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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.
cgnce
plots energies as a function of SCF iteration number (gnuplot required).
cosmoprep
sets up control file for a cosmo run (see Chapter 16).
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 (RHF only).
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.
mdprep
interactive program to prepare for an MD run, checking in particular the mdmaster file (mdprep is actually a FORTRAN program).
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.
raman
calculates vibrational frequencies and Raman intensities. See Section 12.2 for explanation.
screwer
distorts a molecule along a vibrational mode.
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: (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: (MOLDEN).
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).
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.
x2t
converts standard xyz files into TURBOMOLE coordinates.


next up previous contents index
Next: Installation of TURBOMOLE Up: Preface and General Information Previous: Modules and Their Functionality   Contents   Index
TURBOMOLE