-
Notifications
You must be signed in to change notification settings - Fork 15
TREX I/O library
License
BSD-3-Clause, Unknown licenses found
Licenses found
BSD-3-Clause
LICENSE
Unknown
COPYING
TREX-CoE/trexio
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
<?xml version="1.0" encoding="utf-8"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> <!-- 2025-01-09 Thu 14:53 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>TREXIO source code documentation</title> <meta name="author" content="TREX-CoE" /> <meta name="generator" content="Org Mode" /> <style> #content { max-width: 60em; margin: auto; } .title { text-align: center; margin-bottom: .2em; } .subtitle { text-align: center; font-size: medium; font-weight: bold; margin-top:0; } .todo { font-family: monospace; color: red; } .done { font-family: monospace; color: green; } .priority { font-family: monospace; color: orange; } .tag { background-color: #eee; font-family: monospace; padding: 2px; font-size: 80%; font-weight: normal; } .timestamp { color: #bebebe; } .timestamp-kwd { color: #5f9ea0; } .org-right { margin-left: auto; margin-right: 0px; text-align: right; } .org-left { margin-left: 0px; margin-right: auto; text-align: left; } .org-center { margin-left: auto; margin-right: auto; text-align: center; } .underline { text-decoration: underline; } #postamble p, #preamble p { font-size: 90%; margin: .2em; } p.verse { margin-left: 3%; } pre { border: 1px solid #e6e6e6; border-radius: 3px; background-color: #f2f2f2; padding: 8pt; font-family: monospace; overflow: auto; margin: 1.2em; } pre.src { position: relative; overflow: auto; } pre.src:before { display: none; position: absolute; top: -8px; right: 12px; padding: 3px; color: #555; background-color: #f2f2f299; } pre.src:hover:before { display: inline; margin-top: 14px;} /* Languages per Org manual */ pre.src-asymptote:before { content: 'Asymptote'; } pre.src-awk:before { content: 'Awk'; } pre.src-authinfo::before { content: 'Authinfo'; } pre.src-C:before { content: 'C'; } /* pre.src-C++ doesn't work in CSS */ pre.src-clojure:before { content: 'Clojure'; } pre.src-css:before { content: 'CSS'; } pre.src-D:before { content: 'D'; } pre.src-ditaa:before { content: 'ditaa'; } pre.src-dot:before { content: 'Graphviz'; } pre.src-calc:before { content: 'Emacs Calc'; } pre.src-emacs-lisp:before { content: 'Emacs Lisp'; } pre.src-fortran:before { content: 'Fortran'; } pre.src-gnuplot:before { content: 'gnuplot'; } pre.src-haskell:before { content: 'Haskell'; } pre.src-hledger:before { content: 'hledger'; } pre.src-java:before { content: 'Java'; } pre.src-js:before { content: 'Javascript'; } pre.src-latex:before { content: 'LaTeX'; } pre.src-ledger:before { content: 'Ledger'; } pre.src-lisp:before { content: 'Lisp'; } pre.src-lilypond:before { content: 'Lilypond'; } pre.src-lua:before { content: 'Lua'; } pre.src-matlab:before { content: 'MATLAB'; } pre.src-mscgen:before { content: 'Mscgen'; } pre.src-ocaml:before { content: 'Objective Caml'; } pre.src-octave:before { content: 'Octave'; } pre.src-org:before { content: 'Org mode'; } pre.src-oz:before { content: 'OZ'; } pre.src-plantuml:before { content: 'Plantuml'; } pre.src-processing:before { content: 'Processing.js'; } pre.src-python:before { content: 'Python'; } pre.src-R:before { content: 'R'; } pre.src-ruby:before { content: 'Ruby'; } pre.src-sass:before { content: 'Sass'; } pre.src-scheme:before { content: 'Scheme'; } pre.src-screen:before { content: 'Gnu Screen'; } pre.src-sed:before { content: 'Sed'; } pre.src-sh:before { content: 'shell'; } pre.src-sql:before { content: 'SQL'; } pre.src-sqlite:before { content: 'SQLite'; } /* additional languages in org.el's org-babel-load-languages alist */ pre.src-forth:before { content: 