Documentation (citation)

README.md

@@ -5,8 +5,7 @@
 [![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, making it an important tool for researchers in the field of quantum chemistry. In this work, we present an overview of the TREXIO file format and library. 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, and OCaml programming languages. In addition, a suite of tools has been developed to facilitate the use of the TREXIO format and library, including converters for popular quantum chemistry codes and utilities for validating and manipulating data stored in TREXIO files. The simplicity, versatility, and ease of use of TREXIO make it a valuable resource for researchers working with quantum chemistry data.
 
 ## Minimal requirements (for users):
 

ocaml/trexio/Makefile

@@ -4,7 +4,10 @@ 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:
 	dune clean

ocaml/trexio/compile-lib.sh

@@ -21,8 +21,10 @@ set -e
 if test "$TASK" = "build" ; then
   tar -zxf trexio-*.tar.gz
   cd trexio-*
-  ./configure --prefix=${PREFIX}
+# ./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-*

ocaml/trexio/dune-project

@@ -1,9 +1,9 @@
 (lang dune 3.1)
 
 (name trexio)
-(version 2.3.0)
+(version 2.3.2)
 
-(generate_opam_files true)
+(generate_opam_files false)
 
 (source
  (github trex-coe/trexio_ocaml))

ocaml/trexio/trexio.opam

@@ -29,6 +29,7 @@ depexts: [
 ]
 build: [
   ["dune" "subst"] {dev}
+  ["./compile-lib.sh" "%{prefix}%" "build"]
   [
     "dune"
     "build"
@@ -41,4 +42,8 @@ build: [
     "@doc" {with-doc}
   ]
 ]
+install: [
+ ["./compile-lib.sh" "%{prefix}%" "install"]
+ ["dune" "install"]
+]
 dev-repo: "git+https://github.com/trex-coe/trexio_ocaml.git"

src/README.org

@@ -19,6 +19,24 @@ 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{posenitskiy_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]].
+
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 #+BEGIN_EXPORT html