======================================================================
Simulation Environment for Atomistic and Molecular Simulations (SEAMM)
======================================================================
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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.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
awards OAC-1547580 and CHE-2136142
.. _MolSSI: https://www.molssi.org
.. _`National Science Foundation`: https://www.nsf.gov
=======
History
=======
2024.5.3.1 -- Bugfix: JSON in Results GUI not set correctly.
2024.5.3 -- Added the time to Results.json
* Adding time into the Results.json file will allow ensuring that the most
recent data is used, when there are duplicates.
2024.5.1 -- Added ability to store results in Results.json file
* Added column in the results tab for saving results to JSON
* Added separators between the columns of the results table to make clearer which
parameters go together.
2024.4.22 -- Moving user preferences to ~/.seamm.d
* To better support Docker, moving ~/.seammrc to ~/.seamm.d/seamrc
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 cause 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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