TURBOMOLE manual
v8.0

1.7 Tools

Note: these tools are very helpful and meaningful for many features of TURBOMOLE.

This is a brief description of additional TURBOMOLE tools. Further information will be available by running the programs with the argument -help.

actual

please use: actual -help

adg

adds data group to control file.
E.g.: ’adg scfinstab ucis’ inserts:
$scfinstab ucis

aoforce2g98

usage: aoforce2g98 aoforce.out > g98.out
converts output from the aoforce program to Gaussian 98 style, which can be interpreted by some molecular viewer (e.g. jmol) to animate the normal coordinates.

bend

example: bend 1 2 3
displays the bending angle of three atoms specified by their number from the control file. Note that unlike in the TURBOMOLE definition of internal coordinates the apex atom is the second!

calcgtens.py

assembles the full g-tensor from three non-collinear two-component calculations, see chapter 18 for usage.

calchfc.py

assembles the full electron-nucleus hyperfine coupling tensor from three non-collinear two-component calculations, see chapter 18 for usage.

cbasopt

optimize auxiliary basis sets for RI-MP2 and RI-CC2 calculations. Uses ricc2 to calculate the error functional and its gradient and relax as optimization module. For further details call cbasopt -h.

cc2cosmo

manages macro iterations for RI-MP2, RI-CC2 or RI-ADC(2) calculations in an equilibrated solvent environment described by cosmo(see Chapter 21.2).

cgnce

plots energies as a function of SCF iteration number (gnuplot required).

cosmoprep

sets up control file for a cosmo run (see Chapter 21.2).

cpt

The Color Prediction Tool predicts color for calculated and measured spectra. Simply type cpt in the directory of a finished TD-DFT calculation to obtain absorption and emission colors within a linear color approximation. However note that cpt is a standalone tool and not strictly bound to TURBOMOLE. It may be used with data obtained from various theoretical programs as well as experimental data by reading in simple ASCII files. A detailed list of functionality is obtained from cpt --help.

dist

example: dist 1 2
calculates atomic distances from TURBOMOLE input files; dist -l 4 gives all interatomic distances to 4 a.u. (5 a.u. is the default).

DRC

automates dynamic reaction coordinate calculations forward and backward along the imaginary vibrational mode of a transition state structure. A transition state optimization with a subsequent frequency calculation is prerequisite.
For further details call DRC -h.

eiger

displays orbital eigenvalues obtained from data group $scfmo. Shows HOMO-LUMO gap, occupation, checks if there are holes in the occupation, and much more.

epreuler.py

calculates the Euler transformations for EPR properties from two-component calculations, see chapter 18 for usage.

evalgrad

reads the gradient file and prints the energies of each cycle versus bond lengths or angles. Five operational modes are possible:
evalgrad             prints the energy.
evalgrad 1          prints the coordinate of atom 1.
evalgrad 1 2       prints the distance between atoms 1 and 2.
evalgrad 1 2 3    prints the bending angle as defined in Bend.
evalgrad 1 2 3 4 prints the torsional angle as defined in Tors.

file2control

This script copies the content of external data groups (file=) into the control file. If $file2control is found, the process is reverted.

finit

initialises the force constant matrix for the next statpt or relax step.

FDE

drives the Frozen Density Embedding calculations.

Fukui

automates the calculations of Fukui functions. The density change is written in dtx files and condensed Fukui functions based on different population analyses are computed.
For further details call Fukui -h.

gallier

converts IR intensities and/or VCD rotational strengths to a spectrum after the corresponding calculation was performed. Intensities can be broadened with Gaussian or Lorentzian functions.

hcore

prepares the control file for a Hamilton core guess.

hfcprep.sh

prepares the input for the non-collinear two-component calculations to evaluate the electron-nucleus hyperfine coupling tensor, see chapter 18 or hfcprep.sh -h for usage.

gtensprep.sh

prepares the input for the non-collinear two-component calculations to evaluate the electron-nucleus hyperfine coupling tensor, see chapter 18 or gtensprep.sh -h for usage.

geohist.pl

can be used with the geometry keywords such as dist to check the history of a given geometry parameter during a structure optimization.

jobex

usage: see Section 5.1
is the TURBOMOLE driver for all kinds of optimizations.

jobbsse

usage: see jobbsse -h
is the driver for counterpoise corrected calculations.

kdg

example: kdg scfdiis
kills a data group (here $scfdiis) in the control file.

lhfprep

prepares for Localized Hartree-Fock calculations by adjusting parameters of the control file.

log2x

converts the file logging an MD trajectory into coordinates in frames appropriate for jmol animation program.

log2egy

extracts the energy data (KE, total energy, PE) from an MD log file.

log2int

extracts bond lengths or angle from an MD log file.

log2rog

computes the radius of gyration, geometric radius and diameter from an MD log file.

mdprep

interactive program to prepare for an MD run, checking in particular the mdmaster file (mdprep is actually a FORTRAN program).

