This release contains one major and many minor fixes listed below, as well as a new documentation site thanks to GitHub pages. This is by far the most thorough pbqff documentation written thus far, and I intend for it to answer any question related to pbqff usage. So if you find something not covered by the page, please report it as a bug!
There is also an implementation of qffbuddy on the page that was much easier to build than the Python GUI version. I'm tentatively thinking the Python version may be deprecated in favor of the web-based version if people are happy with it.
Breaking Change
A refactor in the handling of queue templates in psqs means that every custom queue_template now needs to specify a *_CMD appropriate to the chemistry program being used. For example, a Molpro PBS queue template might look something like this:
queue_template = """
#!/bin/sh
#PBS -N {{.basename}}
#PBS -S /bin/bash
#PBS -j oe
#PBS -o {{.basename}}.out
#PBS -W umask=022
#PBS -l walltime=1000:00:00
#PBS -l ncpus=1
#PBS -l mem=8gb
#PBS -q workq
module load openpbs molpro
export WORKDIR=$PBS_O_WORKDIR
export TMPDIR=/tmp/$USER/$PBS_JOBID
cd $WORKDIR
mkdir -p $TMPDIR
trap 'rm -rf $TMPDIR' EXIT
export MOLPRO_CMD=\"molpro -t $NCPUS --no-xml-output\" # <- New!
"""$MOLPRO_CMD is used to invoke Molpro for each individual job. The corresponding commands for MOPAC, CFOUR, and DFTB+ are, predictably, MOPAC_CMD, CFOUR_CMD, and DFTB+_CMD. These are used for all three queue types (PBS, Slurm, and Local), so you can actual configure the locations of these programs in the pbqff input file. I export these in most of the examples, but they are only used within the same shell file, so it should be safe to use normal assignments too.
Minor changes
- Improved support for the C2h point group in spectro
- Improved handling of DFTB+ templates
- Fixed a bug where running multiple normal coordinate QFFs in the same directory could introduce file conflicts
- Fixed a bug where MOPAC geometries were truncated to 40 atoms
- Updated built-in queue templates for MCSR users