VMS builds upon the ORCA quantum chemistry software. It parses a user's request (such as: light absorption), submits the appropriate instructions to ORCA, along with a database of molecules, and interprets the results.
The application is to test moleules "in silico" before actually going to the lab, spending precious time and money.
You will need to have ORCA installed
somewhere in your PATH, obviously.
Currently, vms only supports ORCA 3,
and needs to be updated to use ORCA 4.
To install vms itself,
mkdir -p ~/src && cd ~/src
git clone git@github.com:janstary/vms.git
cd vms && make clean installThis will install vms into your $HOME.
You can tweak that (and other stuff) in the Makefile.
VMS should compile on any POSIX-compliant UNIX system.
VMS comes with db.xyz containing just two molecules:
the molecule of water, and the molecule of methan.
An example run of vms can be seen with make test:
./vms -j 2 db.xyz request.single ./single
./vms -j 2 db.xyz request.optimize ./optimize
./vms -j 2 db.xyz request.excited ./excitedThe single request instructs ORCA to run the relatively cheap
single point calculations on the molecules. This is a test that
vms basicaly works. Look into the resulting ./single directory.
The optimize request instructs ORCA to optimize the molecule geometry.
Note the geometry in ./optimize/output, optimized from the
naive structure of H2O and CH4 in db.xyz.
The excited request instructs ORCA to compute excited states,
in order to figure out the absorption of light:
absorb 300 500 0.100 -1.00 -1
This means we are looking for molecules that absorb light
with wavelenghts between 300 and 500 nm, with intesity at least 0.10
(which means, roughly, that a photon has
at least 10% chance of being absorbed);
the higher the absorption the better.
In ./excited/report then, you will see that
molecule 2 from ./excited/molecule.000002: eval 0.039725
003 385.399994 0.127865
This means that the methan molecule, in its third excited state,
absorbs light with a wavelength of 385 nm (violet) with an intensity of 12%,
therefore passing the specification in the request. The molecule of water
does not pass the filter; so ./excited/output only contains the methan.
VMS installs three binaries: vms, ort and ori.
Their manpages describe the details of usage,
the format of the request files, and the structure of the output.
VMS was originaly written by Štěpán Sršeň and later modified and extended by Jonatan Matějka and Jan Starý.