v0.1.0

ComplexMixtures v0.1.0

• added TagBot
• added compat list
• added CompatHelper
• changed version to 0.1.0
• updated docs
• changed MDDF to ComplexMixtures
• updated docs
• updated example files
• Update README.md
• Update README.md

0.0.212

The Chemfiles parser is working apparently. This version has the selection functions which will be deleted subsequently.

• Changed version file to 20.212
• added dependencies
• removed dependencies
• added dependency
• changed uuid
• added Project.toml
• added the AtomSelect module, although the selection of Chemfiles is quite flawed
• added selection function based on Chemfiles
• removed open function because the format can be passed as an empty string
• added the Chemfiles parsers for trajectory formats

0.0.204

This version appears to have the parallel implementation at the frame level working perfectly. All tests passed. Now we need to start implementing the nice output functions, writing output files, and data analysis.

• Changed version file to 20.204
• added reference to default method
• some changes in the example files
• removed sides from FrameData
• fixed initialization of nsamples for self
• fixed definition of npairs inside
• implemented the self parallel and joined the common code with the serial version
• removed debug printing and fixed definition of sides in mddf_frame
• fixed random count sum
• returned linkedcells to serial, and almost done with the implementation of the parallel over frames using spawn

0.0.201

The cutoffdistances is parallelized in a reasonable way, but the speedup is not significant. We need to parallelize at the frame level.

• Changed version file to 20.201
• parallelized the cutoffidistances function only.

0.0.199

This might be called the first actual release. Linked cell methods are functional and everything seems correct. Now we need to proceed to parallelization, output file printing, and data analysis tools.

• Changed version file to 20.199
• tuned example3
• fixed number o random samples in mddf_naive
• changed some comments on examples
• fixed definition of solute center
• fixed centering solute molecule
• many changes, but example 3 is still with problems...
• trying to fix self kbs
• some other fixes
• fixed normalization of random count in self functions
• simplified code
• trying to fix the atom count of naive_self - example3
• added atom counting to linkedcells
• changed conditional
• implemented linked cell self function
• implemented lcell

0.0.193

• remove unused linkdedcells_v2
• Changed version file to 20.193
• various changes, but most importantly found the bug where the box sides were not set correctly
• fixed comment
• removed unused arrays

0.0.190

Wrap coordinates relative to the origin. This is necessary to speedup calculations,
as the wrapping of coordinates to compute distanes will be only necessary for cells
at the borders of the simulation box. Not having the compute minimum images between
pairs of atoms actually speeds up the calculations significantly, because the calculation
of pairwise distances is the most repeated calculation

• Changed version file to 20.190
• removed unused files
• added wrapping of coordinates in initcells

0.0.188

Linked cell method is working fine. Needs to be generalized for multiple solutes, and the self version must be implemented. This version contains still the "linkedcells_v1" set of files, and many test-example files that will be removed in the future.