Cumulative integration over multiple LAMMPS ave/chunk .profile files
integrateProfile.py is a python script that integrates LAMMPS .profile files created with compute chunk and fix chunk styles.
Integrations can be done over several .profile files at a time, summing up the total integral in an additional column. Columns can be weighted using the -q flag. This is intended to be used for number densities of particles, so that the electric field from these particles can be found. Two integrations over number densities gives you the electric potential.
Example of usage:
integrateProfile.py -h
integrateProfile.py -i Na.profile Cl.profile -q [1,-1] -c [2,5] -o efield-NaCl.profile
integrateProfile.py -i efield-NaCl.profile -q [1] -c [1,3] -o potential-NaCl.profile
Restriction: Assumes one chunk, so averages in LAMMPS should be done over one simulation run. E.g:
variable Ne equal 100 # Nevery; use every Ne in averages
variable Ns equal 100000 # Nstep; number of time steps
variable Nr equal ${Ns}/${Ne} # Number of values in average
variable r equal 0.1 # resolution
compute DensityOfWater spce chunk/atom bin/1d z lower ${r} units box region BOX
fix DensityProfileWater spce ave/chunk ${Ne} ${Nr} ${Ns} DensityOfwater density/mass density/number norm all file spce.profile
Easyinstall:
ln -s ~/full/path/to/integrateProfile.py /usr/local/bin/integrateProfile
Dependencies:
- numpy
- scipy
- matplotlib
- Python 2.7