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exercises:2018_ethz_mmm:bf3

Molecular orbitals of Boron trifluoride

Boron trifluoride is a Lewis acid, an electron-pair acceptor. Molecular orbital theory of BF3 must provide an orbital capable of acting as such an acceptor to be consistent with this chemical property.

In this exercise you will visualize molecular orbitals at the Hartree-Fock level for the molecule boron triflouride which has a triangular shape. The orbitals should come out similar to this:

The input file structure is shown below:

&FORCE_EVAL                           ! This section defines method for calculating energy and forces
 
   METHOD Quickstep                   ! Electronic structure method (DFT,...)
   &DFT
    &SCF
      SCF_GUESS RESTART
    &END
      &POISSON                        ! Solver requested for non periodic calculations
         PERIODIC NONE
         PSOLVER  WAVELET             ! Type of solver
      &END POISSON
      &QS                             ! Parameters needed to set up the Quickstep framework
         METHOD GAPW                  ! Method: gaussian and augmented plane waves 
      &END QS
 
#
# Include the exchange and correlation information
#
@INCLUDE './hf.inc'
 
   &PRINT
      &E_DENSITY_CUBE
       FILENAME _SCALE_
      &END
      &MO_CUBES
           FILENAME _SCALE_
           NHOMO 5
           NLUMO 4
      &END MO_CUBES
   &END PRINT
   &END DFT
 
 
   &SUBSYS                            ! This section defines the system
      &CELL                           ! Unit cell set up
         PERIODIC NONE                ! Non periodic calculation
         ABC 10 10 10
      &END CELL
      &TOPOLOGY
        COORD_FILE_NAME BF3.xyz 
        COORD_FILE_FORMAT XYZ
          &CENTER_COORDINATES
          &END
      &END TOPOLOGY
 
      &KIND B                                      ! potential and basis for F 
         &BASIS   
@INCLUDE './B_631GX.inc'
         &END                      
         POTENTIAL ALL
         &POTENTIAL
     4    1    0
     0.43392956    0
         &END 
      &END KIND
      &KIND F                         ! potential and basis for F
         &BASIS
@INCLUDE './F_631GX.inc'
         &END
         POTENTIAL ALL
         &POTENTIAL
     4    5    0
     0.21852465    0
         &END
      &END KIND
   &END SUBSYS
&END FORCE_EVAL                     ! This section defines method for calculating energy and forces
 
&GLOBAL                             ! Section with general information regarding which kind of simulation to perform an parameters for the whole PROGRAM
   PRINT_LEVEL LOW                  ! Global print level
   PROJECT BF3                     ! Name of the project. This word will appear as part of a name of all ouput files (except main ouput file, specified with -o option)
   RUN_TYPE ENERGY                 ! Energy run
&END GLOBAL
 

As usual, you can take the tar file of the exercise directory at the following link. Copy it to the directory $HOME/EXERCISES and untar it:

tar xvf exercise_4.tar

Copy the files to the created directory in your exercise path.

In the directory you will find the following files:
  • BF3.0.inp for the calculation of the orbitals (this is only a template file)
  • compute_bf3_expand to transform the input file and the input geometry, and then launch the job + drawing the orbitals
  • several *.inc file describing the level of theory (exchange and correlation functional) and the basis sets.

The operations are performed by the following bash script:

. /usr/bin/m_functions.bash
a=$1
  m_xyzrescale $a < BF3.opt.xyz > BF3.xyz
  cp BF3.xyz BF3.$a.xyz
  m_replace _SCALE_ $a < BF3.0.inp > BF3.$a.inp
  cp2k.ssmp -i BF3.$a.inp  > BF3.$a.out
 
  mkdir ORB_$a
  for b in 12 13 14 15 16 
     do 
       c=$[16-$b]
       vmd BF3-"$a"-WFN_000"$b"_1-1_0.cube -e orb.vmd
       ST=HOMO-"$c"
       convert out.tga -gravity South -background YellowGreen -splice 0x18 -annotate +0+2  $ST out1.tga
       mv out1.tga ORB_$a/$ST.tga
     done
 
  for c in 17 18 19 20
     do 
       d=$[$c-17]
       vmd BF3-"$a"-WFN_000"$c"_1-1_0.cube -e orb.vmd >& vmd.log
       ST=LUMO+"$d"
       convert out.tga -gravity South -background YellowGreen -splice 0x18 -annotate +0+2  $ST out1.tga
       mv out1.tga ORB_$a/$ST.tga
     done
   vmd BF3-"$a"-ELECTRON_DENSITY-1_0.cube -e dens.vmd >& vmd.log
   convert dens.tga -gravity South -background YellowGreen -splice 0x18 -annotate +0+2  'ELECTRON DENSITY' dens1.tga
 
   mv dens1.tga ORB_$a/dens1.tga
   montage ORB_$a/*tga -geometry 800x600 ORB_$a/all_$a.jpg
   mv BF3-"$a"*.cube ORB_$a/
 
 
 rm *bak*

The command to launch the job with an expansion factor of ALPHA (replace it with the required factor)

 ./compute_bf3_expand ALPHA
Assignments:
  1. Run the script with ALPHA=1.0 (meaning: no expansion of the molecule)
  2. Look into the BF3.ALPHA.out file to verify the energies of the occupied and unoccupied orbitals: do you see degenerate orbitals (with the same energy)
  3. What is the homo-lumo gap (distance between highest occupied and lowest unoccupied orbital (remember: it is in Hartree — write it in eV
  4. The script produces a directory ORB_ALPHA with the orbitals and the density. Compare the orbitals what the illustration above.
  5. Repeat the job with ALPHA=2.5
  6. What do you observe in the plots? Which differences? Why?
exercises/2018_ethz_mmm/bf3.txt · Last modified: 2018/04/16 12:31 by dpasserone