pbqff

pbqff automates the construction of quartic force fields (QFFs) and the process of generating spectral data from them

Installation

Assuming you have the Rust toolchain installed, run

make install

As you can see in the Makefile, this simply runs

cargo build --features vers --bin rust-pbqff --release
sudo ln -s target/release/rust-pbqff /usr/bin/pbqff

to build the binary in release mode, and link it into your $PATH under the name pbqff.

Dependencies

If you're installing pbqff on a "normal" machine, you're very likely to have most of these programs already. But if you install on a fresh, minimal Ubuntu installation (like I do in this video), you might need to install some or all of these:

• curl (for rustup install)
• rust nightly toolchain
• git
• make
• openssl (on arch) or libssl-dev (on ubuntu) (for vers feature)
• pkg-config (for locating openssl)
• gcc (for linking)
• python3, python3-tk, idle3 (for qffbuddy)
• cmake, gfortran, libblas-dev, liblapack-dev (for MOPAC)

For installing or building pbqff itself, you can skip this last set, which are required for building MOPAC from source. However, if you want to run the tests for pbqff, you will need MOPAC installed at /opt/mopac/mopac, so these dependencies are necessary in that case.

Coordinate Types

pbqff supports running QFFs in the following coordinate systems:

• Symmetry-internal coordinates (SICs) via intder
• Cartesian coordinates
• Normal coordinates

The normal coordinates are determined automatically by running a Cartesian harmonic force field.

Programs and Queues

pbqff supports Molpro and Mopac for computing single-point energies and the PBS and Slurm queuing systems via psqs

Input

An example input file for a Mopac QFF on c-C₃H₂ looks like:

geometry = """
C
C 1 CC
C 1 CC 2 CCC
H 2 CH 1 HCC 3 180.0
H 3 CH 1 HCC 2 180.0

CC =                  1.42101898
CCC =                55.60133141
CH =                  1.07692776
HCC =               147.81488230
"""
optimize = true
charge = 0
step_size = 0.005
coord_type = "sic"
program = "mopac"
queue = "slurm"
sleep_int = 2
job_limit = 2048
chunk_size = 1
template = """scfcrt=1.D-21 aux(precision=14 comp xp xs xw) PM6 THREADS=1 \
external=testfiles/params.dat"""
check_int = 100%

qffbuddy

An optional GUI for preparing input files and running pbqff is also included in the qffbuddy directory

Citations

For pbqff itself, please cite B. R. Westbrook and R. C. Fortenberry. "pbqff: Push-Button Quartic Force Fields." J. Chem. Theory Comput., 2023. DOI: 10.1021/acs.jctc.3c00129

@article{Westbrook23_pbqff,
  author = {Brent R. Westbrook and Ryan C. Fortenberry},
  title = {pbqff: Push-Button Quartic Force Fields},
  journal = {J. Chem. Theory Comput.},
  volume = 19,
  number = 9,
  pages = {2606-2615},
  year = 2023,
}

If you use symmetry-internal coordinates, you may also want to cite the original INTDER code by Wesley Allen:

@misc{intder,
 author = {W. D. Allen and coworkers},
 note = {$INTDER\ 2005$ is a General Program Written by W. D. Allen and Coworkers, which Performs Vibrational Analysis and Higher-Order Non-Linear Transformations.},
 year = {2005}
}

And for the original VPT2 code in SPECTRO, you can cite

@incollection{spectro91,
 address = {Greenwich, Connecticut},
 author = {J. F. Gaw and A. Willets and W. H. Green and N. C. Handy},
 booktitle = {Advances in Molecular Vibrations and Collision Dynamics},
 editor = {Joel M. Bowman and Mark A. Ratner},
 pages = {170-185},
 publisher = {JAI Press, Inc.},
 title = {{SPECTRO: A} Program for the Derivation of Spectroscopic Constants From Provided Quartic Force Fields and Cubic Dipole Fields},
 year = {1991}
}

TODOs

• factor out commonality in first part of CoordType::run
• use or delete Fitted trait
  • Findiff actually has some default methods that make it useful, but Fitted doesn't provide any default methods and isn't used as a bound