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.

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. The .bashrc covers the main setup of the PSI4, VASP, CRYSTAL, and COSMO-RS software as well as the configuration of thread usage and memory limits so these programs run with a fixed number of CPU threads and enough stack space to avoid crashes. Additonally, 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):

#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

# make modules available
. ${BASH_ENV} > /dev/null

# 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/COSMOthermX19/COSMOtherm/BIN-LINUX/:$PATH

# Set thread counts and use a larger stack
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 .cosmothermrc you will need is as follows:

ctd = BP_TZVP_19.ctd cdir = "/opt/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/opt/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
EFILE VPFILE
f = toluene.cosmo fdir=/opt/COSMOlogic/COSMOthermX19/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, gCP, TURBOMOLE, and DFTD3

GFN-xTB, gCP, TURBOMOLE, and DFTD3 can be made available via the following commands.

module load xtb/prak

module load gcp

module load turbomole

module load dftd3

Please make sure to have these lines added to your .bashrc :

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

As mentioned above, these lines make the programs use a set number of CPU threads and give them plenty of memory so they run smoothly without running out of stack space.

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. If you encounter significant imaginary frequencies, try to optimize the created xtbhess file e.g. xtbhess.coord and use the optimized structure for another Hessian calculation.

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.

Please note that for cif2crystal to work as intended, it expects a working python interpreter which we provide for you in a suitable conda environment that you can activate as follows.

module load conda

conda activate py27

You should now see a (py27) appear in the lower left corner as part of your shell prompt.