Welcome to the github page of AIM! Here, you can download the newest version, request or submit changes, discuss or ask questions about the code, and more!
AIM is capable of extracting the vibrational Hamiltonian from a molecular dynamics (MD) trajectory. The current version allows for calculating the amide I Hamiltonian immediately, but also allows you to add your own methods (without changing the main code) to calculate other types of Hamiltonians. These vibrational Hamiltonians can be used to calculate infrared absorption (IR) spectra and 2-dimensional infrared (2DIR) spectra using the NISE code.
The manual can be found in the support_files folder above. It contains all information about the program, much more than this page!
There is two ways to download AIM. You can download it directly using the git clone command in the terminal/command prompt. Alternatively, at the top of this page, there is a big green button with the text 'Code'. Click it, and select the option 'download ZIP'. Move the zip to the correct location and unzip.
The main script that should be called when running this code is called AIM.py and can be found in the folder called AIM above.
Don't worry, we know! There is now an installable version of the program, where you can install (and create a very useful alias) in a single command. It lives in another branch (named installable), and we'd love you give it a try! Let us know if it worked well (and intuitively) for you, because once we're certain it does, it'll probably become the main version.
When using the program, please cite J. Chem. Theory Comput. 2022, 18, 5, 3089–3098. It's the paper about the AIM program itself. Please, also don't forget to cite the papers that provided the maps applied by AIM. These references are generated by AIM during runs. More information on this can be found in the FAQ in the manual.
If you have discovered a bug or other issue with the code, please use the issues section. Please check if the issue is already known. If not, feel free to make a new issue! For more information on how to make the issues most helpful for us, please check the manual.
If you have a general question/remark/suggestion, please uses the discussions section. If others had the same question, the answer might already be there. Otherwise, feel free to ask! Active discussions are shown automatically, answered questions can be found by setting the filter to 'closed', or 'all'.
In order to use AIM, you need to have a MD trajectory. These can be generated using MD packages. AIM is currently tested for the following MD packages (you only need one, not all):
Similarly, you need some spectral software to convert the hamiltonian trajectory to a spectrum. The format currently generated by AIM is supported by the NISE package.
AIM requires you to have a python installation. You can get it here. Please make sure you get a version starting with 3. Next to the python installation, AIM also makes use of the following modules, which have to be installed separately. Instructions for this can be found on their webpages, and are very familiar to python users: all allow using pip or conda.
We'd like to encourage the growth of an engaged community. This list will feature examples of ways to extend the capabilities of AIM. Please note that the linked projects are not an official part of AIM, and we take no responsibility in maintaining, updating, or managing them.
- This is a simple way of running AIM in parallel. We hope to add parallel capabilities to AIM soon, but this should help in the meantime.