NEB (nudged elastic band) calculation

The diffusion barrier for Li on graphene.

There are three steps, the first step is “RELAX” calculation for initial and final states, the second is “SCF” calculation, and the third is “NEB” calculation.

First Step: “RELAX” calculation for initial and final states

Initial state relaxation

Input files

atom.config

   51
 LATTICE
     12.30000019     0.00000000     0.00000000
     -6.15000010    10.65211263     0.00000000
      0.00000000     0.00000000    20.00000000
 POSITION
   6     0.13302763     0.06631131     0.50001912 1 1 1
   6     0.13244991     0.26622178     0.50007744 1 1 1
   6     0.13302290     0.46671968     0.50002064 1 1 1
   ...
   6     0.86685591     0.73343720     0.50000920 1 1 1
   6     0.86668410     0.93331589     0.49999358 1 1 1
   3     0.39999999     0.39999999     0.58526884 1 1 1

etot.input

 2  2
 JOB = RELAX
 IN.PSP1 = C.SG15.PBE.UPF
 IN.PSP2 = Li.SG15.PBE.UPF
 IN.ATOM = atom.config
 RELAX_DETAIL = 1 100 0.01
 Ecut = 50
 Ecut2 = 200
 MP_N123 = 3 3 1 0 0 0
 XCFUNCTIONAL = PBE
 SYS_TYPE = 2

SYS_TYPE: specifies type of the system and automatically adjust the parameter “FERMIDE”,

1: semiconductor or insulator (default, FERMIDE=0.025);

2: metallic (FERMIDE=0.2).

C.SG15.PBE.UPF, Li.SG15.PBE.UPF

Calculations

You can submit PWmat tasks in different ways:

   mpirun -np 4 PWmat | tee output

Run the command directly

   #!/bin/bash
   #PBS -N SCF
   #PBS -l nodes=1:ppn=4
   #PBS -q batch
   #PBS -l walltime=100:00:00
 
   ulimit -s unlimited
   cd $PBS_O_WORKDIR
 
   mpirun -np 4 PWmat | tee output

Submit the task with a pbs script

Obtain the final.config file, which contains the position of the last ionic step of the relaxation, and can be used for step two “SCF” calculation.

Final state relaxation

Input files

atom.config

   51
 LATTICE
     12.30000019     0.00000000     0.00000000
     -6.15000010    10.65211263     0.00000000
      0.00000000     0.00000000    20.00000000
 POSITION
   6     0.13330299     0.06669701     0.49998566 1 1 1
   6     0.13316367     0.26655079     0.50000705 1 1 1
   6     0.13316402     0.46660047     0.50000705 1 1 1
   ...
   6     0.86753884     0.73377247     0.50007857 1 1 1
   6     0.86696519     0.93367340     0.50002931 1 1 1
   3     0.60000002     0.60000002     0.58521177 1 1 1

etot.input

 2  2
 JOB = RELAX
 IN.PSP1 = C.SG15.PBE.UPF
 IN.PSP2 = Li.SG15.PBE.UPF
 IN.ATOM = atom.config
 RELAX_DETAIL = 1 100 0.01
 Ecut = 50
 Ecut2 = 200
 MP_N123 = 3 3 1 0 0 0
 XCFUNCTIONAL = PBE
 SYS_TYPE = 2

C.SG15.PBE.UPF, Li.SG15.PBE.UPF

Calculations

You can submit PWmat tasks in different ways:

   mpirun -np 4 PWmat | tee output

Run the command directly

   #!/bin/bash
   #PBS -N SCF
   #PBS -l nodes=1:ppn=4
   #PBS -q batch
   #PBS -l walltime=100:00:00
 
   ulimit -s unlimited
   cd $PBS_O_WORKDIR
 
   mpirun -np 4 PWmat | tee output

Submit the task with a pbs script

Obtain the final.config file, which contains the position of the last ionic step of the relaxation, and can be used for step two “SCF” calculation.

Second Step: “SCF” calculation for initial and finial states

Initial state scf

Input files

atom.config

       51 atoms,Iteration =   8, Etot,Ep,Ek =  -0.7946015575E+04  -0.7946015575E+04   0.0000000000E+00, Average Force=  0.15454E-02, Max force=  0.33836E-02
 Lattice vector (Angstrom), stress(eV/natom)
   0.1230000019E+02    0.0000000000E+00    0.0000000000E+00
  -0.6150000100E+01    0.1065211263E+02    0.0000000000E+00
   0.0000000000E+00    0.0000000000E+00    0.2000000000E+02
 Position, move_x, move_y, move_z
   6      0.133312758      0.066687242      0.499990024     1  1  1
   6      0.133149613      0.266557805      0.500008510     1  1  1
   6      0.133149503      0.466579100      0.500008574     1  1  1
   ...
   6      0.867547638      0.733777090      0.500077817     1  1  1
   6      0.866970187      0.933684078      0.500023723     1  1  1
   3      0.600000020      0.600000020      0.585322202     1  1  1

