MDCraft 1.3.2

v1.3.2

Update pyproject.toml

MDCraft 1.2.0

This release is primarily for the Journal of Open Source Software review process.

Changelog

mdcraft.analysis module

mdcraft.analysis.reader submodule

• Added a LAMMPS dump reader that supports multithreaded reading and reading extra attributes.

MDCraft 1.1.0

In this release, there are a number of under-the-hood optimizations, new features, and bug fixes. As a result, there are unfortunately some backwards-incompatible changes despite this being a minor version update. Moving forward, these types of breaking changes will be minimized as much as possible, if not avoided completely, to adhere to semantic versioning guidelines.

Changelog

mdcraft.algorithm module

mdcraft.algorithm.accelerated submodule

• Rearranged and renamed functions.
  • Added the Numba-accelerated functions numba_histogram_bin_edges and numba_histogram for histogramming discrete data.
  • Renamed the dot_1d_1d, inner_2d_2d, and inner_parallel_2d_2d functions to numba_dot, numba_inner, and numba_inner_parallel, respectively.
  • Moved the delta_fourier_transform_1d_1d, pythagorean_trigonometric_identity_1d, pythagorean_trigonometric_identity_1d_1d, cosine_sum_1d, and sine_sum_1d functions to the openmm.analysis.structure submodule, and renamed them to numba_delta_fourier_transform, numba_pythagorean_trigonometric_identity, numba_cross_pythagorean_trigonometric_identity, numba_cosine_sum, and numba_sine_sum, respectively.
  • Combined and moved the delta_fourier_transform_sum_2d_2d/delta_fourier_transform_sum_parallel_2d_2d, cosine_sum_2d/cosine_sum_parallel_2d, cosine_sum_inplace_2d/cosine_sum_inplace_parallel_2d, sine_sum_2d/sine_sum_parallel_2d, and sine_sum_inplace_2d/sine_sum_inplace_parallel_2d functions to the mdcraft.analysis.structure submodule, and renamed them to numba_delta_fourier_transform, cosine_column_sum, cosine_column_sum_inplace, sine_column_sum, and sine_column_sum_inplace, respectively.

mdcraft.algorithm.topology submodule

• Added the convert_cell_representation and reduce_box_vectors functions for manipulating representations of triclinic simulation boxes.

mdcraft.algorithm.unit submodule

• Renamed the get_scaling_factors and get_lj_scaling_factors functions to get_scale_factors and get_lj_scale_factors, respectively.

mdcraft.algorithm.utility submodule

• Added the is_lower_triangular function. Useful for checking if box vectors are in their reduced forms.

mdcraft.analysis module

• All units stored in the results.units attribute of analysis classes are now accessed using keys without the results. prefix. For example, the unit for profile.DensityProfile.results.number_densities is now obtained using profile.DensityProfile.results.units["number_densities"] instead of profile.DensityProfile.results.units["results.number_densities"].

mdcraft.analysis.electrostatics submodule

• Fixed issue in the DipoleMoment analysis class where the wrong volumes are used for systems with varying dimensions.
  • Removed the dimensions keyword-only argument since it restricted the analysis to only constant-volume systems. Now, the system dimensions/volumes are obtained directly from the trajectory.
  • Renamed the scales keyword-only argument to the more descriptive dim_scales.

mdcraft.analysis.polymer submodule

• Fixed an issue in the EndToEndVector analysis class where the time lags in results.times are are determined incorrectly when specific frames are specified for the analysis.
• Fixed two issues in the Gyradius analysis class.
  • Fixed issue where the wrong volumes are used for systems with varying dimensions when unwrap=True.
    • Removed the dimensions keyword-only argument since it restricted the analysis to only constant-volume systems. Now, the system dimensions are obtained directly from the trajectory.
  • Fixed issue where the wrong number of chains and chain lengths are used when "residues" in groupings, unwrap=True, and parallel=True.
• Refactored the SingleChainStructureFactor analysis class.
  • Removed the unwrap keyword-only argument since it is unnecessary to unwrap atom positions when the simulation system is cuboid.
  • Replaced the parallel implementation with a Numba-accelerated one similar to that used in the mdcraft.analysis.structure.StructureFactor analysis class.

mdcraft.analysis.profile submodule

• Refactored the DensityProfile analysis class.
  • Renamed the scales keyword-only argument to the more descriptive dim_scales.
  • Removed the dt keyword-only argument. The times can now only be obtained directly from the trajectory. This change shouldn't pose any issues since the times are not explicitly used in the analysis.
  • Both serial and parallel implementations now use the Numba-accelerated mdcraft.algorithm.accelerated.numba_histogram function for histogramming, which can provide a significant speedup for large trajectories.
  • The number density, charge density, and potential profiles are now stored in dicts instead of lists for more logical access using axis labels, i.e. "x", "y", and "z", instead of axis indices, i.e. 0, 1, and 2. This change also enables using different numbers of histogram bins in each dimension with the parallel implementation.

mdcraft.analysis.structure submodule

• Replaced numpy.histogram call in the radial_histogram function with the Numba-accelerated mdcraft.algorithm.accelerated.numba_histogram for better performance.
• Renamed the x_i and x_j arguments in the calculate_structure_factor function and RadialDistributionFunction.calculate_structure_factor method to x_a and x_b, respectively, to avoid confusion with the notation used in the documentation.
• Added the generate_spherical_wavevectors function, which supports non-cubic simulation systems and will be used in the StructureFactor, IntermediateScatteringFunction, and mdcraft.analysis.polymer.SingleChainStructureFactor analysis classes in a future MDCraft release.

mdcraft.analysis.transport submodule

• Renamed the calculate_electrophoretic_mobility and calculate_transference_number functions to calculate_electrophoretic_mobilities and calculate_transference_numbers, respectively, to reflect the plural nature of the return values.
• Refactored the Onsager analysis class.
  • Fixed an issue where the time lags in results.times are determined incorrectly when specific frames are specified for the analysis.
  • Renamed the results.conductivities attribute to results.conductivity.
  • Renamed the calculate_electrophoretic_mobility and calculate_transference_number methods to calculate_electrophoretic_mobilities and calculate_transference_numbers, respectively, to reflect the plural nature of the return values.

MDCraft 1.0.0

Initial release.