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Merge branch 'master' into optional-hdf5
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commit
7d00b87ad8
4
.github/workflows/actions.yml
vendored
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.github/workflows/actions.yml
vendored
@ -23,7 +23,7 @@ jobs:
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- name: configure with autotools
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run: |
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./autogen.sh
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TREXIO_DEVEL=1 ./configure --enable-silent-rules
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./configure --enable-silent-rules
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- name: compile TREXIO
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run: make -j 2
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@ -63,7 +63,7 @@ jobs:
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- name: configure with autotools
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run: |
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./autogen.sh
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TREXIO_DEVEL=1 ./configure FC=gfortran-10 --enable-silent-rules
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./configure FC=gfortran-10 --enable-silent-rules
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- name: compile TREXIO
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run: make -j 2
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22
README.md
22
README.md
@ -20,7 +20,7 @@ TREX library for efficient I/O.
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1. Download the `trexio-<version>.tar.gz` file
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2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
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3. `cd trexio-<version>`
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4. `./configure --enable-silent-rules`
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4. `./configure`
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5. `make`
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6. `make check`
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7. `sudo make install`
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@ -40,7 +40,7 @@ TREX library for efficient I/O.
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1. `git clone https://github.com/TREX-CoE/trexio.git`
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2. `cd trexio`
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3. `./autogen.sh`
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4. `TREXIO_DEVEL=1 ./configure --enable-maintainer-mode`
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4. `./configure`
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5. `make`
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6. `make check`
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7. `sudo make install`
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@ -54,7 +54,7 @@ Once installed, add `-ltrexio` to the list of compiler options.
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In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
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In order to link the program against TREXIO, the search paths can be modified as follows:
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`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
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`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
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(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
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@ -78,28 +78,28 @@ The primary TREXIO API is composed of the following functions:
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- `trexio_has_[group]_[variable]`
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- `trexio_close`
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where `[group]` and `[variable]` substitutions correspond to the contents of the `trex.json` configuration file
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where `[group]` and `[variable]` substitutions correspond to the contents of the `trex.json` configuration file
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(for more details, see the corresponding [documentation](https://trex-coe.github.io/trexio/trex.html) page).
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For example, consider the `coord` variable (array), which belongs to the `nucleus` group. The TREXIO user can write or read it using `trexio_write_nucleus_coord` or `trexio_read_nucleus_coord` functions, respectively.
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Note: the `[variable]` names have to be unique only within the corresponding parent `[group]`.
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There is no naming conflict when, for example, `num` variable exists both in the `nucleus` group (i.e. the number of nuclei) and in the `mo` group (i.e. the number of molecular orbitals).
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Note: the `[variable]` names have to be unique only within the corresponding parent `[group]`.
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There is no naming conflict when, for example, `num` variable exists both in the `nucleus` group (i.e. the number of nuclei) and in the `mo` group (i.e. the number of molecular orbitals).
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These quantities can be accessed using the corresponding `trexio_[has|read|write]_nucleus_num` and `trexio_[has|read|write]_mo_num`, respectively.
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## Python API
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For more details regarding the installation and usage of the TREXIO Python API,
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For more details regarding the installation and usage of the TREXIO Python API,
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see [this page](python/README.md).
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## Tutorial
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TREXIO tutorials in Jupyter notebook format can be found in the
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TREXIO tutorials in Jupyter notebook format can be found in the
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[corresponding GitHub repository](https://github.com/TREX-CoE/trexio-tutorials)
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or on [Binder](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD).
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For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
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For example, the tutorial covering TREXIO basics using benzene molecule as an example can be viewed and executed online by clicking on this badge:
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[](https://mybinder.org/v2/gh/TREX-CoE/trexio-tutorials/HEAD?filepath=notebooks%2Ftutorial_benzene.ipynb)
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@ -110,8 +110,8 @@ For example, the tutorial covering TREXIO basics using benzene molecule as an ex
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### Miscellaneous
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Note: The code should be compliant with the C99
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[CERT C coding standard](https://resources.sei.cmu.edu/downloads/secure-coding/assets/sei-cert-c-coding-standard-2016-v01.pdf).
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Note: The code should be compliant with the C99
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[CERT C coding standard](https://resources.sei.cmu.edu/downloads/secure-coding/assets/sei-cert-c-coding-standard-2016-v01.pdf).
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This can be checked with the `cppcheck` tool.
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39
configure.ac
39
configure.ac
@ -4,6 +4,15 @@
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AC_PREREQ([2.69])
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AC_INIT([trexio], [2.0.0], [https://github.com/TREX-CoE/trexio/issues])
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AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
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AM_MAINTAINER_MODE()
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# Activate developer mode when the source is the git repository.
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# Otherwise, it is the source distribution and the developer mode should not be activated.
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TEST_IFEXISTS=".git"
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AC_CHECK_FILE([$TEST_IFEXISTS],
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[enable_maintainer_mode="yes"],
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)
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AM_MAINTAINER_MODE()
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LT_PREREQ([2.2])
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LT_INIT
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@ -25,7 +34,7 @@ AC_DEFINE_UNQUOTED(TREXIO_USER_NAME, ["${UNAME}"], [user name])
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AC_SUBST([UNAME])
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## -------------------
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## Checks for programs
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## Checks for programs
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## -------------------
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AC_LANG(C)
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@ -129,11 +138,16 @@ AC_TYPE_UINT64_T
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AC_FUNC_MALLOC
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AC_CHECK_FUNCS([memset mkdir strerror])
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if test "x$enable_maintainer_mode" == "xyes"; then
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TREXIO_DEVEL=" -- Developer mode"
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else
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TREXIO_DEVEL=""
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fi
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AM_CONDITIONAL([TREXIO_DEVEL],[test "x$TREXIO_DEVEL" != x])
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if test "x${TREXIO_DEVEL}" != "x"; then
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TREXIO_DEVEL=" -- Developer mode"
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AC_PROG_AWK
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AM_PATH_PYTHON([3.0])
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@ -155,23 +169,6 @@ if test "x${TREXIO_DEVEL}" != "x"; then
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HAS_CPPCHECK=1
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fi
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else
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# Throw an error message if the user attempts to configure the GitHub repo clone not in the developer mode.
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# Developer mode is required to generate the TREXIO source files from the org-mode templates.
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TEST_IFEXISTS=".gitmodules"
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AC_CHECK_FILE([$TEST_IFEXISTS],
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[AC_MSG_ERROR([
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----------------------------------------------------------------
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Installation with the current configuration is not possible.
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Activate developer mode: TREXIO_DEVEL=1 ./configure
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| OR |
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Download the tarball with the source code distribution.
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----------------------------------------------------------------
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])],
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[]
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)
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fi
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## Libm
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@ -212,7 +209,7 @@ Package features:
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Now type 'make @<:@<target>@:>@'
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where the optional <target> is:
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all - build C library and Fortran binding
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check - run unit tests
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install - install the library
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check - run unit tests
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install - install the library
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--------------------------------------------------"
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