant_coefficient_size(file, &coeff_size);
assert(rc == TREXIO_SUCCESS);
assert(determinant_num == coeff_size);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the allocated memeory
free(det_list);
free(det_coef);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_determinant(const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// now check that previously written determinant_list exists
rc = trexio_has_determinant_list(file);
assert(rc==TREXIO_SUCCESS);
rc = trexio_has_state_id(file);
assert(rc==TREXIO_SUCCESS);
// now check that previously written determinant_coefficient exists
rc = trexio_has_determinant_coefficient(file);
assert(rc==TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_determinant (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// compute how many integer bit fields is needed per determinant (for a given spin)
int64_t mo_num;
rc = trexio_read_mo_num_64(file, &mo_num);
assert (rc == TREXIO_SUCCESS);
assert (mo_num == MO_NUM);
int int_num;
rc = trexio_get_int64_num(file, &int_num);
assert (rc == TREXIO_SUCCESS);
assert (int_num == (MO_NUM - 1)/64 + 1);
// define arrays to read into
int64_t* det_list_read;
double* det_coef_read;
double check_diff;
uint64_t size_r = 40L;
det_list_read = (int64_t*) calloc(2*int_num*size_r,sizeof(int64_t));
det_coef_read = (double*) calloc(size_r,sizeof(double));
// specify the read parameters, here:
// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
int64_t chunk_read = 10L;
int64_t offset_file_read = 40L;
int offset_data_read = 5;
int64_t read_size_check;
read_size_check = chunk_read;
if (offset != 0L) offset_file_read += offset;
// read one chunk using the aforementioned parameters
rc = trexio_read_determinant_list(file, offset_file_read, &chunk_read, &det_list_read[2*int_num*offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
assert(det_list_read[0] == 0);
assert(det_list_read[2*int_num*offset_data_read] == 2 * int_num * (int64_t) (offset_file_read-offset));
rc = trexio_read_determinant_coefficient(file, offset_file_read, &chunk_read, &det_coef_read[offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
check_diff = det_coef_read[0] - 0.;
assert(check_diff*check_diff < 1e-14);
check_diff = det_coef_read[offset_data_read] - (3.14 + (double) (offset_file_read-offset));
//printf("%lf %lf\n", check_diff, det_coef_read[offset_data_read]);
assert(check_diff*check_diff < 1e-14);
int32_t state_id = 666;
rc = trexio_read_state_id(file, &state_id);
assert(rc == TREXIO_SUCCESS);
assert(state_id == STATE_TEST);
// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
offset_file_read = 97L;
offset_data_read = 1;
int64_t eof_read_size_check = SIZE - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
if (offset != 0L) offset_file_read += offset;
chunk_read = read_size_check;
// read one chunk that will reach EOF and return TREXIO_END code
rc = trexio_read_determinant_list(file, offset_file_read, &chunk_read, &det_list_read[2*int_num*offset_data_read]);
/*
printf("%s\n", trexio_string_of_error(rc));
for (int i=0; i<size_r; i++) {
printf("%lld %lld\n", det_list_read[6*i], det_list_read[6*i+5]);
}
*/
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
assert(det_list_read[2*int_num*size_r-1] == 0);
assert(det_list_read[2*int_num*offset_data_read] == 2 * int_num * (int64_t) (offset_file_read-offset));
chunk_read = read_size_check;
rc = trexio_read_determinant_coefficient(file, offset_file_read, &chunk_read, &det_coef_read[offset_data_read]);
/*
printf("%s\n", trexio_string_of_error(rc));
for (int i=0; i<size_r; i++) {
printf("%lf\n", det_coef_read[i]);
}
*/
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
check_diff= det_coef_read[size_r-1] - 0.;
//printf("%lf %lf\n", check_diff, det_coef_read[size_r-1]);
assert(check_diff*check_diff < 1e-14);
// check the value of determinant_num
int32_t det_num = 0;
int32_t size_check = SIZE;
if (offset != 0L) size_check += offset;
rc = trexio_read_determinant_num(file, &det_num);
assert(rc == TREXIO_SUCCESS);
assert(det_num == size_check);
// check conversion of determinants into orbital lists
int64_t size_list = TREXIO_NORB_PER_INT * int_num;
int32_t* orb_list_up = (int32_t*) calloc(size_list, sizeof(int32_t));
int32_t* orb_list_dn = (int32_t*) calloc(size_list, sizeof(int32_t));
int32_t occ_num_up, occ_num_dn;
rc = trexio_to_orbital_list_up_dn (int_num, &det_list_read[2*int_num*5], orb_list_up, orb_list_dn, &occ_num_up, &occ_num_dn);
assert (rc == TREXIO_SUCCESS);
assert (occ_num_up == 14);
assert (occ_num_dn == 17);
/* // DEBUG printing
printf("occ_num_up : %d ; occ_num_dn : %d \n", occ_num_up, occ_num_dn);
for (int i=0; i<occ_num_up; i++) {
printf("%d ", orb_list_up[i]);
}
printf("| ");
for (int i=0; i<occ_num_dn; i++) {
printf("%d ", orb_list_dn[i]);
}
printf("\n");
*/
// check conversion of one orbital list into the bitfield determinant representation
int64_t* det_list_check = (int64_t*) calloc(int_num, sizeof(int64_t));
rc = trexio_to_bitfield_list (orb_list_up, occ_num_up, det_list_check, int_num);
assert (rc == TREXIO_SUCCESS);
for (int i=0; i<int_num; i++) {
assert (det_list_check[i] == det_list_read[2*int_num*5+i]);
}
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the memory
free(det_list_read);
free(det_coef_read);
free(det_list_check);
free(orb_list_up);
free(orb_list_dn);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_determinant (TREXIO_FILE, TEST_BACKEND, 0);
test_has_determinant (TREXIO_FILE, TEST_BACKEND);
test_read_determinant (TREXIO_FILE, TEST_BACKEND, 0);
// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_determinant (TREXIO_FILE, TEST_BACKEND, SIZE);
test_read_determinant (TREXIO_FILE, TEST_BACKEND, SIZE);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with numerical (floating point) values into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
if (rc != TREXIO_SUCCESS) {
printf("%s\n", trexio_string_of_error(rc));
}
assert (rc == TREXIO_SUCCESS);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical dataset in a file
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset exists
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// check that another dataset does not exist
rc = trexio_has_mo_coefficient(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with numerical (floating point) values from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
double* coord;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical (floating point) dataset from the file
coord = (double*) calloc(3*num, sizeof(double));
rc = trexio_read_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-14 );
free(coord);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

152
tests/io_dset_float_hdf5.c
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@ -1,148 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_dset_f.h5"
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with numerical (floating point) values into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical dataset in a file
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset exists
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// check that another dataset does not exist
rc = trexio_has_mo_coefficient(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with numerical (floating point) values from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
double* coord;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical (floating point) dataset from the file
coord = (double*) calloc(3*num, sizeof(double));
rc = trexio_read_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-14 );
free(coord);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_dset_float"
#include "test_macros.h"
#include "io_dset_float.c"

150
tests/io_dset_float_text.c
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@ -1,146 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_dset_f.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with numerical (floating point) values into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical dataset in a file
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset exists
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// check that another dataset does not exist
rc = trexio_has_mo_coefficient(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with numerical (floating point) values from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
double* coord;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical (floating point) dataset from the file
coord = (double*) calloc(3*num, sizeof(double));
rc = trexio_read_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-14 );
free(coord);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_dset_float"
#include "test_macros.h"
#include "io_dset_float.c"

147
tests/io_dset_int.c Normal file
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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with numerical (int) values into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// 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 ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_basis_shell_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical (integer) dataset in a file
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);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the group exists
rc = trexio_has_basis(file);
assert(rc==TREXIO_SUCCESS);
// check that the group does not exist
rc = trexio_has_mo(file);
assert(rc==TREXIO_HAS_NOT);
// check that the previously written dataset exists
rc = trexio_has_basis_nucleus_index(file);
assert (rc == TREXIO_SUCCESS);
// check that another dataset does not exist
rc = trexio_has_mo_coefficient(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with numericali (int) values from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num = 0;
int* nucl_index = NULL;
int state_id = 0;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_basis_shell_num(file, &num);
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);
assert (rc == TREXIO_SUCCESS);
assert (nucl_index[num-1] == num-1);
free(nucl_index);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

144
tests/io_dset_int_hdf5.c
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@ -1,140 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_dset_i.h5"
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with numerical (int) values into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_basis_shell_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical (integer) dataset in a file
rc = trexio_write_basis_nucleus_index(file, nucl_index);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the group exists
rc = trexio_has_basis(file);
assert(rc==TREXIO_SUCCESS);
// check that the group does not exist
rc = trexio_has_mo(file);
assert(rc==TREXIO_HAS_NOT);
// check that the previously written dataset exists
rc = trexio_has_basis_nucleus_index(file);
assert (rc == TREXIO_SUCCESS);
// check that another dataset does not exist
rc = trexio_has_mo_coefficient(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with numericali (int) values from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
int* nucl_index;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_basis_shell_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical dataset from the file
nucl_index = (int*) calloc(num, sizeof(int));
rc = trexio_read_basis_nucleus_index(file, nucl_index);
assert (rc == TREXIO_SUCCESS);
assert (nucl_index[num-1] == num-1);
free(nucl_index);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_dset_int"
#include "test_macros.h"
#include "io_dset_int.c"

144
tests/io_dset_int_text.c
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@ -1,140 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_dset_i.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with numerical (int) values into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_basis_shell_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write numerical (integer) dataset in a file
rc = trexio_write_basis_nucleus_index(file, nucl_index);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the group exists
rc = trexio_has_basis(file);
assert(rc==TREXIO_SUCCESS);
// check that the group does not exist
rc = trexio_has_mo(file);
assert(rc==TREXIO_HAS_NOT);
// check that the previously written dataset exists
rc = trexio_has_basis_nucleus_index(file);
assert (rc == TREXIO_SUCCESS);
// check that another dataset does not exist
rc = trexio_has_mo_coefficient(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with numericali (int) values from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
int* nucl_index;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_basis_shell_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical dataset from the file
nucl_index = (int*) calloc(num, sizeof(int));
rc = trexio_read_basis_nucleus_index(file, nucl_index);
assert (rc == TREXIO_SUCCESS);
assert (nucl_index[num-1] == num-1);
free(nucl_index);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_dset_int"
#include "test_macros.h"
#include "io_dset_int.c"

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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define N_CHUNKS 4
static int test_write_dset_sparse (const char* file_name, const back_end_t backend, const int64_t offset, const int64_t mo_num) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// parameters to be written
int32_t* index;
double* value;
int64_t size = mo_num/2;
index = calloc(4L*size, sizeof(int32_t));
value = calloc(size, sizeof(double));
for(int i=0; i<size; i++){
index[4*i] = i;
index[4*i+1] = i+1;
index[4*i+2] = i+2;
index[4*i+3] = i+3;
value[i] = 3.14 + (double) i;
}
// write mo_num which will be used to determine the optimal size of int indices
if (trexio_has_mo_num(file) == TREXIO_HAS_NOT) {
rc = trexio_write_mo_num(file, mo_num);
assert(rc == TREXIO_SUCCESS);
}
// write dataset chunks of sparse data in the file (including FAKE statements)
uint64_t chunk_size = (uint64_t) size/N_CHUNKS;
chunk_size = chunk_size > 0 ? chunk_size : (uint64_t) size;
int n_chunks = size/chunk_size;
printf("chunk_size = %ld\n", (long) chunk_size);
printf("n_chunks = %d\n", n_chunks);
uint64_t offset_f = 0UL + offset;
uint64_t offset_d = 0UL;
// write n_chunks times using write_sparse
while(offset_d < size) {
if (offset_d+chunk_size > size) chunk_size = size-offset_d;
printf("chunk_size = %ld\n", (long) chunk_size);
if (chunk_size == 0L) break;
rc = trexio_write_mo_2e_int_eri(file, offset_f, chunk_size, &index[4*offset_d], &value[offset_d]);
printf("%5d: %s\n", __LINE__, trexio_string_of_error(rc));
assert(rc == TREXIO_SUCCESS);
offset_d += chunk_size;
offset_f += chunk_size;
}
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the allocated memeory
free(index);
free(value);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset_sparse (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// check that the group exists
rc = trexio_has_mo_2e_int(file);
assert(rc==TREXIO_SUCCESS);
// check that the group does not exist
rc = trexio_has_rdm(file);
assert(rc==TREXIO_HAS_NOT);
// first check that mo_2e_int_eri_lr (we only write non-lr component in this unit test)
rc = trexio_has_mo_2e_int_eri_lr(file);
assert(rc==TREXIO_HAS_NOT);
// check that previous call to has_sparse did not create a file/dset
rc = trexio_has_mo_2e_int_eri_lr(file);
assert(rc==TREXIO_HAS_NOT);
// now check that previously written mo_2e_int_eri exists
rc = trexio_has_mo_2e_int_eri(file);
assert(rc==TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_sparse (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
int32_t mo_num = 0;
rc = trexio_read_mo_num(file, &mo_num);
assert(rc == TREXIO_SUCCESS);
printf("%5d: mo_num = %d\n", __LINE__, mo_num);
const int64_t size = mo_num/2;
// define arrays to read into
int32_t* index_read;
double* value_read;
uint64_t size_r = mo_num;
index_read = (int32_t*) calloc(4L*size_r,sizeof(int32_t));
value_read = (double*) calloc(size_r,sizeof(double));
// specify the read parameters, here:
// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
int64_t chunk_read = size/3;
chunk_read = chunk_read < 2 ? 2 : chunk_read;
int64_t offset_file_read = 1;
int64_t read_size_check;
read_size_check = chunk_read;
if (offset != 0L) offset_file_read += offset;
// read one chunk using the aforementioned parameters
rc = trexio_read_mo_2e_int_eri(file, offset_file_read, &chunk_read, &index_read[0], &value_read[0]);
printf("%5d: %s\n", __LINE__, trexio_string_of_error(rc));
/*
for (int i=0 ; i<chunk_read ; ++i) {
printf("%d %d | %ld %ld %ld\n", i, index_read[i], (long) offset, (long) offset_file_read, (long) chunk_read);
}
*/
//assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
assert(index_read[0] == offset_file_read-offset);
// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
int64_t size_max;
rc = trexio_read_mo_2e_int_eri_size(file, &size_max);
assert(rc == TREXIO_SUCCESS);
offset_file_read = size_max-chunk_read+1;
int64_t eof_read_size_check = size_max - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
// read one chunk that will reach EOF and return TREXIO_END code
rc = trexio_read_mo_2e_int_eri(file, offset_file_read, &chunk_read, &index_read[0], &value_read[0]);
printf("%5d: %s\n", __LINE__, trexio_string_of_error(rc));
assert(rc == TREXIO_END);
printf("%d %d x\n", (int32_t) index_read[0], (int32_t) (4L*offset_file_read));
printf("%ld %ld\n", (long) chunk_read, (long) eof_read_size_check);
assert(chunk_read == eof_read_size_check);
printf("%d %d\n", index_read[0] , (int32_t) (offset_file_read - offset));
assert(index_read[0] == (int32_t) offset_file_read - offset);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the memory
free(index_read);
free(value_read);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_sparse_size (const char* file_name, const back_end_t backend, const int64_t size_check) {
/* Try to read a size of the dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// define the variable to read into
int64_t size_written;
// read one chunk using the aforementioned parameters
rc = trexio_read_mo_2e_int_eri_size(file, &size_written);
assert(rc == TREXIO_SUCCESS);
printf("%5d: %ld %ld\n", __LINE__, (long) size_written, (long) size_check);
assert(size_written == size_check);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
int32_t mo_num[8] = {6,12,30,62,252,510,1020,9000};
for (int i=0 ; i<8 ; ++i) {
printf("%5d: mo_num = %d\n", __LINE__, mo_num[i]);
const int64_t size = mo_num[i]/2;
// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND, 0, mo_num[i]);
test_has_dset_sparse (TREXIO_FILE, TEST_BACKEND);
test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND, 0);
test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, size);
// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND, size, mo_num[i]);
test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND, size);
test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, 2*size);
rc = system(RM_COMMAND);
assert (rc == 0);
}
return 0;
}