Copy final.config from previous initial state RELAX calculation, and rename atom.config

etot.input

 2  2
 JOB = SCF
 IN.PSP1 = C.SG15.PBE.UPF
 IN.PSP2 = Li.SG15.PBE.UPF
 IN.ATOM = atom.config
 Ecut = 50
 Ecut2 = 200
 MP_N123 = 3 3 1 0 0 0
 XCFUNCTIONAL = PBE
 E_ERROR = 0
 SYS_TYPE = 2

C.SG15.PBE.SOC.UPF, Li.SG15.PBE.SOC.UPF

Calculations

You can submit PWmat tasks in different ways:

   mpirun -np 4 PWmat | tee output

Run the command directly

   #!/bin/bash
   #PBS -N SCF
   #PBS -l nodes=1:ppn=4
   #PBS -q batch
   #PBS -l walltime=100:00:00
 
   ulimit -s unlimited
   cd $PBS_O_WORKDIR
 
   mpirun -np 4 PWmat | tee output

Submit the task with a pbs script

<HTML><ol start=“2” style=“list-style-type: decimal;”></HTML> <HTML><li></HTML>Read total energy from REPORT, and as input parameter for next NEB calculation.<HTML></li></HTML><HTML></ol></HTML>

grep "E_tot(eV)" REPORT | tail -1
>>> E_tot(eV)    = -.79460153820497E+04    -.3343E-03

Final state scf

Input files

atom.config

       51 atoms,Iteration =   8, Etot,Ep,Ek =  -0.7946015575E+04  -0.7946015575E+04   0.0000000000E+00, Average Force=  0.15454E-02, Max force=  0.33836E-02
 Lattice vector (Angstrom), stress(eV/natom)
   0.1230000019E+02    0.0000000000E+00    0.0000000000E+00
  -0.6150000100E+01    0.1065211263E+02    0.0000000000E+00
   0.0000000000E+00    0.0000000000E+00    0.2000000000E+02
 Position, move_x, move_y, move_z
   6      0.133312758      0.066687242      0.499990024     1  1  1
   6      0.133149613      0.266557805      0.500008510     1  1  1
   6      0.133149503      0.466579100      0.500008574     1  1  1
   ...
   6      0.867547638      0.733777090      0.500077817     1  1  1
   6      0.866970187      0.933684078      0.500023723     1  1  1
   3      0.600000020      0.600000020      0.585322202     1  1  1

Copy final.config from previous final state RELAX calculation, and rename atom.config

etot.input

 2  2
 JOB = SCF
 IN.PSP1 = C.SG15.PBE.UPF
 IN.PSP2 = Li.SG15.PBE.UPF
 IN.ATOM = atom.config
 Ecut = 50
 Ecut2 = 200
 MP_N123 = 3 3 1 0 0 0
 XCFUNCTIONAL = PBE
 E_ERROR = 0
 SYS_TYPE = 2

C.SG15.PBE.SOC.UPF, Li.SG15.PBE.SOC.UPF

Calculations

You can submit PWmat tasks in different ways:

   mpirun -np 4 PWmat | tee output

Run the command directly

   #!/bin/bash
   #PBS -N SCF
   #PBS -l nodes=1:ppn=4
   #PBS -q batch
   #PBS -l walltime=100:00:00
 
   ulimit -s unlimited
   cd $PBS_O_WORKDIR
 
   mpirun -np 4 PWmat | tee output

Submit the task with a pbs script

Read total energy from REPORT, and as input parameter for next NEB calculation.

grep "E_tot(eV)" REPORT | tail -1
>>> E_tot(eV)    = -.79460153754978E+04    -.3548E-03

Third Step: “NEB” calculation

Input files

atom_initial.config

       51 atoms,Iteration =   8, Etot,Ep,Ek =  -0.7946015575E+04  -0.7946015575E+04   0.0000000000E+00, Average Force=  0.15454E-02, Max force=  0.33836E-02
 Lattice vector (Angstrom), stress(eV/natom)
   0.1230000019E+02    0.0000000000E+00    0.0000000000E+00
  -0.6150000100E+01    0.1065211263E+02    0.0000000000E+00
   0.0000000000E+00    0.0000000000E+00    0.2000000000E+02
 Position, move_x, move_y, move_z
   6      0.133312758      0.066687242      0.499990024     1  1  1
   6      0.133149613      0.266557805      0.500008510     1  1  1
   6      0.133149503      0.466579100      0.500008574     1  1  1
   ...
   6      0.867547638      0.733777090      0.500077817     1  1  1
   6      0.866970187      0.933684078      0.500023723     1  1  1
   3      0.600000020      0.600000020      0.585322202     1  1  1

