Bulk Ice Classification Using the CHILL+ Criterion¶
The trajectory file for this example is here on figshare. The trajectory file details a portion of a long run of 4096 molecules of a perfect Ic (cubic ice) lattice. In this example, the all 4096 molecules are identified as Ic, according to the CHILL+ algorithm . On running the example, an output top-level directory named runOne is created.
Steps to Run the Example¶
In order to run this example, without making any changes to the example files, please follow the steps below.
- Download the LAMMPS trajectory file from here on figshare. Copy the downloaded trajectory file, entitled nucleation.lammpstrj, into the traj folder inside the top-level directory input. Alternatively, you could change the path to the trajectory file in the conf.yaml file:
- You can obtain the other input files required from example_lua/chillPlus folder. Copy the contents of the chillPlus into the top-level lua_inputs directory.
- You can change the frames to be analyzed by updating the options in the vars.lua file. The starting and ending frames are inclusive, starting from 1 onwards, irrespective of the timestep number.
- A custom volume slice can also be defined in the vars.lua file.
- The functions.lua file actually contains the Lua functions which interface with the C++ backend.
Analyzing the Output¶
Inside the output directory, a file called clusterStats.dat contains the cluster statistics for each frame. Each frame is also written out to a LAMMPS trajectory file called waterChillP.lammpstrj, containing the classified atoms, and the largestIce.lammpstrj, which has the particles in the largest ice cluster. These trajectory files can be visualized in OVITO or VMD. Inside the bop directory, chillPlus.txt contains the number of particles identified as cubic ice (Ic), hexagonal ice (Ih), interfacial ice (Interfacial), clathrates (Clath), interfacial clathrates (InterClath), water and the total number of molecules (Total).
- Nguyen, A. H., & Molinero, V. (2014). Identification of Clathrate Hydrates, Hexagonal Ice, Cubic Ice, and Liquid Water in Simulations: the CHILL+ Algorithm. The Journal of Physical Chemistry B, 119(29), 9369-9376. doi:10.1021/jp510289t