Liquid Si - Standard MD: Difference between revisions

Revision as of 17:03, 14 June 2019

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

Generating liquid Si by melting of the crystalline structure via molecular dynamics.

Input

POSCAR

We start this example by making a POSCAR using the conventional unit cell with 8 atoms which should look like this:

Si cubic diamond conventional cell
  5.43100000000000
 1.00000000 0.00000000 0.00000000
 0.00000000 1.00000000 0.00000000
 0.00000000 0.00000000 1.00000000
  Si
  8
Direct
  0.00000000 0.00000000 0.00000000
  0.75000000 0.25000000 0.75000000
  0.00000000 0.50000000 0.50000000
  0.75000000 0.75000000 0.25000000
  0.50000000 0.00000000 0.50000000
  0.25000000 0.25000000 0.25000000
  0.50000000 0.50000000 0.00000000
  0.25000000 0.75000000 0.75000000

We obtain a sufficiently large supercell (2x2x2 containing 64 atoms) by following the description in: Preparing a Super Cell.
The new POSCAR file of the two 2x2x2 super cell of the conventional cell should look like this:

Si cubic diamond 2x2x2 super cell of conventional cell
     5.43090000000000
    2.00000000   0.00000000   0.00000000
    0.00000000   2.00000000   0.00000000
    0.00000000   0.00000000   2.00000000
   Si
   64
Direct
   0.00000000   0.00000000   0.00000000
   0.50000000   0.00000000   0.00000000
   0.00000000   0.50000000   0.00000000
   0.50000000   0.50000000   0.00000000
   0.00000000   0.00000000   0.50000000
   0.50000000   0.00000000   0.50000000
   0.00000000   0.50000000   0.50000000
   0.50000000   0.50000000   0.50000000
   0.37500000   0.12500000   0.37500000
   0.87500000   0.12500000   0.37500000
   0.37500000   0.62500000   0.37500000
   0.87500000   0.62500000   0.37500000
   0.37500000   0.12500000   0.87500000
   0.87500000   0.12500000   0.87500000
   0.37500000   0.62500000   0.87500000
   0.87500000   0.62500000   0.87500000
   0.00000000   0.25000000   0.25000000
   0.50000000   0.25000000   0.25000000
   0.00000000   0.75000000   0.25000000
   0.50000000   0.75000000   0.25000000
   0.00000000   0.25000000   0.75000000
   0.50000000   0.25000000   0.75000000
   0.00000000   0.75000000   0.75000000
   0.50000000   0.75000000   0.75000000
   0.37500000   0.37500000   0.12500000
   0.87500000   0.37500000   0.12500000
   0.37500000   0.87500000   0.12500000
   0.87500000   0.87500000   0.12500000
   0.37500000   0.37500000   0.62500000
   0.87500000   0.37500000   0.62500000
   0.37500000   0.87500000   0.62500000
   0.87500000   0.87500000   0.62500000
   0.25000000   0.00000000   0.25000000
   0.75000000   0.00000000   0.25000000
   0.25000000   0.50000000   0.25000000
   0.75000000   0.50000000   0.25000000
   0.25000000   0.00000000   0.75000000
   0.75000000   0.00000000   0.75000000 
   0.25000000   0.50000000   0.75000000
   0.75000000   0.50000000   0.75000000
   0.12500000   0.12500000   0.12500000
   0.62500000   0.12500000   0.12500000
   0.12500000   0.62500000   0.12500000
   0.62500000   0.62500000   0.12500000
   0.12500000   0.12500000   0.62500000
   0.62500000   0.12500000   0.62500000
   0.12500000   0.62500000   0.62500000
   0.62500000   0.62500000   0.62500000
   0.25000000   0.25000000   0.00000000
   0.75000000   0.25000000   0.00000000
   0.25000000   0.75000000   0.00000000
   0.75000000   0.75000000   0.00000000
   0.25000000   0.25000000   0.50000000
   0.75000000   0.25000000   0.50000000
   0.25000000   0.75000000   0.50000000
   0.75000000   0.75000000   0.50000000
   0.12500000   0.37500000   0.37500000
   0.62500000   0.37500000   0.37500000
   0.12500000   0.87500000   0.37500000
   0.62500000   0.87500000   0.37500000
   0.12500000   0.37500000   0.87500000
   0.62500000   0.37500000   0.87500000
   0.12500000   0.87500000   0.87500000
   0.62500000   0.87500000   0.87500000

KPOINTS

K-Points
 0
Gamma
 1  1  1
 0  0  0

Since a sufficiently large super cell is used in this example, it is ok in this case to use only a single k-point in the calculations. Hence it is also possible to use the $\Gamma$ -point only version which is significantly faster than the standard version.

INCAR

ISMEAR = 0
IBRION = 0
MDALGO = 2
ISIF = 2
SMASS = 1.0
SIGMA = 0.1
LREAL = Auto
ALGO = VeryFast
PREC = Low
ISYM = 0
TEBEG = 2000
NSW = 100
POTIM = 3.0

To select a molecular dynamics calculation set {IBRION=0.
By selecting MDALGO=2 and ISIF=2 we select the NVT ensemble using the Nose-Hoover thermostat.
The tag SMASS specifies the Nose mass, which is a ficitional mass for the fictional coordinate of the heat bath. The choice of SMASS=1.0 should work well for this tutorial.
Since we are dealing with a super cell, we set LREAL=Auto. In this mode the projection operators are evaluated in real space. This should speed up the calculation while being slightly less accurate then the evaluation of the operators in reciprocal space.
To significantly speed up the calculations we use ALGO=VeryFast and PREC=Low. This is perfectly ok for this tutorial example but for more precise results these flags should be used with caution.
A time step of 3 femtoseconds (POTIM=3.0) is employed in this example, which should be ok for many applications of Si.

Calculation

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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

@@ Line 128: / Line 128: @@
 *To select a molecular dynamics calculation set {{{TAGBL|IBRION}}=0.
 *By selecting {{TAG|MDALGO}}=2 and {{TAG|ISIF}}=2 we select the {{TAG|NVT ensemble}} using the {{TAG|Nose-Hoover thermostat}}.
-*The tag {{TAG|SMASS}} specifies the Nose mass, which is a ficitional mass for the fictional coordinate of the heat bath. The setting of {{TAGBL|SMASS}}=1.0 should work well for this tutorial.
+*The tag {{TAG|SMASS}} specifies the Nose mass, which is a ficitional mass for the fictional coordinate of the heat bath. The choice of {{TAGBL|SMASS}}=1.0 should work well for this tutorial.
 *Since we are dealing with a super cell, we set {{TAGBL|LREAL}}=Auto. In this mode the projection operators are evaluated in real space. This should speed up the calculation while being slightly less accurate then the evaluation of the operators in reciprocal space.
 *To significantly speed up the calculations we use {{TAGBL|ALGO}}=''VeryFast'' and {{TAGBL|PREC}}=''Low''. This is perfectly ok for this tutorial example but for more precise results these flags should be used with caution.