Do you know this problem: A paper draft has seen changes by many different authors over an extended period of time and now has a bunch of old figure files that still lurk around in the file system but that are no longer relevant to the manuscript? Here’s a way […]
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Molecules are commonly treated as (undirected, colored and connected) graphs. If two graphs are identical, they are called isomorphisms of each other. In recent work, I had to remove duplicate graphs/molecules from a long list of several million molecules. The straight-forward albei naive approach would be to do (n^2-n)/2 isomorphism […]
To run the quantum-chemistry code MRCC in the Windows Subsystem for Linux requires two steps, since the MRCC binaries do not work. The underlying problem is that WSL has some trouble running statically compiled binaries, so no issue MRCC can fix. As a workaround, just compile MRCC from the source: […]
When evaluating an integral on a grid, the finite resolution thereof can affect the accuracy of the result. In the context of atomistic simulation, this is because a slight change in nuclear coordinates will affect the mapping on the grid. For smooth properties like the electron density, there is a […]
First, install the dependencies: Then prepare the Makefile Some adjustments are required. Please edit the Makefile and change these lines: to
Hard drives are slow. It does not matter whether we are talking HDD or SDD drives, it matters what we compare it to. In the context of high-performance computing, this means memory (RAM). To set this into perspective, here are some common approximate timings alongside a more intuitive “human scale” […]
The electron density of a molecule is very far from an equally distributed charge density. Therefore, the common density sampling on a regular grid for visualisation purposes is not useful for cases where numerical properties of the density distribution are sought after. In that case, integration grids as Becke-Lebedev grids […]
Many people in Switzerland commute and most of them use SBB to do so. The only catch: SBB has no interest in being fast: “Not as fast as possible, but as fast as necessary.” This means that for a typical commuter between Zurich and Basel, SBB thinks it is acceptable […]
When screening large numbers of compounds, it might be required to quickly assess whether a molecule is planar. Since they can be arbitrarily rotated, it is not immediately obvious how to do that. One way however is to calculate the volume and surface area of the convex hull. From those […]
Alchemical calculations allow to obtain electron densities and total electron energies of a set of isoelectronic target molecules without evaluating the electron density of the target molecule explicitly in a self-consistent fashion. While the theoretical background is detailed in aforementioned reference, this is more about the practical approach how to […]
Duplicating the whole TeX distribution on both Windows and Windows Subsystem for Linux (WSL) is not only a waste of disk space, it is also a maintainability nightmare. Now to build LaTeX documents from Sublime Text 3 as Windows application is quite easy if you have WSL with texlive up […]
The default method of RDKit uses valence considerations to detect the hybridisation state of an atom, since geometries are optional for the molecular structures. While there are geometry criteria for hybridisation states, they are not implemented in rdkit. Here is an example how to use these criteria (number of bonded […]