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Fixed README
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README.md
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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. `./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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[![Binder](https://mybinder.org/badge_logo.svg)](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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