Utilities

Utility scripts and other resources for the ONETEP linear-scaling DFT code. Download this straight into the utils directory of your ONETEP installation.

Interpretation of ONETEP runs

• summarise: Makes a summary of an output produced with output_detail VERBOSE.

  Bash/awk script by Nicholas Hine. Extracts the results of the NGWF CG optimisation steps from an output file (which may still be running) and outputs them in a format as if you were running with output_detail BRIEF or looking at the calculation summary.

• geomconv: Helps investigate convergence indicators of ONETEP geometry optimisation.

  Bash/awk script by Nicholas Hine. Extracts the convergence indicators of a ONETEP BFGS geometry optimisation calculation from the output file, and compares them to the convergence tolerances. The results are coloured to indicate which parameters are converged and which are not.

  Note: This script needs another script to be present in your PATH: summarise.

• kern_vs_ngwf: Helps investigate convergence indicators of a ONETEP single point energy run.

  Bash/awk script by Nicholas Hine. Views the convergence of an ongoing ONETEP calculation, and displays various coloured indicators as to the convergence of the calculation. Examine the results to view decreases in energy, commutator, and ratio of optimisation energy gain from kernel and NGWF optimisation and spot common problems (requires some experience to use successfully).

• occ_check: Diagnoses any potential issues with occupancies.

  Bask/awk script by Jacek Dziedzic. Reads a ONETEP .out file and scans the final bandstructure output near the Fermi level to see if it follows the Aufbau principle, essentially reporting on any spurious electrons above the band gap. This is meant to be used only for insulating systems -- in metals we obviously expect non-fractional occupancies.

  Note: This script needs another script to be present in your PATH: getcol.

Format conversion

• dat2xsf: Converts .dat files for ONETEP into .xsf files for direct loading into xcrysden.

  Bash/awk script by Nicholas Hine. See the header of this script for detailed instructions.

• geom2xsf: Converts .geom or .md files produced by ONETEP into .xsf files for loading into xcrysden.

  Bash/awk script by Nicholas Hine. See the header of this script for detailed instructions.

• geom2xyz: Converts .geom or .md files from ONETEP or CASTEP into .xyz for animation in xmol.

  Perl script by Greg Pearce. This is from 2002 and no longer maintained. It might not function correctly in this day and age.

• dat2xyz: Converts the coordinates in a ONETEP .dat file to a .xyz file.

  See below, under 'Operations on input (.dat) files'.

• out2charge: Extracts atomic charges (Mulliken, NPA/NBO or DDEC) from a ONETEP .out file.

  Bash/awk script by Jacek Dziedzic. Extracts atomic charges (Mulliken, NPA/NBO or DDEC) from a ONETEP .out file. Additionally, if an .xyz file exists, it is used, together with the charges to generate a .vtf file that is readily understood by VMD and where 'Coloring method -> charge' simply works. This can be used to easily visualise any kinds of atomic charges in VMD.

  Bash/awk script by Jacek Dziedzic. Extracts atomic charges (Mulliken, NPA/NBO or DDEC) from a ONETEP .out file.

• pdb2dat: Creates a ONETEP input (.dat) file from a .pdb file.

  Bash/awk script by Jacek Dziedzic. Converts the coordinates and atom types from a .pdb file to a ONETEP input (.dat) file. ONETEP keywords to go into the .dat file are read from separate file -- pdb2dat.header, so that they can be changed without having to modify the script itself. If pdb2dat.header is absent, the script looks for it in the directory the script itself is located in. Box size and atom translation can be adjusted with the command line arguments. Run this script with no arguments for help.

• xyz2dat: Creates a ONETEP input (.dat) file from an .xyz file.

  Bash/awk script by Jacek Dziedzic. Converts the coordinates and atom types from a .xyz file to a ONETEP input (.dat) file. ONETEP keywords to go into the .dat file are read from separate file -- xyz2dat.header, so that they can be changed without having to modify the script itself. If xyz2dat.header is absent, the script looks for it in the directory the script itself is located in. Box size and atom translation can be adjusted with the command line arguments. Run this script with no arguments for help.

• usp2upf: Converts a pseudopotential in the CASTEP .usp form to unified pseudopotential format.

