Restarting finite differences calculations: Difference between revisions
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Latest revision as of 15:07, 4 March 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_FD. 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.
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Input
There are several options for the CHECKPOINT_FD tag:
CHECKPOINT_FD = NONE- disables checkpoint functionality entirely, reproducing the behavior of VASP before 6.6.0. No vaspcheckfd.h5 file is written.CHECKPOINT_FD = RESET(default) - overwrites the vaspcheckfd.h5 file and then updates the file during the calculation after each displacement.CHECKPOINT_FD = 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_FD = 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_FD = SINGLE- used for running the individual displacement calculations created byCHECKPOINT_FD = 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 Calong with a 4x4x1 k-mesh in our KPOINTS file:
K points
0
Gamma
4 4 1
0 0 0and 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_FD = 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_FD = 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:
- Preparing the separate displacements -
CHECKPOINT_FD = PREPARE - Single displacement calculations -
CHECKPOINT_FD = SINGLE - Collected finite differences -
CHECKPOINT_FD = CONTINUE
1. Preparing the displacements
The displacements can be prepared using the CHECKPOINT_FD = 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_FD = 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}
2. 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_FD = 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_FD = 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
3. Collected finite differences
Returning to the parent directory, you can combine these separate displacements into one finite difference calculation using the CHECKPOINT_FD = 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_FD = 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 MB, 16 MB, and 16 MB, respectively. This already sums to 11 GB for a relatively small calculation.
Related tags and sections
CHECKPOINT_FD, vaspcheckfd.h5, IBRION, CONTCAR_disp-N