Setup and QC Software

This section will give a short introduction and an overview of the general Linux setup, as well as Quantum Chemistry programs that will be used in this practical course.

Contents

• Setup and QC Software

  • Creating your working environment

    • Program Packages

    • General Setup

    • COSMOtherm

    • GFN-xTB

  • Specific usage instructions

    • GFN-xTB

    • Calculating the k-Grid

Creating your working environment

Program Packages

The following programs are going to be used:

program	executable
PSI4	psi4
TURBOMOLE 7.6	ridft, ricc2
COSMOtherm	cosmosolv_prak (script that calls COSMOtherm)
CRYSTAL14	crystal_interface
VASP5.4	used via crystal interface
DFTB3	used via crystal interface
xTB (WP12 version)	xtb_prak
gCP	gcp
DFTD3	dftd3

For the usage of these programs, you can take a look at the respective manuals or (in most cases) use the -h option.

Hint

You can also find some additional information about TURBOMOLE in our QC II script.

General Setup

The file .bashrc is a configuration file loaded every time a terminal is opened. The .bashrc is designed to generally set the PATH variable or add scripts that can facilitate working in the terminal. You can find further information in the Ubuntu wiki.

To be able to use a program, the system needs to know where to find it. You can achieve this by modifying the PATH environment variable via the .bashrc in your /home/$USER/ directory. Most of the executables we need are in the /home/abt-grimme/AK-bin/ directory. For the usage of PSI4, the respective conda environment has to be activated. The .bashrc should look like the following and can also be found in the config directory in the WP12 GitHub Repository (if it does not exist, create it):

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

# TURBOMOLE.7.6
export TURBODIR=/home/abt-grimme/TURBOMOLE.7.6/
source $TURBODIR/Config_turbo_env

#PSI4
. /software/psi4conda/etc/profile.d/conda.sh
conda activate
PSIS=/tmp1/$USER/.psi4_tmp
if [ ! -e $PSIS ]; then
   mkdir $PSIS
fi
export PSI_SCRATCH=$PSIS

# VASP5.4
export PATH=/home/abt-grimme/AK-bin/vasp/bin:$PATH

# CRYSTAL14
export PATH=/home/abt-grimme/crystal/14:$PATH

# COSMORS
export PATH=/opt/COSMOlogic/COSMOthermX16/COSMOtherm/BIN-LINUX/:$PATH

# MPICH2
export LD_LIBRARY_PATH=/home/abt-grimme/mpich2/lib:$LD_LIBRARY_PATH
export PATH=/home/abt-grimme/mpich2/bin:$PATH

#xTB
export OMP_NUM_THREADS=4
export MKL_NUM_THREADS=4
ulimit -s unlimited
export OMP_STACKSIZE=1000m

Important

Changes only apply to shells opened after changing your .bashrc.

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

source ~/.bashrc

COSMOtherm

The cosmosolv script needs the .cosmothermrc file in which parameters for the solvents are specified. The .comsothermrc you will need is as follows:

ctd =BP_TZVP_C30_1601.ctd cdir = /opt/COSMOlogic/COSMOthermX16/COSMOtherm/CTDATA-FILES
EFILE VPFILE
f = toluene.cosmo fdir=/opt/COSMOlogic/COSMOthermX16/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO autoc
f = out.ccf
henry xh={ 1.0 0.0 } tc=-50.0 Gsolv
henry xh={ 1.0 0.0 } tc=-10.0 Gsolv
henry xh={ 1.0 0.0 } tc=0.0 Gsolv
henry xh={ 1.0 0.0 } tc=10.0 Gsolv
henry xh={ 1.0 0.0 } tc=20.0 Gsolv
henry xh={ 1.0 0.0 } tc=25.0 Gsolv
henry xh={ 1.0 0.0 } tc=30.0 Gsolv
henry xh={ 1.0 0.0 } tc=40.0 Gsolv
henry xh={ 1.0 0.0 } tc=50.0 Gsolv
henry xh={ 1.0 0.0 } tc=60.0 Gsolv

Create this file in your /home/$USER/ directory.

Hint

This is a general input file for the COSMOtherm program. The cosmosolv copies this file as an input for your calculation. If you are interested, you can find further information about COSMOtherm input files in the COSMOtherm manual.

GFN-xTB

First, make sure that the xtb_prak program is in your PATH variable. You can test this with the command

which xtb_prak

This shows the path to the program. If everything was set up correctly it should in our case show the path

/home/abt-grimme/AK-bin/xtb_prak

If this doesn’t show up check the PATH setup again.

Add the following to the .bashrc :

export OMP_NUM_THREADS=4
export MKL_NUM_THREADS=4
ulimit -s unlimited
export OMP_STACKSIZE=1000m

This sets up GFN-xTB correctly and sources the parameter files.

Specific usage instructions

GFN-xTB

GFN-xTB can be called by:

xtb_prak <coord_input> [options]

where <coord_input> is a valid file of TM or Xmol format.

In exercise 2.3 you need to first optimize a structure and then calculate the second derivatives to get the vibrational contributions in the rigid-rotor-harmonic-oscillator model.

You can do that, by using the following options:

--opt : structure optimization at the GFN2-xTB level,

--hess : compute Hessian at the GFN2-xTB level (second derivatives) or

--ohess : do both with one command.

Please note that after the optimization the input structure, e.g., the coord file is not overwritten and will be on the file xtbopt.coord. You will have to use this file for the calculation of the Hessian.

Calculating the k-Grid

To set the k points the SHRINK block has to be modified in the input file. The k points are calculated differently depending on whether CRYSTAL or VASP is used.

\[\begin{split}VASP: \ \ \ \kappa_{ij} = \frac{2i-s_j-1}{2s_j} \\\\ CRYSTAL: \ \ \ \kappa_{ij} = \frac{2i-s_j}{2s_j}\end{split}\]

where s_j are the shrinking factors in reciprocal space. Further information is given in the lecture (solid state part).

You can calculate the shrinking parameter based on the k-point density ρ_k [Bohr^-1] and the unit cell vectors a ⃗₁ , a ⃗₂ and a ⃗₃ (e.g. taken from the fort.34 file):

\[s_i \approx \frac{1}{|\vec{a}_i|*\rho_\kappa}\]

where s_i are the corresponding dimensionless SHRINK parameter, rounded to the next non-zero integer. Note that the a ⃗_i in fort.34 are in Ångström. When converting a .cif file with cif2crystal you will receive the k-mesh density and the SHRINK parameters corrsponding to the structure automatically.