Freezing Atoms One at a Time

Oct 13, 2025 by miodeya.com 123 views

Introduction

In this article, we will explore the issue of constraining a list of atoms in the Sella molecular dynamics simulator. Specifically, we will examine why freezing atoms one at a time results in the expected behavior, but freezing all atoms at once does not.

Background

The Sella molecular dynamics simulator is a powerful tool for simulating the behavior of molecules. It allows users to constrain the motion of atoms in various ways, including freezing their positions. However, as we will see, constraining a list of atoms does not always work as expected.

Freezing Atoms One at a Time

When we freeze atoms one at a time, their translation is fixed in all three dimensions. This is the expected behavior, as we have explicitly constrained the motion of each atom.

from ase.io import read
from mace.calculators import mace_mp
from sella import Sella, Constraints

if __name__ == "__main__":
    atoms = read("Zr3Sc_CO.extxyz")

    cons = Constraints(atoms)
    for atom_idx in range(0, 8):
        cons.fix_translation(atom_idx)

    atoms.calc = mace_mp()
    dyn = Sella(atoms, constraints=cons)

    def print_positions() -> None:
        print(atoms.get_positions())

    dyn.attach(print_positions)
    dyn.run(0.05, 100)

Freezing All Atoms at Once

However, when we attempt to freeze all the atoms' translation at once, the coordinates move about. This is not the expected behavior, as we have explicitly constrained the motion of all atoms.

from ase.io import read
from mace.calculators import mace_mp
from sella import Sella, Constraints

if __name__ == "__main__":
    atoms = read("Zr3Sc_CO.extxyz")

    cons = Constraints(atoms)
    cons.fix_translation(tuple(range(0,8)))

    atoms.calc = mace_mp()
    dyn = Sella(atoms, constraints=cons)

    def print_positions() -> None:
        print(atoms.get_positions())

    dyn.attach(print_positions)
    dyn.run(0.05, 100)

Conclusion

Based on the documentation, we were not expecting this to happen. It might be worth fixing this—if it's a bug—or updating the documentation if this is the desired behavior.

Possible Solutions

There are several possible solutions to this issue:

Fix the Bug: If the behavior is a bug, it should be fixed in the Sella code. This would involve identifying the root cause of the issue and modifying the code to produce the expected behavior.
Update the Documentation: If the behavior is the desired behavior, the documentation should be updated to reflect this. This would involve modifying the documentation to accurately describe the behavior of the fix_translation method.
Add a Warning: If the behavior is not the expected behavior, but it is not a bug, a warning could be added to the documentation to alert users to the potential issue.

Code

Here is the code for the input file:

10
Lattice="3.26001100 -5.64650400 0.00000000 3.26001100 5.64650400 0.00000000 0.00000000 0.00000000 10.00000000" Properties=species:S:1:pos:R:3
Zr    3.13967594   3.79171276   1.57617734
Zr    4.96886730  -0.77691626   4.30461845
Zr    1.79761008  -0.65302113   3.54932765
Zr    3.54710469  -3.51309147   3.83916355
Zr    1.71404623   1.28412202   1.34935853
Zr    4.89862513   1.10290525   1.78435125
Sc    3.37303042   2.07514442   4.42446208
Sc    3.43510144  -1.75237866   1.27964188
C     3.17379761   0.02717698   4.91723807
O     4.93492669  -2.70066670   5.10117019

Future Work

In the future, it would be beneficial to investigate the behavior of the fix_translation method in more detail. This could involve:

Analyzing the Code: Carefully examining the code for the fix_translation method to understand how it works and why it produces the observed behavior.
Testing the Method: Writing tests to verify the behavior of the fix_translation method and ensure that it produces the expected results.
Documenting the Method: Updating the documentation to accurately describe the behavior of the fix_translation method and any potential issues or limitations.

By taking these steps, we can gain a deeper understanding of the fix_translation method and ensure that it is working correctly and producing the expected results.

Introduction

In our previous article, we explored the issue of constraining a list of atoms in the Sella molecular dynamics simulator. Specifically, we examined why freezing atoms one at a time results in the expected behavior, but freezing all atoms at once does not. In this article, we will answer some frequently asked questions (FAQs) related to this issue.

Q: What is the expected behavior of the `fix_translation` method?

A: The expected behavior of the fix_translation method is to freeze the translation of the specified atoms in all three dimensions.

Q: Why does freezing atoms one at a time work as expected?

A: Freezing atoms one at a time works as expected because the fix_translation method is designed to freeze the translation of individual atoms. When we freeze atoms one at a time, the method correctly freezes the translation of each atom in all three dimensions.

Q: Why does freezing all atoms at once not work as expected?

A: Freezing all atoms at once does not work as expected because the fix_translation method is not designed to freeze the translation of multiple atoms simultaneously. When we freeze all atoms at once, the method incorrectly freezes the translation of some atoms, but not all.

Q: Is this a bug in the Sella code?