'Forth'; } pre.src-io:before { content: 'IO'; } pre.src-J:before { content: 'J'; } pre.src-makefile:before { content: 'Makefile'; } pre.src-maxima:before { content: 'Maxima'; } pre.src-perl:before { content: 'Perl'; } pre.src-picolisp:before { content: 'Pico Lisp'; } pre.src-scala:before { content: 'Scala'; } pre.src-shell:before { content: 'Shell Script'; } pre.src-ebnf2ps:before { content: 'ebfn2ps'; } /* additional language identifiers per "defun org-babel-execute" in ob-*.el */ pre.src-cpp:before { content: 'C++'; } pre.src-abc:before { content: 'ABC'; } pre.src-coq:before { content: 'Coq'; } pre.src-groovy:before { content: 'Groovy'; } /* additional language identifiers from org-babel-shell-names in ob-shell.el: ob-shell is the only babel language using a lambda to put the execution function name together. */ pre.src-bash:before { content: 'bash'; } pre.src-csh:before { content: 'csh'; } pre.src-ash:before { content: 'ash'; } pre.src-dash:before { content: 'dash'; } pre.src-ksh:before { content: 'ksh'; } pre.src-mksh:before { content: 'mksh'; } pre.src-posh:before { content: 'posh'; } /* Additional Emacs modes also supported by the LaTeX listings package */ pre.src-ada:before { content: 'Ada'; } pre.src-asm:before { content: 'Assembler'; } pre.src-caml:before { content: 'Caml'; } pre.src-delphi:before { content: 'Delphi'; } pre.src-html:before { content: 'HTML'; } pre.src-idl:before { content: 'IDL'; } pre.src-mercury:before { content: 'Mercury'; } pre.src-metapost:before { content: 'MetaPost'; } pre.src-modula-2:before { content: 'Modula-2'; } pre.src-pascal:before { content: 'Pascal'; } pre.src-ps:before { content: 'PostScript'; } pre.src-prolog:before { content: 'Prolog'; } pre.src-simula:before { content: 'Simula'; } pre.src-tcl:before { content: 'tcl'; } pre.src-tex:before { content: 'TeX'; } pre.src-plain-tex:before { content: 'Plain TeX'; } pre.src-verilog:before { content: 'Verilog'; } pre.src-vhdl:before { content: 'VHDL'; } pre.src-xml:before { content: 'XML'; } pre.src-nxml:before { content: 'XML'; } /* add a generic configuration mode; LaTeX export needs an additional (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */ pre.src-conf:before { content: 'Configuration File'; } table { border-collapse:collapse; } caption.t-above { caption-side: top; } caption.t-bottom { caption-side: bottom; } td, th { vertical-align:top; } th.org-right { text-align: center; } th.org-left { text-align: center; } th.org-center { text-align: center; } td.org-right { text-align: right; } td.org-left { text-align: left; } td.org-center { text-align: center; } dt { font-weight: bold; } .footpara { display: inline; } .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } .equation-container { display: table; text-align: center; width: 100%; } .equation { vertical-align: middle; } .equation-label { display: table-cell; text-align: right; vertical-align: middle; } .inlinetask { padding: 10px; border: 2px solid gray; margin: 10px; background: #ffffcc; } #org-div-home-and-up { text-align: right; font-size: 70%; white-space: nowrap; } textarea { overflow-x: auto; } .linenr { font-size: smaller } .code-highlighted { background-color: #ffff00; } .org-info-js_info-navigation { border-style: none; } #org-info-js_console-label { font-size: 10px; font-weight: bold; white-space: nowrap; } .org-info-js_search-highlight { background-color: #ffff00; color: #000000; font-weight: bold; } .org-svg { } </style> <link rel="stylesheet" title="Standard" href="trexio.css" type="text/css" /> <script src="org-info.js"> // @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&dn=gpl-3.0.txt GPL-v3-or-Later // @license-end </script> <script> // @license magnet:?xt=urn:btih:1f739d935676111cfff4b4693e3816e664797050&dn=gpl-3.0.txt