optavc was originally written by Dr. Copan to facilitate optimizations and hessian calculations by finite difference. It is primarily meant for internal use by the CCQC on our clusters and computing resources. Psi4 and QCArchive have developed more robust alternatives to optavc, but we have not gotten around to configuring our clusters to use these solutions.
optavc is meant to run Psi4, Molpro, Cfour, and Orca QM calculations on the Sapelo and Vulcan clusters. These clusters have, over time, utilized the PBS/TORQUE, SLURM, and SGE queuing systems so the submission scripts and cluster infrastructure should work easily with other clusters of these types. The submission scripts and specific program names would likely need to be adjusted. Submission scripts for these queuing systems are generated from program specific templates.
For help beyond this document, please see the documentation a PDF can be found here
In order to run this, you must have Psi4 installed as an importable Python module. Instructions can be found on the Psi4 wiki page 8_FAQ_Contents.
This version of optavc should be used with Psi4 >= 1.7
To install psi4 1.8
mamba install psi4 <anything else you might want> -c conda-forge -c conda-forge/label/libint_dev
There are no planned releases for optavc currently. For development purposes, please fork the GitHub repository using the GitHub website. For general usage just clone CCQC/optavc master branch.
clone the GitHub rep to whatever directory you keep python libraries. For instance, in general I recommend
mkdir ~/github cd ~/github git clone https://github.com/CCQC/optavc.git
The directory containing this package must also be added to your PYTHONPATH, in which case the modules are importable as follows.
import optavc.<module name>optavc is, fundamentally, a python module. Therefore there isn't really a input file for optavc. It is generally easiest to write and then execute a python script in your current working directory.
Basic Requirements:
a python dict of options (see the options chapter for the bare required options).
a template file. For the purposes of explanation optavc "only" RUNS this template file. The template file must be
completely sufficient to run whatever singlepoint, gradient, or hessian calculation you are interested in running.
The easiest way to run optavc is as a background process on the login node of a cluster. This is not ideal, but optavc spends alot of time sleeping, and is not particularly resource intensive for the kinds of molecules we treat.
To run this way write a simple python script to call optavc like::
import optavc
options_kwargs = {
'template_file_path': "template.dat",
'energy_regex' : r"\s*@DF-RHF Final Energy:\s+(-\d+\.\d+)",
'program' : "psi4",
'maxiter' : 20,
}
optavc.run_optavc("OPT", options_kwargs)
Then run this python script from cmd line as::
nohup python -u <name.py> &
nohup or (no hangup) prevents your process from being terminated by the shell it's running in closing. nohup places all printing to stdout in nohup.out so all of optavc's output will be placed there. optavc makes calls to psi4 to perform the finite difference procedure, extrapolations, optimizations etc. All output produced from psi4 will be placed by default in output.dat
Directories like HESS and STEP00 will be created in the current working directory which contain either input and
output files or contain directories for each displacement which contain input and output files. Look there to check on
how the calculations themselves are going.
This version works with latest Psi4 with findif overhaul -jdw 8-31-18
Optavc is designed to run on SLURM, PBS_torque, and SGE clusters. Due to software issues encountered by the CCQC singlepoints can be resubmitted if the job fails for any reason. This makes optavc a rather dangerous tool. When making modifications to optavc watch the pytest suite closely to ensure that changes have not affected the re-submission code. An error could submit hundreds to thousands of singlepoints.
For members of the CCQC, if modifying please make sure to test on all currently used clusters Sapelo, Vulcan etc... The test suite will detect which cluster you are currently using.
A few important changes and quirks that users should be notified about:
UNITS - defaults to Angstrom. Optavc does not pay attention to the units set in the template file make sure to set units if Bohr.
SUCCESS REGEXES - The corresponded keyword has been abandoned in favor of using the energy regex as the only indicator
that a job has finished. This is because some programs don't have reliable, consistent success strings. If you're
worried about your energy regex run a single gradient than test_input=True as seen in the documentation above for
run_optavc
ENERGY REGEXES - In order to speedup optavc, optavc now run's by default in MULTI-LINE mode. ENERGY REGEXES must be matched then from the beginning of the line this includes white space.
MEMORY - OPTAVC now only uses #SBATCH --mem={memory} for Sapelo submit scripts. Please make sure to determine the total amount
of memory your job uses if using a program such as Molpro which specifies memory in a per task fashion.
Reorientation - New keywords fix_com and fix_orientation have been added. optavc just runs calculations for Psi4 and
fills the results (gradients, energy, etc...) in the correct psi4 data structures. Since this whole process
is taken care of by Psi4, its normally okay for Psi4 to reorient the molecule (translationally and rotationally) as
it sees fit. The harmonic frequencies will not be affected despite the structure being rotated behind the scenes;
however, the normal mode coordinates will not necessarily align with your molecules. You'd want to visualize the normal
modes with the molecular coordinates Psi4 used (these can be found in output.dat). In geometry optimization, the
final converged geometry you fetch from output.dat will have been rotated by Psi4 as well.
If this behavior is not acceptable (for instance when comparing force constants or gradients numerically against other
programs) you can use the above keywords. When optavc creates a Psi4 molecule object, the molecule will not be
allowed to move if these options are specified.
Optavc can perform optimizations and hessian calculations through Psi4.
Optimizations can be performed with Analytic Gradients or by Finite Differences of Singlepoints
Hessians can be calculated Analytically or by Finite Differences of Gradients or Singlepoints.
Basis set extrapolation and additive corrections can be applied at the level of the Gradient and Hessian.
Aside from the actual calculation of the Energy, Gradient, or Hessian most functionality is obtained through Psi4 and QCDB.
Finite Difference Displacements are generated by psi4 and calculations for each displacements. Thermochemical and Vibrational analysis is also performed by Psi4. Optimization is performed by the Optking python module which comes packages with Psi4 >= 1.7.