Utilities
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.
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| Last updated | 8 May 2007 |
| Download | cpi2recpot.tar.gz (13K)
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usp2upf
| Authors | Nicholas Hine |
| Description | The usp2upf utility is a pseudopotential converter that converts pseudopotentials generated by the CASTEP on-the-fly pseudopotential generator in the .usp format to .upf files to be read by the Quantum Espresso package Quantum Espresso.
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| Last updated | 5th Mar 2009 |
| Download | usp2upf.tar.gz (13K)
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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 | 06 Jul 2011 |
| Download | summarise (13K)
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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)
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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)
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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)
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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)
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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)
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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)
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utils
| Author | Jacek Dziedzic |
| Description | Various scripts and utilities.
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.
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.
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.
gaussian2dat -- Converts simple Gaussian input files to a .dat file. gaussian2pdb -- Converts simple Gaussian input files to a .pdb file.
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.
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.
out2pqr -- Reconstructs an input .pqr file given an .out file. unitconv -- Converts units. |
| Last updated | 31 Jan 2011 |
| Download | utils.tar.gz (4.9M)
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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.
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| Last updated | 3rd Feb 2011 |
| Download | vdw-opt.tar.gz (115K)
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