View source for Restarting finite differences calculations

{{Available|6.6.0}}
{{NB|important|This feature requires [[:Category:HDF5_support | HDF5 support]].}}
Since VASP 6.6.0, it has been possible to restart finite difference calculations using {{TAG|IBRION|6}} and {{TAG|CHECKPOINT}}. The displacements are written to a {{FILE|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. 
{{NB|important|This can only be done using {{TAG|IBRION|6}} currently. We recommend using this generally over {{TAG|IBRION|5}}.}}

== Input ==

There are several options for the {{TAG|CHECKPOINT}} tag:
*{{TAG|CHECKPOINT|LEGACY}} - finite difference calculation are performed as those in VASP 6.5.1. No {{FILE|vaspcheck.h5}} is written.
*{{TAG|CHECKPOINT|RESET}} ''(default)'' - The {{FILE|vaspcheck.h5}} file is overwritten or created, and the displacements are written to it.
*{{TAG|CHECKPOINT|CONTINUE}} - used for restarting a finite differences calculation from a {{FILE|vaspcheck.h5}} file.
*{{TAG|CHECKPOINT|PREPARE}} - used for splitting a finite differences calculation.
*{{TAG|CHECKPOINT|SINGLE}} - used for running a single displacement after splitting with {{TAG|CHECKPOINT|PREPARE}}.

We will describe the restart procedure and splitting a calculation below. As an example, we take a 3x3x1 graphene supercell {{FILE|POSCAR}} file from the [https://www.vasp.at/tutorials/latest/phonon/part1/#phonon-e02 phonon tutorials]:

<syntaxhighlight>
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
</syntaxhighlight>

along with a 4x4x1 '''k'''-mesh in our {{FILE|KPOINTS}} file:

<syntaxhighlight>
K points
 0
Gamma
4  4  1
0  0  0
</syntaxhighlight>

and <code>PAW C_s 04May1998</code> {{FILE|POTCAR}}. 

The following {{FILE|INCAR}} file with modifications will be used thoughout:

 {{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

== 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 {{FILE|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 {{TAG|CHECKPOINT|CONTINUE}} to the {{FILE|INCAR}}:

 {{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}} = CONTINUE

You can resubmit your calculation in the directory, e.g., with a job script: <code>sbatch job.sh</code>, 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 is done in three steps:

# Preparing the separate displacements - {{TAG|CHECKPOINT|PREPARE}}
# Single displacement calculations - {{TAG|CHECKPOINT|SINGLE}}
# Collected finite differences - {{TAG|CHECKPOINT|CONTINUE}}

==== Preparing the displacements ====
The displacements can be prepared using the {{TAG|CHECKPOINT|PREPARE}} tag:

 {{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}} = PREPARE

This will create {{TAGBL|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 {{FILE|vaspcheck.h5}} file:

 h5ls vaspcheck.h5
 
 metadata                 Group
 subdir_prefix            Dataset {SCALAR}
 total_count              Dataset {SCALAR}

==== Single displacement calculations ====
You can then create different directories for each of these {{TAGBL|CONTCAR}}_disp-N and run them separately. For this, you will need to set {{TAG|CHECKPOINT|SINGLE}}:

<syntaxhighlight lang="bash">
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
</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
{{NB|important|You can set different {{TAG|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 {{FILE|vaspcheck.h5}} file:

 h5ls vaspcheck.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 {{TAG|CHECKPOINT|CONTINUE}} tag:

 {{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}} = CONTINUE
{{NB|warning|You can do this calculation in a different directory but you must include the {{FILE|vaspcheck.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 {{FILE|vaspcheck.h5}} file:

 h5ls vaspcheck.h5
 
 metadata                 Group
 subdir_prefix            Dataset {SCALAR}
 total_count              Dataset {SCALAR}

You can find information about the computed phonon modes under <code>Eigenvectors and eigenvalues of the dynamical matrix</code> 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 [[:Category:electron-phonon interactions | electron-phonon]] calculations. 
* You can set different {{TAG|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 {{FILE|vaspcheck.h5}} file with each calculation, particularly the split calculation. If data is read from an inappropriate {{FILE|vaspcheck.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 vaspcheck.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 {{FILE|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 [[https://www.vasp.at/tutorials/latest/transition_states/part2/#transition_states-e07 chabazite]], there are 42 atoms, resulting in 126 phonon modes, and so 252 total displacements. If loose settings and the &Gamma;-point only are used for an ab initio calculation, the {{FILE|CHG}}, {{FILE|CHGCAR}}, and {{FILE|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 ==
{{TAG|CHECKPOINT}},
{{FILE|vaspcheck.h5}},
{{TAG|IBRION}}

[[Phonons: Theory]]

<!--[[Category:Phonons]][[Category:Electron-phonon interactions]][[Category:Howto]]-->