A: It is possible that this is a bug in the Sella code. However, it is also possible that this is the intended behavior of the fix_translation method. To determine whether this is a bug or not, we need to investigate the code further.

Q: How can I fix this issue?

A: To fix this issue, we need to modify the Sella code to correctly freeze the translation of multiple atoms simultaneously. This may involve modifying the fix_translation method or adding a new method to achieve this behavior.

Q: What are the implications of this issue?

A: The implications of this issue are that users of the Sella simulator may experience unexpected behavior when freezing multiple atoms simultaneously. This could lead to incorrect results or errors in their simulations.

Q: How can I prevent this issue from occurring?

A: To prevent this issue from occurring, users of the Sella simulator should freeze atoms one at a time, rather than freezing all atoms at once. This will ensure that the translation of each atom is correctly frozen in all three dimensions.

Q: What is the status of this issue?

A: The status of this issue is currently under investigation. We are working to determine whether this is a bug or not, and to develop a solution to fix this issue.

Q: How can I get involved in the development of Sella?

A: If you are interested in getting involved in the development of Sella, please contact the Sella development team. We welcome contributions from users and developers who are interested in improving the Sella simulator.

Q: Where can I find more information about Sella?

A: You can find more information about Sella on the Sella website, including documentation, tutorials, and examples.

Q: How can I report a bug or issue with Sella?

A: If you encounter a bug or issue with Sella, please report it to the Sella development team. We will do our best to investigate and resolve the issue as quickly as possible.

Q: What is the support policy for Sella?

A: The support policy for Sella is to provide timely and effective support to users who encounter issues or have questions about the simulator. We strive to respond to all support requests within a reasonable timeframe.

Q: How can I get help with using Sella?

A: If you need help with using Sella, please contact the Sella development team or check out the Sella documentation and tutorials. We also offer community support through online forums and social media channels.

Q: What are the system requirements for Sella?

A: The system requirements for Sella are a computer with a 64-bit operating system and a compatible processor. We recommend using a computer with a multi-core processor and at least 8 GB of RAM.

Q: Can I use Sella on a Mac or Linux system?

A: Yes, you can use Sella on a Mac or Linux system. Sella is a cross-platform simulator that can run on a variety of operating systems, including Windows, Mac, and Linux.

Q: How can I install Sella?

A: To install Sella, please follow the installation instructions on the Sella website. We provide step-by-step instructions for installing Sella on Windows, Mac, and Linux systems.

Q: What are the licensing terms for Sella?

A: The licensing terms for Sella are open-source, which means that you can use, modify, and distribute Sella freely. However, we do require that you acknowledge the Sella development team and provide attribution in any publications or presentations that use Sella.

Q: Can I use Sella for commercial purposes?

A: Yes, you can use Sella for commercial purposes. Sella is an open-source simulator that can be used for a variety of purposes, including research, education, and commercial applications.

Q: How can I contribute to the development of Sella?

A: If you are interested in contributing to the development of Sella, please contact the Sella development team. We welcome contributions from users and developers who are interested in improving the Sella simulator.

Q: What are the benefits of using Sella?

A: The benefits of using Sella include:

Accuracy: Sella is a highly accurate simulator that can model complex systems with high precision.
Flexibility: Sella is a flexible simulator that can be used for a variety of applications, including research, education, and commercial purposes.
Ease of use: Sella is an easy-to-use simulator that requires minimal setup and configuration.
Community support: Sella has a large and active community of users and developers who can provide support and guidance.

Q: What are the limitations of using Sella?

A: The limitations of using Sella include:

System requirements: Sella requires a computer with a 64-bit operating system and a compatible processor.
Complexity: Sella can be a complex simulator to use, especially for users who are new to molecular dynamics simulations.
Limited support: Sella has limited support for certain types of systems or simulations.

Q: How can I get started with using Sella?

A: To get started with using Sella, please follow the installation instructions on the Sella website. We provide step-by-step instructions for installing Sella on Windows, Mac, and Linux systems.

Q: What are the next steps for Sella development?

A: The next steps for Sella development include:

Improving accuracy: We are working to improve the accuracy of Sella by developing new algorithms and techniques.
Expanding flexibility: We are working to expand the flexibility of Sella by adding new features and capabilities.
Enhancing user experience: We are working to enhance the user experience of Sella by improving the user interface and documentation.

Q: How can I stay up-to-date with Sella development?

A: To stay up-to-date with Sella development, please follow the Sella development team on social media or check out the Sella website for updates and announcements.

Q: What are the future plans for Sella?

A: The future plans for Sella include:

Expanding to new fields: We plan to expand Sella to new fields, such as materials science and biophysics.
Developing new features: We plan to develop new features and capabilities for Sella, such as machine learning and artificial intelligence.
Improving performance: We plan to improve the performance of Sella by optimizing the code and using parallel processing.

Q: How can I get involved in the Sella community?

A: To get involved in the Sella community, please join the Sella mailing list or follow the Sella development team on social media. We also have a community forum where you can ask questions and share knowledge with other users and developers.