Setting up QCxMS

Setup

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 only runs 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 QCEIMS 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 Visualization program was developed. It can be found 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.

Quantum Chemistry Codes Required

The low cost QC methods GFN1-xTB and GFN2-xTB are implemented in QCxMS. No further rights or installations of third-party software is required and the methods can be called directly by the program. For this reason, using GFN2-xTB is set to run as default.

To run other QC methods, QCxMS needs ORCA or TURBOMOLE to function. If available, place the following QC 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.

(xTB)

Optional. Newer xTB can be called upon if needed.

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

Building the program

The source code will be provided in the future, as soon as most bugs have been cleared. A special release note will be provided accordingly.

Untar the compressed source archive:

tar -xvzf QCxMS_v.X.X.tar.gz

Enter the newly created folder. All source files can be found in the qcxms folder. To build the program, run the following commands:

cd QCxMS/qcxms/
make

This will build the program and creates the executable in the QCxMS/exe/ folder.