seamm 2024.8.21

The core of the SEAMM environment and graphical interface.

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

2024.8.21 – Bugfix: Error using variable in stucture handling

• The standard structure handling widgets and methods had an error is the approach was a variable rather than one of the choices.

2024.8.17 – Enhancements to line graphs

• Added multiple axes to line graphs.

• Updated to correct version of plotly. ‘latest’ is actually not.

2024.7.28 – Updating standard parameters for systems and configurations

• Cleaned up and add to the standard parameters used for naming system and configurations. ‘title’ refers to the title in the file, if it exists.

2024.7.21 – Allows capital letters in variables and columns for results

• Allows capital letters for the variables, column names, etc. that results are stored in. For example, ‘T’, ‘P’, and ‘V’.

2024.6.27 – Added support for using local data files.

• Added support in the Flowchart and Node classes for using local data files for e.g. forcefields. This allows the user to specify a local file, which is copied to the working directory of the job.

• Also added a flag to both the Flowchart and Node classes indicating that the job is running in the JobServer rather than command-line.

2024.5.27 – Bugfix: Error saving results table.

2024.5.26 – Bugfix: Error when clicking “Cancel” on some dialogs

• Dialogs that have a Results tab – mainly the computational engines – raised an error if the “Cancel” button was clicked. “OK” worked. This fixes the problem.

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.