1.5 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

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!

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 equilibriated solvent environment described by cosmo(see Chapter 19).

cgnce

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

cosmoprep

sets up control file for a cosmo run (see Chapter 19).

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.

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.

FDE

drives the Frozen Density Embedding calculations.

hcore

prepares the control file for a Hamilton core guess.

jobex

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

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.

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.

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.

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 13.2 for explanation.

screwer

distorts a molecule along a vibrational mode.

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.

vibration

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

sdg

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

sysname

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

stati

prepares the control file for a statistics run.

t2x

converts TURBOMOLE coordinates to xyz format.

tm2aomix

creates an input file for the AOMix program. AOMix a software the analysis of molecular orbitals. For more information
see: (http://www.sg-chem.net/aomix).

tm2molden

creates a molden format input file for the Molden program. 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).

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 LATEXtables (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).

uhfuse

transforms the UHF MOs from a given symmetry to another symmetry, which is C1 by default (just enter uhfuse). but can be specified (e.g. as C2v) by entering uhfuse -s c2v. Now this functionality is included in the MO definition menu of define program, see Section 4.3.1.

woelfling-job

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

x2t

converts standard xyz files into TURBOMOLE coordinates.