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.
please use: actual -help
adds data group to control file.
E.g.: ’adg scfinstab ucis’ inserts:
$scfinstab ucis
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.
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!
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.
manages macro iterations for RI-MP2, RI-CC2 or RI-ADC(2) calculations in an equilibrated solvent environment described by cosmo(see Chapter 17.2).
plots energies as a function of SCF iteration number (gnuplot required).
sets up control file for a cosmo run (see Chapter 17.2).
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).
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.
displays orbital eigenvalues obtained from data group $scfmo. Shows HOMO-LUMO gap, occupation, checks if there are holes in the occupation, and much more.
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.
initialises the force constant matrix for the next statpt or relax step.
drives the Frozen Density Embedding calculations.
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.
converts IR intensities and/or VCD rotational strenghts to a spectrum after the corresponding calculation was performed. Intensities can be broadened with Gaussian or Lorentzian functions.
prepares the control file for a Hamilton core guess.
usage: see Section 5.1
is the TURBOMOLE driver for all kinds of optimizations.
usage: see jobbsse -h
is the driver for counterpoise corrected calculations.
example: kdg scfdiis
kills a data group (here $scfdiis) in the control file.
prepares for Localized Hartree-Fock calculations by adjusting parameters of the control file.
extracts the energy data (KE, total energy, PE) from an MD log file.
extracts bond lengths or angle from an MD log file.
computes the rotational constants and Ray’s kappa from an MD log file.
computes the radius of gyration, geometric radius and diameter from an MD log file.
converts the file logging an MD trajectory into coordinates in frames appropriate for jmol animation program.
interactive program to prepare for an MD run, checking in particular the mdmaster file (mdprep is actually a FORTRAN program).
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.
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.
prepares MP2 calculations interactively by adjusting parameters of the control file according to your system resources.
calculates numerically force constants, vibrational frequencies, and IR intensities. (Note that the name of the shell script is NumForce with capital F.)
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.
converts energies and oscillator strengths to a spectrum broadened by gaussian functions and/or calculates non-relaxed difference densities of excitations.
translates and rotates coordinates in the principal axis system and prints out the rotational constants.
calculates vibrational frequencies and Raman intensities. See Section 14.2 for explanation.
distorts a molecule along a vibrational mode.
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.
distorts a molecule along a vibrational mode or generates a plot of an IR spectrum (gnuplot required)
shows data group from control file:
for example sdg energy shows the list of calculated energies.
returns the name of your system, used in almost all TURBOMOLE scripts.
prepares the control file for a statistics run.
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).
Uses tm2molden as described below by automatically adding the
$aomix keyword to the control file.
is a versatile tool to create
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.
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.
is used to convert timings output files from TURBOBENCH calculations to LATEXtables (for options please type TBTIM –help).
is used to produce summaries of timings from TURBOBENCH calculations to LATEXformat. (for options please type TBLIST –help).
deprecated command, present in the current version for compatibility
reasons only.
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.
calculates VCD rotational strengths. See Section 14.3 for explanation.
optimizes a reaction path with woelfling.
For further information please type woelfling-job -h.