jaythedog / qcxms

Quantum mechanic mass spectrometry calculation program

QCxMS

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.

Untar the zipped archive:

tar -xvzf QCxMS.vX.X.tar.xz

The following files are being extracted: qcxms pqcxms q-batch getres .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).

Conda

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

Meson

Using meson 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 version 1.10 or newer.

export FC=ifort CC=icc
meson setup build -Dfortran_link_args=-static
ninja -C build 

This will build a static linked binary in the build folder. Copy the binary from build/qcxms file into a directory in your path, e.g. ~/bin/.

Documentation

A more detailed documentation on topics like input settings can be fond at read-the-docs. Examples to test QCxMS can be found in the EXAMPLES folder. Here, input and coordinate files are provided for either EI or CID run modes.

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.
• Collision induced dissociation (CID) calculations are now available. Set cid in the qcxms.in file (see documentation)

The tblite library for xTB calculations

• The tblite library has been included into the program code. This keeps xtb up-to-date and decreases the computational time for calculations done with GFN1- and GFN2-xTB when compared to earlier versions.

Plotting Spectra

To evaluate the results and create a spectrum, download and use the PlotMS program. The documentation explains the basic functionalities of the program.

The program provides mass.agr, JCAMP-DX and .csv are files that can be analyzed. For visualization of the calculated spectra, we recommend the usage of the xmgrace program.

Updates

Versions PlotMS v.6.0 and higher now provide exact masses. Experimental files in .csv format can now be read and plotted against the computed spectra. The .mass_raw.agr file was moved to the PlotMS repository.