From b55c05d6e4c813c93cdd125a30fef5076d2979de Mon Sep 17 00:00:00 2001 From: Geoff Hutchison Date: Mon, 23 May 2022 14:56:08 -0400 Subject: [PATCH] Fix broken links and 2021 survey results --- _posts/2018-08-25-ugm-materials.md | 12 +-- _posts/2021-06-02-avogadro-1-94-release.md | 4 +- _posts/2021-07-28-community-survey-results.md | 102 ++++++++++++++++-- _posts/2021-08-16-avogadro-1-95-release.md | 4 +- _posts/2022-01-15-two-avogadro-website.md | 2 +- 5 files changed, 106 insertions(+), 18 deletions(-) diff --git a/_posts/2018-08-25-ugm-materials.md b/_posts/2018-08-25-ugm-materials.md index a8d25b3..ded41d6 100644 --- a/_posts/2018-08-25-ugm-materials.md +++ b/_posts/2018-08-25-ugm-materials.md @@ -7,7 +7,7 @@ date: 2018-08-25 ![2018 UGM Title](/images/2018UGM.png) -Materials from our first User Group Meeting are available through GitHub: https://github.com/openchemistry/avogadro-ugm2018 +Materials from our first User Group Meeting are available through GitHub: ## Talks @@ -20,14 +20,14 @@ Materials from our first User Group Meeting are available through GitHub: https: ## Tutorials -- Sending RPC calls: https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/tutorials/JSON-RPC.md -- Input Generators: https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/tutorials/Generators.md -- Command Scripts: https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/tutorials/Scripts.md +- Sending RPC calls: +- Input Generators: +- Command Scripts: ## Example Input Generators -- https://github.com/OpenChemistry/avogadro-ugm2018/tree/master/generators +- ## Example Command Scripts -- https://github.com/OpenChemistry/avogadro-ugm2018/tree/master/commands \ No newline at end of file +- \ No newline at end of file diff --git a/_posts/2021-06-02-avogadro-1-94-release.md b/_posts/2021-06-02-avogadro-1-94-release.md index 75ae45d..80fadea 100644 --- a/_posts/2021-06-02-avogadro-1-94-release.md +++ b/_posts/2021-06-02-avogadro-1-94-release.md @@ -15,9 +15,9 @@ including new input generators, molecule fragments, and build and analysis commands. These scripts make it much easier to integrate Avogadro with many open source chemistry Python tools, including RDKit, ASE, etc. -Draft developer documentation can be found at https://two.avogadro.cc +Draft developer documentation can be found at -If you have comments or suggestions, please join us at https://discuss.avogadro.cc +If you have comments or suggestions, please join us at We anticipate several more releases over the summer and early fall 2021. diff --git a/_posts/2021-07-28-community-survey-results.md b/_posts/2021-07-28-community-survey-results.md index 3dfa287..82399cf 100644 --- a/_posts/2021-07-28-community-survey-results.md +++ b/_posts/2021-07-28-community-survey-results.md @@ -12,14 +12,102 @@ avogadro mailing lists. ## Quick Summary (tldr) -- Many users find Avogadro from a friend, peer or instructor (~45%) -- By far, most download binaries (>80%) - - Many use package managers (42%) -- Responses were heavily from Linux (71%) and Mac (60%) users, despite most SourceForge downloads from Windows users (66%) -- Heavily educated, with >90% of responses with at least a graduate degree -- Many can code: >40% report Python knowledge, >10% report C/C++ knowledge +- 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 (~57% use at least weekly) +- 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 + diff --git a/_posts/2021-08-16-avogadro-1-95-release.md b/_posts/2021-08-16-avogadro-1-95-release.md index 160b5e0..eb4ce1f 100644 --- a/_posts/2021-08-16-avogadro-1-95-release.md +++ b/_posts/2021-08-16-avogadro-1-95-release.md @@ -15,9 +15,9 @@ Thanks to many for suggestions, bug reports, and discussions. This release includes many new features, including new protein ribbon / cartoon renderings and the new "Layer" system as part of Google Summer of Code by @serk12. -Draft developer documentation can be found at https://two.avogadro.cc +Draft developer documentation can be found at -If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions +If you have comments or suggestions, please join us at and as always, help and contributions in many forms are very welcome, **particularly if you'd like to help with user documentation.** diff --git a/_posts/2022-01-15-two-avogadro-website.md b/_posts/2022-01-15-two-avogadro-website.md index 6ed96ca..95c3ea8 100644 --- a/_posts/2022-01-15-two-avogadro-website.md +++ b/_posts/2022-01-15-two-avogadro-website.md @@ -7,7 +7,7 @@ date: 2022-01-15 There is now a website to coordinate development on Avogadro2: -https://two.avogadro.cc/ + Developer documentation on Avogadro2, including download links for beta releases and nightly builds, as well as Python plugin documentation and C++ API are now available.