Python-based tool to calculate instantaneous interfaces and concentration/orientation profiles from molecular simulation trajectories in slab geometry.
The method is described by A.P. Willard and D. Chandler in Instantaneous Liquid Interfaces [1]. The tool uses the Lewiner marching cubes algorithm [2] and is partly an adaptation of the willard-chandler module of the pytim code [3] with the addition of a routine to calculate the orientational distribution of free O-H groups at the interface [4].
The Jupyter Notebook example.ipynb shows how to use the code to analyze and visualize the interfaces of a NaSCN aqueous solution in slab geometry.
To calculate concentration profiles, orientational distributions of linear ions and free OH groups w.r.t. the rough instantaneous interface:
python ./willardchandler.py -s TOPOLOGY -t TRAJECTORY -o OUTPUT PICKLE FILE -b FIRST FRAME -e FRAME INTERVAL -m MOLECULES -l LAYERS
for example (NaSCN aqueous solution)
python ./willardchandler.py -s npt.gro -t npt.xtc -o out.p -b 1000 -e 10 -m 'H1 O' 'NA' 'S1 C2 N3' -l -0.1 0.1 0.3 0.5
To calculate concentration profiles, orientational distributions of linear ions and free OH groups w.r.t. the planar Gibbs dividing surface:
python ./gds.py -s TOPOLOGY -t TRAJECTORY -o OUTPUT PICKLE FILE -b FIRST FRAME -e FRAME INTERVAL -m MOLECULES -l LAYERS
for example (NaSCN aqueous solution)
python ./willardchandler.py -s npt.gro -t npt.xtc -o out.p -b 1000 -e 10 -m 'H1 O' 'NA' 'S1 C2 N3' -l -0.1 0.1 0.3 0.5
- A. P. Willard and D. Chandler, “Instantaneous liquid interfaces”, The Journal of Physical Chemistry B 114, 1954–1958 (2010)
- T. Lewiner, H. Lopes, A. W. Vieira, and G. Tavares, “Efficient implementation of marching cubes' cases with topological guarantees”, Journal of Graphics Tools 8, 1–15 (2003)
- M. Sega, G. Hantal, B. Fábián, and P. Jedlovszky, “Pytim: A python package for the interfacial analysis of molecular simulations”, Journal of Computational Chemistry 39(25), 2118–2125 (2018)
- F. Tang, T. Ohto, T. Hasegawa, W. J. Xie, L. Xu, M. Bonn, and Y. Nagata, “Definition of free O-H groups of water at the air–water interface”, Journal of Chemical Theory and Computation 14, 357–364 (2017)