Copy final.config from previous initial state RELAX calculation, and rename atom.config

atom_final.config

       51 atoms,Iteration =   8, Etot,Ep,Ek =  -0.7946015575E+04  -0.7946015575E+04   0.0000000000E+00, Average Force=  0.15454E-02, Max force=  0.33836E-02
 Lattice vector (Angstrom), stress(eV/natom)
   0.1230000019E+02    0.0000000000E+00    0.0000000000E+00
  -0.6150000100E+01    0.1065211263E+02    0.0000000000E+00
   0.0000000000E+00    0.0000000000E+00    0.2000000000E+02
 Position, move_x, move_y, move_z
   6      0.133312758      0.066687242      0.499990024     1  1  1
   6      0.133149613      0.266557805      0.500008510     1  1  1
   6      0.133149503      0.466579100      0.500008574     1  1  1
   ...
   6      0.867547638      0.733777090      0.500077817     1  1  1
   6      0.866970187      0.933684078      0.500023723     1  1  1
   3      0.600000020      0.600000020      0.585322202     1  1  1

Copy final.config from previous initial state RELAX calculation, and rename atom.config

etot.input

 2  2
 JOB = NEB
 IN.PSP1 = C.SG15.PBE.UPF
 IN.PSP2 = Li.SG15.PBE.UPF
 IN.ATOM = atom_initial.config
 NEB_DETAIL = 5, 100, 0.02, 5, 0.1, 1, -.79460153820497E+04, -.79460153754978E+04, 1, atom_final.config #IMTH, NSTEP, FORCE_TOL, NIMAGE, AK, TYPE_SPRING, E0, EN, ITYPE_AT2, ATOM2.CONFIG
 Ecut = 50
 Ecut2 = 200
 MP_N123 = 3 3 1 0 0 0 2
 XCFUNCTIONAL = PBE
 SYS_TYPE = 2

JOB = NEB: specifies NEB or CI-NEB calculation.
IMTH: the algorithm used for atomic relaxation..
NSTEP: the maximum number of line-minimization steps in the relaxation process.
FORCE_TOL: the atomic force tolerance ($$eV/\text{\AA}$$) to stop the relaxation.
NIMAGE: the number of images in the NEB.
AK: the spring constant for the image string ($$eV/\text{\AA}^2$$) .
TYPE_SPRING: the type of string used in NEB algorithm.
E0,EN: the precalculated energy of initial and final configurations.
ITYPE_AT2: the type of ATOM2.CONFIG
ATOM2.CONFIG: if ITYPE_AT2=1, ATOM2.CONFIG is the configuraton of final state; if ITYPE_AT2=2, ATOM2.CONFIG should contain all the NIMAGE, initial and final images. It can copy from MOVEMENT.

C.SG15.PBE.SOC.UPF, Li.SG15.PBE.SOC.UPF

Calculations

You can submit PWmat tasks in different ways:

   mpirun -np 4 PWmat | tee output

Run the command directly

   #!/bin/bash
   #PBS -N SCF
   #PBS -l nodes=1:ppn=4
   #PBS -q batch
   #PBS -l walltime=100:00:00
 
   ulimit -s unlimited
   cd $PBS_O_WORKDIR
 
   mpirun -np 4 PWmat | tee output

Submit the task with a pbs script

For NEB calculation, the main report file is NEB.BARRIER, which concisely report the energies along the images for different relaxation interation steps. A typical NEB.BARRIER file looks like:

iter=           0  Etot(eV),dist(Bohr),angle(cos(th))
    0      -0.79460153820497E+04    0.775127E+00   0.000000E+00
    1      -0.79458967676866E+04    0.775511E+00   0.999799E+00
    2      -0.79456608594139E+04    0.775152E+00   0.999772E+00
    3      -0.79455479350017E+04    0.775153E+00   0.999044E+00
    4      -0.79456646396218E+04    0.775533E+00   0.999760E+00
    5      -0.79458997436463E+04    0.775116E+00   0.999770E+00
    6      -0.79460153754978E+04    0.000000E+00   0.000000E+00
--------------------------------------
...
...
...
iter=          46  Etot(eV),dist(Bohr),angle(cos(th))
    0      -0.79460153820497E+04    0.872956E+00   0.000000E+00
    1      -0.79459501924940E+04    0.880202E+00   0.460050E+00
    2      -0.79458020191154E+04    0.876583E+00   0.843128E+00
    3      -0.79457334923844E+04    0.876550E+00   0.978611E+00
    4      -0.79458018757778E+04    0.883367E+00   0.838971E+00
    5      -0.79459501006750E+04    0.876284E+00   0.451718E+00
    6      -0.79460153754978E+04    0.000000E+00   0.000000E+00
--------------------------------------

Etot(eV)(second column): the total energy of the image.
dist(Bohr)(third column): the distance between the neighboring images.
angle(cos(th))(fourth column): the $$\cos{\theta}$$ of the angle theta between two R(image + 1) - R(image), and R(image) - R(image - 1).

目录

NEB (nudged elastic band) calculation

First Step: “RELAX” calculation for initial and final states

Initial state relaxation

Input files

Calculations

Final state relaxation

Input files

Calculations

Second Step: “SCF” calculation for initial and finial states

Initial state scf

Input files

Calculations

Final state scf

Input files

Calculations

Third Step: “NEB” calculation

Input files

Calculations