GPL-v3-or-Later org_html_manager.set("TOC_DEPTH", "4"); org_html_manager.set("LINK_HOME", "index.html"); org_html_manager.set("LINK_UP", ""); org_html_manager.set("LOCAL_TOC", "1"); org_html_manager.set("VIEW_BUTTONS", "0"); org_html_manager.set("MOUSE_HINT", "underline"); org_html_manager.set("FIXED_TOC", "0"); org_html_manager.set("TOC", "0"); org_html_manager.set("VIEW", "info"); org_html_manager.setup(); // activate after the parameters are set // @license-end </script> </head> <body> <div id="org-div-home-and-up"> <a accesskey="h" href=""> UP </a> | <a accesskey="H" href="index.html"> HOME </a> </div><div id="content" class="content"> <h1 class="title">TREXIO source code documentation</h1> <hr /> <script async src="https://cse.google.com/cse.js?cx=a67f8ab65a66f97f2"></script> <div class="gcse-search"></div> <hr /> <p> 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. </p> <p> 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. </p> <p> TREXIO can be downloaded here: <a href="https://github.com/TREX-CoE/trexio/releases/latest">https://github.com/TREX-CoE/trexio/releases/latest</a> </p> <p> If you use TREXIO, please cite this article published in the <a href="https://doi.org/10.1063/5.0148161">Journal of Chemical Physics</a>: </p> <div class="org-src-container"> <pre class="src src-latex">@article{trexio_2023, author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Micha{<span style="color: #a020f0;">\l</span>} and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josu{<span style="color: #a020f0;">\'</span>{e}} and Filippi, Claudia and Nakano, Kosuke and Kohul{<span style="color: #a020f0;">\'</span>{a}}k, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and R{<span style="color: #a020f0;">\'</span>{<span style="color: #a020f0;">\i</span>}}os, Pablo L{<span style="color: #a020f0;">\'</span>{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} } </pre> </div> <p> If you don't have access to the journal, you can access the manuscript on <a href="https://doi.org/10.48550/arXiv.2302.14793">arXiv:2302.14793</a>. </p> <hr /> <table style="width:100%"> <tr><td style="width:50%"> <ul class="org-ul"> <li><a href="./intro.html">Motivation</a></li> <li><a href="./lib.html">The TREXIO library</a></li> <li><a href="./trex.html">Data stored with TREXIO</a></li> <li><a href="./tutorial_benzene.html">Tutorial</a></li> <li><a href="./examples.html">Examples</a></li> <li><a href="./templator_front.html">Front end API</a></li> <li><a href="./templator_hdf5.html">HDF5 back end</a></li> <li><a href="./templator_text.html">TEXT back end</a></li> </ul> </td> <td> <img src="trexio.png" alt="T-Rex talking about chemistry" align="right" width="300"/> </td></tr> </table> <hr /> <p> The source code of the library is available at <a href="https://github.com/trex-coe/trexio">https://github.com/trex-coe/trexio</a> and bug reports should be submitted at <a href="https://github.com/trex-coe/trexio/issues">https://github.com/trex-coe/trexio/issues</a>. </p> <p> The TREXIO library is licensed under the open-source 3-clause BSD license. </p> <hr /> <p> <img src="https://trex-coe.eu/sites/default/files/inline-images/euflag.jpg" alt="euflag.jpg" /> <a href="https://trex-coe.eu">TREX: Targeting Real Chemical Accuracy at the Exascale</a> 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. </p> </div> <div id="postamble" class="status"> <p class="author">Author: TREX-CoE</p> <p class="date">Created: 2025-01-09 Thu 14:53</p> <p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p> </div> </body> </html>
About
TREX I/O library
Topics
Resources
License
BSD-3-Clause, Unknown licenses found
Licenses found
BSD-3-Clause
LICENSE
Unknown
COPYING
Stars
Watchers
Forks
Packages 0
No packages published