Tuesday, Sept. 12, 2023
Release Information and Documentation: https://molssi.github.io/QCFractal/

The Molecular Sciences Software Institute is excited to announce the release of QCArchive v0.50. QCArchive is a MolSSI open-source software product that allows users to run a large number of QM calculations and archive the results. This release has numerous new improvements and features:

• Enhanced, more consistent interface
• Better performance for dataset operations
• More calculation types
• New dataset management features
• Improved server performance

Want to learn more about QCArchive and see how it could benefit your research team? Join us for a free online webinar on September 21.

Join us on Thursday, Sept. 21 from 1-3 pm ET (10 am – 12 pm PT) for a webinar introducing the newly released QCArchive software.  QCArchive is a MolSSI open-source software product that helps users run large numbers of QM calculations and archive the results.  In this interactive webinar, we will introduce the features, use cases, and fundamentals of QCArchive. Each participant will gain hands-on experience using QCArchive, so you can see how QCArchive could benefit your research team.  No prior experience with QCArchive is required; this workshop will start from the very beginning.  Register here.

Prerequisites: No prior experience using QCArchive is needed to participate in the webinar.  The interactive portion of the workshop will use Python, so basic understanding of Python syntax is recommended.  The level of Python knowledge required is very basic; completing the Introduction lesson of the MolSSI Python Scripting workshop would be sufficient. Information about installing the software using conda will be set out to all participants ahead of the workshop.  

Space is limited and preregistration is required!  Registration form

MolSSI Community Highlights spotlight exceptional examples of research and education enabled by MolSSI software and educational resources.

Dr. Jeffrey Wagner (Technical lead at the Open Force Field Consortium) and his team focus on the development of accurate and transferable molecular mechanics force fields using a combination of quantum mechanics (QM) and experimental data. In this post, Dr. Wagner tells us how MolSSI tools have played a role in advancing the development and validation of molecular forcefields.

MolSSI:

Hi Dr. Wagner, thank you for taking the time to chat with us! Your research area seems fascinating. Could you provide a brief introduction to your research area and share what your team is currently focusing on?

Dr. Wagner:

The Open Force Field Consortium (OpenFF) is a collaboration of academic and industrial researchers that aims to develop accurate and transferable molecular mechanics force fields using a combination of quantum mechanics (QM) and experimental data. The consortium’s ultimate goal is to enable more accurate computational simulations of molecular systems in a variety of fields, including drug discovery and materials science. 

To achieve this goal, we use a variety of computational and experimental techniques, including QM calculations, molecular dynamics simulations, and machine learning methods, to generate and validate force field parameters. We also work to develop best practices and standards for force field development, validation, and sharing.

MolSSI:

Can you share how MolSSI software tools or resources have been utilized to accomplish specific research objectives in your projects?

Dr. Wagner:

The Open Force Field Consortium (OpenFF) heavily relies on the MolSSI software tools and resources to achieve specific research goals. The Parsley and Sage force field lines, which are used in many of our research projects, were developed based on quantum chemical data calculated on the MolSSI QCArchive. This data serves as a reference to validate and improve our force fields. Furthermore, the OpenFF QCSubmit package and qca-dataset-submission pipeline interface with the MolSSI APIs to allow us to easily create cross-ecosystem workflows, making it possible to use the MolSSI ecosystem tools to fit and validate force fields that interact with the OpenMM and other toolkits. Many of our lead employees were trained in software development at MolSSI, which has greatly contributed to the development of the OpenFF toolkits.

We also make heavy use of the MolSSI QCArchive and general QC ecosystem to generate and share quantum chemical datasets for force field fitting. This includes using the QCSubmit package to automatically submit calculations to the QCArchive for small molecule and protein systems. The QCArchive provides us with access to a large database of computed molecular properties, which allows us to validate and benchmark our force fields against accurate reference data. In addition, many of our repositories, including the OpenFF toolkit, are based on the MolSSI project cookiecutter. Overall, the collaboration between OpenFF and MolSSI has been instrumental in our research endeavors, allowing us to develop more accurate and transferable force fields and to improve the accessibility and sharing of quantum chemical datasets.

MolSSI:

It’s great to see the impact of MolSSI resources on your work. Could you please share some of your significant findings or results facilitated by the MolSSI software tools or resources?

Dr. Wagner:

We have published several papers incorporating MolSSI software tools and resources, including the development and benchmarking of the Parsley and Sage small molecule force fields. 

MolSSI

MolSSI greatly values our collaboration with the Open Force Field Consortium. We extend our thanks to Dr. Wagner for sharing his insights with our community. We’re excited to continue supporting their important work in developing accurate molecular mechanics force fields.

