Restarting finite differences calculations: Difference between revisions

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  {{TAGBL|CHECKPOINT}} = PREPARE
  {{TAGBL|CHECKPOINT}} = PREPARE


This will create {{TAGBL|CONTCAR}}_disp-N files containing each of the displacements. You can then create different directories for each of these calculations and run them separately. For this, you will need to set {{TAGBL|CHECKPOINT|SINGLE}}:
This will create {{TAGBL|CONTCAR}}_disp-N files containing each of the displacements in the parent directory:
 
h5ls vaspcheck.h5
displacements            Group
subdir_prefix            Dataset {SCALAR}
symmetry                Group
total_count              Dataset {SCALAR}
 
You can then create different directories for each of these calculations and run them separately. For this, you will need to set {{TAGBL|CHECKPOINT|SINGLE}}:


<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
Line 160: Line 169:
   cp CONTCAR_disp-$i disp-$i/POSCAR
   cp CONTCAR_disp-$i disp-$i/POSCAR
   cp INCAR POTCAR KPOINTS CHG CHGCAR WAVECAR vasp.run disp-$i/
   cp INCAR POTCAR KPOINTS CHG CHGCAR WAVECAR vasp.run disp-$i/
   sed -i 's/prepare/single/g' disp-$i/INCAR
   sed -i 's/PREPARE/SINGLE/g' disp-$i/INCAR
done
done
</syntaxhighlight>
</syntaxhighlight>
Each {{FILE|INCAR}} file in the directories will then look like:
{{TAGBL|SYSTEM}} = graphene
{{TAGBL|ENCUT}} = 400
# electronic
{{TAGBL|PREC}} = Accurate
{{TAGBL|NELMIN}} = 5
{{TAGBL|EDIFF}} = 1e-8
{{TAGBL|ISMEAR}} = -1
{{TAGBL|SIGMA}} = 0.2
{{TAGBL|LREAL}} = .FALSE.
{{TAGBL|LWAVE}} = .FALSE.
{{TAGBL|LCHARG}} = .FALSE.
# ionic (finite differences)
{{TAGBL|IBRION}} = 6
{{TAGBL|POTIM}} = 0.015
{{TAGBL|CHECKPOINT}} = SINGLE
In each individual directory, you can see a single displacement has been recorded to the


We assume that this calculation has failed after a certain point or accidentally been cancelled:
We assume that this calculation has failed after a certain point or accidentally been cancelled:
Line 174: Line 208:
slurmstepd-test01: error: *** STEP 254054.0 ON test01 CANCELLED AT 2026-01-19T16:25:49 ***
slurmstepd-test01: error: *** STEP 254054.0 ON test01 CANCELLED AT 2026-01-19T16:25:49 ***
</syntaxhighlight>
</syntaxhighlight>


If you look in the directory, you will see the {{FILE|vaspcheck.h5}} file. Inside it will contain the displacement calculations that have been completed up to the point of the crash:
If you look in the directory, you will see the {{FILE|vaspcheck.h5}} file. Inside it will contain the displacement calculations that have been completed up to the point of the crash:

Revision as of 14:05, 21 January 2026

Mind: Available as of VASP 6.6.0
Important: This feature requires HDF5 support.

Since VASP 6.6.0, it has been possible to restart finite difference calculations using IBRION = 6 and CHECKPOINT. The displacements are written to a vaspcheck.h5 file. For details of a general finite difference calculation, see the phonons from finite differences HowTo. In this HowTo, we will concern ourselves with restarting and splitting finite difference calculations.

Important: This can only be done using IBRION = 6 currently. We recommend using this generally over IBRION = 5.

Input

There are several options for the CHECKPOINT tag:

  • CHECKPOINT = LEGACY - finite difference calculation are performed as those in VASP 6.5.1. No vaspcheck.h5 is written.
  • CHECKPOINT = RESET (default) - The vaspcheck.h5 file is overwritten or created, and the displacements are written to it.
  • CHECKPOINT = CONTINUE - used for restarting a finite differences calculation from a vaspcheck.h5 file.
  • CHECKPOINT = PREPARE - used for splitting a finite differences calculation.
  • CHECKPOINT = SINGLE - used for running a single displacement after splitting with CHECKPOINT = PREPARE.