242
tests/io_dset_sparse_hdf5.c
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@ -1,238 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_dset_sparse.h5"
#define RM_COMMAND "rm -f -- " TREXIO_FILE
#define SIZE 100
#define N_CHUNKS 5
static int test_write_dset_sparse (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// parameters to be written
int32_t* index;
double* value;
index = calloc(4L*SIZE, sizeof(int32_t));
value = calloc(SIZE, sizeof(double));
for(int i=0; i<SIZE; i++){
index[4*i] = 4*i;
index[4*i+1] = 4*i+1;
index[4*i+2] = 4*i+2;
index[4*i+3] = 4*i+3;
value[i] = 3.14 + (double) i;
}
// write mo_num which will be used to determine the optimal size of int indices
if (trexio_has_mo_num(file) == TREXIO_HAS_NOT) {
rc = trexio_write_mo_num(file, 1000);
assert(rc == TREXIO_SUCCESS);
}
// write dataset chunks of sparse data in the file (including FAKE statements)
uint64_t chunk_size = (uint64_t) SIZE/N_CHUNKS;
uint64_t offset_f = 0UL;
uint64_t offset_d = 0UL;
if (offset != 0L) offset_f += offset;
// write n_chunks times using write_sparse
for(int i=0; i<N_CHUNKS; ++i){
rc = trexio_write_mo_2e_int_eri(file, offset_f, chunk_size, &index[4*offset_d], &value[offset_d]);
assert(rc == TREXIO_SUCCESS);
offset_d += chunk_size;
offset_f += chunk_size;
}
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the allocated memeory
free(index);
free(value);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset_sparse (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// check that the group exists
rc = trexio_has_mo_2e_int(file);
assert(rc==TREXIO_SUCCESS);
// check that the group does not exist
rc = trexio_has_rdm(file);
assert(rc==TREXIO_HAS_NOT);
// first check that mo_2e_int_eri_lr (we only write non-lr component in this unit test)
rc = trexio_has_mo_2e_int_eri_lr(file);
assert(rc==TREXIO_HAS_NOT);
// check that previous call to has_sparse did not create a file/dset
rc = trexio_has_mo_2e_int_eri_lr(file);
assert(rc==TREXIO_HAS_NOT);
// now check that previously written mo_2e_int_eri exists
rc = trexio_has_mo_2e_int_eri(file);
assert(rc==TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_sparse (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// define arrays to read into
int32_t* index_read;
double* value_read;
uint64_t size_r = 40L;
index_read = (int32_t*) calloc(4L*size_r,sizeof(int32_t));
value_read = (double*) calloc(size_r,sizeof(double));
// specify the read parameters, here:
// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
int64_t chunk_read = 10L;
int64_t offset_file_read = 40L;
int offset_data_read = 5;
int64_t read_size_check;
read_size_check = chunk_read;
if (offset != 0L) offset_file_read += offset;
// read one chunk using the aforementioned parameters
rc = trexio_read_mo_2e_int_eri(file, offset_file_read, &chunk_read, &index_read[4*offset_data_read], &value_read[offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
assert(index_read[0] == 0);
assert(index_read[4*offset_data_read] == 4 * (int32_t) (offset_file_read-offset));
// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
offset_file_read = 97L;
offset_data_read = 1;
int64_t eof_read_size_check = SIZE - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
if (offset != 0L) offset_file_read += offset;
// read one chunk that will reach EOF and return TREXIO_END code
rc = trexio_read_mo_2e_int_eri(file, offset_file_read, &chunk_read, &index_read[4*offset_data_read], &value_read[offset_data_read]);
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
assert(index_read[4*size_r-1] == 0);
assert(index_read[4*offset_data_read] == 4 * (int32_t) (offset_file_read-offset));
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the memory
free(index_read);
free(value_read);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_sparse_size (const char* file_name, const back_end_t backend, const int64_t size_check) {
/* Try to read a size of the dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// define the variable to read into
int64_t size_written;
// read one chunk using the aforementioned parameters
rc = trexio_read_mo_2e_int_eri_size(file, &size_written);
assert(rc == TREXIO_SUCCESS);
assert(size_written == size_check);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND, 0);
test_has_dset_sparse (TREXIO_FILE, TEST_BACKEND);
test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND, 0);
test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, SIZE);
// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND, SIZE);
test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND, SIZE);
test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, SIZE*2);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_dset_sparse"
#include "test_macros.h"
#include "io_dset_sparse.c"

242
tests/io_dset_sparse_text.c
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@ -1,238 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_dset_sparse.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
#define SIZE 100
#define N_CHUNKS 5
static int test_write_dset_sparse (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// parameters to be written
int32_t* index;
double* value;
index = calloc(4L*SIZE, sizeof(int32_t));
value = calloc(SIZE, sizeof(double));
for(int i=0; i<SIZE; i++){
index[4*i] = 4*i;
index[4*i+1] = 4*i+1;
index[4*i+2] = 4*i+2;
index[4*i+3] = 4*i+3;
value[i] = 3.14 + (double) i;
}
// write mo_num which will be used to determine the optimal size of int indices
if (trexio_has_mo_num(file) == TREXIO_HAS_NOT) {
rc = trexio_write_mo_num(file, 1000);
assert(rc == TREXIO_SUCCESS);
}
// write dataset chunks of sparse data in the file (including FAKE statements)
uint64_t chunk_size = (uint64_t) SIZE/N_CHUNKS;
uint64_t offset_f = 0UL;
uint64_t offset_d = 0UL;
if (offset != 0L) offset_f += offset;
// write n_chunks times using write_sparse
for(int i=0; i<N_CHUNKS; ++i){
rc = trexio_write_mo_2e_int_eri(file, offset_f, chunk_size, &index[4*offset_d], &value[offset_d]);
assert(rc == TREXIO_SUCCESS);
offset_d += chunk_size;
offset_f += chunk_size;
}
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the allocated memeory
free(index);
free(value);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset_sparse (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// check that the group exists
rc = trexio_has_mo_2e_int(file);
assert(rc==TREXIO_SUCCESS);
// check that the group does not exist
rc = trexio_has_rdm(file);
assert(rc==TREXIO_HAS_NOT);
// first check that mo_2e_int_eri_lr (we only write non-lr component in this unit test)
rc = trexio_has_mo_2e_int_eri_lr(file);
assert(rc==TREXIO_HAS_NOT);
// check that previous call to has_sparse did not create a file/dset
rc = trexio_has_mo_2e_int_eri_lr(file);
assert(rc==TREXIO_HAS_NOT);
// now check that previously written mo_2e_int_eri exists
rc = trexio_has_mo_2e_int_eri(file);
assert(rc==TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_sparse (const char* file_name, const back_end_t backend, const int64_t offset) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// define arrays to read into
int32_t* index_read;
double* value_read;
uint64_t size_r = 40L;
index_read = (int32_t*) calloc(4L*size_r,sizeof(int32_t));
value_read = (double*) calloc(size_r,sizeof(double));
// specify the read parameters, here:
// 1 chunk of 10 elements using offset of 40 (i.e. lines No. 40--59) into elements of the array starting from 5
int64_t chunk_read = 10L;
int64_t offset_file_read = 40L;
int offset_data_read = 5;
int64_t read_size_check;
read_size_check = chunk_read;
if (offset != 0L) offset_file_read += offset;
// read one chunk using the aforementioned parameters
rc = trexio_read_mo_2e_int_eri(file, offset_file_read, &chunk_read, &index_read[4*offset_data_read], &value_read[offset_data_read]);
assert(rc == TREXIO_SUCCESS);
assert(chunk_read == read_size_check);
assert(index_read[0] == 0);
assert(index_read[4*offset_data_read] == 4 * (int32_t) (offset_file_read-offset));
// now attempt to read so that one encounters end of file during reading (i.e. offset_file_read + chunk_read > size_max)
offset_file_read = 97L;
offset_data_read = 1;
int64_t eof_read_size_check = SIZE - offset_file_read; // if offset_file_read=97 => only 3 integrals will be read out of total of 100
if (offset != 0L) offset_file_read += offset;
// read one chunk that will reach EOF and return TREXIO_END code
rc = trexio_read_mo_2e_int_eri(file, offset_file_read, &chunk_read, &index_read[4*offset_data_read], &value_read[offset_data_read]);
assert(rc == TREXIO_END);
assert(chunk_read == eof_read_size_check);
assert(index_read[4*size_r-1] == 0);
assert(index_read[4*offset_data_read] == 4 * (int32_t) (offset_file_read-offset));
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// free the memory
free(index_read);
free(value_read);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_sparse_size (const char* file_name, const back_end_t backend, const int64_t size_check) {
/* Try to read a size of the dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// define the variable to read into
int64_t size_written;
// read one chunk using the aforementioned parameters
rc = trexio_read_mo_2e_int_eri_size(file, &size_written);
assert(rc == TREXIO_SUCCESS);
assert(size_written == size_check);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
// check the first write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND, 0);
test_has_dset_sparse (TREXIO_FILE, TEST_BACKEND);
test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND, 0);
test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, SIZE);
// check the second write attempt (SIZE elements written in N_CHUNKS chunks)
test_write_dset_sparse (TREXIO_FILE, TEST_BACKEND, SIZE);
test_read_dset_sparse (TREXIO_FILE, TEST_BACKEND, SIZE);
test_read_dset_sparse_size(TREXIO_FILE, TEST_BACKEND, SIZE*2);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_dset_sparse"
#include "test_macros.h"
#include "io_dset_sparse.c"

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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
static int test_write_dset_str (const char* file_name, const back_end_t backend) {
/* Try to write an array of strings into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
const char* labels[] = {"C" ,
"Na FAKE" ,
"C" ,
"C" ,
"C" ,
"C" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H FAKE" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write dataset of string in the file (including FAKE statements)
int max_str_len = 16;
rc = trexio_write_nucleus_label(file, labels, max_str_len);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset_str (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of strings in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset of strings exists
rc = trexio_has_nucleus_label(file);
assert (rc == TREXIO_SUCCESS);
// check that the dataset of strings does not exist
rc = trexio_has_mo_symmetry(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_str (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with strings from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
char** labels;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read the arrays of strings truncated to max_str_len=2 symbols
int max_str_len = 2;
labels = (char**) malloc(num*sizeof(char*));
for (int i=0; i<num; i++){
labels[i] = (char*) malloc((max_str_len+1)*sizeof(char));
}
rc = trexio_read_nucleus_label(file, labels, max_str_len);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(labels[0], "C") == 0);
assert (strcmp(labels[1], "Na") == 0);
for (int i=0; i<num; i++){
free(labels[i]);
}
free(labels);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset_str (TREXIO_FILE, TEST_BACKEND);
test_has_dset_str (TREXIO_FILE, TEST_BACKEND);
test_read_dset_str (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

160
tests/io_dset_str_hdf5.c
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@ -1,157 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_dset_s.h5"
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_write_dset_str (const char* file_name, const back_end_t backend) {
/* Try to write an array of strings into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
const char* labels[] = {"C" ,
"Na FAKE" ,
"C" ,
"C" ,
"C" ,
"C" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H FAKE" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write dataset of string in the file (including FAKE statements)
int max_str_len = 16;
rc = trexio_write_nucleus_label(file, labels, max_str_len);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset_str (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of strings in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset of strings exists
rc = trexio_has_nucleus_label(file);
assert (rc == TREXIO_SUCCESS);
// check that the dataset of strings does not exist
rc = trexio_has_mo_symmetry(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_str (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with strings from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
char** labels;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read the arrays of strings truncated to max_str_len=2 symbols
int max_str_len = 2;
labels = (char**) malloc(num*sizeof(char*));
for (int i=0; i<num; i++){
labels[i] = (char*) malloc((max_str_len+1)*sizeof(char));
}
rc = trexio_read_nucleus_label(file, labels, max_str_len);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(labels[0], "C") == 0);
assert (strcmp(labels[1], "Na") == 0);
for (int i=0; i<num; i++){
free(labels[i]);
}
free(labels);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset_str (TREXIO_FILE, TEST_BACKEND);
test_has_dset_str (TREXIO_FILE, TEST_BACKEND);
test_read_dset_str (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_dset_str"
#include "test_macros.h"
#include "io_dset_str.c"

159
tests/io_dset_str_text.c
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@ -1,155 +1,4 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_dset_s.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_dset_str (const char* file_name, const back_end_t backend) {
/* Try to write an array of strings into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
const char* labels[] = {"C" ,
"Na FAKE" ,
"C" ,
"C" ,
"C" ,
"C" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H FAKE" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
// write dataset of string in the file (including FAKE statements)
int max_str_len = 16;
rc = trexio_write_nucleus_label(file, labels, max_str_len);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset_str (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset of strings in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset of strings exists
rc = trexio_has_nucleus_label(file);
assert (rc == TREXIO_SUCCESS);
// check that the dataset of strings does not exist
rc = trexio_has_mo_symmetry(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset_str (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with strings from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
char **labels;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read the arrays of strings truncated to max_str_len=2 symbols
int max_str_len = 2;
labels = (char**) malloc(num*sizeof(char*));
for (int i=0; i<num; i++){
labels[i] = (char*) malloc((max_str_len+1)*sizeof(char));
}
rc = trexio_read_nucleus_label(file, labels, max_str_len);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(labels[0], "C") == 0);
assert (strcmp(labels[1], "Na") == 0);
for (int i=0; i<num; i++){
free(labels[i]);
}
free(labels);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset_str (TREXIO_FILE, TEST_BACKEND);
test_has_dset_str (TREXIO_FILE, TEST_BACKEND);
test_read_dset_str (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_dset_str"
#include "test_macros.h"
#include "io_dset_str.c"

