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120 changes: 112 additions & 8 deletions CONTRIBUTING.md
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# Contributing to QCxMS

The source code will be uploaded soon. Contributions will be possible hereafter.
First off, thank you for considering contributing to `QCxMS`.
Please take a moment to review this guidelines to make the contribution process
simple and effective for all involved.

Respecting these guidelines helps communicate that you respect the time of
the developers who manage and develop this open source project.
In return, they should return this respect by addressing your problem,
evaluating changes, and helping you handle your pull requests.

## Reporting a Bug

Bug reports are welcome. Good bug reports are extremely valuable for us - thank you!
A bug is a *demonstratable problem* caused by the code in this repository.
Good bug reports are extremely valuable for us - thank you!

However, a good bug report should not leave others needing to chase you up for more information. Please try to pinpoint the problem as clear as possible.
Before opening a bug report:

## Contributors
1. Check if the issue has already been reported.
2. Check if it still is an issue or has already been fixed?
Try to reproduce it with the latest version from the `master` branch.
3. Isolate the problem and create a reduced test case.

- V. Asgeirsson
- C.A. Bauer
- J. Koopman (@jaythedog)
- S. Grimme
A good bug report should not leave others needing to chase you up for more
information. So please try to be as detailed as possible in your report,
answer at least these questions:

1. Which version of `QCxMS` are you using? The current version is always
a subject to change, so be more specific.
2. What is your environment (your laptop, the cluster of the university)?
3. What steps will reproduce the issue?
We have to reproduce the issue, so we need all the input files.
4. What would be the expected outcome?
5. What did you see instead?

All these details will help people to fix any potential bugs.

## Suggesting a New Feature

Feature requests are welcome. But take a moment to find out if your idea fits
the scope and goals of the project. It is up to you to provide a strong
argument to convince the project's developers of the benefits of this feature.
Please provide as much detail and context as possible.

## Implementing a New Feature

Contributions are welcome via Github pull requests.

- Each pull request should implement *one* feature or fix *one* bug.
If you want to add or fix more than one thing, submit more than one
pull request.
- Do not commit changes to files that are irrelevant to your feature or
bugfix (*e.g.* `.gitignore`).
- Be willing to accept criticism and work on improving your code.
- Do not add third-party dependencies, the `QCxMS` binary should be usable as
standalone.
- Make sure the code compiles and the tests run successful on more than
your local machine (*e.g.* on cluster of your university).

Please sign-off your commits

### For New Contributors

If you never created a pull request before, welcome :tada:.
You can learn how from [this great tutorial](https://app.egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github)


## Sign Your Work

The sign-off is a simple line at the end of the explanation for a commit. All
commits needs to be signed. Your signature certifies that you wrote the patch or
otherwise have the right to contribute the material. The rules are pretty simple,
if you can certify the below (from [developercertificate.org](https://developercertificate.org/)):

```
Developer Certificate of Origin
Version 1.1
Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.
Developer's Certificate of Origin 1.1
By making a contribution to this project, I certify that:
(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or
(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or
(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
it.
(d) I understand and agree that this project and the contribution
are public and that a record of the contribution (including all
personal information I submit with it, including my sign-off) is
maintained indefinitely and may be redistributed consistent with
this project or the open source license(s) involved.
```

Then you just add a line to every git commit message:

Signed-off-by: Joe Smith <joe.smith@example.com>

Use your real name (sorry, no pseudonyms or anonymous contributions.)

If you set your `user.name` and `user.email` git configs, you can sign your
commit automatically with `git commit -s`.
2 changes: 1 addition & 1 deletion COPYING
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GNU GENERAL PUBLIC LICENSE
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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165 changes: 165 additions & 0 deletions COPYING.LESSER
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GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.


This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.

0. Additional Definitions.

As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.

"The Library" refers to a covered work governed by this License,
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An "Application" is any work that makes use of an interface provided
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A "Combined Work" is a work produced by combining or linking an
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The "Minimal Corresponding Source" for a Combined Work means the
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The "Corresponding Application Code" for a Combined Work means the
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1. Exception to Section 3 of the GNU GPL.

You may convey a covered work under sections 3 and 4 of this License
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2. Conveying Modified Versions.

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23 changes: 20 additions & 3 deletions README.md
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# QCxMS
[![License](https://img.shields.io/github/license/qcxms/qcxms)](https://github.com/grimme-lab/xtb/blob/main/COPYING)
[![Latest Version](https://img.shields.io/github/v/release/qcxms/qcxms)](https://github.com/qcxms/QCxMS/releases/latest)
[![DOI](https://img.shields.io/badge/DOI-10.1002%2Fanie.201300158%20-blue)](https://doi.org/10.1002/anie.201300158) [![DOI](https://img.shields.io/badge/DOI-10.1021%2Facsomega.9b02011%20-blue)](https://doi.org/10.1021/acsomega.9b02011)

This is the download repository for the QCxMS program. Currently, only the executeable is provided on the [latest release page](https://github.com/qcxms/QCxMS/releases/tag/latest). The source code will be uploaded soon as well.
This is the download repository for the QCxMS program.

**Installation**

### Binary

Statically linked binaries (Intel Compiler 21.3.0) can be found at the [latest release page](https://github.com/qcxms/QCxMS/releases/latest).

Untar the zipped archive:

```bash
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The following files are being extracted: `qcxms` `pqcxms` `q-batch` `getres` `.mass_raw.agr` `.XTBPARAM` `EXAMPLE`

Place the executables into your ``$HOME/bin/`` directory or path. Place the `.XTBPARAM` folder and `.mass_raw.arg` file into your `$HOME` directory (these files can appear to be hidden).
To evaluate the results and create a spectrum, download and use the [PlotMS](https://github.com/qcxms/PlotMS) program. For visualization of the calculated spectra, we recommend the useage of the **xmgrace** program. Examples for an input file and coordinate file can found in the `EXAMPLES` file.
To evaluate the results and create a spectrum, download and use the [PlotMS](https://github.com/qcxms/PlotMS) program. For visualization of the calculated spectra, we recommend the usage of the **xmgrace** program. Examples for an input file and coordinate file can found in the `EXAMPLES` folder.


### Meson

Using [meson](https://mesonbuild.com/) as build system requires you to install a fairly new version like 0.57.2 or newer.
To use the default backend of meson you have to install [ninja](https://ninja-build.org/) version 1.10 or newer.

```bash
export FC=ifort CC=icc
meson setup build -Dfortran_link_args=-static
ninja -C build
```
Copy the binary from the `build/qcxms` file into a directory in your path, e.g. `~/bin/`.

**Documentation**

A more detailed documentation on topics like installation and input settings can be fond at [read-the-docs](https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html).



**From QCEIMS to QCxMS:**
- All names have been changed from `qceims.xxx` to `qcxms.xxx`.
- The `q-batch`, `pqcxms` and `plotms` script have been updated.
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