The core of the SEAMM environment and graphical interface.
Project description
Simulation Environment for Atomistic and Molecular Simulations (SEAMM)
The MolSSI Simulation Environment for computational molecular and materials science (CMS)
Free software: GNU Lesser General Public License v3
Documentation: https://molssi-seamm.github.io/seamm/index.html
Features
TODO
Credits
This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.
Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under awards OAC-1547580 and CHE-2136142
History
- 2024.1.2 – Corrected issue with citations in development versions
Fixed an issue getting the date of a plug-in for development versions of the plug-in. This did not affect end users, but did casue issues for development.
- 2023.12.18 – Moving execution of flowcharts to seamm-exec
Moved execution of flowcharts to seamm-exec to consolidate execution in one place. This will allow easier, faster developement for running in queues, etc.
Switched the dependency on PMW from CondaForge to PIP since the version on CondaForge is poorly maintained.
- 2023.12.12 – Moving ~/.seammrc to ~/.seamm.d/seammrc
Should have no effect on users. The seammrc file will be moved automatically to its new location. This change is necessary to be able to run SEAMM in containers.
- 2023.11.15 – Add boolean options when submitting jobs
Added boolean control parameters when submitting jobs.
Bugfix: The previous change to allow running “flowchart.flow” in the current directory caused a bug in other scenarios.
- 2023.11.12 – Allowing running flowchart.flow in current directory
There was a feature which prevented running a flowchart named “flowchart.flow” in the current directory when running from the commandline.
- 2023.11.11 – Incorporating changes to Zenodo
Zenodo updated and made small changes to their API, which required changes in SEAMM.
Consolidated all private information about the user and their keys for Zenodo in ~/.seammrc
- 2023.11.7 – Bugfix: initialization of Dashboard
Fixed a crash that occurred the very first time submitting to the Dashboard.
- 2023.10.30 – Extending and cleaning up handling of configurations
Added ability to name systems and configurations with the IUPAC name, InChI, or InChIKey of the configuration.
Generally cleanedup and streamlined the code handling new systems and configurations.
- 2023.9.26.1 – Bugfix: system naming
Fixed a bug with keeping the current name when updating a system.
- 2023.9.26 – Added units to header in tables, and bugfixes.
The headers for table columns now include units when generated automatically when writing results. Existing columns are not changed.
Changed the join step image and added the code to enable deleting it.
Fixed an issue with the sizie of subwindows in edit dialogs
- 2023.8.30 – Added support for keyed columns in table output
Caught errors when writing out the final structures for viewing and improved messages in such cases.
Keyed columns in table output are used for e.g. the diffusion coefficients of multi-component fluids, where the column is expanded for each component.
- 2023.7.10 – Adding JSON for properties in the database and tabels; bugfixes
Handle non-scalar results using JSON so they can be output to tables and added to the properties in the database.
Fixed error submitting jobs to Dashboard the user doesn’t have a login for.
Ask for credentials when adding a new dashboard to job dialog.
Fixed bug creating a new project.
- 2023.6.28 – Improved error handling contacting Dashboards.
Trap and display errors when contacting Dashboards
Allow SEAMM to continue despite such errors
2023.5.29 – Fixed bug with missing directories when executing codes
- 2023.4.24 – Enhancements for thermal conductivity
Enhanced handling of command-line options to supported self contained flowcharts.
Various enhancements to graphs to better present results.
Added tracebacks to error report to identify the code responsible for the issue.
Correctly remember the filename for flowcharts opened from disk.
- 2023.4.6 – Bugfix: issue running standalone
When a description was not provided in either the command-line or the flowchart, running standlone crashed.
- 2023.3.31 – Bugfix: formatting of dates
Fixed a minor issue with formatting the dates in Job.out.
- 2023.3.23 – Updates for new JobServer
Jobs running from the JobServer now update their status in the datastore as they finish. This helps support jobs continuing if the JobServer crashes or stops.
- 2023.3.8 – Fixed bug running from command-line (Incorrectly labeled 2023.4.8!)
Fixed bug running from the command-line when giving project so the job is put in the datastore.
Improved handling of title and description both when running from the command-line and GUI, defaulting to the title and description of the flowchart.
- 2023.2.15 –
Improved handling of structures
Added ability to run simulations engine in a given directory, typically the step directory. This allows users to see the outputs during the simulation rather than having to wait until the end.
Added support allowing a flowchart to be run as a sub-flowchart.
- 2022.10.23 – Simplified plug-ins
Better support for plug-ins and the SEAMM cookiecutter:
Automated most handling of results and properties, based on metadata
Simplified handling of sub-flowcharts.
- 2022.10.20 – Properties in database
Added support for handling properties the database.
- 2022.9.13 – Bugfix: reading MOPAC .mop files
Fixed a bug that impacted read-structure-step finding MOPAC to use as a helper when reading .mop files.
- 2022.9.8 – Remembering location of flowcharts
Added memory of where you were last opening flowcharts, and directories that you use, to make it a bit easier.
- 2022.7.25 – DOS and Band Structure graphs
Adding support for combined bandstructure/DOS graphs.
- 2022.6.9 – Addeded –version option
Added a –version argument to print version and stop. by @paulsaxe in #130
Switched to reusable GitHub workflows (internal development improvement).
- 0.1.0 (2018-01-20) – Initial Release!
First release on PyPI.
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