Exception: Duplicates in permutation
Dear all,
I am trying to use the trajectories of AIMD as reference data for training. As a trial I started without using supercell. I read and write the structures via ase
as:
from ase.io import read, write
prim = read('POSCAR-unitcell') #unitcell
atoms_ideal = prim #no supercell
structures_aimd = read("OUTCAR", format='vasp-out', index=":") #AIMD on unitcell
# save structures
write('prim.extxyz', prim)
write('supercell_ideal.extxyz', atoms_ideal)
write('supercells_rattled.extxyz', structures_aimd)
However, when I try to construct the fcp
as following
# read structures containing displacements and forces
prim = read('prim.extxyz')
atoms_ideal = read('supercell_ideal.extxyz')
rattled_structures = read('supercells_rattled.extxyz', index=':')
# set up cluster space
cutoffs = [3.8, 3.8, 3.8] #for fc2, fc3, fc4
cs = ClusterSpace(prim, cutoffs)
# set up structure container
structures = prepare_structures(rattled_structures, atoms_ideal)
...
I get the following error
File "/home/saleh/clacs/2_construct_fcp.py", line 27, in <module>
structures = prepare_structures(rattled_structures, atoms_ideal)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/saleh/miniconda3/envs/hiphive/lib/python3.12/site-packages/hiphive-1.2-py3.12.egg/hiphive/utilities.py", line 180, in prepare_structures
File "/home/saleh/miniconda3/envs/hiphive/lib/python3.12/site-packages/hiphive-1.2-py3.12.egg/hiphive/utilities.py", line 120, in prepare_structure
File "/home/saleh/miniconda3/envs/hiphive/lib/python3.12/site-packages/hiphive-1.2-py3.12.egg/hiphive/utilities.py", line 208, in find_permutation
Exception: Duplicates in permutation
I get this error when I use AIMD at 400K and 800K. Strangely, when the AIMD is performed at T=10K, I do not get this error. There is a similar issue.
I had to pass check_permutation=False
to prepare_structures
, but I am worried about the effect of such a choice.
Edited by Mohamed Saleh