Here are some publications that incorporate MolSSI software tools or resources from The Open Force Field Consortium:

• Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field: https://doi.org/10.26434/chemrxiv-2022-n2z1c 
• Collaborative assessment of molecular geometries and energies from the Open Force Field: https://doi.org/10.1021/acs.jcim.2c01185 
• Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale: https://doi.org/10.1021/acs.jcim.2c01153 
• Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field https://doi.org/10.1021/acs.jctc.1c00571 
• End-to-end differentiable construction of molecular mechanics force field https://doi.org/10.1039/D2SC02739A 
• Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans https://doi.org/10.1101/2020.08.27.270934 
• Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields https://doi.org/10.12688/f1000research.27141.1 
• Driving torsion scans with wavefront propagation https://doi.org/10.1063/5.0009232 

All of the Parsley and Sage force fields here: https://zenodo.org/record/7889050

After reviewing many impressive applications, the MolSSI is delighted to announce that the Science and Software Advisory Board has selected our new 2023-24 Software Fellows! They are:

• Anja Conev, Rice University;
• Jeremy Leung, University of Pittsburgh;
• Diego Kleiman, University of Illinois, Urbana-Champaign;
• Ericka Miller, Case Western Reserve University;
• Augustine Onyema, Graduate Center, City University of New York;
• David Poole, Georgia Tech;
• Evan Pretti, University of California, Santa Barbara;
• Zhengkai Tu, Massachusetts Institute of Technology;
• Valeria Rios Vargas, Rutgers University.

Our new MolSSI Software Fellows will receive a full year of support and mentoring by the MolSSI’s Software Scientist team. The many exceptional applicants made the selection process extremely difficult. We are confident that our new Fellows will use this opportunity to excel in their research areas, and grow as researchers & scientists in their individual fields. For a summary of their project titles, visit this link. Congratulations to all our new fellows; we’re incredibly excited to have you on board!

MolSSI Community Highlights spotlight exceptional examples of research and education enabled by MolSSI software and educational resources.

Dr. Danny Perez (Scientist IV in the Theory Division at Los Alamos National Laboratory) and his group focus on the development, implementation, and applications of long-timescale methods for atomistic simulation of materials through their work with the Exascale Atomistic Capability for Accuracy, Length, and Time (EXAALT) project. In this post, Dr. Perez tells us how he is using the MolSSI Driver Interface Project (MDI)  to unlock access to many different DFT software packages to  orchestrate the execution of very large numbers of calculations. Dr. Perez’s work has applications in the study of materials in extreme conditions and the generation of transferable datasets to parameterize machine learning potentials for materials.

MolSSI:

Hi Dr. Perez, we appreciate you taking the time to talk to us today! Your research field seems intriguing. Could you provide a brief introduction to your research area and share what your team is currently focusing on?

Dr. Perez:

My research focuses on the development, implementation, and applications of long-timescale methods for atomistic simulation of materials. I am especially interested in materials in extreme conditions, such as materials for fission and fusion energy, or particle accelerators. Recently, I became interested in the generation of transferable datasets to parameterize machine learning potentials for materials. I am also interested in applications of petascale and exascale computing in materials science.

MolSSI:

Can you share how MolSSI software tools or resources have been utilized to accomplish specific research objectives in your projects?

Dr. Perez:

I have collaborated with the MolSSI team as part of my role as PI in the Exascale Atomistic Capability for Accuracy, Length, and Time (EXAALT) project, which is one of the application projects supported by the DOE’s Exascale Computing Project. One of our objectives is to significantly decrease the time required to obtain reliable interatomic potentials for materials by integrating all steps, generation of training configurations, characterization with density functional theory, training of the potential, and validation. Our objective is to design scalable workflows to integrate and automate all of these steps.

MolSSI:

For this particular project, which MolSSI software tools or resources did your team employ, and what aspects or features did you find most beneficial?

Dr. Perez:

We are designing our workflows using MolSSI Driver Interface (MDI). We are especially interested in the plugin mode of MDI which enables us to control large numbers of instances of DFT and/or MD codes at scale using MPI without having to resort to file or socket-based mechanisms.

MolSSI:

How did MolSSI resources influence your software development efforts, and what led you to choose MolSSI resources for this purpose?

Dr. Perez:

In our case, we wanted to be able to orchestrate the execution of very large numbers of DFT calculations as part of an integrated workflow tool that can run at scale. The solution we converged to was to support engine codes that can be called through an API that can receive existing MPI communicators. Since such APIs are still not common or standardized, we faced the prospect of having to write specific code to support multiple engines. We quickly learned that the MolSSI MDI team aimed at standardizing such APIs, which would greatly simplify our work. After engaging with the MDI team, they endeavored to implement a new plugin mode which perfectly met our requirements in terms of integration with MPI codes at scale. This has led to a tremendous simplification of our code, as we only have to support MDI to unlock a whole ecosystem, instead of having to write engine-specific code.

MolSSI:

It’s fantastic to see the role MolSSI’s software has played in your project’s development! Could you share any scientific findings or results that your workflows have facilitated?