We will describe the restart procedure and splitting a calculation below. As an example, we take a 3x3x1 graphene supercell POSCAR file from the phonon tutorials: 

C18
1.0
   7.3521657209830806    0.0000000000000000    0.0000000000000000
  -3.6760828604915403    6.3671622872044793    0.0000000000000000
   0.0000000000000000    0.0000000000000000    8.0000000000000000
C
18
direct
   0.1111111111111133    0.2222222222222200    0.0000000000000000 C
   0.1111111111111133    0.5555555555555532    0.0000000000000000 C
   0.1111111111111133    0.8888888888888866    0.0000000000000000 C
   0.4444444444444466    0.2222222222222200    0.0000000000000000 C
   0.4444444444444466    0.5555555555555532    0.0000000000000000 C
   0.4444444444444466    0.8888888888888866    0.0000000000000000 C
   0.7777777777777801    0.2222222222222200    0.0000000000000000 C
   0.7777777777777799    0.5555555555555532    0.0000000000000000 C
   0.7777777777777799    0.8888888888888866    0.0000000000000000 C
   0.2222222222222200    0.1111111111111133    0.0000000000000000 C
   0.2222222222222200    0.4444444444444466    0.0000000000000000 C
   0.2222222222222199    0.7777777777777799    0.0000000000000000 C
   0.5555555555555532    0.1111111111111133    0.0000000000000000 C
   0.5555555555555534    0.4444444444444466    0.0000000000000000 C
   0.5555555555555532    0.7777777777777799    0.0000000000000000 C
   0.8888888888888866    0.1111111111111133    0.0000000000000000 C
   0.8888888888888866    0.4444444444444466    0.0000000000000000 C
   0.8888888888888866    0.7777777777777799    0.0000000000000000 C

along with a 4x4x1 k-mesh in our KPOINTS file: 

K points
 0
Gamma
4  4  1
0  0  0

and PAW C_s 04May1998 POTCAR. We can use the following INCAR file: 

SYSTEM = graphene
ENCUT = 400

# electronic
PREC = Accurate
NELMIN = 5
EDIFF = 1e-8
ISMEAR = -1
SIGMA = 0.2
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.

# ionic (finite differences)
IBRION = 6
POTIM = 0.015

Calculations

Restarting a finite difference calculation

We assume that this calculation has failed after a certain point or accidentally been cancelled: 

DAV:   9    -0.181350430125E+03   -0.25600E-06   -0.38452E-08   848   0.118E-03    0.774E-04
DAV:  10    -0.181350430581E+03   -0.45554E-06   -0.20686E-08   864   0.738E-04    0.208E-04
DAV:  11    -0.181350430676E+03   -0.94857E-07   -0.22346E-09   704   0.354E-04    0.207E-04
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd-test01: error: *** JOB 254054 ON test01 CANCELLED AT 2026-01-19T16:25:49 ***
slurmstepd-test01: error: *** STEP 254054.0 ON test01 CANCELLED AT 2026-01-19T16:25:49 ***

If you look in the directory, you will see the vaspcheck.h5 file. Inside, it will contain the displacement calculations that have been completed up to the point of the crash: 

h5ls vaspcheck.h5

data-1                   Group
displacements            Group
symmetry                 Group

The calculation can then be restarted by adding CHECKPOINT = CONTINUE to the INCAR: 

SYSTEM = graphene
ENCUT = 400

# electronic
PREC = Accurate
NELMIN = 5
EDIFF = 1e-8
ISMEAR = -1
SIGMA = 0.2
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.

# ionic (finite differences)
IBRION = 6
POTIM = 0.015
CHECKPOINT = CONTINUE

You can resubmit your calculation in the directory, e.g., with a job script: sbatch job.sh, and the finite differences calculation will continue from there after an SCF step has been done: 

Continuing from previous run

The calculation will then continue as normal until all displacements have been completed and the phonon modes calculated: 

h5ls vaspcheck.h5

data-1                   Group
data-2                   Group
data-3                   Group
data-4                   Group
displacements            Group
symmetry                 Group

Splitting a finite difference calculation

For some large structures, it may be easier to split the displacements into separate calculations. This can be done with the CHECKPOINT = PREPARE tag: 

SYSTEM = graphene
ENCUT = 400

# electronic
PREC = Accurate
NELMIN = 5
EDIFF = 1e-8
ISMEAR = -1
SIGMA = 0.2
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.

# ionic (finite differences)
IBRION = 6
POTIM = 0.015
CHECKPOINT = PREPARE

This will create CONTCAR_disp-N files containing each of the displacements in the parent directory: 

h5ls vaspcheck.h5

displacements            Group
subdir_prefix            Dataset {SCALAR}
symmetry                 Group
total_count              Dataset {SCALAR}

You can then create different directories for each of these calculations and run them separately. For this, you will need to set CHECKPOINT: 

max=$(printf "%s\n" CONTCAR_disp-* | sed 's/.*-//' | sort -n | tail -1)

for i in $(seq 1 $max); do
  mkdir -p disp-$i
  cp CONTCAR_disp-$i disp-$i/POSCAR
  cp INCAR POTCAR KPOINTS CHG CHGCAR WAVECAR vasp.run disp-$i/
  sed -i 's/PREPARE/SINGLE/g' disp-$i/INCAR
done

Each INCAR file in the directories will then look like: 

SYSTEM = graphene
ENCUT = 400

# electronic
PREC = Accurate
NELMIN = 5
EDIFF = 1e-8
ISMEAR = -1
SIGMA = 0.2
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.