  Fortran program by PWSCF group. Distributed under the terms of the GNU General Public license.

Molecular dynamics

• md2thermo: Calculates thermodynamical quantities from a ONETEP .md file.

  Bash/awk script by Jacek Dziedzic. Can be used to process an MD trajectory (.md file) to get statistical information on energy conservation and temperature.

  Note: This script needs several other scripts to be present in your PATH. These are: getcol, getline, findmin, findmax, findavg, findrmsavg, findabsmax, findstddev, format_as, and linear_fit. These scripts are also provided here.

• md2vel: Extracts velocities from a ONETEP .md file.

  Bash/awk script by Jacek Dziedzic. Processes a .md trajectory file and extracts atomic velocities into a form compatible with a multi-frame .xyz file.

• md_clean_duplicates: Cleans up an .md trajectory from multiple restarts.

  Bash/awk script by Jacek Dziedzic. Reads an .md trajectory file, copying input to output, except for duplicate steps (those with identical times), which are removed. Only the first instance of any time is retained. This is useful for processing .md files combined from multiple runs, where global history has been used, leading to short time intervals present at the end of one run, and then again at the beginning of a restared run.

Manipulation of input (.dat) files

• dat2bounds: Shows information about the geometry of a ONETEP .dat file.

  Bask/awk script by Jacek Dziedzic. Shows information about the geometry of a ONETEP .dat file, including margins to box sides and recommended settings for cutoff Coulomb. This is a simple, limited script -- e.g. it only works for orthorhombic boxes, it expects the box to be specified in atomic units, not angstroem; it also assumes 7a0 NGWFs, but it's easy to manually correct the results.

• dat2xyz: Converts the coordinates in a ONETEP .dat file to an .xyz file.

  Bask/awk script by Jacek Dziedzic. Reads the %positions_abs and %lattice_cart blocks, and produces an .xyz file corresponding to the system defined by the .dat file. This is a simple, limited script -- e.g. it only works for orthorhombic boxes, it expects the box to be specified in atomic units, not angstroem.

  Note: This script needs another script to be present in your PATH: getcol.

• datcentre: Centres the system in a .dat file.

  Bash/awk script by Jacek Dziedzic. Translates all atoms in a .dat file to move the geometric centre of the system to the centre of the box. This is a simple, limited script -- e.g. it only works for orthorhombic boxes, it expects the box to be specified in atomic units, not angstroem.

  Note: This script needs another script to be present in your PATH: dat2bounds.

• datshift: Moves the system in a .dat file by an offset.

  Bash/awk script by Jacek Dziedzic. Translates all atoms in a .dat file by offsets specified separately for all Cartesian directions. Leaves the box unchanged. This is a simple, limited script -- e.g. it only works for orthorhombic boxes, it expects the box to be specified in atomic units, not angstroem.

Processing .cube and .dx scalarfield files

• edd_cube: Calculates the electron density difference between two .cube files.

  Fortran program by Max Phipps. Similar functionality, and more, is offered by dxsum.

• dx2cube: Converts a .dx file to a .cube file.

  C++ program by Jacek Dziedzic. Binary available on request from J.Dziedzic@soton.ac.uk. Converts data in a .dx file to a .cube file. Optionally reads a .dat file to extract also atomic positions to be included in the .cube file. Handles requisite unit conversions and sign convention changes automatically.

• dxaxpy: Computes a*x+y for data x in a .dx file, outputting results to a .dx file.

  C++ program by Jacek Dziedzic. Binary available on request from J.Dziedzic@soton.ac.uk. Provides an easy way to scale and shift the values in .dx files.

• dxchop: Zeroes values above or below a threshold in a .dx file.

  C++ program by Jacek Dziedzic. Binary available on request from J.Dziedzic@soton.ac.uk.

• dxcoarsen: Coarsens (keeps only every $n$-th point) in a .dx file.

  Bash/awk script by Jacek Dziedzic. Provides an easy way of making .dx files more lightweight should they prove to be too large to handle, e.g. by VMD. Typically used to reduce the resolution by a factor of 2 along every direction.

• dxgeom: Provides details about the geometry of a .dx file.

  Bash/awk script by Jacek Dziedzic.

