Quantum Chemistry Software

This section will give a short introduction and an overview of the Quantum Chemistry programs that will be used in this practical course.

Setting up the Software

In order to gain access to the needed software packages, you need to make some changes to your system. The .bashrc file located in your home directory is sourced every time you open a new shell. While you can directly execute any program by giving the full path, it is more convenient to tell the system where to look for the binaries by saving the location in the $PATH variable. Additionally, some programs need global variables. All those are usually set in the .bashrc. In order to gain access to all the needed software, add the following lines to your .bashrc:

# make environment modules available
export BASH_ENV=/usr/share/lmod/lmod/init/bash
. ${BASH_ENV} > /dev/null

module use /home/abt-grimme/modulefiles
module load turbomole orca
alias molden='/software/bin/molden'

# AKbin
export PATH=/home/abt-grimme/AK-bin:$PATH
export PATH=/home/$USER/bin:$PATH

# XTB
export OMP_NUM_THREADS=2
export MKL_NUM_THREADS=2
export OMP_STACKSIZE=500m
ulimit -s unlimited

Be sure to create a directory called bin in your home directory by typing:

mkdir ~/bin

Important

All changes apply to shells opened afterwards.

If you want to apply the changes to your current shell, you need to run:

source ~/.bashrc

Program Packages

TURBOMOLE

To run a basic calculation with TURBOMOLE, you will only need the following two files:

• coord: Molecular geometry in atomic units

• control: All data required for the calculation (method, parameters, … )

For more sophisticated calculation settings, TURBOMOLE provides an interactive input generator called define which only needs the coord file to create the control file. Basis set and orbital files, that are also necessary for the calculation, are created during the calculation or by define, respectively. These are:

• basis (and auxbasis): Basis set (and auxiliary basis set for RI)

• mos or alpha and beta: Orbitals (MO coefficients) for restricted and unrestricted treatment, respectively

In this course, all calculations can be prepared manually by only providing a coord and a control file containing all the necessary information.

TURBOMOLE has different binaries and scripts for different jobs. While they do not need an explicit input file when called, you should always pipe the output into a file, e.g.:

ridft > ridft.out &

The most important scripts that come along with the TURBOMOLE program package are listed in the following table.

TURBOMOLE script	Functionality
Most important scripts for calculations
ridft	DFT and HF SCF calculations with the RI-approximation
dscf	DFT and HF SCF calculations without the RI-approximation
ricc2	Module for second-order correlated WF methods (MP2, CC2)
ccsdf12	Module for coupled cluster methods (CCSD, CCSD(T), …)
rdgrad, grad	Calculate gradients (with and without RI)
aoforce	Calculate analytical vibrational frequencies
statpt	Coordinate/Hessian update for stationary point searches
jobex	Script for geometry optimizations
Scripts for visualization purposes
eiger	Show the orbital energies and the HOMO-LUMO gap
x2t	Convert a *.xyz (in Å) file to coord (in bohr)
t2x	Convert a coord (in bohr) file to *.xyz (in Å)
tm2molden	Generate a molden input

Important

Each TURBOMOLE calculation needs its own directory.

The control file

While coord stores the molecular geometry, the control file contains all the specifications and settings for the desired calculation. It contains keywords indicated with a $ symbol followed by some setting. Related specifications sometimes follow in the next line and are indented. Every control file must end with the $end keyword in the last line. An example input for a simple DFT calculation on the BLYP/def2-TZVP level of theory can look as follows:

$coord file=coord
$atoms
  basis = def2-TZVP
$dft
  functional b-lyp
$end

In the following exercises, some proper TURBOMOLE input will always be given (at least partially) in the text. Additionally, you can find a short list of all keywords needed in this course in the Keywords in control section below.

