25 September 2015
Molecules

Due that molecules has no periodicity, VASP is not the best code to calculate molecule electronic properties. Due to the molecule non periodicity the calculation becomes time consuming. Nevertheless it is necesary to make a molecule relaxation if, in the future plans, an interaction between a surface and a molecule will be done.

Molecule Relaxation

POSCAR construction

Lets relax the benzene molecule, with a cell that has the same size that the one that contains the anatase [101]. The cell size will made easy the merge between the two systems.
We only need one K-point to calculate molecules, because the Bloch theorem does not apply. Use any of the GUI editors we mention before.

Figure 2.Benzene molecule in a box. Made it on VESTA .

It's easy if you build your molecule on cartesian coordinates, and then in Vesta, transform it into direct coordinates

POSCAR construction

Please refer to the manual of your desired builder, this example was constructed on VESTA.

POSCAR FILE

Benzene
1.0
       11.1524000168         0.0000000000         0.0000000000
       -2.5919744258         7.1481640748         0.0000000000
        0.0000000000         0.0000000000        17.9026985168
    C    H
    6    6
Direct
     0.559710026         0.692732990         0.239644006
     0.645358026         0.595155001         0.239644006
     0.600000024         0.400000006         0.239644006
     0.468995005         0.302421987         0.239644006
     0.383347005         0.400000006         0.239644006
     0.428705007         0.595155001         0.239644006
     0.595466018         0.846576989         0.239644006
     0.748636007         0.672083974         0.239644006
     0.667518973         0.323071003         0.239644006
     0.433239013         0.148578003         0.239644006
     0.280068994         0.323071003         0.239644006
     0.361185998         0.672083974         0.239644006


INCAR preparation

In this example we are going to relax the ion possition in the cell, because symmetry is broken and the number of atoms increase, VASP will take more ion relaxation steps, so be patient. The INCAR file must have the followin directives.

- ISTART= 0 New Job.
- ISIF = 2 Ions relaxation.
- IBRION= 2 DFT Conjugate Gradient.
- NSW = 55 Maximum Optimization steps.
- EDIFF & EDIFFG Convergence Criteria.

- ICHARG=2 Initial charge distribution are the atomic charges.

INCAR FILE

# Benzene Molecule Relaxation
#===========================================

# General Setup
  System = benzene    # Calculation Title
  PREC   = NORMAL     # Options: Normal, Medium, High, Low
  ENCUT  = 400        # Carbon Kinetic Energy Cutoff [eV]
  ISTART = 0          # Job: 0-new  1-cont  2-samecut
  ICHARG = 2          # initial charge density: 1-file 2-atom 10-cons 11-DOS
  ISPIN  = 1          # Spin Polarize: 1-No 2-Yes

# Electronic Relaxation (SCF)
  NELM     = 60       # Max Number of Elec Self Cons Steps  
    NELMIN = 2        # Min Number of ESC steps
    NELMDL = 10       # Number of non-SC at the beginning
  EDIFF    = 1.0E-04  # Stopping criteria for ESC
  LREAL    = .TRUE.   # Real space projection
  IALGO    = 48       # Electronic algorithm minimization
  VOSKOWN  = 1        # 1- uses VWN exact correlation
  ADDGRID  = .TRUE.   # Improve the grid accuracy

# Ionic Relaxation 
  EDIFFG   = -1.0E-04  # Stopping criteria for ionic self cons steps
  NSW      = 55       # Max Number of ISC steps: 0- Single Point
  IBRION   = 2        # Ionic Relaxation Method: 0-MD 1-qNewton-RaphsonElectronic 2-CG
  ISIF     = 2        # Stress and Relaxation: 2-Ion 3-cell+ion
  ADDGRID  = .TRUE.   # Improve the grid accuracy
  SIGMA    = 0.10     # Insulators/semiconductors=0.1  metals=0.05 
  ISMEAR   = 1        # Partial Occupancies for each Orbital
                      # -5 DOS, -2 from file, -1 Fermi Smear, 0 Gaussian Smear
# Parallelization
  NPAR=8
  NCORE=8   # Search the NPAR of your system
  NSIM = 4


POTCAR

We have to combine the potential files of C and H. To do that copy the POTCAR files into your work directory with diferent name. Potential files are in the directory where you install VASP. Finally just concatenate both files into a new file called POTCAR. Remember conserve the order that we impose in the POSCAR.

[user@machine WRKDIR]$ cp ~/VASP/vasp5.x/Potential/PBE/C/POTCAR POTCAR_C
[user@machine WRKDIR]$ cp ~/VASP/vasp5.x/Potential/PBE/H/POTCAR POTCAR_H
[user@machine WRKDIR]$ cat POTCAR_C POTCAR_H >> POTCAR



KPOINTS file

We are going to generate an automatic K-mesh with 64 K-points distributed in all directions.

Gamma-Point Only for Molecules # Generates Automatically the K-mesh
  1            # One k-point
rec            # Units of reciprocal lattice
  0  0  0  1   # Three coordinates and weight


Job administrator (only for torque or sge users)

If you have a queue administrator you have to set the queue file. FamaLab has torque as default job manager. Please paste the queue file .pbs or .sge into your work directory.

The file has as main directives the jobname, the number of cpu you are requesting, the time is going to take your calculation, and which of the vasp programs you will use.

#PBS -N name_identifier
#PBS -o vasp.out
#PBS -j oe
#PBS -e vasp.err
#PBS -l walltime=8760:00:00
#PBS -l nodes=1:ppn=8
#PBS -q batch

#Elegir la version de vasp:
VASP=vasp_gamma     #Volume=vasp_complex, supercell=vasp_cd, molecules=vasp_gamma


Now he have to run vasp and wait for the relaxation

You can download the build files here:
INCAR POTCAR KPOINTS POSCAR