Clustering

A highly optimized package for generating optimal microstates.

Installation

  • conda
  • compilation
            
	        $ conda install moldyn-clustering -c conda-forge
	    
            
                $ git clone https://github.com/moldyn/Clustering.git

                $ cd clustering

                $ mkdir build

                $ cd build

                $ cmake .. -DCMAKE_INSTALL_PREFIX=/my/installation/path 

                $ make

Fast & Light

Highly optimized C++11 code which can be easily executed on remote.

User-friendly

The user interface was completely revised to reduce mistakes and make it more intuitive.

Parallelized

This package gets the best performance out of your hardware by running in parallel based on OpenMP and CUDA.

Open-Source

The methods are reliable and comprehensible documented with doxygen.

Theoretical foundation

All implemented methods were discussed and published in well-known journals.

Made with love

This package was made with a lot of love and coffee. We care about it, because we use it frequently.

Read our documentation for further information.

Get Started

Changelog

v1.3.2

9/17/2021
  • Coring: fix iterative coring with \(\tau_\text{cor}=0\:\text{frame}\).
  • MPP: Add to linkage matrix header comments.

v1.3.1

12/10/2020
  • Coring: fix iterative coring with \(\tau_\text{cor}=1\:\text{frame}\).

v1.3.0

7/3/2020
  • Coring: add iterative coring mode.
  • Filter: add nRandom for extracting only a few random frames per state.
  • Tutorial: Minor improvemnts to be more precise.

v1.2.2

11/22/2019
  • MPP: bug fix. correct normalization if concat_limits are given.

v1.2.1

9/30/2019
  • Stats: add number of leaving states
  • Stats: Do not count entering/leaving a state at the beginning/ending of the trajectory

v1.2.0

9/30/2019
  • Coring: add option to input coring window as integer directly
  • Coring: bugfix, enforce correct coring at the beginning and end of a trajectory
  • Stats/Coring/Noise: store information of limits to prevent incosistency
  • Documentation: Update and minor improvements

v1.1.2

8/26/2019
  • Noise: open correct highest cluster file (10>9 now)
  • Stats: use concat-limits for counting transitions
  • Documentation: Minor improvements

v1.1.1

5/16/2019
  • Noise: allow relative paths
  • Coring: minor bug fix
  • Documentation: Minor improvements

v1.1

3/27/2019
  • Stats: a new module to check stats of state trajectory
  • Filter: a new interface for the filter module with enhanced functionality
  • Added filter and stats module to documentation.
  • Updated tutorial
  • Minor improvements

v1.0.1

3/25/2019
  • Improved help strings
  • Coring: bug fix - print correct number of changed frames
  • Network: use fe_max from header string to load only corresponding files
  • Noise: use fe_max from header string to load corresponding file

v1.0

1/14/2019
  • Improved UI
  • Added noise module
  • Improved concat limits
  • Added comments in output
  • Bug fixes

v0.13

05/16/2017
  • Complete rewrittend density module
  • Added CUDA support
  • Added MPP by Jain et al.
  • Multiple bug fixed
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