MECPprep

prepares the input for minimum-energy crossing point calculations. The subdirectories state1 and state2 will be created. Multiplicity and charge for the two states can be set.
For further details call MECPprep -h.

MECPopt

driver for geometry optimizations of minimum-energy crossing points. The electronic structure calculations are carried out in the subdirectories state1 and state2 and the optimizer step is performed in the starting directory.
For further details call MECPopt -h.

mos2html

a Python3 script which generates a single, self-contained HTML file for interactively visualizing molecular orbitals (MOs). It automates the process of generating cube files for specified MOs and embeds them, along with a 3D viewer, into a HTML document.

mp2prep

prepares MP2 calculations interactively by adjusting parameters of the control file according to your system resources.

NumForce

calculates numerically force constants, vibrational frequencies, and IR intensities. (Note that the name of the shell script is NumForce with capital F.)

outp

example: outp 1 2 3 4
displays the out-of-plan angle between atom1 and the plane that is defined by the last three atoms. atom1 is fixed at atom4.

panama

converts energies and oscillator strengths to a spectrum broadened by Gaussian functions and/or calculates non-relaxed difference densities of excitations.

past

translates and rotates coordinates in the principal axis system and prints out the rotational constants.

raman

calculates vibrational frequencies and Raman intensities. See Section 15.2 for explanation.

redox

automates the calculation of reduction/oxidation potentials functions w.r.t. the standard hydrogen electrode by computing the electron affinities/ionization energies in the gas phase and Gibbs free energy of solvation with DCOSMO-RS. As a side product electron reorganisation energies are printed.
For further details call redox -h.

r2u

converts a closed-shell occupation of the control file to an unrestricted HF/KS input.

scanprep

prepares a series of control files with frozen internal coordinates. The data group $constraints (e.g. provided by TmoleX) is evaluated.
For further details call scanprep -h.

screwer

distorts a molecule along a vibrational mode.

sdg

shows data group from control file:
for example sdg energy shows the list of calculated energies.

similaritycheck

checks the similarity of two structures. For further details call similaritycheck -h.

stati

prepares the control file for a statistics run (obsolete).

sysname

returns the name of your system, used in almost all TURBOMOLE scripts.

u2r

converts UHF/UKS with the same number of alpha and beta electrons to an RHF/RKS input.

t2x

converts TURBOMOLE coordinates to xyz format.

t2aomix

creates an input file for the AOMix program. AOMix is a software the analysis of molecular orbitals. For more information
see: (http://www.sg-chem.net/aomix).
Uses tm2molden as described below by automatically adding the $aomix keyword to the control file.

tm2molden

is a versatile tool to create

  • molden format input file for the Molden program,

  • AOMix input files or

  • detailed information about the largest AO contributions to the MOs.

Molden is a graphical interface for displaying the molecular density, MOs, normal modes, and reaction paths. For more information about molden see: http://www.cmbi.ru.nl/molden/molden.html.
This format is also often used as input for other program packages or property tools.
NOTE: The default normalization of molecular orbitals of d-type (and beyond) when using tm2molden is different to what Molden expects. To generate Molden input files with the Molden-own normalization, please call tm2molden norm, the default name of the resulting file will be molden_std.input rather than molden.input.
If tm2molden finds the keyword $aomix in the control file, it will write out an AOMix input file, see: http://www.sg-chem.net/aomix
Finally, tm2molden can be used to print out the largest contributions of the AO basis functions to the molecular orbitals.
Usage:
tm2molden mostat [molist] [above <threshold>]
e.g.:
tm2molden mostat 230-240,251,255
tm2molden mostat 434-440 above 0.001
tm2molden mostat above 0.02
Only contributions which are larger than a certain percentage (default is 1%) are printed, this value can be changed with the above option (as absolute value, so 1% is 0.01). Without a list of orbitals (the numbering follows the output of eiger) all MOs are printed.

tors

is a script to query a dihedral angle in a molecular structure:
e.g. tors 1 2 3 4 gives the torsional angle of atom 4 out of the plane of atoms 1, 2 and 3.

tbtim

is used to convert timings output files from Turbobench calculations to LaTeX tables (for options please type TBTIM --help).

tblist

is used to produce summaries of timings from Turbobench calculations to LaTeXformat. (for options please type TBLIST --help).

vcd

calculates VCD rotational strengths. See Section 15.3 for explanation.

vibration

distorts a molecule along a vibrational mode or generates a plot of an IR spectrum (gnuplot required)

woelfling-job

optimizes a reaction path with woelfling. 
For further information please type woelfling-job -h.

x2t

converts standard xyz files into TURBOMOLE coordinates.