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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
static int test_write_jastrow (const char* file_name, const back_end_t backend) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
#define nucleus_num 3
#define ee_num 2
#define en_num 3
#define een_num 6
rc = trexio_write_nucleus_num(file, nucleus_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_type(file, "CHAMP", 6);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_ee_num(file, ee_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_en_num(file, en_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_een_num(file, een_num);
assert (rc == TREXIO_SUCCESS);
double ee [2] = { 0.5, 2. };
rc = trexio_write_jastrow_ee(file, ee);
assert (rc == TREXIO_SUCCESS);
double en [3] = { 1., 2., 3. };
rc = trexio_write_jastrow_en(file, en);
assert (rc == TREXIO_SUCCESS);
double een [6] = { 11., 12., 13., 14., 15., 16. };
rc = trexio_write_jastrow_een(file, een);
assert (rc == TREXIO_SUCCESS);
int en_nucleus [3] = { 0, 1, 2 };
rc = trexio_write_jastrow_en_nucleus(file, en_nucleus);
assert (rc == TREXIO_SUCCESS);
int een_nucleus [6] = { 0, 0, 1, 1, 2, 2 };
rc = trexio_write_jastrow_een_nucleus(file, een_nucleus);
assert (rc == TREXIO_SUCCESS);
double ee_scaling = 1.0;
rc = trexio_write_jastrow_ee_scaling(file, ee_scaling);
assert (rc == TREXIO_SUCCESS);
double en_scaling[3] = { 0.5, 1.0, 0.5 };
rc = trexio_write_jastrow_en_scaling(file, en_scaling);
assert (rc == TREXIO_SUCCESS);
#undef nucleus_num
#undef ee_num
#undef en_num
#undef een_num
rc = trexio_close(file);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_jastrow (const char* file_name, const back_end_t backend) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
int nucleus_num = 0;
rc = trexio_read_nucleus_num(file, &nucleus_num);
assert (rc == TREXIO_SUCCESS);
assert (nucleus_num == 3);
char type[16] = "";
rc = trexio_read_jastrow_type(file, type, 16);
assert (rc == TREXIO_SUCCESS);
assert (strcmp("CHAMP",type) == 0);
int ee_num = 0;
rc = trexio_read_jastrow_ee_num(file, &ee_num);
assert (rc == TREXIO_SUCCESS);
assert (ee_num == 2);
int en_num = 0;
rc = trexio_read_jastrow_en_num(file, &en_num);
assert (rc == TREXIO_SUCCESS);
assert (en_num == nucleus_num);
int een_num = 0;
rc = trexio_read_jastrow_een_num(file, &een_num);
assert (rc == TREXIO_SUCCESS);
assert (een_num == 2*nucleus_num);
double ee [2] = { 0., 0. };
rc = trexio_read_jastrow_ee(file, ee);
assert (rc == TREXIO_SUCCESS);
assert (ee[0] == 0.5);
assert (ee[1] == 2.0);
double en [3] = { 0., 0., 0. };
rc = trexio_read_jastrow_en(file, en);
assert (rc == TREXIO_SUCCESS);
assert (en[0] == 1.0);
assert (en[1] == 2.0);
assert (en[2] == 3.0);
double een [6];
rc = trexio_read_jastrow_een(file, een);
assert (rc == TREXIO_SUCCESS);
assert (een[0] == 11.0);
assert (een[1] == 12.0);
assert (een[2] == 13.0);
assert (een[3] == 14.0);
assert (een[4] == 15.0);
assert (een[5] == 16.0);
int en_nucleus [3] = { 0, 0, 0 };
rc = trexio_read_jastrow_en_nucleus(file, en_nucleus);
assert (rc == TREXIO_SUCCESS);
assert (en_nucleus[0] == 0);
assert (en_nucleus[1] == 1);
assert (en_nucleus[2] == 2);
int een_nucleus [6] = { 0, 0, 0, 0, 0, 0 };
rc = trexio_read_jastrow_een_nucleus(file, een_nucleus);
assert (rc == TREXIO_SUCCESS);
assert (een_nucleus[0] == 0);
assert (een_nucleus[1] == 0);
assert (een_nucleus[2] == 1);
assert (een_nucleus[3] == 1);
assert (een_nucleus[4] == 2);
assert (een_nucleus[5] == 2);
double ee_scaling = 0.0;
rc = trexio_read_jastrow_ee_scaling(file, &ee_scaling);
assert (rc == TREXIO_SUCCESS);
assert (ee_scaling == 1.0);
double en_scaling[3] = { 0.5, 1.0, 0.5 };
rc = trexio_read_jastrow_en_scaling(file, en_scaling);
assert (rc == TREXIO_SUCCESS);
assert (en_scaling[0] == 0.5);
assert (en_scaling[1] == 1.0);
assert (en_scaling[2] == 0.5);
rc = trexio_close(file);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_jastrow (TREXIO_FILE, TEST_BACKEND);
test_read_jastrow (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

201
tests/io_jastrow_hdf5.c
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@ -1,198 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_jastrow"
#include "test_macros.h"
#include "io_jastrow.c"
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_jastrow.h5"
#define RM_COMMAND "rm -f -- " TREXIO_FILE
static int test_write_jastrow (const char* file_name, const back_end_t backend) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
#define nucleus_num 3
#define ee_num 2
#define en_num 3
#define een_num 6
rc = trexio_write_nucleus_num(file, nucleus_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_type(file, "CHAMP", 6);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_ee_num(file, ee_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_en_num(file, en_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_een_num(file, een_num);
assert (rc == TREXIO_SUCCESS);
double ee [2] = { 0.5, 2. };
rc = trexio_write_jastrow_ee(file, ee);
assert (rc == TREXIO_SUCCESS);
double en [3] = { 1., 2., 3. };
rc = trexio_write_jastrow_en(file, en);
assert (rc == TREXIO_SUCCESS);
double een [6] = { 11., 12., 13., 14., 15., 16. };
rc = trexio_write_jastrow_een(file, een);
assert (rc == TREXIO_SUCCESS);
int en_nucleus [3] = { 0, 1, 2 };
rc = trexio_write_jastrow_en_nucleus(file, en_nucleus);
assert (rc == TREXIO_SUCCESS);
int een_nucleus [6] = { 0, 0, 1, 1, 2, 2 };
rc = trexio_write_jastrow_een_nucleus(file, een_nucleus);
assert (rc == TREXIO_SUCCESS);
double ee_scaling = 1.0;
rc = trexio_write_jastrow_ee_scaling(file, ee_scaling);
assert (rc == TREXIO_SUCCESS);
double en_scaling[3] = { 0.5, 1.0, 0.5 };
rc = trexio_write_jastrow_en_scaling(file, en_scaling);
assert (rc == TREXIO_SUCCESS);
#undef nucleus_num
#undef ee_num
#undef en_num
#undef een_num
rc = trexio_close(file);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_jastrow (const char* file_name, const back_end_t backend) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
int nucleus_num = 0;
rc = trexio_read_nucleus_num(file, &nucleus_num);
assert (rc == TREXIO_SUCCESS);
assert (nucleus_num == 3);
char type[16] = "";
rc = trexio_read_jastrow_type(file, type, 16);
assert (rc == TREXIO_SUCCESS);
assert (strcmp("CHAMP",type) == 0);
int ee_num = 0;
rc = trexio_read_jastrow_ee_num(file, &ee_num);
assert (rc == TREXIO_SUCCESS);
assert (ee_num == 2);
int en_num = 0;
rc = trexio_read_jastrow_en_num(file, &en_num);
assert (rc == TREXIO_SUCCESS);
assert (en_num == nucleus_num);
int een_num = 0;
rc = trexio_read_jastrow_een_num(file, &een_num);
assert (rc == TREXIO_SUCCESS);
assert (een_num == 2*nucleus_num);
double ee [2] = { 0., 0. };
rc = trexio_read_jastrow_ee(file, ee);
assert (rc == TREXIO_SUCCESS);
assert (ee[0] == 0.5);
assert (ee[1] == 2.0);
double en [3] = { 0., 0., 0. };
rc = trexio_read_jastrow_en(file, en);
assert (rc == TREXIO_SUCCESS);
assert (en[0] == 1.0);
assert (en[1] == 2.0);
assert (en[2] == 3.0);
double een [6];
rc = trexio_read_jastrow_een(file, een);
assert (rc == TREXIO_SUCCESS);
assert (een[0] == 11.0);
assert (een[1] == 12.0);
assert (een[2] == 13.0);
assert (een[3] == 14.0);
assert (een[4] == 15.0);
assert (een[5] == 16.0);
int en_nucleus [3] = { 0, 0, 0 };
rc = trexio_read_jastrow_en_nucleus(file, en_nucleus);
assert (rc == TREXIO_SUCCESS);
assert (en_nucleus[0] == 0);
assert (en_nucleus[1] == 1);
assert (en_nucleus[2] == 2);
int een_nucleus [6] = { 0, 0, 0, 0, 0, 0 };
rc = trexio_read_jastrow_een_nucleus(file, een_nucleus);
assert (rc == TREXIO_SUCCESS);
assert (een_nucleus[0] == 0);
assert (een_nucleus[1] == 0);
assert (een_nucleus[2] == 1);
assert (een_nucleus[3] == 1);
assert (een_nucleus[4] == 2);
assert (een_nucleus[5] == 2);
double ee_scaling = 0.0;
rc = trexio_read_jastrow_ee_scaling(file, &ee_scaling);
assert (rc == TREXIO_SUCCESS);
assert (ee_scaling == 1.0);
double en_scaling[3] = { 0.5, 1.0, 0.5 };
rc = trexio_read_jastrow_en_scaling(file, en_scaling);
assert (rc == TREXIO_SUCCESS);
assert (en_scaling[0] == 0.5);
assert (en_scaling[1] == 1.0);
assert (en_scaling[2] == 0.5);
rc = trexio_close(file);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_jastrow (TREXIO_FILE, TEST_BACKEND);
test_read_jastrow (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

201
tests/io_jastrow_text.c
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@ -1,198 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_jastrow"
#include "test_macros.h"
#include "io_jastrow.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_jastrow.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_jastrow (const char* file_name, const back_end_t backend) {
/* Try to write an array of sparse data into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
#define nucleus_num 3
#define ee_num 2
#define en_num 3
#define een_num 6
rc = trexio_write_nucleus_num(file, nucleus_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_type(file, "CHAMP", 6);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_ee_num(file, ee_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_en_num(file, en_num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_jastrow_een_num(file, een_num);
assert (rc == TREXIO_SUCCESS);
double ee [2] = { 0.5, 2. };
rc = trexio_write_jastrow_ee(file, ee);
assert (rc == TREXIO_SUCCESS);
double en [3] = { 1., 2., 3. };
rc = trexio_write_jastrow_en(file, en);
assert (rc == TREXIO_SUCCESS);
double een [6] = { 11., 12., 13., 14., 15., 16. };
rc = trexio_write_jastrow_een(file, een);
assert (rc == TREXIO_SUCCESS);
int en_nucleus [3] = { 0, 1, 2 };
rc = trexio_write_jastrow_en_nucleus(file, en_nucleus);
assert (rc == TREXIO_SUCCESS);
int een_nucleus [6] = { 0, 0, 1, 1, 2, 2 };
rc = trexio_write_jastrow_een_nucleus(file, een_nucleus);
assert (rc == TREXIO_SUCCESS);
double ee_scaling = 1.0;
rc = trexio_write_jastrow_ee_scaling(file, ee_scaling);
assert (rc == TREXIO_SUCCESS);
double en_scaling[3] = { 0.5, 1.0, 0.5 };
rc = trexio_write_jastrow_en_scaling(file, en_scaling);
assert (rc == TREXIO_SUCCESS);
#undef nucleus_num
#undef ee_num
#undef en_num
#undef een_num
rc = trexio_close(file);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_jastrow (const char* file_name, const back_end_t backend) {
/* Try to read one chunk of dataset of sparse data in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
int nucleus_num = 0;
rc = trexio_read_nucleus_num(file, &nucleus_num);
assert (rc == TREXIO_SUCCESS);
assert (nucleus_num == 3);
char type[16] = "";
rc = trexio_read_jastrow_type(file, type, 16);
assert (rc == TREXIO_SUCCESS);
assert (strcmp("CHAMP",type) == 0);
int ee_num = 0;
rc = trexio_read_jastrow_ee_num(file, &ee_num);
assert (rc == TREXIO_SUCCESS);
assert (ee_num == 2);
int en_num = 0;
rc = trexio_read_jastrow_en_num(file, &en_num);
assert (rc == TREXIO_SUCCESS);
assert (en_num == nucleus_num);
int een_num = 0;
rc = trexio_read_jastrow_een_num(file, &een_num);
assert (rc == TREXIO_SUCCESS);
assert (een_num == 2*nucleus_num);
double ee [2] = { 0., 0. };
rc = trexio_read_jastrow_ee(file, ee);
assert (rc == TREXIO_SUCCESS);
assert (ee[0] == 0.5);
assert (ee[1] == 2.0);
double en [3] = { 0., 0., 0. };
rc = trexio_read_jastrow_en(file, en);
assert (rc == TREXIO_SUCCESS);
assert (en[0] == 1.0);
assert (en[1] == 2.0);
assert (en[2] == 3.0);
double een [6];
rc = trexio_read_jastrow_een(file, een);
assert (rc == TREXIO_SUCCESS);
assert (een[0] == 11.0);
assert (een[1] == 12.0);
assert (een[2] == 13.0);
assert (een[3] == 14.0);
assert (een[4] == 15.0);
assert (een[5] == 16.0);
int en_nucleus [3] = { 0, 0, 0 };
rc = trexio_read_jastrow_en_nucleus(file, en_nucleus);
assert (rc == TREXIO_SUCCESS);
assert (en_nucleus[0] == 0);
assert (en_nucleus[1] == 1);
assert (en_nucleus[2] == 2);
int een_nucleus [6] = { 0, 0, 0, 0, 0, 0 };
rc = trexio_read_jastrow_een_nucleus(file, een_nucleus);
assert (rc == TREXIO_SUCCESS);
assert (een_nucleus[0] == 0);
assert (een_nucleus[1] == 0);
assert (een_nucleus[2] == 1);
assert (een_nucleus[3] == 1);
assert (een_nucleus[4] == 2);
assert (een_nucleus[5] == 2);
double ee_scaling = 0.0;
rc = trexio_read_jastrow_ee_scaling(file, &ee_scaling);
assert (rc == TREXIO_SUCCESS);
assert (ee_scaling == 1.0);
double en_scaling[3] = { 0.5, 1.0, 0.5 };
rc = trexio_read_jastrow_en_scaling(file, en_scaling);
assert (rc == TREXIO_SUCCESS);
assert (en_scaling[0] == 0.5);
assert (en_scaling[1] == 1.0);
assert (en_scaling[2] == 0.5);
rc = trexio_close(file);
/*================= END OF TEST ==================*/
return 0;
}
int main(){
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_jastrow (TREXIO_FILE, TEST_BACKEND);
test_read_jastrow (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

150
tests/io_num.c Normal file
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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
static int test_write_num (const char* file_name, const back_end_t backend) {
/* Try to write a dimensioning attribute (num variable) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_repulsion(file, 2.14171677);
assert (rc == TREXIO_SUCCESS);
// attempt to write 0 as dimensioning variable in an empty file; should FAIL and return TREXIO_INVALID_ARG_2
rc = trexio_write_mo_num(file, 0);
assert (rc == TREXIO_INVALID_NUM);
// write numerical attribute ao_cartesian as 0
rc = trexio_write_ao_cartesian(file, 0);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_num (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dimensioning attribute (num variable) in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written num variable exists
rc = trexio_has_nucleus_num(file);
assert (rc == TREXIO_SUCCESS);
rc = trexio_has_nucleus_repulsion(file);
assert (rc == TREXIO_SUCCESS);
// check that the num variable does not exist
rc = trexio_has_mo_num(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_num (const char* file_name, const back_end_t backend) {
/* Try to read a dimensioning attribute (num variable) from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
int cartesian;
float repulsion_32;
double repulsion_64, d;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
rc = trexio_read_nucleus_repulsion_32(file, &repulsion_32);
assert (rc == TREXIO_SUCCESS);
d = repulsion_32 - 2.14171677;
assert( d*d < 1.e-8 );
rc = trexio_read_nucleus_repulsion_64(file, &repulsion_64);
assert (rc == TREXIO_SUCCESS);
d = repulsion_64 - 2.14171677;
assert( d*d < 1.e-14 );
// read non-existing numerical attribute from the file
rc = trexio_read_mo_num(file, &num);
assert (rc == TREXIO_ATTR_MISSING);
// read ao_cartesian (zero) value from the file
rc = trexio_read_ao_cartesian(file, &cartesian);
assert (rc == TREXIO_SUCCESS);
assert (cartesian == 0);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_num (TREXIO_FILE, TEST_BACKEND);
test_has_num (TREXIO_FILE, TEST_BACKEND);
test_read_num (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

