SEAMM: the Simulation Environment for Atomistic and Molecular Modeling
Currently, SEAMM is in the early stages of its deployment and beta testing by the members of the computational molecular sciences community. Although we have made every efforts to minimize errors and glitches in the SEAMM software infrastructure, similar to any open-source software project it its early days, there may be bugs and issues we haven’t seen. If you find something or have a suggestion, please let us know!
There is a forum for reporting problems and sharing ideas and experiences. Thanks to the wonderful people at matsci.org for providing the infrastructure and management for so many useful forums! You can also email us at firstname.lastname@example.org or join the Slack channel.
SEAMM is fully open-source allowing anyone to contribute to its growth by opening issues, forking the repository and submitting pull requests in order to make changes in the code or documentation. SEAMM is also a large-scale and ambitious project with many moving parts. Thus, it will take some time to become truly stable! We appreciate your patience and assistance throughout the development process!
SEAMM is a user-friendly software package for the atomistic simulations of organic molecules, biological systems, fluids, synthetic polymers, and materials such as metals and metal oxides, semiconductors, ceramics and alloys. If you are performing any of these types of simulations, SEAMM can provides an ideal environment for discovery allowing you to focus on the science itself instead of getting bugged down on irrelevant technicalities of the software.
- Installing SEAMM
SEAMM and other simulation engines such as LAMMPS, DFTB+, Psi4, and Packmol can be conveniently installed on Linux or Mac systems. We are doing our best to provide support for the Windows platform.
- User Experience
In addition to its robust command-line interface (CLI), SEAMM provides a graphical user interface (GUI) that exposes its full power and functionality to the users in a user-friendly environment. As such, the GUI is focused on minimizing the need to learn verbose or complicated keywords and languages. Furthermore, the GUI puts chooses reasonable defaults for most parameters used in the available simulation tools. In this way, even if you don’t know much about programming, SEAMM will have you back to quickly get started with your simulation while expecting reasonable results. As you learn more about the details of each model and the corresponding tools, you can further customize your calculations for more accurate outcomes.
- Workflow Features
Flowcharts are a foundational concept in SEAMM offering a high-level and intuitive delineation of the entire workflow. Flowcharts remove the need for shell or python scripting while making the entire process reproducible. In other words, one can run all steps involved in a complex workflow exactly the same as it was originally intended and perform the exact same calculations all over again. While flowcharts are critical for enforcing reproducibility, they are flexible objects allowing users to perform necessary tweaks and changes to the workflow. For example, the same set of calculations within a flowchart can be performed on a variety of molecules and materials without any further changes. In a different scenario, changing parameters can be easily accommodated within an already existing flowchart such as fine-tuning the pressure or temperature variables in a simulation. Flowcharts make all these changes convenient and reproducible.
- Share your work
Because flowcharts are simple text files, the can be easily shared with coworkers and collaborators. This means that you can get flowcharts from experts in the areas that are outside your area of expertise and use them as a starting point for your studies. SEAMM makes workflows publishable and therefore, readily accessible and searchable on Zenono based on unique DOIs. As a cherry on top of the cake, SEAMM allows searching for flowcharts on Zenodo with convenient ways to find and import them within your workflows.
- Track your work
SEAMM provides a datastore as well as a web-based dashboard for storing, monitoring, and managing the calculation results. The datastore organizes each project in its isolated directory on disk and provides a well structured tree that can be monitored and managed effortlessly using the dashboard.
- Manage your data
Most granting agencies require a data management plan for the dissemination of scientific data. With SEAMM, the users will be able to publish their computational campaigns via dashboard for a project or manuscript. We are also working on reducing the task of publishing the results on Zenodo and generating a unique DOI down to pressing a few buttons in the GUI.
- Manage your citations
SEAMM helps you gather the right citations for the codes and parameter sets you used in your computational campaign. Each job creates a list of the appropriate citations for the current task and stores it in a database. We are developing tools to allow merging multiple citations for a single computational campaign.
For further details about SEAMM, refer to the Installing SEAMM and the Whitepapers. Developers interested in incorporating their tools and plug-ins in SEAMM are welcome to read the Developers Documentation.
Users can visit our YouTube channel for tutorials and videos, check our Github repository for the latest software updates and join our Slack channel for sharing software issues and seeking support by clicking on the following badges. Do not forget to check out our MolSSI Guidelines and Best Practices for Data Science, Machine Learning and High-Performance Computing. Be sure to also take a look at our SEAMM flowchart, dataset and model collections in our MolSSI Community platform on Zenodo.