https://github.com/aspuru-guzik-group/xtb-gaussian
A wrapper to run xtb inside Gaussian.
https://github.com/aspuru-guzik-group/xtb-gaussian
chemistry computational-chemistry gaussian16 quantum-chemistry xtb
Last synced: about 1 month ago
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A wrapper to run xtb inside Gaussian.
- Host: GitHub
- URL: https://github.com/aspuru-guzik-group/xtb-gaussian
- Owner: aspuru-guzik-group
- License: mit
- Created: 2020-08-18T16:19:49.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-08-18T16:21:23.000Z (about 5 years ago)
- Last Synced: 2025-04-11T04:04:17.986Z (6 months ago)
- Topics: chemistry, computational-chemistry, gaussian16, quantum-chemistry, xtb
- Language: Perl
- Homepage:
- Size: 3.91 KB
- Stars: 20
- Watchers: 7
- Forks: 8
- Open Issues: 3
-
Metadata Files:
- Readme: README.org
- License: LICENSE.txt
Awesome Lists containing this project
README
* An xtb wrapper for Gaussian
This is a wrapper that allows xtb to be used as part of Gaussian. This is
useful in particular for TS optimizations that xtb doesn't otherwise do, and
that Gaussian does very well.
As xtb already has most of the functionality built-in, we mostly just leverage
that. The only improvement really is the use of some perl scripting to
transform xtb Hessians to Gaussian Hessians, which xtb doesn't do on it's own.
The short script is in ~xtb-gaussian~.
** Usage
The files ~examples/optimize.com~ and ~example/QST2.com~ provide examples of usage
(the optimization of a water molecule and finding an SN2 transition state and
reaction path using quasi-Newton synchronous transit). In short, the Gaussian
input file should have a method line like this one,
#+BEGIN_SRC text
%chk=ts
# external="xtb-gaussian -P 12 --etemp 300.0"
opt=(calcfc,ts,noeigentest,nodownhill,nomicro)
#+END_SRC
Here, we set the number of threads for xtb to 12 (~-P 12~ above) and perform a
transition state search using an initial xtb Hessian and xtb gradient
calculations. Additional arguments to xtb can be passed in the external
variable (like ~--etemp 300.0~ above). Passing ~--log-all~ as the first argument
to ~xtb-gaussian~ will mix in the (often very long) xtb output with the Gaussian
output, which is not done by default for performance and easier parsing of
Gaussian log files.
Note that the molecular charge included in the Gaussian molecule deck is
automatically used the wrapper script. *However, that is not true of the
multiplicity!* The script will warn of non-singlet multiplicity, which you can
technically treat by passing the appropriate ~--uhf~ argument to xtb in the
external string (caveat emptor).
** Installation
Installation consists solely of putting ~xtb-gaussian~ and ~xtb~ both on $PATH so
that they are visible to Gaussian. The only dependency is Perl. This code was
tested against ~xtb 6.2.3~ and ~xtb 6.3.1rc1~ binaries on linux.
** Performance
There are some things to keep in mind to ensure the best possible performance,
mostly because of Gaussian is a bit old-school.
Firstly, passing %CPU to gaussian makes xtb use 1 thread. *So don't do it!*
Furthermore, %NProcShared= will make Gaussian wait busily for xtb using a full
half of the NProcShared cores while xtb is running, but use all the cores for
it's own routines (like Hessian diagonalization). It is best to give only 1 or
2 processes to Gaussian and the rest to xtb using ~-P~ as above if Hessians are
often computed (with xtb parallelization) or the system is large. Otherwise,
allocating some threads to Gaussian can make the code faster.
Secondly, performance is very IO centric as Gaussian and xtb keep writing and
reading files over and over again. The wrapper respects the Gaussian scratch
directory. Running with ~$GAUSS_SCRDIR~ pointing at a fast filesystem (such as
~/dev/shm/~ on linux) makes a huge difference.
* Contributors
I wrote this perl version based on a Python script developed by postdoctoral
fellows [[https://github.com/kjelljorner][Kjell Jorner]] (at AstraZeneca, UK) and [[https://github.com/gabegomes][Gabriel dos Passos Gomes]]
(University of Toronto, Canada).