ORCA

ORCA needs an input file (e.g. myinput.inp) to run. A typical call to perform a calculation with ORCA would be

orca myinput.inp > myinput.out &

The input file is generally structured as follows:

# Comment lines are marked with an '#' and are possible everywhere
! Method Basis and further options

# Input is organized in blocks which start with '%'
# e.g.
%scf
        MaxIter 150 #maximum number of iteration steps in the scf,
                    #default = 50
end
# definition of input geometry
* xyz <charge> <multiplicity>
        cartesian coordinates (Angstroms)
*
or:
* int <charge> <multiplicity>
        Z-Matrix
*
or:
* xyzfile <charge> <multiplicity> <filename.xyz>

Important

Multiplicity = 2S+1 with S being the total spin.

A short reference of ORCA keywords can be found in the section Short ORCA Reference. Further information is accessible from: https://sites.google.com/site/orcainputlibrary/.

Keywords in control

The control file contains all specifications and settings for a calculation with TURBOMOLE. Keywords start with $ and sub-settings are indented. The last line of the file must always be $end. The following table shows the most important keywords that are interesting for this course.

Command	Functionality
essential for all calculations
$coord file=coord	Defines the coord file to be the one containing the molecular structure information.
$atoms basis=<bas>	Defines the basis set for the calculation to be <bas>.
always recommended
$eht charge=<chrg> unpaired=<uhf>	Defines the charge <chrg> and the number of unpaired electrons <uhf> for the extended Hückel guess and the entire rest of the calculation.
$symmetry <sym>	Use the symmetry of pointgroup <sym>. If not stated otherwise, in the scope of this course it is always recommended to use C1 symmetry to avoid technical issues (choose c1).
$rij	Use the resolution of the identity (RI) approximation. Note that you then have to use ridft for single-point calculations and the -ri option for jobex. We recommend using the RI approximation for all exercises in this course.
$energy file=energy $grad file=gradient	For geometry optimizations: The energies and gradient of all optimization cycles will be saved in the files energy and gradient.
DFT calculations
$dft functional <func> grid <grid>	Perform a DFT calculation using the functional <func>. Note that the BYLP, B3YLP and B2PLYP functionals are named b-lyp, b3-lyp and b2-plyp, respectively. Define the integration grid <grid> (optional, the default is m4). For double-hybrid functionals, also include the settings for MP2 calculations listed below ($ricc2 and $denconv blocks).
$disp3 -bj	Use the D3 dispersion correction with Becke-Johnson damping.
Note If the $dft block is missing, a HF calculation will be performed.
Post HF calculations
$scfconv 7 $denconv 1.0d-7	For MP2 and CC calculations, a well-converged SCF run is needed. Therefore, set the convergence threshold of the SCF and the density matrix to \(10^{-7}\) or less.
$ricc2 mp2 geoopt model=mp2	Perform an MP2 single-point calculation. The geoopt model=mp2 keyword is only necessary if a geometry optimization on the MP2 level is desired.
$ricc2 ccsd(t)	Perform a CCSD(T) single-point calculation.
other settings
$cosmo epsilon=<epsilon>	Use the condctor like screening model COSMO with the dielectric constant <epsilon> of the solvent.
$scfiterlimit <limit>	Defines the maximum number of iterations in an SCF calculation (default <limit> is 30). If an SCF did not converge, try increasing this value, e.g. to 100.
$statpt itrvec <imag>	Specify the number of imaginary vibrational frequencies <imag> that shall be obtained by a geometry optimization (default is itrvec 0 for minimum structures). Set to itrvec 1 for transition state optimizations.

Short ORCA Reference

You can find a rough summary of the most important ORCA keywords in the following table. For a complete reference, consult the manual at https://orcaforum.kofo.mpg.de/.

Keyword	Explanation
RHF	Restricted Hartree-Fock
UHF	Unrestricted Hartree-Fock
TPSS	DFT with the functional TPSS (can be any valid functional)
MP2	Do an MP2 calculation.
CCSD(T)	Do a CCSD(T) calculation.
TZVP	Use a TZVP basis. Can be any valid basis set definition
Opt	Do a geometry optimization.
RI	Use the resolution of the identity approximation.
NumFreq	Calculate second derivatives (vibrational frequencies). Also gives an IR spectrum and thermal corrections + ZPE.
NMR	Calculate nuclear magnetic shielding tensors.
TightSCF	Increases the convergence criterion for the SCF.