From 77bee73bb0977d653752eae34949159309f20bc1 Mon Sep 17 00:00:00 2001 From: Geoff Hutchison Date: Mon, 23 May 2022 14:17:57 -0400 Subject: [PATCH] Add recent news --- _posts/2018-04-23-openchemistry-gsoc.md | 2 +- _posts/2018-08-13-gsoc-report.md | 29 +++++ _posts/2018-08-22-avogadro-1-91-release.md | 19 ++++ _posts/2018-08-25-ugm-materials.md | 33 ++++++ _posts/2020-02-05-avogadro-1-93-release.md | 26 +++++ _posts/2021-06-02-avogadro-1-94-release.md | 100 ++++++++++++++++++ _posts/2021-07-28-community-survey-results.md | 25 +++++ _posts/2021-08-16-avogadro-1-95-release.md | 82 ++++++++++++++ _posts/2021-09-13-gsoc-report.md | 25 +++++ _posts/2022-01-15-two-avogadro-website.md | 18 ++++ 10 files changed, 358 insertions(+), 1 deletion(-) create mode 100644 _posts/2018-08-13-gsoc-report.md create mode 100644 _posts/2018-08-22-avogadro-1-91-release.md create mode 100644 _posts/2018-08-25-ugm-materials.md create mode 100644 _posts/2020-02-05-avogadro-1-93-release.md create mode 100644 _posts/2021-06-02-avogadro-1-94-release.md create mode 100644 _posts/2021-07-28-community-survey-results.md create mode 100644 _posts/2021-08-16-avogadro-1-95-release.md create mode 100644 _posts/2021-09-13-gsoc-report.md create mode 100644 _posts/2022-01-15-two-avogadro-website.md diff --git a/_posts/2018-04-23-openchemistry-gsoc.md b/_posts/2018-04-23-openchemistry-gsoc.md index 6b6aea9..543bbce 100644 --- a/_posts/2018-04-23-openchemistry-gsoc.md +++ b/_posts/2018-04-23-openchemistry-gsoc.md @@ -9,4 +9,4 @@ Avogadro and [Open Chemistry](http://openchemistry.org) are part of Google Summe https://summerofcode.withgoogle.com/archive/2018/organizations/6513013473935360/ -I think I speak for everyone that we’re excited to see more progress on Avogadro 2 this summer - and hopefully the first official release of Avogadro 2.0 this fall. +I think I speak for everyone that we’re excited to see more progress on Avogadro 2 this summer. diff --git a/_posts/2018-08-13-gsoc-report.md b/_posts/2018-08-13-gsoc-report.md new file mode 100644 index 0000000..bbaa792 --- /dev/null +++ b/_posts/2018-08-13-gsoc-report.md @@ -0,0 +1,29 @@ +--- +title: "Google Summer of Code 2018: Molecular Dynamics" +categories: News +author: ghutchis +date: 2018-08-13 +--- + +Adarsh Balasubramanian was a strong contributor to Avogadro2 this summer as part of +[Google Summer of Code](https://summerofcode.withgoogle.com/archive/2018/projects/4861646958755840) + +Adarsh contributed a number of key features: +- File import for many trajectory formats including: + - PDB + - LAMMPS dump files + - GROMACS trr trajectories + - DCD trajectory format (CHARMM, OpenMM, NAMD, LAMMPS) + - VASP OUTCAR + - Amber mdcrd files +- LAMMPS Input Generator +- OpenMM Input Generator +- Animation / Player tool overhaul + - Native export to AVI and GIF +- Molecular dynamics analysis + - RMSD VTK chart + - Pair / Radial distribution function chart +- Rendering force vector arrows +- Improved residue classes + +His full report is [online](https://gist.github.com/badarsh2/f72c115062154022020ebc57607e31cb) \ No newline at end of file diff --git a/_posts/2018-08-22-avogadro-1-91-release.md b/_posts/2018-08-22-avogadro-1-91-release.md new file mode 100644 index 0000000..a819d6a --- /dev/null +++ b/_posts/2018-08-22-avogadro-1-91-release.md @@ -0,0 +1,19 @@ +--- +title: "Avogadro 1.91.0 Released" +categories: News +author: cryos +date: 2018-08-22 +--- + +We are very proud to announce the availability of Avogadro 1.91.0, the latest Beta +for Avogadro 2.0. + +Avogadro 2 is a free, open source, cross-platform molecular editor +designed for flexible use in computational chemistry, molecular +modeling, bioinformatics, materials science, and related +areas. Packages are available for Windows, Linux and Mac OS X. The +source code source is available under the 3-clause BSD license. + +This release has a lot of new work completed over the last year, including the results of our first Google Summer of Code where two students worked on projects under the program. + +If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: diff --git a/_posts/2018-08-25-ugm-materials.md b/_posts/2018-08-25-ugm-materials.md new file mode 100644 index 0000000..a8d25b3 --- /dev/null +++ b/_posts/2018-08-25-ugm-materials.md @@ -0,0 +1,33 @@ +--- +title: "2018 Avogadro UGM Materials" +categories: News +author: ghutchis +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 + +## Talks + +- Geoffrey Hutchison, Pitt [Welcome, Intro & Community Feedback](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Hutchison-Overview.pdf) +- Marcus Hanwell, Kitware [Avogadro 2, Open Chemistry](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Avogadro2-OpenChemistry.pdf) +- Patrick Avery, U. Buffalo [Extended Hückel, Solids and Avogadro](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/avogadroWithYaehmop.pdf) +- John Keith, Pitt [Quantum chemistry modeling of local solvation effects](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Keith-SolvationEchem.pdf) +- Chris Wilmer, Pitt [The Need for New Tools for Materials Discovery](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Wilmer-MaterialsCAD.pdf) +- Paul Boone, Pitt [Avogadro Plugins](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Boone-AvogadroPlugins.pdf) + +## 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 + +## 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 diff --git a/_posts/2020-02-05-avogadro-1-93-release.md b/_posts/2020-02-05-avogadro-1-93-release.md new file mode 100644 index 0000000..e9f621b --- /dev/null +++ b/_posts/2020-02-05-avogadro-1-93-release.md @@ -0,0 +1,26 @@ +--- +title: "Avogadro 1.90.0 Released" +categories: News +author: cryos +date: 2016-12-02 +--- + +We are very proud to announce the availability of Avogadro 1.90.0, the latest Beta +for Avogadro 2.0. + +Avogadro 2 is a free, open source, cross-platform molecular editor +designed for flexible use in computational chemistry, molecular +modeling, bioinformatics, materials science, and related +areas. Packages are available for Windows, Linux and Mac OS X. The +source code source is available under the 3-clause BSD license. + +This release has a lot of new work completed over the last year, including the results of our first Google Summer of Code where two students worked on projects under the program. + +If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: + +This is a community project and we couldn't have made this release +without you. Many thanks to all the contributors to Avogadro including +those of you who submitted feedback, bug reports, and code. We +acknowledge that the development of Avogadro 2 has been funded in part by a US +Army SBIR with the Engineering Research Development Center under +contract (W912HZ-12-C-0005) at Kitware, Inc. diff --git a/_posts/2021-06-02-avogadro-1-94-release.md b/_posts/2021-06-02-avogadro-1-94-release.md new file mode 100644 index 0000000..75ae45d --- /dev/null +++ b/_posts/2021-06-02-avogadro-1-94-release.md @@ -0,0 +1,100 @@ +--- +title: "Avogadro 1.90.0 Released" +categories: News +author: cryos +date: 2016-12-02 +--- + +We are very proud to announce the availability of Avogadro 1.95.0, the latest Beta +for Avogadro 2.0. + +More can be found on the [1.94 release page](https://github.com/OpenChemistry/avogadrolibs/releases/tag/1.94.0) including downloads for Mac and Windows. + +As part of the release, we've made it easier to download scripts and data, +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 + +If you have comments or suggestions, please join us at https://discuss.avogadro.cc + +We anticipate several more releases over the summer and early fall 2021. + +## Features + +- Bring back "insert framgent" builder from Avogadro v1 @ghutchis (#591) +- New docs on http://two.avogadro.cc @ghutchis (#568) +- Remove dependency on MoleQueue @cryos (#596) +- Initial Flatpak package @kevinsmia1939 +- Improved download widget @ghutchis (#534) +- Reorganize menus - fix #474 @ghutchis (#564) +- Export to SVG @serk12 (#588) +- Symmetry enhancements @ghutchis (#553) +- Added yaehmop with band structure calc @psavery (#339) +- Cp2k input @ghutchis (#383) +- OpenMM script builder plugin @badarsh2 (#343) +- Handle drag-and-drop of files to the window @ghutchis +- Use native message / dialog boxes on Mac @ghutchis +- Download entries from PDB @ghutchis (#575) +- Allow manipulate to rotate selected fragments @ghutchis (#594) +- Add bestFitPlane on Molecule @dvermd (#500) +- Add centerOfGeometry, centerOfMass and radius methods on Molecule @dvermd (#499) +- Reset view (camera) @serk12 (#450) +- Transparent support for ASE "extended XYZ" files @ghutchis (#603) + +## 🐛 Bug Fixes + +- Switch to using Python 3, fixing #431 @ghutchis (#462) +- Switch Open Babel calls to use CML and non-local numeric format (#471) +- Save background color across sessions and set bg