Welcome to atomistica.online
Articles & Tutorials
Simplifying molecular modeling: Introducing the ORCA launcher and job monitor application from atomistica.online
Welcome to the tutorial about the GUI application for running and monitoring of ORCA calculations. This tutorial will guide you how to use our application to avoid using command prompt when it is necessary to run ORCA calculations or monitor job progress. The application is free and it can be downloaded from the Home page of this website.
If you find this article useful, feel free to cite our article about atomistica.online and support further development of this project:
Stevan Armaković and Sanja J. Armaković
ATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH THE ANVIL PLATFORM
Molecular Simulation, 49 (1) (2023), 117 – 123, DOI: 10.1080/08927022.2022.2126865
To support this project, please consider becoming a patron. Please visit https://www.patreon.com/atomista
Molecular modeling plays a crucial role in simulating and understanding chemical systems. However, running ORCA jobs from the command prompt can be challenging for beginners and may discourage them from exploring the field. To address this issue, we are excited to introduce the ORCA Launcher and Job Monitor from atomistica.online, a graphical user interface (GUI) application that simplifies running ORCA jobs and monitoring their progress.
The motivation for developing this application we found in the fact that running ORCA jobs from the command prompt is sometimes annoying not only for beginners but even for experienced modelers. Scientists spend a lot of time preparing correct input files for various calculations, and it isn’t enjoyable after all that work to start a command prompt and type the correct commands for initiating calculations. Although the command for running ORCA calculations is relatively simple, errors frequently occur in writing the names of the input and output files. That is one thing, but there is also the question of monitoring the progress of the calculation. Yes, there are solutions, but isn’t it the easiest to run jobs and monitor their progress from the same place?
Thirteen years ago, when we started with molecular modeling, such an application was just what we were missing for a successful start. Our first calculations were made with GAMESS code, and at the time, it was a little bit tricky for us even to start calculations using the template input file we found in the tutorials. After a few hours of trying, we managed to initiate calculation, but it took us weeks before we learned how to monitor job progress in real-time.
This application removes the barrier of running jobs from the command prompt by providing a user-friendly GUI. It simplifies the process, making molecular modeling more accessible for beginners.
In this tutorial, we will explore the features and functionalities of the ORCA Launcher and Job Monitor from atomistica.online. We will walk you through the general workflow in molecular modeling, highlight the importance of this application for beginners, and guide you on how to use its various features effectively.
2. Overview of the application
Before going through the features of the application, let’s look at the screenshot of the application.
Elements of this GUI application are grouped in three columns. The first column contains buttons, the second column contains two windows (the File list window and the Running jobs window). The third column contains the Content window. The application also contains a file menu; in the lower right corner, you can find real-time information about your resources.
Feature 1: Selecting the ORCA Folder
The first step in using the ORCA Launcher and Job Monitor from atomistica.online is to select the ORCA folder containing the ORCA executable file (orca.exe). For this step, you go to the File menu and press the Select Orca Folder option. This step ensures that the application always knows where the orca.exe file is, which is a prerequisite for adequately generating commands for running ORCA calculations. Once the ORCA folder is selected, the application automatically generates a settings.ini file, storing the path to orca.exe for future use. Every time you start our application, it will look for the orca.exe file in the generated settings.ini file. This ensures the smooth execution of your ORCA calculations.
If you ever change the location of your ORCA executable file, simply go to the “File” menu and select the “Select ORCA folder” option again. This updates the settings.ini file, allowing the application to integrate seamlessly with ORCA.
Feature 2: Loading, Modifying, and Saving Changes to Files
Once the ORCA folder is set, you can load your input files into the ORCA Launcher and Job Monitor application. Simply click the “Load file” button, select your input file (INP, OUT, or LOG format), and watch as it appears in the File list window. The application supports these file formats, enabling easy viewing and editing of their content. When you click on any of the files loaded to the File list window, its content will be presented in the Content window on the right side.
You can modify the file content directly within the application’s Content window. Whether you need to adjust the computational model or add specific settings, the ORCA Launcher and Job Monitor – atomistica.online provides a convenient interface for effortless file editing.
After making the desired modifications to the file, you can save the changes with a click of a button using the “Save changes” option. This ensures that your modifications are preserved and ready for the next execution. The application also provides visual feedback to confirm that the changes have been successfully saved.
With the ability to modify and save changes to your input files, the ORCA Launcher and Job Monitor – atomistica.online empowers you to fine-tune your calculations and tailor them to your specific needs.
Feature 3: Running and Monitoring Jobs
Running ORCA jobs is a breeze with the ORCA Launcher and Job Monitor from atomistica.online. Clicking on the “Run job” button executes an ORCA job based on the selected input file. The application keeps track of running jobs, displaying the names of output files created by ORCA calculation progress in the “Running jobs” window. By clicking on a job in the “Running jobs” window, the content of the corresponding output file is presented in the “Content window”. The “Content window” is refreshed every second (pointing to the end of the file), enabling real-time monitoring of the calculation.
Feature 4: Real-time System Information
You can monitor CPU, RAM, and HDD usage, ensuring you stay informed about your system’s performance while running intensive calculations.
Feature 5: Stopping Jobs
If you need to stop a running job for any reason (for example, it “eats” memory or it is not converging after many iterations), simply click on the desired job in the “Running jobs” window and hit the “Stop job” button, and the job will be halted. Additionally, the application provides real-time system information in the status bar.
Feature 6: Track Geometry Optimization
Our GUI application also includes a feature called “Track Geometry Optimization.” By clicking on the “Track Geometry Optimization” button, you gain access to a dedicated window that tracks the progress of your geometry optimization calculations.
In this optimization tracker window, you’ll find information about the current optimization cycle, including energy, forces, and convergence criteria. This real-time feedback allows you to assess the convergence of your geometry optimization and make informed decisions about further adjustments or termination of the calculation.
The ORCA Launcher and Job Monitor from atomistica.online makes things easier for beginners in molecular modeling. Its intuitive GUI simplifies the process of running ORCA jobs and monitoring their progress. By eliminating the need for command prompt usage and providing real-time feedback, this application empowers users to explore molecular modeling confidently.
We hope this tutorial has sparked your interest to start with molecular modeling. We also hope this application’s user-friendly interface and capabilities will make it enjoyable for beginners and experienced modelers. Simplify your workflow and unleash the full potential of ORCA calculations with the ORCA Launcher and Job Monitor from atomistica.online.