PhD-tools

Useful codes, scripts and tweaks written by Goran Brekke Svaland

Repository content:

• readlammpstrj.py
  • python class for reading LAMMPS trajectory, frame by frame
• eldip.py
  • python script for computing electric dipolemoment and orientational order parameter Tp, using readlammpstrj.py
• integrateProfile.py
  • python script for integrating LAMMPS profiles generated from ave/time or ave/chunk
• heatmap.py
  • python script for making 2D heatmaps from scattered data
• percolation
  • run_voro++_cl.sh is a script to modify the input .gro file and run voro++ to find neighbors of each atom
  • percolation_cl.py is python script that takes the output of voro++ to cluster atoms based on whether their voronoi cells share a face, and dumps a vmd file that can be sourced by vmd to create atom representations of the clusters found by the code.
  • run_cl_traj.sh is a script to run the percolation code for a trajectory.
  • scripting: sub directory containing some random overlay scripts used to run voro++ and the percolation code.
• BASH-scripts
  • displacemolecules displace two molecules using VMD
  • process_lammpslog process LAMMPS log files
  • GROMACSconfmerge merge two gromacs configurations into one
  • gnuplotting use BASH to plot data via gnuplot
• savitzky-golan-filter
  • smoothing.py filter noisy data using a Savitzky-Golan filter
• avgdataframes
  • avgdataframes.py using pandas Data Frames to average over several data frames.
• 2Drdf
  • 2Drdf.py computes the two dimensional radial distribution function in the xy-plane
• ovitoscripting
  • clustercompute.py utilizes the DXA algorithm in ovito for dislocation analysis
• diffusion-vacf
  • diffusion_vacf.py compute diffusion coefficient from average velocities. Based on the velocity autocorrelation function.
• fepstuff
  • fepstuff.py compute free energy profile of ion in confinement
• piechart
  • example script for plotting a pie chart
• solvate
  • solvate two mineral slabs with water using GROMACS
• fractaldim
  • fractaldim.py compute the fractal dimension of a system using the box counting algorithm
• hist-gauss
  • compute histogram of columnar dataset and make a fit to a gaussian bell curve
• surface-roughness
  • scripts for computing colloidal interaction potential