A selection of Nick's scripts

Most of these scripts work just fine on most UNIX flavors, including Apple's OS X. They were developed and tested mainly under linux, with not-too-old versions of perl and python.

Most scripts provide help and list their available options when invoked with the -h option. None of them is especially smart. Most of them can help you to corrupt/destroy your data, see at the bottom... A few friends and students find them useful, though.

Physics-oriented scripts

• conversion converts energy units such as eV, J, cm^-1, ...
• drude_dielectric_function.py: generate the dielectric function of a Drude metal over a wide spectral range
• optical_response.py: taking ω (rad/s) ε₁ ε₂ (real & imag parts of the dielectric function) in input, outputs real & imag part of the refractive index, the normal reflectivity, and the absorption coeff (in m^-1)
• reciprocal_lattice.py: for a given Bravais lattice, list all reciprocal G vectors of length ≤ maxQ
• phys_const.py: not really a script: load this code inside a python shell (from phys_const import * to have several useful symbols such as hbar, c, amu, etc. acquire the values of the relevant SI physical constants
• semiconductor_carrier_concentration.py: evaluate the chemical potential and carriers concentration for a doped semiconductor, as a function of temperature

Data-oriented scripts

• add_kink_points add linearly extrapolated points to kinky-looking 2-column data files
• average_variance_of_slope evaluate the average slope over slices of an extended 2-column data file (requires fit)
• fit: very handy to go through zillions of data files with linear fits
• fixmp3names.py: organize the filename of mp3 files to fit their tags in a regular format
• gauss_conv: convolve a spectrum with a Gaussian of given width
• histogram: generate the histogram of a 1-column data file
• integral: minimal effort to get some quick approximation to a 1D integration
• interpolate: simple linear interpolation of 2-column data file
• multifit: extracts a smoothed slope out of a "noisy" x-y data file
• peaks: extract all local maxima of a function (typically a spectrum, or a time series) given as a 2-column file
• primitive: brutal 1D integration to calculate the primitive function
• prunedata: cleunup pointlessly long data files with numerically nearly equal points
• replace string1 string2 file(s): does what its name promises... to any number of files!!
• running_average: evaluate a n-point running average of a 2-columns regularly-spaced data file
• scale: generate a sequence of equally-spaced numbers (very similar to the unix utility seq)
• spectrum visualizes a line spectrum out of a list of energies (rather primitive, but contains smart pieces of code, like the autoscale, better than a lot of professional software)
• squarediff computes the square difference of columns 2,3,... Useful (together with integral) e.g. to compare quantitatively 2 functions

Tools to analyze/manipulate .xyz files

• cut_cube_in_xyz: cut a x-y-z box, optionally specifying a time interval
• cut_sphere_in_xyz: as above, but for a sphere
• dat2xyz: generate a .xyz file from a 3-columns numeric text file
• xyz_1atom: extract the coordinates of 1 atom only (e.g. in order to plot its trajectory)
• xyz_bond_length: evaluate and report a specific bond length for all frames
• xyz_color_density: change atomic nature of atoms in regions where the local density is higher than a given threshold
• xyz_color_lattice: change atomic nature of atoms depending on their relation to a 2D (xy) periodic potential function of given lattice parameter
• xyz_color_property.py: change atomic nature of atoms depending on some property, either given as a (extra) column of the xyz file or computed as a function of x, y, z
• xyz_delete_atoms: remove a specific atom from an xyz file
• xyz_delete_close_atoms.py: in an xyz file, remove atoms which have accidentally bumped into each other, due to e.g. a merge of 2 xyz files, or to position randomization
• xyz_displacement: (i) evaluate displacements between successive frames or (ii) change atomic nature of atoms which move more than a given threshold
• xyz_first_last: keep only first and last frame
• xyz_gofr.py: evaluate the 2D or 3D g(r) correlation function averaging over all frames and taking a periodic box into consideration
• xyz_in_cell: translate all positions back into one arbitrary primitive cell (in a loose sense, the converse of xyz_lattice_translate)
• xyz_join.py: merge (frame by frame) two (or more) xyz files
• xyz_lattice_translate: replicate the atoms according to translations of a Bravais lattice
• xyz_mark_atom: change the chemical nature of one specific atom in an xyz file
• xyz_motion_enhance.py: amplify displacements (by a user-set factor) relative to the linear interpolation between the first and the last frame
• xyz_rotate.py: rigidly rotate an xyz file around an axis by an angle
• xyz_select_frame: choose 1 frame out of a loooong xyz file
• xyz_skip: keep only one frame every n and discard the rest
• xyz_sphere_density: evaluate the average number density in a sphere (circle) for particles given in an xyz file
• xyz_scattering_intensity.py: evaluate the (neutron scattering) structure factor S(q) for an array of Dirac deltas at the particles positions provided by an xyz file. To spare time, compute half q space. You can then use symmetrize_scattering_intensity.py to restore the missing half q space.
• xyz_statistics.py: generate statistical info
• xyz_stretch: generate an xyz file stretched by a factor (optionally in a given direction)
• xyz_structure_factor.py: evaluate the X-rays structure factor S(q) for atoms at the particles positions provided by an xyz file. Useful to compute the scattering intensity from a polyatomic cell, to be then multiplied by the Bragg pattern generated by xyz_scattering_intensity.py
• xyz_translate.py: translate rigidly an xyz file in any direction
• xyz_utils.py: a python library for reading/writing xyz files

