Setting up QCxMS

Pre-compiled binaries from GitHub

A pre-compiled executable of the latest program version can be found on the latest release page on GitHub. Follow the instructions to use QCxMS without the need of installing or building anything.

Untar the zipped archive:

> tar -xvzf QCxMS_v.X.X.tar.xz

Replace the X.X with the current version number. The program is designed to run on Linux operating systems.

The following files are being extracted:

qcxms

main program (executable)

pqcxms

script that runs trajectories in parallel locally (executable)

q-batch

script that runs trajectories on a cluster with a queueing system (executable)

getres

script that gives the status of the parallel QCxMS production run (executable)

.mass_raw.agr

xmgrace template

.XTBPARAM

folder involving the xTB-parameterfiles .param_gfn.xtb, .param_gfn2.xtb and .param_ipea.xtb

EXAMPLE

folder hosting an example input and coordinate file.

  1. Place the executables into your $HOME/bin directory or path.

  2. Place the .XTBPARAM folder and .mass_raw.arg file into your $HOME directory (these files can appear to be hidden).

For easy visualization of the calculated spectra, the PlotMS program was developed. An instruction can be found in section Visualization and the program can be downloaded at the PlotMS repository. To display the results, we recommend the useage of xmgrace. Exemplary input and coordinate files can be found in the EXAMPLES folder.

Installing with Conda

Note

To bootstrap a conda installation we recommend to either use the conda-forge distribution miniforge or the anaconda distribution miniconda.

Installing qcxms from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge

Once the conda-forge channel has been enabled, qcxms can be installed with:

conda install qcxms

It is possible to list all of the versions of qcxms available on your platform with:

conda search qcxms --channel conda-forge

Note

The conda package manager can become quite slow when adding large channels like conda-forge, for a more performant alternative you can try to use mamba instead, which can be conveniently installed from the conda-forge channel with

conda install mamba -c conda-forge

Alternatively, the mambaforge installed can be used to bootstrap a conda installation with mamba preinstalled.

Quantum Chemistry Codes Required

The low cost QC methods GFN1-xTB and GFN2-xTB are directly implemented into QCxMS via the tblite framework. With this, no further installations of third-party software is required to create a spectrum at the semi-empirical level of theory. GFN2-xTB is set to run as default for QCxMS calculations.

To run other QC methods (e.g. DFT), ORCA or TURBOMOLE have to be installed on your system, either by using enviornment modules or by placing the executables in /usr/local/bin.

MNDO99

DFTB+

place Slater-Koster parameters atom-atom.spl in /usr/local/dftb+

ORCA

All orca utilities must also be in your path.

TURBOMOLE

The ridft and rdgrad programs of Turbomole 7.3 are used.

Please contact the development teams of these programs directly for executables since we do not have the right to distribute them.