157
tests/io_num_hdf5.c
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@ -1,154 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_num"
#include "test_macros.h"
#include "io_num.c"
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_num.h5"
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_write_num (const char* file_name, const back_end_t backend) {
/* Try to write a dimensioning attribute (num variable) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_repulsion(file, 2.14171677);
assert (rc == TREXIO_SUCCESS);
// attempt to write 0 as dimensioning variable in an empty file; should FAIL and return TREXIO_INVALID_ARG_2
rc = trexio_write_mo_num(file, 0);
assert (rc == TREXIO_INVALID_NUM);
// write numerical attribute ao_cartesian as 0
rc = trexio_write_ao_cartesian(file, 0);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_num (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dimensioning attribute (num variable) in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written num variable exists
rc = trexio_has_nucleus_num(file);
assert (rc == TREXIO_SUCCESS);
rc = trexio_has_nucleus_repulsion(file);
assert (rc == TREXIO_SUCCESS);
// check that the num variable does not exist
rc = trexio_has_mo_num(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_num (const char* file_name, const back_end_t backend) {
/* Try to read a dimensioning attribute (num variable) from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
int cartesian;
float repulsion_32;
double repulsion_64, d;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
rc = trexio_read_nucleus_repulsion_32(file, &repulsion_32);
assert (rc == TREXIO_SUCCESS);
d = repulsion_32 - 2.14171677;
assert( d*d < 1.e-8 );
rc = trexio_read_nucleus_repulsion_64(file, &repulsion_64);
assert (rc == TREXIO_SUCCESS);
d = repulsion_64 - 2.14171677;
assert( d*d < 1.e-14 );
// read non-existing numerical attribute from the file
rc = trexio_read_mo_num(file, &num);
assert (rc == TREXIO_ATTR_MISSING);
// read ao_cartesian (zero) value from the file
rc = trexio_read_ao_cartesian(file, &cartesian);
assert (rc == TREXIO_SUCCESS);
assert (cartesian == 0);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_num (TREXIO_FILE, TEST_BACKEND);
test_has_num (TREXIO_FILE, TEST_BACKEND);
test_read_num (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

157
tests/io_num_text.c
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@ -1,154 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_num"
#include "test_macros.h"
#include "io_num.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_num.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_num (const char* file_name, const back_end_t backend) {
/* Try to write a dimensioning attribute (num variable) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_repulsion(file, 2.14171677);
assert (rc == TREXIO_SUCCESS);
// attempt to write 0 as dimensioning variable in an empty file; should FAIL and return TREXIO_INVALID_ARG_2
rc = trexio_write_mo_num(file, 0);
assert (rc == TREXIO_INVALID_NUM);
// write numerical attribute ao_cartesian as 0
rc = trexio_write_ao_cartesian(file, 0);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_num (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dimensioning attribute (num variable) in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written num variable exists
rc = trexio_has_nucleus_num(file);
assert (rc == TREXIO_SUCCESS);
rc = trexio_has_nucleus_repulsion(file);
assert (rc == TREXIO_SUCCESS);
// check that the num variable does not exist
rc = trexio_has_mo_num(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_num (const char* file_name, const back_end_t backend) {
/* Try to read a dimensioning attribute (num variable) from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
int cartesian;
float repulsion_32;
double repulsion_64, d;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
rc = trexio_read_nucleus_repulsion_32(file, &repulsion_32);
assert (rc == TREXIO_SUCCESS);
d = repulsion_32 - 2.14171677;
assert( d*d < 1.e-8 );
rc = trexio_read_nucleus_repulsion_64(file, &repulsion_64);
assert (rc == TREXIO_SUCCESS);
d = repulsion_64 - 2.14171677;
assert( d*d < 1.e-14 );
// read non-existing numerical attribute from the file
rc = trexio_read_mo_num(file, &num);
assert (rc == TREXIO_ATTR_MISSING);
// read ao_cartesian (zero) value from the file
rc = trexio_read_ao_cartesian(file, &cartesian);
assert (rc == TREXIO_SUCCESS);
assert (cartesian == 0);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_num (TREXIO_FILE, TEST_BACKEND);
test_has_num (TREXIO_FILE, TEST_BACKEND);
test_read_num (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

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tests/io_safe_dset_float.c Normal file
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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with floating point values into the TREXIO file using safe API */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
/* write numerical dataset with an unsafe dimension
* this should return TREXIO_UNSAFE_ARRAY_DIM indicating
* that access beyong allocated memory is likely to occur */
uint64_t dim_unsafe = num * 12;
rc = trexio_write_safe_nucleus_coord(file, coord, dim_unsafe);
assert (rc == TREXIO_UNSAFE_ARRAY_DIM);
/* write numerical dataset with a safe dimension
* this should return TREXIO_SUCCESS */
uint64_t dim_safe = num * 3;
rc = trexio_write_safe_nucleus_coord(file, coord, dim_safe);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset exists
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with floating point values from the TREXIO file using safe API */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
double* coord;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical (floating point) dataset from the file
coord = (double*) calloc(3*num, sizeof(double));
/* write numerical dataset with an unsafe dimension
* this should return TREXIO_UNSAFE_ARRAY_DIM indicating
* that access beyong allocated memory is likely to occur */
uint64_t dim_unsafe = num * 12;
rc = trexio_read_safe_nucleus_coord(file, coord, dim_unsafe);
assert (rc == TREXIO_UNSAFE_ARRAY_DIM);
/* write numerical dataset with a safe dimension
* this should return TREXIO_SUCCESS */
uint64_t dim_safe = num * 3;
rc = trexio_read_safe_nucleus_coord(file, coord, dim_safe);
assert (rc == TREXIO_SUCCESS);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-14 );
free(coord);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

168
tests/io_safe_dset_float_hdf5.c
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@ -1,165 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_safe_dset_f.h5"
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with floating point values into the TREXIO file using safe API */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
/* write numerical dataset with an unsafe dimension
* this should return TREXIO_UNSAFE_ARRAY_DIM indicating
* that access beyong allocated memory is likely to occur */
uint64_t dim_unsafe = num * 12;
rc = trexio_write_safe_nucleus_coord(file, coord, dim_unsafe);
assert (rc == TREXIO_UNSAFE_ARRAY_DIM);
/* write numerical dataset with a safe dimension
* this should return TREXIO_SUCCESS */
uint64_t dim_safe = num * 3;
rc = trexio_write_safe_nucleus_coord(file, coord, dim_safe);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset exists
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with floating point values from the TREXIO file using safe API */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
double* coord;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical (floating point) dataset from the file
coord = (double*) calloc(3*num, sizeof(double));
/* write numerical dataset with an unsafe dimension
* this should return TREXIO_UNSAFE_ARRAY_DIM indicating
* that access beyong allocated memory is likely to occur */
uint64_t dim_unsafe = num * 12;
rc = trexio_read_safe_nucleus_coord(file, coord, dim_unsafe);
assert (rc == TREXIO_UNSAFE_ARRAY_DIM);
/* write numerical dataset with a safe dimension
* this should return TREXIO_SUCCESS */
uint64_t dim_safe = num * 3;
rc = trexio_read_safe_nucleus_coord(file, coord, dim_safe);
assert (rc == TREXIO_SUCCESS);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-14 );
free(coord);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_safe_dset_float"
#include "test_macros.h"
#include "io_safe_dset_float.c"

166
tests/io_safe_dset_float_text.c
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@ -1,163 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_safe_dset_float"
#include "test_macros.h"
#include "io_safe_dset_float.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_safe_dset_f.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_dset (const char* file_name, const back_end_t backend) {
/* Try to write a dataset with floating point values into the TREXIO file using safe API */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write numerical attribute in an empty file
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
/* write numerical dataset with an unsafe dimension
* this should return TREXIO_UNSAFE_ARRAY_DIM indicating
* that access beyong allocated memory is likely to occur */
uint64_t dim_unsafe = num * 12;
rc = trexio_write_safe_nucleus_coord(file, coord, dim_unsafe);
assert (rc == TREXIO_UNSAFE_ARRAY_DIM);
/* write numerical dataset with a safe dimension
* this should return TREXIO_SUCCESS */
uint64_t dim_safe = num * 3;
rc = trexio_write_safe_nucleus_coord(file, coord, dim_safe);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_dset (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a dataset in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written dataset exists
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_dset (const char* file_name, const back_end_t backend) {
/* Try to read a dataset with floating point values from the TREXIO file using safe API */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
int num;
double* coord;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read numerical attribute from the file
rc = trexio_read_nucleus_num(file, &num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// read numerical (floating point) dataset from the file
coord = (double*) calloc(3*num, sizeof(double));
/* write numerical dataset with an unsafe dimension
* this should return TREXIO_UNSAFE_ARRAY_DIM indicating
* that access beyong allocated memory is likely to occur */
uint64_t dim_unsafe = num * 12;
rc = trexio_read_safe_nucleus_coord(file, coord, dim_unsafe);
assert (rc == TREXIO_UNSAFE_ARRAY_DIM);
/* write numerical dataset with a safe dimension
* this should return TREXIO_SUCCESS */
uint64_t dim_safe = num * 3;
rc = trexio_read_safe_nucleus_coord(file, coord, dim_safe);
assert (rc == TREXIO_SUCCESS);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-14 );
free(coord);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_dset (TREXIO_FILE, TEST_BACKEND);
test_has_dset (TREXIO_FILE, TEST_BACKEND);
test_read_dset (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

129
tests/io_str.c Normal file
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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
static int test_write_str (const char* file_name, const back_end_t backend) {
/* Try to write a string attribute (single variable-length string) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
const char* sym = "B3U with some comments";
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write string attribute in an empty file
int max_str_len = 32;
rc = trexio_write_nucleus_point_group(file, sym, max_str_len);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_str (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a string attribute in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written string attribute exists
rc = trexio_has_nucleus_point_group(file);
assert (rc == TREXIO_SUCCESS);
// check that another string attribute does not exist
rc = trexio_has_mo_type(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_str (const char* file_name, const back_end_t backend) {
/* Try to read a string attribute from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
char* sym;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read string attribute from the file
int max_str_len = 32;
sym = (char*) malloc(max_str_len*sizeof(char));
rc = trexio_read_nucleus_point_group(file, sym, max_str_len);
assert (rc == TREXIO_SUCCESS);
char * pch;
pch = strtok(sym, " ");
assert (strcmp(pch, "B3U") == 0);
/* alternative test when 3 symbols are read from the file to sym */
/*rc = trexio_read_nucleus_point_group(file, sym, 3);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(sym, "B3U") == 0 );*/
free(sym);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_str (TREXIO_FILE, TEST_BACKEND);
test_has_str (TREXIO_FILE, TEST_BACKEND);
test_read_str (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

136
tests/io_str_hdf5.c
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@ -1,133 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_str.h5"
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_write_str (const char* file_name, const back_end_t backend) {
/* Try to write a string attribute (single variable-length string) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
const char* sym = "B3U with some comments";
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write string attribute in an empty file
int max_str_len = 32;
rc = trexio_write_nucleus_point_group(file, sym, max_str_len);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_str (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a string attribute in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written string attribute exists
rc = trexio_has_nucleus_point_group(file);
assert (rc == TREXIO_SUCCESS);
// check that another string attribute does not exist
rc = trexio_has_mo_type(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_str (const char* file_name, const back_end_t backend) {
/* Try to read a string attribute from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
char* sym;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read string attribute from the file
int max_str_len = 32;
sym = (char*) malloc(max_str_len*sizeof(char));
rc = trexio_read_nucleus_point_group(file, sym, max_str_len);
assert (rc == TREXIO_SUCCESS);
char * pch;
pch = strtok(sym, " ");
assert (strcmp(pch, "B3U") == 0);
/* alternative test when 3 symbols are read from the file to sym */
/*rc = trexio_read_nucleus_point_group(file, sym, 3);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(sym, "B3U") == 0 );*/
free(sym);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_str (TREXIO_FILE, TEST_BACKEND);
test_has_str (TREXIO_FILE, TEST_BACKEND);
test_read_str (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "io_str"
#include "test_macros.h"
#include "io_str.c"

134
tests/io_str_text.c
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@ -1,131 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "io_str"
#include "test_macros.h"
#include "io_str.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_str.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write_str (const char* file_name, const back_end_t backend) {
/* Try to write a string attribute (single variable-length string) into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
const char* sym = "B3U with some comments";
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write string attribute in an empty file
int max_str_len = 32;
rc = trexio_write_nucleus_point_group(file, sym, max_str_len);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_has_str (const char* file_name, const back_end_t backend) {
/* Try to check the existence of a string attribute in the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// check that the previously written string attribute exists
rc = trexio_has_nucleus_point_group(file);
assert (rc == TREXIO_SUCCESS);
// check that another string attribute does not exist
rc = trexio_has_mo_type(file);
assert (rc == TREXIO_HAS_NOT);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_read_str (const char* file_name, const back_end_t backend) {
/* Try to read a string attribute from the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be read
char* sym;
/*================= START OF TEST ==================*/
// open file in 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read string attribute from the file
int max_str_len = 32;
sym = (char*) malloc(max_str_len*sizeof(char));
rc = trexio_read_nucleus_point_group(file, sym, max_str_len);
assert (rc == TREXIO_SUCCESS);
char * pch;
pch = strtok(sym, " ");
assert (strcmp(pch, "B3U") == 0);
/* alternative test when 3 symbols are read from the file to sym */
/*rc = trexio_read_nucleus_point_group(file, sym, 3);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(sym, "B3U") == 0 );*/
free(sym);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write_str (TREXIO_FILE, TEST_BACKEND);
test_has_str (TREXIO_FILE, TEST_BACKEND);
test_read_str (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

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tests/open.c Normal file
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#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TREXIO_VOID "non_existing_" TREXIO_FILE
static int test_open_w (const char* file_name, const back_end_t backend) {
/* Try to open the TREXIO file in 'write' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_r (const char* file_name, const back_end_t backend) {
/* Try to open the TREXIO file in 'read' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_auto (const char* file_name) {
/* Try to open the TREXIO file in 'read' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'r', TREXIO_AUTO, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_errors (const back_end_t backend) {
/* Try to call trexio_open with bad arguments */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open non-existing file in 'r' (read) mode, should return TREXIO_OPEN_ERROR
file = trexio_open(TREXIO_VOID, 'r', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_OPEN_ERROR);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open file with empty file name, should return TREXIO_INVALID_ARG_1
file = trexio_open("", 'w', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_1);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open existing file in non-supported I/O mode, should return TREXIO_INVALID_ARG_2
file = trexio_open(TREXIO_FILE, 'k', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_2);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open existing file with non-supported back end, should return TREXIO_INVALID_ARG_3
file = trexio_open(TREXIO_FILE, 'w', 666, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_3);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
/*================= END OF TEST ==================*/
return 0;
}
static int test_inquire (const back_end_t backend) {
/* Try to call trexio_inquire function */
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// inquire non-existing file
rc = trexio_inquire(TREXIO_VOID);
assert (rc == TREXIO_FAILURE);
// inquire existing file
rc = trexio_inquire(TREXIO_FILE);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_open_w (TREXIO_FILE, TEST_BACKEND);
test_open_r (TREXIO_FILE, TEST_BACKEND);
test_open_auto (TREXIO_FILE);
test_open_errors(TEST_BACKEND);
test_inquire (TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

166
tests/open_hdf5.c
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@ -1,163 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "open"
#include "test_macros.h"
#include "open.c"
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_open.h5"
#define TREXIO_VOID "non_existing_" TREXIO_FILE
#define RM_COMMAND "rm -rf " TREXIO_FILE
static int test_open_w (const char* file_name, const back_end_t backend) {
/* Try to open the TREXIO file in 'write' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_r (const char* file_name, const back_end_t backend) {
/* Try to open the TREXIO file in 'read' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_auto (const char* file_name) {
/* Try to open the TREXIO file in 'read' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'r', TREXIO_AUTO, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_errors (const back_end_t backend) {
/* Try to call trexio_open with bad arguments */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open non-existing file in 'r' (read) mode, should return TREXIO_OPEN_ERROR
file = trexio_open(TREXIO_VOID, 'r', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_OPEN_ERROR);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open file with empty file name, should return TREXIO_INVALID_ARG_1
file = trexio_open("", 'w', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_1);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open existing file in non-supported I/O mode, should return TREXIO_INVALID_ARG_2
file = trexio_open(TREXIO_FILE, 'k', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_2);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open existing file with non-supported back end, should return TREXIO_INVALID_ARG_3
file = trexio_open(TREXIO_FILE, 'w', 666, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_3);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
/*================= END OF TEST ==================*/
return 0;
}
static int test_inquire (const back_end_t backend) {
/* Try to call trexio_inquire function */
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// inquire non-existing file
rc = trexio_inquire(TREXIO_VOID);
assert (rc == TREXIO_FAILURE);
// inquire existing file
rc = trexio_inquire(TREXIO_FILE);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_open_w (TREXIO_FILE, TEST_BACKEND);
test_open_r (TREXIO_FILE, TEST_BACKEND);
test_open_auto (TREXIO_FILE);
test_open_errors(TEST_BACKEND);
test_inquire (TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

