Results from 2021 Community Survey

We recently posted our second “community survey” to gather feedback. The survey was highlighted on Twitter and on the avogadro mailing lists.

Quick Summary (tldr)

• Many users find Avogadro from a friend, peer or instructor (~50%)
• By far, most download binaries (>70%)
  • Many use package managers (50%)
• Responses were heavily from Linux (79%) and Windows (56%) users, with a strong cohort of Mac users (23.5%)
• Worldwide use
• Heavily educated, with >80% of responses with at least a graduate degree
• Many can code: >60% report Python knowledge, >20% report C/C++ knowledge
• High bias towards research applications
• Most responses use Avogadro frequently (>70% use at least weekly)
• Many complaints about stability, crashes, and scalability to large systems
• Some suggestions to add features that already exist!
• Over 80% haven’t contributed previously
• Interest in physical copies and online workshops
• Less than 50% have used Avogadro2 betas ever (or rarely)

Detailed Comments

Avogadro’s Best Strengths

• It is free and offers many tools
• Lightweight program
• Plotting of orbitals, visualization of calculation results, it’s faster and generally more stable than other visualization programs.
• Light weight, easy entry, clean GUI, great compatibility
• The interactive geometry optimization is excellent.
• Input generation
• reads quite a variety of inputs formats; easy to learn
• reading several file types, input generation for several programs, opensource
• Lightweight interface, easy to manipulate structures compared to other software, and a variety of visualization modes (vdw radius is very useful)
• Easy to use; free
• Potential as an interface for QM programs
• Molecular structure manipulation (esp Bond Centric Manipulation)
• Accessibility for my students
• Building molecules
• Rapid drawing that and be converted to many file types
• creating/editing molecules, easy minimalization (at least in Avogadro 1.2, I am not sure if Avogadro 2 has this feature)
• Simple intuitive use
• Molecular orbital rendering
• Flexibility

Most Needs Improvement

• isosurface visualization, editing optimization, documentation
• Crashes
• show both alpha and beta spin orbitals for unrestricted calculations, show TDDFT data, improve builder for solid state materials (crashes easily in windows), builder is in general very cumbersome (compared to Gview e.g.)
• The latest version is lacking a lot of functionality. Molecular editing tools, such as dihedral rotations are missing. Aligning multiple structures (such as confomers) would be great. Gridded view of multiple molecules.
• MEP with better colours
• Stability
• Molecule editing
• Visualizing trajectories, rendering
• Stability
• Saving of modified files in different formats and write out Z-matrices, which was previously available
• It crashes regularly. It is too hard to select and delete segments of the molecule, especially in Avogadro2.
• input generation and different force fields assignment
• I might be wrong but Avogadro 2 seems to be lacking the constraints feature for force field optimization which is a useful feature I use very often in the older Avogadro 1. Also, being able to view conformer ensembles would be useful as I currently rely on other tools to do that (Jmol)
• Avogadro 2 could handle CIF files and crystal lattice manipulation more smoothly. It’s better than the previous version but it still has a long way to go.
• Ubuntu 20.04 snap, editing molecules
• Interface
• Molecule building and editing is clunky
• Interface for QM programs
• Stability and ease-of-plugin-development
• Ability to display/view energy calculations from forcefield optimization.
• Fixing of random crashes, Visualisation of ORCA 5 outputs
• stability
• UI/UX Design
• Avogadro 2 should have at least the same features as Avogadro 1.2
• Builder isn’t as good as other programs
• Avogadro 2 lacks some basic features compared to Avogadro 1
• ESP surfaces are terrible! Can we add a density of state feature?
• To be significantly better than vmd in specific areas

Suggestions for Getting the Word Out

• Be more active on social media, offer workshops on it, offer tips and talk about what’s new on recent releases
• contest for building weird and funny molecules, collaborate with developer of one of the quantum chemical programs to promote each other, boost connection to renders like povray.
• Pushing avogadro to stem education and schools. It’s really the ideal tool!
• The curious will look for an intuitive, accessible interface for using molecular modeling. Many of the tutorials from folks like Jan Jansen are very helpful to getting started, but may be dated. I think that making Avogadro part of a wider learning resource or learning community will result in those learning materials being promoted by educators and researchers.
• Try to reach more people through social media
• Citing its use in publications
• Encouraging/improving features for classroom use would help me “sell” Avogadro to my teaching colleagues.
• Collaborate more with the ORCA community.
• I recommend it to all my students and peers.

Missing Priority Features in Avogadro2

• as mentioned plot both alpha and beta spin orbitals for open shell systems
• Aligning coordinates of multi-xyz files. Rotating/translating systems with respect to given atoms for editing. Quick tools for adding common systems such as aryls or cyclohexyls. Tools for editing the atom order easily. Changing colors of atoms easily. Changing bond types for visualization.
• I need a good MEP Support and orbitals Integration, with and further Installation
• Enhanced treatment of biomolecules
• Easier to select and delete molecule segments
• Direct job submission to HPC,
• Importing and manipulating CIF files
• Creation of a combinatorial library without programming
• Perhaps make it as versatile as VMD but much easier to use.
• Insert Background Image
• Visualize/output FF energy calculations, slow optimization so students can “watch” molecule optimize (like in Avogadro v1), bring back molecular dynamics.
• Delete atoms by selection
• Similar tools as v1, minimalization protocols and easy editing/creating molecules