Velocity-Velocity autocorrelation function for AdResS¶
One purpose of our project is to promote GC-AdResS as a method. It is an advanced method, for people with experience, and once the simulation is done there are several properties and checks to consider to make sure that the simulation was successful.
This module provides the code to run a velocity velocity autocorrelation function on the current geometries available in the Abrupt AdResS implementation. The paper Ref. describes the correlation functions and why they can be used in AdResS. This code is based on that theory and has been developed to check the dynamics of the local thermostat GC-AdResS simulations presented in the paper cited above.
Files are stored here: https://gitlab.e-cam2020.eu/krekeler/analyze.energy. The source code for the velocity autocorrelation function can be found here: https://gitlab.e-cam2020.eu/krekeler/analyze.energy/tree/master/app/cal_vel_acc_adr.cpp
The installation instruction can be found https://gitlab.e-cam2020.eu:10443/krekeler/analyze.energy#installation-instructions.
cal_vel_acc_adr: options: -h , "print this message") -b start time -e end time (=number of MD steps) --x0 lower bound of the interval --x1 upper bound of the interval (--x1 0, use the whole box = atomistic) --frame length of correlation --acc breaks --total number of frames --tf Output Frequency (=Delta_t) -m type of simulation to analyze (adress or atom) -f input .xtc file -o output file
It is important to have the XDR files and setup in the same directory as they have to be specified in the Makefile. The XDR files can be found via the GROMACS web page, see http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library or ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz.