Nucleophile Substitution CH3Cl - Standard MD

Overview >Liquid Si - Standard MD > Liquid Si - Freezing > Nucleophile Substitution CH3Cl - Standard MD > Nuclephile Substitution CH3Cl - mMD1 > Nuclephile Substitution CH3Cl - mMD2 > Nuclephile Substitution CH3Cl - mMD3 > Nuclephile Substitution CH3Cl - SG > Nuclephile Substitution CH3Cl - BM > List of tutorials

Task

The main task of this example is to learn how to monitor distances on the example of a nucleophile substitution of a Cl^- by another Cl^- in CH₃Cl.

Input

POSCAR

CH3Cl                                         
   1.00000000000000     
    12.0000000000000000    0.0000000000000000    0.0000000000000000
     0.0000000000000000   12.0000000000000000    0.0000000000000000
     0.0000000000000000    0.0000000000000000   12.0000000000000000 
C H Cl
   1   3   2
cart
         5.91331371  7.11364924  5.78037960
         5.81982231  8.15982106  5.46969017
         4.92222130  6.65954232  5.88978969
         6.47810398  7.03808479  6.71586385
         4.32824726  8.75151396  7.80743202
         6.84157897  6.18713289  4.46842049

• The starting POSCAR file for this example can be found under POSCAR.init. It will be needed for the script that runs the job (run.sh).
• A sufficiently large cell is chosen to minimize the interactions between neighbouring cells and hence to simulate an isolated molecular reaction.

KPOINTS

Automatic
 0
Gamma
 1  1  1
 0. 0. 0.

• For isolated atoms and molecules interactions between periodic images are negligible (in sufficiently large cells) hence no Brillouin zone sampling is necessary.

INCAR

PREC=Low
EDIFF=1e-6
LWAVE=.FALSE.
LCHARG=.FALSE.
NELECT=22
NELMIN=4
LREAL=.FALSE.
ALGO=VeryFast
ISMEAR=-1
SIGMA=0.0258

############################# MD setting #####################################
IBRION=0                                           # MD simulation
NSW=1000                                           # number of steps
POTIM=1                                            # integration step
TEBEG=300                                          # simulation temperature
MDALGO=11                                          # metaDynamics with Andersen thermostat
ANDERSEN_PROB=0.10                                 # collision probability
##############################################################################

• Molecular dynamics are switched on by the tag IBRION=0.
• The metadynamics tag MDALGO=11 is only used to monitor the two C-Cl distances defined in the ICONST file.
• Simulations are carried out in the NVT ensemble at approximately room temperature (TEBEG=300) and the Andersen thermostat is used for the temperature control. The strength of the coupling is controlled by the collision probability ANDERSEN_PROB=0.10.
• The accuracy of this calculation is kept low (PREC=Low and ALGO=VeryFast), which is completely sufficient for this tutorial. For more quantitative results this tags should be investigated (of course at the cost of higher computational demand).
• A charged system (due to the "incoming" Cl^-) is simulated, so the number of electrons is raised by one compared to the neutral system (NELECT=22). To compensate for the charge a positive homogeneous background charge is assumed.
• Although very light atoms are present in the structure (hydrogen) a time step of 1 fs (POTIM=1) is safe to use. This can be achieved by setting the mass of hydrogen to that of tritium (look for the line "POMASS = 3.016" in the POTCAR file). This is unproblematic since the free energy is independent of the mass of atoms.

ICONST

For this example an ICONST file is used which looks like:

R 1 5 0
R 1 6 0
S 1 -1 7

• First line: This line selects the interatomic distance (R) between the first (C) and the fifth atom (Cl) in the POSCAR file. The 0 at the fourth entry would usually specify that the distances are constrained but if the coordinates are used later for special coordinates the constraining is not applied (for further information see ICONST).
• Second line: Same as the first line but interatomic distance between the first (C) and the sixth atom (Cl) in the POSCAR file is selected.
• Third line: This line selects a linear combination (option S) of the first two coordinates where the second and fourth column specify the coefficients of the coordinates. The setting of 1 and -1 corresponds to the difference between both. The 7 at the fourth entry specifies that difference between these two distances is monitored but no constraints are applied.

Calculation

We are chopping the "relatively" long calculation into smaller peaces. So after each step we have to save the output and copy the CONTCAR file to POSCAR file to restart the calculation. All of this is done by the script run provided with this example:

#run
runvasp="mpirun -np 8 executable_path/vasp_std"

# make sure to always start with the same structure
cp POSCAR.init POSCAR

i=1

while [ $i -le 50 ] 
do
  # start vasp
  $runvasp

  # use the last configuration generated in the previous
  # run as initial configuration for the next run
  cp CONTCAR POSCAR

  # backup some important files
  cp REPORT REPORT.$i
  cp vasprun.xml vasprun.xml.$i

  let i=i+1
done