Restarting finite differences calculations

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 vaspcheckfd.h5 file. For details of a general finite difference calculation, see the phonons from finite differences. In this HowTo, we will concern ourselves with restarting and splitting finite difference calculations.

Mind: 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 - disables checkpoint functionality entirely, reproducing the behavior of VASP before 6.6.0. No vaspcheckfd.h5 file is written.
• CHECKPOINT = RESET (default) - overwrites the vaspcheckfd.h5 file and then updates the file during the calculation after each displacement.
• CHECKPOINT = CONTINUE - reads the existing vaspcheckfd.h5 file (creating a new one if it is not present) and continues from the last completed displacement. Once all displacements are completed, it will perform a single SCF at the equilibrium structure and read all displacement data from the checkpoint file, detecting whether the calculation was done in one run or was split (all displacements must be completed otherwise an error will be given).

used for restarting a finite differences calculation from a vaspcheckfd.h5 file.

• CHECKPOINT = PREPARE - creates or overwrites the vaspcheckfd.h5 file. For each displacement, a CONTCAR_disp-N file is written containing the atomic positions for displacement N.

VASP then stops after completing one SCF cycle for the equilibrium structure. used for splitting a finite differences calculation.

• CHECKPOINT = SINGLE - used for running the individual displacement calculations created by CHECKPOINT = PREPARE. Each run produces a local vaspcheckfd.h5 file in its directory for that specific displacement.

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.

The following INCAR file with modifications will be used thoughout:

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 vaspcheckfd.h5 file. Inside, it will contain the displacement calculations that have been completed up to the point of the crash:

h5ls vaspcheckfd.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 vaspcheckfd.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 is done in three steps:

1. Preparing the separate displacements - CHECKPOINT = PREPARE
2. Single displacement calculations - CHECKPOINT = SINGLE
3. Collected finite differences - CHECKPOINT = CONTINUE

Preparing the displacements

The displacements can be prepared using 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 as you can see in the stdout:

Creating CONTCAR files for finite difference displacements

and the vaspcheckfd.h5 file:

h5ls vaspcheckfd.h5

metadata                 Group
subdir_prefix            Dataset {SCALAR}
total_count              Dataset {SCALAR}

Single displacement calculations

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

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

Important: You can set different NCORE settings in these calculations, offering parallelization that is not otherwise currently possible for finite differences.

In each subdirectory, you can see that a single displacement has been recorded in the stdout:

Computing single independent displacement for finite differences

and to the vaspcheckfd.h5 file:

h5ls vaspcheckfd.h5
 
data-1                   Group

Collected finite differences

Returning to the parent directory, you can combine these separate displacements into one finite difference calculation using the CHECKPOINT = CONTINUE 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 = CONTINUE

Warning: You can do this calculation in a different directory but you must include the vaspcheckfd.h5 from the prepare step there as it contains important metadata.

Running this calculation, you can see that each of the single displacements are combined into one calculation in the stdout:

 Combining displacements from subdirectories

and vaspcheckfd.h5 file:

h5ls vaspcheckfd.h5

metadata                 Group
subdir_prefix            Dataset {SCALAR}
total_count              Dataset {SCALAR}

You can find information about the computed phonon modes under Eigenvectors and eigenvalues of the dynamical matrix as usual.

Practical hints

• The phonon frequencies will differ slightly between one run and the split calculation, on the order of the 4th or 5th significant figure. We do not expect this to be significant.
• You can use this method for any electron-phonon calculations.
• You can set different NCORE settings in these calculations, offering parallelization that is not otherwise currently possible for finite differences.
• Make sure to check that you are using the correct vaspcheckfd.h5 file with each calculation, particularly the split calculation. If data is read from an inappropriate vaspcheckfd.h5 file, you will see it with the following warning:

 -----------------------------------------------------------------------------
|                                                                             |
|     EEEEEEE  RRRRRR   RRRRRR   OOOOOOO  RRRRRR      ###     ###     ###     |
|     E        R     R  R     R  O     O  R     R     ###     ###     ###     |
|     E        R     R  R     R  O     O  R     R     ###     ###     ###     |
|     EEEEE    RRRRRR   RRRRRR   O     O  RRRRRR       #       #       #      |
|     E        R   R    R   R    O     O  R   R                               |
|     E        R    R   R    R   O     O  R    R      ###     ###     ###     |
|     EEEEEEE  R     R  R     R  OOOOOOO  R     R     ###     ###     ###     |
|                                                                             |
|     Checkpoint file vaspcheckfd.h5 is incompatible: NIONS mismatch            |
|     (file=54, current=128). Ensure that your calculational settings are     |
|     identical between runs. In particular, check POSCAR, KPOINTS,           |
|     POTCAR, and INCAR files.                                                |
|                                                                             |
|       ---->  I REFUSE TO CONTINUE WITH THIS SICK JOB ... BYE!!! <----       |
|                                                                             |
 -----------------------------------------------------------------------------

• We recommend using the WAVECAR file from the parent directory of the split calculation for the indiviudal displacements to speed up the calculation. This can easily result in large file sizes. We recommend removing them after each displacement is calculated. E.g., for a finite differences calculation on [chabazite], there are 42 atoms, resulting in 126 phonon modes, and so 252 total displacements. If loose settings and the Γ-point only are used for an ab initio calculation, the CHG, CHGCAR, and WAVECAR files for the equilibrium structure are 11 MD, 16 MD, and 16 MD, respectively. This already sums to 11 GB for a relatively small calculation.

Related tags and sections

CHECKPOINT, vaspcheckfd.h5, IBRION

Phonons: Theory