166
tests/open_text.c
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@ -1,163 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "open"
#include "test_macros.h"
#include "open.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_open.dir"
#define TREXIO_VOID "non_existing_" TREXIO_FILE
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_open_w (const char* file_name, const back_end_t backend) {
/* Try to open the TREXIO file in 'write' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_r (const char* file_name, const back_end_t backend) {
/* Try to open the TREXIO file in 'read' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_auto (const char* file_name) {
/* Try to open the TREXIO file in 'read' mode */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'r', TREXIO_AUTO, &rc);
assert (file != NULL);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_open_errors (const back_end_t backend) {
/* Try to call trexio_open with bad arguments */
trexio_t* file = NULL;
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// open non-existing file in 'r' (read) mode, should return TREXIO_OPEN_ERROR
file = trexio_open(TREXIO_VOID, 'r', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_OPEN_ERROR);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open file with empty file name, should return TREXIO_INVALID_ARG_1
file = trexio_open("", 'w', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_1);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open existing file in non-supported I/O mode, should return TREXIO_INVALID_ARG_2
file = trexio_open(TREXIO_FILE, 'k', backend, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_2);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
// open existing file with non-supported back end, should return TREXIO_INVALID_ARG_3
file = trexio_open(TREXIO_FILE, 'w', 666, &rc);
assert (file == NULL);
assert (rc == TREXIO_INVALID_ARG_3);
fprintf(stderr, "%s \n", trexio_string_of_error(rc));
/*================= END OF TEST ==================*/
return 0;
}
static int test_inquire (const back_end_t backend) {
/* Try to call trexio_inquire function */
trexio_exit_code rc;
/*================= START OF TEST ==================*/
// inquire non-existing file
rc = trexio_inquire(TREXIO_VOID);
assert (rc == TREXIO_FAILURE);
// inquire existing file
rc = trexio_inquire(TREXIO_FILE);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_open_w (TREXIO_FILE, TEST_BACKEND);
test_open_r (TREXIO_FILE, TEST_BACKEND);
test_open_auto (TREXIO_FILE);
test_open_errors(TEST_BACKEND);
test_inquire (TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

262
tests/overwrite_all.c Normal file
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@ -0,0 +1,262 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
static int test_write (const char* file_name, const back_end_t backend) {
/* Try to write a full set of data (num+dset_num+str+dset_str) related to benzene molecule into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
const char* sym = "D6h";
const char* labels[] = {"C" ,
"C" ,
"C" ,
"C" ,
"C" ,
"C" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write the data
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_point_group(file, sym, 4);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_label(file, labels, 2);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_overwrite_unsafe (const char* file_name, const back_end_t backend) {
/* Try to overwrite the data that already exists in the TREXIO file which is open in UNSAFE mode*/
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 5;
double coord[15] = {
0.00000000 , 666.666 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000
};
const char* sym = "Unknown";
const char* labels[] = {"Ru" ,
"U" ,
"Cl" ,
"Na" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'u', backend, &rc);
assert (file != NULL);
// check that the previously written data cannot be overwritten
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_point_group(file, sym, 16);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_label(file, labels, 4);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_overwrite_safe (const char* file_name, const back_end_t backend) {
/* Try to overwrite the data that already exists in the TREXIO file which is open in SAFE mode*/
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 24;
double coord[3] = {
0.00000000 , 666.666, 0.00000000 ,
};
const char* sym = "Unknown";
const char* labels[] = {"Ru" ,
"U" ,
"Cl" ,
"Na" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// check that the previously written data cannot be overwritten
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
rc = trexio_write_nucleus_point_group(file, sym, 16);
assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
rc = trexio_write_nucleus_label(file, labels, 4);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int test_read(const char* file_name, const back_end_t backend) {
/*========= Test read ===========*/
trexio_t* file = NULL;
trexio_exit_code rc;
int num;
double* coord;
char** label;
char* point_group;
/*================= START OF TEST ==================*/
// open existing file on 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read nucleus_num
rc = trexio_read_nucleus_num(file,&num);
assert (rc == TREXIO_SUCCESS);
assert (num == 5);
// read nucleus_coord
coord = (double*) calloc(3*num, sizeof(double));
rc = trexio_read_nucleus_coord(file,coord);
assert (rc == TREXIO_SUCCESS);
double x = coord[1] - 666.666;
assert( x*x < 1.e-14);
free(coord);
// read nucleus_label
label = (char**) malloc(num*sizeof(char*));
for (int i=0; i<num; i++){
label[i] = (char*) malloc(32*sizeof(char));
}
rc = trexio_read_nucleus_label(file, label, 2);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(label[0], "Ru") == 0);
assert (strcmp(label[3], "Na") == 0);
for (int i=0; i<num; i++){
free(label[i]);
}
free(label);
point_group = (char*) malloc(32*sizeof(char));
rc = trexio_read_nucleus_point_group(file, point_group, 10);
assert (rc == TREXIO_SUCCESS);
char * pch;
pch = strtok(point_group, " ");
assert (strcmp(pch, "Unknown") == 0);
/* alternative test when 3 symbols are read from the file to point_group */
/*rc = trexio_read_nucleus_point_group(file, point_group, 3);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(point_group, "B3U") == 0 );*/
free(point_group);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST =====================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write (TREXIO_FILE, TEST_BACKEND);
test_overwrite_safe (TREXIO_FILE, TEST_BACKEND);
test_overwrite_unsafe (TREXIO_FILE, TEST_BACKEND);
test_read (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

269
tests/overwrite_all_hdf5.c
View File

@ -1,266 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "overwrite_all"
#include "test_macros.h"
#include "overwrite_all.c"
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE "test_over.h5"
#define RM_COMMAND "rm -f -- " TREXIO_FILE
static int test_write (const char* file_name, const back_end_t backend) {
/* Try to write a full set of data (num+dset_num+str+dset_str) related to benzene molecule into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
const char* sym = "D6h";
const char* labels[] = {"C" ,
"C" ,
"C" ,
"C" ,
"C" ,
"C" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write the data
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_point_group(file, sym, 4);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_label(file, labels, 2);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_overwrite_unsafe (const char* file_name, const back_end_t backend) {
/* Try to overwrite the data that already exists in the TREXIO file which is open in UNSAFE mode*/
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 5;
double coord[15] = {
0.00000000 , 666.666 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000
};
const char* sym = "Unknown";
const char* labels[] = {"Ru" ,
"U" ,
"Cl" ,
"Na" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'u', backend, &rc);
assert (file != NULL);
// check that the previously written data cannot be overwritten
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_point_group(file, sym, 16);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_label(file, labels, 4);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_overwrite_safe (const char* file_name, const back_end_t backend) {
/* Try to overwrite the data that already exists in the TREXIO file which is open in SAFE mode*/
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 24;
double coord[3] = {
0.00000000 , 666.666, 0.00000000 ,
};
const char* sym = "Unknown";
const char* labels[] = {"Ru" ,
"U" ,
"Cl" ,
"Na" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// check that the previously written data cannot be overwritten
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
rc = trexio_write_nucleus_point_group(file, sym, 16);
assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
rc = trexio_write_nucleus_label(file, labels, 4);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int test_read(const char* file_name, const back_end_t backend) {
/*========= Test read ===========*/
trexio_t* file = NULL;
trexio_exit_code rc;
int num;
double* coord;
char** label;
char* point_group;
/*================= START OF TEST ==================*/
// open existing file on 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read nucleus_num
rc = trexio_read_nucleus_num(file,&num);
assert (rc == TREXIO_SUCCESS);
assert (num == 5);
// read nucleus_coord
coord = (double*) calloc(3*num, sizeof(double));
rc = trexio_read_nucleus_coord(file,coord);
assert (rc == TREXIO_SUCCESS);
double x = coord[1] - 666.666;
assert( x*x < 1.e-14);
free(coord);
// read nucleus_label
label = (char**) malloc(num*sizeof(char*));
for (int i=0; i<num; i++){
label[i] = (char*) malloc(32*sizeof(char));
}
rc = trexio_read_nucleus_label(file, label, 2);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(label[0], "Ru") == 0);
assert (strcmp(label[3], "Na") == 0);
for (int i=0; i<num; i++){
free(label[i]);
}
free(label);
point_group = (char*) malloc(32*sizeof(char));
rc = trexio_read_nucleus_point_group(file, point_group, 10);
assert (rc == TREXIO_SUCCESS);
char * pch;
pch = strtok(point_group, " ");
assert (strcmp(pch, "Unknown") == 0);
/* alternative test when 3 symbols are read from the file to point_group */
/*rc = trexio_read_nucleus_point_group(file, point_group, 3);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(point_group, "B3U") == 0 );*/
free(point_group);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST =====================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write (TREXIO_FILE, TEST_BACKEND);
test_overwrite_safe (TREXIO_FILE, TEST_BACKEND);
test_overwrite_unsafe (TREXIO_FILE, TEST_BACKEND);
test_read (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

269
tests/overwrite_all_text.c
View File

@ -1,266 +1,5 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "overwrite_all"
#include "test_macros.h"
#include "overwrite_all.c"
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE "test_over.dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
static int test_write (const char* file_name, const back_end_t backend) {
/* Try to write a full set of data (num+dset_num+str+dset_str) related to benzene molecule into the TREXIO file */
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 12;
double coord[36] = {
0.00000000 , 1.39250319 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000 ,
1.20594314 , 0.69625160 , 0.00000000 ,
-2.14171677 , 1.23652075 , 0.00000000 ,
-2.14171677 , -1.23652075 , 0.00000000 ,
0.00000000 , -2.47304151 , 0.00000000 ,
2.14171677 , -1.23652075 , 0.00000000 ,
2.14171677 , 1.23652075 , 0.00000000 ,
0.00000000 , 2.47304151 , 0.00000000 ,
};
const char* sym = "D6h";
const char* labels[] = {"C" ,
"C" ,
"C" ,
"C" ,
"C" ,
"C" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// write the data
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_point_group(file, sym, 4);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_label(file, labels, 2);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_overwrite_unsafe (const char* file_name, const back_end_t backend) {
/* Try to overwrite the data that already exists in the TREXIO file which is open in UNSAFE mode*/
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 5;
double coord[15] = {
0.00000000 , 666.666 , 0.00000000 ,
-1.20594314 , 0.69625160 , 0.00000000 ,
-1.20594314 , -0.69625160 , 0.00000000 ,
0.00000000 , -1.39250319 , 0.00000000 ,
1.20594314 , -0.69625160 , 0.00000000
};
const char* sym = "Unknown";
const char* labels[] = {"Ru" ,
"U" ,
"Cl" ,
"Na" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'u', backend, &rc);
assert (file != NULL);
// check that the previously written data cannot be overwritten
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_point_group(file, sym, 16);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_label(file, labels, 4);
assert (rc == TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
static int test_overwrite_safe (const char* file_name, const back_end_t backend) {
/* Try to overwrite the data that already exists in the TREXIO file which is open in SAFE mode*/
trexio_t* file = NULL;
trexio_exit_code rc;
// parameters to be written
int num = 24;
double coord[3] = {
0.00000000 , 666.666, 0.00000000 ,
};
const char* sym = "Unknown";
const char* labels[] = {"Ru" ,
"U" ,
"Cl" ,
"Na" ,
"H" };
/*================= START OF TEST ==================*/
// open file in 'write' mode
file = trexio_open(file_name, 'w', backend, &rc);
assert (file != NULL);
// check that the previously written data cannot be overwritten
rc = trexio_write_nucleus_num(file, num);
assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
rc = trexio_write_nucleus_coord(file, coord);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
rc = trexio_write_nucleus_point_group(file, sym, 16);
assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
rc = trexio_write_nucleus_label(file, labels, 4);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST ==================*/
return 0;
}
int test_read(const char* file_name, const back_end_t backend) {
/*========= Test read ===========*/
trexio_t* file = NULL;
trexio_exit_code rc;
int num;
double* coord;
char** label;
char* point_group;
/*================= START OF TEST ==================*/
// open existing file on 'read' mode
file = trexio_open(file_name, 'r', backend, &rc);
assert (file != NULL);
// read nucleus_num
rc = trexio_read_nucleus_num(file,&num);
assert (rc == TREXIO_SUCCESS);
assert (num == 5);
// read nucleus_coord
coord = (double*) calloc(3*num, sizeof(double));
rc = trexio_read_nucleus_coord(file,coord);
assert (rc == TREXIO_SUCCESS);
double x = coord[1] - 666.666;
assert( x*x < 1.e-14);
free(coord);
// read nucleus_label
label = (char**) malloc(num*sizeof(char*));
for (int i=0; i<num; i++){
label[i] = (char*) malloc(32*sizeof(char));
}
rc = trexio_read_nucleus_label(file, label, 2);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(label[0], "Ru") == 0);
assert (strcmp(label[3], "Na") == 0);
for (int i=0; i<num; i++){
free(label[i]);
}
free(label);
point_group = (char*) malloc(32*sizeof(char));
rc = trexio_read_nucleus_point_group(file, point_group, 10);
assert (rc == TREXIO_SUCCESS);
char * pch;
pch = strtok(point_group, " ");
assert (strcmp(pch, "Unknown") == 0);
/* alternative test when 3 symbols are read from the file to point_group */
/*rc = trexio_read_nucleus_point_group(file, point_group, 3);
assert (rc == TREXIO_SUCCESS);
assert (strcmp(point_group, "B3U") == 0 );*/
free(point_group);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
/*================= END OF TEST =====================*/
return 0;
}
int main(void) {
/*============== Test launcher ================*/
int rc;
rc = system(RM_COMMAND);
assert (rc == 0);
test_write (TREXIO_FILE, TEST_BACKEND);
test_overwrite_safe (TREXIO_FILE, TEST_BACKEND);
test_overwrite_unsafe (TREXIO_FILE, TEST_BACKEND);
test_read (TREXIO_FILE, TEST_BACKEND);
rc = system(RM_COMMAND);
assert (rc == 0);
return 0;
}

5
tests/template_hdf5.c Normal file
View File

@ -0,0 +1,5 @@
#define TEST_BACKEND_HDF5
#define TREXIO_FILE_PREFIX "REPLACE"
#include "test_macros.h"
#include "REPLACE.c"

5
tests/template_text.c Normal file
View File

@ -0,0 +1,5 @@
#define TEST_BACKEND_TEXT
#define TREXIO_FILE_PREFIX "REPLACE"
#include "test_macros.h"
#include "REPLACE.c"

34
tests/test_f.f90
View File

@ -69,8 +69,8 @@ subroutine test_write(file_name, back_end)
double precision :: charge(12)
double precision :: coord(3,12)
character(len=:), allocatable :: sym_str
character(len=:), allocatable :: label(:)
character(len=32), allocatable :: sym_str
character(len=8), allocatable :: label(:)
double precision, allocatable :: energy(:)
integer , allocatable :: spin(:)
@ -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 , &
@ -129,7 +131,19 @@ subroutine test_write(file_name, back_end)
basis_shell_num = 24
basis_nucleus_index = (/ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 /)
label = [character(len=8) :: 'C', 'Na','C', 'C 66', 'C','C', 'H 99', 'Ru', 'H', 'H', 'H', 'H' ]
allocate(label(12))
label(1) = 'C'
label(2) = 'Na'
label(3) = 'C'
label(4) = 'C 66'
label(5) = 'C'
label(6) = 'C'
label(7) = 'H 99'
label(8) = 'Ru'
label(9) = 'H'
label(10)= 'H'
label(11)= 'H'
label(12)= 'H'
sym_str = 'B3U with some comments'
@ -182,6 +196,9 @@ 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 +319,7 @@ 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 +330,7 @@ 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 +398,15 @@ 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)

