v1.0.3

We adjusted the calculate_free_energy method to consider the axis limits specified by the --xlim_inf, --xlim_sup, --ylim_inf, and --ylim_sup arguments during the contour data calculation phase. Now, the grid on which the probability density and free energy are calculated is created based on the specified limits, ensuring that contour data are generated for the entire desired visualization area.

Furthermore, a check was implemented to ensure that the specified limits are respected when plotting the free energy landscape, adjusting the plot_energy_landscape and plot_3D_energy_landscape methods to consistently apply these limits.

v1.0.2

Energy Discretization: Introduction of a new parameter --discretize, allowing for the energy values to be discretized into specified intervals. This feature enhances the visualization of free energy landscapes by marking distinct energy levels with unique colors and markers, facilitating the identification of critical energy thresholds and regions within the landscape.

Customizable Color and Marker Schemes for Discrete Energy Points: The script now supports customizable color and marker schemes for visualizing discrete energy intervals on both 2D and 3D free energy landscapes. This addition provides a more intuitive and visually appealing representation of the energy landscape, making it easier to distinguish between different energy levels.

Enhanced Histogram Normalization: Improved the normalization process for histograms of collective variable (CV) distributions, including a unified scaling mechanism that ensures consistency across different histograms. This change improves the comparative analysis of CV distributions by representing frequency percentages on a unified scale, offering clearer insights into the distribution and prevalence of CV states within the simulation.

Updated 3D Free Energy Landscape Visualization: The 3D visualization of the free energy landscape has been refined to include discretized energy points, providing a richer and more detailed perspective on the energy landscape. This enhancement allows for a more comprehensive analysis of the landscape's topology, including the identification of stable states and energy barriers.

Optimized Data Handling and Parallel Processing: The script now incorporates more efficient data handling and parallel processing techniques, leveraging the joblib library for improved performance. This optimization significantly speeds up the calculation of free energy landscapes, especially for large datasets, by distributing computational tasks across multiple CPU cores.

Improvements
User Interface and Usability: Enhanced the command-line interface to make it more user-friendly and intuitive. New help messages and usage instructions have been added, offering clearer guidance on how to utilize the script and its various options effectively.

Code Optimization and Refactoring: The codebase has undergone significant optimization and refactoring to improve readability, maintainability, and performance. These changes lay the groundwork for future enhancements and make the script more accessible to contributors.

Documentation and Examples: Expanded the documentation to include more examples and detailed descriptions of the new features. The updated documentation aims to assist users in maximizing the script's capabilities and understanding the underlying methodologies of free energy landscape analysis.

Bug Fixes
Addressed and resolved specific issues related to file handling and memory management, ensuring smoother operation and enhanced stability of the script across different platforms and datasets.
These updates collectively enhance the script's functionality, user experience, and performance, making it a more powerful tool for analyzing and visualizing free energy landscapes from molecular dynamics simulations.

v0.0.5

In this update, we implemented significant improvements and fixes to FreeEnergyLandsca pe, a Python module designed to analyze free energy landscapes from molecular dynamics simulations.

Here are highlights of the changes:

Parallelization of Density Calculation: We have implemented parallelization of probability density calculation using joblib. This change significantly improves calculation efficiency by dividing data into chunks and processing them in parallel, using all available CPUs.

Free Energy Calculation and Saving per Frame: We added a calculate_and_sav _free_energy function, which calculates the free energy for each frame and collective variables (CV1 and CV2), and saves the results in a .tsv file. This function also allows the application of an energy threshold to filter the results.

v0.0.4

Minor update.

v0.0.3

We are excited to announce the release of Free Energy Landscape Analysis v0.0.3, a significant update that introduces new features, enhances existing functionalities, and addresses several key issues to improve the user experience and analytical capabilities of the tool. This version marks a milestone in our ongoing effort to provide a comprehensive and user-friendly platform for analyzing the free energy landscape of molecular dynamics simulations.