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
tip
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
Note
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
Note
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
Note
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
Note
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
tip
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
Note
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
Note
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) = -.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
Note
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
Note
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
Note
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
Note
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
Note
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
Note
- 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 () to stop the relaxation.
- NIMAGE: the number of images in the NEB.
- AK: the spring constant for the image string () .
- 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
Note
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
Note
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
--------------------------------------
Note
-
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 of the angle theta between two R(image + 1) - R(image), and R(image) - R(image - 1).