20
tests/test_macros.h Normal file
View File

@ -0,0 +1,20 @@
#include "trexio.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#ifdef TEST_BACKEND_HDF5
#define TEST_BACKEND TREXIO_HDF5
#define TREXIO_FILE TREXIO_FILE_PREFIX ".h5"
#define RM_COMMAND "rm -f -- " TREXIO_FILE
#endif
#ifdef TEST_BACKEND_TEXT
#define TEST_BACKEND TREXIO_TEXT
#define TREXIO_FILE TREXIO_FILE_PREFIX ".dir"
#define RM_COMMAND "rm -f -- " TREXIO_FILE "/*.txt " TREXIO_FILE "/*.txt.size " TREXIO_FILE "/.lock && rm -fd -- " TREXIO_FILE
#endif

4
tools/build_doc.sh
View File

@ -81,7 +81,7 @@ function extract_doc()
${org} \
--load ${CONFIG_TANGLE} \
-f org-html-export-to-html &> /dev/null
mv ${local_html} ${DOCS}
mv -f ${local_html} ${DOCS}
rm -f "${local_html}~"
}
@ -99,7 +99,7 @@ function main() {
# Create documentation
cd ${SRC}
for dir in ${SRC}/templates_*/ ${TREXIO_ROOT}/
for dir in ${SRC}/templates_*/ ${TREXIO_ROOT}/ ${TREXIO_ROOT}/docs
do
dir=${dir%*/}
echo ${dir}

7
tools/generator_tools.py
View File

@ -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
@ -716,7 +721,7 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
if 'index' in datatype:
tmp_dict['is_index'] = 'file->one_based'
else:
tmp_dict['is_index'] = 'false'
tmp_dict['is_index'] = '(false)'
# add the list of dimensions
tmp_dict['dims'] = [dim.replace('.','_') for dim in v[1]]

37
tools/prepare_python.sh
View File

@ -1,11 +1,22 @@
#!/bin/bash
# We want the script to crash on the 1st error:
set -e
# Check that script is executed from tools directory
if [[ $(basename $PWD) != "tools" ]] ; then
echo "This script should run in the tools directory"
exit -1
fi
DO_HDF5=0
if [[ -z ${1} ]] && [[ "${1}" == "--without-hdf5" ]] ; then
echo "Compiling Python API without the HDF5 back end."
DO_HDF5=1
else
echo "Compiling Python API with the HDF5 back end."
fi
TREXIO_ROOT=$(dirname "${PWD}../")
# First define readonly global variables.
@ -14,9 +25,7 @@ readonly INCLUDIR=${TREXIO_ROOT}/include
readonly TOOLS=${TREXIO_ROOT}/tools
readonly PYDIR=${TREXIO_ROOT}/python
readonly PYTREXIODIR=${PYDIR}/pytrexio
# We want the script to crash on the 1st error:
set -e
readonly PYDIR_TREXIO_H=${PYDIR}/src/trexio.h
# Create src and trexio directories in the python folder if not yet done
mkdir -p ${PYDIR}/src
@ -25,22 +34,16 @@ mkdir -p ${PYTREXIODIR}
# Copy all the source code and header files in the corresponding python directory
cp ${SRC}/pytrexio.py ${PYTREXIODIR}/pytrexio.py
cp ${SRC}/trexio.py ${PYDIR}/trexio.py
cp ${SRC}/*.c ${PYDIR}/src
cp ${SRC}/*.h ${PYDIR}/src
cp ${INCLUDIR}/trexio.h ${PYDIR}/src
cp ${SRC}/trexio.c ${SRC}/trexio_s.h ${SRC}/trexio_private.h ${PYDIR}/src
cp ${SRC}/trexio_text.{c,h} ${PYDIR}/src
cp ${SRC}/pytrexio_wrap.c ${PYDIR}/src/pytrexio_wrap.c
cp ${INCLUDIR}/trexio.h ${PYDIR}/src
cp ${INCLUDIR}/config.h ${PYDIR}/src
# fix needed to define HAVE_HDF5 symbol so that Python extension is always compiled with HDF5 (without including config.h)
# add "#define HAVE_HDF5 1" line after "#include stdint.h" using awk and sed
export LINE_NO=$(($(awk '/stdint.h/{print NR}' ${PYDIR}/src/trexio.h) + 1))
# sed on MacOS is different from GNU sed on Linux and requires special treatment
if [[ "$OSTYPE" == "darwin"* ]]; then
sed -i '' -e "$LINE_NO"'i \
#define HAVE_HDF5 1' "${PYDIR}/src/trexio.h"
else
sed -i -e "$LINE_NO"'i \
#define HAVE_HDF5 1' "${PYDIR}/src/trexio.h"
if [[ ${DO_HDF5} == 0 ]] ; then
cp ${SRC}/trexio_hdf5.{c,h} ${PYDIR}/src
fi
# Copy additional info
cp ${TREXIO_ROOT}/AUTHORS ${TREXIO_ROOT}/LICENSE ${PYDIR}

