jobclean | econv | getgeom | mol2inp | conf2xyz | xyz2conf
EaStCHEM Utilities User Guide
This page lists the utilities that are installed on the clusters. They generally automate common tasks encountered when using HPC facilities or computational chemistry software. They are automatically installed along with the EaStCHEM SSP.
jobclean
Tidies up the files left behind by the SGE queuing system. Make sure there is nothing important in them before deleting them!
jobclean <job_id>
Will delete the files ending in o<job_id>, e<job_id>, po<job_id> and/or pe<job_id> if they exist.
jobclean all
Will delete the above files with any <job_id>.
econv
Convert and compare energies. Can use raw energies or read them from electronic structure code output. Usage:
econv [options] energy [energy2]
The options are as follows:
- -u <unit>
Units for the input energy(ies). Valid names are hartree (a.u.), kjm (kJ/mol), kcalm (kcal/mol), wn (cm-1), ev (eV), joule (J), ghz (GHz), kelvin (K). The default input units are a.u. (hartree.)
- -d
- Compute an energy difference. This requires the input of two energies or electronic structure code output files.
- -c <code>
Read the energy(ies) from electronic structure code output. <code> can be one of g03 (Gaussian 03) or gam (GAMESS-UK).
- -f
- In combination with -c option, print the final energy from the output file. This is the default behaviour.
- -i
- In combination with -c option, print the initial energy from the output file.
- -n index
In combination with -c option, print energy #index from the output file.
- -a
- In combination with -c option, print all the energies from the output file in sequence. No energy conversions are performed.
- -help
- Show a quick summary of usage and exit.
For example, the command
econv 0.01234
would convert 0.01234 a.u. to all other energy units. To compute (and convert) an energy difference between two energies in kJ/mol would use something like:
econv -d -u kjm 123.456 124.567
To read (and convert) the final energy from a Gaussian 03 output file we would use:
econv -c g03 test.log
To get (and convert) the difference between the final energies from two GAMESS-UK calculations:
econv -c gam -d test1.out test2.out
getgeom
A utility for extracting geometries from electronic structure code output. Usage:
getgeom [options] input_file output_file
The options are as follows:
- -c <code>
Read the geometry(ies) from <code> which can be one of g03 (Gaussian 03) or gam (GAMESS-UK).
- -o <output format>
Specify the output format for the geometry. Can be one of xyz (XYZ format), g03 (Gaussian 03 input format) or gam (GAMESS-UK input format.) The default is xyz.
- -n <structure number>
Extract geometry number <structure number> from file with multiple structures in (e.g. a geometry optimization.)
- -i
- Get initial structure from file.
- -f
- Get final structure from file. Default behaviour.
- -a
Get all structures from file. Implies -o xyz as this is the only file type that can handle multiple structures.
- -help
- Show a quick summary of usage and exit.
For example
getgeom test.log test.xyz
would get the final geometry in the Gaussian 03 output test.log and save it in the XYZ file test.xyz. To get a geometry optimization sequence in a GAMESS-UK output file we would use:
getgeom -c gam -a test.out
mol2inp
Convert geometries from MOL files to input for electronic structure codes.
mol2inp [options] input_file output_file
The options are as follows:
- -o output format
Specify the output format for the geometry. Can be one of g03 (Gaussian 03 input format) or gam (GAMESS-UK input format.) The default is g03.
- -c calc_type
Specify the calculation type. Valid options are sp (single-point energy), opt (geometry optimization) or freq (geometry optimization followed by frequency calculation). Default is sp.
- -m method
- Specify the SCF calculation method. Default is RHF.
- -f functional
- Specify a DFT functional. This automatically changes the calculation method to DFT. No default.
- -b basis_set
- Specify the basis set to use. Default is 3-21G.
- -help
- Show a quick summary of usage and exit.
For example
mol2inp -o gam molecule.mol molecule.in
Take the geometry from molecule.mol and convert it to GAMESS-UK input in molecule.in for a single-point energy RHF calculation using the 3-21G basis set.
mol2inp -o g03 -c freq -f BLYP -b cc-pVTZ molecule.mol molecule.com
Take the geometry from molecule.mol and convert it to Gaussian 03 input in molecule.com for a DFT geometry optimization followed by a frequency calculation using the BLYP functional and cc-pVTZ basis set.
conf2xyz
Convert geometries from a DL_POLY CONFIG file to XYZ file format
conf2xyz < config_file > xyz_file
NB. As XYZ files contain no PBC information this is lost on conversion.
conf2xyz
Convert geometries from XYZ file format to a DL_POLY CONFIG file.
xyz2conf < xyz_file > config_file
NB. As XYZ files contain no PBC information this must be added to the CONFIG file manually.