# ionic (finite differences)
IBRION = 6
POTIM = 0.015
CHECKPOINT = SINGLE

In each individual directory, you can see a single displacement has been recorded to the



We assume that this calculation has failed after a certain point or accidentally been cancelled: 

DAV:   9    -0.181350430125E+03   -0.25600E-06   -0.38452E-08   848   0.118E-03    0.774E-04
DAV:  10    -0.181350430581E+03   -0.45554E-06   -0.20686E-08   864   0.738E-04    0.208E-04
DAV:  11    -0.181350430676E+03   -0.94857E-07   -0.22346E-09   704   0.354E-04    0.207E-04
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd-test01: error: *** JOB 254054 ON test01 CANCELLED AT 2026-01-19T16:25:49 ***
slurmstepd-test01: error: *** STEP 254054.0 ON test01 CANCELLED AT 2026-01-19T16:25:49 ***


If you look in the directory, you will see the vaspcheck.h5 file. Inside it will contain the displacement calculations that have been completed up to the point of the crash: 

h5ls vaspcheck.h5

data-1                   Group
displacements            Group
symmetry                 Group

The calculation can then be restarted by adding CHECKPOINT = CONTINUE to the INCAR: 

SYSTEM = graphene
ENCUT = 400

# electronic
PREC = Accurate
NELMIN = 5
EDIFF = 1e-8
ISMEAR = -1
SIGMA = 0.2
LREAL = .FALSE.
LWAVE = .FALSE.
LCHARG = .FALSE.

# ionic (finite differences)
IBRION = 6
POTIM = 0.015
CHECKPOINT = CONTINUE

You can resubmit your calculation in the directory, e.g., with a job script: sbatch job.sh, and the finite differences calculation will continue from there after an SCF step has been done: 

Found     2 degrees of freedom:
Finite differences POTIM= 0.01500 DOF=   2
Continuing from previous run

The calculation will then continue as normal until all displacements have been completed and the phonon modes calculated: 

h5ls vaspcheck.h5

data-1                   Group
data-2                   Group
data-3                   Group
data-4                   Group
displacements            Group
symmetry                 Group

Practical hints

The computation of the second-order force constants requires accurate forces. Therefore, the tag PREC=Accurate is recommended in the INCAR. The ADDGRID=TRUE should not be set without careful testing.

A practical way to check for convergence is to monitor the Γ point (q=0) optical mode frequencies while varying the ENCUT, PREC, and k point density (KPOINTS). Additionally, compare the result to phonons from density-functional-perturbation theory (DFPT).

To get the phonon frequencies quickly on the command line, simply type the following: 

grep THz OUTCAR

To get an accurate phonon dispersion, perform the force-constants calculation in a large enough supercell. When increasing the size of the supercell, we recommend decreasing the k-point density in the KPOINTS file to yield the same resolution. For example, for the primitive cell of silicon, a 12x12x12 Gamma-centered k-point mesh is needed to obtain accurate phonon frequencies at the Gamma point. When replicating the unit cell to a 2x2x2 supercell, a 6x6x6 k point mesh will produce an equivalent sampling. For a 4x4x4 supercell, a 3x3x3 k point mesh will suffice.

It is possible to use phonopy[1] to post-process the results of a finite differences calculation done with VASP.[2]

Tip: In contrast to computing phonons within DFPT, the finite difference approach can be used in combination with any Exchange-correlation functional.

IBRION=5, is available as of VASP.4.5, IBRION=6 starting from VASP.5.1. In some older versions (pre VASP.5.1), NSW (number of ionic steps) must be set to 1 in the INCAR file, since NSW=0 sets the IBRION=−1 regardless of the value supplied in the INCAR file. Although VASP.4.6 supports IBRION=5-6, VASP.4.6 does not change the set of k points automatically (often the displaced configurations require a different k-point grid). Hence, the finite difference routine might yield incorrect results in VASP.4.6.

Related tags and sections

IBRION, ISIF, POTIM,

Phonons: Theory

Phonons from density-functional-perturbation theory, Computing the phonon dispersion and DOS

References

  1. ↑ http://phonopy.github.io/phonopy/index.html (2022).
  2. ↑ http://phonopy.github.io/phonopy/vasp-dfpt.html (2022).
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