16
tools/trexio.scm
View 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

654
trex.org
View File

@ -1,58 +1,17 @@
#+TITLE: TREX Configuration file
#+TITLE: Data stored in TREXIO
#+STARTUP: latexpreview
#+SETUPFILE: docs/theme.setup
This page contains information about the general structure of the
TREXIO library. The source code of the library can be automatically
generated based on the contents of the ~trex.json~ configuration file,
which itself is generated from different sections (groups) presented
below.
For simplicity, the singular form is always used for the names of
groups and attributes, and all data are stored in atomic units.
The dimensions of the arrays in the tables below are given in
column-major order (as in Fortran), and the ordering of the dimensions
is reversed in the produced ~trex.json~ configuration file as the
library is written in C.
All quantities are saved in TREXIO files in atomic units. The
dimensions of the arrays in the tables below are given in column-major
order (as in Fortran), and the ordering of the dimensions is reversed
in the produced ~trex.json~ configuration file as the library is
written in C.
TREXIO currently supports ~int~, ~float~ and ~str~ types for both
single attributes and arrays. Note, that some attributes might have
~dim~ type (e.g. ~num~ of the ~nucleus~ group). This type is treated
exactly in the same way as ~int~ with the only difference that ~dim~
variables cannot be negative. This additional constraint is required
because ~dim~ attributes are used internally to allocate memory and to
check array boundaries in the memory-safe API. Most of the times, the
~dim~ variables contain the ~num~ suffix.
You may also encounter some ~dim readonly~ variables.
It means that the value is automatically computed and written by the
TREXIO library, thus it is read-only and cannot be (over)written by the
user.
In Fortran, arrays are 1-based and in most other languages the
arrays are 0-based. Hence, we introduce the ~index~ type which is a
1-based ~int~ in the Fortran interface and 0-based otherwise.
For sparse data structures such as electron replusion integrals,
the data can be too large to fit in memory and the data needs to be
fetched using multiple function calls to perform I/O on buffers.
For more information on how to read/write sparse data structures, see
the [[./examples.html][examples]]. The ~sparse~ data representation implies the
[[https://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_(COO)][coordinate list]] representation, namely the user has to write a list
of indices and values.
For the Configuration Interaction (CI) and Configuration State Function (CSF)
groups, the ~buffered~ data type is introduced, which allows similar incremental
I/O as for ~sparse~ data but without the need to write indices of the sparse values.
For determinant lists (integer bit fields), the ~special~ attribute is present in the type.
This means that the source code is not produced by the generator, but hand-written.
Some data may be complex. In that case, the real part should be stored
in the variable, and the imaginary part will be stored in the variable
with the same name suffixed by ~_im~.
#+begin_src python :tangle trex.json :exports none
#+begin_src python :tangle trex.json :exports none
{
#+end_src
#+end_src
* Metadata (metadata group)
@ -133,11 +92,15 @@ with the same name suffixed by ~_im~.
used in periodic calculations.
#+NAME: cell
| Variable | Type | Dimensions | Description |
|----------+---------+------------+-----------------------|
| ~a~ | ~float~ | ~(3)~ | First lattice vector |
| ~b~ | ~float~ | ~(3)~ | Second lattice vector |
| ~c~ | ~float~ | ~(3)~ | Third lattice vector |
| Variable | Type | Dimensions | Description |
|----------+---------+------------+--------------------------------------------------------------------------|
| ~a~ | ~float~ | ~(3)~ | First real space lattice vector |
| ~b~ | ~float~ | ~(3)~ | Second real space lattice vector |
| ~c~ | ~float~ | ~(3)~ | Third real space lattice vector |
| ~G_a~ | ~float~ | ~(3)~ | First reciprocal space lattice vector |
| ~G_b~ | ~float~ | ~(3)~ | Second reciprocal space lattice vector |
| ~G_c~ | ~float~ | ~(3)~ | Third reciprocal space lattice vector |
| ~two_pi~ | ~int~ | | ~0~ or ~1~. If ~two_pi=1~, $2\pi$ is included in the reciprocal vectors. |
#+CALL: json(data=cell, title="cell")
@ -145,9 +108,13 @@ with the same name suffixed by ~_im~.
:results:
#+begin_src python :tangle trex.json
"cell": {
"a" : [ "float", [ "3" ] ]
, "b" : [ "float", [ "3" ] ]
, "c" : [ "float", [ "3" ] ]
"a" : [ "float", [ "3" ] ]
, "b" : [ "float", [ "3" ] ]
, "c" : [ "float", [ "3" ] ]
, "G_a" : [ "float", [ "3" ] ]
, "G_b" : [ "float", [ "3" ] ]
, "G_c" : [ "float", [ "3" ] ]
, "two_pi" : [ "int" , [] ]
} ,
#+end_src
:end:
@ -177,8 +144,18 @@ with the same name suffixed by ~_im~.
** Electron (electron group)
We consider wave functions expressed in the spin-free formalism, where
the number of \uparrow and \downarrow electrons is fixed.
The chemical system consists of nuclei and electrons, where the
nuclei are considered as fixed point charges with Cartesian
coordinates. The wave function is stored in the spin-free
formalism, and therefore, it is necessary for the user to
explicitly store the number of electrons with spin up
($N_\uparrow$) and spin down ($N_\downarrow$). These numbers
correspond to the normalization of the spin-up and spin-down
single-particle reduced density matrices.
We consider wave functions expressed in the spin-free formalism, where
the number of \uparrow and \downarrow electrons is fixed.
#+NAME:electron
| Variable | Type | Dimensions | Description |
@ -213,13 +190,14 @@ with the same name suffixed by ~_im~.
The ~id~ and ~current_label~ attributes need to be specified for each file.
#+NAME: state
| Variable | Type | Dimensions | Description |
|-----------------+-------+---------------+---------------------------------------------------------------------------------------------|
| ~num~ | ~dim~ | | Number of states (including the ground state) |
| ~id~ | ~int~ | | Index of the current state (0 is ground state) |
| ~current_label~ | ~str~ | | Label of the current state |
| ~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) |
| Variable | Type | Dimensions | Description |
|-----------------+---------+---------------+---------------------------------------------------------------------------------------------|
| ~num~ | ~dim~ | | Number of states (including the ground state) |
| ~id~ | ~index~ | | Index of the current state (0 is ground state) |
| ~energy~ | ~float~ | | Energy of the current state |
| ~current_label~ | ~str~ | | Label of the current state |
| ~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")
@ -227,11 +205,12 @@ with the same name suffixed by ~_im~.
:results:
#+begin_src python :tangle trex.json
"state": {
"num" : [ "dim", [] ]
, "id" : [ "int", [] ]
, "current_label" : [ "str", [] ]
, "label" : [ "str", [ "state.num" ] ]
, "file_name" : [ "str", [ "state.num" ] ]
"num" : [ "dim" , [] ]
, "id" : [ "index", [] ]
, "energy" : [ "float", [] ]
, "current_label" : [ "str" , [] ]
, "label" : [ "str" , [ "state.num" ] ]
, "file_name" : [ "str" , [ "state.num" ] ]
} ,
#+end_src
:end:
@ -241,9 +220,9 @@ with the same name suffixed by ~_im~.
*** Gaussian and Slater-type orbitals
We consider here basis functions centered on nuclei. Hence, we enable
the possibility to define /dummy atoms/ to place basis functions in
random positions.
We consider here basis functions centered on nuclei. Hence, it is
possibile to define /dummy atoms/ to place basis functions in
arbitrary positions.
The atomic basis set is defined as a list of shells. Each shell $s$ is
centered on a center $A$, possesses a given angular momentum $l$ and a
@ -277,35 +256,103 @@ with the same name suffixed by ~_im~.
All the basis set parameters are stored in one-dimensional arrays.
*** Numerical orbitals
Trexio supports numerical atom centered orbitals. The implementation is
based on the approach of FHI-aims [Blum, V. et al; Ab initio molecular
simulations with numeric atom-centered orbitals; Computer Physics
Communications 2009]. These orbitals are
defined by the atom they are centered on, their angular momentum and a
radial function $R_s$, which is of the form
\[
R_s(\mathbf{r}) = \mathcal{N}_s \frac{u_i(\mathbf{r})}{r^{-n_s}}.
\]
Where $u_i(\mathbf{r})$ is numerically tabulated on a dense logarithmic
grid. It is constructed to vanish for any $\mathbf{r}$
outside of the grid. The reference points are stored in ~nao_grid_r~
and ~nao_grid_phi~. Additionaly, a separate spline for the first and second
derivative of $u(\mathbf{r})$ can be stored in ~nao_grid_grad~ and ~nao_grid_lap~.
Storing them in this form allows to calculate the actual first and
second derivatives easily as follows:
\[
\frac{\partial \phi}{\partial x} = \frac{x}{r^2}\left( u^\prime\left(r\right) - \frac{u\left(r\right)}{r}\right)
\]
\[
\frac{\partial^2 \phi}{\partial x^2} = \frac{1}{r^3}\left(x^2 u^{\prime\prime}(r) + \left( 3x^2-r^2\right) \left( \frac{u(r)}{r^2} - \frac{u'(r)}{r}\right) \right)
\]
The index of the first data point for each shell is stored in
~nao_grid_start~, the number of data points per spline is stored
in ~nao_grid_size~ for convenience.
What kind of spline is used can be provided in the ~interpolator_kind~ field.
For example, FHI-aims uses a cubic spline, so the ~interpolator_kind~ is
\"Polynomial\" and the ~interp_coeff_cnt~ is $4$. In this case, the first
interpolation coefficient per data point is the absolute term, the second is for
the linear term etc.
The interpolation coefficients for the wave function are given in the
~interpolator_phi~ array. The ~interpolator_grad~ and ~interpolator_lap~
arrays provide a spline for the gradient and Laplacian, respectively.
The argument passed to the interpolants is on the logarithmic scale of
the reference points: If the argument is an integer $i$, the interpolant
will return the value of $u(\mathbf{r})$ at the $i$th reference point.
A radius is converted to this scale by (note the zero-indexing)
\[
i_{\log} = \frac{1}{c} \cdot \log \left( \frac{r}{r_0} \right)
\]
where
\[
c = \log\left(\frac{r_1}{r_0}\right)
\]
For convenience, this conversion and functions to evaluate the splines
are provided with trexio. Since these implementations are not adapted to
a specific software architecture, a programm using these orbitals should
reimplement them with consideration for its specific needs.
*** Plane waves
A plane wave is defined as
\[
\chi_j(r) = \exp \left( -i \mathbf{k}_j \mathbf{r} \right)
\chi_j(\mathbf{r}) = \exp \left( -i \mathbf{G}_j \cdot \mathbf{r} \right)
\]
The basis set is defined as the array of $k$-points in the
reciprocal space, defined in the ~pbc~ group. The kinetic energy
cutoff ~e_cut~ is the only input data relevant to plane waves.
reciprocal space $\mathbf{G}_j$, defined in the ~pbc~ group. The
kinetic energy cutoff ~e_cut~ is the only input data relevant to
plane waves.
*** Data definitions
#+NAME: basis
| Variable | Type | Dimensions | Description |
|-----------------+---------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater" or "PW" for plane waves |
| ~prim_num~ | ~dim~ | | Total number of primitives |
| ~shell_num~ | ~dim~ | | Total number of shells |
| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices |
| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta |
| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) |
| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) |
| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index |
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations |
| Variable | Type | Dimensions | Description | |
|---------------------+---------+-----------------------------------------------+------------------------------------------------------------------------------+---|
| ~type~ | ~str~ | | Type of basis set: "Gaussian", "Slater", "Numerical" or "PW" for plane waves | |
| ~prim_num~ | ~dim~ | | Total number of primitives | |
| ~shell_num~ | ~dim~ | | Total number of shells | |
| ~nao_grid_num~ | ~dim~ | | Total number of grid points for numerical orbitals | |
| ~interp_coeff_cnt~ | ~dim~ | | Number of coefficients for the numerical orbital interpolator | |
| ~nucleus_index~ | ~index~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and atomic indices | |
| ~shell_ang_mom~ | ~int~ | ~(basis.shell_num)~ | One-to-one correspondence between shells and angular momenta | |
| ~shell_factor~ | ~float~ | ~(basis.shell_num)~ | Normalization factor of each shell ($\mathcal{N}_s$) | |
| ~r_power~ | ~int~ | ~(basis.shell_num)~ | Power to which $r$ is raised ($n_s$) | |
| ~nao_grid_start~ | ~index~ | ~(basis.shell_num)~ | Index of the first data point for a given numerical orbital | |
| ~nao_grid_size~ | ~dim~ | ~(basis.shell_num)~ | Number of data points per numerical orbital | |
| ~shell_index~ | ~index~ | ~(basis.prim_num)~ | One-to-one correspondence between primitives and shell index | |
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) | |
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) | |
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) | |
| ~e_cut~ | ~float~ | | Energy cut-off for plane-wave calculations | |
| ~nao_grid_radius~ | ~float~ | ~(basis.nao_grid_num)~ | Radii of grid points for numerical orbitals | |
| ~nao_grid_phi~ | ~float~ | ~(basis.nao_grid_num)~ | Wave function values for numerical orbitals | |
| ~nao_grid_grad~ | ~float~ | ~(basis.nao_grid_num)~ | Radial gradient of numerical orbitals | |
| ~nao_grid_lap~ | ~float~ | ~(basis.nao_grid_num)~ | Laplacian of numerical orbitals | |
| ~interpolator_kind~ | ~str~ | | Kind of spline, e.g. "Polynomial" | |
| ~interpolator_phi~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital interpolation function | |
| ~interpolator_grad~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital gradient interpolation function | |
| ~interpolator_lap~ | ~float~ | ~(basis.interp_coeff_cnt,basis.nao_grid_num)~ | Coefficients for numerical orbital laplacian interpolation function | |
#+CALL: json(data=basis, title="basis")
@ -313,20 +360,32 @@ with the same name suffixed by ~_im~.
#+RESULTS:
:results:
#+begin_src python :tangle trex.json
"basis": {
"type" : [ "str" , [] ]
, "prim_num" : [ "dim" , [] ]
, "shell_num" : [ "dim" , [] ]
, "nucleus_index" : [ "index", [ "basis.shell_num" ] ]
, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
, "r_power" : [ "int" , [ "basis.shell_num" ] ]
, "shell_index" : [ "index", [ "basis.prim_num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
, "e_cut" : [ "float", [] ]
} ,
"basis": {
"type" : [ "str" , [] ]
, "prim_num" : [ "dim" , [] ]
, "shell_num" : [ "dim" , [] ]
, "nao_grid_num" : [ "dim" , [] ]
, "interp_coeff_cnt" : [ "dim" , [] ]
, "nucleus_index" : [ "index", [ "basis.shell_num" ] ]
, "shell_ang_mom" : [ "int" , [ "basis.shell_num" ] ]
, "shell_factor" : [ "float", [ "basis.shell_num" ] ]
, "r_power" : [ "int" , [ "basis.shell_num" ] ]
, "nao_grid_start" : [ "index", [ "basis.shell_num" ] ]
, "nao_grid_size" : [ "dim" , [ "basis.shell_num" ] ]
, "shell_index" : [ "index", [ "basis.prim_num" ] ]
, "exponent" : [ "float", [ "basis.prim_num" ] ]
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
, "e_cut" : [ "float", [] ]
, "nao_grid_radius" : [ "float", [ "basis.nao_grid_num" ] ]
, "nao_grid_phi" : [ "float", [ "basis.nao_grid_num" ] ]
, "nao_grid_grad" : [ "float", [ "basis.nao_grid_num" ] ]
, "nao_grid_lap" : [ "float", [ "basis.nao_grid_num" ] ]
, "interpolator_kind" : [ "str" , [] ]
, "interpolator_phi" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ]
, "interpolator_grad" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ]
, "interpolator_lap" : [ "float", [ "basis.nao_grid_num", "basis.interp_coeff_cnt" ] ]
} ,
#+end_src
:end:
@ -390,7 +449,7 @@ exponent =
coefficient =
[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0,
0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0, 1.0, 1.0, 1.0 ]
`
prim_factor =
[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01
3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01,
@ -409,20 +468,21 @@ prim_factor =
V_A^{\text{ECP}} =
V_{A \ell_{\max}+1} +
\sum_{\ell=0}^{\ell_{\max}}
\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \left[
V_{A \ell} - V_{A \ell_{\max}+1} \right] \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,
while the remaining terms correspond to the non-local channel projections.
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.
@ -438,14 +498,13 @@ prim_factor =
| ~coefficient~ | ~float~ | ~(ecp.num)~ | $\beta_{A q \ell}$ all ECP coefficients |
| ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers |
There might be some confusion in the meaning of the $\ell_{\max}$.
It can be attributed to the maximum angular momentum occupied in
the core orbitals, which are removed by the ECP. On the other
hand, it can be attributed to the maximum angular momentum of the
ECP that replaces the core electrons.
*Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former.
*Note for developers*: avoid having variables with similar prefix
in their name. The HDF5 back end might cause issues due to the way
~find_dataset~ function works. For example, in the ECP group we
@ -587,58 +646,50 @@ power = [
* Orbitals
** Atomic orbitals (ao group)
Going from the atomic basis set to AOs implies a systematic
construction of all the angular functions of each shell. We
consider two cases for the angular functions: the real-valued
spherical harmonics, and the polynomials in Cartesian coordinates.
In the case of real spherical harmonics, the AOs are ordered as
$0, +1, -1, +2, -2, \dots, +m, -m$ (see [[https://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Real_spherical_harmonics][Wikipedia]]).
In the case of polynomials we
impose the canonical (or alphabetical) ordering), i.e
\begin{eqnarray}
p & : & p_x, p_y, p_z \nonumber \\
d & : & d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz} \nonumber \\
f & : & f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}, f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, …f_{zzz} \nonumber \\
{\rm etc.} \nonumber
\end{eqnarray}
Note that there is no exception for $p$ orbitals in spherical
coordinates: the ordering is $0,+1,-1$ which corresponds $p_z, p_x, p_y$.
AOs are defined as
\[
\chi_i (\mathbf{r}) = \mathcal{N}_i\, P_{\eta(i)}(\mathbf{r})\, R_{\theta(i)} (\mathbf{r})
\chi_i (\mathbf{r}) = \mathcal{N}_i'\, P_{\eta(i)}(\mathbf{r})\, R_{s(i)} (\mathbf{r})
\]
where $i$ is the atomic orbital index,
$P$ encodes for either the
polynomials or the spherical harmonics, $\theta(i)$ returns the
shell on which the AO is expanded, and $\eta(i)$ denotes which
angular function is chosen.
$\mathcal{N}_i$ is a normalization factor that enables the
possibility to have different normalization coefficients within a
shell, as in the GAMESS convention where
$\mathcal{N}_{x^2} \ne \mathcal{N}_{xy}$ because
\[ \left[ \iiint \left(x-X_A \right)^2 R_{\theta(i)}
(\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne
\left[ \iiint \left( x-X_A \right) \left( y-Y_A \right) R_{\theta(i)}
(\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]
where $i$ is the atomic orbital index, $P$ refers to either
polynomials or spherical harmonics, and $s(i)$ specifies the shell
on which the AO is expanded.
$\eta(i)$ denotes the chosen angular function. The AOs can be
expressed using real spherical harmonics or polynomials in Cartesian
coordinates. In the case of real spherical harmonics, the AOs are
ordered as $0, +1, -1, +2, -2, \dots, + m, -m$ (see [[https://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Real_spherical_harmonics][Wikipedia]]). In
the case of polynomials, the canonical (or alphabetical) ordering is
used,
| $p$ | $p_x, p_y, p_z$ |
| $d$ | $d_{xx}, d_{xy}, d_{xz}, d_{yy}, d_{yz}, d_{zz}$ |
| $f$ | $f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}$, |
| | $f_{xzz}, f_{yyy}, f_{yyz}, f_{yzz}, f_{zzz}$ |
| $\vdots$ | |
Note that for \(p\) orbitals in spherical coordinates, the ordering
is $0,+1,-1$ which corresponds to $p_z, p_x, p_y$.
$\mathcal{N}_i'$ is a normalization factor that allows for different
normalization coefficients within a single shell, as in the GAMESS
convention where each individual function is unit-normalized.
Using GAMESS convention, the normalization factor of the shell
$\mathcal{N}_d$ in the ~basis~ group is appropriate for instance
for the $d_z^2$ function (i.e.
$\mathcal{N}_{d}\equiv\mathcal{N}_{z^2}$) but not for the $d_{xy}$
AO, so the correction factor $\mathcal{N}_i'$ for $d_{xy}$ in the
~ao~ groups is the ratio $\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}$.
In such a case, one should set the normalization of the shell (in
the [[Basis set (basis group)][Basis set]] section) to $\mathcal{N}_{z^2}$, which is the
normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the $xy$ function which should be
introduced here should be $\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}$.
#+NAME: ao
| Variable | Type | Dimensions | Description |
|-----------------+---------+------------+---------------------------------|
| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
| ~num~ | ~dim~ | | Total number of atomic orbitals |
| ~shell~ | ~index~ | ~(ao.num)~ | basis set shell for each AO |
| ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factors |