alpha for export @ghutchis +- Add support for cut/copy/clear selected atoms @ghutchis (#510) +- Label toolbar windows for context menu @ghutchis +- Make sure to send Extensions the setActiveWidget call @ghutchis +- Make sure to install Qt image plugins on Mac and Windows @ghutchis +- Fix #483 through stream-specific locale @ghutchis (#549) +- Fix a pile of rendering bugs on high-res by saving viewport @ghutchis (#556) +- Adjust font size for 2D measure labels on hires screens @ghutchis (#548) +- Make sure to check movie sizes for high-dpi screens @ghutchis (#570) +- Fixes silent export on save bug #439 @anubh4v (#517) +- Switch to the navigate tool after pasting coordinates over empty @ghutchis (#593) +- Fix #571 - ensure we read Gaussian files from file, not stream @ghutchis (#592) +- Fix symmetry detection with dummy atoms (e.g, ferrocene example) @ghutchis (#595) + +## 🐍 Python Improvements + +- Add support for a JSON list of selected atoms @ghutchis (#440) +- Simplify wheel building @psavery (#520) +- Update example Avogadro RPC script @ghutchis + +## 🧰 Maintenance + +- Switch to using GitHub actions for continual builds @ghutchis (#461) +- Translations update from Weblate @weblate +- Get rid of bits/stdc++ headers - non-portable GCC header @ghutchis (#463) +- Add fedora patches @ghutchis (#460) +- Allow use of HDF5 >= 1.12.0 @berquist (#488) +- Remove exit calls from qtaim code @ghutchis (#475) +- Switch to include spglib.h with no subdir - fixes build issues @ghutchis (#533) +- Update residues from LigandExpo @ghutchis (#572) +- Make VtkPlot more object-oriented @psavery (#379) + +## Credits + +Thanks to many contributors, including: @Andre870-hub, @ImgBotApp, +@KovalevArtem, @NathanBnm, @Padanian, +@Pietro026, @SantosSi, @SoftwareByRedline, @VeryTastyTomato, @Z-Fikar, +@Zaryob, @adreasnow, @ahmadubuntu, @akyunus, @amandadumi, +@andhikapangestu29, @anubh4v, @badarsh2, @berquist, @borisfaure, +@comradekingu, @crlambda, @cryos, @dnandz, @dvermd, @ghutchis, +@grsousajunior, @hello-malaysia, @imgbot, @joanavieira8, +@kevinsmia1939, @koffevar, @ludovicobesana, @mirosnik1, @niskala5570, +@psavery, @rezaalmanda, @serk12, @shivupa, @tacostea, @tiagomalho, +@udopton, @weblate, @willow88, @yavgech, Alex, Apostol Penkov, Editor +Do Sonic BR, Irina Puscas, J. Lavoie, Jacque Fresco, Jörg S, Kavin +Teenakul, Liu Tao, Michalis, My Random Thoughts, Oğuz Ersen, RIDHO +NURUL ADILLA, Szabolcs Kalapos, Talking Panda, Thomas Koller, Tymofij +Lytvynenko, fikril Ha, phlostically, rahul bahuguna + + +If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: diff --git a/_posts/2021-07-28-community-survey-results.md b/_posts/2021-07-28-community-survey-results.md new file mode 100644 index 0000000..3dfa287 --- /dev/null +++ b/_posts/2021-07-28-community-survey-results.md @@ -0,0 +1,25 @@ +--- +title: "Results from 2021 Community Survey" +categories: News +author: ghutchis +date: 2021-07-28 +toc: true +--- + +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 (~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 +- High bias towards research applications +- Most responses use Avogadro frequently (~57% 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 diff --git a/_posts/2021-08-16-avogadro-1-95-release.md b/_posts/2021-08-16-avogadro-1-95-release.md new file mode 100644 index 0000000..160b5e0 --- /dev/null +++ b/_posts/2021-08-16-avogadro-1-95-release.md @@ -0,0 +1,82 @@ +--- +title: "Avogadro 1.95 Released" +categories: News +author: ghutchis +date: 2021-08-16 +--- + +We are very proud to announce the availability of Avogadro 1.95.0, the latest Beta +for Avogadro 2.0. + +More can be found on the [1.95 release page](https://github.com/OpenChemistry/avogadrolibs/releases/tag/1.95.0) including downloads for Mac and Windows. + +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 + +If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions +in many forms are very welcome, **particularly if you'd like to help with user documentation.