Replace ase ExpCellFilter with FrechetCellFilter in StructOptimizer#101
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Replace ase ExpCellFilter with FrechetCellFilter in StructOptimizer#101
ExpCellFilter with FrechetCellFilter in StructOptimizer#101Conversation
This was referenced Dec 7, 2023
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Just out of curiosity, I understand the improvement in the SiO2's phonon band structure (especially around optic modes) comes better relaxed cell. So, do |
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@lan496 Yes, slightly different (and much faster): from ase.filters import ExpCellFilter, FrechetCellFilter
from pymatgen.core import Structure
from chgnet import ROOT
from chgnet.model import CHGNet, StructOptimizer
relaxer = StructOptimizer()
chgnet = CHGNet.load()
structure = Structure.from_file(f"{ROOT}/examples/mp-18767-LiMnO2.cif")
structure.perturb(0.1)
for ase_filter in (ExpCellFilter, FrechetCellFilter):
result = relaxer.relax(structure, verbose=False, ase_filter=ase_filter)
print(
f"\n{ase_filter.__name__} took {len(result['trajectory'])} steps. Relaxed structure:"
)
print(result["final_structure"])ExpCellFilter took 52 steps. Relaxed structure:
Full Formula (Li2 Mn2 O4)
Reduced Formula: LiMnO2
abc : 2.872010 4.650813 5.834364
angles: 89.984000 90.166300 89.959166
pbc : True True True
Sites (8)
# SP a b c magmom
--- ---- --------- --------- -------- ----------
0 Li+ 0.466097 0.471908 0.378517 0.00247121
1 Li+ 0.979868 0.970313 0.606578 0.00228718
2 Mn3+ 0.484925 0.498502 0.859377 3.87809
3 Mn3+ 0.984186 0.998235 0.126078 3.87656
4 O2- 0.483681 0.009578 0.350723 0.0461
5 O2- -0.012445 0.497563 0.093668 0.0405012
6 O2- 0.484366 -0.001507 0.89173 0.0405898
7 O2- 0.982041 0.509921 0.634653 0.0462106
FrechetCellFilter took 26 steps. Relaxed structure:
Full Formula (Li2 Mn2 O4)
Reduced Formula: LiMnO2
abc : 2.876522 4.657650 5.839542
angles: 90.012820 90.017011 90.010059
pbc : True True True
Sites (8)
# SP a b c magmom
--- ---- --------- --------- -------- ----------
0 Li+ 0.452761 0.467844 0.381994 0.00225034
1 Li+ 0.976853 0.965974 0.60083 0.0018343
2 Mn3+ 0.487451 0.500263 0.862042 3.87584
3 Mn3+ 0.987112 0.997857 0.123798 3.89048
4 O2- 0.483031 0.008843 0.349475 0.0478891
5 O2- -0.008411 0.502525 0.095111 0.0408283
6 O2- 0.489891 -7.2e-05 0.890263 0.0426996
7 O2- 0.984032 0.51128 0.637812 0.0465174
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@janosh Thank you for your detail script. Glad to hear the new filter is working well! |
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ase'sExpCellFilter.get_forcesreturns inconsistent gradients with central differences which was fixed in a newFrechetCellFilteradded by @lan496 in https://gitlab.com/ase/ase/-/merge_requests/3024. See https://gitlab.com/ase/ase/-/issues/1321 for bug details.This PR replaces
ExpCellFilterwithFrechetCellFilterinStructOptimizer.relax().I see a noticeable improvement in CHGNet phonon predictions for SiO2 from this change alone (everything else kept fixed). That's PBE (minus non-analytical correction) in blue and CHGNet in red.
ExpCellFilter (old)
FrechetCellFilter (new)