Dr. Perez:

We are still developing our workflow, but we hope to demonstrate the end-to-end generation of reliable interatomic potentials in under a day.

MolSSI:

Those are impressive goals, and it’s wonderful to see how MolSSI resources have contributed to your group’s success. Thank you for sharing your experiences and insights with us!

Although there are no publications yet that incorporate MolSSI software tools or resources in Dr. Perez’s work, we look forward to seeing the advancements his group will make in the near future.

MolSSI Community Highlights spotlight exceptional examples of research and education enabled by MolSSI software and educational resources.

Dr. Ryan C. Fortenberry, Associate Professor of Chemistry at the University of Mississippi, and his group focus on Theoretical Astrochemistry. They use computers to simulate the way light interacts with molecules and how molecules interact with each other in space. They have utilized MolSSI software in their work with the MOPAC program, an open-source semiempirical thermochemistry software for calculating molecular properties. MOPAC has been developed as commercial software for the last 30 years, and MolSSI has facilitated its transition to an open-source software project that provides it with the opportunity to be maintained and further developed by a community of open-source software developers. In this post, Prof. Fortenberry shares with us how they are leveraging the MolSSI software to reparameterize semi-empirical methods for the computation of anharmonic vibrational frequencies.

MolSSI:

Can you give us a short summary of your research area and what your group is currently working on?

Professor Fortenberry:

My group focuses on Theoretical Astrochemistry. We use computers to simulate the way light interacts with molecules in space and how molecules interact with each other in space. Currently, we have been working to reparameterize semi-empirical methods for the computation of anharmonic vibrational frequencies for the prediction of IR spectra for polycyclic aromatic hydrocarbons (PAHs) with application to ongoing observations from the James Webb Space Telescope (JWST).

MolSSI:

Could you tell us how MolSSI software tools or resources have been employed to meet specific research objectives in your projects?

Professor Fortenberry:

The Basis Set Exchange is used in all of our projects, as the ready translation between quantum chemical packages for basis sets within the exchange is the easiest means of importing new basis sets.  

The MOPAC program is one of the most readily accessible quantum chemical codes that includes semi-empirical methods. Changes to the house-made programs that utilize MOPAC as part of the workflow are able to be run on local computers (rather than only on supercomputer clusters) and even integrated with the GitHub continuous integration features thanks to the fact that MOPAC is now open-source and easily installable.

MolSSI:

Can you tell us about what features of MolSSI’s software were the most useful to you?

Professor Fortenberry:

While semi-empirical computations are available in numerous quantum chemical codes, the open-source nature of MOPAC allows for numerous additions that are unique to our applications. My student, Brent Westbrook, has been able to contribute code to MOPAC to be able to utilize new semi-empirical parameters as part of the input file instead of requiring a separate external file. MOPAC’s flexibility also allows the most useful number of significant digits for the PAH applications to be printed in the output file.  This has allowed Brent to develop an exceptionally streamlined protocol for optimizing the parameters for our PAH IR frequency computations for JWST.

MolSSI:

It’s amazing to see the role MolSSI’s software has played in your project’s development! Could you share any scientific findings or results from your research?

Professor Fortenberry:

Quartic force fields (QFFs) are fourth-order Taylor series expansions of the potential portion of the Watson Hamiltonian.  While sparse compared to a global potential surface, they still scale geometrically with the number of atoms.  Hence, the use of these as a means of computing anharmonic vibrational frequencies has typically been limited to small molecules.  The use of MOPAC and reparameterized semi-empirical methods trained thereon has enabled us to compute fully anharmonic spectra of PAHs of up to 3 rings (~25 atoms; on a laptop!) in preliminary tests with 10 rings a distinct possibility. Our preliminary tests indicate that we may be able to handle PAHs of up to 10 rings.

MolSSI:

Those sound like significant advancements, and it’s fantastic to see how MolSSI resources have helped your research. Thank you for taking the time to share your experiences and insights with us!

If you’d like to read more about Professor Fortenberry’s work, we encourage you to attend the upcoming MOPAC user group meeting and to see the following links and publications.

(1)        Westbrook, B. R.; Layfield, J. P.; Lee, T. J.; Fortenberry, R. C. Reparameterized Semi-Empirical Methods for Computing Anharmonic Vibrational Frequencies of Multiply-Bonded Hydrocarbons. Electron. Struct. 2022, 4 (4), 045003. https://doi.org/10.1088/2516-1075/aca458.

(2)        Westbrook, B. R.; Fortenberry, R. C. Pbqff: Push-Button Quartic Force Fields. J. Chem. Theory Comput. 2023, 19 (9), 2606–2615. https://doi.org/10.1021/acs.jctc.3c00129. Cover Article. GitHub repository: https://github.com/ntBre/pbqff