| Variable | Type | Dimensions | Description |
|-----------------+---------+------------+--------------------------------------|
| ~cartesian~ | ~int~ | | ~1~: true, ~0~: false |
| ~num~ | ~dim~ | | Total number of atomic orbitals |
| ~shell~ | ~index~ | ~(ao.num)~ | Basis set shell for each AO |
| ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factor $\mathcal{N}_i$ |
#+CALL: json(data=ao, title="ao")
@ -671,18 +722,18 @@ power = [
over atomic orbitals.
#+NAME: ao_1e_int
| Variable | Type | Dimensions | Description |
|-----------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) |
| ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
| ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
| ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
| ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
| Variable | Type | Dimensions | Description |
|-----------------------+---------+--------------------+--------------------------------------------------------------------------|
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) |
| ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
| ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
| ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
| ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
#+CALL: json(data=ao_1e_int, title="ao_1e_int")
@ -711,34 +762,32 @@ power = [
The two-electron integrals for a two-electron operator $\hat{O}$ are
\[ \langle p q \vert \hat{O} \vert r s \rangle \] in physicists
notation or \[ ( pr \vert \hat{O} \vert qs ) \] in chemists
notation, where $p,q,r,s$ are indices over atomic orbitals.
Functions are provided to get the indices in physicists or chemists
notation.
# TODO: Physicist / Chemist functions
# TODO: Physicist / Chemist functions
# Functions are provided to get the indices in physicists or chemists
# notation.
- \[ \hat{W}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{1}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron repulsive potential operator.
- \[ \hat{W}^{lr}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}}
\sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i -
\sum_{j=1}^{i-1} \frac{\text{erf}(\mu\, \vert \mathbf{r}_i -
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
The Cholesky decomposition of the integrals can also be stored:
\[
A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
\langle ij | kl \rangle = \sum_{\alpha} G_{ik\alpha} G_{jl\alpha}
\]
#+NAME: ao_2e_int
| Variable | Type | Dimensions | Description |
|-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
| ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals |
| ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range Electron repulsion integrals |
| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
| ~eri_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI |
| ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI |
| ~eri_lr_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI |
| Variable | Type | Dimensions | Description |
|-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
| ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals |
| ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range electron repulsion integrals |
| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
| ~eri_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI |
| ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI |
| ~eri_lr_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI |
#+CALL: json(data=ao_2e_int, title="ao_2e_int")
@ -840,7 +889,7 @@ power = [
| Variable | Type | Dimensions | Description |
|-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
| ~eri~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Electron repulsion integrals |
| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range Electron repulsion integrals |
| ~eri_lr~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Long-range electron repulsion integrals |
| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
| ~eri_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, mo_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI |
| ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI |
@ -861,7 +910,7 @@ power = [
} ,
#+end_src
:end:
* Multi-determinant information
** Slater determinants (determinant group)
@ -959,7 +1008,7 @@ power = [
on a reference wave function $\Psi$, where $\hat{T}_1$ is the single excitation operator,
\[
\hat{T}_1 = \sum_{ia} t_{i}^{a}\, \hat{a}^\dagger_a \hat{a}_i,
\hat{T}_1 = \sum_{ia} t_{i}^{a}\, \hat{a}^\dagger_a \hat{a}_i,
\]
$\hat{T}_2$ is the double excitation operator,
@ -979,7 +1028,7 @@ power = [
\[ |\Phi\rangle = e^{\hat{T}}| \Psi \rangle \]
The reference wave function is stored using the ~determinant~ and/or
The reference wave function is stored using the ~determinant~ and/or
~csf~ groups, and the amplitudes are stored using the current group.
The attributes with the ~exp~ suffix correspond to exponentialized operators.
@ -1036,23 +1085,20 @@ power = [
\gamma_{ij} = \gamma^{\uparrow}_{ij} + \gamma^{\downarrow}_{ij}
\]
The $\uparrow \uparrow$, $\downarrow \downarrow$, $\uparrow \downarrow$, $\downarrow \uparrow$
components of the two-body density matrix are given by
The $\uparrow \uparrow$, $\downarrow \downarrow$, $\uparrow \downarrow$ components of the two-body density matrix are given by
\begin{eqnarray*}
\Gamma_{ijkl}^{\uparrow \uparrow} &=&
\langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\alpha} \hat{a}_{j\alpha}\, \hat{a}_{i\alpha} | \Psi \rangle \\
\Gamma_{ijkl}^{\downarrow \downarrow} &=&
\langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\beta} | \Psi \rangle \\
\Gamma_{ijkl}^{\uparrow \downarrow} &=&
\langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle \\
\Gamma_{ijkl}^{\downarrow \uparrow} &=&
\langle \Psi | \hat{a}^{\dagger}_{k\beta}\, \hat{a}^{\dagger}_{l\alpha} \hat{a}_{j\alpha}\, \hat{a}_{i\beta} | \Psi \rangle \\
\langle \Psi | \hat{a}^{\dagger}_{k\alpha}\, \hat{a}^{\dagger}_{l\beta} \hat{a}_{j\beta}\, \hat{a}_{i\alpha} | \Psi \rangle
+ \langle \Psi | \hat{a}^{\dagger}_{l\alpha}\, \hat{a}^{\dagger}_{k\beta} \hat{a}_{i\beta}\, \hat{a}_{j\alpha} | \Psi \rangle \\
\end{eqnarray*}
and the spin-summed one-body density matrix is
\[
\Gamma_{ijkl} = \Gamma_{ijkl}^{\uparrow \uparrow} +
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow} +
\Gamma_{ijkl}^{\downarrow \uparrow}
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow}.
\]
The total energy can be computed as:
@ -1078,26 +1124,25 @@ power = [
$g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)$.
#+NAME: rdm
| Variable | Type | Dimensions | Description |
|------------------------+----------------+----------------------------------------------+-----------------------------------------------------------------------|
| ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix |
| ~1e_up~ | ~float~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix |
| ~1e_dn~ | ~float~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix |
| ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) |
| ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix |
| ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix |
| ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
| ~2e_dnup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\uparrow component of the two-body reduced density matrix |
| ~2e_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (spin trace) |
| ~2e_upup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_upup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\uparrow\uparrow) |
| ~2e_dndn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_dndn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dndn_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\downarrow\downarrow) |
| ~2e_updn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_updn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_updn_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\uparrow\downarrow) |
| ~2e_dnup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_dnup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dnup_cholesky_num)~ | Cholesky decomposition of the Two-body RDM (\downarrow\uparrow) |
| Variable | Type | Dimensions | Description |
|------------------------+----------------+---------------------------------------------------------+-----------------------------------------------------------------------|
| ~1e~ | ~float~ | ~(mo.num, mo.num)~ | One body density matrix |
| ~1e_up~ | ~float~ | ~(mo.num, mo.num)~ | \uparrow-spin component of the one body density matrix |
| ~1e_dn~ | ~float~ | ~(mo.num, mo.num)~ | \downarrow-spin component of the one body density matrix |
| ~1e_transition~ | ~float~ | ~(mo.num, mo.num, state.num, state.num) | One-particle transition density matrices |
| ~2e~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | Two-body reduced density matrix (spin trace) |
| ~2e_upup~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\uparrow component of the two-body reduced density matrix |
| ~2e_dndn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \downarrow\downarrow component of the two-body reduced density matrix |
| ~2e_updn~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num)~ | \uparrow\downarrow component of the two-body reduced density matrix |
| ~2e_transition~ | ~float sparse~ | ~(mo.num, mo.num, mo.num, mo.num, state.num, state.num) | Two-particle transition density matrices |
| ~2e_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_cholesky_num)~ | Cholesky decomposition of the two-body RDM (spin trace) |
| ~2e_upup_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_upup_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_upup_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\uparrow) |
| ~2e_dndn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_dndn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_dndn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\downarrow\downarrow) |
| ~2e_updn_cholesky_num~ | ~dim~ | | Number of Cholesky vectors |
| ~2e_updn_cholesky~ | ~float sparse~ | ~(mo.num, mo.num, rdm.2e_updn_cholesky_num)~ | Cholesky decomposition of the two-body RDM (\uparrow\downarrow) |
#+CALL: json(data=rdm, title="rdm")
@ -1105,24 +1150,23 @@ power = [
:results:
#+begin_src python :tangle trex.json
"rdm": {
"1e" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_dnup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_cholesky_num" : [ "dim" , [] ]
, "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_upup_cholesky_num" : [ "dim" , [] ]
, "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_dndn_cholesky_num" : [ "dim" , [] ]
, "2e_dndn_cholesky" : [ "float sparse", [ "rdm.2e_dndn_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_updn_cholesky_num" : [ "dim" , [] ]
, "2e_updn_cholesky" : [ "float sparse", [ "rdm.2e_updn_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_dnup_cholesky_num" : [ "dim" , [] ]
, "2e_dnup_cholesky" : [ "float sparse", [ "rdm.2e_dnup_cholesky_num", "mo.num", "mo.num" ] ]
"1e" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_up" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_dn" : [ "float" , [ "mo.num", "mo.num" ] ]
, "1e_transition" : [ "float" , [ "state.num", "state.num", "mo.num", "mo.num" ] ]
, "2e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_upup" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_dndn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_updn" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_transition" : [ "float sparse", [ "state.num", "state.num", "mo.num", "mo.num", "mo.num", "mo.num" ] ]
, "2e_cholesky_num" : [ "dim" , [] ]
, "2e_cholesky" : [ "float sparse", [ "rdm.2e_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_upup_cholesky_num" : [ "dim" , [] ]
, "2e_upup_cholesky" : [ "float sparse", [ "rdm.2e_upup_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_dndn_cholesky_num" : [ "dim" , [] ]
, "2e_dndn_cholesky" : [ "float sparse", [ "rdm.2e_dndn_cholesky_num", "mo.num", "mo.num" ] ]
, "2e_updn_cholesky_num" : [ "dim" , [] ]
, "2e_updn_cholesky" : [ "float sparse", [ "rdm.2e_updn_cholesky_num", "mo.num", "mo.num" ] ]
} ,
#+end_src
:end:
@ -1130,12 +1174,12 @@ power = [
* Correlation factors
** Jastrow factor (jastrow group)
The Jastrow factor is an $N$-electron function to which the CI
expansion is multiplied: $\Psi = \Phi \times \exp(J)$,
The Jastrow factor is an $N$-electron function which multiplies the CI
expansion: $\Psi = \Phi \times \exp(J)$,
In the following, we use the notations $r_{ij} = |\mathbf{r}_i - \mathbf{r}_j|$ and
$R_{i\alpha} = |\mathbf{r}_i - \mathbf{R}_\alpha|$, where indices
$i$ and $j$ correspond to electrons and $\alpha$ to nuclei.
$i$ and $j$ refer to electrons and $\alpha$ to nuclei.
Parameters for multiple forms of Jastrow factors can be saved in
TREXIO files, and are described in the following sections. These
@ -1143,7 +1187,7 @@ power = [
following:
- ~CHAMP~
- ~Mu~
*** CHAMP
The first form of Jastrow factor is the one used in
@ -1152,75 +1196,95 @@ power = [
\[
J(\mathbf{r},\mathbf{R}) = J_{\text{eN}}(\mathbf{r},\mathbf{R}) + J_{\text{ee}}(\mathbf{r}) + J_{\text{eeN}}(\mathbf{r},\mathbf{R})
\]
$J_{\text{eN}}$ contains electron-nucleus terms:
$J_{\text{eN}}$ contains electron-nucleus terms:
\[
J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}}
\frac{a_{1,\alpha}\, g_\alpha(R_{i\alpha})}{1+a_{2,\alpha}\, g_\alpha(R_{i\alpha})} +
\sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, [g_\alpha(R_{i\alpha})]^p - J_{eN}^\infty
J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}}\left[
\frac{a_{1,\alpha}\, f_\alpha(R_{i\alpha})}{1+a_{2,\alpha}\,
f_\alpha(R_{i\alpha})} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, [f_\alpha(R_{i\alpha})]^p - J_{\text{eN}}^\infty
\right]
\]
$J_{\text{ee}}$ contains electron-electron terms:
\[
J_{\text{ee}}(\mathbf{r}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1}
\frac{b_1\, f(r_{ij})}{1+b_2\, f(r_{ij})} +
\sum_{p=2}^{N_\text{ord}^b} a_{p+1}\, [f(r_{ij})]^p - J_{ee}^\infty
\left[
\frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\, f_{\text{ee}}(r_{ij})}{1+b_2\, f_{\text{ee}}(r_{ij})} +
\sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, [f_{\text{ee}}(r_{ij})]^p - J_{\text{ee},ij}^\infty
\right]
\]
$\delta^{\uparrow\downarrow}_{ij}$ is zero when the electrons $i$ and
$j$ have the same spin, and one otherwise.
and $J_{\text{eeN}}$ contains electron-electron-Nucleus terms:
$J_{\text{eeN}}$ contains electron-electron-Nucleus terms:
\[
J_{\text{eeN}}(\mathbf{r},\mathbf{R}) =
J_{\text{eeN}}(\mathbf{r},\mathbf{R}) =
\sum_{\alpha=1}^{N_{\text{nucl}}}
\sum_{i=1}^{N_{\text{elec}}}
\sum_{j=1}^{i-1}
\sum_{p=2}^{N_{\text{ord}}}
\sum_{k=0}^{p-1}
\sum_{l=0}^{p-k-2\delta_{k,0}}
c_{lkp\alpha} \left[ f({r}_{ij}) \right]^k
\left[ \left[ g_\alpha({R}_{i\alpha}) \right]^l + \left[ g_\alpha({R}_{j\alpha}) \right]^l \right]
\left[ g_\alpha({R}_{i\,\alpha}) \, g_\alpha({R}_{j\alpha}) \right]^{(p-k-l)/2}
c_{lkp\alpha} \left[ g_{\text{ee}}({r}_{ij}) \right]^k \nonumber \\
\left[ \left[ g_\alpha({R}_{i\alpha}) \right]^l + \left[ g_\alpha({R}_{j\alpha}) \right]^l \right]
\left[ g_\alpha({R}_{i\,\alpha}) \,
g_\alpha({R}_{j\alpha}) \right]^{(p-k-l)/2}
\]
$c_{lkp\alpha}$ are non-zero only when $p-k-l$ is even.
The terms $J_{\text{ee}}^\infty$ and $J_{\text{eN}}^\infty$ are shifts to ensure that
$J_{\text{ee}}$ and $J_{\text{eN}}$ have an asymptotic value of zero.
The terms $J_{\text{ee},ij}^\infty$ and $J_{\text{eN}}^\infty$ are shifts to ensure that
$J_{\text{eN}}$ and $J_{\text{ee}}$ have an asymptotic value of zero:
\[
J_{\text{eN}}^{\infty} =
\frac{a_{1,\alpha}\, \kappa_\alpha^{-1}}{1+a_{2,\alpha}\,
\kappa_\alpha^{-1}} + \sum_{p=2}^{N_\text{ord}^a} a_{p+1,\alpha}\, \kappa_\alpha^{-p}
\]
\[
J_{\text{ee},ij}^{\infty} =
\frac{\frac{1}{2}\big(1 + \delta^{\uparrow\downarrow}_{ij}\big)\,b_1\,
\kappa_{\text{ee}}^{-1}}{1+b_2\, \kappa_{\text{ee}}^{-1}} +
\sum_{p=2}^{N_\text{ord}^b} b_{p+1}\, \kappa_{\text{ee}}^{-p}
\]
$f$ and $g$ are scaling function defined as
\[
f(r) = \frac{1-e^{-\kappa\, r}}{\kappa} \text{ and }
g_\alpha(r) = e^{-\kappa_\alpha\, r}.
f_\alpha(r) = \frac{1-e^{-\kappa_\alpha\, r}}{\kappa_\alpha} \text{ and }
g_\alpha(r) = e^{-\kappa_\alpha\, r},
\]
*** Mu
[[https://aip.scitation.org/doi/10.1063/5.0044683][Mu-Jastrow]] is based on a one-parameter correlation factor that has
been introduced in the context of transcorrelated methods. This
correlation factor imposes the electron-electron cusp and it is
correlation factor imposes the electron-electron cusp, and it is
built such that the leading order in $1/r_{12}$ of the effective
two-electron potential reproduces the long-range interaction of the
range-separated density functional theory. Its analytical
expression reads
expression reads
\[
J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) +
J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) +
J_{\text{eN}}(\mathbf{r}, \mathbf{R})
\].
The electron-electron cusp is incorporated in the three-body term.
The electron-electron cusp is incorporated in the three-body term
\[
J_\text{eeN} (\mathbf{r}, \mathbf{R}) =
J_\text{eeN} (\mathbf{r}, \mathbf{R}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \,
\Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha})
\Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha}),
\]
$u$ is an electron-electron function given by the symmetric function
where ww$u$ is an electron-electron function
\[
u\left(\mu, r\right) = \frac{r}{2} \, \left[ 1 - \text{erf}(\mu\, r) \right] - \frac{1}{2 \, \mu \, \sqrt{\pi}} \exp \left[ -(\mu \, r)^2 \right].
@ -1231,24 +1295,24 @@ power = [
electrons.
An envelope function has been introduced to cancel out the Jastrow
effects between two-electrons when they are both close to a nucleus
effects between two-electrons when at least one is close to a nucleus
(to perform a frozen-core calculation). The envelope function is
given by
\[
E_\alpha(R) = 1 - \exp\left( - \gamma_{\alpha} \, R^2 \right).
\]
In particular, if the parameters $\gamma_\alpha$ tend to zero, the
Mu-Jastrow factor becomes a two-body Jastrow factor:
\[
J_{\text{ee}}(\mathbf{r}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right)
J_{\text{ee}}(\mathbf{r}) =
\sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right)
\]
and for large $\gamma_\alpha$ it becomes zero.
To increase the flexibility of the Jastrow and improve the
electron density the following electron-nucleus term is added
@ -1261,36 +1325,36 @@ power = [
The parameter $\mu$ is stored in the ~ee~ array, the parameters
$\gamma_\alpha$ are stored in the ~een~ array, and the parameters
$a_\alpha$ are stored in the ~en~ array.
*** Table of values
#+name: jastrow
| Variable | Type | Dimensions | Description |
|---------------+----------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~string~ | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ |
| ~ee_num~ | ~dim~ | | Number of Electron-electron parameters |
| ~en_num~ | ~dim~ | | Number of Electron-nucleus parameters |
| ~een_num~ | ~dim~ | | Number of Electron-electron-nucleus parameters |
| ~ee~ | ~float~ | ~(jastrow.ee_num)~ | Electron-electron parameters |
| ~en~ | ~float~ | ~(jastrow.en_num)~ | Electron-nucleus parameters |
| ~een~ | ~float~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters |
| ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter |
| ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter |
| ~ee_scaling~ | ~float~ | | $\kappa$ value in CHAMP Jastrow for electron-electron distances |
| ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
| Variable | Type | Dimensions | Description |
|---------------+---------+---------------------+-----------------------------------------------------------------|
| ~type~ | ~str~ | | Type of Jastrow factor: ~CHAMP~ or ~Mu~ |
| ~en_num~ | ~dim~ | | Number of Electron-nucleus parameters |
| ~ee_num~ | ~dim~ | | Number of Electron-electron parameters |
| ~een_num~ | ~dim~ | | Number of Electron-electron-nucleus parameters |
| ~en~ | ~float~ | ~(jastrow.en_num)~ | Electron-nucleus parameters |
| ~ee~ | ~float~ | ~(jastrow.ee_num)~ | Electron-electron parameters |
| ~een~ | ~float~ | ~(jastrow.een_num)~ | Electron-electron-nucleus parameters |
| ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter |
| ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter |
| ~ee_scaling~ | ~float~ | | $\kappa$ value in CHAMP Jastrow for electron-electron distances |
| ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
#+CALL: json(data=jastrow, title="jastrow")
#+RESULTS:
:results:
#+begin_src python :tangle trex.json
"jastrow": {
"type" : [ "string", [] ]
, "ee_num" : [ "dim" , [] ]
"type" : [ "str" , [] ]
, "en_num" : [ "dim" , [] ]
, "ee_num" : [ "dim" , [] ]
, "een_num" : [ "dim" , [] ]
, "ee" : [ "float" , [ "jastrow.ee_num" ] ]
, "en" : [ "float" , [ "jastrow.en_num" ] ]
, "ee" : [ "float" , [ "jastrow.ee_num" ] ]
, "een" : [ "float" , [ "jastrow.een_num" ] ]
, "en_nucleus" : [ "index" , [ "jastrow.en_num" ] ]
, "een_nucleus" : [ "index" , [ "jastrow.een_num" ] ]
@ -1331,7 +1395,7 @@ power = [
}
#+end_src
:end:
* Appendix :noexport:
** Python script from table to json

8
version_memo.txt Normal file
View File

@ -0,0 +1,8 @@
To update the version, change:
- configure.ac
- CMakeLists.txt
- ocaml/trexio/trexio.opam
- python/pytrexio/_version.py
- rust/trexio/Cargo.toml