** + + +## ✨ Features + +- New "Layer" system, including custom rendering, locking and hiding parts of the molecule @serk12 (#709) +- Atom and residue labels @serk12 (#715) +- New protein cartoon / ribbon display @serk12 (#660 #694 #716) +- Update render options for Wireframe and Ball-and-Sticks @ghutchis (#700 #720) +- Use MMTF downloads - more efficient than PDB format @ghutchis (#699) +- Add back support for importing crystals @ghutchis (#658 #659) +- Add CJSON support for save/load residues and atom colors @ghutchis (#646) +- Refactor of Python command and input generators, including tabs @ghutchis (#667) +- New View => Apply Colors menu @ghutchis (#640 #723) +- Apply color schemes for residues @ghutchis (#638 #688) +- Add more selection commands, including select by residue @ghutchis (#632 #634) +- Render selected atoms in VdW and licorice modes @ghutchis (#702) +- Detect secondary structure from residues / backbones @ghutchis (#685) +- Save enabled / disabled state of scene / rendering plugins on quit @ghutchis +- Should now download and install translations for @ghutchis + +## 🐛 Bug Fixes + +- Fix Mac builds by turning off COORDGEN library @ghutchis (#606) +- Fix Windows installer to include all needed files @ghutchis +- Save projection type on close #682 @ghutchis +- Add a pass to fix OB plugin library paths on Mac @ghutchis (#627 #628) +- Fix odd behavior on 'Center' command @serk12 (#728) +- Fix several crashes with proteins @ghutchis (#724 #726 #727) +- Fix crash in CJSON reading file without labels @ghutchis (#722) +- Fix bug deleting selected atoms #650 @ghutchis (#672 #677) +- Fix "delete last atom" bug @ghutchis (#691) +- When dragging to create a new atom, use starting coords @ghutchis (#690) +- Fix #679 - incorrect PDB unit cells @ghutchis (#689) +- Fixed problems inserting SMILES without coordinates @ghutchis (#661) +- Fix for transparent widgets @ghutchis (#656) +- Fix #602 - use Molden order for f-orbitals @ghutchis (#649) +- If a chain ID is missing / invalid, skip (to read non-standard PDB) @ghutchis (#647) +- Make sure to reset colors when changing elements @ghutchis (#708) + +## 🧰 Maintenance + +- Make sure to install crystals directory even when it exists @ghutchis (#613) +- Replace NULL/0 with nullptr @e-kwsm (#617) +- Add support for reading partial charge models from obabel @ghutchis (#626) +- Replace obsolescent `LINK_(PRIVATE|PUBLIC)` with `(PRIVATE|PUBLIC)` @e-kwsm (#629) +- Refactor Molecules class @serk12 (#648) +- Don't install cclib script - which was removed @ghutchis (#662 #663) + +## 📚 Translations + +- Fix fuzzy entry for Nihonium (not Zirconium!) @e-kwsm (#618) +- Fix all incorrect fuzzy entries #619 @e-kwsm (#643) +- Remove wrong entries which were fuzzy @e-kwsm (#644) +- Translations update from Weblate @weblate (#625) +- Add a workflow which should update the translation template continuously @ghutchis (#624) + +## Credits + +Thanks to many contributors, including: @12emin34, @GicoProgram, @LihanzUpenn, @NathanBnm, @San4ito, @acunm, @alexrsoares, @danialk03, @dillonschultz93, @e-kwsm, @ghutchis, @grsousajunior, @psavery, @rezaalmanda, @serk12, @tacitcoast, @weblate, Eisuke Kawashima, Jacque Fresco and phlostically + +If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: diff --git a/_posts/2021-09-13-gsoc-report.md b/_posts/2021-09-13-gsoc-report.md new file mode 100644 index 0000000..bae9a18 --- /dev/null +++ b/_posts/2021-09-13-gsoc-report.md @@ -0,0 +1,25 @@ +--- +title: "Google Summer of Code '21: Biomolecular Visualization and Layers" +categories: News +author: ghutchis +date: 2021-09-13 +--- + +Marc P. Masó was a strong contributor to Avogadro2 this summer as part of +[Google Summer of Code](https://summerofcode.withgoogle.com/archive/2021/projects/6688823861313536) + +Marc contributed a number of big features including: +- Protein rendering styles + - Cartoons + - Rope + - Backbone + - Trace + - Tube +- Layers + - Custom rendering per layer + - Assigning atoms to layers to hide / lock (e.g., water molecules, etc.) + - Open / save support in Chemical JSON (CJSON) file format +- Atom and Residue Labels + - New tool to create / edit custom labels + +His full report is [online](https://serk12.github.io/gsoc.html) \ No newline at end of file diff --git a/_posts/2022-01-15-two-avogadro-website.md b/_posts/2022-01-15-two-avogadro-website.md new file mode 100644 index 0000000..6ed96ca --- /dev/null +++ b/_posts/2022-01-15-two-avogadro-website.md @@ -0,0 +1,18 @@ +--- +title: "New Avogadro2 Development Website" +categories: News +author: ghutchis +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. + +We would greatly appreciate help in migrating user documentation from Avgoadro1, +teaching documents, and translation / internationalization. + +If you can help, please introduce yourself on the [Avogadro forum](https://discuss.avogadro.cc) \ No newline at end of file