[ase-users] Running NEB with ASE and CP2K

[Hasan Al-Mahayni]

Hello,

I am running the same file as in the NEB section of the ASE website.
However, I am using CP2K as a calculator, while my initial and final images
are two slabs I created using ASE. I attached the python code "NEB" and the
slab xyz files.

My problem is, whenever I run this file, i get this following error:

"srun: Job 5563956 step creation temporarily disabled, retrying."

After contacting support, they told me that it has to do with cp2k, or this
line to be specific:

image.set_calculator(CP2K(xc='PBE',cutoff=500
,max_scf=200,poisson_solver='none' ,inp=inp))

Anyone had the same problem?

Thanks,
Hasan.
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slab1.xyz file:
20
Lattice="7.65796644025031 0.0 0.0 3.828983220125155 6.6319934785854535 0.0 0.0 0.0 22.08423447177455" Properties=species:S:1:pos:R:3:tags:I:1 pbc="T T F"
Cu       0.00000000       1.47377633      10.00000000        2
Cu       2.55265548       1.47377633      10.00000000        2
Cu       5.10531096       1.47377633      10.00000000        2
Cu       1.27632774       3.68444082      10.00000000        2
Cu       3.82898322       3.68444082      10.00000000        2
Cu       6.38163870       3.68444082      10.00000000        2
Cu       2.55265548       5.89510531      10.00000000        2
Cu       5.10531096       5.89510531      10.00000000        2
Cu       7.65796644       5.89510531      10.00000000        2
Cu       0.00000000       0.00000000      12.08423447        1
Cu       2.55265548       0.00000000      12.08423447        1
Cu       5.10531096       0.00000000      12.08423447        1
Cu       1.27632774       2.21066449      12.08423447        1
Cu       3.82898322       2.21066449      12.08423447        1
Cu       6.38163870       2.21066449      12.08423447        1
Cu       2.55265548       4.42132899      12.08423447        1
Cu       5.10531096       4.42132899      12.08423447        1
Cu       7.65796644       4.42132899      12.08423447        1
O        0.00000000       0.00000000      15.08423447        0
C        0.00000000       0.00000000      13.93389447        0


slab2.xyz file:


20
Lattice="7.65796644025031 0.0 0.0 3.828983220125155 6.6319934785854535 0.0 0.0 0.0 22.08423447177455" Properties=species:S:1:pos:R:3:tags:I:1 pbc="T T F"
Cu       0.00000000       1.47377633      10.00000000        2
Cu       2.55265548       1.47377633      10.00000000        2
Cu       5.10531096       1.47377633      10.00000000        2
Cu       1.27632774       3.68444082      10.00000000        2
Cu       3.82898322       3.68444082      10.00000000        2
Cu       6.38163870       3.68444082      10.00000000        2
Cu       2.55265548       5.89510531      10.00000000        2
Cu       5.10531096       5.89510531      10.00000000        2
Cu       7.65796644       5.89510531      10.00000000        2
Cu       0.00000000       0.00000000      12.08423447        1
Cu       2.55265548       0.00000000      12.08423447        1
Cu       5.10531096       0.00000000      12.08423447        1
Cu       1.27632774       2.21066449      12.08423447        1
Cu       3.82898322       2.21066449      12.08423447        1
Cu       6.38163870       2.21066449      12.08423447        1
Cu       2.55265548       4.42132899      12.08423447        1
Cu       5.10531096       4.42132899      12.08423447        1
Cu       7.65796644       4.42132899      12.08423447        1
O        1.27600000       2.21100000      15.08423447        0
C        1.27600000       2.21100000      13.93389447        0
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from ase import io
from ase.neb import NEB
from ase.optimize import MDMin
from ase.calculators.cp2k import CP2K


inp=  """
!  &EXT_RESTART
 !   RESTART_FILE_NAME cp2k-1.restart
!  &END

&MOTION
&PRINT
      &RESTART
       &EACH
       &END EACH
      &END RESTART
      &TRAJECTORY
         FORMAT XYZ
      &END TRAJECTORY
      &CELL

      &END CELL
   &END PRINT
&END MOTION

           &FORCE_EVAL
            &DFT
              UKS .TRUE.
              CHARGE 0
              MULTIPLICITY 1
              WFN_RESTART_FILE_NAME cp2k-RESTART.kp
             &MGRID
                NGRIDS 5
                RELATIVE_CUTOFF 50
              &END MGRID
              &QS
               EPS_DEFAULT 1.0E-12
               METHOD GPW
               EXTRAPOLATION USE_GUESS
              &END QS
              &SCF
              SCF_GUESS RESTART
              ADDED_MOS 200
              CHOLESKY OFF
                &SMEAR T
                  METHOD FERMI_DIRAC
                  ELECTRONIC_TEMPERATURE 3.0000E+2
                &END SMEAR
                &MIXING T
                 METHOD BROYDEN_MIXING
                 ALPHA     4.0000000000000002E-01
                 BETA     1.5000000000000000E+00
                 NMIXING  5
                 NBUFFER  8
                &END MIXING
              &END SCF
               &POISSON
                POISSON_SOLVER  PERIODIC
                PERIODIC  XYZ
              &END POISSON
              &KPOINTS
                SCHEME  MONKHORST-PACK  8  8  8
               FULL_GRID  .TRUE.
              &END KPOINTS
             &END DFT
           &END FORCE_EVAL

"""

# Read initial and final states:
initial = io.read('slab1.xyz')
final = io.read('slab2.xyz')
# Make a band consisting of 5 images:
images = [initial]
images += [initial.copy() for i in range(3)]
images += [final]
neb = NEB(images)
# Interpolate linearly the potisions of the three middle images:
neb.interpolate()
# Set calculators:
for image in images[1:4]:
    image.set_calculator(CP2K(xc='PBE',cutoff=500 ,max_scf=200,poisson_solver='none' ,inp=inp))
# Optimize:
optimizer = MDMin(neb, trajectory='A2B.traj')
optimizer.run(fmax=0.04)