File/shell-oriented scripts

• backup make a backup: to start it automatically every morning at 1:09, put a line in crontab (edit it by crontab -e) such as:
  9 1 * * 2-6 $HOME/bin/backup >> /tmp/backup.log 2>&1
• crop_pdf, crop a (1 page!) pdf figure, suppressing useless surrounding white bands
• del, sort of rm, but far safer...
• o: super quick file "open": opens arbitray file(s) and URL(s) with the correct application following the user's preferences for their specific media type
• rl: quick remote login (ssh -X), guess-completing the host name from past hints
• supergrep: search for simultaneous occurrence of several patterns in many files, and report the matching filenames
• swap, often better/safer than mv
• synchronizedisks. 2 PC's, e.g. a desktop and a laptop: make sure the same files are on both. Interactive (you control what you copy where). Based on rsync

Latex-oriented scripts

• accenti fix LaTeX accents according to Italian spelling rules
• convert2html quick & efficient for converting LaTeX into html; generate fairly clean and compact html; useful also for LaTeX to .doc/.docx conversion, since MS-Word / libreoffice can import html documents
• convertbiblio or the more refined convertbiblio.py: wanna use BibTeX to sort your \bibitem bibliography automatically, but never quite dared to put them in the horrible bibtex format?
• latexcontinuo: Happy LaTeXing in 3 windows: editor + okular (or evince or gv) + latexcontinuo (possibly minimized). Makes kile lyx and other refined tools unnecessary
• tabletex: n columns of data converted into a formatted LaTeX table, ready to be pasted into a document

Pictures/photography-oriented scripts

• arrange_photo a nifty tool to organize jpg pictures & avi/mpg movies into folders according to their EXIF data
• fix_eps_fonts occasional eps files come with funny fonts which do not display well once included into latex. This script manages to clear them and make them fully latex-compatible
• fix_jpg_tags use exiftool to retrieve and correct the exif data from another picture with the same initial part of the name (e.g. the raw file which originated a jpg picture)
• images2pdf use sam2p to convert (several) bitmapped images into individual pdf files plus one global pdf with one picture per page
• map_photo.py combine foxtrotgps and exiftool to replace or add geolocalization information to a picture with misplaced or lacking GPS-localization exif data
• squeeze_eps reduce the size of those huge eps files, using sam2p

Instructions for unix newbies

1. fire up a command-line terminal;
2. create the appropriate folder [mkdir $HOME/bin] (in case it already exist, no worry, you just get a harmless error message);
3. save the script "scriptname" in your bin, or save it wherever your browser wants. NB! never use cut&paste from the browser screen to download any script: use the browser "Save Page As..." menu command!
4. move it in your bin, e.g. [mv ~/Downloads/scriptname ~/bin];
5. let your computer know it is executable [chmod +x ~/bin/scriptname].

After your log out and log back in "scriptname" should become a legitimate command, exactly like ls or cp, and it should run regardless of the folder you are working in.
If it does not work, most likely your path needs fixing, typically by adding a line of instructions to your ~/.bashrc file. The simplest way to add this instruction is executing the command echo '\nPATH=$HOME/bin:$PATH' >> $HOME/.bashrc . (Please execute this command once only: repeated executions of this line produce a dumb sequence of contradictory lines at the end of "$HOME/.bashrc". In case you accidentally created them, please edit that file and delete all but one line PATH=$HOME/bin:$PATH.) After your next login your "scriptname" should execute fine from the command line.

Whenever it makes sense, these scripts throw their output to stdout, i.e. output appears in the terminal window. Their normal use is therefore
scriptname [options] inputfile [moreinputfiles] > outputfile
For example:
prunedata file_to_be_pruned.dat > pruned_file.dat

In case you forgot to redirect output with > and your terminal happens to be scrolling zillions of lines, then maybe you'd better press CTRL-C to kill execution, and repeat your command line with an appropriate redirection.

A note on redirecting output: command > somefile replaces whatever content was in somefile with the output of command. This may lead to the unwarned irreversible destruction of potentially precious data. If this makes you feel unsafe (it should!), then

1. backup regularly,
2. test scripts in folders where you keep no precious unduplicated data, and
3. think twice before pressing enter!

Comments / debugging / patches are welcome!