Reference files

Atomic Densities for DDEC

Authors Thomas Manz and Nidia Gabaldon Limas
Description Reference ion densities for DDEC3 (density derived electrostatic and chemical) charge analysis.
Last updated 3 June 2015
Download ddec_atomic_densities.tar.gz (912K)

Utilities

onetep_launcher

Authors Jacek Dziedzic
Description This utility makes it easier to launch ONETEP for new users. It takes care of stack sizes, number of OMP threads and some workarounds for defective computational environments. Run this script with no arguments to get help on syntax.
Last updated 30 August 2017
Download onetep_launcher (28K)

cpi2recpot

Authors Peter Haynes & Keith Refson
Description ONETEP uses norm-conserving pseudopotentials in the .recpot format used by CASTEP. The cpi2recpot utility converts pseudopotentials generated by the fhi98PP program in .cpi format to the .recpot format.
Last updated 8 May 2007
Download cpi2recpot.tar.gz (13K)

Scripts

summarise

Author Nicholas Hine
Description 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.
Last updated 29 Aug 2019
Download summarise (13K)

geomconv

Author Nicholas Hine
Description 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.
Last updated 12 Apr 2010
Download geomconv (13K)

kern_vs_ngwf

Author Nicholas Hine
Description 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).
Last updated 12 Apr 2010
Download kern_vs_ngwf (13K)

geom2xyz

Author Greg Pearce
Description Converts .geom or .md files produced by ONETEP into .xyz files for animation in jmol, xcrysden or other visualisers
Last updated 26 Apr 2011
Download geom2xyz (13K)

geom2xsf

Author Nick Hine
Description Converts .geom or .md files produced by ONETEP into .xsf files for xcrysden (see instructions in header)
Last updated 18 Feb 2013
Download geom2xsf (13K)

dat2xsf

Author Nick Hine
Description Converts .dat files for ONETEP into .xsf files for direct loading into xcrysden (see instructions in header)
Last updated 18 Feb 2013
Download dat2xsf (13K)

md2thermo

Author Jacek Dziedzic
Description Reads an .md file produced by ONETEP and displays statistics on temperature, energy, energy conservation. Comes bundled with several auxiliary scripts -- make sure these are in the PATH or in the same directory where md2thermo resides.
Last updated 27 Oct 2011
Download md2thermo.tar.gz (3.5K)

utils

Author Jacek Dziedzic
Description Various scripts and utilities.


Manipulation of .cube files


cube2charge -- Computes the integral of the charge in a .cube file.

cube2dx -- Converts a .cube file to a .dx file. Allows for unit conversion.

cube_wrapper -- Adds an extra layer of gridpoints to a .cube file, realizing PBCs.

cubechop -- Chops (zeroes) value below a certain threshold in a .cube file.


Manipulation of .dx files


dxaxpy -- Performs y = a*x + b, reading x from a .dx file, writing y to a .dx file, a and b are scalars.

dxproduct -- Performs y = a*x1*x2 + b, reading x1 and x2 from .dx files, writing y to a .dx file, a and b are scalars.

dxsum -- Performs y = a1*x1 + a2*x2, reading x1 and x2 from .dx files, writing y to a .dx file, a1 and a2 are scalars.

dxintegrate -- Computes the integral of a quantity in a .dx file.

dxgeom -- Provides details about a geometry of a .dx file.

dxstats -- Provides statistical information for data in a .dx file.

dxgetpart -- Extracts cuboid subsets or supersets from a .dx file.

dxchop -- Chops (zeroes) value below/above a certain threshold in a .dx file.

dxserver -- Serves requested datapoints from a .dx file.

dxcoarsen -- Reduced the resolution of a .dx file.


Manipulation of .pdb files


pdb2box -- Computes the bounding box of a .pdb file.

pdb2dat -- Converts a .pdb file to a .dat file.

pdbstrip -- Strips a desired species or residue from a .pdb file.

pdbtranslate -- Translates atoms in a .pdb file.


Manipulation of Gaussian input files


gaussian2dat -- Converts simple Gaussian input files to a .dat file.

gaussian2pdb -- Converts simple Gaussian input files to a .pdb file.


Manipulation of ONETEP .dat files


dat2bounds -- Calculates the widths (between cores and NGWFs) of a .dat file.

datshift -- Shifts coordinates of all atoms in a .dat file, leaving the box unchanged.

datcentre -- Shifts coordinates of all atoms in a .dat file to align the geometric centre of the molecule with that of the box, leaving the box unchanged.


Energies from ONETEP runs


dE_binding -- Calculates the binding energy given .out files for a complex, host and ligand.

dG_solvation -- Calculates the free energy of solvation given .out files for in-solvent and in-vacuum.

getenergy -- Extracts the converged energy (or any of its components) given an .out file.


Other utilities


out2pqr -- Reconstructs an input .pqr file given an .out file.

unitconv -- Converts units.

Last updated 17 Sep 2015
Download utils.tar.gz (4.9M)

vdw-opt

Authors Quintin Hill
Description This archive contains the source for the optcorrection program which can be used to obtain optimised dispersion (vdw) parameters for use with ONETEP. The optimisation procedure implemented in this program was described in the paper Proc. R. Soc. A 465 2103 (2009), pp. 669-683. Input files needed by the program are also provided in the archive.
Last updated 3rd Feb 2011
Download vdw-opt.tar.gz (115K)

ONETEPConv

Authors Ben Lowe
Description A set of scripts has been made available which assists

in the task of generating convergence testing data by automating convergence-test input file generation.

Last updated 31st March 2015

alphahull

Authors Jolyon Aarons
Description This archive contains the source for the alphahull program which can be used to apply the catalytic descriptor which we describe in Aarons, J., Jones, L., Varambhia, A., MacArthur, K.E., Ozkaya, D., Sarwar, M., Skylaris, C.K. and Nellist, P.D., 2017. Predicting the oxygen-binding properties of platinum nanoparticle ensembles by combining high-precision electron microscopy and density functional theory. Nano Letters, 17(7), pp.4003-4012. An example nanoparticle is included together with useful Matlab scripts
Last updated 12th Oct 2017
Download alphahull_1.tgz (27K)
Page last modified on August 29, 2019, at 09:29 AM