• dxstats: Provides statistical information about data in a .dx file.

  Bash/awk script by Jacek Dziedzic. Prints the number of datapoints, min and max values, average, sum, sum of absolute values, average absolute value, sum of squares and the rms value. Useful for detecting anomalies in .dx files.

• dxintegrate: Integrates the quantity in a .dx file.

  C++ program by Jacek Dziedzic. Binary available on request from J.Dziedzic@soton.ac.uk.

• dxproduct: Multiplies data in two .dx files, producing a .dx file as output.

  C++ program by Jacek Dziedzic. Binary available on request from J.Dziedzic@soton.ac.uk. Computes y=a*x1*x2+b for data x1 in one .dx file and data x2 in another .dx file, with a and b being constants specified as arguments.

• dxsum: Adds data in two .dx files, producing a .dx file as output.

  C++ program by Jacek Dziedzic. Binary available on request from J.Dziedzic@soton.ac.uk. Computes y=a1**x1+a2*x2 for data x1 in one .dx file and data x2 in another .dx file, with a1 and a2 being constants specified as arguments. Note how with a1==1 and a2==-1 you can calculate differences.

• dxsection: Generates a 1D cross-section along one of the Cartesian directions of .dx file.

  Bash/awk script by Jacek Dziedzic. Generates a 1D cross-section along X, Y or Z from a .dx file. Very useful for producing plots.

  Note: This script needs dxserver to be present in your PATH.

DFTB

• dftb: Parameter files for the DFTB method.

QM/MM

• tinktep: Interface between ONETEP and TINKER.

  A set of bash scripts by Jacek Dziedzic. Allows for performing QM/MM calculations with ONETEP as the QM engine and TINKER as the MM engine. Supports GAFF and the AMOEBA polarisable force-field. Mutual polarisation between the QM and MM subsystems is possible. An example is included.

Other

• JTH_v1.0_PAW_datasets: PAW dataset library produced by the developers of ABINIT, converted to a format suitable for ONETEP.

  .tar.gz archives containing .abinit and .atompaw files.

• opium_recpots: A set of pseudopotentials for the most common elements, packaged by Keith Refson.

  .tar.gz archives containing .recpot files.

• devel_doc: Notes and documentation snippets relevant to developers, but not to users of ONETEP.

  .txt files with notes and documentation.

• DDEC_atomic_densities: Reference ion densities for DDEC3 (density derived electrostatic and chemical) charge analysis.

  .coreconf and .refconf files by Thomas Manz and Nidia Gabaldon Limas.

• vdW_params: Van der Waals parameters and a program for their determination for ONETEP's vdwcorrection module.

  Fortran source and data files by Quintin Hill.

• prep_optados_eels: Creates the files necessary to execute optados after a conduction run.

  Bash script by Nicholas Hine.

• 'ver': Shows details about ONETEP version.

  Bash script by Jacek Dziedzic.

• unitconv: Converts units.

  Bash/awk script by Jacek Dziedzic. Helps with unit conversion. Examples of use:

  What is the conversion factor from bohr to angstroem?

  unitconv distance_au distance_A

  How many rydbergs are there in a kcal/mol?

  unitconv energy_kcal_per_mol energy_ry

  How much is 2.5 debye in SI units (Cm)?*

  unitconv dipole_debye dipole_si :2.5

  Convert forces in forces.txt from a0/Ha to eV/A:

  unitconv force_au force_eV_over_A forces.txt

  For a list of supported quantities and units, run the script with no parameters.

Dependencies

Other scripts included here may depend on these being in your PATH. Put them there.

• linear_fit: Calculates a least-squares fit of f(x)=ax+b to XY, 2-column data.

  Returns a, b, their standard errors, and the regression coefficient.

• getcol: Returns the n-th column of a file.

• getline: Returns the n-th line of a file.

• findavg: Finds the average value of a column of numbers.

• findmax: Finds the maximum value of a column of numbers.

• findmin: Finds the minimum value of a column of numbers.

• findrmsavg: Finds the root-mean-square average of a column of numbers.

• findsstddev: Finds the standard deviation of a column of numbers.

• findabsmax: Finds the maximum absolute value of a column of numbers.

• format_as: Prints its argument in a given printf-like format.